class SearchComponentModal(QtPopup):
def __init__(self, image_view: ImageView, search_type: SearchType,
component_num: int, max_components):
super().__init__(image_view)
self.image_view = image_view
self.zoom_to = QEnumComboBox(self, SearchType)
self.zoom_to.setCurrentEnum(search_type)
self.zoom_to.currentEnumChanged.connect(self._component_num_changed)
self.component_selector = QSpinBox()
self.component_selector.valueChanged.connect(
self._component_num_changed)
self.component_selector.setMaximum(max_components)
self.component_selector.setValue(component_num)
layout = QHBoxLayout()
layout.addWidget(QLabel("Component:"))
layout.addWidget(self.component_selector)
layout.addWidget(QLabel("Selection:"))
layout.addWidget(self.zoom_to)
self.frame.setLayout(layout)
def _component_num_changed(self):
if self.zoom_to.currentEnum() == SearchType.Highlight:
self.image_view.component_mark(self.component_selector.value(),
flash=True)
else:
self.image_view.component_zoom(self.component_selector.value())
def closeEvent(self, event):
super().closeEvent(event)
self.image_view.component_unmark(0)
def __init__(self, settings: ViewSettings, start_name: str):
if start_name == "":
raise ValueError(
"ChannelProperty should have non empty start_name")
super().__init__()
self.current_name = start_name
self.current_channel = 0
self._settings = settings
self.widget_dict: typing.Dict[str, ColorComboBoxGroup] = {}
self.minimum_value = CustomSpinBox(self)
self.minimum_value.setRange(-(10**6), 10**6)
self.minimum_value.valueChanged.connect(self.range_changed)
self.maximum_value = CustomSpinBox(self)
self.maximum_value.setRange(-(10**6), 10**6)
self.maximum_value.valueChanged.connect(self.range_changed)
self.fixed = QCheckBox("Fix range")
self.fixed.stateChanged.connect(self.lock_channel)
self.use_filter = QEnumComboBox(enum_class=NoiseFilterType)
self.use_filter.setToolTip("Only current channel")
self.filter_radius = QDoubleSpinBox()
self.filter_radius.setSingleStep(0.1)
self.filter_radius.valueChanged.connect(self.gauss_radius_changed)
self.use_filter.currentIndexChanged.connect(self.gauss_use_changed)
self.gamma_value = QDoubleSpinBox()
self.gamma_value.setRange(0.01, 100)
self.gamma_value.setSingleStep(0.1)
self.gamma_value.valueChanged.connect(self.gamma_value_changed)
self.collapse_widget = CollapseCheckbox("Channel property")
self.collapse_widget.add_hide_element(self.minimum_value)
self.collapse_widget.add_hide_element(self.maximum_value)
self.collapse_widget.add_hide_element(self.fixed)
self.collapse_widget.add_hide_element(self.use_filter)
self.collapse_widget.add_hide_element(self.filter_radius)
self.collapse_widget.add_hide_element(self.gamma_value)
layout = QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.addWidget(self.collapse_widget, 0, 0, 1, 4)
label1 = QLabel("Min bright:")
layout.addWidget(label1, 1, 0)
layout.addWidget(self.minimum_value, 1, 1)
label2 = QLabel("Max bright:")
layout.addWidget(label2, 2, 0)
layout.addWidget(self.maximum_value, 2, 1)
layout.addWidget(self.fixed, 1, 2, 1, 2)
label3 = QLabel("Filter:")
layout.addWidget(label3, 3, 0, 1, 1)
layout.addWidget(self.use_filter, 3, 1, 1, 1)
layout.addWidget(self.filter_radius, 3, 2, 1, 1)
label4 = QLabel("Gamma:")
layout.addWidget(label4, 4, 0, 1, 1)
layout.addWidget(self.gamma_value, 4, 1, 1, 1)
self.setLayout(layout)
self.collapse_widget.add_hide_element(label1)
self.collapse_widget.add_hide_element(label2)
self.collapse_widget.add_hide_element(label3)
self.collapse_widget.add_hide_element(label4)
def __init__(
self,
title,
data_sequence,
unit: Units,
parent=None,
input_type=QDoubleSpinBox,
decimals=2,
data_range=(0, 100000),
single_step=1,
):
"""
:type data_sequence: list[(float)]
:param data_sequence:
:type input_type: () -> (QDoubleSpinBox | QSpinBox)
:param parent:
:type decimals: int|None
:type data_range: (float, float)
:type single_step: float
:type title: str
"""
super().__init__(parent)
layout = QHBoxLayout()
layout.addWidget(QLabel(f"<strong>{title}</strong>"))
self.elements = []
if len(data_sequence) == 2:
data_sequence = (1,) + tuple(data_sequence)
for name, value in zip(["z", "y", "x"], data_sequence):
lab = QLabel(name + ":")
layout.addWidget(lab)
val = input_type()
val.setButtonSymbols(QAbstractSpinBox.NoButtons)
if isinstance(val, QDoubleSpinBox):
val.setDecimals(decimals)
val.setRange(*data_range)
val.setValue(value * UNIT_SCALE[unit.value])
val.setAlignment(Qt.AlignRight)
val.setSingleStep(single_step)
font = val.font()
fm = QFontMetrics(font)
val_len = max(fm.width(str(data_range[0])), fm.width(str(data_range[1]))) + fm.width(" " * 8)
val.setFixedWidth(val_len)
layout.addWidget(val)
self.elements.append(val)
self.units = QEnumComboBox(enum_class=Units)
self.units.setCurrentEnum(unit)
layout.addWidget(self.units)
self.has_units = True
layout.addStretch(1)
self.setLayout(layout)
def __init__(self, image_view: ImageView, search_type: SearchType,
component_num: int, max_components):
super().__init__(image_view)
self.image_view = image_view
self.zoom_to = QEnumComboBox(self, SearchType)
self.zoom_to.setCurrentEnum(search_type)
self.zoom_to.currentEnumChanged.connect(self._component_num_changed)
self.component_selector = QSpinBox()
self.component_selector.valueChanged.connect(
self._component_num_changed)
self.component_selector.setMaximum(max_components)
self.component_selector.setValue(component_num)
layout = QHBoxLayout()
layout.addWidget(QLabel("Component:"))
layout.addWidget(self.component_selector)
layout.addWidget(QLabel("Selection:"))
layout.addWidget(self.zoom_to)
self.frame.setLayout(layout)
def __init__(self, settings: StackSettings, parent=None):
""":type settings: ImageSettings"""
super().__init__(parent)
self._settings = settings
self.path = QTextEdit("<b>Path:</b> example image")
self.path.setWordWrapMode(QTextOption.WrapAnywhere)
self.path.setReadOnly(True)
self.setMinimumHeight(20)
self.spacing = [QDoubleSpinBox() for _ in range(3)]
self.multiple_files = QCheckBox("Show multiple files panel")
self.multiple_files.setChecked(
settings.get("multiple_files_widget", True))
self.multiple_files.stateChanged.connect(self.set_multiple_files)
units_value = self._settings.get("units_value", Units.nm)
for el in self.spacing:
el.setAlignment(Qt.AlignRight)
el.setButtonSymbols(QAbstractSpinBox.NoButtons)
el.setRange(0, 100000)
# noinspection PyUnresolvedReferences
el.valueChanged.connect(self.image_spacing_change)
self.units = QEnumComboBox(enum_class=Units)
self.units.setCurrentEnum(units_value)
# noinspection PyUnresolvedReferences
self.units.currentIndexChanged.connect(self.update_spacing)
self.add_files = AddFiles(settings, btn_layout=FlowLayout)
spacing_layout = QFormLayout()
spacing_layout.addRow("x:", self.spacing[0])
spacing_layout.addRow("y:", self.spacing[1])
spacing_layout.addRow("z:", self.spacing[2])
spacing_layout.addRow("Units:", self.units)
layout = QVBoxLayout()
layout.addWidget(self.path)
layout.addWidget(QLabel("Image spacing:"))
layout.addLayout(spacing_layout)
layout.addWidget(self.add_files)
layout.addStretch(1)
layout.addWidget(self.multiple_files)
self.setLayout(layout)
self._settings.image_changed[str].connect(self.set_image_path)
def __init__(self, settings: StackSettings, parent=None):
super().__init__(parent)
self.settings = settings
self.calculate_btn = QPushButton("Calculate")
self.calculate_btn.clicked.connect(self.calculate)
self.result_view = QTableWidget()
self.channel_select = ChannelComboBox()
self.units_select = QEnumComboBox(enum_class=Units)
self.units_select.setCurrentEnum(
self.settings.get("simple_measurements.units", Units.nm))
self.units_select.currentIndexChanged.connect(self.change_units)
self._shift = 2
layout = QHBoxLayout()
self.measurement_layout = QVBoxLayout()
l1 = QHBoxLayout()
l1.addWidget(QLabel("Units"))
l1.addWidget(self.units_select)
self.measurement_layout.addLayout(l1)
l2 = QHBoxLayout()
l2.addWidget(QLabel("Channel"))
l2.addWidget(self.channel_select)
self.measurement_layout.addLayout(l2)
layout.addLayout(self.measurement_layout)
result_layout = QVBoxLayout()
result_layout.addWidget(self.result_view)
result_layout.addWidget(self.calculate_btn)
layout.addLayout(result_layout)
self.setLayout(layout)
self.setWindowTitle("Measurement")
if self.window() == self:
with suppress(KeyError):
geometry = self.settings.get_from_profile(
"simple_measurement_window_geometry")
self.restoreGeometry(
QByteArray.fromHex(bytes(geometry, "ascii")))
def _get_field_from_value_type(cls, ap: AlgorithmProperty):
if issubclass(ap.value_type, Channel):
res = ChannelComboBox()
res.change_channels_num(10)
elif issubclass(ap.value_type, AlgorithmDescribeBase):
res = SubAlgorithmWidget(ap)
elif issubclass(ap.value_type, bool):
res = QCheckBox()
elif issubclass(ap.value_type, (float, int)):
res = cls._get_numeric_field(ap)
elif issubclass(ap.value_type, Enum):
# noinspection PyTypeChecker
res = QEnumComboBox(enum_class=ap.value_type)
elif issubclass(ap.value_type, str):
res = QLineEdit()
elif issubclass(ap.value_type, ROIExtractionProfile):
res = ProfileSelect()
elif issubclass(ap.value_type, list):
res = QComboBox()
res.addItems(list(map(str, ap.possible_values)))
else:
res = create_widget(annotation=ap.value_type, options={})
return res
class CreatePlan(QWidget):
plan_node_changed = Signal()
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 = QEnumComboBox(enum_class=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 = QEnumComboBox(enum_class=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 = QEnumComboBox(enum_class=Units)
self.units_choose.setCurrentEnum(
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)
self.settings.measurement_profiles_changed.connect(
self._refresh_measurement)
self.settings.roi_profiles_changed.connect(self._refresh_profiles)
self.settings.roi_pipelines_changed.connect(self._refresh_pipelines)
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()
self.refresh_all_profiles()
def change_root_type(self):
value: RootType = self.change_root.currentEnum()
self.calculation_plan.set_root_type(value)
self.plan.update_view()
def change_segmentation_table(self):
index = self.segment_stack.currentIndex()
text = self.segment_stack.tabText(index)
if self.update_element_chk.isChecked():
self.chose_profile_btn.setText("Replace " + text)
else:
self.chose_profile_btn.setText("Add " + text)
self.segment_profile.setCurrentItem(None)
self.pipeline_profile.setCurrentItem(None)
def save_changed(self, text):
text = str(text)
if text == "<none>":
self.save_btn.setText("Save")
self.save_btn.setToolTip("Choose file type")
self.expected_node_type = None
self.save_constructor = None
else:
save_class = self.save_translate_dict.get(text, None)
if save_class is None:
self.save_choose.setCurrentText("<none>")
return
self.save_btn.setText(f"Save to {save_class.get_short_name()}")
self.save_btn.setToolTip("Choose mask create in plan view")
if save_class.need_mask():
self.expected_node_type = NodeType.mask
elif save_class.need_segmentation():
self.expected_node_type = NodeType.segment
else:
self.expected_node_type = NodeType.root
self.save_constructor = Save
self.save_activate()
def save_activate(self):
self.save_btn.setDisabled(True)
if self.node_type == self.expected_node_type:
self.save_btn.setEnabled(True)
def segmentation_from_project(self):
self.calculation_plan.add_step(Operations.reset_to_base)
self.plan.update_view()
def update_names(self):
if self.update_element_chk.isChecked():
self.chose_profile_btn.setText("Replace Profile")
self.add_calculation_btn.setText("Replace set of measurements")
self.generate_mask_btn.setText("Replace mask")
else:
self.chose_profile_btn.setText("Add Profile")
self.add_calculation_btn.setText("Add set of measurements")
self.generate_mask_btn.setText("Generate mask")
def node_type_changed(self):
# self.cmap_save_btn.setDisabled(True)
self.save_btn.setDisabled(True)
self.node_name = ""
if self.plan.currentItem() is None:
self.mask_allow = False
self.file_mask_allow = False
self.segment_allow = False
self.remove_btn.setDisabled(True)
self.plan_node_changed.emit()
logging.debug("[node_type_changed] return")
return
node_type = self.calculation_plan.get_node_type()
self.node_type = node_type
if node_type in [
NodeType.file_mask, NodeType.mask, NodeType.segment,
NodeType.measurement, NodeType.save
]:
self.remove_btn.setEnabled(True)
else:
self.remove_btn.setEnabled(False)
if node_type in (NodeType.mask, NodeType.file_mask):
self.mask_allow = False
self.segment_allow = True
self.file_mask_allow = False
self.node_name = self.calculation_plan.get_node().operation.name
elif node_type == NodeType.segment:
self.mask_allow = True
self.segment_allow = False
self.file_mask_allow = False
self.save_btn.setEnabled(True)
# self.cmap_save_btn.setEnabled(True)
elif node_type == NodeType.root:
self.mask_allow = False
self.segment_allow = True
self.file_mask_allow = True
elif node_type in (NodeType.none, NodeType.measurement, NodeType.save):
self.mask_allow = False
self.segment_allow = False
self.file_mask_allow = False
self.save_activate()
self.plan_node_changed.emit()
def add_save_to_project(self):
save_class = self.save_translate_dict.get(
self.save_choose.currentText(), None)
if save_class is None:
QMessageBox.warning(self, "Save problem", "Not found save class")
dial = FormDialog([
AlgorithmProperty("suffix", "File suffix", ""),
AlgorithmProperty("directory", "Sub directory", "")
] + save_class.get_fields())
if not dial.exec_():
return
values = dial.get_values()
suffix = values["suffix"]
directory = values["directory"]
del values["suffix"]
del values["directory"]
save_elem = Save(suffix, directory, save_class.get_name(),
save_class.get_short_name(), values)
if self.update_element_chk.isChecked():
self.calculation_plan.replace_step(save_elem)
else:
self.calculation_plan.add_step(save_elem)
self.plan.update_view()
def create_mask(self):
text = str(self.mask_name.text()).strip()
if text != "" and text in self.mask_set:
QMessageBox.warning(self, "Already exists",
"Mask with this name already exists",
QMessageBox.Ok)
return
if _check_widget(self.mask_stack, MaskWidget):
mask_ob = MaskCreate(text,
self.segmentation_mask.get_mask_property())
elif _check_widget(self.mask_stack, FileMask):
mask_ob = self.file_mask.get_value(text)
elif _check_widget(self.mask_stack, QEnumComboBox): # existing mask
mask_dialog = TwoMaskDialog
if self.mask_operation.currentEnum(
) == MaskOperation.mask_intersection: # Mask intersection
MaskConstruct = MaskIntersection
else:
MaskConstruct = MaskSum
dial = mask_dialog(self.mask_set)
if not dial.exec_():
return
names = dial.get_result()
mask_ob = MaskConstruct(text, *names)
else:
raise ValueError("Unknowsn widget")
if self.update_element_chk.isChecked():
node = self.calculation_plan.get_node()
name = node.operation.name
if name in self.calculation_plan.get_reused_mask(
) and name != text:
QMessageBox.warning(
self, "Cannot remove",
f"Cannot remove mask '{name}' from plan because it is used in other elements"
)
return
self.mask_set.remove(name)
self.mask_set.add(mask_ob.name)
self.calculation_plan.replace_step(mask_ob)
else:
self.mask_set.add(mask_ob.name)
self.calculation_plan.add_step(mask_ob)
self.plan.update_view()
self.mask_text_changed()
def mask_stack_change(self):
node_type = self.calculation_plan.get_node_type()
if self.update_element_chk.isChecked() and node_type not in [
NodeType.mask, NodeType.file_mask
]:
self.generate_mask_btn.setDisabled(True)
text = self.mask_name.text()
update = self.update_element_chk.isChecked()
if self.node_type == NodeType.none:
self.generate_mask_btn.setDisabled(True)
return
operation = self.calculation_plan.get_node().operation
if (not update and isinstance(operation, (MaskMapper, MaskBase))
and self.calculation_plan.get_node().operation.name == text):
self.generate_mask_btn.setDisabled(True)
return
if _check_widget(self.mask_stack,
MaskWidget): # mask from segmentation
if (not update and node_type == NodeType.segment) or (
update and node_type == NodeType.mask):
self.generate_mask_btn.setEnabled(True)
else:
self.generate_mask_btn.setEnabled(False)
self.generate_mask_btn.setToolTip("Select segmentation")
elif _check_widget(self.mask_stack, FileMask):
if (not update and node_type == NodeType.root) or (
update and node_type == NodeType.file_mask):
self.generate_mask_btn.setEnabled(self.file_mask.is_valid())
else:
self.generate_mask_btn.setEnabled(False)
self.generate_mask_btn.setToolTip("Need root selected")
else: # reuse mask
if len(self.mask_set) > 1 and (
(not update and node_type == NodeType.root) or
(update and node_type == NodeType.file_mask)):
self.generate_mask_btn.setEnabled(True)
else:
self.generate_mask_btn.setEnabled(False)
self.generate_mask_btn.setToolTip(
"Need at least two named mask and root selected")
def mask_name_changed(self, text):
if str(text) in self.mask_set:
self.generate_mask_btn.setDisabled(True)
else:
self.generate_mask_btn.setDisabled(False)
def add_leave_biggest(self):
profile = self.calculation_plan.get_node().operation
profile.leave_biggest_swap()
self.calculation_plan.replace_step(profile)
self.plan.update_view()
def add_segmentation(self):
if self.segment_stack.currentIndex() == 0:
text = str(self.segment_profile.currentItem().text())
if text not in self.settings.roi_profiles:
self.refresh_all_profiles()
return
profile = self.settings.roi_profiles[text]
if self.update_element_chk.isChecked():
self.calculation_plan.replace_step(profile)
else:
self.calculation_plan.add_step(profile)
else: # self.segment_stack.currentIndex() == 1
text = self.pipeline_profile.currentItem().text()
segmentation_pipeline = self.settings.roi_pipelines[text]
pos = self.calculation_plan.current_pos[:]
old_pos = self.calculation_plan.current_pos[:]
for el in segmentation_pipeline.mask_history:
self.calculation_plan.add_step(el.segmentation)
self.plan.update_view()
node = self.calculation_plan.get_node(pos)
pos.append(len(node.children) - 1)
self.calculation_plan.set_position(pos)
self.calculation_plan.add_step(MaskCreate(
"", el.mask_property))
self.plan.update_view()
pos.append(0)
self.calculation_plan.set_position(pos)
self.calculation_plan.add_step(segmentation_pipeline.segmentation)
self.calculation_plan.set_position(old_pos)
self.plan.update_view()
def add_measurement(self):
text = str(self.measurements_list.currentItem().text())
measurement_copy = deepcopy(self.settings.measurement_profiles[text])
prefix = str(self.measurement_name_prefix.text()).strip()
channel = self.choose_channel_for_measurements.currentIndex() - 1
measurement_copy.name_prefix = prefix
# noinspection PyTypeChecker
measurement_calculate = MeasurementCalculate(
channel=channel,
measurement_profile=measurement_copy,
name_prefix=prefix,
units=self.units_choose.currentEnum(),
)
if self.update_element_chk.isChecked():
self.calculation_plan.replace_step(measurement_calculate)
else:
self.calculation_plan.add_step(measurement_calculate)
self.plan.update_view()
def remove_element(self):
conflict_mask, used_mask = self.calculation_plan.get_file_mask_names()
if len(conflict_mask) > 0:
logging.info("Mask in use")
QMessageBox.warning(
self, "In use", "Masks {} are used in other places".format(
", ".join(conflict_mask)))
return
self.mask_set -= used_mask
self.calculation_plan.remove_step()
self.plan.update_view()
def clean_plan(self):
self.calculation_plan = CalculationPlan()
self.plan.set_plan(self.calculation_plan)
self.node_type_changed()
self.mask_set = set()
def mask_text_changed(self):
name = str(self.mask_name.text()).strip()
self.generate_mask_btn.setDisabled(True)
# load mask from file
if self.update_element_chk.isChecked():
if self.node_type not in [NodeType.file_mask, NodeType.mask]:
return
# generate mask from segmentation
if self.node_type == NodeType.mask and (
name == "" or name == self.node_name
or name not in self.mask_set):
self.generate_mask_btn.setEnabled(True)
elif self.mask_allow and (name == "" or name not in self.mask_set):
self.generate_mask_btn.setEnabled(True)
def add_calculation_plan(self, text=None):
if text is None or isinstance(text, bool):
text, ok = QInputDialog.getText(self, "Plan title",
"Set plan title")
else:
text, ok = QInputDialog.getText(
self,
"Plan title",
f"Set plan title. Previous ({text}) is already in use",
text=text)
text = text.strip()
if ok:
if text == "":
QMessageBox.information(
self, "Name cannot be empty",
"Name cannot be empty, Please set correct name",
QMessageBox.Ok)
self.add_calculation_plan()
return
if text in self.settings.batch_plans:
res = QMessageBox.information(
self,
"Name already in use",
"Name already in use. Would like to overwrite?",
QMessageBox.Yes | QMessageBox.No,
)
if res == QMessageBox.No:
self.add_calculation_plan(text)
return
plan = copy(self.calculation_plan)
plan.set_name(text)
self.settings.batch_plans[text] = plan
self.settings.dump()
@staticmethod
def get_index(item: QListWidgetItem, new_values: typing.List[str]) -> int:
if item is None:
return -1
text = item.text()
try:
return new_values.index(text)
except ValueError:
return -1
def refresh_profiles(self, list_widget: QListWidget,
new_values: typing.List[str]):
index = self.get_index(list_widget.currentItem(), new_values)
list_widget.clear()
list_widget.addItems(new_values)
if index != -1:
list_widget.setCurrentRow(index)
@contextmanager
def enable_protect(self):
self.protect = True
yield
self.protect = False
def _refresh_measurement(self):
new_measurements = list(
sorted(self.settings.measurement_profiles.keys(), key=str.lower))
with self.enable_protect():
self.refresh_profiles(self.measurements_list, new_measurements)
def _refresh_profiles(self):
new_profiles = list(
sorted(self.settings.roi_profiles.keys(), key=str.lower))
with self.enable_protect():
self.refresh_profiles(self.segment_profile, new_profiles)
def _refresh_pipelines(self):
new_pipelines = list(
sorted(self.settings.roi_pipelines.keys(), key=str.lower))
with self.enable_protect():
self.refresh_profiles(self.pipeline_profile, new_pipelines)
def refresh_all_profiles(self):
self._refresh_measurement()
self._refresh_profiles()
self._refresh_pipelines()
def show_measurement_info(self, text=None):
if self.protect:
return
if text is None:
if self.measurements_list.currentItem() is not None:
text = str(self.measurements_list.currentItem().text())
else:
return
profile = self.settings.measurement_profiles[text]
self.information.setText(str(profile))
def show_measurement(self):
if self.update_element_chk.isChecked():
if self.node_type == NodeType.measurement:
self.add_calculation_btn.setEnabled(True)
else:
self.add_calculation_btn.setDisabled(True)
elif self.measurements_list.currentItem() is not None:
self.add_calculation_btn.setEnabled(self.mask_allow)
else:
self.add_calculation_btn.setDisabled(True)
def show_segment_info(self, text=None):
if self.protect:
return
if text == "":
return
if self.segment_stack.currentIndex() == 0:
if text is None:
if self.segment_profile.currentItem() is not None:
text = str(self.segment_profile.currentItem().text())
else:
return
profile = self.settings.roi_profiles[text]
else:
if text is None:
if self.pipeline_profile.currentItem() is not None:
text = str(self.pipeline_profile.currentItem().text())
else:
return
profile = self.settings.roi_pipelines[text]
self.information.setText(profile.pretty_print(analysis_algorithm_dict))
def show_segment(self):
if self.update_element_chk.isChecked(
) and self.segment_stack.currentIndex() == 0:
self.get_big_btn.setDisabled(True)
if self.node_type == NodeType.segment:
self.chose_profile_btn.setEnabled(True)
else:
self.chose_profile_btn.setDisabled(True)
else:
if self.node_type == NodeType.segment:
self.get_big_btn.setEnabled(True)
else:
self.get_big_btn.setDisabled(True)
if (self.segment_stack.currentIndex() == 0
and self.segment_profile.currentItem()
) or self.pipeline_profile.currentItem() is not None:
self.chose_profile_btn.setEnabled(self.segment_allow)
else:
self.chose_profile_btn.setDisabled(True)
def edit_plan(self):
plan = self.sender().plan_to_edit # type: CalculationPlan
self.calculation_plan = copy(plan)
self.plan.set_plan(self.calculation_plan)
self.mask_set.clear()
self.calculation_plan.set_position([])
self.mask_set.update(self.calculation_plan.get_mask_names())
class ChannelProperty(QWidget):
"""
For manipulate chanel properties.
1. Apply gaussian blur to channel
2. Fixed range for coloring
In future should be extended
:param settings: for storing internal state. allow keep state between sessions
:param start_name: name used to select proper information from settings object.
Introduced for case with multiple image view.
"""
def __init__(self, settings: ViewSettings, start_name: str):
if start_name == "":
raise ValueError(
"ChannelProperty should have non empty start_name")
super().__init__()
self.current_name = start_name
self.current_channel = 0
self._settings = settings
self.widget_dict: typing.Dict[str, ColorComboBoxGroup] = {}
self.minimum_value = CustomSpinBox(self)
self.minimum_value.setRange(-(10**6), 10**6)
self.minimum_value.valueChanged.connect(self.range_changed)
self.maximum_value = CustomSpinBox(self)
self.maximum_value.setRange(-(10**6), 10**6)
self.maximum_value.valueChanged.connect(self.range_changed)
self.fixed = QCheckBox("Fix range")
self.fixed.stateChanged.connect(self.lock_channel)
self.use_filter = QEnumComboBox(enum_class=NoiseFilterType)
self.use_filter.setToolTip("Only current channel")
self.filter_radius = QDoubleSpinBox()
self.filter_radius.setSingleStep(0.1)
self.filter_radius.valueChanged.connect(self.gauss_radius_changed)
self.use_filter.currentIndexChanged.connect(self.gauss_use_changed)
self.gamma_value = QDoubleSpinBox()
self.gamma_value.setRange(0.01, 100)
self.gamma_value.setSingleStep(0.1)
self.gamma_value.valueChanged.connect(self.gamma_value_changed)
self.collapse_widget = CollapseCheckbox("Channel property")
self.collapse_widget.add_hide_element(self.minimum_value)
self.collapse_widget.add_hide_element(self.maximum_value)
self.collapse_widget.add_hide_element(self.fixed)
self.collapse_widget.add_hide_element(self.use_filter)
self.collapse_widget.add_hide_element(self.filter_radius)
self.collapse_widget.add_hide_element(self.gamma_value)
layout = QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.addWidget(self.collapse_widget, 0, 0, 1, 4)
label1 = QLabel("Min bright:")
layout.addWidget(label1, 1, 0)
layout.addWidget(self.minimum_value, 1, 1)
label2 = QLabel("Max bright:")
layout.addWidget(label2, 2, 0)
layout.addWidget(self.maximum_value, 2, 1)
layout.addWidget(self.fixed, 1, 2, 1, 2)
label3 = QLabel("Filter:")
layout.addWidget(label3, 3, 0, 1, 1)
layout.addWidget(self.use_filter, 3, 1, 1, 1)
layout.addWidget(self.filter_radius, 3, 2, 1, 1)
label4 = QLabel("Gamma:")
layout.addWidget(label4, 4, 0, 1, 1)
layout.addWidget(self.gamma_value, 4, 1, 1, 1)
self.setLayout(layout)
self.collapse_widget.add_hide_element(label1)
self.collapse_widget.add_hide_element(label2)
self.collapse_widget.add_hide_element(label3)
self.collapse_widget.add_hide_element(label4)
def send_info(self):
"""send info to"""
widget = self.widget_dict[self.current_name]
widget.parameters_changed(self.current_channel)
def register_widget(self, widget: "ColorComboBoxGroup") -> None:
"""
Register new viewer by its color combo box group
:param ColorComboBoxGroup widget: viewer widget for color control
"""
if widget.viewer_name in self.widget_dict:
raise ValueError(f"name {widget.viewer_name} already register")
self.widget_dict[widget.viewer_name] = widget
self._settings.connect_to_profile(widget.viewer_name,
self.refresh_values)
self.change_current(widget.viewer_name, 0)
def refresh_values(self, path: typing.Optional[str]):
if path is None or path.startswith(self.current_name):
self.change_current(self.current_name, self.current_channel)
def change_current(self, name: str, channel: int) -> None:
"""
Change to show values connected with channel `channel` from viewer `viewer`
:param str name: name of viewer
:param int channel: channel to which data should be presented
:rtype: None
"""
if name not in self.widget_dict:
raise ValueError(f"name {name} not in register")
self.current_name = name
self.current_channel = channel
block = self.blockSignals(True)
self.minimum_value.blockSignals(True)
self.minimum_value.setValue(
self._settings.get_from_profile(
f"{self.current_name}.range_{self.current_channel}",
(0, 65000))[0])
self.minimum_value.blockSignals(False)
self.maximum_value.setValue(
self._settings.get_from_profile(
f"{self.current_name}.range_{self.current_channel}",
(0, 65000))[1])
self.use_filter.setCurrentEnum(
self._settings.get_from_profile(
f"{self.current_name}.use_filter_{self.current_channel}",
NoiseFilterType.No))
self.filter_radius.setValue(
self._settings.get_from_profile(
f"{self.current_name}.filter_radius_{self.current_channel}",
1))
self.fixed.setChecked(
self._settings.get_from_profile(
f"{self.current_name}.lock_{self.current_channel}", False))
self.gamma_value.setValue(
self._settings.get_from_profile(
f"{self.current_name}.gamma_value_{self.current_channel}", 1))
self.blockSignals(block)
def gamma_value_changed(self):
self._settings.set_in_profile(
f"{self.current_name}.gamma_value_{self.current_channel}",
self.gamma_value.value())
self.send_info()
def gauss_radius_changed(self):
self._settings.set_in_profile(
f"{self.current_name}.filter_radius_{self.current_channel}",
self.filter_radius.value())
if self.use_filter.currentEnum() != NoiseFilterType.No:
self.send_info()
def gauss_use_changed(self):
self._settings.set_in_profile(
f"{self.current_name}.use_filter_{self.current_channel}",
self.use_filter.currentEnum())
if self.use_filter.currentEnum() == NoiseFilterType.Median:
self.filter_radius.setDecimals(0)
self.filter_radius.setSingleStep(1)
else:
self.filter_radius.setDecimals(2)
self.filter_radius.setSingleStep(0.1)
self.send_info()
def lock_channel(self, value):
self._settings.set_in_profile(
f"{self.current_name}.lock_{self.current_channel}", value)
self.send_info()
def range_changed(self):
self._settings.set_in_profile(
f"{self.current_name}.range_{self.current_channel}",
(self.minimum_value.value(), self.maximum_value.value()),
)
if self.fixed.isChecked():
self.send_info()
def __init__(self, settings: ImageSettings, parent=None):
super().__init__(parent)
self.setContentsMargins(0, 0, 0, 0)
self.settings = settings
self.dilate_radius = QSpinBox()
self.dilate_radius.setRange(-100, 100)
# self.dilate_radius.setButtonSymbols(QAbstractSpinBox.NoButtons)
self.dilate_radius.setSingleStep(1)
self.dilate_radius.setDisabled(True)
self.dilate_dim = QEnumComboBox(enum_class=RadiusType)
self.dilate_dim.setToolTip("With minus radius mask will be eroded")
# noinspection PyUnresolvedReferences
self.dilate_dim.currentIndexChanged.connect(
partial(off_widget, self.dilate_radius, self.dilate_dim))
self.radius_information = QLabel()
# noinspection PyUnresolvedReferences
self.dilate_radius.valueChanged.connect(self.dilate_change)
# noinspection PyUnresolvedReferences
self.dilate_dim.currentIndexChanged.connect(self.dilate_change)
self.fill_holes = QEnumComboBox(enum_class=RadiusType)
self.max_hole_size = QSpinBox()
self.max_hole_size.setRange(-1, 10000)
self.max_hole_size.setValue(-1)
self.max_hole_size.setSingleStep(100)
self.max_hole_size.setDisabled(True)
self.max_hole_size.setToolTip(
"Maximum size of holes to be closed. -1 means that all holes will be closed"
)
# noinspection PyUnresolvedReferences
self.fill_holes.currentIndexChanged.connect(
partial(off_widget, self.max_hole_size, self.fill_holes))
self.save_components = QCheckBox()
self.clip_to_mask = QCheckBox()
self.reversed_check = QCheckBox()
# noinspection PyUnresolvedReferences
self.dilate_radius.valueChanged.connect(self.values_changed.emit)
# noinspection PyUnresolvedReferences
self.dilate_dim.currentIndexChanged.connect(self.values_changed.emit)
# noinspection PyUnresolvedReferences
self.fill_holes.currentIndexChanged.connect(self.values_changed.emit)
# noinspection PyUnresolvedReferences
self.max_hole_size.valueChanged.connect(self.values_changed.emit)
self.save_components.stateChanged.connect(self.values_changed.emit)
self.clip_to_mask.stateChanged.connect(self.values_changed.emit)
self.reversed_check.stateChanged.connect(self.values_changed.emit)
layout = QVBoxLayout()
layout1 = QHBoxLayout()
layout1.addWidget(QLabel("Dilate mask:"))
layout1.addWidget(self.dilate_dim)
layout1.addWidget(QLabel("radius (in pix):"))
layout1.addWidget(self.dilate_radius)
layout.addLayout(layout1)
layout2 = QHBoxLayout()
layout2.addWidget(QLabel("Fill holes:"))
layout2.addWidget(self.fill_holes)
layout2.addWidget(QLabel("Max size:"))
layout2.addWidget(self.max_hole_size)
layout.addLayout(layout2)
layout3 = QHBoxLayout()
comp_lab = QLabel("Save components:")
comp_lab.setToolTip(
"save components information in mask. Dilation, "
"holes filing will be done separately for each component")
self.save_components.setToolTip(comp_lab.toolTip())
layout3.addWidget(comp_lab)
layout3.addWidget(self.save_components)
layout3.addStretch()
clip_mask = QLabel("Clip to previous mask:")
clip_mask.setToolTip("Useful dilated new mask")
layout3.addWidget(clip_mask)
layout3.addWidget(self.clip_to_mask)
layout.addLayout(layout3)
layout4 = QHBoxLayout()
layout4.addWidget(QLabel("Reversed mask:"))
layout4.addWidget(self.reversed_check)
layout4.addStretch(1)
layout.addLayout(layout4)
self.setLayout(layout)
self.dilate_change()
def off_widget(widget: QWidget, combo_box: QEnumComboBox):
widget.setDisabled(combo_box.currentEnum() == RadiusType.NO)
class MaskWidget(QWidget):
values_changed = Signal()
def __init__(self, settings: ImageSettings, parent=None):
super().__init__(parent)
self.setContentsMargins(0, 0, 0, 0)
self.settings = settings
self.dilate_radius = QSpinBox()
self.dilate_radius.setRange(-100, 100)
# self.dilate_radius.setButtonSymbols(QAbstractSpinBox.NoButtons)
self.dilate_radius.setSingleStep(1)
self.dilate_radius.setDisabled(True)
self.dilate_dim = QEnumComboBox(enum_class=RadiusType)
self.dilate_dim.setToolTip("With minus radius mask will be eroded")
# noinspection PyUnresolvedReferences
self.dilate_dim.currentIndexChanged.connect(
partial(off_widget, self.dilate_radius, self.dilate_dim))
self.radius_information = QLabel()
# noinspection PyUnresolvedReferences
self.dilate_radius.valueChanged.connect(self.dilate_change)
# noinspection PyUnresolvedReferences
self.dilate_dim.currentIndexChanged.connect(self.dilate_change)
self.fill_holes = QEnumComboBox(enum_class=RadiusType)
self.max_hole_size = QSpinBox()
self.max_hole_size.setRange(-1, 10000)
self.max_hole_size.setValue(-1)
self.max_hole_size.setSingleStep(100)
self.max_hole_size.setDisabled(True)
self.max_hole_size.setToolTip(
"Maximum size of holes to be closed. -1 means that all holes will be closed"
)
# noinspection PyUnresolvedReferences
self.fill_holes.currentIndexChanged.connect(
partial(off_widget, self.max_hole_size, self.fill_holes))
self.save_components = QCheckBox()
self.clip_to_mask = QCheckBox()
self.reversed_check = QCheckBox()
# noinspection PyUnresolvedReferences
self.dilate_radius.valueChanged.connect(self.values_changed.emit)
# noinspection PyUnresolvedReferences
self.dilate_dim.currentIndexChanged.connect(self.values_changed.emit)
# noinspection PyUnresolvedReferences
self.fill_holes.currentIndexChanged.connect(self.values_changed.emit)
# noinspection PyUnresolvedReferences
self.max_hole_size.valueChanged.connect(self.values_changed.emit)
self.save_components.stateChanged.connect(self.values_changed.emit)
self.clip_to_mask.stateChanged.connect(self.values_changed.emit)
self.reversed_check.stateChanged.connect(self.values_changed.emit)
layout = QVBoxLayout()
layout1 = QHBoxLayout()
layout1.addWidget(QLabel("Dilate mask:"))
layout1.addWidget(self.dilate_dim)
layout1.addWidget(QLabel("radius (in pix):"))
layout1.addWidget(self.dilate_radius)
layout.addLayout(layout1)
layout2 = QHBoxLayout()
layout2.addWidget(QLabel("Fill holes:"))
layout2.addWidget(self.fill_holes)
layout2.addWidget(QLabel("Max size:"))
layout2.addWidget(self.max_hole_size)
layout.addLayout(layout2)
layout3 = QHBoxLayout()
comp_lab = QLabel("Save components:")
comp_lab.setToolTip(
"save components information in mask. Dilation, "
"holes filing will be done separately for each component")
self.save_components.setToolTip(comp_lab.toolTip())
layout3.addWidget(comp_lab)
layout3.addWidget(self.save_components)
layout3.addStretch()
clip_mask = QLabel("Clip to previous mask:")
clip_mask.setToolTip("Useful dilated new mask")
layout3.addWidget(clip_mask)
layout3.addWidget(self.clip_to_mask)
layout.addLayout(layout3)
layout4 = QHBoxLayout()
layout4.addWidget(QLabel("Reversed mask:"))
layout4.addWidget(self.reversed_check)
layout4.addStretch(1)
layout.addLayout(layout4)
self.setLayout(layout)
self.dilate_change()
def get_dilate_radius(self):
radius = calculate_operation_radius(self.dilate_radius.value(),
self.settings.image_spacing,
self.dilate_dim.currentEnum())
if isinstance(radius, (list, tuple)):
return [int(x + 0.5) for x in radius]
return int(radius)
def dilate_change(self):
if self.dilate_radius.value() == 0 or self.dilate_dim.currentEnum(
) == RadiusType.NO:
self.radius_information.setText("Dilation radius: 0")
else:
dilate_radius = self.get_dilate_radius()
if isinstance(dilate_radius, list):
self.radius_information.setText(
f"Dilation radius: {dilate_radius[::-1]}")
else:
self.radius_information.setText(
f"Dilation radius: {dilate_radius}")
def get_mask_property(self):
return MaskProperty(
dilate=self.dilate_dim.currentEnum()
if self.dilate_radius.value() != 0 else RadiusType.NO,
dilate_radius=self.dilate_radius.value()
if self.dilate_dim.currentEnum() != RadiusType.NO else 0,
fill_holes=self.fill_holes.currentEnum()
if self.max_hole_size.value() != 0 else RadiusType.NO,
max_holes_size=self.max_hole_size.value()
if self.fill_holes.currentEnum() != RadiusType.NO else 0,
save_components=self.save_components.isChecked(),
clip_to_mask=self.clip_to_mask.isChecked(),
reversed_mask=self.reversed_check.isChecked(),
)
def set_mask_property(self, prop: MaskProperty):
self.dilate_dim.setCurrentEnum(prop.dilate)
self.dilate_radius.setValue(prop.dilate_radius)
self.fill_holes.setCurrentEnum(prop.fill_holes)
self.max_hole_size.setValue(prop.max_holes_size)
self.save_components.setChecked(prop.save_components)
self.clip_to_mask.setChecked(prop.clip_to_mask)
self.reversed_check.setChecked(prop.reversed_mask)
class Properties(QWidget):
def __init__(self, settings: PartSettings):
super().__init__()
self._settings = settings
self.export_btn = QPushButton("Export profile")
self.export_btn.clicked.connect(self.export_profile)
self.import_btn = QPushButton("Import profile")
self.import_btn.clicked.connect(self.import_profiles)
self.export_pipeline_btn = QPushButton("Export pipeline")
self.export_pipeline_btn.clicked.connect(self.export_pipeline)
self.import_pipeline_btn = QPushButton("Import pipeline")
self.import_pipeline_btn.clicked.connect(self.import_pipeline)
self.delete_btn = QPushButton("Delete profile")
self.delete_btn.setDisabled(True)
self.delete_btn.clicked.connect(self.delete_profile)
self.multiple_files_chk = QCheckBox("Show multiple files panel")
self._update_measurement_chk()
self.multiple_files_chk.stateChanged.connect(
self.multiple_files_visibility)
self.rename_btn = QPushButton("Rename profile")
self.rename_btn.clicked.connect(self.rename_profile)
self.rename_btn.setDisabled(True)
self.voxel_size_label = QLabel()
self.info_label = QPlainTextEdit()
self.info_label.setReadOnly(True)
self.profile_list = SearchableListWidget()
self.profile_list.currentTextChanged.connect(self.profile_chosen)
self.pipeline_list = SearchableListWidget()
self.pipeline_list.currentTextChanged.connect(self.profile_chosen)
self.spacing = [QDoubleSpinBox() for _ in range(3)]
self.lock_spacing = LockCheckBox()
self.lock_spacing.stateChanged.connect(self.spacing[1].setDisabled)
self.lock_spacing.stateChanged.connect(self.synchronize_spacing)
# noinspection PyUnresolvedReferences
self.spacing[2].valueChanged.connect(self.synchronize_spacing)
self._settings.roi_profiles_changed.connect(self.update_profile_list)
self._settings.roi_pipelines_changed.connect(self.update_profile_list)
self._settings.connect_("multiple_files_widget",
self._update_measurement_chk)
units_value = self._settings.get("units_value", Units.nm)
for el in self.spacing:
el.setAlignment(Qt.AlignRight)
el.setButtonSymbols(QAbstractSpinBox.NoButtons)
el.setRange(0, 1000000)
# noinspection PyUnresolvedReferences
el.valueChanged.connect(self.image_spacing_change)
self.units = QEnumComboBox(enum_class=Units)
self.units.setCurrentEnum(units_value)
# noinspection PyUnresolvedReferences
self.units.currentIndexChanged.connect(self.update_spacing)
spacing_layout = QHBoxLayout()
spacing_layout.addWidget(self.lock_spacing)
for txt, el in zip(["x", "y", "z"], self.spacing[::-1]):
spacing_layout.addWidget(QLabel(txt + ":"))
spacing_layout.addWidget(el)
spacing_layout.addWidget(self.units)
spacing_layout.addStretch(1)
voxel_size_layout = QHBoxLayout()
voxel_size_layout.addWidget(self.voxel_size_label)
voxel_size_layout.addSpacing(30)
profile_layout = QGridLayout()
profile_layout.setSpacing(0)
profile_layout.addWidget(QLabel("Profiles:"), 0, 0)
profile_layout.addWidget(self.profile_list, 1, 0)
profile_layout.addWidget(QLabel("Pipelines:"), 2, 0)
profile_layout.addWidget(self.pipeline_list, 3, 0, 4, 1)
profile_layout.addWidget(self.info_label, 1, 1, 3, 2)
profile_layout.addWidget(self.export_btn, 4, 1)
profile_layout.addWidget(self.import_btn, 4, 2)
profile_layout.addWidget(self.export_pipeline_btn, 5, 1)
profile_layout.addWidget(self.import_pipeline_btn, 5, 2)
profile_layout.addWidget(self.delete_btn, 6, 1)
profile_layout.addWidget(self.rename_btn, 6, 2)
layout = QVBoxLayout()
layout.addLayout(spacing_layout)
layout.addLayout(voxel_size_layout)
layout.addWidget(self.multiple_files_chk)
layout.addLayout(profile_layout, 1)
self.setLayout(layout)
self.update_profile_list()
@Slot(int)
def multiple_files_visibility(self, val: int):
self._settings.set("multiple_files_widget", val)
# @Slot(str) # PySide bug
def profile_chosen(self, text):
if text == "":
self.delete_btn.setEnabled(False)
self.rename_btn.setEnabled(False)
self.info_label.setPlainText("")
return
try:
if self.sender() == self.profile_list.list_widget:
profile = self._settings.roi_profiles[text]
self.pipeline_list.selectionModel().clear()
self.delete_btn.setText("Delete profile")
self.rename_btn.setText("Rename profile")
elif self.sender() == self.pipeline_list.list_widget:
profile = self._settings.roi_pipelines[text]
self.profile_list.selectionModel().clear()
self.delete_btn.setText("Delete pipeline")
self.rename_btn.setText("Rename pipeline")
else:
return
except KeyError:
return
# TODO update with knowledge from profile dict
self.delete_btn.setEnabled(True)
self.rename_btn.setEnabled(True)
self.info_label.setPlainText(
profile.pretty_print(analysis_algorithm_dict))
def synchronize_spacing(self):
if self.lock_spacing.isChecked():
self.spacing[1].setValue(self.spacing[2].value())
def image_spacing_change(self):
spacing = [
el.value() / UNIT_SCALE[self.units.currentIndex()]
for i, el in enumerate(self.spacing)
]
if not self.spacing[0].isEnabled():
spacing = spacing[1:]
self._settings.image_spacing = spacing
voxel_size = 1
for el in self._settings.image_spacing:
voxel_size *= el * UNIT_SCALE[self.units.currentIndex()]
self.voxel_size_label.setText(
f"Voxel_size: {voxel_size} {self.units.currentEnum().name} <sup>{len(self._settings.image_spacing)}</sup>"
)
def update_spacing(self, index=None):
voxel_size = 1
value = self.units.currentEnum()
if index is not None:
self._settings.set("units_value", value)
for el, sp in zip(self.spacing[::-1],
self._settings.image_spacing[::-1]):
el.blockSignals(True)
current_size = sp * UNIT_SCALE[self.units.currentIndex()]
voxel_size *= current_size
el.setValue(current_size)
el.blockSignals(False)
self.spacing[0].setDisabled(len(self._settings.image_spacing) == 2)
self.voxel_size_label.setText(
f"Voxel_size: {voxel_size} {value.name} <sup>{len(self._settings.image_spacing)}</sup>"
)
def update_profile_list(self):
current_names = set(self._settings.roi_profiles.keys())
self.profile_list.clear()
self.profile_list.addItems(sorted(current_names))
self.pipeline_list.clear()
self.pipeline_list.addItems(
sorted(set(self._settings.roi_pipelines.keys())))
self.delete_btn.setDisabled(True)
self.rename_btn.setDisabled(True)
self.info_label.setPlainText("")
def showEvent(self, _event):
self.update_spacing()
def event(self, event: QEvent):
if event.type() == QEvent.WindowActivate and self.isVisible():
self.update_spacing()
return super().event(event)
@ensure_main_thread
def _update_measurement_chk(self):
self.multiple_files_chk.setChecked(
self._settings.get("multiple_files_widget", False))
def delete_profile(self):
text, dkt = "", {}
if self.profile_list.selectedItems():
text = self.profile_list.selectedItems()[0].text()
dkt = self._settings.roi_profiles
elif self.pipeline_list.selectedItems():
text = self.pipeline_list.selectedItems()[0].text()
dkt = self._settings.roi_pipelines
if text != "":
self.delete_btn.setDisabled(True)
del dkt[text]
self.update_profile_list()
def export_profile(self):
exp = ExportDialog(self._settings.roi_profiles, ProfileDictViewer)
if not exp.exec_():
return
dial = PSaveDialog(
"Segment profile (*.json)",
settings=self._settings,
path=IO_SAVE_DIRECTORY,
caption="Export profile segment",
)
dial.selectFile("segment_profile.json")
if dial.exec_():
file_path = dial.selectedFiles()[0]
data = {
x: self._settings.roi_profiles[x]
for x in exp.get_export_list()
}
with open(file_path, "w", encoding="utf-8") as ff:
json.dump(data,
ff,
cls=self._settings.json_encoder_class,
indent=2)
def import_profiles(self):
dial = PLoadDialog(
"Segment profile (*.json)",
settings=self._settings,
path=IO_SAVE_DIRECTORY,
caption="Import profile segment",
)
if dial.exec_():
file_path = dial.selectedFiles()[0]
profs, err = self._settings.load_part(file_path)
if err:
QMessageBox.warning(
self, "Import error",
"error during importing, part of data were filtered.")
profiles_dict = self._settings.roi_profiles
imp = ImportDialog(profs, profiles_dict, ProfileDictViewer)
if not imp.exec_():
return
for original_name, final_name in imp.get_import_list():
profiles_dict[final_name] = profs[original_name]
self._settings.dump()
self.update_profile_list()
def export_pipeline(self):
exp = ExportDialog(self._settings.roi_pipelines, ProfileDictViewer)
if not exp.exec_():
return
dial = PSaveDialog(
"Segment pipeline (*.json)",
settings=self._settings,
path=IO_SAVE_DIRECTORY,
caption="Export pipeline segment",
)
dial.selectFile("segment_pipeline.json")
if dial.exec_():
file_path = dial.selectedFiles()[0]
data = {
x: self._settings.roi_pipelines[x]
for x in exp.get_export_list()
}
with open(file_path, "w", encoding="utf-8") as ff:
json.dump(data,
ff,
cls=self._settings.json_encoder_class,
indent=2)
def import_pipeline(self):
dial = PLoadDialog(
"Segment pipeline (*.json)",
settings=self._settings,
path=IO_SAVE_DIRECTORY,
caption="Import pipeline segment",
)
if dial.exec_():
file_path = dial.selectedFiles()[0]
profs, err = self._settings.load_part(file_path)
if err:
QMessageBox.warning(
self, "Import error",
"error during importing, part of data were filtered.")
profiles_dict = self._settings.roi_pipelines
imp = ImportDialog(profs, profiles_dict, ProfileDictViewer)
if not imp.exec_():
return
for original_name, final_name in imp.get_import_list():
profiles_dict[final_name] = profs[original_name]
self._settings.dump()
self.update_profile_list()
def rename_profile(self):
profile_name, profiles_dict = "", {}
if self.profile_list.selectedItems():
profile_name = self.profile_list.selectedItems()[0].text()
profiles_dict = self._settings.roi_profiles
elif self.pipeline_list.selectedItems():
profile_name = self.pipeline_list.selectedItems()[0].text()
profiles_dict = self._settings.roi_pipelines
if profile_name == "":
return
text, ok = QInputDialog.getText(self,
"New profile name",
f"New name for {profile_name}",
text=profile_name)
if ok:
text = text.strip()
if text in profiles_dict.keys():
res = QMessageBox.warning(
self,
"Already exist",
f"Profile with name {text} already exist. Would you like to overwrite?",
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No,
)
if res == QMessageBox.No:
self.rename_profile()
return
profiles_dict[text] = profiles_dict.pop(profile_name)
self._settings.dump()
self.update_profile_list()
def __init__(self, settings: PartSettings):
super().__init__()
self._settings = settings
self.export_btn = QPushButton("Export profile")
self.export_btn.clicked.connect(self.export_profile)
self.import_btn = QPushButton("Import profile")
self.import_btn.clicked.connect(self.import_profiles)
self.export_pipeline_btn = QPushButton("Export pipeline")
self.export_pipeline_btn.clicked.connect(self.export_pipeline)
self.import_pipeline_btn = QPushButton("Import pipeline")
self.import_pipeline_btn.clicked.connect(self.import_pipeline)
self.delete_btn = QPushButton("Delete profile")
self.delete_btn.setDisabled(True)
self.delete_btn.clicked.connect(self.delete_profile)
self.multiple_files_chk = QCheckBox("Show multiple files panel")
self._update_measurement_chk()
self.multiple_files_chk.stateChanged.connect(
self.multiple_files_visibility)
self.rename_btn = QPushButton("Rename profile")
self.rename_btn.clicked.connect(self.rename_profile)
self.rename_btn.setDisabled(True)
self.voxel_size_label = QLabel()
self.info_label = QPlainTextEdit()
self.info_label.setReadOnly(True)
self.profile_list = SearchableListWidget()
self.profile_list.currentTextChanged.connect(self.profile_chosen)
self.pipeline_list = SearchableListWidget()
self.pipeline_list.currentTextChanged.connect(self.profile_chosen)
self.spacing = [QDoubleSpinBox() for _ in range(3)]
self.lock_spacing = LockCheckBox()
self.lock_spacing.stateChanged.connect(self.spacing[1].setDisabled)
self.lock_spacing.stateChanged.connect(self.synchronize_spacing)
# noinspection PyUnresolvedReferences
self.spacing[2].valueChanged.connect(self.synchronize_spacing)
self._settings.roi_profiles_changed.connect(self.update_profile_list)
self._settings.roi_pipelines_changed.connect(self.update_profile_list)
self._settings.connect_("multiple_files_widget",
self._update_measurement_chk)
units_value = self._settings.get("units_value", Units.nm)
for el in self.spacing:
el.setAlignment(Qt.AlignRight)
el.setButtonSymbols(QAbstractSpinBox.NoButtons)
el.setRange(0, 1000000)
# noinspection PyUnresolvedReferences
el.valueChanged.connect(self.image_spacing_change)
self.units = QEnumComboBox(enum_class=Units)
self.units.setCurrentEnum(units_value)
# noinspection PyUnresolvedReferences
self.units.currentIndexChanged.connect(self.update_spacing)
spacing_layout = QHBoxLayout()
spacing_layout.addWidget(self.lock_spacing)
for txt, el in zip(["x", "y", "z"], self.spacing[::-1]):
spacing_layout.addWidget(QLabel(txt + ":"))
spacing_layout.addWidget(el)
spacing_layout.addWidget(self.units)
spacing_layout.addStretch(1)
voxel_size_layout = QHBoxLayout()
voxel_size_layout.addWidget(self.voxel_size_label)
voxel_size_layout.addSpacing(30)
profile_layout = QGridLayout()
profile_layout.setSpacing(0)
profile_layout.addWidget(QLabel("Profiles:"), 0, 0)
profile_layout.addWidget(self.profile_list, 1, 0)
profile_layout.addWidget(QLabel("Pipelines:"), 2, 0)
profile_layout.addWidget(self.pipeline_list, 3, 0, 4, 1)
profile_layout.addWidget(self.info_label, 1, 1, 3, 2)
profile_layout.addWidget(self.export_btn, 4, 1)
profile_layout.addWidget(self.import_btn, 4, 2)
profile_layout.addWidget(self.export_pipeline_btn, 5, 1)
profile_layout.addWidget(self.import_pipeline_btn, 5, 2)
profile_layout.addWidget(self.delete_btn, 6, 1)
profile_layout.addWidget(self.rename_btn, 6, 2)
layout = QVBoxLayout()
layout.addLayout(spacing_layout)
layout.addLayout(voxel_size_layout)
layout.addWidget(self.multiple_files_chk)
layout.addLayout(profile_layout, 1)
self.setLayout(layout)
self.update_profile_list()
class MeasurementSettings(QWidget):
"""
:type settings: Settings
"""
def __init__(self, settings: PartSettings, parent=None):
super().__init__(parent)
self.chosen_element: Optional[MeasurementListWidgetItem] = None
self.chosen_element_area: Optional[Tuple[AreaType, float]] = None
self.settings = settings
self.profile_list = QListWidget(self)
self.profile_description = QTextEdit(self)
self.profile_description.setReadOnly(True)
self.profile_options = QListWidget()
self.profile_options_chosen = QListWidget()
self.measurement_area_choose = QEnumComboBox(enum_class=AreaType)
self.per_component = QEnumComboBox(enum_class=PerComponent)
self.power_num = QDoubleSpinBox()
self.power_num.setDecimals(3)
self.power_num.setRange(-100, 100)
self.power_num.setValue(1)
self.choose_butt = QPushButton("→", self)
self.discard_butt = QPushButton("←", self)
self.proportion_butt = QPushButton("Ratio", self)
self.proportion_butt.setToolTip("Create proportion from two parameter")
self.move_up = QPushButton("↑", self)
self.move_down = QPushButton("↓", self)
self.remove_button = QPushButton("Remove")
self.save_butt = QPushButton("Save")
self.save_butt.setToolTip(
"Set name for set and choose at least one parameter")
self.save_butt_with_name = QPushButton(
"Save with custom parameters designation")
self.save_butt_with_name.setToolTip(
"Set name for set and choose at least one parameter")
self.reset_butt = QPushButton("Clear")
self.soft_reset_butt = QPushButton("Remove user parameters")
self.profile_name = QLineEdit(self)
self.delete_profile_butt = QPushButton("Delete ")
self.export_profiles_butt = QPushButton("Export")
self.import_profiles_butt = QPushButton("Import")
self.edit_profile_butt = QPushButton("Edit")
self.choose_butt.setDisabled(True)
self.choose_butt.clicked.connect(self.choose_option)
self.discard_butt.setDisabled(True)
self.discard_butt.clicked.connect(self.discard_option)
self.proportion_butt.setDisabled(True)
self.proportion_butt.clicked.connect(self.proportion_action)
self.save_butt.setDisabled(True)
self.save_butt.clicked.connect(self.save_action)
self.save_butt_with_name.setDisabled(True)
self.save_butt_with_name.clicked.connect(self.named_save_action)
self.profile_name.textChanged.connect(self.name_changed)
self.move_down.setDisabled(True)
self.move_down.clicked.connect(self.move_down_fun)
self.move_up.setDisabled(True)
self.move_up.clicked.connect(self.move_up_fun)
self.remove_button.setDisabled(True)
self.remove_button.clicked.connect(self.remove_element)
self.reset_butt.clicked.connect(self.reset_action)
self.soft_reset_butt.clicked.connect(self.soft_reset)
self.delete_profile_butt.setDisabled(True)
self.delete_profile_butt.clicked.connect(self.delete_profile)
self.export_profiles_butt.clicked.connect(
self.export_measurement_profiles)
self.import_profiles_butt.clicked.connect(
self.import_measurement_profiles)
self.edit_profile_butt.clicked.connect(self.edit_profile)
self.profile_list.itemSelectionChanged.connect(self.profile_chosen)
self.profile_options.itemSelectionChanged.connect(
self.create_selection_changed)
self.profile_options_chosen.itemSelectionChanged.connect(
self.create_selection_chosen_changed)
self.settings.measurement_profiles_changed.connect(
self._refresh_profiles)
layout = QVBoxLayout()
layout.addWidget(QLabel("Measurement set:"))
profile_layout = QHBoxLayout()
profile_layout.addWidget(self.profile_list)
profile_layout.addWidget(self.profile_description)
profile_buttons_layout = QHBoxLayout()
profile_buttons_layout.addWidget(self.delete_profile_butt)
profile_buttons_layout.addWidget(self.export_profiles_butt)
profile_buttons_layout.addWidget(self.import_profiles_butt)
profile_buttons_layout.addWidget(self.edit_profile_butt)
profile_buttons_layout.addStretch()
layout.addLayout(profile_layout)
layout.addLayout(profile_buttons_layout)
heading_layout = QHBoxLayout()
# heading_layout.addWidget(QLabel("Create profile"), 1)
heading_layout.addWidget(h_line(), 6)
layout.addLayout(heading_layout)
name_layout = QHBoxLayout()
name_layout.addWidget(QLabel("Set name:"))
name_layout.addWidget(self.profile_name)
name_layout.addStretch()
name_layout.addWidget(QLabel("Per component:"))
name_layout.addWidget(self.per_component)
name_layout.addWidget(QLabel("Area:"))
name_layout.addWidget(self.measurement_area_choose)
name_layout.addWidget(QLabel("to power:"))
name_layout.addWidget(self.power_num)
layout.addLayout(name_layout)
create_layout = QHBoxLayout()
create_layout.addWidget(self.profile_options)
butt_op_layout = QVBoxLayout()
butt_op_layout.addStretch()
butt_op_layout.addWidget(self.choose_butt)
butt_op_layout.addWidget(self.discard_butt)
butt_op_layout.addWidget(self.proportion_butt)
butt_op_layout.addWidget(self.reset_butt)
butt_op_layout.addStretch()
create_layout.addLayout(butt_op_layout)
create_layout.addWidget(self.profile_options_chosen)
butt_move_layout = QVBoxLayout()
butt_move_layout.addStretch()
butt_move_layout.addWidget(self.move_up)
butt_move_layout.addWidget(self.move_down)
butt_move_layout.addWidget(self.remove_button)
butt_move_layout.addStretch()
create_layout.addLayout(butt_move_layout)
layout.addLayout(create_layout)
save_butt_layout = QHBoxLayout()
save_butt_layout.addWidget(self.soft_reset_butt)
save_butt_layout.addStretch()
save_butt_layout.addWidget(self.save_butt)
save_butt_layout.addWidget(self.save_butt_with_name)
layout.addLayout(save_butt_layout)
self.setLayout(layout)
for profile in MEASUREMENT_DICT.values():
help_text = profile.get_description()
lw = MeasurementListWidgetItem(profile.get_starting_leaf())
lw.setToolTip(help_text)
self.profile_options.addItem(lw)
self._refresh_profiles()
def _refresh_profiles(self):
item = self.profile_list.currentItem()
items = list(self.settings.measurement_profiles.keys())
try:
index = items.index(item.text())
except (ValueError, AttributeError):
index = -1
self.profile_list.clear()
self.profile_list.addItems(items)
self.profile_list.setCurrentRow(index)
if self.profile_list.count() == 0:
self.export_profiles_butt.setDisabled(True)
else:
self.export_profiles_butt.setEnabled(True)
def remove_element(self):
elem = self.profile_options_chosen.currentItem()
if elem is None:
return
index = self.profile_options_chosen.currentRow()
self.profile_options_chosen.takeItem(index)
if self.profile_options_chosen.count() == 0:
self.move_down.setDisabled(True)
self.move_up.setDisabled(True)
self.remove_button.setDisabled(True)
self.discard_butt.setDisabled(True)
self.save_butt.setDisabled(True)
self.save_butt_with_name.setDisabled(True)
def delete_profile(self):
item = self.profile_list.currentItem()
del self.settings.measurement_profiles[str(item.text())]
def profile_chosen(self):
self.delete_profile_butt.setEnabled(True)
if self.profile_list.count() == 0:
self.profile_description.setText("")
return
item = self.profile_list.currentItem()
if item is None:
self.profile_description.setText("")
return
profile = self.settings.measurement_profiles[item.text()]
self.profile_description.setText(str(profile))
def create_selection_changed(self):
self.choose_butt.setEnabled(True)
self.proportion_butt.setEnabled(True)
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.currentEnum(),
self.per_component.currentEnum(),
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.currentEnum()
== self.chosen_element_area.area
and self.per_component.currentEnum()
== 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.currentEnum(),
self.per_component.currentEnum(),
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._add_option(lw)
self.chosen_element.setIcon(QIcon())
self.chosen_element = None
self.chosen_element_area = None
def _add_option(self, item: MeasurementListWidgetItem):
for i in range(self.profile_options_chosen.count()):
if item.text() == self.profile_options_chosen.item(i).text():
return
self.profile_options_chosen.addItem(item)
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_selection_chosen_changed(self):
# print(self.profile_options_chosen.count())
self.remove_button.setEnabled(True)
if self.profile_options_chosen.count() == 0:
self.move_down.setDisabled(True)
self.move_up.setDisabled(True)
self.remove_button.setDisabled(True)
return
self.discard_butt.setEnabled(True)
if self.profile_options_chosen.currentRow() != 0:
self.move_up.setEnabled(True)
else:
self.move_up.setDisabled(True)
if self.profile_options_chosen.currentRow(
) != self.profile_options_chosen.count() - 1:
self.move_down.setEnabled(True)
else:
self.move_down.setDisabled(True)
def good_name(self):
return str(self.profile_name.text()).strip() != ""
def move_down_fun(self):
row = self.profile_options_chosen.currentRow()
item = self.profile_options_chosen.takeItem(row)
self.profile_options_chosen.insertItem(row + 1, item)
self.profile_options_chosen.setCurrentRow(row + 1)
self.create_selection_chosen_changed()
def move_up_fun(self):
row = self.profile_options_chosen.currentRow()
item = self.profile_options_chosen.takeItem(row)
self.profile_options_chosen.insertItem(row - 1, item)
self.profile_options_chosen.setCurrentRow(row - 1)
self.create_selection_chosen_changed()
def name_changed(self):
if self.good_name() and self.profile_options_chosen.count() > 0:
self.save_butt.setEnabled(True)
self.save_butt_with_name.setEnabled(True)
else:
self.save_butt.setDisabled(True)
self.save_butt_with_name.setDisabled(True)
def form_dialog(self, arguments):
return FormDialog(arguments, settings=self.settings, parent=self)
def get_parameters(self, node: Union[Node, Leaf], area: AreaType,
component: PerComponent, power: float):
if isinstance(node, Node):
return node
node = node.replace_(power=power)
if node.area is None:
node = node.replace_(area=area)
if node.per_component is None:
node = node.replace_(per_component=component)
with suppress(KeyError):
arguments = MEASUREMENT_DICT[str(node.name)].get_fields()
if len(arguments) > 0 and len(node.dict) == 0:
dial = self.form_dialog(arguments)
if dial.exec_():
node = node._replace(dict=dial.get_values())
else:
return
return node
def choose_option(self):
selected_item = self.profile_options.currentItem()
# selected_row = self.profile_options.currentRow()
if not isinstance(selected_item, MeasurementListWidgetItem):
raise ValueError(
f"Current item (type: {type(selected_item)} is not instance of MeasurementListWidgetItem"
)
node = deepcopy(selected_item.stat)
# noinspection PyTypeChecker
node = self.get_parameters(node,
self.measurement_area_choose.currentEnum(),
self.per_component.currentEnum(),
self.power_num.value())
if node is None:
return
lw = MeasurementListWidgetItem(node)
lw.setToolTip(selected_item.toolTip())
self._add_option(lw)
def discard_option(self):
selected_item: MeasurementListWidgetItem = self.profile_options_chosen.currentItem(
)
# selected_row = self.profile_options_chosen.currentRow()
lw = MeasurementListWidgetItem(deepcopy(selected_item.stat))
lw.setToolTip(selected_item.toolTip())
self.create_selection_chosen_changed()
for i in range(self.profile_options.count()):
if lw.text() == self.profile_options.item(i).text():
return
self.profile_options.addItem(lw)
def edit_profile(self):
item = self.profile_list.currentItem()
if item is None:
return
profile = self.settings.measurement_profiles[str(item.text())]
self.profile_options_chosen.clear()
self.profile_name.setText(item.text())
for ch in profile.chosen_fields:
self.profile_options_chosen.addItem(
MeasurementListWidgetItem(ch.calculation_tree))
# self.gauss_img.setChecked(profile.use_gauss_image)
self.save_butt.setEnabled(True)
self.save_butt_with_name.setEnabled(True)
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 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 reset_action(self):
self.profile_options.clear()
self.profile_options_chosen.clear()
self.profile_name.setText("")
self.save_butt.setDisabled(True)
self.save_butt_with_name.setDisabled(True)
self.move_down.setDisabled(True)
self.move_up.setDisabled(True)
self.proportion_butt.setDisabled(True)
self.choose_butt.setDisabled(True)
self.discard_butt.setDisabled(True)
for profile in MEASUREMENT_DICT.values():
help_text = profile.get_description()
lw = MeasurementListWidgetItem(profile.get_starting_leaf())
lw.setToolTip(help_text)
self.profile_options.addItem(lw)
def soft_reset(self):
# TODO rim should not be removed
shift = 0
for i in range(self.profile_options.count()):
item = self.profile_options.item(i - shift)
if str(item.text()) not in MEASUREMENT_DICT:
self.profile_options.takeItem(i - shift)
if item == self.chosen_element:
self.chosen_element = None
del item
shift += 1
self.create_selection_changed()
def export_measurement_profiles(self):
exp = ExportDialog(self.settings.measurement_profiles,
StringViewer,
parent=self)
if not exp.exec_():
return
dial = PSaveDialog(
"Measurement profile (*.json)",
settings=self.settings,
path="io.export_directory",
caption="Export settings profiles",
)
dial.selectFile("measurements_profile.json")
if dial.exec_():
file_path = str(dial.selectedFiles()[0])
data = {
x: self.settings.measurement_profiles[x]
for x in exp.get_export_list()
}
with open(file_path, "w", encoding="utf-8") as ff:
json.dump(data,
ff,
cls=self.settings.json_encoder_class,
indent=2)
def import_measurement_profiles(self):
dial = PLoadDialog(
"Measurement profile (*.json)",
settings=self.settings,
path="io.export_directory",
caption="Import settings profiles",
parent=self,
)
if dial.exec_():
file_path = str(dial.selectedFiles()[0])
stat, err = self.settings.load_part(file_path)
if err:
QMessageBox.warning(
self, "Import error",
"error during importing, part of data were filtered.")
measurement_dict = self.settings.measurement_profiles
imp = ImportDialog(stat, measurement_dict, StringViewer)
if not imp.exec_():
return
for original_name, final_name in imp.get_import_list():
measurement_dict[final_name] = stat[original_name]
self.settings.dump()
def __init__(self, settings: PartSettings, parent=None):
super().__init__(parent)
self.chosen_element: Optional[MeasurementListWidgetItem] = None
self.chosen_element_area: Optional[Tuple[AreaType, float]] = None
self.settings = settings
self.profile_list = QListWidget(self)
self.profile_description = QTextEdit(self)
self.profile_description.setReadOnly(True)
self.profile_options = QListWidget()
self.profile_options_chosen = QListWidget()
self.measurement_area_choose = QEnumComboBox(enum_class=AreaType)
self.per_component = QEnumComboBox(enum_class=PerComponent)
self.power_num = QDoubleSpinBox()
self.power_num.setDecimals(3)
self.power_num.setRange(-100, 100)
self.power_num.setValue(1)
self.choose_butt = QPushButton("→", self)
self.discard_butt = QPushButton("←", self)
self.proportion_butt = QPushButton("Ratio", self)
self.proportion_butt.setToolTip("Create proportion from two parameter")
self.move_up = QPushButton("↑", self)
self.move_down = QPushButton("↓", self)
self.remove_button = QPushButton("Remove")
self.save_butt = QPushButton("Save")
self.save_butt.setToolTip(
"Set name for set and choose at least one parameter")
self.save_butt_with_name = QPushButton(
"Save with custom parameters designation")
self.save_butt_with_name.setToolTip(
"Set name for set and choose at least one parameter")
self.reset_butt = QPushButton("Clear")
self.soft_reset_butt = QPushButton("Remove user parameters")
self.profile_name = QLineEdit(self)
self.delete_profile_butt = QPushButton("Delete ")
self.export_profiles_butt = QPushButton("Export")
self.import_profiles_butt = QPushButton("Import")
self.edit_profile_butt = QPushButton("Edit")
self.choose_butt.setDisabled(True)
self.choose_butt.clicked.connect(self.choose_option)
self.discard_butt.setDisabled(True)
self.discard_butt.clicked.connect(self.discard_option)
self.proportion_butt.setDisabled(True)
self.proportion_butt.clicked.connect(self.proportion_action)
self.save_butt.setDisabled(True)
self.save_butt.clicked.connect(self.save_action)
self.save_butt_with_name.setDisabled(True)
self.save_butt_with_name.clicked.connect(self.named_save_action)
self.profile_name.textChanged.connect(self.name_changed)
self.move_down.setDisabled(True)
self.move_down.clicked.connect(self.move_down_fun)
self.move_up.setDisabled(True)
self.move_up.clicked.connect(self.move_up_fun)
self.remove_button.setDisabled(True)
self.remove_button.clicked.connect(self.remove_element)
self.reset_butt.clicked.connect(self.reset_action)
self.soft_reset_butt.clicked.connect(self.soft_reset)
self.delete_profile_butt.setDisabled(True)
self.delete_profile_butt.clicked.connect(self.delete_profile)
self.export_profiles_butt.clicked.connect(
self.export_measurement_profiles)
self.import_profiles_butt.clicked.connect(
self.import_measurement_profiles)
self.edit_profile_butt.clicked.connect(self.edit_profile)
self.profile_list.itemSelectionChanged.connect(self.profile_chosen)
self.profile_options.itemSelectionChanged.connect(
self.create_selection_changed)
self.profile_options_chosen.itemSelectionChanged.connect(
self.create_selection_chosen_changed)
self.settings.measurement_profiles_changed.connect(
self._refresh_profiles)
layout = QVBoxLayout()
layout.addWidget(QLabel("Measurement set:"))
profile_layout = QHBoxLayout()
profile_layout.addWidget(self.profile_list)
profile_layout.addWidget(self.profile_description)
profile_buttons_layout = QHBoxLayout()
profile_buttons_layout.addWidget(self.delete_profile_butt)
profile_buttons_layout.addWidget(self.export_profiles_butt)
profile_buttons_layout.addWidget(self.import_profiles_butt)
profile_buttons_layout.addWidget(self.edit_profile_butt)
profile_buttons_layout.addStretch()
layout.addLayout(profile_layout)
layout.addLayout(profile_buttons_layout)
heading_layout = QHBoxLayout()
# heading_layout.addWidget(QLabel("Create profile"), 1)
heading_layout.addWidget(h_line(), 6)
layout.addLayout(heading_layout)
name_layout = QHBoxLayout()
name_layout.addWidget(QLabel("Set name:"))
name_layout.addWidget(self.profile_name)
name_layout.addStretch()
name_layout.addWidget(QLabel("Per component:"))
name_layout.addWidget(self.per_component)
name_layout.addWidget(QLabel("Area:"))
name_layout.addWidget(self.measurement_area_choose)
name_layout.addWidget(QLabel("to power:"))
name_layout.addWidget(self.power_num)
layout.addLayout(name_layout)
create_layout = QHBoxLayout()
create_layout.addWidget(self.profile_options)
butt_op_layout = QVBoxLayout()
butt_op_layout.addStretch()
butt_op_layout.addWidget(self.choose_butt)
butt_op_layout.addWidget(self.discard_butt)
butt_op_layout.addWidget(self.proportion_butt)
butt_op_layout.addWidget(self.reset_butt)
butt_op_layout.addStretch()
create_layout.addLayout(butt_op_layout)
create_layout.addWidget(self.profile_options_chosen)
butt_move_layout = QVBoxLayout()
butt_move_layout.addStretch()
butt_move_layout.addWidget(self.move_up)
butt_move_layout.addWidget(self.move_down)
butt_move_layout.addWidget(self.remove_button)
butt_move_layout.addStretch()
create_layout.addLayout(butt_move_layout)
layout.addLayout(create_layout)
save_butt_layout = QHBoxLayout()
save_butt_layout.addWidget(self.soft_reset_butt)
save_butt_layout.addStretch()
save_butt_layout.addWidget(self.save_butt)
save_butt_layout.addWidget(self.save_butt_with_name)
layout.addLayout(save_butt_layout)
self.setLayout(layout)
for profile in MEASUREMENT_DICT.values():
help_text = profile.get_description()
lw = MeasurementListWidgetItem(profile.get_starting_leaf())
lw.setToolTip(help_text)
self.profile_options.addItem(lw)
self._refresh_profiles()
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 = QEnumComboBox(enum_class=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 = QEnumComboBox(enum_class=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 = QEnumComboBox(enum_class=Units)
self.units_choose.setCurrentEnum(
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)
self.settings.measurement_profiles_changed.connect(
self._refresh_measurement)
self.settings.roi_profiles_changed.connect(self._refresh_profiles)
self.settings.roi_pipelines_changed.connect(self._refresh_pipelines)
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()
self.refresh_all_profiles()
class SimpleMeasurements(QWidget):
def __init__(self, settings: StackSettings, parent=None):
super().__init__(parent)
self.settings = settings
self.calculate_btn = QPushButton("Calculate")
self.calculate_btn.clicked.connect(self.calculate)
self.result_view = QTableWidget()
self.channel_select = ChannelComboBox()
self.units_select = QEnumComboBox(enum_class=Units)
self.units_select.setCurrentEnum(
self.settings.get("simple_measurements.units", Units.nm))
self.units_select.currentIndexChanged.connect(self.change_units)
self._shift = 2
layout = QHBoxLayout()
self.measurement_layout = QVBoxLayout()
l1 = QHBoxLayout()
l1.addWidget(QLabel("Units"))
l1.addWidget(self.units_select)
self.measurement_layout.addLayout(l1)
l2 = QHBoxLayout()
l2.addWidget(QLabel("Channel"))
l2.addWidget(self.channel_select)
self.measurement_layout.addLayout(l2)
layout.addLayout(self.measurement_layout)
result_layout = QVBoxLayout()
result_layout.addWidget(self.result_view)
result_layout.addWidget(self.calculate_btn)
layout.addLayout(result_layout)
self.setLayout(layout)
self.setWindowTitle("Measurement")
if self.window() == self:
with suppress(KeyError):
geometry = self.settings.get_from_profile(
"simple_measurement_window_geometry")
self.restoreGeometry(
QByteArray.fromHex(bytes(geometry, "ascii")))
def closeEvent(self, event: QCloseEvent) -> None:
"""
Save geometry if widget is used as standalone window.
"""
if self.window() == self:
self.settings.set_in_profile(
"simple_measurement_window_geometry",
self.saveGeometry().toHex().data().decode("ascii"))
super().closeEvent(event)
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 _clean_measurements(self):
selected = set()
for _ in range(self.measurement_layout.count() - self._shift):
# noinspection PyTypeChecker
chk: QCheckBox = self.measurement_layout.takeAt(
self._shift).widget()
if chk.isChecked():
selected.add(chk.text())
chk.deleteLater()
return selected
def refresh_measurements(self):
selected = self._clean_measurements()
for val in MEASUREMENT_DICT.values():
area = val.get_starting_leaf().area
pc = val.get_starting_leaf().per_component
if (val.get_fields() or (area is not None and area != AreaType.ROI)
or (pc is not None and pc != PerComponent.Yes)):
continue
text = val.get_name()
chk = QCheckBox(text)
if text in selected:
chk.setChecked(True)
self.measurement_layout.addWidget(chk)
def keyPressEvent(self, e: QKeyEvent):
if not e.modifiers() & Qt.ControlModifier:
return
selected = self.result_view.selectedRanges()
if e.key() == Qt.Key_C: # copy
s = ""
for r in range(selected[0].topRow(), selected[0].bottomRow() + 1):
for c in range(selected[0].leftColumn(),
selected[0].rightColumn() + 1):
try:
s += str(self.result_view.item(r, c).text()) + "\t"
except AttributeError:
s += "\t"
s = s[:-1] + "\n" # eliminate last '\t'
QApplication.clipboard().setText(s)
def event(self, event: QEvent) -> bool:
if event.type() == QEvent.WindowActivate:
if self.settings.image is not None:
self.channel_select.change_channels_num(
self.settings.image.channels)
self.refresh_measurements()
return super().event(event)
def change_units(self):
self.settings.set("simple_measurements.units",
self.units_select.currentEnum())
class AlgorithmOptions(QWidget):
def __init__(self, settings: StackSettings, image_view: StackImageView):
super().__init__()
self.settings = settings
self.view_name = image_view.name
self.show_result = QEnumComboBox(
enum_class=LabelEnum) # QCheckBox("Show result")
self._set_show_label_from_settings()
self.opacity = QDoubleSpinBox()
self.opacity.setRange(0, 1)
self.opacity.setSingleStep(0.1)
self._set_opacity_from_settings()
self.only_borders = QCheckBox("Only borders")
self._set_border_mode_from_settings()
self.borders_thick = QSpinBox()
self.borders_thick.setRange(1, 25)
self.borders_thick.setSingleStep(1)
self._set_border_thick_from_settings()
self.execute_in_background_btn = QPushButton("Execute in background")
self.execute_in_background_btn.setToolTip(
"Run calculation in background. Put result in multiple files panel"
)
self.execute_btn = QPushButton("Execute")
self.execute_btn.setStyleSheet("QPushButton{font-weight: bold;}")
self.execute_all_btn = QPushButton("Execute all")
self.execute_all_btn.setToolTip(
"Execute in batch mode segmentation with current parameter. File list need to be specified in image tab."
)
self.execute_all_btn.setDisabled(True)
self.save_parameters_btn = QPushButton("Save parameters")
self.block_execute_all_btn = False
self.algorithm_choose_widget = AlgorithmChoose(settings,
mask_algorithm_dict)
self.algorithm_choose_widget.result.connect(self.execution_result_set)
self.algorithm_choose_widget.finished.connect(self.execution_finished)
self.algorithm_choose_widget.progress_signal.connect(
self.progress_info)
# self.stack_layout = QStackedLayout()
self.keep_chosen_components_chk = QCheckBox("Save selected components")
self.keep_chosen_components_chk.setToolTip(
"Save chosen components when loading segmentation form file\n or from multiple file widget."
)
self.keep_chosen_components_chk.stateChanged.connect(
self.set_keep_chosen_components)
self.keep_chosen_components_chk.setChecked(
settings.keep_chosen_components)
self.show_parameters = QPushButton("Show parameters")
self.show_parameters.setToolTip(
"Show parameters of segmentation for each components")
self.show_parameters_widget = SegmentationInfoDialog(
self.settings, self.algorithm_choose_widget.change_algorithm)
self.show_parameters.clicked.connect(self.show_parameters_widget.show)
self.choose_components = ChosenComponents()
self.choose_components.check_change_signal.connect(
image_view.refresh_selected)
self.choose_components.mouse_leave.connect(image_view.component_unmark)
self.choose_components.mouse_enter.connect(image_view.component_mark)
# WARNING works only with one channels algorithms
# SynchronizeValues.add_synchronization("channels_chose", widgets_list)
self.chosen_list = []
self.progress_bar2 = QProgressBar()
self.progress_bar2.setHidden(True)
self.progress_bar = QProgressBar()
self.progress_bar.setHidden(True)
self.progress_info_lab = QLabel()
self.progress_info_lab.setHidden(True)
self.file_list = []
self.batch_process = BatchProceed()
self.batch_process.progress_signal.connect(self.progress_info)
self.batch_process.error_signal.connect(self.execution_all_error)
self.batch_process.execution_done.connect(self.execution_all_done)
self.batch_process.range_signal.connect(self.progress_bar.setRange)
self.is_batch_process = False
self.setContentsMargins(0, 0, 0, 0)
main_layout = QVBoxLayout()
# main_layout.setSpacing(0)
opt_layout = QHBoxLayout()
opt_layout.setContentsMargins(0, 0, 0, 0)
opt_layout.addWidget(self.show_result)
opt_layout.addWidget(right_label("Opacity:"))
opt_layout.addWidget(self.opacity)
main_layout.addLayout(opt_layout)
opt_layout2 = QHBoxLayout()
opt_layout2.setContentsMargins(0, 0, 0, 0)
opt_layout2.addWidget(self.only_borders)
opt_layout2.addWidget(right_label("Border thick:"))
opt_layout2.addWidget(self.borders_thick)
main_layout.addLayout(opt_layout2)
btn_layout = QGridLayout()
btn_layout.setContentsMargins(0, 0, 0, 0)
btn_layout.addWidget(self.execute_btn, 0, 0)
btn_layout.addWidget(self.execute_in_background_btn, 0, 1)
btn_layout.addWidget(self.execute_all_btn, 1, 0)
btn_layout.addWidget(self.save_parameters_btn, 1, 1)
main_layout.addLayout(btn_layout)
main_layout.addWidget(self.progress_bar2)
main_layout.addWidget(self.progress_bar)
main_layout.addWidget(self.progress_info_lab)
main_layout.addWidget(self.algorithm_choose_widget, 1)
# main_layout.addWidget(self.algorithm_choose)
# main_layout.addLayout(self.stack_layout, 1)
main_layout.addWidget(self.choose_components)
down_layout = QHBoxLayout()
down_layout.addWidget(self.keep_chosen_components_chk)
down_layout.addWidget(self.show_parameters)
main_layout.addLayout(down_layout)
main_layout.addStretch()
main_layout.setContentsMargins(0, 0, 0, 0)
# main_layout.setSpacing(0)
self.setLayout(main_layout)
# noinspection PyUnresolvedReferences
self.execute_in_background_btn.clicked.connect(
self.execute_in_background)
self.execute_btn.clicked.connect(self.execute_action)
self.execute_all_btn.clicked.connect(self.execute_all_action)
self.save_parameters_btn.clicked.connect(self.save_parameters)
# noinspection PyUnresolvedReferences
self.opacity.valueChanged.connect(self._set_opacity)
# noinspection PyUnresolvedReferences
self.show_result.currentEnumChanged.connect(self._set_show_label)
self.only_borders.stateChanged.connect(self._set_border_mode)
# noinspection PyUnresolvedReferences
self.borders_thick.valueChanged.connect(self._set_border_thick)
image_view.component_clicked.connect(
self.choose_components.other_component_choose)
settings.chosen_components_widget = self.choose_components
settings.components_change_list.connect(
self.choose_components.new_choose)
settings.image_changed.connect(
self.choose_components.remove_components)
settings.connect_to_profile(
f"{self.view_name}.image_state.only_border",
self._set_border_mode_from_settings)
settings.connect_to_profile(
f"{self.view_name}.image_state.border_thick",
self._set_border_thick_from_settings)
settings.connect_to_profile(f"{self.view_name}.image_state.opacity",
self._set_opacity_from_settings)
settings.connect_to_profile(f"{self.view_name}.image_state.show_label",
self._set_show_label_from_settings)
def _set_border_mode(self, value: bool):
self.settings.set_in_profile(
f"{self.view_name}.image_state.only_border", value)
def _set_border_thick(self, value: int):
self.settings.set_in_profile(
f"{self.view_name}.image_state.border_thick", value)
def _set_opacity(self, value: float):
self.settings.set_in_profile(f"{self.view_name}.image_state.opacity",
value)
def _set_show_label(self, value: LabelEnum):
self.settings.set_in_profile(
f"{self.view_name}.image_state.show_label", value)
def _set_border_mode_from_settings(self):
self.only_borders.setChecked(
self.settings.get_from_profile(
f"{self.view_name}.image_state.only_border", True))
def _set_border_thick_from_settings(self):
self.borders_thick.setValue(
self.settings.get_from_profile(
f"{self.view_name}.image_state.border_thick", 1))
def _set_opacity_from_settings(self):
self.opacity.setValue(
self.settings.get_from_profile(
f"{self.view_name}.image_state.opacity", 1.0))
def _set_show_label_from_settings(self):
self.show_result.setCurrentEnum(
self.settings.get_from_profile(
f"{self.view_name}.image_state.show_label",
LabelEnum.Show_results))
@Slot(int)
def set_keep_chosen_components(self, val):
self.settings.set_keep_chosen_components(val)
def save_parameters(self):
dial = PSaveDialog(io_functions.save_parameters_dict,
system_widget=False,
settings=self.settings,
path=IO_SAVE_DIRECTORY)
if not dial.exec_():
return
res = dial.get_result()
res.save_class.save(res.save_destination,
self.algorithm_choose_widget.current_parameters())
def file_list_change(self, val):
self.file_list = val
if len(self.file_list) > 0 and not self.block_execute_all_btn:
self.execute_all_btn.setEnabled(True)
else:
self.execute_all_btn.setDisabled(True)
def get_chosen_components(self):
return sorted(self.choose_components.get_chosen())
@property
def segmentation(self):
return self.settings.roi
@segmentation.setter
def segmentation(self, val):
self.settings.roi = val
def _image_changed(self):
self.settings.roi = None
self.choose_components.set_chose([], [])
def _execute_in_background_init(self):
if self.batch_process.isRunning():
return
self.progress_bar2.setVisible(True)
self.progress_bar2.setRange(0, self.batch_process.queue.qsize())
self.progress_bar2.setValue(self.batch_process.index)
self.progress_bar.setVisible(True)
self.progress_bar.setValue(0)
self.execute_btn.setDisabled(True)
self.batch_process.start()
def execute_in_background(self):
# TODO check if components are properly passed
widget = self.algorithm_choose_widget.current_widget()
segmentation_profile = widget.get_segmentation_profile()
task = BatchTask(self.settings.get_project_info(),
segmentation_profile, None)
self.batch_process.add_task(task)
self.progress_bar2.setRange(0, self.progress_bar2.maximum() + 1)
self._execute_in_background_init()
def execute_all_action(self):
dial = PSaveDialog(
SaveROI,
settings=self.settings,
system_widget=False,
path="io.save_batch",
file_mode=PSaveDialog.Directory,
)
if not dial.exec_():
return
folder_path = str(dial.selectedFiles()[0])
widget = self.algorithm_choose_widget.current_widget()
save_parameters = dial.values
segmentation_profile = widget.get_segmentation_profile()
for file_path in self.file_list:
task = BatchTask(file_path, segmentation_profile,
(folder_path, save_parameters))
self.batch_process.add_task(task)
self.progress_bar2.setRange(
0,
self.progress_bar2.maximum() + len(self.file_list))
self._execute_in_background_init()
def execution_all_error(self, text):
QMessageBox.warning(self, "Proceed error", text)
def execution_all_done(self):
if not self.batch_process.queue.empty():
self._execute_in_background_init()
return
self.execute_btn.setEnabled(True)
self.block_execute_all_btn = False
if len(self.file_list) > 0:
self.execute_all_btn.setEnabled(True)
self.progress_bar.setHidden(True)
self.progress_bar2.setHidden(True)
self.progress_info_lab.setHidden(True)
def execute_action(self):
self.execute_btn.setDisabled(True)
self.execute_all_btn.setDisabled(True)
self.block_execute_all_btn = True
self.is_batch_process = False
self.progress_bar.setRange(0, 0)
self.choose_components.setDisabled(True)
chosen = sorted(self.choose_components.get_chosen())
blank = get_mask(self.settings.roi, self.settings.mask, chosen)
if blank is not None:
# Problem with handling time data in algorithms
# TODO Fix This
blank = blank[0]
self.progress_bar.setHidden(False)
widget: AlgorithmSettingsWidget = self.algorithm_choose_widget.current_widget(
)
widget.set_mask(blank)
self.progress_bar.setRange(0, widget.algorithm.get_steps_num())
widget.execute()
self.chosen_list = chosen
def progress_info(self, text, num, file_name="", file_num=0):
self.progress_info_lab.setVisible(True)
if file_name != "":
self.progress_info_lab.setText(file_name + "\n" + text)
else:
self.progress_info_lab.setText(text)
self.progress_bar.setValue(num)
self.progress_bar2.setValue(file_num)
def execution_finished(self):
self.execute_btn.setEnabled(True)
self.block_execute_all_btn = False
if len(self.file_list) > 0:
self.execute_all_btn.setEnabled(True)
self.progress_bar.setHidden(True)
self.progress_info_lab.setHidden(True)
self.choose_components.setDisabled(False)
def execution_result_set(self, result):
self.settings.set_segmentation_result(result)
def showEvent(self, _):
widget = self.algorithm_choose_widget.current_widget()
widget.image_changed(self.settings.image)
class ImageInformation(QWidget):
def __init__(self, settings: StackSettings, parent=None):
""":type settings: ImageSettings"""
super().__init__(parent)
self._settings = settings
self.path = QTextEdit("<b>Path:</b> example image")
self.path.setWordWrapMode(QTextOption.WrapAnywhere)
self.path.setReadOnly(True)
self.setMinimumHeight(20)
self.spacing = [QDoubleSpinBox() for _ in range(3)]
self.multiple_files = QCheckBox("Show multiple files panel")
self.multiple_files.setChecked(
settings.get("multiple_files_widget", True))
self.multiple_files.stateChanged.connect(self.set_multiple_files)
units_value = self._settings.get("units_value", Units.nm)
for el in self.spacing:
el.setAlignment(Qt.AlignRight)
el.setButtonSymbols(QAbstractSpinBox.NoButtons)
el.setRange(0, 100000)
# noinspection PyUnresolvedReferences
el.valueChanged.connect(self.image_spacing_change)
self.units = QEnumComboBox(enum_class=Units)
self.units.setCurrentEnum(units_value)
# noinspection PyUnresolvedReferences
self.units.currentIndexChanged.connect(self.update_spacing)
self.add_files = AddFiles(settings, btn_layout=FlowLayout)
spacing_layout = QFormLayout()
spacing_layout.addRow("x:", self.spacing[0])
spacing_layout.addRow("y:", self.spacing[1])
spacing_layout.addRow("z:", self.spacing[2])
spacing_layout.addRow("Units:", self.units)
layout = QVBoxLayout()
layout.addWidget(self.path)
layout.addWidget(QLabel("Image spacing:"))
layout.addLayout(spacing_layout)
layout.addWidget(self.add_files)
layout.addStretch(1)
layout.addWidget(self.multiple_files)
self.setLayout(layout)
self._settings.image_changed[str].connect(self.set_image_path)
@Slot(int)
def set_multiple_files(self, val):
self._settings.set("multiple_files_widget", val)
def update_spacing(self, index=None):
units_value = self.units.currentEnum()
if index is not None:
self._settings.set("units_value", units_value)
for el, val in zip(self.spacing, self._settings.image_spacing[::-1]):
el.blockSignals(True)
el.setValue(val * UNIT_SCALE[units_value.value])
el.blockSignals(False)
if self._settings.is_image_2d():
# self.spacing[2].setValue(0)
self.spacing[2].setDisabled(True)
else:
self.spacing[2].setDisabled(False)
def set_image_path(self, value):
self.path.setText(f"<b>Path:</b> {value}")
self.update_spacing()
def image_spacing_change(self):
self._settings.image_spacing = [
el.value() / UNIT_SCALE[self.units.currentIndex()]
for i, el in enumerate(self.spacing[::-1])
]
def showEvent(self, _a0):
units_value = self._settings.get("units_value", Units.nm)
for el, val in zip(self.spacing, self._settings.image_spacing[::-1]):
el.setValue(val * UNIT_SCALE[units_value.value])
if self._settings.is_image_2d():
self.spacing[2].setValue(0)
self.spacing[2].setDisabled(True)
else:
self.spacing[2].setDisabled(False)
def __init__(self, settings: StackSettings, image_view: StackImageView):
super().__init__()
self.settings = settings
self.view_name = image_view.name
self.show_result = QEnumComboBox(
enum_class=LabelEnum) # QCheckBox("Show result")
self._set_show_label_from_settings()
self.opacity = QDoubleSpinBox()
self.opacity.setRange(0, 1)
self.opacity.setSingleStep(0.1)
self._set_opacity_from_settings()
self.only_borders = QCheckBox("Only borders")
self._set_border_mode_from_settings()
self.borders_thick = QSpinBox()
self.borders_thick.setRange(1, 25)
self.borders_thick.setSingleStep(1)
self._set_border_thick_from_settings()
self.execute_in_background_btn = QPushButton("Execute in background")
self.execute_in_background_btn.setToolTip(
"Run calculation in background. Put result in multiple files panel"
)
self.execute_btn = QPushButton("Execute")
self.execute_btn.setStyleSheet("QPushButton{font-weight: bold;}")
self.execute_all_btn = QPushButton("Execute all")
self.execute_all_btn.setToolTip(
"Execute in batch mode segmentation with current parameter. File list need to be specified in image tab."
)
self.execute_all_btn.setDisabled(True)
self.save_parameters_btn = QPushButton("Save parameters")
self.block_execute_all_btn = False
self.algorithm_choose_widget = AlgorithmChoose(settings,
mask_algorithm_dict)
self.algorithm_choose_widget.result.connect(self.execution_result_set)
self.algorithm_choose_widget.finished.connect(self.execution_finished)
self.algorithm_choose_widget.progress_signal.connect(
self.progress_info)
# self.stack_layout = QStackedLayout()
self.keep_chosen_components_chk = QCheckBox("Save selected components")
self.keep_chosen_components_chk.setToolTip(
"Save chosen components when loading segmentation form file\n or from multiple file widget."
)
self.keep_chosen_components_chk.stateChanged.connect(
self.set_keep_chosen_components)
self.keep_chosen_components_chk.setChecked(
settings.keep_chosen_components)
self.show_parameters = QPushButton("Show parameters")
self.show_parameters.setToolTip(
"Show parameters of segmentation for each components")
self.show_parameters_widget = SegmentationInfoDialog(
self.settings, self.algorithm_choose_widget.change_algorithm)
self.show_parameters.clicked.connect(self.show_parameters_widget.show)
self.choose_components = ChosenComponents()
self.choose_components.check_change_signal.connect(
image_view.refresh_selected)
self.choose_components.mouse_leave.connect(image_view.component_unmark)
self.choose_components.mouse_enter.connect(image_view.component_mark)
# WARNING works only with one channels algorithms
# SynchronizeValues.add_synchronization("channels_chose", widgets_list)
self.chosen_list = []
self.progress_bar2 = QProgressBar()
self.progress_bar2.setHidden(True)
self.progress_bar = QProgressBar()
self.progress_bar.setHidden(True)
self.progress_info_lab = QLabel()
self.progress_info_lab.setHidden(True)
self.file_list = []
self.batch_process = BatchProceed()
self.batch_process.progress_signal.connect(self.progress_info)
self.batch_process.error_signal.connect(self.execution_all_error)
self.batch_process.execution_done.connect(self.execution_all_done)
self.batch_process.range_signal.connect(self.progress_bar.setRange)
self.is_batch_process = False
self.setContentsMargins(0, 0, 0, 0)
main_layout = QVBoxLayout()
# main_layout.setSpacing(0)
opt_layout = QHBoxLayout()
opt_layout.setContentsMargins(0, 0, 0, 0)
opt_layout.addWidget(self.show_result)
opt_layout.addWidget(right_label("Opacity:"))
opt_layout.addWidget(self.opacity)
main_layout.addLayout(opt_layout)
opt_layout2 = QHBoxLayout()
opt_layout2.setContentsMargins(0, 0, 0, 0)
opt_layout2.addWidget(self.only_borders)
opt_layout2.addWidget(right_label("Border thick:"))
opt_layout2.addWidget(self.borders_thick)
main_layout.addLayout(opt_layout2)
btn_layout = QGridLayout()
btn_layout.setContentsMargins(0, 0, 0, 0)
btn_layout.addWidget(self.execute_btn, 0, 0)
btn_layout.addWidget(self.execute_in_background_btn, 0, 1)
btn_layout.addWidget(self.execute_all_btn, 1, 0)
btn_layout.addWidget(self.save_parameters_btn, 1, 1)
main_layout.addLayout(btn_layout)
main_layout.addWidget(self.progress_bar2)
main_layout.addWidget(self.progress_bar)
main_layout.addWidget(self.progress_info_lab)
main_layout.addWidget(self.algorithm_choose_widget, 1)
# main_layout.addWidget(self.algorithm_choose)
# main_layout.addLayout(self.stack_layout, 1)
main_layout.addWidget(self.choose_components)
down_layout = QHBoxLayout()
down_layout.addWidget(self.keep_chosen_components_chk)
down_layout.addWidget(self.show_parameters)
main_layout.addLayout(down_layout)
main_layout.addStretch()
main_layout.setContentsMargins(0, 0, 0, 0)
# main_layout.setSpacing(0)
self.setLayout(main_layout)
# noinspection PyUnresolvedReferences
self.execute_in_background_btn.clicked.connect(
self.execute_in_background)
self.execute_btn.clicked.connect(self.execute_action)
self.execute_all_btn.clicked.connect(self.execute_all_action)
self.save_parameters_btn.clicked.connect(self.save_parameters)
# noinspection PyUnresolvedReferences
self.opacity.valueChanged.connect(self._set_opacity)
# noinspection PyUnresolvedReferences
self.show_result.currentEnumChanged.connect(self._set_show_label)
self.only_borders.stateChanged.connect(self._set_border_mode)
# noinspection PyUnresolvedReferences
self.borders_thick.valueChanged.connect(self._set_border_thick)
image_view.component_clicked.connect(
self.choose_components.other_component_choose)
settings.chosen_components_widget = self.choose_components
settings.components_change_list.connect(
self.choose_components.new_choose)
settings.image_changed.connect(
self.choose_components.remove_components)
settings.connect_to_profile(
f"{self.view_name}.image_state.only_border",
self._set_border_mode_from_settings)
settings.connect_to_profile(
f"{self.view_name}.image_state.border_thick",
self._set_border_thick_from_settings)
settings.connect_to_profile(f"{self.view_name}.image_state.opacity",
self._set_opacity_from_settings)
settings.connect_to_profile(f"{self.view_name}.image_state.show_label",
self._set_show_label_from_settings)