release for 1.6.0

fixes before release
typos, standardization, and file association for project extensions
2026-08-10 18:00:22 -07:00 · 2026-08-10 16:47:32 -07:00 · 2026-08-06 02:00:36 -07:00 · 2026-08-03 22:39:57 -07:00 · 2026-08-03 22:34:41 -07:00 · 2026-08-03 00:46:18 -07:00
25 changed files with 3958 additions and 2368 deletions
@@ -3,13 +3,13 @@ FLARES (fNIRS Lightweight Analysis, Research, & Evaluation Suite)
 FLARES is a lightweight standalone application to extract meaningful data out of .snirf files.
-FLARES is free and open-source software that runs on Windows, MacOS, and Linux. Please read the information regarding each operating system below.
+FLARES is free and open-source software that runs on Windows, macOS, and Linux. Please read the information regarding each operating system below.
 Visit the official [FLARES web site](https://research.dezeeuw.ca/flares).
 [![Python web site](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org)
-# For MacOS Users
+# For macOS Users
 Due to the cost of an Apple Developer account, the application is not certified by Apple. Once the application is extracted and attempted to be launched for the first time you will get a popup stating:
@@ -1,6 +1,76 @@
 # Version 1.6.0
 - 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
 # Version 1.5.2
 - Opening both a file or a folder now contains support for reading some metadata from the BIDS structure. Both options will still function if this metadata is not present
 - Currently only the AGE metadata is grabbed and is auto populated into the participants AGE field and displayed on their bubble
 - If the participants have metadata, a popup will be displayed asking if the user wants to group the participants by their metadata
 - If the user wants to create groups, a dialog box is presented allowing them to do so. Once completed, the GROUP value will be automatically applied to all applicable participants
 - A new options menu item has been added: Regroup Files from Metadata. This will allow the dialog to be opened at a later time with a popup appearing if there is no metadata present
 - Added two new options to the Export to CSV Viewer: Export Configuration to CSV and Paragraph of Configuration
 - Export Configuration to CSV will export the parameters utilized for each file into a CSV formatted file to provide additional validation of what parameters were used
 - Paragraph of Configuration will generate a ready-to-go paragraph explaining in a more friendly and easy to follow manner of what parameters were used
 - Chunked the loading of folders to provide more feedback to the user instead of hanging the application waiting for all files to load
 - New parameters have been added to the right side of the screen! This allows for more flexibility and customizability when processing
 - A new Preference Menu option has been added: Show Advanced Parameters. This keeps some of the parameters hidden when not checked. Since this is a preference, it will be saved when reopening the application
 - Advanced parameters should only be changed if you know what you are doing, and will have a yellow warning symbol next to them to avoid potential confusion on what parameters are advanced
 - Optimized some of the calculations in Scalp Coupling Index to speed up Step 6 by up to ~25% on a per-file basis
 - Removed duplicate/redundant calculations in Peak Spectral Power to speed up Step 8 by up to ~50% on a per-file basis
 - Changed how the figures are generated when processing to speed up Step 28 by up to ~85% on a per-file basis
 - Removed unused methods inside the processing file to slightly speed up application load time
 - Fixed an issue with the build script not properly updating the version string causing the application to falsely think that an update was always available
 - Fixed an issue where parameters that were dependent on SHORT_CHANNELS were not properly being updated
 - Fixed an issue where files that failed processing were not having their progress bar turn red at the step that failed
 - Fixed an issue where progress bars were not updating when MAX_WORKERS was set to a value higher than default
 - Fixed an issue where a high value of MAX_WORKERS was never hit the targeted value due to not being able to spawn the workers fast enough
 - Fixed an issue causing numerous 'Invalid File' popups to appear upon closing the application while files were still having their initial metadata being grabbed
 - Fixed an issue where both 'Update events in snirf file...' windows could not be open at the same time
 - Fixed an issue where externally updating a participant's metadata when they were selected would cause the application to crash
 - Fixed an issue where there was a redundant checking of dependencies when the parameters on the right side of the screen were being calculated
 - Fixed an issue in which clicking menu options too fast would cause the application to hard crash
 - Added a time elapsed message to the status bar denoting how long processing has been going on for. When processing is complete, it will change to be the time elapsed
 - Added a speedup multiplier to show how much time was saved by having MAX_WORKERS not set to 1. This multiplier is calculated using a naive approach and may not be accurate
 - Removed redundant font styling when parameters were changed from their default values
 # Version 1.5.1
- Open a folder is now minimally BIDS compatible. It will recursively go through all folders, but not load external metadata
+- Opening a folder is now minimally BIDS compatible. It will recursively go through all folders, but not load external metadata
 - Renamed options in the Viewer Launcher window to better denote what actions they can perform
 - 2 new analysis options have been added in the viewer launcher window: Inter-Group Stats and Cross-Group Stats
 - Each of these analysis options have lots of text explaining what they do when their respective windows are opened
@@ -9,10 +79,10 @@
 - The description when clicking "Why are these useful?" underneath the per-file parameters is no longer placeholder text. Fixes [Issue 85](https://git.research.dezeeuw.ca/tyler/flares/issues/85)
 - Added a new parameter section "Region of Interest". It has one parameter of "JSON_LOCATION", a json file containing Region of Interest data
 - Temporarily removed the parameter REMOVE_EVENTS due to its functionality being removed because of a memory leak
- Fixed participant metadata remaing in the background when the participant was removed. Fixes [Issue 82](https://git.research.dezeeuw.ca/tyler/flares/issues/82)
+- Fixed participant metadata remaining in the background when the participant was removed. Fixes [Issue 82](https://git.research.dezeeuw.ca/tyler/flares/issues/82)
 - Fixed processing remaining active hidden in the background when the "Clear" button was pushed. Fixes [Issue 81](https://git.research.dezeeuw.ca/tyler/flares/issues/81)
 - Now when "Clear" is pushed while data is processing, a popup will appear ensuring that the user understands that pushing "Clear" will stop processing
- Reset to Default Configuration will now properly reset all of the parameters to their default values. [Issue 90](https://git.research.dezeeuw.ca/tyler/flares/issues/90)
+- Reset to Default Configuration will now properly reset all of the parameters to their default values. Fixes [Issue 90](https://git.research.dezeeuw.ca/tyler/flares/issues/90)
 - A confirmation popup will now display once the application has been reset to default in addition to the status bar message
 - Changed the improper display text of "Cross Validation" to now properly read as "Coefficient of Variation"
 - Changed the parameters "CV" and "CV_THRESHOLD" to now be "COEFF_VAR and COEFF_VAR_THRESHOLD"
@@ -20,8 +90,8 @@
 - Changed the parameters "SHORT_CHANNEL", "SHORT_CHANNEL_THRESH", and "LONG_CHANNEL_THRESH" to now be "SHORT_CHANNELS", "SHORT_CHANNELS_THRESHOLD", and "LONG_CHANNELS_THRESHOLD"
 - Changed the parameter section "Channel Variance" to now be "Sensor Dropout" to better reflect the action it performs, not the method employed to calculate it
 - Changed the parameters "CHANNEL_VAR" and "CHANNEL_THRESH" to now be "SENSOR_DROPOUT" and "SENSOR_DROPOUT_VARIANCE_THRESHOLD"
- Changed the messaged displayed when the application crashes to better reflect what occured
+- Changed the messaged displayed when the application crashes to better reflect what occurred
- Changed the processing stages 25-27 and updates their messages to better reflect their actions that they now perforn
+- Changed the processing stages 25-27 and updates their messages to better reflect their actions that they now perform
 - Changed stage 25 from "Generate Channel Significance" to "Generate Channel Results"
 - Changed stage 26 from "Generate Channel, Region of Interest, and Contrast Results" to "Generate Region of Interest Results"
 - Changed stage 27 from "Compute Contrast Results" to "Generate Contrast Results"
@@ -31,7 +101,7 @@
 - Fixed a crucial bug where short channels were not being processed and filtered the same way as long channels before being used as regressors
 - Fixed a crucial bug where short channels were being presented to the design matrix as normal long channels
 - Fixed a crucial bug where long channels could be interpolated from short channels. Short channels are still potentially interpolated from long channels. See [this link](https://git.research.dezeeuw.ca/tyler/flares/issues/80) for more information regarding this issue.
- Decreased unnecessary processing time when fOLDing channels by an order of magnitude
+- Decreased unnecessary processing time when fOLDing channels by an order of magnitude. Fixes [Issue 84](https://git.research.dezeeuw.ca/tyler/flares/issues/84)
 - Added a welcome message when the terminal is opened, resized the terminal, and added more commands
@@ -41,16 +111,16 @@
 - This release features an almost complete rewrite of backend files. If you encounter any problems, please raise an issue at [this link.](https://git.research.dezeeuw.ca/tyler/flares/issues/new)
 - New configuration file has been added! Now your choices of preferences will be saved when the application is closed and re-opened. If the configuration file is missing, a new one will be generated
 - Recent files and recent projects are now saved and appear under the File menu for quick resuming
- The new option "Reset to Default Configuration" under the Options menu will reset the configuration file back to it's default values and remove any recent files
+- The new option "Reset to Default Configuration" under the Options menu will reset the configuration file back to its default values and remove any recent files
 - A welcome dialog will now display the changelog on first startup and after every update. This popup will only appear once but can be reopened under the Options menu through the button "Show Update Changelog"
 - Changed the hotkey for "Update optodes in snirf file..." to be F9 instead of F6
 - Revamped the fOLD channels window. Images containing the pie charts are now interactable! Click whitespace to expand the whole image and click a chart to expand it.
 - fOLD progress bar when processing now updates the percentages live. Fixes [Issue 76](https://git.research.dezeeuw.ca/tyler/flares/issues/76)
- Overall pie charts on an individal and global basis are now genereted. Fixes [Issue 78](https://git.research.dezeeuw.ca/tyler/flares/issues/78)
+- Overall pie charts on an individual and global basis are now generated. Fixes [Issue 78](https://git.research.dezeeuw.ca/tyler/flares/issues/78)
 - Brodmann images are now available when examining a pie chart to understand which area is being reported. Fixes [Issue 77](https://git.research.dezeeuw.ca/tyler/flares/issues/77)
 - Added a new option 'Folding Bypass' to the Preferences Menu. This skips most processing steps and the only analysis option available will be to fold. Parameters on the right will be ignored. Fixes [Issue 75](https://git.research.dezeeuw.ca/tyler/flares/issues/75)
 - Fixed an issue where the fOLD analysis progress window would go unresponsive before processing participants. Fixes [Issue 45](https://git.research.dezeeuw.ca/tyler/flares/issues/45), Fixes [Issue 34](https://git.research.dezeeuw.ca/tyler/flares/issues/34)
- Added a feature to hover over the 28 stage progress bar and see which state the progress bar is at. Fixes [Issue 74](https://git.research.dezeeuw.ca/tyler/flares/issues/74)
+- Added a feature to hover over the 28-stage progress bar and see which state the progress bar is at. Fixes [Issue 74](https://git.research.dezeeuw.ca/tyler/flares/issues/74)
 - Loading a broken snirf file no longer hangs its processing and can now be removed from the list. Fixes [Issue 73](https://git.research.dezeeuw.ca/tyler/flares/issues/73)
@@ -72,7 +142,7 @@
 # Version 1.4.1
- Hotfix to fix a recursive child loop that would cause the MacOS version to not open
+- Hotfix to fix a recursive child loop that would cause the macOS version to not open
 # Version 1.4.0
@@ -81,7 +151,7 @@
 - It is still possible to load older saves by enabling 'Incompatible Save Bypass' from the Preferences menu, but your mileage may vary
 - AGE, GENDER, GROUP, loaded files, and all the parameters on the right side of the screen can now be saved before any data has been processed
 - If processing has not been completed, the process button will be visible. If processing has completed, the analysis button will be visible
- If the values fail to load, they will fallback to the previous logic of retreiving these values after processing has occured. Fixes [Issue 66](https://git.research.dezeeuw.ca/tyler/flares/issues/66)
+- If the values fail to load, they will fallback to the previous logic of retrieving these values after processing has occurred. Fixes [Issue 66](https://git.research.dezeeuw.ca/tyler/flares/issues/66)
 - Added new parameters to the right side of the screen: MAX_SHIFT, T_MIN, T_MAX, MAX_BAD_CHANNELS. Fixes [Issue 69](https://git.research.dezeeuw.ca/tyler/flares/issues/69)
 - Participants that are bad on channels will no longer continue to the GLM stage. Fixes [Issue 18](https://git.research.dezeeuw.ca/tyler/flares/issues/18)
 - Added new sections to the right side of the screen to mark bad channels: Cross Validation, Median Absolute Deviation, PSD Noise, & Channel Variance
@@ -90,7 +160,7 @@
 - Added feedback when clicking an analysis option that opens up a new window. Fixes [Issue 20](https://git.research.dezeeuw.ca/tyler/flares/issues/20)
 - Fixed an issue where projects can not be saved to a different drive letter on windows. Fixes [Issue 71](https://git.research.dezeeuw.ca/tyler/flares/issues/71)
 - Fixed an issue where the fOLD files were not included in the Windows version. Fixes [Issue 60](https://git.research.dezeeuw.ca/tyler/flares/issues/60)
- Fixed an issue where the MacOS version would fail to perform some analysis options. Fixes [Issue 63](https://git.research.dezeeuw.ca/tyler/flares/issues/63)
+- Fixed an issue where the macOS version would fail to perform some analysis options. Fixes [Issue 63](https://git.research.dezeeuw.ca/tyler/flares/issues/63)
 - Fixed an issue where processing too many participants would cause the analysis button to not appear. Fixes [Issue 61](https://git.research.dezeeuw.ca/tyler/flares/issues/61)
 - Fixed an issue where the error message when a participant fails would not appear. Fixes [Issue 68](https://git.research.dezeeuw.ca/tyler/flares/issues/68)
 - Fixed an issue where changes would not be saved if a project was originally loaded from a save. Fixes [Issue 44](https://git.research.dezeeuw.ca/tyler/flares/issues/44)
@@ -107,7 +177,7 @@
 - This is potentially a save-changing release due to a new parameter being saved. 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
 - Fixed workers not releasing memory when processing multiple participants. Fixes [Issue 55](https://git.research.dezeeuw.ca/tyler/flares/issues/55)
- Fixed part of an issue where memory could increase over time despite clicking the clear button. There is still some edge cases where this can occur 
+- Fixed part of an issue where memory could increase over time despite clicking the clear button. There are still some edge cases where this can occur 
 - Fixed an issue when clearing a bubble, reloading the same file, and clicking it again would cause the app to crash. Fixes [Issue 57](https://git.research.dezeeuw.ca/tyler/flares/issues/57)
 - Picking a .txt or .xlsx file now has both in the same file selection instead of having to select which extension was desired
 - Added a new parameter to the right side of the screen: EPOCH_HANDLING. Fixes [Issue 58](https://git.research.dezeeuw.ca/tyler/flares/issues/58)
@@ -115,10 +185,10 @@
 - The label for ENHANCE_NEGATIVE_CORRELATION no longer gets cut off by its dropdown selection
 - Loading in files and folders have changes to immediately show their bubbles having a respective loading symbol on each bubble
 - Once the file has been completely loaded and processed, the loading symbol will change to a green checkmark and clicking will be enabled
- The metadata in the File infomation widget is now saved to prevent recalculations every time the bubble is selected
+- The metadata in the File information widget is now saved to prevent recalculations every time the bubble is selected
 - The status bar will now say loading while the bubbles are being processed, and loaded once the processing has completed
 - This new loading method will prevent the application from hanging when loading lots of files at once. Fixes [Issue 59](https://git.research.dezeeuw.ca/tyler/flares/issues/59)
- Fixed text allignment for the first paragraph when a bubble is selected in the 'File information' widget
+- Fixed text alignment for the first paragraph when a bubble is selected in the 'File information' widget
 - The three main widgets are now resizable! All of them have minimum widths to ensure they do not get too squished
 - Added a new option 'Reset Window Layout' under the View menu that will resize all widgets back to their default sizes
 - Added a new terminal command 'version' that will print the applications current version
@@ -128,7 +198,7 @@
 - Added 'Update events in snirf file (BLAZES)...' and renamed 'Update events in snirf file...' to 'Update events in snirf file (BORIS)...' under the Options menu
 - The BLAZES option will assign events that are exported directly from the software [BLAZES](https://git.research.dezeeuw.ca/tyler/blazes)
- Moved the updating logic to a seperate file for better reusability and generalization
+- Moved the updating logic to a separate file for better reusability and generalization
 - Fixed 'Toggle Status Bar' having no effect on the visibility of the status bar
 - Fixed a bug when updating optode positions that would prevent .txt files from being selected. Fixes [Issue 54](https://git.research.dezeeuw.ca/tyler/flares/issues/54)
 - Fixed a missing dependency in the standalone application when attempting to use an .xlsx file to update optode positions
@@ -161,7 +231,7 @@
 - These parameters include SHOW_OPTODE_NAMES, SECONDS_TO_STRIP_HR, MAX_LOW_HR, MAX_HIGH_HR, SMOOTHING_WINDOW_HR, HEART_RATE_WINDOW, BAD_CHANNELS_HANDLING, MAX_DIST, MIN_NEIGHBORS, L_TRANS_BANDWIDTH, H_TRANS_BANDWIDTH, RESAMPLE, RESAMPLE_FREQ, STIM_DUR, HRF_MODEL, HIGH_PASS, DRIFT_ORDER, FIR_DELAYS, MIN_ONSET, OVERSAMPLING, SHORT_CHANNEL_REGRESSION, NOISE_MODEL, BINS, and VERBOSITY.
 - Certain parameters now have dependencies on other parameters and will now grey out if they are not used
 - All the new parameters have default values matching the underlying values in version 1.1.7
- The order of the parameters have changed to match the order that the code runs when the Process button is clicked
+- The order of the parameters has been changed to match the order that the code runs when the Process button is clicked
 - Moved TIME_WINDOW_START and TIME_WINDOW_END to the 'Other' category
 - Fixed a bug causing SCI to not work when HEART_RATE was set to False
 - Bad channels can now be dealt with by taking no action, removing them completely, or interpolating them based on their neighbours. Interpolation remains the default option
@@ -171,11 +241,11 @@
 - Fixed a crash when attempting to fOLD channels without the fOLD dataset installed
 - Lowered the number of rectangles in the progress bar to 24 after combining some actions
 - Fixed the User Guide window to properly display information about the 24 stages and added a link to the Git wiki page
- MAX_WORKERS should now properly repect the value set
+- MAX_WORKERS should now properly respect the value set
 - Added a new CSV export option to be used by other applications
 - Added support for updating optode positions directly from an .xlsx file from a Polhemius system
 - Fixed an issue where the dropdowns in the Viewer windows would immediately open and close when using a trackpad
- glover and spm hrf models now function as intended without crashing. Currently, group analysis is still only supported by fir. Fixes [Issue 8](https://git.research.dezeeuw.ca/tyler/flares/issues/8)
+- glover and spm HRF models now function as intended without crashing. Currently, group analysis is still only supported by fir. Fixes [Issue 8](https://git.research.dezeeuw.ca/tyler/flares/issues/8)
 - Clicking 'Clear' should now properly clear all data. Fixes [Issue 9](https://git.research.dezeeuw.ca/tyler/flares/issues/9)
 - Revamped the fold channels viewer to not hang the application and to better process multiple participants at once. Fixes [Issue 34](https://git.research.dezeeuw.ca/tyler/flares/issues/34), [Issue 31](https://git.research.dezeeuw.ca/tyler/flares/issues/31)
 - Added a Preferences menu to the navigation bar
@@ -214,13 +284,13 @@
 - Fixed Windows saves not being able to be opened by a Mac (hopefully the other way too!)
 - Added the option to right click loaded snirf files to reveal them in a file browser or delete them if they are no longer desired
- Changed the way folders are opened to store the files seperately rather than the folder as a whole to allow for the removal of files
+- Changed the way folders are opened to store the files separately rather than the folder as a whole to allow for the removal of files
 - Fixed issues with dropdowns and bubbles not populating correctly when opening a single file and temporarily removed the option to open multiple folders
 - Improved crash handling and the message that is displayed to the user if the application crashes
 - Progress bar will now colour the stage that fails as red if a file fails during processing
 - A warning message will be displayed when a file fails to process with information on what went wrong. This message does not halt the rest of the processing of the other files
 - Fixed the number of rectangles in the progress bar to 20 (was incorrect in v1.1.1)
- Added validation to ensure loaded files do not have 2 dimensional data when clicking process to prevent inaccurate results from being generated
+- Added validation to ensure loaded files do not have 2-dimensional data when clicking process to prevent inaccurate results from being generated
 - Added more metadata information to the top left information panel
 - Changed the Status Bar message when processing is complete to state how many were successful and how many were not
 - Added a clickable link below the selected file's metadata explaining the independent parameters and why they are useful
@@ -283,7 +353,7 @@
 # Version 1.0.1
 - Two new options have been added when clicking on a participant's file.
- First new option is Age which allows the option to specify age on a per-file basis to calculate DPF by using the Scholkmann & Wolf calculation instead of having one DPF for all files. Fixes [Issue 1](https://git.research.dezeeuw.ca/tyler/flares/issues/1). This also allows for proper calculation of DPF for the two seperate wavelengths.
+- First new option is Age which allows the option to specify age on a per-file basis to calculate DPF by using the Scholkmann & Wolf calculation instead of having one DPF for all files. Fixes [Issue 1](https://git.research.dezeeuw.ca/tyler/flares/issues/1). This also allows for proper calculation of DPF for the two separate wavelengths.
 - If no age is set by the user, the code will fall back to the age of 25
 - Second new option is Gender to be used in future analysis options (currently not implemented).
 - UI elements have been shuffled to make room for the new parameters.
@@ -1,53 +1,35 @@
-# Version 1.5.1
+# Version 1.6.0
- Open a folder is now minimally BIDS compatible. It will recursively go through all folders, but not load external metadata
+- 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
- Renamed options in the Viewer Launcher window to better denote what actions they can perform
+- It is still possible to load older saves by enabling 'Incompatible Save Bypass' from the Preferences menu, but your mileage may vary
- 2 new analysis options have been added in the viewer launcher window: Inter-Group Stats and Cross-Group Stats
+- Optimized calculations being performed when calculating the Heart Rate to speed up step 5 by up to ~35% on a per-file basis
- Each of these analysis options have lots of text explaining what they do when their respective windows are opened
+- 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 parameter input dialog in the analysis windows will now be able to scroll down when lots of parameters are required
+- The Group Stats Viewer windows will now properly load the Right/Left or Front/Back fallback ROIs if JSON_LOCATION is not set
- When a project is saved, it automatically will populate into the Recent Projects menu. Fixes [Issue 86](https://git.research.dezeeuw.ca/tyler/flares/issues/86)
+- Changed the warning message for lots of short channels and changed when it shows to be percentage based (35%) instead of numerical based (6)
- The description when clicking "Why are these useful?" underneath the per-file parameters is no longer placeholder text. Fixes [Issue 85](https://git.research.dezeeuw.ca/tyler/flares/issues/85)
+- Renames GENDER to SEX to better represent the values that the field expects and to be more BIDS compliant
- Added a new parameter section "Region of Interest". It has one parameter of "JSON_LOCATION", a json file containing Region of Interest data
+- 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
- Temporarily removed the parameter REMOVE_EVENTS due to its functionality being removed because of a memory leak
+- Added a new metadata value of HAND to allow for grouping participants based on their handiness
- Fixed participant metadata remaing in the background when the participant was removed. Fixes [Issue 82](https://git.research.dezeeuw.ca/tyler/flares/issues/82)
+- Updated the layout of the participant metadata area to better accommodate current and future metadata values
- Fixed processing remaining active hidden in the background when the "Clear" button was pushed. Fixes [Issue 81](https://git.research.dezeeuw.ca/tyler/flares/issues/81)
+- 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
- Now when "Clear" is pushed while data is processing, a popup will appear ensuring that the user understands that pushing "Clear" will stop processing
+- 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'
- Reset to Default Configuration will now properly reset all of the parameters to their default values. [Issue 90](https://git.research.dezeeuw.ca/tyler/flares/issues/90)
+- 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
- A confirmation popup will now display once the application has been reset to default in addition to the status bar message
+- 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
- Changed the improper display text of "Cross Validation" to now properly read as "Coefficient of Variation"
+- 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)
- Changed the parameters "CV" and "CV_THRESHOLD" to now be "COEFF_VAR and COEFF_VAR_THRESHOLD"
+- 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)
- Changed the improper display text of "Mean Absolute Deviation" to now properly read as "Median Absolute Deviation"
+- Added an icon to the 'Toggle Status Bar' view option
- Changed the parameters "SHORT_CHANNEL", "SHORT_CHANNEL_THRESH", and "LONG_CHANNEL_THRESH" to now be "SHORT_CHANNELS", "SHORT_CHANNELS_THRESHOLD", and "LONG_CHANNELS_THRESHOLD"
+- 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)
- Changed the parameter section "Channel Variance" to now be "Sensor Dropout" to better reflect the action it performs, not the method employed to calculate it
+- The popup that appeared when a project was saved has now been moved to a message displayed from the status bar
- Changed the parameters "CHANNEL_VAR" and "CHANNEL_THRESH" to now be "SENSOR_DROPOUT" and "SENSOR_DROPOUT_VARIANCE_THRESHOLD"
+- 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 messaged displayed when the application crashes to better reflect what occured
+- Changed the working of some messages on the status bar to better reflect what has occurred
- Changed the processing stages 25-27 and updates their messages to better reflect their actions that they now perforn
+- Added a new terminal command 'assoc' to associate .flare files to the application. This is undergoing testing and may not function correctly.
- Changed stage 25 from "Generate Channel Significance" to "Generate Channel Results"
+- 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)
- Changed stage 26 from "Generate Channel, Region of Interest, and Contrast Results" to "Generate Region of Interest Results"
+- 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
- Changed stage 27 from "Compute Contrast Results" to "Generate Contrast Results"
+- Fixed an issue where participants could be skipped when processing multiple participants at once which could prevent overall processing from completing
- Changed backend code to only load required methods and not load all methods every time
+- Fixed an issue where when loading a save file some list dropdowns could go blue and bold even if the value was default
- Fixed string parameters not going blue and bold when their value was different than 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 all parameters not going blue and bold when a save file is loaded containing values that differ from default
+- 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 a crucial bug where short channels were not being processed and filtered the same way as long channels before being used as regressors
+- Fixed an issue where some popup windows would not properly display the application name when they would open
- Fixed a crucial bug where short channels were being presented to the design matrix as normal long channels
+- Fixed an issue where the welcome dialog image would not display correctly on macOS
- Fixed a crucial bug where long channels could be interpolated from short channels. Short channels are still potentially interpolated from long channels. See [this link](https://git.research.dezeeuw.ca/tyler/flares/issues/80) for more information regarding this issue.
+- Fixed an issue where the Linux version would fail at 0 seconds when attempting to process files
- Added a welcome message when the terminal is opened, resized the terminal, and added more commands
+- 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
 # Version 1.5.0
 - This release introduces a new configuration file that may break existing installs. If your application does not update correctly, please download fresh from [this link.](https://git.research.dezeeuw.ca/tyler/flares/releases/)
 - This release features an almost complete rewrite of backend files. If you encounter any problems, please raise an issue at [this link.](https://git.research.dezeeuw.ca/tyler/flares/issues/new)
 - New configuration file has been added! Now your choices of preferences will be saved when the application is closed and re-opened. If the configuration file is missing, a new one will be generated
 - Recent files and recent projects are now saved and appear under the File menu for quick resuming
 - The new option "Reset to Default Configuration" under the Options menu will reset the configuration file back to it's default values and remove any recent files
 - A welcome dialog will now display the changelog on first startup and after every update. This popup will only appear once but can be reopened under the Options menu through the button "Show Update Changelog"
 - Changed the hotkey for "Update optodes in snirf file..." to be F9 instead of F6
 - Revamped the fOLD channels window. Images containing the pie charts are now interactable! Click whitespace to expand the whole image and click a chart to expand it.
 - fOLD progress bar when processing now updates the percentages live. Fixes [Issue 76](https://git.research.dezeeuw.ca/tyler/flares/issues/76)
 - Overall pie charts on an individal and global basis are now genereted. Fixes [Issue 78](https://git.research.dezeeuw.ca/tyler/flares/issues/78)
 - Brodmann images are now available when examining a pie chart to understand which area is being reported. Fixes [Issue 77](https://git.research.dezeeuw.ca/tyler/flares/issues/77)
 - Added a new option 'Folding Bypass' to the Preferences Menu. This skips most processing steps and the only analysis option available will be to fold. Parameters on the right will be ignored. Fixes [Issue 75](https://git.research.dezeeuw.ca/tyler/flares/issues/75)
 - Fixed an issue where the fOLD analysis progress window would go unresponsive before processing participants. Fixes [Issue 45](https://git.research.dezeeuw.ca/tyler/flares/issues/45), Fixes [Issue 34](https://git.research.dezeeuw.ca/tyler/flares/issues/34)
 - Added a feature to hover over the 28 stage progress bar and see which state the progress bar is at. Fixes [Issue 74](https://git.research.dezeeuw.ca/tyler/flares/issues/74)
 - Loading a broken snirf file no longer hangs its processing and can now be removed from the list. Fixes [Issue 73](https://git.research.dezeeuw.ca/tyler/flares/issues/73)
@@ -0,0 +1,393 @@
 """
 Filename: file_ext_registration.py
 Description: Registers the extension of project files with the application
 Note: Compliant with pylance strict type checking
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 # Built-in imports
 import os
 import sys
 import plistlib
 import subprocess
 from typing import Optional, Tuple
 # External library imports
 from src.shared.shareddata import APP_NAME, PLATFORM_NAME
 ELEVATION_FLAG = "--register_file_association_elevated"
 def register_file_association(ext: Optional[str] = None,
    prog_id: Optional[str] = None,
    app_name: Optional[str] = None,
    bundle_id: Optional[str] = None,
    force_admin: bool = False,
 ) -> Tuple[bool, str]:
    """
    Registers a custom file extension across Windows, Linux, and macOS.
    Handles non-admin Windows users by falling back to local user registry.
    """
    clean_app = APP_NAME.replace(" ", "").lower()[:-1]
    if ext is None:
        ext = f".{clean_app}"
    if prog_id is None:
        prog_id = f"{APP_NAME.upper().replace(' ', '')}.ProjectFile"
    if app_name is None:
        app_name = APP_NAME
    # Ensure extension starts with dot and contains no spaces
    ext = f".{ext.lstrip('.').replace(' ', '').lower()}"
    if PLATFORM_NAME == "windows":
        return _register_windows(ext, prog_id, app_name, force_admin=force_admin)
    elif PLATFORM_NAME == "linux":
        return _register_linux(ext, prog_id, app_name)
    elif PLATFORM_NAME == "darwin":  # macOS
        if bundle_id is None:
            bundle_id = f"com.{clean_app}.app"
        return _register_macos(ext, app_name, bundle_id)
    else:
        return False, f"Unsupported OS: {PLATFORM_NAME}"
 def _dev_windowless_executable() -> str:
    """
    Windows dev-mode only: returns pythonw.exe alongside the current
    interpreter if it exists, otherwise falls back to sys.executable.
    """
    if getattr(sys, 'frozen', False):
        return sys.executable
    exe_dir = os.path.dirname(sys.executable)
    windowless = os.path.join(exe_dir, "pythonw.exe")
    return windowless if os.path.exists(windowless) else sys.executable
 def is_windows_admin() -> bool:
    """
    Returns True if currently running elevated on Windows. Always False on
    macOS/Linux, and False (rather than raising) if the check itself fails.
    """
    if PLATFORM_NAME != "windows":
        return False
    import ctypes
    try:
        return ctypes.windll.shell32.IsUserAnAdmin() != 0
    except Exception:
        return False
 def _relaunch_elevated(ext: str, prog_id: str, app_name: str) -> Optional[int]:
    """
    Triggers a UAC prompt and re-launches this process elevated with the
    registration args.
    """
    import ctypes
    from ctypes import wintypes
    if getattr(sys, 'frozen', False):
        exe = sys.executable
        params = [ELEVATION_FLAG, ext, prog_id, app_name]
    else:
        exe = _dev_windowless_executable()
        script_path = os.path.abspath(sys.argv[0])
        params = [script_path, ELEVATION_FLAG, ext, prog_id, app_name]
    param_str = " ".join(f'"{p}"' for p in params)
    SEE_MASK_NOCLOSEPROCESS = 0x00000040
    SW_SHOWNORMAL = 1
    class SHELLEXECUTEINFO(ctypes.Structure):
        _fields_ = [
            ("cbSize", wintypes.DWORD),
            ("fMask", ctypes.c_ulong),
            ("hwnd", wintypes.HWND),
            ("lpVerb", wintypes.LPCWSTR),
            ("lpFile", wintypes.LPCWSTR),
            ("lpParameters", wintypes.LPCWSTR),
            ("lpDirectory", wintypes.LPCWSTR),
            ("nShow", ctypes.c_int),
            ("hInstApp", wintypes.HINSTANCE),
            ("lpIDList", ctypes.c_void_p),
            ("lpClass", wintypes.LPCWSTR),
            ("hKeyClass", wintypes.HKEY),
            ("dwHotKey", wintypes.DWORD),
            ("hIconOrMonitor", wintypes.HANDLE),
            ("hProcess", wintypes.HANDLE),
        ]
    sei = SHELLEXECUTEINFO()
    sei.cbSize = ctypes.sizeof(sei)
    sei.fMask = SEE_MASK_NOCLOSEPROCESS
    sei.lpVerb = "runas"
    sei.lpFile = exe
    sei.lpParameters = param_str
    sei.nShow = SW_SHOWNORMAL
    if not ctypes.windll.shell32.ShellExecuteExW(ctypes.byref(sei)):
        # User clicked "No" on the UAC prompt, or elevation failed outright.
        return None
    WAIT_INFINITE = 0xFFFFFFFF
    ctypes.windll.kernel32.WaitForSingleObject(sei.hProcess, WAIT_INFINITE)
    exit_code = wintypes.DWORD()
    ctypes.windll.kernel32.GetExitCodeProcess(sei.hProcess, ctypes.byref(exit_code))
    ctypes.windll.kernel32.CloseHandle(sei.hProcess)
    return exit_code.value
 def _delete_key_recursive(root_key: int, path: str) -> None:
    """Recursively deletes a registry key and all its subkeys, if present."""
    import winreg
    try:
        with winreg.OpenKey(root_key, path, 0, winreg.KEY_ALL_ACCESS) as key:
            while True:
                try:
                    subkey_name = winreg.EnumKey(key, 0)
                except OSError:
                    break
                _delete_key_recursive(root_key, f"{path}\\{subkey_name}")
        winreg.DeleteKey(root_key, path)
    except FileNotFoundError:
        pass
 def _cleanup_stale_hkcu_entries(ext: str, prog_id: str) -> None:
    """
    Removes any leftover per-user (HKCU) association for this ext/prog_id.
    Windows prefers HKCU\\Software\\Classes over HKEY_CLASSES_ROOT for a
    given user, so a stale non-admin dev-time registration can silently
    keep shadowing a correct system-wide (admin) registration.
    """
    import winreg
    _delete_key_recursive(winreg.HKEY_CURRENT_USER, f"Software\\Classes\\{ext}")
    _delete_key_recursive(winreg.HKEY_CURRENT_USER, f"Software\\Classes\\{prog_id}")
 def _register_windows(ext: str, prog_id: str, app_name: str, force_admin: bool = False) -> Tuple[bool, str]:
    """
    Registers the file extension with the application on Windows.
    """
    import winreg
    import ctypes
    is_admin = is_windows_admin()
    if force_admin and not is_admin:
        exit_code = _relaunch_elevated(ext, prog_id, app_name)
        if exit_code is None:
            return False, "Elevation was cancelled or the UAC prompt could not be shown."
        if exit_code != 0:
            return False, f"Elevated registration process exited with code {exit_code}."
        return True, f"Successfully registered {ext} on Windows (System-wide, via elevated relaunch)!"
    # Windows is the one platform where unfrozen invocation is supported
    if getattr(sys, 'frozen', False):
        command_str = f'"{sys.executable}" "%1"'
    else:
        script_path = os.path.abspath(sys.argv[0])
        command_str = f'"{_dev_windowless_executable()}" "{script_path}" "%1"'
    root_key = winreg.HKEY_CLASSES_ROOT if is_admin else winreg.HKEY_CURRENT_USER
    base_path = "" if is_admin else "Software\\Classes\\"
    try:
        # 1. Map extension -> ProgID
        ext_path = f"{base_path}{ext}"
        with winreg.CreateKey(root_key, ext_path) as key:
            winreg.SetValue(key, "", winreg.REG_SZ, prog_id)
        # 2. Add to OpenWithProgids (Forces Windows 10/11 to show in 'Open With')
        open_with_path = f"{base_path}{ext}\\OpenWithProgids"
        with winreg.CreateKey(root_key, open_with_path) as key:
            winreg.SetValueEx(key, prog_id, 0, winreg.REG_SZ, "")
        # 3. Set friendly type description (shown as "Type" in File Explorer)
        type_description = f"{app_name.upper()} Project File"
        prog_path = f"{base_path}{prog_id}"
        with winreg.CreateKey(root_key, prog_path) as key:
            winreg.SetValue(key, "", winreg.REG_SZ, type_description)
        # 4. Set launch command
        cmd_path = f"{base_path}{prog_id}\\shell\\open\\command"
        with winreg.CreateKey(root_key, cmd_path) as key:
            winreg.SetValue(key, "", winreg.REG_SZ, command_str)
        # 5. Notify Shell (SHCNE_ASSOCCHANGED = 0x08000000, SHCNF_IDLIST = 0x0000)
        try:
            ctypes.windll.shell32.SHChangeNotify(0x08000000, 0x0000, 0, 0)
        except Exception:
            pass
        # 6. If we just wrote a system-wide entry, clean up any stale per-user entry that would otherwise shadow it.
        if is_admin:
            try:
                _cleanup_stale_hkcu_entries(ext, prog_id)
            except Exception:
                # Non-fatal: the system-wide write above already succeeded.
                pass
        scope = "System-wide" if is_admin else "Local User (Non-Admin)"
        return True, f"Successfully registered {ext} on Windows ({scope})!"
    except Exception as e:
        return False, f"Windows Registration failed: {str(e)}"
 # TODO: Validate
 def _register_linux(ext: str, prog_id: str, app_name: str) -> Tuple[bool, str]:
    """
    Registers the file extension with the application on Linux based platforms.
    """
    clean_ext = ext.lstrip('.')
    mime_type = f"application/x-{clean_ext}"
    desktop_file_name = f"{prog_id.lower()}.desktop"
    # Linux build is always a frozen PyInstaller executable
    exe_path = f'"{sys.executable}"'
    apps_dir = os.path.expanduser("~/.local/share/applications")
    mime_dir = os.path.expanduser("~/.local/share/mime/packages")
    os.makedirs(apps_dir, exist_ok=True)
    os.makedirs(mime_dir, exist_ok=True)
    try:
        # 1. Create XML MIME definition
        mime_xml_path = os.path.join(mime_dir, f"{prog_id.lower()}.xml")
        xml_content = f"""<?xml version="1.0" encoding="UTF-8"?>
            <mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">
            <mime-type type="{mime_type}">
                <comment>{app_name} File</comment>
                <glob pattern="*.{clean_ext}"/>
            </mime-type>
            </mime-info>"""
        with open(mime_xml_path, "w") as f:
            f.write(xml_content)
        # 2. Create .desktop file
        desktop_path = os.path.join(apps_dir, desktop_file_name)
        desktop_content = f"""[Desktop Entry]
            Name={app_name}
            Exec={exe_path} %f
            Type=Application
            MimeType={mime_type};
            Terminal=false
            """
        with open(desktop_path, "w") as f:
            f.write(desktop_content)
        # 3. Update the shared-mime-info database and check it actually worked
        mime_result = subprocess.run(
            ["update-mime-database", os.path.expanduser("~/.local/share/mime")],
            capture_output=True, text=True,
        )
        if mime_result.returncode != 0:
            return False, f"update-mime-database failed: {mime_result.stderr.strip()}"
        # 4. Set as default handler and check it actually worked
        xdg_result = subprocess.run(
            ["xdg-mime", "default", desktop_file_name, mime_type],
            capture_output=True, text=True,
        )
        if xdg_result.returncode != 0:
            return False, f"xdg-mime default failed: {xdg_result.stderr.strip()}"
        return True, f"Successfully registered {ext} on Linux (Local User)!"
    except FileNotFoundError as e:
        return False, (
            f"Required tool not found ({str(e)}). Is shared-mime-info / "
            f"xdg-utils installed on this system?"
        )
    except Exception as e:
        return False, f"Linux Registration failed: {str(e)}"
 # TODO: Validate
 def _register_macos(ext: str, app_name: str, bundle_id: str) -> Tuple[bool, str]:
    """
    Registers the file extension with the application on macOS.
    """
    if not getattr(sys, 'frozen', False):
        return False, "macOS file association requires app to be packaged as a .app bundle."
    exe_path = sys.executable
    app_bundle_path = os.path.abspath(os.path.join(exe_path, "../../../"))
    if not app_bundle_path.endswith(".app"):
        return False, "Could not locate outer .app bundle."
    info_plist_path = os.path.join(app_bundle_path, "Contents", "Info.plist")
    if not os.path.exists(info_plist_path):
        return False, f"Info.plist not found at {info_plist_path}"
    clean_ext = ext.lstrip('.')
    uti = f"{bundle_id}.{clean_ext}"
    try:
        with open(info_plist_path, "rb") as f:
            plist = plistlib.load(f)
        # Tell macOS this app can open files with our UTI
        doc_types = plist.get("CFBundleDocumentTypes", [])
        if not any(uti in dt.get("LSItemContentTypes", []) for dt in doc_types):
            doc_types.append({
                "CFBundleTypeName": f"{app_name} Project File",
                "CFBundleTypeRole": "Editor",
                "LSHandlerRank": "Owner",
                "LSItemContentTypes": [uti],
            })
        plist["CFBundleDocumentTypes"] = doc_types
        # Declare the UTI itself (required — without this the type is unknown to LS)
        exported_types = plist.get("UTExportedTypeDeclarations", [])
        if not any(t.get("UTTypeIdentifier") == uti for t in exported_types):
            exported_types.append({
                "UTTypeIdentifier": uti,
                "UTTypeDescription": f"{app_name} File",
                "UTTypeConformsTo": ["public.data"],
                "UTTypeTagSpecification": {"public.filename-extension": [clean_ext]},
            })
        plist["UTExportedTypeDeclarations"] = exported_types
        with open(info_plist_path, "wb") as f:
            plistlib.dump(plist, f)
    except Exception as e:
        return False, f"Failed to update Info.plist: {str(e)}"
    try:
        lsregister_path = (
            "/System/Library/Frameworks/CoreServices.framework/Frameworks/"
            "LaunchServices.framework/Support/lsregister"
        )
        subprocess.run(
            [lsregister_path, "-f", app_bundle_path],
            check=True, capture_output=True,
        )
        return True, f"Registered {ext} with {app_bundle_path} via macOS Launch Services!"
    except subprocess.CalledProcessError as e:
        stderr = e.stderr.decode(errors="ignore") if e.stderr else str(e)
        return False, f"macOS Launch Services registration failed: {stderr}"
    except Exception as e:
        return False, f"macOS Registration failed: {str(e)}"
@@ -0,0 +1 @@
 <svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M160-360v-80h400v80H160Zm0-160v-80h640v80H160Z"/></svg>
@@ -10,7 +10,7 @@ from pathlib import Path
 import numpy as np
 from scipy import linalg
-from scipy.special import lpmv, sph_harm
+from scipy.special import lpmv, sph_harm_y
 from .. import __version__
 from .._fiff.compensator import make_compensator
@@ -1487,7 +1487,7 @@ def _sss_basis_basic(exp, coils, mag_scale=100.0, method="standard"):
            S_in_out = list()
            grads_in_out = list()
            # Same spherical harmonic is used for both internal and external
-            sph = sph_harm(order, degree, az, pol)
+            sph = sph_harm_y(order, degree, az, pol)
            sph_norm = _sph_harm_norm(order, degree)
            # Compute complex gradient for all integration points
            # in spherical coordinates (Eq. 6). The gradient for rad, az, pol
@@ -0,0 +1,826 @@
 """
 Filename: project_manager.py
 Description: Manager file for anything project related
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 # Built-in imports
 import os
 import sys
 import copy
 import pickle
 import concurrent
 from pathlib import Path, PurePosixPath
 # External library imports
 import pandas as pd
 from PySide6.QtWidgets import QMessageBox, QVBoxLayout, QFileDialog, QLabel, QDialog
 from PySide6.QtCore import QThread, Signal, Qt, QTimer
 from PySide6.QtGui import QAction
 from mne.io import read_raw_snirf
 from mne.preprocessing.nirs import source_detector_distances
 from mne_nirs.channels import get_short_channels  # type: ignore
 from src.shared.flaresbasewidget import ProgressBubble
 from src.shared.shareddata import APP_NAME, CURRENT_VERSION, PLATFORM_NAME, DATA_SCHEMA
 class SaveProjectThread(QThread):
    finished_signal = Signal(str)
    error_signal = Signal(str)
    def __init__(self, filename, project_data):
        super().__init__()
        self.filename = filename
        self.project_data = project_data
    def run(self):
        try:
            with open(self.filename, "wb") as f:
                pickle.dump(self.project_data, f)
            self.finished_signal.emit(self.filename)
        except Exception as e:
            self.error_signal.emit(str(e))
 class SavingOverlay(QDialog):
    def __init__(self, parent=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("Saving 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 ProjectManager:
    """
    Central manager for all I/O operations:
    - File loading (individual files & folders)
    - Project loading & saving (Save vs Save As)
    - Relative / absolute path utilities
    - State baseline synchronization (dirty tracking)
    """
    def __init__(self, app, file_cfg, cfg_path):
        self.app = app
        self.file_cfg = file_cfg
        self.cfg_path = cfg_path
    # =========================================================================
    # Path Utilities
    # =========================================================================
    def get_safe_path(self, target_path, project_dir):
        """Converts an absolute file path to a relative path relative to project_dir."""
        try:
            target = Path(target_path).resolve()
            proj = Path(project_dir).resolve()
            return str(PurePosixPath(target.relative_to(proj)))
        except ValueError:
            # Fall back to absolute path string if on a different drive/volume
            return str(PurePosixPath(Path(target_path).resolve()))
    # =========================================================================
    # File & Folder Opening Dialogs
    # =========================================================================
    def open_file_dialog(self):
        """Opens dialog to pick a single .snirf file."""
        file_path, _ = QFileDialog.getOpenFileName(
            self.app, "Open File", "", "SNIRF Files (*.snirf);;All Files (*)"
        )
        if file_path:
            self._load_files_into_pipeline([os.path.normpath(file_path)])
    def open_folder_dialog(self):
        """Recursively finds all .snirf files in a selected directory."""
        folder_path = QFileDialog.getExistingDirectory(self.app, "Select Folder", "")
        if folder_path:
            snirf_files = [os.path.normpath(str(f)) for f in Path(folder_path).rglob("*.snirf")]
            self._load_files_into_pipeline(snirf_files)
    def _load_files_into_pipeline(self, file_paths):
        """Loads .snirf files into UI using chunked batches and background workers."""
        app = self.app
        if not file_paths:
            return
        # 1. Warm up the executor if needed
        if not hasattr(app, "file_executor") or app.file_executor is None:
            app.file_executor = concurrent.futures.ProcessPoolExecutor(max_workers=1)
        # 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
        if not hasattr(app, "bubble_widgets"):
            app.bubble_widgets = {}
        if not hasattr(app, "selected_paths"):
            app.selected_paths = []
        if not hasattr(app, "metadata_cache"):
            app.metadata_cache = {}
        # Filter out files already in the UI to avoid duplicates
        new_files = [p for p in file_paths if p not in app.selected_paths]
        if not new_files:
            return
        # Update the pending count for the current load batch
        if not hasattr(app, "pending_files_count"):
            app.pending_files_count = 0
        app.pending_files_count += len(new_files)
        app.button1.setVisible(True)
        app.statusBar().showMessage(f"Loading {len(new_files)} new file(s)...")
        # Queue chunked widget creation
        CHUNK_SIZE = 10
        def process_chunk(file_queue):
            chunk = file_queue[:CHUNK_SIZE]
            remaining = file_queue[CHUNK_SIZE:]
            for path in chunk:
                app.selected_paths.append(path)
                self.add_to_recent_files(path)
                display_name = os.path.basename(path)
                bubble = ProgressBubble(display_name, path)
                bubble.setCursor(Qt.CursorShape.WaitCursor)
                bubble.set_loading_state(True)
                app.bubble_widgets[path] = bubble
                app.bubble_layout.addWidget(bubble)
                # Submit background task as each bubble is constructed
                future = app.file_executor.submit(extract_metadata_worker, path)
                future.add_done_callback(
                    lambda f, p=path, s=current_session: app._on_metadata_ready(f, p, s)
                )
            app.files_are_dirty = True
            app.is_saved = False
            if hasattr(app, "check_if_app_is_dirty"):
                app.check_if_app_is_dirty()
            elif hasattr(app, "update_window_title"):
                app.update_window_title()
            # Schedule remaining files
            if remaining:
                QTimer.singleShot(0, lambda: process_chunk(remaining))
        process_chunk(new_files)
    def add_files_to_project(self, file_paths):
        """Adds file paths to the application state, creating bubble UI items."""
        app = self.app
        normalized_paths = [os.path.normpath(p) for p in file_paths]
        # Merge with existing selected paths avoiding duplicates
        existing_paths = getattr(app, "selected_paths", [])
        new_paths = [p for p in normalized_paths if p not in existing_paths]
        if not new_paths:
            return
        app.selected_paths = existing_paths + new_paths
        # Render file bubbles in UI if method exists
        if hasattr(app, "show_files_as_bubbles_from_list"):
            progress_states = getattr(app, "progress_states", {})
            current_project = getattr(app, "current_project_path", "")
            app.show_files_as_bubbles_from_list(
                app.selected_paths, progress_states, current_project
            )
        # Record in recent files menu
        for path in new_paths:
            self.add_to_recent_files(path)
        # Trigger dirty check
        if hasattr(app, "check_if_app_is_dirty"):
            app.check_if_app_is_dirty()
    # =========================================================================
    # Project Loading
    # =========================================================================
    def load_project_dialog(self):
        """Prompts for a project file and loads it."""
        app = self.app
        filename, _ = QFileDialog.getOpenFileName(
            app, "Load Project", "", "FLARE Project (*.flare)"
        )
        if filename:
            self.load_project(filename)
    def load_project(self, filename):
        """Loads a .flare project file into the application."""
        app = self.app
        try:
            with open(filename, "rb") as f:
                data = pickle.load(f)
            checks = [
                ("version", "<=1.1.7"),
                ("file_metadata", "<=1.2.2"),
                ("file_parameters", "<=1.3.0"),
                ("roi_channel_map_dict", "<=1.5.2"),
            ]
            for key, ver_str in checks:
                if key not in data:
                    msg = (
                        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):
                        QMessageBox.warning(
                            app, f"Warning - {APP_NAME.upper()}", msg + "Attempting load."
                        )
                        break
                    else:
                        QMessageBox.critical(
                            app,
                            f"Error - {APP_NAME.upper()}",
                            msg + "Enable bypass in Preferences to load.",
                        )
                        return
            # Clear existing UI bubbles
            if hasattr(app, "bubble_widgets"):
                for bubble in list(app.bubble_widgets.values()):
                    bubble.setParent(None)
                    bubble.deleteLater()
                app.bubble_widgets.clear()
            app.selected_paths = []
            app.current_project_path = filename
            # Restore Data Schema
            for item in DATA_SCHEMA:
                setattr(app, item["key"], data.get(item["key"], {}))
            project_dir = Path(filename).parent
            saved_cache = data.get("file_metadata", {})
            raw_params = data.get("file_parameters", {})
            app.metadata_cache = {}
            app.file_metadata = {}
            for rel_path, meta_content in saved_cache.items():
                abs_path = str((project_dir / Path(rel_path)).resolve())
                app.metadata_cache[abs_path] = meta_content
            file_list = [
                str((project_dir / Path(rel_path)).resolve()) for rel_path in data["file_list"]
            ]
            raw_progress = data.get("progress_states", {})
            progress_states = {
                str((project_dir / Path(rel_path)).resolve()): step
                for rel_path, step in raw_progress.items()
            }
            for rel_path in data["file_list"]:
                abs_path = str((project_dir / Path(rel_path)).resolve())
                if rel_path in raw_params:
                    app.file_metadata[abs_path] = raw_params[rel_path]
                elif hasattr(app, "config_dict") and abs_path in app.config_dict:
                    old_cfg = app.config_dict[abs_path]
                    app.file_metadata[abs_path] = {
                        "AGE": str(old_cfg.get("AGE", "")),
                        "SEX": str(old_cfg.get("SEX", "")),
                        "HAND": str(old_cfg.get("HAND", "")),
                        "GROUP": str(old_cfg.get("GROUP", "")),
                    }
                else:
                    app.file_metadata[abs_path] = {
                        "AGE": "",
                        "SEX": "",
                        "HAND": "",
                        "GROUP": "",
                    }
            app.show_files_as_bubbles_from_list(file_list, progress_states, filename)
            if "current_ui_params" in data:
                app.restore_sections_from_config(data["current_ui_params"])
            elif getattr(app, "config_dict", None):
                first_file = next(iter(app.config_dict.keys()))
                app.restore_sections_from_config(app.config_dict[first_file])
            has_data = any(len(getattr(app, item["key"], {})) > 0 for item in DATA_SCHEMA)
            if hasattr(app, "button1"):
                app.button1.setVisible(not has_data)
            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}")
    # =========================================================================
    # Project Saving (Save / Save As)
    # =========================================================================
    def save_project(self, onCrash=False, ask=False):
        """
        Saves the project to disk.
        - ask=False: Quick Save to self.app.current_project_path (prompts if unsaved).
        - ask=True: Save As (always prompts for location).
        """
        app = self.app
        # 1. Sync active text fields into active metadata dict
        if hasattr(app, "current_file") and app.current_file and hasattr(app, "meta_fields"):
            if not hasattr(app, "file_metadata"):
                app.file_metadata = {}
            app.file_metadata[app.current_file] = {
                key: field.text().strip() for key, field in app.meta_fields.items()
            }
        # 2. Check if saveable state exists
        has_files = len(getattr(app, "selected_paths", [])) > 0
        has_metadata = any(
            any(val for val in m.values()) for m in getattr(app, "file_metadata", {}).values()
        )
        has_param_changes = any(
            s.has_any_changes() for s in getattr(app, "param_sections", [])
        )
        has_processed_data = any(
            len(getattr(app, item["key"], {})) > 0 for item in DATA_SCHEMA
        )
        if not (has_files or has_processed_data or has_metadata or has_param_changes):
            if not onCrash:
                QMessageBox.warning(
                    app,
                    "Save Project",
                    "There is no data or configuration to save.",
                )
            return
        # 3. Path Resolution
        filename = None
        if not onCrash:
            existing_path = getattr(app, "current_project_path", None)
            if ask or not existing_path:
                start_dir = existing_path if existing_path else ""
                filename, _ = QFileDialog.getSaveFileName(
                    app, "Save Project", start_dir, "FLARE Project (*.flare)"
                )
                if not filename:
                    return
            else:
                filename = existing_path
        else:
            if PLATFORM_NAME == "darwin":
                filename = os.path.join(
                    os.path.dirname(sys.executable), "../../../flares_autosave.flare"
                )
            else:
                filename = os.path.join(os.getcwd(), "flares_autosave.flare")
        try:
            if not filename.endswith(".flare"):
                filename += ".flare"
            project_path = Path(filename).resolve()
            project_dir = project_path.parent
            # 4. Convert Paths to Relative
            bubble_widgets = getattr(app, "bubble_widgets", {})
            file_list = [
                self.get_safe_path(b.file_path, project_dir) for b in bubble_widgets.values()
            ]
            progress_states = {
                self.get_safe_path(b.file_path, project_dir): getattr(b, "current_step", 0)
                for b in bubble_widgets.values()
            }
            rel_metadata = {}
            for full_path, meta in getattr(app, "metadata_cache", {}).items():
                try:
                    rel_metadata[self.get_safe_path(full_path, project_dir)] = meta
                except Exception as e:
                    print(f"Metadata conversion failed for {full_path}: {e}")
            rel_file_params = {
                self.get_safe_path(f_path, project_dir): meta
                for f_path, meta in getattr(app, "file_metadata", {}).items()
            }
            current_params = app.get_all_current_ui_params()
            if not current_params and getattr(app, "config_dict", None):
                first_file = next(iter(app.config_dict.keys()))
                current_params = app.config_dict[first_file]
            # 5. Build Serialized Payload
            project_data = {
                item["key"]: getattr(app, item["key"], {}) for item in DATA_SCHEMA
            }
            project_data.update({
                "version": CURRENT_VERSION,
                "file_list": file_list,
                "progress_states": progress_states,
                "file_metadata": rel_metadata,
                "file_parameters": rel_file_params,
                "current_ui_params": current_params,
            })
            def sanitize(obj):
                if isinstance(obj, Path):
                    return str(PurePosixPath(obj))
                elif isinstance(obj, dict):
                    return {sanitize(k): sanitize(v) for k, v in obj.items()}
                elif isinstance(obj, list):
                    return [sanitize(i) for i in obj]
                return obj
            project_data = sanitize(project_data)
            self.add_to_recent_projects(os.path.normpath(filename))
            # 6. Background Saving Execution
            if not onCrash:
                app.saving_overlay = SavingOverlay(app)
                app.saving_overlay.resize(app.size())
                app.saving_overlay.show()
            app.save_thread = SaveProjectThread(filename, project_data)
            def _on_save_success(saved_file):
                if hasattr(app, "saving_overlay"):
                    app.saving_overlay.close()
                self.add_to_recent_projects(os.path.normpath(saved_file))
                app.current_project_path = saved_file
                self.reset_all_dirty_states()
                if not onCrash:
                    QMessageBox.information(
                        app, "Success", f"Project saved to:\n{saved_file}"
                    )
            def _on_save_error(error_msg):
                if hasattr(app, "saving_overlay"):
                    app.saving_overlay.close()
                if not onCrash:
                    QMessageBox.critical(
                        app, "Error", f"Failed to save project:\n{error_msg}"
                    )
            app.save_thread.finished_signal.connect(_on_save_success)
            app.save_thread.error_signal.connect(_on_save_error)
            app.save_thread.start()
        except Exception as e:
            if not onCrash:
                QMessageBox.critical(app, "Error", f"Failed to save project:\n{e}")
    def update_recent_projects_menu(self):
        """Clears and rebuilds the Recent Projects submenu items."""
        app = self.app
        if not hasattr(app, "recent_projects_menu"):
            return
        app.recent_projects_menu.clear()
        raw_projects = self.file_cfg.get("File", "recent_projects", fallback="")
        projects = [p.strip() for p in raw_projects.split(",") if p.strip()]
        if not projects:
            no_recent = app.recent_projects_menu.addAction(
                "No Recent Projects"
            )
            no_recent.setEnabled(False)
            return
        for i, project_path in enumerate(projects):
            action = QAction(f"{i+1}: {project_path}", app)
            action.setToolTip(project_path)
            action.triggered.connect(
                lambda checked, path=project_path: self.open_recent_project(path)
            )
            app.recent_projects_menu.addAction(action)
    def add_to_recent_projects(self, project_path):
        """Adds a project path, moves it to the top, and hard caps at 10."""
        raw_projects = self.file_cfg.get("File", "recent_projects", fallback="")
        projects = [p.strip() for p in raw_projects.split(",") if p.strip()]
        if project_path in projects:
            projects.remove(project_path)
        projects.insert(0, project_path)
        projects = projects[:10]  # Hard cap of 10 items
        self.file_cfg.set("File", "recent_projects", ",".join(projects))
        try:
            with open(self.cfg_path, "w") as f:
                self.file_cfg.write(f)
        except Exception as e:
            print(f"Warning: Could not save config history: {e}")
        self.update_recent_projects_menu()
    def open_recent_project(self, project_path):
        """The slot that executes when a recent project entry is clicked."""
        if os.path.exists(project_path):
            print(f"Opening recent project: {project_path}")
            # Route project loading through ProjectManager or app's loader
            if hasattr(self.app, "project_loader"):
                self.app.project_loader(project_path)
            else:
                self.load_project(project_path)
            self.add_to_recent_projects(project_path)
        else:
            QMessageBox.warning(
                self.app,
                "Project Not Found",
                f"The project file could not be found:\n{project_path}",
            )
            # Clean out the broken path
            raw_projects = self.file_cfg.get("File", "recent_projects", fallback="")
            projects = [
                p.strip()
                for p in raw_projects.split(",")
                if p.strip() and p.strip() != project_path
            ]
            self.file_cfg.set("File", "recent_projects", ",".join(projects))
            self.update_recent_projects_menu()
    # =========================================================================
    # Recent Files Operations
    # =========================================================================
    def update_recent_files_menu(self):
        """Clears and rebuilds the Recent Files submenu items."""
        app = self.app
        if not hasattr(app, "recent_files_menu"):
            return
        app.recent_files_menu.clear()
        raw_files = self.file_cfg.get("File", "recent_files", fallback="")
        files = [f.strip() for f in raw_files.split(",") if f.strip()]
        if not files:
            no_recent = app.recent_files_menu.addAction("No Recent Files")
            no_recent.setEnabled(False)
            return
        for i, file_path in enumerate(files):
            action = QAction(f"{i+1}: {file_path}", app)
            action.triggered.connect(
                lambda checked, path=file_path: self.open_recent_file(path)
            )
            app.recent_files_menu.addAction(action)
    def add_to_recent_files(self, file_path):
        """Adds a path, moves it to the top, and hard caps the list at 10."""
        raw_files = self.file_cfg.get("File", "recent_files", fallback="")
        files = [f.strip() for f in raw_files.split(",") if f.strip()]
        if file_path in files:
            files.remove(file_path)
        files.insert(0, file_path)
        files = files[:10]
        self.file_cfg.set("File", "recent_files", ",".join(files))
        try:
            with open(self.cfg_path, "w") as f:
                self.file_cfg.write(f)
        except Exception as e:
            print(f"Warning: Could not save config history: {e}")
        self.update_recent_files_menu()
    def open_recent_file(self, file_path):
        """The slot that executes when someone clicks a recent file entry."""
        if os.path.exists(file_path):
            print(f"Opening recent file: {file_path}")
            self._load_files_into_pipeline([os.path.normpath(file_path)])
            # Refresh position to top
            self.add_to_recent_files(file_path)
        else:
            QMessageBox.warning(
                self.app,
                "File Not Found",
                f"The file could not be found:\n{file_path}",
            )
            # Clean up the broken link from history
            raw_files = self.file_cfg.get("File", "recent_files", fallback="")
            files = [
                f.strip()
                for f in raw_files.split(",")
                if f.strip() and f.strip() != file_path
            ]
            self.file_cfg.set("File", "recent_files", ",".join(files))
            self.update_recent_files_menu()
    # =========================================================================
    # Baseline Synchronization & Dirty Checks
    # =========================================================================
    def sync_metadata_baseline(self):
        """Captures current file_metadata state as baseline."""
        self.app.saved_file_metadata = copy.deepcopy(getattr(self.app, "file_metadata", {}))
    def is_metadata_dirty(self):
        """Returns True if file metadata has been modified relative to saved baseline."""
        current_meta = getattr(self.app, "file_metadata", {})
        saved_meta = getattr(self.app, "saved_file_metadata", {})
        if current_meta != saved_meta:
            return True
        if (
            hasattr(self.app, "current_file")
            and self.app.current_file
            and hasattr(self.app, "meta_fields")
        ):
            active_saved = saved_meta.get(self.app.current_file, {})
            for key, field in getattr(self.app, "meta_fields", {}).items():
                if field.text().strip() != active_saved.get(key, "").strip():
                    return True
        return False
    def reset_all_dirty_states(self):
        """Resets parameter, file, and metadata baselines after load/save."""
        # 1. Sync file list baseline
        self.app.saved_selected_paths = copy.deepcopy(getattr(self.app, "selected_paths", []))
        self.app.files_are_dirty = False
        # 2. Sync metadata baseline
        self.sync_metadata_baseline()
        # 3. Sync parameter baselines
        for section_widget in getattr(self.app, "param_sections", []):
            if hasattr(section_widget, "save_current_as_baseline"):
                section_widget.save_current_as_baseline()
        # 4. Clear dirty status & update UI title
        self.app.is_saved = True
        if hasattr(self.app, "update_window_title"):
            self.app.update_window_title()
 def _get_bids_demographics(snirf_path: str) -> dict[str, str]:
    """Traverses the path of a SNIRF file to extract age/sex/hand from BIDS TSV files.
    'hand' is only included if a value is present and isn't 'n/a' (case-insensitive) -
    many datasets leave it unset/inapplicable, so surfacing 'n/a' explicitly just adds noise.
    """
    path = Path(snirf_path)
    fields = ["age", "sex", "hand"]
    # Extract sub-XX and ses-YY labels from the path
    sub_id = next((part for part in path.parts if part.startswith("sub-")), None)
    ses_id = next((part for part in path.parts if part.startswith("ses-")), None)
    if not sub_id:
        return {}
    def _row_to_dict(row) -> dict[str, str]:
        result = {}
        for field in fields:
            if field not in row:
                continue
            val = row[field]
            if pd.isna(val):
                continue
            val_str = str(val).strip()
            if field == "hand" and val_str.lower() in ("n/a", "na", ""):
                continue
            result[field] = val_str
        return result
    # 1. Look for sub-<id>/sub-<id>_sessions.tsv
    sub_dir = next((p for p in path.parents if p.name == sub_id), None)
    if sub_dir and ses_id:
        sessions_tsv = sub_dir / f"{sub_id}_sessions.tsv"
        if sessions_tsv.exists():
            try:
                df = pd.read_csv(sessions_tsv, sep="\t")
                matching = df[df["session_id"].astype(str).str.replace("ses-", "") == ses_id.replace("ses-", "")]
                if not matching.empty:
                    result = _row_to_dict(matching.iloc[0])
                    if result:
                        return result
            except Exception:
                pass
    # 2. Fallback: Check dataset root participants.tsv
    bids_root = sub_dir.parent if sub_dir else None
    if bids_root:
        participants_tsv = bids_root / "participants.tsv"
        if participants_tsv.exists():
            try:
                df = pd.read_csv(participants_tsv, sep="\t")
                matching = df[df["participant_id"].astype(str).str.replace("sub-", "") == sub_id.replace("sub-", "")]
                if not matching.empty:
                    result = _row_to_dict(matching.iloc[0])
                    if result:
                        return result
            except Exception:
                pass
    return {}
 def extract_metadata_worker(file_name):
    """Runs in the separate worker process. Returns a clean dict."""
    # 1. Use preload=False! We only need metadata.
    raw = None
    try:
        raw = read_raw_snirf(file_name, preload=False, verbose="ERROR")
        snirf_info = {}
        # 2. Measurement date
        snirf_info['Measurement Date'] = str(raw.info.get('meas_date'))
        # 3. Short Channels
        try:
            short_chans = get_short_channels(raw, max_dist=0.015)
            names = list(short_chans.ch_names)
            snirf_info['Short Channels'] = f"Likely - {names}"
            total_chans = len(raw.ch_names)
            pct_short = (len(names) / total_chans * 100) if total_chans else 0
            if pct_short > 35:
                snirf_info['Short Channels'] += "\n There are a lot of short channels. Perhaps the optode distances are incorrect?"
        except:
            snirf_info['Short Channels'] = "Unlikely"
        # 4. Distances
        dist_vals = source_detector_distances(raw.info)
        snirf_info['Source-Detector Distances'] = [
            f"{name}: {d:.4f} m" for name, d in zip(raw.info['ch_names'], dist_vals)
        ]
        # 5. Digitization
        dig = raw.info.get('dig', None)
        if dig is not None:
            snirf_info['Digitization Points'] = [
                f"Kind: {p['kind']}, ID: {p['ident']}, Coord: {p['r']}" for p in dig
            ]
        else:
            snirf_info['Digitization Points'] = "Not found"
        # 6. Annotations (using our copy-to-string trick)
        if raw.annotations is not None and len(raw.annotations) > 0:
            snirf_info['Annotations'] = [
                f"Onset: {o:.2f}s, Duration: {d:.2f}s, Description: {str(desc)}"
                for o, d, desc in zip(raw.annotations.onset, raw.annotations.duration, raw.annotations.description)
            ]
        else:
            snirf_info['Annotations'] = "No annotations found"
        demographics = _get_bids_demographics(file_name)
        if "age" in demographics:
            snirf_info["BIDS - Age"] = demographics["age"]
        if "sex" in demographics:
            snirf_info["BIDS - Sex"] = demographics["sex"]
        if "hand" in demographics:
            snirf_info["BIDS - Handedness"] = demographics["hand"]
        return snirf_info
    except Exception as e:
        print(f"Worker safely caught failure on {file_name}: {str(e)}")
        return {'status': 'error', 'reason': str(e)}
    finally:
        if raw is not None:
            try:
                raw.close()
            except:
                pass
@@ -152,8 +152,8 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
        df_ind_dict: dict[str, DataFrame],
        design_matrix_dict: dict[str, DataFrame],
        contrast_results_dict: dict[str, dict[str, Any]],
        roi_channel_map_dict: dict[str, dict[str, str]],
        group_dict: dict[str, str],
        json_location: str | Path
    ) -> None:
        super().__init__("CrossGroupStats")
@@ -163,14 +163,14 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
        self.df_ind_dict = df_ind_dict
        self.design_matrix_dict = design_matrix_dict
        self.contrast_results_dict = contrast_results_dict
-        # self.group_dict = group_dict
+        self.roi_channel_map_dict = roi_channel_map_dict
-        self.json_location = json_location
+        self.group_dict = group_dict
        self.setup_cross_group_ui(["0 (Raw ROI Comparison)", "1 (Laterality Comparison)", "2 (Contrast Comparison)",], placeholder_text=DESCRIPTION)
    def process_request(self):
-        request = self.get_common_request_data(PARAMETERIZED_INDEXES, self.json_location, self.contrast_results_dict)
+        request = self.get_common_request_data(PARAMETERIZED_INDEXES, self.df_ind_dict, self.contrast_results_dict)
        if request is None:
            return
@@ -200,6 +200,12 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
                target_chroma = params.get("target_chroma", "hbo")
                threshold_topo = params.get("threshold_topo", False)
                selected_roi_maps = {
                    fp: self.roi_channel_map_dict[fp]
                    for fp in (file_paths_a + file_paths_b)
                    if fp in self.roi_channel_map_dict
                }
                run_cross_group_second_level_analysis(
                    df_roi_all=df_ind_combined,  # Individual stats dataframe
                    file_paths_a=file_paths_a,
@@ -213,7 +219,7 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
                    correction_method=correction_method,
                    target_chroma=target_chroma,
                    selected_event=selected_event,
-                    roi_config=self.json_location,
+                    roi_channel_maps=selected_roi_maps,
                    threshold_topo=threshold_topo  # Shows the raw difference map (Unthresholded)
                )
            elif idx == 1:
@@ -318,11 +324,26 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
                    print("No contrast data found for one or both groups.")
                    continue
                roi_maps_a = {
                    fp: self.roi_channel_map_dict[fp]
                    for fp in file_paths_a
                    if fp in self.roi_channel_map_dict
                }
                roi_maps_b = {
                    fp: self.roi_channel_map_dict[fp]
                    for fp in file_paths_b
                    if fp in self.roi_channel_map_dict
                }
                if not roi_maps_a or not roi_maps_b:
                    print("No channel-to-ROI mapping available for one or both groups.")
                    continue
                run_cross_group_contrast_analysis(
                    df_contrasts_a=df_contrasts_a,
                    df_contrasts_b=df_contrasts_b,
                    contrast_name=contrast_name,
-                    roi_json_path=self.json_location,
+                    roi_channel_maps_a=roi_maps_a,
                    roi_channel_maps_b=roi_maps_b,
                    group_a_name=self.group_a_dropdown.currentText(),
                    group_b_name=self.group_b_dropdown.currentText(),
                    target_chroma=target_chroma,
@@ -33,6 +33,7 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
        design_matrix_dict: dict[str, DataFrame],
        contrast_results_dict: dict[str, dict[str, Any]],
        group_dict: dict[str, str],
        config_dict: dict[str, str],
    ) -> None:
        super().__init__("ExportToCSV")
@@ -43,8 +44,9 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
        # self.design_matrix = design_matrix_dict
        # self.contrast_results_dict = contrast_results_dict
        # self.group = group_dict
        self.config_dict = config_dict
-        self.setup_csv_ui(["0 (Export Data to CSV)", "1 (CSV for SPARKS)",])
+        self.setup_csv_ui(["0 (Export Data to CSV)", "1 (CSV for SPARKS)", "2 (Export Configuration to CSV)", "3 (Paragraph of Configuration)"])
    def process_request(self):
@@ -91,10 +93,26 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
                            success_count += 1
                    elif idx == 1:
-                            # SPARKS Export
+                        # SPARKS Export
-                            save_path = os.path.join(output_dir, f"{base_filename}_sparks.csv")
+                        save_path = os.path.join(output_dir, f"{base_filename}_sparks.csv")
-                            sparks_csv_export(haemo_obj, save_path)
+                        sparks_csv_export(haemo_obj, save_path)
-                            success_count += 1
+                        success_count += 1
                    elif idx == 2:
                        formatted_data = {
                            os.path.basename(path.replace("\\", "/")): inner_dict
                            for path, inner_dict in self.config_dict.items()
                        }
                        df = DataFrame(formatted_data)
                        df.index.name = "Parameter"
                        save_path = os.path.join(output_dir, f"{APP_NAME}_configuration.csv")
                        df.to_csv(save_path)
                        success_count += 1
                    elif idx == 3:
                        first_params = next(iter(self.config_dict.values()))
                        magic_string = self.gen_magic_str(first_params)
                        self.placeholder_label.setText(magic_string)
                    else:
                        print(f"No method defined for index {idx}")
@@ -114,3 +132,65 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
            #         caller="Video Alignment Tool"
            #     )
            #     win.show()
    def gen_magic_str(self, all_params):
            magic_str = "To start, the data was loaded into the application. "
            if all_params['DOWNSAMPLE']:
                magic_str += f"The data was downsampled to {all_params['DOWNSAMPLE_FREQUENCY']}hz. "
            else:
                magic_str += "The data was not downsampled and was retained at its original sampling frequency. "
            if all_params['TRIM']:
                magic_str += f"The data was then trimmed to only keep {all_params['SECONDS_TO_KEEP']} seconds before the first event, as the earlier data with no events would not be needed. "
            else:
                magic_str += "The data was not trimmed and was retained at its original length. "
            if all_params['OPTODE_PLACEMENT']:
                magic_str += f"A visualization check of the optode locations in 3D space was performed to ensure that they were at the correct location. "
            if all_params['SHORT_CHANNELS']:
                magic_str += f"A short channel(s) was specified with the maximum length of a short channel being {all_params['SHORT_CHANNELS_THRESHOLD']} metres. Channels that were over this distance but under {all_params['LONG_CHANNELS_THRESHOLD']} metres were retained. "
            else:
                magic_str += f"No short channel was specified. Channels between the lengths of {all_params['SHORT_CHANNELS_THRESHOLD']} and {all_params['LONG_CHANNELS_THRESHOLD']} meters were used with all other channles being discarded. "
            if all_params['HEART_RATE']:
                magic_str += f"The heart rate of the participant was attempted to be calculated. {all_params['SECONDS_TO_STRIP_HR']} seconds were ignored from the start of the file to avoid motion artifacts. "
                magic_str += f"The heart rate had hard limits of {all_params['MAX_LOW_HR']} to {all_params['MAX_HIGH_HR']} and was smoothed across {all_params['SMOOTHING_WINDOW_HR']} samples. "
            else:
                magic_str += "The heart rate of the participants was not attempted to be calculated. "
            if all_params['SCI']:
                magic_str += f"The Scalp Coupling Index was calculated over {all_params['SCI_TIME_WINDOW']} second windows. The threshold value was {all_params['SCI_THRESHOLD']}. "
            else:
                magic_str += "Scalp Coupling Index was not used. "
            if all_params['SNR']:
                magic_str += f"The Signal to Noise Ratio was calculated. The threshold value was set to {all_params['SNR_THRESHOLD']}db. "
            else:
                magic_str += "The Signal to Noise Ratio was not used. "
            if all_params['PSP']:
                magic_str += f"Peak Spectral Power was calculated over {all_params['PSP_TIME_WINDOW']} second windows. The threshold value was {all_params['PSP_THRESHOLD']}. "
            else:
                magic_str += "Peak Spectral Power was not used. "
            if all_params['COEFF_VAR']:
                magic_str += f"The Coefficient of Variation was calculated. The threshold value was set to {all_params['COEFF_VAR_THRESHOLD']}. "
            else:
                magic_str += "The Coefficient of Variation was not used. "
            if all_params['MAD']:
                magic_str += f"Median Absolute Deviation was calculated. The threshold value was set to {all_params['MAD_THRESHOLD']}. "
            else:
                magic_str += "Median Absolute Deviation was not used. "
            if all_params['PSD_NOISE']:
                magic_str += f"Power Spectral Density Noise was calculated with a target frequency divisor of {all_params['TARGET_FREQ_DIV']} and a decibal limit of {all_params['DB_LIMIT']}. "
            else:
                magic_str += f"Power Spectral Density Noise was not used. "
            magic_str += "More coming soon."
            return magic_str
@@ -21,7 +21,7 @@ from mne.io.base import BaseRaw
 from flares import aggregate_fnirs_group_geometry, plot_fir_model_results, brain_3d_visualization
 from src.shared.flaresbasewidget import InterGroupUIMixin, FlaresBaseWidget
 from src.shared.shareddata import APP_NAME
-from mne.io import BaseRaw
+
 PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
    0: [
@@ -81,7 +81,6 @@ PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
 }
 class InterGroupBrainImageWidget(InterGroupUIMixin, FlaresBaseWidget):
    def __init__(
        self,
@@ -100,7 +99,7 @@ class InterGroupBrainImageWidget(InterGroupUIMixin, FlaresBaseWidget):
        self.df_ind_dict = df_ind_dict
        self.design_matrix_dict = design_matrix_dict
        self.contrast_results_dict = contrast_results_dict
-        # self.group_dict = group_dict
+        self.group_dict = group_dict
        self.setup_inter_group_ui(["0 (GLM Results)", "1 (Significance)", "2 (Brain Activity Visualization)",])
@@ -39,7 +39,6 @@ PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
 }
 class InterGroupFunctionalConnectivityWidget(InterGroupUIMixin, FlaresBaseWidget):
    def __init__(
        self,
@@ -157,7 +157,6 @@ DESCRIPTION = """0. ROI vs. Zero (run_roi_second_level_analysis)
 class InterGroupStatsWidget(InterGroupUIMixin, FlaresBaseWidget):
    def __init__(
        self, 
        haemo_dict: dict[str | Path, BaseRaw], 
@@ -165,8 +164,8 @@ class InterGroupStatsWidget(InterGroupUIMixin, FlaresBaseWidget):
        df_ind_dict: dict[str, DataFrame],
        design_matrix_dict: dict[str, DataFrame],
        contrast_results_dict: dict[str, dict[str, Any]],
        roi_channel_map_dict: dict[str, dict[str, str]],
        group_dict: dict[str, str],
        json_location: str | Path
    ) -> None:
        super().__init__("InterGroupStats")
@@ -176,14 +175,14 @@ class InterGroupStatsWidget(InterGroupUIMixin, FlaresBaseWidget):
        self.df_ind_dict = df_ind_dict
        self.design_matrix_dict = design_matrix_dict
        self.contrast_results_dict = contrast_results_dict
        self.roi_channel_map_dict = roi_channel_map_dict
        self.group_dict = group_dict
        self.json_location = json_location
        self.setup_inter_group_ui(["0 (ROI vs. Zero)", "1 (Paired ROI Contrast)", "2 (Joint Contrast, ROI-Aggregated)"], placeholder_text=DESCRIPTION)
    def process_request(self):
-        request = self.get_common_request_data(PARAMETERIZED_INDEXES, self.json_location, self.contrast_results_dict)
+        request = self.get_common_request_data(PARAMETERIZED_INDEXES, self.df_ind_dict, self.contrast_results_dict)
        if request is None:
            return
@@ -276,7 +275,6 @@ class InterGroupStatsWidget(InterGroupUIMixin, FlaresBaseWidget):
                    correction_method=correction_method,
                    target_chroma=target_chroma,
                    graph_bounds=graph_bounds if graph_bounds > 0.0 else None,
                    roi_config=self.json_location
                )
            elif idx == 1:
@@ -359,10 +357,19 @@ class InterGroupStatsWidget(InterGroupUIMixin, FlaresBaseWidget):
                df_contrasts = pd.concat(all_contrasts, ignore_index=True)
                selected_roi_maps = {
                    fp: self.roi_channel_map_dict[fp]
                    for fp in selected_file_paths
                    if fp in self.roi_channel_map_dict
                }
                if not selected_roi_maps:
                    print("No channel-to-ROI mapping available for selected participants.")
                    continue
                try:
                    roi_theta = aggregate_channel_contrasts_to_roi(
                        df_contrasts,
-                        roi_json_path=self.json_location,
+                        roi_channel_maps=selected_roi_maps,
                        weighted=weighted,
                    )
@@ -87,7 +87,6 @@ PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
 }
 class ParticipantFunctionalConnectivityWidget(ParticipantUIMixin, FlaresBaseWidget):
    def __init__(
        self,
@@ -106,7 +105,6 @@ class ParticipantFunctionalConnectivityWidget(ParticipantUIMixin, FlaresBaseWidg
        self.setup_participant_ui(["0 (Spectral Connectivity Epochs)", "1 (Envelope Correlation)", "2 (Betas)", "3 (Spectral Connectivity Epochs)",])
    def process_request(self):
        request = self.get_common_request_data(PARAMETERIZED_INDEXES)
        if request is None:
@@ -138,7 +136,6 @@ class ParticipantFunctionalConnectivityWidget(ParticipantUIMixin, FlaresBaseWidg
                    print(f"Skipping {self.participant_map[file_path]}: Event '{selected_event}' not found.")
                    continue
            for idx in selected_indexes:
                if idx == 0:
@@ -85,7 +85,6 @@ class ParticipantImageViewerWidget(FlaresBaseWidget):
        self.showMaximized()
    def show_selected_images(self):
        # Clear previous images
        while self.grid_layout.count():
@@ -13,7 +13,7 @@ import sys
 import platform
-CURRENT_VERSION = "1.5.0"
+CURRENT_VERSION = "1.6.0"
 APP_NAME = "flares"
 APP_NAME_EXPANDED = "fNIRS Lightweight Analysis, Research, & Evaluation Suite"
 API_URL = f"https://git.research.dezeeuw.ca/api/v1/repos/tyler/{APP_NAME}/releases"
@@ -55,6 +55,20 @@ PIPELINE_STAGES = [
 ]
 DATA_SCHEMA = [
    {"key": "raw_haemo_dict",        "help": "Dict[file_path, MNE RawArray]: Haemodynamic raw data"},
    {"key": "epochs_dict",           "help": "Dict[file_path, MNE Epochs]: Time-locked epoch data"},
    {"key": "cha_dict",              "help": "Dict[file_path, DataFrame]: Channel analysis results"},
    {"key": "df_ind_dict",           "help": "Dict[file_path, DataFrame]: Individual-level data/ROI results"},
    {"key": "design_matrix_dict",    "help": "Dict[file_path, DataFrame]: GLM design matrices"},
    {"key": "config_dict",           "help": "Dict[file_path, dict]: Processing configuration parameters"},
    {"key": "fig_bytes_dict",        "help": "Dict[file_path, dict]: Serialized figure data"},
    {"key": "contrast_results_dict", "help": "Dict[file_path, dict]: Calculated contrast statistical results"},
    {"key": "roi_channel_map_dict",  "help": "Dict[file_path, dict]: Calculated contrast statistical results"},
    {"key": "valid_dict",            "help": "Dict[file_path, bool]: Boolean validity status per file"}
 ]
 def resource_path(relative_path: str) -> str:
    """
    Get absolute path to resource regardless of running directly or packaged using PyInstaller
@@ -7,11 +7,13 @@ Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 # External library imports
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel
 from PySide6.QtCore import Qt
 from src.shared.shareddata import APP_NAME, APP_NAME_EXPANDED, CURRENT_VERSION
 class AboutWindow(QWidget):
    """
    Simple About window displaying basic application information.
@@ -7,16 +7,38 @@ Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 # Built-in imports
 from typing import Any, Callable
 # External library imports
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QTextEdit, QLineEdit
-from PySide6.QtCore import Qt
+from PySide6.QtCore import Qt, QThread, Signal
 from file_ext_registration import register_file_association, is_windows_admin
 from src.shared.shareddata import API_URL, API_URL_SECONDARY, APP_NAME, CURRENT_VERSION, PLATFORM_NAME
 from src.window.about import AboutWindow
 from updater import UpdateManager
 class _AssocWorker(QThread):
    """
    Runs register_file_association() off the UI thread. Only actually
    needed for the force_admin=True path, since that blocks on
    WaitForSingleObject while the UAC prompt is up and the elevated
    child process runs — which would otherwise freeze the terminal
    window. Used for the non-elevated path too for consistency.
    """
    result_ready = Signal(bool, str)
    def __init__(self, force_admin: bool, parent: QWidget | None = None) -> None:
        super().__init__(parent)
        self._force_admin = force_admin
    def run(self) -> None:
        ok, msg = register_file_association(force_admin=self._force_admin)
        self.result_ready.emit(ok, msg)
 class TerminalWindow(QWidget):
    def __init__(self, parent: QWidget | None = None) -> None:
        super().__init__(parent, Qt.WindowType.Window)
@@ -38,9 +60,13 @@ class TerminalWindow(QWidget):
            "help": self.cmd_help,
            "version": self.cmd_version,
            "about": self.cmd_about,
            "assoc": self.cmd_assoc,
            "update": self.cmd_update,
        }
        self._pending_assoc_confirmation: bool = False
        self._assoc_worker: _AssocWorker | None = None
        self.output_area.append(f"Welcome to {APP_NAME.upper()}. You are running version {CURRENT_VERSION}.")
        self.output_area.append("Type 'help' for a list of available commands.\n")
@@ -52,6 +78,12 @@ class TerminalWindow(QWidget):
        self.input_line.clear()
        self.output_area.append(f"> {command_text}")
        if self._pending_assoc_confirmation:
            self._pending_assoc_confirmation = False
            self._handle_assoc_confirmation(command_text.strip().lower())
            return
        parts = command_text.strip().split()
        if not parts:
            return
@@ -102,3 +134,33 @@ class TerminalWindow(QWidget):
        self.updater.manual_check_for_updates()
        return "See status bar for update information."
    def cmd_assoc(self, *args: Any) -> str | None:
        # Non-Windows platforms don't have the admin/non-admin split —
        # just register directly.
        if PLATFORM_NAME != "windows" or is_windows_admin():
            self._run_assoc(force_admin=False)
            return None
        self._pending_assoc_confirmation = True
        return "Not running as admin. Register system-wide via UAC elevation? (y/n)"
    def _handle_assoc_confirmation(self, answer: str) -> None:
        if answer in ("y", "yes"):
            self._run_assoc(force_admin=True)
        elif answer in ("n", "no"):
            self._run_assoc(force_admin=False)
        else:
            self.output_area.append("Please answer 'y' or 'n'. Run 'assoc' again to retry.")
    def _run_assoc(self, force_admin: bool) -> None:
        if force_admin:
            self.output_area.append("Requesting elevation. Check for a UAC prompt...")
        self._assoc_worker = _AssocWorker(force_admin=force_admin, parent=self)
        self._assoc_worker.result_ready.connect(self._on_assoc_result)
        self._assoc_worker.start()
    def _on_assoc_result(self, ok: bool, msg: str) -> None:
        self.output_area.append(msg)
        self._assoc_worker = None
@@ -1,11 +1,13 @@
 """
 Filename: userguide.py
-Description: User guide for FLARES
+Description: User guide window
 Note: Compliant with pylance strict type checking
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 # External library imports
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel
 from PySide6.QtCore import Qt
@@ -24,7 +24,7 @@ from src.shared.shareddata import APP_NAME
 class ViewerLauncherWidget(QWidget):
-    def __init__(self, haemo_dict, epochs_dict, cha_dict, df_ind_dict, design_matrix_dict, config_dict, fig_bytes_dict, contrast_results_dict, folding_bypass, json_location):
+    def __init__(self, haemo_dict, epochs_dict, cha_dict, df_ind_dict, design_matrix_dict, config_dict, fig_bytes_dict, contrast_results_dict, roi_channel_map_dict, folding_bypass):
        super().__init__()
        self.setWindowTitle(f"Viewer Launcher - {APP_NAME.upper()}")
@@ -36,11 +36,11 @@ class ViewerLauncherWidget(QWidget):
            ("Participant Fold Channels Viewer", ParticipantFoldChannelsWidget, [haemo_dict, cha_dict], False),
            ("Participant Functional Connectivity Viewer [BETA]", ParticipantFunctionalConnectivityWidget, [haemo_dict, epochs_dict], True),
            ("Inter-Group Functional Connectivity Viewer [BETA]", InterGroupFunctionalConnectivityWidget, [haemo_dict, group_dict, config_dict], True),
-            ("Inter-Group Stats Viewer", InterGroupStatsWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, json_location], True),
+            ("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),
-            ("Cross-Group Stats Viewer", CrossGroupStatsWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, json_location], True),
+            ("Cross-Group Stats Viewer", CrossGroupStatsWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, roi_channel_map_dict, group_dict], True),
            ("Inter-Group Brain and Image Viewer", InterGroupBrainImageWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict], True),
            ("Cross-Group Brain and Image Viewer", CrossGroupBrainImageWidget, [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], True)
+            ("Export To CSV Viewer", ExportToCSVWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, config_dict], True)
        ]
        layout = QVBoxLayout(self)
@@ -1,18 +1,19 @@
 """
 Filename: welcome.py
-Description: Welcome dialog for FLARES
+Description: Welcome dialog window
 Note: Compliant with pylance strict type checking
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 # External library imports
 from PySide6.QtWidgets import QTextBrowser, QVBoxLayout, QLabel, QDialog, QHBoxLayout, QPushButton
 from PySide6.QtGui import QDesktopServices, QIcon
 from PySide6.QtCore import QUrl
 from PySide6.QtNetwork import QNetworkAccessManager, QNetworkRequest, QNetworkReply
-from src.shared.shareddata import APP_NAME, CURRENT_VERSION, CHANGELOG_URL, resource_path
+from src.shared.shareddata import APP_NAME, PLATFORM_NAME, CURRENT_VERSION, CHANGELOG_URL, resource_path
 class WelcomeDialog(QDialog):
@@ -27,8 +28,8 @@ class WelcomeDialog(QDialog):
        header_layout = QHBoxLayout()
        logo_label = QLabel(self)
-        # NOTE: might not work on mac and need the icns file
+        icon_ext = "icns" if PLATFORM_NAME == "darwin" else "ico"
-        logo_label.setPixmap(QIcon(resource_path("icons/main.ico")).pixmap(48, 48))
+        logo_label.setPixmap(QIcon(resource_path(f"icons/main.{icon_ext}")).pixmap(48, 48))
        if first:
            title_label = QLabel(f"<h2>Welcome to {APP_NAME.upper()}!</h2>", self)
        elif direct:
@@ -0,0 +1,41 @@
 """
 Filename: startup_args.py
 Description: Parses the startup arguments for the application
 Note: Compliant with pylance strict type checking
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 import os
 from dataclasses import dataclass
@dataclass
 class StartupArgs:
    finish_update: bool
    initial_file: str | None
 def parse_startup_args(argv: list[str]) -> StartupArgs:
    """
    Parses the command-line flags.
    Recognizes:
      --finish-update   set by the updater when relaunching post-update
      <path>            a project file to open on startup — the first
                         argument that doesn't start with '-', found
                         anywhere in argv rather than assumed to be at
                         a fixed position, so it survives regardless of
                         whether --finish-update precedes it.
    """
    finish_update = "--finish-update" in argv[1:]
    initial_file = None
    for arg in argv[1:]:
        if not arg.startswith("-"):
            initial_file = os.path.abspath(arg)
            break
    return StartupArgs(finish_update=finish_update, initial_file=initial_file)
@@ -416,12 +416,12 @@ def wait_for_process_to_exit(process_name, timeout=10):
    return False
-def finish_update_if_needed(platform_name, app_name, cfg_path):
+def finish_update_if_needed(platform_name, app_name, cfg_path, finish_update):
    """
    Completes a pending application update if '--finish-update' is present in the command-line arguments.
    """
-    if "--finish-update" in sys.argv:
+    if finish_update:
        print("Finishing update...")
        update_cfg = configparser.ConfigParser()
Author	SHA1	Message	Date
tyler	d2a595d0d0	release for 1.6.0	2026-08-10 18:00:22 -07:00
tyler	1e7fca49f2	fixes before release	2026-08-10 16:47:32 -07:00
tyler	074a0681b9	typos, standardization, and file association for project extensions	2026-08-06 02:00:36 -07:00
tyler	68e34484ee	late and too many typos to ignore	2026-08-03 22:39:57 -07:00
tyler	a0199737f5	improved project saving capabilities	2026-08-03 22:34:41 -07:00
tyler	0b52d2b0bc	more metadata	2026-08-03 00:46:18 -07:00
tyler	7c456e31e7	fix to stats when no json file is defined	2026-08-03 00:01:21 -07:00
tyler	61a9ea2f34	fix rare bug	2026-08-01 19:20:49 -07:00
tyler	defd4ec1c8	1.5.2 time	2026-07-31 01:17:29 -07:00
tyler	3e0d83ca9b	implement the new preferences in the backend	2026-07-30 16:15:33 -07:00
tyler	ebd13927e2	new preferences and bug fixes	2026-07-30 14:18:26 -07:00
tyler	f15a5d9433	improvements for 1.5.2	2026-07-29 17:20:23 -07:00
		`@@ -0,0 +1 @@`
							`<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M160-360v-80h400v80H160Zm0-160v-80h640v80H160Z"/></svg>`