def proportion_action(self):
# TODO use get_parameters
if self.chosen_element is None:
item = self.profile_options.currentItem()
self.chosen_element_area = self.get_parameters(
deepcopy(item.stat),
self.measurement_area_choose.get_value(),
self.per_component.get_value(),
self.power_num.value(),
)
if self.chosen_element_area is None:
return
self.chosen_element = item
item.setIcon(QIcon(os.path.join(icons_dir, "task-accepted.png")))
elif (self.profile_options.currentItem() == self.chosen_element
and self.measurement_area_choose.get_value()
== self.chosen_element_area.area
and self.per_component.get_value()
== self.chosen_element_area.per_component):
self.chosen_element.setIcon(QIcon())
self.chosen_element = None
else:
item: MeasurementListWidgetItem = self.profile_options.currentItem(
)
leaf = self.get_parameters(
deepcopy(item.stat),
self.measurement_area_choose.get_value(),
self.per_component.get_value(),
self.power_num.value(),
)
if leaf is None:
return
lw = MeasurementListWidgetItem(
Node(op="/", left=self.chosen_element_area, right=leaf))
lw.setToolTip("User defined")
self.profile_options_chosen.addItem(lw)
self.chosen_element.setIcon(QIcon())
self.chosen_element = None
self.chosen_element_area = None
if self.good_name():
self.save_butt.setEnabled(True)
self.save_butt_with_name.setEnabled(True)
if self.profile_options.count() == 0:
self.choose_butt.setDisabled(True)
def create_calculation_plan():
parameters = {
"channel": 1,
"minimum_size": 200,
"threshold": {
"name": "Base/Core",
"values": {
"core_threshold": {
"name": "Manual",
"values": {
"threshold": 30000
}
},
"base_threshold": {
"name": "Manual",
"values": {
"threshold": 13000
}
},
},
},
"noise_filtering": {
"name": "Gauss",
"values": {
"dimension_type": DimensionType.Layer,
"radius": 1.0
}
},
"side_connection": False,
"sprawl_type": {
"name": "Euclidean",
"values": {}
},
}
segmentation = ROIExtractionProfile(
name="test",
algorithm="Lower threshold with watershed",
values=parameters)
mask_suffix = MaskSuffix(name="", suffix="_mask")
chosen_fields = [
MeasurementEntry(
name="Segmentation Volume",
calculation_tree=Leaf(name="Volume",
area=AreaType.ROI,
per_component=PerComponent.No),
),
MeasurementEntry(
name="Segmentation Volume/Mask Volume",
calculation_tree=Node(
left=Leaf(name="Volume",
area=AreaType.ROI,
per_component=PerComponent.No),
op="/",
right=Leaf(name="Volume",
area=AreaType.Mask,
per_component=PerComponent.No),
),
),
MeasurementEntry(
"Segmentation Components Number",
calculation_tree=Leaf("Components number",
area=AreaType.ROI,
per_component=PerComponent.No),
),
]
statistic = MeasurementProfile(name="base_measure",
chosen_fields=chosen_fields,
name_prefix="")
statistic_calculate = MeasurementCalculate(
channel=0,
units=Units.µm,
measurement_profile=statistic,
name_prefix="")
tree = CalculationTree(
RootType.Image,
[
CalculationTree(mask_suffix, [
CalculationTree(segmentation,
[CalculationTree(statistic_calculate, [])])
])
],
)
return CalculationPlan(tree=tree, name="test")