Feat/fastecentroid

Cargo.toml

@@ -8,7 +8,7 @@ license = "Apache-2.0"
 timsrust = "=0.4.1"
 rayon = "1.5"
 nohash-hasher = "=0.2.0"
-indicatif = { version = "0.17.8", features = ["rayon"] }
+indicatif = { version = "0.17.9", features = ["rayon"] }
 
 clap = { version = "4.5.17", features = ["derive"], optional = true }
 serde = { version = "1.0.204", features = ["derive"] }
@@ -27,6 +27,7 @@ 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 }
+tabled = "0.17.0"
 
 
 [features]
@@ -43,6 +44,10 @@ name = "benchmark_indices"
 path = "benches/benchmark_indices.rs"
 required-features = ["bench"]
 
+[[bin]]
+name = "benchmark_centroiding"
+path = "benches/benchmark_centroiding.rs"
+
 [profile.release]
 opt-level = 3
 lto = 'fat'

benches/benchmark_centroiding.rs

@@ -0,0 +1,64 @@
+use std::env;
+use std::time::Instant;
+use timsquery::models::frames::expanded_frame::{
+    par_expand_and_arrange_frames,
+    par_expand_and_centroid_frames,
+    warn_and_skip_badframes,
+    FrameProcessingConfig,
+};
+use timsrust::readers::{
+    FrameReader,
+    MetadataReader,
+};
+use timsrust::MSLevel;
+use tracing::subscriber::set_global_default;
+use tracing_bunyan_formatter::{
+    BunyanFormattingLayer,
+    JsonStorageLayer,
+};
+use tracing_subscriber::prelude::*;
+use tracing_subscriber::registry::Registry;
+use tracing_subscriber::EnvFilter;
+
+fn main() {
+    // "TIMS_DATA_FILE"
+    // Read from env
+    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 tims_data_file = env::var("TIMS_DATA_FILE").expect("TIMS_DATA_FILE not set");
+    let sql_path = std::path::Path::new(&tims_data_file).join("analysis.tdf");
+    let meta_converters = MetadataReader::new(&sql_path).unwrap();
+    let centroiding_config = FrameProcessingConfig::default_centroided();
+    let centroiding_config = centroiding_config
+        .with_converters(meta_converters.im_converter, meta_converters.mz_converter);
+
+    let frame_reader = FrameReader::new(&tims_data_file).unwrap();
+    let ms1_iter = frame_reader.parallel_filter(|x| x.ms_level == MSLevel::MS1);
+    let ms1_iter = warn_and_skip_badframes(ms1_iter);
+    let start = Instant::now();
+    println!("Starting expansion");
+    let _expanded_ms1_frames = match centroiding_config {
+        FrameProcessingConfig::Centroided {
+            settings,
+            ims_converter,
+            mz_converter,
+        } => par_expand_and_centroid_frames(
+            ms1_iter,
+            settings.ims_tol_pct,
+            settings.mz_tol_ppm,
+            settings.window_width,
+            &ims_converter.unwrap(),
+            &mz_converter.unwrap(),
+        ),
+        FrameProcessingConfig::NotCentroided => par_expand_and_arrange_frames(ms1_iter),
+    };
+    let elapsed = start.elapsed();
+    println!("Elapsed: {:.2?}", elapsed);
+}