improvements

.gitignore

@@ -174,3 +174,4 @@ cython_debug/
 # PyPI configuration file
 .pypirc
 
+/individual_images

changelog.md

@@ -1,3 +1,15 @@
+# Version 1.2.0
+- Added new parameters to the right side of the screen
+- These parameters include SHOW_OPTODE_NAMES, SECONDS_TO_STRIP_HR, MAX_LOW_HR, MAX_HIGH_HR, SMOTHING_WINDOW_HR, HEART_RATE_WINDOW, BAD_CHANNELS_HANDLING, MAX_DIST, MIN_NEIGHBORS, L_TRANS_BANDWIDTH, H_TRANS_BANDWIDTH, RESAMPLE, RESAMPLE_FREQ, STIM_DUR, HRF_MODEL, HIGH_PASS, DRIFT_ORDER, FIR_DELAYS, MIN_ONSET, OVERSAMPLING, SHORT_CHANNEL_REGRESSION, NOISE_MODEL, and BINS.
+- All the new parameters have default values matching the underlying values in version 1.1.7
+- The order of the parameters have changed to match the order that the code runs when the Process button is clicked
+- Moved TIME_WINDOW_START and TIME_WINDOW_END to the 'Other' category
+- Fixed a bug causing SCI to not work when HEART_RATE was set to False
+- 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 issue causing some overlay elements to not render on the brain for certain devices
+
+
 # Version 1.1.7
 
 - Fixed a bug where having both a L_FREQ and H_FREQ would cause only the L_FREQ to be used

flares.py

@@ -21,6 +21,7 @@ import os.path as op
 import re
 import traceback
 from concurrent.futures import ProcessPoolExecutor, as_completed
+from queue import Empty
 
 # External library imports
 import matplotlib.pyplot as plt
@@ -53,7 +54,7 @@ from scipy.signal import welch, butter, filtfilt # type: ignore
 import pywt # type: ignore
 import neurokit2 as nk # type: ignore
 
-# Backen visualization needed to be defined for pyinstaller
+# Backend visualization needed to be defined for pyinstaller
 import pyvistaqt # type: ignore
 import vtkmodules.util.data_model
 import vtkmodules.util.execution_model
@@ -89,9 +90,10 @@ from mne_nirs.io.fold import fold_channel_specificity  # type: ignore
 from mne_nirs.preprocessing import peak_power  # type: ignore
 from mne_nirs.statistics._glm_level_first import RegressionResults  # type: ignore
 
-
+# Needs to be set for men
 os.environ["SUBJECTS_DIR"] = str(data_path()) + "/subjects" # type: ignore
 
+# TODO: Tidy this up
 FIXED_CATEGORY_COLORS = {
     "SCI only": "skyblue",
     "PSP only": "salmon",
@@ -112,10 +114,6 @@ FIXED_CATEGORY_COLORS = {
 }
 
 
-AGE: float
-GENDER: str
-
-# SECONDS_TO_STRIP: int
 DOWNSAMPLE: bool
 DOWNSAMPLE_FREQUENCY: int
 
@@ -123,21 +121,37 @@ TRIM: bool
 SECONDS_TO_KEEP: float
 
 OPTODE_PLACEMENT: bool
+SHOW_OPTODE_NAMES: bool
 
 HEART_RATE: bool
 
+SHORT_CHANNEL: bool
+SHORT_CHANNEL_THRESH: float
+LONG_CHANNEL_THRESH: float
+
+HEART_RATE: bool
+SECONDS_TO_STRIP_HR: int
+MAX_LOW_HR: int
+MAX_HIGH_HR: int
+SMOOTHING_WINDOW_HR: int
+HEART_RATE_WINDOW: int
+
 SCI: bool
 SCI_TIME_WINDOW: int
 SCI_THRESHOLD: float
 
 SNR: bool
-# SNR_TIME_WINDOW : int
+# SNR_TIME_WINDOW : int #TODO: is this needed?
 SNR_THRESHOLD: float
 
 PSP: bool
 PSP_TIME_WINDOW: int
 PSP_THRESHOLD: float
 
+BAD_CHANNELS_HANDLING: str
+MAX_DIST: float
+MIN_NEIGHBORS: int
+
 TDDR: bool
 
 WAVELET: bool
@@ -145,57 +159,39 @@ IQR: float
 WAVELET_TYPE: str
 WAVELET_LEVEL: int
 
-HEART_RATE = True                                                   # True if heart rate should be calculated. This helps the SCI, PSP, and SNR methods to be more accurate.
-SECONDS_TO_STRIP_HR =5                                             # Amount of seconds to temporarily strip from the data to calculate heart rate more effectively. Useful if participant removed cap while still recording.
-MAX_LOW_HR = 40                                                # Any heart rate values lower than this will be set to this value.
-MAX_HIGH_HR = 200                                                   # Any heart rate values higher than this will be set to this value.
-SMOOTHING_WINDOW_HR = 100                                               # Heart rate will be calculated as a rolling average over this many amount of samples.
-HEART_RATE_WINDOW = 25                                                 # Amount of BPM above and below the calculated average to use for a range of resting BPM.
-
 ENHANCE_NEGATIVE_CORRELATION: bool
 
 FILTER: bool
 L_FREQ: float
 H_FREQ: float
+L_TRANS_BANDWIDTH: float
+H_TRANS_BANDWIDTH: float
 
-SHORT_CHANNEL: bool
+STIM_DUR: float
-SHORT_CHANNEL_THRESH: float
+HRF_MODEL: str
-LONG_CHANNEL_THRESH: float
+DRIFT_MODEL: str
-
+HIGH_PASS: float
+DRIFT_ORDER: int
+FIR_DELAYS: range
+MIN_ONSET: int
+OVERSAMPLING: int
 REMOVE_EVENTS: list
+SHORT_CHANNEL_REGRESSION: bool
+
+NOISE_MODEL: str
+BINS: int
+N_JOBS: int
 
 TIME_WINDOW_START: int
 TIME_WINDOW_END: int
 
-DRIFT_MODEL: str
-
 VERBOSITY = True
 
-# FIXME: Shouldn't need each ordering - just order it before checking
+AGE = 25    # Assume 25 if not set from the GUI. This will result in a reasonable PPF
-FIXED_CATEGORY_COLORS = {
-    "SCI only": "skyblue",
-    "PSP only": "salmon",
-    "SNR only": "lightgreen",
-    "PSP + SCI": "orange",
-    "SCI + SNR": "violet",
-    "PSP + SNR": "gold",
-    "SCI + PSP": "orange",
-    "SNR + SCI": "violet",
-    "SNR + PSP": "gold",
-    "PSP + SNR + SCI": "gray",
-    "SCI + PSP + SNR": "gray",
-    "SCI + SNR + PSP": "gray",
-    "PSP + SCI + SNR": "gray",
-    "PSP + SNR + SCI": "gray",
-    "SNR + SCI + PSP": "gray",
-    "SNR + PSP + SCI": "gray",
-}
-
-
-AGE = 25
 GENDER = ""
 GROUP = "Default"
 
+# These are parameters that are required for the analysis
 REQUIRED_KEYS: dict[str, Any] = {
         
     # "SECONDS_TO_STRIP": int,
@@ -262,7 +258,7 @@ PLATFORM_NAME = platform.system().lower()
 # Configure logging to file with timestamps and realtime flush
 if PLATFORM_NAME == 'darwin':
     logging.basicConfig(
-        filename=os.path.join(os.path.dirname(sys.executable), "../../../fnirs_analysis.log"),
+        filename=os.path.join(os.path.dirname(sys.executable), "../../../fnirs_analysis.log"),  # Needed to get out of the bundled application
         level=logging.INFO,
         format='%(asctime)s - %(processName)s - %(levelname)s - %(message)s',
         datefmt='%Y-%m-%d %H:%M:%S',
@@ -320,8 +316,6 @@ def set_metadata(file_path, metadata: dict[str, Any]) -> None:
             val = file_metadata.get(key, None)
             if val not in (None, '', [], {}, ()):  # check for "empty" values
                 globals()[key] = val
-from queue import Empty  # This works with multiprocessing.Manager().Queue()
-
 
 def gui_entry(config: dict[str, Any], gui_queue: Queue, progress_queue: Queue) -> None:
     def forward_progress():
@@ -825,7 +819,7 @@ def get_hbo_hbr_picks(raw):
     return hbo_picks, hbr_picks, hbo_wl, hbr_wl
 
 
-def interpolate_fNIRS_bads_weighted_average(raw, bad_channels, max_dist=0.03, min_neighbors=2):
+def interpolate_fNIRS_bads_weighted_average(raw, max_dist=0.03, min_neighbors=2):
     """
     Interpolate bad fNIRS channels using a distance-weighted average of nearby good channels.
 
@@ -1117,17 +1111,17 @@ def mark_bads(raw, bad_sci, bad_snr, bad_psp):
 
 
 def filter_the_data(raw_haemo):
-        # --- STEP 5: Filtering (0.01–0.2 Hz bandpass) ---
+        # --- STEP 5: Filtering (0.01-0.2 Hz bandpass) ---
     fig_filter = raw_haemo.compute_psd(fmax=3).plot(
         average=True, color="r", show=False, amplitude=True
     )
     
     if L_FREQ == 0 and H_FREQ != 0:
-        raw_haemo = raw_haemo.filter(l_freq=None, h_freq=H_FREQ, h_trans_bandwidth=0.02)
+        raw_haemo = raw_haemo.filter(l_freq=None, h_freq=H_FREQ, h_trans_bandwidth=H_TRANS_BANDWIDTH)
     elif L_FREQ != 0 and H_FREQ == 0:
-        raw_haemo = raw_haemo.filter(l_freq=L_FREQ, h_freq=None, l_trans_bandwidth=0.002)
+        raw_haemo = raw_haemo.filter(l_freq=L_FREQ, h_freq=None, l_trans_bandwidth=L_TRANS_BANDWIDTH)
     elif L_FREQ != 0 and H_FREQ != 0:
-        raw_haemo = raw_haemo.filter(l_freq=L_FREQ, h_freq=H_FREQ, l_trans_bandwidth=0.002, h_trans_bandwidth=0.02)
+        raw_haemo = raw_haemo.filter(l_freq=L_FREQ, h_freq=H_FREQ, l_trans_bandwidth=L_TRANS_BANDWIDTH, h_trans_bandwidth=H_TRANS_BANDWIDTH)
     else:
         print("No filter")
     #raw_haemo = raw_haemo.filter(l_freq=None, h_freq=0.4, h_trans_bandwidth=0.2)
@@ -1307,6 +1301,19 @@ def epochs_calculations(raw_haemo, events, event_dict):
 
 def make_design_matrix(raw_haemo, short_chans):
 
+    events_to_remove = REMOVE_EVENTS
+        
+    filtered_annotations = [ann for ann in raw_haemo.annotations if ann['description'] not in events_to_remove]
+    
+    new_annot = Annotations(
+        onset=[ann['onset'] for ann in filtered_annotations],
+        duration=[ann['duration'] for ann in filtered_annotations],
+        description=[ann['description'] for ann in filtered_annotations]
+    )
+    
+    # Set the new annotations
+    raw_haemo.set_annotations(new_annot)
+
     raw_haemo.resample(1, npad="auto")
     raw_haemo._data = raw_haemo._data * 1e6
     # 2) Create design matrix
@@ -1314,26 +1321,28 @@ def make_design_matrix(raw_haemo, short_chans):
         short_chans.resample(1)
         design_matrix = make_first_level_design_matrix(
             raw=raw_haemo,
-            hrf_model='fir',
+            stim_dur=STIM_DUR,
-            stim_dur=0.5,
+            hrf_model=HRF_MODEL,
-            fir_delays=range(15),
             drift_model=DRIFT_MODEL,
-            high_pass=0.01,
+            high_pass=HIGH_PASS,
-            oversampling=1,
+            drift_order=DRIFT_ORDER,
-            min_onset=-125,
+            fir_delays=range(15),
             add_regs=short_chans.get_data().T,
-            add_reg_names=short_chans.ch_names
+            add_reg_names=short_chans.ch_names,
+            min_onset=MIN_ONSET,
+            oversampling=OVERSAMPLING
         )
     else:
         design_matrix = make_first_level_design_matrix(
             raw=raw_haemo,
-            hrf_model='fir',
+            stim_dur=STIM_DUR,
-            stim_dur=0.5,
+            hrf_model=HRF_MODEL,
-            fir_delays=range(15),
             drift_model=DRIFT_MODEL,
-            high_pass=0.01,
+            high_pass=HIGH_PASS,
-            oversampling=1,
+            drift_order=DRIFT_ORDER,
-            min_onset=-125,
+            fir_delays=range(15),
+            min_onset=MIN_ONSET,
+            oversampling=OVERSAMPLING
         )
 
     print(design_matrix.head())
@@ -3310,18 +3319,20 @@ def hr_calc(raw):
     return fig, hr1, hr2, low, high
 
 
+
+
 def process_participant(file_path, progress_callback=None):
 
     fig_individual: dict[str, Figure] = {}
 
-    # Step 1: Load
+    # Step 1: Preprocessing
     raw = load_snirf(file_path)
     fig_raw = raw.plot(duration=raw.times[-1], n_channels=raw.info['nchan'], title="Loaded Raw", show=False)
     fig_individual["Loaded Raw"] = fig_raw
     if progress_callback: progress_callback(1)
-    logger.info("1")
+    logger.info("Step 1 Completed.")
-    
     
+    # Step 2: Trimming
     if TRIM:
         if hasattr(raw, 'annotations') and len(raw.annotations) > 0:
             # Get time of first event
@@ -3329,17 +3340,16 @@ def process_participant(file_path, progress_callback=None):
             trim_time = max(0, first_event_time - SECONDS_TO_KEEP)  # Ensure we don't go negative
             raw.crop(tmin=trim_time)
             # Shift annotation onsets to match new t=0
-            import mne
 
             ann = raw.annotations
-            ann_shifted = mne.Annotations(
+            ann_shifted = Annotations(
                 onset=ann.onset - trim_time,  # shift to start at zero
                 duration=ann.duration,
                 description=ann.description
             )
             data = raw.get_data()
             info = raw.info.copy()
-            raw = mne.io.RawArray(data, info)
+            raw = RawArray(data, info)
             raw.set_annotations(ann_shifted)
 
             logger.info(f"Trimmed raw data: start at {trim_time}s (5s before first event), t=0 at new start")
@@ -3349,169 +3359,162 @@ def process_participant(file_path, progress_callback=None):
         fig_trimmed = raw.plot(duration=raw.times[-1], n_channels=raw.info['nchan'], title="Trimmed Raw", show=False)
         fig_individual["Trimmed Raw"] = fig_trimmed
     if progress_callback: progress_callback(2)
-    logger.info("2")
+    logger.info("Step 2 Completed.")
 
-    # Step 1.5: Verify optode positions
+    # Step 3: Verify Optode Placement
     if OPTODE_PLACEMENT:
-        fig_optodes = raw.plot_sensors(show_names=True, to_sphere=True, show=False) # type: ignore
+        fig_optodes = raw.plot_sensors(show_names=SHOW_OPTODE_NAMES, to_sphere=True, show=False) # type: ignore
         fig_individual["Plot Sensors"] = fig_optodes
     if progress_callback: progress_callback(3)
-    logger.info("3")
+    logger.info("Step 3 Completed.")
 
-    # Step 2: Bad from SCI
+    # Step 4: Short/Long Channels
+    if SHORT_CHANNEL:
+        short_chans = get_short_channels(raw, max_dist=SHORT_CHANNEL_THRESH)
+        fig_short_chans = short_chans.plot(duration=raw.times[-1], n_channels=raw.info['nchan'], title="Short Channels Only", show=False)
+        fig_individual["short"] = fig_short_chans
+    else:
+        short_chans = None
+    get_long_channels(raw, min_dist=SHORT_CHANNEL_THRESH, max_dist=LONG_CHANNEL_THRESH) # Don't update the existing raw
+    if progress_callback: progress_callback(4)
+    logger.info("Step 4 Completed.")
+
+    # Step 5: Heart Rate
     if HEART_RATE:
         fig, hr1, hr2, low, high = hr_calc(raw)
         fig_individual["PSD"] = fig
         fig_individual['HeartRate_PSD'] = hr1
         fig_individual['HeartRate_Time'] = hr2
-    if progress_callback: progress_callback(4)
+    if progress_callback: progress_callback(5)
-    logger.info("4")    
+    logger.info("Step 5 Completed.")    
         
+    # Step 6: Scalp Coupling Index    
     bad_sci = []
     if SCI:
-        bad_sci, fig_sci_1, fig_sci_2 = calculate_scalp_coupling(raw, low, high)
+        if HEART_RATE:
+            bad_sci, fig_sci_1, fig_sci_2 = calculate_scalp_coupling(raw, low, high)
+        else:
+            bad_sci, fig_sci_1, fig_sci_2 = calculate_scalp_coupling(raw)
         fig_individual["SCI1"] = fig_sci_1
         fig_individual["SCI2"] = fig_sci_2
-    if progress_callback: progress_callback(5)
+    if progress_callback: progress_callback(6)
-    logger.info("5")
+    logger.info("Step 6 Completed.")
 
-    # Step 2: Bad from SNR
+    # Step 7: Signal to Noise Ratio
     bad_snr = []
     if SNR:
         bad_snr, fig_snr = calculate_signal_noise_ratio(raw)
         fig_individual["SNR1"] = fig_snr
-    if progress_callback: progress_callback(6)
+    if progress_callback: progress_callback(7)
-    logger.info("6")
+    logger.info("Step 7 Completed.")
 
-    # Step 3: Bad from PSP
+    # Step 8: Peak Spectral Power
     bad_psp = []
     if PSP:
         bad_psp, fig_psp1, fig_psp2 = calculate_peak_power(raw)
         fig_individual["PSP1"] = fig_psp1
         fig_individual["PSP2"] = fig_psp2
-    if progress_callback: progress_callback(7)
-    logger.info("7")
-
-    # Step 4: Mark the bad channels
-    raw, fig_dropped, fig_raw_before, bad_channels = mark_bads(raw, bad_sci, bad_snr, bad_psp)
-    if fig_dropped and fig_raw_before is not None:
-        fig_individual["fig2"] = fig_dropped
-        fig_individual["fig3"] = fig_raw_before
     if progress_callback: progress_callback(8)
-    logger.info("8")
+    logger.info("Step 8 Completed.")
+
+    # Step 9: Bad Channels Handling
+    if BAD_CHANNELS_HANDLING != "None":
+        raw, fig_dropped, fig_raw_before, bad_channels = mark_bads(raw, bad_sci, bad_snr, bad_psp)
+        if fig_dropped and fig_raw_before is not None:
+            fig_individual["fig2"] = fig_dropped
+            fig_individual["fig3"] = fig_raw_before
+        if bad_channels:
+            if BAD_CHANNELS_HANDLING == "Interpolate":
+                raw, fig_raw_after = interpolate_fNIRS_bads_weighted_average(raw, max_dist=MAX_DIST, min_neighbors=MIN_NEIGHBORS)
+                fig_individual["fig4"] = fig_raw_after
+            elif BAD_CHANNELS_HANDLING == "Remove":
+                pass
+                #TODO: Is there more needed here?
 
-    # Step 5: Interpolate the bad channels
-    if bad_channels:
-        raw, fig_raw_after = interpolate_fNIRS_bads_weighted_average(raw, bad_channels)
-        fig_individual["fig4"] = fig_raw_after
     if progress_callback: progress_callback(9)
-    logger.info("9")
+    logger.info("Step 9 Completed.")
 
-    # Step 6: Optical Density
+    # Step 10: Optical Density
     raw_od = optical_density(raw)
     fig_raw_od = raw_od.plot(duration=raw.times[-1], n_channels=raw.info['nchan'], title="Optical Density", show=False)
     fig_individual["Optical Density"] = fig_raw_od
     if progress_callback: progress_callback(10)
-    logger.info("10")
+    logger.info("Step 10 Completed.")
 
-    # Step 7: TDDR
+    # Step 11: Temporal Derivative Distribution Repair Filtering
     if TDDR:
         raw_od = temporal_derivative_distribution_repair(raw_od)
         fig_raw_od_tddr = raw_od.plot(duration=raw.times[-1], n_channels=raw.info['nchan'], title="After TDDR (Motion Correction)", show=False)
         fig_individual["TDDR"] = fig_raw_od_tddr
     if progress_callback: progress_callback(11)
-    logger.info("11")
+    logger.info("Step 11 Completed.")
-    
     
+    # Step 12: Wavelet Filtering
     if WAVELET:
         raw_od, fig = calculate_and_apply_wavelet(raw_od)
         fig_individual["Wavelet"] = fig
     if progress_callback: progress_callback(12)
-    logger.info("12")
+    logger.info("Step 12 Completed.")
 
-
+    # Step 13: Haemoglobin Concentration
-    # Step 8: BLL
     raw_haemo = beer_lambert_law(raw_od, ppf=calculate_dpf(file_path))
     fig_raw_haemo_bll = raw_haemo.plot(duration=raw_haemo.times[-1], n_channels=raw_haemo.info['nchan'], title="HbO and HbR Signals", show=False)
     fig_individual["BLL"] = fig_raw_haemo_bll
     if progress_callback: progress_callback(13)
-    logger.info("13")
+    logger.info("Step 13 Completed.")
 
-    # Step 9: ENC
+    # Step 14: Enhance Negative Correlation
     if ENHANCE_NEGATIVE_CORRELATION:
         raw_haemo = enhance_negative_correlation(raw_haemo)
-        fig_raw_haemo_enc = raw_haemo.plot(duration=raw_haemo.times[-1], n_channels=raw_haemo.info['nchan'], title="HbO and HbR Signals", show=False)
+        fig_raw_haemo_enc = raw_haemo.plot(duration=raw_haemo.times[-1], n_channels=raw_haemo.info['nchan'], title="Enhance Negative Correlation", show=False)
         fig_individual["ENC"] = fig_raw_haemo_enc
     if progress_callback: progress_callback(14)
-    logger.info("14")
+    logger.info("Step 14 Completed.")
     
-    # Step 10: Filter
+    # Step 15: Filter
     if FILTER:
         raw_haemo, fig_filter, fig_raw_haemo_filter = filter_the_data(raw_haemo)
         fig_individual["filter1"] = fig_filter
         fig_individual["filter2"] = fig_raw_haemo_filter
     if progress_callback: progress_callback(15)
-    logger.info("15")
+    logger.info("Step 15 Completed.")
 
-    # Step 11: Get short / long channels
+    # Step 16: Extracting Events
-    if SHORT_CHANNEL:
-        short_chans = get_short_channels(raw_haemo, max_dist=SHORT_CHANNEL_THRESH)
-        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, min_dist=SHORT_CHANNEL_THRESH, max_dist=LONG_CHANNEL_THRESH)
-    if progress_callback: progress_callback(16)
-    logger.info("16")
-
-    # Step 12: Events from annotations
     events, event_dict = events_from_annotations(raw_haemo)
     fig_events = plot_events(events, event_id=event_dict, sfreq=raw_haemo.info["sfreq"], show=False)
     fig_individual["events"] = fig_events
-    if progress_callback: progress_callback(17)
+    if progress_callback: progress_callback(16)
-    logger.info("17")
+    logger.info("Step 16 Completed.")
 
-    # Step 13: Epoch calculations
+    # Step 17: Epoch Calculations
     epochs, fig_epochs = epochs_calculations(raw_haemo, events, event_dict)
-    for name, fig in fig_epochs:  # Unpack the tuple here
+    for name, fig in fig_epochs:
-        fig_individual[f"epochs_{name}"] = fig  # Store only the figure, not the name
+        fig_individual[f"epochs_{name}"] = fig
-    if progress_callback: progress_callback(18)
+    if progress_callback: progress_callback(17)
-    logger.info("18")
+    logger.info("Step 17 Completed.")
-
-    # Step 14: Design Matrix
-    events_to_remove = REMOVE_EVENTS
-        
-    filtered_annotations = [ann for ann in raw.annotations if ann['description'] not in events_to_remove]
-    
-    new_annot = Annotations(
-        onset=[ann['onset'] for ann in filtered_annotations],
-        duration=[ann['duration'] for ann in filtered_annotations],
-        description=[ann['description'] for ann in filtered_annotations]
-    )
-    
-    # Set the new annotations
-    raw_haemo.set_annotations(new_annot)
 
+    # Step 18: Design Matrix
     design_matrix, fig_design_matrix = make_design_matrix(raw_haemo, short_chans)
     fig_individual["Design Matrix"] = fig_design_matrix
-    if progress_callback: progress_callback(19)
+    if progress_callback: progress_callback(18)
-    logger.info("19")
+    logger.info("Step 18 Completed.")
 
-    # Step 15: Run GLM
+
-    glm_est = run_glm(raw_haemo, design_matrix)
+    # Step 19: Run GLM
+    glm_est = run_glm(raw_haemo, design_matrix, noise_model=NOISE_MODEL, bins=BINS, n_jobs=N_JOBS, verbose=VERBOSITY)
     # Not used AppData\Local\Packages\PythonSoftwareFoundation.Python.3.13_qbz5n2kfra8p0\LocalCache\local-packages\Python313\site-packages\nilearn\glm\contrasts.py
     # Yes used AppData\Local\Packages\PythonSoftwareFoundation.Python.3.13_qbz5n2kfra8p0\LocalCache\local-packages\Python313\site-packages\mne_nirs\utils\_io.py
 
-    # The p-value is calculated from this t-statistic using the Student’s t-distribution with appropriate degrees of freedom.
+    # The p-value is calculated from this t-statistic using the Student's t-distribution with appropriate degrees of freedom.
     # p_value = 2 * stats.t.cdf(-abs(t_statistic), df)
     # It is a two-tailed p-value.
     # It says how likely it is to observe the effect you did (or something more extreme) if the true effect was zero (null hypothesis).
-    # A small p-value (e.g., < 0.05) suggests the effect is unlikely to be zero — it’s "statistically significant."
+    # A small p-value (e.g., < 0.05) suggests the effect is unlikely to be zero — it's "statistically significant."
     # A large p-value means the data do not provide strong evidence that the effect is different from zero.
 
 
-    if progress_callback: progress_callback(20)
+    if progress_callback: progress_callback(19)
-    logger.info("20")
+    logger.info("19")
 
     # Step 16: Plot GLM results
     fig_glm_result = plot_glm_results(file_path, raw_haemo, glm_est, design_matrix)

main.py

@@ -23,10 +23,9 @@ from pathlib import Path, PurePosixPath
 from datetime import datetime
 from multiprocessing import Process, current_process, freeze_support, Manager
 
+# External library imports
 import numpy as np
 import pandas as pd
-
-# External library imports
 import psutil
 import requests
 
@@ -46,7 +45,7 @@ from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleVa
 from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
 
 
-CURRENT_VERSION = "1.0.0"
+CURRENT_VERSION = "1.2.0"
 
 API_URL = "https://git.research.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
 API_URL_SECONDARY = "https://git.research2.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
@@ -58,7 +57,6 @@ SECTIONS = [
     {
         "title": "Preprocessing",
         "params": [
-            # {"name": "SECONDS_TO_STRIP", "default": 0, "type": int, "help": "Seconds to remove from beginning of all loaded snirf files. Setting this to 0 will remove nothing from the files."},
             {"name": "DOWNSAMPLE", "default": True, "type": bool, "help": "Should the snirf files be downsampled? If this is set to True, DOWNSAMPLE_FREQUENCY will be used as the target frequency to downsample to."},
             {"name": "DOWNSAMPLE_FREQUENCY", "default": 25, "type": int, "help": "Frequency (Hz) to downsample to. If this is set higher than the input data, new data will be interpolated. Only used if DOWNSAMPLE is set to True"},
         ]
@@ -74,12 +72,26 @@ SECTIONS = [
         "title": "Verify Optode Placement",
         "params": [
             {"name": "OPTODE_PLACEMENT", "default": True, "type": bool, "help": "Generate an image for each participant outlining their optode placement."},
+            {"name": "SHOW_OPTODE_NAMES", "default": True, "type": bool, "help": "Should the optode names be written next to their location or not."},
+        ]
+    },
+    {
+        "title": "Short/Long Channels",
+        "params": [
+            {"name": "SHORT_CHANNEL", "default": True, "type": bool, "help": "This should be set to True if the data has a short channel present in the data."},
+            {"name": "SHORT_CHANNEL_THRESH", "default": 0.015, "type": float, "help": "The maximum distance the short channel can be in metres."},
+            {"name": "LONG_CHANNEL_THRESH", "default": 0.045, "type": float, "help": "The maximum distance the long channel can be in metres."},
         ]
     },
     {
         "title": "Heart Rate",
         "params": [
             {"name": "HEART_RATE", "default": True, "type": bool, "help": "Attempt to calculate the participants heart rate."},
+            {"name": "SECONDS_TO_STRIP_HR", "default": 5, "type": int, "help": "Will remove this many seconds from the start and end of the file. Useful if recording before cap is firmly placed, or participant removes cap while still recording."},
+            {"name": "MAX_LOW_HR", "default": 40, "type": int, "help": "Any heart rate windows that average below this value will be rounded up to this value."},
+            {"name": "MAX_HIGH_HR", "default": 200, "type": int, "help": "Any heart rate windows that average above this value will be rounded down to this value."},
+            {"name": "SMOOTHING_WINDOW_HR", "default": 100, "type": int, "help": "How many individual data points to smooth into a single window."},
+            {"name": "HEART_RATE_WINDOW", "default": 25, "type": int, "help": "Used for visualization. Shows the range of the calculated heart rate +- this value."},
         ]
     },
     {
@@ -94,14 +106,12 @@ SECTIONS = [
         "title": "Signal to Noise Ratio",
         "params": [
             {"name": "SNR", "default": True, "type": bool, "help": "Calculate and mark channels bad based on their Signal to Noise Ratio. This metric calculates how much of the observed signal was noise versus how much of it was a useful signal."},
-            # {"name": "SNR_TIME_WINDOW", "default": -1, "type": int, "help": "SNR time window."},
             {"name": "SNR_THRESHOLD", "default": 5.0, "type": float, "help": "SNR threshold (dB). A typical scale would be 0-25, but it is possible for values to be both above and below this range. Higher values correspond to a better signal. If SNR is True, any channels lower than this value will be marked as bad."},
         ]
     },
     {
         "title": "Peak Spectral Power",
         "params": [
-
             {"name": "PSP", "default": True, "type": bool, "help": "Calculate and mark channels bad based on their Peak Spectral Power. This metric calculates the amplitude or strength of a frequency component that is most prominent in a particular frequency range or spectrum."},
             {"name": "PSP_TIME_WINDOW", "default": 3, "type": int, "help": "Independent PSP calculations will be perfomed in a time window for the duration of the value provided, until the end of the file is reached."},
             {"name": "PSP_THRESHOLD", "default": 0.1, "type": float, "help": "PSP threshold. A typical scale would be 0-0.5, but it is possible for values to be above this range. Higher values correspond to a better signal. If PSP is True, any channels lower than this value will be marked as bad."},
@@ -110,15 +120,15 @@ SECTIONS = [
     {
         "title": "Bad Channels Handling",
         "params": [
-            # {"name": "NOT_IMPLEMENTED", "default": True, "type": bool, "help": "Calculate Peak Spectral Power."},
+            {"name": "BAD_CHANNELS_HANDLING", "default": [], "type": list, "options": ["Interpolate", "Remove", "None"], "exclusive": True, "help": "How should we deal with the bad channels that occurred? Note: Some analysis options will only work when this is set to 'Interpolate'."},
-            # {"name": "NOT_IMPLEMENTED", "default": 3, "type": int, "help": "PSP time window."},
+            {"name": "MAX_DIST", "default": 0.03, "type": float, "help": "The maximum distance to look for neighbours when interpolating. Used only when BAD_CHANNELS_HANDLING is set to 'Interpolate'."},
-            # {"name": "NOT_IMPLEMENTED", "default": 0.1, "type": float, "help": "PSP threshold."},
+            {"name": "MIN_NEIGHBORS", "default": 2, "type": int, "help": "The minimumn amount of neighbours needed within the MAX_DIST parameter. Used only when BAD_CHANNELS_HANDLING is set to 'Interpolate'."},
         ]
     },
     {
         "title": "Optical Density",
         "params": [
-            # Intentionally empty (TODO)
+            # NOTE: Intentionally empty
         ]
     },
     {
@@ -139,7 +149,7 @@ SECTIONS = [
     {
         "title": "Haemoglobin Concentration",
         "params": [
-            # Intentionally empty (TODO)
+            # NOTE: Intentionally empty
         ]
     },
     {
@@ -154,24 +164,18 @@ SECTIONS = [
             {"name": "FILTER", "default": True, "type": bool, "help": "Filter the data."},
             {"name": "L_FREQ", "default": 0.005, "type": float, "help": "Any frequencies lower than this value will be removed."},
             {"name": "H_FREQ", "default": 0.3, "type": float, "help": "Any frequencies higher than this value will be removed."},
+            {"name": "L_TRANS_BANDWIDTH", "default": 0.002, "type": float, "help": "How wide the transitional period should be so the data doesn't just drop off on the lower bound."},
+            {"name": "H_TRANS_BANDWIDTH", "default": 0.002, "type": float, "help": "How wide the transitional period should be so the data doesn't just drop off on the upper bound."},
         ]
     },
     {
-        "title": "Short/Long Channels",
+        "title": "Extracting Events*",
-        "params": [
-            {"name": "SHORT_CHANNEL", "default": True, "type": bool, "help": "This should be set to True if the data has a short channel present in the data."},
-            {"name": "SHORT_CHANNEL_THRESH", "default": 0.015, "type": float, "help": "The maximum distance the short channel can be in metres."},
-            {"name": "LONG_CHANNEL_THRESH", "default": 0.045, "type": float, "help": "The maximum distance the long channel can be in metres."},
-        ]
-    },
-    {
-        "title": "Extracting Events",
         "params": [
             #{"name": "EVENTS", "default": True, "type": bool, "help": "Calculate Peak Spectral Power."},
         ]
     },
     {
-        "title": "Epoch Calculations",
+        "title": "Epoch Calculations*",
         "params": [
             #{"name": "EVENTS", "default": True, "type": bool, "help": "Calculate Peak Spectral Power."},
         ]
@@ -179,18 +183,27 @@ SECTIONS = [
     {
         "title": "Design Matrix",
         "params": [
+            {"name": "RESAMPLE", "default": True, "type": bool, "help": "The length of your stimulus."},
+            {"name": "RESAMPLE_FREQ", "default": 1, "type": int, "help": "The length of your stimulus."},
+            
+            {"name": "STIM_DUR", "default": 0.5, "type": float, "help": "The length of your stimulus."},
+            {"name": "HRF_MODEL", "default": "fir", "type": str, "help": "Specifies the hemodynamic response function."},
+            {"name": "DRIFT_MODEL", "default": "cosine", "type": str, "help": "Specifies the desired drift model."},
+            {"name": "HIGH_PASS", "default": 0.01, "type": float, "help": "High-pass frequency in case of a cosine model (in Hz)."},
+            {"name": "DRIFT_ORDER", "default": 1, "type": int, "help": "Order of the drift model (in case it is polynomial)"},
+            {"name": "FIR_DELAYS", "default": "None", "type": range, "help": "In case of FIR design, yields the array of delays used in the FIR model (in scans)."},
+            {"name": "MIN_ONSET", "default": -24, "type": int, "help": "Minimal onset relative to frame times (in seconds)"},
+            {"name": "OVERSAMPLING", "default": 50, "type": int, "help": "Oversampling factor used in temporal convolutions."},
             {"name": "REMOVE_EVENTS", "default": "None", "type": list, "help": "Remove events matching the names provided before generating the Design Matrix"},
-            {"name": "DRIFT_MODEL", "default": "cosine", "type": str, "help": "Drift model for GLM."},
+            {"name": "SHORT_CHANNEL_REGRESSION", "default": True, "type": bool, "help": "Whether to use short channel regression and regress out the short channels. Requires SHORT_CHANNELS to be True and at least one short channel to be found."},
-            # {"name": "DURATION_BETWEEN_ACTIVITIES", "default": 35, "type": int, "help": "Time between activities (s)."},
-            # {"name": "SHORT_CHANNEL_REGRESSION", "default": True, "type": bool, "help": "Use short channel regression."},
         ]
     },
     {
         "title": "General Linear Model",
         "params": [
-            {"name": "TIME_WINDOW_START", "default": "0", "type": int, "help": "Where to start averaging the fir model bins. Only affects the significance and contrast images."},
+            {"name": "NOISE_MODEL", "default": "ar1", "type": str, "help": "Number of jobs for GLM processing."},
-            {"name": "TIME_WINDOW_END", "default": "15", "type": int, "help": "Where to end averaging the fir model bins. Only affects the significance and contrast images."},
+            {"name": "BINS", "default": 0, "type": int, "help": "Number of jobs for GLM processing."},
-            #{"name": "N_JOBS", "default": 1, "type": int, "help": "Number of jobs for GLM processing."},
+            {"name": "N_JOBS", "default": 1, "type": int, "help": "Number of jobs for GLM processing."},
         ]
     },
         {
@@ -202,6 +215,8 @@ SECTIONS = [
     {
         "title": "Other",
         "params": [
+            {"name": "TIME_WINDOW_START", "default": "0", "type": int, "help": "Where to start averaging the fir model bins. Only affects the significance and contrast images."},
+            {"name": "TIME_WINDOW_END", "default": "15", "type": int, "help": "Where to end averaging the fir model bins. Only affects the significance and contrast images."},
             {"name": "MAX_WORKERS", "default": 4, "type": int, "help": "Number of files to be processed at once. Lowering this value may help on underpowered systems."},
         ]
     },
@@ -485,6 +500,7 @@ class UserGuideWindow(QWidget):
         label = QLabel("Progress Bar Stages:", self)
         label2 = QLabel("Stage 1: Load the snirf file\n"
                         "Stage 2: Check the optode positions\n"
+                        "Stage 12: Get Short/Long Channels\n"
                         "Stage 3: Scalp Coupling Index\n"
                         "Stage 4: Signal to Noise Ratio\n"
                         "Stage 5: Peak Spectral Power\n"
@@ -494,7 +510,6 @@ class UserGuideWindow(QWidget):
                         "Stage 9: Temporal Derivative Distribution Repair\n"
                         "Stage 10: Beer Lambert Law\n"
                         "Stage 11: Heart Rate Filtering\n"
-                        "Stage 12: Get Short/Long Channels\n"
                         "Stage 13: Calculate Events from Annotations\n"
                         "Stage 14: Epoch Calculations\n"
                         "Stage 15: Design Matrix\n"
@@ -1358,7 +1373,12 @@ class ParamSection(QWidget):
                 widget.setValidator(QDoubleValidator())
                 widget.setText(str(param["default"]))
             elif param["type"] == list:
-                widget = self._create_multiselect_dropdown(None)
+                if param.get("exclusive", True):
+                    widget = QComboBox()
+                    widget.addItems(param.get("options", []))
+                    widget.setCurrentText(str(param.get("default", "<None Selected>")))
+                else:
+                    widget = self._create_multiselect_dropdown(None)
             else: 
                 widget = QLineEdit()
                 widget.setText(str(param["default"]))
@@ -1466,7 +1486,10 @@ class ParamSection(QWidget):
             if expected_type == bool:
                 values[name] = widget.currentText() == "True"
             elif expected_type == list:
-                values[name] = [x.strip() for x in widget.lineEdit().text().split(",") if x.strip()]
+                if isinstance(widget, FullClickComboBox):
+                    values[name] = [x.strip() for x in widget.lineEdit().text().split(",") if x.strip()]
+                elif isinstance(widget, QComboBox):
+                    values[name] = widget.currentText()
             else:
                 raw_text = widget.text()
                 try:

mne/viz/_3d.py

@@ -1025,7 +1025,7 @@ def _handle_sensor_types(meg, eeg, fnirs):
         fnirs=dict(channels="fnirs", pairs="fnirs_pairs"),
     )
     sensor_alpha = {
-        key: dict(meg_helmet=0.25, meg=0.25).get(key, 0.8)
+        key: dict(meg_helmet=0.25, meg=0.25).get(key, 1.0)
         for ch_dict in alpha_map.values()
         for key in ch_dict.values()
     }

mne/viz/backends/_pyvista.py

@@ -586,7 +586,7 @@ class _PyVistaRenderer(_AbstractRenderer):
                 color = None
             else:
                 scalars = None
-            tube = line.tube(radius, n_sides=self.tube_n_sides)
+            tube = line.tube(radius=radius, n_sides=self.tube_n_sides)
             actor = _add_mesh(
                 plotter=self.plotter,
                 mesh=tube,

version_main.txt

@@ -18,7 +18,7 @@ VSVersionInfo(
            StringStruct('FileDescription', 'FLARES main application'),
            StringStruct('FileVersion', '1.0.0.0'),
            StringStruct('InternalName', 'flares.exe'),
-           StringStruct('LegalCopyright', '© 2025 Tyler de Zeeuw'),
+           StringStruct('LegalCopyright', '© 2025-2026 Tyler de Zeeuw'),
            StringStruct('OriginalFilename', 'flares.exe'),
            StringStruct('ProductName', 'FLARES'),
            StringStruct('ProductVersion', '1.0.0.0')])

version_updater.txt

@@ -18,7 +18,7 @@ VSVersionInfo(
            StringStruct('FileDescription', 'FLARES updater application'),
            StringStruct('FileVersion', '1.0.0.0'),
            StringStruct('InternalName', 'main.exe'),
-           StringStruct('LegalCopyright', '© 2025 Tyler de Zeeuw'),
+           StringStruct('LegalCopyright', '© 2025-2026 Tyler de Zeeuw'),
            StringStruct('OriginalFilename', 'flares_updater.exe'),
            StringStruct('ProductName', 'FLARES Updater'),
            StringStruct('ProductVersion', '1.0.0.0')])