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implement the new preferences in the backend

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tyler
2026-07-30 16:15:33 -07:00
parent ebd13927e2
commit 3e0d83ca9b
3 changed files with 351 additions and 165 deletions
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main.py
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@@ -109,7 +109,7 @@ SECTIONS = [
{"name": "SHORT_CHANNELS", "default": True, "type": bool, "advanced": False, "help": "This should be set to True if the data has a short channel present in the data. For more information about short channels, please visit the Wiki."},
{"name": "LONG_CHANNELS", "default": True, "type": bool, "advanced": True, "help": "Should channels exceeding the maximum allowed distance be removed?"},
{"name": "SHORT_CHANNELS_THRESHOLD", "default": 0.015, "type": float, "depends_on": "SHORT_CHANNELS", "advanced": False, "help": "The maximum distance the short channel can be in metres before it is no longer considered a short channel."},
{"name": "LONG_CHANNELS_THRESHOLD", "default": 0.045, "type": float, "advanced": False, "help": "The maximum distance channels can be in metres. Any channel longer than this distance will be discarded."},
{"name": "LONG_CHANNELS_THRESHOLD", "default": 0.045, "type": float, "depends_on": "LONG_CHANNELS", "advanced": False, "help": "The maximum distance channels can be in metres. Any channel longer than this distance will be discarded."},
]
},
{
@@ -131,7 +131,7 @@ SECTIONS = [
"title": "Scalp Coupling Index",
"params": [
{"name": "SCI", "default": True, "type": bool, "advanced": False, "help": "Calculate and mark channels bad based on their Scalp Coupling Index. This metric calculates the quality of the connection between the optode and the scalp."},
{"name": "SCI_USE_HEART_RATE_BAND", "default": True, "type": bool, "depends_on": "SCI", "advanced": False, "help": "Adjust the SCI frequency band using the participant's estimated heart rate."},
{"name": "SCI_USE_HEART_RATE_BAND", "default": True, "type": bool, "depends_on": [{"parent_name": "SCI"}, {"parent_name": "HEART_RATE"}], "advanced": False, "help": "Adjust the SCI frequency band using the participant's estimated heart rate."},
{"name": "SCI_LOW_FREQ", "default": 0.7, "type": float, "depends_on": "SCI_USE_HEART_RATE_BAND", "depends_value": False,"advanced": True, "help": "Lower frequency cutoff for SCI bandpass filtering (Hz)."},
{"name": "SCI_HIGH_FREQ", "default": 1.5, "type": float, "depends_on": "SCI_USE_HEART_RATE_BAND", "depends_value": False, "advanced": True, "help": "Upper frequency cutoff for SCI bandpass filtering (Hz)."},
{"name": "SCI_TIME_WINDOW", "default": 3, "type": int, "depends_on": "SCI", "advanced": False, "help": "Duration of each independent SCI calculation window in seconds."},
@@ -147,7 +147,6 @@ SECTIONS = [
{"name": "SNR_SIGNAL_HIGH_FREQ", "default": 0.5, "type": float, "depends_on": "SNR", "advanced": True, "help": "Upper frequency bound for the signal band used in SNR calculation (Hz)."},
{"name": "SNR_NOISE_LOW_FREQ", "default": 1.0, "type": float, "depends_on": "SNR", "advanced": True, "help": "Lower frequency bound for the noise band used in SNR calculation (Hz)."},
{"name": "SNR_NOISE_HIGH_FREQ", "default": 10.0, "type": float, "depends_on": "SNR", "advanced": True, "help": "Upper frequency bound for the noise band used in SNR calculation (Hz)."},
{"name": "SNR_PLOT_MAX", "default": 20.0, "type": float, "depends_on": "SNR", "advanced": True, "help": "Maximum SNR value displayed on the plot scale (dB)."},
]
},
{
@@ -216,9 +215,9 @@ SECTIONS = [
"title": "Wavelet filtering",
"params": [
{"name": "WAVELET", "default": True, "type": bool, "advanced": False, "help": "Apply Wavelet filtering. It is a method to filter involving decomposition, threholding, and reconstruction."},
{"name": "IQR", "default": 1.5, "type": float, "depends_on": "WAVELET", "advanced": False, "help": "Scaling factor for the Inter-Quartile Range."},
{"name": "WAVELET_TYPE", "default": "db4", "type": str, "depends_on": "WAVELET", "advanced": False, "help": "Wavelet type. Valid values are ['bior1.1', 'bior1.3', 'bior1.5', 'bior2.2', 'bior2.4', 'bior2.6', 'bior2.8', 'bior3.1', 'bior3.3', 'bior3.5', 'bior3.7', 'bior3.9', 'bior4.4', 'bior5.5', 'bior6.8', 'coif1', 'coif2', 'coif3', 'coif4', 'coif5', 'coif6', 'coif7', 'coif8', 'coif9', 'coif10', 'coif11', 'coif12', 'coif13', 'coif14', 'coif15', 'coif16', 'coif17', 'db1', 'db2', 'db3', 'db4', 'db5', 'db6', 'db7', 'db8', 'db9', 'db10', 'db11', 'db12', 'db13', 'db14', 'db15', 'db16', 'db17', 'db18', 'db19', 'db20', 'db21', 'db22', 'db23', 'db24', 'db25', 'db26', 'db27', 'db28', 'db29', 'db30', 'db31', 'db32', 'db33', 'db34', 'db35', 'db36', 'db37', 'db38', 'dmey', 'haar', 'rbio1.1', 'rbio1.3', 'rbio1.5', 'rbio2.2', 'rbio2.4', 'rbio2.6', 'rbio2.8', 'rbio3.1', 'rbio3.3', 'rbio3.5', 'rbio3.7', 'rbio3.9', 'rbio4.4', 'rbio5.5', 'rbio6.8', 'sym2', 'sym3', 'sym4', 'sym5', 'sym6', 'sym7', 'sym8', 'sym9', 'sym10', 'sym11', 'sym12', 'sym13', 'sym14', 'sym15', 'sym16', 'sym17', 'sym18', 'sym19', 'sym20']"},
{"name": "WAVELET_LEVEL", "default": 3, "type": int, "depends_on": "WAVELET", "advanced": False, "help": "Wavelet Decomposition level (must be >= 0)."},
{"name": "IQR", "default": 1.5, "type": float, "depends_on": "WAVELET", "advanced": False, "help": "Scaling factor for the Inter-Quartile Range."},
]
},
{
@@ -239,43 +238,43 @@ SECTIONS = [
"title": "Filtering",
"params": [
{"name": "FILTER", "default": True, "type": bool, "advanced": False, "help": "Should the data be bandpass filtered?"},
{"name": "FILTER_ALGORITHM", "default": ["FIR"], "type": list, "options": ["FIR", "IIR"], "exclusive": True, "advanced": False, "help": "Filtering algorithm."},
{"name": "FILTER_ALGORITHM", "default": ["fir"], "type": list, "options": ["fir", "iir"], "exclusive": True, "advanced": False, "help": "Filtering algorithm."},
{"name": "L_FREQ", "default": 0.005, "type": float, "depends_on": "FILTER", "advanced": False, "help": "Any frequencies lower than this value will be removed."},
{"name": "H_FREQ", "default": 0.3, "type": float, "depends_on": "FILTER", "advanced": False, "help": "Any frequencies higher than this value will be removed."},
{"name": "L_TRANS_BANDWIDTH", "default": 0.002, "type": float, "depends_on": "FILTER", "advanced": True, "help": "Width of the lower transition band to prevent abrupt filter cutoff."},
{"name": "H_TRANS_BANDWIDTH", "default": 0.002, "type": float, "depends_on": "FILTER", "advanced": True, "help": "Width of the upper transition band to prevent abrupt filter cutoff."},
{"name": "IIR_TYPE", "default": ["butterworth"], "type": list, "options": ["butterworth", "chebyshev1", "chebyshev2", "elliptic", "bessel"], "exclusive": True, "depends_on": "FILTER_ALGORITHM", "depends_value": "IIR", "advanced": True, "help": "IIR filter design."},
{"name": "IIR_ORDER", "default": 4, "type": int, "depends_on": "FILTER_ALGORITHM", "depends_value": "IIR", "advanced": True, "help": "Order of the IIR filter."},
# {"name": "IIR_TYPE", "default": ["butterworth"], "type": list, "options": ["butterworth", "chebyshev1", "chebyshev2", "elliptic", "bessel"], "exclusive": True, "depends_on": "FILTER_ALGORITHM", "depends_value": "IIR", "advanced": True, "help": "IIR filter design."},
# {"name": "IIR_ORDER", "default": 4, "type": int, "depends_on": "FILTER_ALGORITHM", "depends_value": "IIR", "advanced": True, "help": "Order of the IIR filter."},
{"name": "FILTER_LENGTH", "default": "auto", "type": str, "depends_on": "FILTER_ALGORITHM", "depends_value": "FIR", "advanced": True, "help": "Length of the FIR filter. 'auto' allows automatic selection."},
{"name": "FILTER_PHASE", "default": ["zero"], "type": list, "options": ["zero", "zero-double", "minimum", "minimum-half"], "exclusive": True, "depends_on": "FILTER_ALGORITHM", "depends_value": "FIR", "advanced": True, "help": "Phase response of the FIR filter."},
{"name": "FILTER_PHASE", "default": ["zero"], "type": list, "options": ["zero", "zero-double", "minimum", "minimum-half", "linear"], "exclusive": True, "depends_on": "FILTER_ALGORITHM", "depends_value": "FIR", "advanced": True, "help": "Phase response of the FIR filter."},
{"name": "FIR_WINDOW", "default": ["hamming"], "type": list, "options": ["hamming", "hann", "blackman"], "exclusive": True, "depends_on": "FILTER_ALGORITHM", "depends_value": "FIR", "advanced": True, "help": "Window function used when designing the FIR filter."},
{"name": "FIR_DESIGN", "default": ["firwin"], "type": list, "options": ["firwin", "firwin2"], "exclusive": True, "depends_on": "FILTER_ALGORITHM", "depends_value": "FIR", "advanced": True, "help": "Method used to design the FIR filter."},
{"name": "IIR_OUTPUT", "default": ["sos"], "type": list, "options": ["sos", "ba", "zpk"], "exclusive": True, "depends_on": "FILTER_ALGORITHM", "depends_value": "IIR", "advanced": True, "help": "Representation used for IIR filter coefficients."},
{"name": "PASSBAND_RIPPLE", "default": 1.0, "type": float, "depends_on": "IIR_TYPE", "depends_value": ["chebyshev1", "elliptic"], "advanced": True, "help": "Maximum allowed ripple in the passband (dB)."},
{"name": "STOPBAND_ATTENUATION", "default": 40.0, "type": float, "depends_on": "IIR_TYPE", "depends_value": ["chebyshev2", "elliptic"], "advanced": True, "help": "Minimum attenuation in the stopband (dB)."},
# {"name": "IIR_OUTPUT", "default": ["sos"], "type": list, "options": ["sos", "ba", "zpk"], "exclusive": True, "depends_on": "FILTER_ALGORITHM", "depends_value": "IIR", "advanced": True, "help": "Representation used for IIR filter coefficients."},
# {"name": "PASSBAND_RIPPLE", "default": 1.0, "type": float, "depends_on": "IIR_TYPE", "depends_value": ["chebyshev1", "elliptic"], "advanced": True, "help": "Maximum allowed ripple in the passband (dB)."},
# {"name": "STOPBAND_ATTENUATION", "default": 40.0, "type": float, "depends_on": "IIR_TYPE", "depends_value": ["chebyshev2", "elliptic"], "advanced": True, "help": "Minimum attenuation in the stopband (dB)."},
{"name": "FILTER_PAD", "default": ["reflect_limited"], "type": list, "options": ["reflect_limited", "reflect", "edge", "constant"], "exclusive": True, "depends_on": "FILTER", "advanced": True, "help": "Padding strategy used during filtering to reduce edge artifacts."},
{"name": "SKIP_BY_ANNOTATION", "default": ["edge", "bad_acq_skip"], "type": list, "depends_on": "FILTER", "advanced": True, "help": "Annotations that should be skipped when applying the filter."},
# {"name": "SKIP_BY_ANNOTATION", "default": ["edge", "bad_acq_skip"], "type": list, "depends_on": "FILTER", "advanced": True, "help": "Annotations that should be skipped when applying the filter."},
{"name": "FILTER_N_JOBS", "default": 1, "type": int, "advanced": True, "help": "Number of parallel jobs used during filtering. Use -1 to use all available CPUs."},
]
},
{
"title": "Extracting Events*",
"title": "Extracting Events",
"params": [
{"name": "EVENTS", "default": True, "type": bool, "advanced": False, "help": "Extract events from annotations for visualization and downstream event-based analysis."},
{"name": "EVENTS", "default": True, "type": bool, "advanced": True, "help": "Extract events from annotations for visualization and downstream event-based analysis."},
{"name": "EVENT_ID", "default": "auto", "type": str, "advanced": True, "help": "Controls how annotation descriptions are converted into event identifiers. Use 'auto' for automatic event detection."},
{"name": "EVENT_REGEX", "default": "^(?![Bb][Aa][Dd]|[Ee][Dd][Gg][Ee]).*$", "type": str, "advanced": True, "help": "Regular expression used to select which annotations are converted into events. By default, bad and edge annotations are ignored."},
{"name": "EVENT_CHUNK_DURATION", "default": None, "type": float, "advanced": True, "help": "If provided, creates repeated events at this interval within longer annotations instead of only using annotation onset times."},
{"name": "EVENT_REGEX", "default": r"^(?![Bb][Aa][Dd]|[Ee][Dd][Gg][Ee]).*$", "type": str, "advanced": True, "help": "Regular expression used to select which annotations are converted into events. By default, bad and edge annotations are ignored."},
# {"name": "EVENT_CHUNK_DURATION", "default": 0.0, "type": float, "advanced": True, "help": "If provided, creates repeated events at this interval within longer annotations instead of only using annotation onset times."},
]
},
{
"title": "Epoch Calculations",
"params": [
{"name": "EPOCHS", "default": True, "type": bool, "advanced": False, "help": "Create epochs around extracted events for condition-based analysis."},
{"name": "EPOCHS", "default": True, "type": bool, "depends_on": "EVENTS", "advanced": True, "help": "Create epochs around extracted events for condition-based analysis."},
{"name": "EPOCH_HANDLING", "default": ["shift"], "type": list, "options": ["shift", "strict", "drop"], "exclusive": True, "advanced": False, "help": "How to handle events occurring at the same sample. Shift moves conflicting events forward, strict raises an error, and drop removes conflicting events."},
{"name": "MAX_SHIFT", "default": 5, "type": int, "depends_on": "EPOCH_HANDLING", "depends_value": "shift", "advanced": True, "help": "Maximum number of samples to shift conflicting events before failing."},
{"name": "T_MIN", "default": -5.0, "type": float, "advanced": False, "help": "Time in seconds before each event to include in the epoch."},
{"name": "T_MAX", "default": 15.0, "type": float, "advanced": False, "help": "Time in seconds after each event to include in the epoch."},
{"name": "BASELINE", "default": ["pre_event"], "type": list, "options": ["none", "pre_event"], "exclusive": True, "advanced": False, "help": "Baseline correction applied to epochs. Pre-event uses the period before the event as baseline."},
# {"name": "BASELINE", "default": ["pre_event"], "type": list, "options": ["none", "pre_event"], "exclusive": True, "advanced": False, "help": "Baseline correction applied to epochs. Pre-event uses the period before the event as baseline."},
{"name": "REJECT_EPOCHS", "default": True, "type": bool, "advanced": False, "help": "Automatically reject epochs containing excessively large haemoglobin amplitude changes."},
{"name": "REJECT_HBO_THRESHOLD", "default": 80e-7, "type": float, "depends_on": "REJECT_EPOCHS", "advanced": True, "help": "Maximum allowed HbO amplitude before an epoch is rejected."},
]
@@ -310,13 +309,6 @@ SECTIONS = [
{"name": "JSON_LOCATION", "default": "", "type": "json_file", "advanced": False, "help": "Location of the JSON file containing region of interest results for significance calculations."},
]
},
{
"title": "Contrast",
"params": [
{"name": "CONTRAST_BASELINE", "default": True, "type": bool, "advanced": True, "help": "Calculate contrasts comparing each condition against zero/baseline. This may not always represent a meaningful physiological baseline in fNIRS."},
{"name": "CONTRAST_PAIRWISE", "default": True, "type": bool, "advanced": True, "help": "Calculate contrasts comparing each experimental condition against every other condition. The number of contrasts increases with the number of conditions."}
]
},
{
"title": "Other",
"params": [
@@ -1445,7 +1437,7 @@ class MainApplication(QMainWindow):
if self.advanced_parameters:
self.update_sections(0)
if hasattr(self, 'recent_files_menu'):
self.update_recent_files_menu()