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updating plotprobe GUI to include tstat thresholding #131

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172 changes: 141 additions & 31 deletions src/cedalion/vis/misc/plot_probe_gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
import numpy as np
from matplotlib.backends.backend_qtagg import FigureCanvas
from matplotlib.backends.backend_qtagg import NavigationToolbar2QT as NavigationToolbar
from matplotlib.backends.qt_compat import QtWidgets
from matplotlib.backends.qt_compat import QtWidgets, QtGui
from matplotlib.figure import Figure

import cedalion
Expand All @@ -26,10 +26,11 @@


class _MAIN_GUI(QtWidgets.QMainWindow):
def __init__(self, snirfData=None, geo2d=None, geo3d=None):
def __init__(self, snirfData=None, stderr=None, geo2d=None, geo3d=None):
# Initialize
super().__init__()
self.snirfData = snirfData
self.stderr = stderr
self.geo2d = geo2d
self.geo3d = geo3d

Expand All @@ -43,7 +44,7 @@ def __init__(self, snirfData=None, geo2d=None, geo3d=None):
window_layout.setSpacing(10)

# Set Minimum Size
self.setMinimumSize(1000, 850)
self.setMinimumSize(800, 600)

# Set Window Title
self.setWindowTitle("Plot Probe")
Expand Down Expand Up @@ -139,6 +140,28 @@ def __init__(self, snirfData=None, geo2d=None, geo3d=None):
## Add Prune Channels
control_panel_layout.addWidget(prune_channels, stretch=1)

# Create t-stat thresh control - only if standard error is provided
if self.stderr is not None:
tstat_control = QtWidgets.QGroupBox("T-Stat Threshold")
tstat_control_layout = QtWidgets.QVBoxLayout()
tstat_control_layout.setSpacing(10)
tstat_control.setLayout(tstat_control_layout)

## Set up T-stat threshold controller
tstat_threshold_layout = QtWidgets.QHBoxLayout()
self.tstat_threshold = QtWidgets.QDoubleSpinBox()
self.tstat_threshold.setValue(0) # Default: no threshold
self.tstat_threshold.setRange(-100, 100)
self.tstat_threshold.setSingleStep(0.5)
self.tstat_threshold.setDecimals(2)
self.tstat_threshold.valueChanged.connect(self._tstat_threshold_changed)
tstat_threshold_layout.addWidget(QtWidgets.QLabel("Threshold"))
tstat_threshold_layout.addWidget(self.tstat_threshold)
tstat_control_layout.addLayout(tstat_threshold_layout)

## Add T-stat control
control_panel_layout.addWidget(tstat_control, stretch=1)

# Create Probe Control
probe_control = QtWidgets.QGroupBox("Probe")
probe_control_layout = QtWidgets.QVBoxLayout()
Expand Down Expand Up @@ -186,7 +209,7 @@ def __init__(self, snirfData=None, geo2d=None, geo3d=None):
# control_panel_layout.addWidget(ref_point,stretch=1)

# Create button action for opening file
open_btn = QtWidgets.QAction("Open...", self)
open_btn = QtGui.QAction("Open...", self)
open_btn.setStatusTip("Open SNIRF file")
open_btn.triggered.connect(self._open_dialog)

Expand All @@ -199,9 +222,10 @@ def __init__(self, snirfData=None, geo2d=None, geo3d=None):
file_menu.addAction(open_btn)

if self.snirfData is not None:
time_dim = 'reltime' if 'reltime' in self.snirfData.dims else 'time' # Detect time dimension
if np.shape(self.snirfData)[1] != len(self.snirfData.channel):
self.snirfData = self.snirfData.transpose(
"trial_type", "channel", "chromo", "reltime"
"trial_type", "channel", "chromo", time_dim
)

self.sPos = self.geo2d.sel(
Expand Down Expand Up @@ -272,6 +296,25 @@ def _init_calc(self):
self.fade_factor = 0.3 ##### Connect?
self.lineWidth = 0.7 ##### Connect?

if 'reltime' in self.snirfData.dims: # handle 'time' or 'reltime'
self.time_dim = 'reltime'
elif 'time' in self.snirfData.dims:
self.time_dim = 'time'
else:
raise ValueError("Data must have either 'time' or 'reltime' dimension")


# T-stat calculation
self.tstat_thresh = 0 # Initialize threshold
if self.stderr is not None:
# Calculate t-statistic: mean / stderr
self.tstat = self.snirfData / self.stderr
# Get max absolute t-stat per channel across time for thresholding
self.tstat_max = np.abs(self.tstat).max(dim=self.time_dim) # Max across time
else:
self.tstat = None
self.tstat_max = None

self.conditions.clear()
self.opt2circ.setChecked(False)
self.measline.setChecked(False)
Expand Down Expand Up @@ -354,14 +397,21 @@ def _init_calc(self):

# Extract time information
try:
self.t = self.snirfData.time.values
except Exception:
pass

try:
self.t = self.snirfData.reltime.values
self.t = self.snirfData[self.time_dim].values # CHANGE to use self.time_dim
except Exception:
pass
# Fallback to trying both
try:
self.t = self.snirfData.time.values
except Exception:
self.t = self.snirfData.reltime.values
# try:
# self.t = self.snirfData.time.values
# except Exception:
# pass
# try:
# self.t = self.snirfData.reltime.values
# except Exception:
# pass

self.minT = min(self.t)
self.maxT = max(self.t)
Expand Down Expand Up @@ -424,37 +474,86 @@ def _init_calc(self):
self._draw_hrf()
self.conditions.setCurrentRow(0)

# def _change_hrf_vis(self): # orig
# for i_con in range(self.trial_types):
# if i_con == self.conditions.currentRow():
# for i_ch in range(self.channels):
# if (
# self.chan_dist[i_ch] >= self.channel_min_dist
# and self.chan_dist[i_ch] <= self.ssFadeThres
# ):
# for i_col in range(self.chromophores):
# self.hrf[
# i_con * self.channels * self.chromophores
# + i_ch * self.chromophores
# + i_col
# ].set_color(self.chrom[i_col] + [self.fade_factor])
# elif (
# self.chan_dist[i_ch] >= self.ssFadeThres
# and self.chan_dist[i_ch] <= self.channel_max_dist
# ):
# for i_col in range(self.chromophores):
# self.hrf[
# i_con * self.channels * self.chromophores
# + i_ch * self.chromophores
# + i_col
# ].set_color(self.chrom[i_col] + [1])
# else:
# for i_col in range(self.chromophores):
# self.hrf[
# i_con * self.channels * self.chromophores
# + i_ch * self.chromophores
# + i_col
# ].set_color(self.chrom[i_col] + [0])
# else:
# for i_ch in range(self.channels):
# for i_col in range(self.chromophores):
# self.hrf[
# i_con * self.channels * self.chromophores
# + i_ch * self.chromophores
# + i_col
# ].set_color(self.chrom[i_col] + [0])

# self._ax.figure.canvas.draw()

def _change_hrf_vis(self):
for i_con in range(self.trial_types):
if i_con == self.conditions.currentRow():
for i_ch in range(self.channels):
# Check if channel meets t-stat threshold
meets_tstat = True
if self.tstat_max is not None:
# Check if ANY chromophore meets threshold for this channel
meets_tstat = any(
self.tstat_max.sel(trial_type=self.snirfData.trial_type[i_con]).values[i_ch, i_col] >= self.tstat_thresh
for i_col in range(self.chromophores)
)

# Determine alpha based on distance and t-stat
if (
self.chan_dist[i_ch] >= self.channel_min_dist
and self.chan_dist[i_ch] <= self.ssFadeThres
):
for i_col in range(self.chromophores):
self.hrf[
i_con * self.channels * self.chromophores
+ i_ch * self.chromophores
+ i_col
].set_color(self.chrom[i_col] + [self.fade_factor])
base_alpha = self.fade_factor
elif (
self.chan_dist[i_ch] >= self.ssFadeThres
and self.chan_dist[i_ch] <= self.channel_max_dist
):
for i_col in range(self.chromophores):
self.hrf[
i_con * self.channels * self.chromophores
+ i_ch * self.chromophores
+ i_col
].set_color(self.chrom[i_col] + [1])
base_alpha = 1
else:
for i_col in range(self.chromophores):
self.hrf[
i_con * self.channels * self.chromophores
+ i_ch * self.chromophores
+ i_col
].set_color(self.chrom[i_col] + [0])
base_alpha = 0

# Apply t-stat threshold: fade if doesn't meet threshold
if not meets_tstat and base_alpha > 0:
base_alpha = base_alpha * 0.5 # Further fade channels below threshold

# Set color for each chromophore
for i_col in range(self.chromophores):
self.hrf[
i_con * self.channels * self.chromophores
+ i_ch * self.chromophores
+ i_col
].set_color(self.chrom[i_col] + [base_alpha])
else:
for i_ch in range(self.channels):
for i_col in range(self.chromophores):
Expand Down Expand Up @@ -491,6 +590,8 @@ def _toggle_circles(self):
if self.opt2circ.isChecked():
self.src_optodes.set_color([1, 0, 0])
self.det_optodes.set_color([0, 0, 1])
self.src_optodes.set_markersize(3) # ADD THIS - Make circles smaller
self.det_optodes.set_markersize(3) # ADD THIS - Make circles smaller

for idx, source in enumerate(self.sPos.label):
self.src_label[idx].set_color([1, 0, 0, 0])
Expand All @@ -499,6 +600,8 @@ def _toggle_circles(self):
else:
self.src_optodes.set_color([1, 0, 0, 0])
self.det_optodes.set_color([0, 0, 1, 0])
self.src_optodes.set_markersize(5) # ADD THIS - Reset to original size
self.det_optodes.set_markersize(5) # ADD THIS - Reset to original size

for idx, source in enumerate(self.sPos.label):
self.src_label[idx].set_color([1, 0, 0, 1])
Expand Down Expand Up @@ -567,6 +670,11 @@ def _ssfade_changed(self, i):
self.ssFadeThres = i
self._change_hrf_vis()

def _tstat_threshold_changed(self, i):
# Pass the new t-stat threshold and update HRF visibility
self.tstat_thresh = i
self._change_hrf_vis()

def _draw_hrf(self):
print("Plotting Optodes!")
t0 = time.time()
Expand Down Expand Up @@ -656,6 +764,7 @@ def run_vis(
blockaverage: cdt.NDTimeSeries,
geo2d: cdt.LabeledPoints,
geo3d: cdt.LabeledPoints,
stderr: cdt.NDTimeSeries = None, # optional standerr input
):
"""Opens the visualization GUI.

Expand All @@ -666,6 +775,7 @@ def run_vis(
"""

app = QtWidgets.QApplication(sys.argv)
main_gui = _MAIN_GUI(snirfData=blockaverage, geo2d=geo2d, geo3d=geo3d)
#main_gui = _MAIN_GUI(snirfData=blockaverage, geo2d=geo2d, geo3d=geo3d)
main_gui = _MAIN_GUI(snirfData=blockaverage, stderr=stderr, geo2d=geo2d, geo3d=geo3d)
main_gui.show()
sys.exit(app.exec())
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