mosamatic2 2.0.12__py3-none-any.whl → 2.0.13__py3-none-any.whl

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/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/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/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/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/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/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/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/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/ui/mainwindow.py

@@ -23,6 +23,7 @@ from mosamatic2.ui.widgets.panels.tasks.createdicomsummarytaskpanel import Creat
 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.pipelines.boadockerpipelinepanel import BoaDockerPipelinePanel
 from mosamatic2.ui.widgets.panels.visualizations.slicevisualization.slicevisualization import SliceVisualization
 
 LOG = LogManager()
@@ -44,6 +45,7 @@ class MainWindow(QMainWindow):
         self._select_slice_from_scans_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()
 
@@ -102,9 +104,12 @@ class MainWindow(QMainWindow):
         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)
@@ -134,6 +139,7 @@ class MainWindow(QMainWindow):
             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.boa_docker_pipeline_panel(), 'boadockerpipelinepanel')
             self._main_panel.add_panel(self.slice_visualization(), 'slicevisualization')
             self._main_panel.select_panel('defaultpipelinepanel')
         return self._main_panel
@@ -190,6 +196,11 @@ 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:
@@ -230,6 +241,9 @@ class MainWindow(QMainWindow):
     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')
 
@@ -248,6 +262,7 @@ class MainWindow(QMainWindow):
         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.boa_docker_pipeline_panel().save_inputs_and_parameters()
         self.slice_visualization().save_inputs_and_parameters()
         return super().closeEvent(event)
 

mosamatic2/ui/resources/VERSION

@@ -1 +1 @@
-2.0.12 
+2.0.13 

mosamatic2/ui/widgets/panels/pipelines/boadockerpipelinepanel.py

@@ -0,0 +1,185 @@
+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.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 BoaDockerPipeline
+
+LOG = LogManager()
+
+PANEL_TITLE = 'BoaDockerPipeline'
+PANEL_NAME = 'boadockerpipeline'
+
+
+class BoaDockerPipelinePanel(PipelinePanel):
+    def __init__(self):
+        super(BoaDockerPipelinePanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._scans_dir_line_edit = None
+        self._images_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_pipeline_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._scans_dir_line_edit.setText(self.settings().get(f'{PANEL_NAME}/scans_dir'))
+        return self._scans_dir_line_edit
+    
+    def scans_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_scans_dir_select_button)
+        return self._images_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 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_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):
+        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('Output directory', output_dir_layout)
+        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_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_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 = BoaDockerPipeline(
+                inputs={'scans': self.scans_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_pipeline_button().setEnabled(True)
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.scans_dir_line_edit().text() == '':
+            errors.append('Empty scans directory path')
+        elif 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')
+        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')
+        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}/output_dir', self.output_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())

mosamatic2/ui/widgets/panels/pipelines/defaultdockerpipelinepanel.py

@@ -182,7 +182,6 @@ class DefaultDockerPipelinePanel(PipelinePanel):
         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())
@@ -289,23 +288,10 @@ class DefaultDockerPipelinePanel(PipelinePanel):
             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())

{mosamatic2-2.0.12.dist-info → mosamatic2-2.0.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.12
+Version: 2.0.13
 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)

{mosamatic2-2.0.12.dist-info → mosamatic2-2.0.13.dist-info}/RECORD

@@ -1,13 +1,15 @@
 models.py,sha256=Kx6oWKt7IpTTxrhBDrX61X-ZX12J7yPkJFuhVDsDHoQ,8807
 mosamatic2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/app.py,sha256=RIUa5tvMYFcmEII4xZPLZZdx9dXWqBvwkxkl_R97Jkw,860
-mosamatic2/cli.py,sha256=EhGBs8AZjgZBBDFkWBNRuKd9o37Zo116DlKHHFBhoBo,1444
+mosamatic2/cli.py,sha256=Fzsz1-uziNRabnBRvqyRcXFpQ7CGLF1dt4w7Js-Y1u8,1614
 mosamatic2/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mosamatic2/commands/boadockerpipeline.py,sha256=-k9rQlhixfcqGUy29SsKYVXxZFri6DcnWaV6utJ6mhI,1344
 mosamatic2/commands/calculatescores.py,sha256=Lb8Q8L2yq7Tt6VBJ6_lltRuldrev_pac6fcgF-xzZyE,1984
 mosamatic2/commands/createdicomsummary.py,sha256=qbVgWGIJPBL8vTBcAxfThloQ_q15OfQy5ohMprzZL4E,1955
 mosamatic2/commands/createpngsfromsegmentations.py,sha256=uUAQJVTqOkBCfENzi21RBNYvf6_nuesx1MeR3j_-7dM,1682
+mosamatic2/commands/defaultdockerpipeline.py,sha256=IxnpnIIsFH2u3aBLKgrHUb_Au72ajlIzzVe6Y0MFHJU,2025
 mosamatic2/commands/defaultpipeline.py,sha256=-kQRSXbEDimAdy_kT1qMxRlZWUoXdu3PkWf70PCIS5Y,1734
-mosamatic2/commands/dicom2nifti.py,sha256=t0EYUqNpPs7OCtPk4KMZrppZQdiaGnfh0HJKKnYJ8CY,1084
+mosamatic2/commands/dicom2nifti.py,sha256=uzI3-QT8_HtwXKkX5kRJzMKssM5dvJGUjZ1Z-XkwLYc,1366
 mosamatic2/commands/rescaledicomimages.py,sha256=25QdCzB5s0sRwkTb3o5zco2bIwy6LttNf7i97kGBDYQ,1280
 mosamatic2/commands/segmentmusclefatl3tensorflow.py,sha256=CdScmA_EQicaN4GY5bBUOYwfhDPqy9om2sxY3WrtmM0,1424
 mosamatic2/commands/selectslicefromscans.py,sha256=3398PM2uBcxF6wpb0-c-Itp_qxoAxBf0SE2nDDI3Ct4,1715
@@ -26,9 +28,11 @@ mosamatic2/core/data/numpyimage.py,sha256=bnG6WVGSRxNdzIlb2DNj5u6Gv4BAYscIj2Buyj
 mosamatic2/core/managers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/core/managers/logmanager.py,sha256=NEaXvhl0aILjBbK710GaWanVuuNvB51HpHhE5rgYvng,1391
 mosamatic2/core/managers/logmanagerlistener.py,sha256=Gaig07yjBnyQq9I8sN85olTEeDCDyCFQnEJdwzvmgvc,99
-mosamatic2/core/pipelines/__init__.py,sha256=2RjHG0xLO-_QK-yw0RHrJe85B-SZ4oAKUJWrDzrLdGI,190
+mosamatic2/core/pipelines/__init__.py,sha256=YPlyO5L_DMrTyO2-2TBq_Bdg-bbMHQiicXJafn66Dg8,283
+mosamatic2/core/pipelines/boadockerpipeline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mosamatic2/core/pipelines/boadockerpipeline/boadockerpipeline.py,sha256=KFZk_L_0KaTdUqHjqGW8MysbCIOKlUKWP8S-T9xyvis,2939
 mosamatic2/core/pipelines/defaultdockerpipeline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mosamatic2/core/pipelines/defaultdockerpipeline/defaultdockerpipeline.py,sha256=gb-rez0Y3jY6_c7llfwN2IDnl9l5Fz3XyvScLmWA7Y4,1490
+mosamatic2/core/pipelines/defaultdockerpipeline/defaultdockerpipeline.py,sha256=m_f9c7MmvSRqERF6n-nLGxa6xP13xtoSihW53d387zU,1315
 mosamatic2/core/pipelines/defaultpipeline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/core/pipelines/defaultpipeline/defaultpipeline.py,sha256=Bme0r_shnrllWYCYDNc6cLM2fQC2yD8RJKpRdoh_6Uc,3077
 mosamatic2/core/pipelines/pipeline.py,sha256=mRxKXLKwgKDpc8R9mCI6gDKGJ2lKVxRQ__Sf0Mfn_Qc,384
@@ -41,7 +45,7 @@ mosamatic2/core/tasks/createdicomsummarytask/createdicomsummarytask.py,sha256=kc
 mosamatic2/core/tasks/createpngsfromsegmentationstask/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/core/tasks/createpngsfromsegmentationstask/createpngsfromsegmentationstask.py,sha256=1UpOsp1CH668BQ0g4tALou_tFgisC306VcvqOKSDuTo,1884
 mosamatic2/core/tasks/dicom2niftitask/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mosamatic2/core/tasks/dicom2niftitask/dicom2niftitask.py,sha256=DC6yNX0RCIJMWcFHkzV51KF8khITYvFQTCsbOr60xGI,1305
+mosamatic2/core/tasks/dicom2niftitask/dicom2niftitask.py,sha256=jvkgC5rkSC0kAy_OXM10RsjAUYi6A76dYjCXQmpycFY,1436
 mosamatic2/core/tasks/rescaledicomimagestask/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/core/tasks/rescaledicomimagestask/rescaledicomimagestask.py,sha256=vGSpMJoXFtE-IHGxTEO9DMkerMJcfG5r9tXgtvkxm6Y,3053
 mosamatic2/core/tasks/segmentmusclefatl3tensorflowtask/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -50,15 +54,15 @@ mosamatic2/core/tasks/segmentmusclefatl3tensorflowtask/segmentmusclefatl3tensorf
 mosamatic2/core/tasks/selectslicefromscanstask/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/core/tasks/selectslicefromscanstask/selectslicefromscanstask.py,sha256=EIEHhWoGL30rcz8qckFl465rU40P-pIkvhMOfSud7Yw,7253
 mosamatic2/core/tasks/task.py,sha256=APPnid6dpSGkPuDqU1vm2RIMR5vkpvbP1CPHUMjympg,1691
-mosamatic2/core/utils.py,sha256=9wY1itpLIEWV8KtwZeD5c4gH4shzOkZEkCA0rSwRI4Q,11897
+mosamatic2/core/utils.py,sha256=y8ujz-sX5nMH2eqvCyzXK2AqYCVVppvJFmGi0UgFXTk,12170
 mosamatic2/server.py,sha256=-cZ9BPsZUXoINKqwhCHN8c59mlvzzDXzTVxsYt9au70,4644
 mosamatic2/ui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mosamatic2/ui/mainwindow.py,sha256=H1X1pLJjqd2DhxJY0ZU6QkktX28zl0pmtFflmOxrGZA,14048
+mosamatic2/ui/mainwindow.py,sha256=XpVqNpOvfULXVaXYHjey4RMhgh4zvvVWfxKFIjTXwO4,14925
 mosamatic2/ui/resources/icons/mosamatic2.icns,sha256=OfhC-diJTIgaNMOezxKKilGsY7mRkaGdU5dGr0MOjIA,2994125
 mosamatic2/ui/resources/icons/mosamatic2.ico,sha256=ySD3RYluHK3pgS0Eas7eKrVk_AskdLQ4qs_IT-wNhq4,12229
 mosamatic2/ui/resources/icons/spinner.gif,sha256=rvaac6GUZauHSPFSOLWr0RmLfjmtZih2Q8knQ2WP3Po,16240
 mosamatic2/ui/resources/images/body-composition.jpg,sha256=KD-BudbXwThB4lJOZZN-ad5-TZRaaZ5cKTH0Ar1TOZs,21227
-mosamatic2/ui/resources/VERSION,sha256=faSzNrbz8BB4kaBpCeyQhoMmfWqpb8tKPPbsfcvfHOA,9
+mosamatic2/ui/resources/VERSION,sha256=haUTerigaCYg0i4VyXT58-MrbAbBF_QkcCNhH9O8PxU,9
 mosamatic2/ui/settings.py,sha256=YEVHYJIfNsqMO3v1pjzgh7Pih9GGoUX7S9s8S-sBNUk,2121
 mosamatic2/ui/utils.py,sha256=6bbPIrh4RJ_yhQKNZrgPbL4XeUEogjIjbk_e5c3QS5g,853
 mosamatic2/ui/widgets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -70,7 +74,8 @@ mosamatic2/ui/widgets/panels/defaultpanel.py,sha256=Ry32Xv6ibxm6NdZ7eBOCcisWNcmn
 mosamatic2/ui/widgets/panels/logpanel.py,sha256=ogswJ6_ryb6u7JeVnOsh2Ez8KWg6jtCFZwij8s87xO4,1861
 mosamatic2/ui/widgets/panels/mainpanel.py,sha256=KqI8dA7GpLFd2unqVRTBkNxdnh6AWGpVPwQuaEg8PmI,2431
 mosamatic2/ui/widgets/panels/pipelines/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mosamatic2/ui/widgets/panels/pipelines/defaultdockerpipelinepanel.py,sha256=SRS6gBhnymgRM6TmaqJgzHzHfffkWucMCjsuzDgJdBg,14415
+mosamatic2/ui/widgets/panels/pipelines/boadockerpipelinepanel.py,sha256=bsyyt-42Qho6D4rpSjo9sBJBM9ISOChX-N8QWc3j2s0,7711
+mosamatic2/ui/widgets/panels/pipelines/defaultdockerpipelinepanel.py,sha256=smEymbmYQ1wy0lgkhjGAGhXQedIhE8wjiX2TqYF6VB8,13284
 mosamatic2/ui/widgets/panels/pipelines/defaultpipelinepanel.py,sha256=qkfI4BnLIXqE_YvSQj4sO_FjnK0eVdIMqAZ8sktgI-8,13727
 mosamatic2/ui/widgets/panels/pipelines/pipelinepanel.py,sha256=SlkKme8Wv2Bvp2Alen98mFjv3F5eZCwJylj294gd5uU,178
 mosamatic2/ui/widgets/panels/stackedpanel.py,sha256=dK1YWuHUzxRhVb5gP0Lu9rAiW4XagjcHmGF__5Lpufk,657
@@ -91,7 +96,7 @@ mosamatic2/ui/widgets/panels/visualizations/slicevisualization/slicevisualizatio
 mosamatic2/ui/widgets/panels/visualizations/visualization.py,sha256=JvqTJi7cCGYK1-wrN2oURdCOBoPS2clVUyYglhkoVJg,178
 mosamatic2/ui/widgets/splashscreen.py,sha256=MS-OczOWfwwEQNQd-JWe9_Mh57css0cSQgbu973rwQo,4056
 mosamatic2/ui/worker.py,sha256=v7e3gq7MUudgpB1BJW-P7j5wurzu6-HG5m7I6WHgJp0,699
-mosamatic2-2.0.12.dist-info/entry_points.txt,sha256=MCUpKkgbej1clgp8EqlLQGs0BIKwGPcBPiVWLfGz9Gw,126
-mosamatic2-2.0.12.dist-info/METADATA,sha256=VwD0JrQc0gdfEC46CqJlD82m3K6TZ1dxAAERa2k4MsY,1490
-mosamatic2-2.0.12.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-mosamatic2-2.0.12.dist-info/RECORD,,
+mosamatic2-2.0.13.dist-info/entry_points.txt,sha256=MCUpKkgbej1clgp8EqlLQGs0BIKwGPcBPiVWLfGz9Gw,126
+mosamatic2-2.0.13.dist-info/METADATA,sha256=XbbE0-CmpimvfTRszW3lSFBavSLHjMhcmSuGZ-R6WaU,1512
+mosamatic2-2.0.13.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+mosamatic2-2.0.13.dist-info/RECORD,,