fixes before release

changelog.md

@@ -5,7 +5,7 @@
 - Optimized calculations being performed when calculating the Heart Rate to speed up step 5 by up to ~35% on a per-file basis
 - Optimized calculations being performed when running the General Linear Model to speed up step 5 by up to ~35% on a per-file basis
 - The Group Stats Viewer windows will now properly load the Right/Left or Front/Back fallback ROIs if JSON_LOCATION is not set
-- Changed the warning message for lots of short channels to be percentage based (25%) instead of numerical based (6)
+- Changed the warning message for lots of short channels and changed when it shows to be percentage based (35%) instead of numerical based (6)
 - Renames GENDER to SEX to better represent the values that the field expects and to be more BIDS compliant
 - Changed the Assign Groups by AGE window to now be the Assign Groups by Metadata window and added support for grouping by other metadata values
 - Added a new metadata value of HAND to allow for grouping participants based on their handiness
@@ -24,8 +24,10 @@
 - Fixed an issue where when loading a save file some list dropdowns could go blue and bold even if the value was default
 - Fixed an issue where the Analysis button would not be clickable if the user had previously pushed Clear. Fixes [Issue 83](https://git.research.dezeeuw.ca/tyler/flares/issues/83)
 - Fixed an issue where some popup windows would not properly display the application name when they would open
-- Fixed instances of the word MacOS to now read macOS to match Apple branding
+- Fixed an issue where the welcome dialog image would not display correctly on macOS
-- Fixed welcom dialog application image not displaying correctly on macOS
+- Fixed an issue where the Linux version would fail at 0 seconds when attempting to process files
+- Fixed an issue where fOLDing channels could cause the same channels to be repeated misaligning the labels
+- Fixed all instances of the word MacOS to now read macOS to match Apple branding
 
 
 # Version 1.5.2

flares.py

@@ -1840,7 +1840,8 @@ def fold_channels(raw: BaseRaw, p_name: str, atlas: str='Brodmann', progress_que
     channel_results = {}
     step_idx = 0
 
-    for cidx, channel_name in enumerate(hbo_channel_names):
+    for channel_name in hbo_channel_names:
+        cidx = raw.ch_names.index(channel_name)
         tbl = _source_detector_fold_table(
             raw, cidx, reference_locations, fold_tbl, interpolate=True
         )
@@ -2179,8 +2180,14 @@ def brain_3d_visualization(
 
 
 
-def brain_landmarks_3d(raw_haemo: BaseRaw, show_optodes: Literal['sensors', 'labels', 'none', 'all'] = 'all', show_brodmann: bool = True) -> None:
+def brain_landmarks_3d(raw_haemo: BaseRaw, show_optodes: Literal['sensors', 'labels', 'none', 'all'] = 'all', show_brodmann: bool = True, subjects_dir = None) -> None:
 
+    if subjects_dir is None:
+        subjects_dir = os.environ.get("SUBJECTS_DIR")
+        if subjects_dir is None:
+            subjects_dir = str(data_path()) + "/subjects" # type: ignore
+            os.environ["SUBJECTS_DIR"] = subjects_dir
+            
     brain = Brain("fsaverage", background="white", size=(800, 700))  # type: ignore
 
     distances = source_detector_distances(raw_haemo.info)

main.py

@@ -19,7 +19,7 @@ from queue import Empty
 from copy import deepcopy
 from pathlib import Path
 from datetime import datetime
-from multiprocessing import Process, current_process, freeze_support, Queue
+from multiprocessing import Process, current_process, freeze_support, Queue, set_start_method
 
 # External library imports
 import psutil
@@ -2038,7 +2038,7 @@ class MainApplication(QMainWindow):
         msgbox.setWindowTitle(f"Warning - {APP_NAME.upper()}")
         
         message = (
-            f"{APP_NAME.upper} has encountered an error processing the file {title}.<br><br>"
+            f"{APP_NAME.upper()} has encountered an error processing the file {title}.<br><br>"
             "This error was likely due to incorrect parameters on the right side of the screen and not an error with your data. "
             "Processing of the remaining files continues in the background and this participant will be ignored in the analysis. "
             f"If you think the parameters on the right side are correct for your data, raise an issue <a href='https://git.research.dezeeuw.ca/tyler/{APP_NAME}/issues'>here</a>.<br><br>"
@@ -2449,8 +2449,9 @@ def exception_hook(exc_type, exc_value, exc_traceback):
     show_critical_error(error_msg)
 
     # Exit the app after user acknowledges
-    sys.exit(1)
+    if getattr(sys, 'frozen', False):
-
+        sys.exit(1)
+    
 
 def show_critical_error(error_msg):
     msg_box = QMessageBox()
@@ -2459,22 +2460,25 @@ def show_critical_error(error_msg):
     
     if PLATFORM_NAME == "darwin":
         log_path = os.path.join(os.path.dirname(sys.executable), "../../../flares.log")
-        log_path2 = os.path.join(os.path.dirname(sys.executable), "../../../flares_error.log")
+        error_path = os.path.join(os.path.dirname(sys.executable), "../../../flares_error.log")
         save_path = os.path.join(os.path.dirname(sys.executable), "../../../flares_autosave.flare")
 
     else:
         log_path = os.path.join(os.getcwd(), "flares.log")
-        log_path2 = os.path.join(os.getcwd(), "flares_error.log")
+        error_path = os.path.join(os.getcwd(), "flares_error.log")
         save_path = os.path.join(os.getcwd(), "flares_autosave.flare")
 
 
-    shutil.copy(log_path, log_path2)
+    shutil.copy(log_path, error_path)
-    log_path2 = Path(log_path2).absolute().as_posix()
+    error_path = Path(error_path).absolute().as_posix()
     autosave_path = Path(save_path).absolute().as_posix()
-    log_link = f"file:///{log_path2}"
+    error_link = f"file:///{error_path}"
     autosave_link = f"file:///{autosave_path}"
-    
+
-    window.save_project(True) #TODO: If the window is the one to crash, the file can't get saved. Could be fine as the window is what was storing the data to begin with?
+    try:
+        window.project_manager.save_project(True)
+    except:
+        pass
 
     message = (
         f"{APP_NAME.upper()} has encountered an unrecoverable error and needs to close.<br><br>"
@@ -2482,7 +2486,7 @@ def show_critical_error(error_msg):
         "If the file was saved, it still may not be intact, openable, or contain the correct data. Use the autosave at your own discretion.<br><br>"
         f"This unrecoverable error was due to an error with {APP_NAME.upper()} and not your data.<br>"
         f"If this crash occured inside a [BETA] branch, it is likely to eventually be fixed.<br>"
-        f"Please raise an issue <a href='https://git.research.dezeeuw.ca/tyler/{APP_NAME}/issues'>here</a> and attach the error file located at <a href='{log_link}'>{log_path2}</a><br><br>"
+        f"Please raise an issue <a href='https://git.research.dezeeuw.ca/tyler/{APP_NAME}/issues'>here</a> and attach the error file located at <a href='{error_link}'>{error_path}</a><br><br>"
         f"<pre>{error_msg}</pre>"
     )
 
@@ -2583,6 +2587,7 @@ if __name__ == "__main__":
     config_init()
 
     freeze_support()  # Required for PyInstaller + multiprocessing
+    set_start_method('spawn', force=True)
     
     # Only run GUI in the main process
     if current_process().name == 'MainProcess':

project_manager.py

@@ -776,8 +776,8 @@ def extract_metadata_worker(file_name):
             snirf_info['Short Channels'] = f"Likely - {names}"
             total_chans = len(raw.ch_names)
             pct_short = (len(names) / total_chans * 100) if total_chans else 0
-            if pct_short > 25:
+            if pct_short > 35:
-                snirf_info['Short Channels'] += "\n There are a lot of short channels. Optode distances are likely incorrect!"
+                snirf_info['Short Channels'] += "\n There are a lot of short channels. Perhaps the optode distances are incorrect?"
         except:
             snirf_info['Short Channels'] = "Unlikely"
 

src/analysis/intergroupbrainimage.py

@@ -99,7 +99,7 @@ class InterGroupBrainImageWidget(InterGroupUIMixin, FlaresBaseWidget):
         self.df_ind_dict = df_ind_dict
         self.design_matrix_dict = design_matrix_dict
         self.contrast_results_dict = contrast_results_dict
-        # self.group_dict = group_dict
+        self.group_dict = group_dict
                
         self.setup_inter_group_ui(["0 (GLM Results)", "1 (Significance)", "2 (Brain Activity Visualization)",])
 

src/shared/flaresbasewidget.py

@@ -50,7 +50,7 @@ class ClickableLabel(QLabel):
     
     def mousePressEvent(self, event):
         viewer = QWidget()
-        viewer.setWindowTitle(f"Expanded View" - {APP_NAME.upper()})
+        viewer.setWindowTitle(f"Expanded View - {APP_NAME.upper()}")
         layout = QVBoxLayout(viewer)
         label = QLabel()
         label.setPixmap(self._pixmap_full)