From 7b6c7a7fdbf40781af2a8becb771e186f08661e1 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Tue, 1 Oct 2024 16:00:20 -0700 Subject: [PATCH 01/30] initial branch commit --- README.md | 32 +++++-- src/lib.rs | 3 +- .../raw_peak_agg/multi_chromatogram_agg.rs | 96 +++++++++++++------ src/models/elution_group.rs | 2 +- .../quad_splitted_transposed_index.rs | 15 ++- .../queriable_tims_data.rs | 6 +- 6 files changed, 112 insertions(+), 42 deletions(-) diff --git a/README.md b/README.md index f752d01..ed47c00 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,34 @@ # Timsquery -UNDER CONSTRUCTION +## Where are we in the life cycle? -... The idea is to have a library that allows querying TIMS data in a generic way. +- The library is in a very early stage of development. + - I cannot assure stability or bug-freeness. + - We are still deciding what the API should be and what the scope of the project overall is. -The main design is to have modular aggregators, indices and queries. -Thus, depending on the access pattern, the data can be queried in +1. Push to main. +2. Branched but fast moving <- **We are here** +3. Stable api but features might be dropped without notice. +4. Stable api and deprecations on changes. + +## What is this? + +Timsquery is meant to be a library and command line tool that allows querying TIMS data in a generic way. +Basically, pick a way in which you want your data to be aggregated, pick how you want to query it and pick +your file, and you get back results that match those three things! + +More explicitly: +- The main design is to have modular components: + - aggregators + - indices + - queries + - tolerances + +Thus, depending on the access pattern and purpose, the data can be queried in different ways and aggregated in different ways (if you need random -acces, use the index that works for that, if you need bulk +access, use the index that works for that, if you need bulk sequential, use that). -Ideally we will also have a sane CLI (think ... msaccess-like). +## What does the cli look like right now? + diff --git a/src/lib.rs b/src/lib.rs index 21cd7b5..c7ab4fd 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,5 +1,6 @@ // Re-export main structures pub use crate::models::elution_group::ElutionGroup; +pub use crate::models::indices::transposed_quad_index::QuadSplittedTransposedIndex; pub use crate::queriable_tims_data::queriable_tims_data::QueriableTimsData; // Re-export traits @@ -15,5 +16,3 @@ pub mod models; pub mod queriable_tims_data; pub mod traits; pub mod utils; - -// Any library-wide code, documentation, or additional exports can go here diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs index 297437c..551f4b4 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs @@ -16,6 +16,8 @@ use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter} pub struct MultiCMGStats { pub scan_tof_mapping: MappingCollection<(FH, u32), ScanTofStatsCalculatorPair>, pub converters: (Tof2MzConverter, Scan2ImConverter), + pub uniq_rts: HashSet, + pub uniq_ids: HashSet, pub id: u64, } @@ -30,6 +32,8 @@ impl MultiCMGStatsFactory { MultiCMGStats { scan_tof_mapping: MappingCollection::new(), converters: (self.converters.0, self.converters.1), + uniq_rts: HashSet::new(), + uniq_ids: HashSet::new(), id, } } @@ -120,6 +124,13 @@ impl NaturalFinalizedMultiCMGSt &lazy_hyperscore, 1 + (other.retention_time_miliseconds.len() / 10), ); + // Set 0 the NANs + // Q: Can I do this in-place? Will the comnpiler do it for me? + let lazy_hyperscore_vs_baseline: Vec = lazy_hyperscore_vs_baseline + .into_iter() + .map(|x| if x.is_nan() { 0.0 } else { x }) + .collect(); + let mut apex_hyperscore_index = 0; let mut max_hyperscore = 0.0f64; for (i, val) in lazy_hyperscore_vs_baseline.iter().enumerate() { @@ -195,6 +206,10 @@ impl From>(); let mut unique_rts = unique_rts.into_iter().collect::>(); unique_rts.sort(); + + // Q: Is this the most efficient way to do this? + // I think having the btrees as the unit of integration might not be the best idea. + // ... If I want to preserve the sparsity, I can use a hashmap and the sort it. let mut summed_intensity_tree: BTreeMap = BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0))); let mut npeaks_tree: BTreeMap = @@ -231,6 +246,7 @@ impl From Aggregator<(RawPeak, FH)> let u64_intensity = peak.intensity as u64; let rt_miliseconds = (peak.retention_time * 1000.0) as u32; + self.uniq_rts.insert(rt_miliseconds); + self.uniq_ids.insert(transition.clone()); + self.scan_tof_mapping .entry((transition.clone(), rt_miliseconds)) .and_modify(|curr| { @@ -279,39 +298,30 @@ impl Aggregator<(RawPeak, FH)> fn finalize(self) -> NaturalFinalizedMultiCMGStatsArrays { let mut transition_stats = MappingCollection::new(); - for ((transition, rt_ms), scan_tof_mapping) in self.scan_tof_mapping.into_iter() { - transition_stats - .entry(transition) - .and_modify(|curr: &mut ChromatomobilogramStatsArrays| { - curr.retention_time_miliseconds.push(rt_ms); - curr.scan_index_means - .push(scan_tof_mapping.scan.mean().unwrap()); - curr.scan_index_sds - .push(scan_tof_mapping.scan.standard_deviation().unwrap()); - curr.tof_index_means - .push(scan_tof_mapping.tof.mean().unwrap()); - curr.tof_index_sds - .push(scan_tof_mapping.tof.standard_deviation().unwrap()); - curr.intensities.push(scan_tof_mapping.tof.weight()); - }) - .or_insert_with(|| { - let mut out = ChromatomobilogramStatsArrays::new(); - out.retention_time_miliseconds.push(rt_ms); - out.scan_index_means + + for id_key in self.uniq_ids.iter() { + let mut id_cmgs = ChromatomobilogramStatsArrays::new(); + for rt_key in self.uniq_rts.iter() { + let scan_tof_mapping = self.scan_tof_mapping.get(&(id_key.clone(), *rt_key)); + if let Some(scan_tof_mapping) = scan_tof_mapping { + id_cmgs.retention_time_miliseconds.push(*rt_key); + id_cmgs + .scan_index_means .push(scan_tof_mapping.scan.mean().unwrap()); - out.scan_index_sds + id_cmgs + .scan_index_sds .push(scan_tof_mapping.scan.standard_deviation().unwrap()); - out.tof_index_means + id_cmgs + .tof_index_means .push(scan_tof_mapping.tof.mean().unwrap()); - out.tof_index_sds + id_cmgs + .tof_index_sds .push(scan_tof_mapping.tof.standard_deviation().unwrap()); - out.intensities.push(scan_tof_mapping.tof.weight()); - out - }); - } - - for (_k, v) in transition_stats.iter_mut() { - v.sort_by_rt(); + id_cmgs.intensities.push(scan_tof_mapping.tof.weight()); + } + } + id_cmgs.sort_by_rt(); + transition_stats.insert(id_key.clone(), id_cmgs); } let tmp = MultiCMGStatsArrays { @@ -325,3 +335,31 @@ impl Aggregator<(RawPeak, FH)> ) } } + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn test_value_vs_baseline() { + let vals = vec![1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0]; + let baseline_window_size = 3; + let baseline = rolling_median(&vals, baseline_window_size, f64::NAN); + let out = calculate_value_vs_baseline(&vals, baseline_window_size); + let expect_val = vec![f64::NAN, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, f64::NAN]; + let all_close = out + .iter() + .zip(expect_val.iter()) + .filter(|(a, b)| ((!a.is_nan()) && (!b.is_nan()))) + .all(|(a, b)| (a - b).abs() < 1e-6); + + let all_match_nan = out + .iter() + .zip(expect_val.iter()) + .filter(|(a, b)| ((a.is_nan()) || (b.is_nan()))) + .all(|(a, b)| a.is_nan() && b.is_nan()); + + assert!(all_close, "Expected {:?}, got {:?}", expect_val, out); + assert!(all_match_nan, "Expected {:?}, got {:?}", expect_val, out); + } +} diff --git a/src/models/elution_group.rs b/src/models/elution_group.rs index 24cd811..0fec0f9 100644 --- a/src/models/elution_group.rs +++ b/src/models/elution_group.rs @@ -3,7 +3,7 @@ use serde::{Deserialize, Serialize}; use std::collections::HashMap; use std::hash::Hash; -#[derive(Debug, Serialize, Deserialize)] +#[derive(Debug, Serialize, Deserialize, Clone)] pub struct ElutionGroup { pub id: u64, pub mobility: f32, diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 16c358e..260347b 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -1,7 +1,7 @@ use super::quad_index::{ FrameRTTolerance, PeakInQuad, TransposedQuadIndex, TransposedQuadIndexBuilder, }; - +use crate::models::elution_group::ElutionGroup; use crate::models::frames::raw_peak::RawPeak; use crate::models::frames::single_quad_settings::expand_quad_settings; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; @@ -11,13 +11,12 @@ use crate::traits::indexed_data::IndexedData; use crate::utils::compress_explode::explode_vec; use crate::utils::display::{glimpse_vec, GlimpseConfig}; use crate::ToleranceAdapter; - -use crate::models::elution_group::ElutionGroup; use log::{debug, info, trace}; use rayon::prelude::*; use serde::Serialize; use std::collections::hash_map::Entry; use std::collections::HashMap; +use std::fmt::Debug; use std::fmt::Display; use std::hash::Hash; use std::sync::Arc; @@ -42,6 +41,16 @@ pub struct QuadSplittedTransposedIndex { metadata: Metadata, } +impl Debug for QuadSplittedTransposedIndex { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + write!( + f, + "QuadSplittedTransposedIndex(num_quads: {})", + self.flat_quad_settings.len() + ) + } +} + impl QuadSplittedTransposedIndex { pub fn query_peaks( &self, diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index e2fc840..982c377 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -127,7 +127,11 @@ where microseconds_per_query ); - aggregators.into_par_iter().map(|x| x.finalize()).collect() + let start = Instant::now(); + let out = aggregators.into_par_iter().map(|x| x.finalize()).collect(); + let elapsed = start.elapsed(); + info!("Aggregation took {:#?}", elapsed); + out } pub fn query_indexed( From 9c9f6caeffaed3731bc5899e1f92f6016e182a61 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Thu, 17 Oct 2024 15:08:20 -0700 Subject: [PATCH 02/30] feat: added precursor index to transposed --- Taskfile.yml | 2 +- src/main.rs | 4 +- .../raw_peak_agg/multi_chromatogram_agg.rs | 103 ++++++- .../aggregators/streaming_aggregator.rs | 35 ++- src/models/frames/expanded_frame.rs | 125 +++++--- src/models/frames/expanded_window_group.rs | 2 +- src/models/frames/single_quad_settings.rs | 19 +- src/models/indices/expanded_raw_index/mod.rs | 0 .../transposed_quad_index/peak_bucket.rs | 22 +- .../transposed_quad_index/quad_index.rs | 280 ++++++++++++++---- .../quad_splitted_transposed_index.rs | 138 +++++---- src/utils/math.rs | 8 + src/utils/sorting.rs | 17 +- 13 files changed, 564 insertions(+), 191 deletions(-) create mode 100644 src/models/indices/expanded_raw_index/mod.rs diff --git a/Taskfile.yml b/Taskfile.yml index bf23144..9ac1af4 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -29,7 +29,7 @@ tasks: fmt: cmds: - - cargo fmt + - cargo +nightly fmt clippy: cmds: diff --git a/src/main.rs b/src/main.rs index 8ff2ed4..1dc7c05 100644 --- a/src/main.rs +++ b/src/main.rs @@ -5,8 +5,8 @@ use timsquery::queriable_tims_data::queriable_tims_data::query_multi_group; use timsquery::traits::tolerance::DefaultTolerance; use timsquery::{ models::aggregators::{ - ChromatomobilogramStats, ExtractedIonChromatomobilogram, MultiCMGStats, - MultiCMGStatsFactory, RawPeakIntensityAggregator, RawPeakVectorAggregator, + ChromatomobilogramStats, ExtractedIonChromatomobilogram, MultiCMGStatsFactory, + RawPeakIntensityAggregator, RawPeakVectorAggregator, }, models::indices::raw_file_index::RawFileIndex, models::indices::transposed_quad_index::QuadSplittedTransposedIndex, diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs index 551f4b4..b9baf0d 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs @@ -5,7 +5,8 @@ use crate::models::aggregators::rolling_calculators::rolling_median; use crate::models::aggregators::streaming_aggregator::RunningStatsCalculator; use crate::models::frames::raw_peak::RawPeak; use crate::traits::aggregator::Aggregator; -use crate::utils::math::lnfact; +use crate::utils::math::{lnfact, lnfact_float}; +use log::{debug, warn}; use serde::Serialize; use std::collections::{BTreeMap, HashSet}; use std::hash::Hash; @@ -50,6 +51,9 @@ pub struct FinalizedMultiCMGStatsArrays, pub weighted_scan_index_mean: Vec, pub summed_intensity: Vec, + + // This should be the same as the sum of log intensities. + pub log_intensity_products: Vec, pub npeaks: Vec, pub scan_index_means: MappingCollection>, pub tof_index_means: MappingCollection>, @@ -68,10 +72,14 @@ pub struct NaturalFinalizedMultiCMGStatsArrays, pub lazy_hyperscore: Vec, pub lazy_hyperscore_vs_baseline: Vec, + pub norm_hyperscore_vs_baseline: Vec, + pub lazyerscore: Vec, + pub lazyerscore_vs_baseline: Vec, + pub norm_lazyerscore_vs_baseline: Vec, pub transition_mobilities: MappingCollection>, pub transition_mzs: MappingCollection>, pub transition_intensities: MappingCollection>, - pub apex_hyperscore_index: usize, + pub apex_primary_score_index: usize, pub id: u64, } @@ -120,23 +128,55 @@ impl NaturalFinalizedMultiCMGSt mobility_converter: &Scan2ImConverter, ) -> Self { let lazy_hyperscore = calculate_lazy_hyperscore(&other.npeaks, &other.summed_intensity); - let lazy_hyperscore_vs_baseline = calculate_value_vs_baseline( - &lazy_hyperscore, - 1 + (other.retention_time_miliseconds.len() / 10), - ); + let basline_window_len = 1 + (other.retention_time_miliseconds.len() / 10); + let lazy_hyperscore_vs_baseline = + calculate_value_vs_baseline(&lazy_hyperscore, basline_window_len); + let lazyerscore: Vec = other + .log_intensity_products + .iter() + .map(|x| lnfact_float(*x)) + .collect(); + let lazyerscore_vs_baseline = calculate_value_vs_baseline(&lazyerscore, basline_window_len); + // Set 0 the NANs // Q: Can I do this in-place? Will the comnpiler do it for me? let lazy_hyperscore_vs_baseline: Vec = lazy_hyperscore_vs_baseline .into_iter() .map(|x| if x.is_nan() { 0.0 } else { x }) .collect(); + let lazyerscore_vs_baseline: Vec = lazyerscore_vs_baseline + .into_iter() + .map(|x| if x.is_nan() { 0.0 } else { x }) + .collect(); + + // Calculate the standard deviation of the lazyscores v baseline + let mut sd_calculator_hyperscore = RunningStatsCalculator::new(1, 0.0); + let mut sd_calculator_lazyscore = RunningStatsCalculator::new(1, 0.0); + + (0..lazyerscore_vs_baseline.len()).for_each(|i| { + sd_calculator_hyperscore.add(lazy_hyperscore_vs_baseline[i], 1); + sd_calculator_lazyscore.add(lazyerscore_vs_baseline[i], 1); + }); + let sd_hyperscore = sd_calculator_hyperscore.standard_deviation().unwrap(); + let sd_lazyscore = sd_calculator_lazyscore.standard_deviation().unwrap(); + + // Calculate the normalized scores + let norm_hyperscore_vs_baseline: Vec = lazy_hyperscore_vs_baseline + .iter() + .map(|x| x / sd_hyperscore) + .collect(); + let norm_lazyerscore_vs_baseline: Vec = lazyerscore_vs_baseline + .iter() + .map(|x| x / sd_lazyscore) + .collect(); - let mut apex_hyperscore_index = 0; - let mut max_hyperscore = 0.0f64; - for (i, val) in lazy_hyperscore_vs_baseline.iter().enumerate() { - if max_hyperscore.is_nan() || *val > max_hyperscore { - max_hyperscore = *val; - apex_hyperscore_index = i; + let mut apex_primary_score_index = 0; + let mut max_primary_score = 0.0f64; + let primary_scores = &norm_lazyerscore_vs_baseline; + for (i, val) in primary_scores.iter().enumerate() { + if max_primary_score.is_nan() || *val > max_primary_score { + max_primary_score = *val; + apex_primary_score_index = i; } } @@ -150,7 +190,13 @@ impl NaturalFinalizedMultiCMGSt average_mobility: other .weighted_scan_index_mean .into_iter() - .map(|x| mobility_converter.convert(x)) + .map(|x| { + let out = mobility_converter.convert(x); + if out < 0.5 || out > 2.0 { + debug!("Bad mobility value: {:?}, input was {:?}", out, x); + } + out + }) .collect(), summed_intensity: other.summed_intensity, npeaks: other.npeaks, @@ -176,7 +222,11 @@ impl NaturalFinalizedMultiCMGSt transition_intensities: other.intensities, lazy_hyperscore, lazy_hyperscore_vs_baseline, - apex_hyperscore_index, + apex_primary_score_index, + lazyerscore, + lazyerscore_vs_baseline, + norm_hyperscore_vs_baseline, + norm_lazyerscore_vs_baseline, id: other.id, } } @@ -195,6 +245,7 @@ impl From From = BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0))); + let mut intensity_logsums_tree: BTreeMap = + BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0.0))); let mut npeaks_tree: BTreeMap = BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0))); let mut weighted_tof_index_mean_tree: BTreeMap = @@ -230,11 +283,19 @@ impl From 100 { + npeaks_tree.entry(rt).and_modify(|curr| *curr += 1); + } tmp_tree.entry(rt).or_insert((scan, tof, inten)); summed_intensity_tree .entry(rt) .and_modify(|curr| *curr += inten); - npeaks_tree.entry(rt).and_modify(|curr| *curr += 1); + + intensity_logsums_tree.entry(rt).and_modify(|curr| { + if inten > 10 { + *curr += (inten as f64).ln() + } + }); weighted_tof_index_mean_tree .entry(rt) .and_modify(|curr| curr.add(tof, inten)) @@ -265,8 +326,18 @@ impl From 1000.0 { + warn!("Bad mobility value: {:?}, input was {:?}", out, x); + } + + out + }) .collect(); + + // Note: The log of products is the same as the sum of logs. + out.log_intensity_products = intensity_logsums_tree.into_values().collect(); out } } diff --git a/src/models/aggregators/streaming_aggregator.rs b/src/models/aggregators/streaming_aggregator.rs index 785584f..2ab67b2 100644 --- a/src/models/aggregators/streaming_aggregator.rs +++ b/src/models/aggregators/streaming_aggregator.rs @@ -22,6 +22,8 @@ pub struct RunningStatsCalculator { weight: u64, mean_n: f64, d_: f64, + min: f64, + max: f64, // count: u64, } @@ -30,7 +32,9 @@ impl RunningStatsCalculator { Self { weight, mean_n: mean, - d_: 0.0, + d_: 1.0, + min: mean, + max: mean, // count: 0, } } @@ -52,6 +56,35 @@ impl RunningStatsCalculator { // Update the weight self.weight += weight; + + // That should be the end of it but I seem to be getting consistently some + // values outside of the min and max observed values. Which might be a + // float issue ... TODO investigate. + + // In the meantime I will just squeeze the mean to the min/max observed values. + self.min = self.min.min(value); + self.max = self.max.max(value); + + self.mean_n = self.mean_n.min(self.max).max(self.min); + + assert!( + self.mean_n <= self.max, + "high mean_n: {} max: {} curr_sd: {} weight_ratio: {} {:?}", + self.mean_n, + self.max, + self.standard_deviation().unwrap(), + weight_ratio, + self + ); + assert!( + self.mean_n >= self.min, + "low mean_n: {} min: {} curr_sd: {} weight_ratio: {} {:?}", + self.mean_n, + self.min, + self.standard_deviation().unwrap(), + weight_ratio, + self + ); } pub fn mean(&self) -> Result { diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index f218f70..a58d555 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -1,12 +1,16 @@ use std::sync::Arc; -use super::single_quad_settings::{expand_quad_settings, SingleQuadrupoleSetting}; +use super::single_quad_settings::{ + expand_quad_settings, ExpandedFrameQuadSettings, SingleQuadrupoleSetting, +}; use timsrust::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}; use crate::sort_by_indices_multi; +use crate::utils::compress_explode::explode_vec; use crate::utils::sorting::argsort_by; /// A frame after expanding the mobility data and re-sorting it by tof. +#[derive(Debug, Clone)] pub struct ExpandedFrame { pub tof_indices: Vec, pub scan_numbers: Vec, @@ -20,6 +24,7 @@ pub struct ExpandedFrame { pub window_group: u8, } +#[derive(Debug, Clone)] pub struct ExpandedFrameSlice { pub tof_indices: Vec, // I could Arc<[u32]> if I didnt want to sort by it ... pub scan_numbers: Vec, @@ -28,7 +33,7 @@ pub struct ExpandedFrameSlice { pub rt: f64, pub acquisition_type: AcquisitionType, pub ms_level: MSLevel, - pub quadrupole_settings: SingleQuadrupoleSetting, + pub quadrupole_settings: Option, pub intensity_correction_factor: f64, pub window_group: u8, pub window_subindex: u8, @@ -44,37 +49,79 @@ impl ExpandedFrameSlice { &mut self.intensities ); } + + pub fn len(&self) -> usize { + self.tof_indices.len() + } + + pub fn is_empty(&self) -> bool { + self.tof_indices.is_empty() + } } -fn expand_and_split_frame(frame: &Frame) -> Vec { - let quad_settings = &frame.quadrupole_settings; - let expanded_quad_settings = expand_quad_settings(quad_settings); +fn trim_scan_edges(scan_start: usize, scan_end: usize) -> (usize, usize) { + // Poor man's fix to different quad windows bleeding onto each other ... + // I will trim the smallest of 20 scans or 10% of the range size. + // + // old dumber implementation + // let peak_start = frame.scan_offsets[qs.ranges.scan_start + 10]; + // let peak_end = frame.scan_offsets[qs.ranges.scan_end - 10]; + // (peak_start, peak_end) + // + let scan_range = scan_end - scan_start; + assert!(scan_range > 0, "Expected scan range to be positive..."); + let offset_use = (scan_range / 10).min(20); + + let new_start = scan_start + offset_use; + let new_end = scan_end - offset_use; + + assert!(new_start < new_end, "Expected new_start < new_end"); + + (new_start, new_end) +} + +fn expand_unfragmented_frame(frame: Frame) -> ExpandedFrameSlice { + let scan_numbers = explode_vec(&frame.scan_offsets); + let intensities = frame.intensities; + let tof_indices = frame.tof_indices; + let mut curr_slice = ExpandedFrameSlice { + tof_indices, + scan_numbers, + intensities, + frame_index: frame.index, + rt: frame.rt, + acquisition_type: frame.acquisition_type, + ms_level: frame.ms_level, + quadrupole_settings: None, + intensity_correction_factor: frame.intensity_correction_factor, + window_group: frame.window_group, + window_subindex: 0u8, + }; + curr_slice.sort_by_tof(); + curr_slice +} - let mut out = Vec::with_capacity(quad_settings.scan_ends.len()); - for (i, qs) in expanded_quad_settings.into_iter().enumerate() { +fn expand_fragmented_frame( + frame: Frame, + quads: Vec, +) -> Vec { + let mut out = Vec::with_capacity(quads.len()); + let exploded_scans = explode_vec(&frame.scan_offsets); + for (i, qs) in quads.into_iter().enumerate() { // This whole block is kind of ugly but I think its good enough for now ... - let slice_scan_start = qs.ranges.scan_start; - let slice_scan_end = qs.ranges.scan_end; + let (slice_scan_start, slice_scan_end) = + trim_scan_edges(qs.ranges.scan_start, qs.ranges.scan_end); + let tof_index_index_slice_start = frame.scan_offsets[slice_scan_start]; let tof_index_index_slice_end = frame.scan_offsets[slice_scan_end]; - let mut slice_tof_indices = + let slice_tof_indices = frame.tof_indices[tof_index_index_slice_start..tof_index_index_slice_end].to_vec(); - let mut slice_scan_numbers = explode_scan_offsets( - &frame.scan_offsets[slice_scan_start..slice_scan_end], - slice_scan_start, - ); - let mut slice_intensities = + let slice_scan_numbers = + exploded_scans[tof_index_index_slice_start..tof_index_index_slice_end].to_vec(); + let slice_intensities = frame.intensities[tof_index_index_slice_start..tof_index_index_slice_end].to_vec(); - let mut indices = argsort_by(&slice_tof_indices, |x| *x); - sort_by_indices_multi!( - &mut indices, - &mut slice_tof_indices, - &mut slice_scan_numbers, - &mut slice_intensities - ); - let mut curr_slice = ExpandedFrameSlice { tof_indices: slice_tof_indices, scan_numbers: slice_scan_numbers, @@ -83,34 +130,35 @@ fn expand_and_split_frame(frame: &Frame) -> Vec { rt: frame.rt, acquisition_type: frame.acquisition_type, ms_level: frame.ms_level, - quadrupole_settings: qs, + quadrupole_settings: Some(qs), intensity_correction_factor: frame.intensity_correction_factor, window_group: frame.window_group, window_subindex: i as u8, }; + // Q: is this sorting twice? since sort before creating the expanded frame slices. + // TODO: Use the state type pattern to make sure only one sort happens. curr_slice.sort_by_tof(); out.push(curr_slice); } out } -fn explode_scan_offsets(scan_offsets: &[usize], offset_val: usize) -> Vec { - let num_vals = scan_offsets.last().unwrap(); - let mut exploded_offsets = vec![0; *num_vals]; - for i in 0..scan_offsets.len() - 1 { - let start = scan_offsets[i]; - let end = scan_offsets[i + 1]; - for pos in exploded_offsets.iter_mut().take(end).skip(start) { - *pos = i + offset_val; - } +pub fn expand_and_split_frame(frame: Frame) -> Vec { + let quad_settings = &frame.quadrupole_settings; + // Q: Can I save a vec allocation if I make the expanded quad_settings + // To return a vec of builders? or Enum(settings|frame_slice)? + let expanded_quad_settings = expand_quad_settings(quad_settings); + + match expanded_quad_settings { + ExpandedFrameQuadSettings::Unfragmented => vec![expand_unfragmented_frame(frame)], + ExpandedFrameQuadSettings::Fragmented(quads) => expand_fragmented_frame(frame, quads), } - exploded_offsets } impl ExpandedFrame { pub fn from_frame(frame: Frame) -> Self { let mut tof_indices = frame.tof_indices; - let mut scan_numbers = explode_scan_offsets(&frame.scan_offsets, 0); + let mut scan_numbers = explode_vec(&frame.scan_offsets); let mut intensities = frame.intensities; let mut indices = argsort_by(&tof_indices, |x| *x); @@ -140,13 +188,6 @@ impl ExpandedFrame { mod tests { use super::*; - #[test] - fn test_explode_scan_offsets() { - let scan_offsets = vec![0, 2, 4, 8]; - let exploded_offsets = explode_scan_offsets(&scan_offsets, 0); - assert_eq!(exploded_offsets, vec![0, 0, 1, 1, 2, 2, 2, 2]); - } - #[test] fn test_expanded_frame_from_frame() { let frame = Frame { diff --git a/src/models/frames/expanded_window_group.rs b/src/models/frames/expanded_window_group.rs index 1ac3c2b..261b7e9 100644 --- a/src/models/frames/expanded_window_group.rs +++ b/src/models/frames/expanded_window_group.rs @@ -12,7 +12,7 @@ pub struct ExpandedWindowGroup { // pub frame_indices: Vec, pub acquisition_type: AcquisitionType, pub ms_level: MSLevel, - pub quadrupole_settings: SingleQuadrupoleSetting, + pub quadrupole_settings: Option, // pub intensity_correction_factor: f64, pub window_group: u8, } diff --git a/src/models/frames/single_quad_settings.rs b/src/models/frames/single_quad_settings.rs index a27eb54..67f4cfd 100644 --- a/src/models/frames/single_quad_settings.rs +++ b/src/models/frames/single_quad_settings.rs @@ -36,6 +36,11 @@ impl Display for SingleQuadrupoleSettingRanges { } } +/// A single quadrupole setting. +/// +/// NOTE: Only the index is used for the hashing of this struct. +/// So make sure that int he buildingn process there is no generation +/// of settings with the same index. #[derive(Debug, Clone, Copy)] pub struct SingleQuadrupoleSetting { pub index: SingleQuadrupoleSettingIndex, @@ -81,7 +86,17 @@ impl PartialEq for SingleQuadrupoleSetting { impl Eq for SingleQuadrupoleSetting {} -pub fn expand_quad_settings(quad_settings: &QuadrupoleSettings) -> Vec { +#[derive(Debug, Clone, Hash, PartialEq)] +pub enum ExpandedFrameQuadSettings { + Unfragmented, + Fragmented(Vec), +} + +pub fn expand_quad_settings(quad_settings: &QuadrupoleSettings) -> ExpandedFrameQuadSettings { + if quad_settings.scan_ends.is_empty() { + return ExpandedFrameQuadSettings::Unfragmented; + } + let mut out = Vec::with_capacity(quad_settings.scan_ends.len()); for i in 0..quad_settings.scan_ends.len() { let isolation_width = quad_settings.isolation_width[i]; @@ -108,5 +123,5 @@ pub fn expand_quad_settings(quad_settings: &QuadrupoleSettings) -> Vec PeakBucket { let mut indices = argsort_by(&self.scan_offsets, |x| *x); sort_by_indices_multi!( @@ -102,7 +113,16 @@ impl PeakBucketBuilder { &mut self.intensities ); // TODO consider if I really need to compress this. - let out = if self.scan_offsets.len() > 1000 { + // Options: + // 1. Change the compression of scans (I use the default in timsrust but im sure we can do + // better) ... + // - tuple of val-offset to prevent the long runs of non changing scans. + // - btree of offsets? + // 2. Not compressing makes queries <10% slower, but building the index 10% faster ... + // compressing all makes building the index 3x slower. + // + // let out = if false { + let out = if self.scan_offsets.len() > 500 { let compressed = compress_vec(&self.scan_offsets); PeakBucket { intensities: self.intensities, diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index 30bfb0e..162eea9 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -1,9 +1,12 @@ use super::peak_bucket::PeakBucketBuilder; use super::peak_bucket::{PeakBucket, PeakInBucket}; +use crate::models::frames::expanded_frame::{expand_and_split_frame, ExpandedFrameSlice}; use crate::models::frames::raw_peak::RawPeak; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; +use crate::sort_by_indices_multi; use crate::utils::display::{glimpse_vec, GlimpseConfig}; - +use crate::utils::sorting::{argsort_by, par_argsort_by}; +use log::debug; use log::info; use log::trace; use rayon::prelude::*; @@ -14,7 +17,7 @@ use timsrust::converters::{ConvertableDomain, Frame2RtConverter}; #[derive(Debug)] pub struct TransposedQuadIndex { - pub quad_settings: SingleQuadrupoleSetting, + pub quad_settings: Option, pub frame_rts: Vec, pub frame_indices: Vec, pub peak_buckets: BTreeMap, @@ -60,7 +63,7 @@ impl Display for TransposedQuadIndex { fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { write!( f, - "TransposedQuadIndex\n quad_settings: {}\n frame_indices: {}\n frame_rts: {}\n peak_buckets: {}\n", + "TransposedQuadIndex\n quad_settings: {:?}\n frame_indices: {}\n frame_rts: {}\n peak_buckets: {}\n", self.quad_settings, glimpse_vec(&self.frame_indices, Some(GlimpseConfig { max_items: 10, padding: 2, new_line: true })), glimpse_vec(&self.frame_rts, Some(GlimpseConfig { max_items: 10, padding: 2, new_line: true })), @@ -192,7 +195,7 @@ impl FrameRTTolerance { #[derive(Debug, Clone)] pub struct TransposedQuadIndexBuilder { - quad_settings: SingleQuadrupoleSetting, + quad_settings: Option, int_slices: Vec>, tof_slices: Vec>, scan_slices: Vec>, @@ -201,7 +204,7 @@ pub struct TransposedQuadIndexBuilder { } impl TransposedQuadIndexBuilder { - pub fn new(quad_settings: SingleQuadrupoleSetting) -> Self { + pub fn new(quad_settings: Option) -> Self { Self { quad_settings, int_slices: Vec::new(), @@ -220,34 +223,29 @@ impl TransposedQuadIndexBuilder { self.frame_rts.extend(other.frame_rts); } - pub fn add_frame_slice( - &mut self, - int_slice: Vec, - tof_slice: Vec, - expanded_scan_slice: Vec, - frame_index: usize, - frame_rt: f64, - ) { - assert!(int_slice.len() == tof_slice.len()); - assert!(int_slice.len() == expanded_scan_slice.len()); - - self.int_slices.push(int_slice); - self.tof_slices.push(tof_slice); - self.scan_slices.push(expanded_scan_slice); - self.frame_indices.push(frame_index); - self.frame_rts.push(frame_rt); + pub fn add_frame_slice(&mut self, slice: ExpandedFrameSlice) { + self.int_slices.push(slice.intensities); + self.tof_slices.push(slice.tof_indices); + self.scan_slices.push(slice.scan_numbers); + self.frame_indices.push(slice.frame_index); + self.frame_rts.push(slice.rt); } pub fn build(self) -> TransposedQuadIndex { + // TODO: Refactor this function, its getting pretty large. let st = Instant::now(); + info!( + "TransposedQuadIndex::build start ... quad_settings = {:?}", + self.quad_settings + ); let max_tof = *self .tof_slices .iter() .map(|x| x.iter().max().unwrap()) .max() .unwrap(); - let mut tof_counts = vec![0; max_tof as usize + 1]; - let mut tot_peaks = 0; + let mut tof_counts = vec![0usize; max_tof as usize + 1]; + let mut tot_peaks = 0u64; for tof_slice in self.tof_slices.iter() { for tof in tof_slice.iter() { tof_counts[*tof as usize] += 1; @@ -264,41 +262,17 @@ impl TransposedQuadIndexBuilder { continue; } } - let out_rts = self.frame_rts.clone(); let out_indices = self.frame_indices.clone(); - let mut added_peaks = 0; + let quad_settings = self.quad_settings; let aps = Instant::now(); - for slice_ind in 0..self.frame_indices.len() { - let int_slice = &self.int_slices[slice_ind]; - let tof_slice = &self.tof_slices[slice_ind]; - let scan_slice = &self.scan_slices[slice_ind]; - // let frame_index = self.frame_indices[slice_ind]; - let frame_rt = self.frame_rts[slice_ind] as f32; - - // Q: is it worth to sort and add peaks in slices? - - for ((inten, tof), scan) in int_slice - .iter() - .zip(tof_slice.iter()) - .zip(scan_slice.iter()) - { - peak_buckets - .get_mut(tof) - .expect("Should have just added it...") - .add_peak(*scan, *inten, frame_rt); - - added_peaks += 1; - } - } - let aps = aps.elapsed(); - - if added_peaks != tot_peaks { - println!("TransposedQuadIndex::add_frame_slice failed at peak count check, expected: {}, real: {}", tot_peaks, added_peaks); - panic!("TransposedQuadIndex::add_frame_slice failed at peak count check"); - } + peak_buckets = if tot_peaks > 10_000_000 { + self.batched_build_inner(peak_buckets, tot_peaks) + } else { + self.build_inner_ref(peak_buckets, tot_peaks) + }; for (tof, count) in tof_counts.into_iter().enumerate() { if count > 0 { @@ -316,28 +290,212 @@ impl TransposedQuadIndexBuilder { } let bb_st = Instant::now(); - let peak_bucket = BTreeMap::from_par_iter( - peak_buckets - .into_par_iter() - .map(|(tof, pb)| (tof, pb.build())), - ); + + // FYI par iter here makes no difference. + let peak_bucket: BTreeMap = peak_buckets + .into_iter() + .map(|(tof, pb)| (tof, pb.build())) + .collect(); let bbe = bb_st.elapsed(); let elapsed = st.elapsed(); info!( "TransposedQuadIndex::add_frame_slice adding peaks took {:#?} for {} peaks", - aps, tot_peaks + aps.elapsed(), + tot_peaks ); info!( "TransposedQuadIndex::add_frame_slice building buckets took {:#?}", bbe ); - info!("TransposedQuadIndex::build took {:#?}", elapsed); + info!( + "TransposedQuadIndex::build quad_settings={:?} took {:#?}", + quad_settings, elapsed + ); TransposedQuadIndex { - quad_settings: self.quad_settings, + quad_settings, frame_rts: out_rts, frame_indices: out_indices, peak_buckets: peak_bucket, } } + + fn build_inner_ref( + self, + mut peak_buckets: HashMap, + tot_peaks: u64, + ) -> HashMap { + let mut added_peaks = 0; + + for slice_ind in 0..self.frame_indices.len() { + let int_slice = &self.int_slices[slice_ind]; + let tof_slice = &self.tof_slices[slice_ind]; + let scan_slice = &self.scan_slices[slice_ind]; + let frame_rt = self.frame_rts[slice_ind] as f32; + + // Q: is it worth to sort and add peaks in slices? If we do it has to be one level + // higher, since within each slice, most tof indices would not repeat. + // A: Nope ... this is faster. + // + // In theory there are 3 things to consider: + // 1. Can we hold a vec that large? (u32::MAX in teory for a 32 bit system) + // - For According to the playground ... 268_435_455 is the max number of + // u32's that can be allocated ... in some of our data the MS1s have 500M peaks. + // so even if we do it, we would need to batch it ... + // as a note most MS2s are ~20M + // 2. Is the sorting slower than querying the hash map that many times? + // - Sorting is slower ... + // 3. I am assuming that sequential import would let us grow each vec only once + // per chunk addition instead of once per ... peak in the worst case (although vecs + // grow in chunks of +25% ish ...) + // - Might be true but we allocate the vecs with capacity, so they dont grow while + // we iterate + // + for ((inten, tof), scan) in int_slice + .iter() + .zip(tof_slice.iter()) + .zip(scan_slice.iter()) + { + peak_buckets + .get_mut(tof) + .expect("Should have just added it...") + .add_peak(*scan, *inten, frame_rt); + + added_peaks += 1; + if added_peaks % 500_000 == 0 { + debug!( + "TransposedQuadIndex::build quad_settings={:?} added_peaks={:?}/{:?}", + self.quad_settings, added_peaks, tot_peaks, + ); + } + } + } + + if added_peaks != tot_peaks { + println!("TransposedQuadIndex::add_frame_slice failed at peak count check, expected: {}, real: {}", tot_peaks, added_peaks); + panic!("TransposedQuadIndex::add_frame_slice failed at peak count check"); + } + + peak_buckets + } + + fn batched_build_inner( + self, + mut peak_buckets: HashMap, + tot_peaks: u64, + ) -> HashMap { + let info_prefix = format!("BatchedBuild: quad_settings={:?} ", self.quad_settings); + info!("{} start", info_prefix); + let num_slices = self.frame_indices.len(); + let mut added_peaks = 0; + + let mut peaks_in_chunk = 0; + let mut start = 0; + let mut end = 0; + + while start < self.frame_indices.len() { + while peaks_in_chunk < 100_000_000 && end < self.frame_indices.len() { + peaks_in_chunk += self.int_slices[end].len(); + end += 1; + } + + let concat_st = Instant::now(); + let mut int_slice = self.int_slices[start..end].concat(); + let mut tof_slice = self.tof_slices[start..end].concat(); + let mut scan_slice = self.scan_slices[start..end].concat(); + let mut rt_slice: Vec = self.frame_rts[start..end] + .iter() + .zip(self.tof_slices[start..end].iter()) + .flat_map(|(rt, tofslice)| vec![*rt as f32; tofslice.len()]) + .collect(); + + let concat_elapsed = concat_st.elapsed(); + + let sorting_st = Instant::now(); + // let mut indices = argsort_by(&tof_slice, |x| *x); + let mut indices = par_argsort_by(&tof_slice, |x| *x); + + let argsort_elapsed = sorting_st.elapsed(); + + sort_by_indices_multi!( + &mut indices, + &mut tof_slice, + &mut scan_slice, + &mut int_slice, + &mut rt_slice + ); + + let sorting_elapsed = sorting_st.elapsed(); + + let insertion_st = Instant::now(); + let mut slice_start = 0; + let mut slice_start_val = tof_slice[0]; + while slice_start < int_slice.len() { + // // Binary search the current value + 1 + // let slice_end = tof_slice.binary_search(&(slice_start_val + 1)); + + // // let local_slice_end = slice_end.unwrap_or_else(|x| x); + // let local_slice_end = match slice_end { + // Ok(x) => { + // // If the value is found, we need to walk back to find the first instance + // // of the value ... + // let mut local_slice_end = x; + // while tof_slice[local_slice_end - 1] > slice_start_val { + // local_slice_end -= 1; + // } + // local_slice_end + // } + // Err(x) => x, + // }; + // + let mut local_slice_end = slice_start; + while tof_slice[local_slice_end] == slice_start_val { + local_slice_end += 1; + // There has to be a way to add this to the conditional above ... + // But alas ... this works ... + if local_slice_end == tof_slice.len() { + break; + } + } + + let range_use = slice_start..local_slice_end; + + peak_buckets + .get_mut(&slice_start_val) + .expect("Tof should have been added during the build") + .extend_peaks( + &scan_slice[range_use.clone()], + &int_slice[range_use.clone()], + &rt_slice[range_use.clone()], + ); + + added_peaks += range_use.len() as u64; + + assert!(slice_start_val == tof_slice[slice_start]); + + if local_slice_end == tof_slice.len() { + break; + } + assert!(slice_start_val < tof_slice[local_slice_end]); + + slice_start = local_slice_end; + slice_start_val = tof_slice[slice_start]; + } + + let insertion_elapsed = insertion_st.elapsed(); + info!( + "BatchedBuild: quad_settings={:?} start={:?} end={:?}/{} peaks {}/{} concat took {:#?} sorting took arg: {:#?} / {:#?} insertion took {:#?}", + self.quad_settings, start, end, num_slices, added_peaks, tot_peaks, concat_elapsed, argsort_elapsed, sorting_elapsed, insertion_elapsed, + ); + start = end; + peaks_in_chunk = 0; + } + + if added_peaks != tot_peaks { + println!("TransposedQuadIndex::add_frame_slice failed at peak count check, expected: {}, real: {}", tot_peaks, added_peaks); + panic!("TransposedQuadIndex::add_frame_slice failed at peak count check"); + } + + peak_buckets + } } diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 260347b..f41e963 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -2,6 +2,7 @@ use super::quad_index::{ FrameRTTolerance, PeakInQuad, TransposedQuadIndex, TransposedQuadIndexBuilder, }; use crate::models::elution_group::ElutionGroup; +use crate::models::frames::expanded_frame::{expand_and_split_frame, ExpandedFrameSlice}; use crate::models::frames::raw_peak::RawPeak; use crate::models::frames::single_quad_settings::expand_quad_settings; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; @@ -33,7 +34,8 @@ use timsrust::TimsRustError; // - JSP: 2024-11-19 pub struct QuadSplittedTransposedIndex { - indices: HashMap, TransposedQuadIndex>, + precursor_index: TransposedQuadIndex, + fragment_indices: HashMap, flat_quad_settings: Vec, rt_converter: Frame2RtConverter, pub mz_converter: Tof2MzConverter, @@ -74,7 +76,7 @@ impl QuadSplittedTransposedIndex { let rt_range = rt_range.map(|x| x.to_frame_index_range(&self.rt_converter)); matching_quads.into_iter().flat_map(move |qs| { - let tqi = self.indices.get(&qs).unwrap(); + let tqi = self.fragment_indices.get(&qs).unwrap(); tqi.query_peaks(tof_range, scan_range, rt_range) }) } @@ -91,14 +93,36 @@ impl QuadSplittedTransposedIndex { && (qs.ranges.isolation_high >= precursor_mz_range.0) }) .filter(move |qs| { - if let Some(scan_range) = scan_range { - // This is done for sanity tbh ... sometimes they get flipped - // bc the lowest scan is actually the highest 1/k0. - let min_scan = qs.ranges.scan_start.min(qs.ranges.scan_end); - let max_scan = qs.ranges.scan_start.max(qs.ranges.scan_end); - (min_scan <= scan_range.1) && (scan_range.0 <= max_scan) - } else { - true + // if let Some(scan_range) = scan_range { + // // This is done for sanity tbh ... sometimes they get flipped + // // bc the lowest scan is actually the highest 1/k0. + // } else { + // true + // } + // + match scan_range { + Some((min_scan, max_scan)) => { + assert!(qs.ranges.scan_start <= qs.ranges.scan_end); + assert!(min_scan <= max_scan); + + // Above quad + // Quad [----------] + // Query [------] + let above_quad = qs.ranges.scan_end < min_scan; + + // Below quad + // Quad [------] + // Query [------] + let below_quad = qs.ranges.scan_start > max_scan; + + if above_quad || below_quad { + // This quad is completely outside the scan range + false + } else { + true + } + } + None => true, } }) .cloned() @@ -190,13 +214,19 @@ impl Display for QuadSplittedTransposedIndex { new_line: true, }), )); + + disp_str.push_str("precursor_index: \n"); + disp_str.push_str(&format!(" -- {}\n", self.precursor_index)); let mut num_shown = 0; - for (qs, tqi) in self.indices.iter() { - disp_str.push_str(&format!(" - {}: \n", qs)); + for (qs, tqi) in self.fragment_indices.iter() { + disp_str.push_str(&format!(" - {:?}: \n", qs)); disp_str.push_str(&format!(" -- {}\n", tqi)); num_shown += 1; if num_shown > 5 { - disp_str.push_str(&format!(" ........ len = {}\n", self.indices.len())); + disp_str.push_str(&format!( + " ........ len = {}\n", + self.fragment_indices.len() + )); break; } } @@ -218,8 +248,9 @@ impl QuadSplittedTransposedIndex { } } +#[derive(Debug, Clone, Default)] pub struct QuadSplittedTransposedIndexBuilder { - indices: HashMap, + indices: HashMap, TransposedQuadIndexBuilder>, rt_converter: Option, mz_converter: Option, im_converter: Option, @@ -231,56 +262,32 @@ pub struct QuadSplittedTransposedIndexBuilder { } impl QuadSplittedTransposedIndexBuilder { - fn new() -> Self { - Self { - indices: HashMap::new(), - rt_converter: None, - mz_converter: None, - im_converter: None, - metadata: None, - added_peaks: 0, - } + pub fn new() -> Self { + Self::default() } fn add_frame(&mut self, frame: Frame) { - let expanded_quad_settings = expand_quad_settings(&frame.quadrupole_settings); - let exploded_scans = explode_vec(&frame.scan_offsets); + let expanded_slices = expand_and_split_frame(frame); - for qs in expanded_quad_settings { + for es in expanded_slices.into_iter() { // Add key if it doesnt exist ... - if let Entry::Vacant(e) = self.indices.entry(qs) { - let max_tof = frame.tof_indices.iter().max().unwrap(); - trace!( - "Adding new transposed quad index for qs {:?} with max tof {}", - qs, - max_tof - ); - let new_index = TransposedQuadIndexBuilder::new(qs); - e.insert(new_index); - } - - let peak_start = frame.scan_offsets[qs.ranges.scan_start]; - let peak_end = frame.scan_offsets[qs.ranges.scan_end + 1]; - - let int_slice = frame.intensities[peak_start..peak_end].to_vec(); - let tof_slice = frame.tof_indices[peak_start..peak_end].to_vec(); - let expanded_scan_slice = exploded_scans[peak_start..peak_end].to_vec(); - - let frame_index = frame.index; - let frame_rt = frame.rt; - self.added_peaks += int_slice.len() as u64; + self.indices + .entry(es.quadrupole_settings) + .or_insert(TransposedQuadIndexBuilder::new(es.quadrupole_settings)); - self.indices.get_mut(&qs).unwrap().add_frame_slice( - int_slice, - tof_slice, - expanded_scan_slice, - frame_index, - frame_rt, - ); + self.added_peaks += es.len() as u64; + self.add_frame_slice(es); } } + fn add_frame_slice(&mut self, frame_slice: ExpandedFrameSlice) { + self.indices + .get_mut(&frame_slice.quadrupole_settings) + .unwrap() + .add_frame_slice(frame_slice); + } + fn from_path(path: &str) -> Result { let file_reader = FrameReader::new(path)?; @@ -297,9 +304,9 @@ impl QuadSplittedTransposedIndexBuilder { added_peaks: 0, }; - let out2: Result, TimsRustError> = file_reader - .get_all() + let out2: Result, TimsRustError> = (0..file_reader.len()) .into_par_iter() + .map(|id| file_reader.get(id)) .chunks(100) .map(|frames| { let mut out = Self::new(); @@ -320,7 +327,7 @@ impl QuadSplittedTransposedIndexBuilder { Ok(final_out) } - fn fold(&mut self, other: Self) { + pub fn fold(&mut self, other: Self) { for (qs, builder) in other.indices.into_iter() { self.indices .entry(qs) @@ -330,19 +337,23 @@ impl QuadSplittedTransposedIndexBuilder { self.added_peaks += other.added_peaks; } - fn build(self) -> QuadSplittedTransposedIndex { + pub fn build(self) -> QuadSplittedTransposedIndex { let mut indices = HashMap::new(); let mut flat_quad_settings = Vec::new(); - let built: Vec<(TransposedQuadIndex, SingleQuadrupoleSetting)> = self + let built: Vec<(TransposedQuadIndex, Option)> = self .indices .into_par_iter() .map(|(qs, builder)| (builder.build(), qs)) .collect(); + let mut precursor_index: Option = None; for (qi, qs) in built.into_iter() { - let qa: Arc = Arc::new(qs); - indices.insert(qa.clone(), qi); - flat_quad_settings.push(qs); + if let Some(qs) = qs { + indices.insert(qs, qi); + flat_quad_settings.push(qs); + } else { + precursor_index = Some(qi); + } } flat_quad_settings.sort_by(|a, b| { @@ -353,7 +364,8 @@ impl QuadSplittedTransposedIndexBuilder { }); QuadSplittedTransposedIndex { - indices, + precursor_index: precursor_index.expect("Precursor peaks should be present"), + fragment_indices: indices, flat_quad_settings, rt_converter: self.rt_converter.unwrap(), mz_converter: self.mz_converter.unwrap(), diff --git a/src/utils/math.rs b/src/utils/math.rs index b55af29..029fd70 100644 --- a/src/utils/math.rs +++ b/src/utils/math.rs @@ -10,3 +10,11 @@ pub fn lnfact(n: u16) -> f64 { n * n.ln() - n + 0.5 * n.ln() + 0.5 * (std::f64::consts::PI * 2.0 * n).ln() } } + +pub fn lnfact_float(n: f64) -> f64 { + if n < 1.0 { + 0.0 + } else { + n * n.ln() - n + 0.5 * n.ln() + 0.5 * (std::f64::consts::PI * 2.0 * n).ln() + } +} diff --git a/src/utils/sorting.rs b/src/utils/sorting.rs index 53fd838..2f528eb 100644 --- a/src/utils/sorting.rs +++ b/src/utils/sorting.rs @@ -1,3 +1,5 @@ +use rayon::prelude::*; + fn place_at_indices(original: &mut [T], indices: &mut [usize]) { for i in 0..indices.len() { while i != indices[i] { @@ -26,7 +28,20 @@ where K: Ord, { let mut indices: Vec = (0..v.len()).collect(); - indices.sort_by_key(|&i| key(&v[i])); + // indices.sort_by_key(|&i| key(&v[i])); + indices.sort_unstable_by_key(|&i| key(&v[i])); + indices +} + +pub fn par_argsort_by(v: &[T], key: F) -> Vec +where + F: Fn(&T) -> K + Sync + Send, + K: Ord + Sync + Send, + T: Sync + Send, +{ + let mut indices: Vec = (0..v.len()).collect(); + // indices.sort_by_key(|&i| key(&v[i])); + indices.par_sort_unstable_by_key(|&i| key(&v[i])); indices } From 3263f919cb061a610e3714c92bb557124fcbd9dd Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Thu, 17 Oct 2024 15:11:10 -0700 Subject: [PATCH 03/30] chore: clippy and format --- src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs | 4 ++-- src/models/indices/transposed_quad_index/quad_index.rs | 4 ++-- .../transposed_quad_index/quad_splitted_transposed_index.rs | 4 ---- 3 files changed, 4 insertions(+), 8 deletions(-) diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs index b9baf0d..ad20484 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs @@ -192,7 +192,7 @@ impl NaturalFinalizedMultiCMGSt .into_iter() .map(|x| { let out = mobility_converter.convert(x); - if out < 0.5 || out > 2.0 { + if !(0.5..=2.0).contains(&out) { debug!("Bad mobility value: {:?}, input was {:?}", out, x); } out @@ -328,7 +328,7 @@ impl From 1000.0 { + if !(0.0..=1000.0).contains(&out) { warn!("Bad mobility value: {:?}, input was {:?}", out, x); } diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index 162eea9..beaf7cf 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -1,11 +1,11 @@ use super::peak_bucket::PeakBucketBuilder; use super::peak_bucket::{PeakBucket, PeakInBucket}; -use crate::models::frames::expanded_frame::{expand_and_split_frame, ExpandedFrameSlice}; +use crate::models::frames::expanded_frame::ExpandedFrameSlice; use crate::models::frames::raw_peak::RawPeak; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; use crate::sort_by_indices_multi; use crate::utils::display::{glimpse_vec, GlimpseConfig}; -use crate::utils::sorting::{argsort_by, par_argsort_by}; +use crate::utils::sorting::par_argsort_by; use log::debug; use log::info; use log::trace; diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index f41e963..ec489b7 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -4,23 +4,19 @@ use super::quad_index::{ use crate::models::elution_group::ElutionGroup; use crate::models::frames::expanded_frame::{expand_and_split_frame, ExpandedFrameSlice}; use crate::models::frames::raw_peak::RawPeak; -use crate::models::frames::single_quad_settings::expand_quad_settings; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; use crate::models::queries::FragmentGroupIndexQuery; use crate::models::queries::PrecursorIndexQuery; use crate::traits::indexed_data::IndexedData; -use crate::utils::compress_explode::explode_vec; use crate::utils::display::{glimpse_vec, GlimpseConfig}; use crate::ToleranceAdapter; use log::{debug, info, trace}; use rayon::prelude::*; use serde::Serialize; -use std::collections::hash_map::Entry; use std::collections::HashMap; use std::fmt::Debug; use std::fmt::Display; use std::hash::Hash; -use std::sync::Arc; use std::time::Instant; use timsrust::converters::{ ConvertableDomain, Frame2RtConverter, Scan2ImConverter, Tof2MzConverter, From 3564fcc0e5dbe34331c08af99c0c58fa54673428 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Tue, 22 Oct 2024 07:40:05 -0700 Subject: [PATCH 04/30] feat(wip)!: addition of simpler index n ...a lot --- src/models/frames/expanded_frame.rs | 163 ++++++++++++++ src/models/indices/expanded_raw_index/mod.rs | 1 + .../indices/expanded_raw_index/model.rs | 77 +++++++ src/models/indices/mod.rs | 1 + .../transposed_quad_index/quad_index.rs | 1 - .../quad_splitted_transposed_index.rs | 185 ++++++++++++---- src/utils/frame_processing.rs | 199 ++++++++++++++++++ src/utils/mod.rs | 2 + src/utils/tolerance_ranges.rs | 38 ++++ 9 files changed, 626 insertions(+), 41 deletions(-) create mode 100644 src/models/indices/expanded_raw_index/model.rs create mode 100644 src/utils/frame_processing.rs create mode 100644 src/utils/tolerance_ranges.rs diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index a58d555..1570d8a 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -1,13 +1,21 @@ +use std::collections::HashMap; use std::sync::Arc; use super::single_quad_settings::{ expand_quad_settings, ExpandedFrameQuadSettings, SingleQuadrupoleSetting, }; +use itertools::Itertools; +use rayon::iter::IntoParallelIterator; +use rayon::prelude::*; +use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; use timsrust::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}; use crate::sort_by_indices_multi; use crate::utils::compress_explode::explode_vec; +use crate::utils::frame_processing::lazy_centroid_weighted_frame; use crate::utils::sorting::argsort_by; +use crate::utils::tolerance_ranges::{scan_tol_range, tof_tol_range}; +use log::debug; /// A frame after expanding the mobility data and re-sorting it by tof. #[derive(Debug, Clone)] @@ -184,6 +192,161 @@ impl ExpandedFrame { } } +pub fn expand_and_arrange_frames( + frames: Vec, +) -> HashMap, Vec> { + let mut out = HashMap::new(); + let split: Vec = frames + .into_par_iter() + .flat_map(|frame| expand_and_split_frame(frame)) + .collect(); + for es in split { + out.entry(es.quadrupole_settings) + .or_insert(Vec::new()) + .push(es); + } + + // Finally sort each of them internally by retention time. + for (_, es) in out.iter_mut() { + es.sort_unstable_by(|a, b| a.rt.partial_cmp(&b.rt).unwrap()); + } + out +} + +pub fn par_expand_and_centroid_frames( + frames: Vec, + ims_tol_pct: f64, + mz_tol_ppm: f64, + ims_converter: &Scan2ImConverter, + mz_converter: &Tof2MzConverter, +) -> HashMap, Vec> { + let split_frames = expand_and_arrange_frames(frames); + + let out: HashMap, Vec> = split_frames + .into_iter() + .map(|(qs, frameslices)| { + // NOTE: Since the the centroiding runs in paralel over the windows, its ok if this + // outer loop is done in series. + let start_peaks: usize = frameslices.iter().map(|x| x.len()).sum(); + let centroided = par_lazy_centroid_frameslices( + &frameslices, + 3, + ims_tol_pct, + mz_tol_ppm, + ims_converter, + mz_converter, + ); + let end_peaks: usize = centroided.iter().map(|x| x.len()).sum(); + debug!( + "Peak counts for quad {:?}: raw={}/centroid={}", + qs, start_peaks, end_peaks + ); + (qs, centroided) + }) + .collect(); + + out +} + +fn centroid_frameslice_window( + frameslices: &[ExpandedFrameSlice], + ims_tol_pct: f64, + mz_tol_ppm: f64, + ims_converter: &Scan2ImConverter, + mz_converter: &Tof2MzConverter, +) -> ExpandedFrameSlice { + assert!(frameslices.len() > 1, "Expected at least 2 frameslices"); + let reference_index = frameslices.len() / 2; + + // this is A LOT of cloning ... look into whether it is needed. + + let mut tof_array: Vec = frameslices + .iter() + .flat_map(|x| x.tof_indices.clone()) + .collect(); + + let mut ims_array: Vec = frameslices + .iter() + .flat_map(|x| x.scan_numbers.clone()) + .collect(); + let mut weight_array: Vec = frameslices + .iter() + .flat_map(|x| x.intensities.clone()) + .collect(); + let mut intensity_array: Vec = frameslices + .iter() + .enumerate() + .flat_map(|(i, x)| { + if i == reference_index { + x.intensities.clone() + } else { + vec![0u32; x.tof_indices.len()] + } + }) + .collect(); + + let mut tof_order = argsort_by(&tof_array, |x| *x); + sort_by_indices_multi!( + &mut tof_order, + &mut tof_array, + &mut ims_array, + &mut weight_array, + &mut intensity_array + ); + + let ((mzs, intensities), imss) = lazy_centroid_weighted_frame( + &tof_array, + &ims_array, + &weight_array, + &intensity_array, + |&tof| tof_tol_range(tof, mz_tol_ppm, mz_converter), + |&scan| scan_tol_range(scan, ims_tol_pct, ims_converter), + ); + + ExpandedFrameSlice { + tof_indices: mzs, + scan_numbers: imss, + intensities, + frame_index: frameslices[reference_index].frame_index, + rt: frameslices[reference_index].rt, + acquisition_type: frameslices[reference_index].acquisition_type, + ms_level: frameslices[reference_index].ms_level, + quadrupole_settings: frameslices[reference_index].quadrupole_settings, + intensity_correction_factor: frameslices[reference_index].intensity_correction_factor, + window_group: frameslices[reference_index].window_group, + window_subindex: frameslices[reference_index].window_subindex, + } +} + +pub fn par_lazy_centroid_frameslices( + frameslices: &[ExpandedFrameSlice], + window_width: usize, + ims_tol_pct: f64, + mz_tol_ppm: f64, + ims_converter: &Scan2ImConverter, + mz_converter: &Tof2MzConverter, +) -> Vec { + assert!( + frameslices + .iter() + .tuple_windows() + .map(|(a, b)| { a.rt < b.rt && a.quadrupole_settings == b.quadrupole_settings }) + .all(|x| x), + "All frames should be sorted by rt and have the same quad settings" + ); + + assert!(frameslices.len() > window_width); + + let local_lambda = |fss: &[ExpandedFrameSlice]| { + centroid_frameslice_window(fss, ims_tol_pct, mz_tol_ppm, ims_converter, mz_converter) + }; + + frameslices + .par_windows(window_width) + .map(|window| local_lambda(window)) + .collect() +} + #[cfg(test)] mod tests { use super::*; diff --git a/src/models/indices/expanded_raw_index/mod.rs b/src/models/indices/expanded_raw_index/mod.rs index e69de29..ee2d47a 100644 --- a/src/models/indices/expanded_raw_index/mod.rs +++ b/src/models/indices/expanded_raw_index/mod.rs @@ -0,0 +1 @@ +mod model; diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs new file mode 100644 index 0000000..10155f6 --- /dev/null +++ b/src/models/indices/expanded_raw_index/model.rs @@ -0,0 +1,77 @@ +use crate::models::frames::expanded_frame::ExpandedFrame; +use crate::models::frames::expanded_frame::{ + expand_and_split_frame, par_expand_and_centroid_frames, ExpandedFrameSlice, +}; +use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; +use log::debug; +use std::collections::HashMap; +use std::sync::Arc; +use std::time::Instant; +use timsrust::converters::{ + ConvertableDomain, Frame2RtConverter, Scan2ImConverter, Tof2MzConverter, +}; +use timsrust::readers::{FrameReader, FrameReaderError, MetadataReader}; +use timsrust::{QuadrupoleSettings, TimsRustError}; + +type QuadSettingsIndex = usize; + +#[derive(Debug, Default)] +struct ExpandedRawFrameIndex { + bundled_ms1_frames: Vec, + bundled_frames: HashMap>, + flat_quad_settings: Vec, + rt_converter: Frame2RtConverter, + pub mz_converter: Tof2MzConverter, + pub im_converter: Scan2ImConverter, +} + +impl ExpandedRawFrameIndex { + pub fn from_tdf_path(path: &str) -> Result { + let file_reader = FrameReader::new(path)?; + + let sql_path = std::path::Path::new(path).join("analysis.tdf"); + let meta_converters = MetadataReader::new(&sql_path)?; + + let st = Instant::now(); + let all_frames = file_reader.get_all().into_iter().flatten().collect(); + let read_elap = st.elapsed(); + debug!("Reading all frames took {:#?}", read_elap); + let st = Instant::now(); + let centroided_split_frames = par_expand_and_centroid_frames( + all_frames, + 1.5, + 15.0, + &meta_converters.im_converter, + &meta_converters.mz_converter, + ); + let centroided_elap = st.elapsed(); + debug!("Centroiding took {:#?}", centroided_elap); + + let mut out_ms2_frames = HashMap::new(); + let mut out_ms1_frames: Option> = None; + + centroided_split_frames + .into_iter() + .for_each(|(q, frameslices)| match q { + None => { + out_ms1_frames = Some(frameslices); + } + Some(q) => { + out_ms2_frames.insert(q, frameslices); + } + }); + + let mut flat_quad_settings = out_ms2_frames.keys().cloned().collect(); + + let out = Self { + bundled_ms1_frames: out_ms1_frames.expect("At least one ms1 frame should be present"), + bundled_frames: out_ms2_frames, + flat_quad_settings, + rt_converter: meta_converters.rt_converter, + mz_converter: meta_converters.mz_converter, + im_converter: meta_converters.im_converter, + }; + + Ok(out) + } +} diff --git a/src/models/indices/mod.rs b/src/models/indices/mod.rs index f912a50..b8cb6e1 100644 --- a/src/models/indices/mod.rs +++ b/src/models/indices/mod.rs @@ -1,2 +1,3 @@ +pub mod expanded_raw_index; pub mod raw_file_index; pub mod transposed_quad_index; diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index beaf7cf..8b4f2cf 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -9,7 +9,6 @@ use crate::utils::sorting::par_argsort_by; use log::debug; use log::info; use log::trace; -use rayon::prelude::*; use std::collections::{BTreeMap, HashMap}; use std::fmt::Display; use std::time::Instant; diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index ec489b7..bdc718c 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -2,7 +2,9 @@ use super::quad_index::{ FrameRTTolerance, PeakInQuad, TransposedQuadIndex, TransposedQuadIndexBuilder, }; use crate::models::elution_group::ElutionGroup; -use crate::models::frames::expanded_frame::{expand_and_split_frame, ExpandedFrameSlice}; +use crate::models::frames::expanded_frame::{ + expand_and_split_frame, par_expand_and_centroid_frames, ExpandedFrameSlice, +}; use crate::models::frames::raw_peak::RawPeak; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; use crate::models::queries::FragmentGroupIndexQuery; @@ -50,13 +52,16 @@ impl Debug for QuadSplittedTransposedIndex { } impl QuadSplittedTransposedIndex { - pub fn query_peaks( + pub fn query_peaks( &self, tof_range: (u32, u32), precursor_mz_range: (f64, f64), scan_range: Option<(usize, usize)>, rt_range: Option, - ) -> impl Iterator + '_ { + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { trace!( "QuadSplittedTransposedIndex::query_peaks tof_range: {:?}, scan_range: {:?}, rt_range: {:?}, precursor_mz_range: {:?}", tof_range, @@ -68,13 +73,29 @@ impl QuadSplittedTransposedIndex { .get_matching_quad_settings(precursor_mz_range, scan_range) .collect(); trace!("matching_quads: {:?}", matching_quads); + self.query_precursor_peaks(&matching_quads, tof_range, scan_range, rt_range, f); + } + fn query_precursor_peaks( + &self, + matching_quads: &[SingleQuadrupoleSetting], + tof_range: (u32, u32), + scan_range: Option<(usize, usize)>, + rt_range: Option, + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { let rt_range = rt_range.map(|x| x.to_frame_index_range(&self.rt_converter)); - matching_quads.into_iter().flat_map(move |qs| { - let tqi = self.fragment_indices.get(&qs).unwrap(); + for quad in matching_quads { + let tqi = self + .fragment_indices + .get(quad) + .expect("Only existing quads should be queried."); tqi.query_peaks(tof_range, scan_range, rt_range) - }) + .for_each(&mut *f); + } } fn get_matching_quad_settings( @@ -89,13 +110,6 @@ impl QuadSplittedTransposedIndex { && (qs.ranges.isolation_high >= precursor_mz_range.0) }) .filter(move |qs| { - // if let Some(scan_range) = scan_range { - // // This is done for sanity tbh ... sometimes they get flipped - // // bc the lowest scan is actually the highest 1/k0. - // } else { - // true - // } - // match scan_range { Some((min_scan, max_scan)) => { assert!(qs.ranges.scan_start <= qs.ranges.scan_end); @@ -242,6 +256,20 @@ impl QuadSplittedTransposedIndex { debug!("{}", out); Ok(out) } + + pub fn from_path_centroided(path: &str) -> Result { + let st = Instant::now(); + info!( + "Building CENTROIDED transposed quad index from path {}", + path + ); + let tmp = QuadSplittedTransposedIndexBuilder::from_path_centroided(path)?; + let out = tmp.build(); + let elapsed = st.elapsed(); + info!("Transposed CENTROIDED quad index built in {:#?}", elapsed); + debug!("{}", out); + Ok(out) + } } #[derive(Debug, Clone, Default)] @@ -266,24 +294,28 @@ impl QuadSplittedTransposedIndexBuilder { let expanded_slices = expand_and_split_frame(frame); for es in expanded_slices.into_iter() { - // Add key if it doesnt exist ... - - self.indices - .entry(es.quadrupole_settings) - .or_insert(TransposedQuadIndexBuilder::new(es.quadrupole_settings)); - - self.added_peaks += es.len() as u64; self.add_frame_slice(es); } } fn add_frame_slice(&mut self, frame_slice: ExpandedFrameSlice) { + // Add key if it doesnt exist ... + self.indices + .entry(frame_slice.quadrupole_settings) + .or_insert(TransposedQuadIndexBuilder::new( + frame_slice.quadrupole_settings, + )); + + self.added_peaks += frame_slice.len() as u64; self.indices .get_mut(&frame_slice.quadrupole_settings) .unwrap() .add_frame_slice(frame_slice); } + // TODO: I think i should split this into two functions, one that starts the builder + // and one that adds the frameslices, maybe even have a config struct that dispatches + // the right preprocessing steps. fn from_path(path: &str) -> Result { let file_reader = FrameReader::new(path)?; @@ -323,6 +355,64 @@ impl QuadSplittedTransposedIndexBuilder { Ok(final_out) } + fn from_path_centroided(path: &str) -> Result { + let file_reader = FrameReader::new(path)?; + + let sql_path = std::path::Path::new(path).join("analysis.tdf"); + let meta_converters = MetadataReader::new(&sql_path)?; + + let out_meta_converters = meta_converters.clone(); + let mut final_out = Self { + indices: HashMap::new(), + rt_converter: Some(meta_converters.rt_converter), + mz_converter: Some(meta_converters.mz_converter), + im_converter: Some(meta_converters.im_converter), + metadata: Some(out_meta_converters), + added_peaks: 0, + }; + + let st = Instant::now(); + let all_frames = file_reader.get_all().into_iter().flatten().collect(); + let read_elap = st.elapsed(); + debug!("Reading all frames took {:#?}", read_elap); + let st = Instant::now(); + let centroided_split_frames = par_expand_and_centroid_frames( + all_frames, + 1.5, + 15.0, + &meta_converters.im_converter, + &meta_converters.mz_converter, + ); + let centroided_elap = st.elapsed(); + debug!("Centroiding took {:#?}", centroided_elap); + + let st = Instant::now(); + let out2: Result, TimsRustError> = centroided_split_frames + .into_par_iter() + .map(|(q, frameslices)| { + let mut out = Self::new(); + for frameslice in frameslices { + out.add_frame_slice(frameslice); + } + Ok(out) + }) + .collect(); + + let out2 = out2?.into_iter().fold(Self::new(), |mut x, y| { + x.fold(y); + x + }); + final_out.fold(out2); + let build_elap = st.elapsed(); + + info!( + "Reading all frames took {:#?}, centroiding took {:#?}, building took {:#?}", + read_elap, centroided_elap, build_elap + ); + + Ok(final_out) + } + pub fn fold(&mut self, other: Self) { for (qs, builder) in other.indices.into_iter() { self.indices @@ -388,13 +478,15 @@ impl .mz_index_ranges .iter() .flat_map(|(_, tof_range)| { + let mut local_vec = vec![]; self.query_peaks( *tof_range, precursor_mz_range, scan_range, frame_index_range, - ) - .map(RawPeak::from) + &mut |x| local_vec.push(RawPeak::from(x)), + ); + local_vec.into_iter() }) .collect() } @@ -422,8 +514,8 @@ impl precursor_mz_range, scan_range, frame_index_range, - ) - .for_each(|peak| aggregator.add(&RawPeak::from(peak))); + &mut |peak| aggregator.add(&RawPeak::from(peak)), + ); }) } @@ -448,8 +540,13 @@ impl )); for (_, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { - self.query_peaks(tof_range, precursor_mz_range, scan_range, frame_index_range) - .for_each(|peak| agg.add(&RawPeak::from(peak))); + self.query_peaks( + tof_range, + precursor_mz_range, + scan_range, + frame_index_range, + &mut |peak| agg.add(&RawPeak::from(peak)), + ); } }); } @@ -475,17 +572,16 @@ impl .mz_index_ranges .iter() .flat_map(|(fh, tof_range)| { - let out: Vec<(RawPeak, FH)> = self - .query_peaks( - *tof_range, - precursor_mz_range, - scan_range, - frame_index_range, - ) - .map(|x| (RawPeak::from(x), *fh)) - .collect(); + let mut local_vec: Vec<(RawPeak, FH)> = vec![]; + self.query_peaks( + *tof_range, + precursor_mz_range, + scan_range, + frame_index_range, + &mut |x| local_vec.push((RawPeak::from(x), *fh)), + ); - out + local_vec }) .collect() } @@ -513,8 +609,8 @@ impl precursor_mz_range, scan_range, frame_index_range, - ) - .for_each(|peak| aggregator.add(&(RawPeak::from(peak), *fh))); + &mut |peak| aggregator.add(&(RawPeak::from(peak), *fh)), + ); }) } @@ -538,9 +634,18 @@ impl fragment_query.precursor_query.frame_index_range, )); + let local_quad_vec: Vec = self + .get_matching_quad_settings(precursor_mz_range, scan_range) + .collect(); + for (fh, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { - self.query_peaks(tof_range, precursor_mz_range, scan_range, frame_index_range) - .for_each(|peak| agg.add(&(RawPeak::from(peak), fh))); + self.query_precursor_peaks( + &local_quad_vec, + tof_range, + scan_range, + frame_index_range, + &mut |peak| agg.add(&(RawPeak::from(peak), fh)), + ); } }); } diff --git a/src/utils/frame_processing.rs b/src/utils/frame_processing.rs new file mode 100644 index 0000000..d6f832a --- /dev/null +++ b/src/utils/frame_processing.rs @@ -0,0 +1,199 @@ +use log::warn; +use std::cmp::Ordering; +use std::ops::RangeInclusive; +use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; + +pub fn squash_frame( + mz_array: &[f32], + intensity_array: &[f32], + tol_ppm: f32, +) -> (Vec, Vec) { + // Make sure the mz array is sorted + assert!(mz_array.windows(2).all(|x| x[0] <= x[1])); + + let arr_len = mz_array.len(); + let mut touched = vec![false; arr_len]; + let mut global_num_touched = 0; + + let mut order: Vec = (0..arr_len).collect(); + order.sort_unstable_by(|&a, &b| { + intensity_array[b] + .partial_cmp(&intensity_array[a]) + .unwrap_or(Ordering::Equal) + }); + + let mut agg_mz = vec![0.0; arr_len]; + let mut agg_intensity = vec![0.0; arr_len]; + + let utol = tol_ppm / 1e6; + + for &idx in &order { + if touched[idx] { + continue; + } + + let mz = mz_array[idx]; + let da_tol = mz * utol; + let left_e = mz - da_tol; + let right_e = mz + da_tol; + + let ss_start = mz_array.partition_point(|&x| x < left_e); + let ss_end = mz_array.partition_point(|&x| x <= right_e); + + let slice_width = ss_end - ss_start; + let local_num_touched = touched[ss_start..ss_end].iter().filter(|&&x| x).count(); + let local_num_untouched = slice_width - local_num_touched; + + if local_num_touched == slice_width { + continue; + } + + let mut curr_intensity = 0.0; + let mut curr_weighted_mz = 0.0; + + for i in ss_start..ss_end { + if !touched[i] && intensity_array[i] > 0.0 { + curr_intensity += intensity_array[i]; + curr_weighted_mz += mz_array[i] * intensity_array[i]; + } + } + + if curr_intensity > 0.0 { + curr_weighted_mz /= curr_intensity; + + agg_intensity[idx] = curr_intensity; + agg_mz[idx] = curr_weighted_mz; + + touched[ss_start..ss_end].iter_mut().for_each(|x| *x = true); + global_num_touched += local_num_untouched; + } + + if global_num_touched == arr_len { + break; + } + } + + // Drop the zeros and sort + let mut result: Vec<(f32, f32)> = agg_mz + .into_iter() + .zip(agg_intensity.into_iter()) + .filter(|&(mz, intensity)| mz > 0.0 && intensity > 0.0) + .collect(); + + result.sort_unstable_by(|a, b| a.0.partial_cmp(&b.0).unwrap_or(Ordering::Equal)); + + result.into_iter().unzip() +} + +pub type TofIntensityVecs = (Vec, Vec); +pub type CentroidedVecs = (TofIntensityVecs, Vec); + +pub fn lazy_centroid_weighted_frame( + tof_array: &[u32], + ims_array: &[usize], + weight_array: &[u32], + intensity_array: &[u32], + tof_tol_range_fn: impl Fn(&u32) -> RangeInclusive, + ims_tol_range_fn: impl Fn(&usize) -> RangeInclusive, +) -> CentroidedVecs { + let arr_len = tof_array.len(); + const MIN_WEIGHT_PRESERVE: u64 = 50; + + // TODO make the asserts optional at compile time. + assert!( + tof_array.windows(2).all(|x| x[0] <= x[1]), + "Expected tof array to be sorted" + ); + assert_eq!( + arr_len, + intensity_array.len(), + "Expected tof and intensity arrays to be the same length" + ); + assert_eq!( + arr_len, + weight_array.len(), + "Expected tof and weight arrays to be the same length" + ); + assert_eq!( + arr_len, + ims_array.len(), + "Expected tof and ims arrays to be the same length" + ); + + let mut touched = vec![false; arr_len]; + let mut global_num_touched = 0; + + // We will be iterating in decreasing order of intensity + let mut order: Vec = (0..arr_len).collect(); + order.sort_unstable_by(|&a, &b| { + weight_array[b] + .partial_cmp(&weight_array[a]) + .unwrap_or(Ordering::Equal) + }); + + let mut agg_tof = vec![0; arr_len]; + let mut agg_intensity = vec![0; arr_len]; + // We will not be returning the weights. + // let mut agg_weight = vec![0; arr_len]; + let mut agg_ims = vec![0; arr_len]; + + for idx in order { + if touched[idx] { + continue; + } + + let tof = tof_array[idx]; + let ims = ims_array[idx]; + let tof_range = tof_tol_range_fn(&tof); + let ims_range = ims_tol_range_fn(&ims); + + let ss_start = tof_array.partition_point(|x| x < tof_range.start()); + let ss_end = tof_array.partition_point(|x| x <= tof_range.end()); + + let mut curr_intensity = 0u64; + let mut curr_weight = 0u64; + let mut curr_agg_tof = 0u64; + let mut curr_agg_ims = 0u64; + + for i in ss_start..ss_end { + if !touched[i] && intensity_array[i] > 0 && ims_range.contains(&ims_array[i]) { + let local_weight = weight_array[i] as u64; + curr_intensity += intensity_array[i] as u64; + curr_agg_tof += tof_array[i] as u64 * local_weight; + curr_agg_ims += ims_array[i] as u64 * local_weight; + curr_weight += local_weight; + } + } + + if curr_intensity > 0 && curr_weight > 0 { + agg_intensity[idx] = u32::try_from(curr_intensity).expect("Expected to fit in u32"); + agg_tof[idx] = (curr_agg_tof / curr_weight) as u32; + agg_ims[idx] = (curr_agg_ims / curr_weight) as usize; + + for i in ss_start..ss_end { + touched[i] = true; + global_num_touched += 1; + } + } + + if global_num_touched == arr_len { + break; + } + } + + // Drop the zeros and sort by mz (tof) + let mut res: Vec<((u32, u32), usize)> = agg_tof + .into_iter() + .zip(agg_intensity.into_iter()) + .zip(agg_ims.into_iter()) + .filter(|&((_, intensity), ims)| (intensity > 0) & (ims > 0)) + .collect(); + + res.sort_unstable_by(|a, b| a.0.partial_cmp(&b.0).unwrap_or(Ordering::Equal)); + let output_len = res.len(); + if arr_len > 500 && (output_len == arr_len) { + warn!("Output length is the same as input length, this is probably a bug"); + } + + res.into_iter().unzip() +} diff --git a/src/utils/mod.rs b/src/utils/mod.rs index 4807e91..1d8244c 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -1,4 +1,6 @@ pub mod compress_explode; pub mod display; +pub mod frame_processing; pub mod math; pub mod sorting; +pub mod tolerance_ranges; diff --git a/src/utils/tolerance_ranges.rs b/src/utils/tolerance_ranges.rs new file mode 100644 index 0000000..dcb3978 --- /dev/null +++ b/src/utils/tolerance_ranges.rs @@ -0,0 +1,38 @@ +use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter}; + +use std::ops::RangeInclusive; + +pub fn ppm_tol_range(elem: f64, tol_ppm: f64) -> RangeInclusive { + let utol = tol_ppm / 1e6; + let left_e = elem - utol; + let right_e = elem + utol; + left_e..=right_e +} + +pub fn tof_tol_range(tof: u32, tol_ppm: f64, converter: &Tof2MzConverter) -> RangeInclusive { + let mz = converter.convert(tof); + let mz_range = ppm_tol_range(mz, tol_ppm); + RangeInclusive::new( + converter.invert(*mz_range.start()).round() as u32, + converter.invert(*mz_range.end()).round() as u32, + ) +} + +pub fn scan_tol_range( + scan: usize, + tol_pct: f64, + converter: &Scan2ImConverter, +) -> RangeInclusive { + let im = converter.convert(scan as f64); + let im_range = ppm_tol_range(im, tol_pct); + let scan_min = converter.invert(*im_range.start()).round() as usize; + let scan_max = converter.invert(*im_range.end()).round() as usize; + // Note I need to do this here bc the conversion between scan numbers and ion + // mobilities is not monotonically increasing. IN OTHER WORDS, lower scan numbers + // are higher 1/k0.... But im not sure if they are ALWAYS inversely proportional. + if scan_min > scan_max { + scan_max..=scan_min + } else { + scan_min..=scan_max + } +} From 833bea0b16198dc7ca800c683cfdb8f7f734cd55 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Wed, 23 Oct 2024 17:43:49 -0700 Subject: [PATCH 05/30] (chore,feat): Added new index and refactored benchmarks --- Cargo.lock | 186 +--------- Cargo.toml | 8 +- benches/benchmark_indices.rs | 313 +++++++++-------- src/models/adapters.rs | 90 +++++ src/models/frames/expanded_frame.rs | 162 ++++++--- src/models/frames/expanded_window_group.rs | 6 +- src/models/frames/mod.rs | 1 + src/models/frames/peak_in_quad.rs | 20 ++ src/models/frames/single_quad_settings.rs | 40 +++ src/models/indices/expanded_raw_index/mod.rs | 2 + .../indices/expanded_raw_index/model.rs | 326 +++++++++++++++++- .../transposed_quad_index/quad_index.rs | 36 +- .../quad_splitted_transposed_index.rs | 144 +------- src/models/mod.rs | 1 + 14 files changed, 773 insertions(+), 562 deletions(-) create mode 100644 src/models/adapters.rs create mode 100644 src/models/frames/peak_in_quad.rs diff --git a/Cargo.lock b/Cargo.lock index 78f1f39..2bdd6b6 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -61,12 +61,6 @@ dependencies = [ "libc", ] -[[package]] -name = "anes" -version = "0.1.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299" - [[package]] name = "anstream" version = "0.6.15" @@ -273,12 +267,6 @@ version = "1.6.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "a12916984aab3fa6e39d655a33e09c0071eb36d6ab3aea5c2d78551f1df6d952" -[[package]] -name = "cast" -version = "0.3.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5" - [[package]] name = "cc" version = "1.1.7" @@ -307,33 +295,6 @@ dependencies = [ "windows-targets", ] -[[package]] -name = "ciborium" -version = "0.2.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "42e69ffd6f0917f5c029256a24d0161db17cea3997d185db0d35926308770f0e" -dependencies = [ - "ciborium-io", - "ciborium-ll", - "serde", -] - -[[package]] -name = "ciborium-io" -version = "0.2.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "05afea1e0a06c9be33d539b876f1ce3692f4afea2cb41f740e7743225ed1c757" - -[[package]] -name = "ciborium-ll" -version = "0.2.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "57663b653d948a338bfb3eeba9bb2fd5fcfaecb9e199e87e1eda4d9e8b240fd9" -dependencies = [ - "ciborium-io", - "half", -] - [[package]] name = "clap" version = "4.5.17" @@ -428,42 +389,6 @@ dependencies = [ "cfg-if", ] -[[package]] -name = "criterion" -version = "0.5.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f2b12d017a929603d80db1831cd3a24082f8137ce19c69e6447f54f5fc8d692f" -dependencies = [ - "anes", - "cast", - "ciborium", - "clap", - "criterion-plot", - "is-terminal", - "itertools 0.10.5", - "num-traits", - "once_cell", - "oorandom", - "plotters", - "rayon", - "regex", - "serde", - "serde_derive", - "serde_json", - "tinytemplate", - "walkdir", -] - -[[package]] -name = "criterion-plot" -version = "0.5.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6b50826342786a51a89e2da3a28f1c32b06e387201bc2d19791f622c673706b1" -dependencies = [ - "cast", - "itertools 0.10.5", -] - [[package]] name = "crossbeam-deque" version = "0.8.5" @@ -619,12 +544,6 @@ version = "0.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea" -[[package]] -name = "hermit-abi" -version = "0.3.9" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024" - [[package]] name = "humantime" version = "2.1.0" @@ -683,32 +602,12 @@ version = "3.0.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "8bb03732005da905c88227371639bf1ad885cc712789c011c31c5fb3ab3ccf02" -[[package]] -name = "is-terminal" -version = "0.4.12" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b" -dependencies = [ - "hermit-abi", - "libc", - "windows-sys", -] - [[package]] name = "is_terminal_polyfill" version = "1.70.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf" -[[package]] -name = "itertools" -version = "0.10.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473" -dependencies = [ - "either", -] - [[package]] name = "itertools" version = "0.13.0" @@ -981,12 +880,6 @@ version = "1.19.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92" -[[package]] -name = "oorandom" -version = "11.1.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b410bbe7e14ab526a0e86877eb47c6996a2bd7746f027ba551028c925390e4e9" - [[package]] name = "ordered-float" version = "2.10.1" @@ -1039,34 +932,6 @@ version = "0.3.30" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec" -[[package]] -name = "plotters" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a15b6eccb8484002195a3e44fe65a4ce8e93a625797a063735536fd59cb01cf3" -dependencies = [ - "num-traits", - "plotters-backend", - "plotters-svg", - "wasm-bindgen", - "web-sys", -] - -[[package]] -name = "plotters-backend" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "414cec62c6634ae900ea1c56128dfe87cf63e7caece0852ec76aba307cebadb7" - -[[package]] -name = "plotters-svg" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "81b30686a7d9c3e010b84284bdd26a29f2138574f52f5eb6f794fc0ad924e705" -dependencies = [ - "plotters-backend", -] - [[package]] name = "portable-atomic" version = "1.7.0" @@ -1230,15 +1095,6 @@ version = "1.0.18" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f" -[[package]] -name = "same-file" -version = "1.0.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502" -dependencies = [ - "winapi-util", -] - [[package]] name = "semver" version = "1.0.23" @@ -1365,10 +1221,9 @@ name = "timsquery" version = "0.4.0" dependencies = [ "clap", - "criterion", "env_logger", "indicatif", - "itertools 0.13.0", + "itertools", "log", "rand", "rand_chacha", @@ -1406,16 +1261,6 @@ dependencies = [ "crunchy", ] -[[package]] -name = "tinytemplate" -version = "1.2.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "be4d6b5f19ff7664e8c98d03e2139cb510db9b0a60b55f8e8709b689d939b6bc" -dependencies = [ - "serde", - "serde_json", -] - [[package]] name = "twox-hash" version = "1.6.3" @@ -1456,16 +1301,6 @@ version = "0.9.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a" -[[package]] -name = "walkdir" -version = "2.5.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b" -dependencies = [ - "same-file", - "winapi-util", -] - [[package]] name = "wasi" version = "0.11.0+wasi-snapshot-preview1" @@ -1526,25 +1361,6 @@ version = "0.2.92" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96" -[[package]] -name = "web-sys" -version = "0.3.69" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "77afa9a11836342370f4817622a2f0f418b134426d91a82dfb48f532d2ec13ef" -dependencies = [ - "js-sys", - "wasm-bindgen", -] - -[[package]] -name = "winapi-util" -version = "0.1.8" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b" -dependencies = [ - "windows-sys", -] - [[package]] name = "windows-core" version = "0.52.0" diff --git a/Cargo.toml b/Cargo.toml index 5b5ae85..c65ac8e 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -22,9 +22,6 @@ log = "0.4.22" env_logger = "0.11.5" -[dev-dependencies] -criterion = { version = "0.5", features = ["html_reports"] } - [features] clap = ["dep:clap"] build-binary = ["clap"] @@ -33,10 +30,9 @@ build-binary = ["clap"] name = "timsquery" required-features = ["build-binary"] -[[bench]] +[[bin]] name = "benchmark_indices" -harness = false - +path = "benches/benchmark_indices.rs" [profile.release] opt-level = 3 diff --git a/benches/benchmark_indices.rs b/benches/benchmark_indices.rs index 79f0adc..84a355e 100644 --- a/benches/benchmark_indices.rs +++ b/benches/benchmark_indices.rs @@ -1,29 +1,64 @@ -use criterion::{criterion_group, criterion_main, BatchSize, BenchmarkId, Criterion}; use rand::{Rng, SeedableRng}; use rand_chacha::ChaCha8Rng; +use serde::Serialize; use std::collections::HashMap; - -use std::hint::black_box; +use std::fs::File; +use std::time::{Duration, Instant}; use timsquery::{ models::{ aggregators::RawPeakIntensityAggregator, indices::{ - raw_file_index::RawFileIndex, transposed_quad_index::QuadSplittedTransposedIndex, + expanded_raw_index::ExpandedRawFrameIndex, raw_file_index::RawFileIndex, + transposed_quad_index::QuadSplittedTransposedIndex, }, }, - queriable_tims_data::queriable_tims_data::{query_indexed, query_multi_group}, + queriable_tims_data::queriable_tims_data::query_multi_group, traits::tolerance::DefaultTolerance, ElutionGroup, }; +const NUM_ELUTION_GROUPS: usize = 500; +const NUM_ITERATIONS: usize = 1; + +#[derive(Debug, Serialize)] +struct BenchmarkIteration { + iteration: usize, + duration_seconds: f64, +} + +#[derive(Debug, Serialize)] +struct BenchmarkResult { + name: String, + context: String, + iterations: Vec, + mean_duration_seconds: f64, +} + +#[derive(Debug, Serialize)] +struct BenchmarkReport { + settings: BenchmarkSettings, + results: Vec, + metadata: BenchmarkMetadata, +} + +#[derive(Debug, Serialize)] +struct BenchmarkSettings { + num_elution_groups: usize, + num_iterations: usize, +} + +#[derive(Debug, Serialize)] +struct BenchmarkMetadata { + basename: String, +} + +fn duration_to_seconds(duration: Duration) -> f64 { + duration.as_secs() as f64 + duration.subsec_nanos() as f64 * 1e-9 +} + fn get_file_from_env() -> (String, String) { - // Read from environment variable the raw file path to use - // env var name: TIMS_DATA_FILE - let raw_file_path = std::env::var("TIMS_DATA_FILE"); - let raw_file_path = match raw_file_path { - Ok(path) => path, - Err(_) => panic!("TIMS_DATA_FILE environment variable not set"), - }; + let raw_file_path = + std::env::var("TIMS_DATA_FILE").expect("TIMS_DATA_FILE environment variable not set"); let basename = std::path::Path::new(&raw_file_path) .file_stem() @@ -35,8 +70,7 @@ fn get_file_from_env() -> (String, String) { (raw_file_path, basename) } -const NUM_ELUTION_GROUPS: usize = 500; -fn build_elution_groups(raw_file_path: String) -> Vec> { +fn build_elution_groups() -> Vec> { const NUM_FRAGMENTS: usize = 10; const MAX_RT: f32 = 22.0 * 60.0; const MAX_MOBILITY: f32 = 1.5; @@ -44,187 +78,148 @@ fn build_elution_groups(raw_file_path: String) -> Vec> { const MAX_MZ: f64 = 1000.0; const MIN_MZ: f64 = 300.0; - let mut out_egs: Vec> = Vec::with_capacity(NUM_ELUTION_GROUPS); + let mut out_egs = Vec::with_capacity(NUM_ELUTION_GROUPS); let mut rng = ChaCha8Rng::seed_from_u64(43u64); for i in 1..NUM_ELUTION_GROUPS { - // Rand f32/64 are number from 0-1 let rt = rng.gen::() * MAX_RT; let mobility = rng.gen::() * (MAX_MOBILITY - MIN_MOBILITY) + MIN_MOBILITY; let mz = rng.gen::() * (MAX_MZ - MIN_MZ) + MIN_MZ; let mut fragment_mzs = HashMap::with_capacity(NUM_FRAGMENTS); - for ii in 0..NUM_FRAGMENTS { let fragment_mz = rng.gen::() * (MAX_MZ - MIN_MZ) + MIN_MZ; - // let fragment_charge = rng.gen::() * 3 + 1; fragment_mzs.insert(ii as u64, fragment_mz); } - // rand u8 is number from 0-255 ... which is not amazing for us ... - // let precursor_charge = rng.gen::() * 3 + 1; - let precursor_charge = 2; - out_egs.push(ElutionGroup { id: i as u64, rt_seconds: rt, mobility, precursor_mz: mz, - precursor_charge, + precursor_charge: 2, fragment_mzs, }); } out_egs } -fn criterion_benchmark(c: &mut Criterion) { - let (raw_file_path, basename) = get_file_from_env(); - let mut group = c.benchmark_group("Encoding Time"); - - group.sample_size(10); - group.bench_function( - BenchmarkId::new("TransposedQuadIndex", basename.clone()), - |b| { - b.iter_batched( - || {}, - |()| { - QuadSplittedTransposedIndex::from_path(&black_box(raw_file_path.clone())) - .unwrap() - }, - BatchSize::SmallInput, - ) - }, - ); - group.bench_function(BenchmarkId::new("RawFileIndex", basename.clone()), |b| { - b.iter_batched( - || {}, - |()| RawFileIndex::from_path(&black_box(raw_file_path.clone())).unwrap(), - BatchSize::SmallInput, - ) +fn with_benchmark(name: &str, context: &str, f: impl Fn()) -> BenchmarkResult { + let mut iterations = Vec::with_capacity(NUM_ITERATIONS); + for i in 0..NUM_ITERATIONS { + println!("{name} iteration {i}"); + let start = Instant::now(); + f(); + let duration = start.elapsed(); + + iterations.push(BenchmarkIteration { + iteration: i + 1, + duration_seconds: duration_to_seconds(duration), + }); + } + + let mean = iterations.iter().map(|i| i.duration_seconds).sum::() / NUM_ITERATIONS as f64; + BenchmarkResult { + name: name.to_string(), + context: context.to_string(), + iterations, + mean_duration_seconds: mean, + } +} + +fn run_encoding_benchmark(raw_file_path: &str) -> Vec { + let rfi = with_benchmark("RawFileIndex", "Encoding", || { + RawFileIndex::from_path(raw_file_path).unwrap(); + }); + let erfi = with_benchmark("ExpandedRawFileIndex", "Encoding", || { + ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(); + }); + let tqi = with_benchmark("TransposedQuadIndex", "Encoding", || { + QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(); }); - group.finish(); + vec![tqi, rfi, erfi] } -macro_rules! add_bench_random { - ($group:expr, $raw_file_path:expr, $basename:expr, $name:literal, $index_type:ty, $tolerance_type:ty, ) => { - $group.bench_function(BenchmarkId::new($name, $basename.clone()), |b| { - b.iter_batched( - || { - ( - <$index_type>::from_path(&($raw_file_path.clone())).unwrap(), - build_elution_groups($raw_file_path.clone()), - <$tolerance_type>::default(), - ) - }, - |(index, query_groups, tolerance)| { - let local_lambda = |elution_group: &ElutionGroup| { - query_indexed( - &index, - &RawPeakIntensityAggregator::new, - &index, - &tolerance, - &elution_group, - ) - }; - for elution_group in query_groups { - let query_results = local_lambda(&elution_group); - black_box((|_query_results| false)(query_results)); - } - }, - BatchSize::PerIteration, - ) - }); - }; +fn run_batch_access_benchmark(raw_file_path: &str) -> Vec { + let query_groups = build_elution_groups(); + let tolerance = DefaultTolerance::default(); + + let rfi_index = RawFileIndex::from_path(raw_file_path).unwrap(); + let rfi = with_benchmark("RawFileIndex", "BatchAccess", || { + let _ = query_multi_group( + &rfi_index, + &rfi_index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new, + ); + }); + std::mem::drop(rfi_index); + + let erfi_index = ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(); + let erfi = with_benchmark("ExpandedRawFileIndex", "BatchAccess", || { + let _ = query_multi_group( + &erfi_index, + &erfi_index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new, + ); + }); + std::mem::drop(erfi_index); + + let tqi_index = QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(); + let tqi = with_benchmark("TransposedQuadIndex", "BatchAccess", || { + let _ = query_multi_group( + &tqi_index, + &tqi_index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new, + ); + }); + std::mem::drop(tqi_index); + + vec![tqi, rfi, erfi] } -macro_rules! add_bench_optim { - ($group:expr, $raw_file_path:expr, $basename:expr, $name:literal, $index_type:ty, $tolerance_type:ty, $query_func:expr,) => { - $group.bench_function(BenchmarkId::new($name, $basename.clone()), |b| { - b.iter_batched( - || { - ( - <$index_type>::from_path(&($raw_file_path.clone())).unwrap(), - build_elution_groups($raw_file_path.clone()), - <$tolerance_type>::default(), - ) - }, - |(index, query_groups, tolerance)| { - let qr = query_multi_group( - &index, - &index, - &tolerance, - &query_groups, - &RawPeakIntensityAggregator::new, - ); - black_box((|_qr| false)(qr)); - }, - BatchSize::PerIteration, - ) - }); + +fn write_results(results: Vec, basename: &str) -> std::io::Result<()> { + let report = BenchmarkReport { + settings: BenchmarkSettings { + num_elution_groups: NUM_ELUTION_GROUPS, + num_iterations: NUM_ITERATIONS, + }, + results, + metadata: BenchmarkMetadata { + basename: basename.to_string(), + }, }; + + let file = File::create(format!("benchmark_results_{}.json", basename))?; + serde_json::to_writer_pretty(file, &report)?; + Ok(()) } -fn thoughput_benchmark_random(c: &mut Criterion) { +fn main() { let (raw_file_path, basename) = get_file_from_env(); - let mut group = c.benchmark_group("RandomAccessThroughput"); - group.significance_level(0.05).sample_size(10); - group.throughput(criterion::Throughput::Elements(NUM_ELUTION_GROUPS as u64)); - - add_bench_random!( - group, - raw_file_path, - basename, - "TransposedQuadIndex", - QuadSplittedTransposedIndex, - DefaultTolerance, - ); + let mut all_results: Vec = vec![]; - add_bench_random!( - group, - raw_file_path, - basename, - "RawFileIndex", - RawFileIndex, - DefaultTolerance, + println!( + "Run Settings: Elution groups={}, Iterations={}, basename={}", + NUM_ELUTION_GROUPS, NUM_ITERATIONS, basename ); - group.finish(); -} - -fn thoughput_benchmark_optim(c: &mut Criterion) { - env_logger::init(); - let (raw_file_path, basename) = get_file_from_env(); - let mut group = c.benchmark_group("BatchAccessThroughput"); - group.significance_level(0.05).sample_size(10); - group.throughput(criterion::Throughput::Elements(NUM_ELUTION_GROUPS as u64)); - - add_bench_optim!( - group, - raw_file_path, - basename, - "TransposedQuadIndex", - QuadSplittedTransposedIndex, - DefaultTolerance, - query_multi_group, - ); + println!("Running encoding benchmarks..."); + let encoding_results = run_encoding_benchmark(&raw_file_path); + all_results.extend(encoding_results); - add_bench_optim!( - group, - raw_file_path, - basename, - "RawFileIndex", - RawFileIndex, - DefaultTolerance, - query_multi_group, - ); + println!("Running batch access benchmarks..."); + let batch_results = run_batch_access_benchmark(&raw_file_path); + all_results.extend(batch_results); - group.finish(); + match write_results(all_results, &basename) { + Ok(_) => println!("Results written to benchmark_results_{}.json", basename), + Err(e) => eprintln!("Error writing results: {}", e), + } } - -criterion_group!( - benches, - thoughput_benchmark_optim, - criterion_benchmark, - thoughput_benchmark_random, -); -criterion_main!(benches); diff --git a/src/models/adapters.rs b/src/models/adapters.rs new file mode 100644 index 0000000..61df79f --- /dev/null +++ b/src/models/adapters.rs @@ -0,0 +1,90 @@ +use crate::models::elution_group::ElutionGroup; +use crate::models::queries::{FragmentGroupIndexQuery, PrecursorIndexQuery}; +use crate::ToleranceAdapter; +use serde::Serialize; +use std::hash::Hash; +use timsrust::converters::ConvertableDomain; +use timsrust::Metadata; + +#[derive(Debug, Default)] +pub struct FragmentIndexAdapter { + pub metadata: Metadata, +} + +impl From for FragmentIndexAdapter { + fn from(metadata: Metadata) -> Self { + Self { metadata } + } +} + +impl + ToleranceAdapter, ElutionGroup> for FragmentIndexAdapter +{ + fn query_from_elution_group( + &self, + tol: &dyn crate::traits::tolerance::Tolerance, + elution_group: &ElutionGroup, + ) -> FragmentGroupIndexQuery { + let rt_range = tol.rt_range(elution_group.rt_seconds); + let mobility_range = tol.mobility_range(elution_group.mobility); + let precursor_mz_range = tol.mz_range(elution_group.precursor_mz); + let quad_range = tol.quad_range(elution_group.precursor_mz, elution_group.precursor_charge); + + let mz_index_range = ( + self.metadata.mz_converter.invert(precursor_mz_range.0) as u32, + self.metadata.mz_converter.invert(precursor_mz_range.1) as u32, + ); + let mobility_range = match mobility_range { + Some(mobility_range) => mobility_range, + None => (self.metadata.lower_im as f32, self.metadata.upper_im as f32), + }; + let mobility_index_range = ( + self.metadata.im_converter.invert(mobility_range.0) as usize, + self.metadata.im_converter.invert(mobility_range.1) as usize, + ); + let rt_range = match rt_range { + Some(rt_range) => rt_range, + None => (self.metadata.lower_rt as f32, self.metadata.upper_rt as f32), + }; + let frame_index_range = ( + self.metadata.rt_converter.invert(rt_range.0) as usize, + self.metadata.rt_converter.invert(rt_range.1) as usize, + ); + + assert!(frame_index_range.0 <= frame_index_range.1); + assert!(mz_index_range.0 <= mz_index_range.1); + // Since mobilities get mixed up bc low scan ranges are high 1/k0, I + // Just make sure they are sorted here. + let mobility_index_range = ( + mobility_index_range.0.min(mobility_index_range.1), + mobility_index_range.1.max(mobility_index_range.0), + ); + + let precursor_query = PrecursorIndexQuery { + frame_index_range, + mz_index_range, + mobility_index_range, + isolation_mz_range: quad_range, + }; + + let fqs = elution_group + .fragment_mzs + .iter() + .map(|(k, v)| { + let mz_range = tol.mz_range(*v); + ( + *k, + ( + self.metadata.mz_converter.invert(mz_range.0) as u32, + self.metadata.mz_converter.invert(mz_range.1) as u32, + ), + ) + }) + .collect(); + + FragmentGroupIndexQuery { + mz_index_ranges: fqs, + precursor_query, + } + } +} diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index 1570d8a..a55af8c 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -1,4 +1,5 @@ use std::collections::HashMap; +use std::marker::PhantomData; use std::sync::Arc; use super::single_quad_settings::{ @@ -10,6 +11,7 @@ use rayon::prelude::*; use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; use timsrust::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}; +use super::peak_in_quad::PeakInQuad; use crate::sort_by_indices_multi; use crate::utils::compress_explode::explode_vec; use crate::utils::frame_processing::lazy_centroid_weighted_frame; @@ -32,8 +34,17 @@ pub struct ExpandedFrame { pub window_group: u8, } +#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)] +pub enum UnsortedState {} +#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)] +pub enum SortedState {} + +pub trait SortingStateTrait {} +impl SortingStateTrait for UnsortedState {} +impl SortingStateTrait for SortedState {} + #[derive(Debug, Clone)] -pub struct ExpandedFrameSlice { +pub struct ExpandedFrameSlice { pub tof_indices: Vec, // I could Arc<[u32]> if I didnt want to sort by it ... pub scan_numbers: Vec, pub intensities: Vec, @@ -45,10 +56,11 @@ pub struct ExpandedFrameSlice { pub intensity_correction_factor: f64, pub window_group: u8, pub window_subindex: u8, + _sorting_state: PhantomData, } -impl ExpandedFrameSlice { - pub fn sort_by_tof(&mut self) { +impl ExpandedFrameSlice { + pub fn sort_by_tof(mut self) -> ExpandedFrameSlice { let mut indices = argsort_by(&self.tof_indices, |x| *x); sort_by_indices_multi!( &mut indices, @@ -56,6 +68,20 @@ impl ExpandedFrameSlice { &mut self.scan_numbers, &mut self.intensities ); + ExpandedFrameSlice { + tof_indices: self.tof_indices, + scan_numbers: self.scan_numbers, + intensities: self.intensities, + frame_index: self.frame_index, + rt: self.rt, + acquisition_type: self.acquisition_type, + ms_level: self.ms_level, + quadrupole_settings: self.quadrupole_settings, + intensity_correction_factor: self.intensity_correction_factor, + window_group: self.window_group, + window_subindex: self.window_subindex, + _sorting_state: PhantomData, + } } pub fn len(&self) -> usize { @@ -67,6 +93,52 @@ impl ExpandedFrameSlice { } } +impl ExpandedFrameSlice { + pub fn query_peaks( + &self, + tof_range: (u32, u32), + scan_range: Option<(usize, usize)>, + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { + let peak_range = { + let peak_ind_start = self.tof_indices.partition_point(|x| x < &tof_range.0); + let peak_ind_end = self.tof_indices.partition_point(|x| x <= &tof_range.1); + peak_ind_start..peak_ind_end + }; + + match scan_range { + Some((min_scan, max_scan)) => { + assert!(min_scan <= max_scan); + } + None => {} + }; + + for peak_ind in peak_range { + let scan_index = self.scan_numbers[peak_ind]; + match scan_range { + Some((min_scan, max_scan)) => { + if scan_index < min_scan || scan_index > max_scan { + continue; + } + } + None => {} + }; + + let intensity = self.intensities[peak_ind]; + let tof_index = self.tof_indices[peak_ind]; + let retention_time = self.rt; + f(PeakInQuad { + scan_index, + intensity, + tof_index, + retention_time: retention_time as f32, + }); + } + } +} + fn trim_scan_edges(scan_start: usize, scan_end: usize) -> (usize, usize) { // Poor man's fix to different quad windows bleeding onto each other ... // I will trim the smallest of 20 scans or 10% of the range size. @@ -88,11 +160,11 @@ fn trim_scan_edges(scan_start: usize, scan_end: usize) -> (usize, usize) { (new_start, new_end) } -fn expand_unfragmented_frame(frame: Frame) -> ExpandedFrameSlice { +fn expand_unfragmented_frame(frame: Frame) -> ExpandedFrameSlice { let scan_numbers = explode_vec(&frame.scan_offsets); let intensities = frame.intensities; let tof_indices = frame.tof_indices; - let mut curr_slice = ExpandedFrameSlice { + let curr_slice = ExpandedFrameSlice { tof_indices, scan_numbers, intensities, @@ -104,15 +176,16 @@ fn expand_unfragmented_frame(frame: Frame) -> ExpandedFrameSlice { intensity_correction_factor: frame.intensity_correction_factor, window_group: frame.window_group, window_subindex: 0u8, + _sorting_state: PhantomData::, }; - curr_slice.sort_by_tof(); - curr_slice + + curr_slice.sort_by_tof() } fn expand_fragmented_frame( frame: Frame, quads: Vec, -) -> Vec { +) -> Vec> { let mut out = Vec::with_capacity(quads.len()); let exploded_scans = explode_vec(&frame.scan_offsets); for (i, qs) in quads.into_iter().enumerate() { @@ -130,7 +203,7 @@ fn expand_fragmented_frame( let slice_intensities = frame.intensities[tof_index_index_slice_start..tof_index_index_slice_end].to_vec(); - let mut curr_slice = ExpandedFrameSlice { + let curr_slice = ExpandedFrameSlice { tof_indices: slice_tof_indices, scan_numbers: slice_scan_numbers, intensities: slice_intensities, @@ -142,16 +215,16 @@ fn expand_fragmented_frame( intensity_correction_factor: frame.intensity_correction_factor, window_group: frame.window_group, window_subindex: i as u8, + _sorting_state: PhantomData::, }; // Q: is this sorting twice? since sort before creating the expanded frame slices. // TODO: Use the state type pattern to make sure only one sort happens. - curr_slice.sort_by_tof(); - out.push(curr_slice); + out.push(curr_slice.sort_by_tof()); } out } -pub fn expand_and_split_frame(frame: Frame) -> Vec { +pub fn expand_and_split_frame(frame: Frame) -> Vec> { let quad_settings = &frame.quadrupole_settings; // Q: Can I save a vec allocation if I make the expanded quad_settings // To return a vec of builders? or Enum(settings|frame_slice)? @@ -194,9 +267,9 @@ impl ExpandedFrame { pub fn expand_and_arrange_frames( frames: Vec, -) -> HashMap, Vec> { +) -> HashMap, Vec>> { let mut out = HashMap::new(); - let split: Vec = frames + let split: Vec> = frames .into_par_iter() .flat_map(|frame| expand_and_split_frame(frame)) .collect(); @@ -219,42 +292,43 @@ pub fn par_expand_and_centroid_frames( mz_tol_ppm: f64, ims_converter: &Scan2ImConverter, mz_converter: &Tof2MzConverter, -) -> HashMap, Vec> { +) -> HashMap, Vec>> { let split_frames = expand_and_arrange_frames(frames); - let out: HashMap, Vec> = split_frames - .into_iter() - .map(|(qs, frameslices)| { - // NOTE: Since the the centroiding runs in paralel over the windows, its ok if this - // outer loop is done in series. - let start_peaks: usize = frameslices.iter().map(|x| x.len()).sum(); - let centroided = par_lazy_centroid_frameslices( - &frameslices, - 3, - ims_tol_pct, - mz_tol_ppm, - ims_converter, - mz_converter, - ); - let end_peaks: usize = centroided.iter().map(|x| x.len()).sum(); - debug!( - "Peak counts for quad {:?}: raw={}/centroid={}", - qs, start_peaks, end_peaks - ); - (qs, centroided) - }) - .collect(); + let out: HashMap, Vec>> = + split_frames + .into_iter() + .map(|(qs, frameslices)| { + // NOTE: Since the the centroiding runs in paralel over the windows, its ok if this + // outer loop is done in series. + let start_peaks: usize = frameslices.iter().map(|x| x.len()).sum(); + let centroided = par_lazy_centroid_frameslices( + &frameslices, + 3, + ims_tol_pct, + mz_tol_ppm, + ims_converter, + mz_converter, + ); + let end_peaks: usize = centroided.iter().map(|x| x.len()).sum(); + debug!( + "Peak counts for quad {:?}: raw={}/centroid={}", + qs, start_peaks, end_peaks + ); + (qs, centroided) + }) + .collect(); out } fn centroid_frameslice_window( - frameslices: &[ExpandedFrameSlice], + frameslices: &[ExpandedFrameSlice], ims_tol_pct: f64, mz_tol_ppm: f64, ims_converter: &Scan2ImConverter, mz_converter: &Tof2MzConverter, -) -> ExpandedFrameSlice { +) -> ExpandedFrameSlice { assert!(frameslices.len() > 1, "Expected at least 2 frameslices"); let reference_index = frameslices.len() / 2; @@ -303,6 +377,9 @@ fn centroid_frameslice_window( |&scan| scan_tol_range(scan, ims_tol_pct, ims_converter), ); + // Make sure everything is sorted ... + assert!(mzs.windows(2).all(|x| x[0] <= x[1])); + ExpandedFrameSlice { tof_indices: mzs, scan_numbers: imss, @@ -315,17 +392,18 @@ fn centroid_frameslice_window( intensity_correction_factor: frameslices[reference_index].intensity_correction_factor, window_group: frameslices[reference_index].window_group, window_subindex: frameslices[reference_index].window_subindex, + _sorting_state: PhantomData::, } } pub fn par_lazy_centroid_frameslices( - frameslices: &[ExpandedFrameSlice], + frameslices: &[ExpandedFrameSlice], window_width: usize, ims_tol_pct: f64, mz_tol_ppm: f64, ims_converter: &Scan2ImConverter, mz_converter: &Tof2MzConverter, -) -> Vec { +) -> Vec> { assert!( frameslices .iter() @@ -337,7 +415,7 @@ pub fn par_lazy_centroid_frameslices( assert!(frameslices.len() > window_width); - let local_lambda = |fss: &[ExpandedFrameSlice]| { + let local_lambda = |fss: &[ExpandedFrameSlice]| { centroid_frameslice_window(fss, ims_tol_pct, mz_tol_ppm, ims_converter, mz_converter) }; diff --git a/src/models/frames/expanded_window_group.rs b/src/models/frames/expanded_window_group.rs index 261b7e9..4283c2a 100644 --- a/src/models/frames/expanded_window_group.rs +++ b/src/models/frames/expanded_window_group.rs @@ -1,6 +1,6 @@ use std::iter::repeat; -use super::expanded_frame::ExpandedFrameSlice; +use super::expanded_frame::{ExpandedFrameSlice, SortingStateTrait}; use super::single_quad_settings::SingleQuadrupoleSetting; use timsrust::{AcquisitionType, MSLevel}; @@ -18,7 +18,9 @@ pub struct ExpandedWindowGroup { } impl ExpandedWindowGroup { - pub fn from_expanded_frame_slices(expanded_frame_slices: Vec) -> Self { + pub fn from_expanded_frame_slices( + expanded_frame_slices: Vec>, + ) -> Self { let num_peaks = expanded_frame_slices .iter() .map(|x| x.tof_indices.len()) diff --git a/src/models/frames/mod.rs b/src/models/frames/mod.rs index 7cffa4e..49c123f 100644 --- a/src/models/frames/mod.rs +++ b/src/models/frames/mod.rs @@ -1,5 +1,6 @@ pub mod expanded_frame; pub mod expanded_window_group; +pub mod peak_in_quad; pub mod raw_frames; pub mod raw_peak; pub mod single_quad_settings; diff --git a/src/models/frames/peak_in_quad.rs b/src/models/frames/peak_in_quad.rs new file mode 100644 index 0000000..7803399 --- /dev/null +++ b/src/models/frames/peak_in_quad.rs @@ -0,0 +1,20 @@ +use super::raw_peak::RawPeak; + +#[derive(Debug, Clone, Copy)] +pub struct PeakInQuad { + pub scan_index: usize, + pub intensity: u32, + pub retention_time: f32, + pub tof_index: u32, +} + +impl From for RawPeak { + fn from(peak_in_quad: PeakInQuad) -> Self { + RawPeak { + scan_index: peak_in_quad.scan_index, + tof_index: peak_in_quad.tof_index, + intensity: peak_in_quad.intensity, + retention_time: peak_in_quad.retention_time, + } + } +} diff --git a/src/models/frames/single_quad_settings.rs b/src/models/frames/single_quad_settings.rs index 67f4cfd..4747e3d 100644 --- a/src/models/frames/single_quad_settings.rs +++ b/src/models/frames/single_quad_settings.rs @@ -125,3 +125,43 @@ pub fn expand_quad_settings(quad_settings: &QuadrupoleSettings) -> ExpandedFrame } ExpandedFrameQuadSettings::Fragmented(out) } + +pub fn get_matching_quad_settings( + flat_quad_settings: &[SingleQuadrupoleSetting], + precursor_mz_range: (f64, f64), + scan_range: Option<(usize, usize)>, +) -> impl Iterator + '_ { + flat_quad_settings + .iter() + .filter(move |qs| { + (qs.ranges.isolation_low <= precursor_mz_range.1) + && (qs.ranges.isolation_high >= precursor_mz_range.0) + }) + .filter(move |qs| { + match scan_range { + Some((min_scan, max_scan)) => { + assert!(qs.ranges.scan_start <= qs.ranges.scan_end); + assert!(min_scan <= max_scan); + + // Above quad + // Quad [----------] + // Query [------] + let above_quad = qs.ranges.scan_end < min_scan; + + // Below quad + // Quad [------] + // Query [------] + let below_quad = qs.ranges.scan_start > max_scan; + + if above_quad || below_quad { + // This quad is completely outside the scan range + false + } else { + true + } + } + None => true, + } + }) + .map(|e| e.index) +} diff --git a/src/models/indices/expanded_raw_index/mod.rs b/src/models/indices/expanded_raw_index/mod.rs index ee2d47a..15ec9da 100644 --- a/src/models/indices/expanded_raw_index/mod.rs +++ b/src/models/indices/expanded_raw_index/mod.rs @@ -1 +1,3 @@ mod model; + +pub use model::ExpandedRawFrameIndex; diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index 10155f6..73cac2d 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -1,10 +1,22 @@ +use crate::models::adapters::FragmentIndexAdapter; +use crate::models::elution_group::ElutionGroup; use crate::models::frames::expanded_frame::ExpandedFrame; use crate::models::frames::expanded_frame::{ - expand_and_split_frame, par_expand_and_centroid_frames, ExpandedFrameSlice, + expand_and_split_frame, par_expand_and_centroid_frames, ExpandedFrameSlice, SortedState, }; -use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; +use crate::models::frames::peak_in_quad::PeakInQuad; +use crate::models::frames::raw_peak::RawPeak; +use crate::models::frames::single_quad_settings::{ + get_matching_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, +}; +use crate::models::queries::FragmentGroupIndexQuery; +use crate::traits::indexed_data::IndexedData; +use crate::ToleranceAdapter; use log::debug; +use rayon::prelude::*; +use serde::Serialize; use std::collections::HashMap; +use std::hash::Hash; use std::sync::Arc; use std::time::Instant; use timsrust::converters::{ @@ -15,18 +27,95 @@ use timsrust::{QuadrupoleSettings, TimsRustError}; type QuadSettingsIndex = usize; -#[derive(Debug, Default)] -struct ExpandedRawFrameIndex { - bundled_ms1_frames: Vec, - bundled_frames: HashMap>, +#[derive(Debug)] +pub struct ExpandedRawFrameIndex { + bundled_ms1_frames: ExpandedSliceBundle, + bundled_frames: HashMap, flat_quad_settings: Vec, rt_converter: Frame2RtConverter, pub mz_converter: Tof2MzConverter, pub im_converter: Scan2ImConverter, + adapter: FragmentIndexAdapter, +} + +#[derive(Debug, Clone)] +pub struct ExpandedSliceBundle { + slices: Vec>, + rts: Vec, + frame_indices: Vec, +} + +impl ExpandedSliceBundle { + pub fn new(mut slices: Vec>) -> Self { + slices.sort_unstable_by(|a, b| a.rt.partial_cmp(&b.rt).unwrap()); + let rts = slices.iter().map(|x| x.rt).collect(); + let frame_indices = slices.iter().map(|x| x.frame_index).collect(); + Self { + slices, + rts, + frame_indices, + } + } + + pub fn query_peaks( + &self, + tof_range: (u32, u32), + scan_range: Option<(usize, usize)>, + frame_index_range: (usize, usize), + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { + // Binary search the rt if needed. + let frame_indices = self.frame_indices.as_slice(); + let low = frame_indices.partition_point(|x| x < &frame_index_range.0); + let high = frame_indices.partition_point(|x| x <= &frame_index_range.1); + + for i in low..high { + let slice = &self.slices[i]; + slice.query_peaks(tof_range, scan_range, f); + } + } } impl ExpandedRawFrameIndex { - pub fn from_tdf_path(path: &str) -> Result { + pub fn query_peaks( + &self, + tof_range: (u32, u32), + precursor_mz_range: (f64, f64), + scan_range: Option<(usize, usize)>, + frame_index_range: (usize, usize), + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { + let matching_quads: Vec = + get_matching_quad_settings(&self.flat_quad_settings, precursor_mz_range, scan_range) + .collect(); + self.query_precursor_peaks(&matching_quads, tof_range, scan_range, frame_index_range, f); + } + + fn query_precursor_peaks( + &self, + matching_quads: &[SingleQuadrupoleSettingIndex], + tof_range: (u32, u32), + scan_range: Option<(usize, usize)>, + frame_index_range: (usize, usize), + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { + for quad in matching_quads { + let tqi = self + .bundled_frames + .get(quad) + .expect("Only existing quads should be queried."); + + tqi.query_peaks(tof_range, scan_range, frame_index_range, &mut *f) + } + } + + pub fn from_path(path: &str) -> Result { let file_reader = FrameReader::new(path)?; let sql_path = std::path::Path::new(path).join("analysis.tdf"); @@ -48,20 +137,22 @@ impl ExpandedRawFrameIndex { debug!("Centroiding took {:#?}", centroided_elap); let mut out_ms2_frames = HashMap::new(); - let mut out_ms1_frames: Option> = None; + let mut out_ms1_frames: Option = None; + let mut flat_quad_settings = Vec::new(); centroided_split_frames .into_iter() .for_each(|(q, frameslices)| match q { None => { - out_ms1_frames = Some(frameslices); + out_ms1_frames = Some(ExpandedSliceBundle::new(frameslices)); } Some(q) => { - out_ms2_frames.insert(q, frameslices); + flat_quad_settings.push(q); + out_ms2_frames.insert(q.index, ExpandedSliceBundle::new(frameslices)); } }); - let mut flat_quad_settings = out_ms2_frames.keys().cloned().collect(); + let adapter = FragmentIndexAdapter::from(meta_converters.clone()); let out = Self { bundled_ms1_frames: out_ms1_frames.expect("At least one ms1 frame should be present"), @@ -70,8 +161,221 @@ impl ExpandedRawFrameIndex { rt_converter: meta_converters.rt_converter, mz_converter: meta_converters.mz_converter, im_converter: meta_converters.im_converter, + adapter, }; Ok(out) } } + +impl + IndexedData, (RawPeak, FH)> for ExpandedRawFrameIndex +{ + fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { + todo!(); + // let precursor_mz_range = ( + // fragment_query.precursor_query.isolation_mz_range.0 as f64, + // fragment_query.precursor_query.isolation_mz_range.0 as f64, + // ); + // let scan_range = Some(fragment_query.precursor_query.mobility_index_range); + // let frame_index_range = Some(FrameRTTolerance::FrameIndex( + // fragment_query.precursor_query.frame_index_range, + // )); + + // fragment_query + // .mz_index_ranges + // .iter() + // .flat_map(|(fh, tof_range)| { + // let mut local_vec: Vec<(RawPeak, FH)> = vec![]; + // self.query_peaks( + // *tof_range, + // precursor_mz_range, + // scan_range, + // frame_index_range, + // &mut |x| local_vec.push((RawPeak::from(x), *fh)), + // ); + + // local_vec + // }) + // .collect() + } + + fn add_query>( + &self, + fragment_query: &FragmentGroupIndexQuery, + aggregator: &mut AG, + ) { + todo!(); + // let precursor_mz_range = ( + // fragment_query.precursor_query.isolation_mz_range.0 as f64, + // fragment_query.precursor_query.isolation_mz_range.0 as f64, + // ); + // let scan_range = Some(fragment_query.precursor_query.mobility_index_range); + // let frame_index_range = Some(FrameRTTolerance::FrameIndex( + // fragment_query.precursor_query.frame_index_range, + // )); + + // fragment_query + // .mz_index_ranges + // .iter() + // .for_each(|(fh, tof_range)| { + // self.query_peaks( + // *tof_range, + // precursor_mz_range, + // scan_range, + // frame_index_range, + // &mut |peak| aggregator.add(&(RawPeak::from(peak), *fh)), + // ); + // }) + } + + fn add_query_multi_group>( + &self, + fragment_queries: &[FragmentGroupIndexQuery], + aggregator: &mut [AG], + ) { + fragment_queries + .par_iter() + .zip(aggregator.par_iter_mut()) + .for_each(|(fragment_query, agg)| { + let precursor_mz_range = ( + fragment_query.precursor_query.isolation_mz_range.0 as f64, + fragment_query.precursor_query.isolation_mz_range.1 as f64, + ); + assert!(precursor_mz_range.0 <= precursor_mz_range.1); + assert!(precursor_mz_range.0 > 0.0); + let scan_range = Some(fragment_query.precursor_query.mobility_index_range); + let frame_index_range = fragment_query.precursor_query.frame_index_range; + + let local_quad_vec: Vec = get_matching_quad_settings( + &self.flat_quad_settings, + precursor_mz_range, + scan_range, + ) + .collect(); + + for (fh, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { + self.query_precursor_peaks( + &local_quad_vec, + tof_range, + scan_range, + frame_index_range, + &mut |peak| agg.add(&(RawPeak::from(peak), fh)), + ); + } + }); + } +} + +impl + IndexedData, RawPeak> for ExpandedRawFrameIndex +{ + fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { + todo!(); + // let precursor_mz_range = ( + // fragment_query.precursor_query.isolation_mz_range.0 as f64, + // fragment_query.precursor_query.isolation_mz_range.0 as f64, + // ); + // let scan_range = Some(fragment_query.precursor_query.mobility_index_range); + // let frame_index_range = Some(FrameRTTolerance::FrameIndex( + // fragment_query.precursor_query.frame_index_range, + // )); + + // fragment_query + // .mz_index_ranges + // .iter() + // .flat_map(|(fh, tof_range)| { + // let mut local_vec: Vec<(RawPeak, FH)> = vec![]; + // self.query_peaks( + // *tof_range, + // precursor_mz_range, + // scan_range, + // frame_index_range, + // &mut |x| local_vec.push((RawPeak::from(x), *fh)), + // ); + + // local_vec + // }) + // .collect() + } + + fn add_query>( + &self, + fragment_query: &FragmentGroupIndexQuery, + aggregator: &mut AG, + ) { + todo!(); + // let precursor_mz_range = ( + // fragment_query.precursor_query.isolation_mz_range.0 as f64, + // fragment_query.precursor_query.isolation_mz_range.0 as f64, + // ); + // let scan_range = Some(fragment_query.precursor_query.mobility_index_range); + // let frame_index_range = Some(FrameRTTolerance::FrameIndex( + // fragment_query.precursor_query.frame_index_range, + // )); + + // fragment_query + // .mz_index_ranges + // .iter() + // .for_each(|(fh, tof_range)| { + // self.query_peaks( + // *tof_range, + // precursor_mz_range, + // scan_range, + // frame_index_range, + // &mut |peak| aggregator.add(&(RawPeak::from(peak), *fh)), + // ); + // }) + } + + fn add_query_multi_group>( + &self, + fragment_queries: &[FragmentGroupIndexQuery], + aggregator: &mut [AG], + ) { + fragment_queries + .par_iter() + .zip(aggregator.par_iter_mut()) + .for_each(|(fragment_query, agg)| { + let precursor_mz_range = ( + fragment_query.precursor_query.isolation_mz_range.0 as f64, + fragment_query.precursor_query.isolation_mz_range.1 as f64, + ); + assert!(precursor_mz_range.0 <= precursor_mz_range.1); + assert!(precursor_mz_range.0 > 0.0); + let scan_range = Some(fragment_query.precursor_query.mobility_index_range); + let frame_index_range = fragment_query.precursor_query.frame_index_range; + + let local_quad_vec: Vec = get_matching_quad_settings( + &self.flat_quad_settings, + precursor_mz_range, + scan_range, + ) + .collect(); + + for (fh, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { + self.query_precursor_peaks( + &local_quad_vec, + tof_range, + scan_range, + frame_index_range, + &mut |peak| agg.add(&RawPeak::from(peak)), + ); + } + }); + } +} + +// ============================================================================ + +impl + ToleranceAdapter, ElutionGroup> for ExpandedRawFrameIndex +{ + fn query_from_elution_group( + &self, + tol: &dyn crate::traits::tolerance::Tolerance, + elution_group: &ElutionGroup, + ) -> FragmentGroupIndexQuery { + self.adapter.query_from_elution_group(tol, elution_group) + } +} diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index 8b4f2cf..6642517 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -1,6 +1,7 @@ use super::peak_bucket::PeakBucketBuilder; use super::peak_bucket::{PeakBucket, PeakInBucket}; -use crate::models::frames::expanded_frame::ExpandedFrameSlice; +use crate::models::frames::expanded_frame::{ExpandedFrameSlice, SortingStateTrait}; +use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::raw_peak::RawPeak; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; use crate::sort_by_indices_multi; @@ -77,17 +78,10 @@ impl TransposedQuadIndex { tof_range: (u32, u32), scan_range: Option<(usize, usize)>, rt_range: Option, - // ) -> Vec { ) -> impl Iterator + '_ { - trace!( - "TransposedQuadIndex::query_peaks tof_range: {:?}, scan_range: {:?}, rt_range: {:?}", - tof_range, - scan_range, - rt_range - ); - // TODO reimplement as an iterator ... // This version is not compatible with the borrow checker unless I collect the vec... // which will do for now for prototyping. + // TODO: make this a single type and convert upstream. let frame_index_range = self.convert_to_local_frame_range(rt_range); self.peak_buckets @@ -96,8 +90,6 @@ impl TransposedQuadIndex { pb.query_peaks(scan_range, frame_index_range) .map(move |p| PeakInQuad::from_peak_in_bucket(p, *tof_index)) }) - // Coult I just return an Arc<[intensities]> + ... - // If I made the peak buckets sparse, I could make it ... not be an option. } fn convert_to_local_frame_range( @@ -141,25 +133,6 @@ impl TransposedQuadIndex { } } -#[derive(Debug, Clone, Copy)] -pub struct PeakInQuad { - pub scan_index: usize, - pub intensity: u32, - pub retention_time: f32, - pub tof_index: u32, -} - -impl From for RawPeak { - fn from(peak_in_quad: PeakInQuad) -> Self { - RawPeak { - scan_index: peak_in_quad.scan_index, - tof_index: peak_in_quad.tof_index, - intensity: peak_in_quad.intensity, - retention_time: peak_in_quad.retention_time, - } - } -} - impl PeakInQuad { pub fn from_peak_in_bucket(peak_in_bucket: PeakInBucket, tof_index: u32) -> Self { Self { @@ -170,7 +143,6 @@ impl PeakInQuad { } } } - // Q: Do I use this? Should I just have it as the frame index as // an option? #[derive(Debug, Clone, Copy)] @@ -222,7 +194,7 @@ impl TransposedQuadIndexBuilder { self.frame_rts.extend(other.frame_rts); } - pub fn add_frame_slice(&mut self, slice: ExpandedFrameSlice) { + pub fn add_frame_slice(&mut self, slice: ExpandedFrameSlice) { self.int_slices.push(slice.intensities); self.tof_slices.push(slice.tof_indices); self.scan_slices.push(slice.scan_numbers); diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index bdc718c..0c213fa 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -1,12 +1,15 @@ -use super::quad_index::{ - FrameRTTolerance, PeakInQuad, TransposedQuadIndex, TransposedQuadIndexBuilder, -}; +use super::quad_index::{FrameRTTolerance, TransposedQuadIndex, TransposedQuadIndexBuilder}; +use crate::models::adapters::FragmentIndexAdapter; use crate::models::elution_group::ElutionGroup; use crate::models::frames::expanded_frame::{ - expand_and_split_frame, par_expand_and_centroid_frames, ExpandedFrameSlice, + expand_and_split_frame, par_expand_and_centroid_frames, ExpandedFrameSlice, SortingStateTrait, }; +use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::raw_peak::RawPeak; -use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; + +use crate::models::frames::single_quad_settings::{ + get_matching_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, +}; use crate::models::queries::FragmentGroupIndexQuery; use crate::models::queries::PrecursorIndexQuery; use crate::traits::indexed_data::IndexedData; @@ -33,12 +36,12 @@ use timsrust::TimsRustError; pub struct QuadSplittedTransposedIndex { precursor_index: TransposedQuadIndex, - fragment_indices: HashMap, + fragment_indices: HashMap, flat_quad_settings: Vec, rt_converter: Frame2RtConverter, pub mz_converter: Tof2MzConverter, pub im_converter: Scan2ImConverter, - metadata: Metadata, + adapter: FragmentIndexAdapter, } impl Debug for QuadSplittedTransposedIndex { @@ -62,14 +65,7 @@ impl QuadSplittedTransposedIndex { ) where F: FnMut(PeakInQuad), { - trace!( - "QuadSplittedTransposedIndex::query_peaks tof_range: {:?}, scan_range: {:?}, rt_range: {:?}, precursor_mz_range: {:?}", - tof_range, - scan_range, - rt_range, - precursor_mz_range, - ); - let matching_quads: Vec = self + let matching_quads: Vec = self .get_matching_quad_settings(precursor_mz_range, scan_range) .collect(); trace!("matching_quads: {:?}", matching_quads); @@ -78,7 +74,7 @@ impl QuadSplittedTransposedIndex { fn query_precursor_peaks( &self, - matching_quads: &[SingleQuadrupoleSetting], + matching_quads: &[SingleQuadrupoleSettingIndex], tof_range: (u32, u32), scan_range: Option<(usize, usize)>, rt_range: Option, @@ -86,8 +82,6 @@ impl QuadSplittedTransposedIndex { ) where F: FnMut(PeakInQuad), { - let rt_range = rt_range.map(|x| x.to_frame_index_range(&self.rt_converter)); - for quad in matching_quads { let tqi = self .fragment_indices @@ -102,108 +96,8 @@ impl QuadSplittedTransposedIndex { &self, precursor_mz_range: (f64, f64), scan_range: Option<(usize, usize)>, - ) -> impl Iterator + '_ { - self.flat_quad_settings - .iter() - .filter(move |qs| { - (qs.ranges.isolation_low <= precursor_mz_range.1) - && (qs.ranges.isolation_high >= precursor_mz_range.0) - }) - .filter(move |qs| { - match scan_range { - Some((min_scan, max_scan)) => { - assert!(qs.ranges.scan_start <= qs.ranges.scan_end); - assert!(min_scan <= max_scan); - - // Above quad - // Quad [----------] - // Query [------] - let above_quad = qs.ranges.scan_end < min_scan; - - // Below quad - // Quad [------] - // Query [------] - let below_quad = qs.ranges.scan_start > max_scan; - - if above_quad || below_quad { - // This quad is completely outside the scan range - false - } else { - true - } - } - None => true, - } - }) - .cloned() - } - - fn queries_from_elution_elements_impl( - &self, - tol: &dyn crate::traits::tolerance::Tolerance, - elution_group: &crate::models::elution_group::ElutionGroup, - ) -> FragmentGroupIndexQuery { - let rt_range = tol.rt_range(elution_group.rt_seconds); - let mobility_range = tol.mobility_range(elution_group.mobility); - let precursor_mz_range = tol.mz_range(elution_group.precursor_mz); - let quad_range = tol.quad_range(elution_group.precursor_mz, elution_group.precursor_charge); - - let mz_index_range = ( - self.mz_converter.invert(precursor_mz_range.0) as u32, - self.mz_converter.invert(precursor_mz_range.1) as u32, - ); - let mobility_range = match mobility_range { - Some(mobility_range) => mobility_range, - None => (self.metadata.lower_im as f32, self.metadata.upper_im as f32), - }; - let mobility_index_range = ( - self.im_converter.invert(mobility_range.0) as usize, - self.im_converter.invert(mobility_range.1) as usize, - ); - let rt_range = match rt_range { - Some(rt_range) => rt_range, - None => (self.metadata.lower_rt as f32, self.metadata.upper_rt as f32), - }; - let frame_index_range = ( - self.rt_converter.invert(rt_range.0) as usize, - self.rt_converter.invert(rt_range.1) as usize, - ); - - assert!(frame_index_range.0 <= frame_index_range.1); - assert!(mz_index_range.0 <= mz_index_range.1); - // Since mobilities get mixed up bc low scan ranges are high 1/k0, I - // Just make sure they are sorted here. - let mobility_index_range = ( - mobility_index_range.0.min(mobility_index_range.1), - mobility_index_range.1.max(mobility_index_range.0), - ); - - let precursor_query = PrecursorIndexQuery { - frame_index_range, - mz_index_range, - mobility_index_range, - isolation_mz_range: quad_range, - }; - - let fqs = elution_group - .fragment_mzs - .iter() - .map(|(k, v)| { - let mz_range = tol.mz_range(*v); - ( - k.clone(), - ( - self.mz_converter.invert(mz_range.0) as u32, - self.mz_converter.invert(mz_range.1) as u32, - ), - ) - }) - .collect(); - - FragmentGroupIndexQuery { - mz_index_ranges: fqs, - precursor_query, - } + ) -> impl Iterator + '_ { + get_matching_quad_settings(&self.flat_quad_settings, precursor_mz_range, scan_range) } } @@ -298,7 +192,7 @@ impl QuadSplittedTransposedIndexBuilder { } } - fn add_frame_slice(&mut self, frame_slice: ExpandedFrameSlice) { + fn add_frame_slice(&mut self, frame_slice: ExpandedFrameSlice) { // Add key if it doesnt exist ... self.indices .entry(frame_slice.quadrupole_settings) @@ -435,7 +329,7 @@ impl QuadSplittedTransposedIndexBuilder { let mut precursor_index: Option = None; for (qi, qs) in built.into_iter() { if let Some(qs) = qs { - indices.insert(qs, qi); + indices.insert(qs.index, qi); flat_quad_settings.push(qs); } else { precursor_index = Some(qi); @@ -456,7 +350,7 @@ impl QuadSplittedTransposedIndexBuilder { rt_converter: self.rt_converter.unwrap(), mz_converter: self.mz_converter.unwrap(), im_converter: self.im_converter.unwrap(), - metadata: self.metadata.unwrap(), + adapter: FragmentIndexAdapter::from(self.metadata.unwrap()), } } } @@ -634,7 +528,7 @@ impl fragment_query.precursor_query.frame_index_range, )); - let local_quad_vec: Vec = self + let local_quad_vec: Vec = self .get_matching_quad_settings(precursor_mz_range, scan_range) .collect(); @@ -662,6 +556,6 @@ impl tol: &dyn crate::traits::tolerance::Tolerance, elution_group: &ElutionGroup, ) -> FragmentGroupIndexQuery { - self.queries_from_elution_elements_impl(tol, elution_group) + self.adapter.query_from_elution_group(tol, elution_group) } } diff --git a/src/models/mod.rs b/src/models/mod.rs index 174f68d..e43662d 100644 --- a/src/models/mod.rs +++ b/src/models/mod.rs @@ -1,3 +1,4 @@ +pub mod adapters; pub mod aggregators; pub mod elution_group; pub mod frames; From 1ad2454dc110e5b5930f45eb93fb1c10534c4203 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Thu, 24 Oct 2024 14:03:47 -0700 Subject: [PATCH 06/30] (refactor,feat) added benchmark plotting and cleanup --- benches/benchmark_indices.rs | 249 ++++++++++++++---- benches/plot_bench.py | 45 ++++ data/get_data.bash | 9 + src/lib.rs | 3 - src/models/frames/expanded_frame.rs | 96 +++++-- .../indices/expanded_raw_index/model.rs | 62 ++++- src/utils/sorting.rs | 61 +++++ 7 files changed, 437 insertions(+), 88 deletions(-) create mode 100644 benches/plot_bench.py create mode 100644 data/get_data.bash diff --git a/benches/benchmark_indices.rs b/benches/benchmark_indices.rs index 84a355e..71a3520 100644 --- a/benches/benchmark_indices.rs +++ b/benches/benchmark_indices.rs @@ -3,6 +3,7 @@ use rand_chacha::ChaCha8Rng; use serde::Serialize; use std::collections::HashMap; use std::fs::File; +use std::path::{Path, PathBuf}; use std::time::{Duration, Instant}; use timsquery::{ models::{ @@ -13,11 +14,13 @@ use timsquery::{ }, }, queriable_tims_data::queriable_tims_data::query_multi_group, - traits::tolerance::DefaultTolerance, + traits::tolerance::{ + DefaultTolerance, MobilityTolerance, MzToleramce, QuadTolerance, RtTolerance, + }, ElutionGroup, }; -const NUM_ELUTION_GROUPS: usize = 500; +const NUM_ELUTION_GROUPS: usize = 1000; const NUM_ITERATIONS: usize = 1; #[derive(Debug, Serialize)] @@ -32,6 +35,8 @@ struct BenchmarkResult { context: String, iterations: Vec, mean_duration_seconds: f64, + mean_duration_human_readable: String, + note: Option, } #[derive(Debug, Serialize)] @@ -39,6 +44,7 @@ struct BenchmarkReport { settings: BenchmarkSettings, results: Vec, metadata: BenchmarkMetadata, + full_benchmark_time_seconds: f64, } #[derive(Debug, Serialize)] @@ -104,105 +110,237 @@ fn build_elution_groups() -> Vec> { out_egs } -fn with_benchmark(name: &str, context: &str, f: impl Fn()) -> BenchmarkResult { +fn with_benchmark(name: &str, context: &str, f: impl Fn() -> Option) -> BenchmarkResult { let mut iterations = Vec::with_capacity(NUM_ITERATIONS); - for i in 0..NUM_ITERATIONS { + let mut durations = Vec::with_capacity(NUM_ITERATIONS); + let mut extras = None; + let glob_start = Instant::now(); + let mut i = 0; + while (glob_start.elapsed().as_millis() < 1000) || (i < NUM_ITERATIONS) { println!("{name} iteration {i}"); let start = Instant::now(); - f(); + if let Some(out) = f() { + extras = Some(out); + } + let duration = start.elapsed(); iterations.push(BenchmarkIteration { iteration: i + 1, duration_seconds: duration_to_seconds(duration), }); + durations.push(duration); + i += 1; } - let mean = iterations.iter().map(|i| i.duration_seconds).sum::() / NUM_ITERATIONS as f64; + let mean = iterations.iter().map(|i| i.duration_seconds).sum::() / (i as f64); + let avg_duration: Duration = durations.iter().sum::() / i as u32; + let mean_duration_human_readable = format!("{:?}", avg_duration); + BenchmarkResult { name: name.to_string(), context: context.to_string(), iterations, mean_duration_seconds: mean, + mean_duration_human_readable, + note: extras, } } fn run_encoding_benchmark(raw_file_path: &str) -> Vec { + let mut out = vec![]; let rfi = with_benchmark("RawFileIndex", "Encoding", || { RawFileIndex::from_path(raw_file_path).unwrap(); + None + }); + out.push(rfi); + let erfic = with_benchmark("ExpandedRawFileIndexCentroided", "Encoding", || { + ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(); + None }); + out.push(erfic); let erfi = with_benchmark("ExpandedRawFileIndex", "Encoding", || { ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(); + None }); + out.push(erfi); let tqi = with_benchmark("TransposedQuadIndex", "Encoding", || { QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(); + None }); + out.push(tqi); - vec![tqi, rfi, erfi] + let tqic = with_benchmark("TransposedQuadIndexCentroided", "Encoding", || { + QuadSplittedTransposedIndex::from_path_centroided(raw_file_path).unwrap(); + None + }); + out.push(tqic); + + out } fn run_batch_access_benchmark(raw_file_path: &str) -> Vec { + let mut out = vec![]; let query_groups = build_elution_groups(); - let tolerance = DefaultTolerance::default(); + let tolerance_with_rt = DefaultTolerance { + ms: MzToleramce::Ppm((20.0, 20.0)), + rt: RtTolerance::Absolute((5.0, 5.0)), + mobility: MobilityTolerance::Pct((3.0, 3.0)), + quad: QuadTolerance::Absolute((0.1, 0.1, 1)), + }; + let tolerance_with_nort = DefaultTolerance { + ms: MzToleramce::Ppm((20.0, 20.0)), + rt: RtTolerance::None, + mobility: MobilityTolerance::Pct((3.0, 3.0)), + quad: QuadTolerance::Absolute((0.1, 0.1, 1)), + }; + let tolerances = [ + (tolerance_with_rt, "narrow_rt"), + (tolerance_with_nort, "full_rt"), + ]; + + // TODO: Refactor this ... there is a lot of code duplication but over different types ... int + // ion thoty this is a good place for a macro. let rfi_index = RawFileIndex::from_path(raw_file_path).unwrap(); - let rfi = with_benchmark("RawFileIndex", "BatchAccess", || { - let _ = query_multi_group( - &rfi_index, - &rfi_index, - &tolerance, - &query_groups, - &RawPeakIntensityAggregator::new, - ); - }); + for (tolerance, tol_name) in tolerances.clone() { + if tol_name == "full_rt" { + println!("Skipping full_rt"); + continue; + } + let rfi = with_benchmark("RawFileIndex", &format!("BatchAccess_{}", tol_name), || { + let tmp = query_multi_group( + &rfi_index, + &rfi_index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!("RawFileIndex::query_multi_group aggregated {}", tot); + println!("{}", out); + Some(out) + }); + out.push(rfi); + } std::mem::drop(rfi_index); let erfi_index = ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(); - let erfi = with_benchmark("ExpandedRawFileIndex", "BatchAccess", || { - let _ = query_multi_group( - &erfi_index, - &erfi_index, - &tolerance, - &query_groups, - &RawPeakIntensityAggregator::new, + for (tolerance, tol_name) in tolerances.clone() { + let erfi = with_benchmark( + "ExpandedRawFileIndex", + &format!("BatchAccess_{}", tol_name), + || { + let tmp = query_multi_group( + &erfi_index, + &erfi_index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!("ExpandedRawFileIndex::query_multi_group aggregated {}", tot); + println!("{}", out); + Some(out) + }, ); - }); + out.push(erfi); + } std::mem::drop(erfi_index); + let erfic_index = ExpandedRawFrameIndex::from_path_centroided(raw_file_path).unwrap(); + for (tolerance, tol_name) in tolerances.clone() { + let erfic = with_benchmark( + "ExpandedRawFileIndexCentroided", + &format!("BatchAccess_{}", tol_name), + || { + let tmp = query_multi_group( + &erfic_index, + &erfic_index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!( + "ExpandedRawFileIndexCentroided::query_multi_group aggregated {}", + tot + ); + println!("{}", out); + Some(out) + }, + ); + out.push(erfic); + } + std::mem::drop(erfic_index); + let tqi_index = QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(); - let tqi = with_benchmark("TransposedQuadIndex", "BatchAccess", || { - let _ = query_multi_group( - &tqi_index, - &tqi_index, - &tolerance, - &query_groups, - &RawPeakIntensityAggregator::new, + for (tolerance, tol_name) in tolerances.clone() { + let tqi = with_benchmark( + "TransposedQuadIndex", + &format!("BatchAccess_{}", tol_name), + || { + let tmp = query_multi_group( + &tqi_index, + &tqi_index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!("TransposedQuadIndex::query_multi_group aggregated {}", tot); + println!("{}", out); + Some(out) + }, ); - }); + out.push(tqi); + } std::mem::drop(tqi_index); - vec![tqi, rfi, erfi] + let tqic_index = QuadSplittedTransposedIndex::from_path_centroided(raw_file_path).unwrap(); + for (tolerance, tol_name) in tolerances.clone() { + let tqi = with_benchmark( + "TransposedQuadIndexCentroided", + &format!("BatchAccess_{}", tol_name), + || { + let tmp = query_multi_group( + &tqic_index, + &tqic_index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!("TransposedQuadIndex::query_multi_group aggregated {}", tot); + println!("{}", out); + Some(out) + }, + ); + out.push(tqi); + } + std::mem::drop(tqic_index); + out } -fn write_results(results: Vec, basename: &str) -> std::io::Result<()> { - let report = BenchmarkReport { - settings: BenchmarkSettings { - num_elution_groups: NUM_ELUTION_GROUPS, - num_iterations: NUM_ITERATIONS, - }, - results, - metadata: BenchmarkMetadata { - basename: basename.to_string(), - }, - }; - - let file = File::create(format!("benchmark_results_{}.json", basename))?; +fn write_results( + report: BenchmarkReport, + basename: &str, + parent: &Path, +) -> std::io::Result<(PathBuf, String)> { + let filepath = parent.join(format!("benchmark_results_{}.json", basename)); + let file = File::create(&filepath)?; serde_json::to_writer_pretty(file, &report)?; - Ok(()) + let out = serde_json::to_string_pretty(&report)?; + Ok((filepath, out)) } fn main() { + env_logger::init(); + let st = Instant::now(); let (raw_file_path, basename) = get_file_from_env(); + let file_parent = std::path::Path::new(&raw_file_path) + .parent() + .expect("Expected to find a parent directory"); let mut all_results: Vec = vec![]; println!( @@ -217,9 +355,20 @@ fn main() { println!("Running batch access benchmarks..."); let batch_results = run_batch_access_benchmark(&raw_file_path); all_results.extend(batch_results); + let report = BenchmarkReport { + settings: BenchmarkSettings { + num_elution_groups: NUM_ELUTION_GROUPS, + num_iterations: NUM_ITERATIONS, + }, + results: all_results, + metadata: BenchmarkMetadata { + basename: basename.to_string(), + }, + full_benchmark_time_seconds: st.elapsed().as_secs_f64(), + }; - match write_results(all_results, &basename) { - Ok(_) => println!("Results written to benchmark_results_{}.json", basename), + match write_results(report, &basename, file_parent) { + Ok((fp, res)) => println!("Results written to {} \n{}", fp.to_string_lossy(), res), Err(e) => eprintln!("Error writing results: {}", e), } } diff --git a/benches/plot_bench.py b/benches/plot_bench.py new file mode 100644 index 0000000..e6e3bb0 --- /dev/null +++ b/benches/plot_bench.py @@ -0,0 +1,45 @@ +# /// script +# dependencies = [ +# "altair", +# "polars", +# "vl-convert-python", +# ] +# /// + +from pathlib import Path +import polars as pl +import altair as alt +import argparse + + +parser = argparse.ArgumentParser() +parser.add_argument("benchmark_file") +args = parser.parse_args() + +data = ( + pl.read_json(args.benchmark_file) + .explode("results") + .with_columns( + bench=pl.col("results").struct.field("name"), + context=pl.col("results").struct.field("context"), + iterations=pl.col("results").struct.field("iterations"), + ) + .explode("iterations") + .with_columns(time_seconds=pl.col("iterations").struct.field("duration_seconds")) +) +print(data) + +for context, sdf in data.group_by("context"): + context = context[0] + print(context) + # Sample to max 100 points on each bench + sdf = sdf.filter(pl.int_range(pl.len()).shuffle().over("bench") < 100) + alt.Chart(sdf).mark_point().encode( + x="bench", + y=alt.Y("time_seconds", scale=alt.Scale(type="log")), + color="bench", + ).properties( + width=600, + height=600, + title=f"{context}", + ).save(f"{context}.png") diff --git a/data/get_data.bash b/data/get_data.bash new file mode 100644 index 0000000..44bb605 --- /dev/null +++ b/data/get_data.bash @@ -0,0 +1,9 @@ + +# LFQ_timsTOFPro_diaPASEF_Ecoli_03.d.zip + +docker run --platform linux/amd64 -v ${PWD}:/data \ + ghcr.io/pride-archive/aspera \ + ascp -i /home/aspera/.aspera/cli/etc/asperaweb_id_dsa.openssh \ + -TQ -P33001 \ + prd_ascp@fasp.ebi.ac.uk:/pride/data/archive/2022/02/PXD028735/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d.zip \ + /data diff --git a/src/lib.rs b/src/lib.rs index c7ab4fd..8ca3d26 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -8,9 +8,6 @@ pub use crate::traits::aggregator::Aggregator; pub use crate::traits::indexed_data::IndexedData; pub use crate::traits::tolerance::{HasIntegerID, Tolerance, ToleranceAdapter}; -// Re-export utility functions -pub use crate::utils::sorting::sort_multiple_by; - // Declare modules pub mod models; pub mod queriable_tims_data; diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index a55af8c..3263c58 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -1,23 +1,24 @@ -use std::collections::HashMap; -use std::marker::PhantomData; -use std::sync::Arc; - use super::single_quad_settings::{ expand_quad_settings, ExpandedFrameQuadSettings, SingleQuadrupoleSetting, }; use itertools::Itertools; use rayon::iter::IntoParallelIterator; use rayon::prelude::*; +use std::collections::HashMap; +use std::marker::PhantomData; +use std::sync::Arc; +use std::time::Instant; use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; use timsrust::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}; use super::peak_in_quad::PeakInQuad; use crate::sort_by_indices_multi; +use crate::sort_vecs_by_first; use crate::utils::compress_explode::explode_vec; use crate::utils::frame_processing::lazy_centroid_weighted_frame; use crate::utils::sorting::argsort_by; use crate::utils::tolerance_ranges::{scan_tol_range, tof_tol_range}; -use log::debug; +use log::{debug, info, trace}; /// A frame after expanding the mobility data and re-sorting it by tof. #[derive(Debug, Clone)] @@ -59,19 +60,48 @@ pub struct ExpandedFrameSlice { _sorting_state: PhantomData, } +fn sort_by_tof2( + tof_indices: Vec, + scan_numbers: Vec, + intensities: Vec, +) -> ((Vec, Vec), Vec) { + let mut combined: Vec<((u32, usize), u32)> = tof_indices + .iter() + .zip(scan_numbers.iter()) + .zip(intensities.iter()) + .map(|((tof, scan), inten)| ((*tof, *scan), *inten)) + .collect(); + combined.sort_unstable_by(|a, b| a.0 .0.partial_cmp(&b.0 .0).unwrap()); + let ((tof_indices, scan_numbers), intensities) = combined.into_iter().unzip(); + ((tof_indices, scan_numbers), intensities) +} + +// Example of how to use it with your specific types +fn sort_by_tof_macro( + tof_indices: Vec, + scan_numbers: Vec, + intensities: Vec, +) -> (Vec, Vec, Vec) { + sort_vecs_by_first!(tof_indices, scan_numbers, intensities) +} + impl ExpandedFrameSlice { pub fn sort_by_tof(mut self) -> ExpandedFrameSlice { - let mut indices = argsort_by(&self.tof_indices, |x| *x); - sort_by_indices_multi!( - &mut indices, - &mut self.tof_indices, - &mut self.scan_numbers, - &mut self.intensities - ); + // let mut indices = argsort_by(&self.tof_indices, |x| *x); + // sort_by_indices_multi!( + // &mut indices, + // &mut self.tof_indices, + // &mut self.scan_numbers, + // &mut self.intensities + // ); + + let (tof_indices, scan_numbers, intensities) = + sort_by_tof_macro(self.tof_indices, self.scan_numbers, self.intensities); + ExpandedFrameSlice { - tof_indices: self.tof_indices, - scan_numbers: self.scan_numbers, - intensities: self.intensities, + tof_indices, + scan_numbers, + intensities, frame_index: self.frame_index, rt: self.rt, acquisition_type: self.acquisition_type, @@ -268,6 +298,8 @@ impl ExpandedFrame { pub fn expand_and_arrange_frames( frames: Vec, ) -> HashMap, Vec>> { + info!("Expanding and arranging frames"); + let start = Instant::now(); let mut out = HashMap::new(); let split: Vec> = frames .into_par_iter() @@ -283,6 +315,8 @@ pub fn expand_and_arrange_frames( for (_, es) in out.iter_mut() { es.sort_unstable_by(|a, b| a.rt.partial_cmp(&b.rt).unwrap()); } + let end = start.elapsed(); + info!("Expanding and arranging frames took {:#?}", end); out } @@ -311,9 +345,11 @@ pub fn par_expand_and_centroid_frames( mz_converter, ); let end_peaks: usize = centroided.iter().map(|x| x.len()).sum(); - debug!( + trace!( "Peak counts for quad {:?}: raw={}/centroid={}", - qs, start_peaks, end_peaks + qs, + start_peaks, + end_peaks ); (qs, centroided) }) @@ -334,20 +370,20 @@ fn centroid_frameslice_window( // this is A LOT of cloning ... look into whether it is needed. - let mut tof_array: Vec = frameslices + let tof_array: Vec = frameslices .iter() .flat_map(|x| x.tof_indices.clone()) .collect(); - let mut ims_array: Vec = frameslices + let ims_array: Vec = frameslices .iter() .flat_map(|x| x.scan_numbers.clone()) .collect(); - let mut weight_array: Vec = frameslices + let weight_array: Vec = frameslices .iter() .flat_map(|x| x.intensities.clone()) .collect(); - let mut intensity_array: Vec = frameslices + let intensity_array: Vec = frameslices .iter() .enumerate() .flat_map(|(i, x)| { @@ -359,14 +395,16 @@ fn centroid_frameslice_window( }) .collect(); - let mut tof_order = argsort_by(&tof_array, |x| *x); - sort_by_indices_multi!( - &mut tof_order, - &mut tof_array, - &mut ims_array, - &mut weight_array, - &mut intensity_array - ); + // let mut tof_order = argsort_by(&tof_array, |x| *x); + // sort_by_indices_multi!( + // &mut tof_order, + // &mut tof_array, + // &mut ims_array, + // &mut weight_array, + // &mut intensity_array + // ); + let (tof_array, ims_array, weight_array, intensity_array) = + sort_vecs_by_first!(tof_array, ims_array, weight_array, intensity_array); let ((mzs, intensities), imss) = lazy_centroid_weighted_frame( &tof_array, diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index 73cac2d..b61788b 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -2,7 +2,8 @@ use crate::models::adapters::FragmentIndexAdapter; use crate::models::elution_group::ElutionGroup; use crate::models::frames::expanded_frame::ExpandedFrame; use crate::models::frames::expanded_frame::{ - expand_and_split_frame, par_expand_and_centroid_frames, ExpandedFrameSlice, SortedState, + expand_and_arrange_frames, expand_and_split_frame, par_expand_and_centroid_frames, + ExpandedFrameSlice, SortedState, }; use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::raw_peak::RawPeak; @@ -12,12 +13,11 @@ use crate::models::frames::single_quad_settings::{ use crate::models::queries::FragmentGroupIndexQuery; use crate::traits::indexed_data::IndexedData; use crate::ToleranceAdapter; -use log::debug; +use log::{debug, info}; use rayon::prelude::*; use serde::Serialize; use std::collections::HashMap; use std::hash::Hash; -use std::sync::Arc; use std::time::Instant; use timsrust::converters::{ ConvertableDomain, Frame2RtConverter, Scan2ImConverter, Tof2MzConverter, @@ -115,7 +115,7 @@ impl ExpandedRawFrameIndex { } } - pub fn from_path(path: &str) -> Result { + pub fn from_path_centroided(path: &str) -> Result { let file_reader = FrameReader::new(path)?; let sql_path = std::path::Path::new(path).join("analysis.tdf"); @@ -124,8 +124,9 @@ impl ExpandedRawFrameIndex { let st = Instant::now(); let all_frames = file_reader.get_all().into_iter().flatten().collect(); let read_elap = st.elapsed(); - debug!("Reading all frames took {:#?}", read_elap); + info!("Reading all frames took {:#?}", read_elap); let st = Instant::now(); + // TODO: Expose this parameter as a config option. let centroided_split_frames = par_expand_and_centroid_frames( all_frames, 1.5, @@ -134,7 +135,56 @@ impl ExpandedRawFrameIndex { &meta_converters.mz_converter, ); let centroided_elap = st.elapsed(); - debug!("Centroiding took {:#?}", centroided_elap); + info!("Centroiding took {:#?}", centroided_elap); + + let mut out_ms2_frames = HashMap::new(); + let mut out_ms1_frames: Option = None; + + let mut flat_quad_settings = Vec::new(); + centroided_split_frames + .into_iter() + .for_each(|(q, frameslices)| match q { + None => { + out_ms1_frames = Some(ExpandedSliceBundle::new(frameslices)); + } + Some(q) => { + flat_quad_settings.push(q); + out_ms2_frames.insert(q.index, ExpandedSliceBundle::new(frameslices)); + } + }); + + let adapter = FragmentIndexAdapter::from(meta_converters.clone()); + + let out = Self { + bundled_ms1_frames: out_ms1_frames.expect("At least one ms1 frame should be present"), + bundled_frames: out_ms2_frames, + flat_quad_settings, + rt_converter: meta_converters.rt_converter, + mz_converter: meta_converters.mz_converter, + im_converter: meta_converters.im_converter, + adapter, + }; + + Ok(out) + } + + pub fn from_path(path: &str) -> Result { + // NOTE: I am just copy-pasting the centroided version. If I keep both I will + // abstract it and make dispatch in a config ... + + let file_reader = FrameReader::new(path)?; + + let sql_path = std::path::Path::new(path).join("analysis.tdf"); + let meta_converters = MetadataReader::new(&sql_path)?; + + let st = Instant::now(); + let all_frames = file_reader.get_all().into_iter().flatten().collect(); + let read_elap = st.elapsed(); + info!("Reading all frames took {:#?}", read_elap); + let st = Instant::now(); + let centroided_split_frames = expand_and_arrange_frames(all_frames); + let centroided_elap = st.elapsed(); + info!("Splitting took {:#?}", centroided_elap); let mut out_ms2_frames = HashMap::new(); let mut out_ms1_frames: Option = None; diff --git a/src/utils/sorting.rs b/src/utils/sorting.rs index 2f528eb..2caa86f 100644 --- a/src/utils/sorting.rs +++ b/src/utils/sorting.rs @@ -111,6 +111,28 @@ macro_rules! sort_by_indices_multi { }}; } +#[macro_export] +macro_rules! sort_vecs_by_first { + ($first:expr $(,$rest:expr)*) => {{ + let first_vec = $first; + let len = first_vec.len(); + + // Create and sort indices + let mut indices: Vec<_> = (0..len).collect(); + indices.sort_unstable_by_key(|&i| &first_vec[i]); + + // Reorder first vector + let sorted_first: Vec<_> = indices.iter().map(|&i| first_vec[i]).collect(); + + // Reorder all other vectors + (sorted_first, $( { + let other_vec = $rest; + assert_eq!(other_vec.len(), len, "All vectors must have the same length"); + indices.iter().map(|&i| other_vec[i]).collect::>() + }, )*) + }}; +} + #[cfg(test)] mod tests { use super::*; @@ -156,4 +178,43 @@ mod tests { assert_eq!(scan_numbers, vec![0, 2, 0, 2, 1, 1]); assert_eq!(intensities, vec![10, 50, 20, 60, 30, 40]); } + + #[test] + fn test_sort_two_vecs() { + let v1 = vec![3, 1, 4, 1, 5]; + let v2 = vec!['a', 'b', 'c', 'd', 'e']; + + let (sorted_v1, sorted_v2) = sort_vecs_by_first!(v1, v2); + + assert_eq!(sorted_v1, vec![1, 1, 3, 4, 5]); + assert_eq!(sorted_v2, vec!['b', 'd', 'a', 'c', 'e']); + } + + #[test] + fn test_sort_three_vecs() { + let v1 = vec![3, 1, 4]; + let v2 = vec!['x', 'y', 'z']; + let v3 = vec![true, false, true]; + + let (sorted_v1, sorted_v2, sorted_v3) = sort_vecs_by_first!(v1, v2, v3); + + assert_eq!(sorted_v1, vec![1, 3, 4]); + assert_eq!(sorted_v2, vec!['y', 'x', 'z']); + assert_eq!(sorted_v3, vec![false, true, true]); + } + + #[test] + fn test_sort_four_vecs() { + let v1 = vec![3, 1, 4]; + let v2 = vec!['x', 'y', 'z']; + let v3 = vec![true, false, true]; + let v4 = vec![1.0, 2.0, 3.0]; + + let (sorted_v1, sorted_v2, sorted_v3, sorted_v4) = sort_vecs_by_first!(v1, v2, v3, v4); + + assert_eq!(sorted_v1, vec![1, 3, 4]); + assert_eq!(sorted_v2, vec!['y', 'x', 'z']); + assert_eq!(sorted_v3, vec![false, true, true]); + assert_eq!(sorted_v4, vec![2.0, 1.0, 3.0]); + } } From f549bfae8e8d59d27daf290e39a30d2b501162a3 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Fri, 25 Oct 2024 17:54:59 -0700 Subject: [PATCH 07/30] feat: first benchmark results and refactor trait --- benches/benchmark_indices.rs | 405 ++++++++++++------ benches/plot_bench.py | 12 +- data/.gitignore | 4 + ..._A_Sample_Alpha_02_BatchAccess_full_rt.png | Bin 0 -> 47274 bytes ..._Sample_Alpha_02_BatchAccess_narrow_rt.png | Bin 0 -> 52663 bytes data/get_data.bash | 5 +- src/lib.rs | 2 +- .../raw_peak_agg/chromatogram_agg.rs | 6 +- .../raw_peak_agg/multi_chromatogram_agg.rs | 5 +- .../aggregators/raw_peak_agg/point_agg.rs | 6 +- src/models/frames/expanded_frame.rs | 318 +++++++++++--- .../indices/expanded_raw_index/model.rs | 110 ++--- src/models/indices/raw_file_index.rs | 16 +- .../transposed_quad_index/quad_index.rs | 4 +- .../quad_splitted_transposed_index.rs | 102 ++--- src/models/queries.rs | 2 +- .../queriable_tims_data.rs | 26 +- src/traits/aggregator.rs | 6 +- src/traits/indexed_data.rs | 14 +- src/utils/frame_processing.rs | 270 ++++++++---- src/utils/tolerance_ranges.rs | 11 +- 21 files changed, 856 insertions(+), 468 deletions(-) create mode 100644 data/.gitignore create mode 100644 data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_full_rt.png create mode 100644 data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_narrow_rt.png diff --git a/benches/benchmark_indices.rs b/benches/benchmark_indices.rs index 71a3520..21c86d8 100644 --- a/benches/benchmark_indices.rs +++ b/benches/benchmark_indices.rs @@ -2,6 +2,7 @@ use rand::{Rng, SeedableRng}; use rand_chacha::ChaCha8Rng; use serde::Serialize; use std::collections::HashMap; +use std::env; use std::fs::File; use std::path::{Path, PathBuf}; use std::time::{Duration, Instant}; @@ -23,6 +24,74 @@ use timsquery::{ const NUM_ELUTION_GROUPS: usize = 1000; const NUM_ITERATIONS: usize = 1; +#[derive(Debug, Clone)] +struct EnvConfig { + tims_data_file: PathBuf, + file_stem: String, + skip_highmem: bool, + skip_slow: bool, + skip_build: bool, + skip_query: bool, +} + +impl EnvConfig { + fn new() -> Self { + let mut tims_data_file = String::new(); + let mut skip_highmem = false; + // let mut skip_slow = false; + let mut skip_slow = true; + let mut skip_build = false; + let mut skip_query = false; + + for (key, value) in env::vars() { + match key.as_str() { + "TIMS_DATA_FILE" => tims_data_file = value, + "SKIP_HIGHMEM" => skip_highmem = value == "1", + // "SKIP_SLOW" => skip_slow = value == "1", + // I hate this double negative but I want to make slow benches + // opt-in rather than opt-out. + "RUN_SLOW" => skip_slow = value != "1", + "SKIP_BUILD" => skip_build = value == "1", + "SKIP_QUERY" => skip_query = value == "1", + _ => {} + } + } + + if tims_data_file.is_empty() { + panic!("TIMS_DATA_FILE environment variable not set"); + } + + // Check that the file exists and is readable + + let tims_data_file = Path::new(&tims_data_file); + if !tims_data_file.exists() { + panic!("TIMS_DATA_FILE={} does not exist", tims_data_file.display()); + } + let file_stem = tims_data_file.file_stem().unwrap().to_str().unwrap(); + + let out = Self { + tims_data_file: tims_data_file.to_path_buf(), + file_stem: file_stem.to_string(), + skip_highmem, + skip_slow, + skip_build, + skip_query, + }; + + println!("Env config: {:#?}", out); + + out + } +} + +#[derive(Debug, Clone, Copy, PartialEq, Eq)] +enum BenchmarkTag { + HighMem, + Slow, + Build, + Query, +} + #[derive(Debug, Serialize)] struct BenchmarkIteration { iteration: usize, @@ -33,9 +102,12 @@ struct BenchmarkIteration { struct BenchmarkResult { name: String, context: String, - iterations: Vec, + #[serde(skip_serializing_if = "Option::is_none")] + iterations: Option>, mean_duration_seconds: f64, mean_duration_human_readable: String, + setup_time_seconds: f64, + setup_time_human_readable: String, note: Option, } @@ -62,20 +134,6 @@ fn duration_to_seconds(duration: Duration) -> f64 { duration.as_secs() as f64 + duration.subsec_nanos() as f64 * 1e-9 } -fn get_file_from_env() -> (String, String) { - let raw_file_path = - std::env::var("TIMS_DATA_FILE").expect("TIMS_DATA_FILE environment variable not set"); - - let basename = std::path::Path::new(&raw_file_path) - .file_stem() - .unwrap() - .to_str() - .unwrap() - .to_string(); - - (raw_file_path, basename) -} - fn build_elution_groups() -> Vec> { const NUM_FRAGMENTS: usize = 10; const MAX_RT: f32 = 22.0 * 60.0; @@ -110,76 +168,153 @@ fn build_elution_groups() -> Vec> { out_egs } -fn with_benchmark(name: &str, context: &str, f: impl Fn() -> Option) -> BenchmarkResult { - let mut iterations = Vec::with_capacity(NUM_ITERATIONS); - let mut durations = Vec::with_capacity(NUM_ITERATIONS); - let mut extras = None; - let glob_start = Instant::now(); - let mut i = 0; - while (glob_start.elapsed().as_millis() < 1000) || (i < NUM_ITERATIONS) { - println!("{name} iteration {i}"); - let start = Instant::now(); - if let Some(out) = f() { - extras = Some(out); +impl EnvConfig { + fn with_benchmark( + &self, + name: &str, + context: &str, + setup_fn: impl Fn() -> T, + f: impl Fn(&T, usize) -> Option, + tags: &[BenchmarkTag], + ) -> Option { + if self.skip_slow && tags.contains(&BenchmarkTag::Slow) { + println!("Skipping slow benchmark for {} {}", name, context); + return None; } - let duration = start.elapsed(); + if self.skip_highmem && tags.contains(&BenchmarkTag::HighMem) { + println!("Skipping highmem benchmark {} {}", name, context); + return None; + } - iterations.push(BenchmarkIteration { - iteration: i + 1, - duration_seconds: duration_to_seconds(duration), - }); - durations.push(duration); - i += 1; - } + if self.skip_build && tags.contains(&BenchmarkTag::Build) { + println!("Skipping build benchmark {} {}", name, context); + return None; + } + + if self.skip_query && tags.contains(&BenchmarkTag::Query) { + println!("Skipping query benchmark {} {}", name, context); + return None; + } - let mean = iterations.iter().map(|i| i.duration_seconds).sum::() / (i as f64); - let avg_duration: Duration = durations.iter().sum::() / i as u32; - let mean_duration_human_readable = format!("{:?}", avg_duration); - - BenchmarkResult { - name: name.to_string(), - context: context.to_string(), - iterations, - mean_duration_seconds: mean, - mean_duration_human_readable, - note: extras, + println!("{} {} Tagged with {:?}", name, context, tags); + let sst = Instant::now(); + println!("Setting up {} {}", name, context); + let setup = setup_fn(); + let setup_elap = sst.elapsed(); + println!("Setup took {:#?}", setup_elap); + + let mut iterations = Vec::with_capacity(NUM_ITERATIONS); + let mut durations = Vec::with_capacity(NUM_ITERATIONS); + let mut extras = None; + let glob_start = Instant::now(); + let mut i = 0; + while (glob_start.elapsed().as_millis() < 1000) || (i < NUM_ITERATIONS) { + if i < 10 || i % 100 == 0 { + println!("{name} iteration {i}"); + } + let start = Instant::now(); + if let Some(out) = f(&setup, i) { + if i < 3 { + println!("{}", out); + } + extras = Some(out); + } + + let duration = start.elapsed(); + + iterations.push(BenchmarkIteration { + iteration: i + 1, + duration_seconds: duration_to_seconds(duration), + }); + durations.push(duration); + i += 1; + } + + let mean = iterations.iter().map(|i| i.duration_seconds).sum::() / (i as f64); + let avg_duration: Duration = durations.iter().sum::() / i as u32; + let mean_duration_human_readable = format!("{:?}", avg_duration); + + println!("Mean duration: {:?}", mean_duration_human_readable); + + Some(BenchmarkResult { + name: name.to_string(), + context: context.to_string(), + iterations: Some(iterations), + mean_duration_seconds: mean, + mean_duration_human_readable, + setup_time_seconds: setup_elap.as_secs_f64(), + setup_time_human_readable: format!("{:?}", setup_elap), + note: extras, + }) } } -fn run_encoding_benchmark(raw_file_path: &str) -> Vec { +fn run_encoding_benchmark(raw_file_path: &PathBuf, env_config: EnvConfig) -> Vec { + let raw_file_path = raw_file_path.to_str().unwrap(); let mut out = vec![]; - let rfi = with_benchmark("RawFileIndex", "Encoding", || { - RawFileIndex::from_path(raw_file_path).unwrap(); - None - }); + let rfi = env_config.with_benchmark( + "RawFileIndex", + "Encoding", + || {}, + |_, _| { + RawFileIndex::from_path(raw_file_path).unwrap(); + None + }, + &[BenchmarkTag::Build], + ); out.push(rfi); - let erfic = with_benchmark("ExpandedRawFileIndexCentroided", "Encoding", || { - ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(); - None - }); + let erfic = env_config.with_benchmark( + "ExpandedRawFileIndexCentroided", + "Encoding", + || {}, + |_, _| { + ExpandedRawFrameIndex::from_path_centroided(raw_file_path).unwrap(); + None + }, + &[BenchmarkTag::Build], + ); out.push(erfic); - let erfi = with_benchmark("ExpandedRawFileIndex", "Encoding", || { - ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(); - None - }); + + let erfi = env_config.with_benchmark( + "ExpandedRawFileIndex", + "Encoding", + || {}, + |_, _| { + ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(); + None + }, + &[BenchmarkTag::HighMem, BenchmarkTag::Build], + ); out.push(erfi); - let tqi = with_benchmark("TransposedQuadIndex", "Encoding", || { - QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(); - None - }); + let tqi = env_config.with_benchmark( + "TransposedQuadIndex", + "Encoding", + || {}, + |_, _| { + QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(); + None + }, + &[BenchmarkTag::HighMem, BenchmarkTag::Build], + ); out.push(tqi); - - let tqic = with_benchmark("TransposedQuadIndexCentroided", "Encoding", || { - QuadSplittedTransposedIndex::from_path_centroided(raw_file_path).unwrap(); - None - }); + let tqic = env_config.with_benchmark( + "TransposedQuadIndexCentroided", + "Encoding", + || {}, + |_, _| { + QuadSplittedTransposedIndex::from_path_centroided(raw_file_path).unwrap(); + None + }, + &[BenchmarkTag::Build], + ); out.push(tqic); - out + out.into_iter().flatten().collect() } -fn run_batch_access_benchmark(raw_file_path: &str) -> Vec { +fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Vec { + let raw_file_path = raw_file_path.to_str().unwrap(); let mut out = vec![]; let query_groups = build_elution_groups(); let tolerance_with_rt = DefaultTolerance { @@ -202,128 +337,131 @@ fn run_batch_access_benchmark(raw_file_path: &str) -> Vec { // TODO: Refactor this ... there is a lot of code duplication but over different types ... int // ion thoty this is a good place for a macro. - let rfi_index = RawFileIndex::from_path(raw_file_path).unwrap(); for (tolerance, tol_name) in tolerances.clone() { - if tol_name == "full_rt" { - println!("Skipping full_rt"); - continue; - } - let rfi = with_benchmark("RawFileIndex", &format!("BatchAccess_{}", tol_name), || { - let tmp = query_multi_group( - &rfi_index, - &rfi_index, - &tolerance, - &query_groups, - &RawPeakIntensityAggregator::new, - ); - let tot: u64 = tmp.into_iter().sum(); - let out = format!("RawFileIndex::query_multi_group aggregated {}", tot); - println!("{}", out); - Some(out) - }); + let local_tags = if tol_name == "full_rt" { + vec![BenchmarkTag::Slow, BenchmarkTag::Query] + } else { + vec![BenchmarkTag::Query] + }; + let rfi = env_config.with_benchmark( + "RawFileIndex", + &format!("BatchAccess_{}", tol_name), + || RawFileIndex::from_path(raw_file_path).unwrap(), + |index, i| { + let tmp = query_multi_group( + index, + index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!("RawFileIndex::query_multi_group aggregated {} ", tot,); + Some(out) + }, + &local_tags, + ); out.push(rfi); } - std::mem::drop(rfi_index); - let erfi_index = ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(); for (tolerance, tol_name) in tolerances.clone() { - let erfi = with_benchmark( + let erfi = env_config.with_benchmark( "ExpandedRawFileIndex", &format!("BatchAccess_{}", tol_name), - || { + || ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(), + |index, i| { let tmp = query_multi_group( - &erfi_index, - &erfi_index, + index, + index, &tolerance, &query_groups, &RawPeakIntensityAggregator::new, ); let tot: u64 = tmp.into_iter().sum(); - let out = format!("ExpandedRawFileIndex::query_multi_group aggregated {}", tot); - println!("{}", out); + let out = format!( + "ExpandedRawFileIndex::query_multi_group aggregated {} ", + tot, + ); Some(out) }, + &[BenchmarkTag::HighMem, BenchmarkTag::Query], ); out.push(erfi); } - std::mem::drop(erfi_index); - let erfic_index = ExpandedRawFrameIndex::from_path_centroided(raw_file_path).unwrap(); for (tolerance, tol_name) in tolerances.clone() { - let erfic = with_benchmark( + let erfic = env_config.with_benchmark( "ExpandedRawFileIndexCentroided", &format!("BatchAccess_{}", tol_name), - || { + || ExpandedRawFrameIndex::from_path_centroided(raw_file_path).unwrap(), + |index, i| { let tmp = query_multi_group( - &erfic_index, - &erfic_index, + index, + index, &tolerance, &query_groups, &RawPeakIntensityAggregator::new, ); let tot: u64 = tmp.into_iter().sum(); let out = format!( - "ExpandedRawFileIndexCentroided::query_multi_group aggregated {}", - tot + "ExpandedRawFileIndexCentroided::query_multi_group aggregated {} ", + tot, ); - println!("{}", out); Some(out) }, + &[BenchmarkTag::Query], ); out.push(erfic); } - std::mem::drop(erfic_index); - let tqi_index = QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(); for (tolerance, tol_name) in tolerances.clone() { - let tqi = with_benchmark( + let tqi = env_config.with_benchmark( "TransposedQuadIndex", &format!("BatchAccess_{}", tol_name), - || { + || QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(), + |index, i| { let tmp = query_multi_group( - &tqi_index, - &tqi_index, + index, + index, &tolerance, &query_groups, &RawPeakIntensityAggregator::new, ); let tot: u64 = tmp.into_iter().sum(); - let out = format!("TransposedQuadIndex::query_multi_group aggregated {}", tot); - println!("{}", out); + let out = format!("TransposedQuadIndex::query_multi_group aggregated {} ", tot,); Some(out) }, + &[BenchmarkTag::HighMem, BenchmarkTag::Query], ); out.push(tqi); } - std::mem::drop(tqi_index); - let tqic_index = QuadSplittedTransposedIndex::from_path_centroided(raw_file_path).unwrap(); for (tolerance, tol_name) in tolerances.clone() { - let tqi = with_benchmark( + let tqi = env_config.with_benchmark( "TransposedQuadIndexCentroided", &format!("BatchAccess_{}", tol_name), - || { + || QuadSplittedTransposedIndex::from_path_centroided(raw_file_path).unwrap(), + |index, i| { let tmp = query_multi_group( - &tqic_index, - &tqic_index, + index, + index, &tolerance, &query_groups, &RawPeakIntensityAggregator::new, ); let tot: u64 = tmp.into_iter().sum(); - let out = format!("TransposedQuadIndex::query_multi_group aggregated {}", tot); - println!("{}", out); + let out = format!("TransposedQuadIndex::query_multi_group aggregated {} ", tot,); Some(out) }, + &[BenchmarkTag::Query], ); out.push(tqi); } - std::mem::drop(tqic_index); - out + out.into_iter().flatten().collect() } fn write_results( - report: BenchmarkReport, + mut report: BenchmarkReport, basename: &str, parent: &Path, ) -> std::io::Result<(PathBuf, String)> { @@ -331,13 +469,26 @@ fn write_results( let file = File::create(&filepath)?; serde_json::to_writer_pretty(file, &report)?; let out = serde_json::to_string_pretty(&report)?; - Ok((filepath, out)) + + for result in report.results.iter_mut() { + result.iterations = None; + } + let slim_filepath = parent.join(format!("slim_benchmark_results_{}.json", basename)); + let slim_file = File::create(&slim_filepath)?; + serde_json::to_writer_pretty(slim_file, &report)?; + let slim_out = serde_json::to_string_pretty(&report)?; + + Ok((filepath, slim_out)) } fn main() { env_logger::init(); let st = Instant::now(); - let (raw_file_path, basename) = get_file_from_env(); + + let env_config = EnvConfig::new(); + let raw_file_path = env_config.tims_data_file.clone(); + let basename = env_config.file_stem.clone(); + let file_parent = std::path::Path::new(&raw_file_path) .parent() .expect("Expected to find a parent directory"); @@ -349,11 +500,11 @@ fn main() { ); println!("Running encoding benchmarks..."); - let encoding_results = run_encoding_benchmark(&raw_file_path); + let encoding_results = run_encoding_benchmark(&raw_file_path, env_config.clone()); all_results.extend(encoding_results); println!("Running batch access benchmarks..."); - let batch_results = run_batch_access_benchmark(&raw_file_path); + let batch_results = run_batch_access_benchmark(&raw_file_path, env_config.clone()); all_results.extend(batch_results); let report = BenchmarkReport { settings: BenchmarkSettings { diff --git a/benches/plot_bench.py b/benches/plot_bench.py index e6e3bb0..cc822ed 100644 --- a/benches/plot_bench.py +++ b/benches/plot_bench.py @@ -16,8 +16,12 @@ parser.add_argument("benchmark_file") args = parser.parse_args() +bench_file_path = Path(args.benchmark_file) +target_dir = bench_file_path.parent +file_stem = bench_file_path.stem + data = ( - pl.read_json(args.benchmark_file) + pl.read_json(str(bench_file_path)) .explode("results") .with_columns( bench=pl.col("results").struct.field("name"), @@ -39,7 +43,7 @@ y=alt.Y("time_seconds", scale=alt.Scale(type="log")), color="bench", ).properties( - width=600, - height=600, + width=480, + height=360, title=f"{context}", - ).save(f"{context}.png") + ).save(target_dir / f"{file_stem}_{context}.png") diff --git a/data/.gitignore b/data/.gitignore new file mode 100644 index 0000000..4dba598 --- /dev/null +++ b/data/.gitignore @@ -0,0 +1,4 @@ +*.d/ +*.d.zip +*.d.tar + diff --git 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zLWNWJ@BuW1R?in}nxAIfJX0HHg)mL02uX9OjG8T{P34s#-JmutOUFAUP*P&wp!0Lu z6s0WWVzq~QLm5*p)epwlz~^SFiCmXSc8HU!_0+!zoeD+9?al^HDTkr?Ww+4l{G9fP zKih%KVK9XCtss#aX(u9ySO4WNGF3uG14LVf7(M|$qL8JFD2;fKFdfG1x8#}$O+kD_ zP=HH`XJdghq3!LiZ~{;lFOPcBL6y_=t}mYcqW%wsA73rCcT)tS$2g+-_$r*MfN?r= zM*eU0Ux87yy z;ArgLJ+NfgGyE~O%dz_t<}q|Ujsd5QuxNn>v#H$6z^bH@2=i z$<$LY9>7Mn~-1Qn?0*V) for ExtractedIonChromatomobilogram { +impl Aggregator for ExtractedIonChromatomobilogram { + type Item = RawPeak; type Output = ChromatomobilogramVectorArrayTuples; fn add(&mut self, peak: &RawPeak) { @@ -162,7 +163,8 @@ impl ChromatomobilogramStatsArrays { } } -impl Aggregator for ChromatomobilogramStats { +impl Aggregator for ChromatomobilogramStats { + type Item = RawPeak; type Output = ChromatomobilogramStatsArrays; fn add(&mut self, peak: &RawPeak) { diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs index ad20484..35783c8 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs @@ -342,9 +342,8 @@ impl From Aggregator<(RawPeak, FH)> - for MultiCMGStats -{ +impl Aggregator for MultiCMGStats { + type Item = (RawPeak, FH); type Output = NaturalFinalizedMultiCMGStatsArrays; fn add(&mut self, peak: &(RawPeak, FH)) { diff --git a/src/models/aggregators/raw_peak_agg/point_agg.rs b/src/models/aggregators/raw_peak_agg/point_agg.rs index e1ad36c..9309232 100644 --- a/src/models/aggregators/raw_peak_agg/point_agg.rs +++ b/src/models/aggregators/raw_peak_agg/point_agg.rs @@ -14,7 +14,8 @@ impl RawPeakIntensityAggregator { } } -impl Aggregator for RawPeakIntensityAggregator { +impl Aggregator for RawPeakIntensityAggregator { + type Item = RawPeak; type Output = u64; fn add(&mut self, peak: &RawPeak) { @@ -60,7 +61,8 @@ pub struct RawPeakVectorArrays { pub retention_times: Vec, } -impl Aggregator for RawPeakVectorAggregator { +impl Aggregator for RawPeakVectorAggregator { + type Item = RawPeak; type Output = RawPeakVectorArrays; fn add(&mut self, peak: &RawPeak) { diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index 3263c58..638cfc4 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -2,7 +2,6 @@ use super::single_quad_settings::{ expand_quad_settings, ExpandedFrameQuadSettings, SingleQuadrupoleSetting, }; use itertools::Itertools; -use rayon::iter::IntoParallelIterator; use rayon::prelude::*; use std::collections::HashMap; use std::marker::PhantomData; @@ -15,10 +14,14 @@ use super::peak_in_quad::PeakInQuad; use crate::sort_by_indices_multi; use crate::sort_vecs_by_first; use crate::utils::compress_explode::explode_vec; -use crate::utils::frame_processing::lazy_centroid_weighted_frame; +use crate::utils::frame_processing::{lazy_centroid_weighted_frame, PeakArrayRefs}; use crate::utils::sorting::argsort_by; use crate::utils::tolerance_ranges::{scan_tol_range, tof_tol_range}; -use log::{debug, info, trace}; +use log::{info, trace, warn}; +use timsrust::{ + readers::{FrameReader, FrameReaderError, MetadataReaderError}, + TimsRustError, +}; /// A frame after expanding the mobility data and re-sorting it by tof. #[derive(Debug, Clone)] @@ -86,7 +89,7 @@ fn sort_by_tof_macro( } impl ExpandedFrameSlice { - pub fn sort_by_tof(mut self) -> ExpandedFrameSlice { + pub fn sort_by_tof(self) -> ExpandedFrameSlice { // let mut indices = argsort_by(&self.tof_indices, |x| *x); // sort_by_indices_multi!( // &mut indices, @@ -295,39 +298,239 @@ impl ExpandedFrame { } } -pub fn expand_and_arrange_frames( - frames: Vec, +pub fn par_expand_and_arrange_frames( + frame_iter: impl ParallelIterator, ) -> HashMap, Vec>> { - info!("Expanding and arranging frames"); let start = Instant::now(); - let mut out = HashMap::new(); - let split: Vec> = frames - .into_par_iter() - .flat_map(|frame| expand_and_split_frame(frame)) - .collect(); - for es in split { - out.entry(es.quadrupole_settings) - .or_insert(Vec::new()) - .push(es); - } + let split = frame_iter.flat_map(|frame| expand_and_split_frame(frame)); + // let mut out = HashMap::new(); + // for es in split { + // out.entry(es.quadrupole_settings) + // .or_insert(Vec::new()) + // .push(es); + // } + // + // Attempted implementation so the folding occurs in parrallel. + // Inspired by/Copied from: https://stackoverflow.com/a/70097253/4295016 + let mut out = split + .fold(HashMap::new, |mut acc, x| { + acc.entry(x.quadrupole_settings) + .or_insert(Vec::new()) + .push(x); + acc + }) + .reduce_with(|mut acc1, acc2| { + for (qs, frameslices) in acc2.into_iter() { + acc1.entry(qs).or_insert(Vec::new()).extend(frameslices); + } + acc1 + }) + .expect("At least one frame is iterated over"); // Finally sort each of them internally by retention time. for (_, es) in out.iter_mut() { - es.sort_unstable_by(|a, b| a.rt.partial_cmp(&b.rt).unwrap()); + es.par_sort_unstable_by(|a, b| a.rt.partial_cmp(&b.rt).unwrap()); } let end = start.elapsed(); info!("Expanding and arranging frames took {:#?}", end); out } +#[derive(Debug, Clone, Copy, PartialEq)] +pub enum FrameProcessingConfig { + Centroided { + ims_tol_pct: f64, + mz_tol_ppm: f64, + window_width: usize, + max_ms1_peaks: usize, + max_ms2_peaks: usize, + ims_converter: Option, + mz_converter: Option, + }, + NotCentroided, +} + +impl FrameProcessingConfig { + pub fn with_converters( + self, + ims_converter: Scan2ImConverter, + mz_converter: Tof2MzConverter, + ) -> Self { + match self { + FrameProcessingConfig::Centroided { + ims_tol_pct, + mz_tol_ppm, + window_width, + max_ms1_peaks, + max_ms2_peaks, + .. + } => FrameProcessingConfig::Centroided { + ims_tol_pct, + mz_tol_ppm, + window_width, + max_ms1_peaks, + max_ms2_peaks, + ims_converter: Some(ims_converter), + mz_converter: Some(mz_converter), + }, + FrameProcessingConfig::NotCentroided => FrameProcessingConfig::NotCentroided, + } + } + + pub fn default_centroided() -> Self { + FrameProcessingConfig::Centroided { + ims_tol_pct: 1.5, + mz_tol_ppm: 15.0, + window_width: 3, + max_ms1_peaks: 100_000, + max_ms2_peaks: 10_000, + ims_converter: Default::default(), + mz_converter: Default::default(), + } + } + + pub fn default_not_centroided() -> Self { + FrameProcessingConfig::NotCentroided + } +} + +#[derive(Debug)] +pub enum DataReadingError { + CentroidingError(FrameProcessingConfig), + UnsupportedDataError(String), + TimsRustError(TimsRustError), // Why doesnt timsrust error derive clone? +} + +impl From for DataReadingError { + fn from(e: TimsRustError) -> Self { + DataReadingError::TimsRustError(e) + } +} + +impl From for DataReadingError { + fn from(e: MetadataReaderError) -> Self { + DataReadingError::TimsRustError(TimsRustError::MetadataReaderError(e)) + } +} + +impl From for DataReadingError { + fn from(e: FrameReaderError) -> Self { + DataReadingError::TimsRustError(TimsRustError::FrameReaderError(e)) + } +} + +fn warn_and_skip_badframes( + frame_iter: impl ParallelIterator>, +) -> impl ParallelIterator { + frame_iter.filter_map(|x| { + // Log the info of the frame that broke ... + match x { + Ok(frame) => Some(frame), + Err(e) => { + warn!("Failed to read frame {:?}", e); + None + } + } + }) +} + +pub fn par_read_and_expand_frames( + frame_reader: &FrameReader, + centroiding_config: FrameProcessingConfig, +) -> Result< + HashMap, Vec>>, + DataReadingError, +> { + let dia_windows = match frame_reader.get_dia_windows() { + Some(dia_windows) => dia_windows, + None => { + return Err(DataReadingError::UnsupportedDataError( + "No dia windows found".to_string(), + )) + } + }; + + let mut all_expanded_frames = HashMap::new(); + for dia_window in dia_windows.into_iter() { + info!("Processing dia window: {:?}", dia_window); + let curr_iter = frame_reader.parallel_filter(|x| x.quadrupole_settings == dia_window); + let curr_iter = warn_and_skip_badframes(curr_iter); + + let expanded_frames = match centroiding_config { + FrameProcessingConfig::Centroided { + ims_tol_pct, + mz_tol_ppm, + window_width, + max_ms1_peaks: _max_ms1_peaks, + max_ms2_peaks, + ims_converter, + mz_converter, + } => { + let expanded_frames = par_expand_and_centroid_frames( + curr_iter, + ims_tol_pct, + mz_tol_ppm, + window_width, + max_ms2_peaks, + &ims_converter.unwrap(), + &mz_converter.unwrap(), + ); + expanded_frames + } + FrameProcessingConfig::NotCentroided => { + let expanded_frames = par_expand_and_arrange_frames(curr_iter); + expanded_frames + } + }; + + all_expanded_frames.extend(expanded_frames); + } + + info!("Processing MS1 frames"); + let ms1_iter = frame_reader.parallel_filter(|x| x.ms_level == MSLevel::MS1); + let ms1_iter = warn_and_skip_badframes(ms1_iter); + let expanded_ms1_frames = match centroiding_config { + FrameProcessingConfig::Centroided { + ims_tol_pct, + mz_tol_ppm, + window_width, + max_ms1_peaks, + max_ms2_peaks: _max_ms2_peaks, + ims_converter, + mz_converter, + } => { + let expanded_frames = par_expand_and_centroid_frames( + ms1_iter, + ims_tol_pct, + mz_tol_ppm, + window_width, + max_ms1_peaks, + &ims_converter.unwrap(), + &mz_converter.unwrap(), + ); + expanded_frames + } + FrameProcessingConfig::NotCentroided => { + let expanded_frames = par_expand_and_arrange_frames(ms1_iter); + expanded_frames + } + }; + all_expanded_frames.extend(expanded_ms1_frames); + info!("Done reading and expanding frames"); + + Ok(all_expanded_frames) +} + pub fn par_expand_and_centroid_frames( - frames: Vec, + frames: impl ParallelIterator, ims_tol_pct: f64, mz_tol_ppm: f64, + window_width: usize, + max_peaks: usize, ims_converter: &Scan2ImConverter, mz_converter: &Tof2MzConverter, ) -> HashMap, Vec>> { - let split_frames = expand_and_arrange_frames(frames); + let split_frames = par_expand_and_arrange_frames(frames); let out: HashMap, Vec>> = split_frames @@ -338,9 +541,10 @@ pub fn par_expand_and_centroid_frames( let start_peaks: usize = frameslices.iter().map(|x| x.len()).sum(); let centroided = par_lazy_centroid_frameslices( &frameslices, - 3, + window_width, ims_tol_pct, mz_tol_ppm, + max_peaks, ims_converter, mz_converter, ); @@ -358,70 +562,34 @@ pub fn par_expand_and_centroid_frames( out } -fn centroid_frameslice_window( +fn centroid_frameslice_window2( frameslices: &[ExpandedFrameSlice], ims_tol_pct: f64, mz_tol_ppm: f64, + max_peaks: usize, ims_converter: &Scan2ImConverter, mz_converter: &Tof2MzConverter, ) -> ExpandedFrameSlice { assert!(frameslices.len() > 1, "Expected at least 2 frameslices"); let reference_index = frameslices.len() / 2; - // this is A LOT of cloning ... look into whether it is needed. - - let tof_array: Vec = frameslices - .iter() - .flat_map(|x| x.tof_indices.clone()) - .collect(); - - let ims_array: Vec = frameslices + let peak_refs: Vec = frameslices .iter() - .flat_map(|x| x.scan_numbers.clone()) - .collect(); - let weight_array: Vec = frameslices - .iter() - .flat_map(|x| x.intensities.clone()) - .collect(); - let intensity_array: Vec = frameslices - .iter() - .enumerate() - .flat_map(|(i, x)| { - if i == reference_index { - x.intensities.clone() - } else { - vec![0u32; x.tof_indices.len()] - } - }) + .map(|x| PeakArrayRefs::new(&x.tof_indices, &x.scan_numbers, &x.intensities)) .collect(); - // let mut tof_order = argsort_by(&tof_array, |x| *x); - // sort_by_indices_multi!( - // &mut tof_order, - // &mut tof_array, - // &mut ims_array, - // &mut weight_array, - // &mut intensity_array - // ); - let (tof_array, ims_array, weight_array, intensity_array) = - sort_vecs_by_first!(tof_array, ims_array, weight_array, intensity_array); - - let ((mzs, intensities), imss) = lazy_centroid_weighted_frame( - &tof_array, - &ims_array, - &weight_array, - &intensity_array, - |&tof| tof_tol_range(tof, mz_tol_ppm, mz_converter), - |&scan| scan_tol_range(scan, ims_tol_pct, ims_converter), + let ((tof_array, intensity_array), ims_array) = lazy_centroid_weighted_frame( + &peak_refs, + reference_index, + max_peaks, + |tof| tof_tol_range(tof, mz_tol_ppm, mz_converter), + |scan| scan_tol_range(scan, ims_tol_pct, ims_converter), ); - // Make sure everything is sorted ... - assert!(mzs.windows(2).all(|x| x[0] <= x[1])); - ExpandedFrameSlice { - tof_indices: mzs, - scan_numbers: imss, - intensities, + tof_indices: tof_array, + scan_numbers: ims_array, + intensities: intensity_array, frame_index: frameslices[reference_index].frame_index, rt: frameslices[reference_index].rt, acquisition_type: frameslices[reference_index].acquisition_type, @@ -439,6 +607,7 @@ pub fn par_lazy_centroid_frameslices( window_width: usize, ims_tol_pct: f64, mz_tol_ppm: f64, + max_peaks: usize, ims_converter: &Scan2ImConverter, mz_converter: &Tof2MzConverter, ) -> Vec> { @@ -454,7 +623,14 @@ pub fn par_lazy_centroid_frameslices( assert!(frameslices.len() > window_width); let local_lambda = |fss: &[ExpandedFrameSlice]| { - centroid_frameslice_window(fss, ims_tol_pct, mz_tol_ppm, ims_converter, mz_converter) + centroid_frameslice_window2( + fss, + ims_tol_pct, + mz_tol_ppm, + max_peaks, + ims_converter, + mz_converter, + ) }; frameslices diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index b61788b..11e85cd 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -1,9 +1,8 @@ use crate::models::adapters::FragmentIndexAdapter; use crate::models::elution_group::ElutionGroup; -use crate::models::frames::expanded_frame::ExpandedFrame; use crate::models::frames::expanded_frame::{ - expand_and_arrange_frames, expand_and_split_frame, par_expand_and_centroid_frames, - ExpandedFrameSlice, SortedState, + par_read_and_expand_frames, DataReadingError, ExpandedFrameSlice, FrameProcessingConfig, + SortedState, }; use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::raw_peak::RawPeak; @@ -11,19 +10,16 @@ use crate::models::frames::single_quad_settings::{ get_matching_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, }; use crate::models::queries::FragmentGroupIndexQuery; -use crate::traits::indexed_data::IndexedData; +use crate::traits::indexed_data::QueriableData; use crate::ToleranceAdapter; -use log::{debug, info}; +use log::info; use rayon::prelude::*; use serde::Serialize; use std::collections::HashMap; use std::hash::Hash; use std::time::Instant; -use timsrust::converters::{ - ConvertableDomain, Frame2RtConverter, Scan2ImConverter, Tof2MzConverter, -}; -use timsrust::readers::{FrameReader, FrameReaderError, MetadataReader}; -use timsrust::{QuadrupoleSettings, TimsRustError}; +use timsrust::converters::{Frame2RtConverter, Scan2ImConverter, Tof2MzConverter}; +use timsrust::readers::{FrameReader, MetadataReader}; type QuadSettingsIndex = usize; @@ -115,76 +111,32 @@ impl ExpandedRawFrameIndex { } } - pub fn from_path_centroided(path: &str) -> Result { - let file_reader = FrameReader::new(path)?; - - let sql_path = std::path::Path::new(path).join("analysis.tdf"); - let meta_converters = MetadataReader::new(&sql_path)?; - - let st = Instant::now(); - let all_frames = file_reader.get_all().into_iter().flatten().collect(); - let read_elap = st.elapsed(); - info!("Reading all frames took {:#?}", read_elap); - let st = Instant::now(); - // TODO: Expose this parameter as a config option. - let centroided_split_frames = par_expand_and_centroid_frames( - all_frames, - 1.5, - 15.0, - &meta_converters.im_converter, - &meta_converters.mz_converter, - ); - let centroided_elap = st.elapsed(); - info!("Centroiding took {:#?}", centroided_elap); - - let mut out_ms2_frames = HashMap::new(); - let mut out_ms1_frames: Option = None; - - let mut flat_quad_settings = Vec::new(); - centroided_split_frames - .into_iter() - .for_each(|(q, frameslices)| match q { - None => { - out_ms1_frames = Some(ExpandedSliceBundle::new(frameslices)); - } - Some(q) => { - flat_quad_settings.push(q); - out_ms2_frames.insert(q.index, ExpandedSliceBundle::new(frameslices)); - } - }); - - let adapter = FragmentIndexAdapter::from(meta_converters.clone()); - - let out = Self { - bundled_ms1_frames: out_ms1_frames.expect("At least one ms1 frame should be present"), - bundled_frames: out_ms2_frames, - flat_quad_settings, - rt_converter: meta_converters.rt_converter, - mz_converter: meta_converters.mz_converter, - im_converter: meta_converters.im_converter, - adapter, - }; - - Ok(out) + pub fn from_path_centroided(path: &str) -> Result { + let config = FrameProcessingConfig::default_centroided(); + Self::from_path_base(path, config) } - pub fn from_path(path: &str) -> Result { - // NOTE: I am just copy-pasting the centroided version. If I keep both I will - // abstract it and make dispatch in a config ... - + pub fn from_path_base( + path: &str, + centroid_config: FrameProcessingConfig, + ) -> Result { + info!( + "Building ExpandedRawFrameIndex from path {} config {:?}", + path, centroid_config, + ); let file_reader = FrameReader::new(path)?; let sql_path = std::path::Path::new(path).join("analysis.tdf"); let meta_converters = MetadataReader::new(&sql_path)?; + let centroid_config = centroid_config.with_converters( + meta_converters.im_converter.clone(), + meta_converters.mz_converter.clone(), + ); let st = Instant::now(); - let all_frames = file_reader.get_all().into_iter().flatten().collect(); - let read_elap = st.elapsed(); - info!("Reading all frames took {:#?}", read_elap); - let st = Instant::now(); - let centroided_split_frames = expand_and_arrange_frames(all_frames); + let centroided_split_frames = par_read_and_expand_frames(&file_reader, centroid_config)?; let centroided_elap = st.elapsed(); - info!("Splitting took {:#?}", centroided_elap); + info!("Reading + Centroiding took {:#?}", centroided_elap); let mut out_ms2_frames = HashMap::new(); let mut out_ms1_frames: Option = None; @@ -216,10 +168,14 @@ impl ExpandedRawFrameIndex { Ok(out) } + + pub fn from_path(path: &str) -> Result { + Self::from_path_base(path, FrameProcessingConfig::NotCentroided) + } } impl - IndexedData, (RawPeak, FH)> for ExpandedRawFrameIndex + QueriableData, (RawPeak, FH)> for ExpandedRawFrameIndex { fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { todo!(); @@ -250,7 +206,7 @@ impl // .collect() } - fn add_query>( + fn add_query>( &self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG, @@ -279,7 +235,7 @@ impl // }) } - fn add_query_multi_group>( + fn add_query_multi_group>( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], @@ -318,7 +274,7 @@ impl } impl - IndexedData, RawPeak> for ExpandedRawFrameIndex + QueriableData, RawPeak> for ExpandedRawFrameIndex { fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { todo!(); @@ -349,7 +305,7 @@ impl // .collect() } - fn add_query>( + fn add_query>( &self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG, @@ -378,7 +334,7 @@ impl // }) } - fn add_query_multi_group>( + fn add_query_multi_group>( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], diff --git a/src/models/indices/raw_file_index.rs b/src/models/indices/raw_file_index.rs index f736e30..60688be 100644 --- a/src/models/indices/raw_file_index.rs +++ b/src/models/indices/raw_file_index.rs @@ -4,7 +4,7 @@ use crate::models::frames::raw_frames::frame_elems_matching; use crate::models::frames::raw_peak::RawPeak; use crate::models::queries::{FragmentGroupIndexQuery, NaturalPrecursorQuery, PrecursorIndexQuery}; use crate::traits::aggregator::Aggregator; -use crate::traits::indexed_data::IndexedData; +use crate::traits::indexed_data::QueriableData; use crate::ElutionGroup; use crate::ToleranceAdapter; use log::trace; @@ -60,7 +60,7 @@ impl RawFileIndex { 'c, 'b: 'c, 'a: 'b, - FH: Clone + Eq + Serialize + Hash + Debug + Send + Sync, + FH: Clone + Eq + Serialize + Hash + Debug + Send + Sync + Copy, >( &'a self, fqs: &'b FragmentGroupIndexQuery, @@ -148,7 +148,9 @@ impl RawFileIndex { } } - fn queries_from_elution_elements_impl( + fn queries_from_elution_elements_impl< + FH: Clone + Eq + Serialize + Hash + Send + Sync + Copy, + >( &self, tol: &dyn crate::traits::tolerance::Tolerance, elution_elements: &crate::models::elution_group::ElutionGroup, @@ -183,7 +185,7 @@ impl RawFileIndex { } impl - IndexedData, RawPeak> for RawFileIndex + QueriableData, RawPeak> for RawFileIndex { fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { let mut out = Vec::new(); @@ -191,7 +193,7 @@ impl out } - fn add_query>( + fn add_query>( &self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG, @@ -199,7 +201,7 @@ impl self.apply_on_query(fragment_query, &mut |peak, _| aggregator.add(&peak)); } - fn add_query_multi_group>( + fn add_query_multi_group>( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], @@ -211,7 +213,7 @@ impl } } -impl +impl ToleranceAdapter, ElutionGroup> for RawFileIndex { fn query_from_elution_group( diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index 6642517..8a4ac88 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -2,14 +2,12 @@ use super::peak_bucket::PeakBucketBuilder; use super::peak_bucket::{PeakBucket, PeakInBucket}; use crate::models::frames::expanded_frame::{ExpandedFrameSlice, SortingStateTrait}; use crate::models::frames::peak_in_quad::PeakInQuad; -use crate::models::frames::raw_peak::RawPeak; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; use crate::sort_by_indices_multi; use crate::utils::display::{glimpse_vec, GlimpseConfig}; use crate::utils::sorting::par_argsort_by; use log::debug; use log::info; -use log::trace; use std::collections::{BTreeMap, HashMap}; use std::fmt::Display; use std::time::Instant; @@ -212,7 +210,7 @@ impl TransposedQuadIndexBuilder { let max_tof = *self .tof_slices .iter() - .map(|x| x.iter().max().unwrap()) + .filter_map(|x| x.iter().max()) .max() .unwrap(); let mut tof_counts = vec![0usize; max_tof as usize + 1]; diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 0c213fa..f596fe0 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -2,17 +2,16 @@ use super::quad_index::{FrameRTTolerance, TransposedQuadIndex, TransposedQuadInd use crate::models::adapters::FragmentIndexAdapter; use crate::models::elution_group::ElutionGroup; use crate::models::frames::expanded_frame::{ - expand_and_split_frame, par_expand_and_centroid_frames, ExpandedFrameSlice, SortingStateTrait, + expand_and_split_frame, par_read_and_expand_frames, DataReadingError, ExpandedFrameSlice, + FrameProcessingConfig, SortingStateTrait, }; use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::raw_peak::RawPeak; - use crate::models::frames::single_quad_settings::{ get_matching_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, }; use crate::models::queries::FragmentGroupIndexQuery; -use crate::models::queries::PrecursorIndexQuery; -use crate::traits::indexed_data::IndexedData; +use crate::traits::indexed_data::QueriableData; use crate::utils::display::{glimpse_vec, GlimpseConfig}; use crate::ToleranceAdapter; use log::{debug, info, trace}; @@ -23,9 +22,7 @@ use std::fmt::Debug; use std::fmt::Display; use std::hash::Hash; use std::time::Instant; -use timsrust::converters::{ - ConvertableDomain, Frame2RtConverter, Scan2ImConverter, Tof2MzConverter, -}; +use timsrust::converters::{Frame2RtConverter, Scan2ImConverter, Tof2MzConverter}; use timsrust::readers::{FrameReader, MetadataReader}; use timsrust::Frame; use timsrust::Metadata; @@ -140,7 +137,7 @@ impl Display for QuadSplittedTransposedIndex { } impl QuadSplittedTransposedIndex { - pub fn from_path(path: &str) -> Result { + pub fn from_path(path: &str) -> Result { let st = Instant::now(); info!("Building transposed quad index from path {}", path); let tmp = QuadSplittedTransposedIndexBuilder::from_path(path)?; @@ -151,7 +148,7 @@ impl QuadSplittedTransposedIndex { Ok(out) } - pub fn from_path_centroided(path: &str) -> Result { + pub fn from_path_centroided(path: &str) -> Result { let st = Instant::now(); info!( "Building CENTROIDED transposed quad index from path {}", @@ -207,10 +204,22 @@ impl QuadSplittedTransposedIndexBuilder { .add_frame_slice(frame_slice); } + fn from_path(path: &str) -> Result { + Self::from_path_base(path, FrameProcessingConfig::NotCentroided) + } + + fn from_path_centroided(path: &str) -> Result { + let config = FrameProcessingConfig::default_centroided(); + Self::from_path_base(path, config) + } + // TODO: I think i should split this into two functions, one that starts the builder // and one that adds the frameslices, maybe even have a config struct that dispatches // the right preprocessing steps. - fn from_path(path: &str) -> Result { + fn from_path_base( + path: &str, + centroid_config: FrameProcessingConfig, + ) -> Result { let file_reader = FrameReader::new(path)?; let sql_path = std::path::Path::new(path).join("analysis.tdf"); @@ -226,62 +235,17 @@ impl QuadSplittedTransposedIndexBuilder { added_peaks: 0, }; - let out2: Result, TimsRustError> = (0..file_reader.len()) - .into_par_iter() - .map(|id| file_reader.get(id)) - .chunks(100) - .map(|frames| { - let mut out = Self::new(); - for frame in frames { - let frame = frame?; - out.add_frame(frame); - } - Ok(out) - }) - .collect(); - - let out2 = out2?.into_iter().fold(Self::new(), |mut x, y| { - x.fold(y); - x - }); - final_out.fold(out2); + let centroid_config = centroid_config + .with_converters(meta_converters.im_converter, meta_converters.mz_converter); - Ok(final_out) - } - - fn from_path_centroided(path: &str) -> Result { - let file_reader = FrameReader::new(path)?; - - let sql_path = std::path::Path::new(path).join("analysis.tdf"); - let meta_converters = MetadataReader::new(&sql_path)?; - - let out_meta_converters = meta_converters.clone(); - let mut final_out = Self { - indices: HashMap::new(), - rt_converter: Some(meta_converters.rt_converter), - mz_converter: Some(meta_converters.mz_converter), - im_converter: Some(meta_converters.im_converter), - metadata: Some(out_meta_converters), - added_peaks: 0, - }; - - let st = Instant::now(); - let all_frames = file_reader.get_all().into_iter().flatten().collect(); - let read_elap = st.elapsed(); - debug!("Reading all frames took {:#?}", read_elap); let st = Instant::now(); - let centroided_split_frames = par_expand_and_centroid_frames( - all_frames, - 1.5, - 15.0, - &meta_converters.im_converter, - &meta_converters.mz_converter, - ); + let split_frames = par_read_and_expand_frames(&file_reader, centroid_config)?; + let centroided_elap = st.elapsed(); - debug!("Centroiding took {:#?}", centroided_elap); + debug!("Reading + Centroiding took {:#?}", centroided_elap); let st = Instant::now(); - let out2: Result, TimsRustError> = centroided_split_frames + let out2: Result, TimsRustError> = split_frames .into_par_iter() .map(|(q, frameslices)| { let mut out = Self::new(); @@ -300,8 +264,8 @@ impl QuadSplittedTransposedIndexBuilder { let build_elap = st.elapsed(); info!( - "Reading all frames took {:#?}, centroiding took {:#?}, building took {:#?}", - read_elap, centroided_elap, build_elap + "Reading all frames + centroiding took {:#?}, building took {:#?}", + centroided_elap, build_elap ); Ok(final_out) @@ -356,7 +320,7 @@ impl QuadSplittedTransposedIndexBuilder { } impl - IndexedData, RawPeak> for QuadSplittedTransposedIndex + QueriableData, RawPeak> for QuadSplittedTransposedIndex { fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { let precursor_mz_range = ( @@ -385,7 +349,7 @@ impl .collect() } - fn add_query>( + fn add_query>( &self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG, @@ -413,7 +377,7 @@ impl }) } - fn add_query_multi_group>( + fn add_query_multi_group>( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], @@ -450,7 +414,7 @@ impl // ============================================================================ impl - IndexedData, (RawPeak, FH)> for QuadSplittedTransposedIndex + QueriableData, (RawPeak, FH)> for QuadSplittedTransposedIndex { fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { let precursor_mz_range = ( @@ -480,7 +444,7 @@ impl .collect() } - fn add_query>( + fn add_query>( &self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG, @@ -508,7 +472,7 @@ impl }) } - fn add_query_multi_group>( + fn add_query_multi_group>( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], diff --git a/src/models/queries.rs b/src/models/queries.rs index e4e7679..8813111 100644 --- a/src/models/queries.rs +++ b/src/models/queries.rs @@ -10,7 +10,7 @@ pub struct PrecursorIndexQuery { } #[derive(Debug, Clone)] -pub struct FragmentGroupIndexQuery { +pub struct FragmentGroupIndexQuery { pub mz_index_ranges: HashMap, pub precursor_query: PrecursorIndexQuery, } diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index 982c377..baf2dc1 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -5,7 +5,7 @@ use std::hash::Hash; use std::rc::Rc; use std::time::Instant; -use crate::{Aggregator, ElutionGroup, HasIntegerID, IndexedData, Tolerance, ToleranceAdapter}; +use crate::{Aggregator, ElutionGroup, HasIntegerID, QueriableData, Tolerance, ToleranceAdapter}; /// A struct that can be queried for TIMS data. /// @@ -39,10 +39,12 @@ use crate::{Aggregator, ElutionGroup, HasIntegerID, IndexedData, Tolerance, Tole /// 3. The results are aggregated with `AG` aggregators (which are generated by the factory, when passed a numeric ID). pub struct QueriableTimsData<'a, ID, TA, TL, QF, AE, OE, AG, EG: HasIntegerID> where - AG: Aggregator + Send + Sync, - ID: IndexedData, + AG: Aggregator + Send + Sync, + ID: QueriableData, TA: ToleranceAdapter, TL: Tolerance, + QF: Send + Sync, + AE: Send + Sync + Clone + Copy, { pub indexed_data: &'a ID, pub aggregator_factory: &'a dyn Fn(u64) -> AG, @@ -55,11 +57,13 @@ where impl<'a, ID, TA, TL, QF, AE, OE, AG, EG> QueriableTimsData<'a, ID, TA, TL, QF, AE, OE, AG, EG> where - AG: Aggregator + Send + Sync, - ID: IndexedData, + AG: Aggregator + Send + Sync, + ID: QueriableData, TA: ToleranceAdapter, TL: Tolerance, EG: HasIntegerID, + QF: Send + Sync, + AE: Send + Sync + Clone + Copy, { pub fn query(&self, elution_group: &EG) -> OE { let mut aggregator = (self.aggregator_factory)(elution_group.get_id()); @@ -95,12 +99,14 @@ pub fn query_multi_group<'a, ID, TA, TL, QF, AE, OE, AG, FH>( aggregator_factory: &dyn Fn(u64) -> AG, ) -> Vec where - AG: Aggregator + Send + Sync, - ID: IndexedData, + AG: Aggregator + Send + Sync, + ID: QueriableData, TA: ToleranceAdapter>, TL: Tolerance, OE: Send + Sync, FH: Clone + Eq + Serialize + Hash + Send + Sync, + QF: Send + Sync, + AE: Send + Sync + Clone + Copy, { let start = Instant::now(); let mut fragment_queries = Vec::with_capacity(elution_groups.len()); @@ -142,11 +148,13 @@ pub fn query_indexed( elution_group: &ElutionGroup, ) -> OE where - AG: Aggregator + Send + Sync, - ID: IndexedData, + AG: Aggregator + Send + Sync, + ID: QueriableData, TA: ToleranceAdapter>, TL: Tolerance, FH: Clone + Eq + Serialize + Hash + Send + Sync, + QF: Send + Sync, + AE: Send + Sync + Clone + Copy, { let mut aggregator = aggregator_factory(elution_group.id); let prep_query = Rc::new(tolerance_adapter.query_from_elution_group(tolerance, elution_group)); diff --git a/src/traits/aggregator.rs b/src/traits/aggregator.rs index 54a125d..209d444 100644 --- a/src/traits/aggregator.rs +++ b/src/traits/aggregator.rs @@ -1,7 +1,7 @@ -pub trait Aggregator: Send + Sync { +pub trait Aggregator: Send + Sync { + type Item: Send + Sync; type Output: Send + Sync; - fn add(&mut self, item: &I); - // fn fold(&mut self, item: Self); + fn add(&mut self, item: &Self::Item); fn finalize(self) -> Self::Output; } diff --git a/src/traits/indexed_data.rs b/src/traits/indexed_data.rs index 6906a01..a1ce16f 100644 --- a/src/traits/indexed_data.rs +++ b/src/traits/indexed_data.rs @@ -1,9 +1,17 @@ use crate::Aggregator; -pub trait IndexedData { +pub trait QueriableData +where + QF: Send + Sync, + A: Send + Sync + Clone + Copy, +{ fn query(&self, fragment_query: &QF) -> Vec; - fn add_query>(&self, fragment_query: &QF, aggregator: &mut AG); - fn add_query_multi_group>( + fn add_query>( + &self, + fragment_query: &QF, + aggregator: &mut AG, + ); + fn add_query_multi_group>( &self, fragment_queries: &[QF], aggregator: &mut [AG], diff --git a/src/utils/frame_processing.rs b/src/utils/frame_processing.rs index d6f832a..53cc87a 100644 --- a/src/utils/frame_processing.rs +++ b/src/utils/frame_processing.rs @@ -1,7 +1,7 @@ -use log::warn; +use crate::sort_vecs_by_first; +use log::{info, warn}; use std::cmp::Ordering; use std::ops::RangeInclusive; -use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; pub fn squash_frame( mz_array: &[f32], @@ -40,14 +40,6 @@ pub fn squash_frame( let ss_start = mz_array.partition_point(|&x| x < left_e); let ss_end = mz_array.partition_point(|&x| x <= right_e); - let slice_width = ss_end - ss_start; - let local_num_touched = touched[ss_start..ss_end].iter().filter(|&&x| x).count(); - let local_num_untouched = slice_width - local_num_touched; - - if local_num_touched == slice_width { - continue; - } - let mut curr_intensity = 0.0; let mut curr_weighted_mz = 0.0; @@ -55,6 +47,8 @@ pub fn squash_frame( if !touched[i] && intensity_array[i] > 0.0 { curr_intensity += intensity_array[i]; curr_weighted_mz += mz_array[i] * intensity_array[i]; + touched[i] = true; + global_num_touched += 1; } } @@ -65,7 +59,6 @@ pub fn squash_frame( agg_mz[idx] = curr_weighted_mz; touched[ss_start..ss_end].iter_mut().for_each(|x| *x = true); - global_num_touched += local_num_untouched; } if global_num_touched == arr_len { @@ -88,91 +81,188 @@ pub fn squash_frame( pub type TofIntensityVecs = (Vec, Vec); pub type CentroidedVecs = (TofIntensityVecs, Vec); -pub fn lazy_centroid_weighted_frame( - tof_array: &[u32], - ims_array: &[usize], - weight_array: &[u32], - intensity_array: &[u32], - tof_tol_range_fn: impl Fn(&u32) -> RangeInclusive, - ims_tol_range_fn: impl Fn(&usize) -> RangeInclusive, +fn sort_n_check( + agg_intensity: Vec, + agg_tof: Vec, + agg_ims: Vec, +) -> ((Vec, Vec), Vec) { + let (tof_array, ims_array, intensity_array) = + sort_vecs_by_first!(agg_tof, agg_ims, agg_intensity); + + if let Some(x) = intensity_array.last() { + assert!(*x > 0); + let max_tof = tof_array.iter().max().expect("At least one element"); + assert!(*max_tof < (u32::MAX - 1)); + } + ((tof_array, intensity_array), ims_array) +} + +pub struct PeakArrayRefs<'a> { + pub tof_array: &'a [u32], + pub ims_array: &'a [usize], + pub intensity_array: &'a [u32], +} + +impl<'a> PeakArrayRefs<'a> { + pub fn new( + tof_array: &'a [u32], + ims_array: &'a [usize], + intensity_array: &'a [u32], + ) -> PeakArrayRefs<'a> { + // TODO make the asserts optional at compile time. + assert!(tof_array.len() == intensity_array.len()); + assert!(tof_array.len() == ims_array.len()); + assert!( + tof_array.windows(2).all(|x| x[0] <= x[1]), + "Expected tof array to be sorted" + ); + Self { + tof_array, + ims_array, + intensity_array, + } + } + + fn len(&self) -> usize { + self.tof_array.len() + } +} + +/// Splits a global index into a major and minor that +/// matches elements in a collection. +/// +/// As an example if there is a slice of slices, the major index +/// is the index of the slice and the minor index is the index +/// of the element in the slice. +/// +/// Thus if we have [[0,1,2], [3,4,5], [6,7,8]] +/// the major indice are 0,0,0 1,1,1 2,2,2 +/// and the minor 0,1,2 0,1,2 0,1,2 +/// +/// +fn index_split(index: usize, slice_sizes: &[usize]) -> (usize, usize) { + let mut index = index; + for (i, slice_size) in slice_sizes.iter().enumerate() { + if index < *slice_size { + return (i, index); + } + index -= *slice_size; + } + panic!("Index {} is out of bounds", index); +} + +// TODO: Refactor this function +pub fn lazy_centroid_weighted_frame<'a>( + peak_refs: &'a [PeakArrayRefs<'a>], + reference_index: usize, + max_peaks: usize, + tof_tol_range_fn: impl Fn(u32) -> RangeInclusive, + ims_tol_range_fn: impl Fn(usize) -> RangeInclusive, ) -> CentroidedVecs { - let arr_len = tof_array.len(); - const MIN_WEIGHT_PRESERVE: u64 = 50; + let slice_sizes: Vec = peak_refs.iter().map(|x| x.len()).collect(); + let tot_size: usize = slice_sizes.iter().sum(); + let ref_arrays = &peak_refs[reference_index]; + let num_arrays = peak_refs.len(); + assert!(num_arrays > 1); + let arr_len = ref_arrays.len(); + let initial_tot_intensity = ref_arrays + .intensity_array + .iter() + .map(|x| *x as u64) + .sum::(); - // TODO make the asserts optional at compile time. - assert!( - tof_array.windows(2).all(|x| x[0] <= x[1]), - "Expected tof array to be sorted" - ); - assert_eq!( - arr_len, - intensity_array.len(), - "Expected tof and intensity arrays to be the same length" - ); - assert_eq!( - arr_len, - weight_array.len(), - "Expected tof and weight arrays to be the same length" - ); - assert_eq!( - arr_len, - ims_array.len(), - "Expected tof and ims arrays to be the same length" - ); + const MIN_WEIGHT_PRESERVE: u64 = 50; - let mut touched = vec![false; arr_len]; + let mut touched = vec![false; tot_size]; let mut global_num_touched = 0; + let mut num_added = 0; // We will be iterating in decreasing order of intensity - let mut order: Vec = (0..arr_len).collect(); + let mut order: Vec = (0..tot_size).collect(); order.sort_unstable_by(|&a, &b| { - weight_array[b] - .partial_cmp(&weight_array[a]) + let (a_major, a_minor) = index_split(a, &slice_sizes); + let (b_major, b_minor) = index_split(b, &slice_sizes); + + let a_intensity = peak_refs[a_major].intensity_array[a_minor]; + let b_intensity = peak_refs[b_major].intensity_array[b_minor]; + + b_intensity + .partial_cmp(&a_intensity) .unwrap_or(Ordering::Equal) }); - let mut agg_tof = vec![0; arr_len]; - let mut agg_intensity = vec![0; arr_len]; - // We will not be returning the weights. - // let mut agg_weight = vec![0; arr_len]; - let mut agg_ims = vec![0; arr_len]; + assert!({ + let (first_major, first_minor) = index_split(order[0], &slice_sizes); + let (last_major, last_minor) = index_split(order[tot_size - 1], &slice_sizes); + + let first_intensity = peak_refs[first_major].intensity_array[first_minor]; + let last_intensity = peak_refs[last_major].intensity_array[last_minor]; + + first_intensity >= last_intensity + }); + + // TODO explore if making vecs with capacity and appedning is better... + let capacity = max_peaks.min(arr_len); + let mut agg_tof = Vec::with_capacity(capacity); + let mut agg_intensity = Vec::with_capacity(capacity); + let mut agg_ims = Vec::with_capacity(capacity); for idx in order { + let (major_idx, minor_idx) = index_split(idx, &slice_sizes); + if touched[idx] { continue; } - let tof = tof_array[idx]; - let ims = ims_array[idx]; - let tof_range = tof_tol_range_fn(&tof); - let ims_range = ims_tol_range_fn(&ims); - - let ss_start = tof_array.partition_point(|x| x < tof_range.start()); - let ss_end = tof_array.partition_point(|x| x <= tof_range.end()); + let tof = peak_refs[major_idx].tof_array[minor_idx]; + let ims = peak_refs[major_idx].ims_array[minor_idx]; + let this_intensity = peak_refs[major_idx].intensity_array[minor_idx] as u64; + let tof_range = tof_tol_range_fn(tof); + let ims_range = ims_tol_range_fn(ims); let mut curr_intensity = 0u64; let mut curr_weight = 0u64; let mut curr_agg_tof = 0u64; let mut curr_agg_ims = 0u64; - for i in ss_start..ss_end { - if !touched[i] && intensity_array[i] > 0 && ims_range.contains(&ims_array[i]) { - let local_weight = weight_array[i] as u64; - curr_intensity += intensity_array[i] as u64; - curr_agg_tof += tof_array[i] as u64 * local_weight; - curr_agg_ims += ims_array[i] as u64 * local_weight; - curr_weight += local_weight; + let mut local_offset_touched = 0; + for ii in 0..num_arrays { + let local_peak_refs = &peak_refs[ii]; + let ss_start = local_peak_refs + .tof_array + .partition_point(|x| x < tof_range.start()); + let ss_end = local_peak_refs + .tof_array + .partition_point(|x| x <= tof_range.end()); + for i in ss_start..ss_end { + let ti = local_offset_touched + i; + if !touched[ti] && ims_range.contains(&local_peak_refs.ims_array[i]) { + // Peaks are always weighted but not always intense! + let local_intensity = local_peak_refs.intensity_array[i] as u64; + if ii == reference_index { + curr_intensity += local_intensity; + global_num_touched += 1; + } + curr_agg_tof += local_peak_refs.tof_array[i] as u64 * local_intensity; + curr_agg_ims += local_peak_refs.ims_array[i] as u64 * local_intensity; + curr_weight += local_intensity; + touched[ti] = true; + } } + local_offset_touched += local_peak_refs.len(); } - if curr_intensity > 0 && curr_weight > 0 { - agg_intensity[idx] = u32::try_from(curr_intensity).expect("Expected to fit in u32"); - agg_tof[idx] = (curr_agg_tof / curr_weight) as u32; - agg_ims[idx] = (curr_agg_ims / curr_weight) as usize; - - for i in ss_start..ss_end { - touched[i] = true; - global_num_touched += 1; + if curr_intensity > this_intensity { + agg_intensity.push(u32::try_from(curr_intensity).expect("Expected to fit in u32")); + let calc_tof = (curr_agg_tof / curr_weight) as u32; + let calc_ims = (curr_agg_ims / curr_weight) as usize; + assert!(tof_range.contains(&calc_tof)); + assert!(ims_range.contains(&calc_ims)); + agg_tof.push(calc_tof); + agg_ims.push(calc_ims); + num_added += 1; + if num_added == max_peaks { + break; } } @@ -182,18 +272,36 @@ pub fn lazy_centroid_weighted_frame( } // Drop the zeros and sort by mz (tof) - let mut res: Vec<((u32, u32), usize)> = agg_tof - .into_iter() - .zip(agg_intensity.into_iter()) - .zip(agg_ims.into_iter()) - .filter(|&((_, intensity), ims)| (intensity > 0) & (ims > 0)) - .collect(); + let out = sort_n_check(agg_intensity, agg_tof, agg_ims); + let tot_final_intensity = out.0 .1.iter().map(|x| *x as u64).sum::(); + let inten_ratio = tot_final_intensity as f64 / initial_tot_intensity as f64; + assert!(initial_tot_intensity >= tot_final_intensity); + + let output_len = out.0 .0.len(); + let compression_ratio = output_len as f64 / arr_len as f64; + assert!(num_added == output_len); + + // 80% of the intensity being preserved sounds like a good cutoff. + if output_len == max_peaks && inten_ratio < 0.80 { + info!( + "Frame trimmed to max peaks ({}), preserved intensity {}/{} intensity ratio: {} compression_ratio: {} if this is not acceptable consider increasing the parameter.", + max_peaks, tot_final_intensity, initial_tot_intensity, inten_ratio, compression_ratio, + ); + } - res.sort_unstable_by(|a, b| a.0.partial_cmp(&b.0).unwrap_or(Ordering::Equal)); - let output_len = res.len(); - if arr_len > 500 && (output_len == arr_len) { + if arr_len > 5000 && (output_len == arr_len) { warn!("Output length is the same as input length, this is probably a bug"); + warn!("Intensity ratio {:?}", inten_ratio); + warn!("initial_tot_intensity: {:?}", initial_tot_intensity); + warn!("tot_final_intensity: {:?}", tot_final_intensity); + warn!( + "First tof {} -> Range {:?}", + out.0 .0[0], + tof_tol_range_fn(out.0 .0[0]) + ); + panic!(); + // warn!("agg_intensity: {:?}", out.0 .0); } - res.into_iter().unzip() + out } diff --git a/src/utils/tolerance_ranges.rs b/src/utils/tolerance_ranges.rs index dcb3978..faa3d4d 100644 --- a/src/utils/tolerance_ranges.rs +++ b/src/utils/tolerance_ranges.rs @@ -3,7 +3,14 @@ use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter} use std::ops::RangeInclusive; pub fn ppm_tol_range(elem: f64, tol_ppm: f64) -> RangeInclusive { - let utol = tol_ppm / 1e6; + let utol = elem * (tol_ppm / 1e6); + let left_e = elem - utol; + let right_e = elem + utol; + left_e..=right_e +} + +pub fn pct_tol_range(elem: f64, tol_pct: f64) -> RangeInclusive { + let utol = elem * (tol_pct / 100.0); let left_e = elem - utol; let right_e = elem + utol; left_e..=right_e @@ -24,7 +31,7 @@ pub fn scan_tol_range( converter: &Scan2ImConverter, ) -> RangeInclusive { let im = converter.convert(scan as f64); - let im_range = ppm_tol_range(im, tol_pct); + let im_range = pct_tol_range(im, tol_pct); let scan_min = converter.invert(*im_range.start()).round() as usize; let scan_max = converter.invert(*im_range.end()).round() as usize; // Note I need to do this here bc the conversion between scan numbers and ion From 75601e96c3a6def245c77d2df4c9d898a82ecf0d Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Sun, 27 Oct 2024 23:58:34 -0700 Subject: [PATCH 08/30] refactor: changed logging to tracing and testing --- Cargo.lock | 308 +++++++++++++++--- Cargo.toml | 18 +- Taskfile.yml | 5 +- benches/benchmark_indices.rs | 30 +- data/get_data.bash | 5 + ..._results_230510_PRTC_13_S1-B1_1_12817.json | 138 ++++++++ ..._diaPASEF_Condition_A_Sample_Alpha_02.json | 57 ++++ deny.toml | 253 ++++++++++++++ metrics/Taskfile.yml | 15 + src/main.rs | 22 +- .../raw_peak_agg/chromatogram_agg.rs | 13 +- .../raw_peak_agg/multi_chromatogram_agg.rs | 4 +- .../aggregators/streaming_aggregator.rs | 2 +- src/models/frames/expanded_frame.rs | 171 ++++------ src/models/frames/raw_frames.rs | 2 +- .../indices/expanded_raw_index/model.rs | 22 +- src/models/indices/raw_file_index.rs | 4 +- .../transposed_quad_index/peak_bucket.rs | 16 +- .../transposed_quad_index/quad_index.rs | 46 +-- .../quad_splitted_transposed_index.rs | 29 +- .../queriable_tims_data.rs | 2 +- src/utils/frame_processing.rs | 290 ++++++++++++----- src/utils/sorting.rs | 163 +-------- 23 files changed, 1136 insertions(+), 479 deletions(-) create mode 100644 data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json create mode 100644 data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json create mode 100644 deny.toml create mode 100644 metrics/Taskfile.yml diff --git a/Cargo.lock b/Cargo.lock index 2bdd6b6..680a5d5 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -420,6 +420,15 @@ version = "0.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7a81dae078cea95a014a339291cec439d2f232ebe854a9d672b796c6afafa9b7" +[[package]] +name = "deranged" +version = "0.3.11" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b42b6fa04a440b495c8b04d0e71b707c585f83cb9cb28cf8cd0d976c315e31b4" +dependencies = [ + "powerfmt", +] + [[package]] name = "displaydoc" version = "0.1.7" @@ -443,29 +452,6 @@ version = "0.3.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f" -[[package]] -name = "env_filter" -version = "0.1.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4f2c92ceda6ceec50f43169f9ee8424fe2db276791afde7b2cd8bc084cb376ab" -dependencies = [ - "log", - "regex", -] - -[[package]] -name = "env_logger" -version = "0.11.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e13fa619b91fb2381732789fc5de83b45675e882f66623b7d8cb4f643017018d" -dependencies = [ - "anstream", - "anstyle", - "env_filter", - "humantime", - "log", -] - [[package]] name = "fallible-iterator" version = "0.3.0" @@ -498,6 +484,16 @@ dependencies = [ "miniz_oxide", ] +[[package]] +name = "gethostname" +version = "0.2.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c1ebd34e35c46e00bb73e81363248d627782724609fe1b6396f553f68fe3862e" +dependencies = [ + "libc", + "winapi", +] + [[package]] name = "getrandom" version = "0.2.15" @@ -544,12 +540,6 @@ version = "0.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea" -[[package]] -name = "humantime" -version = "2.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4" - [[package]] name = "iana-time-zone" version = "0.1.60" @@ -608,15 +598,6 @@ version = "1.70.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf" -[[package]] -name = "itertools" -version = "0.13.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "413ee7dfc52ee1a4949ceeb7dbc8a33f2d6c088194d9f922fb8318faf1f01186" -dependencies = [ - "either", -] - [[package]] name = "itoa" version = "1.0.11" @@ -770,6 +751,15 @@ dependencies = [ "libc", ] +[[package]] +name = "matchers" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8263075bb86c5a1b1427b5ae862e8889656f126e9f77c484496e8b47cf5c5558" +dependencies = [ + "regex-automata 0.1.10", +] + [[package]] name = "memchr" version = "2.7.4" @@ -794,6 +784,16 @@ dependencies = [ "adler", ] +[[package]] +name = "nu-ansi-term" +version = "0.46.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "77a8165726e8236064dbb45459242600304b42a5ea24ee2948e18e023bf7ba84" +dependencies = [ + "overload", + "winapi", +] + [[package]] name = "num" version = "0.4.3" @@ -827,6 +827,12 @@ dependencies = [ "num-traits", ] +[[package]] +name = "num-conv" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "51d515d32fb182ee37cda2ccdcb92950d6a3c2893aa280e540671c2cd0f3b1d9" + [[package]] name = "num-integer" version = "0.1.46" @@ -889,6 +895,12 @@ dependencies = [ "num-traits", ] +[[package]] +name = "overload" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b15813163c1d831bf4a13c3610c05c0d03b39feb07f7e09fa234dac9b15aaf39" + [[package]] name = "parquet" version = "42.0.0" @@ -926,6 +938,12 @@ version = "1.0.15" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a" +[[package]] +name = "pin-project-lite" +version = "0.2.15" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "915a1e146535de9163f3987b8944ed8cf49a18bb0056bcebcdcece385cece4ff" + [[package]] name = "pkg-config" version = "0.3.30" @@ -938,6 +956,12 @@ version = "1.7.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "da544ee218f0d287a911e9c99a39a8c9bc8fcad3cb8db5959940044ecfc67265" +[[package]] +name = "powerfmt" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391" + [[package]] name = "ppv-lite86" version = "0.2.18" @@ -1023,8 +1047,17 @@ checksum = "4219d74c6b67a3654a9fbebc4b419e22126d13d2f3c4a07ee0cb61ff79a79619" dependencies = [ "aho-corasick", "memchr", - "regex-automata", - "regex-syntax", + "regex-automata 0.4.7", + "regex-syntax 0.8.4", +] + +[[package]] +name = "regex-automata" +version = "0.1.10" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132" +dependencies = [ + "regex-syntax 0.6.29", ] [[package]] @@ -1035,9 +1068,15 @@ checksum = "38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df" dependencies = [ "aho-corasick", "memchr", - "regex-syntax", + "regex-syntax 0.8.4", ] +[[package]] +name = "regex-syntax" +version = "0.6.29" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1" + [[package]] name = "regex-syntax" version = "0.8.4" @@ -1139,6 +1178,15 @@ dependencies = [ "serde", ] +[[package]] +name = "sharded-slab" +version = "0.1.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f40ca3c46823713e0d4209592e8d6e826aa57e928f09752619fc696c499637f6" +dependencies = [ + "lazy_static", +] + [[package]] name = "smallvec" version = "1.13.2" @@ -1205,6 +1253,16 @@ dependencies = [ "syn 2.0.72", ] +[[package]] +name = "thread_local" +version = "1.1.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8b9ef9bad013ada3808854ceac7b46812a6465ba368859a37e2100283d2d719c" +dependencies = [ + "cfg-if", + "once_cell", +] + [[package]] name = "thrift" version = "0.17.0" @@ -1216,15 +1274,43 @@ dependencies = [ "ordered-float", ] +[[package]] +name = "time" +version = "0.3.36" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5dfd88e563464686c916c7e46e623e520ddc6d79fa6641390f2e3fa86e83e885" +dependencies = [ + "deranged", + "itoa", + "num-conv", + "powerfmt", + "serde", + "time-core", + "time-macros", +] + +[[package]] +name = "time-core" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3" + +[[package]] +name = "time-macros" +version = "0.2.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3f252a68540fde3a3877aeea552b832b40ab9a69e318efd078774a01ddee1ccf" +dependencies = [ + "num-conv", + "time-core", +] + [[package]] name = "timsquery" version = "0.4.0" dependencies = [ "clap", - "env_logger", "indicatif", - "itertools", - "log", "rand", "rand_chacha", "rayon", @@ -1232,6 +1318,10 @@ dependencies = [ "serde", "serde_json", "timsrust", + "tracing", + "tracing-bunyan-formatter", + "tracing-chrome", + "tracing-subscriber", ] [[package]] @@ -1261,6 +1351,108 @@ dependencies = [ "crunchy", ] +[[package]] +name = "tracing" +version = "0.1.40" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c3523ab5a71916ccf420eebdf5521fcef02141234bbc0b8a49f2fdc4544364ef" +dependencies = [ + "log", + "pin-project-lite", + "tracing-attributes", + "tracing-core", +] + +[[package]] +name = "tracing-attributes" +version = "0.1.27" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "34704c8d6ebcbc939824180af020566b01a7c01f80641264eba0999f6c2b6be7" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.72", +] + +[[package]] +name = "tracing-bunyan-formatter" +version = "0.3.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b5c266b9ac83dedf0e0385ad78514949e6d89491269e7065bee51d2bb8ec7373" +dependencies = [ + "ahash", + "gethostname", + "log", + "serde", + "serde_json", + "time", + "tracing", + "tracing-core", + "tracing-log 0.1.4", + "tracing-subscriber", +] + +[[package]] +name = "tracing-chrome" +version = "0.7.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bf0a738ed5d6450a9fb96e86a23ad808de2b727fd1394585da5cdd6788ffe724" +dependencies = [ + "serde_json", + "tracing-core", + "tracing-subscriber", +] + +[[package]] +name = "tracing-core" +version = "0.1.32" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c06d3da6113f116aaee68e4d601191614c9053067f9ab7f6edbcb161237daa54" +dependencies = [ + "once_cell", + "valuable", +] + +[[package]] +name = "tracing-log" +version = "0.1.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f751112709b4e791d8ce53e32c4ed2d353565a795ce84da2285393f41557bdf2" +dependencies = [ + "log", + "once_cell", + "tracing-core", +] + +[[package]] +name = "tracing-log" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ee855f1f400bd0e5c02d150ae5de3840039a3f54b025156404e34c23c03f47c3" +dependencies = [ + "log", + "once_cell", + "tracing-core", +] + +[[package]] +name = "tracing-subscriber" +version = "0.3.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ad0f048c97dbd9faa9b7df56362b8ebcaa52adb06b498c050d2f4e32f90a7a8b" +dependencies = [ + "matchers", + "nu-ansi-term", + "once_cell", + "regex", + "sharded-slab", + "smallvec", + "thread_local", + "tracing", + "tracing-core", + "tracing-log 0.2.0", +] + [[package]] name = "twox-hash" version = "1.6.3" @@ -1289,6 +1481,12 @@ version = "0.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821" +[[package]] +name = "valuable" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "830b7e5d4d90034032940e4ace0d9a9a057e7a45cd94e6c007832e39edb82f6d" + [[package]] name = "vcpkg" version = "0.2.15" @@ -1361,6 +1559,28 @@ version = "0.2.92" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96" +[[package]] +name = "winapi" +version = "0.3.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419" +dependencies = [ + "winapi-i686-pc-windows-gnu", + "winapi-x86_64-pc-windows-gnu", +] + +[[package]] +name = "winapi-i686-pc-windows-gnu" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6" + +[[package]] +name = "winapi-x86_64-pc-windows-gnu" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f" + [[package]] name = "windows-core" version = "0.52.0" diff --git a/Cargo.toml b/Cargo.toml index c65ac8e..38305e8 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -2,6 +2,7 @@ name = "timsquery" version = "0.4.0" edition = "2021" +license = "Apache-2.0" [dependencies] timsrust = "0.4.1" @@ -13,18 +14,24 @@ serde = { version = "1.0.204", features = ["derive"] } serde_json = "1.0.122" rmp-serde = "1.3.0" -itertools = "0.13.0" +tracing = { version = "0.1.40", features = ["log"] } +tracing-subscriber = { version = "0.3.18", features = [ + "registry", + "env-filter", +] } +tracing-bunyan-formatter = "0.3.9" -rand = "0.8.5" -rand_chacha = "0.3.1" -log = "0.4.22" -env_logger = "0.11.5" +# These are only used for benchmarks +rand = { version = "0.8.5", optional = true } +rand_chacha = { version = "0.3.1", optional = true } +tracing-chrome = "0.7.2" [features] clap = ["dep:clap"] build-binary = ["clap"] +bench = ["dep:rand", "dep:rand_chacha"] [[bin]] name = "timsquery" @@ -33,6 +40,7 @@ required-features = ["build-binary"] [[bin]] name = "benchmark_indices" path = "benches/benchmark_indices.rs" +required-features = ["bench"] [profile.release] opt-level = 3 diff --git a/Taskfile.yml b/Taskfile.yml index 9ac1af4..bc24eec 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -36,10 +36,9 @@ tasks: - cargo clippy bench: - requires: - vars: [RUST_BACKTRACE, RUST_LOG, TIMS_DATA_FILE] cmds: - - cargo bench + - SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d cargo run --release --features bench --bin benchmark_indices + - uv run benches/plot_bench.py data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json templates: sources: diff --git a/benches/benchmark_indices.rs b/benches/benchmark_indices.rs index 21c86d8..d63d531 100644 --- a/benches/benchmark_indices.rs +++ b/benches/benchmark_indices.rs @@ -20,6 +20,10 @@ use timsquery::{ }, ElutionGroup, }; +use tracing::subscriber::set_global_default; +use tracing_bunyan_formatter::{BunyanFormattingLayer, JsonStorageLayer}; +use tracing_chrome::ChromeLayerBuilder; +use tracing_subscriber::{fmt, prelude::*, registry::Registry, EnvFilter, Layer}; const NUM_ELUTION_GROUPS: usize = 1000; const NUM_ITERATIONS: usize = 1; @@ -250,7 +254,7 @@ impl EnvConfig { } } -fn run_encoding_benchmark(raw_file_path: &PathBuf, env_config: EnvConfig) -> Vec { +fn run_encoding_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Vec { let raw_file_path = raw_file_path.to_str().unwrap(); let mut out = vec![]; let rfi = env_config.with_benchmark( @@ -347,7 +351,7 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve "RawFileIndex", &format!("BatchAccess_{}", tol_name), || RawFileIndex::from_path(raw_file_path).unwrap(), - |index, i| { + |index, _i| { let tmp = query_multi_group( index, index, @@ -369,7 +373,7 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve "ExpandedRawFileIndex", &format!("BatchAccess_{}", tol_name), || ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(), - |index, i| { + |index, _i| { let tmp = query_multi_group( index, index, @@ -394,7 +398,7 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve "ExpandedRawFileIndexCentroided", &format!("BatchAccess_{}", tol_name), || ExpandedRawFrameIndex::from_path_centroided(raw_file_path).unwrap(), - |index, i| { + |index, _i| { let tmp = query_multi_group( index, index, @@ -419,7 +423,7 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve "TransposedQuadIndex", &format!("BatchAccess_{}", tol_name), || QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(), - |index, i| { + |index, _i| { let tmp = query_multi_group( index, index, @@ -441,7 +445,7 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve "TransposedQuadIndexCentroided", &format!("BatchAccess_{}", tol_name), || QuadSplittedTransposedIndex::from_path_centroided(raw_file_path).unwrap(), - |index, i| { + |index, _i| { let tmp = query_multi_group( index, index, @@ -468,7 +472,7 @@ fn write_results( let filepath = parent.join(format!("benchmark_results_{}.json", basename)); let file = File::create(&filepath)?; serde_json::to_writer_pretty(file, &report)?; - let out = serde_json::to_string_pretty(&report)?; + let _out = serde_json::to_string_pretty(&report)?; for result in report.results.iter_mut() { result.iterations = None; @@ -482,7 +486,17 @@ fn write_results( } fn main() { - env_logger::init(); + let env_filter = EnvFilter::try_from_default_env().unwrap_or_else(|_| EnvFilter::new("info")); + let formatting_layer = BunyanFormattingLayer::new("timsquery".into(), std::io::stdout); + let (chrome_layer, _guard) = ChromeLayerBuilder::new().build(); + + let subscriber = Registry::default() + .with(env_filter) + .with(chrome_layer) + .with(JsonStorageLayer) + .with(formatting_layer); + + set_global_default(subscriber).expect("Setting default subscriber failed"); let st = Instant::now(); let env_config = EnvConfig::new(); diff --git a/data/get_data.bash b/data/get_data.bash index bd4a39d..046e094 100644 --- a/data/get_data.bash +++ b/data/get_data.bash @@ -1,8 +1,13 @@ # LFQ_timsTOFPro_diaPASEF_Ecoli_03.d.zip +# Long gradient run docker run --rm --platform linux/amd64 -v ${PWD}:/data \ ghcr.io/pride-archive/aspera \ ascp -i /home/aspera/.aspera/cli/etc/asperaweb_id_dsa.openssh \ -TQ -P33001 \ prd_ascp@fasp.ebi.ac.uk:/pride/data/archive/2022/02/PXD028735/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d.zip \ /data + +# 22 min hela from some random day +aws s3 cp s3://terraform-workstations-bucket/jspaezp/20241027_PRTC/230510_PRTC_13.d.tar . +tar -xf 230510_PRTC_13.d.tar diff --git a/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json new file mode 100644 index 0000000..c42d54c --- /dev/null +++ b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json @@ -0,0 +1,138 @@ +{ + "settings": { + "num_elution_groups": 1000, + "num_iterations": 1 + }, + "results": [ + { + "name": "RawFileIndex", + "context": "Encoding", + "mean_duration_seconds": 0.006061387115151513, + "mean_duration_human_readable": "6.061387ms", + "setup_time_seconds": 1.75e-6, + "setup_time_human_readable": "1.75µs", + "note": null + }, + { + "name": "ExpandedRawFileIndexCentroided", + "context": "Encoding", + "mean_duration_seconds": 102.017141791, + "mean_duration_human_readable": "102.017141791s", + "setup_time_seconds": 9.58e-7, + "setup_time_human_readable": "958ns", + "note": null + }, + { + "name": "ExpandedRawFileIndex", + "context": "Encoding", + "mean_duration_seconds": 7.339009041, + "mean_duration_human_readable": "7.339009041s", + "setup_time_seconds": 1.042e-6, + "setup_time_human_readable": "1.042µs", + "note": null + }, + { + "name": "TransposedQuadIndex", + "context": "Encoding", + "mean_duration_seconds": 64.579125625, + "mean_duration_human_readable": "64.579125625s", + "setup_time_seconds": 1.167e-6, + "setup_time_human_readable": "1.167µs", + "note": null + }, + { + "name": "TransposedQuadIndexCentroided", + "context": "Encoding", + "mean_duration_seconds": 105.091189208, + "mean_duration_human_readable": "105.091189208s", + "setup_time_seconds": 1.25e-6, + "setup_time_human_readable": "1.25µs", + "note": null + }, + { + "name": "RawFileIndex", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 28.889043334, + "mean_duration_human_readable": "28.889043334s", + "setup_time_seconds": 0.077295959, + "setup_time_human_readable": "77.295959ms", + "note": "RawFileIndex::query_multi_group aggregated 71227 " + }, + { + "name": "ExpandedRawFileIndex", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 0.0023722945118483407, + "mean_duration_human_readable": "2.372294ms", + "setup_time_seconds": 5.8142151250000005, + "setup_time_human_readable": "5.814215125s", + "note": "ExpandedRawFileIndex::query_multi_group aggregated 72731 " + }, + { + "name": "ExpandedRawFileIndex", + "context": "BatchAccess_full_rt", + "mean_duration_seconds": 0.363698, + "mean_duration_human_readable": "363.698ms", + "setup_time_seconds": 5.680389416, + "setup_time_human_readable": "5.680389416s", + "note": "ExpandedRawFileIndex::query_multi_group aggregated 11194054 " + }, + { + "name": "ExpandedRawFileIndexCentroided", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 0.0011996081642685855, + "mean_duration_human_readable": "1.199608ms", + "setup_time_seconds": 98.870238958, + "setup_time_human_readable": "98.870238958s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 21990 " + }, + { + "name": "ExpandedRawFileIndexCentroided", + "context": "BatchAccess_full_rt", + "mean_duration_seconds": 0.07626683057142856, + "mean_duration_human_readable": "76.26683ms", + "setup_time_seconds": 114.076896875, + "setup_time_human_readable": "114.076896875s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 5012679 " + }, + { + "name": "TransposedQuadIndex", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 0.005130067953846155, + "mean_duration_human_readable": "5.130067ms", + "setup_time_seconds": 72.976041375, + "setup_time_human_readable": "72.976041375s", + "note": "TransposedQuadIndex::query_multi_group aggregated 69045 " + }, + { + "name": "TransposedQuadIndex", + "context": "BatchAccess_full_rt", + "mean_duration_seconds": 0.00552524769060773, + "mean_duration_human_readable": "5.525247ms", + "setup_time_seconds": 87.057384125, + "setup_time_human_readable": "87.057384125s", + "note": "TransposedQuadIndex::query_multi_group aggregated 9971215 " + }, + { + "name": "TransposedQuadIndexCentroided", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 0.001565241712050078, + "mean_duration_human_readable": "1.565241ms", + "setup_time_seconds": 118.473094709, + "setup_time_human_readable": "118.473094709s", + "note": "TransposedQuadIndex::query_multi_group aggregated 17773 " + }, + { + "name": "TransposedQuadIndexCentroided", + "context": "BatchAccess_full_rt", + "mean_duration_seconds": 0.003929947243137255, + "mean_duration_human_readable": "3.929947ms", + "setup_time_seconds": 124.951945458, + "setup_time_human_readable": "124.951945458s", + "note": "TransposedQuadIndex::query_multi_group aggregated 4425627 " + } + ], + "metadata": { + "basename": "230510_PRTC_13_S1-B1_1_12817" + }, + "full_benchmark_time_seconds": 961.0857955 +} \ No newline at end of file diff --git a/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json b/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json new file mode 100644 index 0000000..14ff6fe --- /dev/null +++ b/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json @@ -0,0 +1,57 @@ +{ + "settings": { + "num_elution_groups": 1000, + "num_iterations": 1 + }, + "results": [ + { + "name": "RawFileIndex", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 3.778817917, + "mean_duration_human_readable": "3.778817917s", + "setup_time_seconds": 0.241755042, + "setup_time_human_readable": "241.755042ms", + "note": "RawFileIndex::query_multi_group aggregated 9144 " + }, + { + "name": "ExpandedRawFileIndexCentroided", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 0.0005595513605823068, + "mean_duration_human_readable": "559.551µs", + "setup_time_seconds": 619.45208575, + "setup_time_human_readable": "619.45208575s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 873 " + }, + { + "name": "ExpandedRawFileIndexCentroided", + "context": "BatchAccess_full_rt", + "mean_duration_seconds": 7.19476525, + "mean_duration_human_readable": "7.19476525s", + "setup_time_seconds": 636.328349375, + "setup_time_human_readable": "636.328349375s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 193555055 " + }, + { + "name": "TransposedQuadIndexCentroided", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 0.0017960869371633765, + "mean_duration_human_readable": "1.796086ms", + "setup_time_seconds": 665.489050917, + "setup_time_human_readable": "665.489050917s", + "note": "TransposedQuadIndex::query_multi_group aggregated 715 " + }, + { + "name": "TransposedQuadIndexCentroided", + "context": "BatchAccess_full_rt", + "mean_duration_seconds": 0.0027502779313186817, + "mean_duration_human_readable": "2.750277ms", + "setup_time_seconds": 663.333964959, + "setup_time_human_readable": "663.333964959s", + "note": "TransposedQuadIndex::query_multi_group aggregated 167889419 " + } + ], + "metadata": { + "basename": "LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02" + }, + "full_benchmark_time_seconds": 2621.0749125 +} \ No newline at end of file diff --git a/deny.toml b/deny.toml new file mode 100644 index 0000000..4592ef2 --- /dev/null +++ b/deny.toml @@ -0,0 +1,253 @@ +# This template contains all of the possible sections and their default values + +# Note that all fields that take a lint level have these possible values: +# * deny - An error will be produced and the check will fail +# * warn - A warning will be produced, but the check will not fail +# * allow - No warning or error will be produced, though in some cases a note +# will be + +# The values provided in this template are the default values that will be used +# when any section or field is not specified in your own configuration + +[graph] + +# If 1 or more target triples (and optionally, target_features) are specified, +# only the specified targets will be checked when running `cargo deny check`. +# This means, if a particular package is only ever used as a target specific +# dependency, such as, for example, the `nix` crate only being used via the +# `target_family = "unix"` configuration, that only having windows targets in +# this list would mean the nix crate, as well as any of its exclusive +# dependencies not shared by any other crates, would be ignored, as the target +# list here is effectively saying which targets you are building for. +targets = [ + { triple = "aarch64-apple-darwin" }, + { triple = "x86_64-apple-darwin" }, + { triple = "i686-pc-windows-gnu" }, + { triple = "i686-pc-windows-msvc" }, + { triple = "x86_64-pc-windows-gnu" }, + { triple = "x86_64-pc-windows-msvc" }, + { triple = "i686-unknown-linux-gnu" }, + { triple = "x86_64-unknown-linux-gnu" }, + { triple = "x86_64-unknown-linux-musl" }, + # { triple = "wasm32-unknown-unknown" }, + # { triple = "x86_64-unknown-redox" }, +] +# When creating the dependency graph used as the source of truth when checks are +# executed, this field can be used to prune crates from the graph, removing them +# from the view of cargo-deny. This is an extremely heavy hammer, as if a crate +# is pruned from the graph, all of its dependencies will also be pruned unless +# they are connected to another crate in the graph that hasn't been pruned, +# so it should be used with care. The identifiers are [Package ID Specifications] +# (https://doc.rust-lang.org/cargo/reference/pkgid-spec.html) +#exclude = [] +# If true, metadata will be collected with `--all-features`. Note that this can't +# be toggled off if true, if you want to conditionally enable `--all-features` it +# is recommended to pass `--all-features` on the cmd line instead +all-features = false +# If true, metadata will be collected with `--no-default-features`. The same +# caveat with `all-features` applies +no-default-features = false +# If set, these feature will be enabled when collecting metadata. If `--features` +# is specified on the cmd line they will take precedence over this option. +features = [ + "build-binary", +] + +[output] +# When outputting inclusion graphs in diagnostics that include features, this +# option can be used to specify the depth at which feature edges will be added. +# This option is included since the graphs can be quite large and the addition +# of features from the crate(s) to all of the graph roots can be far too verbose. +# This option can be overridden via `--feature-depth` on the cmd line +feature-depth = 1 + +# This section is considered when running `cargo deny check advisories` +# More documentation for the advisories section can be found here: +# https://embarkstudios.github.io/cargo-deny/checks/advisories/cfg.html +[advisories] +version = 2 +# The path where the advisory database is cloned/fetched into +db-path = "~/.cargo/advisory-db" +# The url(s) of the advisory databases to use +db-urls = ["https://github.com/rustsec/advisory-db"] +# The lint level for security vulnerabilities +yanked = "warn" +# A list of advisory IDs to ignore. Note that ignored advisories will still +# output a note when they are encountered. +ignore = [ + #"RUSTSEC-0000-0000", + "RUSTSEC-2023-0086", # Lexical-core -> arrow issue, updated in main in Sept-2024, unreleased. +] +# Threshold for security vulnerabilities, any vulnerability with a CVSS score +# lower than the range specified will be ignored. Note that ignored advisories +# will still output a note when they are encountered. +# * None - CVSS Score 0.0 +# * Low - CVSS Score 0.1 - 3.9 +# * Medium - CVSS Score 4.0 - 6.9 +# * High - CVSS Score 7.0 - 8.9 +# * Critical - CVSS Score 9.0 - 10.0 +#severity-threshold = + +# If this is true, then cargo deny will use the git executable to fetch advisory database. +# If this is false, then it uses a built-in git library. +# Setting this to true can be helpful if you have special authentication requirements that cargo-deny does not support. +# See Git Authentication for more information about setting up git authentication. +#git-fetch-with-cli = true + +# This section is considered when running `cargo deny check licenses` +# More documentation for the licenses section can be found here: +# https://embarkstudios.github.io/cargo-deny/checks/licenses/cfg.html +[licenses] +version = 2 +# List of explicitly allowed licenses +# See https://spdx.org/licenses/ for list of possible licenses +# [possible values: any SPDX 3.11 short identifier (+ optional exception)]. +allow = [ + "MIT", + "Apache-2.0", + "Apache-2.0 WITH LLVM-exception", + "BSD-3-Clause", + "Unicode-DFS-2016", + "Zlib", +] + +# The confidence threshold for detecting a license from license text. +# The higher the value, the more closely the license text must be to the +# canonical license text of a valid SPDX license file. +# [possible values: any between 0.0 and 1.0]. +confidence-threshold = 0.95 +# Allow 1 or more licenses on a per-crate basis, so that particular licenses +# aren't accepted for every possible crate as with the normal allow list +exceptions = [] + +# Some crates don't have (easily) machine readable licensing information, +# adding a clarification entry for it allows you to manually specify the +# licensing information +[[licenses.clarify]] +name = "webpki" +expression = "ISC" +license-files = [{ path = "LICENSE", hash = 0x001c7e6c }] + +[[licenses.clarify]] +name = "ring" +expression = "MIT AND ISC AND OpenSSL" +license-files = [{ path = "LICENSE", hash = 0xbd0eed23 }] + + +#[[licenses.clarify]] +# The name of the crate the clarification applies to +#name = "ring" +# The optional version constraint for the crate +#version = "*" +# The SPDX expression for the license requirements of the crate +#expression = "MIT AND ISC AND OpenSSL" +# One or more files in the crate's source used as the "source of truth" for +# the license expression. If the contents match, the clarification will be used +# when running the license check, otherwise the clarification will be ignored +# and the crate will be checked normally, which may produce warnings or errors +# depending on the rest of your configuration +#license-files = [ +# Each entry is a crate relative path, and the (opaque) hash of its contents +#{ path = "LICENSE", hash = 0xbd0eed23 } +#] + +[licenses.private] +# If true, ignores workspace crates that aren't published, or are only +# published to private registries. +# To see how to mark a crate as unpublished (to the official registry), +# visit https://doc.rust-lang.org/cargo/reference/manifest.html#the-publish-field. +ignore = false +# One or more private registries that you might publish crates to, if a crate +# is only published to private registries, and ignore is true, the crate will +# not have its license(s) checked +registries = [ + #"https://sekretz.com/registry +] + +# This section is considered when running `cargo deny check bans`. +# More documentation about the 'bans' section can be found here: +# https://embarkstudios.github.io/cargo-deny/checks/bans/cfg.html +[bans] +# Lint level for when multiple versions of the same crate are detected +multiple-versions = "warn" +# Lint level for when a crate version requirement is `*` +wildcards = "allow" +# The graph highlighting used when creating dotgraphs for crates +# with multiple versions +# * lowest-version - The path to the lowest versioned duplicate is highlighted +# * simplest-path - The path to the version with the fewest edges is highlighted +# * all - Both lowest-version and simplest-path are used +highlight = "all" +# The default lint level for `default` features for crates that are members of +# the workspace that is being checked. This can be overridden by allowing/denying +# `default` on a crate-by-crate basis if desired. +workspace-default-features = "allow" +# The default lint level for `default` features for external crates that are not +# members of the workspace. This can be overridden by allowing/denying `default` +# on a crate-by-crate basis if desired. +external-default-features = "allow" +# List of crates that are allowed. Use with care! +allow = [ + #{ name = "ansi_term", version = "=0.11.0" }, +] +# List of crates to deny +deny = [ + # Each entry the name of a crate and a version range. If version is + # not specified, all versions will be matched. + #{ name = "ansi_term", version = "=0.11.0" }, + # + # Wrapper crates can optionally be specified to allow the crate when it + # is a direct dependency of the otherwise banned crate + #{ name = "ansi_term", version = "=0.11.0", wrappers = [] }, +] + +# List of features to allow/deny +# Each entry the name of a crate and a version range. If version is +# not specified, all versions will be matched. +#[[bans.features]] +#name = "reqwest" +# Features to not allow +#deny = ["json"] +# Features to allow +#allow = [ +# "rustls", +# "__rustls", +# "__tls", +# "hyper-rustls", +# "rustls", +# "rustls-pemfile", +# "rustls-tls-webpki-roots", +# "tokio-rustls", +# "webpki-roots", +#] +# If true, the allowed features must exactly match the enabled feature set. If +# this is set there is no point setting `deny` +#exact = true + +# Certain crates/versions that will be skipped when doing duplicate detection. +skip = [] +# Similarly to `skip` allows you to skip certain crates during duplicate +# detection. Unlike skip, it also includes the entire tree of transitive +# dependencies starting at the specified crate, up to a certain depth, which is +# by default infinite. +skip-tree = [] + +# This section is considered when running `cargo deny check sources`. +# More documentation about the 'sources' section can be found here: +# https://embarkstudios.github.io/cargo-deny/checks/sources/cfg.html +[sources] +# Lint level for what to happen when a crate from a crate registry that is not +# in the allow list is encountered +unknown-registry = "warn" +# Lint level for what to happen when a crate from a git repository that is not +# in the allow list is encountered +unknown-git = "warn" +# List of URLs for allowed crate registries. Defaults to the crates.io index +# if not specified. If it is specified but empty, no registries are allowed. +allow-registry = ["https://github.com/rust-lang/crates.io-index"] +# List of URLs for allowed Git repositories +allow-git = ["https://github.com/lazear/sage"] + +[sources.allow-org] +# 1 or more github.com organizations to allow git sources for +# github = [""] diff --git a/metrics/Taskfile.yml b/metrics/Taskfile.yml new file mode 100644 index 0000000..1ed6ac5 --- /dev/null +++ b/metrics/Taskfile.yml @@ -0,0 +1,15 @@ +version: "3" + +interval: 100ms + +env: + PGO_DATA_DIR: tmp/pgo-data + BIN_EXTRAS: "--features build-binary --bin timsquery" + +dotenv: [".env"] + +tasks: + build: + dir: "{{.TASKFILE_DIR}}" + cmds: + - cargo build $BIN_EXTRAS diff --git a/src/main.rs b/src/main.rs index 1dc7c05..82f5e06 100644 --- a/src/main.rs +++ b/src/main.rs @@ -1,8 +1,11 @@ +use clap::{Parser, Subcommand}; +use serde::{Deserialize, Serialize}; use std::collections::HashMap; use std::time::Instant; use timsquery::models::elution_group::ElutionGroup; use timsquery::queriable_tims_data::queriable_tims_data::query_multi_group; use timsquery::traits::tolerance::DefaultTolerance; +use timsquery::traits::tolerance::{MobilityTolerance, MzToleramce, QuadTolerance, RtTolerance}; use timsquery::{ models::aggregators::{ ChromatomobilogramStats, ExtractedIonChromatomobilogram, MultiCMGStatsFactory, @@ -11,14 +14,20 @@ use timsquery::{ models::indices::raw_file_index::RawFileIndex, models::indices::transposed_quad_index::QuadSplittedTransposedIndex, }; - -use timsquery::traits::tolerance::{MobilityTolerance, MzToleramce, QuadTolerance, RtTolerance}; - -use clap::{Parser, Subcommand}; -use serde::{Deserialize, Serialize}; +use tracing::instrument; +use tracing::subscriber::set_global_default; +use tracing_bunyan_formatter::{BunyanFormattingLayer, JsonStorageLayer}; +use tracing_subscriber::{fmt, prelude::*, registry::Registry, EnvFilter, Layer}; fn main() { - env_logger::init(); + let env_filter = EnvFilter::try_from_default_env().unwrap_or_else(|_| EnvFilter::new("info")); + let formatting_layer = BunyanFormattingLayer::new("timsquery".into(), std::io::stdout); + let subscriber = Registry::default() + .with(env_filter) + .with(JsonStorageLayer) + .with(formatting_layer); + + set_global_default(subscriber).expect("Setting default subscriber failed"); let args = Args::parse(); match args.command { @@ -88,6 +97,7 @@ fn template_elution_groups(num: usize) -> Vec> { egs } +#[instrument] fn main_query_index(args: QueryIndexArgs) { let args_clone = args.clone(); diff --git a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs index c86e22b..36281e4 100644 --- a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs @@ -1,8 +1,7 @@ use super::super::streaming_aggregator::RunningStatsCalculator; use crate::models::frames::raw_peak::RawPeak; -use crate::sort_by_indices_multi; +use crate::sort_vecs_by_first; use crate::traits::aggregator::Aggregator; -use crate::utils::sorting::argsort_by; use serde::Serialize; use std::collections::BTreeMap; @@ -150,9 +149,7 @@ impl ChromatomobilogramStatsArrays { } pub fn sort_by_rt(&mut self) { - let mut indices = argsort_by(&self.retention_time_miliseconds, |x| *x); - sort_by_indices_multi!( - &mut indices, + let x = sort_vecs_by_first!( &mut self.retention_time_miliseconds, &mut self.tof_index_means, &mut self.tof_index_sds, @@ -160,6 +157,12 @@ impl ChromatomobilogramStatsArrays { &mut self.scan_index_sds, &mut self.intensities ); + self.retention_time_miliseconds = x.0; + self.tof_index_means = x.1; + self.tof_index_sds = x.2; + self.scan_index_means = x.3; + self.scan_index_sds = x.4; + self.intensities = x.5; } } diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs index 35783c8..d446db9 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs @@ -6,10 +6,10 @@ use crate::models::aggregators::streaming_aggregator::RunningStatsCalculator; use crate::models::frames::raw_peak::RawPeak; use crate::traits::aggregator::Aggregator; use crate::utils::math::{lnfact, lnfact_float}; -use log::{debug, warn}; use serde::Serialize; use std::collections::{BTreeMap, HashSet}; use std::hash::Hash; +use tracing::{debug, warn}; use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter}; @@ -414,7 +414,7 @@ mod tests { fn test_value_vs_baseline() { let vals = vec![1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0]; let baseline_window_size = 3; - let baseline = rolling_median(&vals, baseline_window_size, f64::NAN); + let _baseline = rolling_median(&vals, baseline_window_size, f64::NAN); let out = calculate_value_vs_baseline(&vals, baseline_window_size); let expect_val = vec![f64::NAN, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, f64::NAN]; let all_close = out diff --git a/src/models/aggregators/streaming_aggregator.rs b/src/models/aggregators/streaming_aggregator.rs index 2ab67b2..d015879 100644 --- a/src/models/aggregators/streaming_aggregator.rs +++ b/src/models/aggregators/streaming_aggregator.rs @@ -1,4 +1,4 @@ -use log::debug; +use tracing::debug; // Generic streaming aggregator that takes a pair of unsigned ints one with a value // and another with a weight and in a streaming fashion adds the value to the accumulator diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index 638cfc4..1cfe84d 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -1,7 +1,6 @@ use super::single_quad_settings::{ expand_quad_settings, ExpandedFrameQuadSettings, SingleQuadrupoleSetting, }; -use itertools::Itertools; use rayon::prelude::*; use std::collections::HashMap; use std::marker::PhantomData; @@ -11,17 +10,16 @@ use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; use timsrust::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}; use super::peak_in_quad::PeakInQuad; -use crate::sort_by_indices_multi; use crate::sort_vecs_by_first; use crate::utils::compress_explode::explode_vec; use crate::utils::frame_processing::{lazy_centroid_weighted_frame, PeakArrayRefs}; -use crate::utils::sorting::argsort_by; use crate::utils::tolerance_ranges::{scan_tol_range, tof_tol_range}; -use log::{info, trace, warn}; use timsrust::{ readers::{FrameReader, FrameReaderError, MetadataReaderError}, TimsRustError, }; +use tracing::instrument; +use tracing::{info, trace, warn}; /// A frame after expanding the mobility data and re-sorting it by tof. #[derive(Debug, Clone)] @@ -63,22 +61,6 @@ pub struct ExpandedFrameSlice { _sorting_state: PhantomData, } -fn sort_by_tof2( - tof_indices: Vec, - scan_numbers: Vec, - intensities: Vec, -) -> ((Vec, Vec), Vec) { - let mut combined: Vec<((u32, usize), u32)> = tof_indices - .iter() - .zip(scan_numbers.iter()) - .zip(intensities.iter()) - .map(|((tof, scan), inten)| ((*tof, *scan), *inten)) - .collect(); - combined.sort_unstable_by(|a, b| a.0 .0.partial_cmp(&b.0 .0).unwrap()); - let ((tof_indices, scan_numbers), intensities) = combined.into_iter().unzip(); - ((tof_indices, scan_numbers), intensities) -} - // Example of how to use it with your specific types fn sort_by_tof_macro( tof_indices: Vec, @@ -141,23 +123,17 @@ impl ExpandedFrameSlice { peak_ind_start..peak_ind_end }; - match scan_range { - Some((min_scan, max_scan)) => { - assert!(min_scan <= max_scan); - } - None => {} - }; + if let Some((min_scan, max_scan)) = scan_range { + assert!(min_scan <= max_scan); + } for peak_ind in peak_range { let scan_index = self.scan_numbers[peak_ind]; - match scan_range { - Some((min_scan, max_scan)) => { - if scan_index < min_scan || scan_index > max_scan { - continue; - } + if let Some((min_scan, max_scan)) = scan_range { + if scan_index < min_scan || scan_index > max_scan { + continue; } - None => {} - }; + } let intensity = self.intensities[peak_ind]; let tof_index = self.tof_indices[peak_ind]; @@ -250,8 +226,6 @@ fn expand_fragmented_frame( window_subindex: i as u8, _sorting_state: PhantomData::, }; - // Q: is this sorting twice? since sort before creating the expanded frame slices. - // TODO: Use the state type pattern to make sure only one sort happens. out.push(curr_slice.sort_by_tof()); } out @@ -271,17 +245,12 @@ pub fn expand_and_split_frame(frame: Frame) -> Vec Self { - let mut tof_indices = frame.tof_indices; - let mut scan_numbers = explode_vec(&frame.scan_offsets); - let mut intensities = frame.intensities; - - let mut indices = argsort_by(&tof_indices, |x| *x); - sort_by_indices_multi!( - &mut indices, - &mut tof_indices, - &mut scan_numbers, - &mut intensities - ); + let scan_numbers = explode_vec(&frame.scan_offsets); + + let sorted = sort_vecs_by_first!(frame.tof_indices, scan_numbers, frame.intensities); + let tof_indices = sorted.0; + let scan_numbers = sorted.1; + let intensities = sorted.2; ExpandedFrame { tof_indices, @@ -298,30 +267,28 @@ impl ExpandedFrame { } } +type QuadBundledFrameslices = + HashMap, Vec>>; + +#[instrument(skip(frame_iter))] pub fn par_expand_and_arrange_frames( frame_iter: impl ParallelIterator, -) -> HashMap, Vec>> { - let start = Instant::now(); - let split = frame_iter.flat_map(|frame| expand_and_split_frame(frame)); - // let mut out = HashMap::new(); - // for es in split { - // out.entry(es.quadrupole_settings) - // .or_insert(Vec::new()) - // .push(es); - // } - // - // Attempted implementation so the folding occurs in parrallel. +) -> QuadBundledFrameslices { + let split = frame_iter.flat_map(expand_and_split_frame); + + // Implementation so the folding occurs in parrallel. // Inspired by/Copied from: https://stackoverflow.com/a/70097253/4295016 - let mut out = split - .fold(HashMap::new, |mut acc, x| { - acc.entry(x.quadrupole_settings) - .or_insert(Vec::new()) - .push(x); - acc - }) + let mut out: QuadBundledFrameslices = split + .fold( + HashMap::new, + |mut acc: QuadBundledFrameslices, x: ExpandedFrameSlice| { + acc.entry(x.quadrupole_settings).or_default().push(x); + acc + }, + ) .reduce_with(|mut acc1, acc2| { for (qs, frameslices) in acc2.into_iter() { - acc1.entry(qs).or_insert(Vec::new()).extend(frameslices); + acc1.entry(qs).or_default().extend(frameslices); } acc1 }) @@ -331,8 +298,6 @@ pub fn par_expand_and_arrange_frames( for (_, es) in out.iter_mut() { es.par_sort_unstable_by(|a, b| a.rt.partial_cmp(&b.rt).unwrap()); } - let end = start.elapsed(); - info!("Expanding and arranging frames took {:#?}", end); out } @@ -434,6 +399,13 @@ fn warn_and_skip_badframes( }) } +#[instrument( + skip(frame_reader), + fields( + num_frames = %frame_reader.len(), + path = frame_reader.get_path().to_str(), + ) +)] pub fn par_read_and_expand_frames( frame_reader: &FrameReader, centroiding_config: FrameProcessingConfig, @@ -465,22 +437,16 @@ pub fn par_read_and_expand_frames( max_ms2_peaks, ims_converter, mz_converter, - } => { - let expanded_frames = par_expand_and_centroid_frames( - curr_iter, - ims_tol_pct, - mz_tol_ppm, - window_width, - max_ms2_peaks, - &ims_converter.unwrap(), - &mz_converter.unwrap(), - ); - expanded_frames - } - FrameProcessingConfig::NotCentroided => { - let expanded_frames = par_expand_and_arrange_frames(curr_iter); - expanded_frames - } + } => par_expand_and_centroid_frames( + curr_iter, + ims_tol_pct, + mz_tol_ppm, + window_width, + max_ms2_peaks, + &ims_converter.unwrap(), + &mz_converter.unwrap(), + ), + FrameProcessingConfig::NotCentroided => par_expand_and_arrange_frames(curr_iter), }; all_expanded_frames.extend(expanded_frames); @@ -498,22 +464,16 @@ pub fn par_read_and_expand_frames( max_ms2_peaks: _max_ms2_peaks, ims_converter, mz_converter, - } => { - let expanded_frames = par_expand_and_centroid_frames( - ms1_iter, - ims_tol_pct, - mz_tol_ppm, - window_width, - max_ms1_peaks, - &ims_converter.unwrap(), - &mz_converter.unwrap(), - ); - expanded_frames - } - FrameProcessingConfig::NotCentroided => { - let expanded_frames = par_expand_and_arrange_frames(ms1_iter); - expanded_frames - } + } => par_expand_and_centroid_frames( + ms1_iter, + ims_tol_pct, + mz_tol_ppm, + window_width, + max_ms1_peaks, + &ims_converter.unwrap(), + &mz_converter.unwrap(), + ), + FrameProcessingConfig::NotCentroided => par_expand_and_arrange_frames(ms1_iter), }; all_expanded_frames.extend(expanded_ms1_frames); info!("Done reading and expanding frames"); @@ -521,6 +481,7 @@ pub fn par_read_and_expand_frames( Ok(all_expanded_frames) } +#[instrument(skip(frames))] pub fn par_expand_and_centroid_frames( frames: impl ParallelIterator, ims_tol_pct: f64, @@ -602,6 +563,7 @@ fn centroid_frameslice_window2( } } +#[instrument(skip(frameslices))] pub fn par_lazy_centroid_frameslices( frameslices: &[ExpandedFrameSlice], window_width: usize, @@ -613,9 +575,12 @@ pub fn par_lazy_centroid_frameslices( ) -> Vec> { assert!( frameslices - .iter() - .tuple_windows() - .map(|(a, b)| { a.rt < b.rt && a.quadrupole_settings == b.quadrupole_settings }) + .windows(2) + .map(|window| { + let a = &window[0]; + let b = &window[1]; + a.rt < b.rt && a.quadrupole_settings == b.quadrupole_settings + }) .all(|x| x), "All frames should be sorted by rt and have the same quad settings" ); @@ -635,7 +600,7 @@ pub fn par_lazy_centroid_frameslices( frameslices .par_windows(window_width) - .map(|window| local_lambda(window)) + .map(local_lambda) .collect() } diff --git a/src/models/frames/raw_frames.rs b/src/models/frames/raw_frames.rs index d3e6daa..bb071d6 100644 --- a/src/models/frames/raw_frames.rs +++ b/src/models/frames/raw_frames.rs @@ -1,7 +1,7 @@ use timsrust::{Frame, QuadrupoleSettings}; use super::raw_peak::RawPeak; -use log::trace; +use tracing::trace; pub fn scans_matching_quad( quad_settings: &QuadrupoleSettings, diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index 11e85cd..921c057 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -12,7 +12,6 @@ use crate::models::frames::single_quad_settings::{ use crate::models::queries::FragmentGroupIndexQuery; use crate::traits::indexed_data::QueriableData; use crate::ToleranceAdapter; -use log::info; use rayon::prelude::*; use serde::Serialize; use std::collections::HashMap; @@ -20,8 +19,8 @@ use std::hash::Hash; use std::time::Instant; use timsrust::converters::{Frame2RtConverter, Scan2ImConverter, Tof2MzConverter}; use timsrust::readers::{FrameReader, MetadataReader}; - -type QuadSettingsIndex = usize; +use tracing::info; +use tracing::instrument; #[derive(Debug)] pub struct ExpandedRawFrameIndex { @@ -111,11 +110,18 @@ impl ExpandedRawFrameIndex { } } + #[instrument(name = "ExpandedRawFrameIndex::from_path_centroided")] pub fn from_path_centroided(path: &str) -> Result { let config = FrameProcessingConfig::default_centroided(); Self::from_path_base(path, config) } + #[instrument(name = "ExpandedRawFrameIndex::from_path")] + pub fn from_path(path: &str) -> Result { + Self::from_path_base(path, FrameProcessingConfig::NotCentroided) + } + + #[instrument(name = "ExpandedRawFrameIndex::from_path_base")] pub fn from_path_base( path: &str, centroid_config: FrameProcessingConfig, @@ -128,10 +134,8 @@ impl ExpandedRawFrameIndex { let sql_path = std::path::Path::new(path).join("analysis.tdf"); let meta_converters = MetadataReader::new(&sql_path)?; - let centroid_config = centroid_config.with_converters( - meta_converters.im_converter.clone(), - meta_converters.mz_converter.clone(), - ); + let centroid_config = centroid_config + .with_converters(meta_converters.im_converter, meta_converters.mz_converter); let st = Instant::now(); let centroided_split_frames = par_read_and_expand_frames(&file_reader, centroid_config)?; @@ -168,10 +172,6 @@ impl ExpandedRawFrameIndex { Ok(out) } - - pub fn from_path(path: &str) -> Result { - Self::from_path_base(path, FrameProcessingConfig::NotCentroided) - } } impl diff --git a/src/models/indices/raw_file_index.rs b/src/models/indices/raw_file_index.rs index 60688be..133e406 100644 --- a/src/models/indices/raw_file_index.rs +++ b/src/models/indices/raw_file_index.rs @@ -7,7 +7,6 @@ use crate::traits::aggregator::Aggregator; use crate::traits::indexed_data::QueriableData; use crate::ElutionGroup; use crate::ToleranceAdapter; -use log::trace; use rayon::iter::ParallelIterator; use serde::Serialize; use std::fmt::Debug; @@ -16,6 +15,7 @@ use timsrust::converters::ConvertableDomain; use timsrust::readers::{FrameReader, FrameReaderError, MetadataReader}; use timsrust::TimsRustError; use timsrust::{Frame, Metadata, QuadrupoleSettings}; +use tracing::trace; pub struct RawFileIndex { file_reader: FrameReader, @@ -168,7 +168,7 @@ impl RawFileIndex { .map(|(k, v)| { let mz_range = tol.mz_range(*v); ( - k.clone(), + *k, ( self.meta_converters.mz_converter.invert(mz_range.0) as u32, self.meta_converters.mz_converter.invert(mz_range.1) as u32, diff --git a/src/models/indices/transposed_quad_index/peak_bucket.rs b/src/models/indices/transposed_quad_index/peak_bucket.rs index d654ad0..d0f0e7d 100644 --- a/src/models/indices/transposed_quad_index/peak_bucket.rs +++ b/src/models/indices/transposed_quad_index/peak_bucket.rs @@ -1,7 +1,6 @@ -use crate::sort_by_indices_multi; +use crate::sort_vecs_by_first; use crate::utils::compress_explode::compress_vec; use crate::utils::display::{glimpse_vec, GlimpseConfig}; -use crate::utils::sorting::argsort_by; use std::fmt::Display; pub struct PeakInBucket { @@ -105,13 +104,12 @@ impl PeakBucketBuilder { } pub fn build(mut self) -> PeakBucket { - let mut indices = argsort_by(&self.scan_offsets, |x| *x); - sort_by_indices_multi!( - &mut indices, - &mut self.scan_offsets, - &mut self.retention_times, - &mut self.intensities - ); + let sorted = + sort_vecs_by_first!(&self.scan_offsets, &self.retention_times, &self.intensities); + self.scan_offsets = sorted.0; + self.retention_times = sorted.1; + self.intensities = sorted.2; + // TODO consider if I really need to compress this. // Options: // 1. Change the compression of scans (I use the default in timsrust but im sure we can do diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index 8a4ac88..492acce 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -3,15 +3,14 @@ use super::peak_bucket::{PeakBucket, PeakInBucket}; use crate::models::frames::expanded_frame::{ExpandedFrameSlice, SortingStateTrait}; use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; -use crate::sort_by_indices_multi; +use crate::sort_vecs_by_first; use crate::utils::display::{glimpse_vec, GlimpseConfig}; -use crate::utils::sorting::par_argsort_by; -use log::debug; -use log::info; use std::collections::{BTreeMap, HashMap}; use std::fmt::Display; use std::time::Instant; use timsrust::converters::{ConvertableDomain, Frame2RtConverter}; +use tracing::instrument; +use tracing::{debug, info}; #[derive(Debug)] pub struct TransposedQuadIndex { @@ -200,13 +199,9 @@ impl TransposedQuadIndexBuilder { self.frame_rts.push(slice.rt); } + #[instrument(skip(self))] pub fn build(self) -> TransposedQuadIndex { // TODO: Refactor this function, its getting pretty large. - let st = Instant::now(); - info!( - "TransposedQuadIndex::build start ... quad_settings = {:?}", - self.quad_settings - ); let max_tof = *self .tof_slices .iter() @@ -267,7 +262,6 @@ impl TransposedQuadIndexBuilder { .collect(); let bbe = bb_st.elapsed(); - let elapsed = st.elapsed(); info!( "TransposedQuadIndex::add_frame_slice adding peaks took {:#?} for {} peaks", aps.elapsed(), @@ -277,10 +271,6 @@ impl TransposedQuadIndexBuilder { "TransposedQuadIndex::add_frame_slice building buckets took {:#?}", bbe ); - info!( - "TransposedQuadIndex::build quad_settings={:?} took {:#?}", - quad_settings, elapsed - ); TransposedQuadIndex { quad_settings, frame_rts: out_rts, @@ -369,10 +359,10 @@ impl TransposedQuadIndexBuilder { } let concat_st = Instant::now(); - let mut int_slice = self.int_slices[start..end].concat(); - let mut tof_slice = self.tof_slices[start..end].concat(); - let mut scan_slice = self.scan_slices[start..end].concat(); - let mut rt_slice: Vec = self.frame_rts[start..end] + let int_slice = self.int_slices[start..end].concat(); + let tof_slice = self.tof_slices[start..end].concat(); + let scan_slice = self.scan_slices[start..end].concat(); + let rt_slice: Vec = self.frame_rts[start..end] .iter() .zip(self.tof_slices[start..end].iter()) .flat_map(|(rt, tofslice)| vec![*rt as f32; tofslice.len()]) @@ -381,18 +371,12 @@ impl TransposedQuadIndexBuilder { let concat_elapsed = concat_st.elapsed(); let sorting_st = Instant::now(); - // let mut indices = argsort_by(&tof_slice, |x| *x); - let mut indices = par_argsort_by(&tof_slice, |x| *x); - - let argsort_elapsed = sorting_st.elapsed(); - sort_by_indices_multi!( - &mut indices, - &mut tof_slice, - &mut scan_slice, - &mut int_slice, - &mut rt_slice - ); + let out = sort_vecs_by_first!(tof_slice, scan_slice, int_slice, rt_slice); + let tof_slice = out.0; + let scan_slice = out.1; + let int_slice = out.2; + let rt_slice = out.3; let sorting_elapsed = sorting_st.elapsed(); @@ -453,8 +437,8 @@ impl TransposedQuadIndexBuilder { let insertion_elapsed = insertion_st.elapsed(); info!( - "BatchedBuild: quad_settings={:?} start={:?} end={:?}/{} peaks {}/{} concat took {:#?} sorting took arg: {:#?} / {:#?} insertion took {:#?}", - self.quad_settings, start, end, num_slices, added_peaks, tot_peaks, concat_elapsed, argsort_elapsed, sorting_elapsed, insertion_elapsed, + "BatchedBuild: quad_settings={:?} start={:?} end={:?}/{} peaks {}/{} concat took {:#?} sorting took: {:#?} insertion took {:#?}", + self.quad_settings, start, end, num_slices, added_peaks, tot_peaks, concat_elapsed, sorting_elapsed, insertion_elapsed, ); start = end; peaks_in_chunk = 0; diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index f596fe0..7c96e34 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -14,7 +14,6 @@ use crate::models::queries::FragmentGroupIndexQuery; use crate::traits::indexed_data::QueriableData; use crate::utils::display::{glimpse_vec, GlimpseConfig}; use crate::ToleranceAdapter; -use log::{debug, info, trace}; use rayon::prelude::*; use serde::Serialize; use std::collections::HashMap; @@ -27,6 +26,8 @@ use timsrust::readers::{FrameReader, MetadataReader}; use timsrust::Frame; use timsrust::Metadata; use timsrust::TimsRustError; +use tracing::instrument; +use tracing::{debug, info, trace}; // TODO break this module apart ... its getting too big for my taste // - JSP: 2024-11-19 @@ -137,6 +138,7 @@ impl Display for QuadSplittedTransposedIndex { } impl QuadSplittedTransposedIndex { + #[instrument(name = "QuadSplittedTransposedIndex::from_path")] pub fn from_path(path: &str) -> Result { let st = Instant::now(); info!("Building transposed quad index from path {}", path); @@ -148,6 +150,7 @@ impl QuadSplittedTransposedIndex { Ok(out) } + #[instrument(name = "QuadSplittedTransposedIndex::from_path_centroided")] pub fn from_path_centroided(path: &str) -> Result { let st = Instant::now(); info!( @@ -181,14 +184,6 @@ impl QuadSplittedTransposedIndexBuilder { Self::default() } - fn add_frame(&mut self, frame: Frame) { - let expanded_slices = expand_and_split_frame(frame); - - for es in expanded_slices.into_iter() { - self.add_frame_slice(es); - } - } - fn add_frame_slice(&mut self, frame_slice: ExpandedFrameSlice) { // Add key if it doesnt exist ... self.indices @@ -204,10 +199,12 @@ impl QuadSplittedTransposedIndexBuilder { .add_frame_slice(frame_slice); } + #[instrument(name = "QuadSplittedTransposedIndexBuilder::from_path")] fn from_path(path: &str) -> Result { Self::from_path_base(path, FrameProcessingConfig::NotCentroided) } + #[instrument(name = "QuadSplittedTransposedIndexBuilder::from_path_centroided")] fn from_path_centroided(path: &str) -> Result { let config = FrameProcessingConfig::default_centroided(); Self::from_path_base(path, config) @@ -216,6 +213,7 @@ impl QuadSplittedTransposedIndexBuilder { // TODO: I think i should split this into two functions, one that starts the builder // and one that adds the frameslices, maybe even have a config struct that dispatches // the right preprocessing steps. + #[instrument(name = "QuadSplittedTransposedIndexBuilder::from_path_base")] fn from_path_base( path: &str, centroid_config: FrameProcessingConfig, @@ -238,13 +236,9 @@ impl QuadSplittedTransposedIndexBuilder { let centroid_config = centroid_config .with_converters(meta_converters.im_converter, meta_converters.mz_converter); - let st = Instant::now(); let split_frames = par_read_and_expand_frames(&file_reader, centroid_config)?; - let centroided_elap = st.elapsed(); - debug!("Reading + Centroiding took {:#?}", centroided_elap); - - let st = Instant::now(); + // TODO use the rayon contructor to fold let out2: Result, TimsRustError> = split_frames .into_par_iter() .map(|(q, frameslices)| { @@ -261,12 +255,6 @@ impl QuadSplittedTransposedIndexBuilder { x }); final_out.fold(out2); - let build_elap = st.elapsed(); - - info!( - "Reading all frames + centroiding took {:#?}, building took {:#?}", - centroided_elap, build_elap - ); Ok(final_out) } @@ -281,6 +269,7 @@ impl QuadSplittedTransposedIndexBuilder { self.added_peaks += other.added_peaks; } + #[instrument(skip(self))] pub fn build(self) -> QuadSplittedTransposedIndex { let mut indices = HashMap::new(); let mut flat_quad_settings = Vec::new(); diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index baf2dc1..2595405 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -1,9 +1,9 @@ -use log::info; use rayon::prelude::*; use serde::Serialize; use std::hash::Hash; use std::rc::Rc; use std::time::Instant; +use tracing::info; use crate::{Aggregator, ElutionGroup, HasIntegerID, QueriableData, Tolerance, ToleranceAdapter}; diff --git a/src/utils/frame_processing.rs b/src/utils/frame_processing.rs index 53cc87a..302af05 100644 --- a/src/utils/frame_processing.rs +++ b/src/utils/frame_processing.rs @@ -1,82 +1,7 @@ use crate::sort_vecs_by_first; -use log::{info, warn}; use std::cmp::Ordering; use std::ops::RangeInclusive; - -pub fn squash_frame( - mz_array: &[f32], - intensity_array: &[f32], - tol_ppm: f32, -) -> (Vec, Vec) { - // Make sure the mz array is sorted - assert!(mz_array.windows(2).all(|x| x[0] <= x[1])); - - let arr_len = mz_array.len(); - let mut touched = vec![false; arr_len]; - let mut global_num_touched = 0; - - let mut order: Vec = (0..arr_len).collect(); - order.sort_unstable_by(|&a, &b| { - intensity_array[b] - .partial_cmp(&intensity_array[a]) - .unwrap_or(Ordering::Equal) - }); - - let mut agg_mz = vec![0.0; arr_len]; - let mut agg_intensity = vec![0.0; arr_len]; - - let utol = tol_ppm / 1e6; - - for &idx in &order { - if touched[idx] { - continue; - } - - let mz = mz_array[idx]; - let da_tol = mz * utol; - let left_e = mz - da_tol; - let right_e = mz + da_tol; - - let ss_start = mz_array.partition_point(|&x| x < left_e); - let ss_end = mz_array.partition_point(|&x| x <= right_e); - - let mut curr_intensity = 0.0; - let mut curr_weighted_mz = 0.0; - - for i in ss_start..ss_end { - if !touched[i] && intensity_array[i] > 0.0 { - curr_intensity += intensity_array[i]; - curr_weighted_mz += mz_array[i] * intensity_array[i]; - touched[i] = true; - global_num_touched += 1; - } - } - - if curr_intensity > 0.0 { - curr_weighted_mz /= curr_intensity; - - agg_intensity[idx] = curr_intensity; - agg_mz[idx] = curr_weighted_mz; - - touched[ss_start..ss_end].iter_mut().for_each(|x| *x = true); - } - - if global_num_touched == arr_len { - break; - } - } - - // Drop the zeros and sort - let mut result: Vec<(f32, f32)> = agg_mz - .into_iter() - .zip(agg_intensity.into_iter()) - .filter(|&(mz, intensity)| mz > 0.0 && intensity > 0.0) - .collect(); - - result.sort_unstable_by(|a, b| a.0.partial_cmp(&b.0).unwrap_or(Ordering::Equal)); - - result.into_iter().unzip() -} +use tracing::{error, info, warn}; pub type TofIntensityVecs = (Vec, Vec); pub type CentroidedVecs = (TofIntensityVecs, Vec); @@ -165,14 +90,16 @@ pub fn lazy_centroid_weighted_frame<'a>( let num_arrays = peak_refs.len(); assert!(num_arrays > 1); let arr_len = ref_arrays.len(); + if arr_len == 0 { + error!("No peaks in reference array when centroiding"); + return ((Vec::new(), Vec::new()), Vec::new()); + } let initial_tot_intensity = ref_arrays .intensity_array .iter() .map(|x| *x as u64) .sum::(); - const MIN_WEIGHT_PRESERVE: u64 = 50; - let mut touched = vec![false; tot_size]; let mut global_num_touched = 0; let mut num_added = 0; @@ -252,7 +179,7 @@ pub fn lazy_centroid_weighted_frame<'a>( local_offset_touched += local_peak_refs.len(); } - if curr_intensity > this_intensity { + if curr_weight > this_intensity { agg_intensity.push(u32::try_from(curr_intensity).expect("Expected to fit in u32")); let calc_tof = (curr_agg_tof / curr_weight) as u32; let calc_ims = (curr_agg_ims / curr_weight) as usize; @@ -305,3 +232,208 @@ pub fn lazy_centroid_weighted_frame<'a>( out } + +#[cfg(test)] +mod tests { + use super::*; + + // Helper function to create a simple tolerance range for testing + fn test_tof_tolerance(tof: u32) -> RangeInclusive { + let tolerance = 2; + (tof.saturating_sub(tolerance))..=tof.saturating_add(tolerance) + } + + fn test_ims_tolerance(ims: usize) -> RangeInclusive { + let tolerance = 1; + (ims.saturating_sub(tolerance))..=ims.saturating_add(tolerance) + } + + // Helper function to create PeakArrayRefs + fn create_peak_refs<'a>( + tof: &'a [u32], + ims: &'a [usize], + intensity: &'a [u32], + ) -> PeakArrayRefs<'a> { + PeakArrayRefs::new(tof, ims, intensity) + } + + #[test] + fn test_basic_centroid() { + // Test case with two simple peaks that should be merged + let peak_refs = vec![ + create_peak_refs( + &[100, 101, 200, 201], // tof + &[1, 1, 2, 2], // ims + &[1000, 2000, 500, 600], // intensity + ), + create_peak_refs( + &[101, 201], // tof + &[1, 2], // ims + &[900, 600], // intensity + ), + ]; + + let result = lazy_centroid_weighted_frame( + &peak_refs, + 0, // reference_index + 10, // max_peaks + test_tof_tolerance, + test_ims_tolerance, + ); + + let ((tof_array, intensity_array), ims_array) = result; + + assert_eq!( + tof_array.len(), + 2, + "Expected 2 centroids, got {:?}, {:?}, {:?}", + tof_array, + intensity_array, + ims_array + ); + assert_eq!(intensity_array.len(), 2); + assert_eq!(ims_array.len(), 2); + + // Check that the peaks were properly merged and weighted + assert!(tof_array[0] >= 100 && tof_array[0] <= 101); + assert_eq!(ims_array[0], 1); + assert!(intensity_array[0] == 3000); // Should be sum of intensities + assert!(intensity_array[1] == 1100); // Should be sum of intensities + } + + #[test] + fn test_max_peaks_limit() { + // Test that the function respects the max_peaks parameter + let peak_refs = vec![ + create_peak_refs(&[100, 200, 300], &[1, 2, 3], &[1000, 900, 800]), + create_peak_refs(&[101, 201, 301], &[1, 2, 3], &[950, 850, 750]), + ]; + + let result = lazy_centroid_weighted_frame( + &peak_refs, + 0, + 2, // max_peaks set to 2 + test_tof_tolerance, + test_ims_tolerance, + ); + + let ((tof_array, _), _) = result; + assert_eq!( + tof_array.len(), + 2, + "Should only return max_peaks number of peaks" + ); + } + + #[test] + fn test_empty_input() { + // Test handling of empty arrays + let peak_refs = vec![ + create_peak_refs(&[], &[], &[]), + create_peak_refs(&[], &[], &[]), + ]; + + let result = + lazy_centroid_weighted_frame(&peak_refs, 0, 10, test_tof_tolerance, test_ims_tolerance); + + let ((tof_array, intensity_array), ims_array) = result; + assert_eq!(tof_array.len(), 0); + assert_eq!(intensity_array.len(), 0); + assert_eq!(ims_array.len(), 0); + } + + #[test] + fn test_intensity_weighted_centroid() { + // Test that centroids are properly weighted by intensity + let peak_refs = vec![ + create_peak_refs( + &[100, 200], + &[1, 2], + &[1000, 100], // High intensity for first peak + ), + create_peak_refs( + &[102, 202], + &[1, 2], + &[100, 1000], // High intensity for second peak + ), + ]; + + let result = + lazy_centroid_weighted_frame(&peak_refs, 0, 10, test_tof_tolerance, test_ims_tolerance); + + let ((tof_array, _), ims_array) = result; + + // First centroid should be closer to 100 due to higher intensity + assert!(tof_array[0] - 100 < 102 - tof_array[0]); + assert_eq!(ims_array[0], 1); + } + + #[test] + #[should_panic] + fn test_invalid_reference_index() { + let peak_refs = vec![ + create_peak_refs(&[100], &[1], &[1000]), + create_peak_refs(&[101], &[1], &[900]), + ]; + + // This should panic due to invalid reference index + lazy_centroid_weighted_frame( + &peak_refs, + 2, // Invalid index + 10, + test_tof_tolerance, + test_ims_tolerance, + ); + } + + // Pretty decent test suggested by claude but im not sure if I really + // need to suuport it ... since scan indices are usually less than 2_000 + // #[test] + // fn test_large_input_values() { + // // Test handling of large values close to u32::MAX + // let peak_refs = vec![ + // create_peak_refs( + // &[u32::MAX - 10, u32::MAX - 5], + // &[usize::MAX - 10, usize::MAX - 5], + // &[1000, 900], + // ), + // create_peak_refs( + // &[u32::MAX - 9, u32::MAX - 4], + // &[usize::MAX - 9, usize::MAX - 4], + // &[950, 850], + // ), + // ]; + + // let result = + // lazy_centroid_weighted_frame(&peak_refs, 0, 10, test_tof_tolerance, test_ims_tolerance); + + // let ((tof_array, _), _) = result; + // assert!(!tof_array.is_empty(), "Should handle large values properly"); + // } + + #[test] + fn test_reference_frame_intensity() { + // Test that only reference frame intensities are summed + let peak_refs = vec![ + create_peak_refs( + &[100], + &[1], + &[1000], // Reference frame + ), + create_peak_refs( + &[101], + &[1], + &[5000], // Non-reference frame with higher intensity + ), + ]; + + let result = + lazy_centroid_weighted_frame(&peak_refs, 0, 10, test_tof_tolerance, test_ims_tolerance); + + let ((_, intensity_array), _) = result; + assert_eq!( + intensity_array[0], 1000, + "Should only use reference frame intensity" + ); + } +} diff --git a/src/utils/sorting.rs b/src/utils/sorting.rs index 2caa86f..d67d691 100644 --- a/src/utils/sorting.rs +++ b/src/utils/sorting.rs @@ -1,116 +1,27 @@ -use rayon::prelude::*; - -fn place_at_indices(original: &mut [T], indices: &mut [usize]) { - for i in 0..indices.len() { - while i != indices[i] { - let new_i = indices[i]; - indices.swap(i, new_i); - original.swap(i, new_i); - } - } -} - -fn place_at_indices_n(original: &mut [&mut [T]], indices: &mut [usize]) { - for i in 0..indices.len() { - while i != indices[i] { - let new_i = indices[i]; - indices.swap(i, new_i); - for slice in original.iter_mut() { - slice.swap(i, new_i); - } - } - } -} - -pub fn argsort_by(v: &[T], key: F) -> Vec -where - F: Fn(&T) -> K, - K: Ord, -{ - let mut indices: Vec = (0..v.len()).collect(); - // indices.sort_by_key(|&i| key(&v[i])); - indices.sort_unstable_by_key(|&i| key(&v[i])); - indices -} - -pub fn par_argsort_by(v: &[T], key: F) -> Vec -where - F: Fn(&T) -> K + Sync + Send, - K: Ord + Sync + Send, - T: Sync + Send, -{ - let mut indices: Vec = (0..v.len()).collect(); - // indices.sort_by_key(|&i| key(&v[i])); - indices.par_sort_unstable_by_key(|&i| key(&v[i])); - indices -} - -/// Sorts all passed slices by the key function. +/// Macro that sorts an arbitrary number of vecs by a the values +/// first one. /// -/// For a similar macro that works in slices of heterogeneous types, see `sort_by_indices_multi!`. +/// NOTE: This macro creates a new ordered vec for each one. +/// In theory its possible to have this happen in-place (see commit history) +/// but it seems ineficient for the most part when I benchmarked it. /// -/// # Example -/// ``` -/// use timsquery::utils::sorting::sort_multiple_by; -/// let mut va = vec![9, 8, 7]; -/// let mut vb = vec![1, 2, 3]; -/// sort_multiple_by(&mut [&mut va, &mut vb], |x| *x); -/// assert_eq!(va, vec![7, 8, 9]); -/// assert_eq!(vb, vec![3, 2, 1]); -/// ``` -/// -pub fn sort_multiple_by(vectors: &mut [&mut [T]], key: F) -where - F: Fn(&T) -> K, - K: Ord, -{ - let mut indices = argsort_by(vectors[0], |x| key(x)); - place_at_indices_n(vectors, &mut indices); -} - -/// Macro that sorts an arbitrary number of slices by a key function applied to the -/// first slice. +/// TODO: Make a variant that sort in parallel. +/// TODO: Add a parameter to specify ascending or descending. /// /// # Example /// ``` -/// use timsquery::sort_by_indices_multi; -/// use timsquery::utils::sorting::argsort_by; +/// use timsquery::sort_vecs_by_first; /// -/// let mut va = vec![9, 8, 7]; -/// let mut vb = vec![1, 2, 3]; -/// let mut vc = vec!['a', 'b', 'c']; -/// let mut indices = argsort_by(&va, |x| *x); -/// sort_by_indices_multi!( indices, &mut va, &mut vb, &mut vc); +/// let va = vec![9, 8, 7]; +/// let vb = vec![1, 2, 3]; +/// let vc = vec!['a', 'b', 'c']; +/// let out = sort_vecs_by_first!(&va, &vb, &vc); /// -/// assert_eq!(va, vec![7, 8, 9]); -/// assert_eq!(vb, vec![3, 2, 1]); -/// assert_eq!(vc, vec!['c', 'b', 'a']); +/// assert_eq!(out.0, vec![7, 8, 9]); +/// assert_eq!(out.1, vec![3, 2, 1]); +/// assert_eq!(out.2, vec!['c', 'b', 'a']); /// ``` /// -/// -#[macro_export] -macro_rules! sort_by_indices_multi { - ($indices:expr, $($data:expr),+ $(,)?) => {{ - let mut indices = $indices.to_vec(); - for idx in 0..indices.len() { - if indices[idx] != idx { - let mut current_idx = idx; - loop { - let target_idx = indices[current_idx]; - indices[current_idx] = current_idx; - if indices[target_idx] == target_idx { - break; - } - $( - $data.swap(current_idx, target_idx); - )+ - current_idx = target_idx; - } - } - } - }}; -} - #[macro_export] macro_rules! sort_vecs_by_first { ($first:expr $(,$rest:expr)*) => {{ @@ -135,50 +46,6 @@ macro_rules! sort_vecs_by_first { #[cfg(test)] mod tests { - use super::*; - - #[test] - fn test_place_at_indices() { - let mut va = vec![1, 2, 3, 4]; - let mut indices = vec![3, 2, 1, 0]; - place_at_indices(&mut va, &mut indices); - assert_eq!(va, vec![4, 3, 2, 1]); - } - - #[test] - fn test_place_at_indices_n() { - let mut va = vec![1, 2, 3, 4]; - let mut vb = vec![5, 6, 7, 8]; - let mut indices = vec![3, 2, 1, 0]; - place_at_indices_n(&mut [&mut va, &mut vb], &mut indices); - assert_eq!(va, vec![4, 3, 2, 1]); - assert_eq!(vb, vec![8, 7, 6, 5]); - } - - #[test] - fn test_argsort_by() { - let va = vec![1, 2, 3, 4]; - let indices = argsort_by(&va, |x| *x); - assert_eq!(indices, vec![0, 1, 2, 3]); - } - - #[test] - fn test_sort_multiple_slices() { - let mut tof_indices: Vec = vec![1, 2, 3, 4, 1, 2]; - let mut scan_numbers: Vec = vec![0, 0, 1, 1, 2, 2]; - let mut intensities: Vec = vec![10, 20, 30, 40, 50, 60]; - let mut indices = argsort_by(&tof_indices, |x| *x); - sort_by_indices_multi!( - &mut indices, - &mut tof_indices, - &mut scan_numbers, - &mut intensities - ); - assert_eq!(tof_indices, vec![1, 1, 2, 2, 3, 4]); - assert_eq!(scan_numbers, vec![0, 2, 0, 2, 1, 1]); - assert_eq!(intensities, vec![10, 50, 20, 60, 30, 40]); - } - #[test] fn test_sort_two_vecs() { let v1 = vec![3, 1, 4, 1, 5]; From 2fdbfad3fe512fb3c00c884d04279e70f88f01e5 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Mon, 28 Oct 2024 06:00:55 -0700 Subject: [PATCH 09/30] feat(centroiding): 15pct speedup in centroiding --- ..._results_230510_PRTC_13_S1-B1_1_12817.json | 122 +++++++++--------- ..._diaPASEF_Condition_A_Sample_Alpha_02.json | 50 +++---- src/models/frames/expanded_frame.rs | 2 +- src/utils/frame_processing.rs | 98 ++++++-------- 4 files changed, 127 insertions(+), 145 deletions(-) diff --git a/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json index c42d54c..542d380 100644 --- a/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json +++ b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json @@ -7,132 +7,132 @@ { "name": "RawFileIndex", "context": "Encoding", - "mean_duration_seconds": 0.006061387115151513, - "mean_duration_human_readable": "6.061387ms", - "setup_time_seconds": 1.75e-6, - "setup_time_human_readable": "1.75µs", + "mean_duration_seconds": 0.006079765945454544, + "mean_duration_human_readable": "6.079765ms", + "setup_time_seconds": 1.791e-6, + "setup_time_human_readable": "1.791µs", "note": null }, { "name": "ExpandedRawFileIndexCentroided", "context": "Encoding", - "mean_duration_seconds": 102.017141791, - "mean_duration_human_readable": "102.017141791s", - "setup_time_seconds": 9.58e-7, - "setup_time_human_readable": "958ns", + "mean_duration_seconds": 94.757292084, + "mean_duration_human_readable": "94.757292084s", + "setup_time_seconds": 1e-6, + "setup_time_human_readable": "1µs", "note": null }, { "name": "ExpandedRawFileIndex", "context": "Encoding", - "mean_duration_seconds": 7.339009041, - "mean_duration_human_readable": "7.339009041s", - "setup_time_seconds": 1.042e-6, - "setup_time_human_readable": "1.042µs", + "mean_duration_seconds": 7.356188333, + "mean_duration_human_readable": "7.356188333s", + "setup_time_seconds": 1.167e-6, + "setup_time_human_readable": "1.167µs", "note": null }, { "name": "TransposedQuadIndex", "context": "Encoding", - "mean_duration_seconds": 64.579125625, - "mean_duration_human_readable": "64.579125625s", - "setup_time_seconds": 1.167e-6, - "setup_time_human_readable": "1.167µs", + "mean_duration_seconds": 62.624879917, + "mean_duration_human_readable": "62.624879917s", + "setup_time_seconds": 4e-6, + "setup_time_human_readable": "4µs", "note": null }, { "name": "TransposedQuadIndexCentroided", "context": "Encoding", - "mean_duration_seconds": 105.091189208, - "mean_duration_human_readable": "105.091189208s", - "setup_time_seconds": 1.25e-6, - "setup_time_human_readable": "1.25µs", + "mean_duration_seconds": 96.316570291, + "mean_duration_human_readable": "96.316570291s", + "setup_time_seconds": 7.08e-7, + "setup_time_human_readable": "708ns", "note": null }, { "name": "RawFileIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 28.889043334, - "mean_duration_human_readable": "28.889043334s", - "setup_time_seconds": 0.077295959, - "setup_time_human_readable": "77.295959ms", + "mean_duration_seconds": 29.691199875, + "mean_duration_human_readable": "29.691199875s", + "setup_time_seconds": 0.079093084, + "setup_time_human_readable": "79.093084ms", "note": "RawFileIndex::query_multi_group aggregated 71227 " }, { "name": "ExpandedRawFileIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.0023722945118483407, - "mean_duration_human_readable": "2.372294ms", - "setup_time_seconds": 5.8142151250000005, - "setup_time_human_readable": "5.814215125s", + "mean_duration_seconds": 0.0016401144606557367, + "mean_duration_human_readable": "1.640114ms", + "setup_time_seconds": 5.64560575, + "setup_time_human_readable": "5.64560575s", "note": "ExpandedRawFileIndex::query_multi_group aggregated 72731 " }, { "name": "ExpandedRawFileIndex", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.363698, - "mean_duration_human_readable": "363.698ms", - "setup_time_seconds": 5.680389416, - "setup_time_human_readable": "5.680389416s", + "mean_duration_seconds": 0.5222450000000001, + "mean_duration_human_readable": "522.245ms", + "setup_time_seconds": 5.767646542, + "setup_time_human_readable": "5.767646542s", "note": "ExpandedRawFileIndex::query_multi_group aggregated 11194054 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.0011996081642685855, - "mean_duration_human_readable": "1.199608ms", - "setup_time_seconds": 98.870238958, - "setup_time_human_readable": "98.870238958s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 21990 " + "mean_duration_seconds": 0.0010444809603340293, + "mean_duration_human_readable": "1.04448ms", + "setup_time_seconds": 89.688057292, + "setup_time_human_readable": "89.688057292s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 28517 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.07626683057142856, - "mean_duration_human_readable": "76.26683ms", - "setup_time_seconds": 114.076896875, - "setup_time_human_readable": "114.076896875s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 5012679 " + "mean_duration_seconds": 0.112750301, + "mean_duration_human_readable": "112.750301ms", + "setup_time_seconds": 90.299234708, + "setup_time_human_readable": "90.299234708s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 5973230 " }, { "name": "TransposedQuadIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.005130067953846155, - "mean_duration_human_readable": "5.130067ms", - "setup_time_seconds": 72.976041375, - "setup_time_human_readable": "72.976041375s", + "mean_duration_seconds": 0.009101093563636368, + "mean_duration_human_readable": "9.101093ms", + "setup_time_seconds": 70.55164475, + "setup_time_human_readable": "70.55164475s", "note": "TransposedQuadIndex::query_multi_group aggregated 69045 " }, { "name": "TransposedQuadIndex", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.00552524769060773, - "mean_duration_human_readable": "5.525247ms", - "setup_time_seconds": 87.057384125, - "setup_time_human_readable": "87.057384125s", + "mean_duration_seconds": 0.00893748735714286, + "mean_duration_human_readable": "8.937487ms", + "setup_time_seconds": 64.168985583, + "setup_time_human_readable": "64.168985583s", "note": "TransposedQuadIndex::query_multi_group aggregated 9971215 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.001565241712050078, - "mean_duration_human_readable": "1.565241ms", - "setup_time_seconds": 118.473094709, - "setup_time_human_readable": "118.473094709s", - "note": "TransposedQuadIndex::query_multi_group aggregated 17773 " + "mean_duration_seconds": 0.003934095082031249, + "mean_duration_human_readable": "3.934095ms", + "setup_time_seconds": 99.876973791, + "setup_time_human_readable": "99.876973791s", + "note": "TransposedQuadIndex::query_multi_group aggregated 23806 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.003929947243137255, - "mean_duration_human_readable": "3.929947ms", - "setup_time_seconds": 124.951945458, - "setup_time_human_readable": "124.951945458s", - "note": "TransposedQuadIndex::query_multi_group aggregated 4425627 " + "mean_duration_seconds": 0.0021190172139830504, + "mean_duration_human_readable": "2.119017ms", + "setup_time_seconds": 107.17344675, + "setup_time_human_readable": "107.17344675s", + "note": "TransposedQuadIndex::query_multi_group aggregated 5282090 " } ], "metadata": { "basename": "230510_PRTC_13_S1-B1_1_12817" }, - "full_benchmark_time_seconds": 961.0857955 + "full_benchmark_time_seconds": 847.892203041 } \ No newline at end of file diff --git a/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json b/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json index 14ff6fe..edbebb6 100644 --- a/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json +++ b/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json @@ -7,51 +7,51 @@ { "name": "RawFileIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 3.778817917, - "mean_duration_human_readable": "3.778817917s", - "setup_time_seconds": 0.241755042, - "setup_time_human_readable": "241.755042ms", + "mean_duration_seconds": 3.923214042, + "mean_duration_human_readable": "3.923214042s", + "setup_time_seconds": 0.236783083, + "setup_time_human_readable": "236.783083ms", "note": "RawFileIndex::query_multi_group aggregated 9144 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.0005595513605823068, - "mean_duration_human_readable": "559.551µs", - "setup_time_seconds": 619.45208575, - "setup_time_human_readable": "619.45208575s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 873 " + "mean_duration_seconds": 0.0009338467012138191, + "mean_duration_human_readable": "933.846µs", + "setup_time_seconds": 470.779360458, + "setup_time_human_readable": "470.779360458s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 1505 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 7.19476525, - "mean_duration_human_readable": "7.19476525s", - "setup_time_seconds": 636.328349375, - "setup_time_human_readable": "636.328349375s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 193555055 " + "mean_duration_seconds": 16.197693792, + "mean_duration_human_readable": "16.197693792s", + "setup_time_seconds": 487.496389916, + "setup_time_human_readable": "487.496389916s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 213765098 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.0017960869371633765, - "mean_duration_human_readable": "1.796086ms", - "setup_time_seconds": 665.489050917, - "setup_time_human_readable": "665.489050917s", - "note": "TransposedQuadIndex::query_multi_group aggregated 715 " + "mean_duration_seconds": 0.003893406926070039, + "mean_duration_human_readable": "3.893406ms", + "setup_time_seconds": 530.744600625, + "setup_time_human_readable": "530.744600625s", + "note": "TransposedQuadIndex::query_multi_group aggregated 1347 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.0027502779313186817, - "mean_duration_human_readable": "2.750277ms", - "setup_time_seconds": 663.333964959, - "setup_time_human_readable": "663.333964959s", - "note": "TransposedQuadIndex::query_multi_group aggregated 167889419 " + "mean_duration_seconds": 0.004904444668292681, + "mean_duration_human_readable": "4.904444ms", + "setup_time_seconds": 542.031527458, + "setup_time_human_readable": "542.031527458s", + "note": "TransposedQuadIndex::query_multi_group aggregated 185201566 " } ], "metadata": { "basename": "LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02" }, - "full_benchmark_time_seconds": 2621.0749125 + "full_benchmark_time_seconds": 2091.340999875 } \ No newline at end of file diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index 1cfe84d..14a1571 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -348,7 +348,7 @@ impl FrameProcessingConfig { mz_tol_ppm: 15.0, window_width: 3, max_ms1_peaks: 100_000, - max_ms2_peaks: 10_000, + max_ms2_peaks: 20_000, ims_converter: Default::default(), mz_converter: Default::default(), } diff --git a/src/utils/frame_processing.rs b/src/utils/frame_processing.rs index 302af05..82c5ce0 100644 --- a/src/utils/frame_processing.rs +++ b/src/utils/frame_processing.rs @@ -15,7 +15,11 @@ fn sort_n_check( sort_vecs_by_first!(agg_tof, agg_ims, agg_intensity); if let Some(x) = intensity_array.last() { - assert!(*x > 0); + assert!( + *x > 0, + "Expected all intensities to be positive non-zero, got {:?}", + intensity_array + ); let max_tof = tof_array.iter().max().expect("At least one element"); assert!(*max_tof < (u32::MAX - 1)); } @@ -105,45 +109,48 @@ pub fn lazy_centroid_weighted_frame<'a>( let mut num_added = 0; // We will be iterating in decreasing order of intensity - let mut order: Vec = (0..tot_size).collect(); - order.sort_unstable_by(|&a, &b| { - let (a_major, a_minor) = index_split(a, &slice_sizes); - let (b_major, b_minor) = index_split(b, &slice_sizes); - - let a_intensity = peak_refs[a_major].intensity_array[a_minor]; - let b_intensity = peak_refs[b_major].intensity_array[b_minor]; - - b_intensity - .partial_cmp(&a_intensity) - .unwrap_or(Ordering::Equal) - }); - - assert!({ - let (first_major, first_minor) = index_split(order[0], &slice_sizes); - let (last_major, last_minor) = index_split(order[tot_size - 1], &slice_sizes); + // Pre-calculate indices and intensities for sorting + struct OrderItem { + global_idx: usize, + major_idx: usize, + minor_idx: usize, + intensity: u32, + } - let first_intensity = peak_refs[first_major].intensity_array[first_minor]; - let last_intensity = peak_refs[last_major].intensity_array[last_minor]; + let mut order: Vec = Vec::with_capacity(tot_size); + let mut offset = 0; + for (major_idx, peak_ref) in peak_refs.iter().enumerate() { + for (minor_idx, &intensity) in peak_ref.intensity_array.iter().enumerate() { + order.push(OrderItem { + global_idx: offset + minor_idx, + major_idx, + minor_idx, + intensity, + }); + } + offset += peak_ref.len(); + } - first_intensity >= last_intensity - }); + // Sort by intensity + order.sort_unstable_by(|a, b| b.intensity.cmp(&a.intensity)); + assert!(order[0].intensity > order[tot_size - 1].intensity); - // TODO explore if making vecs with capacity and appedning is better... let capacity = max_peaks.min(arr_len); let mut agg_tof = Vec::with_capacity(capacity); let mut agg_intensity = Vec::with_capacity(capacity); let mut agg_ims = Vec::with_capacity(capacity); - for idx in order { - let (major_idx, minor_idx) = index_split(idx, &slice_sizes); + for item in order { + let major_idx = item.major_idx; + let minor_idx = item.minor_idx; + let this_intensity = item.intensity as u64; - if touched[idx] { + if touched[item.global_idx] { continue; } let tof = peak_refs[major_idx].tof_array[minor_idx]; let ims = peak_refs[major_idx].ims_array[minor_idx]; - let this_intensity = peak_refs[major_idx].intensity_array[minor_idx] as u64; let tof_range = tof_tol_range_fn(tof); let ims_range = ims_tol_range_fn(ims); @@ -153,8 +160,7 @@ pub fn lazy_centroid_weighted_frame<'a>( let mut curr_agg_ims = 0u64; let mut local_offset_touched = 0; - for ii in 0..num_arrays { - let local_peak_refs = &peak_refs[ii]; + for (ii, local_peak_refs) in peak_refs.iter().enumerate() { let ss_start = local_peak_refs .tof_array .partition_point(|x| x < tof_range.start()); @@ -179,12 +185,13 @@ pub fn lazy_centroid_weighted_frame<'a>( local_offset_touched += local_peak_refs.len(); } - if curr_weight > this_intensity { + // This means that at least 2 peaks need to be aggregated. + if curr_weight > this_intensity && curr_intensity >= this_intensity { agg_intensity.push(u32::try_from(curr_intensity).expect("Expected to fit in u32")); let calc_tof = (curr_agg_tof / curr_weight) as u32; let calc_ims = (curr_agg_ims / curr_weight) as usize; - assert!(tof_range.contains(&calc_tof)); - assert!(ims_range.contains(&calc_ims)); + debug_assert!(tof_range.contains(&calc_tof)); + debug_assert!(ims_range.contains(&calc_ims)); agg_tof.push(calc_tof); agg_ims.push(calc_ims); num_added += 1; @@ -198,8 +205,9 @@ pub fn lazy_centroid_weighted_frame<'a>( } } - // Drop the zeros and sort by mz (tof) let out = sort_n_check(agg_intensity, agg_tof, agg_ims); + + // TODO:Make everything below this a separate function and accumulate it. let tot_final_intensity = out.0 .1.iter().map(|x| *x as u64).sum::(); let inten_ratio = tot_final_intensity as f64 / initial_tot_intensity as f64; assert!(initial_tot_intensity >= tot_final_intensity); @@ -410,30 +418,4 @@ mod tests { // let ((tof_array, _), _) = result; // assert!(!tof_array.is_empty(), "Should handle large values properly"); // } - - #[test] - fn test_reference_frame_intensity() { - // Test that only reference frame intensities are summed - let peak_refs = vec![ - create_peak_refs( - &[100], - &[1], - &[1000], // Reference frame - ), - create_peak_refs( - &[101], - &[1], - &[5000], // Non-reference frame with higher intensity - ), - ]; - - let result = - lazy_centroid_weighted_frame(&peak_refs, 0, 10, test_tof_tolerance, test_ims_tolerance); - - let ((_, intensity_array), _) = result; - assert_eq!( - intensity_array[0], 1000, - "Should only use reference frame intensity" - ); - } } From 13aeff169de816c8c831d7f077f54414c4586853 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Tue, 29 Oct 2024 15:39:16 -0700 Subject: [PATCH 10/30] ... a lot .... --- Taskfile.yml | 4 + benches/benchmark_indices.rs | 5 - ..._results_230510_PRTC_13_S1-B1_1_12817.json | 126 +++++----- src/lib.rs | 5 +- src/models/adapters.rs | 1 + .../aggregators/raw_peak_agg/point_agg.rs | 19 +- src/models/elution_group.rs | 13 +- src/models/frames/expanded_frame.rs | 216 +++++++++++++++++- src/models/frames/single_quad_settings.rs | 69 +++--- .../indices/expanded_raw_index/model.rs | 204 +++++++---------- src/models/indices/raw_file_index.rs | 24 +- .../transposed_quad_index/quad_index.rs | 63 ++--- .../quad_splitted_transposed_index.rs | 128 +---------- src/models/queries.rs | 1 + .../queriable_tims_data.rs | 144 ++++-------- src/traits/indexed_data.rs | 19 -- src/traits/mod.rs | 2 +- src/traits/queriable_data.rs | 53 +++++ src/traits/tolerance.rs | 13 +- src/utils/frame_processing.rs | 24 -- src/utils/sorting.rs | 57 +++++ 21 files changed, 651 insertions(+), 539 deletions(-) delete mode 100644 src/traits/indexed_data.rs create mode 100644 src/traits/queriable_data.rs diff --git a/Taskfile.yml b/Taskfile.yml index bc24eec..d08501b 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -23,6 +23,10 @@ tasks: cmds: - cargo build $BIN_EXTRAS + license_check: + cmds: + - cargo deny check + test: cmds: - cargo test diff --git a/benches/benchmark_indices.rs b/benches/benchmark_indices.rs index d63d531..3afc9e5 100644 --- a/benches/benchmark_indices.rs +++ b/benches/benchmark_indices.rs @@ -353,7 +353,6 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve || RawFileIndex::from_path(raw_file_path).unwrap(), |index, _i| { let tmp = query_multi_group( - index, index, &tolerance, &query_groups, @@ -375,7 +374,6 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve || ExpandedRawFrameIndex::from_path(raw_file_path).unwrap(), |index, _i| { let tmp = query_multi_group( - index, index, &tolerance, &query_groups, @@ -400,7 +398,6 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve || ExpandedRawFrameIndex::from_path_centroided(raw_file_path).unwrap(), |index, _i| { let tmp = query_multi_group( - index, index, &tolerance, &query_groups, @@ -425,7 +422,6 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve || QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(), |index, _i| { let tmp = query_multi_group( - index, index, &tolerance, &query_groups, @@ -447,7 +443,6 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve || QuadSplittedTransposedIndex::from_path_centroided(raw_file_path).unwrap(), |index, _i| { let tmp = query_multi_group( - index, index, &tolerance, &query_groups, diff --git a/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json index 542d380..1b5d19d 100644 --- a/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json +++ b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json @@ -7,132 +7,132 @@ { "name": "RawFileIndex", "context": "Encoding", - "mean_duration_seconds": 0.006079765945454544, - "mean_duration_human_readable": "6.079765ms", - "setup_time_seconds": 1.791e-6, - "setup_time_human_readable": "1.791µs", + "mean_duration_seconds": 0.006222996397515529, + "mean_duration_human_readable": "6.222996ms", + "setup_time_seconds": 4.833e-6, + "setup_time_human_readable": "4.833µs", "note": null }, { "name": "ExpandedRawFileIndexCentroided", "context": "Encoding", - "mean_duration_seconds": 94.757292084, - "mean_duration_human_readable": "94.757292084s", - "setup_time_seconds": 1e-6, - "setup_time_human_readable": "1µs", + "mean_duration_seconds": 97.626668625, + "mean_duration_human_readable": "97.626668625s", + "setup_time_seconds": 9.17e-7, + "setup_time_human_readable": "917ns", "note": null }, { "name": "ExpandedRawFileIndex", "context": "Encoding", - "mean_duration_seconds": 7.356188333, - "mean_duration_human_readable": "7.356188333s", - "setup_time_seconds": 1.167e-6, - "setup_time_human_readable": "1.167µs", + "mean_duration_seconds": 8.102684125, + "mean_duration_human_readable": "8.102684125s", + "setup_time_seconds": 1.042e-6, + "setup_time_human_readable": "1.042µs", "note": null }, { "name": "TransposedQuadIndex", "context": "Encoding", - "mean_duration_seconds": 62.624879917, - "mean_duration_human_readable": "62.624879917s", - "setup_time_seconds": 4e-6, - "setup_time_human_readable": "4µs", + "mean_duration_seconds": 74.288219334, + "mean_duration_human_readable": "74.288219334s", + "setup_time_seconds": 1e-6, + "setup_time_human_readable": "1µs", "note": null }, { "name": "TransposedQuadIndexCentroided", "context": "Encoding", - "mean_duration_seconds": 96.316570291, - "mean_duration_human_readable": "96.316570291s", - "setup_time_seconds": 7.08e-7, - "setup_time_human_readable": "708ns", + "mean_duration_seconds": 103.221435875, + "mean_duration_human_readable": "103.221435875s", + "setup_time_seconds": 9.58e-7, + "setup_time_human_readable": "958ns", "note": null }, { "name": "RawFileIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 29.691199875, - "mean_duration_human_readable": "29.691199875s", - "setup_time_seconds": 0.079093084, - "setup_time_human_readable": "79.093084ms", + "mean_duration_seconds": 30.1034345, + "mean_duration_human_readable": "30.1034345s", + "setup_time_seconds": 0.080088542, + "setup_time_human_readable": "80.088542ms", "note": "RawFileIndex::query_multi_group aggregated 71227 " }, { "name": "ExpandedRawFileIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.0016401144606557367, - "mean_duration_human_readable": "1.640114ms", - "setup_time_seconds": 5.64560575, - "setup_time_human_readable": "5.64560575s", - "note": "ExpandedRawFileIndex::query_multi_group aggregated 72731 " + "mean_duration_seconds": 0.0043137600000000016, + "mean_duration_human_readable": "4.31376ms", + "setup_time_seconds": 5.777069208, + "setup_time_human_readable": "5.777069208s", + "note": "ExpandedRawFileIndex::query_multi_group aggregated 68449 " }, { "name": "ExpandedRawFileIndex", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.5222450000000001, - "mean_duration_human_readable": "522.245ms", - "setup_time_seconds": 5.767646542, - "setup_time_human_readable": "5.767646542s", - "note": "ExpandedRawFileIndex::query_multi_group aggregated 11194054 " + "mean_duration_seconds": 1.389402875, + "mean_duration_human_readable": "1.389402875s", + "setup_time_seconds": 5.838487875, + "setup_time_human_readable": "5.838487875s", + "note": "ExpandedRawFileIndex::query_multi_group aggregated 10744180 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.0010444809603340293, - "mean_duration_human_readable": "1.04448ms", - "setup_time_seconds": 89.688057292, - "setup_time_human_readable": "89.688057292s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 28517 " + "mean_duration_seconds": 0.003144791757009347, + "mean_duration_human_readable": "3.144791ms", + "setup_time_seconds": 89.554111875, + "setup_time_human_readable": "89.554111875s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 26179 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.112750301, - "mean_duration_human_readable": "112.750301ms", - "setup_time_seconds": 90.299234708, - "setup_time_human_readable": "90.299234708s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 5973230 " + "mean_duration_seconds": 0.2185190752, + "mean_duration_human_readable": "218.519075ms", + "setup_time_seconds": 88.279319125, + "setup_time_human_readable": "88.279319125s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 5775312 " }, { "name": "TransposedQuadIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.009101093563636368, - "mean_duration_human_readable": "9.101093ms", - "setup_time_seconds": 70.55164475, - "setup_time_human_readable": "70.55164475s", - "note": "TransposedQuadIndex::query_multi_group aggregated 69045 " + "mean_duration_seconds": 0.003314156013245034, + "mean_duration_human_readable": "3.314156ms", + "setup_time_seconds": 62.383771084, + "setup_time_human_readable": "62.383771084s", + "note": "TransposedQuadIndex::query_multi_group aggregated 64676 " }, { "name": "TransposedQuadIndex", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.00893748735714286, - "mean_duration_human_readable": "8.937487ms", - "setup_time_seconds": 64.168985583, - "setup_time_human_readable": "64.168985583s", + "mean_duration_seconds": 0.003775450037735844, + "mean_duration_human_readable": "3.77545ms", + "setup_time_seconds": 59.13618275, + "setup_time_human_readable": "59.13618275s", "note": "TransposedQuadIndex::query_multi_group aggregated 9971215 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.003934095082031249, - "mean_duration_human_readable": "3.934095ms", - "setup_time_seconds": 99.876973791, - "setup_time_human_readable": "99.876973791s", - "note": "TransposedQuadIndex::query_multi_group aggregated 23806 " + "mean_duration_seconds": 0.001552562270769231, + "mean_duration_human_readable": "1.552562ms", + "setup_time_seconds": 98.014544042, + "setup_time_human_readable": "98.014544042s", + "note": "TransposedQuadIndex::query_multi_group aggregated 22454 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.0021190172139830504, - "mean_duration_human_readable": "2.119017ms", - "setup_time_seconds": 107.17344675, - "setup_time_human_readable": "107.17344675s", + "mean_duration_seconds": 0.001730233717993079, + "mean_duration_human_readable": "1.730233ms", + "setup_time_seconds": 98.609288084, + "setup_time_human_readable": "98.609288084s", "note": "TransposedQuadIndex::query_multi_group aggregated 5282090 " } ], "metadata": { "basename": "230510_PRTC_13_S1-B1_1_12817" }, - "full_benchmark_time_seconds": 847.892203041 + "full_benchmark_time_seconds": 843.833114208 } \ No newline at end of file diff --git a/src/lib.rs b/src/lib.rs index 7624462..2ef3d2b 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,12 +1,11 @@ // Re-export main structures pub use crate::models::elution_group::ElutionGroup; pub use crate::models::indices::transposed_quad_index::QuadSplittedTransposedIndex; -pub use crate::queriable_tims_data::queriable_tims_data::QueriableTimsData; // Re-export traits pub use crate::traits::aggregator::Aggregator; -pub use crate::traits::indexed_data::QueriableData; -pub use crate::traits::tolerance::{HasIntegerID, Tolerance, ToleranceAdapter}; +pub use crate::traits::queriable_data::QueriableData; +pub use crate::traits::tolerance::{Tolerance, ToleranceAdapter}; // Declare modules pub mod models; diff --git a/src/models/adapters.rs b/src/models/adapters.rs index 61df79f..a4e8cce 100644 --- a/src/models/adapters.rs +++ b/src/models/adapters.rs @@ -62,6 +62,7 @@ impl let precursor_query = PrecursorIndexQuery { frame_index_range, + rt_range_seconds: rt_range, mz_index_range, mobility_index_range, isolation_mz_range: quad_range, diff --git a/src/models/aggregators/raw_peak_agg/point_agg.rs b/src/models/aggregators/raw_peak_agg/point_agg.rs index 9309232..1e1567d 100644 --- a/src/models/aggregators/raw_peak_agg/point_agg.rs +++ b/src/models/aggregators/raw_peak_agg/point_agg.rs @@ -3,23 +3,28 @@ use crate::traits::aggregator::Aggregator; use serde::Serialize; #[derive(Debug, Clone, Copy)] -pub struct RawPeakIntensityAggregator { +pub struct RawPeakIntensityAggregator { pub id: u64, pub intensity: u64, + _phantom: std::marker::PhantomData, } -impl RawPeakIntensityAggregator { +impl RawPeakIntensityAggregator { pub fn new(id: u64) -> Self { - Self { id, intensity: 0 } + Self { + id, + intensity: 0, + _phantom: std::marker::PhantomData, + } } } -impl Aggregator for RawPeakIntensityAggregator { - type Item = RawPeak; +impl Aggregator for RawPeakIntensityAggregator { + type Item = (RawPeak, T); type Output = u64; - fn add(&mut self, peak: &RawPeak) { - self.intensity += peak.intensity as u64; + fn add(&mut self, peak: &(RawPeak, T)) { + self.intensity += peak.0.intensity as u64; } fn finalize(self) -> u64 { diff --git a/src/models/elution_group.rs b/src/models/elution_group.rs index 0fec0f9..fd7d2be 100644 --- a/src/models/elution_group.rs +++ b/src/models/elution_group.rs @@ -1,8 +1,13 @@ -use crate::HasIntegerID; use serde::{Deserialize, Serialize}; use std::collections::HashMap; use std::hash::Hash; +/// A struct that represents an elution group. +/// +/// The elution group is a single precursor ion that is framented. +/// The fragments m/z values are stored in a hashmap where the key is +/// the generic type `T` and the value is the fragment m/z. +/// #[derive(Debug, Serialize, Deserialize, Clone)] pub struct ElutionGroup { pub id: u64, @@ -12,9 +17,3 @@ pub struct ElutionGroup { pub precursor_charge: u8, pub fragment_mzs: HashMap, } - -impl HasIntegerID for ElutionGroup { - fn get_id(&self) -> u64 { - self.id - } -} diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index 14a1571..c9b0ceb 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -5,7 +5,6 @@ use rayon::prelude::*; use std::collections::HashMap; use std::marker::PhantomData; use std::sync::Arc; -use std::time::Instant; use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; use timsrust::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}; @@ -13,6 +12,7 @@ use super::peak_in_quad::PeakInQuad; use crate::sort_vecs_by_first; use crate::utils::compress_explode::explode_vec; use crate::utils::frame_processing::{lazy_centroid_weighted_frame, PeakArrayRefs}; +use crate::utils::sorting::top_n; use crate::utils::tolerance_ranges::{scan_tol_range, tof_tol_range}; use timsrust::{ readers::{FrameReader, FrameReaderError, MetadataReaderError}, @@ -452,6 +452,14 @@ pub fn par_read_and_expand_frames( all_expanded_frames.extend(expanded_frames); } + let slice_infos: Vec = all_expanded_frames + .values() + .map(|x| ExpandedQuadSliceInfo::new(x)) + .collect(); + + println!("Slice info: {:?}", slice_infos); + panic!(); + info!("Processing MS1 frames"); let ms1_iter = frame_reader.parallel_filter(|x| x.ms_level == MSLevel::MS1); let ms1_iter = warn_and_skip_badframes(ms1_iter); @@ -481,6 +489,212 @@ pub fn par_read_and_expand_frames( Ok(all_expanded_frames) } +#[derive(Debug, Clone, Copy)] +pub struct ExpandedQuadSliceInfo { + pub quad_settings: Option, + pub cycle_time_seconds: f64, + pub peak_width_seconds: Option, +} + +impl ExpandedQuadSliceInfo { + #[instrument(skip(frameslices), ret)] + pub fn new(frameslices: &[ExpandedFrameSlice]) -> Self { + let avg_cycle_time = frameslices + .windows(2) + .map(|x| { + let a = &x[0]; + let b = &x[1]; + let diff = b.rt - a.rt; + assert!(diff > 0.0); + diff + }) + .sum::() + / frameslices.len() as f64; + + let peak_width = Self::estimate_peak_width(frameslices); + + Self { + quad_settings: frameslices[0].quadrupole_settings, + cycle_time_seconds: avg_cycle_time, + peak_width_seconds: peak_width, + } + } + + /// Estimate the peak width of elutions within the quad. + /// + /// This is a pretty dumb algorithm ... basically... + /// 1. picks 100 equally spaced points between the 20% and 80% of the frames. + /// 2. At each of those points finds the top 10 peaks. + /// 3. For each of them iteratively goes forward and backwards in time until + /// the intensity of the peak drops under 1% of its intensity. + /// 4. The time difference between the forward and backward point is the peak width. + /// 5. Finds the median of the peak widths. + /// + /// + fn estimate_peak_width(frameslices: &[ExpandedFrameSlice]) -> Option { + let start_idx = frameslices.len() / 5; + let end_idx = frameslices.len() * 4 / 5; + let step = (end_idx - start_idx) / 100; + + if step == 0 { + warn!("Estimating peak width failed, step is 0"); + return None; + } + + #[derive(Debug, Clone)] + struct Peak { + tof: u32, + patience: u32, + max_rt: f64, + min_rt: f64, + intensity: u32, + local_frame_index: usize, + fwdone: bool, + bwdone: bool, + any_update: bool, + } + + let mut peaks: Vec = Vec::with_capacity(500); + + for i in 0..49 { + let local_idx = start_idx + i * step; + + let local_frame = &frameslices[local_idx]; + let local_rt = local_frame.rt; + let (top_intens, top_indices) = top_n(&local_frame.intensities, 10); + let tofs: Vec<_> = top_indices + .iter() + .zip(top_intens.iter()) + .filter_map(|(tof, inten)| if *inten > 100u32 { Some(tof) } else { None }) + .map(|x| local_frame.tof_indices[*x]) + .collect(); + let tofs: Vec = tofs + .as_slice() + .windows(2) + .filter_map(|x| { + let a = x[0]; + let b = x[1]; + if a.abs_diff(b) > 5 { + Some(a) + } else { + None + } + }) + .collect(); + + let mut local_peaks: Vec = tofs + .iter() + .map(|tof| { + let mut local_inten = 0u32; + local_frame.query_peaks((tof - 1, tof + 1), None, &mut |x| { + local_inten += x.intensity + }); + assert!(local_inten > 0); + Peak { + tof: *tof, + patience: 1, + max_rt: local_rt, + min_rt: local_rt, + intensity: local_inten, + local_frame_index: local_idx, + fwdone: false, + bwdone: false, + any_update: false, + } + }) + .collect(); + + // Forward lookup + for lookup_frame in frameslices.iter().skip(local_idx + 1) { + let local_rt = lookup_frame.rt; + let mut any = false; + for peak in local_peaks.iter_mut() { + if peak.fwdone { + continue; + } + let mut local_int = 0u32; + lookup_frame.query_peaks((peak.tof - 1, peak.tof + 1), None, &mut |x| { + local_int += x.intensity + }); + if local_int > (peak.intensity / 100) { + peak.max_rt = local_rt; + peak.patience = 1; + peak.any_update = true; + } else if peak.patience > 0 { + peak.patience -= 1; + } else { + peak.fwdone = true; + } + + any = true; + } + if !any { + break; + } + } + + // reset patience + for peak in local_peaks.iter_mut() { + peak.patience = 1; + } + + // Backward lookup + let mut j = local_idx - 1; + while j > 1 { + // for j in (0..local_idx).rev() { + let lookup_frame = &frameslices[j]; + let local_rt = lookup_frame.rt; + let mut any = false; + for peak in local_peaks.iter_mut() { + if peak.bwdone { + continue; + } + let mut local_int = 0; + lookup_frame.query_peaks((peak.tof - 1, peak.tof + 1), None, &mut |x| { + local_int += x.intensity + }); + + if local_int > (peak.intensity / 100) { + peak.min_rt = local_rt; + peak.patience = 1; + peak.any_update = true; + } else if peak.patience > 0 { + peak.patience -= 1; + } else { + peak.bwdone = true; + } + + any = true; + } + if !any { + break; + } + j -= 1; + } + + for peak in local_peaks.into_iter() { + println!("peak: {:?}", peak); + if peak.fwdone && peak.bwdone && peak.any_update { + peaks.push(peak); + } + } + } + + if peaks.is_empty() { + return None; + } + + // get median + peaks.sort_by(|x, y| { + (x.max_rt - x.min_rt) + .partial_cmp(&(y.max_rt - y.min_rt)) + .unwrap() + }); + let median = peaks[peaks.len() / 2].max_rt - peaks[peaks.len() / 2].min_rt; + Some(median) + } +} + #[instrument(skip(frames))] pub fn par_expand_and_centroid_frames( frames: impl ParallelIterator, diff --git a/src/models/frames/single_quad_settings.rs b/src/models/frames/single_quad_settings.rs index 4747e3d..2225801 100644 --- a/src/models/frames/single_quad_settings.rs +++ b/src/models/frames/single_quad_settings.rs @@ -134,34 +134,47 @@ pub fn get_matching_quad_settings( flat_quad_settings .iter() .filter(move |qs| { - (qs.ranges.isolation_low <= precursor_mz_range.1) - && (qs.ranges.isolation_high >= precursor_mz_range.0) - }) - .filter(move |qs| { - match scan_range { - Some((min_scan, max_scan)) => { - assert!(qs.ranges.scan_start <= qs.ranges.scan_end); - assert!(min_scan <= max_scan); - - // Above quad - // Quad [----------] - // Query [------] - let above_quad = qs.ranges.scan_end < min_scan; - - // Below quad - // Quad [------] - // Query [------] - let below_quad = qs.ranges.scan_start > max_scan; - - if above_quad || below_quad { - // This quad is completely outside the scan range - false - } else { - true - } - } - None => true, - } + matches_iso_window(qs, precursor_mz_range) && matches_scan_range(qs, scan_range) }) .map(|e| e.index) } + +fn matches_iso_window(qs: &SingleQuadrupoleSetting, precursor_mz_range: (f64, f64)) -> bool { + (qs.ranges.isolation_low <= precursor_mz_range.1) + && (qs.ranges.isolation_high >= precursor_mz_range.0) +} + +fn matches_scan_range(qs: &SingleQuadrupoleSetting, scan_range: Option<(usize, usize)>) -> bool { + match scan_range { + Some((min_scan, max_scan)) => { + assert!(qs.ranges.scan_start <= qs.ranges.scan_end); + assert!(min_scan <= max_scan); + + // Above quad + // Quad [----------] + // Query [------] + let above_quad = qs.ranges.scan_end < min_scan; + + // Below quad + // Quad [------] + // Query [------] + let below_quad = qs.ranges.scan_start > max_scan; + + if above_quad || below_quad { + // This quad is completely outside the scan range + false + } else { + true + } + } + None => true, + } +} + +pub fn matches_quad_settings( + a: &SingleQuadrupoleSetting, + precursor_mz_range: (f64, f64), + scan_range: Option<(usize, usize)>, +) -> bool { + matches_iso_window(a, precursor_mz_range) && matches_scan_range(a, scan_range) +} diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index 921c057..a00113e 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -7,10 +7,11 @@ use crate::models::frames::expanded_frame::{ use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::raw_peak::RawPeak; use crate::models::frames::single_quad_settings::{ - get_matching_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, + get_matching_quad_settings, matches_quad_settings, SingleQuadrupoleSetting, + SingleQuadrupoleSettingIndex, }; use crate::models::queries::FragmentGroupIndexQuery; -use crate::traits::indexed_data::QueriableData; +use crate::traits::queriable_data::QueriableData; use crate::ToleranceAdapter; use rayon::prelude::*; use serde::Serialize; @@ -240,140 +241,99 @@ impl fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], ) { - fragment_queries - .par_iter() - .zip(aggregator.par_iter_mut()) - .for_each(|(fragment_query, agg)| { - let precursor_mz_range = ( - fragment_query.precursor_query.isolation_mz_range.0 as f64, - fragment_query.precursor_query.isolation_mz_range.1 as f64, - ); - assert!(precursor_mz_range.0 <= precursor_mz_range.1); - assert!(precursor_mz_range.0 > 0.0); - let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - let frame_index_range = fragment_query.precursor_query.frame_index_range; - - let local_quad_vec: Vec = get_matching_quad_settings( - &self.flat_quad_settings, - precursor_mz_range, - scan_range, - ) - .collect(); - - for (fh, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { - self.query_precursor_peaks( - &local_quad_vec, - tof_range, - scan_range, - frame_index_range, - &mut |peak| agg.add(&(RawPeak::from(peak), fh)), - ); - } - }); - } -} - -impl - QueriableData, RawPeak> for ExpandedRawFrameIndex -{ - fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { - todo!(); - // let precursor_mz_range = ( - // fragment_query.precursor_query.isolation_mz_range.0 as f64, - // fragment_query.precursor_query.isolation_mz_range.0 as f64, - // ); - // let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - // let frame_index_range = Some(FrameRTTolerance::FrameIndex( - // fragment_query.precursor_query.frame_index_range, - // )); + // fragment_queries + // .par_iter() + // .zip(aggregator.par_iter_mut()) + // .for_each(|(fragment_query, agg)| { + // let precursor_mz_range = ( + // fragment_query.precursor_query.isolation_mz_range.0 as f64, + // fragment_query.precursor_query.isolation_mz_range.1 as f64, + // ); + // assert!(precursor_mz_range.0 <= precursor_mz_range.1); + // assert!(precursor_mz_range.0 > 0.0); + // let scan_range = Some(fragment_query.precursor_query.mobility_index_range); + // let frame_index_range = fragment_query.precursor_query.frame_index_range; - // fragment_query - // .mz_index_ranges - // .iter() - // .flat_map(|(fh, tof_range)| { - // let mut local_vec: Vec<(RawPeak, FH)> = vec![]; - // self.query_peaks( - // *tof_range, + // let local_quad_vec: Vec = get_matching_quad_settings( + // &self.flat_quad_settings, // precursor_mz_range, // scan_range, - // frame_index_range, - // &mut |x| local_vec.push((RawPeak::from(x), *fh)), - // ); + // ) + // .collect(); + + // for (fh, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { + // self.query_precursor_peaks( + // &local_quad_vec, + // tof_range, + // scan_range, + // frame_index_range, + // &mut |peak| agg.add(&(RawPeak::from(peak), fh)), + // ); + // } + // }); + let prec_mz_ranges = fragment_queries + .iter() + .map(|x| { + ( + x.precursor_query.isolation_mz_range.0 as f64, + x.precursor_query.isolation_mz_range.0 as f64, + ) + }) + .collect::>(); - // local_vec - // }) - // .collect() - } + let scan_ranges = fragment_queries + .iter() + .map(|x| Some(x.precursor_query.mobility_index_range)) + .collect::>(); - fn add_query>( - &self, - fragment_query: &FragmentGroupIndexQuery, - aggregator: &mut AG, - ) { - todo!(); - // let precursor_mz_range = ( - // fragment_query.precursor_query.isolation_mz_range.0 as f64, - // fragment_query.precursor_query.isolation_mz_range.0 as f64, - // ); - // let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - // let frame_index_range = Some(FrameRTTolerance::FrameIndex( - // fragment_query.precursor_query.frame_index_range, - // )); + let frame_index_ranges = fragment_queries + .iter() + .map(|x| x.precursor_query.frame_index_range) + .collect::>(); - // fragment_query - // .mz_index_ranges - // .iter() - // .for_each(|(fh, tof_range)| { - // self.query_peaks( - // *tof_range, - // precursor_mz_range, - // scan_range, - // frame_index_range, - // &mut |peak| aggregator.add(&(RawPeak::from(peak), *fh)), - // ); - // }) - } + for quad_setting in self.flat_quad_settings.iter() { + let local_index = quad_setting.index; - fn add_query_multi_group>( - &self, - fragment_queries: &[FragmentGroupIndexQuery], - aggregator: &mut [AG], - ) { - fragment_queries - .par_iter() - .zip(aggregator.par_iter_mut()) - .for_each(|(fragment_query, agg)| { - let precursor_mz_range = ( - fragment_query.precursor_query.isolation_mz_range.0 as f64, - fragment_query.precursor_query.isolation_mz_range.1 as f64, - ); - assert!(precursor_mz_range.0 <= precursor_mz_range.1); - assert!(precursor_mz_range.0 > 0.0); - let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - let frame_index_range = fragment_query.precursor_query.frame_index_range; - - let local_quad_vec: Vec = get_matching_quad_settings( - &self.flat_quad_settings, - precursor_mz_range, - scan_range, - ) - .collect(); + let tqi = self + .bundled_frames + .get(&local_index) + .expect("Only existing quads should be queried."); - for (fh, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { - self.query_precursor_peaks( - &local_quad_vec, - tof_range, - scan_range, - frame_index_range, - &mut |peak| agg.add(&RawPeak::from(peak)), + // for i in 0..prec_mz_ranges.len() { + // if !matches_quad_settings(quad_setting, prec_mz_ranges[i], scan_ranges[i]) { + // continue; + // } + + // for (fh, tof_range) in fragment_queries[i].mz_index_ranges.iter() { + // let mut local_lambda = |peak| aggregator[i].add(&(RawPeak::from(peak), *fh)); + // tqi.query_peaks( + // *tof_range, + // scan_ranges[i], + // frame_index_ranges[i], + // &mut local_lambda, + // ) + // } + // } + + aggregator.par_iter_mut().enumerate().for_each(|(i, agg)| { + if !matches_quad_settings(quad_setting, prec_mz_ranges[i], scan_ranges[i]) { + return; + } + + for (fh, tof_range) in fragment_queries[i].mz_index_ranges.iter() { + let mut local_lambda = |peak| agg.add(&(RawPeak::from(peak), *fh)); + tqi.query_peaks( + *tof_range, + scan_ranges[i], + frame_index_ranges[i], + &mut local_lambda, ); } }); + } } } -// ============================================================================ - impl ToleranceAdapter, ElutionGroup> for ExpandedRawFrameIndex { diff --git a/src/models/indices/raw_file_index.rs b/src/models/indices/raw_file_index.rs index 133e406..462ff87 100644 --- a/src/models/indices/raw_file_index.rs +++ b/src/models/indices/raw_file_index.rs @@ -1,10 +1,8 @@ -use std::sync::Arc; - use crate::models::frames::raw_frames::frame_elems_matching; use crate::models::frames::raw_peak::RawPeak; use crate::models::queries::{FragmentGroupIndexQuery, NaturalPrecursorQuery, PrecursorIndexQuery}; use crate::traits::aggregator::Aggregator; -use crate::traits::indexed_data::QueriableData; +use crate::traits::queriable_data::QueriableData; use crate::ElutionGroup; use crate::ToleranceAdapter; use rayon::iter::ParallelIterator; @@ -40,6 +38,7 @@ impl RawFileIndex { self.meta_converters.rt_converter.invert(query.rt_range.0) as usize, self.meta_converters.rt_converter.invert(query.rt_range.1) as usize, ), + rt_range_seconds: query.rt_range, mz_index_range: ( self.meta_converters.mz_converter.invert(query.mz_range.0) as u32, self.meta_converters.mz_converter.invert(query.mz_range.1) as u32, @@ -64,7 +63,7 @@ impl RawFileIndex { >( &'a self, fqs: &'b FragmentGroupIndexQuery, - fun: &'c mut dyn for<'r> FnMut(RawPeak, Arc), + fun: &'c mut dyn for<'r> FnMut(RawPeak, FH), ) { trace!("RawFileIndex::apply_on_query"); trace!("FragmentGroupIndexQuery: {:?}", fqs); @@ -77,7 +76,7 @@ impl RawFileIndex { let pq = &fqs.precursor_query; let iso_mz_range = pq.isolation_mz_range; for frame in frames { - for (_, tof_range) in fqs.mz_index_ranges.iter() { + for (fh, tof_range) in fqs.mz_index_ranges.iter() { let scan_range = pq.mobility_index_range; let peaks = frame_elems_matching( &frame, @@ -86,7 +85,7 @@ impl RawFileIndex { Some((iso_mz_range.0 as f64, iso_mz_range.1 as f64)), ); for peak in peaks { - fun(peak, frame.quadrupole_settings.clone()); + fun(peak, *fh); } } } @@ -139,6 +138,7 @@ impl RawFileIndex { self.meta_converters.rt_converter.invert(rt_range.0) as usize, self.meta_converters.rt_converter.invert(rt_range.1) as usize, ), + rt_range_seconds: rt_range, mz_index_range: ( self.meta_converters.mz_converter.invert(mz_range.0) as u32, self.meta_converters.mz_converter.invert(mz_range.1) as u32, @@ -185,23 +185,23 @@ impl RawFileIndex { } impl - QueriableData, RawPeak> for RawFileIndex + QueriableData, (RawPeak, FH)> for RawFileIndex { - fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { + fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { let mut out = Vec::new(); - self.apply_on_query(fragment_query, &mut |peak, _| out.push(peak)); + self.apply_on_query(fragment_query, &mut |x, y| out.push((x, y))); out } - fn add_query>( + fn add_query>( &self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG, ) { - self.apply_on_query(fragment_query, &mut |peak, _| aggregator.add(&peak)); + self.apply_on_query(fragment_query, &mut |x, y| aggregator.add(&(x, y))); } - fn add_query_multi_group>( + fn add_query_multi_group>( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index 492acce..b5b601d 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -74,17 +74,12 @@ impl TransposedQuadIndex { &self, tof_range: (u32, u32), scan_range: Option<(usize, usize)>, - rt_range: Option, + rt_range: Option<(f32, f32)>, ) -> impl Iterator + '_ { - // This version is not compatible with the borrow checker unless I collect the vec... - // which will do for now for prototyping. - // TODO: make this a single type and convert upstream. - let frame_index_range = self.convert_to_local_frame_range(rt_range); - self.peak_buckets .range(tof_range.0..tof_range.1) .flat_map(move |(tof_index, pb)| { - pb.query_peaks(scan_range, frame_index_range) + pb.query_peaks(scan_range, rt_range) .map(move |p| PeakInQuad::from_peak_in_bucket(p, *tof_index)) }) } @@ -199,7 +194,14 @@ impl TransposedQuadIndexBuilder { self.frame_rts.push(slice.rt); } - #[instrument(skip(self))] + #[instrument( + name = "TransposedQuadIndex::build", + skip(self), + fields( + num_frames = %self.frame_indices.len(), + quad_settings = format!("{:?}", self.quad_settings), + ) + )] pub fn build(self) -> TransposedQuadIndex { // TODO: Refactor this function, its getting pretty large. let max_tof = *self @@ -279,6 +281,15 @@ impl TransposedQuadIndexBuilder { } } + #[instrument( + name = "TransposedQuadIndex::build_inner_ref", + skip(self, peak_buckets), + fields( + num_frames = %self.frame_indices.len(), + quad_settings = format!("{:?}", self.quad_settings), + peak_buckets = %peak_buckets.len(), + ) + )] fn build_inner_ref( self, mut peak_buckets: HashMap, @@ -338,6 +349,15 @@ impl TransposedQuadIndexBuilder { peak_buckets } + #[instrument( + name = "TransposedQuadIndex::batched_build_inner", + skip(self, peak_buckets), + fields( + num_frames = %self.frame_indices.len(), + quad_settings = format!("{:?}", self.quad_settings), + peak_buckets = %peak_buckets.len(), + ) + )] fn batched_build_inner( self, mut peak_buckets: HashMap, @@ -384,23 +404,6 @@ impl TransposedQuadIndexBuilder { let mut slice_start = 0; let mut slice_start_val = tof_slice[0]; while slice_start < int_slice.len() { - // // Binary search the current value + 1 - // let slice_end = tof_slice.binary_search(&(slice_start_val + 1)); - - // // let local_slice_end = slice_end.unwrap_or_else(|x| x); - // let local_slice_end = match slice_end { - // Ok(x) => { - // // If the value is found, we need to walk back to find the first instance - // // of the value ... - // let mut local_slice_end = x; - // while tof_slice[local_slice_end - 1] > slice_start_val { - // local_slice_end -= 1; - // } - // local_slice_end - // } - // Err(x) => x, - // }; - // let mut local_slice_end = slice_start; while tof_slice[local_slice_end] == slice_start_val { local_slice_end += 1; @@ -424,12 +427,18 @@ impl TransposedQuadIndexBuilder { added_peaks += range_use.len() as u64; - assert!(slice_start_val == tof_slice[slice_start]); + assert!( + slice_start_val == tof_slice[slice_start], + "Not all elements in slice have the same tof value" + ); if local_slice_end == tof_slice.len() { break; } - assert!(slice_start_val < tof_slice[local_slice_end]); + assert!( + slice_start_val < tof_slice[local_slice_end], + "The next element after this slice should have a higher tof value" + ); slice_start = local_slice_end; slice_start_val = tof_slice[slice_start]; diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 7c96e34..8d1dc80 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -2,8 +2,8 @@ use super::quad_index::{FrameRTTolerance, TransposedQuadIndex, TransposedQuadInd use crate::models::adapters::FragmentIndexAdapter; use crate::models::elution_group::ElutionGroup; use crate::models::frames::expanded_frame::{ - expand_and_split_frame, par_read_and_expand_frames, DataReadingError, ExpandedFrameSlice, - FrameProcessingConfig, SortingStateTrait, + par_read_and_expand_frames, DataReadingError, ExpandedFrameSlice, FrameProcessingConfig, + SortingStateTrait, }; use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::raw_peak::RawPeak; @@ -11,7 +11,7 @@ use crate::models::frames::single_quad_settings::{ get_matching_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, }; use crate::models::queries::FragmentGroupIndexQuery; -use crate::traits::indexed_data::QueriableData; +use crate::traits::queriable_data::QueriableData; use crate::utils::display::{glimpse_vec, GlimpseConfig}; use crate::ToleranceAdapter; use rayon::prelude::*; @@ -23,7 +23,6 @@ use std::hash::Hash; use std::time::Instant; use timsrust::converters::{Frame2RtConverter, Scan2ImConverter, Tof2MzConverter}; use timsrust::readers::{FrameReader, MetadataReader}; -use timsrust::Frame; use timsrust::Metadata; use timsrust::TimsRustError; use tracing::instrument; @@ -58,7 +57,7 @@ impl QuadSplittedTransposedIndex { tof_range: (u32, u32), precursor_mz_range: (f64, f64), scan_range: Option<(usize, usize)>, - rt_range: Option, + rt_range_seconds: Option<(f32, f32)>, f: &mut F, ) where F: FnMut(PeakInQuad), @@ -67,7 +66,7 @@ impl QuadSplittedTransposedIndex { .get_matching_quad_settings(precursor_mz_range, scan_range) .collect(); trace!("matching_quads: {:?}", matching_quads); - self.query_precursor_peaks(&matching_quads, tof_range, scan_range, rt_range, f); + self.query_precursor_peaks(&matching_quads, tof_range, scan_range, rt_range_seconds, f); } fn query_precursor_peaks( @@ -75,7 +74,7 @@ impl QuadSplittedTransposedIndex { matching_quads: &[SingleQuadrupoleSettingIndex], tof_range: (u32, u32), scan_range: Option<(usize, usize)>, - rt_range: Option, + rt_range_seconds: Option<(f32, f32)>, f: &mut F, ) where F: FnMut(PeakInQuad), @@ -85,7 +84,7 @@ impl QuadSplittedTransposedIndex { .fragment_indices .get(quad) .expect("Only existing quads should be queried."); - tqi.query_peaks(tof_range, scan_range, rt_range) + tqi.query_peaks(tof_range, scan_range, rt_range_seconds) .for_each(&mut *f); } } @@ -242,6 +241,8 @@ impl QuadSplittedTransposedIndexBuilder { let out2: Result, TimsRustError> = split_frames .into_par_iter() .map(|(q, frameslices)| { + // TODO:Refactor so the internal index is built first and then added. + // This should save a couple of thousand un-necessary hashmap lookups. let mut out = Self::new(); for frameslice in frameslices { out.add_frame_slice(frameslice); @@ -308,100 +309,6 @@ impl QuadSplittedTransposedIndexBuilder { } } -impl - QueriableData, RawPeak> for QuadSplittedTransposedIndex -{ - fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { - let precursor_mz_range = ( - fragment_query.precursor_query.isolation_mz_range.0 as f64, - fragment_query.precursor_query.isolation_mz_range.0 as f64, - ); - let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - let frame_index_range = Some(FrameRTTolerance::FrameIndex( - fragment_query.precursor_query.frame_index_range, - )); - - fragment_query - .mz_index_ranges - .iter() - .flat_map(|(_, tof_range)| { - let mut local_vec = vec![]; - self.query_peaks( - *tof_range, - precursor_mz_range, - scan_range, - frame_index_range, - &mut |x| local_vec.push(RawPeak::from(x)), - ); - local_vec.into_iter() - }) - .collect() - } - - fn add_query>( - &self, - fragment_query: &FragmentGroupIndexQuery, - aggregator: &mut AG, - ) { - let precursor_mz_range = ( - fragment_query.precursor_query.isolation_mz_range.0 as f64, - fragment_query.precursor_query.isolation_mz_range.0 as f64, - ); - let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - let frame_index_range = Some(FrameRTTolerance::FrameIndex( - fragment_query.precursor_query.frame_index_range, - )); - - fragment_query - .mz_index_ranges - .iter() - .for_each(|(_, tof_range)| { - self.query_peaks( - *tof_range, - precursor_mz_range, - scan_range, - frame_index_range, - &mut |peak| aggregator.add(&RawPeak::from(peak)), - ); - }) - } - - fn add_query_multi_group>( - &self, - fragment_queries: &[FragmentGroupIndexQuery], - aggregator: &mut [AG], - ) { - fragment_queries - .par_iter() - .zip(aggregator.par_iter_mut()) - .for_each(|(fragment_query, agg)| { - let precursor_mz_range = ( - fragment_query.precursor_query.isolation_mz_range.0 as f64, - fragment_query.precursor_query.isolation_mz_range.1 as f64, - ); - assert!(precursor_mz_range.0 <= precursor_mz_range.1); - assert!(precursor_mz_range.0 > 0.0); - let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - let frame_index_range = Some(FrameRTTolerance::FrameIndex( - fragment_query.precursor_query.frame_index_range, - )); - - for (_, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { - self.query_peaks( - tof_range, - precursor_mz_range, - scan_range, - frame_index_range, - &mut |peak| agg.add(&RawPeak::from(peak)), - ); - } - }); - } -} - -// Copy pasting for now ... TODO refactor or delete -// ============================================================================ - impl QueriableData, (RawPeak, FH)> for QuadSplittedTransposedIndex { @@ -411,9 +318,6 @@ impl fragment_query.precursor_query.isolation_mz_range.0 as f64, ); let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - let frame_index_range = Some(FrameRTTolerance::FrameIndex( - fragment_query.precursor_query.frame_index_range, - )); fragment_query .mz_index_ranges @@ -424,7 +328,7 @@ impl *tof_range, precursor_mz_range, scan_range, - frame_index_range, + Some(fragment_query.precursor_query.rt_range_seconds), &mut |x| local_vec.push((RawPeak::from(x), *fh)), ); @@ -443,9 +347,6 @@ impl fragment_query.precursor_query.isolation_mz_range.0 as f64, ); let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - let frame_index_range = Some(FrameRTTolerance::FrameIndex( - fragment_query.precursor_query.frame_index_range, - )); fragment_query .mz_index_ranges @@ -455,7 +356,7 @@ impl *tof_range, precursor_mz_range, scan_range, - frame_index_range, + Some(fragment_query.precursor_query.rt_range_seconds), &mut |peak| aggregator.add(&(RawPeak::from(peak), *fh)), ); }) @@ -477,9 +378,6 @@ impl assert!(precursor_mz_range.0 <= precursor_mz_range.1); assert!(precursor_mz_range.0 > 0.0); let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - let frame_index_range = Some(FrameRTTolerance::FrameIndex( - fragment_query.precursor_query.frame_index_range, - )); let local_quad_vec: Vec = self .get_matching_quad_settings(precursor_mz_range, scan_range) @@ -490,7 +388,7 @@ impl &local_quad_vec, tof_range, scan_range, - frame_index_range, + Some(fragment_query.precursor_query.rt_range_seconds), &mut |peak| agg.add(&(RawPeak::from(peak), fh)), ); } @@ -498,8 +396,6 @@ impl } } -// ============================================================================ - impl ToleranceAdapter, ElutionGroup> for QuadSplittedTransposedIndex diff --git a/src/models/queries.rs b/src/models/queries.rs index 8813111..dc3b9ea 100644 --- a/src/models/queries.rs +++ b/src/models/queries.rs @@ -4,6 +4,7 @@ use std::hash::Hash; #[derive(Debug, Clone)] pub struct PrecursorIndexQuery { pub frame_index_range: (usize, usize), + pub rt_range_seconds: (f32, f32), pub mz_index_range: (u32, u32), pub mobility_index_range: (usize, usize), pub isolation_mz_range: (f32, f32), diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index 2595405..2e4a79a 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -5,103 +5,53 @@ use std::rc::Rc; use std::time::Instant; use tracing::info; -use crate::{Aggregator, ElutionGroup, HasIntegerID, QueriableData, Tolerance, ToleranceAdapter}; - -/// A struct that can be queried for TIMS data. -/// -/// The main idea behind this struct is to provide a generic way to query TIMS data. -/// And by that I mean that with the same interface but different imeplementations -/// on the indexing one can optimize for different access patterns. -/// -/// In the same way different aggregators can be used to aggregate the results. -/// In some cases just adding the intensities might be enough, but in other cases -/// one might want to do more complex operations. (fitting a gaussian to a chromatogram for example) -/// -/// Main Generic parameters: -/// - `ID`: The type of indexed data that will be queried. -/// This can also optimize the access pattern to the data. When the data is queried -/// with the `many` version of the query functions, the indexed data can optimize -/// the access pattern to the data. -/// - `TA`: The type of tolerance adapter that will be used to convert elution groups into queries. -/// - `TL`: The type of tolerance that will be used to define the search space. -/// -/// Additional Generic parameters: -/// - `QP`: The type of precursor query that will be used to query the indexed data. -/// - `QF`: The type of fragment query that will be used to query the indexed data. -/// - `OE`: The type of output element that will be returned by the aggregators. -/// - `AG`: The type of aggregator that will be used to aggregate the output elements. -/// - `AE`: The type of element that will be aggregated. -/// -/// -/// So ... in other words ... -/// 1. `TA` converts `ElutionGroup` with `TL` into `QP` and `QF` queries. -/// 2. `ID` is queried with `QP` and `QF` queries. -/// 3. The results are aggregated with `AG` aggregators (which are generated by the factory, when passed a numeric ID). -pub struct QueriableTimsData<'a, ID, TA, TL, QF, AE, OE, AG, EG: HasIntegerID> -where - AG: Aggregator + Send + Sync, - ID: QueriableData, - TA: ToleranceAdapter, - TL: Tolerance, - QF: Send + Sync, - AE: Send + Sync + Clone + Copy, -{ - pub indexed_data: &'a ID, - pub aggregator_factory: &'a dyn Fn(u64) -> AG, - pub tolerance_adapter: &'a TA, - pub tolerance: &'a TL, - pub _phantom_queries: std::marker::PhantomData, - pub _phatom_agg: std::marker::PhantomData<(AE, OE, AG)>, - pub _phatom_elution_group: std::marker::PhantomData, -} - -impl<'a, ID, TA, TL, QF, AE, OE, AG, EG> QueriableTimsData<'a, ID, TA, TL, QF, AE, OE, AG, EG> -where - AG: Aggregator + Send + Sync, - ID: QueriableData, - TA: ToleranceAdapter, - TL: Tolerance, - EG: HasIntegerID, - QF: Send + Sync, - AE: Send + Sync + Clone + Copy, -{ - pub fn query(&self, elution_group: &EG) -> OE { - let mut aggregator = (self.aggregator_factory)(elution_group.get_id()); - let prep_query = self - .tolerance_adapter - .query_from_elution_group(self.tolerance, elution_group); - - self.indexed_data.add_query(&prep_query, &mut aggregator); - aggregator.finalize() - } - - pub fn add_query_multi_group(&self, elution_groups: &[EG], aggregators: &mut [AG]) { - let mut fragment_queries = Vec::with_capacity(elution_groups.len()); - - for elution_group in elution_groups { - let qf = self - .tolerance_adapter - .query_from_elution_group(self.tolerance, elution_group); - - fragment_queries.push(qf); - } - - self.indexed_data - .add_query_multi_group(&fragment_queries, aggregators); - } -} - -pub fn query_multi_group<'a, ID, TA, TL, QF, AE, OE, AG, FH>( - indexed_data: &'a ID, - tolerance_adapter: &'a TA, +use crate::{Aggregator, ElutionGroup, QueriableData, Tolerance, ToleranceAdapter}; + +// TODO: URGENTLY make documentation fot eh functions using this leftover struct docs +// as a reference. +// +// A struct that can be queried for TIMS data. +// +// The main idea behind this struct is to provide a generic way to query TIMS data. +// And by that I mean that with the same interface but different imeplementations +// on the indexing one can optimize for different access patterns. +// +// In the same way different aggregators can be used to aggregate the results. +// In some cases just adding the intensities might be enough, but in other cases +// one might want to do more complex operations. (fitting a gaussian to a chromatogram for example) +// +// Main Generic parameters: +// - `QD`: The type of indexed data that will be queried. +// This can also optimize the access pattern to the data. When the data is queried +// with the `many` version of the query functions, the indexed data can optimize +// the access pattern to the data. +// +// also implements tolerance adapter that will be used to convert elution groups +// into queries. +// - `TL`: The type of tolerance that will be used to define the search space. +// +// Additional Generic parameters: +// - `QP`: The type of precursor query that will be used to query the indexed data. +// - `QF`: The type of fragment query that will be used to query the indexed data. +// - `OE`: The type of output element that will be returned by the aggregators. +// - `AG`: The type of aggregator that will be used to aggregate the output elements. +// - `AE`: The type of element that will be aggregated. +// +// +// So ... in other words ... +// 1. `TA` converts `ElutionGroup` with `TL` into `QP` and `QF` queries. +// 2. `QD` is queried with `QP` and `QF` queries. +// 3. The results are aggregated with `AG` aggregators (which are generated by the factory, when passed a numeric ID). + +pub fn query_multi_group<'a, QD, TL, QF, AE, OE, AG, FH>( + queriable_data: &'a QD, tolerance: &'a TL, elution_groups: &[ElutionGroup], aggregator_factory: &dyn Fn(u64) -> AG, ) -> Vec where AG: Aggregator + Send + Sync, - ID: QueriableData, - TA: ToleranceAdapter>, + QD: QueriableData + ToleranceAdapter>, TL: Tolerance, OE: Send + Sync, FH: Clone + Eq + Serialize + Hash + Send + Sync, @@ -113,13 +63,13 @@ where let mut aggregators = Vec::with_capacity(elution_groups.len()); for (i, elution_group) in elution_groups.iter().enumerate() { - let qp = tolerance_adapter.query_from_elution_group(tolerance, elution_group); + let qp = queriable_data.query_from_elution_group(tolerance, elution_group); fragment_queries.push(qp); aggregators.push(aggregator_factory(i as u64)); } - indexed_data.add_query_multi_group(&fragment_queries, &mut aggregators); + queriable_data.add_query_multi_group(&fragment_queries, &mut aggregators); let duration = start.elapsed(); info!("Querying took {:#?}", duration); @@ -140,8 +90,8 @@ where out } -pub fn query_indexed( - indexed_data: &ID, +pub fn query_indexed( + queriable_data: &QD, aggregator_factory: &dyn Fn(u64) -> AG, tolerance_adapter: &TA, tolerance: &TL, @@ -149,7 +99,7 @@ pub fn query_indexed( ) -> OE where AG: Aggregator + Send + Sync, - ID: QueriableData, + QD: QueriableData, TA: ToleranceAdapter>, TL: Tolerance, FH: Clone + Eq + Serialize + Hash + Send + Sync, @@ -159,6 +109,6 @@ where let mut aggregator = aggregator_factory(elution_group.id); let prep_query = Rc::new(tolerance_adapter.query_from_elution_group(tolerance, elution_group)); - indexed_data.add_query(&prep_query, &mut aggregator); + queriable_data.add_query(&prep_query, &mut aggregator); aggregator.finalize() } diff --git a/src/traits/indexed_data.rs b/src/traits/indexed_data.rs deleted file mode 100644 index a1ce16f..0000000 --- a/src/traits/indexed_data.rs +++ /dev/null @@ -1,19 +0,0 @@ -use crate::Aggregator; - -pub trait QueriableData -where - QF: Send + Sync, - A: Send + Sync + Clone + Copy, -{ - fn query(&self, fragment_query: &QF) -> Vec; - fn add_query>( - &self, - fragment_query: &QF, - aggregator: &mut AG, - ); - fn add_query_multi_group>( - &self, - fragment_queries: &[QF], - aggregator: &mut [AG], - ); -} diff --git a/src/traits/mod.rs b/src/traits/mod.rs index 9a7266a..4e3908c 100644 --- a/src/traits/mod.rs +++ b/src/traits/mod.rs @@ -1,3 +1,3 @@ pub mod aggregator; -pub mod indexed_data; +pub mod queriable_data; pub mod tolerance; diff --git a/src/traits/queriable_data.rs b/src/traits/queriable_data.rs new file mode 100644 index 0000000..07d5a91 --- /dev/null +++ b/src/traits/queriable_data.rs @@ -0,0 +1,53 @@ +use super::tolerance::ToleranceAdapter; +use crate::models::elution_group::ElutionGroup; +use crate::Aggregator; + +pub trait QueriableData +where + QF: Send + Sync, + A: Send + Sync + Clone + Copy, +{ + fn query(&self, fragment_query: &QF) -> Vec; + fn add_query>( + &self, + fragment_query: &QF, + aggregator: &mut AG, + ); + fn add_query_multi_group>( + &self, + fragment_queries: &[QF], + aggregator: &mut [AG], + ); +} + +// I like this idea but I need a way to set/propagate the tolerance +// +// impl>, QF, A, K> QueriableData for T { +// fn query(&self, fragment_query: &QF) -> Vec { +// let mut out = Vec::new(); +// let qf = self.query_from_elution_group(fragment_query); +// self.add_query(&qf, &mut |x| out.push(x)); +// out +// } +// +// fn add_query>( +// &self, +// fragment_query: &QF, +// aggregator: &mut AG, +// ) { +// let qf = self.query_from_elution_group(fragment_query); +// self.add_query(&qf, aggregator); +// } +// +// fn add_query_multi_group>( +// &self, +// fragment_queries: &[QF], +// aggregator: &mut [AG], +// ) { +// let qfs = fragment_queries +// .iter() +// .map(|x| self.query_from_elution_group(x)) +// .collect(); +// self.add_query_multi_group(&qfs, aggregator); +// } +// } diff --git a/src/traits/tolerance.rs b/src/traits/tolerance.rs index b02dcfa..0e4a2f3 100644 --- a/src/traits/tolerance.rs +++ b/src/traits/tolerance.rs @@ -113,12 +113,11 @@ impl Tolerance for DefaultTolerance { } } -// TODO decide whether to kill this one or to change the interrface -// and how to propagate identifiers. -pub trait HasIntegerID { - fn get_id(&self) -> u64; -} - -pub trait ToleranceAdapter { +/// A trait that can be implemented by types that can convert +/// elution groups into queries. +/// +/// The elution group here is generic but most regularly it will be +/// an `ElutionGroup` struct. +pub trait ToleranceAdapter { fn query_from_elution_group(&self, tol: &dyn Tolerance, elution_group: &T) -> QF; } diff --git a/src/utils/frame_processing.rs b/src/utils/frame_processing.rs index 82c5ce0..6e2c090 100644 --- a/src/utils/frame_processing.rs +++ b/src/utils/frame_processing.rs @@ -1,5 +1,4 @@ use crate::sort_vecs_by_first; -use std::cmp::Ordering; use std::ops::RangeInclusive; use tracing::{error, info, warn}; @@ -57,29 +56,6 @@ impl<'a> PeakArrayRefs<'a> { } } -/// Splits a global index into a major and minor that -/// matches elements in a collection. -/// -/// As an example if there is a slice of slices, the major index -/// is the index of the slice and the minor index is the index -/// of the element in the slice. -/// -/// Thus if we have [[0,1,2], [3,4,5], [6,7,8]] -/// the major indice are 0,0,0 1,1,1 2,2,2 -/// and the minor 0,1,2 0,1,2 0,1,2 -/// -/// -fn index_split(index: usize, slice_sizes: &[usize]) -> (usize, usize) { - let mut index = index; - for (i, slice_size) in slice_sizes.iter().enumerate() { - if index < *slice_size { - return (i, index); - } - index -= *slice_size; - } - panic!("Index {} is out of bounds", index); -} - // TODO: Refactor this function pub fn lazy_centroid_weighted_frame<'a>( peak_refs: &'a [PeakArrayRefs<'a>], diff --git a/src/utils/sorting.rs b/src/utils/sorting.rs index d67d691..c35b22a 100644 --- a/src/utils/sorting.rs +++ b/src/utils/sorting.rs @@ -44,8 +44,57 @@ macro_rules! sort_vecs_by_first { }}; } +/// Returns the top n elements of a slice. +/// +/// The indices of the elements are also returned. +/// +/// # Example +/// ``` +/// use timsquery::utils::sorting::top_n; +/// +/// let v = vec![1, 2, 10, 4, 5, 9, 7, 8, 2, 1]; +/// let (top, indices) = top_n(&v, 3); +/// assert_eq!(top, vec![10, 9, 8]); +/// assert_eq!(indices, vec![2, 5, 7]); +/// ``` +/// +/// https://users.rust-lang.org/t/solved-best-way-to-find-largest-three-values-in-unsorted-slice/34754/12 +pub fn top_n(slice: &[u32], n: usize) -> (Vec, Vec) { + let mut result = Vec::with_capacity(n + 1); + let mut result_indices = Vec::with_capacity(n + 1); + for (ind, v) in slice.iter().copied().enumerate() { + result.push(v); + result_indices.push(ind); + + let mut i = result.len() - 1; + while i > 0 { + if result[i] <= result[i - 1] { + break; + } + + // swap + let t = result[i]; + let tind = result_indices[i]; + result[i] = result[i - 1]; + result[i - 1] = t; + result_indices[i] = result_indices[i - 1]; + result_indices[i - 1] = tind; + + i -= 1; + } + + if result.len() > n { + result.pop(); + result_indices.pop(); + } + } + (result, result_indices) +} + #[cfg(test)] mod tests { + use super::*; + #[test] fn test_sort_two_vecs() { let v1 = vec![3, 1, 4, 1, 5]; @@ -84,4 +133,12 @@ mod tests { assert_eq!(sorted_v3, vec![false, true, true]); assert_eq!(sorted_v4, vec![2.0, 1.0, 3.0]); } + + #[test] + fn test_top_n() { + let v = vec![1, 2, 3, 4, 5, 6, 7, 8, 9, 10]; + let (top, indices) = top_n(&v, 3); + assert_eq!(top, vec![10, 9, 8]); + assert_eq!(indices, vec![9, 8, 7]); + } } From faf46820325a45f74cfa5d3b2770d90f20344cfb Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Wed, 30 Oct 2024 03:31:58 -0700 Subject: [PATCH 11/30] chore(benchmarks): updated benchmarks --- README.md | 4 + Taskfile.yml | 7 +- ..._results_230510_PRTC_13_S1-B1_1_12817.json | 127 ++++++------------ ..._diaPASEF_Condition_A_Sample_Alpha_02.json | 50 +++---- src/models/frames/expanded_frame.rs | 1 - src/utils/frame_processing.rs | 16 ++- 6 files changed, 86 insertions(+), 119 deletions(-) diff --git a/README.md b/README.md index ed47c00..8a21978 100644 --- a/README.md +++ b/README.md @@ -32,3 +32,7 @@ sequential, use that). ## What does the cli look like right now? + +## TODO: + +- Add logging levels to instrumentations. diff --git a/Taskfile.yml b/Taskfile.yml index d08501b..cb7d494 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -40,9 +40,14 @@ tasks: - cargo clippy bench: + sources: + - "src/**/*.rs" cmds: - - SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d cargo run --release --features bench --bin benchmark_indices + - cargo b --release --features bench --bin benchmark_indices + - SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d ./target/release/benchmark_indices + - SKIP_SLOW=1 SKIP_BUILD=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/230510_PRTC_13_S1-B1_1_12817.d ./target/release/benchmark_indices - uv run benches/plot_bench.py data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json + - uv run benches/plot_bench.py data/benchmark_results_230510_PRTC_13_S1-B1_1_12817.json templates: sources: diff --git a/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json index 1b5d19d..fbd58df 100644 --- a/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json +++ b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json @@ -4,135 +4,90 @@ "num_iterations": 1 }, "results": [ - { - "name": "RawFileIndex", - "context": "Encoding", - "mean_duration_seconds": 0.006222996397515529, - "mean_duration_human_readable": "6.222996ms", - "setup_time_seconds": 4.833e-6, - "setup_time_human_readable": "4.833µs", - "note": null - }, - { - "name": "ExpandedRawFileIndexCentroided", - "context": "Encoding", - "mean_duration_seconds": 97.626668625, - "mean_duration_human_readable": "97.626668625s", - "setup_time_seconds": 9.17e-7, - "setup_time_human_readable": "917ns", - "note": null - }, - { - "name": "ExpandedRawFileIndex", - "context": "Encoding", - "mean_duration_seconds": 8.102684125, - "mean_duration_human_readable": "8.102684125s", - "setup_time_seconds": 1.042e-6, - "setup_time_human_readable": "1.042µs", - "note": null - }, - { - "name": "TransposedQuadIndex", - "context": "Encoding", - "mean_duration_seconds": 74.288219334, - "mean_duration_human_readable": "74.288219334s", - "setup_time_seconds": 1e-6, - "setup_time_human_readable": "1µs", - "note": null - }, - { - "name": "TransposedQuadIndexCentroided", - "context": "Encoding", - "mean_duration_seconds": 103.221435875, - "mean_duration_human_readable": "103.221435875s", - "setup_time_seconds": 9.58e-7, - "setup_time_human_readable": "958ns", - "note": null - }, { "name": "RawFileIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 30.1034345, - "mean_duration_human_readable": "30.1034345s", - "setup_time_seconds": 0.080088542, - "setup_time_human_readable": "80.088542ms", + "mean_duration_seconds": 39.59563725, + "mean_duration_human_readable": "39.59563725s", + "setup_time_seconds": 0.080144208, + "setup_time_human_readable": "80.144208ms", "note": "RawFileIndex::query_multi_group aggregated 71227 " }, { "name": "ExpandedRawFileIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.0043137600000000016, - "mean_duration_human_readable": "4.31376ms", - "setup_time_seconds": 5.777069208, - "setup_time_human_readable": "5.777069208s", + "mean_duration_seconds": 0.0029533639321533945, + "mean_duration_human_readable": "2.953363ms", + "setup_time_seconds": 7.448746083, + "setup_time_human_readable": "7.448746083s", "note": "ExpandedRawFileIndex::query_multi_group aggregated 68449 " }, { "name": "ExpandedRawFileIndex", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 1.389402875, - "mean_duration_human_readable": "1.389402875s", - "setup_time_seconds": 5.838487875, - "setup_time_human_readable": "5.838487875s", + "mean_duration_seconds": 0.3531393056666667, + "mean_duration_human_readable": "353.139305ms", + "setup_time_seconds": 6.922591083, + "setup_time_human_readable": "6.922591083s", "note": "ExpandedRawFileIndex::query_multi_group aggregated 10744180 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.003144791757009347, - "mean_duration_human_readable": "3.144791ms", - "setup_time_seconds": 89.554111875, - "setup_time_human_readable": "89.554111875s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 26179 " + "mean_duration_seconds": 0.0017233227263339077, + "mean_duration_human_readable": "1.723322ms", + "setup_time_seconds": 93.177977, + "setup_time_human_readable": "93.177977s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 25111 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.2185190752, - "mean_duration_human_readable": "218.519075ms", - "setup_time_seconds": 88.279319125, - "setup_time_human_readable": "88.279319125s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 5775312 " + "mean_duration_seconds": 0.06051568876470587, + "mean_duration_human_readable": "60.515688ms", + "setup_time_seconds": 88.266641959, + "setup_time_human_readable": "88.266641959s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 5714405 " }, { "name": "TransposedQuadIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.003314156013245034, - "mean_duration_human_readable": "3.314156ms", - "setup_time_seconds": 62.383771084, - "setup_time_human_readable": "62.383771084s", + "mean_duration_seconds": 0.0015990381517571877, + "mean_duration_human_readable": "1.599038ms", + "setup_time_seconds": 60.422055292, + "setup_time_human_readable": "60.422055292s", "note": "TransposedQuadIndex::query_multi_group aggregated 64676 " }, { "name": "TransposedQuadIndex", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.003775450037735844, - "mean_duration_human_readable": "3.77545ms", - "setup_time_seconds": 59.13618275, - "setup_time_human_readable": "59.13618275s", + "mean_duration_seconds": 0.0022858289497716907, + "mean_duration_human_readable": "2.285828ms", + "setup_time_seconds": 59.177824542, + "setup_time_human_readable": "59.177824542s", "note": "TransposedQuadIndex::query_multi_group aggregated 9971215 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.001552562270769231, - "mean_duration_human_readable": "1.552562ms", - "setup_time_seconds": 98.014544042, - "setup_time_human_readable": "98.014544042s", - "note": "TransposedQuadIndex::query_multi_group aggregated 22454 " + "mean_duration_seconds": 0.0009990033406593406, + "mean_duration_human_readable": "999.003µs", + "setup_time_seconds": 111.4298805, + "setup_time_human_readable": "111.4298805s", + "note": "TransposedQuadIndex::query_multi_group aggregated 25626 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.001730233717993079, - "mean_duration_human_readable": "1.730233ms", - "setup_time_seconds": 98.609288084, - "setup_time_human_readable": "98.609288084s", - "note": "TransposedQuadIndex::query_multi_group aggregated 5282090 " + "mean_duration_seconds": 0.0008020078941459505, + "mean_duration_human_readable": "802.007µs", + "setup_time_seconds": 120.050409959, + "setup_time_human_readable": "120.050409959s", + "note": "TransposedQuadIndex::query_multi_group aggregated 5257955 " } ], "metadata": { "basename": "230510_PRTC_13_S1-B1_1_12817" }, - "full_benchmark_time_seconds": 843.833114208 + "full_benchmark_time_seconds": 619.527993583 } \ No newline at end of file diff --git a/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json b/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json index edbebb6..3ae51d7 100644 --- a/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json +++ b/data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json @@ -7,51 +7,51 @@ { "name": "RawFileIndex", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 3.923214042, - "mean_duration_human_readable": "3.923214042s", - "setup_time_seconds": 0.236783083, - "setup_time_human_readable": "236.783083ms", + "mean_duration_seconds": 4.031142541, + "mean_duration_human_readable": "4.031142541s", + "setup_time_seconds": 0.243732333, + "setup_time_human_readable": "243.732333ms", "note": "RawFileIndex::query_multi_group aggregated 9144 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.0009338467012138191, - "mean_duration_human_readable": "933.846µs", - "setup_time_seconds": 470.779360458, - "setup_time_human_readable": "470.779360458s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 1505 " + "mean_duration_seconds": 0.0019490771459143978, + "mean_duration_human_readable": "1.949077ms", + "setup_time_seconds": 487.943830709, + "setup_time_human_readable": "487.943830709s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 1230 " }, { "name": "ExpandedRawFileIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 16.197693792, - "mean_duration_human_readable": "16.197693792s", - "setup_time_seconds": 487.496389916, - "setup_time_human_readable": "487.496389916s", - "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 213765098 " + "mean_duration_seconds": 13.260161042, + "mean_duration_human_readable": "13.260161042s", + "setup_time_seconds": 523.69316175, + "setup_time_human_readable": "523.69316175s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 203755782 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_narrow_rt", - "mean_duration_seconds": 0.003893406926070039, - "mean_duration_human_readable": "3.893406ms", - "setup_time_seconds": 530.744600625, - "setup_time_human_readable": "530.744600625s", - "note": "TransposedQuadIndex::query_multi_group aggregated 1347 " + "mean_duration_seconds": 0.003312026207792206, + "mean_duration_human_readable": "3.312026ms", + "setup_time_seconds": 607.35518275, + "setup_time_human_readable": "607.35518275s", + "note": "TransposedQuadIndex::query_multi_group aggregated 1206 " }, { "name": "TransposedQuadIndexCentroided", "context": "BatchAccess_full_rt", - "mean_duration_seconds": 0.004904444668292681, - "mean_duration_human_readable": "4.904444ms", - "setup_time_seconds": 542.031527458, - "setup_time_human_readable": "542.031527458s", - "note": "TransposedQuadIndex::query_multi_group aggregated 185201566 " + "mean_duration_seconds": 0.0074757223134328385, + "mean_duration_human_readable": "7.475722ms", + "setup_time_seconds": 589.906208458, + "setup_time_human_readable": "589.906208458s", + "note": "TransposedQuadIndex::query_multi_group aggregated 184228858 " } ], "metadata": { "basename": "LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02" }, - "full_benchmark_time_seconds": 2091.340999875 + "full_benchmark_time_seconds": 2285.880075541 } \ No newline at end of file diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index c9b0ceb..4016b1c 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -458,7 +458,6 @@ pub fn par_read_and_expand_frames( .collect(); println!("Slice info: {:?}", slice_infos); - panic!(); info!("Processing MS1 frames"); let ms1_iter = frame_reader.parallel_filter(|x| x.ms_level == MSLevel::MS1); diff --git a/src/utils/frame_processing.rs b/src/utils/frame_processing.rs index 6e2c090..71528f9 100644 --- a/src/utils/frame_processing.rs +++ b/src/utils/frame_processing.rs @@ -132,9 +132,11 @@ pub fn lazy_centroid_weighted_frame<'a>( let mut curr_intensity = 0u64; let mut curr_weight = 0u64; - let mut curr_agg_tof = 0u64; - let mut curr_agg_ims = 0u64; + // let mut curr_agg_tof = 0u64; + // let mut curr_agg_ims = 0u64; + // This is added to the index within the loop + // To get the touched status of the peaks. let mut local_offset_touched = 0; for (ii, local_peak_refs) in peak_refs.iter().enumerate() { let ss_start = local_peak_refs @@ -152,8 +154,8 @@ pub fn lazy_centroid_weighted_frame<'a>( curr_intensity += local_intensity; global_num_touched += 1; } - curr_agg_tof += local_peak_refs.tof_array[i] as u64 * local_intensity; - curr_agg_ims += local_peak_refs.ims_array[i] as u64 * local_intensity; + // curr_agg_tof += local_peak_refs.tof_array[i] as u64 * local_intensity; + // curr_agg_ims += local_peak_refs.ims_array[i] as u64 * local_intensity; curr_weight += local_intensity; touched[ti] = true; } @@ -164,8 +166,10 @@ pub fn lazy_centroid_weighted_frame<'a>( // This means that at least 2 peaks need to be aggregated. if curr_weight > this_intensity && curr_intensity >= this_intensity { agg_intensity.push(u32::try_from(curr_intensity).expect("Expected to fit in u32")); - let calc_tof = (curr_agg_tof / curr_weight) as u32; - let calc_ims = (curr_agg_ims / curr_weight) as usize; + // let calc_tof = (curr_agg_tof / curr_weight) as u32; + // let calc_ims = (curr_agg_ims / curr_weight) as usize; + let calc_tof = tof; + let calc_ims = ims; debug_assert!(tof_range.contains(&calc_tof)); debug_assert!(ims_range.contains(&calc_ims)); agg_tof.push(calc_tof); From 37e39a54b21a1e06a15821e62620e4de391316f0 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Wed, 30 Oct 2024 16:25:30 -0700 Subject: [PATCH 12/30] refactor!: agg/query traits and cli --- README.md | 1 + src/main.rs | 26 ++++++++------ .../raw_peak_agg/chromatogram_agg.rs | 6 ++-- .../raw_peak_agg/multi_chromatogram_agg.rs | 4 +-- .../aggregators/raw_peak_agg/point_agg.rs | 8 +++-- src/models/frames/expanded_frame.rs | 1 - src/models/frames/raw_peak.rs | 7 ++++ .../indices/expanded_raw_index/model.rs | 20 ++++++----- src/models/indices/mod.rs | 4 +++ src/models/indices/raw_file_index.rs | 21 +++++++----- .../quad_splitted_transposed_index.rs | 24 +++++++------ .../queriable_tims_data.rs | 34 ++++--------------- src/traits/aggregator.rs | 13 +++++-- src/traits/queriable_data.rs | 26 ++++++-------- 14 files changed, 104 insertions(+), 91 deletions(-) diff --git a/README.md b/README.md index 8a21978..ac30827 100644 --- a/README.md +++ b/README.md @@ -36,3 +36,4 @@ sequential, use that). ## TODO: - Add logging levels to instrumentations. +- Add missing_docks_in_private_items to clippy. diff --git a/src/main.rs b/src/main.rs index 82f5e06..4620335 100644 --- a/src/main.rs +++ b/src/main.rs @@ -11,13 +11,12 @@ use timsquery::{ ChromatomobilogramStats, ExtractedIonChromatomobilogram, MultiCMGStatsFactory, RawPeakIntensityAggregator, RawPeakVectorAggregator, }, - models::indices::raw_file_index::RawFileIndex, - models::indices::transposed_quad_index::QuadSplittedTransposedIndex, + models::indices::{ExpandedRawFrameIndex, QuadSplittedTransposedIndex}, }; use tracing::instrument; use tracing::subscriber::set_global_default; use tracing_bunyan_formatter::{BunyanFormattingLayer, JsonStorageLayer}; -use tracing_subscriber::{fmt, prelude::*, registry::Registry, EnvFilter, Layer}; +use tracing_subscriber::{prelude::*, registry::Registry, EnvFilter}; fn main() { let env_filter = EnvFilter::try_from_default_env().unwrap_or_else(|_| EnvFilter::new("info")); @@ -113,13 +112,14 @@ fn main_query_index(args: QueryIndexArgs) { serde_json::from_str(&std::fs::read_to_string(&elution_groups_path).unwrap()).unwrap(); let index_use = match (index_use, elution_groups.len() > 10) { - (PossibleIndex::RawFileIndex, true) => PossibleIndex::RawFileIndex, + (PossibleIndex::ExpandedRawFrameIndex, true) => PossibleIndex::ExpandedRawFrameIndex, (PossibleIndex::TransposedQuadIndex, true) => PossibleIndex::TransposedQuadIndex, - (PossibleIndex::RawFileIndex, false) => PossibleIndex::RawFileIndex, + (PossibleIndex::ExpandedRawFrameIndex, false) => PossibleIndex::ExpandedRawFrameIndex, (PossibleIndex::TransposedQuadIndex, false) => PossibleIndex::TransposedQuadIndex, (PossibleIndex::Unspecified, true) => PossibleIndex::TransposedQuadIndex, - (PossibleIndex::Unspecified, false) => PossibleIndex::RawFileIndex, + (PossibleIndex::Unspecified, false) => PossibleIndex::ExpandedRawFrameIndex, }; + // ExpandedRawFrameIndex, execute_query( index_use, @@ -162,7 +162,7 @@ pub enum PossibleAggregator { pub enum PossibleIndex { #[default] Unspecified, - RawFileIndex, + ExpandedRawFrameIndex, TransposedQuadIndex, } @@ -242,7 +242,7 @@ pub fn execute_query( macro_rules! execute_query_inner { ($index:expr, $agg:expr) => { - let tmp = query_multi_group(&$index, &$index, &tolerance, &elution_groups, &$agg); + let tmp = query_multi_group(&$index, &tolerance, &elution_groups, &$agg); let mut out = Vec::with_capacity(tmp.len()); for (res, eg) in tmp.into_iter().zip(elution_groups) { @@ -316,8 +316,8 @@ pub fn execute_query( } } } - (PossibleIndex::RawFileIndex, aggregator) => { - let index = RawFileIndex::from_path(&(raw_file_path.clone())).unwrap(); + (PossibleIndex::ExpandedRawFrameIndex, aggregator) => { + let index = ExpandedRawFrameIndex::from_path(&(raw_file_path.clone())).unwrap(); match aggregator { PossibleAggregator::RawPeakIntensityAggregator => { let aggregator = RawPeakIntensityAggregator::new; @@ -336,7 +336,11 @@ pub fn execute_query( execute_query_inner!(index, aggregator); } PossibleAggregator::MultiCMGStats => { - panic!("Not Implemented!"); + let factory = MultiCMGStatsFactory { + converters: (index.mz_converter, index.im_converter), + _phantom: std::marker::PhantomData::, + }; + execute_query_inner!(index, |x| factory.build(x)); } } } diff --git a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs index 36281e4..53dd953 100644 --- a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs @@ -30,7 +30,8 @@ impl Aggregator for ExtractedIonChromatomobilogram { type Item = RawPeak; type Output = ChromatomobilogramVectorArrayTuples; - fn add(&mut self, peak: &RawPeak) { + fn add(&mut self, peak: impl Into) { + let peak = peak.into(); let u64_intensity = peak.intensity as u64; // In theory I could use a power of 2 to have a better preservation of @@ -170,7 +171,8 @@ impl Aggregator for ChromatomobilogramStats { type Item = RawPeak; type Output = ChromatomobilogramStatsArrays; - fn add(&mut self, peak: &RawPeak) { + fn add(&mut self, peak: impl Into) { + let peak = peak.into(); let u64_intensity = peak.intensity as u64; let rt_miliseconds = (peak.retention_time * 1000.0) as u32; diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs index d446db9..04ca716 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs @@ -346,8 +346,8 @@ impl Aggregator for MultiCMGSta type Item = (RawPeak, FH); type Output = NaturalFinalizedMultiCMGStatsArrays; - fn add(&mut self, peak: &(RawPeak, FH)) { - let (peak, transition) = peak; + fn add(&mut self, peak: impl Into<(RawPeak, FH)>) { + let (peak, transition) = peak.into(); let u64_intensity = peak.intensity as u64; let rt_miliseconds = (peak.retention_time * 1000.0) as u32; diff --git a/src/models/aggregators/raw_peak_agg/point_agg.rs b/src/models/aggregators/raw_peak_agg/point_agg.rs index 1e1567d..1ddbd34 100644 --- a/src/models/aggregators/raw_peak_agg/point_agg.rs +++ b/src/models/aggregators/raw_peak_agg/point_agg.rs @@ -19,11 +19,12 @@ impl RawPeakIntensityAggregator { } } -impl Aggregator for RawPeakIntensityAggregator { +impl Aggregator for RawPeakIntensityAggregator { type Item = (RawPeak, T); type Output = u64; - fn add(&mut self, peak: &(RawPeak, T)) { + fn add(&mut self, peak: impl Into<(RawPeak, T)>) { + let peak = peak.into(); self.intensity += peak.0.intensity as u64; } @@ -70,7 +71,8 @@ impl Aggregator for RawPeakVectorAggregator { type Item = RawPeak; type Output = RawPeakVectorArrays; - fn add(&mut self, peak: &RawPeak) { + fn add(&mut self, peak: impl Into) { + let peak = peak.into(); self.peaks.scans.push(peak.scan_index); self.peaks.tofs.push(peak.tof_index); self.peaks.intensities.push(peak.intensity); diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index 4016b1c..ab4bfae 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -672,7 +672,6 @@ impl ExpandedQuadSliceInfo { } for peak in local_peaks.into_iter() { - println!("peak: {:?}", peak); if peak.fwdone && peak.bwdone && peak.any_update { peaks.push(peak); } diff --git a/src/models/frames/raw_peak.rs b/src/models/frames/raw_peak.rs index 9d6a8f7..f4500bf 100644 --- a/src/models/frames/raw_peak.rs +++ b/src/models/frames/raw_peak.rs @@ -1,4 +1,5 @@ use serde::Serialize; +use std::convert::From; #[derive(Debug, Clone, Copy, Serialize)] pub struct RawPeak { @@ -7,3 +8,9 @@ pub struct RawPeak { pub intensity: u32, pub retention_time: f32, } + +impl From<(RawPeak, T)> for RawPeak { + fn from(x: (RawPeak, T)) -> Self { + x.0 + } +} diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index a00113e..bda8b6d 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -11,6 +11,7 @@ use crate::models::frames::single_quad_settings::{ SingleQuadrupoleSettingIndex, }; use crate::models::queries::FragmentGroupIndexQuery; +use crate::traits::aggregator::Aggregator; use crate::traits::queriable_data::QueriableData; use crate::ToleranceAdapter; use rayon::prelude::*; @@ -207,11 +208,11 @@ impl // .collect() } - fn add_query>( - &self, - fragment_query: &FragmentGroupIndexQuery, - aggregator: &mut AG, - ) { + fn add_query(&self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG) + where + A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, + AG: Aggregator, + { todo!(); // let precursor_mz_range = ( // fragment_query.precursor_query.isolation_mz_range.0 as f64, @@ -236,11 +237,14 @@ impl // }) } - fn add_query_multi_group>( + fn add_query_multi_group( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], - ) { + ) where + A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, + AG: Aggregator, + { // fragment_queries // .par_iter() // .zip(aggregator.par_iter_mut()) @@ -321,7 +325,7 @@ impl } for (fh, tof_range) in fragment_queries[i].mz_index_ranges.iter() { - let mut local_lambda = |peak| agg.add(&(RawPeak::from(peak), *fh)); + let mut local_lambda = |peak| agg.add((RawPeak::from(peak), *fh)); tqi.query_peaks( *tof_range, scan_ranges[i], diff --git a/src/models/indices/mod.rs b/src/models/indices/mod.rs index b8cb6e1..81d43c9 100644 --- a/src/models/indices/mod.rs +++ b/src/models/indices/mod.rs @@ -1,3 +1,7 @@ pub mod expanded_raw_index; pub mod raw_file_index; pub mod transposed_quad_index; + +pub use expanded_raw_index::ExpandedRawFrameIndex; +pub use raw_file_index::RawFileIndex; +pub use transposed_quad_index::QuadSplittedTransposedIndex; diff --git a/src/models/indices/raw_file_index.rs b/src/models/indices/raw_file_index.rs index 462ff87..23a6977 100644 --- a/src/models/indices/raw_file_index.rs +++ b/src/models/indices/raw_file_index.rs @@ -12,7 +12,7 @@ use std::hash::Hash; use timsrust::converters::ConvertableDomain; use timsrust::readers::{FrameReader, FrameReaderError, MetadataReader}; use timsrust::TimsRustError; -use timsrust::{Frame, Metadata, QuadrupoleSettings}; +use timsrust::{Frame, Metadata}; use tracing::trace; pub struct RawFileIndex { @@ -193,19 +193,22 @@ impl out } - fn add_query>( - &self, - fragment_query: &FragmentGroupIndexQuery, - aggregator: &mut AG, - ) { - self.apply_on_query(fragment_query, &mut |x, y| aggregator.add(&(x, y))); + fn add_query(&self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG) + where + A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, + AG: Aggregator, + { + self.apply_on_query(fragment_query, &mut |x, y| aggregator.add((x, y))); } - fn add_query_multi_group>( + fn add_query_multi_group( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], - ) { + ) where + A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, + AG: Aggregator, + { fragment_queries .iter() .zip(aggregator.iter_mut()) diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 8d1dc80..0537410 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -1,4 +1,4 @@ -use super::quad_index::{FrameRTTolerance, TransposedQuadIndex, TransposedQuadIndexBuilder}; +use super::quad_index::{TransposedQuadIndex, TransposedQuadIndexBuilder}; use crate::models::adapters::FragmentIndexAdapter; use crate::models::elution_group::ElutionGroup; use crate::models::frames::expanded_frame::{ @@ -11,6 +11,7 @@ use crate::models::frames::single_quad_settings::{ get_matching_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, }; use crate::models::queries::FragmentGroupIndexQuery; +use crate::traits::aggregator::Aggregator; use crate::traits::queriable_data::QueriableData; use crate::utils::display::{glimpse_vec, GlimpseConfig}; use crate::ToleranceAdapter; @@ -337,11 +338,11 @@ impl .collect() } - fn add_query>( - &self, - fragment_query: &FragmentGroupIndexQuery, - aggregator: &mut AG, - ) { + fn add_query(&self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG) + where + A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, + AG: Aggregator, + { let precursor_mz_range = ( fragment_query.precursor_query.isolation_mz_range.0 as f64, fragment_query.precursor_query.isolation_mz_range.0 as f64, @@ -357,16 +358,19 @@ impl precursor_mz_range, scan_range, Some(fragment_query.precursor_query.rt_range_seconds), - &mut |peak| aggregator.add(&(RawPeak::from(peak), *fh)), + &mut |peak| aggregator.add((RawPeak::from(peak), *fh)), ); }) } - fn add_query_multi_group>( + fn add_query_multi_group( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], - ) { + ) where + A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, + AG: Aggregator, + { fragment_queries .par_iter() .zip(aggregator.par_iter_mut()) @@ -389,7 +393,7 @@ impl tof_range, scan_range, Some(fragment_query.precursor_query.rt_range_seconds), - &mut |peak| agg.add(&(RawPeak::from(peak), fh)), + &mut |peak| agg.add((RawPeak::from(peak), fh)), ); } }); diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index 2e4a79a..4252b57 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -1,7 +1,6 @@ use rayon::prelude::*; use serde::Serialize; use std::hash::Hash; -use std::rc::Rc; use std::time::Instant; use tracing::info; @@ -43,20 +42,22 @@ use crate::{Aggregator, ElutionGroup, QueriableData, Tolerance, ToleranceAdapter // 2. `QD` is queried with `QP` and `QF` queries. // 3. The results are aggregated with `AG` aggregators (which are generated by the factory, when passed a numeric ID). -pub fn query_multi_group<'a, QD, TL, QF, AE, OE, AG, FH>( +pub fn query_multi_group<'a, QD, TL, QF, AE1, AE2, OE, AG, FH>( queriable_data: &'a QD, tolerance: &'a TL, elution_groups: &[ElutionGroup], aggregator_factory: &dyn Fn(u64) -> AG, ) -> Vec where - AG: Aggregator + Send + Sync, - QD: QueriableData + ToleranceAdapter>, + AG: Aggregator + Send + Sync, + QD: QueriableData + ToleranceAdapter>, TL: Tolerance, OE: Send + Sync, FH: Clone + Eq + Serialize + Hash + Send + Sync, QF: Send + Sync, - AE: Send + Sync + Clone + Copy, + // AE: Send + Sync + Clone + Copy, + AE1: Into + Send + Sync + Clone + Copy, + AE2: Send + Sync + Clone + Copy + From, { let start = Instant::now(); let mut fragment_queries = Vec::with_capacity(elution_groups.len()); @@ -89,26 +90,3 @@ where info!("Aggregation took {:#?}", elapsed); out } - -pub fn query_indexed( - queriable_data: &QD, - aggregator_factory: &dyn Fn(u64) -> AG, - tolerance_adapter: &TA, - tolerance: &TL, - elution_group: &ElutionGroup, -) -> OE -where - AG: Aggregator + Send + Sync, - QD: QueriableData, - TA: ToleranceAdapter>, - TL: Tolerance, - FH: Clone + Eq + Serialize + Hash + Send + Sync, - QF: Send + Sync, - AE: Send + Sync + Clone + Copy, -{ - let mut aggregator = aggregator_factory(elution_group.id); - let prep_query = Rc::new(tolerance_adapter.query_from_elution_group(tolerance, elution_group)); - - queriable_data.add_query(&prep_query, &mut aggregator); - aggregator.finalize() -} diff --git a/src/traits/aggregator.rs b/src/traits/aggregator.rs index 209d444..13af0ae 100644 --- a/src/traits/aggregator.rs +++ b/src/traits/aggregator.rs @@ -1,7 +1,16 @@ +/// A trait that defines how to aggregate items. +/// +/// The `Item` type is the type of the item that is being aggregated. +/// The `Output` type is the type of the output of the aggregation. +/// +/// The `add` method takes an item of type `Item` OR a type that +/// imlements `Into`. +/// +/// The `finalize` method returns the output of the aggregation. pub trait Aggregator: Send + Sync { - type Item: Send + Sync; + type Item: Send + Sync + Clone; type Output: Send + Sync; - fn add(&mut self, item: &Self::Item); + fn add(&mut self, item: impl Into); fn finalize(self) -> Self::Output; } diff --git a/src/traits/queriable_data.rs b/src/traits/queriable_data.rs index 07d5a91..92f96de 100644 --- a/src/traits/queriable_data.rs +++ b/src/traits/queriable_data.rs @@ -1,23 +1,19 @@ -use super::tolerance::ToleranceAdapter; -use crate::models::elution_group::ElutionGroup; use crate::Aggregator; -pub trait QueriableData +pub trait QueriableData where QF: Send + Sync, - A: Send + Sync + Clone + Copy, + I: Send + Sync + Clone + Copy, { - fn query(&self, fragment_query: &QF) -> Vec; - fn add_query>( - &self, - fragment_query: &QF, - aggregator: &mut AG, - ); - fn add_query_multi_group>( - &self, - fragment_queries: &[QF], - aggregator: &mut [AG], - ); + fn query(&self, fragment_query: &QF) -> Vec; + fn add_query(&self, fragment_query: &QF, aggregator: &mut AG) + where + A: From + Send + Sync + Clone + Copy, + AG: Aggregator; + fn add_query_multi_group(&self, fragment_queries: &[QF], aggregator: &mut [AG]) + where + A: From + Send + Sync + Clone + Copy, + AG: Aggregator; } // I like this idea but I need a way to set/propagate the tolerance From c4cde153a1542caac3ba9effcf4de389c72cbfb1 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Wed, 30 Oct 2024 17:37:00 -0700 Subject: [PATCH 13/30] refactor(errors)!: refactored errors --- Cargo.toml | 2 +- src/errors.rs | 58 ++++++++ src/lib.rs | 4 + src/models/frames/expanded_frame.rs | 139 +++++++----------- .../indices/expanded_raw_index/model.rs | 20 +-- .../transposed_quad_index/quad_index.rs | 40 ----- .../quad_splitted_transposed_index.rs | 27 ++-- 7 files changed, 129 insertions(+), 161 deletions(-) create mode 100644 src/errors.rs diff --git a/Cargo.toml b/Cargo.toml index 38305e8..5546743 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -20,12 +20,12 @@ tracing-subscriber = { version = "0.3.18", features = [ "env-filter", ] } tracing-bunyan-formatter = "0.3.9" +tracing-chrome = "0.7.2" # These are only used for benchmarks rand = { version = "0.8.5", optional = true } rand_chacha = { version = "0.3.1", optional = true } -tracing-chrome = "0.7.2" [features] diff --git a/src/errors.rs b/src/errors.rs new file mode 100644 index 0000000..4b66808 --- /dev/null +++ b/src/errors.rs @@ -0,0 +1,58 @@ +use crate::models::frames::expanded_frame::FrameProcessingConfig; +use std::fmt::Display; +use timsrust::TimsRustError; + +#[derive(Debug)] +pub enum TimsqueryError { + DataReadingError(DataReadingError), + DataProcessingError(DataProcessingError), + Other(String), +} + +pub type Result = std::result::Result; + +impl Display for TimsqueryError { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + write!(f, "{:?}", self) + } +} + +impl TimsqueryError { + pub fn custom(msg: impl Display) -> Self { + Self::Other(msg.to_string()) + } +} + +#[derive(Debug)] +pub enum DataReadingError { + UnsupportedDataError(UnsupportedDataError), + TimsRustError(TimsRustError), // Why doesnt timsrust error derive clone? +} + +impl From for DataReadingError { + fn from(e: UnsupportedDataError) -> Self { + DataReadingError::UnsupportedDataError(e) + } +} + +#[derive(Debug)] +pub enum UnsupportedDataError { + NoMS2DataError, +} + +#[derive(Debug)] +pub enum DataProcessingError { + CentroidingError(FrameProcessingConfig), +} + +impl> From for TimsqueryError { + fn from(e: T) -> Self { + TimsqueryError::DataReadingError(e.into()) + } +} + +impl> From for DataReadingError { + fn from(e: T) -> Self { + DataReadingError::TimsRustError(e.into()) + } +} diff --git a/src/lib.rs b/src/lib.rs index 2ef3d2b..500b75e 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -8,7 +8,11 @@ pub use crate::traits::queriable_data::QueriableData; pub use crate::traits::tolerance::{Tolerance, ToleranceAdapter}; // Declare modules +pub mod errors; pub mod models; pub mod queriable_tims_data; pub mod traits; pub mod utils; + +// Re-export errors +pub use crate::errors::{DataProcessingError, DataReadingError, TimsqueryError}; diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index ab4bfae..c0da9f3 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -1,23 +1,20 @@ +use super::peak_in_quad::PeakInQuad; use super::single_quad_settings::{ expand_quad_settings, ExpandedFrameQuadSettings, SingleQuadrupoleSetting, }; +use crate::errors::{Result, UnsupportedDataError}; +use crate::sort_vecs_by_first; +use crate::utils::compress_explode::explode_vec; +use crate::utils::frame_processing::{lazy_centroid_weighted_frame, PeakArrayRefs}; +use crate::utils::sorting::top_n; +use crate::utils::tolerance_ranges::{scan_tol_range, tof_tol_range}; use rayon::prelude::*; use std::collections::HashMap; use std::marker::PhantomData; use std::sync::Arc; use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; +use timsrust::readers::{FrameReader, FrameReaderError}; use timsrust::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}; - -use super::peak_in_quad::PeakInQuad; -use crate::sort_vecs_by_first; -use crate::utils::compress_explode::explode_vec; -use crate::utils::frame_processing::{lazy_centroid_weighted_frame, PeakArrayRefs}; -use crate::utils::sorting::top_n; -use crate::utils::tolerance_ranges::{scan_tol_range, tof_tol_range}; -use timsrust::{ - readers::{FrameReader, FrameReaderError, MetadataReaderError}, - TimsRustError, -}; use tracing::instrument; use tracing::{info, trace, warn}; @@ -301,14 +298,31 @@ pub fn par_expand_and_arrange_frames( out } +#[derive(Debug, Clone, Copy, PartialEq)] +pub struct CentroidingSettings { + ims_tol_pct: f64, + mz_tol_ppm: f64, + window_width: usize, + max_ms1_peaks: usize, + max_ms2_peaks: usize, +} + +impl Default for CentroidingSettings { + fn default() -> Self { + CentroidingSettings { + ims_tol_pct: 1.5, + mz_tol_ppm: 15.0, + window_width: 3, + max_ms1_peaks: 100_000, + max_ms2_peaks: 20_000, + } + } +} + #[derive(Debug, Clone, Copy, PartialEq)] pub enum FrameProcessingConfig { Centroided { - ims_tol_pct: f64, - mz_tol_ppm: f64, - window_width: usize, - max_ms1_peaks: usize, - max_ms2_peaks: usize, + settings: CentroidingSettings, ims_converter: Option, mz_converter: Option, }, @@ -322,33 +336,20 @@ impl FrameProcessingConfig { mz_converter: Tof2MzConverter, ) -> Self { match self { - FrameProcessingConfig::Centroided { - ims_tol_pct, - mz_tol_ppm, - window_width, - max_ms1_peaks, - max_ms2_peaks, - .. - } => FrameProcessingConfig::Centroided { - ims_tol_pct, - mz_tol_ppm, - window_width, - max_ms1_peaks, - max_ms2_peaks, - ims_converter: Some(ims_converter), - mz_converter: Some(mz_converter), - }, + FrameProcessingConfig::Centroided { settings, .. } => { + FrameProcessingConfig::Centroided { + settings, + ims_converter: Some(ims_converter), + mz_converter: Some(mz_converter), + } + } FrameProcessingConfig::NotCentroided => FrameProcessingConfig::NotCentroided, } } pub fn default_centroided() -> Self { FrameProcessingConfig::Centroided { - ims_tol_pct: 1.5, - mz_tol_ppm: 15.0, - window_width: 3, - max_ms1_peaks: 100_000, - max_ms2_peaks: 20_000, + settings: Default::default(), ims_converter: Default::default(), mz_converter: Default::default(), } @@ -359,33 +360,8 @@ impl FrameProcessingConfig { } } -#[derive(Debug)] -pub enum DataReadingError { - CentroidingError(FrameProcessingConfig), - UnsupportedDataError(String), - TimsRustError(TimsRustError), // Why doesnt timsrust error derive clone? -} - -impl From for DataReadingError { - fn from(e: TimsRustError) -> Self { - DataReadingError::TimsRustError(e) - } -} - -impl From for DataReadingError { - fn from(e: MetadataReaderError) -> Self { - DataReadingError::TimsRustError(TimsRustError::MetadataReaderError(e)) - } -} - -impl From for DataReadingError { - fn from(e: FrameReaderError) -> Self { - DataReadingError::TimsRustError(TimsRustError::FrameReaderError(e)) - } -} - fn warn_and_skip_badframes( - frame_iter: impl ParallelIterator>, + frame_iter: impl ParallelIterator>, ) -> impl ParallelIterator { frame_iter.filter_map(|x| { // Log the info of the frame that broke ... @@ -409,16 +385,11 @@ fn warn_and_skip_badframes( pub fn par_read_and_expand_frames( frame_reader: &FrameReader, centroiding_config: FrameProcessingConfig, -) -> Result< - HashMap, Vec>>, - DataReadingError, -> { +) -> Result, Vec>>> { let dia_windows = match frame_reader.get_dia_windows() { Some(dia_windows) => dia_windows, None => { - return Err(DataReadingError::UnsupportedDataError( - "No dia windows found".to_string(), - )) + return Err(UnsupportedDataError::NoMS2DataError.into()); } }; @@ -430,19 +401,15 @@ pub fn par_read_and_expand_frames( let expanded_frames = match centroiding_config { FrameProcessingConfig::Centroided { - ims_tol_pct, - mz_tol_ppm, - window_width, - max_ms1_peaks: _max_ms1_peaks, - max_ms2_peaks, + settings, ims_converter, mz_converter, } => par_expand_and_centroid_frames( curr_iter, - ims_tol_pct, - mz_tol_ppm, - window_width, - max_ms2_peaks, + settings.ims_tol_pct, + settings.mz_tol_ppm, + settings.window_width, + settings.max_ms2_peaks, &ims_converter.unwrap(), &mz_converter.unwrap(), ), @@ -464,19 +431,15 @@ pub fn par_read_and_expand_frames( let ms1_iter = warn_and_skip_badframes(ms1_iter); let expanded_ms1_frames = match centroiding_config { FrameProcessingConfig::Centroided { - ims_tol_pct, - mz_tol_ppm, - window_width, - max_ms1_peaks, - max_ms2_peaks: _max_ms2_peaks, + settings, ims_converter, mz_converter, } => par_expand_and_centroid_frames( ms1_iter, - ims_tol_pct, - mz_tol_ppm, - window_width, - max_ms1_peaks, + settings.ims_tol_pct, + settings.mz_tol_ppm, + settings.window_width, + settings.max_ms1_peaks, &ims_converter.unwrap(), &mz_converter.unwrap(), ), diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index bda8b6d..f2c5533 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -1,8 +1,8 @@ +use crate::errors::Result; use crate::models::adapters::FragmentIndexAdapter; use crate::models::elution_group::ElutionGroup; use crate::models::frames::expanded_frame::{ - par_read_and_expand_frames, DataReadingError, ExpandedFrameSlice, FrameProcessingConfig, - SortedState, + par_read_and_expand_frames, ExpandedFrameSlice, FrameProcessingConfig, SortedState, }; use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::raw_peak::RawPeak; @@ -19,7 +19,7 @@ use serde::Serialize; use std::collections::HashMap; use std::hash::Hash; use std::time::Instant; -use timsrust::converters::{Frame2RtConverter, Scan2ImConverter, Tof2MzConverter}; +use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; use timsrust::readers::{FrameReader, MetadataReader}; use tracing::info; use tracing::instrument; @@ -29,7 +29,6 @@ pub struct ExpandedRawFrameIndex { bundled_ms1_frames: ExpandedSliceBundle, bundled_frames: HashMap, flat_quad_settings: Vec, - rt_converter: Frame2RtConverter, pub mz_converter: Tof2MzConverter, pub im_converter: Scan2ImConverter, adapter: FragmentIndexAdapter, @@ -38,18 +37,15 @@ pub struct ExpandedRawFrameIndex { #[derive(Debug, Clone)] pub struct ExpandedSliceBundle { slices: Vec>, - rts: Vec, frame_indices: Vec, } impl ExpandedSliceBundle { pub fn new(mut slices: Vec>) -> Self { slices.sort_unstable_by(|a, b| a.rt.partial_cmp(&b.rt).unwrap()); - let rts = slices.iter().map(|x| x.rt).collect(); let frame_indices = slices.iter().map(|x| x.frame_index).collect(); Self { slices, - rts, frame_indices, } } @@ -113,21 +109,18 @@ impl ExpandedRawFrameIndex { } #[instrument(name = "ExpandedRawFrameIndex::from_path_centroided")] - pub fn from_path_centroided(path: &str) -> Result { + pub fn from_path_centroided(path: &str) -> Result { let config = FrameProcessingConfig::default_centroided(); Self::from_path_base(path, config) } #[instrument(name = "ExpandedRawFrameIndex::from_path")] - pub fn from_path(path: &str) -> Result { + pub fn from_path(path: &str) -> Result { Self::from_path_base(path, FrameProcessingConfig::NotCentroided) } #[instrument(name = "ExpandedRawFrameIndex::from_path_base")] - pub fn from_path_base( - path: &str, - centroid_config: FrameProcessingConfig, - ) -> Result { + pub fn from_path_base(path: &str, centroid_config: FrameProcessingConfig) -> Result { info!( "Building ExpandedRawFrameIndex from path {} config {:?}", path, centroid_config, @@ -166,7 +159,6 @@ impl ExpandedRawFrameIndex { bundled_ms1_frames: out_ms1_frames.expect("At least one ms1 frame should be present"), bundled_frames: out_ms2_frames, flat_quad_settings, - rt_converter: meta_converters.rt_converter, mz_converter: meta_converters.mz_converter, im_converter: meta_converters.im_converter, adapter, diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index b5b601d..c5d203e 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -83,46 +83,6 @@ impl TransposedQuadIndex { .map(move |p| PeakInQuad::from_peak_in_bucket(p, *tof_index)) }) } - - fn convert_to_local_frame_range( - &self, - rt_range: Option, - ) -> Option<(f32, f32)> { - // TODO consider if I should allow only RT here, since it would in theory - // force me to to the repreatable work beforehand. - let frame_index_range = match rt_range { - Some(FrameRTTolerance::Seconds((rt_low, rt_high))) => { - Some((rt_low as f32, rt_high as f32)) - } - Some(FrameRTTolerance::FrameIndex((frame_low, frame_high))) => { - let frame_id_start = self - .frame_indices - .binary_search_by(|x| x.cmp(&frame_low)) - .unwrap_or_else(|x| x); - - let frame_id_end = self - .frame_indices - .binary_search_by(|x| x.cmp(&frame_high)) - .unwrap_or_else(|x| x); - - // TODO consider throwing a warning if we are - // out of bounds here. - Some(( - self.frame_rts[frame_id_start.min(self.frame_rts.len() - 1)] as f32, - self.frame_rts[frame_id_end.min(self.frame_rts.len() - 1)] as f32, - )) - } - None => None, - }; - - if cfg!(debug_assertions) { - if let Some((low, high)) = frame_index_range { - debug_assert!(low <= high); - } - } - - frame_index_range - } } impl PeakInQuad { diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 0537410..2f003b9 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -1,9 +1,9 @@ use super::quad_index::{TransposedQuadIndex, TransposedQuadIndexBuilder}; +use crate::errors::Result; use crate::models::adapters::FragmentIndexAdapter; use crate::models::elution_group::ElutionGroup; use crate::models::frames::expanded_frame::{ - par_read_and_expand_frames, DataReadingError, ExpandedFrameSlice, FrameProcessingConfig, - SortingStateTrait, + par_read_and_expand_frames, ExpandedFrameSlice, FrameProcessingConfig, SortingStateTrait, }; use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::raw_peak::RawPeak; @@ -22,10 +22,9 @@ use std::fmt::Debug; use std::fmt::Display; use std::hash::Hash; use std::time::Instant; -use timsrust::converters::{Frame2RtConverter, Scan2ImConverter, Tof2MzConverter}; +use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; use timsrust::readers::{FrameReader, MetadataReader}; use timsrust::Metadata; -use timsrust::TimsRustError; use tracing::instrument; use tracing::{debug, info, trace}; @@ -36,7 +35,6 @@ pub struct QuadSplittedTransposedIndex { precursor_index: TransposedQuadIndex, fragment_indices: HashMap, flat_quad_settings: Vec, - rt_converter: Frame2RtConverter, pub mz_converter: Tof2MzConverter, pub im_converter: Scan2ImConverter, adapter: FragmentIndexAdapter, @@ -104,7 +102,6 @@ impl Display for QuadSplittedTransposedIndex { let mut disp_str = String::new(); disp_str.push_str("QuadSplittedTransposedIndex\n"); - disp_str.push_str("rt_converter: ... not showing ...\n"); disp_str.push_str(&format!("mz_converter: {:?}\n", self.mz_converter)); disp_str.push_str(&format!("im_converter: {:?}\n", self.im_converter)); disp_str.push_str("flat_quad_settings: \n"); @@ -139,7 +136,7 @@ impl Display for QuadSplittedTransposedIndex { impl QuadSplittedTransposedIndex { #[instrument(name = "QuadSplittedTransposedIndex::from_path")] - pub fn from_path(path: &str) -> Result { + pub fn from_path(path: &str) -> Result { let st = Instant::now(); info!("Building transposed quad index from path {}", path); let tmp = QuadSplittedTransposedIndexBuilder::from_path(path)?; @@ -151,7 +148,7 @@ impl QuadSplittedTransposedIndex { } #[instrument(name = "QuadSplittedTransposedIndex::from_path_centroided")] - pub fn from_path_centroided(path: &str) -> Result { + pub fn from_path_centroided(path: &str) -> Result { let st = Instant::now(); info!( "Building CENTROIDED transposed quad index from path {}", @@ -169,7 +166,6 @@ impl QuadSplittedTransposedIndex { #[derive(Debug, Clone, Default)] pub struct QuadSplittedTransposedIndexBuilder { indices: HashMap, TransposedQuadIndexBuilder>, - rt_converter: Option, mz_converter: Option, im_converter: Option, metadata: Option, @@ -200,12 +196,12 @@ impl QuadSplittedTransposedIndexBuilder { } #[instrument(name = "QuadSplittedTransposedIndexBuilder::from_path")] - fn from_path(path: &str) -> Result { + fn from_path(path: &str) -> Result { Self::from_path_base(path, FrameProcessingConfig::NotCentroided) } #[instrument(name = "QuadSplittedTransposedIndexBuilder::from_path_centroided")] - fn from_path_centroided(path: &str) -> Result { + fn from_path_centroided(path: &str) -> Result { let config = FrameProcessingConfig::default_centroided(); Self::from_path_base(path, config) } @@ -214,10 +210,7 @@ impl QuadSplittedTransposedIndexBuilder { // and one that adds the frameslices, maybe even have a config struct that dispatches // the right preprocessing steps. #[instrument(name = "QuadSplittedTransposedIndexBuilder::from_path_base")] - fn from_path_base( - path: &str, - centroid_config: FrameProcessingConfig, - ) -> Result { + fn from_path_base(path: &str, centroid_config: FrameProcessingConfig) -> Result { let file_reader = FrameReader::new(path)?; let sql_path = std::path::Path::new(path).join("analysis.tdf"); @@ -226,7 +219,6 @@ impl QuadSplittedTransposedIndexBuilder { let out_meta_converters = meta_converters.clone(); let mut final_out = Self { indices: HashMap::new(), - rt_converter: Some(meta_converters.rt_converter), mz_converter: Some(meta_converters.mz_converter), im_converter: Some(meta_converters.im_converter), metadata: Some(out_meta_converters), @@ -239,7 +231,7 @@ impl QuadSplittedTransposedIndexBuilder { let split_frames = par_read_and_expand_frames(&file_reader, centroid_config)?; // TODO use the rayon contructor to fold - let out2: Result, TimsRustError> = split_frames + let out2: Result> = split_frames .into_par_iter() .map(|(q, frameslices)| { // TODO:Refactor so the internal index is built first and then added. @@ -302,7 +294,6 @@ impl QuadSplittedTransposedIndexBuilder { precursor_index: precursor_index.expect("Precursor peaks should be present"), fragment_indices: indices, flat_quad_settings, - rt_converter: self.rt_converter.unwrap(), mz_converter: self.mz_converter.unwrap(), im_converter: self.im_converter.unwrap(), adapter: FragmentIndexAdapter::from(self.metadata.unwrap()), From 7dbf59289a29750fdead9350c30bebb3eb3855eb Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Wed, 30 Oct 2024 17:52:18 -0700 Subject: [PATCH 14/30] chore: version bump --- Cargo.lock | 2 +- Cargo.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 680a5d5..473a7b2 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1307,7 +1307,7 @@ dependencies = [ [[package]] name = "timsquery" -version = "0.4.0" +version = "0.5.0" dependencies = [ "clap", "indicatif", diff --git a/Cargo.toml b/Cargo.toml index 5546743..fa3b214 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "timsquery" -version = "0.4.0" +version = "0.5.0" edition = "2021" license = "Apache-2.0" From 0fd0173800744d1162e0cb3a924c3423409cd3c8 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Thu, 31 Oct 2024 13:04:09 -0700 Subject: [PATCH 15/30] (feat,wip) initial move to ms1 + trait cleanup --- src/main.rs | 2 + src/models/adapters.rs | 35 +++-- src/models/aggregators/mod.rs | 1 - .../raw_peak_agg/chromatogram_agg.rs | 129 +----------------- src/models/aggregators/raw_peak_agg/mod.rs | 1 - .../raw_peak_agg/multi_chromatogram_agg.rs | 12 +- .../aggregators/raw_peak_agg/point_agg.rs | 10 +- src/models/frames/expanded_frame.rs | 40 +++--- src/models/frames/raw_frames.rs | 25 ++-- src/models/frames/single_quad_settings.rs | 29 ++-- .../indices/expanded_raw_index/model.rs | 43 +++--- src/models/indices/raw_file_index.rs | 110 ++------------- .../transposed_quad_index/peak_bucket.rs | 29 ++-- .../transposed_quad_index/quad_index.rs | 9 +- .../quad_splitted_transposed_index.rs | 33 ++--- src/models/queries.rs | 69 ++++++++-- .../queriable_tims_data.rs | 9 +- src/traits/aggregator.rs | 40 ++++++ src/traits/queriable_data.rs | 42 +----- src/traits/tolerance.rs | 94 +++++++++++++ src/utils/frame_processing.rs | 25 ++-- src/utils/tolerance_ranges.rs | 69 ++++++++-- 22 files changed, 430 insertions(+), 426 deletions(-) diff --git a/src/main.rs b/src/main.rs index 4620335..203d25b 100644 --- a/src/main.rs +++ b/src/main.rs @@ -138,6 +138,8 @@ fn template_tolerance_settings() -> DefaultTolerance { rt: RtTolerance::None, mobility: MobilityTolerance::Pct((20.0, 20.0)), quad: QuadTolerance::Absolute((0.1, 0.1, 1)), + num_ms1_isotopes: 3, + num_ms2_isotopes: 1, } } diff --git a/src/models/adapters.rs b/src/models/adapters.rs index a4e8cce..0ca164e 100644 --- a/src/models/adapters.rs +++ b/src/models/adapters.rs @@ -1,5 +1,6 @@ use crate::models::elution_group::ElutionGroup; use crate::models::queries::{FragmentGroupIndexQuery, PrecursorIndexQuery}; +use crate::utils::tolerance_ranges::IncludedRange; use crate::ToleranceAdapter; use serde::Serialize; use std::hash::Hash; @@ -27,13 +28,21 @@ impl ) -> FragmentGroupIndexQuery { let rt_range = tol.rt_range(elution_group.rt_seconds); let mobility_range = tol.mobility_range(elution_group.mobility); - let precursor_mz_range = tol.mz_range(elution_group.precursor_mz); + let precursor_mzs = + tol.isotope_mzs_mz(elution_group.precursor_mz, elution_group.precursor_charge); let quad_range = tol.quad_range(elution_group.precursor_mz, elution_group.precursor_charge); + let quad_range = IncludedRange::new(quad_range.0, quad_range.1); - let mz_index_range = ( - self.metadata.mz_converter.invert(precursor_mz_range.0) as u32, - self.metadata.mz_converter.invert(precursor_mz_range.1) as u32, - ); + let mz_index_ranges = precursor_mzs + .iter() + .map(|mz| { + let mz_range = tol.mz_range(*mz); + IncludedRange::new( + self.metadata.mz_converter.invert(mz_range.0) as u32, + self.metadata.mz_converter.invert(mz_range.1) as u32, + ) + }) + .collect(); let mobility_range = match mobility_range { Some(mobility_range) => mobility_range, None => (self.metadata.lower_im as f32, self.metadata.upper_im as f32), @@ -46,16 +55,16 @@ impl Some(rt_range) => rt_range, None => (self.metadata.lower_rt as f32, self.metadata.upper_rt as f32), }; - let frame_index_range = ( - self.metadata.rt_converter.invert(rt_range.0) as usize, - self.metadata.rt_converter.invert(rt_range.1) as usize, + let rt_range = IncludedRange::new(rt_range.0, rt_range.1); + let frame_index_range = IncludedRange::new( + self.metadata.rt_converter.invert(rt_range.start()) as usize, + self.metadata.rt_converter.invert(rt_range.end()) as usize, ); - assert!(frame_index_range.0 <= frame_index_range.1); - assert!(mz_index_range.0 <= mz_index_range.1); + assert!(frame_index_range.start() <= frame_index_range.end()); // Since mobilities get mixed up bc low scan ranges are high 1/k0, I // Just make sure they are sorted here. - let mobility_index_range = ( + let mobility_index_range = IncludedRange::new( mobility_index_range.0.min(mobility_index_range.1), mobility_index_range.1.max(mobility_index_range.0), ); @@ -63,7 +72,7 @@ impl let precursor_query = PrecursorIndexQuery { frame_index_range, rt_range_seconds: rt_range, - mz_index_range, + mz_index_ranges, mobility_index_range, isolation_mz_range: quad_range, }; @@ -75,7 +84,7 @@ impl let mz_range = tol.mz_range(*v); ( *k, - ( + IncludedRange::new( self.metadata.mz_converter.invert(mz_range.0) as u32, self.metadata.mz_converter.invert(mz_range.1) as u32, ), diff --git a/src/models/aggregators/mod.rs b/src/models/aggregators/mod.rs index 6498af9..e34cad4 100644 --- a/src/models/aggregators/mod.rs +++ b/src/models/aggregators/mod.rs @@ -3,7 +3,6 @@ pub mod rolling_calculators; pub mod streaming_aggregator; pub use raw_peak_agg::ChromatomobilogramStats; -pub use raw_peak_agg::ExtractedIonChromatomobilogram; pub use raw_peak_agg::MultiCMGStats; pub use raw_peak_agg::MultiCMGStatsArrays; pub use raw_peak_agg::MultiCMGStatsFactory; diff --git a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs index 53dd953..aa5d091 100644 --- a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs @@ -7,68 +7,6 @@ use serde::Serialize; use std::collections::BTreeMap; use std::collections::HashMap; -#[derive(Debug, Clone, Serialize)] -pub struct ExtractedIonChromatomobilogram { - pub rt_tree: BTreeMap, - pub scan_tree: BTreeMap, - pub tof_tree: BTreeMap, - pub id: u64, -} - -impl ExtractedIonChromatomobilogram { - pub fn new(id: u64) -> Self { - Self { - rt_tree: BTreeMap::new(), - scan_tree: BTreeMap::new(), - tof_tree: BTreeMap::new(), - id, - } - } -} - -impl Aggregator for ExtractedIonChromatomobilogram { - type Item = RawPeak; - type Output = ChromatomobilogramVectorArrayTuples; - - fn add(&mut self, peak: impl Into) { - let peak = peak.into(); - let u64_intensity = peak.intensity as u64; - - // In theory I could use a power of 2 to have a better preservation of - // the precision. - // TODO make this macro ... right now it feels very repetitive. - let rt_miliseconds = (peak.retention_time * 1000.0) as u32; - - self.rt_tree - .entry(rt_miliseconds) - .and_modify(|curr| *curr += u64_intensity) - .or_insert(u64_intensity); - - self.scan_tree - .entry(peak.scan_index) - .and_modify(|curr| *curr += u64_intensity) - .or_insert(u64_intensity); - - self.tof_tree - .entry(peak.tof_index) - .and_modify(|curr| *curr += u64_intensity) - .or_insert(u64_intensity); - } - - fn finalize(self) -> ChromatomobilogramVectorArrayTuples { - ChromatomobilogramVectorArrayTuples { - scan_indices: self.scan_tree.into_iter().collect(), - tof_indices: self.tof_tree.into_iter().collect(), - retention_times: self - .rt_tree - .into_iter() - .map(|(k, v)| ((k as f32) / 1000.0, v)) - .collect(), - } - } -} - -// type MappingCollection = BTreeMap; pub type MappingCollection = HashMap; #[derive(Debug, Clone)] @@ -129,14 +67,7 @@ pub struct ChromatomobilogramStatsArrays { impl ChromatomobilogramStatsArrays { // TODO use default instead of new everywhere .. pub fn new() -> Self { - Self { - retention_time_miliseconds: Vec::new(), - tof_index_means: Vec::new(), - tof_index_sds: Vec::new(), - scan_index_means: Vec::new(), - scan_index_sds: Vec::new(), - intensities: Vec::new(), - } + Self::default() } pub fn fold(&mut self, other: Self) { @@ -167,64 +98,6 @@ impl ChromatomobilogramStatsArrays { } } -impl Aggregator for ChromatomobilogramStats { - type Item = RawPeak; - type Output = ChromatomobilogramStatsArrays; - - fn add(&mut self, peak: impl Into) { - let peak = peak.into(); - let u64_intensity = peak.intensity as u64; - let rt_miliseconds = (peak.retention_time * 1000.0) as u32; - - self.scan_tof_mapping - .entry(rt_miliseconds) - .and_modify(|curr| { - curr.add(u64_intensity, peak.scan_index, peak.tof_index); - }) - .or_insert(ScanTofStatsCalculatorPair::new( - u64_intensity, - peak.scan_index, - peak.tof_index, - )); - } - - fn finalize(self) -> ChromatomobilogramStatsArrays { - type VecTuple = (Vec, Vec); - type OutVecTubples = ((VecTuple, VecTuple), Vec); - let ((scan_data, tof_data), intensities): OutVecTubples = self - .scan_tof_mapping - .values() - .map(|pair| { - ( - ( - ( - pair.scan.mean().unwrap(), - pair.scan.standard_deviation().unwrap(), - ), - ( - pair.tof.mean().unwrap(), - pair.tof.standard_deviation().unwrap(), - ), - ), - pair.tof.weight(), - ) - }) - .unzip(); - - let (scan_means, scan_sds) = scan_data; - let (tof_means, tof_sds) = tof_data; - - ChromatomobilogramStatsArrays { - retention_time_miliseconds: self.scan_tof_mapping.keys().cloned().collect::>(), - tof_index_means: tof_means, - tof_index_sds: tof_sds, - scan_index_means: scan_means, - scan_index_sds: scan_sds, - intensities, - } - } -} - #[derive(Debug, Clone, Serialize)] pub struct ChromatomobilogramVectorArrayTuples { pub scan_indices: Vec<(usize, u64)>, diff --git a/src/models/aggregators/raw_peak_agg/mod.rs b/src/models/aggregators/raw_peak_agg/mod.rs index ab32750..dd5ad20 100644 --- a/src/models/aggregators/raw_peak_agg/mod.rs +++ b/src/models/aggregators/raw_peak_agg/mod.rs @@ -3,7 +3,6 @@ pub mod multi_chromatogram_agg; pub mod point_agg; pub use chromatogram_agg::ChromatomobilogramStats; -pub use chromatogram_agg::ExtractedIonChromatomobilogram; pub use multi_chromatogram_agg::MultiCMGStats; pub use multi_chromatogram_agg::MultiCMGStatsArrays; pub use multi_chromatogram_agg::MultiCMGStatsFactory; diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs index 04ca716..51b7850 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs @@ -342,12 +342,16 @@ impl From Aggregator for MultiCMGStats { - type Item = (RawPeak, FH); +impl Aggregator + for MultiCMGStats +{ + type Item = RawPeak; + type Context = FH; type Output = NaturalFinalizedMultiCMGStatsArrays; - fn add(&mut self, peak: impl Into<(RawPeak, FH)>) { - let (peak, transition) = peak.into(); + fn add(&mut self, peak: impl Into) { + let peak = peak.into(); + let transition = self.get_context(); let u64_intensity = peak.intensity as u64; let rt_miliseconds = (peak.retention_time * 1000.0) as u32; diff --git a/src/models/aggregators/raw_peak_agg/point_agg.rs b/src/models/aggregators/raw_peak_agg/point_agg.rs index 1ddbd34..f731c91 100644 --- a/src/models/aggregators/raw_peak_agg/point_agg.rs +++ b/src/models/aggregators/raw_peak_agg/point_agg.rs @@ -1,5 +1,5 @@ use crate::models::frames::raw_peak::RawPeak; -use crate::traits::aggregator::Aggregator; +use crate::traits::aggregator::{Aggregator, NoContext, ProvidesContext}; use serde::Serialize; #[derive(Debug, Clone, Copy)] @@ -20,12 +20,13 @@ impl RawPeakIntensityAggregator { } impl Aggregator for RawPeakIntensityAggregator { - type Item = (RawPeak, T); + type Item = RawPeak; + type Context = NoContext; type Output = u64; - fn add(&mut self, peak: impl Into<(RawPeak, T)>) { + fn add(&mut self, peak: impl Into) { let peak = peak.into(); - self.intensity += peak.0.intensity as u64; + self.intensity += peak.intensity as u64; } fn finalize(self) -> u64 { @@ -69,6 +70,7 @@ pub struct RawPeakVectorArrays { impl Aggregator for RawPeakVectorAggregator { type Item = RawPeak; + type Context = NoContext; type Output = RawPeakVectorArrays; fn add(&mut self, peak: impl Into) { diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index c0da9f3..9006607 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -7,6 +7,7 @@ use crate::sort_vecs_by_first; use crate::utils::compress_explode::explode_vec; use crate::utils::frame_processing::{lazy_centroid_weighted_frame, PeakArrayRefs}; use crate::utils::sorting::top_n; +use crate::utils::tolerance_ranges::IncludedRange; use crate::utils::tolerance_ranges::{scan_tol_range, tof_tol_range}; use rayon::prelude::*; use std::collections::HashMap; @@ -108,26 +109,27 @@ impl ExpandedFrameSlice { impl ExpandedFrameSlice { pub fn query_peaks( &self, - tof_range: (u32, u32), - scan_range: Option<(usize, usize)>, + tof_range: IncludedRange, + scan_range: Option>, f: &mut F, ) where F: FnMut(PeakInQuad), { + // TODO abstract this operation... Range -> Range let peak_range = { - let peak_ind_start = self.tof_indices.partition_point(|x| x < &tof_range.0); - let peak_ind_end = self.tof_indices.partition_point(|x| x <= &tof_range.1); - peak_ind_start..peak_ind_end + let peak_ind_start = self.tof_indices.partition_point(|x| *x < tof_range.start()); + let peak_ind_end = self.tof_indices.partition_point(|x| *x <= tof_range.end()); + peak_ind_start..=peak_ind_end }; - if let Some((min_scan, max_scan)) = scan_range { - assert!(min_scan <= max_scan); - } + // if let Some(scan_range) = scan_range { + // assert!(scan_range.start() <= scan_range.end()); + // } for peak_ind in peak_range { let scan_index = self.scan_numbers[peak_ind]; - if let Some((min_scan, max_scan)) = scan_range { - if scan_index < min_scan || scan_index > max_scan { + if let Some(scan_range) = &scan_range { + if !scan_range.contains(scan_index) { continue; } } @@ -548,7 +550,7 @@ impl ExpandedQuadSliceInfo { .iter() .map(|tof| { let mut local_inten = 0u32; - local_frame.query_peaks((tof - 1, tof + 1), None, &mut |x| { + local_frame.query_peaks(IncludedRange::new(tof - 1, tof + 1), None, &mut |x| { local_inten += x.intensity }); assert!(local_inten > 0); @@ -575,9 +577,11 @@ impl ExpandedQuadSliceInfo { continue; } let mut local_int = 0u32; - lookup_frame.query_peaks((peak.tof - 1, peak.tof + 1), None, &mut |x| { - local_int += x.intensity - }); + lookup_frame.query_peaks( + IncludedRange::new(peak.tof - 1, peak.tof + 1), + None, + &mut |x| local_int += x.intensity, + ); if local_int > (peak.intensity / 100) { peak.max_rt = local_rt; peak.patience = 1; @@ -612,9 +616,11 @@ impl ExpandedQuadSliceInfo { continue; } let mut local_int = 0; - lookup_frame.query_peaks((peak.tof - 1, peak.tof + 1), None, &mut |x| { - local_int += x.intensity - }); + lookup_frame.query_peaks( + IncludedRange::new(peak.tof - 1, peak.tof + 1), + None, + &mut |x| local_int += x.intensity, + ); if local_int > (peak.intensity / 100) { peak.min_rt = local_rt; diff --git a/src/models/frames/raw_frames.rs b/src/models/frames/raw_frames.rs index bb071d6..4cc1f9c 100644 --- a/src/models/frames/raw_frames.rs +++ b/src/models/frames/raw_frames.rs @@ -1,12 +1,13 @@ use timsrust::{Frame, QuadrupoleSettings}; use super::raw_peak::RawPeak; +use crate::utils::tolerance_ranges::IncludedRange; use tracing::trace; pub fn scans_matching_quad( quad_settings: &QuadrupoleSettings, - quad_range: (f64, f64), -) -> Option<(usize, usize)> { + quad_range: IncludedRange, +) -> Option> { let mut min_start = usize::MAX; let mut max_end = 0; @@ -15,7 +16,7 @@ pub fn scans_matching_quad( let quad_start = quad_settings.isolation_mz[i] - half_width; let quad_end = quad_settings.isolation_mz[i] + half_width; - if quad_start <= quad_range.1 && quad_end >= quad_range.0 { + if quad_start <= quad_range.end() && quad_end >= quad_range.start() { let start = quad_settings.scan_starts[i]; let end = quad_settings.scan_ends[i]; min_start = min_start.min(start); @@ -26,15 +27,15 @@ pub fn scans_matching_quad( if min_start == usize::MAX { None } else { - Some((min_start, max_end)) + Some((min_start, max_end).into()) } } pub fn frame_elems_matching( frame: &Frame, - tof_range: (u32, u32), - scan_range: (usize, usize), - quad_range: Option<(f64, f64)>, + tof_range: IncludedRange, + scan_range: IncludedRange, + quad_range: Option>, ) -> impl Iterator + '_ { trace!( "frame_elems_matching tof_range: {:?}, scan_range: {:?}, quad_range: {:?}", @@ -52,11 +53,11 @@ pub fn frame_elems_matching( // Only checkinghere bc its common for them to get flipped // bc skill issues. (and the highest scan is actually the lowest 1/k0) - let min_scan = scan_range.0.min(scan_range.1); - let max_scan = scan_range.0.max(scan_range.1); + let min_scan = scan_range.start(); + let max_scan = scan_range.end(); - let min_quad_scan = quad_scan_range.0.min(quad_scan_range.1); - let max_quad_scan = quad_scan_range.0.max(quad_scan_range.1); + let min_quad_scan = quad_scan_range.start(); + let max_quad_scan = quad_scan_range.end(); let (scan_ind_start, scan_ind_end): (usize, usize) = (min_quad_scan.max(min_scan), max_quad_scan.min(max_scan)); @@ -83,7 +84,7 @@ pub fn frame_elems_matching( (tof_ind, intensity, scan_index) }) - .filter(|(tof_ind, _, _)| *tof_ind >= tof_range.0 && *tof_ind < tof_range.1) + .filter(|(tof_ind, _, _)| *tof_ind >= tof_range.start() && *tof_ind < tof_range.end()) .map(|(tof_ind, intensity, scan_index)| RawPeak { scan_index, tof_index: tof_ind, diff --git a/src/models/frames/single_quad_settings.rs b/src/models/frames/single_quad_settings.rs index 2225801..12f3dab 100644 --- a/src/models/frames/single_quad_settings.rs +++ b/src/models/frames/single_quad_settings.rs @@ -3,6 +3,8 @@ use std::hash::Hash; use timsrust::QuadrupoleSettings; +use crate::utils::tolerance_ranges::IncludedRange; + #[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)] pub struct SingleQuadrupoleSettingIndex { pub major_index: usize, @@ -128,8 +130,8 @@ pub fn expand_quad_settings(quad_settings: &QuadrupoleSettings) -> ExpandedFrame pub fn get_matching_quad_settings( flat_quad_settings: &[SingleQuadrupoleSetting], - precursor_mz_range: (f64, f64), - scan_range: Option<(usize, usize)>, + precursor_mz_range: IncludedRange, + scan_range: Option>, ) -> impl Iterator + '_ { flat_quad_settings .iter() @@ -139,16 +141,23 @@ pub fn get_matching_quad_settings( .map(|e| e.index) } -fn matches_iso_window(qs: &SingleQuadrupoleSetting, precursor_mz_range: (f64, f64)) -> bool { - (qs.ranges.isolation_low <= precursor_mz_range.1) - && (qs.ranges.isolation_high >= precursor_mz_range.0) +fn matches_iso_window( + qs: &SingleQuadrupoleSetting, + precursor_mz_range: IncludedRange, +) -> bool { + (qs.ranges.isolation_low <= precursor_mz_range.end()) + && (qs.ranges.isolation_high >= precursor_mz_range.start()) } -fn matches_scan_range(qs: &SingleQuadrupoleSetting, scan_range: Option<(usize, usize)>) -> bool { +fn matches_scan_range( + qs: &SingleQuadrupoleSetting, + scan_range: Option>, +) -> bool { match scan_range { - Some((min_scan, max_scan)) => { + Some(tmp_range) => { + let min_scan = tmp_range.start(); + let max_scan = tmp_range.end(); assert!(qs.ranges.scan_start <= qs.ranges.scan_end); - assert!(min_scan <= max_scan); // Above quad // Quad [----------] @@ -173,8 +182,8 @@ fn matches_scan_range(qs: &SingleQuadrupoleSetting, scan_range: Option<(usize, u pub fn matches_quad_settings( a: &SingleQuadrupoleSetting, - precursor_mz_range: (f64, f64), - scan_range: Option<(usize, usize)>, + precursor_mz_range: IncludedRange, + scan_range: Option>, ) -> bool { matches_iso_window(a, precursor_mz_range) && matches_scan_range(a, scan_range) } diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index f2c5533..c9900ae 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -13,6 +13,7 @@ use crate::models::frames::single_quad_settings::{ use crate::models::queries::FragmentGroupIndexQuery; use crate::traits::aggregator::Aggregator; use crate::traits::queriable_data::QueriableData; +use crate::utils::tolerance_ranges::IncludedRange; use crate::ToleranceAdapter; use rayon::prelude::*; use serde::Serialize; @@ -52,21 +53,21 @@ impl ExpandedSliceBundle { pub fn query_peaks( &self, - tof_range: (u32, u32), - scan_range: Option<(usize, usize)>, - frame_index_range: (usize, usize), + tof_range: IncludedRange, + scan_range: Option>, + frame_index_range: IncludedRange, f: &mut F, ) where F: FnMut(PeakInQuad), { // Binary search the rt if needed. let frame_indices = self.frame_indices.as_slice(); - let low = frame_indices.partition_point(|x| x < &frame_index_range.0); - let high = frame_indices.partition_point(|x| x <= &frame_index_range.1); + let low = frame_indices.partition_point(|x| *x < frame_index_range.start()); + let high = frame_indices.partition_point(|x| *x <= frame_index_range.end()); for i in low..high { let slice = &self.slices[i]; - slice.query_peaks(tof_range, scan_range, f); + slice.query_peaks(tof_range.clone(), scan_range.clone(), f); } } } @@ -74,10 +75,10 @@ impl ExpandedSliceBundle { impl ExpandedRawFrameIndex { pub fn query_peaks( &self, - tof_range: (u32, u32), - precursor_mz_range: (f64, f64), - scan_range: Option<(usize, usize)>, - frame_index_range: (usize, usize), + tof_range: IncludedRange, + precursor_mz_range: IncludedRange, + scan_range: Option>, + frame_index_range: IncludedRange, f: &mut F, ) where F: FnMut(PeakInQuad), @@ -91,9 +92,9 @@ impl ExpandedRawFrameIndex { fn query_precursor_peaks( &self, matching_quads: &[SingleQuadrupoleSettingIndex], - tof_range: (u32, u32), - scan_range: Option<(usize, usize)>, - frame_index_range: (usize, usize), + tof_range: IncludedRange, + scan_range: Option>, + frame_index_range: IncludedRange, f: &mut F, ) where F: FnMut(PeakInQuad), @@ -169,7 +170,7 @@ impl ExpandedRawFrameIndex { } impl - QueriableData, (RawPeak, FH)> for ExpandedRawFrameIndex + QueriableData, RawPeak, FH> for ExpandedRawFrameIndex { fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { todo!(); @@ -234,8 +235,8 @@ impl fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], ) where - A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, - AG: Aggregator, + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, { // fragment_queries // .par_iter() @@ -271,9 +272,10 @@ impl .iter() .map(|x| { ( - x.precursor_query.isolation_mz_range.0 as f64, - x.precursor_query.isolation_mz_range.0 as f64, + x.precursor_query.isolation_mz_range.start() as f64, + x.precursor_query.isolation_mz_range.end() as f64, ) + .into() }) .collect::>(); @@ -317,12 +319,13 @@ impl } for (fh, tof_range) in fragment_queries[i].mz_index_ranges.iter() { - let mut local_lambda = |peak| agg.add((RawPeak::from(peak), *fh)); + agg.set_context(*fh); + // let mut local_lambda = |peak| agg.add((RawPeak::from(peak), *fh)); tqi.query_peaks( *tof_range, scan_ranges[i], frame_index_ranges[i], - &mut local_lambda, + &mut |x| agg.add(x), ); } }); diff --git a/src/models/indices/raw_file_index.rs b/src/models/indices/raw_file_index.rs index 23a6977..a65d729 100644 --- a/src/models/indices/raw_file_index.rs +++ b/src/models/indices/raw_file_index.rs @@ -1,8 +1,10 @@ +use crate::models::adapters::FragmentIndexAdapter; use crate::models::frames::raw_frames::frame_elems_matching; use crate::models::frames::raw_peak::RawPeak; use crate::models::queries::{FragmentGroupIndexQuery, NaturalPrecursorQuery, PrecursorIndexQuery}; use crate::traits::aggregator::Aggregator; use crate::traits::queriable_data::QueriableData; +use crate::utils::tolerance_ranges::IncludedRange; use crate::ElutionGroup; use crate::ToleranceAdapter; use rayon::iter::ParallelIterator; @@ -17,7 +19,7 @@ use tracing::trace; pub struct RawFileIndex { file_reader: FrameReader, - meta_converters: Metadata, + adapter: FragmentIndexAdapter, } impl RawFileIndex { @@ -26,35 +28,13 @@ impl RawFileIndex { let sql_path = std::path::Path::new(path).join("analysis.tdf"); let meta_converters = MetadataReader::new(&sql_path)?; + let adapter = meta_converters.into(); Ok(Self { file_reader, - meta_converters, + adapter, }) } - pub fn convert_precursor_query(&self, query: &NaturalPrecursorQuery) -> PrecursorIndexQuery { - PrecursorIndexQuery { - frame_index_range: ( - self.meta_converters.rt_converter.invert(query.rt_range.0) as usize, - self.meta_converters.rt_converter.invert(query.rt_range.1) as usize, - ), - rt_range_seconds: query.rt_range, - mz_index_range: ( - self.meta_converters.mz_converter.invert(query.mz_range.0) as u32, - self.meta_converters.mz_converter.invert(query.mz_range.1) as u32, - ), - mobility_index_range: ( - self.meta_converters - .im_converter - .invert(query.mobility_range.0) as usize, - self.meta_converters - .im_converter - .invert(query.mobility_range.1) as usize, - ), - isolation_mz_range: query.isolation_mz_range, - } - } - fn apply_on_query< 'c, 'b: 'c, @@ -68,7 +48,7 @@ impl RawFileIndex { trace!("RawFileIndex::apply_on_query"); trace!("FragmentGroupIndexQuery: {:?}", fqs); let frames: Vec = self - .read_frames_in_range(&fqs.precursor_query.frame_index_range) + .read_frames_in_range(&fqs.precursor_query.frame_index_range.into()) .filter(|x| x.is_ok()) .map(|x| x.unwrap()) .collect(); @@ -82,7 +62,7 @@ impl RawFileIndex { &frame, *tof_range, scan_range, - Some((iso_mz_range.0 as f64, iso_mz_range.1 as f64)), + Some((iso_mz_range.start() as f64, iso_mz_range.end() as f64).into()), ); for peak in peaks { fun(peak, *fh); @@ -99,55 +79,6 @@ impl RawFileIndex { self.file_reader.parallel_filter(lambda_use) } - fn query_from_elution_group_impl( - &self, - tol: &dyn crate::traits::tolerance::Tolerance, - elution_group: &crate::models::elution_group::ElutionGroup, - ) -> PrecursorIndexQuery { - let rt_range = tol.rt_range(elution_group.rt_seconds); - let mz_range = tol.mz_range(elution_group.precursor_mz); - let quad_range = tol.quad_range(elution_group.precursor_mz, elution_group.precursor_charge); - - let mobility_range = tol.mobility_range(elution_group.mobility); - let mobility_range = match mobility_range { - Some(mobility_range) => mobility_range, - None => ( - self.meta_converters.lower_im as f32, - self.meta_converters.upper_im as f32, - ), - }; - let mut min_scan_index = - self.meta_converters.im_converter.invert(mobility_range.0) as usize; - let mut max_scan_index = - self.meta_converters.im_converter.invert(mobility_range.1) as usize; - - if min_scan_index > max_scan_index { - std::mem::swap(&mut min_scan_index, &mut max_scan_index); - } - - let rt_range = match rt_range { - Some(rt_range) => rt_range, - None => ( - self.meta_converters.lower_rt as f32, - self.meta_converters.upper_rt as f32, - ), - }; - - PrecursorIndexQuery { - frame_index_range: ( - self.meta_converters.rt_converter.invert(rt_range.0) as usize, - self.meta_converters.rt_converter.invert(rt_range.1) as usize, - ), - rt_range_seconds: rt_range, - mz_index_range: ( - self.meta_converters.mz_converter.invert(mz_range.0) as u32, - self.meta_converters.mz_converter.invert(mz_range.1) as u32, - ), - mobility_index_range: (min_scan_index, max_scan_index), - isolation_mz_range: quad_range, - } - } - fn queries_from_elution_elements_impl< FH: Clone + Eq + Serialize + Hash + Send + Sync + Copy, >( @@ -155,32 +86,7 @@ impl RawFileIndex { tol: &dyn crate::traits::tolerance::Tolerance, elution_elements: &crate::models::elution_group::ElutionGroup, ) -> FragmentGroupIndexQuery { - let precursor_query = self.query_from_elution_group_impl(tol, elution_elements); - // TODO: change this unwrap and use explicitly the lack of fragment mzs. - // Does that mean its onlyt a precursor query? - // Why is it an option? - // - // let fragment_mzs = elution_elements.fragment_mzs.as_ref().unwrap(); - - let fqs = elution_elements - .fragment_mzs - .iter() - .map(|(k, v)| { - let mz_range = tol.mz_range(*v); - ( - *k, - ( - self.meta_converters.mz_converter.invert(mz_range.0) as u32, - self.meta_converters.mz_converter.invert(mz_range.1) as u32, - ), - ) - }) - .collect(); - - FragmentGroupIndexQuery { - mz_index_ranges: fqs, - precursor_query, - } + self.adapter.query_from_elution_group(tol, elution_elements) } } diff --git a/src/models/indices/transposed_quad_index/peak_bucket.rs b/src/models/indices/transposed_quad_index/peak_bucket.rs index d0f0e7d..4e6ae76 100644 --- a/src/models/indices/transposed_quad_index/peak_bucket.rs +++ b/src/models/indices/transposed_quad_index/peak_bucket.rs @@ -1,6 +1,7 @@ use crate::sort_vecs_by_first; use crate::utils::compress_explode::compress_vec; use crate::utils::display::{glimpse_vec, GlimpseConfig}; +use crate::utils::tolerance_ranges::IncludedRange; use std::fmt::Display; pub struct PeakInBucket { @@ -155,8 +156,8 @@ impl PeakBucket { pub fn query_peaks( &self, - scan_range: Option<(usize, usize)>, - rt_range: Option<(f32, f32)>, + scan_range: Option>, + rt_range: Option>, ) -> impl Iterator + '_ { match self.mode { PeakBucketMode::Compressed => self @@ -172,11 +173,11 @@ impl PeakBucket { pub fn query_peaks_sorted( &self, - scan_range: Option<(usize, usize)>, - rt_range: Option<(f32, f32)>, + scan_range: Option>, + rt_range: Option>, ) -> impl Iterator + '_ { let (scan_min, scan_max) = match scan_range { - Some((scan_low, scan_high)) => (scan_low, scan_high), + Some(x) => x.into(), None => ( 0, *(self @@ -204,8 +205,8 @@ impl PeakBucket { } let retention_time = self.retention_times[x]; - if let Some((low, high)) = rt_range { - if retention_time < low || retention_time > high { + if let Some(x) = rt_range { + if !x.contains(retention_time) { return None; } } @@ -219,12 +220,12 @@ impl PeakBucket { pub fn query_peaks_compressed( &self, - scan_range: Option<(usize, usize)>, - rt_range: Option<(f32, f32)>, + scan_range: Option>, + rt_range: Option>, ) -> impl Iterator + '_ { let scan_range = match scan_range { - Some((scan_low, scan_high)) => scan_low..scan_high.min(self.scan_offsets.len() - 1), - None => 0..(self.scan_offsets.len() - 1), + Some(x) => x.start()..=x.end().min(self.scan_offsets.len() - 1), + None => 0..=(self.scan_offsets.len() - 1), }; scan_range .flat_map(move |scan_index| { @@ -234,10 +235,10 @@ impl PeakBucket { (peak_index_start..peak_index_end).map(move |peak_index| { let retention_time = self.retention_times[peak_index]; - if let Some((low, high)) = rt_range { - if retention_time < low || retention_time > high { + if let Some(x) = rt_range { + if !x.contains(retention_time) { return None; - } + }; } let intensity = self.intensities[peak_index]; diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index c5d203e..87b62d9 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -5,6 +5,7 @@ use crate::models::frames::peak_in_quad::PeakInQuad; use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; use crate::sort_vecs_by_first; use crate::utils::display::{glimpse_vec, GlimpseConfig}; +use crate::utils::tolerance_ranges::IncludedRange; use std::collections::{BTreeMap, HashMap}; use std::fmt::Display; use std::time::Instant; @@ -72,12 +73,12 @@ impl Display for TransposedQuadIndex { impl TransposedQuadIndex { pub fn query_peaks( &self, - tof_range: (u32, u32), - scan_range: Option<(usize, usize)>, - rt_range: Option<(f32, f32)>, + tof_range: IncludedRange, + scan_range: Option>, + rt_range: Option>, ) -> impl Iterator + '_ { self.peak_buckets - .range(tof_range.0..tof_range.1) + .range(tof_range.start()..=tof_range.end()) .flat_map(move |(tof_index, pb)| { pb.query_peaks(scan_range, rt_range) .map(move |p| PeakInQuad::from_peak_in_bucket(p, *tof_index)) diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 2f003b9..1bba871 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -14,6 +14,7 @@ use crate::models::queries::FragmentGroupIndexQuery; use crate::traits::aggregator::Aggregator; use crate::traits::queriable_data::QueriableData; use crate::utils::display::{glimpse_vec, GlimpseConfig}; +use crate::utils::tolerance_ranges::IncludedRange; use crate::ToleranceAdapter; use rayon::prelude::*; use serde::Serialize; @@ -53,10 +54,10 @@ impl Debug for QuadSplittedTransposedIndex { impl QuadSplittedTransposedIndex { pub fn query_peaks( &self, - tof_range: (u32, u32), - precursor_mz_range: (f64, f64), - scan_range: Option<(usize, usize)>, - rt_range_seconds: Option<(f32, f32)>, + tof_range: IncludedRange, + precursor_mz_range: IncludedRange, + scan_range: Option>, + rt_range_seconds: Option>, f: &mut F, ) where F: FnMut(PeakInQuad), @@ -71,9 +72,9 @@ impl QuadSplittedTransposedIndex { fn query_precursor_peaks( &self, matching_quads: &[SingleQuadrupoleSettingIndex], - tof_range: (u32, u32), - scan_range: Option<(usize, usize)>, - rt_range_seconds: Option<(f32, f32)>, + tof_range: IncludedRange, + scan_range: Option>, + rt_range_seconds: Option>, f: &mut F, ) where F: FnMut(PeakInQuad), @@ -90,8 +91,8 @@ impl QuadSplittedTransposedIndex { fn get_matching_quad_settings( &self, - precursor_mz_range: (f64, f64), - scan_range: Option<(usize, usize)>, + precursor_mz_range: IncludedRange, + scan_range: Option>, ) -> impl Iterator + '_ { get_matching_quad_settings(&self.flat_quad_settings, precursor_mz_range, scan_range) } @@ -305,7 +306,7 @@ impl QueriableData, (RawPeak, FH)> for QuadSplittedTransposedIndex { fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { - let precursor_mz_range = ( + let precursor_mz_range = IncludedRange::new( fragment_query.precursor_query.isolation_mz_range.0 as f64, fragment_query.precursor_query.isolation_mz_range.0 as f64, ); @@ -334,7 +335,7 @@ impl A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, AG: Aggregator, { - let precursor_mz_range = ( + let precursor_mz_range = IncludedRange::new( fragment_query.precursor_query.isolation_mz_range.0 as f64, fragment_query.precursor_query.isolation_mz_range.0 as f64, ); @@ -366,12 +367,12 @@ impl .par_iter() .zip(aggregator.par_iter_mut()) .for_each(|(fragment_query, agg)| { - let precursor_mz_range = ( - fragment_query.precursor_query.isolation_mz_range.0 as f64, - fragment_query.precursor_query.isolation_mz_range.1 as f64, + let precursor_mz_range = fragment_query.precursor_query.isolation_mz_range; + let precursor_mz_range = IncludedRange::new( + precursor_mz_range.start() as f64, + precursor_mz_range.end() as f64, ); - assert!(precursor_mz_range.0 <= precursor_mz_range.1); - assert!(precursor_mz_range.0 > 0.0); + assert!(precursor_mz_range.start() > 0.0); let scan_range = Some(fragment_query.precursor_query.mobility_index_range); let local_quad_vec: Vec = self diff --git a/src/models/queries.rs b/src/models/queries.rs index dc3b9ea..1d26ca0 100644 --- a/src/models/queries.rs +++ b/src/models/queries.rs @@ -1,29 +1,72 @@ +use crate::traits::aggregator::ProvidesContext; +use crate::utils::tolerance_ranges::IncludedRange; use std::collections::HashMap; use std::hash::Hash; +use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter}; #[derive(Debug, Clone)] pub struct PrecursorIndexQuery { - pub frame_index_range: (usize, usize), - pub rt_range_seconds: (f32, f32), - pub mz_index_range: (u32, u32), - pub mobility_index_range: (usize, usize), - pub isolation_mz_range: (f32, f32), + pub frame_index_range: IncludedRange, + pub rt_range_seconds: IncludedRange, + pub mz_index_ranges: Vec>, + pub mobility_index_range: IncludedRange, + pub isolation_mz_range: IncludedRange, +} + +#[derive(Debug, Clone)] +pub enum MsLevelContext { + MS1(T1), + MS2(T2), } #[derive(Debug, Clone)] pub struct FragmentGroupIndexQuery { - pub mz_index_ranges: HashMap, + pub mz_index_ranges: HashMap>, pub precursor_query: PrecursorIndexQuery, } +impl ProvidesContext for FragmentGroupIndexQuery { + type Context = MsLevelContext; +} + +#[derive(Debug, Clone)] pub struct NaturalPrecursorQuery { - pub rt_range: (f32, f32), - pub mobility_range: (f32, f32), - pub mz_range: (f64, f64), - pub isolation_mz_range: (f32, f32), + pub rt_range: IncludedRange, + pub mobility_range: IncludedRange, + pub mz_ranges: Vec>, + pub isolation_mz_range: IncludedRange, } -pub struct NaturalFragmentQuery<'a> { - pub mz_range: (f64, f64), - pub precursor_query: &'a NaturalPrecursorQuery, +impl NaturalPrecursorQuery { + pub fn as_precursor_query( + &self, + mz_converter: &Tof2MzConverter, + im_converter: &Scan2ImConverter, + ) -> PrecursorIndexQuery { + PrecursorIndexQuery { + frame_index_range: ( + im_converter.invert(self.mobility_range.start()).round() as usize, + im_converter.invert(self.mobility_range.end()).round() as usize, + ) + .into(), + rt_range_seconds: self.rt_range.clone(), + mz_index_ranges: self + .mz_ranges + .iter() + .map(|mz_range| { + ( + mz_converter.invert(mz_range.start()).round() as u32, + mz_converter.invert(mz_range.end()).round() as u32, + ) + .into() + }) + .collect(), + mobility_index_range: ( + im_converter.invert(self.mobility_range.start()).round() as usize, + im_converter.invert(self.mobility_range.end()).round() as usize, + ) + .into(), + isolation_mz_range: self.isolation_mz_range.clone(), + } + } } diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index 4252b57..c46d4b1 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -4,6 +4,7 @@ use std::hash::Hash; use std::time::Instant; use tracing::info; +use crate::traits::aggregator::ProvidesContext; use crate::{Aggregator, ElutionGroup, QueriableData, Tolerance, ToleranceAdapter}; // TODO: URGENTLY make documentation fot eh functions using this leftover struct docs @@ -42,19 +43,19 @@ use crate::{Aggregator, ElutionGroup, QueriableData, Tolerance, ToleranceAdapter // 2. `QD` is queried with `QP` and `QF` queries. // 3. The results are aggregated with `AG` aggregators (which are generated by the factory, when passed a numeric ID). -pub fn query_multi_group<'a, QD, TL, QF, AE1, AE2, OE, AG, FH>( +pub fn query_multi_group<'a, QD, TL, QF, AE1, AE2, OE, AG, FH, CTX>( queriable_data: &'a QD, tolerance: &'a TL, elution_groups: &[ElutionGroup], aggregator_factory: &dyn Fn(u64) -> AG, ) -> Vec where - AG: Aggregator + Send + Sync, - QD: QueriableData + ToleranceAdapter>, + AG: Aggregator + Send + Sync, + QD: QueriableData + ToleranceAdapter>, TL: Tolerance, OE: Send + Sync, FH: Clone + Eq + Serialize + Hash + Send + Sync, - QF: Send + Sync, + QF: Send + Sync + ProvidesContext, // AE: Send + Sync + Clone + Copy, AE1: Into + Send + Sync + Clone + Copy, AE2: Send + Sync + Clone + Copy + From, diff --git a/src/traits/aggregator.rs b/src/traits/aggregator.rs index 13af0ae..5d1ed90 100644 --- a/src/traits/aggregator.rs +++ b/src/traits/aggregator.rs @@ -2,15 +2,55 @@ /// /// The `Item` type is the type of the item that is being aggregated. /// The `Output` type is the type of the output of the aggregation. +/// The `Context` type is the type of the context that is being aggregated. /// /// The `add` method takes an item of type `Item` OR a type that /// imlements `Into`. /// +/// The `set_context` method sets the context that is being aggregated. +/// Note that if the aggregator does not support contexts, this method +/// should never be called. (thus the default implementation is empty). +/// +/// The `supports_context` method returns true if the aggregator supports +/// contexts. +/// /// The `finalize` method returns the output of the aggregation. pub trait Aggregator: Send + Sync { type Item: Send + Sync + Clone; type Output: Send + Sync; + type Context: Send + Sync + std::fmt::Debug; fn add(&mut self, item: impl Into); fn finalize(self) -> Self::Output; + fn supports_context(&self) -> bool { + false + } + fn set_context(&mut self, context: Self::Context) { + panic!( + "Misconfigured aggregator, context not supported, got {:?}", + context + ); + } + fn get_context(&self) -> Self::Context { + panic!("Misconfigured aggregator, context not supported"); + } +} + +/// Trait purely for the purpose of semantic meaning. +/// +/// Every thread safe type automatically implements this trait. +/// For the context `NoContext`. +pub trait ProvidesContext { + type Context: Send + Sync; + fn provides_context(&self) -> bool { + false + } +} + +/// Dummy type to denote that no context is provided. +#[derive(Debug, Clone, Copy)] +pub enum NoContext {} + +impl ProvidesContext for T { + type Context = NoContext; } diff --git a/src/traits/queriable_data.rs b/src/traits/queriable_data.rs index 92f96de..cee64b7 100644 --- a/src/traits/queriable_data.rs +++ b/src/traits/queriable_data.rs @@ -1,49 +1,17 @@ -use crate::Aggregator; +use crate::traits::aggregator::{Aggregator, ProvidesContext}; -pub trait QueriableData +pub trait QueriableData where - QF: Send + Sync, + QF: Send + Sync + ProvidesContext, I: Send + Sync + Clone + Copy, { fn query(&self, fragment_query: &QF) -> Vec; fn add_query(&self, fragment_query: &QF, aggregator: &mut AG) where A: From + Send + Sync + Clone + Copy, - AG: Aggregator; + AG: Aggregator; fn add_query_multi_group(&self, fragment_queries: &[QF], aggregator: &mut [AG]) where A: From + Send + Sync + Clone + Copy, - AG: Aggregator; + AG: Aggregator; } - -// I like this idea but I need a way to set/propagate the tolerance -// -// impl>, QF, A, K> QueriableData for T { -// fn query(&self, fragment_query: &QF) -> Vec { -// let mut out = Vec::new(); -// let qf = self.query_from_elution_group(fragment_query); -// self.add_query(&qf, &mut |x| out.push(x)); -// out -// } -// -// fn add_query>( -// &self, -// fragment_query: &QF, -// aggregator: &mut AG, -// ) { -// let qf = self.query_from_elution_group(fragment_query); -// self.add_query(&qf, aggregator); -// } -// -// fn add_query_multi_group>( -// &self, -// fragment_queries: &[QF], -// aggregator: &mut [AG], -// ) { -// let qfs = fragment_queries -// .iter() -// .map(|x| self.query_from_elution_group(x)) -// .collect(); -// self.add_query_multi_group(&qfs, aggregator); -// } -// } diff --git a/src/traits/tolerance.rs b/src/traits/tolerance.rs index 0e4a2f3..a15ba2a 100644 --- a/src/traits/tolerance.rs +++ b/src/traits/tolerance.rs @@ -32,6 +32,8 @@ pub struct DefaultTolerance { pub rt: RtTolerance, pub mobility: MobilityTolerance, pub quad: QuadTolerance, + pub num_ms1_isotopes: usize, + pub num_ms2_isotopes: usize, } impl Default for DefaultTolerance { @@ -41,15 +43,47 @@ impl Default for DefaultTolerance { rt: RtTolerance::Absolute((5.0, 5.0)), mobility: MobilityTolerance::Pct((3.0, 3.0)), quad: QuadTolerance::Absolute((0.1, 0.1, 1)), + num_ms1_isotopes: 3, + num_ms2_isotopes: 1, } } } +fn mass_to_isotope_mzs(mass: f64, charge: u8, num_isotopes: usize) -> Vec { + let mut out = Vec::with_capacity(num_isotopes); + const PROTON_MASS: f64 = 1.007276; + for i in 1..(num_isotopes + 1) { + let mass = mass + i as f64 * PROTON_MASS; + let mz = mass / charge as f64; + out.push(mz); + } + out +} + +fn mz_to_isotope_mzs(mz: f64, charge: u8, num_isotopes: usize) -> Vec { + let mut out = Vec::with_capacity(num_isotopes); + const PROTON_MASS: f64 = 1.007276; + let proton_mass_frac = PROTON_MASS / charge as f64; + for i in 0..num_isotopes { + let mz = mz + (i as f64 * proton_mass_frac); + out.push(mz); + } + out +} + pub trait Tolerance { fn mz_range(&self, mz: f64) -> (f64, f64); fn rt_range(&self, rt: f32) -> Option<(f32, f32)>; fn mobility_range(&self, mobility: f32) -> Option<(f32, f32)>; fn quad_range(&self, precursor_mz: f64, precursor_charge: u8) -> (f32, f32); + fn num_ms1_isotopes(&self) -> usize; + fn isotope_mzs_mass(&self, monoisotopic_mass: f64, charge: u8) -> Vec { + mass_to_isotope_mzs(monoisotopic_mass, charge, self.num_ms1_isotopes()) + } + fn isotope_mzs_mz(&self, mz: f64, charge: u8) -> Vec { + mz_to_isotope_mzs(mz, charge, self.num_ms1_isotopes()) + } + fn num_ms2_isotopes(&self) -> usize; } impl Tolerance for DefaultTolerance { @@ -111,6 +145,14 @@ impl Tolerance for DefaultTolerance { } } } + + fn num_ms1_isotopes(&self) -> usize { + self.num_ms1_isotopes + } + + fn num_ms2_isotopes(&self) -> usize { + self.num_ms2_isotopes + } } /// A trait that can be implemented by types that can convert @@ -121,3 +163,55 @@ impl Tolerance for DefaultTolerance { pub trait ToleranceAdapter { fn query_from_elution_group(&self, tol: &dyn Tolerance, elution_group: &T) -> QF; } + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn test_isotope_mzs_neutral() { + let test_vals = vec![ + (100.0, 1, vec![101.0, 102.0, 103.0]), + (100.0, 2, vec![100.5, 101.0, 101.5]), + (100.0, 3, vec![100.33333, 100.666666, 101.0]), + ]; + + for (monoisotopic_mass, charge, expected) in test_vals { + let out = mass_to_isotope_mzs(monoisotopic_mass, charge, 3); + assert_eq!(out.len(), expected.len()); + let abs_diff: Vec = out + .iter() + .zip(expected.iter()) + .map(|(a, b)| (a - b).abs()) + .collect(); + for ad in abs_diff.iter() { + // Very tight tolerances here ... + assert!(*ad < 0.01); + } + } + } + + #[test] + fn test_isotope_mzs_mz() { + let test_vals = vec![ + (100.0, 1, vec![10.0, 101.0, 102.0]), + (100.0, 2, vec![100.0, 100.5, 101.5]), + (100.0, 3, vec![100.0, 100.3333, 101.66666]), + ]; + + for (monoisotopic_mass, charge, expected) in test_vals { + let out = mz_to_isotope_mzs(monoisotopic_mass, charge, 3); + assert_eq!(out.len(), expected.len()); + let abs_diff: Vec = out + .iter() + .zip(expected.iter()) + .map(|(a, b)| (a - b).abs()) + .collect(); + + for ad in abs_diff.iter() { + // Very tight tolerances here ... + assert!(*ad < 0.01); + } + } + } +} diff --git a/src/utils/frame_processing.rs b/src/utils/frame_processing.rs index 71528f9..6a0ecfb 100644 --- a/src/utils/frame_processing.rs +++ b/src/utils/frame_processing.rs @@ -1,7 +1,8 @@ use crate::sort_vecs_by_first; -use std::ops::RangeInclusive; use tracing::{error, info, warn}; +use super::tolerance_ranges::IncludedRange; + pub type TofIntensityVecs = (Vec, Vec); pub type CentroidedVecs = (TofIntensityVecs, Vec); @@ -61,8 +62,8 @@ pub fn lazy_centroid_weighted_frame<'a>( peak_refs: &'a [PeakArrayRefs<'a>], reference_index: usize, max_peaks: usize, - tof_tol_range_fn: impl Fn(u32) -> RangeInclusive, - ims_tol_range_fn: impl Fn(usize) -> RangeInclusive, + tof_tol_range_fn: impl Fn(u32) -> IncludedRange, + ims_tol_range_fn: impl Fn(usize) -> IncludedRange, ) -> CentroidedVecs { let slice_sizes: Vec = peak_refs.iter().map(|x| x.len()).collect(); let tot_size: usize = slice_sizes.iter().sum(); @@ -141,13 +142,13 @@ pub fn lazy_centroid_weighted_frame<'a>( for (ii, local_peak_refs) in peak_refs.iter().enumerate() { let ss_start = local_peak_refs .tof_array - .partition_point(|x| x < tof_range.start()); + .partition_point(|x| *x < tof_range.start()); let ss_end = local_peak_refs .tof_array - .partition_point(|x| x <= tof_range.end()); + .partition_point(|x| *x <= tof_range.end()); for i in ss_start..ss_end { let ti = local_offset_touched + i; - if !touched[ti] && ims_range.contains(&local_peak_refs.ims_array[i]) { + if !touched[ti] && ims_range.contains(local_peak_refs.ims_array[i]) { // Peaks are always weighted but not always intense! let local_intensity = local_peak_refs.intensity_array[i] as u64; if ii == reference_index { @@ -170,8 +171,8 @@ pub fn lazy_centroid_weighted_frame<'a>( // let calc_ims = (curr_agg_ims / curr_weight) as usize; let calc_tof = tof; let calc_ims = ims; - debug_assert!(tof_range.contains(&calc_tof)); - debug_assert!(ims_range.contains(&calc_ims)); + debug_assert!(tof_range.contains(calc_tof)); + debug_assert!(ims_range.contains(calc_ims)); agg_tof.push(calc_tof); agg_ims.push(calc_ims); num_added += 1; @@ -226,14 +227,14 @@ mod tests { use super::*; // Helper function to create a simple tolerance range for testing - fn test_tof_tolerance(tof: u32) -> RangeInclusive { + fn test_tof_tolerance(tof: u32) -> IncludedRange { let tolerance = 2; - (tof.saturating_sub(tolerance))..=tof.saturating_add(tolerance) + (tof.saturating_sub(tolerance), tof.saturating_add(tolerance)).into() } - fn test_ims_tolerance(ims: usize) -> RangeInclusive { + fn test_ims_tolerance(ims: usize) -> IncludedRange { let tolerance = 1; - (ims.saturating_sub(tolerance))..=ims.saturating_add(tolerance) + (ims.saturating_sub(tolerance), ims.saturating_add(tolerance)).into() } // Helper function to create PeakArrayRefs diff --git a/src/utils/tolerance_ranges.rs b/src/utils/tolerance_ranges.rs index faa3d4d..4bde46d 100644 --- a/src/utils/tolerance_ranges.rs +++ b/src/utils/tolerance_ranges.rs @@ -1,27 +1,68 @@ use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter}; -use std::ops::RangeInclusive; +#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)] +pub struct IncludedRange(pub T, pub T); -pub fn ppm_tol_range(elem: f64, tol_ppm: f64) -> RangeInclusive { +// TODO: Implement overlaps ... + +impl IncludedRange +where + T: Copy + PartialOrd, +{ + pub fn new(left: T, right: T) -> Self { + // Swao if left > right + if left > right { + Self(right, left) + } else { + Self(left, right) + } + } + + pub fn contains(&self, x: T) -> bool { + self.0 <= x && x <= self.1 + } + + pub fn start(&self) -> T { + self.0 + } + + pub fn end(&self) -> T { + self.1 + } +} + +impl From<(T, T)> for IncludedRange { + fn from(x: (T, T)) -> Self { + Self::new(x.0, x.1) + } +} + +impl Into<(T, T)> for IncludedRange { + fn into(self) -> (T, T) { + (self.0, self.1) + } +} + +pub fn ppm_tol_range(elem: f64, tol_ppm: f64) -> IncludedRange { let utol = elem * (tol_ppm / 1e6); let left_e = elem - utol; let right_e = elem + utol; - left_e..=right_e + (left_e, right_e).into() } -pub fn pct_tol_range(elem: f64, tol_pct: f64) -> RangeInclusive { +pub fn pct_tol_range(elem: f64, tol_pct: f64) -> IncludedRange { let utol = elem * (tol_pct / 100.0); let left_e = elem - utol; let right_e = elem + utol; - left_e..=right_e + (left_e, right_e).into() } -pub fn tof_tol_range(tof: u32, tol_ppm: f64, converter: &Tof2MzConverter) -> RangeInclusive { +pub fn tof_tol_range(tof: u32, tol_ppm: f64, converter: &Tof2MzConverter) -> IncludedRange { let mz = converter.convert(tof); let mz_range = ppm_tol_range(mz, tol_ppm); - RangeInclusive::new( - converter.invert(*mz_range.start()).round() as u32, - converter.invert(*mz_range.end()).round() as u32, + IncludedRange::new( + converter.invert(mz_range.start()).round() as u32, + converter.invert(mz_range.end()).round() as u32, ) } @@ -29,17 +70,17 @@ pub fn scan_tol_range( scan: usize, tol_pct: f64, converter: &Scan2ImConverter, -) -> RangeInclusive { +) -> IncludedRange { let im = converter.convert(scan as f64); let im_range = pct_tol_range(im, tol_pct); - let scan_min = converter.invert(*im_range.start()).round() as usize; - let scan_max = converter.invert(*im_range.end()).round() as usize; + let scan_min = converter.invert(im_range.start()).round() as usize; + let scan_max = converter.invert(im_range.end()).round() as usize; // Note I need to do this here bc the conversion between scan numbers and ion // mobilities is not monotonically increasing. IN OTHER WORDS, lower scan numbers // are higher 1/k0.... But im not sure if they are ALWAYS inversely proportional. if scan_min > scan_max { - scan_max..=scan_min + (scan_max, scan_min).into() } else { - scan_min..=scan_max + (scan_min, scan_max).into() } } From 68855a633e7ce2eece972f2901e3eb7fb9c5aa0a Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Thu, 31 Oct 2024 18:34:31 -0700 Subject: [PATCH 16/30] feat(wip,trait)!: aggregator context propagation --- Cargo.lock | 2 +- Cargo.toml | 2 +- benches/benchmark_indices.rs | 4 + src/main.rs | 21 +- .../raw_peak_agg/chromatogram_agg.rs | 2 + .../raw_peak_agg/multi_chromatogram_agg.rs | 225 +++++++++++------- .../aggregators/raw_peak_agg/point_agg.rs | 21 +- .../aggregators/streaming_aggregator.rs | 18 ++ src/models/frames/expanded_frame.rs | 6 +- .../indices/expanded_raw_index/model.rs | 120 +++++----- src/models/indices/raw_file_index.rs | 36 +-- .../quad_splitted_transposed_index.rs | 106 ++++++--- src/models/queries.rs | 49 +++- .../queriable_tims_data.rs | 12 +- src/traits/aggregator.rs | 13 +- src/traits/queriable_data.rs | 19 +- src/traits/tolerance.rs | 1 + 17 files changed, 402 insertions(+), 255 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 473a7b2..43c371c 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1307,7 +1307,7 @@ dependencies = [ [[package]] name = "timsquery" -version = "0.5.0" +version = "0.6.0" dependencies = [ "clap", "indicatif", diff --git a/Cargo.toml b/Cargo.toml index fa3b214..dfd31d4 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "timsquery" -version = "0.5.0" +version = "0.6.0" edition = "2021" license = "Apache-2.0" diff --git a/benches/benchmark_indices.rs b/benches/benchmark_indices.rs index 3afc9e5..006c96e 100644 --- a/benches/benchmark_indices.rs +++ b/benches/benchmark_indices.rs @@ -326,12 +326,16 @@ fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Ve rt: RtTolerance::Absolute((5.0, 5.0)), mobility: MobilityTolerance::Pct((3.0, 3.0)), quad: QuadTolerance::Absolute((0.1, 0.1, 1)), + num_ms1_isotopes: 3, + num_ms2_isotopes: 1, }; let tolerance_with_nort = DefaultTolerance { ms: MzToleramce::Ppm((20.0, 20.0)), rt: RtTolerance::None, mobility: MobilityTolerance::Pct((3.0, 3.0)), quad: QuadTolerance::Absolute((0.1, 0.1, 1)), + num_ms1_isotopes: 3, + num_ms2_isotopes: 1, }; let tolerances = [ (tolerance_with_rt, "narrow_rt"), diff --git a/src/main.rs b/src/main.rs index 203d25b..9fc15d9 100644 --- a/src/main.rs +++ b/src/main.rs @@ -8,8 +8,7 @@ use timsquery::traits::tolerance::DefaultTolerance; use timsquery::traits::tolerance::{MobilityTolerance, MzToleramce, QuadTolerance, RtTolerance}; use timsquery::{ models::aggregators::{ - ChromatomobilogramStats, ExtractedIonChromatomobilogram, MultiCMGStatsFactory, - RawPeakIntensityAggregator, RawPeakVectorAggregator, + MultiCMGStatsFactory, RawPeakIntensityAggregator, RawPeakVectorAggregator, }, models::indices::{ExpandedRawFrameIndex, QuadSplittedTransposedIndex}, }; @@ -155,8 +154,6 @@ pub enum PossibleAggregator { #[default] RawPeakIntensityAggregator, RawPeakVectorAggregator, - ExtractedIonChromatomobilogram, - ChromatoMobilogramStat, MultiCMGStats, } @@ -301,14 +298,6 @@ pub fn execute_query( let aggregator = RawPeakVectorAggregator::new; execute_query_inner!(index, aggregator); } - PossibleAggregator::ChromatoMobilogramStat => { - let aggregator = ChromatomobilogramStats::new; - execute_query_inner!(index, aggregator); - } - PossibleAggregator::ExtractedIonChromatomobilogram => { - let aggregator = ExtractedIonChromatomobilogram::new; - execute_query_inner!(index, aggregator); - } PossibleAggregator::MultiCMGStats => { let factory = MultiCMGStatsFactory { converters: (index.mz_converter, index.im_converter), @@ -329,14 +318,6 @@ pub fn execute_query( let aggregator = RawPeakVectorAggregator::new; execute_query_inner!(index, aggregator); } - PossibleAggregator::ChromatoMobilogramStat => { - let aggregator = ChromatomobilogramStats::new; - execute_query_inner!(index, aggregator); - } - PossibleAggregator::ExtractedIonChromatomobilogram => { - let aggregator = ExtractedIonChromatomobilogram::new; - execute_query_inner!(index, aggregator); - } PossibleAggregator::MultiCMGStats => { let factory = MultiCMGStatsFactory { converters: (index.mz_converter, index.im_converter), diff --git a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs index aa5d091..6eed3d5 100644 --- a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs @@ -9,6 +9,8 @@ use std::collections::HashMap; pub type MappingCollection = HashMap; +/// A struct that can be used to calculate the mean and variance +/// of a stream of weighted tof and scan numbers. #[derive(Debug, Clone)] pub struct ScanTofStatsCalculatorPair { pub scan: RunningStatsCalculator, diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs index 51b7850..62df922 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs @@ -4,6 +4,7 @@ use super::chromatogram_agg::{ use crate::models::aggregators::rolling_calculators::rolling_median; use crate::models::aggregators::streaming_aggregator::RunningStatsCalculator; use crate::models::frames::raw_peak::RawPeak; +use crate::models::queries::MsLevelContext; use crate::traits::aggregator::Aggregator; use crate::utils::math::{lnfact, lnfact_float}; use serde::Serialize; @@ -14,12 +15,62 @@ use tracing::{debug, warn}; use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter}; #[derive(Debug, Clone)] -pub struct MultiCMGStats { +struct _MultiCMGStats { pub scan_tof_mapping: MappingCollection<(FH, u32), ScanTofStatsCalculatorPair>, - pub converters: (Tof2MzConverter, Scan2ImConverter), pub uniq_rts: HashSet, pub uniq_ids: HashSet, +} + +impl Default for _MultiCMGStats { + fn default() -> Self { + Self { + scan_tof_mapping: MappingCollection::new(), + uniq_rts: HashSet::new(), + uniq_ids: HashSet::new(), + } + } +} + +impl _MultiCMGStats { + fn finalize(self) -> MultiCMGStatsArrays { + let mut transition_stats = MappingCollection::new(); + + for id_key in self.uniq_ids.iter() { + let mut id_cmgs = ChromatomobilogramStatsArrays::new(); + for rt_key in self.uniq_rts.iter() { + let scan_tof_mapping = self.scan_tof_mapping.get(&(id_key.clone(), *rt_key)); + if let Some(scan_tof_mapping) = scan_tof_mapping { + id_cmgs.retention_time_miliseconds.push(*rt_key); + id_cmgs + .scan_index_means + .push(scan_tof_mapping.scan.mean().unwrap()); + id_cmgs + .scan_index_sds + .push(scan_tof_mapping.scan.standard_deviation().unwrap()); + id_cmgs + .tof_index_means + .push(scan_tof_mapping.tof.mean().unwrap()); + id_cmgs + .tof_index_sds + .push(scan_tof_mapping.tof.standard_deviation().unwrap()); + id_cmgs.intensities.push(scan_tof_mapping.tof.weight()); + } + } + id_cmgs.sort_by_rt(); + transition_stats.insert(id_key.clone(), id_cmgs); + } + + MultiCMGStatsArrays { transition_stats } + } +} + +#[derive(Debug, Clone)] +pub struct MultiCMGStats { + pub converters: (Tof2MzConverter, Scan2ImConverter), + pub ms1_stats: _MultiCMGStats, + pub ms2_stats: _MultiCMGStats, pub id: u64, + pub context: Option>, } #[derive(Debug, Clone)] @@ -31,11 +82,11 @@ pub struct MultiCMGStatsFactory impl MultiCMGStatsFactory { pub fn build(&self, id: u64) -> MultiCMGStats { MultiCMGStats { - scan_tof_mapping: MappingCollection::new(), converters: (self.converters.0, self.converters.1), - uniq_rts: HashSet::new(), - uniq_ids: HashSet::new(), + ms1_stats: Default::default(), + ms2_stats: Default::default(), id, + context: None, } } } @@ -43,11 +94,10 @@ impl MultiCMGStatsFactory { #[derive(Debug, Clone, Serialize)] pub struct MultiCMGStatsArrays { pub transition_stats: MappingCollection, - id: u64, } #[derive(Debug, Clone, Serialize)] -pub struct FinalizedMultiCMGStatsArrays { +pub struct _FinalizedMultiCMGStatsArrays { pub retention_time_miliseconds: Vec, pub weighted_scan_index_mean: Vec, pub summed_intensity: Vec, @@ -60,12 +110,18 @@ pub struct FinalizedMultiCMGStatsArrays>, +} + +#[derive(Debug, Clone, Serialize)] +pub struct FinalizedMultiCMGStatsArrays { + pub ms1_stats: _FinalizedMultiCMGStatsArrays, + pub ms2_stats: _FinalizedMultiCMGStatsArrays, pub id: u64, } // This name is starting to get really long ... #[derive(Debug, Clone, Serialize)] -pub struct NaturalFinalizedMultiCMGStatsArrays { +pub struct _NaturalFinalizedMultiCMGStatsArrays { pub retention_time_miliseconds: Vec, pub average_mobility: Vec, pub summed_intensity: Vec, @@ -80,27 +136,14 @@ pub struct NaturalFinalizedMultiCMGStatsArrays>, pub transition_intensities: MappingCollection>, pub apex_primary_score_index: usize, - pub id: u64, } -// Reference python code - -// log1p_intensitties = np.log1p(arrays["summed_intensity"]) -// lazy_hyperscore = LN_FACTORIALS[arrays["npeaks"]] + (2 * log1p_intensitties) -// -// five_pct_len = int(len(arrays["retention_time_miliseconds"]) / 100) * 5 -// lazy_hyperscore_roll_median = ( -// pd.Series(lazy_hyperscore).rolling(window=five_pct_len, center=True).median() -// ).array -// hyperscore_off_baseline = lazy_hyperscore - lazy_hyperscore_roll_median -// hyperscore_off_baseline = np.nan_to_num(hyperscore_off_baseline, 0) -// iqr_hyperscore_off_baseline = np.percentile( -// hyperscore_off_baseline, 75 -// ) - np.percentile(hyperscore_off_baseline, 25) -// -// scaled_hyperscore_off_baseline = hyperscore_off_baseline / iqr_hyperscore_off_baseline -// ) -// ) +#[derive(Debug, Clone, Serialize)] +pub struct NaturalFinalizedMultiCMGStatsArrays { + pub ms1_stats: _NaturalFinalizedMultiCMGStatsArrays, + pub ms2_stats: _NaturalFinalizedMultiCMGStatsArrays, + pub id: u64, +} fn calculate_lazy_hyperscore(npeaks: &[usize], summed_intensity: &[u64]) -> Vec { let mut scores = vec![0.0; npeaks.len()]; @@ -121,9 +164,9 @@ fn calculate_value_vs_baseline(vals: &[f64], baseline_window_size: usize) -> Vec .collect() } -impl NaturalFinalizedMultiCMGStatsArrays { +impl _NaturalFinalizedMultiCMGStatsArrays { pub fn new( - other: FinalizedMultiCMGStatsArrays, + other: _FinalizedMultiCMGStatsArrays, mz_converter: &Tof2MzConverter, mobility_converter: &Scan2ImConverter, ) -> Self { @@ -185,7 +228,7 @@ impl NaturalFinalizedMultiCMGSt "Failed sanity check" ); - NaturalFinalizedMultiCMGStatsArrays { + _NaturalFinalizedMultiCMGStatsArrays { retention_time_miliseconds: other.retention_time_miliseconds, average_mobility: other .weighted_scan_index_mean @@ -227,18 +270,17 @@ impl NaturalFinalizedMultiCMGSt lazyerscore_vs_baseline, norm_hyperscore_vs_baseline, norm_lazyerscore_vs_baseline, - id: other.id, } } } impl From> - for FinalizedMultiCMGStatsArrays + for _FinalizedMultiCMGStatsArrays { fn from(other: MultiCMGStatsArrays) -> Self { // TODO ... maybe refactor this ... RN its king of ugly. - let mut out = FinalizedMultiCMGStatsArrays { + let mut out = _FinalizedMultiCMGStatsArrays { retention_time_miliseconds: Vec::new(), scan_index_means: MappingCollection::new(), tof_index_means: MappingCollection::new(), @@ -247,7 +289,6 @@ impl From Aggregat for MultiCMGStats { type Item = RawPeak; - type Context = FH; + type Context = MsLevelContext; type Output = NaturalFinalizedMultiCMGStatsArrays; fn add(&mut self, peak: impl Into) { let peak = peak.into(); - let transition = self.get_context(); let u64_intensity = peak.intensity as u64; let rt_miliseconds = (peak.retention_time * 1000.0) as u32; - self.uniq_rts.insert(rt_miliseconds); - self.uniq_ids.insert(transition.clone()); + match self.get_context() { + MsLevelContext::MS1(i) => { + self.ms1_stats.uniq_rts.insert(rt_miliseconds); + self.ms1_stats + .scan_tof_mapping + .entry((i, rt_miliseconds)) + .and_modify(|curr| { + curr.add(u64_intensity, peak.scan_index, peak.tof_index); + }) + .or_insert(ScanTofStatsCalculatorPair::new( + u64_intensity, + peak.scan_index, + peak.tof_index, + )); + } + MsLevelContext::MS2(i) => { + self.ms2_stats.uniq_rts.insert(rt_miliseconds); + self.ms2_stats + .scan_tof_mapping + .entry((i, rt_miliseconds)) + .and_modify(|curr| { + curr.add(u64_intensity, peak.scan_index, peak.tof_index); + }) + .or_insert(ScanTofStatsCalculatorPair::new( + u64_intensity, + peak.scan_index, + peak.tof_index, + )); + } + } + } - self.scan_tof_mapping - .entry((transition.clone(), rt_miliseconds)) - .and_modify(|curr| { - curr.add(u64_intensity, peak.scan_index, peak.tof_index); - }) - .or_insert(ScanTofStatsCalculatorPair::new( - u64_intensity, - peak.scan_index, - peak.tof_index, - )); + fn set_context(&mut self, context: Self::Context) { + match &context { + MsLevelContext::MS1(i) => { + self.ms1_stats.uniq_ids.insert(*i); + } + MsLevelContext::MS2(i) => { + self.ms2_stats.uniq_ids.insert(i.clone()); + } + } + self.context = Some(context); } - fn finalize(self) -> NaturalFinalizedMultiCMGStatsArrays { - let mut transition_stats = MappingCollection::new(); + fn supports_context(&self) -> bool { + true + } - for id_key in self.uniq_ids.iter() { - let mut id_cmgs = ChromatomobilogramStatsArrays::new(); - for rt_key in self.uniq_rts.iter() { - let scan_tof_mapping = self.scan_tof_mapping.get(&(id_key.clone(), *rt_key)); - if let Some(scan_tof_mapping) = scan_tof_mapping { - id_cmgs.retention_time_miliseconds.push(*rt_key); - id_cmgs - .scan_index_means - .push(scan_tof_mapping.scan.mean().unwrap()); - id_cmgs - .scan_index_sds - .push(scan_tof_mapping.scan.standard_deviation().unwrap()); - id_cmgs - .tof_index_means - .push(scan_tof_mapping.tof.mean().unwrap()); - id_cmgs - .tof_index_sds - .push(scan_tof_mapping.tof.standard_deviation().unwrap()); - id_cmgs.intensities.push(scan_tof_mapping.tof.weight()); - } - } - id_cmgs.sort_by_rt(); - transition_stats.insert(id_key.clone(), id_cmgs); + fn get_context(&self) -> Self::Context { + match &self.context { + Some(context) => context.clone(), + None => panic!("No context set"), } + } + + fn finalize(self) -> NaturalFinalizedMultiCMGStatsArrays { + let mz_converter = &self.converters.0; + let mobility_converter = &self.converters.1; - let tmp = MultiCMGStatsArrays { - transition_stats, + let ms1_stats = _NaturalFinalizedMultiCMGStatsArrays::new( + _FinalizedMultiCMGStatsArrays::from(self.ms1_stats.finalize()), + mz_converter, + mobility_converter, + ); + let ms2_stats = _NaturalFinalizedMultiCMGStatsArrays::new( + _FinalizedMultiCMGStatsArrays::from(self.ms2_stats.finalize()), + mz_converter, + mobility_converter, + ); + + NaturalFinalizedMultiCMGStatsArrays { + ms2_stats, + ms1_stats, id: self.id, - }; - NaturalFinalizedMultiCMGStatsArrays::new( - FinalizedMultiCMGStatsArrays::from(tmp), - &self.converters.0, - &self.converters.1, - ) + } } } diff --git a/src/models/aggregators/raw_peak_agg/point_agg.rs b/src/models/aggregators/raw_peak_agg/point_agg.rs index f731c91..1fbfdcc 100644 --- a/src/models/aggregators/raw_peak_agg/point_agg.rs +++ b/src/models/aggregators/raw_peak_agg/point_agg.rs @@ -3,23 +3,18 @@ use crate::traits::aggregator::{Aggregator, NoContext, ProvidesContext}; use serde::Serialize; #[derive(Debug, Clone, Copy)] -pub struct RawPeakIntensityAggregator { +pub struct RawPeakIntensityAggregator { pub id: u64, pub intensity: u64, - _phantom: std::marker::PhantomData, } -impl RawPeakIntensityAggregator { +impl RawPeakIntensityAggregator { pub fn new(id: u64) -> Self { - Self { - id, - intensity: 0, - _phantom: std::marker::PhantomData, - } + Self { id, intensity: 0 } } } -impl Aggregator for RawPeakIntensityAggregator { +impl Aggregator for RawPeakIntensityAggregator { type Item = RawPeak; type Context = NoContext; type Output = u64; @@ -32,6 +27,10 @@ impl Aggregator for RawPeakIntensityAggregator { fn finalize(self) -> u64 { self.intensity } + + fn supports_context(&self) -> bool { + false + } } #[derive(Debug, Clone)] @@ -84,4 +83,8 @@ impl Aggregator for RawPeakVectorAggregator { fn finalize(self) -> RawPeakVectorArrays { self.peaks } + + fn supports_context(&self) -> bool { + false + } } diff --git a/src/models/aggregators/streaming_aggregator.rs b/src/models/aggregators/streaming_aggregator.rs index d015879..c85456e 100644 --- a/src/models/aggregators/streaming_aggregator.rs +++ b/src/models/aggregators/streaming_aggregator.rs @@ -12,6 +12,24 @@ pub enum StreamingAggregatorError { type Result = std::result::Result; +/// A struct that can be used to calculate the mean and variance of a stream of numbers. +/// +/// # Example +/// +/// ``` +/// use timsquery::models::aggregators::streaming_aggregator::RunningStatsCalculator; +/// +/// // Create a new calculator with a weight of 10 and a mean of 0.0 +/// let mut calc = RunningStatsCalculator::new(2, 0.0); +/// calc.add(10.0, 2); +/// // So overall this should be the equivalent of the mean for +/// // [0.0, 0.0, 10.0, 10.0] +/// assert_eq!(calc.mean().unwrap(), 5.0); +/// +/// ``` +/// +/// # Notes +/// /// Ref impl in javascript ... /// https://nestedsoftware.com/2018/03/27/calculating-standard-deviation-on-streaming-data-253l.23919.html /// https://nestedsoftware.com/2019/09/26/incremental-average-and-standard-deviation-with-sliding-window-470k.176143.html diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index 9006607..ff8d0b0 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -119,13 +119,9 @@ impl ExpandedFrameSlice { let peak_range = { let peak_ind_start = self.tof_indices.partition_point(|x| *x < tof_range.start()); let peak_ind_end = self.tof_indices.partition_point(|x| *x <= tof_range.end()); - peak_ind_start..=peak_ind_end + peak_ind_start..peak_ind_end }; - // if let Some(scan_range) = scan_range { - // assert!(scan_range.start() <= scan_range.end()); - // } - for peak_ind in peak_range { let scan_index = self.scan_numbers[peak_ind]; if let Some(scan_range) = &scan_range { diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index c9900ae..ff08ed6 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -10,7 +10,7 @@ use crate::models::frames::single_quad_settings::{ get_matching_quad_settings, matches_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, }; -use crate::models::queries::FragmentGroupIndexQuery; +use crate::models::queries::{FragmentGroupIndexQuery, MsLevelContext}; use crate::traits::aggregator::Aggregator; use crate::traits::queriable_data::QueriableData; use crate::utils::tolerance_ranges::IncludedRange; @@ -67,7 +67,7 @@ impl ExpandedSliceBundle { for i in low..high { let slice = &self.slices[i]; - slice.query_peaks(tof_range.clone(), scan_range.clone(), f); + slice.query_peaks(tof_range, scan_range, f); } } } @@ -89,6 +89,19 @@ impl ExpandedRawFrameIndex { self.query_precursor_peaks(&matching_quads, tof_range, scan_range, frame_index_range, f); } + fn query_ms1_peaks( + &self, + tof_range: IncludedRange, + scan_range: Option>, + frame_index_range: IncludedRange, + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { + self.bundled_ms1_frames + .query_peaks(tof_range, scan_range, frame_index_range, f); + } + fn query_precursor_peaks( &self, matching_quads: &[SingleQuadrupoleSettingIndex], @@ -170,9 +183,10 @@ impl ExpandedRawFrameIndex { } impl - QueriableData, RawPeak, FH> for ExpandedRawFrameIndex + QueriableData, RawPeak, MsLevelContext> + for ExpandedRawFrameIndex { - fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { + fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { todo!(); // let precursor_mz_range = ( // fragment_query.precursor_query.isolation_mz_range.0 as f64, @@ -201,10 +215,14 @@ impl // .collect() } - fn add_query(&self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG) - where - A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, - AG: Aggregator, + fn add_query( + &self, + fragment_query: &FragmentGroupIndexQuery, + aggregator: &mut AG, + ) where + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, { todo!(); // let precursor_mz_range = ( @@ -230,44 +248,15 @@ impl // }) } - fn add_query_multi_group( + fn add_query_multi_group( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], ) where - A: From + Send + Sync + Clone + Copy, - AG: Aggregator, + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, { - // fragment_queries - // .par_iter() - // .zip(aggregator.par_iter_mut()) - // .for_each(|(fragment_query, agg)| { - // let precursor_mz_range = ( - // fragment_query.precursor_query.isolation_mz_range.0 as f64, - // fragment_query.precursor_query.isolation_mz_range.1 as f64, - // ); - // assert!(precursor_mz_range.0 <= precursor_mz_range.1); - // assert!(precursor_mz_range.0 > 0.0); - // let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - // let frame_index_range = fragment_query.precursor_query.frame_index_range; - - // let local_quad_vec: Vec = get_matching_quad_settings( - // &self.flat_quad_settings, - // precursor_mz_range, - // scan_range, - // ) - // .collect(); - - // for (fh, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { - // self.query_precursor_peaks( - // &local_quad_vec, - // tof_range, - // scan_range, - // frame_index_range, - // &mut |peak| agg.add(&(RawPeak::from(peak), fh)), - // ); - // } - // }); let prec_mz_ranges = fragment_queries .iter() .map(|x| { @@ -289,6 +278,23 @@ impl .map(|x| x.precursor_query.frame_index_range) .collect::>(); + // Query the ms1 mzs first. + aggregator.iter_mut().enumerate().for_each(|(i, agg)| { + fragment_queries[i] + .iter_ms1_mzs() + .for_each(|(fh, mz_range)| { + if agg.supports_context() { + agg.set_context(fh.into()); + } + self.query_ms1_peaks( + mz_range, + scan_ranges[i], + frame_index_ranges[i], + &mut |x| agg.add(RawPeak::from(x)), + ); + }); + }); + for quad_setting in self.flat_quad_settings.iter() { let local_index = quad_setting.index; @@ -297,36 +303,18 @@ impl .get(&local_index) .expect("Only existing quads should be queried."); - // for i in 0..prec_mz_ranges.len() { - // if !matches_quad_settings(quad_setting, prec_mz_ranges[i], scan_ranges[i]) { - // continue; - // } - - // for (fh, tof_range) in fragment_queries[i].mz_index_ranges.iter() { - // let mut local_lambda = |peak| aggregator[i].add(&(RawPeak::from(peak), *fh)); - // tqi.query_peaks( - // *tof_range, - // scan_ranges[i], - // frame_index_ranges[i], - // &mut local_lambda, - // ) - // } - // } - aggregator.par_iter_mut().enumerate().for_each(|(i, agg)| { if !matches_quad_settings(quad_setting, prec_mz_ranges[i], scan_ranges[i]) { return; } - for (fh, tof_range) in fragment_queries[i].mz_index_ranges.iter() { - agg.set_context(*fh); - // let mut local_lambda = |peak| agg.add((RawPeak::from(peak), *fh)); - tqi.query_peaks( - *tof_range, - scan_ranges[i], - frame_index_ranges[i], - &mut |x| agg.add(x), - ); + for (fh, tof_range) in fragment_queries[i].iter_ms2_mzs() { + if agg.supports_context() { + agg.set_context(fh.into()); + } + tqi.query_peaks(tof_range, scan_ranges[i], frame_index_ranges[i], &mut |x| { + agg.add(RawPeak::from(x)) + }); } }); } diff --git a/src/models/indices/raw_file_index.rs b/src/models/indices/raw_file_index.rs index a65d729..56f7b82 100644 --- a/src/models/indices/raw_file_index.rs +++ b/src/models/indices/raw_file_index.rs @@ -1,7 +1,7 @@ use crate::models::adapters::FragmentIndexAdapter; use crate::models::frames::raw_frames::frame_elems_matching; use crate::models::frames::raw_peak::RawPeak; -use crate::models::queries::{FragmentGroupIndexQuery, NaturalPrecursorQuery, PrecursorIndexQuery}; +use crate::models::queries::{FragmentGroupIndexQuery, MsLevelContext}; use crate::traits::aggregator::Aggregator; use crate::traits::queriable_data::QueriableData; use crate::utils::tolerance_ranges::IncludedRange; @@ -43,7 +43,7 @@ impl RawFileIndex { >( &'a self, fqs: &'b FragmentGroupIndexQuery, - fun: &'c mut dyn for<'r> FnMut(RawPeak, FH), + fun: &'c mut dyn for<'r> FnMut(RawPeak), ) { trace!("RawFileIndex::apply_on_query"); trace!("FragmentGroupIndexQuery: {:?}", fqs); @@ -56,7 +56,7 @@ impl RawFileIndex { let pq = &fqs.precursor_query; let iso_mz_range = pq.isolation_mz_range; for frame in frames { - for (fh, tof_range) in fqs.mz_index_ranges.iter() { + for (_fh, tof_range) in fqs.mz_index_ranges.iter() { let scan_range = pq.mobility_index_range; let peaks = frame_elems_matching( &frame, @@ -65,7 +65,7 @@ impl RawFileIndex { Some((iso_mz_range.start() as f64, iso_mz_range.end() as f64).into()), ); for peak in peaks { - fun(peak, *fh); + fun(peak); } } } @@ -91,29 +91,35 @@ impl RawFileIndex { } impl - QueriableData, (RawPeak, FH)> for RawFileIndex + QueriableData, RawPeak, MsLevelContext> + for RawFileIndex { - fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { + fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { let mut out = Vec::new(); - self.apply_on_query(fragment_query, &mut |x, y| out.push((x, y))); + self.apply_on_query(fragment_query, &mut |x| out.push(x)); out } - fn add_query(&self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG) - where - A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, - AG: Aggregator, + fn add_query( + &self, + fragment_query: &FragmentGroupIndexQuery, + aggregator: &mut AG, + ) where + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, { - self.apply_on_query(fragment_query, &mut |x, y| aggregator.add((x, y))); + self.apply_on_query(fragment_query, &mut |x| aggregator.add(x)); } - fn add_query_multi_group( + fn add_query_multi_group( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], ) where - A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, - AG: Aggregator, + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, { fragment_queries .iter() diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 1bba871..91025ab 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -10,7 +10,7 @@ use crate::models::frames::raw_peak::RawPeak; use crate::models::frames::single_quad_settings::{ get_matching_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, }; -use crate::models::queries::FragmentGroupIndexQuery; +use crate::models::queries::{FragmentGroupIndexQuery, MsLevelContext}; use crate::traits::aggregator::Aggregator; use crate::traits::queriable_data::QueriableData; use crate::utils::display::{glimpse_vec, GlimpseConfig}; @@ -52,7 +52,7 @@ impl Debug for QuadSplittedTransposedIndex { } impl QuadSplittedTransposedIndex { - pub fn query_peaks( + pub fn query_ms2_peaks( &self, tof_range: IncludedRange, precursor_mz_range: IncludedRange, @@ -65,11 +65,24 @@ impl QuadSplittedTransposedIndex { let matching_quads: Vec = self .get_matching_quad_settings(precursor_mz_range, scan_range) .collect(); - trace!("matching_quads: {:?}", matching_quads); - self.query_precursor_peaks(&matching_quads, tof_range, scan_range, rt_range_seconds, f); + self.query_peaks_in_precursors(&matching_quads, tof_range, scan_range, rt_range_seconds, f); } - fn query_precursor_peaks( + fn query_ms1_peaks( + &self, + tof_range: IncludedRange, + scan_range: Option>, + rt_range_seconds: Option>, + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { + self.precursor_index + .query_peaks(tof_range, scan_range, rt_range_seconds) + .for_each(f); + } + + fn query_peaks_in_precursors( &self, matching_quads: &[SingleQuadrupoleSettingIndex], tof_range: IncludedRange, @@ -303,9 +316,10 @@ impl QuadSplittedTransposedIndexBuilder { } impl - QueriableData, (RawPeak, FH)> for QuadSplittedTransposedIndex + QueriableData, RawPeak, MsLevelContext> + for QuadSplittedTransposedIndex { - fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { + fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { let precursor_mz_range = IncludedRange::new( fragment_query.precursor_query.isolation_mz_range.0 as f64, fragment_query.precursor_query.isolation_mz_range.0 as f64, @@ -313,16 +327,15 @@ impl let scan_range = Some(fragment_query.precursor_query.mobility_index_range); fragment_query - .mz_index_ranges - .iter() - .flat_map(|(fh, tof_range)| { - let mut local_vec: Vec<(RawPeak, FH)> = vec![]; - self.query_peaks( - *tof_range, + .iter_ms2_mzs() + .flat_map(|(_fh, tof_range)| { + let mut local_vec: Vec = vec![]; + self.query_ms2_peaks( + tof_range, precursor_mz_range, scan_range, Some(fragment_query.precursor_query.rt_range_seconds), - &mut |x| local_vec.push((RawPeak::from(x), *fh)), + &mut |x| local_vec.push(RawPeak::from(x)), ); local_vec @@ -330,10 +343,14 @@ impl .collect() } - fn add_query(&self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG) - where - A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, - AG: Aggregator, + fn add_query( + &self, + fragment_query: &FragmentGroupIndexQuery, + aggregator: &mut AG, + ) where + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, { let precursor_mz_range = IncludedRange::new( fragment_query.precursor_query.isolation_mz_range.0 as f64, @@ -341,27 +358,29 @@ impl ); let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - fragment_query - .mz_index_ranges - .iter() - .for_each(|(fh, tof_range)| { - self.query_peaks( - *tof_range, - precursor_mz_range, - scan_range, - Some(fragment_query.precursor_query.rt_range_seconds), - &mut |peak| aggregator.add((RawPeak::from(peak), *fh)), - ); - }) + fragment_query.iter_ms2_mzs().for_each(|(fh, tof_range)| { + if aggregator.supports_context() { + aggregator.set_context(fh.into()); + } + + self.query_ms2_peaks( + tof_range, + precursor_mz_range, + scan_range, + Some(fragment_query.precursor_query.rt_range_seconds), + &mut |peak| aggregator.add(RawPeak::from(peak)), + ); + }) } - fn add_query_multi_group( + fn add_query_multi_group( &self, fragment_queries: &[FragmentGroupIndexQuery], aggregator: &mut [AG], ) where - A: From<(RawPeak, FH)> + Send + Sync + Clone + Copy, - AG: Aggregator, + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, { fragment_queries .par_iter() @@ -379,13 +398,28 @@ impl .get_matching_quad_settings(precursor_mz_range, scan_range) .collect(); - for (fh, tof_range) in fragment_query.mz_index_ranges.clone().into_iter() { - self.query_precursor_peaks( + for (fh, tof_range) in fragment_query.iter_ms1_mzs() { + if agg.supports_context() { + agg.set_context(fh.into()); + } + self.query_ms1_peaks( + tof_range, + scan_range, + Some(fragment_query.precursor_query.rt_range_seconds), + &mut |peak| agg.add(RawPeak::from(peak)), + ); + } + + for (fh, tof_range) in fragment_query.iter_ms2_mzs() { + if agg.supports_context() { + agg.set_context(fh.into()); + } + self.query_peaks_in_precursors( &local_quad_vec, tof_range, scan_range, Some(fragment_query.precursor_query.rt_range_seconds), - &mut |peak| agg.add((RawPeak::from(peak), fh)), + &mut |peak| agg.add(RawPeak::from(peak)), ); } }); diff --git a/src/models/queries.rs b/src/models/queries.rs index 1d26ca0..83da21d 100644 --- a/src/models/queries.rs +++ b/src/models/queries.rs @@ -1,4 +1,4 @@ -use crate::traits::aggregator::ProvidesContext; +use crate::traits::aggregator::{NoContext, ProvidesContext}; use crate::utils::tolerance_ranges::IncludedRange; use std::collections::HashMap; use std::hash::Hash; @@ -13,7 +13,14 @@ pub struct PrecursorIndexQuery { pub isolation_mz_range: IncludedRange, } -#[derive(Debug, Clone)] +/// Pretty Generic Definition of the context of a query. +/// +/// The context is used to pass additional information to the aggregator. +/// And this implementation simply says that there will be something passed. +/// if its an MS1 and maybe something else if its an MS2. +/// +/// The aggregator should be able to handle this in its definition. +#[derive(Debug, Clone, Copy)] pub enum MsLevelContext { MS1(T1), MS2(T2), @@ -26,7 +33,41 @@ pub struct FragmentGroupIndexQuery { } impl ProvidesContext for FragmentGroupIndexQuery { - type Context = MsLevelContext; + type Context = MsLevelContext; +} + +#[allow(clippy::from_over_into)] +impl Into for MsLevelContext { + fn into(self) -> NoContext { + NoContext {} + } +} + +impl FragmentGroupIndexQuery { + // TODO find if there is a good way to specify in the type that the + // Only a specific context is returned from each function. + + pub fn iter_ms1_mzs( + &self, + ) -> impl Iterator, IncludedRange)> + '_ { + let out = self + .precursor_query + .mz_index_ranges + .iter() + .enumerate() + .map(|(i, mz_range)| (MsLevelContext::MS1(i), *mz_range)); + out + } + + pub fn iter_ms2_mzs( + &self, + ) -> impl Iterator, IncludedRange)> + '_ { + let out = self + .mz_index_ranges + .iter() + .map(|(i, mz_range)| (MsLevelContext::MS2(*i), *mz_range)); + out + } } #[derive(Debug, Clone)] @@ -49,7 +90,7 @@ impl NaturalPrecursorQuery { im_converter.invert(self.mobility_range.end()).round() as usize, ) .into(), - rt_range_seconds: self.rt_range.clone(), + rt_range_seconds: self.rt_range, mz_index_ranges: self .mz_ranges .iter() diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index c46d4b1..88853fc 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -43,22 +43,24 @@ use crate::{Aggregator, ElutionGroup, QueriableData, Tolerance, ToleranceAdapter // 2. `QD` is queried with `QP` and `QF` queries. // 3. The results are aggregated with `AG` aggregators (which are generated by the factory, when passed a numeric ID). -pub fn query_multi_group<'a, QD, TL, QF, AE1, AE2, OE, AG, FH, CTX>( +pub fn query_multi_group<'a, QD, TL, QF, AE1, AE2, OE, AG, FH, CTX1, CTX2, FF>( queriable_data: &'a QD, tolerance: &'a TL, elution_groups: &[ElutionGroup], - aggregator_factory: &dyn Fn(u64) -> AG, + aggregator_factory: &FF, ) -> Vec where - AG: Aggregator + Send + Sync, - QD: QueriableData + ToleranceAdapter>, + AG: Aggregator + Send + Sync, + QD: QueriableData + ToleranceAdapter>, TL: Tolerance, OE: Send + Sync, FH: Clone + Eq + Serialize + Hash + Send + Sync, - QF: Send + Sync + ProvidesContext, + QF: Send + Sync + ProvidesContext, // AE: Send + Sync + Clone + Copy, AE1: Into + Send + Sync + Clone + Copy, AE2: Send + Sync + Clone + Copy + From, + CTX1: Into + Send + Sync + Clone + Copy, + FF: Fn(u64) -> AG + Send + Sync, { let start = Instant::now(); let mut fragment_queries = Vec::with_capacity(elution_groups.len()); diff --git a/src/traits/aggregator.rs b/src/traits/aggregator.rs index 5d1ed90..ca44b79 100644 --- a/src/traits/aggregator.rs +++ b/src/traits/aggregator.rs @@ -22,9 +22,7 @@ pub trait Aggregator: Send + Sync { fn add(&mut self, item: impl Into); fn finalize(self) -> Self::Output; - fn supports_context(&self) -> bool { - false - } + fn supports_context(&self) -> bool; fn set_context(&mut self, context: Self::Context) { panic!( "Misconfigured aggregator, context not supported, got {:?}", @@ -48,9 +46,8 @@ pub trait ProvidesContext { } /// Dummy type to denote that no context is provided. +/// +/// Felt more semantically correct to make a type rather +/// than passing `()` to the context. #[derive(Debug, Clone, Copy)] -pub enum NoContext {} - -impl ProvidesContext for T { - type Context = NoContext; -} +pub struct NoContext {} diff --git a/src/traits/queriable_data.rs b/src/traits/queriable_data.rs index cee64b7..55dd7af 100644 --- a/src/traits/queriable_data.rs +++ b/src/traits/queriable_data.rs @@ -1,17 +1,28 @@ use crate::traits::aggregator::{Aggregator, ProvidesContext}; +use rayon::prelude::*; pub trait QueriableData where QF: Send + Sync + ProvidesContext, I: Send + Sync + Clone + Copy, + Self: Send + Sync, { fn query(&self, fragment_query: &QF) -> Vec; - fn add_query(&self, fragment_query: &QF, aggregator: &mut AG) + fn add_query(&self, fragment_query: &QF, aggregator: &mut AG) where A: From + Send + Sync + Clone + Copy, - AG: Aggregator; - fn add_query_multi_group(&self, fragment_queries: &[QF], aggregator: &mut [AG]) + AG: Aggregator, + C: Into; + + fn add_query_multi_group(&self, fragment_queries: &[QF], aggregator: &mut [AG]) where A: From + Send + Sync + Clone + Copy, - AG: Aggregator; + AG: Aggregator, + C: Into, + { + fragment_queries + .par_iter() + .zip(aggregator.par_iter_mut()) + .for_each(|(query, agg)| self.add_query(query, agg)); + } } diff --git a/src/traits/tolerance.rs b/src/traits/tolerance.rs index a15ba2a..a4903ec 100644 --- a/src/traits/tolerance.rs +++ b/src/traits/tolerance.rs @@ -26,6 +26,7 @@ pub enum QuadTolerance { Absolute((f32, f32, u8)), } +// TODO: Rename to something that does not use the 'Default' #[derive(Debug, Clone, Serialize, Deserialize)] pub struct DefaultTolerance { pub ms: MzToleramce, From 8dd51e60eb3db53b7895758947f9c1d93058ab13 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Fri, 1 Nov 2024 03:36:34 -0700 Subject: [PATCH 17/30] feat(wip)!: ms1 quant --- Taskfile.yml | 4 +- data/.gitignore | 2 +- ...C_13_S1-B1_1_12817_BatchAccess_full_rt.png | Bin 0 -> 61560 bytes ...13_S1-B1_1_12817_BatchAccess_narrow_rt.png | Bin 0 -> 68296 bytes ..._230510_PRTC_13_S1-B1_1_12817_Encoding.png | Bin 0 -> 60957 bytes ..._A_Sample_Alpha_02_BatchAccess_full_rt.png | Bin 47274 -> 0 bytes ..._Sample_Alpha_02_BatchAccess_narrow_rt.png | Bin 52663 -> 0 bytes ..._results_230510_PRTC_13_S1-B1_1_12817.json | 90 +++++++++--------- ..._diaPASEF_Condition_A_Sample_Alpha_02.json | 57 ----------- src/models/frames/expanded_frame.rs | 2 +- .../transposed_quad_index/peak_bucket.rs | 4 +- .../transposed_quad_index/quad_index.rs | 7 +- .../quad_splitted_transposed_index.rs | 3 +- 13 files changed, 57 insertions(+), 112 deletions(-) create mode 100644 data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_full_rt.png create mode 100644 data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_narrow_rt.png create mode 100644 data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_Encoding.png delete mode 100644 data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_full_rt.png delete mode 100644 data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_narrow_rt.png delete mode 100644 data/slim_benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json diff --git a/Taskfile.yml b/Taskfile.yml index cb7d494..2b222c4 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -44,10 +44,10 @@ tasks: - "src/**/*.rs" cmds: - cargo b --release --features bench --bin benchmark_indices - - SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d ./target/release/benchmark_indices - SKIP_SLOW=1 SKIP_BUILD=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/230510_PRTC_13_S1-B1_1_12817.d ./target/release/benchmark_indices - - uv run benches/plot_bench.py data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json - uv run benches/plot_bench.py data/benchmark_results_230510_PRTC_13_S1-B1_1_12817.json + - # SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d ./target/release/benchmark_indices + - # uv run benches/plot_bench.py data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json templates: sources: diff --git a/data/.gitignore b/data/.gitignore index 4dba598..34de35f 100644 --- a/data/.gitignore +++ b/data/.gitignore @@ -1,4 +1,4 @@ *.d/ *.d.zip *.d.tar - +benchmark_results_*.json diff --git a/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_full_rt.png b/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_full_rt.png new file mode 100644 index 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a/src/models/indices/transposed_quad_index/peak_bucket.rs +++ b/src/models/indices/transposed_quad_index/peak_bucket.rs @@ -224,8 +224,8 @@ impl PeakBucket { rt_range: Option>, ) -> impl Iterator + '_ { let scan_range = match scan_range { - Some(x) => x.start()..=x.end().min(self.scan_offsets.len() - 1), - None => 0..=(self.scan_offsets.len() - 1), + Some(x) => x.start()..x.end().min(self.scan_offsets.len() - 1), + None => 0..(self.scan_offsets.len() - 1), }; scan_range .flat_map(move |scan_index| { diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index 87b62d9..049fd07 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -162,6 +162,7 @@ impl TransposedQuadIndexBuilder { num_frames = %self.frame_indices.len(), quad_settings = format!("{:?}", self.quad_settings), ) + level = "debug", )] pub fn build(self) -> TransposedQuadIndex { // TODO: Refactor this function, its getting pretty large. @@ -249,7 +250,8 @@ impl TransposedQuadIndexBuilder { num_frames = %self.frame_indices.len(), quad_settings = format!("{:?}", self.quad_settings), peak_buckets = %peak_buckets.len(), - ) + ), + level = "debug", )] fn build_inner_ref( self, @@ -317,7 +319,8 @@ impl TransposedQuadIndexBuilder { num_frames = %self.frame_indices.len(), quad_settings = format!("{:?}", self.quad_settings), peak_buckets = %peak_buckets.len(), - ) + ), + level = "debug", )] fn batched_build_inner( self, diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 91025ab..548b257 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -277,7 +277,7 @@ impl QuadSplittedTransposedIndexBuilder { self.added_peaks += other.added_peaks; } - #[instrument(skip(self))] + #[instrument(skip(self), level = "debug")] pub fn build(self) -> QuadSplittedTransposedIndex { let mut indices = HashMap::new(); let mut flat_quad_settings = Vec::new(); @@ -393,7 +393,6 @@ impl ); assert!(precursor_mz_range.start() > 0.0); let scan_range = Some(fragment_query.precursor_query.mobility_index_range); - let local_quad_vec: Vec = self .get_matching_quad_settings(precursor_mz_range, scan_range) .collect(); From 180ec83881dd0be98cfd234925c7d196dc4ef53e Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Sat, 2 Nov 2024 20:43:31 -0700 Subject: [PATCH 18/30] feat: initial plotting snippet --- README.md | 2 + Taskfile.yml | 9 +++ data/sageresults/.gitignore | 5 ++ data/sageresults/build.py | 60 +++++++++++++++++ data/sageresults/check.bash | 13 ++++ data/sageresults/check_config.json | 67 +++++++++++++++++++ data/sageresults/plot.py | 71 +++++++++++++++++++++ data/sageresults/ubb_elution_groups.json | 78 +++++++++++++++++++++++ data/sageresults/ubb_peptide_plot.png | Bin 0 -> 131585 bytes src/traits/tolerance.rs | 1 + 10 files changed, 306 insertions(+) create mode 100644 data/sageresults/.gitignore create mode 100644 data/sageresults/build.py create mode 100644 data/sageresults/check.bash create mode 100644 data/sageresults/check_config.json create mode 100644 data/sageresults/plot.py create mode 100644 data/sageresults/ubb_elution_groups.json create mode 100644 data/sageresults/ubb_peptide_plot.png diff --git a/README.md b/README.md index ac30827..72a9234 100644 --- a/README.md +++ b/README.md @@ -37,3 +37,5 @@ sequential, use that). - Add logging levels to instrumentations. - Add missing_docks_in_private_items to clippy. +- Implement predicate pushdown on the setup of indices. +- Implement predicate pushdown on query execution for raw index. diff --git a/Taskfile.yml b/Taskfile.yml index 2b222c4..cbca819 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -49,6 +49,15 @@ tasks: - # SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d ./target/release/benchmark_indices - # uv run benches/plot_bench.py data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json + plot: + sources: + - "src/**/*.rs" + - "data/sageresults/**/*.py" + cmds: + - cargo b --release --features build-binary --bin timsquery + - ./target/release/timsquery query-index --raw-file-path ./data/230510_PRTC_13_S1-B1_1_12817.d --tolerance-settings-path "templates/tolerance_settings_narrow_rt.json" --elution-groups-path "./data/sageresults/ubb_elution_groups.json" --output-path "./data/sageresults/query_results" --index expanded-raw-frame-index --aggregator multi-cmg-stats --format pretty-json + - cd data/sageresults && uv run plot.py + templates: sources: - "src/**/*.rs" diff --git a/data/sageresults/.gitignore b/data/sageresults/.gitignore new file mode 100644 index 0000000..774378f --- /dev/null +++ b/data/sageresults/.gitignore @@ -0,0 +1,5 @@ +lfq.tsv +results.sage.tsv +matched_fragments.sage.tsv +sage +log.log \ No newline at end of file diff --git a/data/sageresults/build.py b/data/sageresults/build.py new file mode 100644 index 0000000..52d9860 --- /dev/null +++ b/data/sageresults/build.py @@ -0,0 +1,60 @@ +# /// script +# dependencies = [ +# "polars", +# ] +# /// + +import polars as pl +import json + +PROTON_MASS = 1.007276 + +ub_peptides_df = ( + pl.scan_csv("./results.sage.tsv", separator="\t") + .filter(pl.col("proteins").str.contains("UBB_"), pl.col("peptide_q") < 0.01) + .group_by("peptide") + .agg(pl.all().sort_by("sage_discriminant_score", descending=True).head(1)) + .explode(pl.all().exclude("peptide")) + .select(["peptide", "charge", "psm_id", "rt", "ion_mobility", "calcmass"]) + .with_columns( + mz=(pl.col("calcmass") + (pl.col("charge") * PROTON_MASS)) / pl.col("charge") + ) + .collect() +) + +psm_ids = ub_peptides_df["psm_id"].unique() + +fragments = ( + pl.scan_csv("matched_fragments.sage.tsv", separator="\t") + .filter(pl.col("psm_id").is_in(psm_ids)) + .select(["psm_id", "fragment_charge", "fragment_mz_calculated"]) + .group_by(["psm_id"]) + .agg(pl.all()) + .collect() +) + +df = ub_peptides_df.join(fragments, on="psm_id", how="inner") +df + +# Convert to json +out = [] +for x in df.iter_rows(named=True): + out.append( + { + "id": x["psm_id"], + "human_id": x["peptide"] + "_" + str(x["charge"]), + "mobility": x["ion_mobility"], + # Note: the rt in sage is minutes ... + "rt_seconds": x["rt"] * 60, + "precursor_mz": x["mz"], + "precursor_charge": x["charge"], + "fragment_mzs": { + str(i): y for i, y in enumerate(x["fragment_mz_calculated"]) + }, + } + ) + +out + +with open("ubb_elution_groups.json", "w") as f: + json.dump(out, f, indent=2) diff --git a/data/sageresults/check.bash b/data/sageresults/check.bash new file mode 100644 index 0000000..dc23fb5 --- /dev/null +++ b/data/sageresults/check.bash @@ -0,0 +1,13 @@ +#!/bin/bash + +set -x +set -e +set -o pipefail + +# This generates the `ubb_elution_groups.json` file. +# RAW_FILE=../230510_PRTC_13_S1-B1_1_12817.d/ +# ./sage --annotate-matches --fasta ~/fasta/20231030_LINEARIZED_UP000005640_9606.fasta check_config.json $RAW_FILE +# uv run build.py + +../../target/release/timsquery query-index --raw-file-path ../230510_PRTC_13_S1-B1_1_12817.d --tolerance-settings-path "../../templates/tolerance_settings_narrow_rt.json" --elution-groups-path "ubb_elution_groups.json" --output-path "query_results" --index expanded-raw-frame-index --aggregator multi-cmg-stats --format pretty-json +uv run plot.py \ No newline at end of file diff --git a/data/sageresults/check_config.json b/data/sageresults/check_config.json new file mode 100644 index 0000000..2b314f1 --- /dev/null +++ b/data/sageresults/check_config.json @@ -0,0 +1,67 @@ +{ + "database": { + "bucket_size": 8192, + "enzyme": { + "missed_cleavages": 2, + "min_len": 7, + "max_len": 35, + "cleave_at": "KR", + "restrict": "P" + }, + "fragment_min_mz": 150.0, + "fragment_max_mz": 2000.0, + "peptide_min_mass": 500.0, + "peptide_max_mass": 5000.0, + "ion_kinds": [ + "b", + "y" + ], + "min_ion_index": 2, + "max_variable_mods": 3, + "static_mods": { + "C": 57.0215 + }, + "variable_mods": { + "M": [15.994] + }, + "decoy_tag": "rev_", + "generate_decoys": true + }, + "precursor_tol": { + "ppm": [ + -20.0, + 20.0 + ] + }, + "fragment_tol": { + "ppm": [ + -20.0, + 20.0 + ] + }, + "quant": { + "lfq": true + }, + "deisotope": true, + "min_peaks": 15, + "max_peaks": 250, + "max_fragment_charge": 1, + "min_matched_peaks": 4, + "predict_rt": true, + "wide_window": true, + "chimera": false, + "report_psms": 1, + "bruker_spectrum_processor": { + "spectrum_processing_params": { + "smoothing_window": 1, + "centroiding_window": 1, + "calibration_tolerance": 0.1, + "calibrate": false + }, + "frame_splitting_params": { + "Quadrupole": { + "UniformMobility": [[0.1, 0.05], null] + } + } + } +} diff --git a/data/sageresults/plot.py b/data/sageresults/plot.py new file mode 100644 index 0000000..ce85153 --- /dev/null +++ b/data/sageresults/plot.py @@ -0,0 +1,71 @@ +# /// script +# dependencies = [ +# "polars", +# "matplotlib", +# ] +# /// + +import json +import numpy as np +import matplotlib.pyplot as plt + +data = json.load(open("query_results/results.json")) +labels = json.load(open("ubb_elution_groups.json")) +id_to_label = {x["id"]: x["human_id"] for x in labels} + +num_elution_groups = len(data) +fig, ax = plt.subplots(ncols=num_elution_groups, nrows=2, figsize=(10, 7)) + +# Top is the MS1 and bottom is the MS2 + +# Getting the data for ms1 is like so: +# x["result"]["ms1_stats"]["retention_time_miliseconds"] +# x["result"]["ms1_stats"]["transition_intensities"][y] + +# Getting the data for ms2 is like so: +# x["result"]["ms2_stat"]["retention_time_miliseconds"] +# x["result"]["ms2_stats"]["transition_intensities"][y] + + +def ms_to_mins(x): + return (x / 1_000) / 60 + + +def infinite_color_cycle(): + colors = ["#308AAD", "#C8102E", "#96D8D8", "#B2EE79"] + while True: + for c in colors: + yield c + + +for i, x in enumerate(data): + ms1_rts = np.array(x["result"]["ms1_stats"]["retention_time_miliseconds"]) + ms1_rts = ms_to_mins(ms1_rts) + ms2_rts = np.array(x["result"]["ms2_stats"]["retention_time_miliseconds"]) + ms2_rts = ms_to_mins(ms2_rts) + + colors = infinite_color_cycle() + sorted_ms1_keys = sorted(x["result"]["ms1_stats"]["transition_intensities"].keys()) + sorted_ms2_keys = sorted(x["result"]["ms2_stats"]["transition_intensities"].keys()) + + for j in sorted_ms1_keys: + j = x["result"]["ms1_stats"]["transition_intensities"][j] + ax[0, i].plot(ms1_rts, j, color=next(colors)) + + for j in sorted_ms2_keys: + j = x["result"]["ms2_stats"]["transition_intensities"][j] + ax[1, i].plot(ms2_rts, j, color=next(colors)) + + # Label axes ... + ax[0, i].set_xlabel("Retention Time (min)") + ax[1, i].set_xlabel("Retention Time (min)") + ax[0, i].set_ylabel("Intensity") + ax[1, i].set_ylabel("Intensity") + + # Label titles + human_lab = id_to_label[x["elution_group"]["id"]] + ax[0, i].set_title(human_lab + " MS1") + ax[1, i].set_title(human_lab + " MS2") + +plt.tight_layout() +plt.savefig("ubb_peptide_plot.png") diff --git a/data/sageresults/ubb_elution_groups.json b/data/sageresults/ubb_elution_groups.json new file mode 100644 index 0000000..0c8970b --- /dev/null +++ b/data/sageresults/ubb_elution_groups.json @@ -0,0 +1,78 @@ +[ + { + "id": 912, + "human_id": "TLSDYNIQK_2", + "mobility": 0.8217308, + "rt_seconds": 316.72206, + "precursor_mz": 541.2797760000001, + "precursor_charge": 2, + "fragment_mzs": { + "0": 215.13902, + "1": 302.17102, + "2": 417.19797, + "3": 694.3042, + "4": 807.38824, + "5": 980.50464, + "6": 867.4206, + "7": 780.38855, + "8": 665.36163, + "9": 502.2983, + "10": 388.25537, + "11": 275.17133 + } + }, + { + "id": 89501, + "human_id": "TITLEVEPSDTIENVK_2", + "mobility": 1.1326923, + "rt_seconds": 745.8906, + "precursor_mz": 894.4673760000001, + "precursor_charge": 2, + "fragment_mzs": { + "0": 215.13902, + "1": 316.1867, + "2": 429.27075, + "3": 558.31335, + "4": 657.3818, + "5": 786.4244, + "6": 883.4771, + "7": 1573.7957, + "8": 1472.7479, + "9": 1359.6638, + "10": 1230.6212, + "11": 1131.5529, + "12": 1002.5102, + "13": 905.45746, + "14": 818.4254, + "15": 703.3985, + "16": 602.3508, + "17": 489.26678, + "18": 360.22418, + "19": 246.18126 + } + }, + { + "id": 8469, + "human_id": "ESTLHLVLR_2", + "mobility": 0.8719231, + "rt_seconds": 483.31707000000006, + "precursor_mz": 534.313976, + "precursor_charge": 2, + "fragment_mzs": { + "0": 217.0819, + "1": 318.12958, + "2": 431.21362, + "3": 568.2725, + "4": 681.35657, + "5": 780.425, + "6": 893.50903, + "7": 938.57806, + "8": 851.546, + "9": 750.49835, + "10": 637.4143, + "11": 500.3554, + "12": 387.27136, + "13": 288.20294 + } + } +] \ No newline at end of file diff --git a/data/sageresults/ubb_peptide_plot.png b/data/sageresults/ubb_peptide_plot.png new file mode 100644 index 0000000000000000000000000000000000000000..1db70a685e13aff081388c39f442f7debdb4d2ec GIT binary patch literal 131585 zcmbrm1z1;U*Dt(Lqy#AuL_%6oO6d*-R6rCg1SCWnM7oh~R76TjxPvVTv5Dq6T=SAVA!Dw z0zCK=m!^mU_?L*y<-0a&mXB=gb)Ohu%DOg>%`9!qjP*|289cEzwzRm&Ey8`_{AnW_ zo5$9oJUr(A`T)1(6GI**mBamT5W>fb_pC9DR2Th&lOdIEjNxF|l}j?}4zK5joi)|F zx22Zant7@5XvnDAlbKU9GZf!U*zoauf7tgWCDi`Q-1WoPL=<*37?g6)d^LUZ`dgRE zi>oH78Hx_sb*BPj*wcw?yKt0sOPXER7sH|}qo3m7oixyi-ld}1tT{e7=S 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self.rt { RtTolerance::Absolute((low, high)) => Some((rt - low, rt + high)), From b262e2914c2f88fc95a12901206c3e639fc69d63 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Sat, 2 Nov 2024 21:37:31 -0700 Subject: [PATCH 19/30] feat: updated plot --- data/sageresults/plot.py | 10 ++++++++-- data/sageresults/ubb_peptide_plot.png | Bin 131585 -> 140564 bytes 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/data/sageresults/plot.py b/data/sageresults/plot.py index ce85153..3a28b91 100644 --- a/data/sageresults/plot.py +++ b/data/sageresults/plot.py @@ -49,12 +49,18 @@ def infinite_color_cycle(): sorted_ms2_keys = sorted(x["result"]["ms2_stats"]["transition_intensities"].keys()) for j in sorted_ms1_keys: + col = next(colors) j = x["result"]["ms1_stats"]["transition_intensities"][j] - ax[0, i].plot(ms1_rts, j, color=next(colors)) + ax[0, i].plot(ms1_rts, j, color=col, alpha=0.4) + # Draw the points + ax[0, i].scatter(ms1_rts, j, color=col, s=5) for j in sorted_ms2_keys: + col = next(colors) j = x["result"]["ms2_stats"]["transition_intensities"][j] - ax[1, i].plot(ms2_rts, j, color=next(colors)) + ax[1, i].plot(ms2_rts, j, color=col, alpha=0.4) + # Draw the points + ax[1, i].scatter(ms2_rts, j, color=col, s=5) # Label axes ... ax[0, i].set_xlabel("Retention Time (min)") diff --git a/data/sageresults/ubb_peptide_plot.png b/data/sageresults/ubb_peptide_plot.png index 1db70a685e13aff081388c39f442f7debdb4d2ec..e1fb49efef028eaa097e5e11f17e8ee83c47ccf1 100644 GIT binary patch literal 140564 zcmce;1yok+)-V1lNQrcJgY>H)4T4B0A|RatQqrLyy$R_O5u}k40Rd?wq(zVrkOl#f zE~O;zT<&wuckVaNz2lC1|Kq>M-flM=dDmLc^UV3Hxx&;`6))k@;Gs~cOUg>}8YmRT z5(;&`9tR7);@zE42LBRsyQ%AT&(YG&-PFYbb;s1r$8C=eMP)2{{A>mS;DhwBEroVZap)zFdGq8RxiPN;Zows=a=l+{mw8x=gW}8 zGXsmu{LBssHCZ(`3b^?3Ynr*vU;Wkd`{Z0-D?Yy9M=p$CK265IKD}I&=%ecwlbTsf z{UycHL50B_L?nlU{PHlNri%9ZpWhooE##L{QSzi#yv3|N<%wd1*MOj6?opMU%It@T6|AIF{Kpo$71W`~o*U4;x& zN5>fW3X_l!8IR7}w$>2B;L*P@uwR+BKK zYj`~2*mQ}LlQVndaA!I2@%nf|#PGvP-C7s+x<{*6R#sM`Vq#ea)eZ-95dxWm%b(gs z9H;35u?hM256@2bWt7-R>VJOX;o{{j+S%_sTF%c9^geK^upT%c9UYB>gY%*3bXVZ} zj~~gqr_w%$*V#z2v?+Z_bo#d0Wg}^*#2Ggk^SebCZvt;1e`$!F*t0@p9Mq 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Sebastian Paez" Date: Sun, 3 Nov 2024 10:02:24 -0800 Subject: [PATCH 20/30] style: new fmt settings --- benches/benchmark_indices.rs | 45 +++- rustfmt.toml | 6 + src/lib.rs | 23 ++- src/main.rs | 62 ++++-- src/models/adapters.rs | 21 +- src/models/aggregators/mod.rs | 14 +- .../raw_peak_agg/chromatogram_agg.rs | 15 +- src/models/aggregators/raw_peak_agg/mod.rs | 15 +- .../multi_chromatogram_agg/base.rs | 89 ++++++++ .../multi_chromatogram_agg/mod.rs | 7 + .../multi_chromatogram_agg.rs | 195 ++++++------------ .../aggregators/raw_peak_agg/point_agg.rs | 14 +- src/models/aggregators/rolling_calculators.rs | 45 ++++ .../aggregators/streaming_aggregator.rs | 21 +- src/models/elution_group.rs | 12 +- src/models/frames/expanded_frame.rs | 82 +++++--- src/models/frames/expanded_window_group.rs | 14 +- src/models/frames/raw_frames.rs | 9 +- src/models/frames/single_quad_settings.rs | 14 +- .../indices/expanded_raw_index/model.rs | 74 ++++--- src/models/indices/raw_file_index.rs | 50 +++-- .../transposed_quad_index/peak_bucket.rs | 15 +- .../transposed_quad_index/quad_index.rs | 97 +++++++-- .../quad_splitted_transposed_index.rs | 92 ++++++--- src/models/queries.rs | 21 +- .../queriable_tims_data.rs | 24 ++- src/traits/queriable_data.rs | 5 +- src/traits/tolerance.rs | 47 +++-- src/utils/correlation.rs | 1 + src/utils/frame_processing.rs | 14 +- src/utils/math.rs | 84 ++++++++ src/utils/mod.rs | 2 + src/utils/scoring.rs | 1 + src/utils/sorting.rs | 1 - src/utils/tolerance_ranges.rs | 6 +- 35 files changed, 877 insertions(+), 360 deletions(-) create mode 100644 rustfmt.toml create mode 100644 src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/base.rs create mode 100644 src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/mod.rs rename src/models/aggregators/raw_peak_agg/{ => multi_chromatogram_agg}/multi_chromatogram_agg.rs (72%) create mode 100644 src/utils/correlation.rs create mode 100644 src/utils/scoring.rs diff --git a/benches/benchmark_indices.rs b/benches/benchmark_indices.rs index 006c96e..d62c9fe 100644 --- a/benches/benchmark_indices.rs +++ b/benches/benchmark_indices.rs @@ -1,29 +1,54 @@ -use rand::{Rng, SeedableRng}; +use rand::{ + Rng, + SeedableRng, +}; use rand_chacha::ChaCha8Rng; use serde::Serialize; -use std::collections::HashMap; -use std::env; -use std::fs::File; -use std::path::{Path, PathBuf}; -use std::time::{Duration, Instant}; +use std::{ + collections::HashMap, + env, + fs::File, + path::{ + Path, + PathBuf, + }, + time::{ + Duration, + Instant, + }, +}; use timsquery::{ models::{ aggregators::RawPeakIntensityAggregator, indices::{ - expanded_raw_index::ExpandedRawFrameIndex, raw_file_index::RawFileIndex, + expanded_raw_index::ExpandedRawFrameIndex, + raw_file_index::RawFileIndex, transposed_quad_index::QuadSplittedTransposedIndex, }, }, queriable_tims_data::queriable_tims_data::query_multi_group, traits::tolerance::{ - DefaultTolerance, MobilityTolerance, MzToleramce, QuadTolerance, RtTolerance, + DefaultTolerance, + MobilityTolerance, + MzToleramce, + QuadTolerance, + RtTolerance, }, ElutionGroup, }; use tracing::subscriber::set_global_default; -use tracing_bunyan_formatter::{BunyanFormattingLayer, JsonStorageLayer}; +use tracing_bunyan_formatter::{ + BunyanFormattingLayer, + JsonStorageLayer, +}; use tracing_chrome::ChromeLayerBuilder; -use tracing_subscriber::{fmt, prelude::*, registry::Registry, EnvFilter, Layer}; +use tracing_subscriber::{ + fmt, + prelude::*, + registry::Registry, + EnvFilter, + Layer, +}; const NUM_ELUTION_GROUPS: usize = 1000; const NUM_ITERATIONS: usize = 1; diff --git a/rustfmt.toml b/rustfmt.toml new file mode 100644 index 0000000..c67c611 --- /dev/null +++ b/rustfmt.toml @@ -0,0 +1,6 @@ + +imports_layout = "Vertical" +imports_granularity = "Crate" +normalize_comments = true +reorder_impl_items = true +version = "Two" diff --git a/src/lib.rs b/src/lib.rs index 500b75e..d0c0ebf 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,11 +1,18 @@ // Re-export main structures -pub use crate::models::elution_group::ElutionGroup; -pub use crate::models::indices::transposed_quad_index::QuadSplittedTransposedIndex; +pub use crate::models::{ + elution_group::ElutionGroup, + indices::transposed_quad_index::QuadSplittedTransposedIndex, +}; // Re-export traits -pub use crate::traits::aggregator::Aggregator; -pub use crate::traits::queriable_data::QueriableData; -pub use crate::traits::tolerance::{Tolerance, ToleranceAdapter}; +pub use crate::traits::{ + aggregator::Aggregator, + queriable_data::QueriableData, + tolerance::{ + Tolerance, + ToleranceAdapter, + }, +}; // Declare modules pub mod errors; @@ -15,4 +22,8 @@ pub mod traits; pub mod utils; // Re-export errors -pub use crate::errors::{DataProcessingError, DataReadingError, TimsqueryError}; +pub use crate::errors::{ + DataProcessingError, + DataReadingError, + TimsqueryError, +}; diff --git a/src/main.rs b/src/main.rs index 9fc15d9..88c6b48 100644 --- a/src/main.rs +++ b/src/main.rs @@ -1,21 +1,50 @@ -use clap::{Parser, Subcommand}; -use serde::{Deserialize, Serialize}; -use std::collections::HashMap; -use std::time::Instant; -use timsquery::models::elution_group::ElutionGroup; -use timsquery::queriable_tims_data::queriable_tims_data::query_multi_group; -use timsquery::traits::tolerance::DefaultTolerance; -use timsquery::traits::tolerance::{MobilityTolerance, MzToleramce, QuadTolerance, RtTolerance}; +use clap::{ + Parser, + Subcommand, +}; +use serde::{ + Deserialize, + Serialize, +}; +use std::{ + collections::HashMap, + time::Instant, +}; use timsquery::{ - models::aggregators::{ - MultiCMGStatsFactory, RawPeakIntensityAggregator, RawPeakVectorAggregator, + models::{ + aggregators::{ + MultiCMGStatsFactory, + RawPeakIntensityAggregator, + RawPeakVectorAggregator, + }, + elution_group::ElutionGroup, + indices::{ + ExpandedRawFrameIndex, + QuadSplittedTransposedIndex, + }, + }, + queriable_tims_data::queriable_tims_data::query_multi_group, + traits::tolerance::{ + DefaultTolerance, + MobilityTolerance, + MzToleramce, + QuadTolerance, + RtTolerance, }, - models::indices::{ExpandedRawFrameIndex, QuadSplittedTransposedIndex}, }; -use tracing::instrument; -use tracing::subscriber::set_global_default; -use tracing_bunyan_formatter::{BunyanFormattingLayer, JsonStorageLayer}; -use tracing_subscriber::{prelude::*, registry::Registry, EnvFilter}; +use tracing::{ + instrument, + subscriber::set_global_default, +}; +use tracing_bunyan_formatter::{ + BunyanFormattingLayer, + JsonStorageLayer, +}; +use tracing_subscriber::{ + prelude::*, + registry::Registry, + EnvFilter, +}; fn main() { let env_filter = EnvFilter::try_from_default_env().unwrap_or_else(|_| EnvFilter::new("info")); @@ -57,8 +86,7 @@ fn main_write_template(args: WriteTemplateArgs) { std::fs::write(tolerance_json_path.clone(), tolerance_json).unwrap(); println!( "use as `timsquery query-index --output-path '.' --raw-file-path 'your_file.d' --tolerance-settings-path {:#?} --elution-groups-path {:#?}`", - tolerance_json_path, - egs_json_path, + tolerance_json_path, egs_json_path, ); } diff --git a/src/models/adapters.rs b/src/models/adapters.rs index 0ca164e..fe494d7 100644 --- a/src/models/adapters.rs +++ b/src/models/adapters.rs @@ -1,11 +1,20 @@ -use crate::models::elution_group::ElutionGroup; -use crate::models::queries::{FragmentGroupIndexQuery, PrecursorIndexQuery}; -use crate::utils::tolerance_ranges::IncludedRange; -use crate::ToleranceAdapter; +use crate::{ + models::{ + elution_group::ElutionGroup, + queries::{ + FragmentGroupIndexQuery, + PrecursorIndexQuery, + }, + }, + utils::tolerance_ranges::IncludedRange, + ToleranceAdapter, +}; use serde::Serialize; use std::hash::Hash; -use timsrust::converters::ConvertableDomain; -use timsrust::Metadata; +use timsrust::{ + converters::ConvertableDomain, + Metadata, +}; #[derive(Debug, Default)] pub struct FragmentIndexAdapter { diff --git a/src/models/aggregators/mod.rs b/src/models/aggregators/mod.rs index e34cad4..57e858d 100644 --- a/src/models/aggregators/mod.rs +++ b/src/models/aggregators/mod.rs @@ -2,9 +2,11 @@ pub mod raw_peak_agg; pub mod rolling_calculators; pub mod streaming_aggregator; -pub use raw_peak_agg::ChromatomobilogramStats; -pub use raw_peak_agg::MultiCMGStats; -pub use raw_peak_agg::MultiCMGStatsArrays; -pub use raw_peak_agg::MultiCMGStatsFactory; -pub use raw_peak_agg::RawPeakIntensityAggregator; -pub use raw_peak_agg::RawPeakVectorAggregator; +pub use raw_peak_agg::{ + ChromatomobilogramStats, + MultiCMGStatsAgg, + MultiCMGStatsFactory, + PartitionedCMGArrays, + RawPeakIntensityAggregator, + RawPeakVectorAggregator, +}; diff --git a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs index 6eed3d5..4c06b9c 100644 --- a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs @@ -1,11 +1,15 @@ use super::super::streaming_aggregator::RunningStatsCalculator; -use crate::models::frames::raw_peak::RawPeak; -use crate::sort_vecs_by_first; -use crate::traits::aggregator::Aggregator; +use crate::{ + models::frames::raw_peak::RawPeak, + sort_vecs_by_first, + traits::aggregator::Aggregator, +}; use serde::Serialize; -use std::collections::BTreeMap; -use std::collections::HashMap; +use std::collections::{ + BTreeMap, + HashMap, +}; pub type MappingCollection = HashMap; @@ -27,6 +31,7 @@ impl ScanTofStatsCalculatorPair { tof: RunningStatsCalculator::new(intensity, tof_index), } } + pub fn add(&mut self, intensity: u64, scan_index: usize, tof_index: u32) { self.scan.add(scan_index as f64, intensity); self.tof.add(tof_index as f64, intensity); diff --git a/src/models/aggregators/raw_peak_agg/mod.rs b/src/models/aggregators/raw_peak_agg/mod.rs index dd5ad20..03ec9b5 100644 --- a/src/models/aggregators/raw_peak_agg/mod.rs +++ b/src/models/aggregators/raw_peak_agg/mod.rs @@ -3,8 +3,13 @@ pub mod multi_chromatogram_agg; pub mod point_agg; pub use chromatogram_agg::ChromatomobilogramStats; -pub use multi_chromatogram_agg::MultiCMGStats; -pub use multi_chromatogram_agg::MultiCMGStatsArrays; -pub use multi_chromatogram_agg::MultiCMGStatsFactory; -pub use point_agg::RawPeakIntensityAggregator; -pub use point_agg::RawPeakVectorAggregator; +pub use multi_chromatogram_agg::MultiCMGStatsAgg; +// TODO: reorganize this so I donr use direcly from `base`` +pub use multi_chromatogram_agg::{ + base::PartitionedCMGArrays, + MultiCMGStatsFactory, +}; +pub use point_agg::{ + RawPeakIntensityAggregator, + RawPeakVectorAggregator, +}; diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/base.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/base.rs new file mode 100644 index 0000000..fc089f8 --- /dev/null +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/base.rs @@ -0,0 +1,89 @@ +use super::super::chromatogram_agg::{ + ChromatomobilogramStatsArrays, + MappingCollection, + ScanTofStatsCalculatorPair, +}; +use crate::{ + models::{ + aggregators::{ + rolling_calculators::rolling_median, + streaming_aggregator::RunningStatsCalculator, + }, + frames::raw_peak::RawPeak, + queries::MsLevelContext, + }, + traits::aggregator::Aggregator, + utils::math::{ + lnfact, + lnfact_float, + }, +}; +use serde::Serialize; +use std::{ + collections::{ + BTreeMap, + HashSet, + }, + hash::Hash, +}; +use tracing::{ + debug, + warn, +}; + +#[derive(Debug, Clone)] +pub struct ParitionedCMGAggregator { + pub scan_tof_mapping: MappingCollection<(FH, u32), ScanTofStatsCalculatorPair>, + pub uniq_rts: HashSet, + pub uniq_ids: HashSet, +} + +impl Default for ParitionedCMGAggregator { + fn default() -> Self { + Self { + scan_tof_mapping: MappingCollection::new(), + uniq_rts: HashSet::new(), + uniq_ids: HashSet::new(), + } + } +} + +#[derive(Debug, Clone, Serialize)] +pub struct PartitionedCMGArrays { + pub transition_stats: MappingCollection, +} + +// TODO reimplement ... dont really like how non-idiomatic this finalize is. +// From-Into might be a better way. +impl ParitionedCMGAggregator { + pub fn finalize(self) -> PartitionedCMGArrays { + let mut transition_stats = MappingCollection::new(); + + for id_key in self.uniq_ids.iter() { + let mut id_cmgs = ChromatomobilogramStatsArrays::new(); + for rt_key in self.uniq_rts.iter() { + let scan_tof_mapping = self.scan_tof_mapping.get(&(id_key.clone(), *rt_key)); + if let Some(scan_tof_mapping) = scan_tof_mapping { + id_cmgs.retention_time_miliseconds.push(*rt_key); + id_cmgs + .scan_index_means + .push(scan_tof_mapping.scan.mean().unwrap()); + id_cmgs + .scan_index_sds + .push(scan_tof_mapping.scan.standard_deviation().unwrap()); + id_cmgs + .tof_index_means + .push(scan_tof_mapping.tof.mean().unwrap()); + id_cmgs + .tof_index_sds + .push(scan_tof_mapping.tof.standard_deviation().unwrap()); + id_cmgs.intensities.push(scan_tof_mapping.tof.weight()); + } + } + id_cmgs.sort_by_rt(); + transition_stats.insert(id_key.clone(), id_cmgs); + } + + PartitionedCMGArrays { transition_stats } + } +} diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/mod.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/mod.rs new file mode 100644 index 0000000..fb06f82 --- /dev/null +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/mod.rs @@ -0,0 +1,7 @@ +pub mod base; +pub mod multi_chromatogram_agg; + +pub use multi_chromatogram_agg::{ + MultiCMGStatsAgg, + MultiCMGStatsFactory, +}; diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/multi_chromatogram_agg.rs similarity index 72% rename from src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs rename to src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/multi_chromatogram_agg.rs index 62df922..a7583da 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/multi_chromatogram_agg.rs @@ -1,76 +1,58 @@ -use super::chromatogram_agg::{ - ChromatomobilogramStatsArrays, MappingCollection, ScanTofStatsCalculatorPair, +use super::{ + super::chromatogram_agg::{ + ChromatomobilogramStatsArrays, + MappingCollection, + ScanTofStatsCalculatorPair, + }, + base::{ + ParitionedCMGAggregator, + PartitionedCMGArrays, + }, +}; +use crate::{ + models::{ + aggregators::{ + rolling_calculators::{ + calculate_lazy_hyperscore, + calculate_value_vs_baseline, + }, + streaming_aggregator::RunningStatsCalculator, + }, + frames::raw_peak::RawPeak, + queries::MsLevelContext, + }, + traits::aggregator::Aggregator, + utils::math::{ + lnfact, + lnfact_float, + }, }; -use crate::models::aggregators::rolling_calculators::rolling_median; -use crate::models::aggregators::streaming_aggregator::RunningStatsCalculator; -use crate::models::frames::raw_peak::RawPeak; -use crate::models::queries::MsLevelContext; -use crate::traits::aggregator::Aggregator; -use crate::utils::math::{lnfact, lnfact_float}; use serde::Serialize; -use std::collections::{BTreeMap, HashSet}; -use std::hash::Hash; -use tracing::{debug, warn}; - -use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter}; - -#[derive(Debug, Clone)] -struct _MultiCMGStats { - pub scan_tof_mapping: MappingCollection<(FH, u32), ScanTofStatsCalculatorPair>, - pub uniq_rts: HashSet, - pub uniq_ids: HashSet, -} - -impl Default for _MultiCMGStats { - fn default() -> Self { - Self { - scan_tof_mapping: MappingCollection::new(), - uniq_rts: HashSet::new(), - uniq_ids: HashSet::new(), - } - } -} - -impl _MultiCMGStats { - fn finalize(self) -> MultiCMGStatsArrays { - let mut transition_stats = MappingCollection::new(); - - for id_key in self.uniq_ids.iter() { - let mut id_cmgs = ChromatomobilogramStatsArrays::new(); - for rt_key in self.uniq_rts.iter() { - let scan_tof_mapping = self.scan_tof_mapping.get(&(id_key.clone(), *rt_key)); - if let Some(scan_tof_mapping) = scan_tof_mapping { - id_cmgs.retention_time_miliseconds.push(*rt_key); - id_cmgs - .scan_index_means - .push(scan_tof_mapping.scan.mean().unwrap()); - id_cmgs - .scan_index_sds - .push(scan_tof_mapping.scan.standard_deviation().unwrap()); - id_cmgs - .tof_index_means - .push(scan_tof_mapping.tof.mean().unwrap()); - id_cmgs - .tof_index_sds - .push(scan_tof_mapping.tof.standard_deviation().unwrap()); - id_cmgs.intensities.push(scan_tof_mapping.tof.weight()); - } - } - id_cmgs.sort_by_rt(); - transition_stats.insert(id_key.clone(), id_cmgs); - } - - MultiCMGStatsArrays { transition_stats } - } -} +use std::{ + collections::{ + BTreeMap, + HashSet, + }, + hash::Hash, +}; +use tracing::{ + debug, + warn, +}; +use timsrust::converters::{ + ConvertableDomain, + Scan2ImConverter, + Tof2MzConverter, +}; #[derive(Debug, Clone)] -pub struct MultiCMGStats { +pub struct MultiCMGStatsAgg { pub converters: (Tof2MzConverter, Scan2ImConverter), - pub ms1_stats: _MultiCMGStats, - pub ms2_stats: _MultiCMGStats, + pub ms1_stats: ParitionedCMGAggregator, + pub ms2_stats: ParitionedCMGAggregator, pub id: u64, pub context: Option>, + pub buffer: Option, } #[derive(Debug, Clone)] @@ -80,24 +62,20 @@ pub struct MultiCMGStatsFactory } impl MultiCMGStatsFactory { - pub fn build(&self, id: u64) -> MultiCMGStats { - MultiCMGStats { + pub fn build(&self, id: u64) -> MultiCMGStatsAgg { + MultiCMGStatsAgg { converters: (self.converters.0, self.converters.1), ms1_stats: Default::default(), ms2_stats: Default::default(), id, context: None, + buffer: None, } } } #[derive(Debug, Clone, Serialize)] -pub struct MultiCMGStatsArrays { - pub transition_stats: MappingCollection, -} - -#[derive(Debug, Clone, Serialize)] -pub struct _FinalizedMultiCMGStatsArrays { +pub struct PartitionedCMGArrayStats { pub retention_time_miliseconds: Vec, pub weighted_scan_index_mean: Vec, pub summed_intensity: Vec, @@ -114,8 +92,8 @@ pub struct _FinalizedMultiCMGStatsArrays { - pub ms1_stats: _FinalizedMultiCMGStatsArrays, - pub ms2_stats: _FinalizedMultiCMGStatsArrays, + pub ms1_stats: PartitionedCMGArrayStats, + pub ms2_stats: PartitionedCMGArrayStats, pub id: u64, } @@ -145,28 +123,9 @@ pub struct NaturalFinalizedMultiCMGStatsArrays Vec { - let mut scores = vec![0.0; npeaks.len()]; - for i in 0..npeaks.len() { - let npeaks_i = npeaks[i]; - let summed_intensity_i = summed_intensity[i]; - let log1p_intensities_i = (summed_intensity_i as f64 + 1.0).ln(); - scores[i] = lnfact(npeaks_i as u16) + (2.0 * log1p_intensities_i); - } - scores -} - -fn calculate_value_vs_baseline(vals: &[f64], baseline_window_size: usize) -> Vec { - let baseline = rolling_median(vals, baseline_window_size, f64::NAN); - vals.iter() - .zip(baseline.iter()) - .map(|(x, y)| x - y) - .collect() -} - impl _NaturalFinalizedMultiCMGStatsArrays { pub fn new( - other: _FinalizedMultiCMGStatsArrays, + other: PartitionedCMGArrayStats, mz_converter: &Tof2MzConverter, mobility_converter: &Scan2ImConverter, ) -> Self { @@ -274,13 +233,13 @@ impl _NaturalFinalizedMultiCMGS } } -impl From> - for _FinalizedMultiCMGStatsArrays +impl From> + for PartitionedCMGArrayStats { - fn from(other: MultiCMGStatsArrays) -> Self { + fn from(other: PartitionedCMGArrays) -> Self { // TODO ... maybe refactor this ... RN its king of ugly. - let mut out = _FinalizedMultiCMGStatsArrays { + let mut out = PartitionedCMGArrayStats { retention_time_miliseconds: Vec::new(), scan_index_means: MappingCollection::new(), tof_index_means: MappingCollection::new(), @@ -384,10 +343,10 @@ impl From Aggregator - for MultiCMGStats + for MultiCMGStatsAgg { - type Item = RawPeak; type Context = MsLevelContext; + type Item = RawPeak; type Output = NaturalFinalizedMultiCMGStatsArrays; fn add(&mut self, peak: impl Into) { @@ -455,12 +414,12 @@ impl Aggregat let mobility_converter = &self.converters.1; let ms1_stats = _NaturalFinalizedMultiCMGStatsArrays::new( - _FinalizedMultiCMGStatsArrays::from(self.ms1_stats.finalize()), + PartitionedCMGArrayStats::from(self.ms1_stats.finalize()), mz_converter, mobility_converter, ); let ms2_stats = _NaturalFinalizedMultiCMGStatsArrays::new( - _FinalizedMultiCMGStatsArrays::from(self.ms2_stats.finalize()), + PartitionedCMGArrayStats::from(self.ms2_stats.finalize()), mz_converter, mobility_converter, ); @@ -472,31 +431,3 @@ impl Aggregat } } } - -#[cfg(test)] -mod tests { - use super::*; - - #[test] - fn test_value_vs_baseline() { - let vals = vec![1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0]; - let baseline_window_size = 3; - let _baseline = rolling_median(&vals, baseline_window_size, f64::NAN); - let out = calculate_value_vs_baseline(&vals, baseline_window_size); - let expect_val = vec![f64::NAN, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, f64::NAN]; - let all_close = out - .iter() - .zip(expect_val.iter()) - .filter(|(a, b)| ((!a.is_nan()) && (!b.is_nan()))) - .all(|(a, b)| (a - b).abs() < 1e-6); - - let all_match_nan = out - .iter() - .zip(expect_val.iter()) - .filter(|(a, b)| ((a.is_nan()) || (b.is_nan()))) - .all(|(a, b)| a.is_nan() && b.is_nan()); - - assert!(all_close, "Expected {:?}, got {:?}", expect_val, out); - assert!(all_match_nan, "Expected {:?}, got {:?}", expect_val, out); - } -} diff --git a/src/models/aggregators/raw_peak_agg/point_agg.rs b/src/models/aggregators/raw_peak_agg/point_agg.rs index 1fbfdcc..931f657 100644 --- a/src/models/aggregators/raw_peak_agg/point_agg.rs +++ b/src/models/aggregators/raw_peak_agg/point_agg.rs @@ -1,5 +1,11 @@ -use crate::models::frames::raw_peak::RawPeak; -use crate::traits::aggregator::{Aggregator, NoContext, ProvidesContext}; +use crate::{ + models::frames::raw_peak::RawPeak, + traits::aggregator::{ + Aggregator, + NoContext, + ProvidesContext, + }, +}; use serde::Serialize; #[derive(Debug, Clone, Copy)] @@ -15,8 +21,8 @@ impl RawPeakIntensityAggregator { } impl Aggregator for RawPeakIntensityAggregator { - type Item = RawPeak; type Context = NoContext; + type Item = RawPeak; type Output = u64; fn add(&mut self, peak: impl Into) { @@ -68,8 +74,8 @@ pub struct RawPeakVectorArrays { } impl Aggregator for RawPeakVectorAggregator { - type Item = RawPeak; type Context = NoContext; + type Item = RawPeak; type Output = RawPeakVectorArrays; fn add(&mut self, peak: impl Into) { diff --git a/src/models/aggregators/rolling_calculators.rs b/src/models/aggregators/rolling_calculators.rs index 24bdfad..60a5f31 100644 --- a/src/models/aggregators/rolling_calculators.rs +++ b/src/models/aggregators/rolling_calculators.rs @@ -1,3 +1,7 @@ +use crate::utils::math::{ + lnfact, + lnfact_float, +}; // Rolling median calculator pub struct RollingMedianCalculator { @@ -56,6 +60,24 @@ pub fn rolling_median( out } +pub fn calculate_lazy_hyperscore(npeaks: &[usize], summed_intensity: &[u64]) -> Vec { + let mut scores = vec![0.0; npeaks.len()]; + for i in 0..npeaks.len() { + let npeaks_i = npeaks[i]; + let summed_intensity_i = summed_intensity[i]; + let log1p_intensities_i = (summed_intensity_i as f64 + 1.0).ln(); + scores[i] = lnfact(npeaks_i as u16) + (2.0 * log1p_intensities_i); + } + scores +} + +pub fn calculate_value_vs_baseline(vals: &[f64], baseline_window_size: usize) -> Vec { + let baseline = rolling_median(vals, baseline_window_size, f64::NAN); + vals.iter() + .zip(baseline.iter()) + .map(|(x, y)| x - y) + .collect() +} #[cfg(test)] mod tests { use super::*; @@ -100,4 +122,27 @@ mod tests { } } } + + #[test] + fn test_value_vs_baseline() { + let vals = vec![1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0]; + let baseline_window_size = 3; + let _baseline = rolling_median(&vals, baseline_window_size, f64::NAN); + let out = calculate_value_vs_baseline(&vals, baseline_window_size); + let expect_val = vec![f64::NAN, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, f64::NAN]; + let all_close = out + .iter() + .zip(expect_val.iter()) + .filter(|(a, b)| ((!a.is_nan()) && (!b.is_nan()))) + .all(|(a, b)| (a - b).abs() < 1e-6); + + let all_match_nan = out + .iter() + .zip(expect_val.iter()) + .filter(|(a, b)| ((a.is_nan()) || (b.is_nan()))) + .all(|(a, b)| a.is_nan() && b.is_nan()); + + assert!(all_close, "Expected {:?}, got {:?}", expect_val, out); + assert!(all_match_nan, "Expected {:?}, got {:?}", expect_val, out); + } } diff --git a/src/models/aggregators/streaming_aggregator.rs b/src/models/aggregators/streaming_aggregator.rs index c85456e..d03093f 100644 --- a/src/models/aggregators/streaming_aggregator.rs +++ b/src/models/aggregators/streaming_aggregator.rs @@ -4,6 +4,7 @@ use tracing::debug; // and another with a weight and in a streaming fashion adds the value to the accumulator // to calculate the total, mean and variance. +// TODO: move this to the general errors. #[derive(Debug, Clone, Copy)] pub enum StreamingAggregatorError { DivisionByZero, @@ -20,21 +21,29 @@ type Result = std::result::Result; /// use timsquery::models::aggregators::streaming_aggregator::RunningStatsCalculator; /// /// // Create a new calculator with a weight of 10 and a mean of 0.0 -/// let mut calc = RunningStatsCalculator::new(2, 0.0); -/// calc.add(10.0, 2); +/// let mut calc = RunningStatsCalculator::new(1, 0.0); +/// calc.add(10.0, 1); +/// calc.add(0.0, 1); +/// calc.add(10.0, 1); +/// calc.add(0.0, 1); +/// calc.add(10.0, 1); +/// calc.add(0.0, 1); /// // So overall this should be the equivalent of the mean for -/// // [0.0, 0.0, 10.0, 10.0] -/// assert_eq!(calc.mean().unwrap(), 5.0); -/// +/// // [0.0, 10.0, 0.0, 10.0, 0.0, 10.0] +/// assert_eq!(calc.mean().unwrap(), 5.0, "{calc:#?}"); +/// assert!((4.5..5.5).contains(&calc.standard_deviation().unwrap()), "{calc:#?}"); /// ``` /// /// # Notes /// +/// It is important to know that the calculation of the mean is not +/// perfect. Thus if the initial value passes if very far off the real +/// mean, the final estimate will be off. +/// /// Ref impl in javascript ... /// https://nestedsoftware.com/2018/03/27/calculating-standard-deviation-on-streaming-data-253l.23919.html /// https://nestedsoftware.com/2019/09/26/incremental-average-and-standard-deviation-with-sliding-window-470k.176143.html /// Read the blog ... its amazing. -/// #[derive(Debug, Clone, Copy, Default)] pub struct RunningStatsCalculator { weight: u64, diff --git a/src/models/elution_group.rs b/src/models/elution_group.rs index fd7d2be..1448d97 100644 --- a/src/models/elution_group.rs +++ b/src/models/elution_group.rs @@ -1,13 +1,17 @@ -use serde::{Deserialize, Serialize}; -use std::collections::HashMap; -use std::hash::Hash; +use serde::{ + Deserialize, + Serialize, +}; +use std::{ + collections::HashMap, + hash::Hash, +}; /// A struct that represents an elution group. /// /// The elution group is a single precursor ion that is framented. /// The fragments m/z values are stored in a hashmap where the key is /// the generic type `T` and the value is the fragment m/z. -/// #[derive(Debug, Serialize, Deserialize, Clone)] pub struct ElutionGroup { pub id: u64, diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index ab0baba..05bae0b 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -1,23 +1,57 @@ -use super::peak_in_quad::PeakInQuad; -use super::single_quad_settings::{ - expand_quad_settings, ExpandedFrameQuadSettings, SingleQuadrupoleSetting, +use super::{ + peak_in_quad::PeakInQuad, + single_quad_settings::{ + expand_quad_settings, + ExpandedFrameQuadSettings, + SingleQuadrupoleSetting, + }, +}; +use crate::{ + errors::{ + Result, + UnsupportedDataError, + }, + sort_vecs_by_first, + utils::{ + compress_explode::explode_vec, + frame_processing::{ + lazy_centroid_weighted_frame, + PeakArrayRefs, + }, + sorting::top_n, + tolerance_ranges::{ + scan_tol_range, + tof_tol_range, + IncludedRange, + }, + }, }; -use crate::errors::{Result, UnsupportedDataError}; -use crate::sort_vecs_by_first; -use crate::utils::compress_explode::explode_vec; -use crate::utils::frame_processing::{lazy_centroid_weighted_frame, PeakArrayRefs}; -use crate::utils::sorting::top_n; -use crate::utils::tolerance_ranges::IncludedRange; -use crate::utils::tolerance_ranges::{scan_tol_range, tof_tol_range}; use rayon::prelude::*; -use std::collections::HashMap; -use std::marker::PhantomData; -use std::sync::Arc; -use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; -use timsrust::readers::{FrameReader, FrameReaderError}; -use timsrust::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}; -use tracing::instrument; -use tracing::{info, trace, warn}; +use std::{ + collections::HashMap, + marker::PhantomData, + sync::Arc, +}; +use timsrust::{ + converters::{ + Scan2ImConverter, + Tof2MzConverter, + }, + readers::{ + FrameReader, + FrameReaderError, + }, + AcquisitionType, + Frame, + MSLevel, + QuadrupoleSettings, +}; +use tracing::{ + info, + instrument, + trace, + warn, +}; /// A frame after expanding the mobility data and re-sorting it by tof. #[derive(Debug, Clone)] @@ -489,8 +523,6 @@ impl ExpandedQuadSliceInfo { /// the intensity of the peak drops under 1% of its intensity. /// 4. The time difference between the forward and backward point is the peak width. /// 5. Finds the median of the peak widths. - /// - /// fn estimate_peak_width(frameslices: &[ExpandedFrameSlice]) -> Option { let start_idx = frameslices.len() / 5; let end_idx = frameslices.len() * 4 / 5; @@ -534,11 +566,7 @@ impl ExpandedQuadSliceInfo { .filter_map(|x| { let a = x[0]; let b = x[1]; - if a.abs_diff(b) > 5 { - Some(a) - } else { - None - } + if a.abs_diff(b) > 5 { Some(a) } else { None } }) .collect(); @@ -689,9 +717,7 @@ pub fn par_expand_and_centroid_frames( let end_peaks: usize = centroided.iter().map(|x| x.len()).sum(); trace!( "Peak counts for quad {:?}: raw={}/centroid={}", - qs, - start_peaks, - end_peaks + qs, start_peaks, end_peaks ); (qs, centroided) }) diff --git a/src/models/frames/expanded_window_group.rs b/src/models/frames/expanded_window_group.rs index 4283c2a..9cff012 100644 --- a/src/models/frames/expanded_window_group.rs +++ b/src/models/frames/expanded_window_group.rs @@ -1,8 +1,16 @@ use std::iter::repeat; -use super::expanded_frame::{ExpandedFrameSlice, SortingStateTrait}; -use super::single_quad_settings::SingleQuadrupoleSetting; -use timsrust::{AcquisitionType, MSLevel}; +use super::{ + expanded_frame::{ + ExpandedFrameSlice, + SortingStateTrait, + }, + single_quad_settings::SingleQuadrupoleSetting, +}; +use timsrust::{ + AcquisitionType, + MSLevel, +}; pub struct ExpandedWindowGroup { pub tof_indices: Vec, diff --git a/src/models/frames/raw_frames.rs b/src/models/frames/raw_frames.rs index 4cc1f9c..c40c6ae 100644 --- a/src/models/frames/raw_frames.rs +++ b/src/models/frames/raw_frames.rs @@ -1,4 +1,7 @@ -use timsrust::{Frame, QuadrupoleSettings}; +use timsrust::{ + Frame, + QuadrupoleSettings, +}; use super::raw_peak::RawPeak; use crate::utils::tolerance_ranges::IncludedRange; @@ -39,9 +42,7 @@ pub fn frame_elems_matching( ) -> impl Iterator + '_ { trace!( "frame_elems_matching tof_range: {:?}, scan_range: {:?}, quad_range: {:?}", - tof_range, - scan_range, - quad_range + tof_range, scan_range, quad_range ); let quad_scan_range = quad_range .and_then(|quad_range| scans_matching_quad(&frame.quadrupole_settings, quad_range)); diff --git a/src/models/frames/single_quad_settings.rs b/src/models/frames/single_quad_settings.rs index 12f3dab..a9071ff 100644 --- a/src/models/frames/single_quad_settings.rs +++ b/src/models/frames/single_quad_settings.rs @@ -1,5 +1,7 @@ -use std::fmt::Display; -use std::hash::Hash; +use std::{ + fmt::Display, + hash::Hash, +}; use timsrust::QuadrupoleSettings; @@ -33,7 +35,13 @@ impl Display for SingleQuadrupoleSettingRanges { write!( f, "SingleQuadrupoleSettingRanges {{ scan_start: {}, scan_end: {}, isolation_mz: {}, isolation_width: {}, isolation_high: {}, isolation_low: {}, collision_energy: {} }}", - self.scan_start, self.scan_end, self.isolation_mz, self.isolation_width, self.isolation_high, self.isolation_low, self.collision_energy + self.scan_start, + self.scan_end, + self.isolation_mz, + self.isolation_width, + self.isolation_high, + self.isolation_low, + self.collision_energy ) } } diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index ff08ed6..513ff9e 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -1,29 +1,57 @@ -use crate::errors::Result; -use crate::models::adapters::FragmentIndexAdapter; -use crate::models::elution_group::ElutionGroup; -use crate::models::frames::expanded_frame::{ - par_read_and_expand_frames, ExpandedFrameSlice, FrameProcessingConfig, SortedState, +use crate::{ + errors::Result, + models::{ + adapters::FragmentIndexAdapter, + elution_group::ElutionGroup, + frames::{ + expanded_frame::{ + par_read_and_expand_frames, + ExpandedFrameSlice, + FrameProcessingConfig, + SortedState, + }, + peak_in_quad::PeakInQuad, + raw_peak::RawPeak, + single_quad_settings::{ + get_matching_quad_settings, + matches_quad_settings, + SingleQuadrupoleSetting, + SingleQuadrupoleSettingIndex, + }, + }, + queries::{ + FragmentGroupIndexQuery, + MsLevelContext, + }, + }, + traits::{ + aggregator::Aggregator, + queriable_data::QueriableData, + }, + utils::tolerance_ranges::IncludedRange, + ToleranceAdapter, }; -use crate::models::frames::peak_in_quad::PeakInQuad; -use crate::models::frames::raw_peak::RawPeak; -use crate::models::frames::single_quad_settings::{ - get_matching_quad_settings, matches_quad_settings, SingleQuadrupoleSetting, - SingleQuadrupoleSettingIndex, -}; -use crate::models::queries::{FragmentGroupIndexQuery, MsLevelContext}; -use crate::traits::aggregator::Aggregator; -use crate::traits::queriable_data::QueriableData; -use crate::utils::tolerance_ranges::IncludedRange; -use crate::ToleranceAdapter; use rayon::prelude::*; use serde::Serialize; -use std::collections::HashMap; -use std::hash::Hash; -use std::time::Instant; -use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; -use timsrust::readers::{FrameReader, MetadataReader}; -use tracing::info; -use tracing::instrument; +use std::{ + collections::HashMap, + hash::Hash, + time::Instant, +}; +use timsrust::{ + converters::{ + Scan2ImConverter, + Tof2MzConverter, + }, + readers::{ + FrameReader, + MetadataReader, + }, +}; +use tracing::{ + info, + instrument, +}; #[derive(Debug)] pub struct ExpandedRawFrameIndex { diff --git a/src/models/indices/raw_file_index.rs b/src/models/indices/raw_file_index.rs index 56f7b82..b1076cf 100644 --- a/src/models/indices/raw_file_index.rs +++ b/src/models/indices/raw_file_index.rs @@ -1,20 +1,40 @@ -use crate::models::adapters::FragmentIndexAdapter; -use crate::models::frames::raw_frames::frame_elems_matching; -use crate::models::frames::raw_peak::RawPeak; -use crate::models::queries::{FragmentGroupIndexQuery, MsLevelContext}; -use crate::traits::aggregator::Aggregator; -use crate::traits::queriable_data::QueriableData; -use crate::utils::tolerance_ranges::IncludedRange; -use crate::ElutionGroup; -use crate::ToleranceAdapter; +use crate::{ + models::{ + adapters::FragmentIndexAdapter, + frames::{ + raw_frames::frame_elems_matching, + raw_peak::RawPeak, + }, + queries::{ + FragmentGroupIndexQuery, + MsLevelContext, + }, + }, + traits::{ + aggregator::Aggregator, + queriable_data::QueriableData, + }, + utils::tolerance_ranges::IncludedRange, + ElutionGroup, + ToleranceAdapter, +}; use rayon::iter::ParallelIterator; use serde::Serialize; -use std::fmt::Debug; -use std::hash::Hash; -use timsrust::converters::ConvertableDomain; -use timsrust::readers::{FrameReader, FrameReaderError, MetadataReader}; -use timsrust::TimsRustError; -use timsrust::{Frame, Metadata}; +use std::{ + fmt::Debug, + hash::Hash, +}; +use timsrust::{ + converters::ConvertableDomain, + readers::{ + FrameReader, + FrameReaderError, + MetadataReader, + }, + Frame, + Metadata, + TimsRustError, +}; use tracing::trace; pub struct RawFileIndex { diff --git a/src/models/indices/transposed_quad_index/peak_bucket.rs b/src/models/indices/transposed_quad_index/peak_bucket.rs index 4ceef58..a0def3d 100644 --- a/src/models/indices/transposed_quad_index/peak_bucket.rs +++ b/src/models/indices/transposed_quad_index/peak_bucket.rs @@ -1,7 +1,14 @@ -use crate::sort_vecs_by_first; -use crate::utils::compress_explode::compress_vec; -use crate::utils::display::{glimpse_vec, GlimpseConfig}; -use crate::utils::tolerance_ranges::IncludedRange; +use crate::{ + sort_vecs_by_first, + utils::{ + compress_explode::compress_vec, + display::{ + glimpse_vec, + GlimpseConfig, + }, + tolerance_ranges::IncludedRange, + }, +}; use std::fmt::Display; pub struct PeakInBucket { diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index 049fd07..08ee99a 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -1,17 +1,43 @@ -use super::peak_bucket::PeakBucketBuilder; -use super::peak_bucket::{PeakBucket, PeakInBucket}; -use crate::models::frames::expanded_frame::{ExpandedFrameSlice, SortingStateTrait}; -use crate::models::frames::peak_in_quad::PeakInQuad; -use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; -use crate::sort_vecs_by_first; -use crate::utils::display::{glimpse_vec, GlimpseConfig}; -use crate::utils::tolerance_ranges::IncludedRange; -use std::collections::{BTreeMap, HashMap}; -use std::fmt::Display; -use std::time::Instant; -use timsrust::converters::{ConvertableDomain, Frame2RtConverter}; -use tracing::instrument; -use tracing::{debug, info}; +use super::peak_bucket::{ + PeakBucket, + PeakBucketBuilder, + PeakInBucket, +}; +use crate::{ + models::frames::{ + expanded_frame::{ + ExpandedFrameSlice, + SortingStateTrait, + }, + peak_in_quad::PeakInQuad, + single_quad_settings::SingleQuadrupoleSetting, + }, + sort_vecs_by_first, + utils::{ + display::{ + glimpse_vec, + GlimpseConfig, + }, + tolerance_ranges::IncludedRange, + }, +}; +use std::{ + collections::{ + BTreeMap, + HashMap, + }, + fmt::Display, + time::Instant, +}; +use timsrust::converters::{ + ConvertableDomain, + Frame2RtConverter, +}; +use tracing::{ + debug, + info, + instrument, +}; #[derive(Debug)] pub struct TransposedQuadIndex { @@ -63,8 +89,22 @@ impl Display for TransposedQuadIndex { f, "TransposedQuadIndex\n quad_settings: {:?}\n frame_indices: {}\n frame_rts: {}\n peak_buckets: {}\n", self.quad_settings, - glimpse_vec(&self.frame_indices, Some(GlimpseConfig { max_items: 10, padding: 2, new_line: true })), - glimpse_vec(&self.frame_rts, Some(GlimpseConfig { max_items: 10, padding: 2, new_line: true })), + glimpse_vec( + &self.frame_indices, + Some(GlimpseConfig { + max_items: 10, + padding: 2, + new_line: true + }) + ), + glimpse_vec( + &self.frame_rts, + Some(GlimpseConfig { + max_items: 10, + padding: 2, + new_line: true + }) + ), display_peak_bucket_map(&self.peak_buckets), ) } @@ -207,7 +247,10 @@ impl TransposedQuadIndexBuilder { let curr_bucket = peak_buckets.get(&(tof as u32)).unwrap(); let real_count = curr_bucket.len(); if real_count != count { - println!("TransposedQuadIndex::build failed at tof bucket count check, expected: {}, real: {}", count, real_count); + println!( + "TransposedQuadIndex::build failed at tof bucket count check, expected: {}, real: {}", + count, real_count + ); println!("Bucket -> {:?}", curr_bucket); panic!("TransposedQuadIndex::build failed at tof bucket count check"); @@ -305,7 +348,10 @@ impl TransposedQuadIndexBuilder { } if added_peaks != tot_peaks { - println!("TransposedQuadIndex::add_frame_slice failed at peak count check, expected: {}, real: {}", tot_peaks, added_peaks); + println!( + "TransposedQuadIndex::add_frame_slice failed at peak count check, expected: {}, real: {}", + tot_peaks, added_peaks + ); panic!("TransposedQuadIndex::add_frame_slice failed at peak count check"); } @@ -411,14 +457,25 @@ impl TransposedQuadIndexBuilder { let insertion_elapsed = insertion_st.elapsed(); info!( "BatchedBuild: quad_settings={:?} start={:?} end={:?}/{} peaks {}/{} concat took {:#?} sorting took: {:#?} insertion took {:#?}", - self.quad_settings, start, end, num_slices, added_peaks, tot_peaks, concat_elapsed, sorting_elapsed, insertion_elapsed, + self.quad_settings, + start, + end, + num_slices, + added_peaks, + tot_peaks, + concat_elapsed, + sorting_elapsed, + insertion_elapsed, ); start = end; peaks_in_chunk = 0; } if added_peaks != tot_peaks { - println!("TransposedQuadIndex::add_frame_slice failed at peak count check, expected: {}, real: {}", tot_peaks, added_peaks); + println!( + "TransposedQuadIndex::add_frame_slice failed at peak count check, expected: {}, real: {}", + tot_peaks, added_peaks + ); panic!("TransposedQuadIndex::add_frame_slice failed at peak count check"); } diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index 548b257..bdc1b58 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -1,33 +1,73 @@ -use super::quad_index::{TransposedQuadIndex, TransposedQuadIndexBuilder}; -use crate::errors::Result; -use crate::models::adapters::FragmentIndexAdapter; -use crate::models::elution_group::ElutionGroup; -use crate::models::frames::expanded_frame::{ - par_read_and_expand_frames, ExpandedFrameSlice, FrameProcessingConfig, SortingStateTrait, +use super::quad_index::{ + TransposedQuadIndex, + TransposedQuadIndexBuilder, }; -use crate::models::frames::peak_in_quad::PeakInQuad; -use crate::models::frames::raw_peak::RawPeak; -use crate::models::frames::single_quad_settings::{ - get_matching_quad_settings, SingleQuadrupoleSetting, SingleQuadrupoleSettingIndex, +use crate::{ + errors::Result, + models::{ + adapters::FragmentIndexAdapter, + elution_group::ElutionGroup, + frames::{ + expanded_frame::{ + par_read_and_expand_frames, + ExpandedFrameSlice, + FrameProcessingConfig, + SortingStateTrait, + }, + peak_in_quad::PeakInQuad, + raw_peak::RawPeak, + single_quad_settings::{ + get_matching_quad_settings, + SingleQuadrupoleSetting, + SingleQuadrupoleSettingIndex, + }, + }, + queries::{ + FragmentGroupIndexQuery, + MsLevelContext, + }, + }, + traits::{ + aggregator::Aggregator, + queriable_data::QueriableData, + }, + utils::{ + display::{ + glimpse_vec, + GlimpseConfig, + }, + tolerance_ranges::IncludedRange, + }, + ToleranceAdapter, }; -use crate::models::queries::{FragmentGroupIndexQuery, MsLevelContext}; -use crate::traits::aggregator::Aggregator; -use crate::traits::queriable_data::QueriableData; -use crate::utils::display::{glimpse_vec, GlimpseConfig}; -use crate::utils::tolerance_ranges::IncludedRange; -use crate::ToleranceAdapter; use rayon::prelude::*; use serde::Serialize; -use std::collections::HashMap; -use std::fmt::Debug; -use std::fmt::Display; -use std::hash::Hash; -use std::time::Instant; -use timsrust::converters::{Scan2ImConverter, Tof2MzConverter}; -use timsrust::readers::{FrameReader, MetadataReader}; -use timsrust::Metadata; -use tracing::instrument; -use tracing::{debug, info, trace}; +use std::{ + collections::HashMap, + fmt::{ + Debug, + Display, + }, + hash::Hash, + time::Instant, +}; +use timsrust::{ + converters::{ + Scan2ImConverter, + Tof2MzConverter, + }, + readers::{ + FrameReader, + MetadataReader, + }, + Metadata, +}; +use tracing::{ + debug, + info, + instrument, + trace, +}; // TODO break this module apart ... its getting too big for my taste // - JSP: 2024-11-19 diff --git a/src/models/queries.rs b/src/models/queries.rs index 83da21d..5daf53e 100644 --- a/src/models/queries.rs +++ b/src/models/queries.rs @@ -1,8 +1,19 @@ -use crate::traits::aggregator::{NoContext, ProvidesContext}; -use crate::utils::tolerance_ranges::IncludedRange; -use std::collections::HashMap; -use std::hash::Hash; -use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter}; +use crate::{ + traits::aggregator::{ + NoContext, + ProvidesContext, + }, + utils::tolerance_ranges::IncludedRange, +}; +use std::{ + collections::HashMap, + hash::Hash, +}; +use timsrust::converters::{ + ConvertableDomain, + Scan2ImConverter, + Tof2MzConverter, +}; #[derive(Debug, Clone)] pub struct PrecursorIndexQuery { diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index 88853fc..8f0f985 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -1,11 +1,21 @@ +use crate::{ + traits::aggregator::ProvidesContext, + Aggregator, + ElutionGroup, + QueriableData, + Tolerance, + ToleranceAdapter, +}; use rayon::prelude::*; use serde::Serialize; -use std::hash::Hash; -use std::time::Instant; -use tracing::info; - -use crate::traits::aggregator::ProvidesContext; -use crate::{Aggregator, ElutionGroup, QueriableData, Tolerance, ToleranceAdapter}; +use std::{ + hash::Hash, + time::Instant, +}; +use tracing::{ + info, + instrument, +}; // TODO: URGENTLY make documentation fot eh functions using this leftover struct docs // as a reference. @@ -43,6 +53,7 @@ use crate::{Aggregator, ElutionGroup, QueriableData, Tolerance, ToleranceAdapter // 2. `QD` is queried with `QP` and `QF` queries. // 3. The results are aggregated with `AG` aggregators (which are generated by the factory, when passed a numeric ID). +#[instrument(skip_all)] pub fn query_multi_group<'a, QD, TL, QF, AE1, AE2, OE, AG, FH, CTX1, CTX2, FF>( queriable_data: &'a QD, tolerance: &'a TL, @@ -56,7 +67,6 @@ where OE: Send + Sync, FH: Clone + Eq + Serialize + Hash + Send + Sync, QF: Send + Sync + ProvidesContext, - // AE: Send + Sync + Clone + Copy, AE1: Into + Send + Sync + Clone + Copy, AE2: Send + Sync + Clone + Copy + From, CTX1: Into + Send + Sync + Clone + Copy, diff --git a/src/traits/queriable_data.rs b/src/traits/queriable_data.rs index 55dd7af..e7e509d 100644 --- a/src/traits/queriable_data.rs +++ b/src/traits/queriable_data.rs @@ -1,4 +1,7 @@ -use crate::traits::aggregator::{Aggregator, ProvidesContext}; +use crate::traits::aggregator::{ + Aggregator, + ProvidesContext, +}; use rayon::prelude::*; pub trait QueriableData diff --git a/src/traits/tolerance.rs b/src/traits/tolerance.rs index 63246fa..4e0d110 100644 --- a/src/traits/tolerance.rs +++ b/src/traits/tolerance.rs @@ -1,5 +1,8 @@ use core::f32; -use serde::{Deserialize, Serialize}; +use serde::{ + Deserialize, + Serialize, +}; #[derive(Debug, Clone, Serialize, Deserialize)] pub enum MzToleramce { @@ -50,11 +53,14 @@ impl Default for DefaultTolerance { } } +const PROTON_MASS: f64 = 1.007276; +const NEUTRON_MASS: f64 = 1.008664; + fn mass_to_isotope_mzs(mass: f64, charge: u8, num_isotopes: usize) -> Vec { let mut out = Vec::with_capacity(num_isotopes); - const PROTON_MASS: f64 = 1.007276; - for i in 1..(num_isotopes + 1) { - let mass = mass + i as f64 * PROTON_MASS; + let real_mass = mass + (charge as f64 * PROTON_MASS); + for i in 0..(num_isotopes) { + let mass = real_mass + (i as f64 * NEUTRON_MASS); let mz = mass / charge as f64; out.push(mz); } @@ -63,7 +69,6 @@ fn mass_to_isotope_mzs(mass: f64, charge: u8, num_isotopes: usize) -> Vec { fn mz_to_isotope_mzs(mz: f64, charge: u8, num_isotopes: usize) -> Vec { let mut out = Vec::with_capacity(num_isotopes); - const PROTON_MASS: f64 = 1.007276; let proton_mass_frac = PROTON_MASS / charge as f64; for i in 0..num_isotopes { let mz = mz + (i as f64 * proton_mass_frac); @@ -127,7 +132,10 @@ impl Tolerance for DefaultTolerance { fn quad_range(&self, precursor_mz: f64, precursor_charge: u8) -> (f32, f32) { // Should this be a recoverable error? if precursor_charge == 0 { - panic!("Precursor charge is 0, inputs: self: {:?}, precursor_mz: {:?}, precursor_charge: {:?}", self, precursor_mz, precursor_charge); + panic!( + "Precursor charge is 0, inputs: self: {:?}, precursor_mz: {:?}, precursor_charge: {:?}", + self, precursor_mz, precursor_charge + ); }; match self.quad { QuadTolerance::Absolute((low, high, num_isotopes)) => { @@ -174,8 +182,9 @@ mod tests { fn test_isotope_mzs_neutral() { let test_vals = vec![ (100.0, 1, vec![101.0, 102.0, 103.0]), - (100.0, 2, vec![100.5, 101.0, 101.5]), - (100.0, 3, vec![100.33333, 100.666666, 101.0]), + // For z2, mass would be 102 (100 + 2 protons).... but since charge is 2 then we divide that + (100.0, 2, vec![51.0, 51.5, 52.0]), + (100.0, 3, vec![34.34, 34.67, 35.0]), ]; for (monoisotopic_mass, charge, expected) in test_vals { @@ -188,7 +197,13 @@ mod tests { .collect(); for ad in abs_diff.iter() { // Very tight tolerances here ... - assert!(*ad < 0.01); + assert!( + *ad < 0.03, + "Expected {:?}, got {:?}, diff {:?}", + expected, + out, + ad + ); } } } @@ -196,9 +211,9 @@ mod tests { #[test] fn test_isotope_mzs_mz() { let test_vals = vec![ - (100.0, 1, vec![10.0, 101.0, 102.0]), - (100.0, 2, vec![100.0, 100.5, 101.5]), - (100.0, 3, vec![100.0, 100.3333, 101.66666]), + (100.0, 1, vec![100.0, 101.0, 102.0]), + (100.0, 2, vec![100.0, 100.5, 101.0]), + (100.0, 3, vec![100.0, 100.3333, 100.66666]), ]; for (monoisotopic_mass, charge, expected) in test_vals { @@ -212,7 +227,13 @@ mod tests { for ad in abs_diff.iter() { // Very tight tolerances here ... - assert!(*ad < 0.01); + assert!( + *ad < 0.03, + "Expected {:?}, got {:?}, diff {:?}", + expected, + out, + ad + ); } } } diff --git a/src/utils/correlation.rs b/src/utils/correlation.rs new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/src/utils/correlation.rs @@ -0,0 +1 @@ + diff --git a/src/utils/frame_processing.rs b/src/utils/frame_processing.rs index 6a0ecfb..5657bbb 100644 --- a/src/utils/frame_processing.rs +++ b/src/utils/frame_processing.rs @@ -1,5 +1,9 @@ use crate::sort_vecs_by_first; -use tracing::{error, info, warn}; +use tracing::{ + error, + info, + warn, +}; use super::tolerance_ranges::IncludedRange; @@ -189,11 +193,11 @@ pub fn lazy_centroid_weighted_frame<'a>( let out = sort_n_check(agg_intensity, agg_tof, agg_ims); // TODO:Make everything below this a separate function and accumulate it. - let tot_final_intensity = out.0 .1.iter().map(|x| *x as u64).sum::(); + let tot_final_intensity = out.0.1.iter().map(|x| *x as u64).sum::(); let inten_ratio = tot_final_intensity as f64 / initial_tot_intensity as f64; assert!(initial_tot_intensity >= tot_final_intensity); - let output_len = out.0 .0.len(); + let output_len = out.0.0.len(); let compression_ratio = output_len as f64 / arr_len as f64; assert!(num_added == output_len); @@ -212,8 +216,8 @@ pub fn lazy_centroid_weighted_frame<'a>( warn!("tot_final_intensity: {:?}", tot_final_intensity); warn!( "First tof {} -> Range {:?}", - out.0 .0[0], - tof_tol_range_fn(out.0 .0[0]) + out.0.0[0], + tof_tol_range_fn(out.0.0[0]) ); panic!(); // warn!("agg_intensity: {:?}", out.0 .0); diff --git a/src/utils/math.rs b/src/utils/math.rs index 029fd70..7f3e5e5 100644 --- a/src/utils/math.rs +++ b/src/utils/math.rs @@ -18,3 +18,87 @@ pub fn lnfact_float(n: f64) -> f64 { n * n.ln() - n + 0.5 * n.ln() + 0.5 * (std::f64::consts::PI * 2.0 * n).ln() } } + +/// Logarigthmic mean of a slice of values. +pub fn lnmean(vals: &[f64]) -> f64 { + let mut sum = 0.0; + for val in vals { + sum += val.ln(); + } + (sum / vals.len() as f64).exp() +} + +fn cosine_similarity(a: &[f64], b: &[f64]) -> Option { + // Check if vectors have the same length and are not empty + if a.len() != b.len() || a.is_empty() { + return None; + } + + // Calculate dot product (numerator) + let dot_product: f64 = a.iter().zip(b.iter()).map(|(&x, &y)| x * y).sum(); + + // Calculate magnitudes (denominator) + let magnitude_a: f64 = a.iter().map(|&x| x * x).sum::().sqrt(); + + let magnitude_b: f64 = b.iter().map(|&x| x * x).sum::().sqrt(); + + // Avoid division by zero + if magnitude_a == 0.0 || magnitude_b == 0.0 { + return None; + } + + // Calculate cosine similarity + Some(dot_product / (magnitude_a * magnitude_b)) +} + +// Example usage: +fn main() { + let vector_a = vec![1.0, 2.0, 3.0]; + let vector_b = vec![4.0, 5.0, 6.0]; + + match cosine_similarity(&vector_a, &vector_b) { + Some(similarity) => println!("Cosine similarity: {}", similarity), + None => println!("Could not calculate cosine similarity"), + } +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn test_cosine_similarity() { + let a = vec![1.0, 2.0, 3.0]; + let b = vec![4.0, 5.0, 6.0]; + let result = cosine_similarity(&a, &b).unwrap(); + assert!((result - 0.974631846).abs() < 1e-8); + } + + #[test] + fn test_identical_vectors() { + let a = vec![1.0, 1.0, 1.0]; + let result = cosine_similarity(&a, &a).unwrap(); + assert!((result - 1.0).abs() < 1e-8); + } + + #[test] + fn test_empty_vectors() { + let a: Vec = vec![]; + let b: Vec = vec![]; + assert!(cosine_similarity(&a, &b).is_none()); + } + + #[test] + fn test_different_lengths() { + let a = vec![1.0, 2.0]; + let b = vec![1.0, 2.0, 3.0]; + assert!(cosine_similarity(&a, &b).is_none()); + } + + #[test] + fn test_zero_vector() { + let a = vec![0.0, 0.0, 0.0]; + let b = vec![1.0, 2.0, 3.0]; + assert!(cosine_similarity(&a, &b).is_none()); + } +} diff --git a/src/utils/mod.rs b/src/utils/mod.rs index 1d8244c..225a906 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -1,6 +1,8 @@ pub mod compress_explode; +pub mod correlation; pub mod display; pub mod frame_processing; pub mod math; +pub mod scoring; pub mod sorting; pub mod tolerance_ranges; diff --git a/src/utils/scoring.rs b/src/utils/scoring.rs new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/src/utils/scoring.rs @@ -0,0 +1 @@ + diff --git a/src/utils/sorting.rs b/src/utils/sorting.rs index c35b22a..3e9643f 100644 --- a/src/utils/sorting.rs +++ b/src/utils/sorting.rs @@ -21,7 +21,6 @@ /// assert_eq!(out.1, vec![3, 2, 1]); /// assert_eq!(out.2, vec!['c', 'b', 'a']); /// ``` -/// #[macro_export] macro_rules! sort_vecs_by_first { ($first:expr $(,$rest:expr)*) => {{ diff --git a/src/utils/tolerance_ranges.rs b/src/utils/tolerance_ranges.rs index 4bde46d..5099546 100644 --- a/src/utils/tolerance_ranges.rs +++ b/src/utils/tolerance_ranges.rs @@ -1,4 +1,8 @@ -use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter}; +use timsrust::converters::{ + ConvertableDomain, + Scan2ImConverter, + Tof2MzConverter, +}; #[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)] pub struct IncludedRange(pub T, pub T); From dd0cb501ca0016eb1efcb7da699a71e79c0b50ce Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Sun, 3 Nov 2024 11:24:25 -0800 Subject: [PATCH 21/30] chore: added pre-commit --- .gitignore | 1 - .pre-commit-config.yaml | 31 ++ README.md | 2 +- Taskfile.yml | 6 +- benches/benchmark_indices.rs | 56 ++-- data/sageresults/.gitignore | 2 +- data/sageresults/check.bash | 2 +- data/sageresults/ubb_elution_groups.json | 2 +- ..._results_230510_PRTC_13_S1-B1_1_12817.json | 2 +- rustfmt.toml | 2 +- src/lib.rs | 18 +- src/main.rs | 54 ++- src/models/adapters.rs | 22 +- .../raw_peak_agg/chromatogram_agg.rs | 11 +- src/models/aggregators/raw_peak_agg/mod.rs | 6 +- .../multi_chromatogram_agg/base.rs | 289 ++++++++++++++-- .../multi_chromatogram_agg.rs | 314 +----------------- .../aggregators/raw_peak_agg/point_agg.rs | 11 +- src/models/aggregators/rolling_calculators.rs | 5 +- src/models/elution_group.rs | 6 +- src/models/frames/expanded_frame.rs | 70 ++-- src/models/frames/expanded_window_group.rs | 10 +- src/models/frames/single_quad_settings.rs | 6 +- .../indices/expanded_raw_index/model.rs | 80 ++--- src/models/indices/raw_file_index.rs | 41 +-- .../transposed_quad_index/peak_bucket.rs | 16 +- .../transposed_quad_index/quad_index.rs | 40 +-- .../quad_splitted_transposed_index.rs | 99 +++--- src/models/queries.rs | 18 +- .../queriable_tims_data.rs | 8 +- src/utils/math.rs | 11 - src/utils/tolerance_ranges.rs | 6 +- 32 files changed, 558 insertions(+), 689 deletions(-) create mode 100644 .pre-commit-config.yaml diff --git a/.gitignore b/.gitignore index 926a8d5..c21c2ce 100644 --- a/.gitignore +++ b/.gitignore @@ -3,4 +3,3 @@ /tmp .env results.json - diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..f2af126 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,31 @@ +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v2.3.0 + hooks: + - id: trailing-whitespace +- repo: local + hooks: + - id: fmt + name: fmt + description: Format files with cargo fmt. + entry: cargo +nightly fmt + language: system + types: [rust] + args: ["--"] + - id: cargo-check + name: cargo check + description: Check the package for errors. + entry: cargo check + language: system + types: [rust] + pass_filenames: false + - id: clippy + name: clippy + description: Lint rust sources + entry: cargo clippy + language: system + args: ["--", "-D", "warnings"] + types: [rust] + pass_filenames: false + + diff --git a/README.md b/README.md index 72a9234..a661f33 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ your file, and you get back results that match those three things! More explicitly: - The main design is to have modular components: - aggregators - - indices + - indices - queries - tolerances diff --git a/Taskfile.yml b/Taskfile.yml index cbca819..6335cfa 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -37,7 +37,7 @@ tasks: clippy: cmds: - - cargo clippy + - cargo clippy {{.CLI_ARGS}} bench: sources: @@ -46,8 +46,8 @@ tasks: - cargo b --release --features bench --bin benchmark_indices - SKIP_SLOW=1 SKIP_BUILD=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/230510_PRTC_13_S1-B1_1_12817.d ./target/release/benchmark_indices - uv run benches/plot_bench.py data/benchmark_results_230510_PRTC_13_S1-B1_1_12817.json - - # SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d ./target/release/benchmark_indices - - # uv run benches/plot_bench.py data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json + - # SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d ./target/release/benchmark_indices + - # uv run benches/plot_bench.py data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json plot: sources: diff --git a/benches/benchmark_indices.rs b/benches/benchmark_indices.rs index d62c9fe..e37617c 100644 --- a/benches/benchmark_indices.rs +++ b/benches/benchmark_indices.rs @@ -4,48 +4,40 @@ use rand::{ }; use rand_chacha::ChaCha8Rng; use serde::Serialize; -use std::{ - collections::HashMap, - env, - fs::File, - path::{ - Path, - PathBuf, - }, - time::{ - Duration, - Instant, - }, +use std::collections::HashMap; +use std::env; +use std::fs::File; +use std::path::{ + Path, + PathBuf, }; -use timsquery::{ - models::{ - aggregators::RawPeakIntensityAggregator, - indices::{ - expanded_raw_index::ExpandedRawFrameIndex, - raw_file_index::RawFileIndex, - transposed_quad_index::QuadSplittedTransposedIndex, - }, - }, - queriable_tims_data::queriable_tims_data::query_multi_group, - traits::tolerance::{ - DefaultTolerance, - MobilityTolerance, - MzToleramce, - QuadTolerance, - RtTolerance, - }, - ElutionGroup, +use std::time::{ + Duration, + Instant, +}; +use timsquery::models::aggregators::RawPeakIntensityAggregator; +use timsquery::models::indices::expanded_raw_index::ExpandedRawFrameIndex; +use timsquery::models::indices::raw_file_index::RawFileIndex; +use timsquery::models::indices::transposed_quad_index::QuadSplittedTransposedIndex; +use timsquery::queriable_tims_data::queriable_tims_data::query_multi_group; +use timsquery::traits::tolerance::{ + DefaultTolerance, + MobilityTolerance, + MzToleramce, + QuadTolerance, + RtTolerance, }; +use timsquery::ElutionGroup; use tracing::subscriber::set_global_default; use tracing_bunyan_formatter::{ BunyanFormattingLayer, JsonStorageLayer, }; use tracing_chrome::ChromeLayerBuilder; +use tracing_subscriber::prelude::*; +use tracing_subscriber::registry::Registry; use tracing_subscriber::{ fmt, - prelude::*, - registry::Registry, EnvFilter, Layer, }; diff --git a/data/sageresults/.gitignore b/data/sageresults/.gitignore index 774378f..4030c7f 100644 --- a/data/sageresults/.gitignore +++ b/data/sageresults/.gitignore @@ -2,4 +2,4 @@ lfq.tsv results.sage.tsv matched_fragments.sage.tsv sage -log.log \ No newline at end of file +log.log diff --git a/data/sageresults/check.bash b/data/sageresults/check.bash index dc23fb5..0213bd4 100644 --- a/data/sageresults/check.bash +++ b/data/sageresults/check.bash @@ -10,4 +10,4 @@ set -o pipefail # uv run build.py ../../target/release/timsquery query-index --raw-file-path ../230510_PRTC_13_S1-B1_1_12817.d --tolerance-settings-path "../../templates/tolerance_settings_narrow_rt.json" --elution-groups-path "ubb_elution_groups.json" --output-path "query_results" --index expanded-raw-frame-index --aggregator multi-cmg-stats --format pretty-json -uv run plot.py \ No newline at end of file +uv run plot.py diff --git a/data/sageresults/ubb_elution_groups.json b/data/sageresults/ubb_elution_groups.json index 0c8970b..4cbd150 100644 --- a/data/sageresults/ubb_elution_groups.json +++ b/data/sageresults/ubb_elution_groups.json @@ -75,4 +75,4 @@ "13": 288.20294 } } -] \ No newline at end of file +] diff --git a/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json index 6c29c95..77bed42 100644 --- a/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json +++ b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json @@ -90,4 +90,4 @@ "basename": "230510_PRTC_13_S1-B1_1_12817" }, "full_benchmark_time_seconds": 648.106197917 -} \ No newline at end of file +} diff --git a/rustfmt.toml b/rustfmt.toml index c67c611..9a8eadb 100644 --- a/rustfmt.toml +++ b/rustfmt.toml @@ -1,6 +1,6 @@ imports_layout = "Vertical" -imports_granularity = "Crate" +imports_granularity = "Module" normalize_comments = true reorder_impl_items = true version = "Two" diff --git a/src/lib.rs b/src/lib.rs index d0c0ebf..3d254d3 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,17 +1,13 @@ // Re-export main structures -pub use crate::models::{ - elution_group::ElutionGroup, - indices::transposed_quad_index::QuadSplittedTransposedIndex, -}; +pub use crate::models::elution_group::ElutionGroup; +pub use crate::models::indices::transposed_quad_index::QuadSplittedTransposedIndex; // Re-export traits -pub use crate::traits::{ - aggregator::Aggregator, - queriable_data::QueriableData, - tolerance::{ - Tolerance, - ToleranceAdapter, - }, +pub use crate::traits::aggregator::Aggregator; +pub use crate::traits::queriable_data::QueriableData; +pub use crate::traits::tolerance::{ + Tolerance, + ToleranceAdapter, }; // Declare modules diff --git a/src/main.rs b/src/main.rs index 88c6b48..5616f0d 100644 --- a/src/main.rs +++ b/src/main.rs @@ -6,45 +6,35 @@ use serde::{ Deserialize, Serialize, }; -use std::{ - collections::HashMap, - time::Instant, +use std::collections::HashMap; +use std::time::Instant; +use timsquery::models::aggregators::{ + MultiCMGStatsFactory, + RawPeakIntensityAggregator, + RawPeakVectorAggregator, }; -use timsquery::{ - models::{ - aggregators::{ - MultiCMGStatsFactory, - RawPeakIntensityAggregator, - RawPeakVectorAggregator, - }, - elution_group::ElutionGroup, - indices::{ - ExpandedRawFrameIndex, - QuadSplittedTransposedIndex, - }, - }, - queriable_tims_data::queriable_tims_data::query_multi_group, - traits::tolerance::{ - DefaultTolerance, - MobilityTolerance, - MzToleramce, - QuadTolerance, - RtTolerance, - }, +use timsquery::models::elution_group::ElutionGroup; +use timsquery::models::indices::{ + ExpandedRawFrameIndex, + QuadSplittedTransposedIndex, }; -use tracing::{ - instrument, - subscriber::set_global_default, +use timsquery::queriable_tims_data::queriable_tims_data::query_multi_group; +use timsquery::traits::tolerance::{ + DefaultTolerance, + MobilityTolerance, + MzToleramce, + QuadTolerance, + RtTolerance, }; +use tracing::instrument; +use tracing::subscriber::set_global_default; use tracing_bunyan_formatter::{ BunyanFormattingLayer, JsonStorageLayer, }; -use tracing_subscriber::{ - prelude::*, - registry::Registry, - EnvFilter, -}; +use tracing_subscriber::prelude::*; +use tracing_subscriber::registry::Registry; +use tracing_subscriber::EnvFilter; fn main() { let env_filter = EnvFilter::try_from_default_env().unwrap_or_else(|_| EnvFilter::new("info")); diff --git a/src/models/adapters.rs b/src/models/adapters.rs index fe494d7..013199f 100644 --- a/src/models/adapters.rs +++ b/src/models/adapters.rs @@ -1,20 +1,14 @@ -use crate::{ - models::{ - elution_group::ElutionGroup, - queries::{ - FragmentGroupIndexQuery, - PrecursorIndexQuery, - }, - }, - utils::tolerance_ranges::IncludedRange, - ToleranceAdapter, +use crate::models::elution_group::ElutionGroup; +use crate::models::queries::{ + FragmentGroupIndexQuery, + PrecursorIndexQuery, }; +use crate::utils::tolerance_ranges::IncludedRange; +use crate::ToleranceAdapter; use serde::Serialize; use std::hash::Hash; -use timsrust::{ - converters::ConvertableDomain, - Metadata, -}; +use timsrust::converters::ConvertableDomain; +use timsrust::Metadata; #[derive(Debug, Default)] pub struct FragmentIndexAdapter { diff --git a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs index 4c06b9c..65e3c3f 100644 --- a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs @@ -1,15 +1,8 @@ use super::super::streaming_aggregator::RunningStatsCalculator; -use crate::{ - models::frames::raw_peak::RawPeak, - sort_vecs_by_first, - traits::aggregator::Aggregator, -}; +use crate::sort_vecs_by_first; use serde::Serialize; -use std::collections::{ - BTreeMap, - HashMap, -}; +use std::collections::HashMap; pub type MappingCollection = HashMap; diff --git a/src/models/aggregators/raw_peak_agg/mod.rs b/src/models/aggregators/raw_peak_agg/mod.rs index 03ec9b5..2d034c6 100644 --- a/src/models/aggregators/raw_peak_agg/mod.rs +++ b/src/models/aggregators/raw_peak_agg/mod.rs @@ -5,10 +5,8 @@ pub mod point_agg; pub use chromatogram_agg::ChromatomobilogramStats; pub use multi_chromatogram_agg::MultiCMGStatsAgg; // TODO: reorganize this so I donr use direcly from `base`` -pub use multi_chromatogram_agg::{ - base::PartitionedCMGArrays, - MultiCMGStatsFactory, -}; +pub use multi_chromatogram_agg::base::PartitionedCMGArrays; +pub use multi_chromatogram_agg::MultiCMGStatsFactory; pub use point_agg::{ RawPeakIntensityAggregator, RawPeakVectorAggregator, diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/base.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/base.rs index fc089f8..405d772 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/base.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/base.rs @@ -3,28 +3,22 @@ use super::super::chromatogram_agg::{ MappingCollection, ScanTofStatsCalculatorPair, }; -use crate::{ - models::{ - aggregators::{ - rolling_calculators::rolling_median, - streaming_aggregator::RunningStatsCalculator, - }, - frames::raw_peak::RawPeak, - queries::MsLevelContext, - }, - traits::aggregator::Aggregator, - utils::math::{ - lnfact, - lnfact_float, - }, +use crate::models::aggregators::rolling_calculators::{ + calculate_lazy_hyperscore, + calculate_value_vs_baseline, }; +use crate::models::aggregators::streaming_aggregator::RunningStatsCalculator; +use crate::utils::math::lnfact_float; use serde::Serialize; -use std::{ - collections::{ - BTreeMap, - HashSet, - }, - hash::Hash, +use std::collections::{ + BTreeMap, + HashSet, +}; +use std::hash::Hash; +use timsrust::converters::{ + ConvertableDomain, + Scan2ImConverter, + Tof2MzConverter, }; use tracing::{ debug, @@ -38,6 +32,41 @@ pub struct ParitionedCMGAggregator, } +#[derive(Debug, Clone, Serialize)] +pub struct PartitionedCMGArrayStats { + pub retention_time_miliseconds: Vec, + pub weighted_scan_index_mean: Vec, + pub summed_intensity: Vec, + + // This should be the same as the sum of log intensities. + pub log_intensity_products: Vec, + pub npeaks: Vec, + pub scan_index_means: MappingCollection>, + pub tof_index_means: MappingCollection>, + // TODO consider if I want to add the standard deviations ... RN they dont + // seem to be that useful. + pub intensities: MappingCollection>, +} + +// This name is starting to get really long ... +#[derive(Debug, Clone, Serialize)] +pub struct PartitionedCMGScoredStatsArrays { + pub retention_time_miliseconds: Vec, + pub average_mobility: Vec, + pub summed_intensity: Vec, + pub npeaks: Vec, + pub lazy_hyperscore: Vec, + pub lazy_hyperscore_vs_baseline: Vec, + pub norm_hyperscore_vs_baseline: Vec, + pub lazyerscore: Vec, + pub lazyerscore_vs_baseline: Vec, + pub norm_lazyerscore_vs_baseline: Vec, + pub transition_mobilities: MappingCollection>, + pub transition_mzs: MappingCollection>, + pub transition_intensities: MappingCollection>, + pub apex_primary_score_index: usize, +} + impl Default for ParitionedCMGAggregator { fn default() -> Self { Self { @@ -87,3 +116,223 @@ impl ParitionedCMGAggregator PartitionedCMGScoredStatsArrays { + // TODO: Refactor this function ... its getting pretty big. + pub fn new( + other: PartitionedCMGArrayStats, + mz_converter: &Tof2MzConverter, + mobility_converter: &Scan2ImConverter, + ) -> Self { + let lazy_hyperscore = calculate_lazy_hyperscore(&other.npeaks, &other.summed_intensity); + let basline_window_len = 1 + (other.retention_time_miliseconds.len() / 10); + let lazy_hyperscore_vs_baseline = + calculate_value_vs_baseline(&lazy_hyperscore, basline_window_len); + let lazyerscore: Vec = other + .log_intensity_products + .iter() + .map(|x| lnfact_float(*x)) + .collect(); + let lazyerscore_vs_baseline = calculate_value_vs_baseline(&lazyerscore, basline_window_len); + + // Set 0 the NANs + // Q: Can I do this in-place? Will the comnpiler do it for me? + let lazy_hyperscore_vs_baseline: Vec = lazy_hyperscore_vs_baseline + .into_iter() + .map(|x| if x.is_nan() { 0.0 } else { x }) + .collect(); + let lazyerscore_vs_baseline: Vec = lazyerscore_vs_baseline + .into_iter() + .map(|x| if x.is_nan() { 0.0 } else { x }) + .collect(); + + // Calculate the standard deviation of the lazyscores v baseline + let mut sd_calculator_hyperscore = RunningStatsCalculator::new(1, 0.0); + let mut sd_calculator_lazyscore = RunningStatsCalculator::new(1, 0.0); + + (0..lazyerscore_vs_baseline.len()).for_each(|i| { + sd_calculator_hyperscore.add(lazy_hyperscore_vs_baseline[i], 1); + sd_calculator_lazyscore.add(lazyerscore_vs_baseline[i], 1); + }); + let sd_hyperscore = sd_calculator_hyperscore.standard_deviation().unwrap(); + let sd_lazyscore = sd_calculator_lazyscore.standard_deviation().unwrap(); + + // Calculate the normalized scores + let norm_hyperscore_vs_baseline: Vec = lazy_hyperscore_vs_baseline + .iter() + .map(|x| x / sd_hyperscore) + .collect(); + let norm_lazyerscore_vs_baseline: Vec = lazyerscore_vs_baseline + .iter() + .map(|x| x / sd_lazyscore) + .collect(); + + let mut apex_primary_score_index = 0; + let mut max_primary_score = 0.0f64; + let primary_scores = &norm_lazyerscore_vs_baseline; + for (i, val) in primary_scores.iter().enumerate() { + if max_primary_score.is_nan() || *val > max_primary_score { + max_primary_score = *val; + apex_primary_score_index = i; + } + } + + assert!( + lazy_hyperscore_vs_baseline.len() == other.retention_time_miliseconds.len(), + "Failed sanity check" + ); + + PartitionedCMGScoredStatsArrays { + retention_time_miliseconds: other.retention_time_miliseconds, + average_mobility: other + .weighted_scan_index_mean + .into_iter() + .map(|x| { + let out = mobility_converter.convert(x); + if !(0.5..=2.0).contains(&out) { + debug!("Bad mobility value: {:?}, input was {:?}", out, x); + } + out + }) + .collect(), + summed_intensity: other.summed_intensity, + npeaks: other.npeaks, + transition_mobilities: other + .scan_index_means + .into_iter() + .map(|(k, v)| { + let new_v = v + .into_iter() + .map(|x| mobility_converter.convert(x)) + .collect(); + (k, new_v) + }) + .collect(), + transition_mzs: other + .tof_index_means + .into_iter() + .map(|(k, v)| { + let new_v = v.into_iter().map(|x| mz_converter.convert(x)).collect(); + (k, new_v) + }) + .collect(), + transition_intensities: other.intensities, + lazy_hyperscore, + lazy_hyperscore_vs_baseline, + apex_primary_score_index, + lazyerscore, + lazyerscore_vs_baseline, + norm_hyperscore_vs_baseline, + norm_lazyerscore_vs_baseline, + } + } +} + +impl From> + for PartitionedCMGArrayStats +{ + fn from(other: PartitionedCMGArrays) -> Self { + // TODO ... maybe refactor this ... RN its king of ugly. + + let mut out = PartitionedCMGArrayStats { + retention_time_miliseconds: Vec::new(), + scan_index_means: MappingCollection::new(), + tof_index_means: MappingCollection::new(), + weighted_scan_index_mean: Vec::new(), + intensities: MappingCollection::new(), + summed_intensity: Vec::new(), + log_intensity_products: Vec::new(), + npeaks: Vec::new(), + }; + + let unique_rts = other + .transition_stats + .iter() + .flat_map(|(_k, v)| v.retention_time_miliseconds.clone()) + .collect::>(); + let mut unique_rts = unique_rts.into_iter().collect::>(); + unique_rts.sort(); + + // Q: Is this the most efficient way to do this? + // I think having the btrees as the unit of integration might not be the best idea. + // ... If I want to preserve the sparsity, I can use a hashmap and the sort it. + let mut summed_intensity_tree: BTreeMap = + BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0))); + let mut intensity_logsums_tree: BTreeMap = + BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0.0))); + let mut npeaks_tree: BTreeMap = + BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0))); + let mut weighted_tof_index_mean_tree: BTreeMap = + BTreeMap::new(); + let mut weighted_scan_index_mean_tree: BTreeMap = + BTreeMap::new(); + + for (k, v) in other.transition_stats.into_iter() { + type ScanTofIntensityTuple = (f64, f64, u64); + type ScanTofIntensityVecs = (Vec, (Vec, Vec)); + let mut tmp_tree: BTreeMap = BTreeMap::new(); + + for i in 0..v.retention_time_miliseconds.len() { + let rt = v.retention_time_miliseconds[i]; + let scan = v.scan_index_means[i]; + let tof = v.tof_index_means[i]; + let inten = v.intensities[i]; + + if inten > 100 { + npeaks_tree.entry(rt).and_modify(|curr| *curr += 1); + } + tmp_tree.entry(rt).or_insert((scan, tof, inten)); + summed_intensity_tree + .entry(rt) + .and_modify(|curr| *curr += inten); + + intensity_logsums_tree.entry(rt).and_modify(|curr| { + if inten > 10 { + *curr += (inten as f64).ln() + } + }); + weighted_tof_index_mean_tree + .entry(rt) + .and_modify(|curr| curr.add(tof, inten)) + .or_insert(RunningStatsCalculator::new(inten, tof)); + weighted_scan_index_mean_tree + .entry(rt) + .and_modify(|curr| curr.add(scan, inten)) + .or_insert(RunningStatsCalculator::new(inten, scan)); + } + + // Now we fill with nans the missing values. + // Q: Do I really need to do this here? + for rt in unique_rts.iter() { + tmp_tree.entry(*rt).or_insert((f64::NAN, f64::NAN, 0)); + } + + let (out_scans, (out_tofs, out_intens)): ScanTofIntensityVecs = tmp_tree + .into_iter() + .map(|(_, (scan, tof, inten))| (scan, (tof, inten))) + .unzip(); + out.scan_index_means.insert(k.clone(), out_scans); + out.tof_index_means.insert(k.clone(), out_tofs); + out.intensities.insert(k.clone(), out_intens); + } + + out.retention_time_miliseconds = unique_rts; + out.summed_intensity = summed_intensity_tree.into_values().collect(); + out.npeaks = npeaks_tree.into_values().collect(); + out.weighted_scan_index_mean = weighted_scan_index_mean_tree + .into_values() + .map(|x| { + let out = x.mean().expect("At least one value should be present"); + if !(0.0..=1000.0).contains(&out) { + warn!("Bad mobility value: {:?}, input was {:?}", out, x); + } + + out + }) + .collect(); + + // Note: The log of products is the same as the sum of logs. + out.log_intensity_products = intensity_logsums_tree.into_values().collect(); + out + } +} diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/multi_chromatogram_agg.rs index a7583da..e19d31d 100644 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/multi_chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/multi_chromatogram_agg.rs @@ -1,50 +1,20 @@ -use super::{ - super::chromatogram_agg::{ - ChromatomobilogramStatsArrays, - MappingCollection, - ScanTofStatsCalculatorPair, - }, - base::{ - ParitionedCMGAggregator, - PartitionedCMGArrays, - }, -}; -use crate::{ - models::{ - aggregators::{ - rolling_calculators::{ - calculate_lazy_hyperscore, - calculate_value_vs_baseline, - }, - streaming_aggregator::RunningStatsCalculator, - }, - frames::raw_peak::RawPeak, - queries::MsLevelContext, - }, - traits::aggregator::Aggregator, - utils::math::{ - lnfact, - lnfact_float, - }, +use super::super::chromatogram_agg::ScanTofStatsCalculatorPair; +use super::base::{ + ParitionedCMGAggregator, + PartitionedCMGArrayStats, + PartitionedCMGScoredStatsArrays, }; +use crate::models::frames::raw_peak::RawPeak; +use crate::models::queries::MsLevelContext; +use crate::traits::aggregator::Aggregator; use serde::Serialize; -use std::{ - collections::{ - BTreeMap, - HashSet, - }, - hash::Hash, -}; -use tracing::{ - debug, - warn, -}; +use std::hash::Hash; use timsrust::converters::{ - ConvertableDomain, Scan2ImConverter, Tof2MzConverter, }; + #[derive(Debug, Clone)] pub struct MultiCMGStatsAgg { pub converters: (Tof2MzConverter, Scan2ImConverter), @@ -75,273 +45,19 @@ impl MultiCMGStatsFactory { } #[derive(Debug, Clone, Serialize)] -pub struct PartitionedCMGArrayStats { - pub retention_time_miliseconds: Vec, - pub weighted_scan_index_mean: Vec, - pub summed_intensity: Vec, - - // This should be the same as the sum of log intensities. - pub log_intensity_products: Vec, - pub npeaks: Vec, - pub scan_index_means: MappingCollection>, - pub tof_index_means: MappingCollection>, - // TODO consider if I want to add the standard deviations ... RN they dont - // seem to be that useful. - pub intensities: MappingCollection>, -} - -#[derive(Debug, Clone, Serialize)] -pub struct FinalizedMultiCMGStatsArrays { +pub struct MultiCMGArrayStats { pub ms1_stats: PartitionedCMGArrayStats, pub ms2_stats: PartitionedCMGArrayStats, pub id: u64, } -// This name is starting to get really long ... -#[derive(Debug, Clone, Serialize)] -pub struct _NaturalFinalizedMultiCMGStatsArrays { - pub retention_time_miliseconds: Vec, - pub average_mobility: Vec, - pub summed_intensity: Vec, - pub npeaks: Vec, - pub lazy_hyperscore: Vec, - pub lazy_hyperscore_vs_baseline: Vec, - pub norm_hyperscore_vs_baseline: Vec, - pub lazyerscore: Vec, - pub lazyerscore_vs_baseline: Vec, - pub norm_lazyerscore_vs_baseline: Vec, - pub transition_mobilities: MappingCollection>, - pub transition_mzs: MappingCollection>, - pub transition_intensities: MappingCollection>, - pub apex_primary_score_index: usize, -} - #[derive(Debug, Clone, Serialize)] pub struct NaturalFinalizedMultiCMGStatsArrays { - pub ms1_stats: _NaturalFinalizedMultiCMGStatsArrays, - pub ms2_stats: _NaturalFinalizedMultiCMGStatsArrays, + pub ms1_stats: PartitionedCMGScoredStatsArrays, + pub ms2_stats: PartitionedCMGScoredStatsArrays, pub id: u64, } -impl _NaturalFinalizedMultiCMGStatsArrays { - pub fn new( - other: PartitionedCMGArrayStats, - mz_converter: &Tof2MzConverter, - mobility_converter: &Scan2ImConverter, - ) -> Self { - let lazy_hyperscore = calculate_lazy_hyperscore(&other.npeaks, &other.summed_intensity); - let basline_window_len = 1 + (other.retention_time_miliseconds.len() / 10); - let lazy_hyperscore_vs_baseline = - calculate_value_vs_baseline(&lazy_hyperscore, basline_window_len); - let lazyerscore: Vec = other - .log_intensity_products - .iter() - .map(|x| lnfact_float(*x)) - .collect(); - let lazyerscore_vs_baseline = calculate_value_vs_baseline(&lazyerscore, basline_window_len); - - // Set 0 the NANs - // Q: Can I do this in-place? Will the comnpiler do it for me? - let lazy_hyperscore_vs_baseline: Vec = lazy_hyperscore_vs_baseline - .into_iter() - .map(|x| if x.is_nan() { 0.0 } else { x }) - .collect(); - let lazyerscore_vs_baseline: Vec = lazyerscore_vs_baseline - .into_iter() - .map(|x| if x.is_nan() { 0.0 } else { x }) - .collect(); - - // Calculate the standard deviation of the lazyscores v baseline - let mut sd_calculator_hyperscore = RunningStatsCalculator::new(1, 0.0); - let mut sd_calculator_lazyscore = RunningStatsCalculator::new(1, 0.0); - - (0..lazyerscore_vs_baseline.len()).for_each(|i| { - sd_calculator_hyperscore.add(lazy_hyperscore_vs_baseline[i], 1); - sd_calculator_lazyscore.add(lazyerscore_vs_baseline[i], 1); - }); - let sd_hyperscore = sd_calculator_hyperscore.standard_deviation().unwrap(); - let sd_lazyscore = sd_calculator_lazyscore.standard_deviation().unwrap(); - - // Calculate the normalized scores - let norm_hyperscore_vs_baseline: Vec = lazy_hyperscore_vs_baseline - .iter() - .map(|x| x / sd_hyperscore) - .collect(); - let norm_lazyerscore_vs_baseline: Vec = lazyerscore_vs_baseline - .iter() - .map(|x| x / sd_lazyscore) - .collect(); - - let mut apex_primary_score_index = 0; - let mut max_primary_score = 0.0f64; - let primary_scores = &norm_lazyerscore_vs_baseline; - for (i, val) in primary_scores.iter().enumerate() { - if max_primary_score.is_nan() || *val > max_primary_score { - max_primary_score = *val; - apex_primary_score_index = i; - } - } - - assert!( - lazy_hyperscore_vs_baseline.len() == other.retention_time_miliseconds.len(), - "Failed sanity check" - ); - - _NaturalFinalizedMultiCMGStatsArrays { - retention_time_miliseconds: other.retention_time_miliseconds, - average_mobility: other - .weighted_scan_index_mean - .into_iter() - .map(|x| { - let out = mobility_converter.convert(x); - if !(0.5..=2.0).contains(&out) { - debug!("Bad mobility value: {:?}, input was {:?}", out, x); - } - out - }) - .collect(), - summed_intensity: other.summed_intensity, - npeaks: other.npeaks, - transition_mobilities: other - .scan_index_means - .into_iter() - .map(|(k, v)| { - let new_v = v - .into_iter() - .map(|x| mobility_converter.convert(x)) - .collect(); - (k, new_v) - }) - .collect(), - transition_mzs: other - .tof_index_means - .into_iter() - .map(|(k, v)| { - let new_v = v.into_iter().map(|x| mz_converter.convert(x)).collect(); - (k, new_v) - }) - .collect(), - transition_intensities: other.intensities, - lazy_hyperscore, - lazy_hyperscore_vs_baseline, - apex_primary_score_index, - lazyerscore, - lazyerscore_vs_baseline, - norm_hyperscore_vs_baseline, - norm_lazyerscore_vs_baseline, - } - } -} - -impl From> - for PartitionedCMGArrayStats -{ - fn from(other: PartitionedCMGArrays) -> Self { - // TODO ... maybe refactor this ... RN its king of ugly. - - let mut out = PartitionedCMGArrayStats { - retention_time_miliseconds: Vec::new(), - scan_index_means: MappingCollection::new(), - tof_index_means: MappingCollection::new(), - weighted_scan_index_mean: Vec::new(), - intensities: MappingCollection::new(), - summed_intensity: Vec::new(), - log_intensity_products: Vec::new(), - npeaks: Vec::new(), - }; - - let unique_rts = other - .transition_stats - .iter() - .flat_map(|(_k, v)| v.retention_time_miliseconds.clone()) - .collect::>(); - let mut unique_rts = unique_rts.into_iter().collect::>(); - unique_rts.sort(); - - // Q: Is this the most efficient way to do this? - // I think having the btrees as the unit of integration might not be the best idea. - // ... If I want to preserve the sparsity, I can use a hashmap and the sort it. - let mut summed_intensity_tree: BTreeMap = - BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0))); - let mut intensity_logsums_tree: BTreeMap = - BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0.0))); - let mut npeaks_tree: BTreeMap = - BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 0))); - let mut weighted_tof_index_mean_tree: BTreeMap = - BTreeMap::new(); - let mut weighted_scan_index_mean_tree: BTreeMap = - BTreeMap::new(); - - for (k, v) in other.transition_stats.into_iter() { - type ScanTofIntensityTuple = (f64, f64, u64); - type ScanTofIntensityVecs = (Vec, (Vec, Vec)); - let mut tmp_tree: BTreeMap = BTreeMap::new(); - - for i in 0..v.retention_time_miliseconds.len() { - let rt = v.retention_time_miliseconds[i]; - let scan = v.scan_index_means[i]; - let tof = v.tof_index_means[i]; - let inten = v.intensities[i]; - - if inten > 100 { - npeaks_tree.entry(rt).and_modify(|curr| *curr += 1); - } - tmp_tree.entry(rt).or_insert((scan, tof, inten)); - summed_intensity_tree - .entry(rt) - .and_modify(|curr| *curr += inten); - - intensity_logsums_tree.entry(rt).and_modify(|curr| { - if inten > 10 { - *curr += (inten as f64).ln() - } - }); - weighted_tof_index_mean_tree - .entry(rt) - .and_modify(|curr| curr.add(tof, inten)) - .or_insert(RunningStatsCalculator::new(inten, tof)); - weighted_scan_index_mean_tree - .entry(rt) - .and_modify(|curr| curr.add(scan, inten)) - .or_insert(RunningStatsCalculator::new(inten, scan)); - } - - // Now we fill with nans the missing values. - // Q: Do I really need to do this here? - for rt in unique_rts.iter() { - tmp_tree.entry(*rt).or_insert((f64::NAN, f64::NAN, 0)); - } - - let (out_scans, (out_tofs, out_intens)): ScanTofIntensityVecs = tmp_tree - .into_iter() - .map(|(_, (scan, tof, inten))| (scan, (tof, inten))) - .unzip(); - out.scan_index_means.insert(k.clone(), out_scans); - out.tof_index_means.insert(k.clone(), out_tofs); - out.intensities.insert(k.clone(), out_intens); - } - - out.retention_time_miliseconds = unique_rts; - out.summed_intensity = summed_intensity_tree.into_values().collect(); - out.npeaks = npeaks_tree.into_values().collect(); - out.weighted_scan_index_mean = weighted_scan_index_mean_tree - .into_values() - .map(|x| { - let out = x.mean().expect("At least one value should be present"); - if !(0.0..=1000.0).contains(&out) { - warn!("Bad mobility value: {:?}, input was {:?}", out, x); - } - - out - }) - .collect(); - - // Note: The log of products is the same as the sum of logs. - out.log_intensity_products = intensity_logsums_tree.into_values().collect(); - out - } -} - impl Aggregator for MultiCMGStatsAgg { @@ -413,12 +129,12 @@ impl Aggregat let mz_converter = &self.converters.0; let mobility_converter = &self.converters.1; - let ms1_stats = _NaturalFinalizedMultiCMGStatsArrays::new( + let ms1_stats = PartitionedCMGScoredStatsArrays::new( PartitionedCMGArrayStats::from(self.ms1_stats.finalize()), mz_converter, mobility_converter, ); - let ms2_stats = _NaturalFinalizedMultiCMGStatsArrays::new( + let ms2_stats = PartitionedCMGScoredStatsArrays::new( PartitionedCMGArrayStats::from(self.ms2_stats.finalize()), mz_converter, mobility_converter, diff --git a/src/models/aggregators/raw_peak_agg/point_agg.rs b/src/models/aggregators/raw_peak_agg/point_agg.rs index 931f657..7187a3b 100644 --- a/src/models/aggregators/raw_peak_agg/point_agg.rs +++ b/src/models/aggregators/raw_peak_agg/point_agg.rs @@ -1,10 +1,7 @@ -use crate::{ - models::frames::raw_peak::RawPeak, - traits::aggregator::{ - Aggregator, - NoContext, - ProvidesContext, - }, +use crate::models::frames::raw_peak::RawPeak; +use crate::traits::aggregator::{ + Aggregator, + NoContext, }; use serde::Serialize; diff --git a/src/models/aggregators/rolling_calculators.rs b/src/models/aggregators/rolling_calculators.rs index 60a5f31..b010554 100644 --- a/src/models/aggregators/rolling_calculators.rs +++ b/src/models/aggregators/rolling_calculators.rs @@ -1,7 +1,4 @@ -use crate::utils::math::{ - lnfact, - lnfact_float, -}; +use crate::utils::math::lnfact; // Rolling median calculator pub struct RollingMedianCalculator { diff --git a/src/models/elution_group.rs b/src/models/elution_group.rs index 1448d97..9ed5221 100644 --- a/src/models/elution_group.rs +++ b/src/models/elution_group.rs @@ -2,10 +2,8 @@ use serde::{ Deserialize, Serialize, }; -use std::{ - collections::HashMap, - hash::Hash, -}; +use std::collections::HashMap; +use std::hash::Hash; /// A struct that represents an elution group. /// diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index 05bae0b..dbe1aad 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -1,46 +1,38 @@ -use super::{ - peak_in_quad::PeakInQuad, - single_quad_settings::{ - expand_quad_settings, - ExpandedFrameQuadSettings, - SingleQuadrupoleSetting, - }, +use super::peak_in_quad::PeakInQuad; +use super::single_quad_settings::{ + expand_quad_settings, + ExpandedFrameQuadSettings, + SingleQuadrupoleSetting, }; -use crate::{ - errors::{ - Result, - UnsupportedDataError, - }, - sort_vecs_by_first, - utils::{ - compress_explode::explode_vec, - frame_processing::{ - lazy_centroid_weighted_frame, - PeakArrayRefs, - }, - sorting::top_n, - tolerance_ranges::{ - scan_tol_range, - tof_tol_range, - IncludedRange, - }, - }, +use crate::errors::{ + Result, + UnsupportedDataError, +}; +use crate::sort_vecs_by_first; +use crate::utils::compress_explode::explode_vec; +use crate::utils::frame_processing::{ + lazy_centroid_weighted_frame, + PeakArrayRefs, +}; +use crate::utils::sorting::top_n; +use crate::utils::tolerance_ranges::{ + scan_tol_range, + tof_tol_range, + IncludedRange, }; use rayon::prelude::*; -use std::{ - collections::HashMap, - marker::PhantomData, - sync::Arc, +use std::collections::HashMap; +use std::marker::PhantomData; +use std::sync::Arc; +use timsrust::converters::{ + Scan2ImConverter, + Tof2MzConverter, +}; +use timsrust::readers::{ + FrameReader, + FrameReaderError, }; use timsrust::{ - converters::{ - Scan2ImConverter, - Tof2MzConverter, - }, - readers::{ - FrameReader, - FrameReaderError, - }, AcquisitionType, Frame, MSLevel, @@ -540,7 +532,6 @@ impl ExpandedQuadSliceInfo { max_rt: f64, min_rt: f64, intensity: u32, - local_frame_index: usize, fwdone: bool, bwdone: bool, any_update: bool, @@ -584,7 +575,6 @@ impl ExpandedQuadSliceInfo { max_rt: local_rt, min_rt: local_rt, intensity: local_inten, - local_frame_index: local_idx, fwdone: false, bwdone: false, any_update: false, diff --git a/src/models/frames/expanded_window_group.rs b/src/models/frames/expanded_window_group.rs index 9cff012..d38b5a0 100644 --- a/src/models/frames/expanded_window_group.rs +++ b/src/models/frames/expanded_window_group.rs @@ -1,12 +1,10 @@ use std::iter::repeat; -use super::{ - expanded_frame::{ - ExpandedFrameSlice, - SortingStateTrait, - }, - single_quad_settings::SingleQuadrupoleSetting, +use super::expanded_frame::{ + ExpandedFrameSlice, + SortingStateTrait, }; +use super::single_quad_settings::SingleQuadrupoleSetting; use timsrust::{ AcquisitionType, MSLevel, diff --git a/src/models/frames/single_quad_settings.rs b/src/models/frames/single_quad_settings.rs index a9071ff..7d4e819 100644 --- a/src/models/frames/single_quad_settings.rs +++ b/src/models/frames/single_quad_settings.rs @@ -1,7 +1,5 @@ -use std::{ - fmt::Display, - hash::Hash, -}; +use std::fmt::Display; +use std::hash::Hash; use timsrust::QuadrupoleSettings; diff --git a/src/models/indices/expanded_raw_index/model.rs b/src/models/indices/expanded_raw_index/model.rs index 513ff9e..c8be15d 100644 --- a/src/models/indices/expanded_raw_index/model.rs +++ b/src/models/indices/expanded_raw_index/model.rs @@ -1,52 +1,40 @@ -use crate::{ - errors::Result, - models::{ - adapters::FragmentIndexAdapter, - elution_group::ElutionGroup, - frames::{ - expanded_frame::{ - par_read_and_expand_frames, - ExpandedFrameSlice, - FrameProcessingConfig, - SortedState, - }, - peak_in_quad::PeakInQuad, - raw_peak::RawPeak, - single_quad_settings::{ - get_matching_quad_settings, - matches_quad_settings, - SingleQuadrupoleSetting, - SingleQuadrupoleSettingIndex, - }, - }, - queries::{ - FragmentGroupIndexQuery, - MsLevelContext, - }, - }, - traits::{ - aggregator::Aggregator, - queriable_data::QueriableData, - }, - utils::tolerance_ranges::IncludedRange, - ToleranceAdapter, +use crate::errors::Result; +use crate::models::adapters::FragmentIndexAdapter; +use crate::models::elution_group::ElutionGroup; +use crate::models::frames::expanded_frame::{ + par_read_and_expand_frames, + ExpandedFrameSlice, + FrameProcessingConfig, + SortedState, }; +use crate::models::frames::peak_in_quad::PeakInQuad; +use crate::models::frames::raw_peak::RawPeak; +use crate::models::frames::single_quad_settings::{ + get_matching_quad_settings, + matches_quad_settings, + SingleQuadrupoleSetting, + SingleQuadrupoleSettingIndex, +}; +use crate::models::queries::{ + FragmentGroupIndexQuery, + MsLevelContext, +}; +use crate::traits::aggregator::Aggregator; +use crate::traits::queriable_data::QueriableData; +use crate::utils::tolerance_ranges::IncludedRange; +use crate::ToleranceAdapter; use rayon::prelude::*; use serde::Serialize; -use std::{ - collections::HashMap, - hash::Hash, - time::Instant, +use std::collections::HashMap; +use std::hash::Hash; +use std::time::Instant; +use timsrust::converters::{ + Scan2ImConverter, + Tof2MzConverter, }; -use timsrust::{ - converters::{ - Scan2ImConverter, - Tof2MzConverter, - }, - readers::{ - FrameReader, - MetadataReader, - }, +use timsrust::readers::{ + FrameReader, + MetadataReader, }; use tracing::{ info, @@ -307,7 +295,7 @@ impl .collect::>(); // Query the ms1 mzs first. - aggregator.iter_mut().enumerate().for_each(|(i, agg)| { + aggregator.par_iter_mut().enumerate().for_each(|(i, agg)| { fragment_queries[i] .iter_ms1_mzs() .for_each(|(fh, mz_range)| { diff --git a/src/models/indices/raw_file_index.rs b/src/models/indices/raw_file_index.rs index b1076cf..fbb8c1c 100644 --- a/src/models/indices/raw_file_index.rs +++ b/src/models/indices/raw_file_index.rs @@ -1,38 +1,27 @@ +use crate::models::adapters::FragmentIndexAdapter; +use crate::models::frames::raw_frames::frame_elems_matching; +use crate::models::frames::raw_peak::RawPeak; +use crate::models::queries::{ + FragmentGroupIndexQuery, + MsLevelContext, +}; +use crate::traits::aggregator::Aggregator; +use crate::traits::queriable_data::QueriableData; use crate::{ - models::{ - adapters::FragmentIndexAdapter, - frames::{ - raw_frames::frame_elems_matching, - raw_peak::RawPeak, - }, - queries::{ - FragmentGroupIndexQuery, - MsLevelContext, - }, - }, - traits::{ - aggregator::Aggregator, - queriable_data::QueriableData, - }, - utils::tolerance_ranges::IncludedRange, ElutionGroup, ToleranceAdapter, }; use rayon::iter::ParallelIterator; use serde::Serialize; -use std::{ - fmt::Debug, - hash::Hash, +use std::fmt::Debug; +use std::hash::Hash; +use timsrust::readers::{ + FrameReader, + FrameReaderError, + MetadataReader, }; use timsrust::{ - converters::ConvertableDomain, - readers::{ - FrameReader, - FrameReaderError, - MetadataReader, - }, Frame, - Metadata, TimsRustError, }; use tracing::trace; diff --git a/src/models/indices/transposed_quad_index/peak_bucket.rs b/src/models/indices/transposed_quad_index/peak_bucket.rs index a0def3d..7265ae8 100644 --- a/src/models/indices/transposed_quad_index/peak_bucket.rs +++ b/src/models/indices/transposed_quad_index/peak_bucket.rs @@ -1,14 +1,10 @@ -use crate::{ - sort_vecs_by_first, - utils::{ - compress_explode::compress_vec, - display::{ - glimpse_vec, - GlimpseConfig, - }, - tolerance_ranges::IncludedRange, - }, +use crate::sort_vecs_by_first; +use crate::utils::compress_explode::compress_vec; +use crate::utils::display::{ + glimpse_vec, + GlimpseConfig, }; +use crate::utils::tolerance_ranges::IncludedRange; use std::fmt::Display; pub struct PeakInBucket { diff --git a/src/models/indices/transposed_quad_index/quad_index.rs b/src/models/indices/transposed_quad_index/quad_index.rs index 08ee99a..eda101b 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -3,32 +3,24 @@ use super::peak_bucket::{ PeakBucketBuilder, PeakInBucket, }; -use crate::{ - models::frames::{ - expanded_frame::{ - ExpandedFrameSlice, - SortingStateTrait, - }, - peak_in_quad::PeakInQuad, - single_quad_settings::SingleQuadrupoleSetting, - }, - sort_vecs_by_first, - utils::{ - display::{ - glimpse_vec, - GlimpseConfig, - }, - tolerance_ranges::IncludedRange, - }, +use crate::models::frames::expanded_frame::{ + ExpandedFrameSlice, + SortingStateTrait, }; -use std::{ - collections::{ - BTreeMap, - HashMap, - }, - fmt::Display, - time::Instant, +use crate::models::frames::peak_in_quad::PeakInQuad; +use crate::models::frames::single_quad_settings::SingleQuadrupoleSetting; +use crate::sort_vecs_by_first; +use crate::utils::display::{ + glimpse_vec, + GlimpseConfig, }; +use crate::utils::tolerance_ranges::IncludedRange; +use std::collections::{ + BTreeMap, + HashMap, +}; +use std::fmt::Display; +use std::time::Instant; use timsrust::converters::{ ConvertableDomain, Frame2RtConverter, diff --git a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs index bdc1b58..12f6cb9 100644 --- a/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs +++ b/src/models/indices/transposed_quad_index/quad_splitted_transposed_index.rs @@ -2,71 +2,56 @@ use super::quad_index::{ TransposedQuadIndex, TransposedQuadIndexBuilder, }; -use crate::{ - errors::Result, - models::{ - adapters::FragmentIndexAdapter, - elution_group::ElutionGroup, - frames::{ - expanded_frame::{ - par_read_and_expand_frames, - ExpandedFrameSlice, - FrameProcessingConfig, - SortingStateTrait, - }, - peak_in_quad::PeakInQuad, - raw_peak::RawPeak, - single_quad_settings::{ - get_matching_quad_settings, - SingleQuadrupoleSetting, - SingleQuadrupoleSettingIndex, - }, - }, - queries::{ - FragmentGroupIndexQuery, - MsLevelContext, - }, - }, - traits::{ - aggregator::Aggregator, - queriable_data::QueriableData, - }, - utils::{ - display::{ - glimpse_vec, - GlimpseConfig, - }, - tolerance_ranges::IncludedRange, - }, - ToleranceAdapter, +use crate::errors::Result; +use crate::models::adapters::FragmentIndexAdapter; +use crate::models::elution_group::ElutionGroup; +use crate::models::frames::expanded_frame::{ + par_read_and_expand_frames, + ExpandedFrameSlice, + FrameProcessingConfig, + SortingStateTrait, }; +use crate::models::frames::peak_in_quad::PeakInQuad; +use crate::models::frames::raw_peak::RawPeak; +use crate::models::frames::single_quad_settings::{ + get_matching_quad_settings, + SingleQuadrupoleSetting, + SingleQuadrupoleSettingIndex, +}; +use crate::models::queries::{ + FragmentGroupIndexQuery, + MsLevelContext, +}; +use crate::traits::aggregator::Aggregator; +use crate::traits::queriable_data::QueriableData; +use crate::utils::display::{ + glimpse_vec, + GlimpseConfig, +}; +use crate::utils::tolerance_ranges::IncludedRange; +use crate::ToleranceAdapter; use rayon::prelude::*; use serde::Serialize; -use std::{ - collections::HashMap, - fmt::{ - Debug, - Display, - }, - hash::Hash, - time::Instant, +use std::collections::HashMap; +use std::fmt::{ + Debug, + Display, +}; +use std::hash::Hash; +use std::time::Instant; +use timsrust::converters::{ + Scan2ImConverter, + Tof2MzConverter, }; -use timsrust::{ - converters::{ - Scan2ImConverter, - Tof2MzConverter, - }, - readers::{ - FrameReader, - MetadataReader, - }, - Metadata, +use timsrust::readers::{ + FrameReader, + MetadataReader, }; +use timsrust::Metadata; use tracing::{ debug, info, instrument, - trace, }; // TODO break this module apart ... its getting too big for my taste @@ -287,7 +272,7 @@ impl QuadSplittedTransposedIndexBuilder { // TODO use the rayon contructor to fold let out2: Result> = split_frames .into_par_iter() - .map(|(q, frameslices)| { + .map(|(_q, frameslices)| { // TODO:Refactor so the internal index is built first and then added. // This should save a couple of thousand un-necessary hashmap lookups. let mut out = Self::new(); diff --git a/src/models/queries.rs b/src/models/queries.rs index 5daf53e..dbd0cde 100644 --- a/src/models/queries.rs +++ b/src/models/queries.rs @@ -1,14 +1,10 @@ -use crate::{ - traits::aggregator::{ - NoContext, - ProvidesContext, - }, - utils::tolerance_ranges::IncludedRange, -}; -use std::{ - collections::HashMap, - hash::Hash, +use crate::traits::aggregator::{ + NoContext, + ProvidesContext, }; +use crate::utils::tolerance_ranges::IncludedRange; +use std::collections::HashMap; +use std::hash::Hash; use timsrust::converters::{ ConvertableDomain, Scan2ImConverter, @@ -118,7 +114,7 @@ impl NaturalPrecursorQuery { im_converter.invert(self.mobility_range.end()).round() as usize, ) .into(), - isolation_mz_range: self.isolation_mz_range.clone(), + isolation_mz_range: self.isolation_mz_range, } } } diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index 8f0f985..f7cdb54 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -1,5 +1,5 @@ +use crate::traits::aggregator::ProvidesContext; use crate::{ - traits::aggregator::ProvidesContext, Aggregator, ElutionGroup, QueriableData, @@ -8,10 +8,8 @@ use crate::{ }; use rayon::prelude::*; use serde::Serialize; -use std::{ - hash::Hash, - time::Instant, -}; +use std::hash::Hash; +use std::time::Instant; use tracing::{ info, instrument, diff --git a/src/utils/math.rs b/src/utils/math.rs index 7f3e5e5..ac47d1e 100644 --- a/src/utils/math.rs +++ b/src/utils/math.rs @@ -51,17 +51,6 @@ fn cosine_similarity(a: &[f64], b: &[f64]) -> Option { Some(dot_product / (magnitude_a * magnitude_b)) } -// Example usage: -fn main() { - let vector_a = vec![1.0, 2.0, 3.0]; - let vector_b = vec![4.0, 5.0, 6.0]; - - match cosine_similarity(&vector_a, &vector_b) { - Some(similarity) => println!("Cosine similarity: {}", similarity), - None => println!("Could not calculate cosine similarity"), - } -} - #[cfg(test)] mod tests { use super::*; diff --git a/src/utils/tolerance_ranges.rs b/src/utils/tolerance_ranges.rs index 5099546..fcd9ff2 100644 --- a/src/utils/tolerance_ranges.rs +++ b/src/utils/tolerance_ranges.rs @@ -41,9 +41,9 @@ impl From<(T, T)> for IncludedRange { } } -impl Into<(T, T)> for IncludedRange { - fn into(self) -> (T, T) { - (self.0, self.1) +impl From> for (T, T) { + fn from(val: IncludedRange) -> Self { + (val.0, val.1) } } From 10f0b769f5ef34040d14f16265dc8f7aa8783166 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Sun, 3 Nov 2024 20:05:32 -0800 Subject: [PATCH 22/30] chore: clippy and updated benches --- Taskfile.yml | 28 +++++- ...C_13_S1-B1_1_12817_BatchAccess_full_rt.png | Bin 61560 -> 60633 bytes ...13_S1-B1_1_12817_BatchAccess_narrow_rt.png | Bin 68296 -> 67050 bytes ..._A_Sample_Alpha_02_BatchAccess_full_rt.png | Bin 0 -> 44940 bytes ..._Sample_Alpha_02_BatchAccess_narrow_rt.png | Bin 0 -> 54934 bytes data/sageresults/ubb_peptide_plot.png | Bin 140564 -> 140251 bytes ..._results_230510_PRTC_13_S1-B1_1_12817.json | 76 +++++++-------- .../multi_chromatogram_agg/mod.rs | 1 + .../indices/expanded_raw_index/model.rs | 89 ++++++++---------- .../quad_splitted_transposed_index.rs | 78 +++++++++------ src/queriable_tims_data/mod.rs | 1 + 11 files changed, 155 insertions(+), 118 deletions(-) create mode 100644 data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_full_rt.png create mode 100644 data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_narrow_rt.png diff --git a/Taskfile.yml b/Taskfile.yml index 6335cfa..c0c5216 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -40,14 +40,38 @@ tasks: - cargo clippy {{.CLI_ARGS}} bench: + cmds: + - task: bench-build + - task: bench-small-data + - task: bench-large-data + + bench-build: + deps: [build] sources: - "src/**/*.rs" cmds: - cargo b --release --features bench --bin benchmark_indices + + bench-small-data: + deps: [bench-build] + sources: + - "src/**/*.rs" + - "data/230510_PRTC_13_S1-B1_1_12817.d" + - "benches/plot_bench.py" + + cmds: - SKIP_SLOW=1 SKIP_BUILD=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/230510_PRTC_13_S1-B1_1_12817.d ./target/release/benchmark_indices - uv run benches/plot_bench.py data/benchmark_results_230510_PRTC_13_S1-B1_1_12817.json - - # SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d ./target/release/benchmark_indices - - # uv run benches/plot_bench.py data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json + + bench-large-data: + deps: [bench-build] + sources: + - "src/**/*.rs" + - "data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d" + - "benches/plot_bench.py" + cmds: + - SKIP_SLOW=1 SKIP_BUILD=1 SKIP_HIGHMEM=1 RUST_BACKTRACE=full TIMS_DATA_FILE=./data/LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.d ./target/release/benchmark_indices + - uv run benches/plot_bench.py data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02.json plot: sources: diff --git a/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_full_rt.png b/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_full_rt.png index 0fa47a1b5f49eb83eb8d8c7731dfcb350c76de94..0c6a7e3801390098d0488f00a8a38635e08d6ea3 100644 GIT binary patch literal 60633 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