diff --git a/changelog.md b/changelog.md index 12d8cef..53705eb 100644 --- a/changelog.md +++ b/changelog.md @@ -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 diff --git a/flares.py b/flares.py index e902141..0baf805 100644 --- a/flares.py +++ b/flares.py @@ -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 ) @@ -2179,8 +2180,14 @@ 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 distances = source_detector_distances(raw_haemo.info) diff --git a/main.py b/main.py index d0a8701..f187b3d 100644 --- a/main.py +++ b/main.py @@ -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}.

" + f"{APP_NAME.upper()} has encountered an error processing the file {title}.

" "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 here.

" @@ -2449,8 +2449,9 @@ def exception_hook(exc_type, exc_value, exc_traceback): show_critical_error(error_msg) # Exit the app after user acknowledges - sys.exit(1) - + if getattr(sys, 'frozen', False): + sys.exit(1) + def show_critical_error(error_msg): msg_box = QMessageBox() @@ -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.

" @@ -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.

" f"This unrecoverable error was due to an error with {APP_NAME.upper()} and not your data.
" f"If this crash occured inside a [BETA] branch, it is likely to eventually be fixed.
" - f"Please raise an issue here and attach the error file located at {log_path2}

" + f"Please raise an issue here and attach the error file located at {error_path}

" f"
{error_msg}
" ) @@ -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': diff --git a/project_manager.py b/project_manager.py index 8d71a44..cdfb134 100644 --- a/project_manager.py +++ b/project_manager.py @@ -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" diff --git a/src/analysis/intergroupbrainimage.py b/src/analysis/intergroupbrainimage.py index 10e94b5..8d447e7 100644 --- a/src/analysis/intergroupbrainimage.py +++ b/src/analysis/intergroupbrainimage.py @@ -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)",]) diff --git a/src/shared/flaresbasewidget.py b/src/shared/flaresbasewidget.py index c9d8b4c..a455954 100644 --- a/src/shared/flaresbasewidget.py +++ b/src/shared/flaresbasewidget.py @@ -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)