quick bug fixes

changelog.md

@@ -1,3 +1,60 @@
+# 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
+- Changed the way folders are opened to store the files seperately rather than the folder as a whole to allow for the removal of files
+- Fixed issues with dropdowns and bubbles not populating correctly when opening a single file and temporarily removed the option to open multiple folders
+- Improved crash handling and the message that is displayed to the user if the application crashes
+- Progress bar will now colour the stage that fails as red if a file fails during processing
+- A warning message will be displayed when a file fails to process with information on what went wrong. This message does not halt the rest of the processing of the other files
+- Fixed the number of rectangles in the progress bar to 20 (was incorrect in v1.1.1)
+- Added validation to ensure loaded files do not have 2 dimensional data when clicking process to prevent inaccurate results from being generated
+- Added more metadata information to the top left information panel
+- Changed the Status Bar message when processing is complete to state how many were successful and how many were not
+- 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
+
+- Fixed some display text to now display the correct information
+- A new option under Analysis has been added to export the data from a specified participant as a csv file. Fixes [Issue 19](https://git.research.dezeeuw.ca/tyler/flares/issues/19), [Issue 27](https://git.research.dezeeuw.ca/tyler/flares/issues/27)
+- Added 2 new parameters - TIME_WINDOW_START and TIME_WINDOW_END. Fixes [Issue 29](https://git.research.dezeeuw.ca/tyler/flares/issues/29)
+- These parameters affect the visualization of the significance and contrast images but do not change the total time modeled underneath
+- Fixed the duration of annotations edited from a BORIS file from 0 seconds to their proper duration
+- Added the annotation information to each participant under their "File information" window
+- Fixed Macs not being able to save snirfs attempting to be updated from BORIS files, and in general the updated files not respecting the path chosen by the user
+
+
+# Version 1.1.3
+
+- Added back the ability to use the fOLD dataset. Fixes [Issue 23](https://git.research.dezeeuw.ca/tyler/flares/issues/23)
+- 5th option has been added under Analysis to get to fOLD channels per participant
+- Added an option to cancel the running process. Fixes [Issue 15](https://git.research.dezeeuw.ca/tyler/flares/issues/15)
+- Prevented graph images from showing when participants are being processed. Fixes [Issue 24](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
+- Allow the option to remove all events of a type from all loaded snirfs. Fixes [Issue 25](https://git.research.dezeeuw.ca/tyler/flares/issues/25)
+- Added new icons in the menu bar
+- Added a terminal to interact with the app in a more command-like form
+- Currently the terminal has no functionality but some features for batch operations will be coming soon!
+- Inter-Group viewer now has the option to visualize the average response on the brain of all participants in the group. Fixes [Issue 26](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
+- Fixed the description under "Update events in snirf file..."
+
+
+# Version 1.1.2
+
+- Fixed incorrect colormaps being applied
+- Added functionality to utilize external event markers from a file. Fixes [Issue 6](https://git.research.dezeeuw.ca/tyler/flares/issues/6)
+
+
 # Version 1.1.1
 
 - Fixed the number of rectangles in the progress bar to 19

flares.py

@@ -50,12 +50,12 @@ 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.execution_model
+import vtkmodules.util.data_model
+import vtkmodules.util.execution_model
 
 # External library imports for mne
 from mne import (
-    EvokedArray, SourceEstimate, Info, Epochs, Label,
+    EvokedArray, SourceEstimate, Info, Epochs, Label, Annotations,
     events_from_annotations, read_source_spaces,
     stc_near_sensors, pick_types, grand_average, get_config, set_config, read_labels_from_annot
 )  # type: ignore
@@ -130,8 +130,16 @@ TDDR: bool
 
 ENHANCE_NEGATIVE_CORRELATION: bool
 
+L_FREQ: float
+H_FREQ: float
+
 SHORT_CHANNEL: bool
 
+REMOVE_EVENTS: list
+
+TIME_WINDOW_START: int
+TIME_WINDOW_END: int
+
 VERBOSITY = True
 
 # FIXME: Shouldn't need each ordering - just order it before checking
@@ -179,6 +187,11 @@ REQUIRED_KEYS: dict[str, Any] = {
     "PSP_THRESHOLD": float,
     
     "SHORT_CHANNEL": bool,
+    "REMOVE_EVENTS": list,
+    "TIME_WINDOW_START": int,
+    "TIME_WINDOW_END": int,
+    "L_FREQ": float,
+    "H_FREQ": float,
     # "REJECT_PAIRS": bool,
     # "FORCE_DROP_ANNOTATIONS": list,
     # "FILTER_LOW_PASS": float,
@@ -260,40 +273,42 @@ def set_metadata(file_path, metadata: dict[str, Any]) -> None:
             val = file_metadata.get(key, None)
             if val not in (None, '', [], {}, ()):  # check for "empty" values
                 globals()[key] = val
+from queue import Empty  # This works with multiprocessing.Manager().Queue()
 
 
 def gui_entry(config: dict[str, Any], gui_queue: Queue, progress_queue: Queue) -> None:
-    try:
-        # Start a thread to forward progress messages back to GUI
-        def forward_progress():
-            while True:
-                try:
-                    msg = progress_queue.get(timeout=1)
-                    if msg == "__done__":
-                        break
-                    gui_queue.put(msg)
-                except:
-                    continue
+    def forward_progress():
+        while True:
+            try:
+                msg = progress_queue.get(timeout=1)
+                if msg == "__done__":
+                    break
+                gui_queue.put(msg)
+            except Empty:
+                continue
+            except Exception as e:
+                gui_queue.put({
+                    "type": "error",
+                    "error": f"Forwarding thread crashed: {e}",
+                    "traceback": traceback.format_exc()
+                })
+                break
 
-        t = threading.Thread(target=forward_progress, daemon=True)
-        t.start()
+    t = threading.Thread(target=forward_progress, daemon=True)
+    t.start()
+
+    try:
         file_paths = config['SNIRF_FILES']
         file_params = config['PARAMS']
         file_metadata = config['METADATA']
-
         max_workers = file_params.get("MAX_WORKERS", int(os.cpu_count()/4))
 
-        # Run the actual processing, with progress_queue passed down
-        print("actual call")
-        results = process_multiple_participants(file_paths, file_params, file_metadata, progress_queue, max_workers)
-
-        # Signal end of progress
-        progress_queue.put("__done__")
-        t.join()
+        results = process_multiple_participants(
+            file_paths, file_params, file_metadata, progress_queue, max_workers
+        )
 
         gui_queue.put({"success": True, "result": results})
 
-
     except Exception as e:
         gui_queue.put({
             "success": False,
@@ -301,6 +316,14 @@ def gui_entry(config: dict[str, Any], gui_queue: Queue, progress_queue: Queue) -
             "traceback": traceback.format_exc()
         })
 
+    finally:
+        # Always send done to the thread and avoid hanging
+        try:
+            progress_queue.put("__done__")
+        except:
+            pass
+        t.join(timeout=5)  # prevent permanent hang
+
 
 
 def process_participant_worker(args):
@@ -335,9 +358,16 @@ def process_multiple_participants(file_paths, file_params, file_metadata, progre
             try:
                 file_path, result, error = future.result()
                 if error:
-                    print(f"Error processing {file_path}: {error[0]}")
-                    print(error[1])
+                    error_message, error_traceback = error
+                    if progress_queue:
+                        progress_queue.put({
+                            "type": "error",
+                            "file": file_path,
+                            "error": error_message,
+                            "traceback": error_traceback
+                        })
                     continue
+                
                 results_by_file[file_path] = result
             except Exception as e:
                 print(f"Unexpected error processing {file_path}: {e}")
@@ -1045,7 +1075,16 @@ def filter_the_data(raw_haemo):
         average=True, xscale="log", color="r", show=False, amplitude=False
     )
     
-    raw_haemo = raw_haemo.filter(l_freq=None, h_freq=0.4, h_trans_bandwidth=0.2)
+    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(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
@@ -1074,7 +1113,7 @@ def epochs_calculations(raw_haemo, events, event_dict):
 
     # Plot drop log
     # TODO: Why show this if we never use epochs2?
-    fig_epochs_dropped = epochs2.plot_drop_log()
+    fig_epochs_dropped = epochs2.plot_drop_log(show=False)
     fig_epochs.append(("fig_epochs_dropped", fig_epochs_dropped))
 
     # Plot for each condition
@@ -1470,9 +1509,15 @@ def resource_path(relative_path):
 
 def fold_channels(raw: BaseRaw) -> None:
 
+    # if getattr(sys, 'frozen', False):
+    path = os.path.expanduser("~") + "/mne_data/fOLD/fOLD-public-master/Supplementary"
+    logger.info(path)
+    set_config('MNE_NIRS_FOLD_PATH', resource_path(path)) # type: ignore
 
-    # Locate the fOLD excel files
-    set_config('MNE_NIRS_FOLD_PATH', resource_path("../../mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
+    # # Locate the fOLD excel files
+    # else:
+    #     logger.info("yabba")
+    #     set_config('MNE_NIRS_FOLD_PATH', resource_path("../../mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
 
     output = None
 
@@ -1485,7 +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)
@@ -1534,8 +1578,8 @@ def fold_channels(raw: BaseRaw) -> None:
             "Brain_Outside",
         ]
 
-        cmap1 = plt.cm.get_cmap('tab20')  # First 20 colors
-        cmap2 = plt.cm.get_cmap('tab20b')  # Next 20 colors
+        cmap1 = plt.get_cmap('tab20')  # First 20 colors
+        cmap2 = plt.get_cmap('tab20b')  # Next 20 colors
 
         # Combine the colors from both colormaps
         colors = [cmap1(i) for i in range(20)] + [cmap2(i) for i in range(20)]  # Total 40 colors
@@ -1611,6 +1655,7 @@ def fold_channels(raw: BaseRaw) -> None:
     for ax in axes[len(hbo_channel_names):]:
         ax.axis('off')
     
+    plt.show()
     return fig, legend_fig
 
                 
@@ -2244,21 +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.40-rh": "green",
-            "Brodmann.6-rh": "pink",
-            "Brodmann.7-rh": "orange",
-            "Brodmann.17-rh": "red",
-            "Brodmann.1-rh": "yellow",
-            "Brodmann.2-rh": "yellow",
-            "Brodmann.3-rh": "yellow",
-            "Brodmann.18-rh": "red",
-            "Brodmann.19-rh": "red",
-            "Brodmann.4-rh": "purple",
-            "Brodmann.8-rh": "white"
+            "Brodmann.1-lh": "red",
+            "Brodmann.2-lh": "red",
+            "Brodmann.3-lh": "red",
+            "Brodmann.4-lh": "orange",
+            "Brodmann.5-lh": "green",
+            "Brodmann.6-lh": "yellow",
+            "Brodmann.7-lh": "green",
+            "Brodmann.17-lh": "blue",
+            "Brodmann.18-lh": "blue",
+            "Brodmann.19-lh": "blue",
+            "Brodmann.39-lh": "purple",
+            "Brodmann.40-lh": "pink",
+            "Brodmann.42-lh": "white",
+            "Brodmann.44-lh": "white",
+            "Brodmann.48-lh": "white",
+
         }
 
         for label in labels:
@@ -2795,7 +2844,7 @@ def calculate_dpf(file_path):
     # order is hbo / hbr
     with h5py.File(file_path, 'r') as f:
         wavelengths = f['/nirs/probe/wavelengths'][:]
-        logger.info("Wavelengths (nm):", wavelengths)
+        logger.info(f"Wavelengths (nm): {wavelengths}")
     wavelengths = sorted(wavelengths, reverse=True)
     age = float(AGE)
     logger.info(f"Their age was {AGE}")
@@ -2911,7 +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:
@@ -2935,6 +2984,19 @@ def process_participant(file_path, progress_callback=None):
     logger.info("14")
 
     # Step 14: Design Matrix
+    events_to_remove = REMOVE_EVENTS
+        
+    filtered_annotations = [ann for ann in raw.annotations if ann['description'] not in events_to_remove]
+    
+    new_annot = Annotations(
+        onset=[ann['onset'] for ann in filtered_annotations],
+        duration=[ann['duration'] for ann in filtered_annotations],
+        description=[ann['description'] for ann in filtered_annotations]
+    )
+    
+    # Set the new annotations
+    raw_haemo.set_annotations(new_annot)
+
     design_matrix, fig_design_matrix = make_design_matrix(raw_haemo, short_chans)
     fig_individual["Design Matrix"] = fig_design_matrix
     if progress_callback: progress_callback(15)
@@ -3008,7 +3070,11 @@ def process_participant(file_path, progress_callback=None):
     contrast_dict = {}
 
     for condition in all_conditions:
-        delay_cols = [col for col in all_delay_cols if col.startswith(f"{condition}_delay_")]
+        delay_cols = [
+            col for col in all_delay_cols
+            if col.startswith(f"{condition}_delay_") and
+            TIME_WINDOW_START <= int(col.split("_delay_")[-1]) <= TIME_WINDOW_END
+        ]
 
         if not delay_cols:
             continue  # skip if no columns found (shouldn't happen?)
@@ -3038,4 +3104,15 @@ def process_participant(file_path, progress_callback=None):
     if progress_callback: progress_callback(20)
     logger.info("20")
         
+    sanitize_paths_for_pickle(raw_haemo, epochs)
+
     return raw_haemo, epochs, fig_bytes, cha, contrast_results, df_ind, design_matrix, AGE, GENDER, GROUP, True
+
+def sanitize_paths_for_pickle(raw_haemo, epochs):
+    # Fix raw_haemo._filenames
+    if hasattr(raw_haemo, '_filenames'):
+        raw_haemo._filenames = [str(p) for p in raw_haemo._filenames]
+
+    # Fix epochs._raw._filenames
+    if hasattr(epochs, '_raw') and hasattr(epochs._raw, '_filenames'):
+        epochs._raw._filenames = [str(p) for p in epochs._raw._filenames]

icons/folder_eye_24dp_1F1F1F.svg

@@ -0,0 +1 @@
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icons/remove_24dp_1F1F1F.svg

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icons/terminal_24dp_1F1F1F.svg

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