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tyler
2026-01-14 23:54:03 -08:00
parent 473c945563
commit fe4e8904b4
8 changed files with 225 additions and 186 deletions
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83
main.py
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@@ -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": "NOT_IMPLEMENTED", "default": 3, "type": int, "help": "PSP time window."},
# {"name": "NOT_IMPLEMENTED", "default": 0.1, "type": float, "help": "PSP threshold."},
{"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": "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": "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",
"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",
"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": "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."},
{"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."},
]
},
{
"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": "TIME_WINDOW_END", "default": "15", "type": int, "help": "Where to end averaging the fir model bins. Only affects the significance and contrast images."},
#{"name": "N_JOBS", "default": 1, "type": int, "help": "Number of jobs for GLM processing."},
{"name": "NOISE_MODEL", "default": "ar1", "type": str, "help": "Number of jobs for GLM processing."},
{"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."},
]
},
{
@@ -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: