mosamatic2 2.0.13__tar.gz → 2.0.15__tar.gz

{mosamatic2-2.0.13 → mosamatic2-2.0.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.13
+Version: 2.0.15
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl
@@ -23,6 +23,7 @@ Requires-Dist: pyqtgraph (>=0.13.7)
 Requires-Dist: pyside6-essentials (>=6.9)
 Requires-Dist: python-gdcm (>=3.0.26)
 Requires-Dist: scipy (>=1.15.3)
+Requires-Dist: slicer
 Requires-Dist: tensorboard (==2.15.2)
 Requires-Dist: tensorboard-data-server (==0.7.2)
 Requires-Dist: tensorflow (==2.15.*) ; platform_system == "Linux"

{mosamatic2-2.0.13 → mosamatic2-2.0.15}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.13"
+version = "2.0.15"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}
@@ -35,6 +35,7 @@ dependencies = [
     "pyqtgraph>=0.13.7",
     "moosez",
     "docker",
+    "slicer",
 ]
 
 [tool.poetry]

mosamatic2-2.0.15/src/mosamatic2/commands/totalsegmentator.py

@@ -0,0 +1,68 @@
+import click
+
+from mosamatic2.core.tasks import TotalSegmentatorTask
+
+
+@click.command(help='Run Total Segmentator on CT scans')
+@click.option(
+    '--scans', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Directory with scans (each patient separate subdirectory)',
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--tasks', 
+    default='total',
+    help='Comma-separated list of Total Segmentator tasks to run (no spaces!)'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def totalsegmentator(scans, tasks, output, overwrite):
+    """
+    Run Total Segmentator on CT scans. If you want to run specialized tasks
+    like "liver_segments" or "liver_vessels" you need an educational license.
+    Check out https://github.com/wasserth/TotalSegmentator?tab=readme-ov-file
+    to find out how to get such a license.
+    
+    Parameters
+    ----------
+    --scans : str
+        Directory to scans. Each patient's scan should be in a separate
+        subdirectory. For example:
+
+        /scans
+        /scans/patient1
+        /scans/patient1/file1.dcm
+        /scans/patient1/file2.dcm
+        ...
+        /scans/patient2
+        ...
+
+    --output : str
+        Path to output directory where selected slices will be placed. Each
+        slice's file name will be the same as the scan directory name, so in
+        the example above that would be "patient1", "patient2", etc.
+
+    --tasks : str
+        Comma-separated list of Total Segmentator tasks to run (no spaces!)
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = TotalSegmentatorTask(
+        inputs={'scans': scans},
+        params={'tasks': tasks},
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

{mosamatic2-2.0.13 → mosamatic2-2.0.15}/src/mosamatic2/core/tasks/__init__.py

@@ -4,4 +4,5 @@ from mosamatic2.core.tasks.calculatescorestask.calculatescorestask import Calcul
 from mosamatic2.core.tasks.createpngsfromsegmentationstask.createpngsfromsegmentationstask import CreatePngsFromSegmentationsTask
 from mosamatic2.core.tasks.dicom2niftitask.dicom2niftitask import Dicom2NiftiTask
 from mosamatic2.core.tasks.selectslicefromscanstask.selectslicefromscanstask import SelectSliceFromScansTask
-from mosamatic2.core.tasks.createdicomsummarytask.createdicomsummarytask import CreateDicomSummaryTask
+from mosamatic2.core.tasks.createdicomsummarytask.createdicomsummarytask import CreateDicomSummaryTask
+from mosamatic2.core.tasks.totalsegmentatortask.totalsegmentatortask import TotalSegmentatorTask

mosamatic2-2.0.15/src/mosamatic2/core/tasks/totalsegmentatortask/totalsegmentatortask.py

@@ -0,0 +1,50 @@
+import os
+import shutil
+import tempfile
+from totalsegmentator.python_api import totalsegmentator
+from mosamatic2.core.tasks.task import Task
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
+TOTAL_SEGMENTATOR_OUTPUT_DIR = os.path.join(tempfile.gettempdir(), 'total_segmentator_output')
+
+
+class TotalSegmentatorTask(Task):
+    INPUTS = ['scans']
+    PARAMS = ['tasks']
+
+    def __init__(self, inputs, params, output, overwrite):
+        super(TotalSegmentatorTask, self).__init__(inputs, params, output, overwrite)
+        LOG.info(f'Using temporary output directory: {TOTAL_SEGMENTATOR_OUTPUT_DIR}')
+
+    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)
+        tasks = self.param('tasks').split(",") if self.param('tasks') else []
+        for task in tasks:
+            LOG.info(f'Running task {task}...')
+            totalsegmentator(input=scan_dir, output=TOTAL_SEGMENTATOR_OUTPUT_DIR, task=task)
+
+    def run(self):
+        scan_dirs = self.load_scan_dirs()
+        nr_steps = len(scan_dirs)
+        for step in range(nr_steps):
+            scan_dir = scan_dirs[step]
+            try:
+                self.extract_masks(scan_dir)
+            except Exception as e:
+                LOG.error(f'{scan_dir}: Could not extract masks [{str(e)}]. Skipping scan...')
+            self.set_progress(step, nr_steps)
+            LOG.info(f'Copying temporary output to final output directory...')
+            for f in os.listdir(TOTAL_SEGMENTATOR_OUTPUT_DIR):
+                if f.endswith('.nii') or f.endswith('.nii.gz'):
+                    f_path = os.path.join(TOTAL_SEGMENTATOR_OUTPUT_DIR, f)
+                    shutil.move(f_path, self.output())
+                    LOG.info(f'Copied {f}')

{mosamatic2-2.0.13 → mosamatic2-2.0.15}/src/mosamatic2/core/utils.py

@@ -363,5 +363,9 @@ def is_docker_running():
         return False
     
 
+def is_path_docker_compatible(path):
+    return not ' ' in path
+
+
 def to_unix_path(path):
     return path.replace("\\", "/").replace(" ", "\\ ")

{mosamatic2-2.0.13 → mosamatic2-2.0.15}/src/mosamatic2/ui/mainwindow.py

@@ -21,6 +21,7 @@ from mosamatic2.ui.widgets.panels.tasks.calculatescorestaskpanel import Calculat
 from mosamatic2.ui.widgets.panels.tasks.dicom2niftitaskpanel import Dicom2NiftiTaskPanel
 from mosamatic2.ui.widgets.panels.tasks.createdicomsummarytaskpanel import CreateDicomSummaryTaskPanel
 from mosamatic2.ui.widgets.panels.tasks.selectslicefromscanstaskpanel import SelectSliceFromScansTaskPanel
+from mosamatic2.ui.widgets.panels.tasks.totalsegmentatortaskpanel import TotalSegmentatorTaskPanel
 from mosamatic2.ui.widgets.panels.pipelines.defaultpipelinepanel import DefaultPipelinePanel
 from mosamatic2.ui.widgets.panels.pipelines.defaultdockerpipelinepanel import DefaultDockerPipelinePanel
 from mosamatic2.ui.widgets.panels.pipelines.boadockerpipelinepanel import BoaDockerPipelinePanel
@@ -43,6 +44,7 @@ class MainWindow(QMainWindow):
         self._dicom2nifti_task_panel = None
         self._create_dicom_summary_task_panel = None
         self._select_slice_from_scans_task_panel = None
+        self._total_segmentator_task_panel = None
         self._default_pipeline_panel = None
         self._default_docker_pipeline_panel = None
         self._boa_docker_pipeline_panel = None
@@ -90,6 +92,8 @@ class MainWindow(QMainWindow):
         create_dicom_summary_task_action.triggered.connect(self.handle_create_dicom_summary_task_action)
         select_slice_from_scans_task_action = QAction('SelectSliceFromScansTask', self)
         select_slice_from_scans_task_action.triggered.connect(self.handle_select_slice_from_scans_task_action)
+        total_segmentator_task_action = QAction('TotalSegmentatorTask', self)
+        total_segmentator_task_action.triggered.connect(self.handle_total_segmentator_task_action)
         tasks_menu = self.menuBar().addMenu('Tasks')
         tasks_menu.addAction(rescale_dicom_images_task_action)
         tasks_menu.addAction(segment_muscle_fat_l3_tensorflow_task_action)
@@ -98,6 +102,7 @@ class MainWindow(QMainWindow):
         tasks_menu.addAction(dicom2nifti_task_action)
         tasks_menu.addAction(create_dicom_summary_task_action)
         tasks_menu.addAction(select_slice_from_scans_task_action)
+        tasks_menu.addAction(total_segmentator_task_action)
 
     def init_pipelines_menu(self):
         default_pipeline_action = QAction('DefaultPipeline', self)
@@ -137,6 +142,7 @@ class MainWindow(QMainWindow):
             self._main_panel.add_panel(self.dicom2nifti_task_panel(), 'dicom2niftitaskpanel')
             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.total_segmentator_task_panel(), 'totalsegmentatortaskpanel')
             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.boa_docker_pipeline_panel(), 'boadockerpipelinepanel')
@@ -186,6 +192,11 @@ class MainWindow(QMainWindow):
         if not self._select_slice_from_scans_task_panel:
             self._select_slice_from_scans_task_panel = SelectSliceFromScansTaskPanel()
         return self._select_slice_from_scans_task_panel
+
+    def total_segmentator_task_panel(self):
+        if not self._total_segmentator_task_panel:
+            self._total_segmentator_task_panel = TotalSegmentatorTaskPanel()
+        return self._total_segmentator_task_panel
     
     def default_pipeline_panel(self):
         if not self._default_pipeline_panel:
@@ -235,6 +246,9 @@ class MainWindow(QMainWindow):
     def handle_select_slice_from_scans_task_action(self):
         self.main_panel().select_panel('selectslicefromscanstaskpanel')
 
+    def handle_total_segmentator_task_action(self):
+        self.main_panel().select_panel('totalsegmentatortaskpanel')
+
     def handle_default_pipeline_action(self):
         self.main_panel().select_panel('defaultpipelinepanel')
 
@@ -260,6 +274,7 @@ class MainWindow(QMainWindow):
         self.dicom2nifti_task_panel().save_inputs_and_parameters()
         self.create_dicom_summary_task_panel().save_inputs_and_parameters()
         self.select_slice_from_scans_task_panel().save_inputs_and_parameters()
+        self.total_segmentator_task_panel().save_inputs_and_parameters()
         self.default_pipeline_panel().save_inputs_and_parameters()
         self.default_docker_pipeline_panel().save_inputs_and_parameters()
         self.boa_docker_pipeline_panel().save_inputs_and_parameters()

mosamatic2-2.0.15/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.15 

{mosamatic2-2.0.13 → mosamatic2-2.0.15}/src/mosamatic2/ui/widgets/panels/pipelines/boadockerpipelinepanel.py

@@ -16,6 +16,7 @@ from PySide6.QtCore import (
 )
 
 from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.utils import is_docker_running, is_path_docker_compatible
 from mosamatic2.ui.widgets.panels.pipelines.pipelinepanel import PipelinePanel
 from mosamatic2.ui.settings import Settings
 from mosamatic2.ui.utils import is_macos
@@ -127,6 +128,15 @@ class BoaDockerPipelinePanel(PipelinePanel):
             self.settings().set('last_directory', directory)
 
     def handle_run_pipeline_button(self):
+        if not is_docker_running():
+            QMessageBox.information(self, 'Error', 'Docker is not running. Please start Docker Desktop first')
+            return
+        if not is_path_docker_compatible(self.scans_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to scans directory contains spaces and is not Docker compatible')
+            return
+        if not is_path_docker_compatible(self.output_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to output directory contains spaces and is not Docker compatible')
+            return
         errors = self.check_inputs_and_parameters()
         if len(errors) > 0:
             error_message = 'Following errors were encountered:\n'

{mosamatic2-2.0.13 → mosamatic2-2.0.15}/src/mosamatic2/ui/widgets/panels/pipelines/defaultdockerpipelinepanel.py

@@ -18,6 +18,7 @@ from PySide6.QtCore import (
 )
 
 from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.utils import is_docker_running, is_path_docker_compatible
 from mosamatic2.ui.widgets.panels.pipelines.pipelinepanel import PipelinePanel
 from mosamatic2.ui.settings import Settings
 from mosamatic2.ui.utils import is_macos
@@ -223,6 +224,18 @@ class DefaultDockerPipelinePanel(PipelinePanel):
             self.model_type_combobox().setCurrentText('pytorch')
 
     def handle_run_pipeline_button(self):
+        if not is_docker_running():
+            QMessageBox.information(self, 'Error', 'Docker is not running. Please start Docker Desktop first')
+            return
+        if not is_path_docker_compatible(self.images_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to images directory contains spaces and is not Docker compatible')
+            return
+        if not is_path_docker_compatible(self.model_files_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to model files directory contains spaces and is not Docker compatible')
+            return
+        if not is_path_docker_compatible(self.output_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to output directory contains spaces and is not Docker compatible')
+            return
         errors = self.check_inputs_and_parameters()
         if len(errors) > 0:
             error_message = 'Following errors were encountered:\n'

mosamatic2-2.0.15/src/mosamatic2/ui/widgets/panels/tasks/totalsegmentatortaskpanel.py

@@ -0,0 +1,195 @@
+import os
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QCheckBox,
+    QComboBox,
+    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 TotalSegmentatorTask
+
+LOG = LogManager()
+
+PANEL_TITLE = 'TotalSegmentatorTaskPanel'
+PANEL_NAME = 'totalsegmentatortaskpanel'
+
+
+class TotalSegmentatorTaskPanel(TaskPanel):
+    def __init__(self):
+        super(TotalSegmentatorTaskPanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._scans_dir_line_edit = None
+        self._scans_dir_select_button = None
+        self._tasks_line_edit = 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 scans_dir_line_edit(self):
+        if not self._scans_dir_line_edit:
+            self._scans_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/scans_dir'))
+        return self._scans_dir_line_edit
+    
+    def scans_dir_select_button(self):
+        if not self._scans_dir_select_button:
+            self._scans_dir_select_button = QPushButton('Select')
+            self._scans_dir_select_button.clicked.connect(self.handle_scans_dir_select_button)
+        return self._scans_dir_select_button
+    
+    def tasks_line_edit(self):
+        if not self._tasks_line_edit:
+            self._tasks_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/tasks'))
+            if self._tasks_line_edit.text() == '':
+                self._tasks_line_edit.setText('total')
+        return self._tasks_line_edit
+    
+    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):
+        scans_dir_layout = QHBoxLayout()
+        scans_dir_layout.addWidget(self.scans_dir_line_edit())
+        scans_dir_layout.addWidget(self.scans_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('Scans directory', scans_dir_layout)
+        self.form_layout().addRow('Tasks', self.tasks_line_edit())
+        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_scans_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.scans_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 = TotalSegmentatorTask(
+                inputs={'scans': self.scans_dir_line_edit().text()},
+                params={'tasks': self.tasks_line_edit().text()},
+                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.scans_dir_line_edit().text() == '':
+            errors.append('Empty scans directory path')
+        if not os.path.isdir(self.scans_dir_line_edit().text()):
+            errors.append('Scans 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')
+        if self.tasks_line_edit().text() == '':
+            errors.append('Tasks cannot be empty and must be comma-separated list of values')
+        return errors
+    
+    def save_inputs_and_parameters(self):
+        self.settings().set(f'{PANEL_NAME}/scans_dir', self.scans_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/tasks', self.tasks_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())

{mosamatic2-2.0.13 → mosamatic2-2.0.15}/src/mosamatic2/ui/widgets/panels/visualizations/slicevisualization/sliceviewer.py

@@ -80,9 +80,9 @@ class SliceViewer(QWidget):
         slice.SetMapper(slice_mapper)
         slice_text_actor = self.create_text_actor("", 0.01, 0.01, 12, align_bottom=True, normalized=True)
         usage_text_actor = self.create_text_actor(
-            "- Slice with mouse wheel or Up/Down-Key (first click inside viewer)\n"
+            "- Slice with mouse wheel or Up/Down keys (first click inside viewer)\n"
             "- Zoom with pressed right mouse button while dragging\n"
-            "- Pan with middle mouse button while dragging\n"
+            "- Pan with Shift key and left mouse button while dragging\n"
             "- Change contrast/brightness with pressed left mouse while dragging",
             0.01, 0.99, 12, normalized=True)
         ren = vtk.vtkRenderer()

mosamatic2-2.0.13/src/mosamatic2/ui/resources/VERSION

@@ -1 +0,0 @@
-2.0.13