changed the changelog

changelog.md

@@ -1,3 +1,34 @@
+# 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

@@ -134,6 +134,9 @@ 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
@@ -182,6 +185,8 @@ REQUIRED_KEYS: dict[str, Any] = {
     
     "SHORT_CHANNEL": bool,
     "REMOVE_EVENTS": list,
+    "TIME_WINDOW_START": int,
+    "TIME_WINDOW_END": int
     # "REJECT_PAIRS": bool,
     # "FORCE_DROP_ANNOTATIONS": list,
     # "FILTER_LOW_PASS": float,
@@ -1077,7 +1082,7 @@ 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
@@ -3031,7 +3036,11 @@ 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?)

icons/terminal_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 23.5-56.5T160-800h640q33 0 56.5 23.5T880-720v480q0 33-23.5 56.5T800-160H160Zm0-80h640v-400H160v400Zm140-40-56-56 103-104-104-104 57-56 160 160-160 160Zm180 0v-80h240v80H480Z"/></svg>

icons/upgrade_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="M280-160v-80h400v80H280Zm160-160v-327L336-544l-56-56 200-200 200 200-56 56-104-103v327h-80Z"/></svg>

main.py

@@ -42,9 +42,10 @@ from PySide6.QtWidgets import (
 )
 from PySide6.QtCore import QThread, Signal, Qt, QTimer, QEvent, QSize
 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
 
 
-CURRENT_VERSION = "1.0.1"
+CURRENT_VERSION = "1.0.0"
 
 API_URL = "https://git.research.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
 API_URL_SECONDARY = "https://git.research2.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
@@ -154,6 +155,8 @@ SECTIONS = [
     {
         "title": "General Linear Model",
         "params": [
+            {"name": "TIME_WINDOW_START", "default": "0", "type": int, "help": "Where to start averaging the fir model bins. Only affects the significance and contrast images."},
+            {"name": "TIME_WINDOW_END", "default": "15", "type": int, "help": "Where to end averaging the fir model bins. Only affects the significance and contrast images."},
             #{"name": "N_JOBS", "default": 1, "type": int, "help": "Number of jobs for GLM processing."},
         ]
     },
@@ -173,10 +176,10 @@ SECTIONS = [
 
 
 
-class CommandConsole(QWidget):
+class TerminalWindow(QWidget):
     def __init__(self, parent=None):
         super().__init__(parent, Qt.WindowType.Window)
-        self.setWindowTitle("Custom Console")
+        self.setWindowTitle("Terminal - FLARES")
 
         self.output_area = QTextEdit()
         self.output_area.setReadOnly(True)
@@ -189,10 +192,8 @@ class CommandConsole(QWidget):
         layout.addWidget(self.input_line)
         self.setLayout(layout)
 
-        # Define your commands
         self.commands = {
             "hello": self.cmd_hello,
-            "add": self.cmd_add,
             "help": self.cmd_help
         }
 
@@ -219,12 +220,9 @@ class CommandConsole(QWidget):
         else:
             self.output_area.append(f"[Unknown command] '{command_name}'")
 
-    # Example commands
-    def cmd_hello(self, *args):
-        return "Hello from the console!"
 
-    def cmd_add(self, a, b):
+    def cmd_hello(self, *args):
-        return f"Result: {int(a) + int(b)}"
+        return "Hello from the terminal!"
 
     def cmd_help(self, *args):
         return f"Available commands: {', '.join(self.commands.keys())}"
@@ -734,13 +732,12 @@ class UpdateEventsWindow(QWidget):
         self.description = QLabel()
         self.description.setTextFormat(Qt.TextFormat.RichText)
         self.description.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
-        self.description.setOpenExternalLinks(False) # Handle the click internally
+        self.description.setOpenExternalLinks(True)
             
-        self.description.setText("Some software when creating snirf files will insert a template of optode positions as the correct position of the optodes for the participant.<br>"
+        self.description.setText("The events that are present in a snirf file may not be the events that are to be studied and examined.<br>"
-        "This is rarely correct as each head differs slightly in shape or size, and a lot of calculations require the optodes to be in the correct location.<br>"
+        "Utilizing different software and video recordings, it is easy enough to see when an action actually occured in a file.<br>"
-        "Using a .txt file, we can update the positions in the snirf file to match those of a digitization system such as one from Polhemus or elsewhere.<br>"
+        "The software <a href='https://www.boris.unito.it/'>BORIS</a> is used to add these events to video files, and these events can be applied to the snirf file <br>"
-        "The .txt file should have the fiducials, detectors, and sources clearly labeled, followed by the x, y, and z coordinates seperated by a space.<br>"
+        "selected below by selecting the correct BORIS observation and time syncing it to an event that it shares with the snirf file.")
-        "An example format of what a digitization text file should look like can be found <a href='custom_link'>by clicking here</a>.")
 
         layout.addWidget(self.description)
 
@@ -1021,64 +1018,94 @@ class UpdateEventsWindow(QWidget):
         try:
             raw = read_raw_snirf(snirf_path, preload=True)
 
-            # Build new Annotations from shifted BORIS events
             onsets = []
             durations = []
             descriptions = []
 
+            open_events = {}  # label -> list of start times
             label_counts = {}
 
             used_times = set()
-            
             sfreq = raw.info['sfreq']  # sampling frequency in Hz
             min_shift = 1.0 / sfreq
-            
             max_attempts = 10
 
             for event in boris_events:
                 if not isinstance(event, list) or len(event) < 3:
                     continue
 
-                orig_time = event[0]
+                event_time = event[0]
-                desc = event[2]
+                label = event[2]
 
-                # Count occurrences per event label
+                count = label_counts.get(label, 0) + 1
-                count = label_counts.get(desc, 0)
+                label_counts[label] = count
-                label_counts[desc] = count + 1
 
-                # Only use 1st, 3rd, 5th... (odd occurrences)
+                if label not in open_events:
-                if (count % 2) == 0:
+                    open_events[label] = []
-                    shifted_time = orig_time + time_shift
 
-                    # Ensure unique timestamp by checking and adjusting slightly
+                if count % 2 == 1:
-                    adjusted_time = shifted_time
+                    # Odd occurrence = start event
+                    open_events[label].append(event_time)
+                else:
+                    # Even occurrence = end event
+                    if open_events[label]:
+                        matched_start = open_events[label].pop(0)
+                        duration = event_time - matched_start
 
-                    # Try to find a unique timestamp
+                        if duration <= 0:
+                            print(f"Warning: Duration for {label} is non-positive ({duration}). Skipping.")
+                            continue
+
+                        shifted_start = matched_start + time_shift
+
+                        adjusted_time = shifted_start
                         attempts = 0
                         while round(adjusted_time, 6) in used_times and attempts < max_attempts:
                             adjusted_time += min_shift
                             attempts += 1
 
                         if attempts == max_attempts:
-                        print(f"Warning: Could not find unique timestamp for event '{desc}' at original time {orig_time:.3f}s. Skipping.")
+                            print(f"Warning: Couldn't find unique time for {label} @ {matched_start}s. Skipping.")
-                        continue  # Skip problematic event
+                            continue
 
                         adjusted_time = round(adjusted_time, 6)
                         used_times.add(adjusted_time)
 
-                    print(f"Applying event: {desc} @ {adjusted_time:.3f}s (original: {orig_time:.3f}s)")
+                        print(f"Adding event: {label} @ {adjusted_time:.3f}s for {duration:.3f}s")
 
+                        onsets.append(adjusted_time)
+                        durations.append(duration)
+                        descriptions.append(label)
+                    else:
+                        print(f"Warning: Unmatched end for label '{label}' at {event_time:.3f}s. Skipping.")
+
+            # Optionally warn about any unmatched starts left open
+            for label, starts in open_events.items():
+                for start_time in starts:
+                    shifted_start = start_time + time_shift
+
+                    adjusted_time = shifted_start
+                    attempts = 0
+                    while round(adjusted_time, 6) in used_times and attempts < max_attempts:
+                        adjusted_time += min_shift
+                        attempts += 1
+
+                    if attempts == max_attempts:
+                        print(f"Warning: Couldn't find unique time for unmatched start {label} @ {start_time}s. Skipping.")
+                        continue
+
+                    adjusted_time = round(adjusted_time, 6)
+                    used_times.add(adjusted_time)
+
+                    print(f"Warning: Unmatched start for label '{label}' at {start_time:.3f}s. Adding with duration 0.")
                     onsets.append(adjusted_time)
                     durations.append(0.0)
-                    descriptions.append(desc)
+                    descriptions.append(label)
 
             new_annotations = Annotations(onset=onsets, duration=durations, description=descriptions)
 
-            # Replace annotations in raw object
             raw.set_annotations(new_annotations)
-
+            write_raw_snirf(raw, save_path)
-            # Write a new SNIRF file
-            write_raw_snirf(raw, suggested_name)
 
             QMessageBox.information(self, "Success", "SNIRF file updated with aligned BORIS events.")
 
@@ -1179,6 +1206,11 @@ class ProgressBubble(QWidget):
             else:
                 rect.setStyleSheet("background-color: white; border: 1px solid gray;")
                 
+    def mark_cancelled(self):
+        if 0 <= self.current_step < len(self.rects):
+            rect = self.rects[self.current_step]
+            rect.setStyleSheet("background-color: red; border: 1px solid gray;")
+
     def mousePressEvent(self, event):
         self.clicked.emit(self)
         super().mousePressEvent(event)
@@ -2191,12 +2223,212 @@ class ParticipantFoldChannelsWidget(QWidget):
         self.image_index_dropdown.currentIndexChanged.connect(self.update_image_index_dropdown_label)
 
         self.submit_button = QPushButton("Submit")
-        self.submit_button.clicked.connect(self.show_brain_images)
+        self.submit_button.clicked.connect(self.show_fold_images)
 
         self.top_bar.addWidget(QLabel("Participants:"))
         self.top_bar.addWidget(self.participant_dropdown)
         self.top_bar.addWidget(QLabel("Fold Type:"))
         self.top_bar.addWidget(self.image_index_dropdown)
+        self.top_bar.addWidget(QLabel("This will cause the app to hang for ~30s/Participant!"))
+        self.top_bar.addWidget(self.submit_button)
+
+        self.scroll = QScrollArea()
+        self.scroll.setWidgetResizable(True)
+        self.scroll_content = QWidget()
+        self.grid_layout = QGridLayout(self.scroll_content)
+        self.scroll.setWidget(self.scroll_content)
+        self.layout.addWidget(self.scroll)
+
+        self.thumb_size = QSize(280, 180)
+        self.showMaximized()
+
+    def _create_multiselect_dropdown(self, items):
+        combo = FullClickComboBox()
+        combo.setView(QListView())
+        model = QStandardItemModel()
+        combo.setModel(model)
+        combo.setEditable(True)
+        combo.lineEdit().setReadOnly(True)
+        combo.lineEdit().setPlaceholderText("Select...")
+
+
+        dummy_item = QStandardItem("<None Selected>")
+        dummy_item.setFlags(Qt.ItemIsEnabled)
+        model.appendRow(dummy_item)
+
+        toggle_item = QStandardItem("Toggle Select All")
+        toggle_item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+        toggle_item.setData(Qt.Unchecked, Qt.CheckStateRole)
+        model.appendRow(toggle_item)
+
+        for item in items:
+            standard_item = QStandardItem(item)
+            standard_item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+            standard_item.setData(Qt.Unchecked, Qt.CheckStateRole)
+            model.appendRow(standard_item)
+
+        combo.setInsertPolicy(QComboBox.NoInsert)
+
+
+        def on_view_clicked(index):
+            item = model.itemFromIndex(index)
+            if item.isCheckable():
+                new_state = Qt.Checked if item.checkState() == Qt.Unchecked else Qt.Unchecked
+                item.setCheckState(new_state)
+
+        combo.view().pressed.connect(on_view_clicked)
+
+        self._updating_checkstates = False
+
+        def on_item_changed(item):
+            if self._updating_checkstates:
+                return
+            self._updating_checkstates = True
+
+            normal_items = [model.item(i) for i in range(2, model.rowCount())]  # skip dummy and toggle
+
+            if item == toggle_item:
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                if all_checked:
+                    for i in normal_items:
+                        i.setCheckState(Qt.Unchecked)
+                    toggle_item.setCheckState(Qt.Unchecked)
+                else:
+                    for i in normal_items:
+                        i.setCheckState(Qt.Checked)
+                    toggle_item.setCheckState(Qt.Checked)
+
+            elif item == dummy_item:
+                pass
+
+            else:
+                # When normal items change, update toggle item
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                toggle_item.setCheckState(Qt.Checked if all_checked else Qt.Unchecked)
+
+            # Update label text immediately after change
+            if combo == self.participant_dropdown:
+                self.update_participant_dropdown_label()
+            elif combo == self.image_index_dropdown:
+                self.update_image_index_dropdown_label()
+
+            self._updating_checkstates = False
+
+        model.itemChanged.connect(on_item_changed)
+
+        combo.setInsertPolicy(QComboBox.NoInsert)
+        return combo
+    
+    def _get_checked_items(self, combo):
+        checked = []
+        model = combo.model()
+        for i in range(model.rowCount()):
+            item = model.item(i)
+            # Skip dummy and toggle items:
+            if item.text() in ("<None Selected>", "Toggle Select All"):
+                continue
+            if item.checkState() == Qt.Checked:
+                checked.append(item.text())
+        return checked
+
+    def update_participant_dropdown_label(self):
+        selected = self._get_checked_items(self.participant_dropdown)
+        if not selected:
+            self.participant_dropdown.lineEdit().setText("<None Selected>")
+        else:
+            # Extract just "Participant N" from "Participant N (filename)"
+            selected_short = [s.split(" ")[0] + " " + s.split(" ")[1] for s in selected]
+            self.participant_dropdown.lineEdit().setText(", ".join(selected_short))
+
+    def update_image_index_dropdown_label(self):
+        selected = self._get_checked_items(self.image_index_dropdown)
+        if not selected:
+            self.image_index_dropdown.lineEdit().setText("<None Selected>")
+        else:
+            # Only show the index part
+            index_labels = [s.split(" ")[0] for s in selected]
+            self.image_index_dropdown.lineEdit().setText(", ".join(index_labels))
+
+    def show_fold_images(self):
+        import flares
+
+        selected_display_names = self._get_checked_items(self.participant_dropdown)
+        selected_file_paths = []
+        for display_name in selected_display_names:
+            for fp, short_label in self.participant_map.items():
+                expected_display = f"{short_label} ({os.path.basename(fp)})"
+                if display_name == expected_display:
+                    selected_file_paths.append(fp)
+                    break
+
+        selected_indexes = [
+            int(s.split(" ")[0]) for s in self._get_checked_items(self.image_index_dropdown)
+        ]
+
+        # Pass the necessary arguments to each method
+        for file_path in selected_file_paths:
+            haemo_obj = self.haemo_dict.get(file_path)
+
+            if haemo_obj is None:
+                continue
+
+            #cha = self.cha_dict.get(file_path)
+
+            for idx in selected_indexes:
+                if idx == 0:
+
+                    flares.fold_channels(haemo_obj)
+
+                else:
+                    print(f"No method defined for index {idx}")
+
+
+
+class ExportDataAsCSVViewerWidget(QWidget):
+    def __init__(self, haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict):
+        super().__init__()
+        self.setWindowTitle("FLARES Export Data As CSV Viewer")
+        self.haemo_dict = haemo_dict
+        self.cha_dict = cha_dict
+        self.df_ind = df_ind
+        self.design_matrix = design_matrix
+        self.group = group
+        self.contrast_results_dict = contrast_results_dict
+        
+        # Create mappings: file_path -> participant label and dropdown display text
+        self.participant_map = {}  # file_path -> "Participant 1"
+        self.participant_dropdown_items = []  # "Participant 1 (filename)"
+
+        for i, file_path in enumerate(self.haemo_dict.keys(), start=1):
+            short_label = f"Participant {i}"
+            display_label = f"{short_label} ({os.path.basename(file_path)})"
+            self.participant_map[file_path] = short_label
+            self.participant_dropdown_items.append(display_label)
+
+        self.layout = QVBoxLayout(self)
+        self.top_bar = QHBoxLayout()
+        self.layout.addLayout(self.top_bar)
+
+        self.participant_dropdown = self._create_multiselect_dropdown(self.participant_dropdown_items)
+        self.participant_dropdown.currentIndexChanged.connect(self.update_participant_dropdown_label)
+              
+        self.index_texts = [
+            "0 (Export Data to CSV)",
+            # "1 (second image)",
+            # "2 (third image)",
+            # "3 (fourth image)",
+            ]
+
+        self.image_index_dropdown = self._create_multiselect_dropdown(self.index_texts)
+        self.image_index_dropdown.currentIndexChanged.connect(self.update_image_index_dropdown_label)
+
+        self.submit_button = QPushButton("Submit")
+        self.submit_button.clicked.connect(self.generate_and_save_csv)
+
+        self.top_bar.addWidget(QLabel("Participants:"))
+        self.top_bar.addWidget(self.participant_dropdown)
+        self.top_bar.addWidget(QLabel("Export Type:"))
+        self.top_bar.addWidget(self.image_index_dropdown)
         self.top_bar.addWidget(self.submit_button)
 
         self.scroll = QScrollArea()
@@ -2316,8 +2548,7 @@ class ParticipantFoldChannelsWidget(QWidget):
             index_labels = [s.split(" ")[0] for s in selected]
             self.image_index_dropdown.lineEdit().setText(", ".join(index_labels))
 
-    def show_brain_images(self):
+    def generate_and_save_csv(self):
-        import flares
         
         selected_display_names = self._get_checked_items(self.participant_dropdown)
         selected_file_paths = []
@@ -2332,42 +2563,6 @@ class ParticipantFoldChannelsWidget(QWidget):
             int(s.split(" ")[0]) for s in self._get_checked_items(self.image_index_dropdown)
         ]
 
-
-        parameterized_indexes = {
-            0: [
-                {
-                    "key": "show_optodes",
-                    "label": "Determine what is rendered above the brain. Valid values are 'sensors', 'labels', 'none', 'all'.",
-                    "default": "all",
-                    "type": str,
-                },
-                {
-                    "key": "show_brodmann",
-                    "label": "Show common brodmann areas on the brain.",
-                    "default": "True",
-                    "type": bool,
-                }
-            ],
-        }
-
-        # Inject full_text from index_texts
-        for idx, params_list in parameterized_indexes.items():
-            full_text = self.index_texts[idx] if idx < len(self.index_texts) else f"{idx} (No label found)"
-            for param_info in params_list:
-                param_info["full_text"] = full_text
-
-        indexes_needing_params = {idx: parameterized_indexes[idx] for idx in selected_indexes if idx in parameterized_indexes}
-
-        param_values = {}
-        if indexes_needing_params:
-            dialog = ParameterInputDialog(indexes_needing_params, parent=self)
-            if dialog.exec_() == QDialog.Accepted:
-                param_values = dialog.get_values()
-                if param_values is None:
-                    return
-            else:
-                return
-
         # Pass the necessary arguments to each method
         for file_path in selected_file_paths:
             haemo_obj = self.haemo_dict.get(file_path)
@@ -2375,26 +2570,40 @@ class ParticipantFoldChannelsWidget(QWidget):
             if haemo_obj is None:
                 continue
 
-            #cha = self.cha_dict.get(file_path)
+            cha = self.cha_dict.get(file_path)
 
             for idx in selected_indexes:
                 if idx == 0:
+                    try:
+                        suggested_name = f"{file_path}.csv"
 
-                    params = param_values.get(idx, {})
+                        # Open save dialog
-                    show_optodes = params.get("show_optodes", None)
+                        save_path, _ = QFileDialog.getSaveFileName(
-                    show_brodmann = params.get("show_brodmann", None)
+                            self,
+                            "Save SNIRF File As",
+                            suggested_name,
+                            "CSV Files (*.csv)"
+                        )
 
-                    if show_optodes is None or show_brodmann is None:
+                        if not save_path:
-                        print(f"Missing parameters for index {idx}, skipping.")
+                            print("Save cancelled.")
-                        continue
+                            return
+
+                        if not save_path.lower().endswith(".csv"):
+                            save_path += ".csv"
+                        # Save the CSV here
+                        
+                        cha.to_csv(save_path)
+                        QMessageBox.information(self, "Success", "CSV file has been saved.")
+
+                    except Exception as e:
+                        QMessageBox.critical(self, "Error", f"Failed to update SNIRF file:\n{e}")
 
-                    flares.fold_channels(haemo_obj)
 
                 else:
                     print(f"No method defined for index {idx}")
 
 
-
 class ClickableLabel(QLabel):
     def __init__(self, full_pixmap: QPixmap, thumbnail_pixmap: QPixmap):
         super().__init__()
@@ -2600,7 +2809,7 @@ class GroupViewerWidget(QWidget):
         self.index_texts = [
             "0 (GLM Results)",
             "1 (Significance)",
-            # "2 (third_image)",
+            "2 (Brain Activity Visualization)",
             # "3 (fourth image)",
             ]
 
@@ -2903,6 +3112,32 @@ class GroupViewerWidget(QWidget):
                     "type": float,
                 }
             ],
+            2: [
+                {
+                    "key": "show_optodes",
+                    "label": "Determine what is rendered above the brain. Valid values are 'sensors', 'labels', 'none', 'all'.",
+                    "default": "all",
+                    "type": str,
+                },
+                {
+                    "key": "t_or_theta",
+                    "label": "Specify if t values or theta values should be plotted. Valid values are 't', 'theta'",
+                    "default": "theta",
+                    "type": str,
+                },
+                {
+                    "key": "show_text",
+                    "label": "Display informative text on the top left corner. THIS DOES NOT WORK AND SHOULD BE LEFT AT FALSE",
+                    "default": "False",
+                    "type": bool,
+                },
+                {
+                    "key": "brain_bounds",
+                    "label": "Graph Upper/Lower Limit",
+                    "default": "1.0",
+                    "type": float,
+                }
+            ],
         }
 
         # Inject full_text from index_texts
@@ -2925,8 +3160,13 @@ class GroupViewerWidget(QWidget):
             
 
         all_cha = pd.DataFrame()
-        for fp in selected_file_paths:
+        for file_path in selected_file_paths:
-            cha_df = self.cha.get(fp)
+            haemo_obj = self.haemo_dict.get(file_path)
+
+            if haemo_obj is None:
+                continue
+            
+            cha_df = self.cha.get(file_path)
             if cha_df is not None:
                 all_cha = pd.concat([all_cha, cha_df], ignore_index=True)
 
@@ -2981,6 +3221,20 @@ class GroupViewerWidget(QWidget):
                 df_contrasts = pd.concat(all_contrasts, ignore_index=True)
                 flares.run_second_level_analysis(df_contrasts, p_haemo, p_val, graph_bounds)
 
+            elif idx == 2:
+                params = param_values.get(idx, {})
+                show_optodes = params.get("show_optodes", None)
+                t_or_theta = params.get("t_or_theta", None)
+                show_text = params.get("show_text", None)
+                brain_bounds = params.get("brain_bounds", None)
+
+                if show_optodes is None or t_or_theta is None or show_text is None or brain_bounds is None:
+                    print(f"Missing parameters for index {idx}, skipping.")
+                    continue
+
+                flares.brain_3d_visualization(haemo_obj, all_cha, selected_event, t_or_theta=t_or_theta, show_optodes=show_optodes, show_text=show_text, brain_bounds=brain_bounds)
+
+                
             elif idx == 3:
                 pass
 
@@ -3557,12 +3811,16 @@ class ViewerLauncherWidget(QWidget):
         btn5 = QPushButton("Open Cross Group Brain Viewer")
         btn5.clicked.connect(lambda: self.open_group_brain_viewer(haemo_dict, df_ind, design_matrix, group, contrast_results_dict))
         
+        btn6 = QPushButton("Open Export Data As CSV Viewer")
+        btn6.clicked.connect(lambda: self.open_export_data_as_csv_viewer(haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict))
+
 
         layout.addWidget(btn1)
         layout.addWidget(btn2)
         layout.addWidget(btn3)
         layout.addWidget(btn4)
         layout.addWidget(btn5)
+        layout.addWidget(btn6)
 
     def open_participant_viewer(self, haemo_dict, fig_bytes_dict):
         self.participant_viewer = ParticipantViewerWidget(haemo_dict, fig_bytes_dict)
@@ -3584,6 +3842,10 @@ class ViewerLauncherWidget(QWidget):
         self.participant_brain_viewer = GroupBrainViewerWidget(haemo_dict, df_ind, design_matrix, group, contrast_results_dict)
         self.participant_brain_viewer.show()
 
+    def open_export_data_as_csv_viewer(self, haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict):
+        self.export_data_as_csv_viewer = ExportDataAsCSVViewerWidget(haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict)
+        self.export_data_as_csv_viewer.show()
+
 
 class MainApplication(QMainWindow):
     """
@@ -3606,6 +3868,7 @@ class MainApplication(QMainWindow):
         self.param_sections = []
         self.folder_paths = []
         self.section_widget = None
+        self.first_run = True
 
         self.init_ui()
         self.create_menu_bar()
@@ -3834,8 +4097,8 @@ class MainApplication(QMainWindow):
         options_actions = [
             ("User Guide", "F1", self.user_guide, resource_path("icons/help_24dp_1F1F1F.svg")), 
             ("Check for Updates", "F5", self.manual_check_for_updates, resource_path("icons/update_24dp_1F1F1F.svg")),
-            ("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/update_24dp_1F1F1F.svg")),
+            ("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
-            ("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/update_24dp_1F1F1F.svg")),
+            ("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
             ("About", "F12", self.about_window, resource_path("icons/info_24dp_1F1F1F.svg"))
         ]
 
@@ -3846,9 +4109,7 @@ class MainApplication(QMainWindow):
 
         terminal_menu = menu_bar.addMenu("Terminal")
         terminal_actions = [
-            ("Cut", "Ctrl+X", self.terminal_gui, resource_path("icons/content_cut_24dp_1F1F1F.svg")),
+            ("New Terminal", "Ctrl+Alt+T", self.terminal_gui, resource_path("icons/terminal_24dp_1F1F1F.svg")),
-            ("Copy", "Ctrl+C", self.terminal_gui, resource_path("icons/content_copy_24dp_1F1F1F.svg")),
-            ("Paste", "Ctrl+V", self.terminal_gui, resource_path("icons/content_paste_24dp_1F1F1F.svg"))
         ]
         for name, shortcut, slot, icon in terminal_actions:
             terminal_menu.addAction(make_action(name, shortcut, slot, icon=icon))
@@ -3875,6 +4136,8 @@ class MainApplication(QMainWindow):
 
     def clear_all(self):
         
+        self.cancel_task()
+        
         self.right_column_widget.hide()
         
         # Clear the bubble layout
@@ -3937,7 +4200,7 @@ class MainApplication(QMainWindow):
             
     def terminal_gui(self):
         if self.terminal is None or not self.terminal.isVisible():
-            self.terminal = CommandConsole(self)
+            self.terminal = TerminalWindow(self)
             self.terminal.show()
 
     def update_optode_positions(self):
@@ -4284,8 +4547,52 @@ class MainApplication(QMainWindow):
         return self.file_metadata
 
 
+    def cancel_task(self):
+        self.button1.clicked.disconnect(self.cancel_task)
+        self.button1.setText("Stopping...")
+
+        if hasattr(self, "result_process") and self.result_process.is_alive():
+            parent = psutil.Process(self.result_process.pid)
+            children = parent.children(recursive=True)
+            for child in children:
+                try:
+                    child.kill()
+                except psutil.NoSuchProcess:
+                    pass
+            self.result_process.terminate()
+            self.result_process.join()
+
+        if hasattr(self, "result_timer") and self.result_timer.isActive():
+            self.result_timer.stop()
+        
+        # if hasattr(self, "result_process") and self.result_process.is_alive():
+        #     self.result_process.terminate()  # Forcefully terminate the process
+        #     self.result_process.join()       # Wait for it to properly close
+
+        # # Stop the QTimer if running
+        # if hasattr(self, "result_timer") and self.result_timer.isActive():
+        #     self.result_timer.stop()
+        
+        for bubble in self.bubble_widgets.values():
+            bubble.mark_cancelled()
+
+        self.statusbar.showMessage("Processing cancelled.")
+        self.button1.clicked.connect(self.on_run_task)
+        self.button1.setText("Process")
+
+
     '''MODULE FILE'''
     def on_run_task(self):
+        
+        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()
+        self.first_run = False
+
         # Collect all selected snirf files in a flat list
         snirf_files = []
 
@@ -4608,6 +4915,16 @@ class MainApplication(QMainWindow):
             else:
                 snirf_info['Digitization Points'] = "Not found"
                 
+            if raw.annotations is not None and len(raw.annotations) > 0:
+                annot_info = []
+                for onset, duration, desc in zip(raw.annotations.onset,
+                                                raw.annotations.duration,
+                                                raw.annotations.description):
+                    annot_info.append(f"Onset: {onset:.2f}s, Duration: {duration:.2f}s, Description: {desc}")
+                snirf_info['Annotations'] = annot_info
+            else:
+                snirf_info['Annotations'] = "No annotations found"
+                
             return snirf_info
         except:
             return None
@@ -4813,7 +5130,7 @@ def resource_path(relative_path):
         # PyInstaller bundle path
         base_path = sys._MEIPASS
     else:
-        base_path = os.path.abspath(".")
+        base_path = os.path.dirname(os.path.abspath(__file__))
 
     return os.path.join(base_path, relative_path)