release worthy?

.gitignore

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

changelog.md

@@ -1,7 +1,56 @@
+# 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
-- Fix for instand child process crash on Windows
+- 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
 
 

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')])