CHORE: reorganize specrum reader code

MannLabs · Dec 4, 2024 · d4b71dd · d4b71dd
1 parent 3f49454
commit d4b71dd
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Showing 7 changed files with 132 additions and 111 deletions.
diff --git a/benches/speed_performance.rs b/benches/speed_performance.rs
@@ -2,7 +2,7 @@ use criterion::{black_box, criterion_group, criterion_main, Criterion};
 use rayon::iter::ParallelIterator;
 #[cfg(feature = "tdf")]
 use timsrust::readers::FrameReader;
-use timsrust::readers::{SpectrumReader, SpectrumReaderConfig};
+use timsrust::readers::SpectrumReader;
 
 const DDA_TEST: &str =
     "/mnt/d/data/mpib/tims05_300SPD/20230505_TIMS05_PaSk_MA_HeLa_6min_ddaP_S1-C10_1_2323.d/";

diff --git a/src/errors.rs b/src/errors.rs
@@ -2,7 +2,7 @@
 use crate::io::readers::{
     FrameReaderError, MetadataReaderError, QuadrupoleSettingsReaderError,
 };
-use crate::io::readers::{PrecursorReaderError, SpectrumReaderError};
+use crate::{io::readers::PrecursorReaderError, readers::SpectrumReaderError};
 
 /// An error that is produced by timsrust (uses [thiserror]).
 #[derive(thiserror::Error, Debug)]

diff --git a/src/io/readers/spectrum_reader.rs b/src/io/readers/spectrum_reader.rs
@@ -1,37 +1,35 @@
+mod builder;
+mod config;
+mod errors;
 #[cfg(feature = "minitdf")]
 mod minitdf;
+mod spectrum_trait;
 #[cfg(feature = "tdf")]
 mod tdf;
 
-#[cfg(feature = "minitdf")]
-use minitdf::{MiniTDFSpectrumReader, MiniTDFSpectrumReaderError};
-use rayon::prelude::*;
-#[cfg(feature = "serialize")]
-use serde::{Deserialize, Serialize};
-#[cfg(feature = "tdf")]
-use tdf::{TDFSpectrumReader, TDFSpectrumReaderError};
-
+use super::TimsTofPathLike;
 use crate::ms_data::Spectrum;
-
-#[cfg(feature = "tdf")]
-use super::FrameWindowSplittingConfiguration;
-use super::{TimsTofFileType, TimsTofPath, TimsTofPathLike};
+pub use builder::SpectrumReaderBuilder;
+pub use config::{SpectrumProcessingParams, SpectrumReaderConfig};
+pub use errors::SpectrumReaderError;
+use rayon::prelude::*;
+use spectrum_trait::SpectrumReaderTrait;
 
 pub struct SpectrumReader {
     spectrum_reader: Box<dyn SpectrumReaderTrait>,
 }
 
 impl SpectrumReader {
-    pub fn build() -> SpectrumReaderBuilder {
-        SpectrumReaderBuilder::default()
-    }
-
     pub fn new(
         path: impl TimsTofPathLike,
     ) -> Result<Self, SpectrumReaderError> {
         Self::build().with_path(path).finalize()
     }
 
+    pub fn build() -> SpectrumReaderBuilder {
+        SpectrumReaderBuilder::default()
+    }
+
     pub fn get(&self, index: usize) -> Result<Spectrum, SpectrumReaderError> {
         self.spectrum_reader.get(index)
     }
@@ -60,96 +58,3 @@ impl SpectrumReader {
         self.spectrum_reader.calibrate();
     }
 }
-
-#[derive(Debug, Default, Clone)]
-pub struct SpectrumReaderBuilder {
-    path: Option<TimsTofPath>,
-    config: SpectrumReaderConfig,
-}
-
-impl SpectrumReaderBuilder {
-    pub fn with_path(&self, path: impl TimsTofPathLike) -> Self {
-        // TODO
-        let path = Some(path.to_timstof_path().unwrap());
-        Self {
-            path,
-            ..self.clone()
-        }
-    }
-
-    pub fn with_config(&self, config: SpectrumReaderConfig) -> Self {
-        Self {
-            config: config,
-            ..self.clone()
-        }
-    }
-
-    pub fn finalize(self) -> Result<SpectrumReader, SpectrumReaderError> {
-        let path = match self.path {
-            None => return Err(SpectrumReaderError::NoPath),
-            Some(path) => path,
-        };
-        let spectrum_reader: Box<dyn SpectrumReaderTrait> =
-            match path.file_type() {
-                #[cfg(feature = "minitdf")]
-                TimsTofFileType::MiniTDF => {
-                    Box::new(MiniTDFSpectrumReader::new(path)?)
-                },
-                #[cfg(feature = "tdf")]
-                TimsTofFileType::TDF => {
-                    Box::new(TDFSpectrumReader::new(path, self.config)?)
-                },
-            };
-        let mut reader = SpectrumReader { spectrum_reader };
-        if self.config.spectrum_processing_params.calibrate {
-            reader.calibrate();
-        }
-        Ok(reader)
-    }
-}
-
-trait SpectrumReaderTrait: Sync + Send {
-    fn get(&self, index: usize) -> Result<Spectrum, SpectrumReaderError>;
-    fn len(&self) -> usize;
-    fn calibrate(&mut self);
-}
-
-#[derive(Debug, thiserror::Error)]
-pub enum SpectrumReaderError {
-    #[cfg(feature = "minitdf")]
-    #[error("{0}")]
-    MiniTDFSpectrumReaderError(#[from] MiniTDFSpectrumReaderError),
-    #[cfg(feature = "tdf")]
-    #[error("{0}")]
-    TDFSpectrumReaderError(#[from] TDFSpectrumReaderError),
-    #[error("No path provided")]
-    NoPath,
-}
-
-#[derive(Debug, Clone, Copy)]
-#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
-pub struct SpectrumProcessingParams {
-    pub smoothing_window: u32,
-    pub centroiding_window: u32,
-    pub calibration_tolerance: f64,
-    pub calibrate: bool,
-}
-
-impl Default for SpectrumProcessingParams {
-    fn default() -> Self {
-        Self {
-            smoothing_window: 1,
-            centroiding_window: 1,
-            calibration_tolerance: 0.1,
-            calibrate: false,
-        }
-    }
-}
-
-#[derive(Debug, Default, Clone, Copy)]
-#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
-pub struct SpectrumReaderConfig {
-    pub spectrum_processing_params: SpectrumProcessingParams,
-    #[cfg(feature = "tdf")]
-    pub frame_splitting_params: FrameWindowSplittingConfiguration,
-}
diff --git a/src/io/readers/spectrum_reader/builder.rs b/src/io/readers/spectrum_reader/builder.rs
@@ -0,0 +1,58 @@
+use crate::readers::{TimsTofFileType, TimsTofPath, TimsTofPathLike};
+
+use super::{
+    errors::SpectrumReaderError, SpectrumReader, SpectrumReaderConfig,
+    SpectrumReaderTrait,
+};
+
+#[cfg(feature = "minitdf")]
+use super::minitdf::MiniTDFSpectrumReader;
+#[cfg(feature = "tdf")]
+use super::tdf::TDFSpectrumReader;
+
+#[derive(Debug, Default, Clone)]
+pub struct SpectrumReaderBuilder {
+    path: Option<TimsTofPath>,
+    config: SpectrumReaderConfig,
+}
+
+impl SpectrumReaderBuilder {
+    pub fn with_path(&self, path: impl TimsTofPathLike) -> Self {
+        // TODO
+        let path = Some(path.to_timstof_path().unwrap());
+        Self {
+            path,
+            ..self.clone()
+        }
+    }
+
+    pub fn with_config(&self, config: SpectrumReaderConfig) -> Self {
+        Self {
+            config: config,
+            ..self.clone()
+        }
+    }
+
+    pub fn finalize(self) -> Result<SpectrumReader, SpectrumReaderError> {
+        let path = match self.path {
+            None => return Err(SpectrumReaderError::NoPath),
+            Some(path) => path,
+        };
+        let spectrum_reader: Box<dyn SpectrumReaderTrait> =
+            match path.file_type() {
+                #[cfg(feature = "minitdf")]
+                TimsTofFileType::MiniTDF => {
+                    Box::new(MiniTDFSpectrumReader::new(path)?)
+                },
+                #[cfg(feature = "tdf")]
+                TimsTofFileType::TDF => {
+                    Box::new(TDFSpectrumReader::new(path, self.config)?)
+                },
+            };
+        let mut reader = SpectrumReader { spectrum_reader };
+        if self.config.spectrum_processing_params.calibrate {
+            reader.calibrate();
+        }
+        Ok(reader)
+    }
+}
diff --git a/src/io/readers/spectrum_reader/config.rs b/src/io/readers/spectrum_reader/config.rs
@@ -0,0 +1,33 @@
+#[cfg(feature = "tdf")]
+use super::super::FrameWindowSplittingConfiguration;
+
+#[cfg(feature = "serialize")]
+use serde::{Deserialize, Serialize};
+
+#[derive(Debug, Clone, Copy)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+pub struct SpectrumProcessingParams {
+    pub smoothing_window: u32,
+    pub centroiding_window: u32,
+    pub calibration_tolerance: f64,
+    pub calibrate: bool,
+}
+
+impl Default for SpectrumProcessingParams {
+    fn default() -> Self {
+        Self {
+            smoothing_window: 1,
+            centroiding_window: 1,
+            calibration_tolerance: 0.1,
+            calibrate: false,
+        }
+    }
+}
+
+#[derive(Debug, Default, Clone, Copy)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+pub struct SpectrumReaderConfig {
+    pub spectrum_processing_params: SpectrumProcessingParams,
+    #[cfg(feature = "tdf")]
+    pub frame_splitting_params: FrameWindowSplittingConfiguration,
+}
diff --git a/src/io/readers/spectrum_reader/errors.rs b/src/io/readers/spectrum_reader/errors.rs
@@ -0,0 +1,16 @@
+#[cfg(feature = "minitdf")]
+use super::minitdf::MiniTDFSpectrumReaderError;
+#[cfg(feature = "tdf")]
+use super::tdf::TDFSpectrumReaderError;
+
+#[derive(Debug, thiserror::Error)]
+pub enum SpectrumReaderError {
+    #[cfg(feature = "minitdf")]
+    #[error("{0}")]
+    MiniTDFSpectrumReaderError(#[from] MiniTDFSpectrumReaderError),
+    #[cfg(feature = "tdf")]
+    #[error("{0}")]
+    TDFSpectrumReaderError(#[from] TDFSpectrumReaderError),
+    #[error("No path provided")]
+    NoPath,
+}
diff --git a/src/io/readers/spectrum_reader/spectrum_trait.rs b/src/io/readers/spectrum_reader/spectrum_trait.rs
@@ -0,0 +1,9 @@
+use crate::Spectrum;
+
+use super::errors::SpectrumReaderError;
+
+pub(crate) trait SpectrumReaderTrait: Sync + Send {
+    fn get(&self, index: usize) -> Result<Spectrum, SpectrumReaderError>;
+    fn len(&self) -> usize;
+    fn calibrate(&mut self);
+}