def named_save_action(self):
if self.profile_name.text() in self.settings.measurement_profiles:
ret = QMessageBox.warning(
self,
"Profile exist",
"Profile exist\nWould you like to overwrite it?",
QMessageBox.No | QMessageBox.Yes,
)
if ret == QMessageBox.No:
return
selected_values = []
for i in range(self.profile_options_chosen.count()):
txt = str(self.profile_options_chosen.item(i).text())
selected_values.append((txt, str, txt))
val_dialog = MultipleInput("Set fields name",
list(selected_values),
parent=self)
if val_dialog.exec_():
selected_values = []
for i in range(self.profile_options_chosen.count()):
element: MeasurementListWidgetItem = self.profile_options_chosen.item(
i)
selected_values.append(
MeasurementEntry(val_dialog.result[element.text()],
element.stat))
stat_prof = MeasurementProfile(self.profile_name.text(),
selected_values)
self.settings.measurement_profiles[stat_prof.name] = stat_prof
self.export_profiles_butt.setEnabled(True)
def measurement_profiles():
statistics = [
MeasurementEntry(
"Segmentation Volume",
Volume.get_starting_leaf().replace_(area=AreaType.ROI, per_component=PerComponent.No),
),
MeasurementEntry(
"ROI Components Number",
ComponentsNumber.get_starting_leaf().replace_(area=AreaType.ROI, per_component=PerComponent.No),
),
]
statistics2 = [
MeasurementEntry(
"Mask Volume", Volume.get_starting_leaf().replace_(area=AreaType.Mask, per_component=PerComponent.No)
),
]
return MeasurementProfile("statistic1", statistics), MeasurementProfile("statistic2", statistics + statistics2)
def create_simple_plan(root_type: RootType, save: Save):
parameters = {
"channel": 0,
"minimum_size": 200,
"threshold": {
"name": "Manual",
"values": {
"threshold": 13000
}
},
"noise_filtering": {
"name": "Gauss",
"values": {
"dimension_type": DimensionType.Layer,
"radius": 1.0
}
},
"side_connection": False,
}
segmentation = ROIExtractionProfile(name="test",
algorithm="Lower threshold",
values=parameters)
chosen_fields = [
MeasurementEntry(
name="Segmentation Volume",
calculation_tree=Leaf(name="Volume",
area=AreaType.ROI,
per_component=PerComponent.No),
),
]
statistic = MeasurementProfile(name="base_measure",
chosen_fields=chosen_fields,
name_prefix="")
statistic_calculate = MeasurementCalculate(
channel=-1,
units=Units.µm,
measurement_profile=statistic,
name_prefix="")
tree = CalculationTree(
root_type,
[
CalculationTree(segmentation, [
CalculationTree(statistic_calculate, []),
CalculationTree(save, [])
])
],
)
return CalculationPlan(tree=tree, name="test")
def calculate(self):
if self.settings.roi is None:
QMessageBox.warning(self, "No segmentation",
"need segmentation to work")
return
to_calculate = []
for i in range(self._shift, self.measurement_layout.count()):
# noinspection PyTypeChecker
chk: QCheckBox = self.measurement_layout.itemAt(i).widget()
if chk.isChecked():
leaf: Leaf = MEASUREMENT_DICT[chk.text()].get_starting_leaf()
to_calculate.append(
leaf.replace_(per_component=PerComponent.Yes,
area=AreaType.ROI))
if not to_calculate:
QMessageBox.warning(self, "No measurement",
"Select at least one measurement")
return
profile = MeasurementProfile(
"", [MeasurementEntry(x.name, x) for x in to_calculate])
dial = ExecuteFunctionDialog(
profile.calculate,
kwargs={
"image": self.settings.image,
"channel_num": self.channel_select.get_value(),
"roi": self.settings.roi_info,
"result_units": self.units_select.currentEnum(),
},
)
dial.exec_()
result: MeasurementResult = dial.get_result()
values = result.get_separated()
labels = result.get_labels()
self.result_view.clear()
self.result_view.setColumnCount(len(values) + 1)
self.result_view.setRowCount(len(labels))
for i, val in enumerate(labels):
self.result_view.setItem(i, 0, QTableWidgetItem(val))
for j, values_list in enumerate(values):
for i, val in enumerate(values_list):
self.result_view.setItem(i, j + 1, QTableWidgetItem(str(val)))
def save_action(self):
if self.profile_name.text() in self.settings.measurement_profiles:
ret = QMessageBox.warning(
self,
"Profile exist",
"Profile exist\nWould you like to overwrite it?",
QMessageBox.No | QMessageBox.Yes,
)
if ret == QMessageBox.No:
return
selected_values = []
for i in range(self.profile_options_chosen.count()):
element: MeasurementListWidgetItem = self.profile_options_chosen.item(
i)
selected_values.append(
MeasurementEntry(element.text(), element.stat))
stat_prof = MeasurementProfile(self.profile_name.text(),
selected_values)
self.settings.measurement_profiles[stat_prof.name] = stat_prof
self.settings.dump()
self.export_profiles_butt.setEnabled(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")
