fix to boris events

changelog.md

@@ -1,6 +1,22 @@
+# Version 1.1.1
+
+- Fixed the number of rectangles in the progress bar to 19
+- Fixed a crash when attempting to load a brain image on Windows
+- Removed hardcoded event annotations. Fixes [Issue 16](https://git.research.dezeeuw.ca/tyler/flares/issues/16)
+
+
 # Version 1.1.0
 
-- Changelog details coming soon
+- Revamped the Analysis window
+- 4 Options of Participant, Participant Brain, Inter-Group, and Cross Group Brain are available.
+- Customization is present to query different participants, images, events, brains, etc.
+- Removed preprocessing options and reorganized their order to correlate with the actual order.
+- Most preprocessing options removed will be coming back soon
+- Added a group option when clicking on a participant's file
+- If no group is specified, the participant will be added to the "Default" group
+- Added option to update the optode positions in a snirf file from the Options menu (F6)
+- Fixed [Issue 3](https://git.research.dezeeuw.ca/tyler/flares/issues/3), [Issue 4](https://git.research.dezeeuw.ca/tyler/flares/issues/4), [Issue 17](https://git.research.dezeeuw.ca/tyler/flares/issues/17), [Issue 21](https://git.research.dezeeuw.ca/tyler/flares/issues/21), [Issue 22](https://git.research.dezeeuw.ca/tyler/flares/issues/22)
+
 
 # Version 1.0.1
 

flares.py

@@ -48,6 +48,11 @@ from statsmodels.stats.multitest import multipletests
 from scipy import stats
 from scipy.spatial.distance import cdist
 
+# Backen visualization needed to be defined for pyinstaller
+import pyvistaqt # type: ignore
+# import vtkmodules.util.data_model
+# import vtkmodules.util.execution_model
+
 # External library imports for mne
 from mne import (
     EvokedArray, SourceEstimate, Info, Epochs, Label,
@@ -125,6 +130,8 @@ TDDR: bool
 
 ENHANCE_NEGATIVE_CORRELATION: bool
 
+SHORT_CHANNEL: bool
+
 VERBOSITY = True
 
 # FIXME: Shouldn't need each ordering - just order it before checking
@@ -171,6 +178,7 @@ REQUIRED_KEYS: dict[str, Any] = {
     "PSP_TIME_WINDOW": int,
     "PSP_THRESHOLD": float,
     
+    "SHORT_CHANNEL": bool,
     # "REJECT_PAIRS": bool,
     # "FORCE_DROP_ANNOTATIONS": list,
     # "FILTER_LOW_PASS": float,
@@ -1100,7 +1108,7 @@ def epochs_calculations(raw_haemo, events, event_dict):
     evokeds3 = []
     colors = []
     conditions = list(epochs.event_id.keys())
-    cmap = plt.cm.get_cmap("tab10", len(conditions))
+    cmap = plt.get_cmap("tab10", len(conditions))
 
     for idx, cond in enumerate(conditions):
         evoked = epochs[cond].average(picks="hbo")
@@ -1120,16 +1128,20 @@ def epochs_calculations(raw_haemo, events, event_dict):
     fig.legend(lines, conditions, loc="lower right")
     fig_epochs.append(("evoked_topo", help))  # Store with a unique name
 
-    # Evoked response for specific condition ("Reach")
+    unique_annotations = set(raw_haemo.annotations.description)
-    evoked_stim1 = epochs['Reach'].average()
 
-    fig_evoked_hbo = evoked_stim1.copy().pick(picks='hbo').plot(time_unit='s', show=False)
+    for cond in unique_annotations:
-    fig_evoked_hbr = evoked_stim1.copy().pick(picks='hbr').plot(time_unit='s', show=False)
-    
-    fig_epochs.append(("fig_evoked_hbo", fig_evoked_hbo))  # Store with a unique name
-    fig_epochs.append(("fig_evoked_hbr", fig_evoked_hbr))  # Store with a unique name
 
-    print("Evoked HbO peak amplitude:", evoked_stim1.copy().pick(picks='hbo').data.max())
+        # Evoked response for specific condition ("Activity")
+        evoked_stim1 = epochs[cond].average()
+
+        fig_evoked_hbo = evoked_stim1.copy().pick(picks='hbo').plot(time_unit='s', show=False)
+        fig_evoked_hbr = evoked_stim1.copy().pick(picks='hbr').plot(time_unit='s', show=False)
+        
+        fig_epochs.append((f"fig_evoked_hbo_{cond}", fig_evoked_hbo))  # Store with a unique name
+        fig_epochs.append((f"fig_evoked_hbr_{cond}", fig_evoked_hbr))  # Store with a unique name
+
+        print("Evoked HbO peak amplitude:", evoked_stim1.copy().pick(picks='hbo').data.max())
 
     evokeds = {}
     for condition in epochs2.event_id:
@@ -1200,26 +1212,36 @@ def epochs_calculations(raw_haemo, events, event_dict):
 
 
 
-
-
 def make_design_matrix(raw_haemo, short_chans):
 
     raw_haemo.resample(1, npad="auto")
-    short_chans.resample(1)
     raw_haemo._data = raw_haemo._data * 1e6
     # 2) Create design matrix
-    design_matrix = make_first_level_design_matrix(
+    if SHORT_CHANNEL:
-        raw=raw_haemo,
+        short_chans.resample(1)
-        hrf_model='fir',
+        design_matrix = make_first_level_design_matrix(
-        stim_dur=0.5,
+            raw=raw_haemo,
-        fir_delays=range(15),
+            hrf_model='fir',
-        drift_model='cosine',
+            stim_dur=0.5,
-        high_pass=0.01,
+            fir_delays=range(15),
-        oversampling=1,
+            drift_model='cosine',
-        min_onset=-125,
+            high_pass=0.01,
-        add_regs=short_chans.get_data().T,
+            oversampling=1,
-        add_reg_names=short_chans.ch_names
+            min_onset=-125,
-    )
+            add_regs=short_chans.get_data().T,
+            add_reg_names=short_chans.ch_names
+        )
+    else:
+        design_matrix = make_first_level_design_matrix(
+            raw=raw_haemo,
+            hrf_model='fir',
+            stim_dur=0.5,
+            fir_delays=range(15),
+            drift_model='cosine',
+            high_pass=0.01,
+            oversampling=1,
+            min_onset=-125,
+        )
 
     print(design_matrix.head())
     print(design_matrix.columns)
@@ -1232,10 +1254,6 @@ def make_design_matrix(raw_haemo, short_chans):
 
 
 
-
-
-
-
 def generate_montage_locations():
     """Get standard MNI montage locations in dataframe.
 
@@ -1600,153 +1618,158 @@ def fold_channels(raw: BaseRaw) -> None:
 
 def individual_significance(raw_haemo, glm_est):
 
+    fig_individual_significances = []  # List to store figures
+
     # TODO: BAD!
     cha = glm_est.to_dataframe()
 
-    ch_summary = cha.query("Condition.str.startswith('Reach_delay_') and Chroma == 'hbo'", engine='python')
+    unique_annotations = set(raw_haemo.annotations.description)
 
-    print(ch_summary.head())
+    for cond in unique_annotations:
 
-    channel_averages = ch_summary.groupby('ch_name')['theta'].mean().reset_index()
+        ch_summary = cha.query(f"Condition.str.startswith('{cond}_delay_') and Chroma == 'hbo'", engine='python')
-    print(channel_averages.head())
+
+        print(ch_summary.head())
+
+        channel_averages = ch_summary.groupby('ch_name')['theta'].mean().reset_index()
+        print(channel_averages.head())
 
 
-    reach_ch_summary = ch_summary.query(
+        activity_ch_summary = ch_summary.query(
-        "Chroma == 'hbo' and Condition.str.startswith('Reach_delay_')", engine='python'
+            f"Chroma == 'hbo' and Condition.str.startswith('{cond}_delay_')", engine='python'
-    )
+        )
 
-    # Function to correct p-values per channel
+        # Function to correct p-values per channel
-    def fdr_correct_per_channel(df):
+        def fdr_correct_per_channel(df):
-        df = df.copy()
+            df = df.copy()
-        df['pval_fdr'] = multipletests(df['p_value'], method='fdr_bh')[1]
+            df['pval_fdr'] = multipletests(df['p_value'], method='fdr_bh')[1]
-        return df
+            return df
 
-    # Apply FDR correction grouped by channel
+        # Apply FDR correction grouped by channel
-    corrected = reach_ch_summary.groupby("ch_name", group_keys=False).apply(fdr_correct_per_channel)
+        corrected = activity_ch_summary.groupby("ch_name", group_keys=False).apply(fdr_correct_per_channel)
 
-    # Determine which channels are significant across any delay
+        # Determine which channels are significant across any delay
-    sig_channels = (
+        sig_channels = (
-        corrected.groupby('ch_name')
+            corrected.groupby('ch_name')
-        .apply(lambda df: (df['pval_fdr'] < 0.05).any())
+            .apply(lambda df: (df['pval_fdr'] < 0.05).any())
-        .reset_index(name='significant')
+            .reset_index(name='significant')
-    )
+        )
 
-    # Merge with mean theta (optional for plotting)
+        # Merge with mean theta (optional for plotting)
-    mean_theta = reach_ch_summary.groupby('ch_name')['theta'].mean().reset_index()
+        mean_theta = activity_ch_summary.groupby('ch_name')['theta'].mean().reset_index()
-    sig_channels = sig_channels.merge(mean_theta, on='ch_name')
+        sig_channels = sig_channels.merge(mean_theta, on='ch_name')
-    print(sig_channels)
+        print(sig_channels)
 
 
-    # For example, take the minimum corrected p-value per channel
+        # For example, take the minimum corrected p-value per channel
-    summary_pvals = corrected.groupby('ch_name')['pval_fdr'].min().reset_index()
+        summary_pvals = corrected.groupby('ch_name')['pval_fdr'].min().reset_index()
-    print(summary_pvals)
+        print(summary_pvals)
 
 
-    def parse_ch_name(ch_name):
+        def parse_ch_name(ch_name):
-        # Extract numbers after S and D in names like 'S10_D5 hbo'
+            # Extract numbers after S and D in names like 'S10_D5 hbo'
-        match = re.match(r'S(\d+)_D(\d+)', ch_name)
+            match = re.match(r'S(\d+)_D(\d+)', ch_name)
-        if match:
+            if match:
-            return int(match.group(1)), int(match.group(2))
+                return int(match.group(1)), int(match.group(2))
-        else:
+            else:
-            return None, None
+                return None, None
 
 
-    min_pvals = corrected.groupby('ch_name')['pval_fdr'].min().reset_index()
+        min_pvals = corrected.groupby('ch_name')['pval_fdr'].min().reset_index()
 
-    # Merge the real p-values into sig_channels / avg_df
+        # Merge the real p-values into sig_channels / avg_df
-    avg_df = sig_channels.merge(min_pvals, on='ch_name')
+        avg_df = sig_channels.merge(min_pvals, on='ch_name')
 
-    # Rename columns for consistency
+        # Rename columns for consistency
-    avg_df = avg_df.rename(columns={'theta': 't_or_theta', 'pval_fdr': 'p_value'})
+        avg_df = avg_df.rename(columns={'theta': 't_or_theta', 'pval_fdr': 'p_value'})
 
-    # Add Source and Detector columns again
+        # Add Source and Detector columns again
-    avg_df['Source'], avg_df['Detector'] = zip(*avg_df['ch_name'].map(parse_ch_name))
+        avg_df['Source'], avg_df['Detector'] = zip(*avg_df['ch_name'].map(parse_ch_name))
 
-    # Keep relevant columns
+        # Keep relevant columns
-    avg_df = avg_df[['Source', 'Detector', 't_or_theta', 'p_value']].dropna()
+        avg_df = avg_df[['Source', 'Detector', 't_or_theta', 'p_value']].dropna()
 
-    ABS_SIGNIFICANCE_THETA_VALUE = 1
+        ABS_SIGNIFICANCE_THETA_VALUE = 1
-    ABS_SIGNIFICANCE_T_VALUE = 1
+        ABS_SIGNIFICANCE_T_VALUE = 1
-    P_THRESHOLD = 0.05
+        P_THRESHOLD = 0.05
-    SOURCE_DETECTOR_SEPARATOR = "_"
+        SOURCE_DETECTOR_SEPARATOR = "_"
-    Reach = "Reach"
 
+        t_or_theta = 'theta'
+        for _, row in avg_df.iterrows(): # type: ignore
+            print(f"Source {row['Source']} <-> Detector {row['Detector']}: "
+                f"Avg {t_or_theta}-value = {row['t_or_theta']:.3f}, Avg p-value = {row['p_value']:.3f}")
 
-    t_or_theta = 'theta'
+        # Extract the cource and detector positions from raw
-    for _, row in avg_df.iterrows(): # type: ignore
+        src_pos: dict[int, tuple[float, float]] = {}
-        print(f"Source {row['Source']} <-> Detector {row['Detector']}: "
+        det_pos: dict[int, tuple[float, float]] = {}
-            f"Avg {t_or_theta}-value = {row['t_or_theta']:.3f}, Avg p-value = {row['p_value']:.3f}")
+        for ch in getattr(raw_haemo, "info")["chs"]:
+            ch_name = ch['ch_name']
+            if not ch_name or not ch['loc'].any():
+                continue
+            parts = ch_name.split()[0]
+            src_str, det_str = parts.split(SOURCE_DETECTOR_SEPARATOR)
+            src_num = int(src_str[1:])
+            det_num = int(det_str[1:])
+            src_pos[src_num] = ch['loc'][3:5]
+            det_pos[det_num] = ch['loc'][6:8]
 
-    # Extract the cource and detector positions from raw
+        # Set up the plot
-    src_pos: dict[int, tuple[float, float]] = {}
+        fig, ax = plt.subplots(figsize=(8, 6)) # type: ignore
-    det_pos: dict[int, tuple[float, float]] = {}
-    for ch in getattr(raw_haemo, "info")["chs"]:
-        ch_name = ch['ch_name']
-        if not ch_name or not ch['loc'].any():
-            continue
-        parts = ch_name.split()[0]
-        src_str, det_str = parts.split(SOURCE_DETECTOR_SEPARATOR)
-        src_num = int(src_str[1:])
-        det_num = int(det_str[1:])
-        src_pos[src_num] = ch['loc'][3:5]
-        det_pos[det_num] = ch['loc'][6:8]
 
-    # Set up the plot
+        # Plot the sources
-    fig, ax = plt.subplots(figsize=(8, 6)) # type: ignore
+        for pos in src_pos.values():
+            ax.scatter(pos[0], pos[1], s=120, c='k', marker='o', edgecolors='white', linewidths=1, zorder=3) # type: ignore
 
-    # Plot the sources
+        # Plot the detectors
-    for pos in src_pos.values():
+        for pos in det_pos.values():
-        ax.scatter(pos[0], pos[1], s=120, c='k', marker='o', edgecolors='white', linewidths=1, zorder=3) # type: ignore
+            ax.scatter(pos[0], pos[1], s=120, c='k', marker='s', edgecolors='white', linewidths=1, zorder=3) # type: ignore
 
-    # Plot the detectors
+        # Ensure that the colors stay within the boundaries even if they are over or under the max/min values
-    for pos in det_pos.values():
+        if t_or_theta == 't':
-        ax.scatter(pos[0], pos[1], s=120, c='k', marker='s', edgecolors='white', linewidths=1, zorder=3) # type: ignore
+            norm = mcolors.Normalize(vmin=-ABS_SIGNIFICANCE_T_VALUE, vmax=ABS_SIGNIFICANCE_T_VALUE)
+        elif t_or_theta == 'theta':
+            norm = mcolors.Normalize(vmin=-ABS_SIGNIFICANCE_THETA_VALUE, vmax=ABS_SIGNIFICANCE_THETA_VALUE)
 
-    # Ensure that the colors stay within the boundaries even if they are over or under the max/min values
+        cmap: mcolors.Colormap = plt.get_cmap('seismic')
-    if t_or_theta == 't':
-        norm = mcolors.Normalize(vmin=-ABS_SIGNIFICANCE_T_VALUE, vmax=ABS_SIGNIFICANCE_T_VALUE)
-    elif t_or_theta == 'theta':
-        norm = mcolors.Normalize(vmin=-ABS_SIGNIFICANCE_THETA_VALUE, vmax=ABS_SIGNIFICANCE_THETA_VALUE)
 
-    cmap: mcolors.Colormap = plt.get_cmap('seismic')
+        # Plot connections with avg t-values
+        for row in avg_df.itertuples():
+            src: int = cast(int, row.Source) # type: ignore
+            det: int = cast(int, row.Detector)  # type: ignore
+            tval: float = cast(float, row.t_or_theta) # type: ignore
+            pval: float = cast(float, row.p_value) # type: ignore
+            
 
-    # Plot connections with avg t-values
+            if src in src_pos and det in det_pos:
-    for row in avg_df.itertuples():
+                x = [src_pos[src][0], det_pos[det][0]]
-        src: int = cast(int, row.Source) # type: ignore
+                y = [src_pos[src][1], det_pos[det][1]]
-        det: int = cast(int, row.Detector)  # type: ignore
+                style = '-' if pval <= P_THRESHOLD else '--'
-        tval: float = cast(float, row.t_or_theta) # type: ignore
+                ax.plot(x, y, linestyle=style, color=cmap(norm(tval)), linewidth=4, alpha=0.9, zorder=2) # type: ignore
-        pval: float = cast(float, row.p_value) # type: ignore
+
+        # Format the Colorbar
+        sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
+        sm.set_array([])
+        cbar = plt.colorbar(sm, ax=ax, shrink=0.85) # type: ignore
+        cbar.set_label(f'Average {cond} {t_or_theta} value (hbo)', fontsize=11) # type: ignore
+
+        # Formatting the subplots
+        ax.set_aspect('equal')
+        ax.set_title(f"Average {t_or_theta} values for {cond} (HbO)", fontsize=14) # type: ignore
+        ax.set_xlabel('X position (m)', fontsize=11) # type: ignore
+        ax.set_ylabel('Y position (m)', fontsize=11) # type: ignore
+        ax.grid(True, alpha=0.3) # type: ignore
+
+        # Set axis limits to be 1cm more than the optode positions
+        all_x = [pos[0] for pos in src_pos.values()] + [pos[0] for pos in det_pos.values()]
+        all_y = [pos[1] for pos in src_pos.values()] + [pos[1] for pos in det_pos.values()]
+        ax.set_xlim(min(all_x)-0.01, max(all_x)+0.01)
+        ax.set_ylim(min(all_y)-0.01, max(all_y)+0.01)
+
+        fig.tight_layout()
         
+        fig_individual_significances.append((f"Condition {cond}", fig))
 
-        if src in src_pos and det in det_pos:
+    return fig_individual_significances
-            x = [src_pos[src][0], det_pos[det][0]]
-            y = [src_pos[src][1], det_pos[det][1]]
-            style = '-' if pval <= P_THRESHOLD else '--'
-            ax.plot(x, y, linestyle=style, color=cmap(norm(tval)), linewidth=4, alpha=0.9, zorder=2) # type: ignore
-
-    # Format the Colorbar
-    sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
-    sm.set_array([])
-    cbar = plt.colorbar(sm, ax=ax, shrink=0.85) # type: ignore
-    cbar.set_label(f'Average {Reach} {t_or_theta} value (hbo)', fontsize=11) # type: ignore
-
-    # Formatting the subplots
-    ax.set_aspect('equal')
-    ax.set_title(f"Average {t_or_theta} values for {Reach} (HbO)", fontsize=14) # type: ignore
-    ax.set_xlabel('X position (m)', fontsize=11) # type: ignore
-    ax.set_ylabel('Y position (m)', fontsize=11) # type: ignore
-    ax.grid(True, alpha=0.3) # type: ignore
-
-    # Set axis limits to be 1cm more than the optode positions
-    all_x = [pos[0] for pos in src_pos.values()] + [pos[0] for pos in det_pos.values()]
-    all_y = [pos[1] for pos in src_pos.values()] + [pos[1] for pos in det_pos.values()]
-    ax.set_xlim(min(all_x)-0.01, max(all_x)+0.01)
-    ax.set_ylim(min(all_y)-0.01, max(all_y)+0.01)
-
-    fig.tight_layout()
-    
-
-    return fig
 
 # TODO: Hardcoded
 def group_significance(
@@ -1761,7 +1784,7 @@ def group_significance(
     Args:
         raw_haemo: Raw haemoglobin MNE object (used for optode positions)
         all_cha: DataFrame with columns including 'ID', 'Condition', 'p_value', 'theta', 'df', 'ch_name', 'Chroma'
-        condition: condition prefix, e.g., 'Reach'
+        condition: condition prefix, e.g., 'Activity'
         correction: p-value correction method ('fdr_bh' or 'bonferroni')
 
     Returns:
@@ -1919,7 +1942,12 @@ def group_significance(
 
 def plot_glm_results(file_path, raw_haemo, glm_est, design_matrix):
     
+    fig_glms = []  # List to store figures
+
     dm = design_matrix.copy()
+    logger.info(design_matrix.shape)
+    logger.info(design_matrix.columns)
+    logger.info(design_matrix.head())
 
     rois = dict(AllChannels=range(len(raw_haemo.ch_names)))
     conditions = design_matrix.columns
@@ -1928,72 +1956,83 @@ def plot_glm_results(file_path, raw_haemo, glm_est, design_matrix):
     df_individual["ID"] = file_path
     # df_individual["theta"] = [t * 1.0e6 for t in df_individual["theta"]]
 
-    condition_of_interest="Reach"
+    first_onset_for_cond = {}
+    for onset, desc in zip(raw_haemo.annotations.onset, raw_haemo.annotations.description):
+        if desc not in first_onset_for_cond:
+            first_onset_for_cond[desc] = onset
 
-    # Filter for the condition of interest and FIR delays
+    # Get unique condition names from annotations (descriptions)
-    df_individual["isCondition"] = [condition_of_interest in n for n in df_individual["Condition"]]
+    unique_annotations = set(raw_haemo.annotations.description)
-    df_individual["isDelay"] = ["delay" in n for n in df_individual["Condition"]]
+
-    df_individual = df_individual.query("isDelay and isCondition")
+    for cond in unique_annotations:
-    
+        logger.info(cond)
-    # Remove other conditions from design matrix
+        df_individual_filtered = df_individual.copy()
-    dm_condition_cols = [col for col in dm.columns if condition_of_interest in col]
+
-    dm_cond = dm[dm_condition_cols]
+        # Filter for the condition of interest and FIR delays
+        df_individual_filtered["isCondition"] = [cond in n for n in df_individual_filtered["Condition"]]
+        df_individual_filtered["isDelay"] = ["delay" in n for n in df_individual_filtered["Condition"]]
+        df_individual_filtered = df_individual_filtered.query("isDelay and isCondition")
         
-    # Add a numeric delay column
+        # Remove other conditions from design matrix
-    def extract_delay_number(condition_str):
+        dm_condition_cols = [col for col in dm.columns if cond in col]
-        # Extracts the number at the end of a string like 'Reach_delay_5'
+        dm_cond = dm[dm_condition_cols]
-        return int(condition_str.split("_")[-1])
+            
+        # Add a numeric delay column
+        def extract_delay_number(condition_str):
+            # Extracts the number at the end of a string like 'Activity_delay_5'
+            return int(condition_str.split("_")[-1])
 
-    df_individual["DelayNum"] = df_individual["Condition"].apply(extract_delay_number)
+        df_individual_filtered["DelayNum"] = df_individual_filtered["Condition"].apply(extract_delay_number)
 
-    # Now separate and sort using numeric delay
+        # Now separate and sort using numeric delay
-    df_hbo = df_individual[df_individual["Chroma"] == "hbo"].sort_values("DelayNum")
+        df_hbo = df_individual_filtered[df_individual_filtered["Chroma"] == "hbo"].sort_values("DelayNum")
-    df_hbr = df_individual[df_individual["Chroma"] == "hbr"].sort_values("DelayNum")
+        df_hbr = df_individual_filtered[df_individual_filtered["Chroma"] == "hbr"].sort_values("DelayNum")
 
-    vals_hbo = df_hbo["theta"].values
+        vals_hbo = df_hbo["theta"].values
-    vals_hbr = df_hbr["theta"].values
+        vals_hbr = df_hbr["theta"].values
-    
+        
-    # Create the plot
+        # Create the plot
-    fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(19, 10))
+        fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(19, 10))
-    
+        
-    # Scale design matrix components using numpy arrays instead of pandas operations
+        # Scale design matrix components using numpy arrays instead of pandas operations
-    dm_cond_values = dm_cond.values
+        dm_cond_values = dm_cond.values
-    dm_cond_scaled_hbo = dm_cond_values * vals_hbo.reshape(1, -1)
+        dm_cond_scaled_hbo = dm_cond_values * vals_hbo.reshape(1, -1)
-    dm_cond_scaled_hbr = dm_cond_values * vals_hbr.reshape(1, -1)
+        dm_cond_scaled_hbr = dm_cond_values * vals_hbr.reshape(1, -1)
-    
+        
-    # Create time axis relative to stimulus onset
+        # Create time axis relative to stimulus onset
-    time = dm_cond.index - np.ceil(raw_haemo.annotations.onset[1])
+        time = dm_cond.index - np.ceil(first_onset_for_cond.get(cond, 0))
-    
+        
-    # Plot
+        # Plot
-    axes[0].plot(time, dm_cond_values)
+        axes[0].plot(time, dm_cond_values)
-    axes[1].plot(time, dm_cond_scaled_hbo)
+        axes[1].plot(time, dm_cond_scaled_hbo)
-    axes[2].plot(time, np.sum(dm_cond_scaled_hbo, axis=1), 'r')
+        axes[2].plot(time, np.sum(dm_cond_scaled_hbo, axis=1), 'r')
-    axes[2].plot(time, np.sum(dm_cond_scaled_hbr, axis=1), 'b')
+        axes[2].plot(time, np.sum(dm_cond_scaled_hbr, axis=1), 'b')
-    
+        
-    # Format plots
+        # Format plots
-    for ax in range(3):
+        for ax in range(3):
-        axes[ax].set_xlim(-5, 25)
+            axes[ax].set_xlim(-5, 25)
-        axes[ax].set_xlabel("Time (s)")
+            axes[ax].set_xlabel("Time (s)")
-    axes[0].set_ylim(-0.2, 1.2)
+        axes[0].set_ylim(-0.2, 1.2)
-    axes[1].set_ylim(-0.5, 1)
+        axes[1].set_ylim(-0.5, 1)
-    axes[2].set_ylim(-0.5, 1)
+        axes[2].set_ylim(-0.5, 1)
-    axes[0].set_title(f"FIR Model (Unscaled)")
+        axes[0].set_title(f"FIR Model (Unscaled)")
-    axes[1].set_title(f"FIR Components (Scaled by {condition_of_interest} GLM Estimates)")
+        axes[1].set_title(f"FIR Components (Scaled by {cond} GLM Estimates)")
-    axes[2].set_title(f"Evoked Response ({condition_of_interest})")
+        axes[2].set_title(f"Evoked Response ({cond})")
-    axes[0].set_ylabel("FIR Model")
+        axes[0].set_ylabel("FIR Model")
-    axes[1].set_ylabel("Oxyhaemoglobin (ΔμMol)")
+        axes[1].set_ylabel("Oxyhaemoglobin (ΔμMol)")
-    axes[2].set_ylabel("Haemoglobin (ΔμMol)")
+        axes[2].set_ylabel("Haemoglobin (ΔμMol)")
-    axes[2].legend(["Oxyhaemoglobin", "Deoxyhaemoglobin"])
+        axes[2].legend(["Oxyhaemoglobin", "Deoxyhaemoglobin"])
 
-    
+        
-    print(f"Number of FIR bins: {len(vals_hbo)}")
+        print(f"Number of FIR bins: {len(vals_hbo)}")
-    print(f"Mean theta (HbO): {np.mean(vals_hbo):.4f}")
+        print(f"Mean theta (HbO): {np.mean(vals_hbo):.4f}")
-    print(f"Sum of theta (HbO): {np.sum(vals_hbo):.4f}")
+        print(f"Sum of theta (HbO): {np.sum(vals_hbo):.4f}")
-    print(f"Mean theta (HbR): {np.mean(vals_hbr):.4f}")
+        print(f"Mean theta (HbR): {np.mean(vals_hbr):.4f}")
-    print(f"Sum of theta (HbR): {np.sum(vals_hbr):.4f}")
+        print(f"Sum of theta (HbR): {np.sum(vals_hbr):.4f}")
-    
+        
-    return fig
+        fig_glms.append((f"Condition {cond}", fig))
 
+    return fig_glms
 
 
 def plot_3d_evoked_array(
@@ -2871,9 +2910,12 @@ def process_participant(file_path, progress_callback=None):
     logger.info("11")
 
     # Step 11: Get short / long channels
-    short_chans = get_short_channels(raw_haemo, max_dist=0.015)
+    if SHORT_CHANNEL:
-    fig_short_chans = short_chans.plot(duration=raw_haemo.times[-1], n_channels=raw_haemo.info['nchan'], title="Short Channels Only", show=False)
+        short_chans = get_short_channels(raw_haemo, max_dist=0.015)
-    fig_individual["short"] = fig_short_chans
+        fig_short_chans = short_chans.plot(duration=raw_haemo.times[-1], n_channels=raw_haemo.info['nchan'], title="Short Channels Only", show=False)
+        fig_individual["short"] = fig_short_chans
+    else:
+        short_chans = None
     raw_haemo = get_long_channels(raw_haemo)
     if progress_callback: progress_callback(12)
     logger.info("12")
@@ -2916,13 +2958,15 @@ def process_participant(file_path, progress_callback=None):
 
     # Step 16: Plot GLM results
     fig_glm_result = plot_glm_results(file_path, raw_haemo, glm_est, design_matrix)
-    fig_individual["GLM"] = fig_glm_result
+    for name, fig in fig_glm_result:
+        fig_individual[f"GLM {name}"] = fig
     if progress_callback: progress_callback(17)
     logger.info("17")
 
     # Step 17: Plot channel significance
     fig_significance = individual_significance(raw_haemo, glm_est)
-    fig_individual["Significance"] = fig_significance
+    for name, fig in fig_significance:
+        fig_individual[f"Significance {name}"] = fig
     if progress_callback: progress_callback(18)
     logger.info("18")
 
@@ -2975,6 +3019,9 @@ def process_participant(file_path, progress_callback=None):
 
         contrast_dict[condition] = contrast_vector
 
+    if progress_callback: progress_callback(19)
+    logger.info("19")
+
     # Compute contrast results
     contrast_results = {}
 
@@ -2988,7 +3035,7 @@ def process_participant(file_path, progress_callback=None):
     
     fig_bytes = convert_fig_dict_to_png_bytes(fig_individual)
 
+    if progress_callback: progress_callback(20)
+    logger.info("20")
 
-    return raw_haemo, epochs, fig_bytes, cha, contrast_results, df_ind, design_matrix, AGE, GENDER, GROUP, True
+    return raw_haemo, epochs, fig_bytes, cha, contrast_results, df_ind, design_matrix, AGE, GENDER, GROUP, True
-
-# Not 3000 lines yay!

main.py

@@ -10,6 +10,7 @@ License: GPL-3.0
 import os
 import re
 import sys
+import json
 import time
 import shlex
 import pickle
@@ -33,6 +34,7 @@ from mne.io import read_raw_snirf
 from mne.preprocessing.nirs import source_detector_distances
 from mne_nirs.io import write_raw_snirf
 from mne.channels import make_dig_montage
+from mne import Annotations
 
 from PySide6.QtWidgets import (
     QApplication, QWidget, QMessageBox, QVBoxLayout, QHBoxLayout, QTextEdit, QScrollArea, QComboBox, QGridLayout,
@@ -120,6 +122,12 @@ SECTIONS = [
             #{"name": "FILTER", "default": True, "type": bool, "help": "Calculate Peak Spectral Power."},
         ]
     },
+    {
+        "title": "Short Channels",
+        "params": [
+            {"name": "SHORT_CHANNEL", "default": True, "type": bool, "help": "Does the data have a short channel?"},
+        ]
+    },
     {
         "title": "Extracting Events",
         "params": [
@@ -242,6 +250,9 @@ class UpdateCheckThread(QThread):
     error_occurred = Signal(str)
 
     def run(self):
+        if not getattr(sys, 'frozen', False):
+            self.error_occurred.emit("Application is not frozen (Development mode).")
+            return
         try:
             latest_version, download_url = self.get_latest_release_for_platform()
             if not latest_version:
@@ -615,6 +626,430 @@ class UpdateOptodesWindow(QWidget):
 
 
 
+class UpdateEventsWindow(QWidget):
+
+    def __init__(self, parent=None):
+        super().__init__(parent, Qt.WindowType.Window)
+        self.setWindowTitle("Update event markers")
+        self.resize(760, 200)
+
+        self.label_file_a = QLabel("SNIRF file:")
+        self.line_edit_file_a = QLineEdit()
+        self.line_edit_file_a.setReadOnly(True)
+        self.btn_browse_a = QPushButton("Browse .snirf")
+        self.btn_browse_a.clicked.connect(self.browse_file_a)
+
+        self.label_file_b = QLabel("BORIS file:")
+        self.line_edit_file_b = QLineEdit()
+        self.line_edit_file_b.setReadOnly(True)
+        self.btn_browse_b = QPushButton("Browse .boris")
+        self.btn_browse_b.clicked.connect(self.browse_file_b)
+
+        self.label_suffix = QLabel("Filename in BORIS project file:")
+        self.combo_suffix = QComboBox()
+        self.combo_suffix.setEditable(False)
+        self.combo_suffix.currentIndexChanged.connect(self.on_observation_selected)
+
+        self.label_events = QLabel("Events in selected observation:")
+        self.combo_events = QComboBox()
+        self.combo_events.setEnabled(False)
+        
+        self.label_snirf_events = QLabel("Events in SNIRF file:")
+        self.combo_snirf_events = QComboBox()
+        self.combo_snirf_events.setEnabled(False)
+
+        self.btn_clear = QPushButton("Clear")
+        self.btn_go = QPushButton("Go")
+        self.btn_clear.clicked.connect(self.clear_files)
+        self.btn_go.clicked.connect(self.go_action)
+
+        # --- 
+        layout = QVBoxLayout()
+        self.description = QLabel()
+        self.description.setTextFormat(Qt.TextFormat.RichText)
+        self.description.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
+        self.description.setOpenExternalLinks(False) # Handle the click internally
+            
+        self.description.setText("Some software when creating snirf files will insert a template of optode positions as the correct position of the optodes for the participant.<br>"
+        "This is rarely correct as each head differs slightly in shape or size, and a lot of calculations require the optodes to be in the correct location.<br>"
+        "Using a .txt file, we can update the positions in the snirf file to match those of a digitization system such as one from Polhemus or elsewhere.<br>"
+        "The .txt file should have the fiducials, detectors, and sources clearly labeled, followed by the x, y, and z coordinates seperated by a space.<br>"
+        "An example format of what a digitization text file should look like can be found <a href='custom_link'>by clicking here</a>.")
+
+        layout.addWidget(self.description)
+
+        help_text_a = "Select the SNIRF (.snirf) file to update with new event markers."
+
+        file_a_layout = QHBoxLayout()
+
+        # Help button on the left
+        help_btn_a = QPushButton("?")
+        help_btn_a.setFixedWidth(25)
+        help_btn_a.setToolTip(help_text_a)
+        help_btn_a.clicked.connect(lambda _, text=help_text_a: self.show_help_popup(text))
+        file_a_layout.addWidget(help_btn_a)
+
+        # Container for label + line_edit + browse button with tooltip
+        file_a_container = QWidget()
+        file_a_container_layout = QHBoxLayout()
+        file_a_container_layout.setContentsMargins(0, 0, 0, 0)
+        file_a_container_layout.addWidget(self.label_file_a)
+        file_a_container_layout.addWidget(self.line_edit_file_a)
+        file_a_container_layout.addWidget(self.btn_browse_a)
+        file_a_container.setLayout(file_a_container_layout)
+        file_a_container.setToolTip(help_text_a)
+
+        file_a_layout.addWidget(file_a_container)
+        layout.addLayout(file_a_layout)
+
+
+        help_text_b = "Provide a .boris project file that contains events for this participant."
+
+        file_b_layout = QHBoxLayout()
+
+        help_btn_b = QPushButton("?")
+        help_btn_b.setFixedWidth(25)
+        help_btn_b.setToolTip(help_text_b)
+        help_btn_b.clicked.connect(lambda _, text=help_text_b: self.show_help_popup(text))
+        file_b_layout.addWidget(help_btn_b)
+
+        file_b_container = QWidget()
+        file_b_container_layout = QHBoxLayout()
+        file_b_container_layout.setContentsMargins(0, 0, 0, 0)
+        file_b_container_layout.addWidget(self.label_file_b)
+        file_b_container_layout.addWidget(self.line_edit_file_b)
+        file_b_container_layout.addWidget(self.btn_browse_b)
+        file_b_container.setLayout(file_b_container_layout)
+        file_b_container.setToolTip(help_text_b)
+
+        file_b_layout.addWidget(file_b_container)
+        layout.addLayout(file_b_layout)
+
+
+        help_text_suffix = "This participant from the .boris project file matches the .snirf file."
+
+        suffix_layout = QHBoxLayout()
+
+        help_btn_suffix = QPushButton("?")
+        help_btn_suffix.setFixedWidth(25)
+        help_btn_suffix.setToolTip(help_text_suffix)
+        help_btn_suffix.clicked.connect(lambda _, text=help_text_suffix: self.show_help_popup(text))
+        suffix_layout.addWidget(help_btn_suffix)
+
+        suffix_container = QWidget()
+        suffix_container_layout = QHBoxLayout()
+        suffix_container_layout.setContentsMargins(0, 0, 0, 0)
+        suffix_container_layout.addWidget(self.label_suffix)
+        suffix_container_layout.addWidget(self.combo_suffix)
+        suffix_container.setLayout(suffix_container_layout)
+        suffix_container.setToolTip(help_text_suffix)
+
+        suffix_layout.addWidget(suffix_container)
+        layout.addLayout(suffix_layout)
+
+
+        help_text_suffix = "The events extracted from the BORIS project file for the selected observation."
+
+        suffix2_layout = QHBoxLayout()
+
+        help_btn_suffix = QPushButton("?")
+        help_btn_suffix.setFixedWidth(25)
+        help_btn_suffix.setToolTip(help_text_suffix)
+        help_btn_suffix.clicked.connect(lambda _, text=help_text_suffix: self.show_help_popup(text))
+        suffix2_layout.addWidget(help_btn_suffix)
+        
+        suffix2_container = QWidget()
+        suffix2_container_layout = QHBoxLayout()
+        suffix2_container_layout.setContentsMargins(0, 0, 0, 0)
+        suffix2_container_layout.addWidget(self.label_events)
+        suffix2_container_layout.addWidget(self.combo_events)
+        suffix2_container.setLayout(suffix2_container_layout)
+        suffix2_container.setToolTip(help_text_suffix)
+
+        suffix2_layout.addWidget(suffix2_container)
+        layout.addLayout(suffix2_layout)
+        
+        snirf_events_layout = QHBoxLayout()
+
+        help_text_snirf_events = "The event markers extracted from the SNIRF file."
+        help_btn_snirf_events = QPushButton("?")
+        help_btn_snirf_events.setFixedWidth(25)
+        help_btn_snirf_events.setToolTip(help_text_snirf_events)
+        help_btn_snirf_events.clicked.connect(lambda _, text=help_text_snirf_events: self.show_help_popup(text))
+        snirf_events_layout.addWidget(help_btn_snirf_events)
+
+        snirf_events_container = QWidget()
+        snirf_events_container_layout = QHBoxLayout()
+        snirf_events_container_layout.setContentsMargins(0, 0, 0, 0)
+        snirf_events_container_layout.addWidget(self.label_snirf_events)
+        snirf_events_container_layout.addWidget(self.combo_snirf_events)
+        snirf_events_container.setLayout(snirf_events_container_layout)
+        snirf_events_container.setToolTip(help_text_snirf_events)
+
+        snirf_events_layout.addWidget(snirf_events_container)
+        layout.addLayout(snirf_events_layout)
+
+        buttons_layout = QHBoxLayout()
+        buttons_layout.addStretch()
+        buttons_layout.addWidget(self.btn_clear)
+        buttons_layout.addWidget(self.btn_go)
+        layout.addLayout(buttons_layout)
+
+        self.setLayout(layout)
+
+
+    def show_help_popup(self, text):
+        msg = QMessageBox(self)
+        msg.setWindowTitle("Parameter Info")
+        msg.setText(text)
+        msg.exec()
+
+    def browse_file_a(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, "Select SNIRF File", "", "SNIRF Files (*.snirf)")
+        if file_path:
+            self.line_edit_file_a.setText(file_path)
+            try:
+                raw = read_raw_snirf(file_path, preload=False)
+                annotations = raw.annotations
+
+                # Build individual event entries
+                event_entries = []
+                for onset, description in zip(annotations.onset, annotations.description):
+                    event_str = f"{description} @ {onset:.3f}s"
+                    event_entries.append(event_str)
+
+                if not event_entries:
+                    QMessageBox.information(self, "No Events", "No events found in SNIRF file.")
+                    self.combo_snirf_events.clear()
+                    self.combo_snirf_events.setEnabled(False)
+                    return
+
+                self.combo_snirf_events.clear()
+                self.combo_snirf_events.addItems(event_entries)
+                self.combo_snirf_events.setEnabled(True)
+
+            except Exception as e:
+                QMessageBox.warning(self, "Error", f"Could not read SNIRF file with MNE:\n{str(e)}")
+                self.combo_snirf_events.clear()
+                self.combo_snirf_events.setEnabled(False)
+
+    def browse_file_b(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, "Select BORIS File", "", "BORIS project Files (*.boris)")
+        if file_path:
+            self.line_edit_file_b.setText(file_path)
+            
+            try:
+                with open(file_path, 'r', encoding='utf-8') as f:
+                    data = json.load(f)
+                self.boris_data = data
+
+                observation_keys = self.extract_boris_observation_keys(data)
+                self.combo_suffix.clear()
+                self.combo_suffix.addItems(observation_keys)
+
+            except (json.JSONDecodeError, FileNotFoundError, KeyError) as e:
+                QMessageBox.warning(self, "Error", f"Failed to parse BORIS file:\n{e}")
+                
+    def extract_boris_observation_keys(self, data):
+        if "observations" not in data:
+            raise KeyError("Missing 'observations' key in BORIS file.")
+
+        observations = data["observations"]
+        if not isinstance(observations, dict):
+            raise TypeError("'observations' must be a dictionary.")
+
+        return list(observations.keys())
+    
+    def on_observation_selected(self):
+        selected_obs = self.combo_suffix.currentText()
+        if not selected_obs or not hasattr(self, 'boris_data'):
+            self.combo_events.clear()
+            self.combo_events.setEnabled(False)
+            return
+
+        try:
+            events = self.boris_data["observations"][selected_obs]["events"]
+        except (KeyError, TypeError):
+            self.combo_events.clear()
+            self.combo_events.setEnabled(False)
+            return
+
+        event_entries = []
+        for event in events:
+            if isinstance(event, list) and len(event) >= 3:
+                timestamp = event[0]
+                label = event[2]
+                display = f"{label} @ {timestamp:.3f}"
+                event_entries.append(display)
+
+        self.combo_events.clear()
+        self.combo_events.addItems(event_entries)
+        self.combo_events.setEnabled(bool(event_entries))
+
+    def clear_files(self):
+        self.line_edit_file_a.clear()
+        self.line_edit_file_b.clear()
+    
+    
+    def go_action(self):
+        
+        file_a = self.line_edit_file_a.text()
+        file_b = self.line_edit_file_b.text()
+        suffix = "flare" 
+    
+        if not hasattr(self, "boris_data") or self.combo_events.count() == 0 or self.combo_snirf_events.count() == 0:
+            QMessageBox.warning(self, "Missing data", "Please make sure a BORIS and SNIRF event are selected.")
+            return
+
+        # Extract BORIS anchor
+        try:
+            boris_label, boris_time_str = self.combo_events.currentText().split(" @ ")
+            boris_anchor_time = float(boris_time_str.replace("s", "").strip())
+        except Exception as e:
+            QMessageBox.critical(self, "BORIS Event Error", f"Could not parse BORIS anchor event:\n{e}")
+            return
+
+        # Extract SNIRF anchor
+        try:
+            snirf_label, snirf_time_str = self.combo_snirf_events.currentText().split(" @ ")
+            snirf_anchor_time = float(snirf_time_str.replace("s", "").strip())
+        except Exception as e:
+            QMessageBox.critical(self, "SNIRF Event Error", f"Could not parse SNIRF anchor event:\n{e}")
+            return
+
+        time_shift = snirf_anchor_time - boris_anchor_time
+
+        selected_obs = self.combo_suffix.currentText()
+        if not selected_obs or selected_obs not in self.boris_data["observations"]:
+            QMessageBox.warning(self, "Invalid selection", "Selected observation not found in BORIS file.")
+            return
+
+        boris_events = self.boris_data["observations"][selected_obs].get("events", [])
+        if not boris_events:
+            QMessageBox.warning(self, "No BORIS events", "No events found in selected BORIS observation.")
+            return
+
+        snirf_path = self.line_edit_file_a.text()
+        if not snirf_path:
+            QMessageBox.warning(self, "No SNIRF file", "Please select a SNIRF file.")
+            return
+
+        base_name = os.path.splitext(os.path.basename(file_a))[0]
+        suggested_name = f"{base_name}_{suffix}.snirf"
+
+        # Open save dialog
+        save_path, _ = QFileDialog.getSaveFileName(
+            self,
+            "Save SNIRF File As",
+            suggested_name,
+            "SNIRF Files (*.snirf)"
+        )
+
+        if not save_path:
+            print("Save cancelled.")
+            return
+
+        if not save_path.lower().endswith(".snirf"):
+            save_path += ".snirf"
+
+        try:
+            raw = read_raw_snirf(snirf_path, preload=True)
+
+            # Build new Annotations from shifted BORIS events
+            onsets = []
+            durations = []
+            descriptions = []
+
+            label_counts = {}
+
+            used_times = set()
+            
+            sfreq = raw.info['sfreq']  # sampling frequency in Hz
+            min_shift = 1.0 / sfreq
+            
+            max_attempts = 10
+            
+            for event in boris_events:
+                if not isinstance(event, list) or len(event) < 3:
+                    continue
+
+                orig_time = event[0]
+                desc = event[2]
+
+                # Count occurrences per event label
+                count = label_counts.get(desc, 0)
+                label_counts[desc] = count + 1
+
+                # Only use 1st, 3rd, 5th... (odd occurrences)
+                if (count % 2) == 0:
+                    shifted_time = orig_time + time_shift
+
+                    # Ensure unique timestamp by checking and adjusting slightly
+                    adjusted_time = shifted_time
+
+                    # Try to find a unique timestamp
+                    attempts = 0
+                    while round(adjusted_time, 6) in used_times and attempts < max_attempts:
+                        adjusted_time += min_shift
+                        attempts += 1
+
+                    if attempts == max_attempts:
+                        print(f"Warning: Could not find unique timestamp for event '{desc}' at original time {orig_time:.3f}s. Skipping.")
+                        continue  # Skip problematic event
+
+                    adjusted_time = round(adjusted_time, 6)
+                    used_times.add(adjusted_time)
+
+                    print(f"Applying event: {desc} @ {adjusted_time:.3f}s (original: {orig_time:.3f}s)")
+
+                    onsets.append(adjusted_time)
+                    durations.append(0.0)
+                    descriptions.append(desc)
+
+            new_annotations = Annotations(onset=onsets, duration=durations, description=descriptions)
+
+            # Replace annotations in raw object
+            raw.set_annotations(new_annotations)
+
+            # Write a new SNIRF file
+            write_raw_snirf(raw, suggested_name)
+
+            QMessageBox.information(self, "Success", "SNIRF file updated with aligned BORIS events.")
+
+        except Exception as e:
+            QMessageBox.critical(self, "Error", f"Failed to update SNIRF file:\n{e}")
+
+
+    def update_optode_positions(self, file_a, file_b, save_path):
+                
+        fiducials = {}
+        ch_positions = {}
+
+        # Read the lines from the optode file
+        with open(file_b, 'r') as f:
+            for line in f:
+                if line.strip():
+                    # Split by the semicolon and convert to meters
+                    ch_name, coords_str = line.split(":")
+                    coords = np.array(list(map(float, coords_str.strip().split()))) * 0.001
+
+                    # The key we have is a fiducial
+                    if ch_name.lower() in ['lpa', 'nz', 'rpa']:
+                        fiducials[ch_name.lower()] = coords
+
+                    # The key we have is a source or detector
+                    else:
+                        ch_positions[ch_name.upper()] = coords
+
+        # Create montage with updated coords in head space
+        initial_montage = make_dig_montage(ch_pos=ch_positions, nasion=fiducials.get('nz'), lpa=fiducials.get('lpa'), rpa=fiducials.get('rpa'), coord_frame='head') # type: ignore
+
+        # Read the SNIRF file, set the montage, and write it back
+        raw = read_raw_snirf(file_a, preload=True)
+        raw.set_montage(initial_montage)
+        write_raw_snirf(raw, save_path)
+
+
 class ProgressBubble(QWidget):
     """
     A clickable widget displaying a progress bar made of colored rectangles and a label.
@@ -646,9 +1081,9 @@ class ProgressBubble(QWidget):
         self.progress_layout = QHBoxLayout()
 
         self.rects = []
-        for _ in range(12):
+        for _ in range(19):
             rect = QFrame()
-            rect.setFixedSize(10, 20)
+            rect.setFixedSize(10, 18)
             rect.setStyleSheet("background-color: white; border: 1px solid gray;")
             self.progress_layout.addWidget(rect)
             self.rects.append(rect)
@@ -2627,6 +3062,7 @@ class MainApplication(QMainWindow):
         self.about = None
         self.help = None
         self.optodes = None
+        self.events = None
         self.bubble_widgets = {}
         self.param_sections = []
         self.folder_paths = []
@@ -2859,12 +3295,13 @@ class MainApplication(QMainWindow):
             ("User Guide", "F1", self.user_guide, resource_path("icons/help_24dp_1F1F1F.svg")), 
             ("Check for Updates", "F5", self.manual_check_for_updates, resource_path("icons/update_24dp_1F1F1F.svg")),
             ("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/update_24dp_1F1F1F.svg")),
+            ("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/update_24dp_1F1F1F.svg")),
             ("About", "F12", self.about_window, resource_path("icons/info_24dp_1F1F1F.svg"))
         ]
 
         for i, (name, shortcut, slot, icon) in enumerate(options_actions):
             options_menu.addAction(make_action(name, shortcut, slot, icon=icon))
-            if i == 1 or i == 2:  # after the first 2 actions (0,1)
+            if i == 1 or i == 3:  # after the first 2 actions (0,1)
                 options_menu.addSeparator()
 
         self.statusbar = self.statusBar()
@@ -2955,6 +3392,11 @@ class MainApplication(QMainWindow):
             self.optodes.show()
 
 
+    def update_event_markers(self):
+        if self.events is None or not self.events.isVisible():
+            self.events = UpdateEventsWindow(self)
+            self.events.show()
+
     def open_file_dialog(self):
         file_path, _ = QFileDialog.getOpenFileName(
             self, "Open File", "", "All Files (*);;Text Files (*.txt)"