From d58e46b60a357aeed584e3609df0ea4eb9d6d5da Mon Sep 17 00:00:00 2001
From: Sander Willems <sander.willems@bruker.com>
Date: Tue, 3 Sep 2024 17:03:44 +0200
Subject: [PATCH] FEAT: add serialization to spectrum reader config

---
 src/domain_converters/scan_to_im.rs    | 4 ++++
 src/domain_converters/tof_to_mz.rs     | 3 +++
 src/io/readers/quad_settings_reader.rs | 4 ++++
 src/io/readers/spectrum_reader.rs      | 8 ++++++--
 4 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/domain_converters/scan_to_im.rs b/src/domain_converters/scan_to_im.rs
index 2a9d8bd..62433c9 100644
--- a/src/domain_converters/scan_to_im.rs
+++ b/src/domain_converters/scan_to_im.rs
@@ -1,5 +1,9 @@
+#[cfg(feature = "serialize")]
+use serde::{Deserialize, Serialize};
+
 /// A converter from Scan -> (inversed) ion mobility.
 #[derive(Debug, Default, Clone, Copy, PartialEq)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub struct Scan2ImConverter {
     scan_intercept: f64,
     scan_slope: f64,
diff --git a/src/domain_converters/tof_to_mz.rs b/src/domain_converters/tof_to_mz.rs
index c42078b..8360704 100644
--- a/src/domain_converters/tof_to_mz.rs
+++ b/src/domain_converters/tof_to_mz.rs
@@ -1,7 +1,10 @@
 use linreg::linear_regression;
+#[cfg(feature = "serialize")]
+use serde::{Deserialize, Serialize};
 
 /// A converter from TOF -> m/z.
 #[derive(Debug, Default, Clone, Copy, PartialEq)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub struct Tof2MzConverter {
     tof_intercept: f64,
     tof_slope: f64,
diff --git a/src/io/readers/quad_settings_reader.rs b/src/io/readers/quad_settings_reader.rs
index 147ab84..eb67dfc 100644
--- a/src/io/readers/quad_settings_reader.rs
+++ b/src/io/readers/quad_settings_reader.rs
@@ -1,3 +1,5 @@
+#[cfg(feature = "serialize")]
+use serde::{Deserialize, Serialize};
 use std::path::Path;
 
 use crate::{
@@ -151,6 +153,7 @@ type ScanSpanStep = (usize, usize);
 /// 100 and step 80 between their in the scan number.
 ///
 #[derive(Debug, Copy, Clone)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub enum QuadWindowExpansionStrategy {
     None,
     Even(usize),
@@ -171,6 +174,7 @@ pub enum FrameWindowSplittingStrategy {
 }
 
 #[derive(Debug, Clone, Copy)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub enum FrameWindowSplittingConfiguration {
     Quadrupole(QuadWindowExpansionStrategy),
     Window(QuadWindowExpansionStrategy),
diff --git a/src/io/readers/spectrum_reader.rs b/src/io/readers/spectrum_reader.rs
index 5a625f1..7b125ab 100644
--- a/src/io/readers/spectrum_reader.rs
+++ b/src/io/readers/spectrum_reader.rs
@@ -8,6 +8,8 @@ use core::fmt;
 #[cfg(feature = "minitdf")]
 use minitdf::{MiniTDFSpectrumReader, MiniTDFSpectrumReaderError};
 use rayon::iter::{IntoParallelIterator, ParallelIterator};
+#[cfg(feature = "serialize")]
+use serde::{Deserialize, Serialize};
 use std::path::{Path, PathBuf};
 #[cfg(feature = "tdf")]
 use tdf::{TDFSpectrumReader, TDFSpectrumReaderError};
@@ -135,7 +137,8 @@ pub enum SpectrumReaderError {
     SpectrumReaderFileError(PathBuf),
 }
 
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Copy)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub struct SpectrumProcessingParams {
     pub smoothing_window: u32,
     pub centroiding_window: u32,
@@ -154,7 +157,8 @@ impl Default for SpectrumProcessingParams {
     }
 }
 
-#[derive(Debug, Default, Clone)]
+#[derive(Debug, Default, Clone, Copy)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub struct SpectrumReaderConfig {
     pub spectrum_processing_params: SpectrumProcessingParams,
     #[cfg(feature = "tdf")]