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 = EnumComboBox(Units)
self.units_select.set_value(self.settings.get("simple_measurements.units", Units.nm))
self.units_select.currentIndexChanged.connect(self.change_units)
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:
try:
geometry = self.settings.get_from_profile("simple_measurement_window_geometry")
self.restoreGeometry(QByteArray.fromHex(bytes(geometry, "ascii")))
except KeyError:
pass
def __init__(self, settings, parent=None):
super().__init__(parent)
self.setWindowTitle("Batch processing")
self.settings = settings
self.batch_manager = CalculationManager()
self.file_choose = FileChoose(self.settings, self.batch_manager, self)
self.calculate_planer = CalculatePlaner(self.settings, self)
self.addTab(self.calculate_planer, "Prepare workflow")
self.addTab(self.file_choose, "Input files")
self.working = False
with suppress(KeyError):
geometry = self.settings.get_from_profile("batch_window_geometry")
self.restoreGeometry(QByteArray.fromHex(bytes(geometry, "ascii")))
def __init__(self,
settings: ViewSettings,
image_view_names: List[str],
reload_list=None,
parent=None):
super().__init__(parent)
self.color_control = ColorControl(settings, image_view_names)
self.settings = settings
self.reload_list = reload_list if reload_list is not None else []
self.develop = DevelopTab()
self.addTab(self.color_control, "Color control")
if state_store.develop:
self.addTab(self.develop, "Develop")
if self.window() == self:
with suppress(KeyError):
geometry = self.settings.get_from_profile(
"advanced_window_geometry")
self.restoreGeometry(
QByteArray.fromHex(bytes(geometry, "ascii")))
def __init__(self,
config_folder=CONFIG_FOLDER,
title="PartSeg",
settings=None,
signal_fun=None,
initial_image=None):
super().__init__(config_folder, title, settings,
load_functions.load_dict, signal_fun)
self.channel_info = "result_image"
self.files_num = 2
self.setMinimumWidth(600)
# thi isinstance is only for hinting in IDE
assert isinstance(self.settings, PartSettings) # nosec
self.main_menu = MainMenu(self.settings, self)
self.channel_control2 = ChannelProperty(self.settings,
start_name="result_image")
self.raw_image = CompareImageView(self.settings, self.channel_control2,
"raw_image")
self.measurements = MeasurementWidget(self.settings)
self.left_stack = StackedWidgetWithSelector()
self.left_stack.addWidget(self.raw_image, "Image")
self.left_stack.addWidget(self.measurements, "Measurements")
self.result_image = ResultImageView(self.settings,
self.channel_control2,
"result_image")
self.color_bar = ColorBar(self.settings,
[self.raw_image, self.result_image])
self.info_text = QLabel()
self.info_text.setMinimumHeight(25)
self.raw_image.text_info_change.connect(self.info_text.setText)
self.result_image.text_info_change.connect(self.info_text.setText)
self.synchronize_tool = SynchronizeView(self.raw_image,
self.result_image, self)
self.options_panel = Options(self.settings, self.channel_control2,
self.raw_image, self.synchronize_tool)
# self.main_menu.image_loaded.connect(self.image_read)
self.settings.image_changed.connect(self.image_read)
self.advanced_window = SegAdvancedWindow(self.settings,
reload_list=[self.reload])
self.batch_window = None # BatchWindow(self.settings)
self.multiple_files = MultipleFileWidget(self.settings,
load_functions.load_dict,
True)
self.multiple_files.setVisible(
self.settings.get("multiple_files_widget", False))
if initial_image is None:
reader = TiffImageReader()
im = reader.read(self.initial_image_path)
im.file_path = ""
self.settings.image = im
elif initial_image is not False:
self.settings.image = initial_image
icon = QIcon(os.path.join(PartSegData.icons_dir, "icon.png"))
self.setWindowIcon(icon)
menu_bar = self.menuBar()
file_menu = menu_bar.addMenu("File")
file_menu.addAction("&Open").triggered.connect(
self.main_menu.load_data)
file_menu.addMenu(self.recent_file_menu)
file_menu.addAction("&Save").triggered.connect(
self.main_menu.save_file)
file_menu.addAction("Batch processing").triggered.connect(
self.main_menu.batch_window)
view_menu = menu_bar.addMenu("View")
view_menu.addAction("Settings and Measurement").triggered.connect(
self.main_menu.advanced_window_show)
view_menu.addAction("Additional output").triggered.connect(
self.additional_layers_show)
view_menu.addAction("Additional output with data").triggered.connect(
lambda: self.additional_layers_show(True))
view_menu.addAction("Napari viewer").triggered.connect(
self.napari_viewer_show)
view_menu.addAction("Toggle Multiple Files").triggered.connect(
self.toggle_multiple_files)
view_menu.addAction("Toggle left panel").triggered.connect(
self.toggle_left_panel)
view_menu.addAction("Toggle console").triggered.connect(
self._toggle_console)
action = view_menu.addAction("Screenshot right panel")
action.triggered.connect(self.screenshot(self.result_image))
action.setShortcut(QKeySequence.Print)
view_menu.addAction("Screenshot left panel").triggered.connect(
self.screenshot(self.raw_image))
image_menu = menu_bar.addMenu("Image operations")
image_menu.addAction("Image adjustment").triggered.connect(
self.image_adjust_exec)
image_menu.addAction("Mask manager").triggered.connect(
self.main_menu.mask_manager)
help_menu = menu_bar.addMenu("Help")
help_menu.addAction("State directory").triggered.connect(
self.show_settings_directory)
help_menu.addAction("About").triggered.connect(self.show_about_dialog)
layout = QGridLayout()
layout.setSpacing(0)
info_layout = QHBoxLayout()
info_layout.addWidget(self.left_stack.selector)
info_layout.addWidget(self.options_panel.compare_btn)
info_layout.addWidget(self.info_text, 1, Qt.AlignHCenter)
image_layout = EqualColumnLayout()
image_layout.addWidget(self.left_stack)
image_layout.addWidget(self.result_image)
layout.setSpacing(0)
layout.addWidget(self.main_menu, 0, 0, 1, 3)
layout.addLayout(info_layout, 3, 1, 1, 2)
layout.addWidget(self.multiple_files, 2, 0)
layout.addWidget(self.color_bar, 2, 1)
layout.addLayout(image_layout, 2, 2, 1, 1)
layout.addWidget(self.options_panel, 0, 3, 3, 1)
layout.setColumnStretch(2, 1)
widget = QWidget()
widget.setLayout(layout)
self.setCentralWidget(widget)
with suppress(KeyError):
geometry = self.settings.get_from_profile("main_window_geometry")
self.restoreGeometry(QByteArray.fromHex(bytes(geometry, "ascii")))
def restore_state(self,
stream: QXmlStreamReader,
testing: bool = False) -> bool:
'''
Restores the state from given stream.
Parameters
----------
stream : QXmlStreamReader
testing : bool
If Testing is true, the function only parses the data from the
given stream but does not restore anything. You can use this check
for faulty files before you start restoring the state
Returns
-------
value : bool
'''
is_floating = bool(int(stream.attributes().value("Floating")))
logger.debug('Restore DockContainerWidget Floating %s', is_floating)
if not testing:
self.d._visible_dock_area_count = -1
# invalidate the dock area count and clear the area cache
self.d.dock_areas.clear()
self.d.last_added_area_cache.clear()
if is_floating:
logger.debug('Restore floating widget')
if not stream.readNextStartElement(
) or stream.name() != "Geometry":
return False
geometry_string = stream.readElementText(
QXmlStreamReader.ErrorOnUnexpectedElement)
geometry = QByteArray.fromHex(geometry_string)
if geometry.isEmpty():
return False
if not testing:
floating_widget = self.floating_widget()
floating_widget.restoreGeometry(geometry)
res, new_root_splitter = self.d.restore_child_nodes(stream, testing)
if not res:
return False
if testing:
return True
# If the root splitter is empty, rostoreChildNodes returns a 0 pointer
# and we need to create a new empty root splitter
if not new_root_splitter:
new_root_splitter = self.d.new_splitter(Qt.Horizontal)
self.d.layout.replaceWidget(self.d.root_splitter, new_root_splitter)
old_root = self.d.root_splitter
self.d.root_splitter = new_root_splitter
old_root.deleteLater()
return True
def __init__(self,
config_folder=CONFIG_FOLDER,
title="PartSeg",
settings=None,
signal_fun=None,
initial_image=None):
super().__init__(config_folder, title, settings,
io_functions.load_dict, signal_fun)
self.channel_info = "channelcontrol"
self.channel_control = ChannelProperty(self.settings,
start_name="channelcontrol")
self.image_view = StackImageView(self.settings,
self.channel_control,
name="channelcontrol")
self.image_view.setMinimumWidth(450)
self.info_text = QLabel()
self.info_text.setSizePolicy(QSizePolicy.Ignored,
QSizePolicy.Preferred)
self.image_view.text_info_change.connect(self.info_text.setText)
self.options_panel = Options(self.settings, self.image_view)
self.main_menu = MainMenu(self.settings, self)
self.main_menu.image_loaded.connect(self.image_read)
self.settings.image_changed.connect(self.image_read)
self.color_bar = ColorBar(self.settings, self.image_view)
self.multiple_files = MultipleFileWidget(self.settings,
io_functions.load_dict)
self.multiple_files.setVisible(
self.options_panel.image_properties.multiple_files.isChecked())
self.options_panel.algorithm_options.batch_process.multiple_result.connect(
partial(self.multiple_files.save_state_action, custom_name=False))
icon = QIcon(os.path.join(PartSegData.icons_dir, "icon_stack.png"))
self.setWindowIcon(icon)
menu_bar = self.menuBar()
file_menu = menu_bar.addMenu("File")
file_menu.addAction("&Open").triggered.connect(
self.main_menu.load_image)
file_menu.addMenu(self.recent_file_menu)
file_menu.addAction("&Save segmentation").triggered.connect(
self.main_menu.save_segmentation)
file_menu.addAction("&Save components").triggered.connect(
self.main_menu.save_result)
view_menu = menu_bar.addMenu("View")
view_menu.addAction("Settings and Measurement").triggered.connect(
self.main_menu.show_advanced_window)
view_menu.addAction("Additional output").triggered.connect(
self.additional_layers_show)
view_menu.addAction("Additional output with data").triggered.connect(
lambda: self.additional_layers_show(True))
view_menu.addAction("Napari viewer").triggered.connect(
self.napari_viewer_show)
view_menu.addAction("Toggle Multiple Files").triggered.connect(
self.toggle_multiple_files)
view_menu.addAction("Toggle console").triggered.connect(
self._toggle_console)
action = view_menu.addAction("Screenshot")
action.triggered.connect(self.screenshot(self.image_view))
action.setShortcut(QKeySequence.Print)
image_menu = menu_bar.addMenu("Image operations")
image_menu.addAction("Image adjustment").triggered.connect(
self.image_adjust_exec)
help_menu = menu_bar.addMenu("Help")
help_menu.addAction("State directory").triggered.connect(
self.show_settings_directory)
help_menu.addAction("About").triggered.connect(self.show_about_dialog)
layout = QVBoxLayout()
layout.addWidget(self.main_menu)
sub_layout = QHBoxLayout()
sub2_layout = QVBoxLayout()
sub3_layout = QVBoxLayout()
sub_layout.addWidget(self.multiple_files)
sub_layout.addWidget(self.color_bar, 0)
sub3_layout.addWidget(self.image_view, 1)
sub3_layout.addWidget(self.info_text, 0)
sub2_layout.addWidget(self.options_panel, 1)
sub2_layout.addWidget(self.channel_control, 0)
sub_layout.addLayout(sub3_layout, 1)
sub_layout.addLayout(sub2_layout, 0)
layout.addLayout(sub_layout)
self.widget = QWidget()
self.widget.setLayout(layout)
self.setCentralWidget(self.widget)
if initial_image is None:
reader = TiffImageReader()
im = reader.read(self.initial_image_path)
im.file_path = ""
self.settings.image = im
elif initial_image is not False:
self.settings.image = initial_image
with suppress(KeyError):
geometry = self.settings.get_from_profile("main_window_geometry")
self.restoreGeometry(QByteArray.fromHex(bytes(geometry, "ascii")))
