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 clean_plan(self):
self.calculation_plan = CalculationPlan()
self.plan.set_plan(self.calculation_plan)
self.node_type_changed()
self.mask_set = set()
def __init__(self, settings: PartSettings):
super().__init__()
self.settings = settings
self.save_translate_dict: typing.Dict[str, SaveBase] = {x.get_short_name(): x for x in save_dict.values()}
self.plan = PlanPreview(self)
self.save_plan_btn = QPushButton("Save")
self.clean_plan_btn = QPushButton("Remove all")
self.remove_btn = QPushButton("Remove")
self.update_element_chk = QCheckBox("Update element")
self.change_root = EnumComboBox(RootType)
self.save_choose = QComboBox()
self.save_choose.addItem("<none>")
self.save_choose.addItems(list(self.save_translate_dict.keys()))
self.save_btn = QPushButton("Save")
self.segment_profile = SearchableListWidget()
self.pipeline_profile = SearchableListWidget()
self.segment_stack = QTabWidget()
self.segment_stack.addTab(self.segment_profile, "Profile")
self.segment_stack.addTab(self.pipeline_profile, "Pipeline")
self.generate_mask_btn = QPushButton("Add mask")
self.generate_mask_btn.setToolTip("Mask need to have unique name")
self.mask_name = QLineEdit()
self.mask_operation = EnumComboBox(MaskOperation)
self.chanel_num = QSpinBox()
self.choose_channel_for_measurements = QComboBox()
self.choose_channel_for_measurements.addItems(
["Same as segmentation"] + [str(x + 1) for x in range(MAX_CHANNEL_NUM)]
)
self.units_choose = EnumComboBox(Units)
self.units_choose.set_value(self.settings.get("units_value", Units.nm))
self.chanel_num.setRange(0, 10)
self.expected_node_type = None
self.save_constructor = None
self.chose_profile_btn = QPushButton("Add Profile")
self.get_big_btn = QPushButton("Leave the biggest")
self.get_big_btn.hide()
self.get_big_btn.setDisabled(True)
self.measurements_list = SearchableListWidget(self)
self.measurement_name_prefix = QLineEdit(self)
self.add_calculation_btn = QPushButton("Add measurement calculation")
self.information = QTextEdit()
self.information.setReadOnly(True)
self.protect = False
self.mask_set = set()
self.calculation_plan = CalculationPlan()
self.plan.set_plan(self.calculation_plan)
self.segmentation_mask = MaskWidget(settings)
self.file_mask = FileMask()
self.change_root.currentIndexChanged.connect(self.change_root_type)
self.save_choose.currentTextChanged.connect(self.save_changed)
self.measurements_list.currentTextChanged.connect(self.show_measurement)
self.segment_profile.currentTextChanged.connect(self.show_segment)
self.measurements_list.currentTextChanged.connect(self.show_measurement_info)
self.segment_profile.currentTextChanged.connect(self.show_segment_info)
self.pipeline_profile.currentTextChanged.connect(self.show_segment_info)
self.pipeline_profile.currentTextChanged.connect(self.show_segment)
self.mask_name.textChanged.connect(self.mask_name_changed)
self.generate_mask_btn.clicked.connect(self.create_mask)
self.clean_plan_btn.clicked.connect(self.clean_plan)
self.remove_btn.clicked.connect(self.remove_element)
self.mask_name.textChanged.connect(self.mask_text_changed)
self.chose_profile_btn.clicked.connect(self.add_segmentation)
self.get_big_btn.clicked.connect(self.add_leave_biggest)
self.add_calculation_btn.clicked.connect(self.add_measurement)
self.save_plan_btn.clicked.connect(self.add_calculation_plan)
# self.forgot_mask_btn.clicked.connect(self.forgot_mask)
# self.cmap_save_btn.clicked.connect(self.save_to_cmap)
self.save_btn.clicked.connect(self.add_save_to_project)
self.update_element_chk.stateChanged.connect(self.mask_text_changed)
self.update_element_chk.stateChanged.connect(self.show_measurement)
self.update_element_chk.stateChanged.connect(self.show_segment)
self.update_element_chk.stateChanged.connect(self.update_names)
self.segment_stack.currentChanged.connect(self.change_segmentation_table)
plan_box = QGroupBox("Prepare workflow:")
lay = QVBoxLayout()
lay.addWidget(self.plan)
bt_lay = QGridLayout()
bt_lay.setSpacing(1)
bt_lay.addWidget(self.save_plan_btn, 0, 0)
bt_lay.addWidget(self.clean_plan_btn, 0, 1)
bt_lay.addWidget(self.remove_btn, 1, 0)
bt_lay.addWidget(self.update_element_chk, 1, 1)
lay.addLayout(bt_lay)
plan_box.setLayout(lay)
plan_box.setStyleSheet(group_sheet)
other_box = QGroupBox("Other operations:")
other_box.setContentsMargins(0, 0, 0, 0)
bt_lay = QVBoxLayout()
bt_lay.setSpacing(0)
bt_lay.addWidget(QLabel("Root type:"))
bt_lay.addWidget(self.change_root)
bt_lay.addStretch(1)
bt_lay.addWidget(QLabel("Saving:"))
bt_lay.addWidget(self.save_choose)
bt_lay.addWidget(self.save_btn)
other_box.setLayout(bt_lay)
other_box.setStyleSheet(group_sheet)
mask_box = QGroupBox("Use mask from:")
mask_box.setStyleSheet(group_sheet)
self.mask_stack = QTabWidget()
self.mask_stack.addTab(stretch_widget(self.file_mask), "File")
self.mask_stack.addTab(stretch_widget(self.segmentation_mask), "Current ROI")
self.mask_stack.addTab(stretch_widget(self.mask_operation), "Operations on masks")
self.mask_stack.setTabToolTip(2, "Allows to create mask which is based on masks previously added to plan.")
lay = QGridLayout()
lay.setSpacing(0)
lay.addWidget(self.mask_stack, 0, 0, 1, 2)
label = QLabel("Mask name:")
label.setToolTip("Needed if you would like to reuse this mask in tab 'Operations on masks'")
self.mask_name.setToolTip("Needed if you would like to reuse this mask in tab 'Operations on masks'")
lay.addWidget(label, 1, 0)
lay.addWidget(self.mask_name, 1, 1)
lay.addWidget(self.generate_mask_btn, 2, 0, 1, 2)
mask_box.setLayout(lay)
segment_box = QGroupBox("ROI extraction:")
segment_box.setStyleSheet(group_sheet)
lay = QVBoxLayout()
lay.setSpacing(0)
lay.addWidget(self.segment_stack)
lay.addWidget(self.chose_profile_btn)
lay.addWidget(self.get_big_btn)
segment_box.setLayout(lay)
measurement_box = QGroupBox("Set of measurements:")
measurement_box.setStyleSheet(group_sheet)
lay = QGridLayout()
lay.setSpacing(0)
lay.addWidget(self.measurements_list, 0, 0, 1, 2)
lab = QLabel("Name prefix:")
lab.setToolTip("Prefix added before each column name")
lay.addWidget(lab, 1, 0)
lay.addWidget(self.measurement_name_prefix, 1, 1)
lay.addWidget(QLabel("Channel:"), 2, 0)
lay.addWidget(self.choose_channel_for_measurements, 2, 1)
lay.addWidget(QLabel("Units:"), 3, 0)
lay.addWidget(self.units_choose, 3, 1)
lay.addWidget(self.add_calculation_btn, 4, 0, 1, 2)
measurement_box.setLayout(lay)
info_box = QGroupBox("Information")
info_box.setStyleSheet(group_sheet)
lay = QVBoxLayout()
lay.addWidget(self.information)
info_box.setLayout(lay)
layout = QGridLayout()
fst_col = QVBoxLayout()
fst_col.addWidget(plan_box, 1)
fst_col.addWidget(mask_box)
layout.addWidget(plan_box, 0, 0, 5, 1)
# layout.addWidget(plan_box, 0, 0, 3, 1)
# layout.addWidget(mask_box, 3, 0, 2, 1)
# layout.addWidget(segmentation_mask_box, 1, 1)
layout.addWidget(mask_box, 0, 2, 1, 2)
layout.addWidget(other_box, 0, 1)
layout.addWidget(segment_box, 1, 1, 1, 2)
layout.addWidget(measurement_box, 1, 3)
layout.addWidget(info_box, 3, 1, 1, 3)
self.setLayout(layout)
self.generate_mask_btn.setDisabled(True)
self.chose_profile_btn.setDisabled(True)
self.add_calculation_btn.setDisabled(True)
self.mask_allow = False
self.segment_allow = False
self.file_mask_allow = False
self.node_type = NodeType.root
self.node_name = ""
self.plan_node_changed.connect(self.mask_text_changed)
self.plan.changed_node.connect(self.node_type_changed)
self.plan_node_changed.connect(self.show_segment)
self.plan_node_changed.connect(self.show_measurement)
self.plan_node_changed.connect(self.mask_stack_change)
self.mask_stack.currentChanged.connect(self.mask_stack_change)
self.file_mask.value_changed.connect(self.mask_stack_change)
self.mask_name.textChanged.connect(self.mask_stack_change)
self.node_type_changed()
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")