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Code Issues 16 Pull Requests Actions Packages Projects Releases 22 Wiki Activity

fixes before release

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tyler
2026-08-10 16:47:32 -07:00
parent 074a0681b9
commit 1e7fca49f2
6 changed files with 35 additions and 21 deletions
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changelog.md
+5 -3
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@@ -5,7 +5,7 @@
- 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 to be percentage based (25%) instead of numerical based (6)
- 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
@@ -24,8 +24,10 @@
- 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 some popup windows would not properly display the application name when they would open
- Fixed instances of the word MacOS to now read macOS to match Apple branding
- Fixed welcom dialog application image not displaying correctly on macOS
- 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
flares.py
+9 -2
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@@ -1840,7 +1840,8 @@ def fold_channels(raw: BaseRaw, p_name: str, atlas: str='Brodmann', progress_que
channel_results = {}
step_idx = 0
for cidx, channel_name in enumerate(hbo_channel_names):
for channel_name in hbo_channel_names:
cidx = raw.ch_names.index(channel_name)
tbl = _source_detector_fold_table(
raw, cidx, reference_locations, fold_tbl, interpolate=True
)
@@ -2179,7 +2180,13 @@ def brain_3d_visualization(
def brain_landmarks_3d(raw_haemo: BaseRaw, show_optodes: Literal['sensors', 'labels', 'none', 'all'] = 'all', show_brodmann: bool = True) -> None:
def brain_landmarks_3d(raw_haemo: BaseRaw, show_optodes: Literal['sensors', 'labels', 'none', 'all'] = 'all', show_brodmann: bool = True, subjects_dir = None) -> None:
if subjects_dir is None:
subjects_dir = os.environ.get("SUBJECTS_DIR")
if subjects_dir is None:
subjects_dir = str(data_path()) + "/subjects" # type: ignore
os.environ["SUBJECTS_DIR"] = subjects_dir
brain = Brain("fsaverage", background="white", size=(800, 700)) # type: ignore
main.py
+14 -9
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@@ -19,7 +19,7 @@ from queue import Empty
from copy import deepcopy
from pathlib import Path
from datetime import datetime
from multiprocessing import Process, current_process, freeze_support, Queue
from multiprocessing import Process, current_process, freeze_support, Queue, set_start_method
# External library imports
import psutil
@@ -2038,7 +2038,7 @@ class MainApplication(QMainWindow):
msgbox.setWindowTitle(f"Warning - {APP_NAME.upper()}")
message = (
f"{APP_NAME.upper} has encountered an error processing the file {title}.<br><br>"
f"{APP_NAME.upper()} has encountered an error processing the file {title}.<br><br>"
"This error was likely due to incorrect parameters on the right side of the screen and not an error with your data. "
"Processing of the remaining files continues in the background and this participant will be ignored in the analysis. "
f"If you think the parameters on the right side are correct for your data, raise an issue <a href='https://git.research.dezeeuw.ca/tyler/{APP_NAME}/issues'>here</a>.<br><br>"
@@ -2449,6 +2449,7 @@ def exception_hook(exc_type, exc_value, exc_traceback):
show_critical_error(error_msg)
# Exit the app after user acknowledges
if getattr(sys, 'frozen', False):
sys.exit(1)
@@ -2459,22 +2460,25 @@ def show_critical_error(error_msg):
if PLATFORM_NAME == "darwin":
log_path = os.path.join(os.path.dirname(sys.executable), "../../../flares.log")
log_path2 = os.path.join(os.path.dirname(sys.executable), "../../../flares_error.log")
error_path = os.path.join(os.path.dirname(sys.executable), "../../../flares_error.log")
save_path = os.path.join(os.path.dirname(sys.executable), "../../../flares_autosave.flare")
else:
log_path = os.path.join(os.getcwd(), "flares.log")
log_path2 = os.path.join(os.getcwd(), "flares_error.log")
error_path = os.path.join(os.getcwd(), "flares_error.log")
save_path = os.path.join(os.getcwd(), "flares_autosave.flare")
shutil.copy(log_path, log_path2)
log_path2 = Path(log_path2).absolute().as_posix()
shutil.copy(log_path, error_path)
error_path = Path(error_path).absolute().as_posix()
autosave_path = Path(save_path).absolute().as_posix()
log_link = f"file:///{log_path2}"
error_link = f"file:///{error_path}"
autosave_link = f"file:///{autosave_path}"
window.save_project(True) #TODO: If the window is the one to crash, the file can't get saved. Could be fine as the window is what was storing the data to begin with?
try:
window.project_manager.save_project(True)
except:
pass
message = (
f"{APP_NAME.upper()} has encountered an unrecoverable error and needs to close.<br><br>"
@@ -2482,7 +2486,7 @@ def show_critical_error(error_msg):
"If the file was saved, it still may not be intact, openable, or contain the correct data. Use the autosave at your own discretion.<br><br>"
f"This unrecoverable error was due to an error with {APP_NAME.upper()} and not your data.<br>"
f"If this crash occured inside a [BETA] branch, it is likely to eventually be fixed.<br>"
f"Please raise an issue <a href='https://git.research.dezeeuw.ca/tyler/{APP_NAME}/issues'>here</a> and attach the error file located at <a href='{log_link}'>{log_path2}</a><br><br>"
f"Please raise an issue <a href='https://git.research.dezeeuw.ca/tyler/{APP_NAME}/issues'>here</a> and attach the error file located at <a href='{error_link}'>{error_path}</a><br><br>"
f"<pre>{error_msg}</pre>"
)
@@ -2583,6 +2587,7 @@ if __name__ == "__main__":
config_init()
freeze_support() # Required for PyInstaller + multiprocessing
set_start_method('spawn', force=True)
# Only run GUI in the main process
if current_process().name == 'MainProcess':
project_manager.py
+2 -2
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@@ -776,8 +776,8 @@ def extract_metadata_worker(file_name):
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 > 25:
snirf_info['Short Channels'] += "\n There are a lot of short channels. Optode distances are likely incorrect!"
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"
src/analysis/intergroupbrainimage.py
+1 -1
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@@ -99,7 +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)",])
src/shared/flaresbasewidget.py
+1 -1
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@@ -50,7 +50,7 @@ class ClickableLabel(QLabel):
def mousePressEvent(self, event):
viewer = QWidget()
viewer.setWindowTitle(f"Expanded View" - {APP_NAME.upper()})
viewer.setWindowTitle(f"Expanded View - {APP_NAME.upper()}")
layout = QVBoxLayout(viewer)
label = QLabel()
label.setPixmap(self._pixmap_full)