quick bug fixes

changelog.md

@@ -1,4 +1,11 @@
-# Next Release
+# Version 1.1.6
+
+- Fixed Process button from appearing when no files are selected
+- Fix for instand child process crash on Windows
+- Added L_FREQ and H_FREQ parameters for more user control over low and high pass filtering
+
+
+# Version 1.1.5
 
 - Fixed Windows saves not being able to be opened by a Mac (hopefully the other way too!)
 - Added the option to right click loaded snirf files to reveal them in a file browser or delete them if they are no longer desired
@@ -14,6 +21,7 @@
 - Added a clickable link below the selected file's metadata explaining the independent parameters and why they are useful
 - Updated some tooltips to provide better, more accurate information
 - Added details about the processing steps and their order into the user guide
+- Changed the default bandpass filtering parameters
 
 
 # Version 1.1.4

flares.py

@@ -50,8 +50,8 @@ from scipy.spatial.distance import cdist
 
 # Backen visualization needed to be defined for pyinstaller
 import pyvistaqt # type: ignore
-# import vtkmodules.util.data_model
+import vtkmodules.util.data_model
-# import vtkmodules.util.execution_model
+import vtkmodules.util.execution_model
 
 # External library imports for mne
 from mne import (
@@ -130,6 +130,9 @@ TDDR: bool
 
 ENHANCE_NEGATIVE_CORRELATION: bool
 
+L_FREQ: float
+H_FREQ: float
+
 SHORT_CHANNEL: bool
 
 REMOVE_EVENTS: list
@@ -186,7 +189,9 @@ REQUIRED_KEYS: dict[str, Any] = {
     "SHORT_CHANNEL": bool,
     "REMOVE_EVENTS": list,
     "TIME_WINDOW_START": int,
-    "TIME_WINDOW_END": int
+    "TIME_WINDOW_END": int,
+    "L_FREQ": float,
+    "H_FREQ": float,
     # "REJECT_PAIRS": bool,
     # "FORCE_DROP_ANNOTATIONS": list,
     # "FILTER_LOW_PASS": float,
@@ -1069,9 +1074,17 @@ def filter_the_data(raw_haemo):
     fig_filter = raw_haemo.compute_psd(fmax=2).plot(
         average=True, xscale="log", color="r", show=False, amplitude=False
     )
-
+    
+    if L_FREQ == 0 and H_FREQ != 0:
+        raw_haemo = raw_haemo.filter(l_freq=None, h_freq=H_FREQ, h_trans_bandwidth=0.02)
+    elif L_FREQ != 0 and H_FREQ == 0:
+        raw_haemo = raw_haemo.filter(l_freq=L_FREQ, h_freq=None, l_trans_bandwidth=0.002)
+    elif L_FREQ != 0 and H_FREQ == 0:
+        raw_haemo = raw_haemo.filter(l_freq=L_FREQ, h_freq=H_FREQ, l_trans_bandwidth=0.002, h_trans_bandwidth=0.02)
+        
     #raw_haemo = raw_haemo.filter(l_freq=None, h_freq=0.4, h_trans_bandwidth=0.2)
-    raw_haemo = raw_haemo.filter(0.05, 0.7, h_trans_bandwidth=0.2, l_trans_bandwidth=0.02)
+    #raw_haemo = raw_haemo.filter(l_freq=None, h_freq=0.7, h_trans_bandwidth=0.2)
+    #raw_haemo = raw_haemo.filter(0.005, 0.7, h_trans_bandwidth=0.02, l_trans_bandwidth=0.002)
 
     raw_haemo.compute_psd(fmax=2).plot(
         average=True, xscale="log", axes=fig_filter.axes, color="g", amplitude=False, show=False
@@ -1517,7 +1530,6 @@ def fold_channels(raw: BaseRaw) -> None:
     # Format the output to make it slightly easier to read
 
     if True:
-
         num_channels = len(hbo_channel_names)
         rows, cols = 4, 7  # 6 rows and 4 columns of pie charts
         fig, axes = plt.subplots(rows, cols, figsize=(16, 10), constrained_layout=True)
@@ -2277,21 +2289,25 @@ def brain_landmarks_3d(raw_haemo: BaseRaw, show_optodes: Literal['sensors', 'lab
 
     
     if show_brodmann:# Add Brodmann labels
-        labels = cast(list[Label], read_labels_from_annot("fsaverage", "PALS_B12_Brodmann", "rh", verbose=False)) # type: ignore
+        labels = cast(list[Label], read_labels_from_annot("fsaverage", "PALS_B12_Brodmann", "lh", verbose=False)) # type: ignore
 
         label_colors = {
-            "Brodmann.39-rh": "blue",
+            "Brodmann.1-lh": "red",
-            "Brodmann.40-rh": "green",
+            "Brodmann.2-lh": "red",
-            "Brodmann.6-rh": "pink",
+            "Brodmann.3-lh": "red",
-            "Brodmann.7-rh": "orange",
+            "Brodmann.4-lh": "orange",
-            "Brodmann.17-rh": "red",
+            "Brodmann.5-lh": "green",
-            "Brodmann.1-rh": "yellow",
+            "Brodmann.6-lh": "yellow",
-            "Brodmann.2-rh": "yellow",
+            "Brodmann.7-lh": "green",
-            "Brodmann.3-rh": "yellow",
+            "Brodmann.17-lh": "blue",
-            "Brodmann.18-rh": "red",
+            "Brodmann.18-lh": "blue",
-            "Brodmann.19-rh": "red",
+            "Brodmann.19-lh": "blue",
-            "Brodmann.4-rh": "purple",
+            "Brodmann.39-lh": "purple",
-            "Brodmann.8-rh": "white"
+            "Brodmann.40-lh": "pink",
+            "Brodmann.42-lh": "white",
+            "Brodmann.44-lh": "white",
+            "Brodmann.48-lh": "white",
+
         }
 
         for label in labels:
@@ -2944,7 +2960,7 @@ def process_participant(file_path, progress_callback=None):
 
     # Step 11: Get short / long channels
     if SHORT_CHANNEL:
-        short_chans = get_short_channels(raw_haemo, max_dist=0.015)
+        short_chans = get_short_channels(raw_haemo, max_dist=0.02)
         fig_short_chans = short_chans.plot(duration=raw_haemo.times[-1], n_channels=raw_haemo.info['nchan'], title="Short Channels Only", show=False)
         fig_individual["short"] = fig_short_chans
     else:

main.py

@@ -123,7 +123,10 @@ SECTIONS = [
     {
         "title": "Filtering",
         "params": [
+            {"name": "L_FREQ", "default": 0.005, "type": float, "help": "Any frequencies lower than this value will be removed."},
+            {"name": "H_FREQ", "default": 0.7, "type": float, "help": "Any frequencies higher than this value will be removed."},
             #{"name": "FILTER", "default": True, "type": bool, "help": "Calculate Peak Spectral Power."},
+
         ]
     },
     {
@@ -4044,7 +4047,7 @@ class MainApplication(QMainWindow):
         self.button2.setMinimumSize(100, 40)
         self.button3.setMinimumSize(100, 40)
 
-        # self.button1.setVisible(False)
+        self.button1.setVisible(False)
         self.button3.setVisible(False) 
 
         self.button1.clicked.connect(self.on_run_task)