Don't set widget values in the widgets (as done from file) (#379)

* Remove unnecessary `.setValue` calls

* Check status done by config file

btrack/napari/widgets/_general.py

@@ -86,15 +86,13 @@ 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()
     not_assign.setDecimals(3)
     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"] = (
         "<b>P</b>(not track)",
         not_assign,

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"

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(<b>P</b>)", 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(<b>G</b>)", 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(<b>R</b>)", 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