mosamatic2 2.0.10__tar.gz → 2.0.11__tar.gz

{mosamatic2-2.0.10 → mosamatic2-2.0.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.10
+Version: 2.0.11
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl

{mosamatic2-2.0.10 → mosamatic2-2.0.11}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.10"
+version = "2.0.11"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}

mosamatic2-2.0.11/src/mosamatic2/core/pipelines/__init__.py

@@ -0,0 +1,2 @@
+from mosamatic2.core.pipelines.defaultpipeline.defaultpipeline import DefaultPipeline
+from mosamatic2.core.pipelines.defaultdockerpipeline.defaultdockerpipeline import DefaultDockerPipeline

mosamatic2-2.0.11/src/mosamatic2/core/pipelines/defaultdockerpipeline/defaultdockerpipeline.py

@@ -0,0 +1,42 @@
+import os
+
+from mosamatic2.core.pipelines.pipeline import Pipeline
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
+DOCKER_SCRIPT = """
+docker run --rm ^
+    -v "%IMAGES%":/data/images ^
+    -v "%MODEL_FILES%":/data/model_files ^
+    -v "%OUTPUT%":/data/output ^
+    brecheisen/mosamatic2-cli:%VERSION% defaultpipeline ^
+        --images /data/images --model_files /data/model_files --output /data/output --overwrite true
+"""
+
+
+class DefaultDockerPipeline(Pipeline):
+    INPUTS = [
+        'images',
+        'model_files',
+    ]
+    PARAMS = [
+        'target_size',
+        'file_type',
+        'fig_width',
+        'fig_height',
+        'model_type',
+        'model_version',
+        'version',
+    ]
+    def __init__(self, inputs, params, output, overwrite):
+        super(DefaultDockerPipeline, self).__init__(inputs, params, output, overwrite)
+
+    def run(self):
+        docker_script = 'docker run --rm ' + \
+            '-v "{}":/data/images '.format(self.input('images')) + \
+            '-v "{}":/data/model_files '.format(self.input('model_files')) + \
+            '-v "{}":/data/output '.format(self.output()) + \
+            'brecheisen/mosamatic2-cli:{} defaultpipeline '.format(self.param('version')) + \
+            '--images /data/images --model_files /data/model_files --output /data/output --overwrite true'
+        LOG.info(f'Running Docker script: {docker_script}')
+        os.system(docker_script)

mosamatic2-2.0.11/src/mosamatic2/core/tasks/selectslicefromscanstask/selectslicefromscanstask.py

@@ -0,0 +1,162 @@
+import os
+import math
+import tempfile
+import shutil
+import nibabel as nib
+import numpy as np
+from totalsegmentator.python_api import totalsegmentator
+from mosamatic2.core.tasks.task import Task
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.utils import load_dicom
+
+LOG = LogManager()
+
+TOTAL_SEGMENTATOR_OUTPUT_DIR = os.path.join(tempfile.gettempdir(), 'total_segmentator_output')
+TOTAL_SEGMENTATOR_TASK = 'total'
+Z_DELTA_OFFSETS = {
+    'vertebrae_L3': 0.333,
+    'vertebrae_T4': 0.5,
+}
+
+
+class SelectSliceFromScansTask(Task):
+    INPUTS = ['scans']
+    PARAMS = ['vertebra']
+
+    def __init__(self, inputs, params, output, overwrite):
+        super(SelectSliceFromScansTask, self).__init__(inputs, params, output, overwrite)
+        self._error_dir = os.path.split(self.output())[0]
+        self._error_dir = os.path.join(self._error_dir, 'selectslicefromscanstask_errors')
+        os.makedirs(self._error_dir, exist_ok=True)
+        self._error_file = os.path.join(self._error_dir, 'errors.txt')
+        with open(self._error_file, 'w') as f:
+            f.write('Errors:\n')
+        LOG.info(f'Error directory: {self._error_dir}')
+
+    def write_error(self, message):
+        LOG.error(message)
+        with open(self._error_file, 'a') as f:
+            f.write(message + '\n')
+
+    def load_scan_dirs(self):
+        scan_dirs = []
+        for d in os.listdir(self.input('scans')):
+            scan_dir = os.path.join(self.input('scans'), d)
+            if os.path.isdir(scan_dir):
+                scan_dirs.append(scan_dir)
+        return scan_dirs
+    
+    def extract_masks(self, scan_dir):
+        os.makedirs(TOTAL_SEGMENTATOR_OUTPUT_DIR, exist_ok=True)
+        totalsegmentator(input=scan_dir, output=TOTAL_SEGMENTATOR_OUTPUT_DIR, fast=True)
+        if not os.path.isfile(os.path.join(TOTAL_SEGMENTATOR_OUTPUT_DIR, 'vertebrae_L3.nii.gz')):
+            raise Exception(f'{scan_dir}: vertebrae_L3.nii.gz does not exist')
+        # os.system(f'TotalSegmentator -i {scan_dir} -o {TOTAL_SEGMENTATOR_OUTPUT_DIR} --fast')
+
+    def delete_total_segmentator_output(self):
+        if os.path.exists(TOTAL_SEGMENTATOR_OUTPUT_DIR):
+            shutil.rmtree(TOTAL_SEGMENTATOR_OUTPUT_DIR)
+
+    def get_z_delta_offset_for_mask(self, mask_name):
+        if mask_name not in Z_DELTA_OFFSETS.keys():
+            return None
+        return Z_DELTA_OFFSETS[mask_name]
+
+    def find_slice(self, scan_dir, vertebra):
+        if vertebra == 'L3':
+            vertebral_level = 'vertebrae_L3'
+        elif vertebra == 'T4':
+            vertebral_level = 'vertebrae_T4'
+        else:
+            self.write_error(f'{scan_dir}: Unknown vertbra {vertebra}. Options are "L3" and "T4"')
+            return None
+        # Find Z-positions DICOM images
+        z_positions = {}
+        for f in os.listdir(scan_dir):
+            f_path = os.path.join(scan_dir, f)
+            try:
+                p = load_dicom(f_path, stop_before_pixels=True)
+                if p is not None and hasattr(p, "ImagePositionPatient"):
+                    z_positions[p.ImagePositionPatient[2]] = f_path
+            except Exception as e:
+                self.write_error(f"{scan_dir}: Failed to load DICOM {f_path}: {e}")
+                break
+        if not z_positions:
+            self.write_error(f"{scan_dir}: No valid DICOM z-positions found.")
+            return None
+        # Find Z-position L3 image
+        mask_file = os.path.join(TOTAL_SEGMENTATOR_OUTPUT_DIR, f'{vertebral_level}.nii.gz')
+        if not os.path.exists(mask_file):
+            self.write_error(f"{scan_dir}: Mask file not found: {mask_file}")
+            return None
+        try:
+            mask_obj = nib.load(mask_file)
+            mask = mask_obj.get_fdata()
+            affine_transform = mask_obj.affine
+        except Exception as e:
+            self.write_error(f"{scan_dir}: Failed to load mask {mask_file}: {e}")
+            return None
+        indexes = np.array(np.where(mask == 1))
+        if indexes.size == 0:
+            self.write_error(f"{scan_dir}: No voxels found in mask {mask_file} for {vertebral_level}")
+            return None        
+        try:
+            index_min = indexes.min(axis=1)
+            index_max = indexes.max(axis=1)
+        except ValueError as e:
+            self.write_error(f"{scan_dir}: Invalid indexes array for {vertebral_level}: {e}")
+            return None
+        world_min = nib.affines.apply_affine(affine_transform, index_min)
+        world_max = nib.affines.apply_affine(affine_transform, index_max)
+        z_direction = affine_transform[:3, 2][2]
+        if z_direction == 0:
+            self.write_error(f"{scan_dir}: Affine z-direction is zero.")
+            return None
+        z_sign = math.copysign(1, z_direction)
+        z_delta_offset = self.get_z_delta_offset_for_mask(vertebral_level)
+        if z_delta_offset is None:
+            return None
+        z_delta = 0.333 * abs(world_max[2] - world_min[2]) # This needs to be vertebra-specific perhaps
+        z_l3 = world_max[2] - z_sign * z_delta
+        # Find closest L3 image in DICOM set
+        positions = sorted(z_positions.keys())
+        closest_file = None
+        for z1, z2 in zip(positions[:-1], positions[1:]):
+            if min(z1, z2) <= z_l3 <= max(z1, z2):
+                closest_z = min(z_positions.keys(), key=lambda z: abs(z - z_l3))
+                closest_file = z_positions[closest_z]
+                LOG.info(f'Closest image: {closest_file}')
+                break
+        if closest_file is None:
+            self.write_error(f"{scan_dir}: No matching slice found.")
+        return closest_file
+
+    def run(self):
+        scan_dirs = self.load_scan_dirs()
+        vertebra = self.param('vertebra')
+        nr_steps = len(scan_dirs)
+        for step in range(nr_steps):
+            scan_dir = scan_dirs[step]
+            scan_name = os.path.split(scan_dir)[1]
+            errors = False
+            LOG.info(f'Processing {scan_dir}...')
+            try:
+                self.extract_masks(scan_dir)
+            except Exception as e:
+                self.write_error(f'{scan_dir}: Could not extract masks [{str(e)}]. Skipping scan...')
+                errors = True
+            if not errors:
+                file_path = self.find_slice(scan_dir, vertebra)
+                if file_path is not None:
+                    extension = '' if file_path.endswith('.dcm') else '.dcm'
+                    target_file_path = os.path.join(self.output(), vertebra + '_' + scan_name + extension)
+                    shutil.copyfile(file_path, target_file_path)
+                else:
+                    self.write_error(f'{scan_dir}: Could not find slice for vertebral level: {vertebra}')
+                    errors = True
+                self.delete_total_segmentator_output()
+            if errors:
+                LOG.info(f'Copying problematic scan {scan_dir} to error directory: {self._error_dir}')
+                scan_error_dir = os.path.join(self._error_dir, scan_name)
+                shutil.copytree(scan_dir, scan_error_dir)
+            self.set_progress(step, nr_steps)

{mosamatic2-2.0.10 → mosamatic2-2.0.11}/src/mosamatic2/ui/mainwindow.py

@@ -22,6 +22,7 @@ from mosamatic2.ui.widgets.panels.tasks.dicom2niftitaskpanel import Dicom2NiftiT
 from mosamatic2.ui.widgets.panels.tasks.createdicomsummarytaskpanel import CreateDicomSummaryTaskPanel
 from mosamatic2.ui.widgets.panels.tasks.selectslicefromscanstaskpanel import SelectSliceFromScansTaskPanel
 from mosamatic2.ui.widgets.panels.pipelines.defaultpipelinepanel import DefaultPipelinePanel
+from mosamatic2.ui.widgets.panels.pipelines.defaultdockerpipelinepanel import DefaultDockerPipelinePanel
 from mosamatic2.ui.widgets.panels.visualizations.slicevisualization.slicevisualization import SliceVisualization
 
 LOG = LogManager()
@@ -42,6 +43,7 @@ class MainWindow(QMainWindow):
         self._create_dicom_summary_task_panel = None
         self._select_slice_from_scans_task_panel = None
         self._default_pipeline_panel = None
+        self._default_docker_pipeline_panel = None
         self._slice_visualization = None
         self.init_window()
 
@@ -98,8 +100,11 @@ class MainWindow(QMainWindow):
     def init_pipelines_menu(self):
         default_pipeline_action = QAction('DefaultPipeline', self)
         default_pipeline_action.triggered.connect(self.handle_default_pipeline_action)
+        default_docker_pipeline_action = QAction('DefaultDockerPipeline', self)
+        default_docker_pipeline_action.triggered.connect(self.handle_default_docker_pipeline_action)
         pipelines_menu = self.menuBar().addMenu('Pipelines')
         pipelines_menu.addAction(default_pipeline_action)
+        pipelines_menu.addAction(default_docker_pipeline_action)
 
     def init_visualizations_menu(self):
         slice_visualization_action = QAction('SliceVisualization', self)
@@ -128,6 +133,7 @@ class MainWindow(QMainWindow):
             self._main_panel.add_panel(self.create_dicom_summary_task_panel(), 'createdicomsummarytaskpanel')
             self._main_panel.add_panel(self.select_slice_from_scans_task_panel(), 'selectslicefromscanstaskpanel')
             self._main_panel.add_panel(self.default_pipeline_panel(), 'defaultpipelinepanel')
+            self._main_panel.add_panel(self.default_docker_pipeline_panel(), 'defaultdockerpipelinepanel')
             self._main_panel.add_panel(self.slice_visualization(), 'slicevisualization')
             self._main_panel.select_panel('defaultpipelinepanel')
         return self._main_panel
@@ -179,6 +185,11 @@ class MainWindow(QMainWindow):
         if not self._default_pipeline_panel:
             self._default_pipeline_panel = DefaultPipelinePanel()
         return self._default_pipeline_panel
+
+    def default_docker_pipeline_panel(self):
+        if not self._default_docker_pipeline_panel:
+            self._default_docker_pipeline_panel = DefaultDockerPipelinePanel()
+        return self._default_docker_pipeline_panel
     
     def slice_visualization(self):
         if not self._slice_visualization:
@@ -216,6 +227,9 @@ class MainWindow(QMainWindow):
     def handle_default_pipeline_action(self):
         self.main_panel().select_panel('defaultpipelinepanel')
 
+    def handle_default_docker_pipeline_action(self):
+        self.main_panel().select_panel('defaultdockerpipelinepanel')
+
     def handle_slice_visualization_action(self):
         self.main_panel().select_panel('slicevisualization')
 
@@ -233,6 +247,7 @@ class MainWindow(QMainWindow):
         self.create_dicom_summary_task_panel().save_inputs_and_parameters()
         self.select_slice_from_scans_task_panel().save_inputs_and_parameters()
         self.default_pipeline_panel().save_inputs_and_parameters()
+        self.default_docker_pipeline_panel().save_inputs_and_parameters()
         self.slice_visualization().save_inputs_and_parameters()
         return super().closeEvent(event)
 

mosamatic2-2.0.11/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.11 

mosamatic2-2.0.11/src/mosamatic2/ui/widgets/panels/pipelines/defaultdockerpipelinepanel.py

@@ -0,0 +1,311 @@
+import os
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QSpinBox,
+    QComboBox,
+    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.pipelines.pipelinepanel import PipelinePanel
+from mosamatic2.ui.settings import Settings
+from mosamatic2.ui.utils import is_macos
+from mosamatic2.ui.worker import Worker
+from mosamatic2.core.pipelines import DefaultDockerPipeline
+
+LOG = LogManager()
+
+PANEL_TITLE = 'DefaultDockerPipeline'
+PANEL_NAME = 'defaultdockerpipeline'
+MODEL_TYPE_ITEM_NAMES = ['tensorflow', 'pytorch']
+MODEL_VERSION_ITEM_NAMES = ['1.0', '2.2']
+
+
+class DefaultDockerPipelinePanel(PipelinePanel):
+    def __init__(self):
+        super(DefaultDockerPipelinePanel, 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._target_size_spinbox = None
+        self._model_type_combobox = None
+        self._model_version_combobox = None
+        self._fig_width_spinbox = None
+        self._fig_height_spinbox = None
+        self._full_scan_checkbox = None
+        self._overwrite_checkbox = None
+        self._version_line_edit = None
+        self._form_layout = None
+        self._run_pipeline_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._images_dir_line_edit.setText(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._model_files_dir_line_edit.setText(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._output_dir_line_edit.setText(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 target_size_spinbox(self):
+        if not self._target_size_spinbox:
+            self._target_size_spinbox = QSpinBox()
+            self._target_size_spinbox.setMinimum(0)
+            self._target_size_spinbox.setMaximum(1024)
+            self._target_size_spinbox.setValue(self.settings().get_int(f'{PANEL_NAME}/target_size', 512))
+        return self._target_size_spinbox
+    
+    def model_type_combobox(self):
+        if not self._model_type_combobox:
+            self._model_type_combobox = QComboBox()
+            self._model_type_combobox.addItems(MODEL_TYPE_ITEM_NAMES)
+            self._model_type_combobox.setCurrentText(self.settings().get(f'{PANEL_NAME}/model_type'))
+            self._model_type_combobox.currentTextChanged.connect(self.handle_model_type_combobox)
+        return self._model_type_combobox
+    
+    def model_version_combobox(self):
+        if not self._model_version_combobox:
+            self._model_version_combobox = QComboBox()
+            self._model_version_combobox.addItems(MODEL_VERSION_ITEM_NAMES)
+            self._model_version_combobox.setCurrentText(self.settings().get(f'{PANEL_NAME}/model_version'))
+            self._model_version_combobox.currentTextChanged.connect(self.handle_model_version_combobox)
+        return self._model_version_combobox
+    
+    def fig_width_spinbox(self):
+        if not self._fig_width_spinbox:
+            self._fig_width_spinbox = QSpinBox()
+            self._fig_width_spinbox.setValue(self.settings().get_int(f'{PANEL_NAME}/fig_width', default=10))
+        return self._fig_width_spinbox
+    
+    def fig_height_spinbox(self):
+        if not self._fig_height_spinbox:
+            self._fig_height_spinbox = QSpinBox()
+            self._fig_height_spinbox.setValue(self.settings().get_int(f'{PANEL_NAME}/fig_height', default=10))
+        return self._fig_height_spinbox
+    
+    def full_scan_checkbox(self):
+        if not self._full_scan_checkbox:
+            self._full_scan_checkbox = QCheckBox('')
+            self._full_scan_checkbox.setChecked(self.settings().get_bool(f'{PANEL_NAME}/full_scan', False))
+        return self._full_scan_checkbox
+
+    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 version_line_edit(self):
+        if not self._version_line_edit:
+            self._version_line_edit = QLineEdit()
+            self._version_line_edit.setText(self.settings().get(f'{PANEL_NAME}/version'))
+        return self._version_line_edit
+    
+    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_pipeline_button(self):
+        if not self._run_pipeline_button:
+            self._run_pipeline_button = QPushButton('Run pipeline')
+            self._run_pipeline_button.clicked.connect(self.handle_run_pipeline_button)
+        return self._run_pipeline_button
+    
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+    
+    def init_help_dialog(self):
+        self.help_dialog().set_text('Show some help information')
+    
+    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('Version', self.version_line_edit())
+        self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
+        layout = QVBoxLayout()
+        layout.addLayout(self.form_layout())
+        layout.addWidget(self.run_pipeline_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_model_type_combobox(self, text):
+        if text == 'tensorflow':
+            self.model_version_combobox().setCurrentText('1.0')
+        if text == 'pytorch':
+            self.model_version_combobox().setCurrentText('2.2')
+
+    def handle_model_version_combobox(self, text):
+        if text == '1.0':
+            self.model_type_combobox().setCurrentText('tensorflow')
+        if text == '2.2':
+            self.model_type_combobox().setCurrentText('pytorch')
+
+    def handle_run_pipeline_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 pipeline...')
+            self.run_pipeline_button().setEnabled(False)
+            self.save_inputs_and_parameters()
+            self._task = DefaultDockerPipeline(
+                inputs={
+                    'images': self.images_dir_line_edit().text(),
+                    'model_files': self.model_files_dir_line_edit().text(),
+                },
+                params={
+                    'file_type': 'npy',
+                    'model_type': 'tensorflow',
+                    'model_version': 1.0,
+                    'target_size': 512,
+                    'fig_width': 10,
+                    'fig_height': 10,
+                    'version': '2.0.10',
+                },
+                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_pipeline_button().setEnabled(True)
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.images_dir_line_edit().text() == '':
+            errors.append('Empty images directory path')
+        elif 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')
+        elif not os.path.isdir(self.model_files_dir_line_edit().text()):
+            errors.append('Model files directory does not exist')
+        if self.output_dir_line_edit().text() == '':
+            errors.append('Empty output directory path')
+        elif 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')
+        # if self.version_line_edit().text() == '':
+        #     errors.append('Empty version. Should be same as current Mosamatic version')
+        # if self.target_size_spinbox().value() != 512:
+        #     errors.append('Target size must be 512')
+        # if self.full_scan_checkbox().isChecked():
+        #     errors.append('Full scan support is not available yet')
+        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}/version', self.version_line_edit().text())
+        # self.settings().set(f'{PANEL_NAME}/target_size', self.target_size_spinbox().value())
+        # self.settings().set(f'{PANEL_NAME}/model_type', self.model_type_combobox().currentText())
+        # self.settings().set(f'{PANEL_NAME}/model_version', self.model_version_combobox().currentText())
+        # self.settings().set(f'{PANEL_NAME}/fig_width', self.fig_width_spinbox().value())
+        # self.settings().set(f'{PANEL_NAME}/fig_height', self.fig_height_spinbox().value())
+        # self.settings().set(f'{PANEL_NAME}/full_scan', self.full_scan_checkbox().isChecked())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())

{mosamatic2-2.0.10 → mosamatic2-2.0.11}/src/mosamatic2/ui/widgets/panels/tasks/selectslicefromscanstaskpanel.py

@@ -25,7 +25,7 @@ from mosamatic2.core.tasks import SelectSliceFromScansTask
 
 LOG = LogManager()
 
-PANEL_TITLE = 'Automatically select L3 slice from full CT scan'
+PANEL_TITLE = 'SelectSliceFromScansTaskPanel'
 PANEL_NAME = 'selectslicefromscanstaskpanel'
 
 

mosamatic2-2.0.10/src/mosamatic2/core/pipelines/__init__.py

@@ -1 +0,0 @@
-from mosamatic2.core.pipelines.defaultpipeline.defaultpipeline import DefaultPipeline

mosamatic2-2.0.10/src/mosamatic2/core/tasks/selectslicefromscanstask/selectslicefromscanstask.py

@@ -1,114 +0,0 @@
-import os
-import math
-import tempfile
-import shutil
-import nibabel as nib
-import numpy as np
-from totalsegmentator.python_api import totalsegmentator
-from mosamatic2.core.tasks.task import Task
-from mosamatic2.core.managers.logmanager import LogManager
-from mosamatic2.core.utils import load_dicom
-
-LOG = LogManager()
-
-TOTAL_SEGMENTATOR_OUTPUT_DIR = os.path.join(tempfile.gettempdir(), 'total_segmentator_output')
-TOTAL_SEGMENTATOR_TASK = 'total'
-Z_DELTA_OFFSETS = {
-    'vertebrae_L3': 0.333,
-    'vertebrae_T4': 0.5,
-}
-
-
-class SelectSliceFromScansTask(Task):
-    INPUTS = ['scans']
-    PARAMS = ['vertebra']
-
-    def __init__(self, inputs, params, output, overwrite):
-        super(SelectSliceFromScansTask, self).__init__(inputs, params, output, overwrite)
-
-    def load_scan_dirs(self):
-        scan_dirs = []
-        for d in os.listdir(self.input('scans')):
-            scan_dir = os.path.join(self.input('scans'), d)
-            if os.path.isdir(scan_dir):
-                scan_dirs.append(scan_dir)
-        return scan_dirs
-    
-    def extract_masks(self, scan_dir):
-        os.makedirs(TOTAL_SEGMENTATOR_OUTPUT_DIR, exist_ok=True)
-        totalsegmentator(input=scan_dir, output=TOTAL_SEGMENTATOR_OUTPUT_DIR, fast=True)
-        # os.system(f'TotalSegmentator -i {scan_dir} -o {TOTAL_SEGMENTATOR_OUTPUT_DIR} --fast')
-
-    def delete_total_segmentator_output(self):
-        if os.path.exists(TOTAL_SEGMENTATOR_OUTPUT_DIR):
-            shutil.rmtree(TOTAL_SEGMENTATOR_OUTPUT_DIR)
-
-    def get_z_delta_offset_for_mask(self, mask_name):
-        if mask_name not in Z_DELTA_OFFSETS.keys():
-            return None
-        return Z_DELTA_OFFSETS[mask_name]
-
-    def find_slice(self, scan_dir, vertebra):
-        if vertebra == 'L3':
-            vertebral_level = 'vertebrae_L3'
-        elif vertebra == 'T4':
-            vertebral_level = 'vertebrae_T4'
-        else:
-            raise RuntimeError(f'Unknown vertbra {vertebra}. Options are "L3" and "T4"')
-        # Find Z-positions DICOM images
-        z_positions = {}
-        for f in os.listdir(scan_dir):
-            f_path = os.path.join(scan_dir, f)
-            p = load_dicom(f_path, stop_before_pixels=True)
-            if p is not None:
-                z_positions[p.ImagePositionPatient[2]] = f_path
-        # Find Z-position L3 image
-        mask_file = os.path.join(TOTAL_SEGMENTATOR_OUTPUT_DIR, f'{vertebral_level}.nii.gz')
-        mask_obj = nib.load(mask_file)
-        mask = mask_obj.get_fdata()
-        affine_transform = mask_obj.affine
-        indexes = np.array(np.where(mask == 1))
-        index_min = indexes.min(axis=1)
-        index_max = indexes.max(axis=1)
-        world_min = nib.affines.apply_affine(affine_transform, index_min)
-        world_max = nib.affines.apply_affine(affine_transform, index_max)
-        z_direction = affine_transform[:3, 2][2]
-        z_sign = math.copysign(1, z_direction)
-        z_delta_offset = self.get_z_delta_offset_for_mask(vertebral_level)
-        if z_delta_offset is None:
-            return None
-        z_delta = 0.333 * abs(world_max[2] - world_min[2]) # This needs to be vertebra-specific perhaps
-        z_l3 = world_max[2] - z_sign * z_delta
-        # Find closest L3 image in DICOM set
-        positions = sorted(z_positions.keys())
-        closest_file = None
-        for z1, z2 in zip(positions[:-1], positions[1:]):
-            if min(z1, z2) <= z_l3 <= max(z1, z2):
-                closest_z = min(z_positions.keys(), key=lambda z: abs(z - z_l3))
-                closest_file = z_positions[closest_z]
-                LOG.info(f'Closest image: {closest_file}')
-                break
-        return closest_file
-
-    def run(self):
-        scan_dirs = self.load_scan_dirs()
-        vertebra = self.param('vertebra')
-        nr_steps = len(scan_dirs)
-        for step in range(nr_steps):
-            scan_dir = scan_dirs[step]
-            scan_name = os.path.split(scan_dir)[1]
-            try:
-                self.extract_masks(scan_dir)
-            except Exception as e:
-                LOG.warning(f'Could not extract masks from {scan_dir} [{str(e)}]')
-                self.set_progress(step, nr_steps)
-                continue
-            file_path = self.find_slice(scan_dir, vertebra)
-            if file_path is not None:
-                extension = '' if file_path.endswith('.dcm') else '.dcm'
-                target_file_path = os.path.join(self.output(), vertebra + '_' + scan_name + extension)
-                shutil.copyfile(file_path, target_file_path)
-            else:
-                LOG.error(f'Could not find slice for vertebral level: {vertebra}')
-            self.delete_total_segmentator_output()
-            self.set_progress(step, nr_steps)

mosamatic2-2.0.10/src/mosamatic2/ui/resources/VERSION

@@ -1 +0,0 @@
-2.0.10