mostly finish rewrite

src/analysis/exportcsv.py

@@ -0,0 +1,166 @@
+"""
+Filename: exportcsv.py
+Description: Export data as csv analysis window for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
+import os
+
+import numpy as np
+import pandas as pd
+
+from PySide6.QtWidgets import QFileDialog, QGridLayout, QHBoxLayout, QMessageBox, QPushButton, QScrollArea, QWidget, QVBoxLayout, QLabel
+from PySide6.QtCore import QSize
+
+from src.shared.flaresbasewidget import FlaresBaseWidget
+from src.shared.shareddata import APP_NAME
+
+
+class ExportDataAsCSVViewerWidget(FlaresBaseWidget):
+    def __init__(self, haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict):
+        super().__init__("ExportDataAsCSVViewer")
+        self.setWindowTitle(f"Export Data As CSV Viewer - {APP_NAME.upper()}")
+        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 (CSV for SPARKS)",
+            # "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()
+        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 generate_and_save_csv(self):
+        
+        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)
+        ]
+
+        if not selected_file_paths or not selected_indexes:
+            QMessageBox.warning(self, "Selection Missing", "Please select at least one participant and one export type.")
+            return
+
+        # 2. ASK ONCE: Select Output Directory
+        output_dir = QFileDialog.getExistingDirectory(self, "Select Output Folder for CSV Exports")
+        
+        if not output_dir:
+            print("Export cancelled: No folder selected.")
+            return
+
+        success_count = 0
+
+        # Pass the necessary arguments to each method
+        for file_path in selected_file_paths:
+            base_filename = os.path.splitext(os.path.basename(file_path))[0]
+            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:
+                try:
+                    if idx == 0:
+                        save_path = os.path.join(output_dir, f"{base_filename}_exported.csv")
+                        if cha is not None:
+                            cha.to_csv(save_path)
+                            success_count += 1
+
+
+                    elif idx == 1:
+                            # SPARKS Export
+                            save_path = os.path.join(output_dir, f"{base_filename}_sparks.csv")
+                            if haemo_obj is not None:
+                                raw = haemo_obj
+                                data, times = raw.get_data(return_times=True)
+                                ann_col = np.full(times.shape, "", dtype=object)
+
+                                if raw.annotations is not None and len(raw.annotations) > 0:
+                                    for onset, duration, desc in zip(
+                                        raw.annotations.onset,
+                                        raw.annotations.duration,
+                                        raw.annotations.description
+                                    ):
+                                        mask = (times >= onset) & (times < onset + duration)
+                                        ann_col[mask] = desc
+
+                                df = pd.DataFrame(data.T, columns=raw.ch_names)
+                                df.insert(0, "annotation", ann_col)
+                                df.insert(0, "time", times)
+                                df.to_csv(save_path, index=False)
+                                success_count += 1
+                        
+                    else:
+                        print(f"No method defined for index {idx}")
+                
+                except Exception as e:
+                    print(f"Failed to export {file_path} (Type {idx}): {e}")
+
+        # 4. Final Notification
+        if success_count > 0:
+            QMessageBox.information(self, "Export Complete", f"Successfully saved {success_count} CSV files to:\n{output_dir}")
+            
+            # # If SPARKS export was included, show the Event Window once at the end
+            # if 1 in selected_indexes:
+            #     win = UpdateEventsWindow(
+            #         parent=self,
+            #         mode=EventUpdateMode.WRITE_JSON,
+            #         caller="Video Alignment Tool"
+            #     )
+            #     win.show()
+

src/analysis/group.py

@@ -0,0 +1,306 @@
+"""
+Filename: group.py
+Description: Group analysis window for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
+import os
+
+import pandas as pd
+
+from PySide6.QtWidgets import QComboBox, QDialog, QGridLayout, QHBoxLayout, QPushButton, QScrollArea, QWidget, QVBoxLayout, QLabel
+from PySide6.QtCore import QSize
+
+from src.shared.flaresbasewidget import FlaresBaseWidget, ParameterInputDialog
+from src.shared.shareddata import APP_NAME
+
+
+class GroupViewerWidget(FlaresBaseWidget):
+    def __init__(self, haemo_dict, cha, df_ind, design_matrix, contrast_results, group):
+        super().__init__("GroupViewer")
+        self.setWindowTitle(f"Group Viewer - {APP_NAME.upper()}")
+        self.haemo_dict = haemo_dict
+        self.cha = cha
+        self.df_ind = df_ind
+        self.design_matrix = design_matrix
+        self.contrast_results = contrast_results
+        self.group = group
+        self.show_all_events = True
+        self._updating_checkstates = False
+        
+        # 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.group_to_paths = {}
+        for file_path, group_name in self.group.items():
+            self.group_to_paths.setdefault(group_name, []).append(file_path)
+
+        self.group_names = sorted(self.group_to_paths.keys())
+
+        self.group_dropdown = QComboBox()
+        self.group_dropdown.addItem("<None Selected>")
+        self.group_dropdown.addItems(self.group_names)
+        self.group_dropdown.setCurrentIndex(0)
+        self.group_dropdown.currentIndexChanged.connect(self.update_participant_list_for_group)
+
+        self.participant_dropdown = self._create_multiselect_dropdown(self.participant_dropdown_items)
+        self.participant_dropdown.currentIndexChanged.connect(self.update_participant_dropdown_label)
+        self.participant_dropdown.setEnabled(False)
+
+        self.event_dropdown = QComboBox()
+        self.event_dropdown.addItem("<None Selected>")
+
+        self.index_texts = [
+            "0 (GLM Results)",
+            "1 (Significance)",
+            "2 (Brain Activity Visualization)",
+            # "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.show_brain_images)
+
+        self.top_bar.addWidget(QLabel("Group:"))
+        self.top_bar.addWidget(self.group_dropdown)
+        self.top_bar.addWidget(QLabel("Participants:"))
+        self.top_bar.addWidget(self.participant_dropdown)
+        self.top_bar.addWidget(QLabel("Event:"))
+        self.top_bar.addWidget(self.event_dropdown)
+        self.top_bar.addWidget(QLabel("Image Indexes:"))
+        self.top_bar.addWidget(self.image_index_dropdown)
+        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 show_brain_images(self):
+        import flares as flares
+
+        selected_event = self.event_dropdown.currentText()
+        if selected_event == "<None Selected>":
+            selected_event = None
+
+        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
+
+        if selected_event:
+            valid_paths = []
+            for fp in selected_file_paths:
+                raw = self.haemo_dict.get(fp)
+                # Check if this participant actually has the event in their annotations
+                if raw is not None and hasattr(raw, "annotations"):
+                    if selected_event in raw.annotations.description:
+                        valid_paths.append(fp)
+            
+            selected_file_paths = valid_paths
+
+        selected_indexes = [
+            int(s.split(" ")[0]) for s in self._get_checked_items(self.image_index_dropdown)
+        ]
+
+        if not selected_file_paths:
+            print("No participants selected.")
+            return
+
+        # Only keep indexes 0 and 1 that need parameters
+        parameterized_indexes = {
+            0: [
+                {
+                    "key": "lower_bound",
+                    "label": "Lower bound + <description>",
+                    "default": "-0.3",
+                    "type": float,  # specify int here
+                },
+                {
+                    "key": "upper_bound",
+                    "label": "Upper bound + <description>",
+                    "default": "0.8",
+                    "type": float,  # specify int here
+                }
+            ],
+            1: [
+                {
+                    "key": "p_value",
+                    "label": "Significance threshold P-value (e.g. 0.05)",
+                    "default": "0.05",
+                    "type": float,
+                },
+                {
+                    "key": "graph_bounds",
+                    "label": "Graph Upper/Lower Limit",
+                    "default": "3.0",
+                    "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
+        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
+            
+
+        all_cha = pd.DataFrame()
+        for file_path in selected_file_paths:
+            haemo_obj = self.haemo_dict.get(file_path)
+
+            if selected_event:
+                participant_events = set(haemo_obj.annotations.description)
+                if selected_event not in participant_events:
+                    print(f"Skipping {self.participant_map[file_path]}: Event '{selected_event}' not found.")
+                    continue
+
+            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)
+
+        # Pass the necessary arguments to each method
+        file_path = selected_file_paths[0]
+        p_haemo = self.haemo_dict.get(file_path)
+        p_design_matrix = self.design_matrix.get(file_path)
+
+        df_group = pd.DataFrame()
+
+        if selected_file_paths:
+            for file_path in selected_file_paths:
+                df = self.df_ind.get(file_path)
+                if df is not None:
+                    df_group = pd.concat([df_group, df], ignore_index=True)
+                
+
+        for idx in selected_indexes:
+            if idx == 0:
+                params = param_values.get(idx, {})
+                lower_bound = params.get("lower_bound", None)
+                upper_bound = params.get("upper_bound", None)
+
+                if lower_bound is None or upper_bound is None:
+                    print(f"Missing parameters for index {idx}, skipping.")
+                    continue
+
+
+                flares.plot_fir_model_results(df_group, p_haemo, p_design_matrix, selected_event, lower_bound, upper_bound)
+
+            elif idx == 1:
+                params = param_values.get(idx, {})
+                p_val = params.get("p_value", None)
+                graph_bounds = params.get("graph_bounds", None)
+
+                if p_val is None or graph_bounds is None:
+                    print(f"Missing parameters for index {idx}, skipping.")
+                    continue
+
+                all_contrasts = []
+                for fp in selected_file_paths:
+                    condition_dfs = self.contrast_results.get(fp, {})
+                    if selected_event in condition_dfs:
+                        df = condition_dfs[selected_event].copy()
+                        df["ID"] = fp
+                        all_contrasts.append(df)
+
+                if not all_contrasts:
+                    print("No contrast data found for selected participants and event.")
+                    return
+
+                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
+
+                raw_list = [self.haemo_dict.get(fp) for fp in selected_file_paths]
+                
+                if len(selected_file_paths) > 1:
+                    print(f"Aggregating geometry for {len(selected_file_paths)} participants...")
+                    processed_raw = flares.aggregate_fnirs_group_geometry(raw_list)
+                else:
+                    processed_raw = raw_list[0].copy().pick(picks="hbo")
+
+                flares.brain_3d_visualization(processed_raw, 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
+
+            else:
+                print(f"No method defined for index {idx}")

src/analysis/groupbrain.py

@@ -0,0 +1,311 @@
+"""
+Filename: groupbrain.py
+Description: Group brain analysis window for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
+import os
+
+import pandas as pd
+
+from PySide6.QtWidgets import QComboBox, QDialog, QGridLayout, QHBoxLayout, QPushButton, QScrollArea, QWidget, QVBoxLayout, QLabel
+from PySide6.QtCore import QSize
+
+from src.shared.flaresbasewidget import FlaresBaseWidget, ParameterInputDialog
+from src.shared.shareddata import APP_NAME
+
+
+class GroupBrainViewerWidget(FlaresBaseWidget):
+    def __init__(self, haemo_dict, df_ind, design_matrix, group, contrast_results_dict):
+        super().__init__("GroupBrainViewer")
+        self.setWindowTitle(f"Group Brain Viewer - {APP_NAME.upper()}")
+        self.haemo_dict = haemo_dict
+        self.df_ind = df_ind
+        self.design_matrix = design_matrix
+        self.group = group
+        self.contrast_results_dict = contrast_results_dict
+
+        self.group_to_paths = {}
+        for file_path, group_name in self.group.items():
+            self.group_to_paths.setdefault(group_name, []).append(file_path)
+
+        self.group_names = sorted(self.group_to_paths.keys())
+
+        self.layout = QVBoxLayout(self)
+        self.top_bar = QHBoxLayout()
+        self.layout.addLayout(self.top_bar)
+
+
+        self.group_a_dropdown = QComboBox()
+        self.group_a_dropdown.addItem("<None Selected>")
+        self.group_a_dropdown.addItems(self.group_names)
+        self.group_a_dropdown.currentIndexChanged.connect(self._update_group_a_options)
+
+
+        self.group_b_dropdown = QComboBox()
+        self.group_b_dropdown.addItem("<None Selected>")
+        self.group_b_dropdown.addItems(self.group_names)
+        self.group_b_dropdown.currentIndexChanged.connect(self._update_group_b_options)
+
+
+        self.event_dropdown = QComboBox()
+        self.event_dropdown.addItem("<None Selected>")
+
+        self.participant_dropdown_a = self._create_multiselect_dropdown([])
+        self.participant_dropdown_a.lineEdit().setPlaceholderText("Select participants (Group A)")
+        self.participant_dropdown_a.model().itemChanged.connect(self._on_participants_changed)
+
+
+        self.participant_dropdown_b = self._create_multiselect_dropdown([])
+        self.participant_dropdown_b.lineEdit().setPlaceholderText("Select participants (Group B)")
+        self.participant_dropdown_b.model().itemChanged.connect(self._on_participants_changed)
+
+
+        self.index_texts = [
+            "0 (Contrast Image)",
+            # "1 (3D Brain Contrast)",
+            # "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.show_brain_images)
+
+
+        self.top_bar.addWidget(QLabel("Group A:"))
+        self.top_bar.addWidget(self.group_a_dropdown)
+        self.top_bar.addWidget(QLabel("Participants (Group A):"))
+        self.top_bar.addWidget(self.participant_dropdown_a)
+        self.top_bar.addWidget(QLabel("Group B:"))
+        self.top_bar.addWidget(self.group_b_dropdown)
+        self.top_bar.addWidget(QLabel("Participants (Group B):"))
+        self.top_bar.addWidget(self.participant_dropdown_b)
+        self.top_bar.addWidget(QLabel("Event:"))
+        self.top_bar.addWidget(self.event_dropdown)
+        self.top_bar.addWidget(QLabel("Image Indexes:"))
+        self.top_bar.addWidget(self.image_index_dropdown)
+        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 _update_group_b_options(self):
+        """Triggered when Group B changes: Update Group A to exclude B's choice"""
+        selected_b = self.group_b_dropdown.currentText()
+        
+        # Refresh Group A and exclude what was just picked in Group B
+        self._refresh_group_dropdown(self.group_a_dropdown, exclude=selected_b)
+        
+        # Update the participants for Group B
+        self.update_participant_list_for_group(selected_b, self.participant_dropdown_b)
+        self._update_event_dropdown()
+
+    def _update_group_a_options(self):
+        """Triggered when Group A changes: Update Group B to exclude A's choice"""
+        selected_a = self.group_a_dropdown.currentText()
+        
+        # Refresh Group B and exclude what was just picked in Group A
+        self._refresh_group_dropdown(self.group_b_dropdown, exclude=selected_a)
+        
+        # Update the participants for Group A
+        self.update_participant_list_for_group(selected_a, self.participant_dropdown_a)
+        self._update_event_dropdown()
+
+    def _on_participants_changed(self, item=None):
+        self._update_event_dropdown()
+
+
+    def _refresh_group_dropdown(self, dropdown, exclude):
+        current = dropdown.currentText()
+        dropdown.blockSignals(True)
+        dropdown.clear()
+        dropdown.addItem("<None Selected>")
+        for group in self.group_names:
+            if group != exclude:
+                dropdown.addItem(group)
+        # Restore previous selection if still valid
+        if current != "<None Selected>" and current != exclude and dropdown.findText(current) != -1:
+            dropdown.setCurrentText(current)
+        else:
+            dropdown.setCurrentIndex(0)  # Reset to "<None Selected>"
+        dropdown.blockSignals(False)
+
+
+    def _get_file_paths_from_labels(self, labels, group_name):
+        file_paths = []
+
+        if group_name == self.group_a_dropdown.currentText():
+            participant_map = self.participant_map_a
+        elif group_name == self.group_b_dropdown.currentText():
+            participant_map = self.participant_map_b
+        else:
+            return []
+
+        # Reverse map: display label -> file path
+        reverse_map = {
+            f"{label} ({os.path.basename(fp)})": fp
+            for fp, label in participant_map.items()
+        }
+
+        for label in labels:
+            file_path = reverse_map.get(label)
+            if file_path:
+                file_paths.append(file_path)
+
+        return file_paths
+
+    def show_brain_images(self):
+        import flares as flares
+
+        selected_event = self.event_dropdown.currentText()
+        if selected_event == "<None Selected>":
+            selected_event = None
+
+        # Group A
+        participants_a = self._get_checked_items(self.participant_dropdown_a)
+        file_paths_a = self._get_file_paths_from_labels(participants_a, self.group_a_dropdown.currentText())
+
+        # Group B
+        participants_b = self._get_checked_items(self.participant_dropdown_b)
+        file_paths_b = self._get_file_paths_from_labels(participants_b, self.group_b_dropdown.currentText())
+
+        selected_indexes = [
+            int(s.split(" ")[0]) for s in self._get_checked_items(self.image_index_dropdown)
+        ]
+
+        all_selected_paths = list(set(file_paths_a + file_paths_b))
+        
+        if not all_selected_paths:
+            print("No participants selected.")
+            return
+        
+        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": "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 about the contrast.",
+                    "default": "True",
+                    "type": bool,
+                },
+                {
+                    "key": "brain_bounds",
+                    "label": "Graph Upper/Lower Limit",
+                    "default": "1.0",
+                    "type": float,
+                },
+                {
+                    "key": "is_3d",
+                    "label": "Should we display the results in a 3D interactive window?",
+                    "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
+
+        # Build group-level contrast DataFrames
+        def concat_group_contrasts(file_paths: list[str], event: str | None) -> pd.DataFrame:
+            group_df = pd.DataFrame()
+            for fp in file_paths:
+                print(f"Looking up contrast for: {fp}")
+                event_con_dict = self.contrast_results_dict.get(fp, {})
+                print("Available events for this file:", list(event_con_dict.keys()))
+                if event and event in event_con_dict:
+                    df = event_con_dict[event]
+                    print(f"Appending contrast df for event: {event}")
+                    group_df = pd.concat([group_df, df], ignore_index=True)
+                else:
+                    print(f"Event '{event}' not found for {fp}")
+            return group_df
+
+        print("Selected event:", selected_event)
+        print("File paths A:", file_paths_a)
+        print("File paths B:", file_paths_b)
+
+        contrast_df_a = concat_group_contrasts(file_paths_a, selected_event)
+        contrast_df_b = concat_group_contrasts(file_paths_b, selected_event)
+
+        print("contrast_df_a empty?", contrast_df_a.empty)
+        print("contrast_df_b empty?", contrast_df_b.empty)
+
+        all_raw_objs = [self.haemo_dict.get(fp) for fp in all_selected_paths if self.haemo_dict.get(fp)]
+        
+        if len(all_raw_objs) > 1:
+            processed_raw = flares.aggregate_fnirs_group_geometry(all_raw_objs)
+        else:
+            processed_raw = all_raw_objs[0].copy().pick(picks="hbo")
+
+        # Visualizations
+        for idx in selected_indexes:
+            if idx == 0:
+                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)
+                is_3d = params.get("is_3d", None)
+
+                if show_optodes is None or t_or_theta is None or show_text is None or brain_bounds is None or is_3d is None:
+                    print(f"Missing parameters for index {idx}, skipping.")
+                    continue
+
+                if not contrast_df_a.empty and not contrast_df_b.empty and processed_raw:
+
+                    flares.plot_2d_3d_contrasts_between_groups(
+                        contrast_df_a,
+                        contrast_df_b,
+                        raw_haemo=processed_raw,
+                        group_a_name=self.group_a_dropdown.currentText(),
+                        group_b_name=self.group_b_dropdown.currentText(),
+                        is_3d=is_3d,
+                        t_or_theta=t_or_theta,
+                        show_optodes=show_optodes,
+                        show_text=show_text,
+                        brain_bounds=brain_bounds
+                    )
+                else:
+                    print("no")
+           
+

src/analysis/groupfunctionalconnectivity.py

@@ -1,3 +1,11 @@
+"""
+Filename: groupfunctionalconnectivity.py
+Description: Group functional connectivity analysis window for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 import os
 
 from PySide6.QtWidgets import QComboBox, QDialog, QGridLayout, QHBoxLayout, QPushButton, QScrollArea, QWidget, QVBoxLayout, QLabel, QMessageBox
@@ -10,14 +18,14 @@ from src.shared.shareddata import APP_NAME
 class GroupFunctionalConnectivityWidget(FlaresBaseWidget):
     def __init__(self, haemo_dict, group, config_dict):
         super().__init__("GroupFunctionalConnectivityWidget")
-        self.setWindowTitle(f"{APP_NAME.upper} Group Viewer")
+        self.setWindowTitle(f"Group Functional Connectivity Viewer [BETA] - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.group = group
         self.config_dict = config_dict
         self.show_all_events = True
         self._updating_checkstates = False
 
-        QMessageBox.warning(self, f"Warning - {APP_NAME.upper}", f"Functional Connectivity is still in development and the results should currently be taken with a grain of salt. "
+        QMessageBox.warning(self, f"Warning - {APP_NAME.upper()}", f"Functional Connectivity is still in development and the results should currently be taken with a grain of salt. "
                     "By clicking OK, you accept that the images generated may not be factual.")
 
         

src/analysis/participant.py

@@ -1,3 +1,11 @@
+"""
+Filename: participant.py
+Description: Participant analysis window for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 import os
 from pathlib import Path
 from datetime import datetime
@@ -14,7 +22,7 @@ class ParticipantViewerWidget(FlaresBaseWidget):
     def __init__(self, haemo_dict, fig_bytes_dict):
         super().__init__("ParticipantViewer")
         self.setAttribute(Qt.WidgetAttribute.WA_DeleteOnClose)
-        self.setWindowTitle(f"{APP_NAME.upper} Participant Viewer")
+        self.setWindowTitle(f"Participant Viewer - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.fig_bytes_dict = fig_bytes_dict
 

src/analysis/participantbrain.py

@@ -1,3 +1,11 @@
+"""
+Filename: participantbrain.py
+Description: Participant brain analysis window for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 import os
 
 from PySide6.QtWidgets import QComboBox, QDialog, QGridLayout, QHBoxLayout, QPushButton, QScrollArea, QWidget, QVBoxLayout, QLabel
@@ -10,7 +18,7 @@ from src.shared.shareddata import APP_NAME
 class ParticipantBrainViewerWidget(FlaresBaseWidget):
     def __init__(self, haemo_dict, cha_dict):
         super().__init__("ParticipantBrainViewer")
-        self.setWindowTitle(f"{APP_NAME.upper} Participant Brain Viewer")
+        self.setWindowTitle(f"Participant Brain Viewer - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.cha_dict = cha_dict
 

src/analysis/participantfunctionalconnectivity.py

@@ -1,3 +1,11 @@
+"""
+Filename: participantfunctionalconnectivity.py
+Description: Participant functional connectivity analysis window for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 import os
 
 from PySide6.QtWidgets import QComboBox, QDialog, QGridLayout, QHBoxLayout, QPushButton, QScrollArea, QWidget, QVBoxLayout, QLabel, QMessageBox
@@ -10,11 +18,11 @@ from src.shared.shareddata import APP_NAME
 class ParticipantFunctionalConnectivityWidget(FlaresBaseWidget):
     def __init__(self, haemo_dict, epochs_dict):
         super().__init__("FunctionalConnectivityWidget")
-        self.setWindowTitle(f"{APP_NAME.upper} Functional Connectivity Viewer [BETA]")
+        self.setWindowTitle(f"Functional Connectivity Viewer [BETA] - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.epochs_dict = epochs_dict
 
-        QMessageBox.warning(self, f"Warning - {APP_NAME.upper}", f"Functional Connectivity is still in development and the results should currently be taken with a grain of salt. "
+        QMessageBox.warning(self, f"Warning - {APP_NAME.upper()}", f"Functional Connectivity is still in development and the results should currently be taken with a grain of salt. "
                             "By clicking OK, you accept that the images generated may not be factual.")
 
         # Create mappings: file_path -> participant label and dropdown display text

src/shared/flaresbasewidget.py

@@ -1,3 +1,11 @@
+"""
+Filename: flaresbasewidget.py
+Description: Custom window design and supporting methods for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 import os
 
 from PySide6.QtWidgets import QApplication, QComboBox, QDialog, QHBoxLayout, QLabel, QLineEdit, QListView, QMessageBox, QPushButton, QVBoxLayout, QWidget, QFrame, QSpinBox
@@ -5,7 +13,26 @@ from PySide6.QtGui import QStandardItemModel, QStandardItem, QPixmap, QIntValida
 from PySide6.QtCore import QEvent, Qt
 
 from src.shared.shareddata import APP_NAME
-from src.shared.flaresbasewidget import FullClickComboBox
+
+
+class FullClickComboBox(QComboBox):
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setEditable(True)
+        self.lineEdit().setReadOnly(True)
+        self.lineEdit().installEventFilter(self)
+
+    def eventFilter(self, obj, event):
+        if obj == self.lineEdit():
+            
+            if event.type() == QEvent.MouseButtonPress:
+                return True
+
+            if event.type() == QEvent.MouseButtonRelease:
+                self.showPopup()
+                return True
+                
+        return super().eventFilter(obj, event)
     
 
 class ClickableLabel(QLabel):

src/shared/shareddata.py

@@ -1,3 +1,11 @@
+"""
+Filename: shareddata.py
+Description: Shared constants and methods for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 import sys
 import os
 import platform
@@ -7,6 +15,8 @@ APP_NAME = "flares"
 API_URL = f"https://git.research.dezeeuw.ca/api/v1/repos/tyler/{APP_NAME}/releases"
 API_URL_SECONDARY = f"https://git.research2.dezeeuw.ca/api/v1/repos/tyler/{APP_NAME}/releases"
 PLATFORM_NAME = platform.system().lower()
+CHANGELOG_URL = "https://git.research.dezeeuw.ca/tyler/flares/raw/branch/main/changelog_major.md"
+WIKI_URL = "https://git.research.dezeeuw.ca/tyler/flares/wiki"
 
 PIPELINE_STAGES = [
     "Preprocessing",

src/window/about.py

@@ -1,3 +1,11 @@
+"""
+Filename: about.py
+Description: About window for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel
 from PySide6.QtCore import Qt
 

src/window/terminal.py

@@ -1,3 +1,11 @@
+"""
+Filename: terminal.py
+Description: Terminal window for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QTextEdit, QLineEdit
 from PySide6.QtCore import Qt
 

src/window/updateevents.py

@@ -1,3 +1,11 @@
+"""
+Filename: updateevents.py
+Description: Methods to update snirf events for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 import os
 import json
 from enum import Enum, auto
@@ -26,7 +34,7 @@ class UpdateEventsWindow(QWidget):
 
         self.mode = mode
         self.caller = caller or self.__class__.__name__
-        self.setWindowTitle("Update event markers")
+        self.setWindowTitle(f"Update event markers - {APP_NAME.upper()}")
         self.resize(760, 200)
 
         print("INIT MODE:", mode)
@@ -845,5 +853,3 @@ class UpdateEventsBlazesWindow(QWidget):
                     f"Aligned {len(onsets)} events.\n(Filtered out {skipped_count} short events)")
             except Exception as e:
                 QMessageBox.critical(self, "Error", f"Failed to update SNIRF file:\n{e}")
-
-

src/window/updateoptodes.py

@@ -1,3 +1,11 @@
+"""
+Filename: updateoptodes.py
+Description: Methods to update optode locations for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 import os
 from pathlib import Path
 
@@ -9,6 +17,7 @@ from PySide6.QtCore import Qt
 
 from mne.io import read_raw_snirf
 from mne_nirs.io import write_raw_snirf
+from mne.channels import make_dig_montage
 
 from src.shared.shareddata import APP_NAME
 
@@ -17,7 +26,7 @@ class UpdateOptodesWindow(QWidget):
 
     def __init__(self, parent=None):
         super().__init__(parent, Qt.WindowType.Window)
-        self.setWindowTitle("Update optode positions")
+        self.setWindowTitle(f"Update optode positions - {APP_NAME.upper()}")
         self.resize(760, 200)
 
         self.label_file_a = QLabel("SNIRF file:")
@@ -136,7 +145,7 @@ class UpdateOptodesWindow(QWidget):
 
     def show_help_popup(self, text):
         msg = QMessageBox(self)
-        msg.setWindowTitle(f"Parameter Info - {APP_NAME.upper}")
+        msg.setWindowTitle(f"Parameter Info - {APP_NAME.upper()}")
         msg.setText(text)
         msg.exec()
 

src/window/userguide.py

@@ -1,7 +1,15 @@
+"""
+Filename: userguide.py
+Description: User guide for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel
 from PySide6.QtCore import Qt
 
-from src.shared.shareddata import APP_NAME, PIPELINE_STAGES
+from src.shared.shareddata import APP_NAME, PIPELINE_STAGES, WIKI_URL
 
 
 class UserGuideWindow(QWidget):
@@ -22,7 +30,7 @@ class UserGuideWindow(QWidget):
         label2_text = "\n".join(f"Stage {idx + 1}: {name}" for idx, name in enumerate(PIPELINE_STAGES)) + "\n"
         label2 = QLabel(label2_text, self)
 
-        label3 = QLabel(f"For more information, visit the Git wiki page <a href='https://git.research.dezeeuw.ca/tyler/{APP_NAME}/wiki'>here</a>.", self)
+        label3 = QLabel(f"For more information, visit the Git wiki page <a href='{WIKI_URL}'>here</a>.", self)
         label3.setTextFormat(Qt.TextFormat.RichText)
         label3.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
         label3.setOpenExternalLinks(True)

src/window/viewerlauncher.py

@@ -0,0 +1,122 @@
+"""
+Filename: viewerlauncher.py
+Description: Analysis options launcher for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
+from PySide6.QtWidgets import  QPushButton, QWidget, QVBoxLayout
+from PySide6.QtCore import QTimer
+
+from src.analysis.exportcsv import ExportDataAsCSVViewerWidget
+from src.analysis.group import GroupViewerWidget
+from src.analysis.groupbrain import GroupBrainViewerWidget
+from src.analysis.groupfunctionalconnectivity import GroupFunctionalConnectivityWidget
+from src.analysis.participant import ParticipantViewerWidget
+from src.analysis.participantbrain import ParticipantBrainViewerWidget
+from src.analysis.participantfoldchannels import ParticipantFoldChannelsWidget
+from src.analysis.participantfunctionalconnectivity import ParticipantFunctionalConnectivityWidget
+from src.shared.shareddata import APP_NAME
+
+
+class ViewerLauncherWidget(QWidget):
+    def __init__(self, haemo_dict, config_dict, fig_bytes_dict, cha_dict, contrast_results_dict, df_ind, design_matrix, epochs_dict, folding_bypass):
+        super().__init__()
+        self.setWindowTitle(f"Viewer Launcher - {APP_NAME.upper()}")
+
+        group_dict = {
+            file_path: config.get("GROUP", "Unknown")
+            for file_path, config in config_dict.items()
+        }
+
+        def launch(func, btn, *args):
+            func(*args)
+            self._trigger_success(btn)
+
+        layout = QVBoxLayout(self)
+
+        btn1 = QPushButton("Open Participant Viewer")
+        btn1.clicked.connect(lambda: launch(self.open_participant_viewer, btn1, haemo_dict, fig_bytes_dict))
+        btn1.setEnabled(not folding_bypass)
+
+        btn2 = QPushButton("Open Participant Brain Viewer")
+        btn2.clicked.connect(lambda: launch(self.open_participant_brain_viewer, btn2, haemo_dict, cha_dict))
+        btn2.setEnabled(not folding_bypass)
+
+        btn3 = QPushButton("Open Participant Fold Channels Viewer")
+        btn3.clicked.connect(lambda: launch(self.open_participant_fold_channels_viewer, btn3, haemo_dict, cha_dict))
+
+        btn7 = QPushButton("Open Functional Connectivity Viewer [BETA]")
+        btn7.clicked.connect(lambda: launch(self.open_participant_functional_connectivity_viewer, btn7, haemo_dict, epochs_dict))
+        btn7.setEnabled(not folding_bypass)
+
+        btn8 = QPushButton("Open Group Functional Connectivity Viewer [BETA]")
+        btn8.clicked.connect(lambda: launch(self.open_group_functional_connectivity_viewer, btn8, haemo_dict, group_dict, config_dict))
+        btn8.setEnabled(not folding_bypass)
+
+        btn4 = QPushButton("Open Inter-Group Viewer")
+        btn4.clicked.connect(lambda: launch(self.open_group_viewer, btn4, haemo_dict, cha_dict, df_ind, design_matrix, contrast_results_dict, group_dict))
+        btn4.setEnabled(not folding_bypass)
+        
+        btn5 = QPushButton("Open Cross Group Brain Viewer")
+        btn5.clicked.connect(lambda: launch(self.open_group_brain_viewer, btn5, haemo_dict, df_ind, design_matrix, group_dict, contrast_results_dict))
+        btn5.setEnabled(not folding_bypass)
+        
+        btn6 = QPushButton("Open Export Data As CSV Viewer")
+        btn6.clicked.connect(lambda: launch(self.open_export_data_as_csv_viewer, btn6, haemo_dict, cha_dict, df_ind, design_matrix, group_dict, contrast_results_dict))
+        btn6.setEnabled(not folding_bypass)
+
+        layout.addWidget(btn1)
+        layout.addWidget(btn2)
+        layout.addWidget(btn3)
+        layout.addWidget(btn7)
+        layout.addWidget(btn8)
+        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)
+        self.participant_viewer.show()
+
+    def open_participant_brain_viewer(self, haemo_dict, cha_dict):
+        self.participant_brain_viewer = ParticipantBrainViewerWidget(haemo_dict, cha_dict)
+        self.participant_brain_viewer.show()
+        
+    def open_participant_fold_channels_viewer(self, haemo_dict, cha_dict):
+        self.participant_fold_channels_viewer = ParticipantFoldChannelsWidget(haemo_dict, cha_dict)
+        self.participant_fold_channels_viewer.show()
+
+    def open_participant_functional_connectivity_viewer(self, haemo_dict, epochs_dict):
+        self.participant_brain_viewer = ParticipantFunctionalConnectivityWidget(haemo_dict, epochs_dict)
+        self.participant_brain_viewer.show()
+
+    def open_group_functional_connectivity_viewer(self, haemo_dict, group, config_dict):
+        self.participant_brain_viewer = GroupFunctionalConnectivityWidget(haemo_dict, group, config_dict)
+        self.participant_brain_viewer.show()
+
+    def open_group_viewer(self, haemo_dict, cha_dict, df_ind, design_matrix, contrast_results_dict, group):
+        self.participant_brain_viewer = GroupViewerWidget(haemo_dict, cha_dict, df_ind, design_matrix, contrast_results_dict, group)
+        self.participant_brain_viewer.show()
+
+    def open_group_brain_viewer(self, haemo_dict, df_ind, design_matrix, group, contrast_results_dict):
+        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()
+
+    def _trigger_success(self, button):
+        """Temporarily adds a green checkmark to the button text."""
+        original_text = button.text()
+        button.setText(f"{original_text}  ✔")
+        button.setStyleSheet("color: green; font-weight: bold;")
+        
+        # Revert after 1 second
+        QTimer.singleShot(1000, lambda: self._revert_button(button, original_text))
+
+    def _revert_button(self, button, original_text):
+        button.setText(original_text)
+        button.setStyleSheet("")

src/window/welcome.py

@@ -1,9 +1,17 @@
+"""
+Filename: welcome.py
+Description: Welcome dialog for FLARES
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
 from PySide6.QtWidgets import QTextBrowser, QVBoxLayout, QLabel, QDialog, QHBoxLayout, QPushButton
 from PySide6.QtGui import QDesktopServices, QIcon
 from PySide6.QtCore import QUrl
 from PySide6.QtNetwork import QNetworkAccessManager, QNetworkRequest
 
-from src.shared.shareddata import APP_NAME, CURRENT_VERSION, resource_path
+from src.shared.shareddata import APP_NAME, CURRENT_VERSION, CHANGELOG_URL, resource_path
 
 
 class WelcomeDialog(QDialog):
@@ -13,13 +21,13 @@ class WelcomeDialog(QDialog):
         self.setMinimumSize(550, 450)
         self.resize(800, 500)
         
-        # Main Layout
         layout = QVBoxLayout(self)
         
-        # Header Layout (Logo + App Name)
         header_layout = QHBoxLayout()
         logo_label = QLabel(self)
-        logo_label.setPixmap(QIcon(resource_path("icons/main.ico")).pixmap(48, 48)) # Fits cleanly in a header
+
+        # NOTE: might not work on mac and need the icns file
+        logo_label.setPixmap(QIcon(resource_path("icons/main.ico")).pixmap(48, 48))
         if direct:
             title_label = QLabel(f"<h2>{APP_NAME.upper()} has been sucessfully updated to version {CURRENT_VERSION}!</h2>", self)
         else:
@@ -30,19 +38,19 @@ class WelcomeDialog(QDialog):
         header_layout.addStretch()
         layout.addLayout(header_layout)
         
-        # Text Browser Area (Automatically converts Markdown syntax into clean formatted UI text)
         self.text_browser = QTextBrowser(self)
         self.text_browser.setHtml("<p style='color: gray;'>Loading latest updates from server...</p>")
-        self.text_browser.setOpenLinks(False)  # Don't open links inside the viewer
+
+        # Ensure links open in the default web browser and not in this window
+        self.text_browser.setOpenLinks(False)
         self.text_browser.anchorClicked.connect(QDesktopServices.openUrl)
         layout.addWidget(self.text_browser)
         
-        # Footer Controls Layout
         footer_layout = QHBoxLayout()
         
         ok_button = QPushButton("OK", self)
         ok_button.setDefault(True)
-        ok_button.clicked.connect(self.accept) # Closes the dialog with a success signal
+        ok_button.clicked.connect(self.accept)
         
         footer_layout.addStretch()
         footer_layout.addWidget(ok_button)
@@ -51,18 +59,16 @@ class WelcomeDialog(QDialog):
         # Fetch markdown from the web asynchronously
         self.network_manager = QNetworkAccessManager(self)
         self.network_manager.finished.connect(self._on_download_complete)
-        
+        self.network_manager.get(QNetworkRequest(QUrl(CHANGELOG_URL)))
-        md_url = "https://git.research.dezeeuw.ca/tyler/flares/raw/branch/main/changelog_major.md"
-        self.network_manager.get(QNetworkRequest(QUrl(md_url)))
 
 
     def _on_download_complete(self, reply):
         """Processes the downloaded markdown and drops it into the view frame."""
         if reply.error() == reply.NetworkError.NoError:
             raw_bytes = reply.readAll()
+
             # Convert raw bytes to standard text string
             markdown_text = str(raw_bytes, encoding='utf-8')
-            # Qt's QTextBrowser natively renders markdown arrays beautifully!
             self.text_browser.setMarkdown(markdown_text)
         else:
             self.text_browser.setHtml(