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Code Issues 28 Pull Requests Actions Packages Projects Releases 12 Wiki Activity

crash and documentation fixes

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tyler
2026-01-15 12:04:55 -08:00
parent 2ecd357aca
commit 9779a63a9c
3 changed files with 68 additions and 38 deletions
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4
changelog.md
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@@ -8,6 +8,10 @@
- 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 - 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 underlying deprecation warning
- Fixed an issue causing some overlay elements to not render on the brain for certain devices - 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
# Version 1.1.7 # Version 1.1.7

31
flares.py
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@@ -2578,7 +2578,10 @@ def plot_fir_model_results(df, raw_haemo, dm, selected_event, l_bound, u_bound):
dm_cols_activity = np.where([f"{selected_event}" in c for c in dm.columns])[0] dm_cols_activity = np.where([f"{selected_event}" in c for c in dm.columns])[0]
dm = dm[[dm.columns[i] for i in dm_cols_activity]] dm = dm[[dm.columns[i] for i in dm_cols_activity]]
lme = smf.mixedlm("theta ~ -1 + delay:TidyCond:Chroma", df, groups=df["ID"]).fit() try:
lme = smf.mixedlm("theta ~ -1 + delay:TidyCond:Chroma", df, groups=df["ID"]).fit()
except:
lme = smf.ols("theta ~ -1 + delay:TidyCond:Chroma", df, groups=df["ID"]).fit() # type: ignore
df_sum = statsmodels_to_results(lme) df_sum = statsmodels_to_results(lme)
df_sum["delay"] = [int(n) for n in df_sum["delay"]] df_sum["delay"] = [int(n) for n in df_sum["delay"]]
@@ -3516,21 +3519,21 @@ def process_participant(file_path, progress_callback=None):
if progress_callback: progress_callback(19) if progress_callback: progress_callback(19)
logger.info("19") logger.info("19")
# Step 16: Plot GLM results # Step 20: Generate GLM Results
fig_glm_result = plot_glm_results(file_path, raw_haemo, glm_est, design_matrix) fig_glm_result = plot_glm_results(file_path, raw_haemo, glm_est, design_matrix)
for name, fig in fig_glm_result: for name, fig in fig_glm_result:
fig_individual[f"GLM {name}"] = fig fig_individual[f"GLM {name}"] = fig
if progress_callback: progress_callback(21) if progress_callback: progress_callback(20)
logger.info("21") logger.info("20")
# Step 17: Plot channel significance # Step 21: Generate Channel Significance
fig_significance = individual_significance(raw_haemo, glm_est) fig_significance = individual_significance(raw_haemo, glm_est)
for name, fig in fig_significance: for name, fig in fig_significance:
fig_individual[f"Significance {name}"] = fig fig_individual[f"Significance {name}"] = fig
if progress_callback: progress_callback(22) if progress_callback: progress_callback(21)
logger.info("22") logger.info("21")
# Step 18: cha, con, roi # Step 22: Generate Channel, Region of Interest, and Contrast Results
cha = glm_est.to_dataframe() cha = glm_est.to_dataframe()
# HACK: Comment out line 588 (self._renderer.show()) in _brain.py from MNE # HACK: Comment out line 588 (self._renderer.show()) in _brain.py from MNE
@@ -3583,10 +3586,10 @@ def process_participant(file_path, progress_callback=None):
contrast_dict[condition] = contrast_vector contrast_dict[condition] = contrast_vector
if progress_callback: progress_callback(23) if progress_callback: progress_callback(22)
logger.info("23") logger.info("22")
# Compute contrast results # Step 23: Compute Contrast Results
contrast_results = {} contrast_results = {}
for cond, contrast_vector in contrast_dict.items(): for cond, contrast_vector in contrast_dict.items():
@@ -3597,10 +3600,10 @@ def process_participant(file_path, progress_callback=None):
cha["ID"] = file_path cha["ID"] = file_path
if progress_callback: progress_callback(24) if progress_callback: progress_callback(23)
logger.info("24") logger.info("23")
# Step 24: Finishing Up
fig_bytes = convert_fig_dict_to_png_bytes(fig_individual) fig_bytes = convert_fig_dict_to_png_bytes(fig_individual)
sanitize_paths_for_pickle(raw_haemo, epochs) sanitize_paths_for_pickle(raw_haemo, epochs)

71
main.py
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@@ -498,29 +498,38 @@ class UserGuideWindow(QWidget):
layout = QVBoxLayout() layout = QVBoxLayout()
label = QLabel("Progress Bar Stages:", self) label = QLabel("Progress Bar Stages:", self)
label2 = QLabel("Stage 1: Load the snirf file\n" label2 = QLabel("Stage 1: Preprocessing\n"
"Stage 2: Check the optode positions\n" "Stage 2: Trimming\n"
"Stage 12: Get Short/Long Channels\n" "Stage 3: Verify Optode Placement\n"
"Stage 3: Scalp Coupling Index\n" "Stage 4: Short/Long Cannels\n"
"Stage 4: Signal to Noise Ratio\n" "Stage 5: Heart Rate\n"
"Stage 5: Peak Spectral Power\n" "Stage 6: Scalp Coupling Index\n"
"Stage 6: Identify bad channels\n" "Stage 7: Signal to Noise Ratio\n"
"Stage 7: Interpolate bad channels\n" "Stage 8: Peak Spectral Power\n"
"Stage 8: Optical Density\n" "Stage 9: Bad Channels Handling\n"
"Stage 9: Temporal Derivative Distribution Repair\n" "Stage 10: Optical Density\n"
"Stage 10: Beer Lambert Law\n" "Stage 11: Temporal Derivative Distribution Repair Filtering\n"
"Stage 11: Heart Rate Filtering\n" "Stage 12: Wavelet Filtering\n"
"Stage 13: Calculate Events from Annotations\n" "Stage 13: Haemoglobin Concentration\n"
"Stage 14: Epoch Calculations\n" "Stage 14: Enhance Negative Correlation\n"
"Stage 15: Design Matrix\n" "Stage 15: Filter\n"
"Stage 16: General Linear Model\n" "Stage 16: Extracting Events\n"
"Stage 17: Generate Plots from the GLM\n" "Stage 17: Epoch Calculations\n"
"Stage 18: Individual Significance\n" "Stage 18: Design Matrix\n"
"Stage 19: Channel, Region of Interest, and Contrast Results\n" "Stage 19: General Linear Model\n"
"Stage 20: Image Conversion\n", self) "Stage 20: Generate GLM Results\n"
"Stage 21: Generate Channel Significance\n"
"Stage 22: Generate Channel, Region of Interest, and Contrast Results\n"
"Stage 23: Compute Contrast Results\n"
"Stage 24: Finishing Up\n", self)
label3 = QLabel("For more information, visit the Git wiki page <a href='https://git.research.dezeeuw.ca/tyler/flares/wiki'>here</a>.", self)
label3.setTextFormat(Qt.TextFormat.RichText)
label3.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
label3.setOpenExternalLinks(True)
layout.addWidget(label) layout.addWidget(label)
layout.addWidget(label2) layout.addWidget(label2)
layout.addWidget(label3)
self.setLayout(layout) self.setLayout(layout)
@@ -1244,7 +1253,7 @@ class ProgressBubble(QWidget):
self.progress_layout = QHBoxLayout() self.progress_layout = QHBoxLayout()
self.rects = [] self.rects = []
for _ in range(25): for _ in range(24):
rect = QFrame() rect = QFrame()
rect.setFixedSize(10, 18) rect.setFixedSize(10, 18)
rect.setStyleSheet("background-color: white; border: 1px solid gray;") rect.setStyleSheet("background-color: white; border: 1px solid gray;")
@@ -2445,9 +2454,23 @@ class ParticipantFoldChannelsWidget(QWidget):
for idx in selected_indexes: for idx in selected_indexes:
if idx == 0: if idx == 0:
try:
flares.fold_channels(haemo_obj) flares.fold_channels(haemo_obj)
except:
msg_box = QMessageBox()
msg_box.setIcon(QMessageBox.Icon.Critical)
msg_box.setWindowTitle("Something went wrong!")
message = (
"Unable to locate the fOLD files!<br><br>"
f"Please download the 'Supplementary' folder from <a href='https://github.com/nirx/fOLD-public'>here</a>. "
"Once the folder is downloaded, place it in C:/Users/your username/mne_data/fOLD/fOLD-public-master/Supplementary.<br><br>"
"If you are not using Windows, please go to the FLARES Git page for more information."
)
msg_box.setTextFormat(Qt.TextFormat.RichText)
msg_box.setText(message)
msg_box.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
msg_box.setStandardButtons(QMessageBox.StandardButton.Ok)
msg_box.exec()
else: else:
print(f"No method defined for index {idx}") print(f"No method defined for index {idx}")