class MainWindow(QMainWindow):
def __init__(self, title):
super().__init__()
self.setWindowTitle(title)
self.lib_path = ""
self.final_title = ""
analysis_icon = QIcon(os.path.join(icons_dir, "icon.png"))
stack_icon = QIcon(os.path.join(icons_dir, "icon_stack.png"))
self.analysis_button = QToolButton(self)
self.analysis_button.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
self.analysis_button.setIcon(analysis_icon)
# TODO use more general solution for text wrapping
self.analysis_button.setText(ANALYSIS_NAME.replace(" ", "\n"))
self.analysis_button.setIconSize(QSize(100, 100))
self.mask_button = QToolButton(self)
self.mask_button.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
self.mask_button.setIcon(stack_icon)
self.mask_button.setText(MASK_NAME.replace(" ", "\n"))
self.mask_button.setIconSize(QSize(100, 100))
self.analysis_button.clicked.connect(self.launch_analysis)
self.mask_button.clicked.connect(self.launch_mask)
self.progress = QProgressBar()
self.progress.setHidden(True)
layout = QGridLayout()
layout.addWidget(self.progress, 0, 0, 1, 2)
layout.addWidget(self.analysis_button, 1, 1)
layout.addWidget(self.mask_button, 1, 0)
widget = QWidget()
widget.setLayout(layout)
self.setCentralWidget(widget)
self.setWindowIcon(analysis_icon)
self.prepare = None
self.wind = None
self._update_theme()
def _update_theme(self):
napari_settings = napari_get_settings(state_store.save_folder)
with warnings.catch_warnings():
warnings.simplefilter("ignore", FutureWarning)
theme = get_theme(napari_settings.appearance.theme)
# TODO understand qss overwrite mechanism
self.setStyleSheet(napari_template(get_stylesheet(), **theme))
def _launch_begin(self):
self.progress.setVisible(True)
self.progress.setRange(0, 0)
self.analysis_button.setDisabled(True)
self.mask_button.setDisabled(True)
import_config()
def launch_analysis(self):
self._launch_begin()
self._launch_analysis()
self.prepare.start()
def _launch_analysis(self):
self.lib_path = "PartSeg._roi_analysis.main_window"
self.final_title = f"{APP_NAME} {ANALYSIS_NAME}"
self.prepare = Prepare(self.lib_path)
self.prepare.finished.connect(self.launch)
def launch_mask(self):
self._launch_begin()
self._launch_mask()
self.prepare.start()
def _launch_mask(self):
self.lib_path = "PartSeg._roi_mask.main_window"
self.final_title = f"{APP_NAME} {MASK_NAME}"
self.prepare = Prepare(self.lib_path)
self.prepare.finished.connect(self.launch)
def window_shown(self):
self.close()
def launch(self):
if self.prepare.result is None:
self.close()
return
if self.prepare.errors:
errors_message = QMessageBox()
errors_message.setText("There are errors during start")
errors_message.setInformativeText(
"During load saved state some of data could not be load properly\n"
"The files has prepared backup copies in state directory (Help > State directory)"
)
errors_message.setStandardButtons(QMessageBox.Ok)
text = "\n".join("File: " + x[0] + "\n" + str(x[1])
for x in self.prepare.errors)
errors_message.setDetailedText(text)
errors_message.exec_()
wind = self.prepare.result(title=self.final_title,
signal_fun=self.window_shown)
wind.show()
self.wind = wind
class MainWindow(QMainWindow):
def __init__(self, title):
super().__init__()
self.setWindowTitle(title)
self.lib_path = ""
self.final_title = ""
analysis_icon = QIcon(os.path.join(icons_dir, "icon.png"))
stack_icon = QIcon(os.path.join(icons_dir, "icon_stack.png"))
self.analysis_button = QToolButton(self)
self.analysis_button.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
self.analysis_button.setIcon(analysis_icon)
# TODO use more general solution for text wrapping
self.analysis_button.setText(SEGMENTATION_NAME.replace(" ", "\n"))
self.analysis_button.setIconSize(QSize(100, 100))
self.mask_button = QToolButton(self)
self.mask_button.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
self.mask_button.setIcon(stack_icon)
self.mask_button.setText(MASK_NAME.replace(" ", "\n"))
self.mask_button.setIconSize(QSize(100, 100))
self.analysis_button.clicked.connect(self.launch_analysis)
self.mask_button.clicked.connect(self.launch_mask)
self.progress = QProgressBar()
self.progress.setHidden(True)
layout = QGridLayout()
layout.addWidget(self.progress, 0, 0, 1, 2)
layout.addWidget(self.analysis_button, 1, 1)
layout.addWidget(self.mask_button, 1, 0)
widget = QWidget()
widget.setLayout(layout)
self.setCentralWidget(widget)
self.setWindowIcon(analysis_icon)
self.prepare = None
self.wind = None
def _launch_begin(self):
self.progress.setVisible(True)
self.progress.setRange(0, 0)
self.analysis_button.setDisabled(True)
self.mask_button.setDisabled(True)
import_config()
def launch_analysis(self):
self._launch_begin()
self.lib_path = "PartSeg.segmentation_analysis.main_window"
self.final_title = "PartSeg Segmentation Analysis"
self.prepare = Prepare(self.lib_path)
self.prepare.finished.connect(self.launch)
self.prepare.start()
def launch_mask(self):
self._launch_begin()
self.lib_path = "PartSeg.segmentation_mask.main_window"
self.final_title = "PartSeg Mask Segmentation"
self.prepare = Prepare(self.lib_path)
self.prepare.finished.connect(self.launch)
self.prepare.start()
def window_shown(self):
self.close()
def launch(self):
if self.prepare.result is None:
self.close()
return
if self.prepare.errors:
errors_message = QMessageBox()
errors_message.setText("There are errors during start")
errors_message.setInformativeText(
"During load saved state some of data could not be load properly\n"
"The files has prepared backup copies in state directory (Help > State directory)"
)
errors_message.setStandardButtons(QMessageBox.Ok)
text = "\n".join(["File: " + x[0] + "\n" + str(x[1]) for x in self.prepare.errors])
errors_message.setDetailedText(text)
errors_message.exec()
wind = self.prepare.result(title=self.final_title, signal_fun=self.window_shown)
wind.show()
self.wind = wind
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)