mosamatic2 2.0.24__py3-none-any.whl

mosamatic2/ui/widgets/panels/tasks/segmentationnumpy2niftitaskpanel.py

@@ -0,0 +1,213 @@
+import os
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QCheckBox,
+    QSpinBox,
+    QHBoxLayout,
+    QVBoxLayout,
+    QFormLayout,
+    QPushButton,
+    QFileDialog,
+    QMessageBox,
+)
+from PySide6.QtCore import (
+    QThread, 
+    Slot,
+)
+
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.ui.widgets.panels.tasks.taskpanel import TaskPanel
+from mosamatic2.ui.settings import Settings
+from mosamatic2.ui.utils import is_macos
+from mosamatic2.ui.worker import Worker
+from mosamatic2.core.tasks import SegmentationNumpy2NiftiTask
+
+LOG = LogManager()
+
+PANEL_TITLE = 'SegmentationNumpy2NiftiTask'
+PANEL_NAME = 'segmentationnumpy2niftitaskpanel'
+
+
+class SegmentationNumpy2NiftiTaskPanel(TaskPanel):
+    def __init__(self):
+        super(SegmentationNumpy2NiftiTaskPanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._images_dir_line_edit = None
+        self._images_dir_select_line_button = None
+        self._segmentations_dir_line_edit = None
+        self._segmentations_dir_select_button = None
+        self._output_dir_line_edit = None
+        self._output_dir_select_button = None
+        self._overwrite_checkbox = None
+        self._form_layout = None
+        self._run_task_button = None
+        self._settings = None
+        self._task = None
+        self._worker = None
+        self._thread = None
+        self.init_layout()
+
+    def images_dir_line_edit(self):
+        if not self._images_dir_line_edit:
+            self._images_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/images_dir'))
+        return self._images_dir_line_edit
+    
+    def images_dir_select_button(self):
+        if not self._images_dir_select_line_button:
+            self._images_dir_select_line_button = QPushButton('Select')
+            self._images_dir_select_line_button.clicked.connect(self.handle_images_dir_select_button)
+        return self._images_dir_select_line_button
+    
+    def segmentations_dir_line_edit(self):
+        if not self._segmentations_dir_line_edit:
+            self._segmentations_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/segmentations_dir'))
+        return self._segmentations_dir_line_edit
+    
+    def segmentations_dir_select_button(self):
+        if not self._segmentations_dir_select_button:
+            self._segmentations_dir_select_button = QPushButton('Select')
+            self._segmentations_dir_select_button.clicked.connect(self.handle_segmentations_dir_select_button)
+        return self._segmentations_dir_select_button
+    
+    def output_dir_line_edit(self):
+        if not self._output_dir_line_edit:
+            self._output_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/output_dir'))
+        return self._output_dir_line_edit
+    
+    def output_dir_select_button(self):
+        if not self._output_dir_select_button:
+            self._output_dir_select_button = QPushButton('Select')
+            self._output_dir_select_button.clicked.connect(self.handle_output_dir_select_button)
+        return self._output_dir_select_button
+    
+    def overwrite_checkbox(self):
+        if not self._overwrite_checkbox:
+            self._overwrite_checkbox = QCheckBox('')
+            self._overwrite_checkbox.setChecked(self.settings().get_bool(f'{PANEL_NAME}/overwrite', True))
+        return self._overwrite_checkbox
+    
+    def form_layout(self):
+        if not self._form_layout:
+            self._form_layout = QFormLayout()
+            if is_macos():
+                self._form_layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow)
+        return self._form_layout
+    
+    def run_task_button(self):
+        if not self._run_task_button:
+            self._run_task_button = QPushButton('Run task')
+            self._run_task_button.clicked.connect(self.handle_run_task_button)
+        return self._run_task_button
+    
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+    
+    def init_layout(self):
+        images_dir_layout = QHBoxLayout()
+        images_dir_layout.addWidget(self.images_dir_line_edit())
+        images_dir_layout.addWidget(self.images_dir_select_button())
+        segmentations_dir_layout = QHBoxLayout()
+        segmentations_dir_layout.addWidget(self.segmentations_dir_line_edit())
+        segmentations_dir_layout.addWidget(self.segmentations_dir_select_button())
+        output_dir_layout = QHBoxLayout()
+        output_dir_layout.addWidget(self.output_dir_line_edit())
+        output_dir_layout.addWidget(self.output_dir_select_button())
+        self.form_layout().addRow('Images directory', images_dir_layout)
+        self.form_layout().addRow('Segmentations directory', segmentations_dir_layout)
+        self.form_layout().addRow('Output directory', output_dir_layout)
+        self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
+        layout = QVBoxLayout()
+        layout.addLayout(self.form_layout())
+        layout.addWidget(self.run_task_button())
+        self.setLayout(layout)
+        self.setObjectName(PANEL_NAME)
+
+    def handle_images_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.images_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_segmentations_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.segmentations_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_output_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.output_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_run_task_button(self):
+        errors = self.check_inputs_and_parameters()
+        if len(errors) > 0:
+            error_message = 'Following errors were encountered:\n'
+            for error in errors:
+                error_message += f' - {error}\n'
+            QMessageBox.information(self, 'Error', error_message)
+        else:
+            LOG.info('Running task...')
+            self.run_task_button().setEnabled(False)
+            self.save_inputs_and_parameters()
+            self._task = SegmentationNumpy2NiftiTask(
+                inputs={
+                    'images': self.images_dir_line_edit().text(),
+                    'segmentations': self.segmentations_dir_line_edit().text()
+                },
+                params=None,
+                output=self.output_dir_line_edit().text(),
+                overwrite=self.overwrite_checkbox().isChecked(),
+            )
+            self._worker = Worker(self._task)
+            self._thread = QThread()
+            self._worker.moveToThread(self._thread)
+            self._thread.started.connect(self._worker.run)
+            self._worker.progress.connect(self.handle_progress)
+            self._worker.status.connect(self.handle_status)
+            self._worker.finished.connect(self.handle_finished)
+            self._worker.finished.connect(self._thread.quit)
+            self._worker.finished.connect(self._worker.deleteLater)
+            self._thread.finished.connect(self._thread.deleteLater)
+            self._thread.start()
+
+    @Slot(int)
+    def handle_progress(self, progress):
+        LOG.info(f'Progress: {progress} / 100%')
+
+    @Slot(str)
+    def handle_status(self, status):
+        LOG.info(f'Status: {status}')
+
+    @Slot()
+    def handle_finished(self):
+        self.run_task_button().setEnabled(True)
+
+    # HELPERS
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.images_dir_line_edit().text() == '':
+            errors.append('Empty images directory path')
+        if self.segmentations_dir_line_edit().text() == '':
+            errors.append('Empty segmentations directory path')
+        if not os.path.isdir(self.segmentations_dir_line_edit().text()):
+            errors.append('Segmentations directory does not exist')
+        if self.output_dir_line_edit().text() == '':
+            errors.append('Empty output directory path')
+        if os.path.isdir(self.output_dir_line_edit().text()) and not self.overwrite_checkbox().isChecked():
+            errors.append('Output directory exists but overwrite=False. Please remove output directory first')
+        return errors
+    
+    def save_inputs_and_parameters(self):
+        self.settings().set(f'{PANEL_NAME}/images_dir', self.images_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/segmentations_dir', self.segmentations_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/output_dir', self.output_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())

mosamatic2/ui/widgets/panels/tasks/segmentmusclefatl3tensorflowtaskpanel.py

@@ -0,0 +1,216 @@
+import os
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QCheckBox,
+    QHBoxLayout,
+    QVBoxLayout,
+    QFormLayout,
+    QPushButton,
+    QFileDialog,
+    QMessageBox,
+)
+from PySide6.QtCore import (
+    QThread, 
+    Slot,
+)
+
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.ui.widgets.panels.tasks.taskpanel import TaskPanel
+from mosamatic2.ui.settings import Settings
+from mosamatic2.ui.utils import is_macos
+from mosamatic2.ui.worker import Worker
+from mosamatic2.core.tasks import SegmentMuscleFatL3TensorFlowTask
+
+LOG = LogManager()
+
+PANEL_TITLE = 'SegmentMuscleFatL3TensorFlowTask (TensorFlow)'
+PANEL_NAME = 'segmentmusclefatl3tensorflowtaskpanel'
+
+
+class SegmentMuscleFatL3TensorFlowTaskPanel(TaskPanel):
+    def __init__(self):
+        super(SegmentMuscleFatL3TensorFlowTaskPanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._images_dir_line_edit = None
+        self._images_dir_select_button = None
+        self._model_files_dir_line_edit = None
+        self._model_files_dir_select_button = None
+        self._output_dir_line_edit = None
+        self._output_dir_select_button = None
+        self._overwrite_checkbox = None
+        self._form_layout = None
+        self._run_task_button = None
+        self._settings = None
+        self._task = None
+        self._worker = None
+        self._thread = None
+        self.init_layout()
+
+    def images_dir_line_edit(self):
+        if not self._images_dir_line_edit:
+            self._images_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/images_dir'))
+        return self._images_dir_line_edit
+    
+    def images_dir_select_button(self):
+        if not self._images_dir_select_button:
+            self._images_dir_select_button = QPushButton('Select')
+            self._images_dir_select_button.clicked.connect(self.handle_images_dir_select_button)
+        return self._images_dir_select_button
+    
+    def model_files_dir_line_edit(self):
+        if not self._model_files_dir_line_edit:
+            self._model_files_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/model_files_dir'))
+        return self._model_files_dir_line_edit
+    
+    def model_files_dir_select_button(self):
+        if not self._model_files_dir_select_button:
+            self._model_files_dir_select_button = QPushButton('Select')
+            self._model_files_dir_select_button.clicked.connect(self.handle_model_files_dir_select_button)
+        return self._model_files_dir_select_button
+    
+    def output_dir_line_edit(self):
+        if not self._output_dir_line_edit:
+            self._output_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/output_dir'))
+        return self._output_dir_line_edit
+    
+    def output_dir_select_button(self):
+        if not self._output_dir_select_button:
+            self._output_dir_select_button = QPushButton('Select')
+            self._output_dir_select_button.clicked.connect(self.handle_output_dir_select_button)
+        return self._output_dir_select_button
+    
+    def overwrite_checkbox(self):
+        if not self._overwrite_checkbox:
+            self._overwrite_checkbox = QCheckBox('')
+            self._overwrite_checkbox.setChecked(self.settings().get_bool(f'{PANEL_NAME}/overwrite', True))
+        return self._overwrite_checkbox
+    
+    def form_layout(self):
+        if not self._form_layout:
+            self._form_layout = QFormLayout()
+            if is_macos():
+                self._form_layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow)
+        return self._form_layout
+    
+    def run_task_button(self):
+        if not self._run_task_button:
+            self._run_task_button = QPushButton('Run task')
+            self._run_task_button.clicked.connect(self.handle_run_task_button)
+        return self._run_task_button
+    
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+    
+    def init_layout(self):
+        images_dir_layout = QHBoxLayout()
+        images_dir_layout.addWidget(self.images_dir_line_edit())
+        images_dir_layout.addWidget(self.images_dir_select_button())
+        model_files_dir_layout = QHBoxLayout()
+        model_files_dir_layout.addWidget(self.model_files_dir_line_edit())
+        model_files_dir_layout.addWidget(self.model_files_dir_select_button())
+        output_dir_layout = QHBoxLayout()
+        output_dir_layout.addWidget(self.output_dir_line_edit())
+        output_dir_layout.addWidget(self.output_dir_select_button())
+        self.form_layout().addRow('Images directory', images_dir_layout)
+        self.form_layout().addRow('Model files directory', model_files_dir_layout)
+        self.form_layout().addRow('Output directory', output_dir_layout)
+        self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
+        layout = QVBoxLayout()
+        layout.addLayout(self.form_layout())
+        layout.addWidget(self.run_task_button())
+        self.setLayout(layout)
+        self.setObjectName(PANEL_NAME)
+
+    def handle_images_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.images_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_model_files_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.model_files_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_output_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.output_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_run_task_button(self):
+        errors = self.check_inputs_and_parameters()
+        if len(errors) > 0:
+            error_message = 'Following errors were encountered:\n'
+            for error in errors:
+                error_message += f' - {error}\n'
+            QMessageBox.information(self, 'Error', error_message)
+        else:
+            LOG.info('Running task...')
+            self.run_task_button().setEnabled(False)
+            self.save_inputs_and_parameters()
+            self._task = SegmentMuscleFatL3TensorFlowTask(
+                inputs={
+                    'images': self.images_dir_line_edit().text(),
+                    'model_files': self.model_files_dir_line_edit().text(),
+                },
+                params={'model_version': 1.0},
+                output=self.output_dir_line_edit().text(),
+                overwrite=self.overwrite_checkbox().isChecked(),
+            )
+            self._worker = Worker(self._task)
+            self._thread = QThread()
+            self._worker.moveToThread(self._thread)
+            self._thread.started.connect(self._worker.run)
+            self._worker.progress.connect(self.handle_progress)
+            self._worker.status.connect(self.handle_status)
+            self._worker.finished.connect(self.handle_finished)
+            self._worker.finished.connect(self._thread.quit)
+            self._worker.finished.connect(self._worker.deleteLater)
+            self._thread.finished.connect(self._thread.deleteLater)
+            self._thread.start()
+
+    @Slot(int)
+    def handle_progress(self, progress):
+        LOG.info(f'Progress: {progress} / 100%')
+
+    @Slot(str)
+    def handle_status(self, status):
+        LOG.info(f'Status: {status}')
+
+    @Slot()
+    def handle_finished(self):
+        self.run_task_button().setEnabled(True)
+
+    # HELPERS
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.images_dir_line_edit().text() == '':
+            errors.append('Empty images directory path')
+        if not os.path.isdir(self.images_dir_line_edit().text()):
+            errors.append('Images directory does not exist')
+        if self.model_files_dir_line_edit().text() == '':
+            errors.append('Empty model files directory path')
+        if not os.path.isdir(self.model_files_dir_line_edit().text()):
+            errors.append('Model files directory does not exist')
+        if len(os.listdir(self.model_files_dir_line_edit().text())) != 3:
+            errors.append('Model files directory should ONLY contain "model-1.1.zip", "contour_model-1.1.zip" and "params-1.1.json", nothing else!')
+        if self.output_dir_line_edit().text() == '':
+            errors.append('Empty output directory path')
+        if os.path.isdir(self.output_dir_line_edit().text()) and not self.overwrite_checkbox().isChecked():
+            errors.append('Output directory exists but overwrite=False. Please remove output directory first')
+        return errors
+    
+    def save_inputs_and_parameters(self):
+        self.settings().set(f'{PANEL_NAME}/images_dir', self.images_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/model_files_dir', self.model_files_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/output_dir', self.output_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())

mosamatic2/ui/widgets/panels/tasks/segmentmusclefatt4pytorchtaskpanel.py

@@ -0,0 +1,217 @@
+import os
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QCheckBox,
+    QHBoxLayout,
+    QVBoxLayout,
+    QFormLayout,
+    QPushButton,
+    QFileDialog,
+    QMessageBox,
+)
+from PySide6.QtCore import (
+    QThread, 
+    Slot,
+)
+
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.ui.widgets.panels.tasks.taskpanel import TaskPanel
+from mosamatic2.ui.settings import Settings
+from mosamatic2.ui.utils import is_macos
+from mosamatic2.ui.worker import Worker
+from mosamatic2.core.tasks import SegmentMuscleFatT4PyTorchTask
+
+LOG = LogManager()
+
+PANEL_TITLE = 'SegmentMuscleFatT4PyTorchTask'
+PANEL_NAME = 'segmentmusclefatt4pytorchtaskpanel'
+
+
+class SegmentMuscleFatT4PyTorchTaskPanel(TaskPanel):
+    def __init__(self):
+        super(SegmentMuscleFatT4PyTorchTaskPanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._images_dir_line_edit = None
+        self._images_dir_select_button = None
+        self._model_files_dir_line_edit = None
+        self._model_files_dir_select_button = None
+        self._output_dir_line_edit = None
+        self._output_dir_select_button = None
+        self._overwrite_checkbox = None
+        self._form_layout = None
+        self._run_task_button = None
+        self._settings = None
+        self._task = None
+        self._worker = None
+        self._thread = None
+        self.init_layout()
+
+    def images_dir_line_edit(self):
+        if not self._images_dir_line_edit:
+            self._images_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/images_dir'))
+        return self._images_dir_line_edit
+    
+    def images_dir_select_button(self):
+        if not self._images_dir_select_button:
+            self._images_dir_select_button = QPushButton('Select')
+            self._images_dir_select_button.clicked.connect(self.handle_images_dir_select_button)
+        return self._images_dir_select_button
+    
+    def model_files_dir_line_edit(self):
+        if not self._model_files_dir_line_edit:
+            self._model_files_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/model_files_dir'))
+        return self._model_files_dir_line_edit
+    
+    def model_files_dir_select_button(self):
+        if not self._model_files_dir_select_button:
+            self._model_files_dir_select_button = QPushButton('Select')
+            self._model_files_dir_select_button.clicked.connect(self.handle_model_files_dir_select_button)
+        return self._model_files_dir_select_button
+    
+    def output_dir_line_edit(self):
+        if not self._output_dir_line_edit:
+            self._output_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/output_dir'))
+        return self._output_dir_line_edit
+    
+    def output_dir_select_button(self):
+        if not self._output_dir_select_button:
+            self._output_dir_select_button = QPushButton('Select')
+            self._output_dir_select_button.clicked.connect(self.handle_output_dir_select_button)
+        return self._output_dir_select_button
+    
+    def overwrite_checkbox(self):
+        if not self._overwrite_checkbox:
+            self._overwrite_checkbox = QCheckBox('')
+            self._overwrite_checkbox.setChecked(self.settings().get_bool(f'{PANEL_NAME}/overwrite', True))
+        return self._overwrite_checkbox
+    
+    def form_layout(self):
+        if not self._form_layout:
+            self._form_layout = QFormLayout()
+            if is_macos():
+                self._form_layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow)
+        return self._form_layout
+    
+    def run_task_button(self):
+        if not self._run_task_button:
+            self._run_task_button = QPushButton('Run task')
+            self._run_task_button.clicked.connect(self.handle_run_task_button)
+        return self._run_task_button
+    
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+    
+    def init_layout(self):
+        images_dir_layout = QHBoxLayout()
+        images_dir_layout.addWidget(self.images_dir_line_edit())
+        images_dir_layout.addWidget(self.images_dir_select_button())
+        model_files_dir_layout = QHBoxLayout()
+        model_files_dir_layout.addWidget(self.model_files_dir_line_edit())
+        model_files_dir_layout.addWidget(self.model_files_dir_select_button())
+        output_dir_layout = QHBoxLayout()
+        output_dir_layout.addWidget(self.output_dir_line_edit())
+        output_dir_layout.addWidget(self.output_dir_select_button())
+        self.form_layout().addRow('Images directory', images_dir_layout)
+        self.form_layout().addRow('Model files directory', model_files_dir_layout)
+        self.form_layout().addRow('Output directory', output_dir_layout)
+        self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
+        layout = QVBoxLayout()
+        layout.addLayout(self.form_layout())
+        layout.addWidget(self.run_task_button())
+        self.setLayout(layout)
+        self.setObjectName(PANEL_NAME)
+
+    def handle_images_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.images_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_model_files_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.model_files_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_output_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.output_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_run_task_button(self):
+        errors = self.check_inputs_and_parameters()
+        if len(errors) > 0:
+            error_message = 'Following errors were encountered:\n'
+            for error in errors:
+                error_message += f' - {error}\n'
+            QMessageBox.information(self, 'Error', error_message)
+        else:
+            LOG.info('Running task...')
+            self.run_task_button().setEnabled(False)
+            self.save_inputs_and_parameters()
+            self._task = SegmentMuscleFatT4PyTorchTask(
+                inputs={
+                    'images': self.images_dir_line_edit().text(),
+                    'model_files': self.model_files_dir_line_edit().text(),
+                },
+                params={'model_version': 1.0},
+                output=self.output_dir_line_edit().text(),
+                overwrite=self.overwrite_checkbox().isChecked(),
+            )
+            # self._task.run()
+            self._worker = Worker(self._task)
+            self._thread = QThread()
+            self._worker.moveToThread(self._thread)
+            self._thread.started.connect(self._worker.run)
+            self._worker.progress.connect(self.handle_progress)
+            self._worker.status.connect(self.handle_status)
+            self._worker.finished.connect(self.handle_finished)
+            self._worker.finished.connect(self._thread.quit)
+            self._worker.finished.connect(self._worker.deleteLater)
+            self._thread.finished.connect(self._thread.deleteLater)
+            self._thread.start()
+
+    @Slot(int)
+    def handle_progress(self, progress):
+        LOG.info(f'Progress: {progress} / 100%')
+
+    @Slot(str)
+    def handle_status(self, status):
+        LOG.info(f'Status: {status}')
+
+    @Slot()
+    def handle_finished(self):
+        self.run_task_button().setEnabled(True)
+
+    # HELPERS
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.images_dir_line_edit().text() == '':
+            errors.append('Empty images directory path')
+        if not os.path.isdir(self.images_dir_line_edit().text()):
+            errors.append('Images directory does not exist')
+        if self.model_files_dir_line_edit().text() == '':
+            errors.append('Empty model files directory path')
+        if not os.path.isdir(self.model_files_dir_line_edit().text()):
+            errors.append('Model files directory does not exist')
+        if len(os.listdir(self.model_files_dir_line_edit().text())) != 3:
+            errors.append('Model files directory should ONLY contain "model-1.0.pt", "contour_model-1.0.pt" and "params-1.0.json", nothing else!')
+        if self.output_dir_line_edit().text() == '':
+            errors.append('Empty output directory path')
+        if os.path.isdir(self.output_dir_line_edit().text()) and not self.overwrite_checkbox().isChecked():
+            errors.append('Output directory exists but overwrite=False. Please remove output directory first')
+        return errors
+    
+    def save_inputs_and_parameters(self):
+        self.settings().set(f'{PANEL_NAME}/images_dir', self.images_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/model_files_dir', self.model_files_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/output_dir', self.output_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())