fix to bandpass filter

changelog.md

@@ -1,3 +1,21 @@
+# Next Release
+
+- 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
+
+
 # Version 1.1.4
 
 - Fixed some display text to now display the correct information

flares.py

@@ -268,40 +268,42 @@ 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)
+        results = process_multiple_participants(
+            file_paths, file_params, file_metadata, progress_queue, max_workers
+        )
 
-        # Signal end of progress
-        progress_queue.put("__done__")
-        t.join()
-    
         gui_queue.put({"success": True, "result": results})
 
-
     except Exception as e:
         gui_queue.put({
             "success": False,
@@ -309,6 +311,14 @@ 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):
@@ -343,9 +353,16 @@ 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}")
@@ -1053,7 +1070,8 @@ 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)
+    #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.compute_psd(fmax=2).plot(
         average=True, xscale="log", axes=fig_filter.axes, color="g", amplitude=False, show=False
@@ -2810,7 +2828,7 @@ 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}")
@@ -3069,5 +3087,16 @@ 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
+    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 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M160-160q-33 0-56.5-23.5T80-240v-480q0-33 23.5-56.5T160-800h240l80 80h320q33 0 56.5 23.5T880-640v242q-18-14-38-23t-42-19v-200H447l-80-80H160v480h120v80H160ZM640-40q-91 0-168-48T360-220q35-84 112-132t168-48q91 0 168 48t112 132q-35 84-112 132T640-40Zm0-80q57 0 107.5-26t82.5-74q-32-48-82.5-74T640-320q-57 0-107.5 26T450-220q32 48 82.5 74T640-120Zm0-40q-25 0-42.5-17.5T580-220q0-25 17.5-42.5T640-280q25 0 42.5 17.5T700-220q0 25-17.5 42.5T640-160Zm-480-80v-480 277-37 240Z"/></svg>

icons/remove_24dp_1F1F1F.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M200-440v-80h560v80H200Z"/></svg>

main.py

@@ -19,7 +19,7 @@ import zipfile
 import platform
 import traceback
 import subprocess
-from pathlib import Path
+from pathlib import Path, PurePosixPath
 from datetime import datetime
 from multiprocessing import Process, current_process, freeze_support, Manager
 
@@ -34,13 +34,14 @@ from mne.io import read_raw_snirf
 from mne.preprocessing.nirs import source_detector_distances
 from mne_nirs.io import write_raw_snirf
 from mne.channels import make_dig_montage
+from mne_nirs.channels import get_short_channels  # type: ignore
 from mne import Annotations
 
 from PySide6.QtWidgets import (
     QApplication, QWidget, QMessageBox, QVBoxLayout, QHBoxLayout, QTextEdit, QScrollArea, QComboBox, QGridLayout,
-    QPushButton, QMainWindow, QFileDialog, QLabel, QLineEdit, QFrame, QSizePolicy, QGroupBox, QDialog, QListView,
+    QPushButton, QMainWindow, QFileDialog, QLabel, QLineEdit, QFrame, QSizePolicy, QGroupBox, QDialog, QListView, QMenu
 )
-from PySide6.QtCore import QThread, Signal, Qt, QTimer, QEvent, QSize
+from PySide6.QtCore import QThread, Signal, Qt, QTimer, QEvent, QSize, QPoint
 from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleValidator, QPixmap, QStandardItemModel, QStandardItem
 from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
 
@@ -57,34 +58,34 @@ SECTIONS = [
     {
         "title": "Preprocessing",
         "params": [
-            {"name": "SECONDS_TO_STRIP", "default": 0, "type": int, "help": "Seconds to remove from beginning of file. Setting this to 0 will remove nothing from the file."},
-            {"name": "DOWNSAMPLE", "default": True, "type": bool, "help": "Downsample snirf files."},
-            {"name": "DOWNSAMPLE_FREQUENCY", "default": 25, "type": int, "help": "Frequency (Hz) to downsample to. If this is set higher than the input data, new data will be interpolated."},
+            {"name": "SECONDS_TO_STRIP", "default": 0, "type": int, "help": "Seconds to remove from beginning of all loaded snirf files. Setting this to 0 will remove nothing from the files."},
+            {"name": "DOWNSAMPLE", "default": True, "type": bool, "help": "Should the snirf files be downsampled? If this is set to True, DOWNSAMPLE_FREQUENCY will be used as the target frequency to downsample to."},
+            {"name": "DOWNSAMPLE_FREQUENCY", "default": 25, "type": int, "help": "Frequency (Hz) to downsample to. If this is set higher than the input data, new data will be interpolated. Only used if DOWNSAMPLE is set to True"},
         ]
     },
     {
         "title": "Scalp Coupling Index",
         "params": [
-            {"name": "SCI", "default": True, "type": bool, "help": "Calculate Scalp Coupling Index."},
-            {"name": "SCI_TIME_WINDOW", "default": 3, "type": int, "help": "SCI time window."},
-            {"name": "SCI_THRESHOLD", "default": 0.6, "type": float, "help": "SCI threshold (0-1)."},
+            {"name": "SCI", "default": True, "type": bool, "help": "Calculate and mark channels bad based on their Scalp Coupling Index. This metric calculates the quality of the connection between the optode and the scalp."},
+            {"name": "SCI_TIME_WINDOW", "default": 3, "type": int, "help": "Independent SCI calculations will be perfomed in a time window for the duration of the value provided, until the end of the file is reached."},
+            {"name": "SCI_THRESHOLD", "default": 0.6, "type": float, "help": "SCI threshold on a scale of 0-1. A value of 0 is bad coupling while a value of 1 is perfect coupling. If SCI is True, any channels lower than this value will be marked as bad."},
         ]
     },
     {
         "title": "Signal to Noise Ratio",
         "params": [
-            {"name": "SNR", "default": True, "type": bool, "help": "Calculate Signal to Noise Ratio."},
+            {"name": "SNR", "default": True, "type": bool, "help": "Calculate and mark channels bad based on their Signal to Noise Ratio. This metric calculates how much of the observed signal was noise versus how much of it was a useful signal."},
             # {"name": "SNR_TIME_WINDOW", "default": -1, "type": int, "help": "SNR time window."},
-            {"name": "SNR_THRESHOLD", "default": 5.0, "type": float, "help": "SNR threshold (dB)."},
+            {"name": "SNR_THRESHOLD", "default": 5.0, "type": float, "help": "SNR threshold (dB). A typical scale would be 0-25, but it is possible for values to be both above and below this range. Higher values correspond to a better signal. If SNR is True, any channels lower than this value will be marked as bad."},
         ]
     },
     {
         "title": "Peak Spectral Power",
         "params": [
 
-            {"name": "PSP", "default": True, "type": bool, "help": "Calculate Peak Spectral Power."},
-            {"name": "PSP_TIME_WINDOW", "default": 3, "type": int, "help": "PSP time window."},
-            {"name": "PSP_THRESHOLD", "default": 0.1, "type": float, "help": "PSP threshold."},
+            {"name": "PSP", "default": True, "type": bool, "help": "Calculate and mark channels bad based on their Peak Spectral Power. This metric calculates the amplitude or strength of a frequency component that is most prominent in a particular frequency range or spectrum."},
+            {"name": "PSP_TIME_WINDOW", "default": 3, "type": int, "help": "Independent PSP calculations will be perfomed in a time window for the duration of the value provided, until the end of the file is reached."},
+            {"name": "PSP_THRESHOLD", "default": 0.1, "type": float, "help": "PSP threshold. A typical scale would be 0-0.5, but it is possible for values to be above this range. Higher values correspond to a better signal. If PSP is True, any channels lower than this value will be marked as bad."},
         ]
     },
     {
@@ -104,7 +105,7 @@ SECTIONS = [
     {
         "title": "Temporal Derivative Distribution Repair filtering",
         "params": [
-            {"name": "TDDR", "default": True, "type": bool, "help": "Apply TDDR filtering."},
+            {"name": "TDDR", "default": True, "type": bool, "help": "Apply Temporal Derivitave Distribution Repair filtering - a method that removes baseline shift and spike artifacts from the data."},
         ]
     },
     {
@@ -128,7 +129,7 @@ SECTIONS = [
     {
         "title": "Short Channels",
         "params": [
-            {"name": "SHORT_CHANNEL", "default": True, "type": bool, "help": "Does the data have a short channel?"},
+            {"name": "SHORT_CHANNEL", "default": True, "type": bool, "help": "This should be set to True if the data has a short channel present in the data."},
         ]
     },
     {
@@ -169,7 +170,7 @@ SECTIONS = [
     {
         "title": "Other",
         "params": [
-            {"name": "MAX_WORKERS", "default": 4, "type": int, "help": "Number of files to process at once."},
+            {"name": "MAX_WORKERS", "default": 4, "type": int, "help": "Number of files to be processed at once. Lowering this value may help on underpowered systems."},
         ]
     },
 ]
@@ -445,13 +446,34 @@ class UserGuideWindow(QWidget):
 
     def __init__(self, parent=None):
         super().__init__(parent, Qt.WindowType.Window)
-        self.setWindowTitle("User Guide for FLARES")
+        self.setWindowTitle("User Guide - FLARES")
         self.resize(250, 100)
 
         layout = QVBoxLayout()
-        label = QLabel("No user guide available yet!", self)
+        label = QLabel("Progress Bar Stages:", self)
+        label2 = QLabel("Stage 1: Load the snirf file\n"
+                        "Stage 2: Check the optode positions\n"
+                        "Stage 3: Scalp Coupling Index\n"
+                        "Stage 4: Signal to Noise Ratio\n"
+                        "Stage 5: Peak Spectral Power\n"
+                        "Stage 6: Identify bad channels\n"
+                        "Stage 7: Interpolate bad channels\n"
+                        "Stage 8: Optical Density\n"
+                        "Stage 9: Temporal Derivative Distribution Repair\n"
+                        "Stage 10: Beer Lambert Law\n"
+                        "Stage 11: Heart Rate Filtering\n"
+                        "Stage 12: Get Short/Long Channels\n"
+                        "Stage 13: Calculate Events from Annotations\n"
+                        "Stage 14: Epoch Calculations\n"
+                        "Stage 15: Design Matrix\n"
+                        "Stage 16: General Linear Model\n"
+                        "Stage 17: Generate Plots from the GLM\n"
+                        "Stage 18: Individual Significance\n"
+                        "Stage 19: Channel, Region of Interest, and Contrast Results\n"
+                        "Stage 20: Image Conversion\n", self)
 
         layout.addWidget(label)
+        layout.addWidget(label2)
 
         self.setLayout(layout)
 
@@ -582,7 +604,7 @@ class UpdateOptodesWindow(QWidget):
 
     def show_help_popup(self, text):
         msg = QMessageBox(self)
-        msg.setWindowTitle("Parameter Info")
+        msg.setWindowTitle("Parameter Info - FLARES")
         msg.setText(text)
         msg.exec()
 
@@ -863,7 +885,7 @@ class UpdateEventsWindow(QWidget):
 
     def show_help_popup(self, text):
         msg = QMessageBox(self)
-        msg.setWindowTitle("Parameter Info")
+        msg.setWindowTitle("Parameter Info - FLARES")
         msg.setText(text)
         msg.exec()
 
@@ -1154,7 +1176,8 @@ class ProgressBubble(QWidget):
     """
         
     clicked = Signal(object)
-
+    rightClicked = Signal(object, QPoint)
+    
     def __init__(self, display_name, file_path):
         super().__init__()
 
@@ -1174,7 +1197,7 @@ class ProgressBubble(QWidget):
         self.progress_layout = QHBoxLayout()
 
         self.rects = []
-        for _ in range(19):
+        for _ in range(20):
             rect = QFrame()
             rect.setFixedSize(10, 18)
             rect.setStyleSheet("background-color: white; border: 1px solid gray;")
@@ -1212,7 +1235,10 @@ class ProgressBubble(QWidget):
             rect.setStyleSheet("background-color: red; border: 1px solid gray;")
 
     def mousePressEvent(self, event):
-        self.clicked.emit(self)
+        if event.button() == Qt.MouseButton.LeftButton:
+            self.clicked.emit(self)
+        elif event.button() == Qt.MouseButton.RightButton:
+            self.rightClicked.emit(self, event.globalPosition().toPoint())
         super().mousePressEvent(event)
 
     def setSuffixText(self, suffix):
@@ -1394,7 +1420,7 @@ class ParamSection(QWidget):
 
     def show_help_popup(self, text):
         msg = QMessageBox(self)
-        msg.setWindowTitle("Parameter Info")
+        msg.setWindowTitle("Parameter Info - FLARES")
         msg.setText(text)
         msg.exec()
 
@@ -1529,52 +1555,40 @@ class ParamSection(QWidget):
             # You can customize how you display selected items here:
             widget.lineEdit().setText(", ".join(selected))
         
-    def update_annotation_dropdown_from_folder(self, folder_path):
-        """
-        Reads all EEG files in the given folder, extracts annotations using MNE,
-        and updates the dropdown for the `target_param` with the set of common annotations.
-
-        Args:
-            folder_param (str): The name of the parameter holding the folder path.
-            target_param (str): The name of the multi-select dropdown to update.
-        """
-        # folder_path_widget = self.widgets.get(folder_param, {}).get("widget")
-        # if not folder_path_widget:
-        #     print(f"[ParamSection] Folder path param '{folder_param}' not found.")
-        #     return
-
-        # folder_path = folder_path_widget.text().strip()
-        # if not os.path.isdir(folder_path):
-        #     print(f"[ParamSection] '{folder_path}' is not a valid directory.")
-        #     return
-
+    def update_annotation_dropdown_from_loaded_files(self, bubble_widgets, button1):
         annotation_sets = []
-        for filename in os.listdir(folder_path):
-            full_path = os.path.join(folder_path, filename)
+
+        print(f"[ParamSection] Number of loaded bubbles: {len(bubble_widgets)}")
+        for bubble in bubble_widgets.values():
+            file_path = bubble.file_path
+            print(f"[ParamSection] Trying file: {file_path}")
             try:
-                raw = read_raw_snirf(full_path, preload=False, verbose="ERROR")
+                raw = read_raw_snirf(file_path, preload=False, verbose="ERROR")
                 annotations = raw.annotations
                 if annotations is not None:
+                    print(f"[ParamSection] Found annotations with descriptions: {annotations.description}")
                     labels = set(annotations.description)
                     annotation_sets.append(labels)
-            except Exception as e:
-                print(f"[ParamSection] Skipping file '{filename}' due to error: {e}")
+                else:
+                    print(f"[ParamSection] No annotations found in file: {file_path}")
+            except Exception:
+                raise
 
         if not annotation_sets:
-            print(f"[ParamSection] No annotations found in folder '{folder_path}'")
+            print("[ParamSection] No annotations found in loaded files")
+            self.update_dropdown_items("REMOVE_EVENTS", [])
+            button1.setVisible(False)
             return
 
-        # Get common annotations
         common_annotations = set.intersection(*annotation_sets) if len(annotation_sets) > 1 else annotation_sets[0]
-        common_annotations = sorted(list(common_annotations))  # for consistent order
+        common_annotations = sorted(list(common_annotations))
 
         print(f"[ParamSection] Common annotations: {common_annotations}")
 
-        # Update the dropdown
-        
         self.update_dropdown_items("REMOVE_EVENTS", common_annotations)
 
 
+
 class FullClickLineEdit(QLineEdit):
     def mousePressEvent(self, event):
         combo = self.parent()
@@ -3869,6 +3883,11 @@ class MainApplication(QMainWindow):
         self.folder_paths = []
         self.section_widget = None
         self.first_run = True
+        
+        self.files_total = 0        # total number of files to process
+        self.files_done = set()     # set of file paths done (success or fail)
+        self.files_failed = set()   # set of failed file paths
+        self.files_results = {}     # dict for successful results (if needed)
 
         self.init_ui()
         self.create_menu_bar()
@@ -3938,6 +3957,19 @@ class MainApplication(QMainWindow):
             right_column_layout.addWidget(label)
             right_column_layout.addWidget(field)
 
+        label_desc = QLabel('<a href="#">Why are these useful?</a>')
+        label_desc.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
+        label_desc.setOpenExternalLinks(False)
+
+        def show_info_popup():
+            QMessageBox.information(None, "Parameter Info - FLARES", 
+                "Age: Used to calculate the DPF factor.\nGender: Not currently used. "
+                "Will be able to sort into groups by gender in the near future.\nGroup: Allows contrast "
+                "images to be created comparing one group to another once the processing has completed.")
+
+        label_desc.linkActivated.connect(show_info_popup)        
+        right_column_layout.addWidget(label_desc)
+
         right_column_layout.addStretch()  # Push fields to top
     
         self.right_column_widget.hide()
@@ -4012,7 +4044,7 @@ 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)
@@ -4062,7 +4094,7 @@ class MainApplication(QMainWindow):
         file_actions = [
             ("Open File...", "Ctrl+O", self.open_file_dialog, resource_path("icons/file_open_24dp_1F1F1F.svg")),
             ("Open Folder...", "Ctrl+Alt+O", self.open_folder_dialog, resource_path("icons/folder_24dp_1F1F1F.svg")),
-            ("Open Folders...", "Ctrl+Shift+O", self.open_multiple_folders_dialog, resource_path("icons/folder_copy_24dp_1F1F1F.svg")),
+            # ("Open Folders...", "Ctrl+Shift+O", self.open_folder_dialog, resource_path("icons/folder_copy_24dp_1F1F1F.svg")),
             ("Load Project...", "Ctrl+L", self.load_project, resource_path("icons/article_24dp_1F1F1F.svg")),
             ("Save Project...", "Ctrl+S", self.save_project, resource_path("icons/save_24dp_1F1F1F.svg")),
             ("Save Project As...", "Ctrl+Shift+S", self.save_project, resource_path("icons/save_as_24dp_1F1F1F.svg")),
@@ -4070,7 +4102,7 @@ class MainApplication(QMainWindow):
 
         for i, (name, shortcut, slot, icon) in enumerate(file_actions):
             file_menu.addAction(make_action(name, shortcut, slot, icon=icon))
-            if i == 2:  # after the first 3 actions (0,1,2)
+            if i == 1:  # after the first 3 actions (0,1,2)
                 file_menu.addSeparator()
 
         file_menu.addSeparator()
@@ -4216,26 +4248,59 @@ class MainApplication(QMainWindow):
 
     def open_file_dialog(self):
         file_path, _ = QFileDialog.getOpenFileName(
-            self, "Open File", "", "All Files (*);;Text Files (*.txt)"
+            self, "Open File", "", "SNIRF Files (*.snirf);;All Files (*)"
         )
         if file_path:
-            self.selected_path = file_path  # store the file path
-            self.show_files_as_bubbles(file_path)
+            # Create and display the bubble directly for this file
+            display_name = os.path.basename(file_path)
+            bubble = ProgressBubble(display_name, file_path)
+            bubble.clicked.connect(self.on_bubble_clicked)
+            bubble.rightClicked.connect(self.on_bubble_right_clicked)
+
+            if not hasattr(self, 'bubble_widgets'):
+                self.bubble_widgets = {}
+            if not hasattr(self, 'selected_paths'):
+                self.selected_paths = []
+
+            file_path = os.path.normpath(file_path)
+            self.bubble_widgets[file_path] = bubble
+            self.selected_paths.append(file_path)
+
+            self.bubble_layout.addWidget(bubble)
+            
+            for section_widget in self.param_sections:
+                if hasattr(section_widget, 'update_annotation_dropdown_from_loaded_files'):
+                    if "REMOVE_EVENTS" in section_widget.widgets:
+                        section_widget.update_annotation_dropdown_from_loaded_files(self.bubble_widgets, self.button1)
+                        break
+            else:
+                print("[MainWindow] Could not find ParamSection with 'REMOVE_EVENTS' widget")
         
+        self.statusBar().showMessage(f"{file_path} loaded.")
+
         self.button1.setVisible(True)
 
 
     def open_folder_dialog(self):
-        folder_path = QFileDialog.getExistingDirectory(
-            self, "Select Folder", ""
-        )
+        folder_path = QFileDialog.getExistingDirectory(self, "Select Folder", "")
+        
         if folder_path:
-            self.selected_path = folder_path  # store the folder path
+            snirf_files = [str(f) for f in Path(folder_path).glob("*.snirf")]
+
+            if not hasattr(self, 'selected_paths'):
+                self.selected_paths = []
+
+            for file_path in snirf_files:
+                if file_path not in self.selected_paths:
+                    self.selected_paths.append(file_path)
+
             self.show_files_as_bubbles(folder_path)
+            
             for section_widget in self.param_sections:
-                if "REMOVE_EVENTS" in section_widget.widgets:
-                    section_widget.update_annotation_dropdown_from_folder(folder_path)
-                    break
+                if hasattr(section_widget, 'update_annotation_dropdown_from_loaded_files'):
+                    if "REMOVE_EVENTS" in section_widget.widgets:
+                        section_widget.update_annotation_dropdown_from_loaded_files(self.bubble_widgets, self.button1)
+                        break
             else:
                 print("[MainWindow] Could not find ParamSection with 'REMOVE_EVENTS' widget")
         
@@ -4244,16 +4309,29 @@ class MainApplication(QMainWindow):
 
     def open_multiple_folders_dialog(self):
         while True:
-            folder = QFileDialog.getExistingDirectory(self, "Select Folder")
-            if not folder:
+            folder_path = QFileDialog.getExistingDirectory(self, "Select Folder")
+            if not folder_path:
                 break
+            
+            snirf_files = [str(f) for f in Path(folder_path).glob("*.snirf")]
 
             if not hasattr(self, 'selected_paths'):
                 self.selected_paths = []
-            if folder not in self.selected_paths:
-                self.selected_paths.append(folder)
+            
+            for file_path in snirf_files:
+                if file_path not in self.selected_paths:
+                    self.selected_paths.append(file_path)
 
-            self.show_files_as_bubbles(self.selected_paths)
+            self.show_files_as_bubbles(folder_path)
+            
+            for section_widget in self.param_sections:
+                if hasattr(section_widget, 'update_annotation_dropdown_from_loaded_files'):
+                    if "REMOVE_EVENTS" in section_widget.widgets:
+                        section_widget.update_annotation_dropdown_from_loaded_files(self.bubble_widgets, self.button1)
+                        break
+            else:
+                print("[MainWindow] Could not find ParamSection with 'REMOVE_EVENTS' widget")
+        
 
             # Ask if the user wants to add another
             more = QMessageBox.question(
@@ -4267,21 +4345,42 @@ class MainApplication(QMainWindow):
             
         self.button1.setVisible(True)
 
-    def save_project(self):
 
-        filename, _ = QFileDialog.getSaveFileName(
-            self, "Save Project", "", "FLARE Project (*.flare)"
-        )
-        if not filename:
-            return
+    def save_project(self, onCrash=False):
 
+        if not onCrash:
+            filename, _ = QFileDialog.getSaveFileName(
+                self, "Save Project", "", "FLARE Project (*.flare)"
+            )
+            if not filename:
+                return
+        else:
+            if PLATFORM_NAME == "darwin":
+                filename = os.path.join(os.path.dirname(sys.executable), "../../../flares_autosave.flare")
+            else:
+                filename = os.path.join(os.getcwd(), "flares_autosave.flare")
+                
         try:
-            project_data = {
-                "file_list": [bubble.file_path for bubble in self.bubble_widgets.values()],
-                "progress_states": {
-                    bubble.file_path: bubble.current_step for bubble in self.bubble_widgets.values()
-                },
+            # Ensure the filename has the proper extension
+            if not filename.endswith(".flare"):
+                filename += ".flare"
 
+            project_path = Path(filename).resolve()
+            project_dir = project_path.parent
+            
+            file_list = [
+                str(PurePosixPath(Path(bubble.file_path).resolve().relative_to(project_dir)))
+                for bubble in self.bubble_widgets.values()
+            ]
+
+            progress_states = {
+                str(PurePosixPath(Path(bubble.file_path).resolve().relative_to(project_dir))): bubble.current_step
+                for bubble in self.bubble_widgets.values()
+            }
+
+            project_data = {
+                "file_list": file_list,
+                "progress_states": progress_states,
                 "raw_haemo_dict": self.raw_haemo_dict,
                 "epochs_dict": self.epochs_dict,
                 "fig_bytes_dict": self.fig_bytes_dict,
@@ -4294,6 +4393,17 @@ class MainApplication(QMainWindow):
                 "group_dict": self.group_dict,
                 "valid_dict": self.valid_dict,
             }
+            
+            def sanitize(obj):
+                if isinstance(obj, Path):
+                    return str(PurePosixPath(obj))
+                elif isinstance(obj, dict):
+                    return {sanitize(k): sanitize(v) for k, v in obj.items()}
+                elif isinstance(obj, list):
+                    return [sanitize(i) for i in obj]
+                return obj
+
+            project_data = sanitize(project_data)
 
             with open(filename, "wb") as f:
                 pickle.dump(project_data, f)
@@ -4301,7 +4411,8 @@ class MainApplication(QMainWindow):
             QMessageBox.information(self, "Success", f"Project saved to:\n{filename}")
 
         except Exception as e:
-            QMessageBox.critical(self, "Error", f"Failed to save project:\n{e}")
+            if not onCrash:
+                QMessageBox.critical(self, "Error", f"Failed to save project:\n{e}")
 
 
 
@@ -4328,9 +4439,20 @@ class MainApplication(QMainWindow):
             self.group_dict = data.get("group_dict", {})
             self.valid_dict = data.get("valid_dict", {})
 
-            # Restore bubbles and progress
-            self.show_files_as_bubbles_from_list(data["file_list"], data.get("progress_states", {}), filename)
+            project_dir = Path(filename).parent
 
+            # Convert saved relative paths to absolute paths
+            file_list = [str((project_dir / Path(rel_path)).resolve()) for rel_path in data["file_list"]]
+
+            # Also resolve progress_states with updated paths
+            raw_progress = data.get("progress_states", {})
+            progress_states = {
+                str((project_dir / Path(rel_path)).resolve()): step
+                for rel_path, step in raw_progress.items()
+            }
+
+            self.show_files_as_bubbles_from_list(file_list, progress_states, filename)
+            
             # Re-enable buttons
             # self.button1.setVisible(True)
             self.button3.setVisible(True)
@@ -4348,11 +4470,11 @@ class MainApplication(QMainWindow):
             folder_paths = [folder_paths]
 
         # Clear previous bubbles
-        while self.bubble_layout.count():
-            item = self.bubble_layout.takeAt(0)
-            widget = item.widget()
-            if widget:
-                widget.deleteLater()
+        # while self.bubble_layout.count():
+        #     item = self.bubble_layout.takeAt(0)
+        #     widget = item.widget()
+        #     if widget:
+        #         widget.deleteLater()
 
         temp_bubble = ProgressBubble("Test Bubble", "")  # A dummy bubble for measurement
         temp_bubble.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy. Preferred)
@@ -4364,21 +4486,26 @@ class MainApplication(QMainWindow):
         cols = max(1, available_width // bubble_width)  # Ensure at least 1 column
 
         index = 0
-
+        if not hasattr(self, 'selected_paths'):
+            self.selected_paths = []
+            
         for folder_path in folder_paths:
             if not os.path.isdir(folder_path):
                 continue
 
-            files = os.listdir(folder_path)
-            files = [f for f in files if os.path.isfile(os.path.join(folder_path, f))]
-
-            for filename in files:
-                full_path = os.path.join(folder_path, filename)
-                display_name = f"{os.path.basename(folder_path)} / {filename}"
+            snirf_files = [str(f) for f in Path(folder_path).glob("*.snirf")]
 
+            for full_path in snirf_files:
+                
+                display_name = f"{os.path.basename(folder_path)} / {os.path.basename(full_path)}"
                 bubble = ProgressBubble(display_name, full_path)
                 bubble.clicked.connect(self.on_bubble_clicked)
-                self.bubble_widgets[filename] = bubble
+                bubble.rightClicked.connect(self.on_bubble_right_clicked)
+
+                self.bubble_widgets[full_path] = bubble
+
+                if full_path not in self.selected_paths:
+                    self.selected_paths.append(full_path)
 
                 row = index // cols
                 col = index % cols
@@ -4418,6 +4545,7 @@ class MainApplication(QMainWindow):
             # Create bubble with full path
             bubble = ProgressBubble(display_name, file_path)
             bubble.clicked.connect(self.on_bubble_clicked)
+            bubble.rightClicked.connect(self.on_bubble_right_clicked)
             self.bubble_widgets[file_path] = bubble
 
             step = progress_states.get(file_path, 0)
@@ -4506,6 +4634,77 @@ class MainApplication(QMainWindow):
             field.blockSignals(False)
 
 
+    def on_bubble_right_clicked(self, bubble, global_pos):
+        menu = QMenu(self)
+        action1 = menu.addAction(QIcon(resource_path("icons/folder_eye_24dp_1F1F1F.svg")), "Reveal")
+        action2 = menu.addAction(QIcon(resource_path("icons/remove_24dp_1F1F1F.svg")), "Remove")
+
+        action = menu.exec(global_pos)
+        if action == action1:
+            path = bubble.file_path
+            if os.path.exists(path):
+                if PLATFORM_NAME == "windows":
+                    subprocess.run(["explorer", "/select,", os.path.normpath(path)])
+                elif PLATFORM_NAME == "darwin":  # macOS
+                    subprocess.run(["open", "-R", path])
+                else:  # Linux
+                    folder = os.path.dirname(path)
+                    subprocess.run(["xdg-open", folder])
+            else:
+                print("File not found:", path)
+                
+        elif action == action2:
+            if self.button3.isVisible():
+                reply = QMessageBox.warning(
+                    self,
+                    "Confirm Remove",
+                    "Are you sure you want to remove this file? This will remove the analysis option and the processing will have to be performed again.",
+                    QMessageBox.StandardButton.Ok | QMessageBox.StandardButton.Cancel
+                )
+                if reply != QMessageBox.StandardButton.Ok:
+                    return
+                else:
+                    self.button3.setVisible(False)
+                    
+            self.top_left_widget.clear()
+            self.right_column_widget.hide()
+
+            parent_layout = bubble.parent().layout()
+            if parent_layout is not None:
+                parent_layout.removeWidget(bubble)
+
+            key_to_delete = None
+            for path, b in self.bubble_widgets.items():
+                if b is bubble:
+                    key_to_delete = path
+                    break
+
+            if key_to_delete:
+                del self.bubble_widgets[key_to_delete]
+
+            # Remove from selected_paths
+            if hasattr(self, 'selected_paths'):
+                try:
+                    self.selected_paths.remove(bubble.file_path)
+                except ValueError:
+                    pass
+
+            # Remove from selected_path (if used)
+            if hasattr(self, 'selected_path') and self.selected_path == bubble.file_path:
+                self.selected_path = None
+                
+            for section_widget in self.param_sections:
+                if hasattr(section_widget, 'update_annotation_dropdown_from_loaded_files'):
+                    if "REMOVE_EVENTS" in section_widget.widgets:
+                        section_widget.update_annotation_dropdown_from_loaded_files(self.bubble_widgets, self.button1)
+                        break
+                
+            bubble.setParent(None)
+            bubble.deleteLater()
+            
+            if getattr(self, 'last_clicked_bubble', None) is bubble:
+                self.last_clicked_bubble = None
+            
     def eventFilter(self, watched, event):
         if event.type() == QEvent.Type.MouseButtonPress:
             widget = self.childAt(event.pos())
@@ -4587,10 +4786,11 @@ class MainApplication(QMainWindow):
         self.button1.clicked.disconnect(self.on_run_task)
         self.button1.setText("Cancel")
         self.button1.clicked.connect(self.cancel_task)
-        
+
         if not self.first_run:
             for bubble in self.bubble_widgets.values():
-                bubble.mark_cancelled()
+                pass
+                # bubble.mark_cancelled()
         self.first_run = False
 
         # Collect all selected snirf files in a flat list
@@ -4617,7 +4817,41 @@ class MainApplication(QMainWindow):
         if not snirf_files:
             raise ValueError("No .snirf files found in selection")
 
+        # validate
+        for i in snirf_files:
+            x_coords = set()
+            y_coords = set()
+            z_coords = set()
+            raw = read_raw_snirf(i)
+            dig = raw.info.get('dig', None)
+            if dig is not None:
+                for point in dig:
+                    if point['kind'] == 3:
+                        coord = point['r']
+                        x_coords.add(coord[0])
+                        y_coords.add(coord[1])
+                        z_coords.add(coord[2])
+                        print(f"Coord: {coord}")
+            is_2d = (
+                all(abs(x) < 1e-6 for x in x_coords) or
+                all(abs(y) < 1e-6 for y in y_coords) or
+                all(abs(z) < 1e-6 for z in z_coords)
+            )
 
+            if is_2d:
+                QMessageBox.critical(None, "Error - 2D Data Detected - FLARES", f"Error: 2 dimensional data was found in {i}. "
+                                     "It is not possible to process this file. Please update the coordinates "
+                                     "using the 'Update optodes in snirf file...' option from the Options menu or by pressing 'F6'.")
+                self.button1.clicked.disconnect(self.cancel_task)
+                self.button1.setText("Process")
+                self.button1.clicked.connect(self.on_run_task)
+                return
+            
+        self.files_total = len(snirf_files)
+        self.files_done = set()
+        self.files_failed = set()
+        self.files_results = {}
+        
         all_params = {}
         for section_widget in self.param_sections:
             section_params = section_widget.get_param_values()
@@ -4659,7 +4893,12 @@ class MainApplication(QMainWindow):
 
             if isinstance(msg, dict):
                 if msg.get("success"):
+                    
                     results = msg["result"] # from flares.py
+                    
+                    for file_path, result_tuple in results.items():
+                        self.files_done.add(file_path)
+                        self.files_results[file_path] = result_tuple
 
                     # Initialize storage
                     # TODO: Is this check needed?
@@ -4691,26 +4930,84 @@ class MainApplication(QMainWindow):
                         self.valid_dict[file_path] = valid
 
                         # self.statusbar.showMessage(f"Processing complete! Time elapsed: {elapsed_time:.2f} seconds")
-                        self.statusbar.showMessage(f"Processing complete!")
+                        # self.statusbar.showMessage(f"Processing complete!")
 
                         self.button3.setVisible(True)
+                        
 
-                else:
+                elif msg.get("success") is False:
                     error_msg = msg.get("error", "Unknown error")
-                    print("Error during processing:", error_msg)
-                    self.statusbar.showMessage(f"Processing failed! {error_msg}")
+                    traceback_str = msg.get("traceback", "")
+                    self.show_error_popup("Processing failed!", error_msg, traceback_str)
+                    self.files_done = set(self.files_results.keys())
+                    self.statusbar.showMessage(f"Processing failed!")
+                    self.result_timer.stop()
+                    self.cleanup_after_process()
+                    return
 
-                self.result_timer.stop()
+                elif msg.get("type") == "error":
+                    # Error forwarded from a single file (e.g. from a worker)
+                    file_path = msg.get("file", "Unknown file")
+                    error_msg = msg.get("error", "Unknown error")
+                    traceback_str = msg.get("traceback", "")
+                    
+                    self.files_done.add(file_path)
+                    self.files_failed.add(file_path)
+
+                    self.show_error_popup(f"{file_path}", error_msg, traceback_str)
+                    self.statusbar.showMessage(f"Error processing {file_path}")
+                    if file_path in self.bubble_widgets:
+                        self.bubble_widgets[file_path].mark_cancelled()
+                    
 
-                self.cleanup_after_process()
-                return  
-            
             elif isinstance(msg, tuple) and msg[0] == 'progress':
                 _, file_path, step_index = msg
-                file_name = os.path.basename(file_path)  # extract file name
-                self.progress_update_signal.emit(file_name, step_index)
+                self.progress_update_signal.emit(file_path, step_index)
 
 
+        if len(self.files_done) == self.files_total:
+            self.result_timer.stop()
+            self.cleanup_after_process()
+
+            success_count = len(self.files_results)
+            fail_count = len(self.files_failed)
+
+            summary_msg = f"Processing complete: {success_count} succeeded, {fail_count} failed."
+            self.statusbar.showMessage(summary_msg)
+
+            if success_count > 0:
+                self.button3.setVisible(True)
+                
+            self.button1.clicked.disconnect(self.cancel_task)
+            self.button1.setText("Process")
+            self.button1.clicked.connect(self.on_run_task)
+
+            
+    def show_error_popup(self, title, error_message, traceback_str=""):
+        msgbox = QMessageBox(self)
+        msgbox.setIcon(QMessageBox.Warning)
+        msgbox.setWindowTitle("Warning - FLARES")
+        
+        message = (
+            f"FLARES 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. "
+            "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/flares/issues'>here</a>.<br><br>"
+            f"Error message: {error_message}"
+        )
+
+        msgbox.setTextFormat(Qt.TextFormat.RichText)
+        msgbox.setText(message)
+        msgbox.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
+
+        # Add traceback to detailed text
+        if traceback_str:
+            msgbox.setDetailedText(traceback_str)
+
+        msgbox.setStandardButtons(QMessageBox.Ok)
+        msgbox.exec_()
+        
+        
     def cleanup_after_process(self):
       
         if hasattr(self, 'result_process'):
@@ -4738,8 +5035,9 @@ class MainApplication(QMainWindow):
             self.manager.shutdown()
 
 
-    def update_file_progress(self, filename, step_index):
-        bubble = self.bubble_widgets.get(filename)
+    def update_file_progress(self, file_path, step_index):
+        key = os.path.normpath(file_path)
+        bubble = self.bubble_widgets.get(key)
         if bubble:
             bubble.update_progress(step_index)
 
@@ -4895,6 +5193,14 @@ class MainApplication(QMainWindow):
             # Measurement date
             snirf_info['Measurement Date'] = str(raw.info.get('meas_date'))
 
+            try:
+                short_chans = get_short_channels(raw, max_dist=0.015)
+                snirf_info['Short Channels'] = f"Likely - {short_chans.ch_names}"
+                if len(short_chans.ch_names) > 6:
+                    snirf_info['Short Channels'] += "\n There are a lot of short channels. Optode distances are likely incorrect!"
+            except:
+                snirf_info['Short Channels'] = "Unlikely"
+                
             # Source-detector distances
             distances = source_detector_distances(raw.info)
             distance_info = []
@@ -5169,11 +5475,50 @@ def exception_hook(exc_type, exc_value, exc_traceback):
     if app is None:
         app = QApplication(sys.argv)
 
-    QMessageBox.critical(None, "Unexpected Error", f"An unhandled exception occurred:\n\n{error_msg}")
+    show_critical_error(error_msg)
 
     # Exit the app after user acknowledges
     sys.exit(1)
+
+def show_critical_error(error_msg):
+    msg_box = QMessageBox()
+    msg_box.setIcon(QMessageBox.Icon.Critical)
+    msg_box.setWindowTitle("Something went wrong!")
     
+    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")
+        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")
+        save_path = os.path.join(os.getcwd(), "flares_autosave.flare")
+
+
+    shutil.copy(log_path, log_path2)
+    log_path2 = Path(log_path2).absolute().as_posix()
+    autosave_path = Path(save_path).absolute().as_posix()
+    log_link = f"file:///{log_path2}"
+    autosave_link = f"file:///{autosave_path}"
+    
+    window.save_project(True)
+
+    message = (
+        "FLARES has encountered an unrecoverable error and needs to close.<br><br>"
+        f"We are sorry for the inconvenience. An autosave was attempted to be saved to <a href='{autosave_link}'>{autosave_path}</a>, but it may not have been saved. "
+        "If the file was saved, it still may not be intact, openable, or contain the correct data. Use the autosave at your discretion.<br><br>"
+        "This unrecoverable error was likely due to an error with FLARES and not your data.<br>"
+        f"Please raise an issue <a href='https://git.research.dezeeuw.ca/tyler/flares/issues'>here</a> and attach the error file located at <a href='{log_link}'>{log_path2}</a><br><br>"
+        f"<pre>{error_msg}</pre>"
+    )
+
+    msg_box.setTextFormat(Qt.TextFormat.RichText)
+    msg_box.setText(message)
+    msg_box.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
+    msg_box.setStandardButtons(QMessageBox.StandardButton.Ok)
+
+    msg_box.exec()
 
 if __name__ == "__main__":
     # Redirect exceptions to the popup window