group fc

.gitignore

@@ -174,3 +174,8 @@ cython_debug/
 # PyPI configuration file
 .pypirc
 
+/individual_images
+*.xlsx
+*.csv
+*.snirf
+*.json

changelog.md

@@ -0,0 +1,163 @@
+# Version 1.2.1
+
+- Added a requirements.txt file to ensure compatibility
+- Added new options 'Missing Events Bypass' and 'Analysis Clearing Bypass' to the Preferences Menu
+- Missing Events Bypass allows comparing events in the Group Viewers even if not all participants in the group have the event present. Fixes [Issue 28](https://git.research.dezeeuw.ca/tyler/flares/issues/28)
+- Clicking Process after an analysis has been performed will now clear the existing analysis by default with a popup warning that the analysis will be cleared
+- Analysis Clearing Bypass will prevent the popup and will not clear the existing analysis data. Fixes [Issue 41](https://git.research.dezeeuw.ca/tyler/flares/issues/41)
+- Clicking 'Clear' should now actually properly clear all data. Hopefully fixes [Issue 9](https://git.research.dezeeuw.ca/tyler/flares/issues/9) for good
+- Setting SHORT_CHANNEL to False will now grey out SHORT_CHANNEL_REGRESSION, as it is impossible to regress what does not exist. Sets SHORT_CHANNEL_REGRESSION to False under the hood when it is greyed out regardless of what is displayed. Fixes [Issue 47](https://git.research.dezeeuw.ca/tyler/flares/issues/47)
+- Projects can now be saves if files have different parent folders. Fixes [Issue 48](https://git.research.dezeeuw.ca/tyler/flares/issues/48)
+- It is no longer possible to attempt a save before any data has been processed. A popup will now display if a save is attempted with nothing to save
+- Fixed a bug where LONG_CHANNEL_THRESH was not being applied in the processing steps
+- Added a new option in the Analysis window for Group Functional Connectivity. Implements [Issue 50](https://git.research.dezeeuw.ca/tyler/flares/issues/50)
+- Group Functional connectivity is still in development and the results should currently be taken with a grain of salt
+- A warning is displayed when entering the Group Functional Connectivity Viewer disclosing this
+- 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 bug where the secondary download server would never get contacted if the primary failed
+- Automatic downloads will now ignore prerelease versions. Fixes [Issue 52](https://git.research.dezeeuw.ca/tyler/flares/issues/52)
+
+
+# Version 1.2.0
+
+- This is a save-breaking release due to a new save file format. Please update your project files to ensure compatibility. Fixes [Issue 30](https://git.research.dezeeuw.ca/tyler/flares/issues/30)
+- Added new parameters to the right side of the screen
+- 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
+- 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
+- Fixed an underlying deprecation warning
+- Fixed an issue causing some overlay elements to not render on the brain for certain devices
+- Fixed a crash when rendering some Inter-Group images with only one participant in a group
+- 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
+- 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)
+- 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
+- Two preferences have been added allowing to bypass the warning of 2D data detected and save files being from previous, potentially breaking versions
+- Fixed a typo when saving a CSV that stated a SNIRF was being saved
+- Loading a save file now properly restores AGE, GENDER, and GROUP. Fixes [Issue 40](https://git.research.dezeeuw.ca/tyler/flares/issues/40)
+- Saving a project now no longer makes the main window go not responding. Fixes [Issue 43](https://git.research.dezeeuw.ca/tyler/flares/issues/43)
+- Memory usage should no longer grow when generating lots of images multiple times. Fixes [Issue 36](https://git.research.dezeeuw.ca/tyler/flares/issues/36)
+- Added a new option in the Analysis window for Functional Connectivity
+- Functional connectivity is still in development and the results should currently be taken with a grain of salt
+- A warning is displayed when entering the Functional Connectivity Viewer disclosing this
+
+
+# Version 1.1.7
+
+- Fixed a bug where having both a L_FREQ and H_FREQ would cause only the L_FREQ to be used
+- Changed the default H_FREQ from 0.7 to 0.3
+- Added a PSD graph, along with 2 heart rate images to the individual participant viewer
+- The PSD graph is used to help calculate the heart rate, whereas the other 2 are currently just for show
+- SCI is now done using a .6hz window around the calculated heart rate compared to a window around an average heart rate
+- Fixed an issue with some epochs figures not showing under the participant analysis
+- Removed SECONDS_TO_STRIP from the preprocessing options
+- Added new parameters to the right side of the screen
+- These parameters include TRIM, SECONDS_TO_KEEP, OPTODE_PLACEMENT, HEART_RATE, WAVELET, IQR, WAVELET_TYPE, WAVELET_LEVEL, ENHANCE_NEGATIVE_CORRELATION, SHORT_CHANNEL_THRESH, LONG_CHANNEL_THRESH, and DRIFT_MODEL
+- Changed number of rectangles in the progress bar to 25 to account for the new options
+
+
+# Version 1.1.6
+
+- Fixed Process button from appearing when no files are selected
+- Fixed a bug that would cause an instant child process crash on Windows
+- Added L_FREQ and H_FREQ parameters for more user control over low and high pass filtering
+
+
+# Version 1.1.5
+
+- 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
+- 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 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
+- Updated some tooltips to provide better, more accurate information
+- Added details about the processing steps and their order into the user guide
+- Changed the default bandpass filtering parameters
+
+
+# Version 1.1.4
+
+- Fixed some display text to now display the correct information
+- A new option under Analysis has been added to export the data from a specified participant as a csv file. Fixes [Issue 19](https://git.research.dezeeuw.ca/tyler/flares/issues/19), [Issue 27](https://git.research.dezeeuw.ca/tyler/flares/issues/27)
+- Added 2 new parameters - TIME_WINDOW_START and TIME_WINDOW_END. Fixes [Issue 29](https://git.research.dezeeuw.ca/tyler/flares/issues/29)
+- These parameters affect the visualization of the significance and contrast images but do not change the total time modeled underneath
+- Fixed the duration of annotations edited from a BORIS file from 0 seconds to their proper duration
+- Added the annotation information to each participant under their "File information" window
+- Fixed Macs not being able to save snirfs attempting to be updated from BORIS files, and in general the updated files not respecting the path chosen by the user
+
+
+# Version 1.1.3
+
+- Added back the ability to use the fOLD dataset. Fixes [Issue 23](https://git.research.dezeeuw.ca/tyler/flares/issues/23)
+- 5th option has been added under Analysis to get to fOLD channels per participant
+- Added an option to cancel the running process. Fixes [Issue 15](https://git.research.dezeeuw.ca/tyler/flares/issues/15)
+- Prevented graph images from showing when participants are being processed. Fixes [Issue 24](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
+- Allow the option to remove all events of a type from all loaded snirfs. Fixes [Issue 25](https://git.research.dezeeuw.ca/tyler/flares/issues/25)
+- Added new icons in the menu bar
+- Added a terminal to interact with the app in a more command-like form
+- Currently the terminal has no functionality but some features for batch operations will be coming soon!
+- Inter-Group viewer now has the option to visualize the average response on the brain of all participants in the group. Fixes [Issue 26](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
+- Fixed the description under "Update events in snirf file..."
+
+
+# Version 1.1.2
+
+- Fixed incorrect colormaps being applied
+- Added functionality to utilize external event markers from a file. Fixes [Issue 6](https://git.research.dezeeuw.ca/tyler/flares/issues/6)
+
+
+# Version 1.1.1
+
+- Fixed the number of rectangles in the progress bar to 19
+- Fixed a crash when attempting to load a brain image on Windows
+- Removed hardcoded event annotations. Fixes [Issue 16](https://git.research.dezeeuw.ca/tyler/flares/issues/16)
+
+
+# Version 1.1.0
+
+- Revamped the Analysis window
+- 4 Options of Participant, Participant Brain, Inter-Group, and Cross Group Brain are available.
+- Customization is present to query different participants, images, events, brains, etc.
+- Removed preprocessing options and reorganized their order to correlate with the actual order.
+- Most preprocessing options removed will be coming back soon
+- Added a group option when clicking on a participant's file
+- If no group is specified, the participant will be added to the "Default" group
+- Added option to update the optode positions in a snirf file from the Options menu (F6)
+- Fixed [Issue 3](https://git.research.dezeeuw.ca/tyler/flares/issues/3), [Issue 5](https://git.research.dezeeuw.ca/tyler/flares/issues/5), [Issue 17](https://git.research.dezeeuw.ca/tyler/flares/issues/17), [Issue 21](https://git.research.dezeeuw.ca/tyler/flares/issues/21), [Issue 22](https://git.research.dezeeuw.ca/tyler/flares/issues/22)
+
+
+# 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.
+- 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.
+- Removed the process button from being available until a file or project is opened. Fixes [Issue 2](https://git.research.dezeeuw.ca/tyler/flares/issues/2).
+- Removed the option for PPF under Haemoglobin Concentration as it is no longer used.
+- Added a new category in the options called Other
+- Added MAX_WORKERS to the Other category. This is how many files should be processed at once. Fixes [Issue 13](https://git.research.dezeeuw.ca/tyler/flares/issues/13).
+- Added more information about the snirf file to be displayed when selected
+
+
+# Version 1.0.0
+
+- Initial release.

icons/folder_eye_24dp_1F1F1F.svg

@@ -0,0 +1 @@
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icons/remove_24dp_1F1F1F.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M200-440v-80h560v80H200Z"/></svg>

icons/terminal_24dp_1F1F1F.svg

@@ -0,0 +1 @@
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icons/upgrade_24dp_1F1F1F.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M280-160v-80h400v80H280Zm160-160v-327L336-544l-56-56 200-200 200 200-56 56-104-103v327h-80Z"/></svg>

mne/transforms.py

@@ -12,7 +12,7 @@ from pathlib import Path
 import numpy as np
 from scipy import linalg
 from scipy.spatial.distance import cdist
-from scipy.special import sph_harm
+from scipy.special import sph_harm_y
 
 from ._fiff.constants import FIFF
 from ._fiff.open import fiff_open

mne/viz/_3d.py

@@ -1025,7 +1025,7 @@ def _handle_sensor_types(meg, eeg, fnirs):
         fnirs=dict(channels="fnirs", pairs="fnirs_pairs"),
     )
     sensor_alpha = {
-        key: dict(meg_helmet=0.25, meg=0.25).get(key, 0.8)
+        key: dict(meg_helmet=0.25, meg=0.25).get(key, 1.0)
         for ch_dict in alpha_map.values()
         for key in ch_dict.values()
     }

mne/viz/backends/_pyvista.py

@@ -586,7 +586,7 @@ class _PyVistaRenderer(_AbstractRenderer):
                 color = None
             else:
                 scalars = None
-            tube = line.tube(radius, n_sides=self.tube_n_sides)
+            tube = line.tube(radius=radius, n_sides=self.tube_n_sides)
             actor = _add_mesh(
                 plotter=self.plotter,
                 mesh=tube,

version_main.txt

@@ -18,7 +18,7 @@ VSVersionInfo(
            StringStruct('FileDescription', 'FLARES main application'),
            StringStruct('FileVersion', '1.0.0.0'),
            StringStruct('InternalName', 'flares.exe'),
-           StringStruct('LegalCopyright', '© 2025 Tyler de Zeeuw'),
+           StringStruct('LegalCopyright', '© 2025-2026 Tyler de Zeeuw'),
            StringStruct('OriginalFilename', 'flares.exe'),
            StringStruct('ProductName', 'FLARES'),
            StringStruct('ProductVersion', '1.0.0.0')])

version_updater.txt

@@ -18,7 +18,7 @@ VSVersionInfo(
            StringStruct('FileDescription', 'FLARES updater application'),
            StringStruct('FileVersion', '1.0.0.0'),
            StringStruct('InternalName', 'main.exe'),
-           StringStruct('LegalCopyright', '© 2025 Tyler de Zeeuw'),
+           StringStruct('LegalCopyright', '© 2025-2026 Tyler de Zeeuw'),
            StringStruct('OriginalFilename', 'flares_updater.exe'),
            StringStruct('ProductName', 'FLARES Updater'),
            StringStruct('ProductVersion', '1.0.0.0')])