Merge pull request #28 from MannLabs/develop

Develop

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "timsrust"
-version = "0.3.0"
+version = "0.4.0"
 edition = "2021"
 description = "A crate to read Bruker timsTOF data"
 license = "Apache-2.0"
@@ -14,18 +14,22 @@ keywords = ["MS", "LC-TIMS-TOF", "PASEF"]
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-byteorder = "1.4.3"
-zstd = "0.12.3"
-rusqlite = { version = "0.29.0", features = ["bundled"] }
-rayon = "1.5"
+zstd = "0.13.2"
+rayon = "1.10.0"
 linreg = "0.2.0"
 bytemuck = "1.13.1"
-parquet = "42.0.0"
 thiserror = "1.0.0"
 memmap2 = "0.9.3"
+rusqlite = { version = "0.31.0", features = ["bundled"], optional = true}
+parquet = { version = "42.0.0", optional = true }
+
+[features]
+tdf = ["rusqlite"]
+minitdf = ["parquet"]
+default = ["tdf", "minitdf"]
 
 [dev-dependencies]
-criterion = { version = "0.4", features = ["html_reports"] }
+criterion = { version = "0.5.1", features = ["html_reports"] }
 
 [[bench]]
 name = "speed_performance"

README.md

@@ -6,6 +6,10 @@
 
 A crate to read Bruker TimsTof data.
 
+## Stability
+
+**NOTE**: TimsRust does not yet have a stable version! Use with caution.
+
 ## Installation
 
 Add this crate to your `Cargo.toml`:
@@ -43,3 +47,14 @@ Two file formats are supported:
 ## Python bindings
 
 The [timsrust_pyo3](https://github.com/jspaezp/timsrust_pyo3) package is an example of how the performance of TimsRust can be utilized in Python
+
+## Planned changes for future versions
+TODO
+* Improve docs
+* Improve tests
+* Pase CompressionType1
+* Make Path of TimsTOF data into special type
+* Single access point for all readers?
+* Few unchecked unwraps left
+* Queryable data in all dimensions
+* ...

benches/speed_performance.rs

@@ -1,93 +1,113 @@
 use criterion::{black_box, criterion_group, criterion_main, Criterion};
-use timsrust::FileReader;
+use rayon::iter::ParallelIterator;
+#[cfg(feature = "tdf")]
+use timsrust::readers::FrameReader;
+use timsrust::readers::{SpectrumReader, SpectrumReaderConfig};
 
 const DDA_TEST: &str =
-    "/mnt/c/Users/Sander.Willems/Documents/data/tims05_300SPD/20230505_TIMS05_PaSk_MA_HeLa_6min_ddaP_S1-C10_1_2323.d/";
+    "/mnt/d/data/mpib/tims05_300SPD/20230505_TIMS05_PaSk_MA_HeLa_6min_ddaP_S1-C10_1_2323.d/";
 const DIA_TEST: &str =
     "/mnt/c/Users/Sander.Willems/Documents/data/20230505_TIMS05_PaSk_SA_HeLa_6min_diaP_8scans_S1-D3_1_2329.d/";
 const SYP_TEST: &str =
     "/mnt/c/Users/Sander.Willems/Documents/data/20230505_TIMS05_PaSk_SA_HeLa_6min_syP_5scans_30Da_S1-D4_1_2330.d/";
 
-fn read_all_frames(file_reader: &FileReader) {
-    file_reader.read_all_frames();
+#[cfg(feature = "tdf")]
+fn read_all_frames(frame_reader: &FrameReader) {
+    frame_reader.get_all();
 }
 
-fn read_all_ms1_frames(file_reader: &FileReader) {
-    file_reader.read_all_ms1_frames();
+#[cfg(feature = "tdf")]
+fn read_all_ms1_frames(frame_reader: &FrameReader) {
+    frame_reader.get_all_ms1();
 }
 
-fn read_all_ms2_frames(file_reader: &FileReader) {
-    file_reader.read_all_ms2_frames();
+#[cfg(feature = "tdf")]
+fn read_all_ms2_frames(frame_reader: &FrameReader) {
+    frame_reader.get_all_ms2();
 }
 
-fn read_all_spectra(file_reader: &FileReader) {
-    file_reader.read_all_spectra();
+fn read_all_spectra(spectrum_reader: &SpectrumReader) {
+    spectrum_reader.get_all();
 }
 
-fn criterion_benchmark_dda(c: &mut Criterion) {
+#[cfg(feature = "tdf")]
+fn criterion_benchmark_dda_frames(c: &mut Criterion) {
     // c.bench_function("fib 20", |b| b.iter(|| fibonacci(black_box(20))));
     let mut group = c.benchmark_group("sample-size-example");
     group.significance_level(0.001).sample_size(10);
     let d_folder_name: &str = DDA_TEST;
-    let file_reader: FileReader =
-        FileReader::new(d_folder_name.to_string()).unwrap();
+    let frame_reader = FrameReader::new(d_folder_name).unwrap();
     group.bench_function("DDA read_all_frames 6m", |b| {
-        b.iter(|| read_all_frames(black_box(&file_reader)))
+        b.iter(|| read_all_frames(black_box(&frame_reader)))
     });
     group.bench_function("DDA read_all_ms1_frames 6m", |b| {
-        b.iter(|| read_all_ms1_frames(black_box(&file_reader)))
+        b.iter(|| read_all_ms1_frames(black_box(&frame_reader)))
     });
     group.bench_function("DDA read_all_ms2_frames 6m", |b| {
-        b.iter(|| read_all_ms2_frames(black_box(&file_reader)))
+        b.iter(|| read_all_ms2_frames(black_box(&frame_reader)))
     });
+    group.finish();
+}
+
+#[cfg(feature = "tdf")]
+fn criterion_benchmark_dda_spectra(c: &mut Criterion) {
+    // c.bench_function("fib 20", |b| b.iter(|| fibonacci(black_box(20))));
+    let mut group = c.benchmark_group("sample-size-example");
+    group.significance_level(0.001).sample_size(10);
+    let d_folder_name: &str = DDA_TEST;
+    let spectrum_reader = SpectrumReader::new(d_folder_name).unwrap();
     group.bench_function("DDA read_all_spectra 6m", |b| {
-        b.iter(|| read_all_spectra(black_box(&file_reader)))
+        b.iter(|| read_all_spectra(black_box(&spectrum_reader)))
     });
     group.finish();
 }
 
+#[cfg(feature = "tdf")]
 fn criterion_benchmark_dia(c: &mut Criterion) {
     // c.bench_function("fib 20", |b| b.iter(|| fibonacci(black_box(20))));
     let mut group = c.benchmark_group("sample-size-example");
     group.significance_level(0.001).sample_size(10);
     let d_folder_name: &str = DIA_TEST;
-    let file_reader: FileReader =
-        FileReader::new(d_folder_name.to_string()).unwrap();
+    let frame_reader = FrameReader::new(d_folder_name).unwrap();
+    let spectrum_reader = SpectrumReader::new(d_folder_name).unwrap();
     group.bench_function("DIA read_all_frames 6m", |b| {
-        b.iter(|| read_all_frames(black_box(&file_reader)))
+        b.iter(|| read_all_frames(black_box(&frame_reader)))
     });
     group.bench_function("DIA read_all_ms1_frames 6m", |b| {
-        b.iter(|| read_all_ms1_frames(black_box(&file_reader)))
+        b.iter(|| read_all_ms1_frames(black_box(&frame_reader)))
     });
     group.bench_function("DIA read_all_ms2_frames 6m", |b| {
-        b.iter(|| read_all_ms2_frames(black_box(&file_reader)))
+        b.iter(|| read_all_ms2_frames(black_box(&frame_reader)))
     });
     group.finish();
 }
 
+#[cfg(feature = "tdf")]
 fn criterion_benchmark_syp(c: &mut Criterion) {
     // c.bench_function("fib 20", |b| b.iter(|| fibonacci(black_box(20))));
     let mut group = c.benchmark_group("sample-size-example");
     group.significance_level(0.001).sample_size(10);
     let d_folder_name: &str = SYP_TEST;
-    let file_reader: FileReader =
-        FileReader::new(d_folder_name.to_string()).unwrap();
+    let frame_reader = FrameReader::new(d_folder_name).unwrap();
+    let spectrum_reader = SpectrumReader::new(d_folder_name).unwrap();
     group.bench_function("SYP read_all_frames 6m", |b| {
-        b.iter(|| read_all_frames(black_box(&file_reader)))
+        b.iter(|| read_all_frames(black_box(&frame_reader)))
     });
     group.bench_function("SYP read_all_ms1_frames 6m", |b| {
-        b.iter(|| read_all_ms1_frames(black_box(&file_reader)))
+        b.iter(|| read_all_ms1_frames(black_box(&frame_reader)))
     });
     group.bench_function("SYP read_all_ms2_frames 6m", |b| {
-        b.iter(|| read_all_ms2_frames(black_box(&file_reader)))
+        b.iter(|| read_all_ms2_frames(black_box(&frame_reader)))
     });
     group.finish();
 }
 
+#[cfg(feature = "tdf")]
 criterion_group!(
     benches,
-    criterion_benchmark_dda,
+    criterion_benchmark_dda_spectra,
     // criterion_benchmark_dia,
     // criterion_benchmark_syp
 );
+#[cfg(feature = "tdf")]
 criterion_main!(benches);

src/domain_converters.rs

@@ -10,4 +10,6 @@ pub use tof_to_mz::Tof2MzConverter;
 /// Convert from one domain (e.g. Time of Flight) to another (m/z).
 pub trait ConvertableDomain {
     fn convert<T: Into<f64> + Copy>(&self, value: T) -> f64;
+
+    fn invert<T: Into<f64> + Copy>(&self, value: T) -> f64;
 }

src/domain_converters/frame_to_rt.rs

@@ -1,5 +1,5 @@
 /// A converter from Frame -> retention time.
-#[derive(Debug, Clone)]
+#[derive(Debug, Default, Clone, PartialEq)]
 pub struct Frame2RtConverter {
     rt_values: Vec<f64>,
 }
@@ -16,4 +16,20 @@ impl super::ConvertableDomain for Frame2RtConverter {
         let upper_value: f64 = self.rt_values[value.into().ceil() as usize];
         (lower_value + upper_value) / 2.
     }
+    fn invert<T: Into<f64> + Copy>(&self, value: T) -> f64 {
+        let rt_value = value.into();
+        match self.rt_values.binary_search_by(|probe| {
+            probe.partial_cmp(&rt_value).expect("Cannot handle NaNs")
+        }) {
+            Ok(index) => index as f64,
+            Err(index) => match index {
+                _ if (index > 0) && (index < self.rt_values.len()) => {
+                    let start = self.rt_values[index - 1];
+                    let end = self.rt_values[index];
+                    index as f64 + (rt_value - start) / (end - start)
+                },
+                _ => index as f64,
+            },
+        }
+    }
 }

src/domain_converters/scan_to_im.rs

@@ -1,5 +1,5 @@
 /// A converter from Scan -> (inversed) ion mobility.
-#[derive(Debug, Clone)]
+#[derive(Debug, Default, Clone, Copy, PartialEq)]
 pub struct Scan2ImConverter {
     scan_intercept: f64,
     scan_slope: f64,
@@ -22,7 +22,12 @@ impl Scan2ImConverter {
 
 impl super::ConvertableDomain for Scan2ImConverter {
     fn convert<T: Into<f64> + Copy>(&self, value: T) -> f64 {
-        let scan_index_f64: f64 = value.into();
-        self.scan_intercept + self.scan_slope * scan_index_f64
+        let scan_index: f64 = value.into();
+        self.scan_intercept + self.scan_slope * scan_index
+    }
+
+    fn invert<T: Into<f64> + Copy>(&self, value: T) -> f64 {
+        let im_value: f64 = value.into();
+        (im_value - self.scan_intercept) / self.scan_slope
     }
 }

src/domain_converters/tof_to_mz.rs

@@ -1,7 +1,7 @@
 use linreg::linear_regression;
 
 /// A converter from TOF -> m/z.
-#[derive(Debug, Clone)]
+#[derive(Debug, Default, Clone, Copy, PartialEq)]
 pub struct Tof2MzConverter {
     tof_intercept: f64,
     tof_slope: f64,
@@ -22,7 +22,7 @@ impl Tof2MzConverter {
         }
     }
 
-    pub fn from_pairs(data: &Vec<(f64, u32)>) -> Self {
+    pub fn regress_from_pairs(data: &Vec<(f64, u32)>) -> Self {
         let x: Vec<u32> = data.iter().map(|(_, x_val)| *x_val).collect();
         let y: Vec<f64> =
             data.iter().map(|(y_val, _)| (*y_val).sqrt()).collect();
@@ -36,7 +36,11 @@ impl Tof2MzConverter {
 
 impl super::ConvertableDomain for Tof2MzConverter {
     fn convert<T: Into<f64> + Copy>(&self, value: T) -> f64 {
-        let tof_index_f64: f64 = value.into();
-        (self.tof_intercept + self.tof_slope * tof_index_f64).powi(2)
+        let tof_index: f64 = value.into();
+        (self.tof_intercept + self.tof_slope * tof_index).powi(2)
+    }
+    fn invert<T: Into<f64> + Copy>(&self, value: T) -> f64 {
+        let mz_value: f64 = value.into();
+        (mz_value.sqrt() - self.tof_intercept) / self.tof_slope
     }
 }

src/errors.rs

@@ -1,16 +1,23 @@
-use crate::{
-    file_readers,
-    // io::readers::common::{sql_reader::SqlError, tdf_blobs::TdfBlobError},
+#[cfg(feature = "tdf")]
+use crate::io::readers::{
+    FrameReaderError, MetadataReaderError, QuadrupoleSettingsReaderError,
 };
+use crate::io::readers::{PrecursorReaderError, SpectrumReaderError};
 
 /// An error that is produced by timsrust (uses [thiserror]).
 #[derive(thiserror::Error, Debug)]
-pub enum Error {
-    /// An error to indicate a path is not a Bruker File Format.
-    #[error("FileFormatError: {0}")]
-    FileFormatError(#[from] file_readers::FileFormatError),
-    // #[error("SqlError: {0}")]
-    // SqlError(#[from] SqlError),
-    // #[error("BinError: {0}")]
-    // BinError(#[from] TdfBlobError),
+pub enum TimsRustError {
+    #[cfg(feature = "tdf")]
+    #[error("{0}")]
+    FrameReaderError(#[from] FrameReaderError),
+    #[error("{0}")]
+    SpectrumReaderError(#[from] SpectrumReaderError),
+    #[cfg(feature = "tdf")]
+    #[error("{0}")]
+    MetadataReaderError(#[from] MetadataReaderError),
+    #[error("{0}")]
+    PrecursorReaderError(#[from] PrecursorReaderError),
+    #[cfg(feature = "tdf")]
+    #[error("{0}")]
+    QuadrupoleSettingsReaderError(#[from] QuadrupoleSettingsReaderError),
 }