diff --git a/btrack/napari/widgets/_general.py b/btrack/napari/widgets/_general.py
index 3c6273b6..ab69ea40 100644
--- a/btrack/napari/widgets/_general.py
+++ b/btrack/napari/widgets/_general.py
@@ -86,7 +86,6 @@ def create_update_method_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
max_lost_frames.setToolTip(
"Number of frames without observation before marking as lost"
)
- max_lost_frames.setValue(5)
widgets["max_lost"] = ("max lost", max_lost_frames)
not_assign = QtWidgets.QDoubleSpinBox()
@@ -94,7 +93,6 @@ def create_update_method_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
not_assign.setRange(0, 1)
not_assign.setStepType(QtWidgets.QAbstractSpinBox.AdaptiveDecimalStepType)
not_assign.setToolTip("Default probability to not assign a track")
- not_assign.setValue(0.1)
widgets["prob_not_assign"] = (
"P(not track)",
not_assign,
diff --git a/btrack/napari/widgets/_hypothesis.py b/btrack/napari/widgets/_hypothesis.py
index 07f3a170..a35c5b87 100644
--- a/btrack/napari/widgets/_hypothesis.py
+++ b/btrack/napari/widgets/_hypothesis.py
@@ -23,7 +23,6 @@ def _create_hypotheses_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
widget.addItems([f"{h.replace('_', '(')})" for h in hypotheses])
flags = QtCore.Qt.ItemFlags(QtCore.Qt.ItemIsUserCheckable + QtCore.Qt.ItemIsEnabled)
for i, tooltip in enumerate(tooltips):
- widget.item(i).setCheckState(QtCore.Qt.CheckState.Checked)
widget.item(i).setFlags(flags)
widget.item(i).setToolTip(tooltip)
@@ -32,18 +31,12 @@ def _create_hypotheses_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
QtCore.Qt.ItemIsUserCheckable,
)
- # # P_merge should be disabled by default
- widget.item(hypotheses.index("P_merge")).setCheckState(
- QtCore.Qt.CheckState.Unchecked
- )
-
return {"hypotheses": ("hypotheses", widget)}
def _create_scaling_factor_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
"""Create widgets for setting the scaling factors of the HypothesisModel"""
- widget_values = [5.0, 3.0, 10.0, 50.0]
names = [
"lambda_time",
"lambda_dist",
@@ -64,11 +57,10 @@ def _create_scaling_factor_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]
]
scaling_factor_widgets = {}
- for value, name, label, tooltip in zip(widget_values, names, labels, tooltips):
+ for name, label, tooltip in zip(names, labels, tooltips):
widget = QtWidgets.QDoubleSpinBox()
widget.setStepType(QtWidgets.QAbstractSpinBox.AdaptiveDecimalStepType)
widget.setToolTip(tooltip)
- widget.setValue(value)
scaling_factor_widgets[name] = (label, widget)
return scaling_factor_widgets
@@ -83,7 +75,6 @@ def _create_threshold_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
"A threshold distance from the edge of the field of view to add an "
"initialization or termination hypothesis."
)
- distance_threshold.setValue(20.0)
widgets = {"theta_dist": ("distance threshold", distance_threshold)}
time_threshold = QtWidgets.QDoubleSpinBox()
@@ -92,7 +83,6 @@ def _create_threshold_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
"A threshold time from the beginning or end of movie to add "
"an initialization or termination hypothesis."
)
- time_threshold.setValue(5.0)
widgets["theta_time"] = ("time threshold", time_threshold)
apoptosis_threshold = QtWidgets.QSpinBox()
@@ -101,7 +91,6 @@ def _create_threshold_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
"Number of apoptotic detections to be considered a genuine event.\n"
"Detections are counted consecutively from the back of the track"
)
- apoptosis_threshold.setValue(5)
widgets["apop_thresh"] = ("apoptosis threshold", apoptosis_threshold)
return widgets
@@ -116,7 +105,6 @@ def _create_bin_size_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
"Isotropic spatial bin size for considering hypotheses.\n"
"Larger bin sizes generate more hypothesese for each tracklet."
)
- distance_bin_size.setValue(40.0)
widgets = {"dist_thresh": ("distance bin size", distance_bin_size)}
time_bin_size = QtWidgets.QDoubleSpinBox()
@@ -125,7 +113,6 @@ def _create_bin_size_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
"Temporal bin size for considering hypotheses.\n"
"Larger bin sizes generate more hypothesese for each tracklet."
)
- time_bin_size.setValue(2.0)
widgets["time_thresh"] = ("time bin size", time_bin_size)
return widgets
@@ -149,11 +136,9 @@ def create_hypothesis_model_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]
"Miss rate for the segmentation.\n"
"e.g. 1/100 segmentations incorrect gives a segmentation miss rate of 0.01."
)
- segmentation_miss_rate.setValue(0.1)
widgets["segmentation_miss_rate"] = ("miss rate", segmentation_miss_rate)
relax = QtWidgets.QCheckBox()
- relax.setChecked(True) # noqa: FBT003
relax.setToolTip(
"Disable the time and distance thresholds.\n"
"This means that tracks can initialize or terminate anywhere and"
diff --git a/btrack/napari/widgets/_motion.py b/btrack/napari/widgets/_motion.py
index ee27e23f..a4f1893b 100644
--- a/btrack/napari/widgets/_motion.py
+++ b/btrack/napari/widgets/_motion.py
@@ -12,14 +12,12 @@ def _create_sigma_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
P_sigma.setToolTip(
"Magnitude of error in initial estimates.\nUsed to scale the matrix P."
)
- P_sigma.setValue(150.0)
widgets = {"P_sigma": ("max(P)", P_sigma)}
G_sigma = QtWidgets.QDoubleSpinBox()
G_sigma.setRange(0, 500)
G_sigma.setStepType(QtWidgets.QAbstractSpinBox.AdaptiveDecimalStepType)
G_sigma.setToolTip("Magnitude of error in process\nUsed to scale the matrix G.")
- G_sigma.setValue(15.0)
widgets["G_sigma"] = ("max(G)", G_sigma)
R_sigma = QtWidgets.QDoubleSpinBox()
@@ -28,7 +26,6 @@ def _create_sigma_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
R_sigma.setToolTip(
"Magnitude of error in measurements.\nUsed to scale the matrix R."
)
- R_sigma.setValue(5.0)
widgets["R_sigma"] = ("max(R)", R_sigma)
return widgets
@@ -43,7 +40,6 @@ def create_motion_model_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
accuracy.setRange(0.1, 10)
accuracy.setStepType(QtWidgets.QAbstractSpinBox.AdaptiveDecimalStepType)
accuracy.setToolTip("Integration limits for calculating probabilities")
- accuracy.setValue(7.5)
widgets["accuracy"] = ("accuracy", accuracy)
return widgets