changelog

changelog.md

@@ -1,3 +1,21 @@
+# Version 1.8.0
+
+- Plugin Manager now supports checking and downloading plugin updates to ensure plugins can be updated
+- Plugin Manager now properly uninstalls plugins when requested rather than doing nothing
+- Installing plugins now displays a progress bar when downloading and no longer hangs the application when downloading a big plugin
+- Project loading now displays a loading message when loading big projects and no longer hangs the application when loading
+- New preferences options and menus are now available! All existing preferences have been moved into new sub categories
+- The UI preference category now has the Show Advanced Parameters preference
+- The Updates preference category has two ney options to prevent the automatic checking of application or plugin updates
+- The Theme category has remain untouched and all other preferences have been moved to the Processing category
+- Added a new preference in the Processing category called "Separate Events". This allows events to have their own values, and not be collapsed into a single value
+- Export To CSV Viewer export options now perform the actions they claim rather than having no functionality
+- Logs on a per participant basis are now available to be viewed from within the application
+- They can be accessed by right clicking a participant bubble and selecting "Show Logs". Logs will be empty if they have not been processed
+- Fixed a regression where opening a folder would no longer load all the files in that folder
+- Improved code stability and functionality
+
+
 # Version 1.7.2
 
 - Fixed the Linux build not starting if shared library files were missing from the host machine

flares.py

@@ -108,7 +108,6 @@ from mne_connectivity import envelope_correlation, spectral_connectivity_epochs,
 from src.shared.shareddata import PLATFORM_NAME, resource_path, get_app_dir
 
 
-
 PRIMARY_COLORS = {
     "SCI only": "skyblue",      # Scalp Coupling Index (Standard MNE)
     "SNR only": "lightgreen",   # Signal-to-Noise Ratio (Original)
@@ -301,6 +300,8 @@ GROUP: str = "Default"
 
 FOLDING_BYP: bool = False
 
+SEPARATE_EVENTS: bool = False
+
 FEATURE_1: bool = False
 FEATURE_2: bool = False
 
@@ -326,7 +327,6 @@ logging.basicConfig(
 logger = logging.getLogger()
 
 
-
 def set_config_me(config: dict[str, Any]) -> None:
     """
     Validates and applies the given configuration dictionary.
@@ -422,6 +422,27 @@ def gui_entry(config: dict[str, Any], gui_queue: mp.Queue, progress_queue: mp.Qu
 def process_participant_worker(file_path, file_params, file_metadata, result_queue, progress_queue):
     file_start = time.time()
     stage_tracker = {"value": 0.0}
+
+    class QueueStreamAlt:
+        def __init__(self, fp, q):
+            self.fp = fp
+            self.q = q
+
+        def write(self, msg):
+            if msg and self.q:
+                try:
+                    self.q.put(("log", self.fp, msg))
+                except Exception:
+                    pass
+
+        def flush(self):
+            pass
+
+    old_stdout = sys.stdout
+    old_stderr = sys.stderr
+    sys.stdout = QueueStreamAlt(file_path, progress_queue)
+    sys.stderr = QueueStreamAlt(file_path, progress_queue)
+
     try:
         set_config_me(file_params)
         set_metadata(file_path, file_metadata)
@@ -446,6 +467,8 @@ def process_participant_worker(file_path, file_params, file_metadata, result_que
             pass
 
     finally:
+        sys.stdout = old_stdout
+        sys.stderr = old_stderr
         try:
             plt.close('all')
             gc.collect()
@@ -2101,7 +2124,6 @@ def plot_glm_results(file_path, raw_haemo, glm_est, design_matrix):
         axes[2].set_ylabel("Haemoglobin (ΔμMol)")
         axes[2].legend(["Oxyhaemoglobin", "Deoxyhaemoglobin"])
 
-        
         print(f"Number of FIR bins: {len(vals_hbo)}")
         print(f"Mean theta (HbO): {np.mean(vals_hbo):.4f}")
         print(f"Sum of theta (HbO): {np.sum(vals_hbo):.4f}")
@@ -2372,7 +2394,6 @@ def brain_3d_visualization(
 
     model_df = cast(DataFrame, statsmodels_to_results(ch_model, order=ch_summary["ch_name"].unique()))
 
-    
     valid_channels = ch_summary["ch_name"].unique().tolist() # type: ignore
     raw_for_plot = raw_haemo.copy().pick(picks=valid_channels) # type: ignore
 
@@ -2476,7 +2497,6 @@ def brain_landmarks_3d(raw_haemo: BaseRaw, show_optodes: Literal['sensors', 'lab
                 scale=0.002
             )
 
-    
     if show_brodmann:# Add Brodmann labels
         labels = cast(list[Label], read_labels_from_annot("fsaverage", "PALS_B12_Brodmann", "lh", verbose=False)) # type: ignore
 
@@ -5990,6 +6010,24 @@ def process_participant(file_path, file_start, progress_callback=None):
     logger.info("Step 21 Completed.")
     step_start = lap(step_start, timings, "Step 21")
 
+    # Step 21.5: Make annotations trial-specific for individual trial GLM/FIR
+    if SEPARATE_EVENTS:
+        annots = raw_haemo.annotations
+        if len(annots) > 0:
+            new_descriptions = []
+            cond_counts = {}
+            for desc in annots.description:
+                # Optional: filter for specific task conditions if you have other markers like 'bad' or 'iseg'
+                cond_counts[desc] = cond_counts.get(desc, 0) + 1
+                new_descriptions.append(f"{desc}_trial_{cond_counts[desc]}")
+
+            # Update raw_haemo annotations with trial-specific names
+            raw_haemo.set_annotations(Annotations(
+                onset=annots.onset,
+                duration=annots.duration,
+                description=new_descriptions
+            ))
+
     # Step 22: Design Matrix
     raw_haemo, raw_haemo_dm, df_design_matrix, fig_design_matrix = make_design_matrix(
         raw_haemo=raw_haemo,
@@ -6071,7 +6109,6 @@ def process_participant(file_path, file_start, progress_callback=None):
         except Exception as e:
             logger.warning(f"Step 27.5 Failed to extract FIR features: {e}")
 
-     
     # Step 28: Finishing Up
     png_queue.put(None)   # sentinel
     png_queue.join()      # blocks only on remaining unfinished work
@@ -6404,11 +6441,6 @@ def _log_matrix_diagnostics(name: str, mat: np.ndarray) -> None:
 
 
 
-
-
-
-
-
 # ============================================================================
 # Shared: channel alignment across participants
 # ============================================================================
@@ -6797,13 +6829,6 @@ def run_group_functional_connectivity_epochs(
 
 
 
-
-
-
-
-
-
-
 def sparks_csv_export(
     haemo_obj: BaseRaw,
     save_path: str,
@@ -6828,7 +6853,6 @@ def sparks_csv_export(
     df.to_csv(save_path, index=False)
 
 
- 
 def peak_power_fast(
     raw,
     time_window=10,
@@ -7413,6 +7437,21 @@ def normalize_roi_map(roi_map):
     return {}
 
 
+
+def extract_epoch_features(epochs, file_path, window=(4.0, 12.0)):
+    """One row per (epoch, channel): mean haemoglobin amplitude within `window` seconds."""
+    tmask = (epochs.times >= window[0]) & (epochs.times <= window[1])
+    feat = epochs.get_data()[:, :, tmask].mean(axis=2) * 1e6      # (n_epochs, n_channels), µM
+    id_to_name = {v: k for k, v in epochs.event_id.items()}
+    df = pd.DataFrame(feat, columns=epochs.ch_names)
+    df["Condition"] = [id_to_name[e] for e in epochs.events[:, 2]]
+    df["trial"] = epochs.selection        # index of the epoch in the original event list (survives rejection)
+    long = df.melt(id_vars=["Condition", "trial"], var_name="ch_name", value_name="theta")
+    long["Chroma"] = long["ch_name"].map(dict(zip(epochs.ch_names, epochs.get_channel_types())))
+    long["ID"] = file_path
+    return long[["ch_name", "Chroma", "ID", "Condition", "trial", "theta"]]
+
+
 if __name__ == "__main__":
     print("This file has no functionality when not used in tandem with the FLARES application.")
 

main.py

@@ -15,6 +15,7 @@ import traceback
 import subprocess
 import configparser
 import concurrent.futures
+from typing import Any
 from queue import Empty
 from copy import deepcopy
 from pathlib import Path
@@ -34,11 +35,11 @@ from PySide6.QtWidgets import (
     QPushButton, QMainWindow, QLabel, QLineEdit, QGroupBox, QDialog, QMenu, QSpinBox, QTableWidget, QTableWidgetItem
 )
 from PySide6.QtCore import QEvent, QObject, Signal, Qt, QTimer
-from PySide6.QtGui import QAction, QActionGroup, QFontMetrics, QKeySequence, QIcon
+from PySide6.QtGui import QAction, QActionGroup, QFontMetrics, QKeySequence, QIcon, QTextCursor
 from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
 
 from file_ext_registration import register_file_association, ELEVATION_FLAG
-from plugin_manager import PluginManager
+from plugin_manager import PluginManager, StartupUpdateWorker
 from project_manager import ProjectManager
 from src.window.about import AboutWindow
 from src.window.plugins import PluginsWindow
@@ -49,7 +50,7 @@ from src.window.userguide import UserGuideWindow
 from src.window.viewerlauncher import ViewerLauncherWidget
 from src.window.welcome import WelcomeDialog
 from src.shared.flaresbasewidget import FilePickerWidget, ParamSection, ProgressBubble
-from src.shared.shareddata import API_URL, API_URL_SECONDARY, APP_NAME, CURRENT_VERSION, PLATFORM_NAME, DATA_SCHEMA, get_app_dir
+from src.shared.shareddata import API_URL, API_URL_SECONDARY, APP_NAME, CURRENT_VERSION, PLATFORM_NAME, DATA_SCHEMA, PLUGINS_URL, get_app_dir
 from startup_args import parse_startup_args
 from updater import finish_update_if_needed, UpdateManager, LocalPendingUpdateCheckThread
 
@@ -71,13 +72,19 @@ show_welcome_dialog = false
 first_startup = true
 
 [Preferences]
-theme = auto
-2d_data_bypass = false
-incompatible_save_bypass = false
-missing_events_bypass = false
-analysis_clearing_bypass = false
-folding_bypass = false
-advanced_parameters = false
+theme_mode = auto
+
+processing_2d_data_bypass = false
+processing_incompatible_save_bypass = false
+processing_missing_events_bypass = false
+processing_analysis_clearing_bypass = false
+processing_folding_bypass = false
+processing_separate_events = false
+
+ui_advanced_parameters = false
+
+updates_check_plugins_automatic = true
+updates_check_app_automatic = true
 
 [Terminal]
 
@@ -85,6 +92,7 @@ advanced_parameters = false
 
 """
 
+
 # Selectable parameters on the right side of the window
 SECTIONS = [
     {
@@ -334,6 +342,33 @@ BIDS_FIELD_MAP = {
 
 
 
+class LogWindow(QDialog):
+
+  def __init__(self, title, file_path, log_text, parent=None):
+    super().__init__(parent)
+    self.file_path = file_path
+    self.setWindowTitle(title)
+    self.resize(700, 500)
+
+    layout = QVBoxLayout(self)
+    self.text_edit = QTextEdit(self)
+    self.text_edit.setReadOnly(True)
+    self.text_edit.setPlainText(log_text)
+
+    font = self.text_edit.font()
+    font.setFamily("Courier")
+    self.text_edit.setFont(font)
+
+    layout.addWidget(self.text_edit)
+
+  def append_log(self, text):
+    # Auto-scroll to the bottom and insert incoming text chunk
+    cursor = self.text_edit.textCursor()
+    cursor.movePosition(QTextCursor.MoveOperation.End)
+    self.text_edit.setTextCursor(cursor)
+    self.text_edit.insertPlainText(text)
+
+
 class GroupAssignmentDialog(QDialog):
     """Dialog allowing users to create groups and assign unique metadata values to them."""
 
@@ -366,7 +401,6 @@ class GroupAssignmentDialog(QDialog):
 
     def _init_ui(self):
         layout = QVBoxLayout(self)
-
         # Field selector
         field_box_layout = QHBoxLayout()
         field_box_layout.addWidget(QLabel("Group by:"))
@@ -607,25 +641,34 @@ class MainApplication(QMainWindow):
         self.events_blazes = None
         self.plugins = None
         self.terminal = None
-        self.bubble_widgets = {}
-        self.param_sections = []
-        self.folder_paths = []
         self.section_widget = None
         self.first_run = True
-        self.show_status_bar = False
-        self.is_2d_bypass = False
-        self.incompatible_save_bypass = False
-        self.missing_events_bypass = False
-        self.analysis_clearing_bypass = False
-        self.folding_bypass = False
-        self.advanced_parameters = False
 
         self.is_saved = True
         self.current_project_path = None
+        self.current_file = None
         self.selected_paths = []
         self.saved_selected_paths = []
         self.files_are_dirty = False
 
+        self.file_metadata = {}          # AGE, SEX, HAND, GROUP
+        self.metadata_cache = {}         # Internal file/path information metadata cache
+        self.bubble_widgets = {}         # References to the UI "Bubble" objects
+        self.participant_logs = {}
+
+        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.pending_update_version = None
+        self.pending_update_path = None
+
+        # are these used?
+        self.param_sections = []
+        self.folder_paths = []
+        self.last_clicked_bubble = None
+
         self.project_manager = ProjectManager(self, file_cfg=file_cfg, cfg_path=cfg_path)
         self.plugin_manager = PluginManager(self)
 
@@ -633,18 +676,35 @@ class MainApplication(QMainWindow):
         for item in DATA_SCHEMA:
             setattr(self, item["key"], {})
 
-        self.file_metadata = {}          # AGE, SEX, HAND, GROUP
-        self.metadata_cache = {}         # Internal file/path information metadata cache
-        self.bubble_widgets = {}         # References to the UI "Bubble" objects
-        self.current_file = None         # Tracks the currently selected absolute path
+        config_mappings = {
+            "View": ["status_bar"],
+            "Preferences": [
+                "theme_mode",
+                "processing_2d_data_bypass",
+                "processing_incompatible_save_bypass",
+                "processing_missing_events_bypass",
+                "processing_analysis_clearing_bypass",
+                "processing_folding_bypass",
+                "processing_separate_events",
+                "ui_advanced_parameters",
+                "updates_check_plugins_automatic",
+                "updates_check_app_automatic",
+            ]
+        }
+
+        for section, keys in config_mappings.items():
+            for key in keys:
+                if section == "Preferences" and key == "theme_mode":
+                    val = file_cfg.get(section, key, fallback="auto")
+                elif key in ["status_bar", "updates_check_plugins_automatic", "updates_check_app_automatic"]:
+                    val = file_cfg.getboolean(section, key, fallback=True)
+                else:
+                    val = file_cfg.getboolean(section, key, fallback=False)
+                setattr(self, key, val)
 
         self.metadata_processed.connect(self._safe_ui_update)
         self.metadata_ui_signal.connect(self._handle_metadata_ui_update)
 
-        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.updater = UpdateManager(
             main_window=self,
@@ -658,17 +718,23 @@ class MainApplication(QMainWindow):
 
         self.init_ui()
         self.create_menu_bar()
-
-        self.pending_update_version = None
-        self.pending_update_path = None
-        self.last_clicked_bubble = None
         self.installEventFilter(self)
 
-        # Start local pending update check thread
-        self.local_check_thread = LocalPendingUpdateCheckThread(CURRENT_VERSION, "-" + PLATFORM_NAME, PLATFORM_NAME, APP_NAME)
-        self.local_check_thread.pending_update_found.connect(self.updater.on_pending_update_found)
-        self.local_check_thread.no_pending_update.connect(self.updater.on_no_pending_update)
-        self.local_check_thread.start()
+        # Conditionally start background network threads using the loaded attributes
+        if self.updates_check_app_automatic:
+            self.local_check_thread = LocalPendingUpdateCheckThread(CURRENT_VERSION, "-" + PLATFORM_NAME, PLATFORM_NAME, APP_NAME)
+            self.local_check_thread.pending_update_found.connect(self.updater.on_pending_update_found)
+            self.local_check_thread.no_pending_update.connect(self.updater.on_no_pending_update)
+            self.local_check_thread.start()
+        else:
+            print("[MainApplication] App automatic update check is disabled in preferences.")
+
+        if self.updates_check_plugins_automatic:
+            self._startup_update_worker = StartupUpdateWorker(self.plugin_manager, [PLUGINS_URL])
+            self._startup_update_worker.updates_checked.connect(self._on_startup_updates_found)
+            self._startup_update_worker.start()
+        else:
+            print("[MainApplication] Plugin automatic update check is disabled in preferences.")
 
         self.plugin_manager.reload_plugins()
 
@@ -704,7 +770,6 @@ class MainApplication(QMainWindow):
             self.project_manager.load_project(file_to_open)
 
 
-
     def init_ui(self):
         central = QWidget()
         self.setCentralWidget(central)
@@ -830,19 +895,41 @@ class MainApplication(QMainWindow):
     #     for stat in top_stats[:10]:
     #         print(stat)
 
-    def create_menu_bar(self):
-        '''Menu Bar at the top of the screen'''
+    def _on_startup_updates_found(self, outdated_plugins: list[dict[str, Any]]) -> None:
+        """Safely displays the update popup on the main thread once the background check finishes."""
+        if not outdated_plugins:
+            return
 
+        update_details = "\n".join(
+            f"• {p['name']}: Installed v{p['version']} ➔ New v{p['remote_version']}"
+            for p in outdated_plugins
+        )
+        summary_msg = f"The following plugin updates are available:\n\n{update_details}\n\nYou can update them in the Plugin Manager."
+
+        QMessageBox.information(
+            self,
+            "Plugin Updates Available",
+            summary_msg
+        )
+
+    def create_menu_bar(self):
+        """Menu Bar at the top of the screen built dynamically from a unified schema."""
         menu_bar = self.menuBar()
         self.statusbar = self.statusBar()
 
+        self.view_actions = {}
+        self.pref_actions = {}
+
         def make_action(name, shortcut=None, slot=None, checkable=False, checked=False, icon=None):
             action = QAction(name, self)
-
             if shortcut:
                 action.setShortcut(QKeySequence(shortcut))
             if slot:
-                action.triggered.connect(slot)
+                if checkable:
+                    # Checkable actions use 'toggled' to reliably pass the boolean state
+                    action.toggled.connect(slot)
+                else:
+                    action.triggered.connect(slot)
             if checkable:
                 action.setCheckable(True)
                 action.setChecked(checked)
@@ -850,140 +937,142 @@ class MainApplication(QMainWindow):
                 action.setIcon(QIcon(icon))
             return action
 
-        # File menu and actions
-        file_menu = menu_bar.addMenu("File")
-        file_actions = [
-            ("Open File...", "Ctrl+O", self.project_manager.open_file_dialog, resource_path("icons/file_open_24dp_1F1F1F.svg")),
-            ("Open Folder...", "Ctrl+Alt+O", self.project_manager.open_folder_dialog, resource_path("icons/folder_24dp_1F1F1F.svg")),
-            ("Load Project...", "Ctrl+L", self.project_manager.load_project_dialog, resource_path("icons/article_24dp_1F1F1F.svg")),
-            ("Save Project...", "Ctrl+S", lambda: self.project_manager.save_project(ask=False), resource_path("icons/save_24dp_1F1F1F.svg")),
-            ("Save Project As...", "Ctrl+Shift+S", lambda: self.project_manager.save_project(ask=True), resource_path("icons/save_as_24dp_1F1F1F.svg")),
+        # Unified Menu Bar Schema
+        MENU_BAR_SCHEMA = [
+            # === FILE MENU ===
+            {"menu": "File", "name": "Open File...", "shortcut": "Ctrl+O", "slot": self.project_manager.open_file_dialog, "icon": resource_path("icons/file_open_24dp_1F1F1F.svg")},
+            {"menu": "File", "name": "Open Folder...", "shortcut": "Ctrl+Alt+O", "slot": self.project_manager.open_folder_dialog, "icon": resource_path("icons/folder_24dp_1F1F1F.svg")},
+            {"menu": "File", "type": "recent_files"},
+            {"menu": "File", "type": "separator"},
+            {"menu": "File", "name": "Load Project...", "shortcut": "Ctrl+L", "slot": self.project_manager.load_project_dialog, "icon": resource_path("icons/article_24dp_1F1F1F.svg")},
+            {"menu": "File", "type": "recent_projects"},
+            {"menu": "File", "type": "separator"},
+            {"menu": "File", "name": "Save Project...", "shortcut": "Ctrl+S", "slot": lambda: self.project_manager.save_project(ask=False), "icon": resource_path("icons/save_24dp_1F1F1F.svg")},
+            {"menu": "File", "name": "Save Project As...", "shortcut": "Ctrl+Shift+S", "slot": lambda: self.project_manager.save_project(ask=True), "icon": resource_path("icons/save_as_24dp_1F1F1F.svg")},
+            {"menu": "File", "type": "separator"},
+            {"menu": "File", "name": "Exit", "shortcut": "Ctrl+Q", "slot": QApplication.instance().quit, "icon": resource_path("icons/exit_to_app_24dp_1F1F1F.svg")},
+
+            # === EDIT MENU ===
+            {"menu": "Edit", "name": "Cut", "shortcut": "Ctrl+X", "slot": self.cut_text, "icon": resource_path("icons/content_cut_24dp_1F1F1F.svg")},
+            {"menu": "Edit", "name": "Copy", "shortcut": "Ctrl+C", "slot": self.copy_text, "icon": resource_path("icons/content_copy_24dp_1F1F1F.svg")},
+            {"menu": "Edit", "name": "Paste", "shortcut": "Ctrl+V", "slot": self.paste_text, "icon": resource_path("icons/content_paste_24dp_1F1F1F.svg")},
+
+            # === VIEW MENU ===
+            {"menu": "View", "name": "Toggle Status Bar", "shortcut": "", "slot": self.toggle_statusbar, "checkable": True, "checked": True, "icon": resource_path("icons/short_text_24dp_1F1F1F.svg"), "key": "statusbar"},
+            {"menu": "View", "type": "separator"},
+            {"menu": "View", "name": "Reset Window Layout", "shortcut": "Ctrl+Shift+R", "slot": self.reset_window_layout, "icon": resource_path("icons/grid_layout_side_24dp_1F1F1F.svg")},
+
+            # === OPTIONS MENU ===
+            {"menu": "Options", "name": "User Guide", "shortcut": "F1", "slot": self.user_guide, "icon": resource_path("icons/help_24dp_1F1F1F.svg")},
+            {"menu": "Options", "name": "Regroup Files from Metadata", "shortcut": "F3", "slot": self.group_metadata, "icon": resource_path("icons/help_24dp_1F1F1F.svg")},
+            {"menu": "Options", "name": "Check for Updates", "shortcut": "F5", "slot": self.updater.manual_check_for_updates, "icon": resource_path("icons/update_24dp_1F1F1F.svg")},
+            {"menu": "Options", "name": "Show Update Changelog", "shortcut": "F6", "slot": self.show_update_changelog, "icon": resource_path("icons/article_shortcut_24dp_1F1F1F.svg")},
+            {"menu": "Options", "type": "separator"},
+            {"menu": "Options", "name": "Update events in snirf file (BORIS)...", "shortcut": "F7", "slot": self.update_event_markers, "icon": resource_path("icons/upgrade_24dp_1F1F1F.svg")},
+            {"menu": "Options", "name": "Update events in snirf file (BLAZES)...", "shortcut": "F8", "slot": self.update_event_markers_blazes, "icon": resource_path("icons/upgrade_24dp_1F1F1F.svg")},
+            {"menu": "Options", "name": "Update optodes in snirf file...", "shortcut": "F9", "slot": self.update_optode_positions, "icon": resource_path("icons/upgrade_24dp_1F1F1F.svg")},
+            {"menu": "Options", "type": "separator"},
+            {"menu": "Options", "name": "Reset to Default Configuration", "shortcut": "F10", "slot": self.reset_to_default_configuration, "icon": resource_path("icons/reset_settings_24dp_1F1F1F.svg")},
+            {"menu": "Options", "type": "separator"},
+            {"menu": "Options", "name": "About", "shortcut": "F12", "slot": self.about_window, "icon": resource_path("icons/info_24dp_1F1F1F.svg")},
+
+            # === PREFERENCES: THEME ===
+            {"menu": "Preferences", "submenu": "Theme", "name": "Auto", "mode": "auto", "slot": partial(self.theme_change_func, "auto"), "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg"), "key": "theme_auto", "group": "theme", "checkable": True},
+            {"menu": "Preferences", "submenu": "Theme", "name": "Light", "mode": "light", "slot": partial(self.theme_change_func, "light"), "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg"), "key": "theme_light", "group": "theme", "checkable": True},
+            {"menu": "Preferences", "submenu": "Theme", "name": "Dark", "mode": "dark", "slot": partial(self.theme_change_func, "dark"), "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg"), "key": "theme_dark", "group": "theme", "checkable": True},
+
+            # === PREFERENCES: PROCESSING ===
+            {"menu": "Preferences", "submenu": "Processing", "name": "2D Data Bypass", "key": "processing_2d_data_bypass", "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg")},
+            {"menu": "Preferences", "submenu": "Processing", "name": "Incompatible Save Bypass", "key": "processing_incompatible_save_bypass", "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg")},
+            {"menu": "Preferences", "submenu": "Processing", "name": "Missing Events Bypass", "key": "processing_missing_events_bypass", "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg")},
+            {"menu": "Preferences", "submenu": "Processing", "name": "Analysis Clearing Bypass", "key": "processing_analysis_clearing_bypass", "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg")},
+            {"menu": "Preferences", "submenu": "Processing", "name": "Folding Bypass", "key": "processing_folding_bypass", "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg")},
+            {"menu": "Preferences", "submenu": "Processing", "name": "Separate Events", "key": "processing_separate_events", "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg")},
+
+            # === PREFERENCES: UI ===
+            {"menu": "Preferences", "submenu": "UI", "name": "Show Advanced Parameters", "key": "ui_advanced_parameters", "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg")},
+
+            # === PREFERENCES: UPDATES ===
+            {"menu": "Preferences", "submenu": "Updates", "name": "Automatic App Updates", "key": "updates_check_app_automatic", "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg")},
+            {"menu": "Preferences", "submenu": "Updates", "name": "Automatic Plugin Updates", "key": "updates_check_plugins_automatic", "icon": resource_path("icons/warning_off_24dp_1F1F1F.svg")},
+
+            # === PLUGINS MENU ===
+            {"menu": "Plugins", "name": "Plugin Manager", "shortcut": "Ctrl+Alt+P", "slot": self.plugins_gui, "icon": resource_path("icons/terminal_24dp_1F1F1F.svg")},
+
+            # === TERMINAL MENU ===
+            {"menu": "Terminal", "name": "New Terminal", "shortcut": "Ctrl+Alt+T", "slot": self.terminal_gui, "icon": resource_path("icons/terminal_24dp_1F1F1F.svg")},
         ]
 
-        for i, (name, shortcut, slot, icon) in enumerate(file_actions):
-            file_menu.addAction(make_action(name, shortcut, slot, icon=icon))
-            if i == 1:
-                self.recent_files_menu = file_menu.addMenu("Recent Files")
-                self.recent_files_menu.setIcon(QIcon(resource_path("icons/history_24dp_1F1F1F.svg"))) # optional icon
-                file_menu.addSeparator()
-            elif i == 2:
-                self.recent_projects_menu = file_menu.addMenu("Recent Projects")
-                self.recent_projects_menu.setIcon(QIcon(resource_path("icons/history_2_24dp_1F1F1F.svg")))
-                file_menu.addSeparator()
-
-        file_menu.addSeparator()
-        file_menu.addAction(make_action("Exit", "Ctrl+Q", QApplication.instance().quit, icon=resource_path("icons/exit_to_app_24dp_1F1F1F.svg")))
-
-        # Edit menu
-        edit_menu = menu_bar.addMenu("Edit")
-        edit_actions = [
-            ("Cut", "Ctrl+X", self.cut_text, resource_path("icons/content_cut_24dp_1F1F1F.svg")),
-            ("Copy", "Ctrl+C", self.copy_text, resource_path("icons/content_copy_24dp_1F1F1F.svg")),
-            ("Paste", "Ctrl+V", self.paste_text, resource_path("icons/content_paste_24dp_1F1F1F.svg"))
-        ]
-        for name, shortcut, slot, icon in edit_actions:
-            edit_menu.addAction(make_action(name, shortcut, slot, icon=icon))
-
-        # View menu
-        
-        self.view_actions = {}
-
-        view_menu = menu_bar.addMenu("View")
-        toggle_statusbar_action = make_action("Toggle Status Bar", "", self.toggle_statusbar, True, True, resource_path("icons/short_text_24dp_1F1F1F.svg"))
-        view_menu.addAction(toggle_statusbar_action)
-        self.view_actions["statusbar"] = toggle_statusbar_action
-
-        # Reset Layout Action
-        view_menu.addSeparator()
-        reset_layout_action = make_action(
-            "Reset Window Layout", 
-            "Ctrl+Shift+R", 
-            self.reset_window_layout, 
-            icon=resource_path("icons/grid_layout_side_24dp_1F1F1F.svg")
-        )
-        view_menu.addAction(reset_layout_action)
-
-        # Options menu (Help & About)
-        options_menu = menu_bar.addMenu("Options")
-
-        options_actions = [
-            ("User Guide", "F1", self.user_guide, resource_path("icons/help_24dp_1F1F1F.svg")), 
-            ("Regroup Files from Metadata", "F3", self.group_metadata, resource_path("icons/help_24dp_1F1F1F.svg")), 
-            ("Check for Updates", "F5", self.updater.manual_check_for_updates, resource_path("icons/update_24dp_1F1F1F.svg")),
-            ("Show Update Changelog", "F6", self.show_update_changelog, resource_path("icons/article_shortcut_24dp_1F1F1.svg")),
-            ("Update events in snirf file (BORIS)...", "F7", self.update_event_markers, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
-            ("Update events in snirf file (BLAZES)...", "F8", self.update_event_markers_blazes, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
-            ("Update optodes in snirf file...", "F9", self.update_optode_positions, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
-            ("Reset to Default Configuration", "F10", self.reset_to_default_configuration, resource_path("icons/reset_settings_24dp_1F1F1F.svg")),
-            ("About", "F12", self.about_window, resource_path("icons/info_24dp_1F1F1F.svg"))
-        ]
-
-        for i, (name, shortcut, slot, icon) in enumerate(options_actions):
-            options_menu.addAction(make_action(name, shortcut, slot, icon=icon))
-            if i == 3 or i == 6 or i == 7:
-                options_menu.addSeparator()
-
-        self.pref_actions = {}
-
-        preferences_menu = menu_bar.addMenu("Preferences")
-        theme_menu = preferences_menu.addMenu("Theme")
-
+        # Container references for submenus and groups
+        menus = {}
+        submenus = {}
         theme_group = QActionGroup(self)
         theme_group.setExclusive(True)
 
-        # 4. Define actions for the submenu
-        theme_actions = [
-            ("Auto", "", "auto", resource_path("icons/warning_off_24dp_1F1F1F.svg"), "theme_auto"),
-            ("Light", "", "light", resource_path("icons/warning_off_24dp_1F1F1F.svg"), "theme_light"),
-            ("Dark", "", "dark", resource_path("icons/warning_off_24dp_1F1F1F.svg"), "theme_dark"),
-        ]
+        for item in MENU_BAR_SCHEMA:
+            menu_name = item["menu"]
+            if menu_name not in menus:
+                menus[menu_name] = menu_bar.addMenu(menu_name)
+            parent_menu = menus[menu_name]
 
-        for name, shortcut, mode, icon, config_key in theme_actions:
-            # Use partial to pass 'mode' to self.theme_change_func on click
-            slot = partial(self.theme_change_func, mode)
+            # Handle Submenus (e.g. Preferences -> Theme/Processing/Updates)
+            if "submenu" in item:
+                sub_name = item["submenu"]
+                sub_key = f"{menu_name}_{sub_name}"
+                if sub_key not in submenus:
+                    submenus[sub_key] = parent_menu.addMenu(sub_name)
+                parent_menu = submenus[sub_key]
 
-            action = make_action(name, shortcut, slot, icon=icon, checkable=True)
-            theme_menu.addAction(action)
-            theme_group.addAction(action)
+            # Handle Special Types (Separators & Dynamic Submenus)
+            item_type = item.get("type")
+            if item_type == "separator":
+                parent_menu.addSeparator()
+                continue
+            elif item_type == "recent_files":
+                self.recent_files_menu = parent_menu.addMenu("Recent Files")
+                self.recent_files_menu.setIcon(QIcon(resource_path("icons/history_24dp_1F1F1F.svg")))
+                parent_menu.addSeparator()
+                continue
+            elif item_type == "recent_projects":
+                self.recent_projects_menu = parent_menu.addMenu("Recent Projects")
+                self.recent_projects_menu.setIcon(QIcon(resource_path("icons/history_2_24dp_1F1F1F.svg")))
+                parent_menu.addSeparator()
+                continue
 
-            self.pref_actions[config_key] = action
+            # Handle Normal/Preference/View Actions
+            name = item["name"]
+            shortcut = item.get("shortcut", "")
+            key = item.get("key")
 
-        # Set default selection (e.g., Auto)
-        self.pref_actions["theme_auto"].setChecked(True)
+            # If it's a preference toggle item without an explicit slot, bind it to _set_preference
+            slot = item.get("slot")
+            checkable = item.get("checkable", False)
+            checked = item.get("checked", False)
 
-        preferences_actions = [
-            ("2D Data Bypass", "", self.is_2d_bypass_func, resource_path("icons/warning_off_24dp_1F1F1F.svg"), "2d_data_bypass"),
-            ("Incompatible Save Bypass", "", self.incompatable_save_bypass_func, resource_path("icons/warning_off_24dp_1F1F1F.svg"), "incompatible_save_bypass"),
-            ("Missing Events Bypass", "", self.missing_events_bypass_func, resource_path("icons/warning_off_24dp_1F1F1F.svg"), "missing_events_bypass"),
-            ("Analysis Clearing Bypass", "", self.analysis_clearing_bypass_func, resource_path("icons/warning_off_24dp_1F1F1F.svg"), "analysis_clearing_bypass"),
-            ("Folding Bypass", "", self.folding_bypass_func, resource_path("icons/warning_off_24dp_1F1F1F.svg"), "folding_bypass"),
-            ("Show Advanced Parameters", "", self.advanced_parameters_func, resource_path("icons/warning_off_24dp_1F1F1F.svg"), "advanced_parameters"),
-        ]
+            if not slot and key and "theme_" not in key:
+                slot = partial(self._set_preference, key)
+                checkable = True
+                checked = getattr(self, key, False)
 
-        for name, shortcut, slot, icon, config_key in preferences_actions:
-            action = make_action(name, shortcut, slot, icon=icon, checkable=True)
-            preferences_menu.addAction(action)
-            self.pref_actions[config_key] = action
+            action = make_action(name, shortcut, slot, checkable=checkable, checked=checked, icon=item.get("icon"))
+            parent_menu.addAction(action)
 
-        plugins_menu = menu_bar.addMenu("Plugins")
-        plugins_actions = [
-            ("Plugin Manager", "Ctrl+Alt+P", self.plugins_gui, resource_path("icons/terminal_24dp_1F1F1F.svg")),
-        ]
-        for name, shortcut, slot, icon in plugins_actions:
-            plugins_menu.addAction(make_action(name, shortcut, slot, icon=icon))
+            # Register into appropriate tracking dictionaries
+            if key == "statusbar":
+                self.view_actions["statusbar"] = action
+            elif item.get("group") == "theme":
+                theme_group.addAction(action)
+                self.pref_actions[key] = action
+            elif key:
+                self.pref_actions[key] = action
 
-        terminal_menu = menu_bar.addMenu("Terminal")
-        terminal_actions = [
-            ("New Terminal", "Ctrl+Alt+T", self.terminal_gui, resource_path("icons/terminal_24dp_1F1F1F.svg")),
-        ]
-        for name, shortcut, slot, icon in terminal_actions:
-            terminal_menu.addAction(make_action(name, shortcut, slot, icon=icon))
+        # Set default theme selection if available
+        if "theme_auto" in self.pref_actions:
+            self.pref_actions["theme_auto"].setChecked(True)
 
         self.sync_app_with_config()
-
         self.statusbar.showMessage("Ready")
 
-
     def update_theme(self):
         text = self.label_desc.text()
         self.label_desc.setText("")
@@ -1039,7 +1128,7 @@ class MainApplication(QMainWindow):
             #     self.update_window_title()
 
         # Defensive dictionary lookup for the preference action
-        pref_action = getattr(self, "pref_actions", {}).get("advanced_parameters")
+        pref_action = getattr(self, "pref_actions", {}).get("ui_advanced_parameters")
         show_advanced = pref_action.isChecked() if pref_action is not None else False
 
         # Toggle visibility on all built sections
@@ -1280,7 +1369,7 @@ class MainApplication(QMainWindow):
             data_map["roi_channel_map_dict"],
             data_map["fir_feature_dict"],
             data_map["qc_dict"],
-            self.folding_bypass,
+            self.processing_folding_bypass,
         ]
 
         self.launcher_window = ViewerLauncherWidget(*args)
@@ -1298,19 +1387,25 @@ class MainApplication(QMainWindow):
         self.top_left_widget.paste()  # Trigger paste
         self.statusbar.showMessage("Pasted from clipboard")  # Show status message
 
-    def theme_change_func(self, mode):
+    def theme_change_func(self, mode: str, checked: bool = True) -> None:
+        """Handles theme switching when toggled from the menu."""
+        if not checked:
+            return  # Ignore the 'False' state when an option gets unchecked
+
         app = QApplication.instance()
         style_hints = app.styleHints()
 
         if mode == "auto":
             style_hints.setColorScheme(Qt.ColorScheme.Unknown)
-
         elif mode == "light":
             style_hints.setColorScheme(Qt.ColorScheme.Light)
-
         elif mode == "dark":
             style_hints.setColorScheme(Qt.ColorScheme.Dark)
 
+        # Save the change to your config file
+        self.theme_mode = mode
+        self._update_config_setting("Preferences", "theme_mode", mode)
+
     def _update_config_setting(self, group, key, value):
         """Helper to update memory configuration and save to disk."""
         # configparser expects string values
@@ -1326,30 +1421,12 @@ class MainApplication(QMainWindow):
         self._update_config_setting("View", "status_bar", checked)
         self.statusbar.setVisible(checked)
 
-    def is_2d_bypass_func(self, checked):
-        self.is_2d_bypass = checked
-        self._update_config_setting("Preferences", "2d_data_bypass", checked)
-
-    def incompatable_save_bypass_func(self, checked):
-        self.incompatible_save_bypass = checked
-        self._update_config_setting("Preferences", "incompatible_save_bypass", checked)
-
-    def missing_events_bypass_func(self, checked):
-        self.missing_events_bypass = checked
-        self._update_config_setting("Preferences", "missing_events_bypass", checked)
-
-    def analysis_clearing_bypass_func(self, checked):
-        self.analysis_clearing_bypass = checked
-        self._update_config_setting("Preferences", "analysis_clearing_bypass", checked)
-
-    def folding_bypass_func(self, checked):
-        self.folding_bypass = checked
-        self._update_config_setting("Preferences", "folding_bypass", checked)
-
-    def advanced_parameters_func(self, checked):
-        self.advanced_parameters = checked
-        self._update_config_setting("Preferences", "advanced_parameters", checked)
-        self.update_sections(0)
+    def _set_preference(self, config_key: str, checked: bool) -> None:
+        """Generic handler for updating boolean preferences and config settings."""
+        setattr(self, config_key, checked)
+        self._update_config_setting("Preferences", config_key, checked)
+        if config_key == "ui_advanced_parameters":
+            self.update_sections(0)
 
     def about_window(self):
         if self.about is None or not self.about.isVisible():
@@ -1454,32 +1531,65 @@ class MainApplication(QMainWindow):
 
 
     def sync_app_with_config(self):
-        """Reads values from file_cfg and updates both internal variables and UI checkmarks."""
-        # 1. Sync internal application state variables
-        self.is_2d_bypass = file_cfg.getboolean("Preferences", "2d_data_bypass", fallback=False)
-        self.incompatible_save_bypass = file_cfg.getboolean("Preferences", "incompatible_save_bypass", fallback=False)
-        self.missing_events_bypass = file_cfg.getboolean("Preferences", "missing_events_bypass", fallback=False)
-        self.analysis_clearing_bypass = file_cfg.getboolean("Preferences", "analysis_clearing_bypass", fallback=False)
-        self.folding_bypass = file_cfg.getboolean("Preferences", "folding_bypass", fallback=False)
-        self.advanced_parameters = file_cfg.getboolean("Preferences", "advanced_parameters", fallback=False)
+        """Reads values from file_cfg and updates both internal variables and UI checkmarks, 
+        using fallbacks parsed directly from DEFAULT_CONFIG."""
 
-        self.show_status_bar = file_cfg.getboolean("View", "status_bar", fallback=False)
-        self.main_h_ratio = file_cfg.getfloat("View", "main_h_ratio", fallback=26 / 45)
-        self.left_v_ratio = file_cfg.getfloat("View", "left_v_ratio", fallback=0.30)
+        # Parse DEFAULT_CONFIG to use as the single source of truth for fallbacks
+        default_parser = configparser.ConfigParser()
+        default_parser.read_string(DEFAULT_CONFIG)
 
-        # 2. Sync the UI Menu checkmarks visually
-        if hasattr(self, 'pref_actions'):
-            self.pref_actions["2d_data_bypass"].setChecked(self.is_2d_bypass)
-            self.pref_actions["incompatible_save_bypass"].setChecked(self.incompatible_save_bypass)
-            self.pref_actions["missing_events_bypass"].setChecked(self.missing_events_bypass)
-            self.pref_actions["analysis_clearing_bypass"].setChecked(self.analysis_clearing_bypass)
-            self.pref_actions["folding_bypass"].setChecked(self.folding_bypass)
-            self.pref_actions["advanced_parameters"].setChecked(self.advanced_parameters)
+        # Define mapping of sections, keys, and their expected type
+        config_mappings = {
+            "View": [
+                ("status_bar", "boolean"), 
+                ("main_h_ratio", "float"), 
+                ("left_v_ratio", "float")
+            ],
+            "Preferences": [
+                ("theme_mode", "string"),
+                ("processing_2d_data_bypass", "boolean"),
+                ("processing_incompatible_save_bypass", "boolean"),
+                ("processing_missing_events_bypass", "boolean"),
+                ("processing_analysis_clearing_bypass", "boolean"),
+                ("processing_folding_bypass", "boolean"),
+                ("processing_separate_events", "boolean"),
+                ("ui_advanced_parameters", "boolean"),
+                ("updates_check_plugins_automatic", "boolean"),
+                ("updates_check_app_automatic", "boolean"),
+            ]
+        }
 
-        if hasattr(self, 'view_actions'):
-            self.view_actions["statusbar"].setChecked(self.show_status_bar)
+        # 1. Sync internal state variables and UI checkmarks dynamically
+        for section, items in config_mappings.items():
+            for key, val_type in items:
+                # Retrieve the exact fallback specified in DEFAULT_CONFIG
+                if val_type == "boolean":
+                    fallback = default_parser.getboolean(section, key)
+                    val = file_cfg.getboolean(section, key, fallback=fallback)
+                elif val_type == "float":
+                    fallback = default_parser.getfloat(section, key)
+                    val = file_cfg.getfloat(section, key, fallback=fallback)
+                else:
+                    fallback = default_parser.get(section, key)
+                    val = file_cfg.get(section, key, fallback=fallback)
 
-        if self.advanced_parameters:
+                # Set attribute on self
+                setattr(self, key, val)
+
+                # Sync UI Menu checkmarks visually
+                if key in self.pref_actions:
+                    self.pref_actions[key].setChecked(val)
+                elif key == "status_bar" and "statusbar" in self.view_actions:
+                    self.view_actions["statusbar"].setChecked(val)
+
+        # 2. Sync Theme Radio Action Group based on theme_mode string (e.g., "auto", "light", "dark")
+        theme_mode = getattr(self, "theme_mode", "auto")
+        theme_action_key = f"theme_{theme_mode}"
+        if theme_action_key in self.pref_actions:
+            self.pref_actions[theme_action_key].setChecked(True)
+
+        # 3. Trigger dependent UI updates and handlers
+        if getattr(self, "ui_advanced_parameters", False):
             self.update_sections(0)
 
         if hasattr(self, 'recent_files_menu'):
@@ -1489,6 +1599,7 @@ class MainApplication(QMainWindow):
             self.project_manager.update_recent_projects_menu()
 
         QTimer.singleShot(0, self.apply_splitter_ratios)
+        self.statusbar.showMessage("Ready")
 
 
     def save_splitter_ratios(self):
@@ -1814,6 +1925,7 @@ class MainApplication(QMainWindow):
         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")
+        action3 = menu.addAction(QIcon(resource_path("icons/remove_24dp_1F1F1F.svg")), "View Logs")
 
         action = menu.exec(global_pos)
         if action == action1:
@@ -1899,6 +2011,36 @@ class MainApplication(QMainWindow):
 
             self.check_files_dirty_state()
 
+        elif action == action3:
+            self.open_log_window(bubble)
+
+
+    def open_log_window(self, bubble):
+        target_path = bubble.file_path
+        log_content = getattr(self, "participant_logs", {}).get(
+            target_path, "No logs generated yet for this participant."
+        )
+
+        window_title = f"Logs — {os.path.basename(target_path)}"
+
+        if not hasattr(self, "active_log_windows"):
+            self.active_log_windows = []
+        self.active_log_windows = [
+            w for w in self.active_log_windows if w.isVisible()
+        ]
+
+        # If a log window for this specific file is already open, focus it instead of opening a new one
+        for win in self.active_log_windows:
+            if getattr(win, "file_path", None) == target_path:
+                win.raise_()
+                win.activateWindow()
+                return
+
+        log_win = LogWindow(window_title, target_path, log_content, self)
+        log_win.show()
+        self.active_log_windows.append(log_win)
+
+
     def check_files_dirty_state(self):
         """Compares currently loaded files against the saved baseline list."""
         if not hasattr(self, "saved_selected_paths"):
@@ -2010,7 +2152,7 @@ class MainApplication(QMainWindow):
     def on_run_task(self):
 
         #do the check
-        if not self.analysis_clearing_bypass:
+        if not self.processing_analysis_clearing_bypass:
             if self.button3.isVisible():
                 msg = QMessageBox(self)
                 msg.setWindowTitle("Confirm - FLARES")
@@ -2120,9 +2262,12 @@ class MainApplication(QMainWindow):
         for section_widget in self.param_sections:
             section_params = section_widget.get_param_values()
             all_params.update(section_params)        
-        if self.folding_bypass:
+        if self.processing_folding_bypass:
             all_params['FOLDING_BYP'] = True
 
+        if self.processing_separate_events:
+            all_params['SEPARATE_EVENTS'] = True
+
         collected_data = {
             "SNIRF_FILES": snirf_files,
             "PARAMS": all_params,  # add this line
@@ -2258,6 +2403,36 @@ class MainApplication(QMainWindow):
                     _, file_path, step_index = msg
                     self.progress_update_signal.emit(file_path, step_index)
 
+                elif isinstance(msg, tuple) and len(msg) == 3 and msg[0] == "log":
+                    _, file_path, text = msg
+                    if not hasattr(self, 'participant_logs'):
+                        self.participant_logs = {}
+                    if file_path not in self.participant_logs:
+                        self.participant_logs[file_path] = ""
+                    self.participant_logs[file_path] += text
+
+                    # Push live update to any open log window for this file
+                    if hasattr(self, 'active_log_windows'):
+                        for win in self.active_log_windows:
+                            if getattr(win, 'file_path', None) == file_path:
+                                win.append_log(text)
+
+                elif isinstance(msg, dict) and msg.get("type") == "log":
+                    file_path = msg.get("file")
+                    text = msg.get("message")
+                    if file_path:
+                        if not hasattr(self, 'participant_logs'):
+                            self.participant_logs = {}
+                        if file_path not in self.participant_logs:
+                            self.participant_logs[file_path] = ""
+                        self.participant_logs[file_path] += text
+
+                        # Push live update to any open log window for this file
+                        if hasattr(self, 'active_log_windows'):
+                            for win in self.active_log_windows:
+                                if getattr(win, 'file_path', None) == file_path:
+                                    win.append_log(text)
+
 
         except Exception as e:
             print(f"Error in timer loop: {e}")
@@ -2847,4 +3022,4 @@ if __name__ == "__main__":
         window.show()
         sys.exit(app.exec())
 
-# Not 2800 lines yay!
+# Not 3100 lines yay!

plugin_manager.py

@@ -22,7 +22,7 @@ from typing import Any, cast
 
 # External library imports
 import certifi
-from PySide6.QtCore import QObject, QUrl, Signal
+from PySide6.QtCore import QObject, QThread, QUrl, Signal
 from PySide6.QtGui import QDesktopServices
 from PySide6.QtWidgets import QMainWindow, QMenu, QMessageBox
 
@@ -329,3 +329,98 @@ class PluginManager(QObject):
         if self.plugins_dir.exists():
             return QDesktopServices.openUrl(QUrl.fromLocalFile(str(self.plugins_dir)))
         return False
+
+    def check_for_updates(self, repo_urls: list[str]) -> list[dict[str, Any]]:
+        """
+        Fetches remote repositories and compares server plugin versions
+        against installed plugins, returning the installed plugins list
+        enriched with update metadata.
+        """
+        installed_plugins = self.get_installed_plugins_info()
+        remote_data, _ = self.fetch_remote_repositories(repo_urls)
+
+        # Index remote plugins by their ID (fallback to name if id is missing)
+        remote_map: dict[str, dict[str, Any]] = {}
+        for remote_plugin in remote_data:
+            plugin_id = remote_plugin.get("id") or remote_plugin.get("name")
+            if plugin_id:
+                remote_map[str(plugin_id)] = remote_plugin
+
+        # Compare versions and annotate each installed plugin dictionary
+        for plugin in installed_plugins:
+            plugin_id = str(plugin.get("id", ""))
+            local_version_str = str(plugin.get("version", "0.0.0"))
+            local_tuple = parse_version(local_version_str)
+
+            remote_plugin = remote_map.get(plugin_id)
+            if remote_plugin:
+                remote_version_str = str(remote_plugin.get("version", "0.0.0"))
+                remote_tuple = parse_version(remote_version_str)
+
+                if remote_tuple > local_tuple:
+                    plugin["update_available"] = True
+                    plugin["remote_version"] = remote_version_str
+                    plugin["download_url"] = str(remote_plugin.get("download_url", ""))
+                else:
+                    plugin["update_available"] = False
+                    plugin["remote_version"] = remote_version_str
+                    plugin["download_url"] = ""
+            else:
+                plugin["update_available"] = False
+                plugin["remote_version"] = None
+                plugin["download_url"] = ""
+
+        return installed_plugins
+
+
+class StartupUpdateWorker(QThread):
+    updates_checked = Signal(list)
+
+    def __init__(self, manager: Any, repo_urls: list[str]) -> None:
+        super().__init__()
+        self.manager = manager
+        self.repo_urls = repo_urls
+
+    def run(self) -> None:
+        try:
+            print("[StartupWorker] Starting background update check...")
+            installed_plugins = self.manager.get_installed_plugins_info()
+            print(f"[StartupWorker] Found {len(installed_plugins)} installed local plugins.")
+
+            remote_data, all_failed = self.manager.fetch_remote_repositories(self.repo_urls)
+            print(f"[StartupWorker] Fetch remote complete. Failed: {all_failed}, Items fetched: {len(remote_data)}")
+
+            if all_failed or not remote_data:
+                print("[StartupWorker] Aborting: Remote fetch failed or returned empty data.")
+                return
+
+            remote_map: dict[str, dict[str, Any]] = {}
+            for raw_plugin in remote_data:
+                if isinstance(raw_plugin, dict):
+                    remote_plugin = cast(dict[str, Any], raw_plugin)
+
+                    plugin_id = remote_plugin.get("id") or remote_plugin.get("name")
+                    if isinstance(plugin_id, str):
+                        remote_map[plugin_id] = remote_plugin
+
+            outdated_plugins: list[dict[str, Any]] = []
+            for plugin in installed_plugins:
+                plugin_id = str(plugin.get("id", ""))
+                local_version_str = str(plugin.get("version", "0.0.0"))
+                local_tuple = parse_version(local_version_str)
+
+                remote_plugin = remote_map.get(plugin_id)
+                if remote_plugin:
+                    remote_version_str = str(remote_plugin.get("version", "0.0.0"))
+                    remote_tuple = parse_version(remote_version_str)
+                    print(f"[StartupWorker] Comparing '{plugin.get('name')}': Local v{local_version_str} vs Remote v{remote_version_str}")
+
+                    if remote_tuple > local_tuple:
+                        plugin["remote_version"] = remote_version_str
+                        plugin["download_url"] = str(remote_plugin.get("download_url", ""))
+                        outdated_plugins.append(plugin)
+
+            print(f"[StartupWorker] Outdated plugins found: {len(outdated_plugins)}")
+            self.updates_checked.emit(outdated_plugins)
+        except Exception as e:
+            print(f"[StartupWorker] Error during startup update check: {e}")

project_manager.py

@@ -38,6 +38,23 @@ if TYPE_CHECKING:
     from main import MainApplication
 
 
+class LoadProjectThread(QThread):
+    finished_signal = Signal(object)  # Emits the loaded project data dictionary
+    error_signal = Signal(str)  # Emits the error message string
+
+    def __init__(self, filename: str) -> None:
+        super().__init__()
+        self.filename = filename
+
+    def run(self) -> None:
+        try:
+            with open(self.filename, "rb") as f:
+                project_data = pickle.load(f)
+            self.finished_signal.emit(project_data)
+        except Exception as e:
+            self.error_signal.emit(str(e))
+
+
 class SaveProjectThread(QThread):
     finished_signal = Signal(str)
     error_signal = Signal(str)
@@ -56,6 +73,25 @@ class SaveProjectThread(QThread):
             self.error_signal.emit(str(e))
 
 
+class LoadingOverlay(QDialog):
+    def __init__(self, parent: Optional[QWidget] = None) -> None:
+        super().__init__(parent)
+        self.setWindowFlags(Qt.WindowType.Dialog | Qt.WindowType.FramelessWindowHint)
+        self.setModal(True)
+        self.setWindowModality(Qt.WindowModality.ApplicationModal)
+        self.setAttribute(Qt.WidgetAttribute.WA_TranslucentBackground)
+
+        layout = QVBoxLayout()
+        layout.setAlignment(Qt.AlignmentFlag.AlignCenter)
+
+        label = QLabel("Loading Project…")
+        label.setStyleSheet(
+            "font-size: 18px; color: white; background-color: rgba(0,0,0,150);"
+            " padding: 20px; border-radius: 10px;"
+        )
+        layout.addWidget(label)
+        self.setLayout(layout)
+
 
 class SavingOverlay(QDialog):
     def __init__(self, parent: Optional[QWidget] = None) -> None:
@@ -171,6 +207,8 @@ class ProjectManager:
             )
             return
 
+        self._load_files_into_pipeline(snirf_files)
+
     def load_dropped_files(self, file_paths: List[str]) -> None:
         """Public entry point for handling files or folders dropped onto the UI."""
         if not file_paths:
@@ -339,12 +377,31 @@ class ProjectManager:
             self.load_project(filename)
 
     def load_project(self, filename: str) -> None:
-        """Loads a .flare project file into the application."""
+        """Triggers asynchronous loading of a .flare project file."""
+        app = self.app
+
+        # 1. Show the custom loading overlay matching your saver design
+        self.loading_overlay = LoadingOverlay(app)
+        self.loading_overlay.resize(app.size())
+        self.loading_overlay.move(app.pos())
+        self.loading_overlay.show()
+
+        # 2. Fire up the background thread for pickle loading
+        self.loader_thread = LoadProjectThread(filename)
+        self.loader_thread.finished_signal.connect(
+            lambda data: self._handle_loaded_data(filename, data)
+        )
+        self.loader_thread.error_signal.connect(self._handle_load_error)
+        self.loader_thread.start()
+
+    def _handle_loaded_data(self, filename: str, data: dict) -> None:
+        # Close overlay
+        if hasattr(self, "loading_overlay"):
+            self.loading_overlay.close()
+            self.loading_overlay.deleteLater()
+
         app = self.app
         try:
-            with open(filename, "rb") as f:
-                data = pickle.load(f)
-
             checks = [
                 ("version", "<=1.1.7"),
                 ("file_metadata", "<=1.2.2"),
@@ -358,7 +415,7 @@ class ProjectManager:
                         f"This project was saved in an earlier version of {APP_NAME.upper()} ({ver_str}) "
                         "and is potentially not compatible with this version. "
                     )
-                    if getattr(app, "incompatible_save_bypass", False):
+                    if getattr(app, "processing_incompatible_save_bypass", False):
                         QMessageBox.warning(
                             app, f"Warning - {APP_NAME.upper()}", msg + "Attempting load."
                         )
@@ -438,16 +495,19 @@ class ProjectManager:
             if hasattr(app, "button3"):
                 app.button3.setVisible(has_data)
 
-            
             self.add_to_recent_projects(os.path.normpath(filename))
-
-            # Reset baselines cleanly
             self.reset_all_dirty_states()
 
             QMessageBox.information(app, "Loaded", f"Project loaded from:\n{filename}")
 
         except Exception as e:
-            QMessageBox.critical(app, "Error", f"Failed to load project:\n{e}")
+            QMessageBox.critical(app, "Error", f"Failed to process loaded project data:\n{e}")
+
+    def _handle_load_error(self, error_msg: str) -> None:
+        if hasattr(self, "loading_overlay"):
+            self.loading_overlay.close()
+            self.loading_overlay.deleteLater()
+        QMessageBox.critical(self.app, "Error", f"Failed to read project file:\n{error_msg}")
 
     # =========================================================================
     # Project Saving (Save / Save As)
@@ -863,7 +923,6 @@ def _get_bids_demographics(snirf_path: str) -> dict[str, str]:
     return {}
 
 
-
 def extract_metadata_worker(file_name: str) -> dict[str, Any]:
     """Runs in the separate worker process. Returns a clean dict."""
 

src/analysis/exporttocsv.py

@@ -12,6 +12,7 @@ import os
 from typing import Any
 
 # External library imports
+from mne import Epochs
 from pandas import DataFrame
 
 from mne.io.base import BaseRaw
@@ -27,6 +28,7 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
     def __init__(
         self,
         haemo_dict: dict[str, BaseRaw],
+        epochs_dict: dict[str, Epochs],
         cha_dict: dict[str, DataFrame],
         df_ind_dict: dict[str, DataFrame],
         design_matrix_dict: dict[str, DataFrame],
@@ -40,6 +42,7 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
         super().__init__("ExportToCSV")
         self.setWindowTitle(f"Export To CSV Viewer - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
+        self.epochs_dict = epochs_dict
         self.cha_dict = cha_dict
         self.df_ind_dict = df_ind_dict
         self.design_matrix = design_matrix_dict
@@ -50,8 +53,7 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
         self.qc_dict = qc_dict
 
         self.setup_csv_ui(["0 (Export Data to CSV)", "1 (CSV for SPARKS)", "2 (Export Configuration to CSV)", "3 (Paragraph of Configuration)", "4 (Export FIR Waveform Features to CSV)",
-            "5 (Export Quality Control Metrics to CSV)",
-            "6 (Export Master Consolidated Matrix [All Participants into 1 CSV])"
+            "5 (Export Quality Control Metrics to CSV)", "6 (Export Master Consolidated Matrix [All Participants into 1 CSV])"
         ])
 
 
@@ -120,67 +122,67 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
                         magic_string = self.gen_magic_str(first_params)
                         self.placeholder_label.setText(magic_string)
 
-                    # elif idx == 4:
-                    #     # FIR Waveform Features Export
-                    #     fir_data = self.fir_feature_dict.get(file_path)
-                    #     if fir_data and isinstance(fir_data, dict):
-                    #         names = fir_data.get("feature_names", [])
-                    #         vals = fir_data.get("features", [])
-                    #         chans = fir_data.get("feature_channels", [])
+                    elif idx == 4:
+                        # FIR Waveform Features Export
+                        fir_data = self.fir_feature_dict.get(file_path)
+                        if fir_data:
+                            names = fir_data.get("feature_names", [])
+                            vals = fir_data.get("features", [])
+                            chans = fir_data.get("feature_channels", [])
 
-                    #         fir_df = DataFrame({
-                    #             "Feature_Name": names,
-                    #             "Channel": chans if len(chans) == len(names) else ["N/A"] * len(names),
-                    #             "Value": vals
-                    #         })
-                    #         save_path = os.path.join(output_dir, f"{base_filename}_fir_features.csv")
-                    #         fir_df.to_csv(save_path, index=False)
-                    #         success_count += 1
+                            fir_df = DataFrame({
+                                "Feature_Name": names,
+                                "Channel": chans if len(chans) == len(names) else ["N/A"] * len(names),
+                                "Value": vals
+                            })
+                            save_path = os.path.join(output_dir, f"{base_filename}_fir_features.csv")
+                            fir_df.to_csv(save_path, index=False)
+                            success_count += 1
 
-                    # elif idx == 5:
-                    #     # Quality Control (QC) Metrics Export
-                    #     qc_data = self.qc_dict.get(file_path)
-                    #     if qc_data and isinstance(qc_data, dict):
-                    #         qc_df = DataFrame(list(qc_data.items()), columns=["Metric", "Value"])
-                    #         save_path = os.path.join(output_dir, f"{base_filename}_qc_metrics.csv")
-                    #         qc_df.to_csv(save_path, index=False)
-                    #         success_count += 1
+                    elif idx == 5:
+                        # Quality Control (QC) Metrics Export
+                        qc_data = self.qc_dict.get(file_path)
+                        if qc_data and isinstance(qc_data, dict):
+                            qc_df = DataFrame(list(qc_data.items()), columns=["Metric", "Value"])
+                            save_path = os.path.join(output_dir, f"{base_filename}_qc_metrics.csv")
+                            qc_df.to_csv(save_path, index=False)
+                            success_count += 1
 
-                    # elif idx == 6:
-                    #     # Master Consolidated Matrix (1 single CSV combining all selected participants)
-                    #     save_path = os.path.join(output_dir, f"{APP_NAME}_master_consolidated.csv")
-                    #     if not os.path.exists(save_path):
-                    #         master_rows: list[dict[str, Any]] = []
-                    #         for fp in selected_file_paths:
-                    #             abs_path = os.path.abspath(fp)
-                    #             grp = self.group_dict.get(fp, "Unknown")
-                    #             row: dict[str, Any] = {"Participant": abs_path, "Group": grp}
+                    elif idx == 6:
+                        # Master Consolidated Matrix (1 single CSV combining all selected participants)
+                        save_path = os.path.join(output_dir, f"{APP_NAME}_master_consolidated.csv")
+                        if not os.path.exists(save_path):
+                            master_rows: list[dict[str, Any]] = []
+                            for fp in selected_file_paths:
+                                abs_path = os.path.abspath(fp)
+                                grp = self.group_dict.get(fp, "Unknown")
+                                row: dict[str, Any] = {"Participant": abs_path, "Group": grp}
 
-                    #             # QC Metrics
-                    #             qc_info = self.qc_dict.get(fp, {})
-                    #             if isinstance(qc_info, dict):
-                    #                 for mk, mv in qc_info.items():
-                    #                     row[f"QC_{mk}"] = mv
+                                # QC Metrics
+                                qc_info = self.qc_dict.get(fp, {})
+                                if isinstance(qc_info, dict):
+                                    for mk, mv in qc_info.items():
+                                        row[f"QC_{mk}"] = mv
 
-                    #             # FIR Features
-                    #             fir_info = self.fir_feature_dict.get(fp, {})
-                    #             print("1")
-                    #             if isinstance(fir_info, dict):
-                    #                 print("2")
-                    #                 f_names = fir_info.get("feature_names", [])
-                    #                 f_vals = fir_info.get("features", [])
-                    #                 print("3")
-                    #                 if len(f_names) == len(f_vals):
-                    #                     print("4")
-                    #                     for fn, fv in zip(f_names, f_vals):
-                    #                         row[f"FIR_{fn}"] = fv
+                                # FIR Features
+                                fir_info = self.fir_feature_dict.get(fp, {})
+                                print("1")
+                                if isinstance(fir_info, dict):
+                                    print("2")
+                                    f_names = fir_info.get("feature_names", [])
+                                    f_vals = fir_info.get("features", [])
+                                    print("3")
+                                    if len(f_names) == len(f_vals):
+                                        print("4")
+                                        for fn, fv in zip(f_names, f_vals):
+                                            row[f"FIR_{fn}"] = fv
 
-                    #             master_rows.append(row)
+                                master_rows.append(row)
 
-                    #         if master_rows:
-                    #             df_master = DataFrame(master_rows)
-                    #             df_master.to_csv(save_path, index=False)
-                    #             success_count += 1
+                            if master_rows:
+                                df_master = DataFrame(master_rows)
+                                df_master.to_csv(save_path, index=False)
+                                success_count += 1
 
                     else:
                         print(f"No method defined for index {idx}")

src/analysis/intragroupstats.py

@@ -211,7 +211,6 @@ class IntraGroupStatsWidget(IntraGroupUIMixin, FlaresBaseWidget):
                     continue
 
 
-            
             cha_df = self.cha_dict.get(file_path)
             if cha_df is not None:
                 all_cha = pd.concat([all_cha, cha_df], ignore_index=True)

src/analysis/participantfoldchannels.py

@@ -283,7 +283,6 @@ class StaticChannelCanvas(FigureCanvas):
             self.draw_idle()
 
 
-
 class StandaloneLegendDialog(QWidget):
     def __init__(self, canvas_engine: Any, title_prefix: str, parent: QWidget | None = None) -> None:
         super().__init__(None)
@@ -317,7 +316,7 @@ class InteractiveParticipantGridCanvas(FigureCanvas):
 
         num_channels = len(channels_data)
 
-        # --- FIX: DYNAMICALLY CALCULATE OPTIMAL 16:9 COLUMNS ---
+        # Dynamically calculate best ratio for 16:9
         target_ratio = 16 / 9
         best_cols = 4
         min_ratio_error = float('inf')
@@ -678,7 +677,6 @@ class InteractiveParticipantGridCanvas(FigureCanvas):
         scroll_layout.setSpacing(6)
         scroll_layout.setContentsMargins(0, 0, 0, 0)
 
-
         true_color_map = get_landmark_color_map()
 
         # Iterate over the sorted keys directly from your method

src/shared/flaresbasewidget.py

@@ -14,11 +14,12 @@ import pandas as pd
 from pandas import DataFrame
 
 from PySide6.QtWidgets import QApplication, QComboBox, QDialog, QGridLayout, QHBoxLayout, QLabel, QLineEdit, QListView, QMessageBox, QPushButton, QScrollArea, QSizePolicy, QVBoxLayout, QWidget, QFrame, QSpinBox, QFileDialog
-from PySide6.QtGui import QPalette, QStandardItemModel, QStandardItem, QPixmap, QIntValidator, QDoubleValidator
+from PySide6.QtGui import QStandardItemModel, QStandardItem, QPixmap, QIntValidator, QDoubleValidator
 from PySide6.QtCore import QEvent, QPoint, QSize, QTimer, Qt, Signal
 
 from src.shared.shareddata import APP_NAME, PIPELINE_STAGES
 
+
 class FullClickComboBox(QComboBox):
     def __init__(self, parent=None):
         super().__init__(parent)
@@ -1290,7 +1291,6 @@ class FlaresBaseWidget(QWidget):
         model.itemChanged.connect(on_item_changed)
 
 
-
     def update_participant_list_for_group(self, group_name=None, combo=None):
 
         target_combo = combo if combo is not None else getattr(self, "participant_dropdown", None)
@@ -1492,8 +1492,6 @@ class InterGroupUIMixin:
         dropdown.blockSignals(False)
 
 
-
-
     def _get_file_paths_from_labels(self, labels, group_name):
         file_paths = []
 
@@ -1868,7 +1866,6 @@ class IntraGroupUIMixin:
                     param_info["options"] = dynamic_contrasts
                     param_info["default"] = dynamic_contrasts[0] if dynamic_contrasts else ""
 
-        
         param_values = {}
         if indexes_needing_params:
             dialog = ParameterInputDialog(indexes_needing_params, parent=self)
@@ -1886,6 +1883,7 @@ class IntraGroupUIMixin:
             param_values,
         )
 
+
 class ParticipantUIMixin:
     def setup_participant_ui(
         self,
@@ -1913,7 +1911,6 @@ class ParticipantUIMixin:
         self.event_dropdown = QComboBox()
         self.event_dropdown.addItem("<None Selected>")
 
-                
         self.index_texts = index_texts
 
         self.image_index_dropdown = self._create_multiselect_dropdown(self.index_texts)
@@ -1968,8 +1965,6 @@ class ParticipantUIMixin:
         ]
 
 
-        
-
         # 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)"
@@ -1989,8 +1984,8 @@ class ParticipantUIMixin:
                 return
 
         return (
-        selected_event,
-        selected_file_paths,
-        selected_indexes,
-        param_values,
+            selected_event,
+            selected_file_paths,
+            selected_indexes,
+            param_values,
         )

src/window/plugins.py

@@ -8,6 +8,10 @@ License: GPL-3.0
 """
 
 # Built-in imports
+import io
+import shutil
+import urllib.request
+import zipfile
 from pathlib import Path
 from typing import Any, cast
 
@@ -15,26 +19,95 @@ from typing import Any, cast
 from PySide6.QtCore import Qt, QThread, Signal
 from PySide6.QtGui import QColor
 from PySide6.QtWidgets import (
-    QHBoxLayout, QLabel, QLineEdit, QListWidget, QListWidgetItem,
-    QMessageBox, QPushButton, QTabWidget, QTextBrowser, QVBoxLayout, QWidget
+    QHBoxLayout, QLabel, QLineEdit, QListWidget, QListWidgetItem, QMessageBox,
+    QPushButton, QTabWidget, QTextBrowser, QVBoxLayout, QWidget, QProgressDialog
 )
 
-from plugin_manager import PluginManager, parse_version
+from plugin_manager import PluginManager, get_ssl_context, parse_version
 from src.shared.shareddata import APP_NAME, CURRENT_VERSION, PLUGINS_URL
 
 
 class RemoteFetchWorker(QThread):
     """Background thread to fetch remote repository data without lagging the main UI."""
-    fetched = Signal(list, bool)  # (plugins_data, all_failed)
+    fetched = Signal(list, bool, str)  # (plugins_data, all_failed, fetch_type)
 
-    def __init__(self, manager: PluginManager, urls: list[str]) -> None:
+    def __init__(self, manager: PluginManager, urls: list[str], fetch_type: str = "browser") -> None:
         super().__init__()
         self.manager = manager
         self.urls = urls
+        self.fetch_type = fetch_type
 
     def run(self) -> None:
         plugins, all_failed = self.manager.fetch_remote_repositories(self.urls)
-        self.fetched.emit(plugins, all_failed)
+        self.fetched.emit(plugins, all_failed, self.fetch_type)
+
+
+class PluginInstallWorker(QThread):
+    """Background worker to download, unpack, and install/update plugins with progress reporting."""
+    progress = Signal(int, int)  # (downloaded_bytes, total_bytes)
+    status_message = Signal(str)
+    finished = Signal(bool, str)  # (success, message_or_path)
+
+    def __init__(
+        self,
+        manager: PluginManager,
+        download_url: str,
+        plugin_id: str,
+        is_update: bool = False,
+        plugin_path_to_remove: Path | None = None
+    ) -> None:
+        super().__init__()
+        self.manager = manager
+        self.download_url = download_url
+        self.plugin_id = plugin_id
+        self.is_update = is_update
+        self.plugin_path_to_remove = plugin_path_to_remove
+
+    def run(self) -> None:
+        try:
+            self.status_message.emit("Connecting to server...")
+            req = urllib.request.Request(
+                self.download_url,
+                headers={"User-Agent": f"{APP_NAME}-PluginManager"},
+            )
+
+            with urllib.request.urlopen(req, timeout=30, context=get_ssl_context()) as response:
+                if response.status != 200:
+                    self.finished.emit(False, f"Download failed with HTTP status code {response.status}")
+                    return
+
+                total_size_str = response.headers.get("Content-Length")
+                total_size = int(total_size_str) if total_size_str and total_size_str.isdigit() else 0
+
+                self.status_message.emit("Downloading plugin archive...")
+                chunk_size = 8192
+                downloaded = 0
+                buffer = io.BytesIO()
+
+                while True:
+                    chunk = response.read(chunk_size)
+                    if not chunk:
+                        break
+                    buffer.write(chunk)
+                    downloaded += len(chunk)
+                    self.progress.emit(downloaded, total_size)
+
+                zip_bytes = buffer.getvalue()
+
+            if self.is_update and self.plugin_path_to_remove and self.plugin_path_to_remove.exists():
+                self.status_message.emit("Removing old version...")
+                if self.plugin_path_to_remove.is_dir():
+                    shutil.rmtree(self.plugin_path_to_remove)
+                else:
+                    self.plugin_path_to_remove.unlink()
+
+            self.status_message.emit("Unpacking and extracting files...")
+            with zipfile.ZipFile(io.BytesIO(zip_bytes)) as zip_ref:
+                zip_ref.extractall(self.manager.plugins_dir)
+
+            self.finished.emit(True, str(self.manager.plugins_dir))
+        except Exception as e:
+            self.finished.emit(False, str(e))
 
 
 class PluginsWindow(QWidget):
@@ -52,6 +125,8 @@ class PluginsWindow(QWidget):
         self.remote_plugins_data: list[dict[str, Any]] = []
         self._has_fetched_remote: bool = False
         self._fetch_worker: RemoteFetchWorker | None = None
+        self._install_worker: PluginInstallWorker | None = None
+        self._progress_dialog: QProgressDialog | None = None
 
         # Refresh UI automatically if manager updates state
         self.manager.plugins_changed.connect(self.refresh_installed_plugins)
@@ -70,40 +145,75 @@ class PluginsWindow(QWidget):
         self.setLayout(main_layout)
 
         self.refresh_installed_plugins()
+        self.check_installed_updates()
+
+    def check_installed_updates(self) -> None:
+        """Asynchronously checks remote repositories for installed plugin updates."""
+        if self._fetch_worker is not None and self._fetch_worker.isRunning():
+            return
+
+        self._fetch_worker = RemoteFetchWorker(self.manager, self.repository_urls, fetch_type="updates")
+        self._fetch_worker.fetched.connect(self._on_remote_fetched)
+        self._fetch_worker.start()
 
     def refresh_installed_plugins(self) -> None:
-        """Refreshes installed list using metadata from PluginManager."""
+        """Refreshes installed list using metadata from PluginManager and attaches update info."""
         self.installed_list.clear()
         plugins_info = self.manager.get_installed_plugins_info()
 
+        remote_map: dict[str, dict[str, Any]] = {}
+        if self._has_fetched_remote and self.remote_plugins_data:
+            for p in self.remote_plugins_data:
+                p_id = p.get("id") or p.get("name")
+                if p_id:
+                    remote_map[str(p_id)] = p
+
         for info in plugins_info:
+            p_id = str(info.get("id", ""))
+            local_tuple = parse_version(str(info.get("version", "0.0.0")))
+
+            remote_plugin = remote_map.get(p_id)
+            if remote_plugin:
+                remote_ver = str(remote_plugin.get("version", "0.0.0"))
+                if parse_version(remote_ver) > local_tuple:
+                    info["update_available"] = True
+                    info["remote_version"] = remote_ver
+                    info["download_url"] = str(remote_plugin.get("download_url", ""))
+
             display_text = f"{info['name']} (v{info.get('version', '1.0.0')})"
+            if info.get("update_available"):
+                display_text += f" [Update Available: v{info.get('remote_version')}]"
             if info["is_disabled"]:
                 display_text += " [Disabled]"
 
             item = QListWidgetItem(display_text, self.installed_list)
             item.setData(Qt.ItemDataRole.UserRole, info)
 
-            if info["is_disabled"]:
+            if info.get("update_available"):
+                item.setForeground(QColor("#1976d2"))
+            elif info["is_disabled"]:
                 item.setForeground(QColor("#757575"))
 
         if self.installed_list.count() == 0:
             self.installed_list.addItem("No plugins installed.")
             self._clear_details_panel()
 
-        # Re-populate browser list if remote data was already fetched to reflect newly installed/uninstalled plugins
-        if self._has_fetched_remote and self.remote_plugins_data:
+        if not self._has_fetched_remote:
+            self.check_installed_updates()
+        elif self.remote_plugins_data:
             self._populate_browser_list()
 
     def _on_installed_item_changed(self, current: QListWidgetItem | None, _: Any) -> None:
         """Updates the right-hand details panel when a plugin is selected."""
         if not current:
             self._clear_details_panel()
+            self.btn_update_plugin.setEnabled(False)
             return
 
         info = current.data(Qt.ItemDataRole.UserRole)
         if not isinstance(info, dict):
             self._clear_details_panel()
+            self.btn_update_plugin.setEnabled(False)
             return
 
         plugin_info = cast(dict[str, Any], info)
@@ -114,83 +224,161 @@ class PluginsWindow(QWidget):
         desc = str(plugin_info.get("description", "No description provided."))
         is_disabled = bool(plugin_info.get("is_disabled", False))
         path = str(plugin_info.get("path", ""))
+        update_available = bool(plugin_info.get("update_available", False))
 
         self.lbl_plugin_title.setText(name)
         self.lbl_plugin_meta.setText(f"<b>Version:</b> {version} &nbsp;|&nbsp; <b>Author:</b> {author}")
 
-        if is_disabled:
+        if update_available:
+            rem_ver = plugin_info.get("remote_version", "")
+            self.lbl_plugin_status.setText(f"<font color='#1976d2'><b>Status: Update v{rem_ver} Available!</b></font>")
+        elif is_disabled:
             self.lbl_plugin_status.setText("<font color='#d32f2f'><b>Status: Disabled</b></font>")
         else:
             self.lbl_plugin_status.setText("<font color='#2e7d32'><b>Status: Active</b></font>")
 
         self.txt_plugin_desc.setHtml(desc)
         self.lbl_plugin_path.setText(f"<b>Path:</b> <code>{path}</code>")
+        self.btn_update_plugin.setEnabled(update_available)
 
-    def _clear_details_panel(self) -> None:
-        """Clears details display when nothing is selected."""
-        self.lbl_plugin_title.setText("Select a plugin")
-        self.lbl_plugin_meta.setText("")
-        self.lbl_plugin_status.setText("")
-        self.txt_plugin_desc.clear()
-        self.lbl_plugin_path.setText("")
+    def execute_plugin_installation(self, download_url: str, plugin_id: str, plugin_name: str, is_update: bool, plugin_path: Path | None) -> None:
+        """Sets up the progress dialog and starts the background installation/update worker."""
+        if self._install_worker is not None and self._install_worker.isRunning():
+            return
 
-    def toggle_enable_disable(self) -> None:
+        self._installation_finished_flag = False
+        action_label = "Updating" if is_update else "Installing"
+
+        self._progress_dialog = QProgressDialog(f"{action_label} '{plugin_name}'...", "Cancel", 0, 100, self)
+        self._progress_dialog.setMinimumDuration(0)  # Show the progress dialog instantly
+        self._progress_dialog.setWindowTitle(f"{action_label} Plugin")
+        self._progress_dialog.setWindowModality(Qt.WindowModality.WindowModal)
+        self._progress_dialog.setAutoClose(False)
+        self._progress_dialog.setAutoReset(False)
+        self._progress_dialog.canceled.connect(self._cancel_installation)
+        self._progress_dialog.show()
+
+        self._install_worker = PluginInstallWorker(self.manager, download_url, plugin_id, is_update, plugin_path)
+        self._install_worker.progress.connect(self._on_install_progress)
+        self._install_worker.status_message.connect(self._on_install_status)
+        self._install_worker.finished.connect(lambda success, msg: self._on_install_finished(success, msg, plugin_name, is_update))
+        self._install_worker.start()
+
+
+    def _cancel_installation(self) -> None:
+        """Handles manual user cancellation of the download/install progress."""
+        if getattr(self, "_installation_finished_flag", False):
+            return  # Ignore if triggered by closing the dialog programmatically on success
+
+        if self._install_worker and self._install_worker.isRunning():
+            self._install_worker.terminate()
+            self._install_worker.wait()
+            QMessageBox.warning(self, "Cancelled", "Plugin installation was cancelled.")
+
+    def _on_install_finished(self, success: bool, message: str, plugin_name: str, is_update: bool) -> None:
+        self._installation_finished_flag = True  # Prevent false cancellation triggers
+
+        if self._progress_dialog:
+            self._progress_dialog.close()
+            self._progress_dialog.deleteLater()
+            self._progress_dialog = None
+
+        action_word = "updated" if is_update else "installed"
+        action_verb = "update" if is_update else "install"
+
+        if success:
+            self.manager.reload_plugins()
+            QMessageBox.information(self, "Success", f"Successfully {action_word} '{plugin_name}'!")
+            self.refresh_installed_plugins()
+            if self._has_fetched_remote:
+                self._populate_browser_list()
+        else:
+            QMessageBox.critical(self, "Installation Failed", f"Could not {action_verb} plugin:\n{message}")
+
+    def _on_install_progress(self, downloaded: int, total: int) -> None:
+        if self._progress_dialog:
+            if total > 0:
+                self._progress_dialog.setMaximum(total)
+                self._progress_dialog.setValue(downloaded)
+                mb_down = downloaded / (1024 * 1024)
+                mb_total = total / (1024 * 1024)
+                self._progress_dialog.setLabelText(f"Downloading... ({mb_down:.2f} MB / {mb_total:.2f} MB)")
+            else:
+                self._progress_dialog.setMaximum(0)  # Infinite marquee progress if size is unknown
+                mb_down = downloaded / (1024 * 1024)
+                self._progress_dialog.setLabelText(f"Downloading... ({mb_down:.2f} MB downloaded)")
+
+    def _on_install_status(self, message: str) -> None:
+        if self._progress_dialog:
+            self._progress_dialog.setLabelText(message)
+
+
+    def update_selected_plugin(self) -> None:
+        """Triggers the background update process for the selected installed plugin."""
         selected = self.installed_list.currentItem()
         if not selected:
             return
         raw_info = selected.data(Qt.ItemDataRole.UserRole)
-        if isinstance(raw_info, dict):
-            info = cast(dict[str, Any], raw_info)
-            plugin_path = info.get("path")
-            if isinstance(plugin_path, str) and plugin_path:
-                self.manager.toggle_plugin_state(Path(plugin_path))
-
-    def uninstall_plugin(self) -> None:
-        selected = self.installed_list.currentItem()
-        if not selected:
-            return
-        
-        raw_info = selected.data(Qt.ItemDataRole.UserRole)
         if not isinstance(raw_info, dict):
             return
 
         info = cast(dict[str, Any], raw_info)
+        download_url = info.get("download_url", "")
+        plugin_id = info.get("id", "unnamed")
+        plugin_name = info.get("name", "Plugin")
         plugin_path = info.get("path")
-        plugin_name = info.get("name", "this plugin")
 
-        if not isinstance(plugin_path, str) or not plugin_path:
+        if not download_url:
+            QMessageBox.warning(self, "Update Failed", "No download URL provided for this update.")
             return
 
-        reply = QMessageBox.question(
-            self, 
-            "Confirm Uninstall",
-            f"Are you sure you want to delete '{plugin_name}'?",
-            QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
-        )
-        if reply == QMessageBox.StandardButton.Yes:
-            self.manager.uninstall_plugin(Path(plugin_path))
+        path_obj = Path(plugin_path) if isinstance(plugin_path, str) and plugin_path else (plugin_path if isinstance(plugin_path, Path) else None)
+        self.execute_plugin_installation(download_url, plugin_id, plugin_name, is_update=True, plugin_path=path_obj)
 
-    def fetch_remote_plugins(self) -> None:
-        """Asynchronously fetches remote plugins on a background thread."""
-        if self._fetch_worker is not None and self._fetch_worker.isRunning():
+    def install_selected_plugin(self) -> None:
+        """Triggers the background installation/update process from the browser tab."""
+        selected = self.browser_list.currentItem()
+        if not selected:
+            return
+        data = selected.data(Qt.ItemDataRole.UserRole)
+        if not isinstance(data, dict):
             return
 
-        self.browser_list.clear()
-        self.browser_list.addItem("Fetching remote repositories...")
-        self.btn_install.setEnabled(False)
-        self.btn_fetch.setEnabled(False)
+        plugin_data = cast(dict[str, Any], data)
 
-        # Defer network call to background worker to avoid UI freeze
-        self._fetch_worker = RemoteFetchWorker(self.manager, self.repository_urls)
-        self._fetch_worker.fetched.connect(self._on_remote_fetched)
-        self._fetch_worker.start()
+        update_available = bool(selected.data(Qt.ItemDataRole.UserRole + 3))
+        plugin_id = str(plugin_data.get("id", "unnamed"))
+        plugin_name = str(plugin_data.get("name", "Plugin"))
+        download_url = str(plugin_data.get("download_url", ""))
 
-    def _on_remote_fetched(self, plugins: list[dict[str, Any]], all_failed: bool) -> None:
+        if not download_url:
+            QMessageBox.warning(self, "Error", "No download URL provided for this plugin.")
+            return
+
+        # Find existing local path if updating an installed plugin
+        existing_path: Path | None = None
+        installed_info = self.manager.get_installed_plugins_info()
+        for info in installed_info:
+            if info.get("id") == plugin_id or info.get("name") == plugin_name:
+                p = info.get("path")
+                if isinstance(p, Path):
+                    existing_path = p
+                elif isinstance(p, str):
+                    existing_path = Path(p)
+                break
+
+        self.execute_plugin_installation(download_url, plugin_id, plugin_name, is_update=update_available, plugin_path=existing_path)
+
+    def _on_remote_fetched(self, plugins: list[dict[str, Any]], all_failed: bool, fetch_type: str) -> None:
         """Callback executed on the main UI thread when remote fetching finishes."""
         self.remote_plugins_data = plugins
         self._has_fetched_remote = True
         self.btn_fetch.setEnabled(True)
 
+        if fetch_type == "updates":
+            self.refresh_installed_plugins()
+            return
+
         if plugins:
             self._populate_browser_list()
         elif all_failed:
@@ -200,13 +388,33 @@ class PluginsWindow(QWidget):
             self.browser_list.clear()
             self.browser_list.addItem("No plugins found across configured repositories.")
 
+    def fetch_remote_plugins(self) -> None:
+        """Asynchronously fetches remote plugins on a background thread for the browser."""
+        if self._fetch_worker is not None and self._fetch_worker.isRunning():
+            return
+
+        self.browser_list.clear()
+        self.browser_list.addItem("Fetching remote repositories...")
+        self.btn_install.setEnabled(False)
+        self.btn_fetch.setEnabled(False)
+
+        self._fetch_worker = RemoteFetchWorker(self.manager, self.repository_urls, fetch_type="browser")
+        self._fetch_worker.fetched.connect(self._on_remote_fetched)
+        self._fetch_worker.start()
+
     def _populate_browser_list(self) -> None:
-        """Populates the browser tab list and evaluates compatibility and installation state."""
+        """Populates the browser tab list and evaluates compatibility, installation, and updates."""
         self.browser_list.clear()
 
         installed_info = self.manager.get_installed_plugins_info()
-        installed_ids = {p.get("id") for p in installed_info if p.get("id")}
-        installed_names = {p.get("name") for p in installed_info if p.get("name")}
+        installed_map: dict[str, dict[str, Any]] = {}
+        for p in installed_info:
+            p_id = p.get("id")
+            p_name = p.get("name")
+            if p_id:
+                installed_map[str(p_id)] = p
+            if p_name:
+                installed_map[str(p_name)] = p
 
         for plugin in self.remote_plugins_data:
             name = plugin.get("name", "Unknown")
@@ -220,7 +428,6 @@ class PluginsWindow(QWidget):
             is_version_ok = self.manager.current_app_version >= parse_version(min_v_str)
             is_compatible = is_platform_ok and is_version_ok
 
-            # Evaluate reasons for incompatibility
             incompat_reasons: list[str] = []
             if not is_platform_ok:
                 plat_str = ", ".join(platforms) if isinstance(platforms, list) else str(platforms)
@@ -228,10 +435,20 @@ class PluginsWindow(QWidget):
             if not is_version_ok:
                 incompat_reasons.append(f"Requires App v{min_v_str}+")
 
-            is_installed = (bool(p_id) and p_id in installed_ids) or (bool(name) and name in installed_names)
+            installed_match = installed_map.get(str(p_id)) or installed_map.get(str(name))
+            is_installed = installed_match is not None
+
+            update_available = False
+            remote_ver_str = str(plugin.get("version", "0.0.0"))
+            if is_installed:
+                local_ver_str = str(installed_match.get("version", "0.0.0"))
+                if parse_version(remote_ver_str) > parse_version(local_ver_str):
+                    update_available = True
 
             display_text = f"{name} (v{version}) - {desc}"
-            if is_installed:
+            if update_available:
+                display_text += f" [Update Available: v{remote_ver_str}]"
+            elif is_installed:
                 display_text += " [Installed]"
             elif incompat_reasons:
                 reason_str = "; ".join(incompat_reasons)
@@ -241,28 +458,14 @@ class PluginsWindow(QWidget):
             item.setData(Qt.ItemDataRole.UserRole, plugin)
             item.setData(Qt.ItemDataRole.UserRole + 1, is_compatible)
             item.setData(Qt.ItemDataRole.UserRole + 2, is_installed)
+            item.setData(Qt.ItemDataRole.UserRole + 3, update_available)
 
-            if is_installed:
-                item.setForeground(QColor("#2e7d32"))  # Green for installed
+            if update_available:
+                item.setForeground(QColor("#1976d2"))
+            elif is_installed:
+                item.setForeground(QColor("#2e7d32"))
             elif not is_compatible:
-                item.setForeground(QColor("#d32f2f"))  # Red for incompatible
-
-    def install_selected_plugin(self) -> None:
-        selected = self.browser_list.currentItem()
-        if not selected:
-            return
-        data = selected.data(Qt.ItemDataRole.UserRole)
-        if not data:
-            return
-
-        try:
-            target_path = self.manager.install_plugin_from_url(
-                data.get("download_url", ""),
-                data.get("id", "unnamed")
-            )
-            QMessageBox.information(self, "Success", f"Installed plugin to:\n{target_path}")
-        except Exception as e:
-            QMessageBox.critical(self, "Installation Failed", f"Could not install plugin:\n{e}")
+                item.setForeground(QColor("#d32f2f"))
 
     def _on_tab_changed(self, index: int) -> None:
         if index == 1 and not self._has_fetched_remote:
@@ -272,10 +475,19 @@ class PluginsWindow(QWidget):
         if current:
             is_compatible = bool(current.data(Qt.ItemDataRole.UserRole + 1))
             is_installed = bool(current.data(Qt.ItemDataRole.UserRole + 2))
+            update_available = bool(current.data(Qt.ItemDataRole.UserRole + 3))
 
-            # Button lights up ONLY if plugin is compatible and NOT yet installed
-            self.btn_install.setEnabled(is_compatible and not is_installed)
+            if update_available:
+                self.btn_install.setText("Update Plugin")
+                self.btn_install.setEnabled(is_compatible)
+            elif is_installed:
+                self.btn_install.setText("Install Plugin")
+                self.btn_install.setEnabled(False)
+            else:
+                self.btn_install.setText("Install Plugin")
+                self.btn_install.setEnabled(is_compatible)
         else:
+            self.btn_install.setText("Install Plugin")
             self.btn_install.setEnabled(False)
 
     def _on_add_repo(self) -> None:
@@ -334,14 +546,19 @@ class PluginsWindow(QWidget):
 
         btn_layout = QHBoxLayout()
         btn_refresh = QPushButton("Refresh List", tab)
+        self.btn_update_plugin = QPushButton("Update Plugin", tab)
+        self.btn_update_plugin.setEnabled(False)
+        self.btn_update_plugin.setStyleSheet("font-weight: bold; color: #1976d2;")
         btn_enable = QPushButton("Enable / Disable", tab)
         btn_uninstall = QPushButton("Uninstall", tab)
 
         btn_refresh.clicked.connect(self.refresh_installed_plugins)
+        self.btn_update_plugin.clicked.connect(self.update_selected_plugin)
         btn_enable.clicked.connect(self.toggle_enable_disable)
         btn_uninstall.clicked.connect(self.uninstall_plugin)
 
         btn_layout.addWidget(btn_refresh)
+        btn_layout.addWidget(self.btn_update_plugin)
         btn_layout.addStretch()
         btn_layout.addWidget(btn_enable)
         btn_layout.addWidget(btn_uninstall)
@@ -389,3 +606,53 @@ class PluginsWindow(QWidget):
         layout.addWidget(self.browser_list)
         layout.addLayout(btn_layout)
         return tab
+
+    def toggle_enable_disable(self) -> None:
+        selected = self.installed_list.currentItem()
+        if not selected:
+            return
+        raw_info = selected.data(Qt.ItemDataRole.UserRole)
+        if isinstance(raw_info, dict):
+            info = cast(dict[str, Any], raw_info)
+            plugin_path = info.get("path")
+            if isinstance(plugin_path, str) and plugin_path:
+                self.manager.toggle_plugin_state(Path(plugin_path))
+            elif isinstance(plugin_path, Path):
+                self.manager.toggle_plugin_state(plugin_path)
+
+    def uninstall_plugin(self) -> None:
+        selected = self.installed_list.currentItem()
+        if not selected:
+            return
+
+        raw_info = selected.data(Qt.ItemDataRole.UserRole)
+        if not isinstance(raw_info, dict):
+            return
+
+        info = cast(dict[str, Any], raw_info)
+        plugin_path = info.get("path")
+        plugin_name = info.get("name", "this plugin")
+
+        if not plugin_path:
+            return
+
+        reply = QMessageBox.question(
+            self,
+            "Confirm Uninstall",
+            f"Are you sure you want to delete '{plugin_name}'?",
+            QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
+        )
+        if reply == QMessageBox.StandardButton.Yes:
+            if isinstance(plugin_path, str):
+                self.manager.uninstall_plugin(Path(plugin_path))
+            elif isinstance(plugin_path, Path):
+                self.manager.uninstall_plugin(plugin_path)
+
+
+    def _clear_details_panel(self) -> None:
+        """Clears details display when nothing is selected."""
+        self.lbl_plugin_title.setText("Select a plugin")
+        self.lbl_plugin_meta.setText("")
+        self.lbl_plugin_status.setText("")
+        self.txt_plugin_desc.clear()
+        self.lbl_plugin_path.setText("")

src/window/viewerlauncher.py

@@ -64,7 +64,7 @@ class ViewerLauncherWidget(QWidget):
             ("Inter-Group Stats Viewer", InterGroupStatsWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, roi_channel_map_dict, group_dict], True),
             ("Intra-Group Brain and Image Viewer", IntraGroupBrainImageWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict], True),
             ("Inter-Group Brain and Image Viewer", InterGroupBrainImageWidget, [haemo_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict], True),
-            ("Export To CSV Viewer", ExportToCSVWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, config_dict, fir_feature_dict, qc_dict], True)
+            ("Export To CSV Viewer", ExportToCSVWidget, [haemo_dict, epochs_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, config_dict, fir_feature_dict, qc_dict], True)
         ]
 
         layout = QVBoxLayout(self)