crash and documentation fixes
This commit is contained in:
@@ -8,6 +8,10 @@
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- 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
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- Fixed an underlying deprecation warning
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- Fixed an issue causing some overlay elements to not render on the brain for certain devices
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- Fixed a crash when rendering some Inter-Group images with only one participant in a group
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- Fixed a crash when attempting to fOLD channels without the fOLD dataset installed
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- Lowered the number of rectangles in the progress bar to 24 after combining some actions
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- Fixed the User Guide window to properly display information about the 24 stages and added a link to the Git wiki page
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# Version 1.1.7
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31
flares.py
31
flares.py
@@ -2578,7 +2578,10 @@ def plot_fir_model_results(df, raw_haemo, dm, selected_event, l_bound, u_bound):
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dm_cols_activity = np.where([f"{selected_event}" in c for c in dm.columns])[0]
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dm = dm[[dm.columns[i] for i in dm_cols_activity]]
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lme = smf.mixedlm("theta ~ -1 + delay:TidyCond:Chroma", df, groups=df["ID"]).fit()
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try:
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lme = smf.mixedlm("theta ~ -1 + delay:TidyCond:Chroma", df, groups=df["ID"]).fit()
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except:
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lme = smf.ols("theta ~ -1 + delay:TidyCond:Chroma", df, groups=df["ID"]).fit() # type: ignore
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df_sum = statsmodels_to_results(lme)
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df_sum["delay"] = [int(n) for n in df_sum["delay"]]
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@@ -3516,21 +3519,21 @@ def process_participant(file_path, progress_callback=None):
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if progress_callback: progress_callback(19)
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logger.info("19")
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# Step 16: Plot GLM results
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# Step 20: Generate GLM Results
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fig_glm_result = plot_glm_results(file_path, raw_haemo, glm_est, design_matrix)
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for name, fig in fig_glm_result:
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fig_individual[f"GLM {name}"] = fig
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if progress_callback: progress_callback(21)
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logger.info("21")
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if progress_callback: progress_callback(20)
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logger.info("20")
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# Step 17: Plot channel significance
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# Step 21: Generate Channel Significance
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fig_significance = individual_significance(raw_haemo, glm_est)
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for name, fig in fig_significance:
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fig_individual[f"Significance {name}"] = fig
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if progress_callback: progress_callback(22)
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logger.info("22")
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if progress_callback: progress_callback(21)
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logger.info("21")
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# Step 18: cha, con, roi
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# Step 22: Generate Channel, Region of Interest, and Contrast Results
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cha = glm_est.to_dataframe()
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# HACK: Comment out line 588 (self._renderer.show()) in _brain.py from MNE
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@@ -3583,10 +3586,10 @@ def process_participant(file_path, progress_callback=None):
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contrast_dict[condition] = contrast_vector
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if progress_callback: progress_callback(23)
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logger.info("23")
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if progress_callback: progress_callback(22)
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logger.info("22")
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# Compute contrast results
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# Step 23: Compute Contrast Results
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contrast_results = {}
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for cond, contrast_vector in contrast_dict.items():
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@@ -3597,10 +3600,10 @@ def process_participant(file_path, progress_callback=None):
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cha["ID"] = file_path
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if progress_callback: progress_callback(24)
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logger.info("24")
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if progress_callback: progress_callback(23)
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logger.info("23")
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# Step 24: Finishing Up
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fig_bytes = convert_fig_dict_to_png_bytes(fig_individual)
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sanitize_paths_for_pickle(raw_haemo, epochs)
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71
main.py
71
main.py
@@ -498,29 +498,38 @@ class UserGuideWindow(QWidget):
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layout = QVBoxLayout()
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label = QLabel("Progress Bar Stages:", self)
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label2 = QLabel("Stage 1: Load the snirf file\n"
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"Stage 2: Check the optode positions\n"
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"Stage 12: Get Short/Long Channels\n"
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"Stage 3: Scalp Coupling Index\n"
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"Stage 4: Signal to Noise Ratio\n"
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"Stage 5: Peak Spectral Power\n"
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"Stage 6: Identify bad channels\n"
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"Stage 7: Interpolate bad channels\n"
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"Stage 8: Optical Density\n"
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"Stage 9: Temporal Derivative Distribution Repair\n"
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"Stage 10: Beer Lambert Law\n"
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"Stage 11: Heart Rate Filtering\n"
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"Stage 13: Calculate Events from Annotations\n"
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"Stage 14: Epoch Calculations\n"
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"Stage 15: Design Matrix\n"
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"Stage 16: General Linear Model\n"
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"Stage 17: Generate Plots from the GLM\n"
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"Stage 18: Individual Significance\n"
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"Stage 19: Channel, Region of Interest, and Contrast Results\n"
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"Stage 20: Image Conversion\n", self)
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label2 = QLabel("Stage 1: Preprocessing\n"
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"Stage 2: Trimming\n"
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"Stage 3: Verify Optode Placement\n"
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"Stage 4: Short/Long Cannels\n"
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"Stage 5: Heart Rate\n"
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"Stage 6: Scalp Coupling Index\n"
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"Stage 7: Signal to Noise Ratio\n"
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"Stage 8: Peak Spectral Power\n"
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"Stage 9: Bad Channels Handling\n"
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"Stage 10: Optical Density\n"
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"Stage 11: Temporal Derivative Distribution Repair Filtering\n"
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"Stage 12: Wavelet Filtering\n"
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"Stage 13: Haemoglobin Concentration\n"
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"Stage 14: Enhance Negative Correlation\n"
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"Stage 15: Filter\n"
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"Stage 16: Extracting Events\n"
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"Stage 17: Epoch Calculations\n"
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"Stage 18: Design Matrix\n"
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"Stage 19: General Linear Model\n"
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"Stage 20: Generate GLM Results\n"
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"Stage 21: Generate Channel Significance\n"
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"Stage 22: Generate Channel, Region of Interest, and Contrast Results\n"
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"Stage 23: Compute Contrast Results\n"
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"Stage 24: Finishing Up\n", self)
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label3 = QLabel("For more information, visit the Git wiki page <a href='https://git.research.dezeeuw.ca/tyler/flares/wiki'>here</a>.", self)
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label3.setTextFormat(Qt.TextFormat.RichText)
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label3.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
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label3.setOpenExternalLinks(True)
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layout.addWidget(label)
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layout.addWidget(label2)
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layout.addWidget(label3)
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self.setLayout(layout)
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@@ -1244,7 +1253,7 @@ class ProgressBubble(QWidget):
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self.progress_layout = QHBoxLayout()
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self.rects = []
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for _ in range(25):
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for _ in range(24):
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rect = QFrame()
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rect.setFixedSize(10, 18)
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rect.setStyleSheet("background-color: white; border: 1px solid gray;")
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@@ -2445,9 +2454,23 @@ class ParticipantFoldChannelsWidget(QWidget):
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for idx in selected_indexes:
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if idx == 0:
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flares.fold_channels(haemo_obj)
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try:
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flares.fold_channels(haemo_obj)
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except:
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msg_box = QMessageBox()
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msg_box.setIcon(QMessageBox.Icon.Critical)
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msg_box.setWindowTitle("Something went wrong!")
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message = (
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"Unable to locate the fOLD files!<br><br>"
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f"Please download the 'Supplementary' folder from <a href='https://github.com/nirx/fOLD-public'>here</a>. "
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"Once the folder is downloaded, place it in C:/Users/your username/mne_data/fOLD/fOLD-public-master/Supplementary.<br><br>"
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"If you are not using Windows, please go to the FLARES Git page for more information."
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)
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msg_box.setTextFormat(Qt.TextFormat.RichText)
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msg_box.setText(message)
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msg_box.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
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msg_box.setStandardButtons(QMessageBox.StandardButton.Ok)
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msg_box.exec()
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else:
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print(f"No method defined for index {idx}")
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