Merge pull request #111 from Roestlab/bug/mrmpeakpicking_none_smoother

Bug/mrmpeakpicking none smoother

massdash/constants.py

@@ -24,4 +24,13 @@
 URL_TEST_PQP = "https://github.com/Roestlab/massdash/raw/dev/test/test_data/example_dia/openswath/lib/test.pqp"
 URL_TEST_RAW_MZML = "https://github.com/Roestlab/massdash/raw/dev/test/test_data/example_dia/raw/test_raw_1.mzML"
 URL_TEST_DREAMDIA_REPORT = "https://github.com/Roestlab/massdash/raw/dev/test/test_data/example_dia/dreamdia/test_dreamdia_report.tsv"
-URL_PRETRAINED_CONFORMER = "https://github.com/Roestlab/massdash/releases/download/v0.0.1-alpha/base_cape.onnx"
+URL_PRETRAINED_CONFORMER = "https://github.com/Roestlab/massdash/releases/download/v0.0.1-alpha/base_cape.onnx"
+
+######################
+## Data Handling
+
+# Data Smoothing
+SMOOTHING_DICT = {'No Smoothing': {'type': 'none'},
+                  'Savitzky-Golay': {'type': 'sgolay', 'sgolay_polynomial_order': 3, 'sgolay_frame_length': 11},
+                  'Gaussian': {'type': 'gauss', 'gaussian_sigma': 2.0, 'gaussian_window': 11}
+                 }

massdash/plotting/GenericPlotter.py

@@ -45,7 +45,7 @@ def __init__(self):
         self.subtitle = None
         self.x_axis_label = "Retention Time"
         self.y_axis_label = "Intensity"
-        self.smoothing_dict = {'type': ['sgolay', 'gaussian'], 'sgolay_polynomial_order': 3,
+        self.smoothing_dict = {'type': ['sgolay', 'gauss'], 'sgolay_polynomial_order': 3,
                                'sgolay_frame_length': 11, 'gaussian_sigma': 2.0, 'gaussian_window': 11}
 
         self.x_range = None

massdash/plotting/InteractivePlotter.py

@@ -103,7 +103,7 @@ def process_chrom(self, p: figure, chrom: Chromatogram, label: str, color: str='
                 else:
                     raise ValueError(error_message)
 
-        elif self.smoothing_dict['type'] == 'gaussian':
+        elif self.smoothing_dict['type'] == 'gauss':
             try:
                 window = gaussian(self.smoothing_dict['gaussian_window'], std=self.smoothing_dict['gaussian_sigma'])
                 intensity = convolve(intensity, window, mode='same') / window.sum()

massdash/structs/TransitionGroup.py

@@ -181,7 +181,7 @@ def adjust_length(self, length: int) -> None:
 
     def plot(self, 
              transitionGroupFeatures: Optional[List[TransitionGroupFeature]] = None, 
-             smoothing: Optional[Literal['none', 'sgolay', 'gaussian']] = 'none',
+             smoothing: Optional[Literal['none', 'sgolay', 'gauss']] = 'none',
              gaussian_sigma: float = 2.0,
              gaussian_window: int = 11,
              sgolay_polynomial_order: int = 3,

massdash/ui/ChromatogramPlotUISettings.py

@@ -5,6 +5,9 @@
 
 import streamlit as st
 
+# Constants
+from ..constants import SMOOTHING_DICT
+
 class ChromatogramPlotUISettings:
     """
     A class for managing the settings for a chromatogram plot.
@@ -105,10 +108,10 @@ def create_ui(self, include_raw_data_settings: bool=False, is_ion_mobility_data:
                 self.set_y_range = st.checkbox("Share y-range", value=self.set_y_range, help="Share the y-range of the plots.")
 
             # Perform Smoothing of the chromatograms
-            self.do_smoothing = st.selectbox("Smoothing", ['none', 'sgolay', 'gaussian'], help="The type of smoothing to apply to the chromatograms.")
-
-            self.smoothing_dict['type'] = self.do_smoothing
-            if self.do_smoothing == 'sgolay':
+            self.do_smoothing = st.selectbox("Smoothing", list(SMOOTHING_DICT.keys()), help="The type of smoothing to apply to the chromatograms.")
+            
+            self.smoothing_dict = SMOOTHING_DICT[self.do_smoothing]
+            if self.smoothing_dict['type'] == 'sgolay':
                 # Create two columns for side-by-side widgets
                 col1, col2 = st.columns(2)
 
@@ -118,7 +121,7 @@ def create_ui(self, include_raw_data_settings: bool=False, is_ion_mobility_data:
                 # Add widget for sgolay_frame_length in the second column
                 self.smoothing_dict['sgolay_frame_length'] = col2.number_input("Frame Length", min_value=1, max_value=50, value=11, step=1, help="The length of the frame to use for smoothing the chromatograms.")
 
-            if self.do_smoothing == 'gaussian':
+            if self.smoothing_dict['type'] == 'gauss':
                 # Create two columns for side-by-side widgets
                 col1, col2 = st.columns(2)
 

massdash/ui/MRMTransitionGroupPickerUISettings.py

@@ -64,9 +64,13 @@ def create_ui(self, plot_settings: ChromatogramPlotUISettings):
                     self.sgolay_frame_length = st.number_input("Savitzky-Golay Frame Length", value=11, step=2, min_value=1, help="Savitzky-Golay frame length.")
                     self.sgolay_polynomial_order = st.number_input("Savitzky-Golay Polynomial Order", value=3, min_value=1, help="Savitzky-Golay polynomial order.")
         else:
-            self.smoother = plot_settings.do_smoothing
+            self.smoother = plot_settings.smoothing_dict['type']
             if self.smoother == "gauss":
-                self.gauss_width = st.number_input("Width of the Gaussian smoothing", min_value=0.0, value=30.0, help="Width of the Gaussian smoothing.")
+                self.gauss_width = plot_settings.smoothing_dict['gaussian_window']
             elif self.smoother == "sgolay":
                 self.sgolay_frame_length = plot_settings.smoothing_dict['sgolay_frame_length']
                 self.sgolay_polynomial_order = plot_settings.smoothing_dict['sgolay_polynomial_order']
+            elif self.smoother == "none":
+                self.smoother = "original"
+            else:
+                st.error(f"Unknown supported smoothing type for MRMTransitionGroupPicker: {self.smoother}. Needs to be one of 'Savitzky-Golay' or 'Gaussian'.")