bug fixes

changelog.md

@@ -1,8 +1,11 @@
 # Version 1.7.1
 
+- Added support for Plugins! Plugins can be downloaded from the official repository or from custom ones. Support for creating a plugin can be found on the wiki
 - Fixed an issue where the application could not automatically update between versions 1.5.1 to 1.7.1. Sorry! 1.7.1 upgrading onward should be fixed and more robust
 - Fixed an issue where some log files would not generate, or would generate in an incorrect location
 - Fixed an issue where updating events in a snirf file would not release memory properly
+- Fixed an issue where loading multiple files in quick succession could cause some of the files to never finish loading
+- Fixed an issue where loading a saved project, pushing clear, and re-opening snirf files would cause them to appear incorrectly in the loaded files area
 
 
 # Version 1.7.0

changelog_major.md

@@ -1,35 +1,34 @@
-# Version 1.6.0
+# Version 1.7.0
 
-- This is potentially a save-changing release due to adding more data into the save file, renaming existing data, and changing what part of the code saves data. Please update your project files to ensure compatibility
-- It is still possible to load older saves by enabling 'Incompatible Save Bypass' from the Preferences menu, but your mileage may vary
-- Optimized calculations being performed when calculating the Heart Rate to speed up step 5 by up to ~35% on a per-file basis
-- Optimized calculations being performed when running the General Linear Model to speed up step 5 by up to ~35% on a per-file basis
-- The Group Stats Viewer windows will now properly load the Right/Left or Front/Back fallback ROIs if JSON_LOCATION is not set
-- Changed the warning message for lots of short channels and changed when it shows to be percentage based (35%) instead of numerical based (6)
-- Renames GENDER to SEX to better represent the values that the field expects and to be more BIDS compliant
-- Changed the Assign Groups by AGE window to now be the Assign Groups by Metadata window and added support for grouping by other metadata values
-- Added a new metadata value of HAND to allow for grouping participants based on their handiness
-- Updated the layout of the participant metadata area to better accommodate current and future metadata values
-- Updated the message displayed when "Why are these useful?" is clicked to better represent what the values are used for and to accommodate the new metadata values
-- Changed the application title to now show what project you are working on. If you are not working on a project, it will display 'Untitled'
-- Tracking of current save states is now present and an asterisk will now appear in the title bar when a project has not been saved
-- Currently tracking is only supported on loaded files, parameters on the right side of the screen, and when processing has completed. Per-file metadata or processing stages are not currently implemented
-- Clicking close on the Main Window will now properly close all sub windows when closing the application and closing the application with unsaved changes will now prompt to save a project or discard changes. Fixes [Issue 87](https://git.research.dezeeuw.ca/tyler/flares/issues/87)
-- The Save button under the File menu no longer asks for a destination if a saved project was already loaded. Fixes [Issue 72](https://git.research.dezeeuw.ca/tyler/flares/issues/72)
-- Added an icon to the 'Toggle Status Bar' view option
-- Status bar visibility and window layout sizes are now stored between application sessions. Fixes [Issue 88](https://git.research.dezeeuw.ca/tyler/flares/issues/88)
-- The popup that appeared when a project was saved has now been moved to a message displayed from the status bar
-- Moved all loading of files, loading of folders, loading of projects, and saving of projects to a new file for easier future development
-- Changed the working of some messages on the status bar to better reflect what has occurred
-- Added a new terminal command 'assoc' to associate .flare files to the application. This is undergoing testing and may not function correctly.
-- Removed the debug flag from the application package, which may speed up the application. Fixes [Issue 11](https://git.research.dezeeuw.ca/tyler/flares/issues/11)
-- Fixed an issue where the two Group Stats Viewer windows would crash the application once attempted to be opened if JSON_LOCATION was not set
-- Fixed an issue where participants could be skipped when processing multiple participants at once which could prevent overall processing from completing
-- Fixed an issue where when loading a save file some list dropdowns could go blue and bold even if the value was default
-- Fixed an issue where the Analysis button would not be clickable if the user had previously pushed Clear. Fixes [Issue 83](https://git.research.dezeeuw.ca/tyler/flares/issues/83)
-- Fixed an issue where removing all files via their right click feature would cause the Process button to still be visible. Fixes [Issue 91](https://git.research.dezeeuw.ca/tyler/flares/issues/91)
-- Fixed an issue where some popup windows would not properly display the application name when they would open
-- Fixed an issue where the welcome dialog image would not display correctly on macOS
-- Fixed an issue where the Linux version would fail at 0 seconds when attempting to process files
-- Fixed an issue where fOLDing channels could cause the same channels to be repeated misaligning the labels
-- Fixed all instances of the word MacOS to now read macOS to match Apple branding
+- This is potentially a save-changing release due to adding more data into the save file. Please update your project files to ensure compatibility
+- Renamed all instances of "Inter" to properly read as "Intra" and changed "Cross" to now read as "Inter"
+- Changed RESAMPLE to only apply where it is required to avoid having Functional Connectivity analysis methods running on data that has been resampled
+- Added parameters that appear when attempting to generate results from the Participant and Intra-Group Functional Connectivity viewers and removed the non-functional placeholder parameters
+- Modified the Participant and Intra-Group Functional Connectivity analysis options to better perform their expected tasks. This remains as a BETA feature
+- Removed the existing Intra-Group Functional Connectivity option and replaced it with two new ones: Beta-Series Correlation and Spectral Coherence (epochs)
+- Updated the names of the methods provided for the Participant Functional Connectivity Viewer to better match the actions they perform
+- Updated the warnings for the Functional Connectivity Viewers to better represent the challenges these analysis options now face
+- Added basic unit testing to hopefully prevent any accidental processing changes from occurring in the future
+- Added a new parameter to the PSP section on the right side of the screen: PSP_USE_HEART_RATE_BAND. This functions similarly to the existing SCI_USE_HEART_RATE_BAND
+- Added description text to the Inter-Group and Intra-Group Brain and Image Viewers, as well as the Functional Connectivity windows to explain what output can be expected
+- Added a new Preference option of Theme. Allows from selecting Auto (System default), Light, or Dark. Fixes [Issue 7](https://git.research.dezeeuw.ca/tyler/flares/issues/7)
+- Removed image index 1 (Significance) from the Intra-Group Brain and Image Viewer as it is now provided more in depth with the Stats viewers
+- Modified the timeout when waiting for the application to close while performing updates down to a reasonable number
+- Modified the help messages for parameters in the SCI and PSP areas to better reflect how the parameters are used
+- Modified the heart rate calculation to be more precise and correct when dealing with good data and not messy data
+- Modified the heart rate calculation to not take only one channel in the data to use, but rather an average of channels. This still prefers short channels if they are present
+- Fixed an issue where loading a project from a saved project file would not allow the data to be reprocessed with new parameters
+- Fixed an issue where the "Hand" BIDS metadata value would not populate on bubbles correctly
+- Fixed an issue where performing PSP could ignore the bad channels that were marked by SCI and SNR
+- Fixed an issue where the heart rate calculation would disregard all calculations and fall back to an extremely rudimentary calculation
+- Fixed an issue that could prevent log file generation while the application was in the middle of an update
+- Fixed an issue where a rare crash could occur while the application was in the middle of an update
+- Fixed an issue that could have passed multiple conditions when generating an Intra-Group Stats image
+- Fixed an issue that could pass NaN values when attempting to collapse channels
+- Fixed an issue that was causing the OLS model to always be used for brain images with multiple participants, and not the MixedLM model
+- Fixed an issue that could cause the Wavelet filtering step to crash
+- Fixed an issue where file associations appeared to work as intended but would not load the project on macOS and only open the application
+- Fixed an issue where file associations would refuse to associate on macOS once they have attempted to be associated
+- Fixed an issue where certain parameters would not enable or disable depending on other parameters when they should've
+- Fixed an issue where not all widgets would close when attempting to close the application causing the application to crash
+- Fixed an issue where events were not created correctly after the data had been resampled by the design matrix

main.py

@@ -1661,7 +1661,7 @@ class MainApplication(QMainWindow):
             bubble.update_progress(step, active=False)
 
             # Add to layout
-            self.bubble_layout.addWidget(bubble, index, 1)
+            self.bubble_layout.addWidget(bubble, index, 0)
 
         # 4. Status Bar
         msg = f"Project loaded: {len(file_list)} files."

project_manager.py

@@ -136,7 +136,6 @@ class ProjectManager:
         # 2. Track this session to prevent ghost updates
         if not hasattr(app, "loading_session_id"):
             app.loading_session_id = 0
-        app.loading_session_id += 1
         current_session = app.loading_session_id
 
         # 3. Setup internal tracking if not exists

src/window/plugins.py

@@ -1,6 +1,6 @@
 """
 Filename: plugins.py
-Description: Plugins window with deferred remote fetching and installation state checks.
+Description: Plugins window
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
@@ -43,7 +43,7 @@ class PluginsWindow(QWidget):
         self.main_app_window = parent
         self.manager: PluginManager = plugin_manager
         
-        self.setWindowTitle(f"Plugins - {APP_NAME.upper()}")
+        self.setWindowTitle(f"{APP_NAME.upper()} - Plugins")
         self.resize(750, 500)
 
         self.repository_urls: list[str] = [PLUGINS_URL]
@@ -157,7 +157,7 @@ class PluginsWindow(QWidget):
     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():
-            return  # Fetch operation already in progress
+            return
 
         self.browser_list.clear()
         self.browser_list.addItem("Fetching remote repositories...")
@@ -185,10 +185,9 @@ class PluginsWindow(QWidget):
             self.browser_list.addItem("No plugins found across configured repositories.")
 
     def _populate_browser_list(self) -> None:
-        """Populates the browser tab list and checks if each plugin is already installed."""
+        """Populates the browser tab list and evaluates compatibility and installation state."""
         self.browser_list.clear()
 
-        # Gather set of currently installed identifiers (by ID and Name)
         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")}
@@ -205,14 +204,22 @@ 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
 
-            # Check if plugin is already installed locally
+            # Evaluate reasons for incompatibility
+            incompat_reasons: list[str] = []
+            if not is_platform_ok:
+                plat_str = ", ".join(platforms) if isinstance(platforms, list) else str(platforms)
+                incompat_reasons.append(f"Requires platform: {plat_str}")
+            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)
 
             display_text = f"{name} (v{version}) - {desc}"
             if is_installed:
                 display_text += " [Installed]"
-            elif not is_compatible:
-                display_text += " [Incompatible]"
+            elif incompat_reasons:
+                reason_str = "; ".join(incompat_reasons)
+                display_text += f" [Incompatible: {reason_str}]"
 
             item = QListWidgetItem(display_text, self.browser_list)
             item.setData(Qt.ItemDataRole.UserRole, plugin)
@@ -250,7 +257,7 @@ class PluginsWindow(QWidget):
             is_compatible = bool(current.data(Qt.ItemDataRole.UserRole + 1))
             is_installed = bool(current.data(Qt.ItemDataRole.UserRole + 2))
             
-            # Disable install button if plugin is incompatible OR ALREADY INSTALLED
+            # Button lights up ONLY if plugin is compatible and NOT yet installed
             self.btn_install.setEnabled(is_compatible and not is_installed)
         else:
             self.btn_install.setEnabled(False)
@@ -267,7 +274,6 @@ class PluginsWindow(QWidget):
         tab = QWidget()
         layout = QVBoxLayout(tab)
 
-        # Header bar with directory path and Open Folder button
         path_layout = QHBoxLayout()
         path_label = QLabel(f"<b>Plugins Directory:</b> <code>{self.manager.plugins_dir}</code>", tab)
         btn_open_folder = QPushButton("Open Folder", tab)
@@ -278,13 +284,11 @@ class PluginsWindow(QWidget):
         path_layout.addStretch()
         path_layout.addWidget(btn_open_folder)
 
-        # Splitter Layout: Left side List, Right side Detail Panel
         content_layout = QHBoxLayout()
 
         self.installed_list = QListWidget(tab)
         self.installed_list.currentItemChanged.connect(self._on_installed_item_changed)
 
-        # Right-side Details Panel
         self.details_panel = QWidget(tab)
         details_layout = QVBoxLayout(self.details_panel)
         details_layout.setContentsMargins(10, 0, 0, 0)
@@ -312,7 +316,6 @@ class PluginsWindow(QWidget):
         content_layout.addWidget(self.installed_list, stretch=1)
         content_layout.addWidget(self.details_panel, stretch=1)
 
-        # Bottom Action Buttons
         btn_layout = QHBoxLayout()
         btn_refresh = QPushButton("Refresh List", tab)
         btn_enable = QPushButton("Enable / Disable", tab)