class ImageReaderThread(ProgressTread):
"""
thread for reading files. Useful for reading from disc
"""
image_read_finish = Signal(Image)
def __init__(self, file_path=None, mask_path=None):
super().__init__()
self.reader = TiffImageReader(self.info_function)
self.file_path = file_path
self.mask_path = mask_path
self.image = None
def set_path(self, file_path, mask_path=None):
self.file_path = file_path
self.mask_path = mask_path
def run(self):
if self.file_path is None:
return
try:
self.image = self.reader.read(self.file_path, self.mask_path)
self.image_read_finish.emit(self.image)
except Exception as e:
self.error_signal.emit(e)
def run(self):
if self.module != "":
from .. import plugins
plugins.register()
main_window_module = importlib.import_module(self.module)
main_window: BaseMainWindow = main_window_module.MainWindow
settings: BaseSettings = main_window.get_setting_class()(main_window_module.CONFIG_FOLDER)
self.errors = settings.load()
reader = TiffImageReader()
im = reader.read(main_window.initial_image_path)
im.file_path = ""
self.result = partial(main_window, settings=settings, initial_image=im)
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 __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")))