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/Cargo.lock b/Cargo.lock index 78f1f39..415629c 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" @@ -495,6 +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" @@ -518,29 +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" @@ -573,6 +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" @@ -619,18 +540,6 @@ 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" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4" - [[package]] name = "iana-time-zone" version = "0.1.60" @@ -683,41 +592,12 @@ 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" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "413ee7dfc52ee1a4949ceeb7dbc8a33f2d6c088194d9f922fb8318faf1f01186" -dependencies = [ - "either", -] - [[package]] name = "itoa" version = "1.0.11" @@ -871,6 +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" @@ -895,6 +784,22 @@ dependencies = [ "adler", ] +[[package]] +name = "nohash-hasher" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2bf50223579dc7cdcfb3bfcacf7069ff68243f8c363f62ffa99cf000a6b9c451" + +[[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" @@ -928,6 +833,12 @@ 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" @@ -981,12 +892,6 @@ 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" @@ -996,6 +901,12 @@ 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" @@ -1034,38 +945,16 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a" [[package]] -name = "pkg-config" -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" +name = "pin-project-lite" +version = "0.2.15" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "414cec62c6634ae900ea1c56128dfe87cf63e7caece0852ec76aba307cebadb7" +checksum = "915a1e146535de9163f3987b8944ed8cf49a18bb0056bcebcdcece385cece4ff" [[package]] -name = "plotters-svg" -version = "0.3.6" +name = "pkg-config" +version = "0.3.30" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "81b30686a7d9c3e010b84284bdd26a29f2138574f52f5eb6f794fc0ad924e705" -dependencies = [ - "plotters-backend", -] +checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec" [[package]] name = "portable-atomic" @@ -1073,6 +962,12 @@ 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" @@ -1158,8 +1053,17 @@ 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]] @@ -1170,9 +1074,15 @@ 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" @@ -1230,15 +1140,6 @@ 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" @@ -1283,6 +1184,15 @@ 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" @@ -1349,6 +1259,16 @@ 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" @@ -1360,16 +1280,44 @@ 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" +version = "0.9.0" dependencies = [ "clap", - "criterion", - "env_logger", "indicatif", - "itertools 0.13.0", - "log", + "nohash-hasher", "rand", "rand_chacha", "rayon", @@ -1377,6 +1325,10 @@ dependencies = [ "serde", "serde_json", "timsrust", + "tracing", + "tracing-bunyan-formatter", + "tracing-chrome", + "tracing-subscriber", ] [[package]] @@ -1407,13 +1359,105 @@ dependencies = [ ] [[package]] -name = "tinytemplate" -version = "1.2.1" +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 = "be4d6b5f19ff7664e8c98d03e2139cb510db9b0a60b55f8e8709b689d939b6bc" +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]] @@ -1444,6 +1488,12 @@ 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" @@ -1456,16 +1506,6 @@ 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" @@ -1527,23 +1567,26 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96" [[package]] -name = "web-sys" -version = "0.3.69" +name = "winapi" +version = "0.3.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "77afa9a11836342370f4817622a2f0f418b134426d91a82dfb48f532d2ec13ef" +checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419" dependencies = [ - "js-sys", - "wasm-bindgen", + "winapi-i686-pc-windows-gnu", + "winapi-x86_64-pc-windows-gnu", ] [[package]] -name = "winapi-util" -version = "0.1.8" +name = "winapi-i686-pc-windows-gnu" +version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b" -dependencies = [ - "windows-sys", -] +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" diff --git a/Cargo.toml b/Cargo.toml index 0c3a062..4513811 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,12 +1,13 @@ [package] name = "timsquery" -version = "0.4.0" +version = "0.9.0" edition = "2021" license = "Apache-2.0" [dependencies] -timsrust = "0.4.1" +timsrust = "=0.4.1" rayon = "1.5" +nohash-hasher = "=0.2.0" indicatif = { version = "0.17.8", features = ["rayon"] } clap = { version = "4.5.17", features = ["derive"], optional = true } @@ -14,30 +15,33 @@ 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" +tracing-chrome = "0.7.2" -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 } -[dev-dependencies] -criterion = { version = "0.5", features = ["html_reports"] } - [features] clap = ["dep:clap"] build-binary = ["clap"] +bench = ["dep:rand", "dep:rand_chacha"] [[bin]] name = "timsquery" required-features = ["build-binary"] -[[bench]] +[[bin]] name = "benchmark_indices" -harness = false - +path = "benches/benchmark_indices.rs" +required-features = ["bench"] [profile.release] opt-level = 3 diff --git a/README.md b/README.md index f752d01..a661f33 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,41 @@ # 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? + + +## TODO: + +- 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 bf23144..24d0f70 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -14,32 +14,96 @@ tasks: sources: - "src/**/*.rs" cmds: - - task: build + - task: bin-build + - task: lib-build - task: test - task: fmt - task: clippy - build: + bin-build: cmds: - cargo build $BIN_EXTRAS + bin-build-release: + deps: [test, fmt] + sources: + - "src/**/*.rs" + cmds: + - cargo b --release --features build-binary --bin timsquery + + lib-build: + cmds: + - cargo build --lib + + license_check: + cmds: + - cargo deny check + test: cmds: - cargo test fmt: cmds: - - cargo fmt + - cargo +nightly fmt clippy: cmds: - - cargo clippy + - cargo clippy {{.CLI_ARGS}} bench: - requires: - vars: [RUST_BACKTRACE, RUST_LOG, TIMS_DATA_FILE] cmds: - - cargo bench + - task: bench-build + - task: bench-small-data + - task: bench-large-data + + bench-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 + + 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: + deps: [bin-build-release] + sources: + - "data/sageresults/**/*.py" + - "src/**/*.rs" + cmds: + - for: ["expanded-raw-frame-index", "transposed-quad-index"] + cmd: ./target/release/timsquery query-index + --aggregator multi-cmg-stats --format pretty-json + --raw-file-path ./data/230510_PRTC_13_S1-B1_1_12817.d + --tolerance-settings-path "templates/tolerance_settings.json" + --elution-groups-path "./data/sageresults/ubb_elution_groups.json" + --output-path "./data/sageresults/{{ .ITEM }}_query_results" + --index {{ .ITEM }} + - for: ["expanded-raw-frame-index", "transposed-quad-index"] + cmd: cd data/sageresults && + uv run plot.py + --query-results {{ .ITEM }}_query_results/results.json + --elution-groups ubb_elution_groups.json + --output ubb_peptide_plot{{ .ITEM }}.png templates: sources: diff --git a/benches/benchmark_indices.rs b/benches/benchmark_indices.rs index 79f0adc..65ca109 100644 --- a/benches/benchmark_indices.rs +++ b/benches/benchmark_indices.rs @@ -1,42 +1,161 @@ -use criterion::{criterion_group, criterion_main, BatchSize, BenchmarkId, Criterion}; -use rand::{Rng, SeedableRng}; +use rand::{ + Rng, + SeedableRng, +}; use rand_chacha::ChaCha8Rng; +use serde::Serialize; use std::collections::HashMap; - -use std::hint::black_box; -use timsquery::{ - models::{ - aggregators::RawPeakIntensityAggregator, - indices::{ - raw_file_index::RawFileIndex, transposed_quad_index::QuadSplittedTransposedIndex, - }, - }, - queriable_tims_data::queriable_tims_data::{query_indexed, query_multi_group}, - traits::tolerance::DefaultTolerance, - ElutionGroup, +use std::env; +use std::fs::File; +use std::path::{ + Path, + PathBuf, +}; +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, + EnvFilter, + Layer, }; -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"), - }; +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, +} - let basename = std::path::Path::new(&raw_file_path) - .file_stem() - .unwrap() - .to_str() - .unwrap() - .to_string(); +#[derive(Debug, Serialize)] +struct BenchmarkIteration { + iteration: usize, + duration_seconds: f64, +} + +#[derive(Debug, Serialize)] +struct BenchmarkResult { + name: String, + context: String, + #[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, +} + +#[derive(Debug, Serialize)] +struct BenchmarkReport { + settings: BenchmarkSettings, + results: Vec, + metadata: BenchmarkMetadata, + full_benchmark_time_seconds: f64, +} + +#[derive(Debug, Serialize)] +struct BenchmarkSettings { + num_elution_groups: usize, + num_iterations: usize, +} - (raw_file_path, basename) +#[derive(Debug, Serialize)] +struct BenchmarkMetadata { + basename: String, } -const NUM_ELUTION_GROUPS: usize = 500; -fn build_elution_groups(raw_file_path: String) -> Vec> { +fn duration_to_seconds(duration: Duration) -> f64 { + duration.as_secs() as f64 + duration.subsec_nanos() as f64 * 1e-9 +} + +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 +163,390 @@ 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_mzs: vec![mz], fragment_mzs, + expected_fragment_intensity: None, + expected_precursor_intensity: None, }); } 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, - ) +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; + } + + if self.skip_highmem && tags.contains(&BenchmarkTag::HighMem) { + println!("Skipping highmem benchmark {} {}", name, context); + return None; + } + + 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; + } + + 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: &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( + "RawFileIndex", + "Encoding", + || {}, + |_, _| { + RawFileIndex::from_path(raw_file_path).unwrap(); + None + }, + &[BenchmarkTag::Build], + ); + out.push(rfi); + let erfic = env_config.with_benchmark( + "ExpandedRawFileIndexCentroided", + "Encoding", + || {}, + |_, _| { + ExpandedRawFrameIndex::from_path_centroided(raw_file_path).unwrap(); + None + }, + &[BenchmarkTag::Build], + ); + out.push(erfic); + + 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 = env_config.with_benchmark( + "TransposedQuadIndex", + "Encoding", + || {}, + |_, _| { + QuadSplittedTransposedIndex::from_path(raw_file_path).unwrap(); + None }, + &[BenchmarkTag::HighMem, BenchmarkTag::Build], ); - group.bench_function(BenchmarkId::new("RawFileIndex", basename.clone()), |b| { - b.iter_batched( - || {}, - |()| RawFileIndex::from_path(&black_box(raw_file_path.clone())).unwrap(), - BatchSize::SmallInput, - ) - }); - - group.finish(); + out.push(tqi); + let tqic = env_config.with_benchmark( + "TransposedQuadIndexCentroided", + "Encoding", + || {}, + |_, _| { + QuadSplittedTransposedIndex::from_path_centroided(raw_file_path).unwrap(); + None + }, + &[BenchmarkTag::Build], + ); + out.push(tqic); + + out.into_iter().flatten().collect() } -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()), - <$tolerance_type>::default(), - ) - }, - |(index, query_groups, tolerance)| { - let local_lambda = |elution_group: &ElutionGroup| { - query_indexed( - &index, - &RawPeakIntensityAggregator::new, - &index, - &tolerance, - &elution_group, - ) - }; - for elution_group in query_groups { - let query_results = local_lambda(&elution_group); - black_box((|_query_results| false)(query_results)); - } - }, - BatchSize::PerIteration, - ) - }); +fn run_batch_access_benchmark(raw_file_path: &Path, env_config: EnvConfig) -> Vec { + let raw_file_path = raw_file_path.to_str().unwrap(); + let mut out = vec![]; + let query_groups = build_elution_groups(); + let tolerance_with_rt = DefaultTolerance { + ms: MzToleramce::Ppm((20.0, 20.0)), + rt: RtTolerance::Absolute((5.0, 5.0)), + mobility: MobilityTolerance::Pct((3.0, 3.0)), + quad: QuadTolerance::Absolute((0.1, 0.1)), }; -} -macro_rules! add_bench_optim { - ($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, - ) - }); + 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)), }; -} + let tolerances = [ + (tolerance_with_rt, "narrow_rt"), + (tolerance_with_nort, "full_rt"), + ]; -fn thoughput_benchmark_random(c: &mut Criterion) { - 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)); + // 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. - add_bench_random!( - group, - raw_file_path, - basename, - "TransposedQuadIndex", - QuadSplittedTransposedIndex, - DefaultTolerance, - ); + for (tolerance, tol_name) in tolerances.clone() { + 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, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new_with_elution_group, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!("RawFileIndex::query_multi_group aggregated {} ", tot,); + Some(out) + }, + &local_tags, + ); + out.push(rfi); + } - add_bench_random!( - group, - raw_file_path, - basename, - "RawFileIndex", - RawFileIndex, - DefaultTolerance, - ); + for (tolerance, tol_name) in tolerances.clone() { + 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( + index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new_with_elution_group, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!( + "ExpandedRawFileIndex::query_multi_group aggregated {} ", + tot, + ); + Some(out) + }, + &[BenchmarkTag::HighMem, BenchmarkTag::Query], + ); + out.push(erfi); + } + + for (tolerance, tol_name) in tolerances.clone() { + 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( + index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new_with_elution_group, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!( + "ExpandedRawFileIndexCentroided::query_multi_group aggregated {} ", + tot, + ); + Some(out) + }, + &[BenchmarkTag::Query], + ); + out.push(erfic); + } - group.finish(); + for (tolerance, tol_name) in tolerances.clone() { + 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( + index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new_with_elution_group, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!("TransposedQuadIndex::query_multi_group aggregated {} ", tot,); + Some(out) + }, + &[BenchmarkTag::HighMem, BenchmarkTag::Query], + ); + out.push(tqi); + } + + for (tolerance, tol_name) in tolerances.clone() { + 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( + index, + &tolerance, + &query_groups, + &RawPeakIntensityAggregator::new_with_elution_group, + ); + let tot: u64 = tmp.into_iter().sum(); + let out = format!("TransposedQuadIndex::query_multi_group aggregated {} ", tot,); + Some(out) + }, + &[BenchmarkTag::Query], + ); + out.push(tqi); + } + out.into_iter().flatten().collect() } -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, - ); +fn write_results( + mut 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)?; + let _out = serde_json::to_string_pretty(&report)?; - add_bench_optim!( - group, - raw_file_path, - basename, - "RawFileIndex", - RawFileIndex, - DefaultTolerance, - query_multi_group, - ); + 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)?; - group.finish(); + Ok((filepath, slim_out)) } -criterion_group!( - benches, - thoughput_benchmark_optim, - criterion_benchmark, - thoughput_benchmark_random, -); -criterion_main!(benches); +fn main() { + 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(); + 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"); + let mut all_results: Vec = vec![]; + + println!( + "Run Settings: Elution groups={}, Iterations={}, basename={}", + NUM_ELUTION_GROUPS, NUM_ITERATIONS, basename + ); + + println!("Running encoding benchmarks..."); + 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, env_config.clone()); + 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(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..cc822ed --- /dev/null +++ b/benches/plot_bench.py @@ -0,0 +1,49 @@ +# /// 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() + +bench_file_path = Path(args.benchmark_file) +target_dir = bench_file_path.parent +file_stem = bench_file_path.stem + +data = ( + pl.read_json(str(bench_file_path)) + .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=480, + height=360, + title=f"{context}", + ).save(target_dir / f"{file_stem}_{context}.png") diff --git a/data/.gitignore b/data/.gitignore new file mode 100644 index 0000000..34de35f --- /dev/null +++ b/data/.gitignore @@ -0,0 +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 0000000..0e94dcc Binary files /dev/null and b/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_full_rt.png differ diff --git a/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_narrow_rt.png b/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_narrow_rt.png new file mode 100644 index 0000000..1b1e7eb Binary files /dev/null and b/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_BatchAccess_narrow_rt.png differ diff --git a/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_Encoding.png b/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_Encoding.png new file mode 100644 index 0000000..b0dee17 Binary files /dev/null and b/data/benchmark_results_230510_PRTC_13_S1-B1_1_12817_Encoding.png differ diff --git a/data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_full_rt.png b/data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_full_rt.png new file mode 100644 index 0000000..c0e73a9 Binary files /dev/null and b/data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_full_rt.png differ diff --git a/data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_narrow_rt.png b/data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_narrow_rt.png new file mode 100644 index 0000000..bd8a0f8 Binary files /dev/null and b/data/benchmark_results_LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02_BatchAccess_narrow_rt.png differ diff --git a/data/get_data.bash b/data/get_data.bash new file mode 100644 index 0000000..046e094 --- /dev/null +++ b/data/get_data.bash @@ -0,0 +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/sageresults/.gitignore b/data/sageresults/.gitignore new file mode 100644 index 0000000..4030c7f --- /dev/null +++ b/data/sageresults/.gitignore @@ -0,0 +1,5 @@ +lfq.tsv +results.sage.tsv +matched_fragments.sage.tsv +sage +log.log diff --git a/data/sageresults/build.py b/data/sageresults/build.py new file mode 100644 index 0000000..b906d88 --- /dev/null +++ b/data/sageresults/build.py @@ -0,0 +1,84 @@ +# /// script +# dependencies = [ +# "polars", +# ] +# /// + +import polars as pl +import json + +PROTON_MASS = 1.007276 +NEUTRON_MASS = 1.008664 + +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", + "fragment_intensity", + ] + ) + .group_by(["psm_id"]) + .agg(pl.all()) + .collect() +) + +df = ub_peptides_df.join(fragments, on="psm_id", how="inner") + +# Convert to json +out = [] +for x in df.iter_rows(named=True): + mzs = [x["mz"] + (z * (NEUTRON_MASS / x["charge"])) for z in range(4)] + expected_ms1_intensities = (0.491, 0.334, 0.129, 0.036) + expected_intensities = {str(i): y for i, y in enumerate(x["fragment_intensity"])} + + 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_mzs": mzs, + "precursor_charge": x["charge"], + "fragment_mzs": { + str(i): y for i, y in enumerate(x["fragment_mz_calculated"]) + }, + "expected_fragment_intensity": expected_intensities, + "expected_precursor_intensity": expected_ms1_intensities, + } + ) + + +out.sort(key=lambda x: x["rt_seconds"]) +print(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..0213bd4 --- /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 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..b60db07 --- /dev/null +++ b/data/sageresults/plot.py @@ -0,0 +1,117 @@ +# /// script +# dependencies = [ +# "polars", +# "matplotlib", +# ] +# /// + +import json +import numpy as np +import matplotlib.pyplot as plt +import argparse + + +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 + + +def build_parser(): + parser = argparse.ArgumentParser() + parser.add_argument("--elution-groups", type=str, default="ubb_elution_groups.json") + parser.add_argument( + "--query-results", type=str, default="query_results/results.json" + ) + parser.add_argument("--output", type=str, default="ubb_peptide_plot.png") + return parser + + +def main(args): + data = json.load(open(args.query_results)) + labels = json.load(open(args.elution_groups)) + 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)) + + 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() + ) + + rt_plot_center = x["elution_group"]["rt_seconds"] / 60 + rt_plot_right = rt_plot_center + 0.5 + rt_plot_left = rt_plot_center - 0.5 + max_ms1 = 0 + max_ms2 = 0 + + for j in sorted_ms1_keys: + col = next(colors) + j = x["result"]["ms1_stats"]["transition_intensities"][j] + max_ms1 = max(max_ms1, max(j)) + 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] + max_ms2 = max(max_ms2, max(j)) + 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) + + ax[0, i].set_xlim(rt_plot_left, rt_plot_right) + ax[1, i].set_xlim(rt_plot_left, rt_plot_right) + + ax[0, i].vlines( + rt_plot_center, + 0, + max_ms1, + colors="red", + linestyles="dashed", + alpha=0.3, + ) + ax[1, i].vlines( + rt_plot_center, + 0, + max_ms2, + colors="red", + linestyles="dashed", + alpha=0.3, + ) + + # 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(args.output) + + +if __name__ == "__main__": + parser = build_parser() + args = parser.parse_args() + main(args) diff --git a/data/sageresults/ubb_elution_groups.json b/data/sageresults/ubb_elution_groups.json new file mode 100644 index 0000000..f5339a5 --- /dev/null +++ b/data/sageresults/ubb_elution_groups.json @@ -0,0 +1,163 @@ +[ + { + "id": 912, + "human_id": "TLSDYNIQK_2", + "mobility": 0.8217308, + "rt_seconds": 316.72206, + "precursor_mzs": [ + 541.2797760000001, + 541.7841080000001, + 542.28844, + 542.7927720000001 + ], + "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 + }, + "expected_fragment_intensity": { + "0": 10859.0, + "1": 3455.0, + "2": 2128.0, + "3": 1312.0, + "4": 2445.0, + "5": 13072.0, + "6": 374172.0, + "7": 42041.0, + "8": 37806.0, + "9": 13536.0, + "10": 11156.0, + "11": 14119.0 + }, + "expected_precursor_intensity": [ + 0.491, + 0.334, + 0.129, + 0.036 + ] + }, + { + "id": 8469, + "human_id": "ESTLHLVLR_2", + "mobility": 0.8719231, + "rt_seconds": 483.31707000000006, + "precursor_mzs": [ + 534.313976, + 534.818308, + 535.32264, + 535.8269720000001 + ], + "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 + }, + "expected_fragment_intensity": { + "0": 1188.0, + "1": 10631.0, + "2": 1731.0, + "3": 12942.0, + "4": 11920.0, + "5": 5894.0, + "6": 3753.0, + "7": 47939.0, + "8": 26996.0, + "9": 30928.0, + "10": 119102.0, + "11": 107218.0, + "12": 42401.0, + "13": 10389.0 + }, + "expected_precursor_intensity": [ + 0.491, + 0.334, + 0.129, + 0.036 + ] + }, + { + "id": 89501, + "human_id": "TITLEVEPSDTIENVK_2", + "mobility": 1.1326923, + "rt_seconds": 745.8906, + "precursor_mzs": [ + 894.4673760000001, + 894.971708, + 895.47604, + 895.9803720000001 + ], + "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 + }, + "expected_fragment_intensity": { + "0": 208.0, + "1": 750.0, + "2": 607.0, + "3": 1998.0, + "4": 1227.0, + "5": 949.0, + "6": 252.0, + "7": 363.0, + "8": 440.0, + "9": 231.0, + "10": 535.0, + "11": 701.0, + "12": 2148.0, + "13": 274.0, + "14": 236.0, + "15": 316.0, + "16": 93.0, + "17": 452.0, + "18": 254.0, + "19": 92.0 + }, + "expected_precursor_intensity": [ + 0.491, + 0.334, + 0.129, + 0.036 + ] + } +] \ 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 0000000..7772c92 Binary files /dev/null and b/data/sageresults/ubb_peptide_plot.png differ diff --git a/data/sageresults/ubb_peptide_plotexpanded-raw-frame-index.png b/data/sageresults/ubb_peptide_plotexpanded-raw-frame-index.png new file mode 100644 index 0000000..ad8cb4d Binary files /dev/null and b/data/sageresults/ubb_peptide_plotexpanded-raw-frame-index.png differ diff --git a/data/sageresults/ubb_peptide_plottransposed-quad-index.png b/data/sageresults/ubb_peptide_plottransposed-quad-index.png new file mode 100644 index 0000000..c31aa64 Binary files /dev/null and b/data/sageresults/ubb_peptide_plottransposed-quad-index.png differ 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..c6c3ed2 --- /dev/null +++ b/data/slim_benchmark_results_230510_PRTC_13_S1-B1_1_12817.json @@ -0,0 +1,93 @@ +{ + "settings": { + "num_elution_groups": 1000, + "num_iterations": 1 + }, + "results": [ + { + "name": "RawFileIndex", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 32.022435916, + "mean_duration_human_readable": "32.022435916s", + "setup_time_seconds": 0.078233583, + "setup_time_human_readable": "78.233583ms", + "note": "RawFileIndex::query_multi_group aggregated 68182 " + }, + { + "name": "ExpandedRawFileIndex", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 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0000000..31a2813 --- /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": 3.913134625, + "mean_duration_human_readable": "3.913134625s", + "setup_time_seconds": 0.241788791, + "setup_time_human_readable": "241.788791ms", + "note": "RawFileIndex::query_multi_group aggregated 8809 " + }, + { + "name": "ExpandedRawFileIndexCentroided", + "context": "BatchAccess_narrow_rt", + "mean_duration_seconds": 0.0037595285112781963, + "mean_duration_human_readable": "3.759528ms", + "setup_time_seconds": 456.581050083, + "setup_time_human_readable": "456.581050083s", + "note": "ExpandedRawFileIndexCentroided::query_multi_group aggregated 1570 " + }, + { + "name": "ExpandedRawFileIndexCentroided", + "context": "BatchAccess_full_rt", + 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"LFQ_timsTOFPro_diaPASEF_Condition_A_Sample_Alpha_02" + }, + "full_benchmark_time_seconds": 2070.526848583 +} \ 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/rustfmt.toml b/rustfmt.toml new file mode 100644 index 0000000..9a8eadb --- /dev/null +++ b/rustfmt.toml @@ -0,0 +1,6 @@ + +imports_layout = "Vertical" +imports_granularity = "Module" +normalize_comments = true +reorder_impl_items = true +version = "Two" diff --git a/src/errors.rs b/src/errors.rs new file mode 100644 index 0000000..4d9b82b --- /dev/null +++ b/src/errors.rs @@ -0,0 +1,68 @@ +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), + ExpectedVectorLength { real: usize, expected: usize }, + ExpectedNonEmptyData, + InsufficientData { real: usize, expected: usize }, + ExpectedVectorSameLength(usize, usize), +} + +impl From for TimsqueryError { + fn from(e: DataProcessingError) -> Self { + TimsqueryError::DataProcessingError(e) + } +} + +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 21cd7b5..3d254d3 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,19 +1,25 @@ // Re-export main structures pub use crate::models::elution_group::ElutionGroup; -pub use crate::queriable_tims_data::queriable_tims_data::QueriableTimsData; +pub use crate::models::indices::transposed_quad_index::QuadSplittedTransposedIndex; // Re-export traits 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; +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; -// Any library-wide code, documentation, or additional exports can go here +// Re-export errors +pub use crate::errors::{ + DataProcessingError, + DataReadingError, + TimsqueryError, +}; diff --git a/src/main.rs b/src/main.rs index 8ff2ed4..83d8322 100644 --- a/src/main.rs +++ b/src/main.rs @@ -1,24 +1,50 @@ +use clap::{ + Parser, + Subcommand, +}; +use serde::{ + Deserialize, + Serialize, +}; use std::collections::HashMap; use std::time::Instant; +use timsquery::models::aggregators::{ + MultiCMGStatsFactory, + RawPeakIntensityAggregator, + RawPeakVectorAggregator, +}; use timsquery::models::elution_group::ElutionGroup; +use timsquery::models::indices::{ + ExpandedRawFrameIndex, + QuadSplittedTransposedIndex, +}; 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, - }, - models::indices::raw_file_index::RawFileIndex, - models::indices::transposed_quad_index::QuadSplittedTransposedIndex, +use timsquery::traits::tolerance::{ + DefaultTolerance, + MobilityTolerance, + MzToleramce, + QuadTolerance, + RtTolerance, }; - -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::prelude::*; +use tracing_subscriber::registry::Registry; +use tracing_subscriber::EnvFilter; 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 { @@ -50,8 +76,7 @@ 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, ); } @@ -73,21 +98,22 @@ fn template_elution_groups(num: usize) -> Vec> { let rt = min_rt + (i as f32 * rt_step); let mobility = min_mobility + (i as f32 * mobility_step); let mz = min_mz + (i as f64 * mz_step); - let precursor_charge = 2; let fragment_mzs = (0..10).map(|x| (x as usize, mz + x as f64)); let fragment_mzs = HashMap::from_iter(fragment_mzs); egs.push(ElutionGroup { id: i as u64, rt_seconds: rt, mobility, - precursor_mz: mz, - precursor_charge, + precursor_mzs: vec![mz], fragment_mzs, + expected_fragment_intensity: None, + expected_precursor_intensity: None, }); } egs } +#[instrument] fn main_query_index(args: QueryIndexArgs) { let args_clone = args.clone(); @@ -99,17 +125,18 @@ fn main_query_index(args: QueryIndexArgs) { let tolerance_settings: DefaultTolerance = serde_json::from_str(&std::fs::read_to_string(&tolerance_settings_path).unwrap()).unwrap(); - let elution_groups: Vec> = + let elution_groups: Vec> = 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, @@ -123,11 +150,11 @@ fn main_query_index(args: QueryIndexArgs) { fn template_tolerance_settings() -> DefaultTolerance { DefaultTolerance { - ms: MzToleramce::Ppm((50.0, 50.0)), + ms: MzToleramce::Ppm((15.0, 15.0)), // rt: RtTolerance::Absolute((120.0, 120.0)), rt: RtTolerance::None, - mobility: MobilityTolerance::Pct((20.0, 20.0)), - quad: QuadTolerance::Absolute((0.1, 0.1, 1)), + mobility: MobilityTolerance::Pct((10.0, 10.0)), + quad: QuadTolerance::Absolute((0.1, 0.1)), } } @@ -143,8 +170,6 @@ pub enum PossibleAggregator { #[default] RawPeakIntensityAggregator, RawPeakVectorAggregator, - ExtractedIonChromatomobilogram, - ChromatoMobilogramStat, MultiCMGStats, } @@ -152,7 +177,7 @@ pub enum PossibleAggregator { pub enum PossibleIndex { #[default] Unspecified, - RawFileIndex, + ExpandedRawFrameIndex, TransposedQuadIndex, } @@ -215,7 +240,7 @@ enum Commands { #[derive(Debug, Serialize, Deserialize)] struct ElutionGroupResults { - elution_group: ElutionGroup, + elution_group: ElutionGroup, result: T, } @@ -224,7 +249,7 @@ pub fn execute_query( aggregator: PossibleAggregator, raw_file_path: String, tolerance: DefaultTolerance, - elution_groups: Vec>, + elution_groups: Vec>, args: QueryIndexArgs, ) { let output_path = args.output_path; @@ -232,7 +257,7 @@ 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) { @@ -282,51 +307,39 @@ pub fn execute_query( let index = QuadSplittedTransposedIndex::from_path(&(raw_file_path.clone())).unwrap(); match aggregator { PossibleAggregator::RawPeakIntensityAggregator => { - let aggregator = RawPeakIntensityAggregator::new; + let aggregator = RawPeakIntensityAggregator::new_with_elution_group; execute_query_inner!(index, aggregator); } PossibleAggregator::RawPeakVectorAggregator => { - 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; + let aggregator = RawPeakVectorAggregator::new_with_elution_group; execute_query_inner!(index, aggregator); } PossibleAggregator::MultiCMGStats => { let factory = MultiCMGStatsFactory { converters: (index.mz_converter, index.im_converter), - _phantom: std::marker::PhantomData::, + _phantom: std::marker::PhantomData::, }; - execute_query_inner!(index, |x| factory.build(x)); + execute_query_inner!(index, |x| factory.build_with_elution_group(x)); } } } - (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; + let aggregator = RawPeakIntensityAggregator::new_with_elution_group; execute_query_inner!(index, aggregator); } PossibleAggregator::RawPeakVectorAggregator => { - 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; + let aggregator = RawPeakVectorAggregator::new_with_elution_group; 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_with_elution_group(x)); } } } diff --git a/src/models/adapters.rs b/src/models/adapters.rs new file mode 100644 index 0000000..8f955df --- /dev/null +++ b/src/models/adapters.rs @@ -0,0 +1,102 @@ +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; +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 quad_range = tol.quad_range(elution_group.get_precursor_mz_limits()); + let quad_range = IncludedRange::new(quad_range.0, quad_range.1); + + let mz_index_ranges = elution_group + .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), + }; + 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 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.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 = IncludedRange::new( + 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, + rt_range_seconds: rt_range, + mz_index_ranges, + 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(), + IncludedRange::new( + 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/aggregators/mod.rs b/src/models/aggregators/mod.rs index 6498af9..3af0fba 100644 --- a/src/models/aggregators/mod.rs +++ b/src/models/aggregators/mod.rs @@ -2,10 +2,10 @@ pub mod raw_peak_agg; 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; -pub use raw_peak_agg::RawPeakIntensityAggregator; -pub use raw_peak_agg::RawPeakVectorAggregator; +pub use raw_peak_agg::{ + ChromatomobilogramStats, + MultiCMGStatsAgg, + MultiCMGStatsFactory, + 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 f4f47e9..1c6c4d7 100644 --- a/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs +++ b/src/models/aggregators/raw_peak_agg/chromatogram_agg.rs @@ -1,75 +1,13 @@ use super::super::streaming_aggregator::RunningStatsCalculator; -use crate::models::frames::raw_peak::RawPeak; -use crate::sort_by_indices_multi; -use crate::traits::aggregator::Aggregator; -use crate::utils::sorting::argsort_by; +use crate::sort_vecs_by_first; +use nohash_hasher::BuildNoHashHasher; use serde::Serialize; -use std::collections::BTreeMap; use std::collections::HashMap; +use std::hash::BuildHasherDefault; -#[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 Output = ChromatomobilogramVectorArrayTuples; - - fn add(&mut self, peak: &RawPeak) { - 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; - +/// 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, @@ -86,6 +24,7 @@ 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); @@ -102,19 +41,25 @@ pub struct ChromatomobilogramStats { // In theory we can optimize this to make a single aggregator struct // that shares the weight (intensity), since all will have the same weight // and retention times. - pub scan_tof_mapping: MappingCollection, + pub scan_tof_mapping: HashMap>, pub id: u64, + pub expected_tof_index: u32, + pub expected_scan_index: usize, } impl ChromatomobilogramStats { - pub fn new(id: u64) -> Self { + pub fn new(id: u64, expected_tof_index: u32, expected_scan_index: usize) -> Self { Self { - scan_tof_mapping: MappingCollection::new(), + scan_tof_mapping: HashMap::with_hasher(BuildHasherDefault::default()), id, + expected_tof_index, + expected_scan_index, } } } +/// A struct that calculates stores the mean/sd of an isolation window (transition) +/// across the chromatogram. #[derive(Debug, Clone, Serialize, Default)] pub struct ChromatomobilogramStatsArrays { pub retention_time_miliseconds: Vec, @@ -123,35 +68,19 @@ pub struct ChromatomobilogramStatsArrays { pub scan_index_means: Vec, pub scan_index_sds: Vec, pub intensities: Vec, + pub expected_intensity: Option, + pub expected_tof_index: u32, + pub expected_scan_index: usize, } 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(), - } - } - - pub fn fold(&mut self, other: Self) { - self.retention_time_miliseconds - .extend(other.retention_time_miliseconds); - self.tof_index_means.extend(other.tof_index_means); - self.tof_index_sds.extend(other.tof_index_sds); - self.scan_index_means.extend(other.scan_index_means); - self.scan_index_sds.extend(other.scan_index_sds); - self.intensities.extend(other.intensities); + Self::default() } 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, @@ -159,62 +88,26 @@ 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; } -} - -impl Aggregator for ChromatomobilogramStats { - type Output = ChromatomobilogramStatsArrays; - - fn add(&mut self, peak: &RawPeak) { - 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, - )); + pub fn is_sorted(&self) -> bool { + self.retention_time_miliseconds + .windows(2) + .all(|x| x[0] <= x[1]) } - 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; + pub fn len(&self) -> usize { + self.retention_time_miliseconds.len() + } - 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, - } + pub fn is_empty(&self) -> bool { + self.retention_time_miliseconds.is_empty() } } diff --git a/src/models/aggregators/raw_peak_agg/mod.rs b/src/models/aggregators/raw_peak_agg/mod.rs index ab32750..5ac89c7 100644 --- a/src/models/aggregators/raw_peak_agg/mod.rs +++ b/src/models/aggregators/raw_peak_agg/mod.rs @@ -3,9 +3,10 @@ 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::MultiCMGStatsAgg; +// TODO: reorganize this so I donr use direcly from `base`` pub use multi_chromatogram_agg::MultiCMGStatsFactory; -pub use point_agg::RawPeakIntensityAggregator; -pub use point_agg::RawPeakVectorAggregator; +pub use point_agg::{ + RawPeakIntensityAggregator, + RawPeakVectorAggregator, +}; diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs deleted file mode 100644 index 297437c..0000000 --- a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg.rs +++ /dev/null @@ -1,327 +0,0 @@ -use super::chromatogram_agg::{ - ChromatomobilogramStatsArrays, MappingCollection, ScanTofStatsCalculatorPair, -}; -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 serde::Serialize; -use std::collections::{BTreeMap, HashSet}; -use std::hash::Hash; - -use timsrust::converters::{ConvertableDomain, Scan2ImConverter, Tof2MzConverter}; - -#[derive(Debug, Clone)] -pub struct MultiCMGStats { - pub scan_tof_mapping: MappingCollection<(FH, u32), ScanTofStatsCalculatorPair>, - pub converters: (Tof2MzConverter, Scan2ImConverter), - pub id: u64, -} - -#[derive(Debug, Clone)] -pub struct MultiCMGStatsFactory { - pub converters: (Tof2MzConverter, Scan2ImConverter), - pub _phantom: std::marker::PhantomData, -} - -impl MultiCMGStatsFactory { - pub fn build(&self, id: u64) -> MultiCMGStats { - MultiCMGStats { - scan_tof_mapping: MappingCollection::new(), - converters: (self.converters.0, self.converters.1), - id, - } - } -} - -#[derive(Debug, Clone, Serialize)] -pub struct MultiCMGStatsArrays { - pub transition_stats: MappingCollection, - id: u64, -} - -#[derive(Debug, Clone, Serialize)] -pub struct FinalizedMultiCMGStatsArrays { - pub retention_time_miliseconds: Vec, - pub weighted_scan_index_mean: Vec, - pub summed_intensity: 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>, - 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 transition_mobilities: MappingCollection>, - pub transition_mzs: MappingCollection>, - pub transition_intensities: MappingCollection>, - pub apex_hyperscore_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 -// ) -// ) - -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 -} - -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, - mz_converter: &Tof2MzConverter, - 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 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; - } - } - - 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| mobility_converter.convert(x)) - .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_hyperscore_index, - id: other.id, - } - } -} - -impl From> - for FinalizedMultiCMGStatsArrays -{ - fn from(other: MultiCMGStatsArrays) -> Self { - // TODO ... maybe refactor this ... RN its king of ugly. - - let mut out = FinalizedMultiCMGStatsArrays { - 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(), - npeaks: Vec::new(), - id: other.id, - }; - - 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(); - let mut summed_intensity_tree: BTreeMap = - BTreeMap::from_iter(unique_rts.iter().map(|x| (*x, 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]; - - 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); - 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. - 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| x.mean().expect("At least one value should be present")) - .collect(); - out - } -} - -impl Aggregator<(RawPeak, FH)> - for MultiCMGStats -{ - type Output = NaturalFinalizedMultiCMGStatsArrays; - - fn add(&mut self, peak: &(RawPeak, FH)) { - let (peak, transition) = peak; - let u64_intensity = peak.intensity as u64; - let rt_miliseconds = (peak.retention_time * 1000.0) as u32; - - 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 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 - .push(scan_tof_mapping.scan.mean().unwrap()); - out.scan_index_sds - .push(scan_tof_mapping.scan.standard_deviation().unwrap()); - out.tof_index_means - .push(scan_tof_mapping.tof.mean().unwrap()); - out.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(); - } - - let tmp = MultiCMGStatsArrays { - transition_stats, - id: self.id, - }; - NaturalFinalizedMultiCMGStatsArrays::new( - FinalizedMultiCMGStatsArrays::from(tmp), - &self.converters.0, - &self.converters.1, - ) - } -} diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/aggregator.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/aggregator.rs new file mode 100644 index 0000000..8d7f5ec --- /dev/null +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/aggregator.rs @@ -0,0 +1,123 @@ +use super::super::chromatogram_agg::{ + ChromatomobilogramStatsArrays, + ScanTofStatsCalculatorPair, +}; +use crate::errors::Result; +use nohash_hasher::BuildNoHashHasher; +use serde::Serialize; +use std::collections::HashMap; +use std::hash::Hash; + +type SparseRTCollection = HashMap>; + +#[derive(Debug, Clone)] +pub struct ParitionedCMGAggregator< + FH: Clone + Eq + Serialize + Hash + Send + Sync + std::fmt::Debug, +> { + pub scan_tof_calc: Vec>, + pub keys: Vec, + pub context_key_num: usize, + pub expected_intensities: Option>, + pub expected_scan_index: usize, + pub expected_tof_indices: Vec, + pub context_buffer: SparseRTCollection, +} + +impl + ParitionedCMGAggregator +{ + pub fn new( + keys: Vec, + expected_intensities: Option>, + expected_scan_index: usize, + expected_tof_indices: Vec, + ) -> Self { + let mut scan_tof_calc = Vec::with_capacity(keys.len()); + for _ in 0..keys.len() { + scan_tof_calc.push(None); + } + if let Some(exp_intens) = expected_intensities.as_ref() { + assert!(exp_intens.len() == keys.len()); + } + assert!(expected_tof_indices.len() == keys.len()); + + Self { + scan_tof_calc, + keys, + context_key_num: 0, + expected_intensities, + expected_scan_index, + expected_tof_indices, + context_buffer: SparseRTCollection::with_hasher(BuildNoHashHasher::default()), + } + } + + pub fn flush_buffer(&mut self) { + if !self.context_buffer.is_empty() { + // Swap the buffer with the current one. + let mut new_buffer = SparseRTCollection::with_hasher(BuildNoHashHasher::default()); + if self.scan_tof_calc[self.context_key_num].is_none() { + self.scan_tof_calc[self.context_key_num] = Some(new_buffer); + std::mem::swap( + &mut self.context_buffer, + self.scan_tof_calc[self.context_key_num].as_mut().unwrap(), + ); + } else { + std::mem::swap(&mut self.context_buffer, &mut new_buffer); + for (rt, calc) in new_buffer.into_iter() { + self.scan_tof_calc[self.context_key_num] + .as_mut() + .unwrap() + .entry(rt) + .and_modify(|curr| { + curr.add( + calc.weight(), + calc.scan.mean().unwrap() as usize, + calc.tof.mean().unwrap() as u32, + ); + }) + .or_insert(calc); + } + + assert!(self.context_buffer.is_empty()); + // panic!( + // "Same context used multiple times, currently not supported \ncurr: {:?}, \nkeys: {:?}", + // self.context_key_num, self.keys, + // ); + } + } + } + + pub fn set_context(&mut self, context: FH) -> Result<()> { + self.flush_buffer(); + + // Find the position in the keys. + let pos = self.keys.iter().position(|x| x == &context); + if let Some(pos) = pos { + self.context_key_num = pos; + Ok(()) + } else { + let msg = format!( + "Context Not Found, wante any of {:?}, got {:?}", + self.keys, context + ); + Err(crate::TimsqueryError::Other(msg)) + } + } + + pub fn add(&mut self, rt_ms: u32, scan_index: usize, tof_index: u32, intensity: u64) { + self.context_buffer + .entry(rt_ms) + .and_modify(|curr| { + curr.add(intensity, scan_index, tof_index); + }) + .or_insert(ScanTofStatsCalculatorPair::new( + intensity, scan_index, tof_index, + )); + } +} + +#[derive(Debug, Clone, Serialize)] +pub struct PartitionedCMGArrays { + pub transition_stats: HashMap, +} diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/arrays.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/arrays.rs new file mode 100644 index 0000000..cb90db5 --- /dev/null +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/arrays.rs @@ -0,0 +1,285 @@ +use super::super::chromatogram_agg::ChromatomobilogramStatsArrays; +use super::aggregator::ParitionedCMGAggregator; +use crate::models::aggregators::streaming_aggregator::RunningStatsCalculator; +use crate::utils::correlation::cosine_similarity; +use serde::Serialize; +use std::collections::{ + BTreeMap, + HashMap, + HashSet, +}; +use std::f64; +use std::hash::Hash; +use tracing::warn; + +#[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: HashMap>, + pub tof_index_means: HashMap>, + // TODO consider if I want to add the standard deviations ... RN they dont + // seem to be that useful. + pub intensities: HashMap>, + pub cosine_similarity: Option>, + + pub expected_tof_index: HashMap, + pub expected_scan_index: usize, +} + +#[derive(Debug, Clone, Serialize)] +pub struct PartitionedCMGArrays { + pub transition_stats: Vec, + pub transition_keys: Vec, + pub expected_scan_index: usize, + pub expected_tof_indices: Vec, + pub expected_intensities: Option>, +} + +fn cosine_sim(expected: &[f64], nested_observed: &[Vec]) -> Vec { + assert!( + expected.len() == nested_observed.len(), + "Expected and observed have different lengths {:?} {:?}", + expected.len(), + nested_observed.len(), + ); + let nested_len = nested_observed[0].len(); + for x in nested_observed.iter() { + assert!( + x.len() == nested_len, + "Nested observed vectors have different lengths {:?} {:?}", + x.len(), + nested_len, + ); + } + if nested_len == 0 { + panic!("Expected at least one element in the nested vector"); + } + + let mut buffer = vec![0.0; nested_observed.len()]; + let mut out = Vec::with_capacity(nested_len); + for rt_i in 0..nested_len { + // buffer.clear(); + for (i, x) in nested_observed.iter().enumerate() { + buffer[i] = x[rt_i] as f64; + } + out.push(cosine_similarity(expected, &buffer).unwrap()); + } + out +} + +impl + From> for PartitionedCMGArrays +{ + fn from(mut item: ParitionedCMGAggregator) -> Self { + item.flush_buffer(); + let mut transition_stats = Vec::with_capacity(item.keys.len()); + let mut uniq_rts: Vec = item + .scan_tof_calc + .iter() + .flatten() + .flatten() + .map(|x| *x.0) + .collect(); + uniq_rts.sort_unstable(); + uniq_rts.dedup(); + let mut out_expected_intensities: Vec = Vec::with_capacity(item.keys.len()); + let mut out_expected_tof_indices: Vec = Vec::with_capacity(item.keys.len()); + + for (id_ind, _id_key) in item.keys.iter().enumerate() { + let mut id_cmgs = ChromatomobilogramStatsArrays::new(); + let local_id_mapping = &item.scan_tof_calc[id_ind]; + if local_id_mapping.is_none() { + continue; + } + if item.expected_intensities.is_some() { + out_expected_intensities.push(item.expected_intensities.as_ref().unwrap()[id_ind]); + } + out_expected_tof_indices.push(item.expected_tof_indices[id_ind]); + let local_id_mapping = local_id_mapping.as_ref().unwrap(); + + for rt_key in uniq_rts.iter() { + let scan_tof_mapping = local_id_mapping.get(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.push(id_cmgs); + } + + let out_expected_intensities = if out_expected_intensities.is_empty() { + None + } else { + Some(out_expected_intensities) + }; + + Self { + transition_stats, + transition_keys: item.keys, + expected_intensities: out_expected_intensities, + expected_tof_indices: out_expected_tof_indices, + expected_scan_index: item.expected_scan_index, + } + } +} + +impl From> + for PartitionedCMGArrayStats +{ + fn from(other: PartitionedCMGArrays) -> Self { + // TODO ... maybe refactor this ... RN its king of ugly. + + // TODO: make a constructor to make sure everything here + // Is actually getting added and is the right size/shape. + let expected_tof_index = other + .transition_keys + .iter() + .zip(other.expected_tof_indices.iter()) + .map(|(k, v)| (k.clone(), *v)) + .collect(); + let mut out = PartitionedCMGArrayStats { + retention_time_miliseconds: Vec::new(), + scan_index_means: HashMap::new(), + tof_index_means: HashMap::new(), + weighted_scan_index_mean: Vec::new(), + intensities: HashMap::new(), + summed_intensity: Vec::new(), + log_intensity_products: Vec::new(), + npeaks: Vec::new(), + cosine_similarity: None, + expected_tof_index, + expected_scan_index: other.expected_scan_index, + }; + + let unique_rts = other + .transition_stats + .iter() + .flat_map(|v| v.retention_time_miliseconds.clone()) + // This is quite a bit of cloning ... I should re-write it to something more + // performant. + .collect::>(); + let mut unique_rts = unique_rts.into_iter().collect::>(); + unique_rts.sort(); + + let mut summed_intensity_vec: Vec = vec![0; unique_rts.len()]; + let mut intensity_logsums_vec: Vec = vec![0.0; unique_rts.len()]; + let mut npeaks_tree: Vec = vec![0; unique_rts.len()]; + let mut weighted_scan_index_mean_vec: Vec> = + vec![None; unique_rts.len()]; + + let mut tmp_transition_intensities: Vec> = Vec::new(); + + for (v, k) in other + .transition_stats + .into_iter() + .zip(other.transition_keys.iter()) + { + type ScanTofIntensityTuple = (f64, f64, u64); + type ScanTofIntensityVecs = (Vec, (Vec, Vec)); + // TODO: replace with a 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 final_index = unique_rts + .binary_search(&rt) + .expect("All RTs should be registered above."); + + let scan = v.scan_index_means[i]; + let tof = v.tof_index_means[i]; + let inten = v.intensities[i]; + + if inten > 100 { + npeaks_tree[final_index] += 1; + } + tmp_tree.entry(rt).or_insert((scan, tof, inten)); + summed_intensity_vec[final_index] += inten; + if inten > 10 { + intensity_logsums_vec[final_index] += (inten as f64).ln(); + } + + if let Some(mut x) = weighted_scan_index_mean_vec[final_index] { + x.add(scan, inten); + } else { + weighted_scan_index_mean_vec[final_index] = + Some(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); + tmp_transition_intensities.push(out_intens); + } + + out.retention_time_miliseconds = unique_rts; + out.summed_intensity = summed_intensity_vec; + out.npeaks = npeaks_tree; + + let weighted_scan_index_mean = weighted_scan_index_mean_vec + .into_iter() + .map(|x| { + let out = x + .expect("At least one value should be given for every RT") + .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(); + out.weighted_scan_index_mean = weighted_scan_index_mean; + + // Note: The log of products is the same as the sum of logs. + out.log_intensity_products = intensity_logsums_vec; + + out.cosine_similarity = if other.expected_intensities.is_none() { + None + } else { + let expect_inten: Vec = other + .expected_intensities + .unwrap() + .iter() + .map(|x| *x as f64) + .collect(); + Some(cosine_sim(&expect_inten, &tmp_transition_intensities)) + }; + + out.intensities = other + .transition_keys + .into_iter() + .zip(tmp_transition_intensities) + .collect(); + out + } +} 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..7d7ea93 --- /dev/null +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/mod.rs @@ -0,0 +1,10 @@ +pub mod aggregator; +pub mod arrays; +#[allow(clippy::module_inception)] +pub mod multi_chromatogram_agg; +pub mod scored_arrays; + +pub use multi_chromatogram_agg::{ + MultiCMGStatsAgg, + MultiCMGStatsFactory, +}; 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 new file mode 100644 index 0000000..2a15c7a --- /dev/null +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/multi_chromatogram_agg.rs @@ -0,0 +1,239 @@ +use super::super::chromatogram_agg::ScanTofStatsCalculatorPair; +use super::aggregator::ParitionedCMGAggregator; +use super::arrays::{ + PartitionedCMGArrayStats, + PartitionedCMGArrays, +}; +use super::scored_arrays::{ + PartitionedCMGScoredStatsArrays, + ScoresAtTime, +}; +use crate::errors::Result; +use crate::models::elution_group::ElutionGroup; +use crate::models::frames::raw_peak::RawPeak; +use crate::models::queries::MsLevelContext; +use crate::traits::aggregator::Aggregator; +use serde::Serialize; +use std::hash::Hash; + +use timsrust::converters::{ + ConvertableDomain, + Scan2ImConverter, + Tof2MzConverter, +}; + +#[derive(Debug, Clone)] +pub struct MultiCMGStatsAgg { + pub converters: (Tof2MzConverter, Scan2ImConverter), + pub ms1_stats: ParitionedCMGAggregator, + pub ms2_stats: ParitionedCMGAggregator, + pub id: u64, + pub context: Option>, + pub buffer: Option, + // TODO: Make this a reference instead of a clone.... maybe. + pub elution_group_ref: ElutionGroup, +} + +#[derive(Debug, Clone)] +pub struct MultiCMGStatsFactory { + pub converters: (Tof2MzConverter, Scan2ImConverter), + pub _phantom: std::marker::PhantomData, +} + +impl MultiCMGStatsFactory { + pub fn build_with_elution_group( + &self, + elution_group: &ElutionGroup, + ) -> MultiCMGStatsAgg { + // TODO: RN this is a super hacky ... IDEALLY we would either keep a reference OR + // preserve only the expected intensities. + let elution_group_ref = elution_group.clone(); + + let (fragment_keys, fragment_tof): (Vec, Vec) = elution_group + .fragment_mzs + .iter() + .map(|(k, v)| { + let tof = self.converters.0.invert(*v) as u32; + (k.clone(), tof) + }) + .unzip(); + + let (precursor_keys, precursor_tof): (Vec, Vec) = elution_group + .precursor_mzs + .iter() + .enumerate() + .map(|(i, v)| (i, self.converters.0.invert(*v) as u32)) + .unzip(); + + let expect_scan_index = self.converters.1.invert(elution_group.mobility) as usize; + + let exp_fragment_intensities: Option> = + if elution_group.expected_fragment_intensity.is_some() { + let tmp_expect_inten = elution_group.expected_fragment_intensity.as_ref().unwrap(); + let out = fragment_keys + .iter() + .map(|x| *(tmp_expect_inten.get(x).unwrap_or(&0.0))) + .collect(); + Some(out) + } else { + None + }; + + MultiCMGStatsAgg { + converters: (self.converters.0, self.converters.1), + ms1_stats: ParitionedCMGAggregator::new( + precursor_keys, + elution_group.expected_precursor_intensity.to_owned(), + expect_scan_index, + precursor_tof, + ), + ms2_stats: ParitionedCMGAggregator::new( + fragment_keys, + exp_fragment_intensities, + expect_scan_index, + fragment_tof, + ), + id: elution_group.id, + context: None, + buffer: None, + elution_group_ref, + } + } +} + +#[derive(Debug, Clone, Serialize)] +pub struct MultiCMGArrayStats { + pub ms1_stats: PartitionedCMGArrayStats, + pub ms2_stats: PartitionedCMGArrayStats, + pub id: u64, +} + +#[derive(Debug, Clone, Serialize)] +pub struct NaturalFinalizedMultiCMGStatsArrays { + pub ms1_stats: PartitionedCMGScoredStatsArrays, + pub ms2_stats: PartitionedCMGScoredStatsArrays, + pub cross_ms1: Vec, + pub cross_ms2: Vec, + pub id: u64, +} + +#[derive(Debug, Clone, Serialize)] +pub struct ApexScores { + pub ms1_scores: ScoresAtTime, + pub ms2_scores: ScoresAtTime, + pub main_score: f64, +} + +impl + NaturalFinalizedMultiCMGStatsArrays +{ + pub fn finalized_score(&self) -> Result { + let main_score = self.cross_ms2.as_slice(); + let main_score_rts = self.ms1_stats.retention_time_miliseconds.as_slice(); + let apex_cross_ms2_index = main_score + .iter() + .enumerate() + .max_by(|x, y| x.1.partial_cmp(y.1).unwrap()) + .unwrap(); + + let apex_rt = main_score_rts[apex_cross_ms2_index.0]; + + let ms1_scores = self.ms1_stats.scores_at_rt(apex_rt); + let ms2_scores = self.ms2_stats.scores_at_rt(apex_rt); + + let out = ApexScores { + ms1_scores, + ms2_scores, + main_score: *apex_cross_ms2_index.1, + }; + + if out.main_score.is_infinite() { + panic!("Main score is infinite, main_score: {:?}", main_score); + } + Ok(out) + } +} + +impl Aggregator + for MultiCMGStatsAgg +{ + type Context = MsLevelContext; + type Item = RawPeak; + type Output = NaturalFinalizedMultiCMGStatsArrays; + + 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; + + match self.get_context() { + MsLevelContext::MS1(_i) => { + self.ms1_stats.add( + rt_miliseconds, + peak.scan_index, + peak.tof_index, + u64_intensity, + ); + } + MsLevelContext::MS2(_i) => { + self.ms2_stats.add( + rt_miliseconds, + peak.scan_index, + peak.tof_index, + u64_intensity, + ); + } + } + } + + fn set_context(&mut self, context: Self::Context) { + match &context { + MsLevelContext::MS1(i) => { + self.ms1_stats.set_context(*i).unwrap(); + } + MsLevelContext::MS2(i) => { + self.ms2_stats.set_context(i.clone()).unwrap(); + } + } + self.context = Some(context); + } + + fn supports_context(&self) -> bool { + true + } + + 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; + + // TODO clean this up ... 4 conversions in one line is feeling a bit weird. + let ms1_stats = PartitionedCMGScoredStatsArrays::new( + PartitionedCMGArrayStats::from(PartitionedCMGArrays::from(self.ms1_stats)), + mz_converter, + mobility_converter, + ); + let ms2_stats = PartitionedCMGScoredStatsArrays::new( + PartitionedCMGArrayStats::from(PartitionedCMGArrays::from(self.ms2_stats)), + mz_converter, + mobility_converter, + ); + + let cross_ms1 = ms2_stats.cross_scores(&ms1_stats).unwrap_or(vec![]); + let cross_ms2 = ms1_stats.cross_scores(&ms2_stats).unwrap_or(vec![]); + + NaturalFinalizedMultiCMGStatsArrays { + ms2_stats, + ms1_stats, + cross_ms1, + cross_ms2, + id: self.id, + } + } +} diff --git a/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/scored_arrays.rs b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/scored_arrays.rs new file mode 100644 index 0000000..a539dcc --- /dev/null +++ b/src/models/aggregators/raw_peak_agg/multi_chromatogram_agg/scored_arrays.rs @@ -0,0 +1,367 @@ +use super::arrays::PartitionedCMGArrayStats; +use crate::errors::{ + DataProcessingError, + Result, +}; +use crate::models::aggregators::rolling_calculators::{ + calculate_lazy_hyperscore, + calculate_value_vs_baseline, +}; +use crate::models::aggregators::streaming_aggregator::RunningStatsCalculator; +use crate::sort_vecs_by_first; +use crate::utils::dtw::dtw_max; +use crate::utils::math::lnfact_float; +use serde::Serialize; +use std::collections::HashMap; +use std::f64; +use std::hash::Hash; +use timsrust::converters::{ + ConvertableDomain, + Scan2ImConverter, + Tof2MzConverter, +}; +use tracing::debug; + +// 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 scores: ChromatogramScores, + pub transition_mobilities: HashMap>, + pub transition_mzs: HashMap>, + pub expected_mzs: HashMap, + pub expected_mobility: f64, + pub transition_intensities: HashMap>, + pub apex_primary_score_index: usize, +} + +#[derive(Debug, Clone, Serialize, Default)] +pub struct ScoresAtTime { + pub lazyerscore: f64, + pub lazyerscore_vs_baseline: f64, + pub norm_lazyerscore_vs_baseline: f64, + pub cosine_similarity: f64, + pub npeaks: u8, + pub retention_time_miliseconds: u32, + pub average_mobility: f64, + pub summed_intensity: u64, + pub mz_errors: Vec, + pub mobility_errors: Vec, + pub transition_intensities: Vec, +} + +#[derive(Debug, Clone, Serialize)] +pub struct ChromatogramScores { + pub lazy_hyperscore: Vec, + pub lazyerscore: Vec, + pub lazy_hyperscore_vs_baseline: Vec, + pub lazyerscore_vs_baseline: Vec, + pub norm_hyperscore_vs_baseline: Vec, + pub norm_lazyerscore_vs_baseline: Vec, + pub npeaks: Vec, + pub cosine_similarity: Option>, +} + +impl ScoresAtTime { + pub fn sorted_transition_intensities(&self) -> (Vec, Vec, Vec) { + let sorted_vecs = sort_vecs_by_first!( + &self.transition_intensities, + &self.mobility_errors, + &self.mz_errors + ); + + let partition_point = sorted_vecs.0.partition_point(|&x| x < 10); + let mut transition_intensities = sorted_vecs.0[partition_point..].to_vec(); + transition_intensities.reverse(); + let mut mobility_errors = sorted_vecs.2[partition_point..].to_vec(); + mobility_errors.reverse(); + let mut mz_errors = sorted_vecs.1[partition_point..].to_vec(); + mz_errors.reverse(); + + (transition_intensities, mobility_errors, mz_errors) + } +} + +impl ChromatogramScores { + pub fn new( + arrays: &PartitionedCMGArrayStats, + ) -> Self { + let lazy_hyperscore = calculate_lazy_hyperscore(&arrays.npeaks, &arrays.summed_intensity); + let basline_window_len = 1 + (arrays.retention_time_miliseconds.len() / 20); + let lazy_hyperscore_vs_baseline = + calculate_value_vs_baseline(&lazy_hyperscore, basline_window_len); + let lazyerscore: Vec = arrays + .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(); + + // Make sure all arrays are the same length + assert!( + lazy_hyperscore_vs_baseline.len() == arrays.retention_time_miliseconds.len(), + "Failed sanity check" + ); + assert!( + lazyerscore_vs_baseline.len() == arrays.retention_time_miliseconds.len(), + "Failed sanity check" + ); + + ChromatogramScores { + lazy_hyperscore, + lazyerscore, + lazy_hyperscore_vs_baseline, + lazyerscore_vs_baseline, + norm_hyperscore_vs_baseline, + norm_lazyerscore_vs_baseline, + npeaks: arrays.npeaks.to_owned(), + cosine_similarity: arrays.cosine_similarity.to_owned(), + } + } + + fn get_apex_score_index(&self) -> usize { + let mut apex_primary_score_index = 0; + let mut max_primary_score = 0.0f64; + let primary_scores = &self.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; + } + } + apex_primary_score_index + } +} + +impl + PartitionedCMGScoredStatsArrays +{ + pub fn index_at_rt(&self, rt_miliseconds: u32) -> usize { + let part_point = self + .retention_time_miliseconds + .partition_point(|x| x < &rt_miliseconds); + if part_point == 0 { 0 } else { part_point - 1 } + } + + pub fn scores_at_rt(&self, rt_miliseconds: u32) -> ScoresAtTime { + let index = self.index_at_rt(rt_miliseconds); + let lazyerscore = self.scores.lazyerscore[index]; + let lazyerscore_vs_baseline = self.scores.lazyerscore_vs_baseline[index]; + let norm_lazyerscore_vs_baseline = self.scores.norm_lazyerscore_vs_baseline[index]; + let cosine_similarity = match self.scores.cosine_similarity.as_ref() { + Some(x) => x[index], + None => 0.0, + }; + let npeaks = self.scores.npeaks[index]; + let retention_time_miliseconds = self.retention_time_miliseconds[index]; + // TODO decide whether to report errors where the expected val is 0. + + let transition_msz: HashMap = self + .transition_mzs + .iter() + .map(|x| (x.0.clone(), x.1[index])) + .collect(); + let transition_mobilities: HashMap = self + .transition_mobilities + .iter() + .map(|x| (x.0.clone(), x.1[index])) + .collect(); + let transition_intensities_map: HashMap = self + .transition_intensities + .iter() + .map(|x| (x.0.clone(), x.1[index])) + .collect(); + + let key_order: Vec = self.transition_intensities.keys().cloned().collect(); + let mz_errors: Vec = key_order + .iter() + .map(|x| self.expected_mzs[x] - transition_msz[x]) + .collect(); + let mobility_errors: Vec = key_order + .iter() + .map(|x| self.expected_mobility - transition_mobilities[x]) + .collect(); + let transition_intensities: Vec = key_order + .iter() + .map(|x| transition_intensities_map[x]) + .collect(); + + let summed_intensity = self.summed_intensity[index]; + let average_mobility = self.average_mobility[index]; + + ScoresAtTime { + lazyerscore, + lazyerscore_vs_baseline, + norm_lazyerscore_vs_baseline, + cosine_similarity, + npeaks, + retention_time_miliseconds, + mz_errors, + mobility_errors, + average_mobility, + summed_intensity, + transition_intensities, + } + } + + /// Calculates the cross score between the two partitioned arrays. + /// + /// USES THE OTHER ARRAYS LAZYERSCORE AND PROJECTS ONTO THE SELF SPACE. + /// + /// In brief .. it is + /// (self.cosine_similarity * other.cosine_similarity) * other.lazyerscore_vs_baseline + /// + /// But it projects the 'self' values to the 'other' values. + pub fn cross_scores( + &self, + other: &PartitionedCMGScoredStatsArrays, + ) -> Result> { + let self_cosine = match self.scores.cosine_similarity.as_ref() { + Some(x) => x, + None => return Err(DataProcessingError::ExpectedNonEmptyData.into()), + }; + let self_rt = self.retention_time_miliseconds.as_slice(); + let other_cosine = match other.scores.cosine_similarity.as_ref() { + Some(x) => x, + None => return Err(DataProcessingError::ExpectedNonEmptyData.into()), + }; + let other_rt = other.retention_time_miliseconds.as_slice(); + let other_lzb = other.scores.lazyerscore_vs_baseline.as_slice(); + + // Should I project self -> other or other -> self? + let proj_other_cosine = dtw_max(self_rt, other_rt, other_cosine)?; + let proj_other_lzb = dtw_max(self_rt, other_rt, other_lzb)?; + + assert!(proj_other_cosine.len() == proj_other_lzb.len()); + assert!(proj_other_cosine.len() == self_rt.len()); + + let mut out = Vec::with_capacity(proj_other_cosine.len()); + for (self_cos, (other_cos, other_lzb)) in self_cosine + .iter() + .zip(proj_other_cosine.iter().zip(proj_other_lzb.iter())) + { + // TODO fix this a layer deeper ... + // maybe two ... 1. Either prevent needing to wrap the extensions by having + // The aggregator map to the closest cycle, rather than the frame. + // 2. Fix the wrapping to not generate -inf values. + let score = self_cos * other_cos * other_lzb; + if score.is_infinite() { + out.push(0.0); + continue; + } + out.push(score); + } + + // Check if there are infinite values + if out.iter().any(|x| x.is_infinite()) { + let infinite_indices = out + .iter() + .enumerate() + .filter(|(_, x)| x.is_infinite()) + .collect::>(); + panic!( + "Cross scores contain infinite values at indices: \n\n>>> {:?}", + infinite_indices, + ); + } + + Ok(out) + } +} + +impl PartitionedCMGScoredStatsArrays { + pub fn new( + other: PartitionedCMGArrayStats, + mz_converter: &Tof2MzConverter, + mobility_converter: &Scan2ImConverter, + ) -> Self { + let scores = ChromatogramScores::new(&other); + let apex_primary_score_index = scores.get_apex_score_index(); + let 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(); + + let 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(); + + let 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(); + + let expected_mobility = mobility_converter.convert(other.expected_scan_index as f64); + let expected_mzs = other + .expected_tof_index + .into_iter() + .map(|x| (x.0, mz_converter.convert(x.1 as f64))) + .collect(); + + PartitionedCMGScoredStatsArrays { + retention_time_miliseconds: other.retention_time_miliseconds, + average_mobility, + summed_intensity: other.summed_intensity, + transition_mobilities, + transition_mzs, + transition_intensities: other.intensities, + apex_primary_score_index, + scores, + expected_mzs, + expected_mobility, + } + } +} diff --git a/src/models/aggregators/raw_peak_agg/point_agg.rs b/src/models/aggregators/raw_peak_agg/point_agg.rs index e1ad36c..8438d50 100644 --- a/src/models/aggregators/raw_peak_agg/point_agg.rs +++ b/src/models/aggregators/raw_peak_agg/point_agg.rs @@ -1,5 +1,9 @@ +use crate::models::elution_group; use crate::models::frames::raw_peak::RawPeak; -use crate::traits::aggregator::Aggregator; +use crate::traits::aggregator::{ + Aggregator, + NoContext, +}; use serde::Serialize; #[derive(Debug, Clone, Copy)] @@ -12,18 +16,36 @@ impl RawPeakIntensityAggregator { pub fn new(id: u64) -> Self { Self { id, intensity: 0 } } + + pub fn new_with_elution_group< + T: Send + Sync + std::hash::Hash + Clone + Eq + PartialEq + Serialize + std::fmt::Debug, + >( + elution_group: &elution_group::ElutionGroup, + ) -> Self { + Self { + id: elution_group.id, + intensity: 0, + } + } } -impl Aggregator for RawPeakIntensityAggregator { +impl Aggregator for RawPeakIntensityAggregator { + type Context = NoContext; + type Item = RawPeak; type Output = u64; - fn add(&mut self, peak: &RawPeak) { + fn add(&mut self, peak: impl Into) { + let peak = peak.into(); self.intensity += peak.intensity as u64; } fn finalize(self) -> u64 { self.intensity } + + fn supports_context(&self) -> bool { + false + } } #[derive(Debug, Clone)] @@ -39,6 +61,14 @@ impl RawPeakVectorAggregator { peaks: RawPeakVectorArrays::new(), } } + + pub fn new_with_elution_group< + T: Send + Sync + std::hash::Hash + Clone + Eq + PartialEq + Serialize + std::fmt::Debug, + >( + elution_group: &elution_group::ElutionGroup, + ) -> Self { + Self::new(elution_group.id) + } } impl RawPeakVectorArrays { @@ -60,10 +90,13 @@ pub struct RawPeakVectorArrays { pub retention_times: Vec, } -impl Aggregator for RawPeakVectorAggregator { +impl Aggregator for RawPeakVectorAggregator { + type Context = NoContext; + 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); @@ -73,4 +106,8 @@ impl Aggregator for RawPeakVectorAggregator { fn finalize(self) -> RawPeakVectorArrays { self.peaks } + + fn supports_context(&self) -> bool { + false + } } diff --git a/src/models/aggregators/rolling_calculators.rs b/src/models/aggregators/rolling_calculators.rs index 24bdfad..58b53b1 100644 --- a/src/models/aggregators/rolling_calculators.rs +++ b/src/models/aggregators/rolling_calculators.rs @@ -1,3 +1,4 @@ +use crate::utils::math::lnfact; // Rolling median calculator pub struct RollingMedianCalculator { @@ -56,6 +57,24 @@ pub fn rolling_median( out } +pub fn calculate_lazy_hyperscore(npeaks: &[u8], 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 +119,27 @@ 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 785584f..d03093f 100644 --- a/src/models/aggregators/streaming_aggregator.rs +++ b/src/models/aggregators/streaming_aggregator.rs @@ -1,9 +1,10 @@ -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 // to calculate the total, mean and variance. +// TODO: move this to the general errors. #[derive(Debug, Clone, Copy)] pub enum StreamingAggregatorError { DivisionByZero, @@ -12,16 +13,44 @@ 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(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, 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, mean_n: f64, d_: f64, + min: f64, + max: f64, // count: u64, } @@ -30,7 +59,9 @@ impl RunningStatsCalculator { Self { weight, mean_n: mean, - d_: 0.0, + d_: 1.0, + min: mean, + max: mean, // count: 0, } } @@ -52,6 +83,35 @@ 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/elution_group.rs b/src/models/elution_group.rs index 24cd811..fd2a47f 100644 --- a/src/models/elution_group.rs +++ b/src/models/elution_group.rs @@ -1,20 +1,38 @@ -use crate::HasIntegerID; -use serde::{Deserialize, Serialize}; +use serde::{ + Deserialize, + Serialize, +}; use std::collections::HashMap; use std::hash::Hash; -#[derive(Debug, Serialize, Deserialize)] -pub struct ElutionGroup { +/// 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, pub mobility: f32, pub rt_seconds: f32, - pub precursor_mz: f64, - pub precursor_charge: u8, + pub precursor_mzs: Vec, pub fragment_mzs: HashMap, + pub expected_fragment_intensity: Option>, + pub expected_precursor_intensity: Option>, } -impl HasIntegerID for ElutionGroup { - fn get_id(&self) -> u64 { - self.id +impl ElutionGroup { + pub fn get_precursor_mz_limits(&self) -> (f64, f64) { + let mut min_precursor_mz = f64::MAX; + let mut max_precursor_mz = f64::MIN; + for precursor_mz in self.precursor_mzs.iter() { + if *precursor_mz < min_precursor_mz { + min_precursor_mz = *precursor_mz; + } + if *precursor_mz > max_precursor_mz { + max_precursor_mz = *precursor_mz; + } + } + (min_precursor_mz, max_precursor_mz) } } diff --git a/src/models/frames/expanded_frame.rs b/src/models/frames/expanded_frame.rs index f218f70..dbe1aad 100644 --- a/src/models/frames/expanded_frame.rs +++ b/src/models/frames/expanded_frame.rs @@ -1,12 +1,52 @@ +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, + IncludedRange, +}; +use rayon::prelude::*; +use std::collections::HashMap; +use std::marker::PhantomData; use std::sync::Arc; - -use super::single_quad_settings::{expand_quad_settings, SingleQuadrupoleSetting}; -use timsrust::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}; - -use crate::sort_by_indices_multi; -use crate::utils::sorting::argsort_by; +use timsrust::converters::{ + Scan2ImConverter, + Tof2MzConverter, +}; +use timsrust::readers::{ + FrameReader, + FrameReaderError, +}; +use timsrust::{ + 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)] pub struct ExpandedFrame { pub tof_indices: Vec, pub scan_numbers: Vec, @@ -20,7 +60,17 @@ pub struct ExpandedFrame { pub window_group: u8, } -pub struct ExpandedFrameSlice { +#[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 tof_indices: Vec, // I could Arc<[u32]> if I didnt want to sort by it ... pub scan_numbers: Vec, pub intensities: Vec, @@ -28,54 +78,162 @@ 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, + _sorting_state: PhantomData, } -impl ExpandedFrameSlice { - pub fn sort_by_tof(&mut self) { - 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 - ); +// 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(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 (tof_indices, scan_numbers, intensities) = + sort_by_tof_macro(self.tof_indices, self.scan_numbers, self.intensities); + + ExpandedFrameSlice { + tof_indices, + scan_numbers, + 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 { + 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); +impl ExpandedFrameSlice { + pub fn query_peaks( + &self, + 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.start()); + let peak_ind_end = self.tof_indices.partition_point(|x| *x <= tof_range.end()); + peak_ind_start..peak_ind_end + }; + + for peak_ind in peak_range { + let scan_index = self.scan_numbers[peak_ind]; + if let Some(scan_range) = &scan_range { + if !scan_range.contains(scan_index) { + continue; + } + } + + 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. + // + // 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 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, + _sorting_state: PhantomData::, + }; + + curr_slice.sort_by_tof() +} - 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 { + let curr_slice = ExpandedFrameSlice { tof_indices: slice_tof_indices, scan_numbers: slice_scan_numbers, intensities: slice_intensities, @@ -83,43 +241,37 @@ 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, + _sorting_state: PhantomData::, }; - curr_slice.sort_by_tof(); - out.push(curr_slice); + out.push(curr_slice.sort_by_tof()); } 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 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, @@ -136,17 +288,519 @@ impl ExpandedFrame { } } +type QuadBundledFrameslices = + HashMap, Vec>>; + +#[instrument(skip(frame_iter))] +pub fn par_expand_and_arrange_frames( + frame_iter: impl ParallelIterator, +) -> 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: 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_default().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.par_sort_unstable_by(|a, b| a.rt.partial_cmp(&b.rt).unwrap()); + } + 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 { + settings: CentroidingSettings, + 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 { 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 { + settings: Default::default(), + ims_converter: Default::default(), + mz_converter: Default::default(), + } + } + + pub fn default_not_centroided() -> Self { + FrameProcessingConfig::NotCentroided + } +} + +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 + } + } + }) +} + +#[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, +) -> Result, Vec>>> { + let dia_windows = match frame_reader.get_dia_windows() { + Some(dia_windows) => dia_windows, + None => { + return Err(UnsupportedDataError::NoMS2DataError.into()); + } + }; + + 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 { + settings, + ims_converter, + mz_converter, + } => par_expand_and_centroid_frames( + curr_iter, + settings.ims_tol_pct, + settings.mz_tol_ppm, + settings.window_width, + settings.max_ms2_peaks, + &ims_converter.unwrap(), + &mz_converter.unwrap(), + ), + FrameProcessingConfig::NotCentroided => par_expand_and_arrange_frames(curr_iter), + }; + + 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); + + 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 { + settings, + ims_converter, + mz_converter, + } => par_expand_and_centroid_frames( + ms1_iter, + settings.ims_tol_pct, + settings.mz_tol_ppm, + settings.window_width, + settings.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"); + + 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, level = "debug")] + 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, + 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(IncludedRange::new(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, + 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( + 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; + 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( + 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; + 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() { + 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, + 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 = par_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, + window_width, + ims_tol_pct, + mz_tol_ppm, + max_peaks, + ims_converter, + mz_converter, + ); + let end_peaks: usize = centroided.iter().map(|x| x.len()).sum(); + trace!( + "Peak counts for quad {:?}: raw={}/centroid={}", + qs, start_peaks, end_peaks + ); + (qs, centroided) + }) + .collect(); + + out +} + +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; + + let peak_refs: Vec = frameslices + .iter() + .map(|x| PeakArrayRefs::new(&x.tof_indices, &x.scan_numbers, &x.intensities)) + .collect(); + + 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), + ); + + ExpandedFrameSlice { + 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, + 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, + _sorting_state: PhantomData::, + } +} + +#[instrument(skip(frameslices))] +pub fn par_lazy_centroid_frameslices( + frameslices: &[ExpandedFrameSlice], + window_width: usize, + ims_tol_pct: f64, + mz_tol_ppm: f64, + max_peaks: usize, + ims_converter: &Scan2ImConverter, + mz_converter: &Tof2MzConverter, +) -> Vec> { + assert!( + frameslices + .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" + ); + + assert!(frameslices.len() > window_width); + + let local_lambda = |fss: &[ExpandedFrameSlice]| { + centroid_frameslice_window2( + fss, + ims_tol_pct, + mz_tol_ppm, + max_peaks, + ims_converter, + mz_converter, + ) + }; + + frameslices + .par_windows(window_width) + .map(local_lambda) + .collect() +} + #[cfg(test)] 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..d38b5a0 100644 --- a/src/models/frames/expanded_window_group.rs +++ b/src/models/frames/expanded_window_group.rs @@ -1,8 +1,14 @@ 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}; +use timsrust::{ + AcquisitionType, + MSLevel, +}; pub struct ExpandedWindowGroup { pub tof_indices: Vec, @@ -12,13 +18,15 @@ 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, } 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/raw_frames.rs b/src/models/frames/raw_frames.rs index d3e6daa..c40c6ae 100644 --- a/src/models/frames/raw_frames.rs +++ b/src/models/frames/raw_frames.rs @@ -1,12 +1,16 @@ -use timsrust::{Frame, QuadrupoleSettings}; +use timsrust::{ + Frame, + QuadrupoleSettings, +}; use super::raw_peak::RawPeak; -use log::trace; +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 +19,7 @@ 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); @@ -26,21 +30,19 @@ 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: {:?}", - 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)); @@ -52,11 +54,11 @@ 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 +85,7 @@ 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/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/frames/single_quad_settings.rs b/src/models/frames/single_quad_settings.rs index a27eb54..7d4e819 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, @@ -31,11 +33,22 @@ 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 ) } } +/// 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 +94,17 @@ 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 +131,65 @@ pub fn expand_quad_settings(quad_settings: &QuadrupoleSettings) -> Vec, + scan_range: Option>, +) -> impl Iterator + '_ { + flat_quad_settings + .iter() + .filter(move |qs| { + 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: 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>, +) -> bool { + match scan_range { + Some(tmp_range) => { + let min_scan = tmp_range.start(); + let max_scan = tmp_range.end(); + assert!(qs.ranges.scan_start <= qs.ranges.scan_end); + + // 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: 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/mod.rs b/src/models/indices/expanded_raw_index/mod.rs new file mode 100644 index 0000000..15ec9da --- /dev/null +++ b/src/models/indices/expanded_raw_index/mod.rs @@ -0,0 +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 new file mode 100644 index 0000000..7ba0431 --- /dev/null +++ b/src/models/indices/expanded_raw_index/model.rs @@ -0,0 +1,343 @@ +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; +use std::hash::Hash; +use std::time::Instant; +use timsrust::converters::{ + Scan2ImConverter, + Tof2MzConverter, +}; +use timsrust::readers::{ + FrameReader, + MetadataReader, +}; +use tracing::{ + info, + instrument, +}; + +#[derive(Debug)] +pub struct ExpandedRawFrameIndex { + bundled_ms1_frames: ExpandedSliceBundle, + bundled_frames: HashMap, + flat_quad_settings: Vec, + pub mz_converter: Tof2MzConverter, + pub im_converter: Scan2ImConverter, + adapter: FragmentIndexAdapter, +} + +#[derive(Debug, Clone)] +pub struct ExpandedSliceBundle { + slices: 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 frame_indices = slices.iter().map(|x| x.frame_index).collect(); + Self { + slices, + frame_indices, + } + } + + pub fn query_peaks( + &self, + 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.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); + } + } +} + +impl ExpandedRawFrameIndex { + pub fn query_peaks( + &self, + tof_range: IncludedRange, + precursor_mz_range: IncludedRange, + scan_range: Option>, + frame_index_range: IncludedRange, + 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_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], + tof_range: IncludedRange, + scan_range: Option>, + frame_index_range: IncludedRange, + 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) + } + } + + #[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) -> 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, meta_converters.mz_converter); + + let st = Instant::now(); + let centroided_split_frames = par_read_and_expand_frames(&file_reader, centroid_config)?; + let centroided_elap = st.elapsed(); + info!("Reading + 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, + mz_converter: meta_converters.mz_converter, + im_converter: meta_converters.im_converter, + adapter, + }; + + Ok(out) + } +} + +impl + QueriableData, RawPeak, MsLevelContext> + for ExpandedRawFrameIndex +{ + 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, + ) + .into(); + 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 = vec![]; + self.query_peaks( + *tof_range, + precursor_mz_range, + scan_range, + fragment_query.precursor_query.frame_index_range, + &mut |x| local_vec.push(RawPeak::from(x)), + ); + + local_vec + }) + .collect() + } + + 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 = ( + fragment_query.precursor_query.isolation_mz_range.0 as f64, + fragment_query.precursor_query.isolation_mz_range.0 as f64, + ) + .into(); + 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, + fragment_query.precursor_query.frame_index_range, + &mut |peak| aggregator.add(RawPeak::from(peak)), + ); + }) + } + + fn add_query_multi_group( + &self, + fragment_queries: &[FragmentGroupIndexQuery], + aggregator: &mut [AG], + ) where + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, + { + let prec_mz_ranges = fragment_queries + .iter() + .map(|x| { + ( + x.precursor_query.isolation_mz_range.start() as f64, + x.precursor_query.isolation_mz_range.end() as f64, + ) + .into() + }) + .collect::>(); + + let scan_ranges = fragment_queries + .iter() + .map(|x| Some(x.precursor_query.mobility_index_range)) + .collect::>(); + + let frame_index_ranges = fragment_queries + .iter() + .map(|x| x.precursor_query.frame_index_range) + .collect::>(); + + // Query the ms1 mzs first. + aggregator.par_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; + + let tqi = self + .bundled_frames + .get(&local_index) + .expect("Only existing quads should be queried."); + + 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].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)) + }); + } + }); + } + } +} + +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/mod.rs b/src/models/indices/mod.rs index f912a50..81d43c9 100644 --- a/src/models/indices/mod.rs +++ b/src/models/indices/mod.rs @@ -1,2 +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 f736e30..327b9e1 100644 --- a/src/models/indices/raw_file_index.rs +++ b/src/models/indices/raw_file_index.rs @@ -1,25 +1,34 @@ -use std::sync::Arc; - +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::indexed_data::IndexedData; -use crate::ElutionGroup; -use crate::ToleranceAdapter; -use log::trace; +use crate::traits::queriable_data::QueriableData; +use crate::{ + 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, QuadrupoleSettings}; +use timsrust::readers::{ + FrameReader, + FrameReaderError, + MetadataReader, +}; +use timsrust::{ + Frame, + TimsRustError, +}; +use tracing::trace; pub struct RawFileIndex { file_reader: FrameReader, - meta_converters: Metadata, + adapter: FragmentIndexAdapter, } impl RawFileIndex { @@ -28,48 +37,27 @@ 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, - ), - 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, 'a: 'b, - FH: Clone + Eq + Serialize + Hash + Debug + Send + Sync, + FH: Clone + Eq + Serialize + Hash + Debug + Send + Sync + Copy, >( &'a self, fqs: &'b FragmentGroupIndexQuery, - fun: &'c mut dyn for<'r> FnMut(RawPeak, Arc), + fun: &'c mut dyn for<'r> FnMut(RawPeak), ) { 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(); @@ -77,16 +65,16 @@ 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, *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, frame.quadrupole_settings.clone()); + fun(peak); } } } @@ -100,110 +88,48 @@ 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, - ), - 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( + fn queries_from_elution_elements_impl< + FH: Clone + Eq + Serialize + Hash + Send + Sync + Copy + std::fmt::Debug, + >( &self, 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.clone(), - ( - 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) } } impl - IndexedData, RawPeak> for RawFileIndex + QueriableData, RawPeak, MsLevelContext> + for RawFileIndex { fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { let mut out = Vec::new(); - self.apply_on_query(fragment_query, &mut |peak, _| out.push(peak)); + self.apply_on_query(fragment_query, &mut |x| out.push(x)); 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)); + ) where + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, + { + 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 + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, + { fragment_queries .iter() .zip(aggregator.iter_mut()) @@ -211,7 +137,7 @@ impl } } -impl +impl ToleranceAdapter, ElutionGroup> for RawFileIndex { fn query_from_elution_group( diff --git a/src/models/indices/transposed_quad_index/peak_bucket.rs b/src/models/indices/transposed_quad_index/peak_bucket.rs index d39db0c..7265ae8 100644 --- a/src/models/indices/transposed_quad_index/peak_bucket.rs +++ b/src/models/indices/transposed_quad_index/peak_bucket.rs @@ -1,7 +1,10 @@ -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 crate::utils::display::{ + glimpse_vec, + GlimpseConfig, +}; +use crate::utils::tolerance_ranges::IncludedRange; use std::fmt::Display; pub struct PeakInBucket { @@ -93,16 +96,35 @@ impl PeakBucketBuilder { self.scan_offsets.push(scan_index); } + pub fn extend_peaks( + &mut self, + scan_indices: &[usize], + intensities: &[u32], + retention_times: &[f32], + ) { + self.scan_offsets.extend(scan_indices); + self.intensities.extend(intensities); + self.retention_times.extend(retention_times); + } + 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. - 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, @@ -137,8 +159,8 @@ 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 @@ -154,11 +176,11 @@ 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 @@ -186,8 +208,8 @@ 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; } } @@ -201,11 +223,11 @@ 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), + Some(x) => x.start()..x.end().min(self.scan_offsets.len() - 1), None => 0..(self.scan_offsets.len() - 1), }; scan_range @@ -216,10 +238,10 @@ 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 30bfb0e..eda101b 100644 --- a/src/models/indices/transposed_quad_index/quad_index.rs +++ b/src/models/indices/transposed_quad_index/quad_index.rs @@ -1,20 +1,39 @@ -use super::peak_bucket::PeakBucketBuilder; -use super::peak_bucket::{PeakBucket, PeakInBucket}; -use crate::models::frames::raw_peak::RawPeak; +use super::peak_bucket::{ + PeakBucket, + PeakBucketBuilder, + 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::utils::display::{glimpse_vec, GlimpseConfig}; - -use log::info; -use log::trace; -use rayon::prelude::*; -use std::collections::{BTreeMap, HashMap}; +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 timsrust::converters::{ + ConvertableDomain, + Frame2RtConverter, +}; +use tracing::{ + debug, + info, + instrument, +}; #[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, @@ -60,10 +79,24 @@ 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 })), + 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), ) } @@ -72,89 +105,16 @@ impl Display for TransposedQuadIndex { impl TransposedQuadIndex { pub fn query_peaks( &self, - tof_range: (u32, u32), - scan_range: Option<(usize, usize)>, - rt_range: Option, - // ) -> Vec { + tof_range: IncludedRange, + scan_range: Option>, + rt_range: Option>, ) -> 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. - let frame_index_range = self.convert_to_local_frame_range(rt_range); - 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, frame_index_range) + pb.query_peaks(scan_range, rt_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( - &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 - } -} - -#[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, - } } } @@ -168,7 +128,6 @@ impl PeakInQuad { } } } - // Q: Do I use this? Should I just have it as the frame index as // an option? #[derive(Debug, Clone, Copy)] @@ -192,7 +151,7 @@ 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 +160,7 @@ 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 +179,33 @@ 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); } + #[instrument( + name = "TransposedQuadIndex::build", + skip(self), + fields( + num_frames = %self.frame_indices.len(), + quad_settings = format!("{:?}", self.quad_settings), + ) + level = "debug", + )] pub fn build(self) -> TransposedQuadIndex { - let st = Instant::now(); + // TODO: Refactor this function, its getting pretty large. 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![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; @@ -264,48 +222,27 @@ 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 { 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"); @@ -316,28 +253,224 @@ 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); TransposedQuadIndex { - quad_settings: self.quad_settings, + quad_settings, frame_rts: out_rts, frame_indices: out_indices, peak_buckets: peak_bucket, } } + + #[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(), + ), + level = "debug", + )] + 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 + } + + #[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(), + ), + level = "debug", + )] + 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 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()]) + .collect(); + + let concat_elapsed = concat_st.elapsed(); + + let sorting_st = Instant::now(); + + 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(); + + let insertion_st = Instant::now(); + let mut slice_start = 0; + let mut slice_start_val = tof_slice[0]; + while slice_start < int_slice.len() { + 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], + "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], + "The next element after this slice should have a higher tof value" + ); + + 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: {:#?} 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; + } + + 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 16c358e..d3ef6f0 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 @@ -1,167 +1,140 @@ use super::quad_index::{ - FrameRTTolerance, PeakInQuad, TransposedQuadIndex, TransposedQuadIndexBuilder, + 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 crate::models::frames::peak_in_quad::PeakInQuad; 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::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::display::{ + glimpse_vec, + GlimpseConfig, +}; +use crate::utils::tolerance_ranges::IncludedRange; 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::Display; +use std::fmt::{ + Debug, + Display, +}; use std::hash::Hash; -use std::sync::Arc; use std::time::Instant; use timsrust::converters::{ - ConvertableDomain, Frame2RtConverter, Scan2ImConverter, Tof2MzConverter, + Scan2ImConverter, + Tof2MzConverter, +}; +use timsrust::readers::{ + FrameReader, + MetadataReader, }; -use timsrust::readers::{FrameReader, MetadataReader}; -use timsrust::Frame; use timsrust::Metadata; -use timsrust::TimsRustError; +use tracing::{ + debug, + info, + instrument, +}; // TODO break this module apart ... its getting too big for my taste // - 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, pub im_converter: Scan2ImConverter, - metadata: Metadata, + adapter: FragmentIndexAdapter, +} + +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( + pub fn query_ms2_peaks( &self, - tof_range: (u32, u32), - precursor_mz_range: (f64, f64), - scan_range: Option<(usize, usize)>, - rt_range: Option, - ) -> impl Iterator + '_ { - 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 + tof_range: IncludedRange, + precursor_mz_range: IncludedRange, + scan_range: Option>, + rt_range_seconds: Option>, + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { + let matching_quads: Vec = self .get_matching_quad_settings(precursor_mz_range, scan_range) .collect(); - trace!("matching_quads: {:?}", matching_quads); - - 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(); - tqi.query_peaks(tof_range, scan_range, rt_range) - }) + self.query_peaks_in_precursors(&matching_quads, tof_range, scan_range, rt_range_seconds, f); } - fn get_matching_quad_settings( + fn query_ms1_peaks( &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| { - 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 - } - }) - .cloned() + 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 queries_from_elution_elements_impl( + fn query_peaks_in_precursors( &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, + matching_quads: &[SingleQuadrupoleSettingIndex], + tof_range: IncludedRange, + scan_range: Option>, + rt_range_seconds: Option>, + f: &mut F, + ) where + F: FnMut(PeakInQuad), + { + 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_seconds) + .for_each(&mut *f); } } + + fn get_matching_quad_settings( + &self, + precursor_mz_range: IncludedRange, + scan_range: Option>, + ) -> impl Iterator + '_ { + get_matching_quad_settings(&self.flat_quad_settings, precursor_mz_range, scan_range) + } } impl Display for QuadSplittedTransposedIndex { @@ -169,7 +142,6 @@ 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"); @@ -181,13 +153,19 @@ 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; } } @@ -197,7 +175,8 @@ impl Display for QuadSplittedTransposedIndex { } impl QuadSplittedTransposedIndex { - pub fn from_path(path: &str) -> Result { + #[instrument(name = "QuadSplittedTransposedIndex::from_path")] + 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)?; @@ -207,11 +186,26 @@ impl QuadSplittedTransposedIndex { debug!("{}", out); Ok(out) } + + #[instrument(name = "QuadSplittedTransposedIndex::from_path_centroided")] + 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)] pub struct QuadSplittedTransposedIndexBuilder { - indices: HashMap, - rt_converter: Option, + indices: HashMap, TransposedQuadIndexBuilder>, mz_converter: Option, im_converter: Option, metadata: Option, @@ -222,57 +216,41 @@ 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); - - for qs in expanded_quad_settings { - // 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(); + 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); + } - let frame_index = frame.index; - let frame_rt = frame.rt; - self.added_peaks += int_slice.len() as u64; + #[instrument(name = "QuadSplittedTransposedIndexBuilder::from_path")] + fn from_path(path: &str) -> Result { + Self::from_path_base(path, FrameProcessingConfig::NotCentroided) + } - self.indices.get_mut(&qs).unwrap().add_frame_slice( - int_slice, - tof_slice, - expanded_scan_slice, - frame_index, - frame_rt, - ); - } + #[instrument(name = "QuadSplittedTransposedIndexBuilder::from_path_centroided")] + fn from_path_centroided(path: &str) -> Result { + let config = FrameProcessingConfig::default_centroided(); + Self::from_path_base(path, config) } - fn from_path(path: &str) -> Result { + // 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) -> Result { let file_reader = FrameReader::new(path)?; let sql_path = std::path::Path::new(path).join("analysis.tdf"); @@ -281,22 +259,26 @@ 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), added_peaks: 0, }; - let out2: Result, TimsRustError> = file_reader - .get_all() + let centroid_config = centroid_config + .with_converters(meta_converters.im_converter, meta_converters.mz_converter); + + let split_frames = par_read_and_expand_frames(&file_reader, centroid_config)?; + + // TODO use the rayon contructor to fold + let out2: Result> = split_frames .into_par_iter() - .chunks(100) - .map(|frames| { + .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 frame in frames { - let frame = frame?; - out.add_frame(frame); + for frameslice in frameslices { + out.add_frame_slice(frameslice); } Ok(out) }) @@ -311,7 +293,7 @@ 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) @@ -321,19 +303,24 @@ impl QuadSplittedTransposedIndexBuilder { self.added_peaks += other.added_peaks; } - fn build(self) -> QuadSplittedTransposedIndex { + #[instrument(skip(self), level = "debug")] + 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.index, qi); + flat_quad_settings.push(qs); + } else { + precursor_index = Some(qi); + } } flat_quad_settings.sort_by(|a, b| { @@ -344,194 +331,144 @@ 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(), im_converter: self.im_converter.unwrap(), - metadata: self.metadata.unwrap(), + adapter: FragmentIndexAdapter::from(self.metadata.unwrap()), } } } -impl - IndexedData, RawPeak> for QuadSplittedTransposedIndex +impl + QueriableData, RawPeak, MsLevelContext> + for QuadSplittedTransposedIndex { fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec { - 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, ); 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)| { - 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, - frame_index_range, - ) - .map(RawPeak::from) + Some(fragment_query.precursor_query.rt_range_seconds), + &mut |x| local_vec.push(RawPeak::from(x)), + ); + + local_vec }) .collect() } - fn add_query>( + fn add_query( &self, fragment_query: &FragmentGroupIndexQuery, aggregator: &mut AG, - ) { - let precursor_mz_range = ( + ) 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, 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, - ) - .for_each(|peak| aggregator.add(&RawPeak::from(peak))); - }) + 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], - ) { - 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) - .for_each(|peak| agg.add(&RawPeak::from(peak))); - } - }); - } -} - -// Copy pasting for now ... TODO refactor or delete -// ============================================================================ - -impl - IndexedData, (RawPeak, FH)> for QuadSplittedTransposedIndex -{ - fn query(&self, fragment_query: &FragmentGroupIndexQuery) -> Vec<(RawPeak, FH)> { - 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 + ) where + A: From + Send + Sync + Clone + Copy, + AG: Aggregator, + MsLevelContext: Into, + { + let prec_mz_ranges = fragment_queries .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(); - - out + .map(|x| { + ( + x.precursor_query.isolation_mz_range.start() as f64, + x.precursor_query.isolation_mz_range.end() as f64, + ) + .into() }) - .collect() - } + .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, - )); + let scan_ranges = fragment_queries + .iter() + .map(|x| Some(x.precursor_query.mobility_index_range)) + .collect::>(); - fragment_query - .mz_index_ranges + let rt_ranges = fragment_queries .iter() - .for_each(|(fh, tof_range)| { - self.query_peaks( - *tof_range, - precursor_mz_range, - scan_range, - frame_index_range, - ) - .for_each(|peak| aggregator.add(&(RawPeak::from(peak), *fh))); - }) - } + .map(|x| x.precursor_query.rt_range_seconds) + .collect::>(); + + // Query the ms1 mzs first. + aggregator.par_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], Some(rt_ranges[i]), &mut |x| { + agg.add(RawPeak::from(x)) + }); + }); + }); - 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 quad_setting in self.flat_quad_settings.iter() { + let local_index = quad_setting.index; + + let tqi = self + .fragment_indices + .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_peaks(tof_range, precursor_mz_range, scan_range, frame_index_range) - .for_each(|peak| agg.add(&(RawPeak::from(peak), fh))); + 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].iter_ms2_mzs() { + if agg.supports_context() { + agg.set_context(fh.into()); + } + tqi.query_peaks(tof_range, scan_ranges[i], Some(rt_ranges[i])) + .for_each(|x| agg.add(RawPeak::from(x))); } }); + } } } -// ============================================================================ - -impl +impl ToleranceAdapter, ElutionGroup> for QuadSplittedTransposedIndex { @@ -540,6 +477,6 @@ 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; diff --git a/src/models/queries.rs b/src/models/queries.rs index e4e7679..8ef750c 100644 --- a/src/models/queries.rs +++ b/src/models/queries.rs @@ -1,28 +1,134 @@ +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, +}; #[derive(Debug, Clone)] pub struct PrecursorIndexQuery { - pub frame_index_range: (usize, usize), - 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, +} + +/// 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)] +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; +} + +#[allow(clippy::from_over_into)] +impl Into for MsLevelContext { + fn into(self) -> NoContext { + NoContext {} + } +} + +#[allow(clippy::from_over_into)] +impl Into for MsLevelContext { + fn into(self) -> NoContext { + NoContext {} + } +} + +#[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.clone()), *mz_range)); + out + } +} + +#[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, + 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, + } + } } diff --git a/src/queriable_tims_data/mod.rs b/src/queriable_tims_data/mod.rs index 4ebfc69..2045234 100644 --- a/src/queriable_tims_data/mod.rs +++ b/src/queriable_tims_data/mod.rs @@ -1 +1,2 @@ +#[allow(clippy::module_inception)] pub mod queriable_tims_data; diff --git a/src/queriable_tims_data/queriable_tims_data.rs b/src/queriable_tims_data/queriable_tims_data.rs index e2fc840..5e1b88d 100644 --- a/src/queriable_tims_data/queriable_tims_data.rs +++ b/src/queriable_tims_data/queriable_tims_data.rs @@ -1,119 +1,87 @@ -use log::info; +use crate::traits::aggregator::ProvidesContext; +use crate::{ + Aggregator, + ElutionGroup, + QueriableData, + Tolerance, + ToleranceAdapter, +}; use rayon::prelude::*; use serde::Serialize; use std::hash::Hash; -use std::rc::Rc; use std::time::Instant; - -use crate::{Aggregator, ElutionGroup, HasIntegerID, IndexedData, 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: IndexedData, - TA: ToleranceAdapter, - TL: Tolerance, -{ - 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: IndexedData, - TA: ToleranceAdapter, - TL: Tolerance, - EG: HasIntegerID, -{ - 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 tracing::{ + info, + instrument, +}; + +// 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). + +#[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, elution_groups: &[ElutionGroup], - aggregator_factory: &dyn Fn(u64) -> AG, + aggregator_factory: &FF, ) -> Vec where - AG: Aggregator + Send + Sync, - ID: IndexedData, - TA: ToleranceAdapter>, + AG: Aggregator + Send + Sync, + QD: QueriableData + ToleranceAdapter>, TL: Tolerance, OE: Send + Sync, - FH: Clone + Eq + Serialize + Hash + Send + Sync, + FH: Clone + Eq + Serialize + Hash + Send + Sync + std::fmt::Debug, + QF: Send + Sync + ProvidesContext, + AE1: Into + Send + Sync + Clone + Copy, + AE2: Send + Sync + Clone + From + Copy, + CTX1: Into + Send + Sync + Clone, + FF: Fn(&ElutionGroup) -> AG + Send + Sync, { let start = Instant::now(); let mut fragment_queries = Vec::with_capacity(elution_groups.len()); 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); + for elution_group in elution_groups.iter() { + let qp = queriable_data.query_from_elution_group(tolerance, elution_group); fragment_queries.push(qp); - aggregators.push(aggregator_factory(i as u64)); + aggregators.push(aggregator_factory(elution_group)); } - 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); @@ -127,26 +95,9 @@ where microseconds_per_query ); - aggregators.into_par_iter().map(|x| x.finalize()).collect() -} - -pub fn query_indexed( - indexed_data: &ID, - aggregator_factory: &dyn Fn(u64) -> AG, - tolerance_adapter: &TA, - tolerance: &TL, - elution_group: &ElutionGroup, -) -> OE -where - AG: Aggregator + Send + Sync, - ID: IndexedData, - TA: ToleranceAdapter>, - TL: Tolerance, - FH: Clone + Eq + Serialize + Hash + Send + Sync, -{ - 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); - aggregator.finalize() + let start = Instant::now(); + let out = aggregators.into_par_iter().map(|x| x.finalize()).collect(); + let elapsed = start.elapsed(); + info!("Aggregation took {:#?}", elapsed); + out } diff --git a/src/traits/aggregator.rs b/src/traits/aggregator.rs index 54a125d..ca44b79 100644 --- a/src/traits/aggregator.rs +++ b/src/traits/aggregator.rs @@ -1,7 +1,53 @@ -pub trait Aggregator: Send + Sync { +/// 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 `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: &I); - // fn fold(&mut self, item: Self); + fn add(&mut self, item: impl Into); fn finalize(self) -> Self::Output; + fn supports_context(&self) -> bool; + 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. +/// +/// Felt more semantically correct to make a type rather +/// than passing `()` to the context. +#[derive(Debug, Clone, Copy)] +pub struct NoContext {} diff --git a/src/traits/indexed_data.rs b/src/traits/indexed_data.rs deleted file mode 100644 index 6906a01..0000000 --- a/src/traits/indexed_data.rs +++ /dev/null @@ -1,11 +0,0 @@ -use crate::Aggregator; - -pub trait IndexedData { - 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..e7e509d --- /dev/null +++ b/src/traits/queriable_data.rs @@ -0,0 +1,31 @@ +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) + where + A: From + Send + Sync + Clone + Copy, + 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, + 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 b02dcfa..63e03f3 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 { @@ -23,9 +26,10 @@ pub enum MobilityTolerance { #[derive(Debug, Clone, Serialize, Deserialize)] pub enum QuadTolerance { - Absolute((f32, f32, u8)), + Absolute((f32, f32)), } +// TODO: Rename to something that does not use the 'Default' #[derive(Debug, Clone, Serialize, Deserialize)] pub struct DefaultTolerance { pub ms: MzToleramce, @@ -40,7 +44,7 @@ impl Default for 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)), + quad: QuadTolerance::Absolute((0.1, 0.1)), } } } @@ -49,7 +53,7 @@ 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 quad_range(&self, precursor_mz_range: (f64, f64)) -> (f32, f32); } impl Tolerance for DefaultTolerance { @@ -64,6 +68,7 @@ impl Tolerance for DefaultTolerance { } } + // TODO add an unit ... fn rt_range(&self, rt: f32) -> Option<(f32, f32)> { match self.rt { RtTolerance::Absolute((low, high)) => Some((rt - low, rt + high)), @@ -88,24 +93,17 @@ 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); - }; + fn quad_range(&self, precursor_mz_range: (f64, f64)) -> (f32, f32) { match self.quad { - QuadTolerance::Absolute((low, high, num_isotopes)) => { - let max_offset = (1.0 / precursor_charge as f32) * num_isotopes as f32; - let f32_mz = precursor_mz as f32; - let mz_low = f32_mz - low - max_offset; - let mz_high = f32_mz + high + max_offset; + QuadTolerance::Absolute((low, high)) => { + let mz_low = precursor_mz_range.0.min(precursor_mz_range.1) as f32 - low; + let mz_high = precursor_mz_range.1.max(precursor_mz_range.0) as f32 + high; assert!(mz_low <= mz_high); assert!( mz_low > 0.0, - "Precursor mz is 0 or less, inputs: self: {:?}, precursor_mz: {:?}, precursor_charge: {:?}", + "Precursor mz is 0 or less, inputs: self: {:?}, precursor_mz_range: {:?}", self, - precursor_mz, - precursor_charge + precursor_mz_range, ); (mz_low, mz_high) } @@ -113,12 +111,11 @@ 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/correlation.rs b/src/utils/correlation.rs new file mode 100644 index 0000000..655f937 --- /dev/null +++ b/src/utils/correlation.rs @@ -0,0 +1,253 @@ +use std::f64; + +use crate::errors::{ + DataProcessingError, + Result, +}; + +/// Calculates the cosine similarity between two vectors of the same size. +/// +/// # Example +/// +/// ``` +/// use timsquery::utils::correlation::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_eq!(result, 0.9746318461970762); +/// ``` +pub fn cosine_similarity(a: &[f64], b: &[f64]) -> Result { + // Check if vectors have the same length and are not empty + if a.len() != b.len() || a.is_empty() { + return Err(DataProcessingError::ExpectedVectorSameLength(a.len(), b.len()).into()); + } + + // 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 Ok(f64::NAN); + } + + // Calculate cosine similarity + Ok(dot_product / (magnitude_a * magnitude_b)) +} + +/// Calculates the cosine similarity at every window for two vectors. +/// +/// This means that for every window of size `window_size` the cosine similarity +/// is calculated between the two vectors. (and is padded with f64::NAN) +/// The output is a vector of the same length as the input. +/// +/// # Example +/// +/// ``` +/// use timsquery::utils::correlation::rolling_cosine_similarity; +/// +/// let a = vec![1.0, 2.0, 3.0, 1.0, 2.0, 3.0, 1.0, 2.0, 3.0]; +/// let b = vec![4.0, 5.0, 6.0, 4.0, 5.0, 6.0, 4.0, 5.0, 6.0]; +/// let expect_res: [f64; 9] = [ +/// f64::NAN, +/// 0.97463184, // Note that this is the same as above +/// 0.97823, +/// 0.95065, +/// 0.97463184, // And this one +/// 0.97823, +/// 0.95065, +/// 0.97463184, +/// f64::NAN, +/// ]; +/// let results = rolling_cosine_similarity(&a, &b, 3).unwrap(); +/// assert_eq!(results.len(), expect_res.len()); +/// ``` +pub fn rolling_cosine_similarity(a: &[f64], b: &[f64], window_size: usize) -> Result> { + // Check if vectors have the same length and are long enough for the window + if a.len() != b.len() { + return Err(DataProcessingError::ExpectedVectorSameLength(a.len(), b.len()).into()); + } + if a.len() < window_size { + return Err(DataProcessingError::InsufficientData { + real: a.len(), + expected: window_size, + } + .into()); + } + + let offset = window_size / 2; + let mut results = vec![f64::NAN; a.len()]; + + // Initialize the first window + let mut dot_product = 0.0; + let mut sum_a_squared = 0.0; + let mut sum_b_squared = 0.0; + + // Calculate initial values for first window + for i in 0..window_size { + dot_product += a[i] * b[i]; + sum_a_squared += a[i] * a[i]; + sum_b_squared += b[i] * b[i]; + } + + // Calculate similarity for first window + results[offset] = calculate_similarity(dot_product, sum_a_squared, sum_b_squared); + + // Roll the window + for i in (offset + 1)..(a.len() - offset) { + // Remove contribution of element leaving the window + let leaving_idx = i - offset; + dot_product -= a[leaving_idx] * b[leaving_idx]; + sum_a_squared -= a[leaving_idx] * a[leaving_idx]; + sum_b_squared -= b[leaving_idx] * b[leaving_idx]; + + // Add contribution of new element + dot_product += a[i] * b[i]; + sum_a_squared += a[i] * a[i]; + sum_b_squared += b[i] * b[i]; + + // Calculate similarity for current window + results[i] = calculate_similarity(dot_product, sum_a_squared, sum_b_squared); + } + + Ok(results) +} + +#[inline(always)] +fn calculate_similarity(dot_product: f64, sum_a_squared: f64, sum_b_squared: f64) -> f64 { + let magnitude_a = sum_a_squared.sqrt(); + let magnitude_b = sum_b_squared.sqrt(); + + if magnitude_a == 0.0 || magnitude_b == 0.0 { + 0.0 + } else { + dot_product / (magnitude_a * magnitude_b) + } +} + +#[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_err()); + } + + #[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_err()); + } + + #[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).unwrap().is_nan()); + } + + #[test] + fn test_rolling_cosine_similarity() { + let a = vec![1.0, 2.0, 3.0, 1.0, 2.0, 3.0, 1.0, 2.0, 3.0]; + let b = vec![4.0, 5.0, 6.0, 4.0, 5.0, 6.0, 4.0, 5.0, 6.0]; + let expect_res: [f64; 9] = [ + f64::NAN, + 0.97463184, // Note that this is the same as above + 0.97823, + 0.95065, + 0.97463184, // And this one + 0.97823, + 0.95065, + 0.97463184, + f64::NAN, + ]; + let results = rolling_cosine_similarity(&a, &b, 3).unwrap(); + assert_eq!(results.len(), expect_res.len()); + + for (result, expect) in results.iter().zip(expect_res.iter()) { + if result.is_nan() { + assert!(expect.is_nan()); + } else { + assert!( + (result - expect).abs() < 1e-3, + "Expected {:?}, got {:?}", + expect_res, + results, + ); + } + } + } + + #[test] + fn test_rolling_basic() { + let a = vec![1.0, 2.0, 3.0, 4.0]; + let b = vec![1.0, 2.0, 3.0, 4.0]; + let expect_res: [f64; 4] = [f64::NAN, 1.0, 1.0, f64::NAN]; + let results = rolling_cosine_similarity(&a, &b, 2).unwrap(); + assert_eq!(results.len(), 4); + for result in results.iter().zip(expect_res.iter()) { + if result.0.is_nan() { + assert!(result.1.is_nan()); + } else { + assert!( + (result.0 - result.1).abs() < 1e-8, + "Expected {:?}, got {:?}", + results, + expect_res + ); + } + } + } + + #[test] + fn test_rolling_window_too_large() { + let a = vec![1.0, 2.0]; + let b = vec![1.0, 2.0]; + let results = rolling_cosine_similarity(&a, &b, 3); + assert!(results.is_err()); + } + + #[test] + fn test_rolling_different_lengths() { + let a = vec![1.0, 2.0, 3.0]; + let b = vec![1.0, 2.0]; + let results = rolling_cosine_similarity(&a, &b, 2); + assert!(results.is_err()); + } + + #[test] + fn test_rolling_zero_window() { + let a = vec![0.0, 0.0, 1.0, 1.0]; + let b = vec![0.0, 0.0, 1.0, 1.0]; + let results = rolling_cosine_similarity(&a, &b, 2).unwrap(); + assert_eq!(results.len(), 4); + assert!(results[0].is_nan()); + assert!(results[3].is_nan()); + assert_eq!(results[1], 0.0, "{:?}", results); + assert_eq!(results[2], 1.0, "{:?}", results); + } +} diff --git a/src/utils/dtw.rs b/src/utils/dtw.rs new file mode 100644 index 0000000..a3cf3be --- /dev/null +++ b/src/utils/dtw.rs @@ -0,0 +1,287 @@ +use crate::errors::{ + DataProcessingError, + Result, +}; +use std::ops::{ + Add, + Sub, +}; + +/// Defines how values should be combined when warping +pub trait WarpingStrategy { + /// Combines two values according to the warping strategy + fn combine(&self, current: f64, new_value: f64) -> f64; + + /// Provides the initial value for the warping operation + fn initial_value(&self) -> f64; +} + +pub trait WarpingX< + T: PartialOrd + Copy + Clone + std::ops::Sub + std::ops::Add, +> +{ + fn maxval() -> T; +} + +impl WarpingX for f64 { + fn maxval() -> f64 { + f64::MAX + } +} + +impl WarpingX for u64 { + fn maxval() -> u64 { + u64::MAX + } +} + +impl WarpingX for u32 { + fn maxval() -> u32 { + u32::MAX + } +} + +/// Strategy that keeps the maximum value when warping +#[derive(Debug, Clone, Copy)] +pub struct MaxWarping; + +impl WarpingStrategy for MaxWarping { + fn combine(&self, current: f64, new_value: f64) -> f64 { + current.max(new_value) + } + + fn initial_value(&self) -> f64 { + f64::NEG_INFINITY + } +} + +/// Strategy that adds values when warping +#[derive(Debug, Clone, Copy)] +pub struct AddWarping; + +impl WarpingStrategy for AddWarping { + fn combine(&self, current: f64, new_value: f64) -> f64 { + if current == self.initial_value() { + new_value + } else { + current + new_value + } + } + + fn initial_value(&self) -> f64 { + 0.0 + } +} + +/// Generic Dynamic Time Warping implementation that uses a specified warping strategy +pub fn dtw_with_strategy< + S: WarpingStrategy, + T: WarpingX + PartialOrd + Copy + Clone + Sub + Add, +>( + ref_x: &[T], + target_x: &[T], + target_vals: &[f64], + strategy: &S, +) -> Result> { + // Check if vectors have the same length and are not empty + if target_vals.len() != target_x.len() { + return Err(DataProcessingError::ExpectedVectorSameLength( + target_vals.len(), + target_x.len(), + ) + .into()); + } + + // Initialize output with strategy's initial value + let mut output = vec![strategy.initial_value(); ref_x.len()]; + let defval = T::maxval(); + + let mut target_i = 0; + for (ref_i, ref_x_val) in ref_x.iter().enumerate() { + let next_ref_val = ref_x.get(ref_i + 1).unwrap_or(&defval); + // 1. If out target is lower than the current reference add. + // 2. If our value is between the current and next reference add to the closest one. + // 3. If our value is larget than the next reference, skip. + // Once we exhaust the target values add everything to the last one. + + while target_i < target_x.len() && target_x[target_i] < *ref_x_val { + output[ref_i] = strategy.combine(output[ref_i], target_vals[target_i]); + target_i += 1; + } + + while target_i < target_x.len() && target_x[target_i] < *next_ref_val { + let left_diff = target_x[target_i] - *ref_x_val; + let right_diff = *next_ref_val - target_x[target_i]; + if left_diff < right_diff { + output[ref_i] = strategy.combine(output[ref_i], target_vals[target_i]); + } else { + output[ref_i + 1] = strategy.combine(output[ref_i + 1], target_vals[target_i]); + } + target_i += 1; + } + } + + Ok(output) +} + +/// Dynamic Time Warping to max +/// +/// Attempts to align the values in `target_vals` which correspond +/// to the positions in `target_x` to the positions in `ref_x`. +/// +/// This version preseves the maximum value of the `target_vals` +/// in each position of the `target_x` array. +/// +/// # Note +/// This assumes that `ref_x` and `target_x` are sorted (monotonically increasing). +/// +/// Thus .... If the reference is shorter: +/// +/// If ref_x = [1, 2, 3, 4, 5, 6, 7, 8, 10] +/// If target_x = [1, 2, 4, 5, 6, 7, 10] +/// If target_vals = [5, 3, 2, 1, 2, 4, 9] +/// +/// Then the output would be: +/// [5, 3, 3, 2, 1, 2, 4, 4, 9] // Length = ref_x.len() +/// +/// Thus .... If the reference is longer: +/// +/// If ref_x = [1, 2, 4, 5, 6, 7, 10] +/// If target_x = [1, 2, 3, 4, 5, 6, 7, 8, 10] +/// If target_vals = [5, 3, 1, 2, 1, 2, 4, 4, 9] +/// +/// Then the output would be: +/// [5, 3, 2, 1, 2, 4, 9] // Length = ref_x.len() +pub fn dtw_max + PartialOrd + Copy + Clone + Sub + Add>( + ref_x: &[T], + target_x: &[T], + target_vals: &[f64], +) -> Result> { + dtw_with_strategy(ref_x, target_x, target_vals, &MaxWarping) +} + +/// Dynamic Time Warping to Sum +/// +/// Attempts to align the values in `target_vals` which correspond +/// to the positions in `target_x` to the positions in `ref_x`. +/// +/// This version preseves the maximum value of the `target_vals` +/// in each position of the `target_x` array. +/// +/// # Note +/// This assumes that `ref_x` and `target_x` are sorted (monotonically increasing). +/// +/// Thus .... If the reference is shorter: +/// +/// If ref_x = [1, 2, 3, 4, 5, 6, 7, 8, 10] +/// If target_x = [1, 2, 4, 5, 6, 7, 10] +/// If target_vals = [5, 3, 2, 1, 2, 4, 9] +/// +/// Then the output would be: +/// [5, 3, 3, 2, 1, 2, 4, 4, 9] // Length = ref_x.len() +/// +/// Thus .... If the reference is longer: +/// +/// If ref_x = [1, 2, 4, 5, 6, 7, 10] +/// If target_x = [1, 2, 3, 4, 5, 6, 7, 8, 10] +/// If target_vals = [5, 3, 1, 2, 1, 2, 4, 4, 9] +/// +/// Then the output would be: +/// [5, 4, 2, 1, 2, 4, 13] // Length = ref_x.len() +pub fn dtw_add + PartialOrd + Copy + Clone + Sub + Add>( + ref_x: &[T], + target_x: &[T], + target_vals: &[f64], +) -> Result> { + dtw_with_strategy(ref_x, target_x, target_vals, &AddWarping) +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + #[rustfmt::skip] + fn test_dtw_max_reference_shorter() { + let ref_x = vec![1.0, 2.0, 4.0, 5.0, 6.0, 7.0, 10.0]; + let target_x = vec![1.1, 2.1, 3.1, 4.1, 5.1, 6.1, 7.1, 8.1, 10.1]; + let target_vals = vec![5.0, 3.0, 1.0, 2.0, 1.0, 2.0, 4.0, 11.0,9.0]; + // -> <- + let expected = vec![5.0, 3.0, 2.0, 1.0, 2.0, 11.0, 9.0]; + + let result = dtw_max(&ref_x, &target_x, &target_vals).unwrap(); + assert_eq!(ref_x.len(), result.len()); + assert_eq!(result, expected, "Expected {:?} got {:?}", result, expected); + } + + #[test] + #[rustfmt::skip] + fn test_dtw_max_reference_longer() { + let ref_x = vec![1.0, 2.0, 4.0, 5.0, 6.0, 7.0, 10.0]; + let target_x = vec![1.1, 2.1, 3.1, 4.1, 5.1, 6.1, 7.1, 8.1, 10.1]; + let target_vals = vec![5.0, 1.0, 3.0, 2.0, 1.0, 2.0, 7.0, 11.0, 9.0]; + // -> <- + let expected = vec![5.0, 1.0, 3.0, 1.0, 2.0, 11.0, 9.0]; + + let result = dtw_max(&ref_x, &target_x, &target_vals).unwrap(); + assert_eq!(ref_x.len(), result.len()); + assert_eq!(result, expected, "Expected {:?} got {:?}", result, expected); + } + + #[test] + #[rustfmt::skip] + fn test_dtw_add_reference_shorter() { + let ref_x = vec![1.0, 2.0, 4.0, 5.0, 6.0, 7.0, 10.0]; + let target_x = vec![1.1, 2.1, 3.1, 4.1, 5.1, 6.1, 7.1, 8.1, 10.1]; + let target_vals = vec![5.0, 3.0, 1.0, 2.0, 1.0, 2.0, 4.0, 4.0, 9.0]; + // -> <- + let expect_out = vec![5.0, 3.0, 3.0, 1.0, 2.0, 8.0, 9.0]; + // Here 3 and 4 should add to the same value (of 4), same for 7 and 8. + + let result = dtw_add(&ref_x, &target_x, &target_vals).unwrap(); + assert_eq!(ref_x.len(), result.len()); + // Values get added when they map to the same reference point + for (l, r) in result.iter().zip(expect_out.iter()) { + assert!( + (l - r).abs() < 1e-6, + "Expected {:?} got {:?}", + result, + expect_out + ); + } + } + + #[test] + fn test_custom_strategy() { + // Example of a custom strategy that multiplies values + struct MultiplyWarping; + impl WarpingStrategy for MultiplyWarping { + fn combine(&self, current: f64, new_value: f64) -> f64 { + if current == self.initial_value() { + new_value + } else { + current * new_value + } + } + + fn initial_value(&self) -> f64 { + 1.0 + } + } + + let ref_x = vec![1.0, 2.0, 3.0]; + let target_x = vec![1.0, 1.1, 2.0, 2.1, 3.0]; + let target_vals = vec![2.0, 2.0, 3.0, 10.0, 4.0]; + + let result = dtw_with_strategy(&ref_x, &target_x, &target_vals, &MultiplyWarping).unwrap(); + let expected_out = vec![4.0, 30.0, 4.0]; + for (l, r) in result.iter().zip(expected_out.iter()) { + assert!( + (l - r).abs() < 1e-6, + "Expected {:?} got {:?}", + result, + expected_out + ); + } + } +} diff --git a/src/utils/frame_processing.rs b/src/utils/frame_processing.rs new file mode 100644 index 0000000..5657bbb --- /dev/null +++ b/src/utils/frame_processing.rs @@ -0,0 +1,406 @@ +use crate::sort_vecs_by_first; +use tracing::{ + error, + info, + warn, +}; + +use super::tolerance_ranges::IncludedRange; + +pub type TofIntensityVecs = (Vec, Vec); +pub type CentroidedVecs = (TofIntensityVecs, Vec); + +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, + "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)); + } + ((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() + } +} + +// 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) -> 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(); + let ref_arrays = &peak_refs[reference_index]; + 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::(); + + 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 + // Pre-calculate indices and intensities for sorting + struct OrderItem { + global_idx: usize, + major_idx: usize, + minor_idx: usize, + intensity: u32, + } + + 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(); + } + + // Sort by intensity + order.sort_unstable_by(|a, b| b.intensity.cmp(&a.intensity)); + assert!(order[0].intensity > order[tot_size - 1].intensity); + + 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 item in order { + let major_idx = item.major_idx; + let minor_idx = item.minor_idx; + let this_intensity = item.intensity as u64; + + 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 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; + + // 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 + .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(); + } + + // 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 = tof; + let calc_ims = 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; + if num_added == max_peaks { + break; + } + } + + if global_num_touched == arr_len { + break; + } + } + + 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); + + 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, + ); + } + + 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); + } + + out +} + +#[cfg(test)] +mod tests { + use super::*; + + // Helper function to create a simple tolerance range for testing + fn test_tof_tolerance(tof: u32) -> IncludedRange { + let tolerance = 2; + (tof.saturating_sub(tolerance), tof.saturating_add(tolerance)).into() + } + + fn test_ims_tolerance(ims: usize) -> IncludedRange { + let tolerance = 1; + (ims.saturating_sub(tolerance), ims.saturating_add(tolerance)).into() + } + + // 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"); + // } +} diff --git a/src/utils/math.rs b/src/utils/math.rs index b55af29..03a491e 100644 --- a/src/utils/math.rs +++ b/src/utils/math.rs @@ -10,3 +10,20 @@ 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() + } +} + +/// 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() +} diff --git a/src/utils/mod.rs b/src/utils/mod.rs index 4807e91..dc4aadd 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -1,4 +1,9 @@ pub mod compress_explode; +pub mod correlation; pub mod display; +pub mod dtw; +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 53fd838..3e9643f 100644 --- a/src/utils/sorting.rs +++ b/src/utils/sorting.rs @@ -1,99 +1,93 @@ -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 -} - -/// Sorts all passed slices by the key function. +/// Macro that sorts an arbitrary number of vecs by a the values +/// first one. +/// +/// 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. /// -/// For a similar macro that works in slices of heterogeneous types, see `sort_by_indices_multi!`. +/// TODO: Make a variant that sort in parallel. +/// TODO: Add a parameter to specify ascending or descending. /// /// # 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]); -/// ``` +/// use timsquery::sort_vecs_by_first; /// -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); +/// 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!(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_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 = $rest; + assert_eq!(other_vec.len(), len, "All vectors must have the same length"); + indices.iter().map(|&i| other_vec[i]).collect::>() + }, )*) + }}; } -/// Macro that sorts an arbitrary number of slices by a key function applied to the -/// first slice. +/// Returns the top n elements of a slice. +/// +/// The indices of the elements are also returned. /// /// # Example /// ``` -/// use timsquery::sort_by_indices_multi; -/// use timsquery::utils::sorting::argsort_by; -/// -/// let mut va = vec![9, 8, 7]; -/// let mut vb = vec![1, 2, 3]; -/// let mut vc = vec!['a', 'b', 'c']; -/// let mut indices = argsort_by(&va, |x| *x); -/// sort_by_indices_multi!( indices, &mut va, &mut vb, &mut vc); +/// use timsquery::utils::sorting::top_n; /// -/// assert_eq!(va, vec![7, 8, 9]); -/// assert_eq!(vb, vec![3, 2, 1]); -/// assert_eq!(vc, vec!['c', 'b', 'a']); +/// let v = vec![1, 2, 10, 4, 5, 9, 7, 8, 2, 1]; +/// let (top, indices) = top_n(&v, 3); +/// assert_eq!(top, vec![10, 9, 8]); +/// assert_eq!(indices, vec![2, 5, 7]); /// ``` /// -/// -#[macro_export] -macro_rules! sort_by_indices_multi { - ($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; - } +/// 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)] @@ -101,44 +95,49 @@ 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]); + 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_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]); + 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_argsort_by() { - let va = vec![1, 2, 3, 4]; - let indices = argsort_by(&va, |x| *x); - assert_eq!(indices, vec![0, 1, 2, 3]); + 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]); } #[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]); + 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]); } } diff --git a/src/utils/tolerance_ranges.rs b/src/utils/tolerance_ranges.rs new file mode 100644 index 0000000..fcd9ff2 --- /dev/null +++ b/src/utils/tolerance_ranges.rs @@ -0,0 +1,90 @@ +use timsrust::converters::{ + ConvertableDomain, + Scan2ImConverter, + Tof2MzConverter, +}; + +#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)] +pub struct IncludedRange(pub T, pub T); + +// 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 From> for (T, T) { + fn from(val: IncludedRange) -> Self { + (val.0, val.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).into() +} + +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).into() +} + +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); + IncludedRange::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, +) -> 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; + // 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).into() + } else { + (scan_min, scan_max).into() + } +} diff --git a/trace-1730278950486075.json b/trace-1730278950486075.json new file mode 100644 index 0000000..3426beb --- /dev/null +++ b/trace-1730278950486075.json @@ -0,0 +1,18837 @@ +[ +{"args":{"name":"main"},"name":"thread_name","ph":"M","pid":1,"tid":0}, +{".file":"src/queriable_tims_data/queriable_tims_data.rs",".line":74,"cat":"timsquery::queriable_tims_data::queriable_tims_data","name":"event src/queriable_tims_data/queriable_tims_data.rs:74","ph":"i","pid":1,"s":"t","tid":0,"ts":39675871.584}, +{".file":"src/queriable_tims_data/queriable_tims_data.rs",".line":80,"cat":"timsquery::queriable_tims_data::queriable_tims_data","name":"event src/queriable_tims_data/queriable_tims_data.rs:80","ph":"i","pid":1,"s":"t","tid":0,"ts":39675906.75}, 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