mosamatic2 2.0.12__tar.gz → 2.0.14__tar.gz

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.12
+Version: 2.0.14
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl
@@ -9,6 +9,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: antspyx (>=0.5.4)
 Requires-Dist: dicom2nifti (>=2.6.2)
+Requires-Dist: docker
 Requires-Dist: flask (>=3.1.2)
 Requires-Dist: moosez
 Requires-Dist: nibabel (>=5.3.2)
@@ -22,6 +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"

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.12"
+version = "2.0.14"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}
@@ -34,6 +34,8 @@ dependencies = [
     "vtk>=9.5.1",
     "pyqtgraph>=0.13.7",
     "moosez",
+    "docker",
+    "slicer",
 ]
 
 [tool.poetry]

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/src/mosamatic2/cli.py

@@ -8,6 +8,8 @@ from mosamatic2.commands import (
     selectslicefromscans,
     createdicomsummary,
     defaultpipeline,
+    defaultdockerpipeline,
+    boadockerpipeline,
 )
 from mosamatic2.core.utils import show_doc_command
 
@@ -37,4 +39,6 @@ main.add_command(dicom2nifti.dicom2nifti)
 main.add_command(selectslicefromscans.selectslicefromscans)
 main.add_command(createdicomsummary.createdicomsummary)
 main.add_command(defaultpipeline.defaultpipeline)
+main.add_command(defaultdockerpipeline.defaultdockerpipeline)
+main.add_command(boadockerpipeline.boadockerpipeline)
 main.add_command(show_doc_command(main)) # Special command to show long description for command

mosamatic2-2.0.14/src/mosamatic2/commands/boadockerpipeline.py

@@ -0,0 +1,48 @@
+import click
+
+from mosamatic2.core.pipelines import BoaDockerPipeline
+
+
+@click.command(help='Runs 3D body composition analysis pipeline using BOA algorithm')
+@click.option(
+    '--scans', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Root directory with scan directories for each patient (no spaces allowed)',
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory (no spaces allowed)'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def boadockerpipeline(scans, output, overwrite):
+    """
+    Runs 3D body composition analysis pipeline using BOA algorithm.
+    
+    Parameters
+    ----------
+    --scans : str
+        Root directory with scan directories for each patient. Each scan directory should 
+        contain DICOM images for a single scan only and nothing else. Also, the directory
+        paths cannot contain any spaces.
+
+    --output : str
+        Path to output directory. No spaces allowed.
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    pipeline = BoaDockerPipeline(
+        inputs={'scans': scans},
+        params=None,
+        output=output,
+        overwrite=overwrite,
+    )
+    pipeline.run()

mosamatic2-2.0.14/src/mosamatic2/commands/defaultdockerpipeline.py

@@ -0,0 +1,73 @@
+import click
+
+from mosamatic2.core.pipelines import DefaultDockerPipeline
+
+
+@click.command(help='Runs default L3 analysis pipeline through Docker')
+@click.option(
+    '--images', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Directory with L3 images (no spaces allowed)',
+)
+@click.option(
+    '--model_files', 
+    required=True, 
+    type=click.Path(), 
+    help='Input directory with AI model files (no spaces allowed)'
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory (no spaces allowed)'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def defaultdockerpipeline(images, model_files, output, overwrite):
+    """
+    Runs default L3 analysis pipeline through Docker
+    
+    Parameters
+    ----------
+    --images : str
+        Directory with L3 images. Warning: This directory path cannot contain any spaces!
+        Docker has issues working with that.
+
+    --model_files : str
+        Directory with AI model files. This directory can ONLY contain the following
+        files:
+
+        (1) contour_model-1.0.zip
+        (2) model-1.0.zip
+        (3) params-1.0.json
+
+        These files can be downloaded from:
+        https://mosamatic.rbeesoft.nl/wordpress/mosamatic/installation/
+
+        Warning: This directory path cannot contain any spaces!
+
+    --output : str
+        Path to output directory (no spaces!)
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    pipeline = DefaultDockerPipeline(
+        inputs={'images': images, 'model_files': model_files},
+        params={
+            'target_size': 512,
+            'model_type': 'tensorflow',
+            'model_version': 1.0,
+            'file_type': 'npy',
+            'fig_width': 10,
+            'fig_height': 10,
+        },
+        output=output,
+        overwrite=overwrite,
+    )
+    pipeline.run()

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/src/mosamatic2/commands/dicom2nifti.py

@@ -10,6 +10,12 @@ from mosamatic2.core.tasks import Dicom2NiftiTask
     type=click.Path(exists=True), 
     help='Root directory with DICOM scans (one for each patient)',
 )
+@click.option(
+    '--compressed', 
+    type=click.BOOL, 
+    default=True, 
+    help='Compress with gzip [true|false] (default: True)'
+)
 @click.option(
     '--output', 
     required=True, 
@@ -22,7 +28,7 @@ from mosamatic2.core.tasks import Dicom2NiftiTask
     default=False, 
     help='Overwrite [true|false]'
 )
-def dicom2nifti(scans, output, overwrite):
+def dicom2nifti(scans, compressed, output, overwrite):
     """
     Converts DICOM scans to NIFTI format.
     
@@ -31,6 +37,9 @@ def dicom2nifti(scans, output, overwrite):
     --scans : str
         Root directory with DICOM scans (one subdirectory for each patient)
 
+    --compressed : bool
+        Whether to compress the NIFTI file with gzip or not (default: True)
+
     --output : str
         Path to output directory
 
@@ -39,7 +48,7 @@ def dicom2nifti(scans, output, overwrite):
     """
     task = Dicom2NiftiTask(
         inputs={'scans': scans},
-        params=None,
+        params={'compressed': compressed},
         output=output,
         overwrite=overwrite,
     )

mosamatic2-2.0.14/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()

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/src/mosamatic2/core/pipelines/__init__.py

@@ -1,2 +1,3 @@
 from mosamatic2.core.pipelines.defaultpipeline.defaultpipeline import DefaultPipeline
-from mosamatic2.core.pipelines.defaultdockerpipeline.defaultdockerpipeline import DefaultDockerPipeline
+from mosamatic2.core.pipelines.defaultdockerpipeline.defaultdockerpipeline import DefaultDockerPipeline
+from mosamatic2.core.pipelines.boadockerpipeline.boadockerpipeline import BoaDockerPipeline

mosamatic2-2.0.14/src/mosamatic2/core/pipelines/boadockerpipeline/boadockerpipeline.py

@@ -0,0 +1,70 @@
+import os
+from mosamatic2.core.pipelines.pipeline import Pipeline
+from mosamatic2.core.tasks import Dicom2NiftiTask
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.utils import (
+    is_docker_running, 
+    to_unix_path,
+    current_time_in_seconds,
+    elapsed_time_in_seconds,
+    duration,
+)
+
+LOG = LogManager()
+
+
+class BoaDockerPipeline(Pipeline):
+    INPUTS = ['scans']
+    PARAMS = []
+
+    def __init__(self, inputs, params, output, overwrite):
+        super(BoaDockerPipeline, self).__init__(inputs, params, output, overwrite)
+
+    def load_nifti_files(self):
+        nifti_files_dir = os.path.join(self.output(), 'dicom2niftitask')
+        nifti_files = []
+        for f in os.listdir(nifti_files_dir):
+            f_path = os.path.join(nifti_files_dir, f)
+            if f.endswith('.nii') or f.endswith('.nii.gz'):
+                nifti_files.append(f_path)
+        return nifti_files
+
+    def run(self):
+        assert is_docker_running()
+        # First convert DICOM series to NIFTI format
+        dicom2nifti_task = Dicom2NiftiTask(
+            inputs={'scans': self.input('scans')},
+            params={'compressed': True},
+            output=self.output(),
+            overwrite=self.overwrite(),
+        )
+        dicom2nifti_task.run()
+        # Load NIFTI file paths
+        nifti_files = self.load_nifti_files()
+        workspaces_dir = to_unix_path(os.path.join(self.output(), 'workspaces'))
+        os.makedirs(workspaces_dir, exist_ok=True)
+        weights_dir = to_unix_path(os.path.join(self.output(), 'weights'))
+        start_time = current_time_in_seconds()
+        for f in nifti_files:
+            start_time_f = current_time_in_seconds()
+            f = to_unix_path(f)
+            dir_name = os.path.split(f)[1][:-7]
+            workspace = to_unix_path(os.path.join(workspaces_dir, dir_name))
+            # Build Docker script
+            docker_script = 'docker run --rm ' + \
+                '-v "{}":/image.nii.gz '.format(f) + \
+                '-v "{}":/workspace '.format(workspace) + \
+                '-v "{}":/app/weights '.format(weights_dir) + \
+                '--gpus all ' + \
+                '--network host ' + \
+                '--shm-size=8g --ulimit memlock=-1 --ulimit stack=67108864 ' + \
+                '--entrypoint /bin/sh ' + \
+                'shipai/boa-cli -c ' + \
+                '"python body_organ_analysis --input-image /image.nii.gz --output-dir /workspace/ --models all --verbose"'
+            LOG.info(f'Running BOA Docker script: {docker_script}')
+            # Run Docker script
+            os.system(docker_script)
+            elapsed_f = elapsed_time_in_seconds(start_time_f)
+            LOG.info(f'Elapsed {dir_name}: {duration(elapsed_f)}')
+        elapsed_total = elapsed_time_in_seconds(start_time)
+        LOG.info(f'Elapsed total: {duration(elapsed_total)}')

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/src/mosamatic2/core/pipelines/defaultdockerpipeline/defaultdockerpipeline.py

@@ -1,17 +1,9 @@
 import os
-
 from mosamatic2.core.pipelines.pipeline import Pipeline
 from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.utils import is_docker_running, to_unix_path
 
 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):
@@ -32,10 +24,11 @@ class DefaultDockerPipeline(Pipeline):
         super(DefaultDockerPipeline, self).__init__(inputs, params, output, overwrite)
 
     def run(self):
+        assert is_docker_running()
         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()) + \
+            '-v "{}":/data/images '.format(to_unix_path(self.input('images'))) + \
+            '-v "{}":/data/model_files '.format(to_unix_path(self.input('model_files'))) + \
+            '-v "{}":/data/output '.format(to_unix_path(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}')

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/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

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/src/mosamatic2/core/tasks/dicom2niftitask/dicom2niftitask.py

@@ -9,7 +9,7 @@ LOG = LogManager()
 
 class Dicom2NiftiTask(Task):
     INPUTS = ['scans']
-    PARAMS = []
+    PARAMS = ['compressed']
 
     def __init__(self, inputs, params, output, overwrite):
         super(Dicom2NiftiTask, self).__init__(inputs, params, output, overwrite)
@@ -28,7 +28,10 @@ class Dicom2NiftiTask(Task):
         for step in range(nr_steps):
             scan_dir = scan_dirs[step]
             scan_name = os.path.split(scan_dir)[1]
-            nifti_file_name = scan_name + '.nii.gz'
+            if self.param('compressed'):
+                nifti_file_name = scan_name + '.nii.gz'
+            else:
+                nifti_file_name = scan_name + '.nii'
             LOG.info(f'Converting DICOM series in {scan_dir} to {nifti_file_name}')
             dicom2nifti.dicom_series_to_nifti(
                 scan_dir,

mosamatic2-2.0.14/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}')

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/src/mosamatic2/core/utils.py

@@ -350,4 +350,18 @@ def convert_numpy_array_to_png_image(
         png_file_name += '.png'
     png_file_path = os.path.join(output_dir_path, png_file_name)
     image.save(png_file_path)
-    return png_file_path
+    return png_file_path
+
+
+def is_docker_running():
+    import docker
+    try:
+        client = docker.from_env()
+        client.ping()
+        return True
+    except Exception:
+        return False
+    
+
+def to_unix_path(path):
+    return path.replace("\\", "/").replace(" ", "\\ ")

{mosamatic2-2.0.12 → mosamatic2-2.0.14}/src/mosamatic2/ui/mainwindow.py

@@ -21,8 +21,10 @@ 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
 from mosamatic2.ui.widgets.panels.visualizations.slicevisualization.slicevisualization import SliceVisualization
 
 LOG = LogManager()
@@ -42,8 +44,10 @@ 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
         self._slice_visualization = None
         self.init_window()
 
@@ -88,6 +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)
@@ -96,15 +102,19 @@ 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)
         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)
+        boa_docker_pipeline_action = QAction('BoaDockerPipeline', self)
+        boa_docker_pipeline_action.triggered.connect(self.handle_boa_docker_pipeline_action)
         pipelines_menu = self.menuBar().addMenu('Pipelines')
         pipelines_menu.addAction(default_pipeline_action)
         pipelines_menu.addAction(default_docker_pipeline_action)
+        pipelines_menu.addAction(boa_docker_pipeline_action)
 
     def init_visualizations_menu(self):
         slice_visualization_action = QAction('SliceVisualization', self)
@@ -132,8 +142,10 @@ 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')
             self._main_panel.add_panel(self.slice_visualization(), 'slicevisualization')
             self._main_panel.select_panel('defaultpipelinepanel')
         return self._main_panel
@@ -180,6 +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:
@@ -190,6 +207,11 @@ class MainWindow(QMainWindow):
         if not self._default_docker_pipeline_panel:
             self._default_docker_pipeline_panel = DefaultDockerPipelinePanel()
         return self._default_docker_pipeline_panel
+
+    def boa_docker_pipeline_panel(self):
+        if not self._boa_docker_pipeline_panel:
+            self._boa_docker_pipeline_panel = BoaDockerPipelinePanel()
+        return self._boa_docker_pipeline_panel
     
     def slice_visualization(self):
         if not self._slice_visualization:
@@ -224,12 +246,18 @@ 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')
 
     def handle_default_docker_pipeline_action(self):
         self.main_panel().select_panel('defaultdockerpipelinepanel')
 
+    def handle_boa_docker_pipeline_action(self):
+        self.main_panel().select_panel('boadockerpipelinepanel')
+
     def handle_slice_visualization_action(self):
         self.main_panel().select_panel('slicevisualization')
 
@@ -246,8 +274,10 @@ 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()
         self.slice_visualization().save_inputs_and_parameters()
         return super().closeEvent(event)
 

mosamatic2-2.0.14/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.14