mosamatic2 2.0.16__tar.gz → 2.0.18__tar.gz

{mosamatic2-2.0.16 → mosamatic2-2.0.18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.16
+Version: 2.0.18
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl
@@ -9,9 +9,9 @@ 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: docker (>=7.1.0)
 Requires-Dist: flask (>=3.1.2)
-Requires-Dist: moosez
+Requires-Dist: moosez (>=3.0.29)
 Requires-Dist: nibabel (>=5.3.2)
 Requires-Dist: numpy (>=1.26.4)
 Requires-Dist: openpyxl (>=3.1.5)
@@ -23,7 +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: slicer (>=0.0.8)
 Requires-Dist: tensorboard (==2.15.2)
 Requires-Dist: tensorboard-data-server (==0.7.2)
 Requires-Dist: tensorflow (==2.15.*) ; platform_system == "Linux"

{mosamatic2-2.0.16 → mosamatic2-2.0.18}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.16"
+version = "2.0.18"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}
@@ -33,9 +33,9 @@ dependencies = [
     "antspyx>=0.5.4",
     "vtk>=9.5.1",
     "pyqtgraph>=0.13.7",
-    "moosez",
-    "docker",
-    "slicer",
+    "moosez>=3.0.29",
+    "docker>=7.1.0",
+    "slicer>=0.0.8",
 ]
 
 [tool.poetry]

{mosamatic2-2.0.16 → mosamatic2-2.0.18}/src/mosamatic2/cli.py

@@ -1,6 +1,7 @@
 import click
 from mosamatic2.commands import (
     calculatescores,
+    calculatemaskstatistics,
     rescaledicomimages,
     segmentmusclefatl3tensorflow,
     createpngsfromsegmentations,
@@ -10,6 +11,8 @@ from mosamatic2.commands import (
     defaultpipeline,
     defaultdockerpipeline,
     boadockerpipeline,
+    liveranalysispipeline,
+    totalsegmentator,
 )
 from mosamatic2.core.utils import show_doc_command
 
@@ -32,6 +35,7 @@ def main():
 
 
 main.add_command(calculatescores.calculatescores)
+main.add_command(calculatemaskstatistics.calculatemaskstatistics)
 main.add_command(rescaledicomimages.rescaledicomimages)
 main.add_command(segmentmusclefatl3tensorflow.segmentmusclefatl3tensorflow)
 main.add_command(createpngsfromsegmentations.createpngsfromsegmentations)
@@ -41,4 +45,6 @@ main.add_command(createdicomsummary.createdicomsummary)
 main.add_command(defaultpipeline.defaultpipeline)
 main.add_command(defaultdockerpipeline.defaultdockerpipeline)
 main.add_command(boadockerpipeline.boadockerpipeline)
+main.add_command(liveranalysispipeline.liveranalysispipeline)
+main.add_command(totalsegmentator.totalsegmentator)
 main.add_command(show_doc_command(main)) # Special command to show long description for command

mosamatic2-2.0.18/src/mosamatic2/commands/calculatemaskstatistics.py

@@ -0,0 +1,59 @@
+import click
+
+from mosamatic2.core.tasks import CalculateMaskStatisticsTask
+
+
+@click.command(help='Calculates segmentation mask statistics')
+@click.option(
+    '--scans', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Directory with scans in NIFTI format',
+)
+@click.option(
+    '--masks',
+    required=True,
+    type=click.Path(exists=True), 
+    help='Directory with segmentation mask files in NIFTI format',
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def calculatemaskstatistics(scans, masks, output, overwrite):
+    """
+    Calculates segmentation mask statistics. The following metrics are calculated:
+
+    (1) Mean radiation attenuation (HU)
+    (2) Standard deviation radiation attenuation (HU)
+    (3) Segmentation mask volume (mL)
+    
+    Parameters
+    ----------
+    --scans : str
+        Directory with scans in NIFTI format
+
+    --masks : str
+        Directory with segmentation mask files in NIFTI format
+
+    --output : str
+        Path to output directory
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = CalculateMaskStatisticsTask(
+        inputs={'scans': scans, 'masks': masks},
+        params=None,
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

{mosamatic2-2.0.16 → mosamatic2-2.0.18}/src/mosamatic2/commands/defaultdockerpipeline.py

@@ -16,6 +16,11 @@ from mosamatic2.core.pipelines import DefaultDockerPipeline
     type=click.Path(), 
     help='Input directory with AI model files (no spaces allowed)'
 )
+@click.option(
+    '--version', 
+    required=True, 
+    help='Docker image version'
+)
 @click.option(
     '--output', 
     required=True, 
@@ -28,7 +33,7 @@ from mosamatic2.core.pipelines import DefaultDockerPipeline
     default=False, 
     help='Overwrite [true|false]'
 )
-def defaultdockerpipeline(images, model_files, output, overwrite):
+def defaultdockerpipeline(images, model_files, version, output, overwrite):
     """
     Runs default L3 analysis pipeline through Docker
     
@@ -51,6 +56,11 @@ def defaultdockerpipeline(images, model_files, output, overwrite):
 
         Warning: This directory path cannot contain any spaces!
 
+    --version : str
+        Docker image version, e.g., 2.0.16
+        Check https://hub.docker.com/repository/docker/brecheisen/mosamatic2-cli/general
+        for the latest version and older versions.
+
     --output : str
         Path to output directory (no spaces!)
 
@@ -66,6 +76,7 @@ def defaultdockerpipeline(images, model_files, output, overwrite):
             'file_type': 'npy',
             'fig_width': 10,
             'fig_height': 10,
+            'version': version,
         },
         output=output,
         overwrite=overwrite,

mosamatic2-2.0.18/src/mosamatic2/commands/liveranalysispipeline.py

@@ -0,0 +1,61 @@
+import click
+
+from mosamatic2.core.pipelines import LiverAnalysisPipeline
+
+
+@click.command(help='Runs liver analysis pipeline')
+@click.option(
+    '--scans', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Root directory with scan directories for each patient (no spaces allowed)',
+)
+@click.option(
+    '--compressed', 
+    default=True,
+    help='Whether to produce compressed NIFTI file or not (default: True)'
+)
+@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 liveranalysispipeline(scans, compressed, output, overwrite):
+    """
+    Runs liver analysis pipeline. This pipeline run the following steps on each scan: 
+
+    (1) DICOM to NIFTI conversion
+    (2) Extract liver segments using Total Segmentator
+    (3) Calculate segment statistics, e.g., volume (mL), mean HU, std HU and PNG image
+        of each segments HU histogram.
+    
+    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.
+
+    --compressed : str
+        Whether to produce compressed NIFTI file or not (default: True)
+
+    --output : str
+        Path to output directory. No spaces allowed.
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    pipeline = LiverAnalysisPipeline(
+        inputs={'scans': scans},
+        params={'compressed': compressed},
+        output=output,
+        overwrite=overwrite,
+    )
+    pipeline.run()

{mosamatic2-2.0.16 → mosamatic2-2.0.18}/src/mosamatic2/commands/totalsegmentator.py

@@ -21,13 +21,18 @@ from mosamatic2.core.tasks import TotalSegmentatorTask
     default='total',
     help='Comma-separated list of Total Segmentator tasks to run (no spaces!)'
 )
+@click.option(
+    '--format',
+    default='dicom',
+    help='Process scans in DICOM or NIFTI format [dicom|nifti] (default: dicom)'
+)
 @click.option(
     '--overwrite', 
     type=click.BOOL, 
     default=False, 
     help='Overwrite [true|false]'
 )
-def totalsegmentator(scans, tasks, output, overwrite):
+def totalsegmentator(scans, tasks, format, 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.
@@ -56,12 +61,16 @@ def totalsegmentator(scans, tasks, output, overwrite):
     --tasks : str
         Comma-separated list of Total Segmentator tasks to run (no spaces!)
 
+    --format : str
+        Process scans in DICOM or NIFTI format. Options: [dicom|nifti]
+        Default is 'dicom'.
+
     --overwrite : bool
         Overwrite contents output directory [true|false]
     """
     task = TotalSegmentatorTask(
         inputs={'scans': scans},
-        params={'tasks': tasks},
+        params={'tasks': tasks, 'format': format},
         output=output,
         overwrite=overwrite,
     )

{mosamatic2-2.0.16 → mosamatic2-2.0.18}/src/mosamatic2/core/pipelines/__init__.py

@@ -1,3 +1,4 @@
 from mosamatic2.core.pipelines.defaultpipeline.defaultpipeline import DefaultPipeline
 from mosamatic2.core.pipelines.defaultdockerpipeline.defaultdockerpipeline import DefaultDockerPipeline
-from mosamatic2.core.pipelines.boadockerpipeline.boadockerpipeline import BoaDockerPipeline
+from mosamatic2.core.pipelines.boadockerpipeline.boadockerpipeline import BoaDockerPipeline
+from mosamatic2.core.pipelines.liveranalysispipeline.liveranalysispipeline import LiverAnalysisPipeline

{mosamatic2-2.0.16 → mosamatic2-2.0.18}/src/mosamatic2/core/pipelines/defaultdockerpipeline/defaultdockerpipeline.py

@@ -11,15 +11,8 @@ class DefaultDockerPipeline(Pipeline):
         'images',
         'model_files',
     ]
-    PARAMS = [
-        'target_size',
-        'file_type',
-        'fig_width',
-        'fig_height',
-        'model_type',
-        'model_version',
-        'version',
-    ]
+    PARAMS = ['version']
+    
     def __init__(self, inputs, params, output, overwrite):
         super(DefaultDockerPipeline, self).__init__(inputs, params, output, overwrite)
 

mosamatic2-2.0.18/src/mosamatic2/core/pipelines/liveranalysispipeline/liveranalysispipeline.py

@@ -0,0 +1,48 @@
+import os
+from mosamatic2.core.pipelines.pipeline import Pipeline
+from mosamatic2.core.tasks import (
+    Dicom2NiftiTask,
+    TotalSegmentatorTask,
+    CalculateMaskStatisticsTask,
+)
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
+
+
+class LiverAnalysisPipeline(Pipeline):
+    INPUTS = ['scans']
+    PARAMS = ['compressed']
+
+    def __init__(self, inputs, params, output, overwrite):
+        super(LiverAnalysisPipeline, self).__init__(inputs, params, output, overwrite)
+        self.add_task(
+            Dicom2NiftiTask(
+                inputs={'scans': self.input('scans')},
+                params={'compressed': self.param('compressed')},
+                output=self.output(),
+                overwrite=self.overwrite(),
+            )
+        )
+        self.add_task(
+            TotalSegmentatorTask(
+                inputs={'scans': os.path.join(self.output(), 'dicom2niftitask')},
+                params={
+                    'tasks': 'liver_segments', 
+                    'format': 'nifti',
+                },
+                output=self.output(),
+                overwrite=self.overwrite(),
+            )
+        )
+        self.add_task(
+            CalculateMaskStatisticsTask(
+                inputs={
+                    'scans': os.path.join(self.output(), 'dicom2niftitask'),
+                    'masks': os.path.join(self.output(), 'totalsegmentatortask'),
+                },
+                params=None,
+                output=self.output(),
+                overwrite=self.overwrite(),
+            )
+        )

{mosamatic2-2.0.16 → mosamatic2-2.0.18}/src/mosamatic2/core/tasks/__init__.py

@@ -5,4 +5,5 @@ from mosamatic2.core.tasks.createpngsfromsegmentationstask.createpngsfromsegment
 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.totalsegmentatortask.totalsegmentatortask import TotalSegmentatorTask
+from mosamatic2.core.tasks.totalsegmentatortask.totalsegmentatortask import TotalSegmentatorTask
+from mosamatic2.core.tasks.calculatemaskstatisticstask.calculatemaskstatisticstask import CalculateMaskStatisticsTask

mosamatic2-2.0.18/src/mosamatic2/core/tasks/calculatemaskstatisticstask/calculatemaskstatisticstask.py

@@ -0,0 +1,104 @@
+import os
+import numpy as np
+import nibabel as nb
+import pandas as pd
+import matplotlib.pyplot as plt
+from mosamatic2.core.tasks.task import Task
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
+
+
+class CalculateMaskStatisticsTask(Task):
+    INPUTS = ['scans', 'masks']
+    PARAMS = []
+
+    def __init__(self, inputs, params, output, overwrite):
+        super(CalculateMaskStatisticsTask, self).__init__(inputs, params, output, overwrite)
+
+    def load_scans(self):
+        scans = []
+        for f in os.listdir(self.input('scans')):
+            if f.endswith('.nii.gz'):
+                scan = os.path.join(self.input('scans'), f)
+                if os.path.isfile(scan):
+                    scans.append(scan)
+        return scans
+
+    def load_mask_files(self):
+        mask_files = []
+        for f in os.listdir(self.input('masks')):
+            if f.endswith('.nii.gz'):
+                mask_file = os.path.join(self.input('masks'), f)
+                if os.path.isfile(mask_file):
+                    mask_files.append(mask_file)
+        return mask_files
+    
+    def collect_scan_mask_file_pairs(self, scans, mask_files):
+        scan_mask_file_pairs = []
+        for scan in scans:
+            scan_name = os.path.split(scan)[1][:-7]
+            for mask_file in mask_files:
+                mask_file_name = os.path.split(mask_file)[1][:-7]
+                if scan_name in mask_file_name:
+                    scan_mask_file_pairs.append((scan, mask_file))
+        return scan_mask_file_pairs
+    
+    def get_masked_voxels(self, scan_mask_file_pair):
+        scan_image_file = scan_mask_file_pair[0]
+        scan_image = nb.load(scan_image_file)
+        scan_image_data = scan_image.get_fdata()
+        mask_file_image_file = scan_mask_file_pair[1]
+        mask_file_image_file_name = os.path.split(mask_file_image_file)[1]
+        mask_file_image = nb.load(mask_file_image_file)
+        mask_file_image_data = mask_file_image.get_fdata()
+        mask = mask_file_image_data > 0
+        masked_voxels = scan_image_data[mask]
+        return masked_voxels, mask_file_image_file_name
+    
+    def calculate_volume_in_mL(self, mask_file):
+        nifti_image = nb.load(mask_file)
+        nifti_image_data = nifti_image.get_fdata()
+        voxel_dims = nifti_image.header.get_zooms()[:3]
+        voxel_volume = np.prod(voxel_dims)
+        num_voxels = np.sum(nifti_image_data > 0.5)
+        mask_volume = num_voxels * voxel_volume / 1000.0
+        return mask_volume
+    
+    def create_histogram_png(self, masked_voxels, file_name):
+        histogram_png_file = os.path.join(self.output(), f'{file_name}.png')
+        plt.figure(figsize=(8,6))
+        plt.hist(masked_voxels, bins=100, color='steelblue', edgecolor='black')
+        plt.title(f'Histogram of HU values inside {file_name}')
+        plt.xlabel('HU')
+        plt.ylabel('Frequency')
+        plt.savefig(histogram_png_file, dpi=300, bbox_inches='tight')
+        plt.close()
+
+    def save_data_to_file(self, data):
+        csv_file_path = os.path.join(self.output(), 'statistics.csv')
+        xls_file_path = os.path.join(self.output(), 'statistics.xlsx')
+        df = pd.DataFrame(data=data)
+        df.to_csv(csv_file_path, index=False, sep=';')
+        df.to_excel(xls_file_path, index=False, engine='openpyxl')
+
+    def run(self):
+        scans = self.load_scans()
+        mask_files = self.load_mask_files()
+        scan_mask_file_pairs = self.collect_scan_mask_file_pairs(scans, mask_files)
+        nr_steps = len(scan_mask_file_pairs)
+        data = {
+            'file': [],
+            'mean_HU': [],
+            'std_HU': [],
+            'volume_mL': [],
+        }
+        for step in range(nr_steps):
+            masked_voxels, file_name = self.get_masked_voxels(scan_mask_file_pairs[step])
+            data['file'].append(file_name)
+            data['mean_HU'].append(round(np.mean(masked_voxels)))
+            data['std_HU'].append(round(np.std(masked_voxels)))
+            data['volume_mL'].append(round(self.calculate_volume_in_mL(scan_mask_file_pairs[step][1])))
+            self.create_histogram_png(masked_voxels, file_name)
+            self.set_progress(step, nr_steps)
+        self.save_data_to_file(data)

mosamatic2-2.0.18/src/mosamatic2/core/tasks/totalsegmentatortask/totalsegmentatortask.py

@@ -0,0 +1,75 @@
+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', 'format']
+
+    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 load_scans(self):
+        scans = []
+        for f in os.listdir(self.input('scans')):
+            if f.endswith('.nii.gz'):
+                scan = os.path.join(self.input('scans'), f)
+                if os.path.isfile(scan):
+                    scans.append(scan)
+        return scans
+    
+    def extract_masks(self, scan_dir_or_file):
+        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_or_file, output=TOTAL_SEGMENTATOR_OUTPUT_DIR, task=task)
+
+    def delete_total_segmentator_output(self):
+        if os.path.exists(TOTAL_SEGMENTATOR_OUTPUT_DIR):
+            shutil.rmtree(TOTAL_SEGMENTATOR_OUTPUT_DIR)
+
+    def run(self):
+        if self.param('format') == 'dicom':
+            scan_dirs_or_files = self.load_scan_dirs()
+        elif self.param('format') == 'nifti':
+            scan_dirs_or_files = self.load_scans()
+        else:
+            LOG.error('Unknown format: {}'.format(self.param('format')))
+            return
+        nr_steps = len(scan_dirs_or_files)
+        for step in range(nr_steps):
+            scan_dir_or_file = scan_dirs_or_files[step]
+            scan_dir_or_file_name = os.path.split(scan_dir_or_file)[1]
+            if self.param('format') == 'nifti':
+                scan_dir_or_file_name = scan_dir_or_file_name[:-7]
+            try:
+                self.extract_masks(scan_dir_or_file)
+            except Exception as e:
+                LOG.error(f'{scan_dir_or_file}: 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)
+                    target_file = os.path.join(self.output(), f'{scan_dir_or_file_name}_{f}')
+                    shutil.copyfile(f_path, target_file)
+                    LOG.info(f'Copied {f} to {target_file}')
+            LOG.info('Cleaning up Total Segmentator temporary output...')
+            self.delete_total_segmentator_output()

{mosamatic2-2.0.16 → mosamatic2-2.0.18}/src/mosamatic2/ui/mainwindow.py

@@ -22,9 +22,11 @@ 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.tasks.totalsegmentatortaskpanel import TotalSegmentatorTaskPanel
+from mosamatic2.ui.widgets.panels.tasks.calculatemaskstatisticstaskpanel import CalculateMaskStatisticsTaskPanel
 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.pipelines.liveranalysispipelinepanel import LiverAnalysisPipelinePanel
 from mosamatic2.ui.widgets.panels.visualizations.slicevisualization.slicevisualization import SliceVisualization
 
 LOG = LogManager()
@@ -45,9 +47,11 @@ class MainWindow(QMainWindow):
         self._create_dicom_summary_task_panel = None
         self._select_slice_from_scans_task_panel = None
         self._total_segmentator_task_panel = None
+        self._calculate_mask_statistics_task_panel = None
         self._default_pipeline_panel = None
         self._default_docker_pipeline_panel = None
         self._boa_docker_pipeline_panel = None
+        self._liver_analysis_pipeline_panel = None
         self._slice_visualization = None
         self.init_window()
 
@@ -94,6 +98,8 @@ class MainWindow(QMainWindow):
         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)
+        calculate_mask_statistics_task_action = QAction('CalculateMaskStatisticsTask', self)
+        calculate_mask_statistics_task_action.triggered.connect(self.handle_calculate_mask_statistics_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)
@@ -103,6 +109,7 @@ class MainWindow(QMainWindow):
         tasks_menu.addAction(create_dicom_summary_task_action)
         tasks_menu.addAction(select_slice_from_scans_task_action)
         tasks_menu.addAction(total_segmentator_task_action)
+        tasks_menu.addAction(calculate_mask_statistics_task_action)
 
     def init_pipelines_menu(self):
         default_pipeline_action = QAction('DefaultPipeline', self)
@@ -111,10 +118,13 @@ class MainWindow(QMainWindow):
         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)
+        liver_analysis_pipeline_action = QAction('LiverAnalysisPipeline', self)
+        liver_analysis_pipeline_action.triggered.connect(self.handle_liver_analysis_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)
+        pipelines_menu.addAction(liver_analysis_pipeline_action)
 
     def init_visualizations_menu(self):
         slice_visualization_action = QAction('SliceVisualization', self)
@@ -143,9 +153,11 @@ 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.total_segmentator_task_panel(), 'totalsegmentatortaskpanel')
+            self._main_panel.add_panel(self.calculate_mask_statistics_task_panel(), 'calculatemaskstatisticstaskpanel')
             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.liver_analysis_pipeline_panel(), 'liveranalysispipelinepanel')
             self._main_panel.add_panel(self.slice_visualization(), 'slicevisualization')
             self._main_panel.select_panel('defaultpipelinepanel')
         return self._main_panel
@@ -198,6 +210,11 @@ class MainWindow(QMainWindow):
             self._total_segmentator_task_panel = TotalSegmentatorTaskPanel()
         return self._total_segmentator_task_panel
     
+    def calculate_mask_statistics_task_panel(self):
+        if not self._calculate_mask_statistics_task_panel:
+            self._calculate_mask_statistics_task_panel = CalculateMaskStatisticsTaskPanel()
+        return self._calculate_mask_statistics_task_panel
+    
     def default_pipeline_panel(self):
         if not self._default_pipeline_panel:
             self._default_pipeline_panel = DefaultPipelinePanel()
@@ -213,6 +230,11 @@ class MainWindow(QMainWindow):
             self._boa_docker_pipeline_panel = BoaDockerPipelinePanel()
         return self._boa_docker_pipeline_panel
     
+    def liver_analysis_pipeline_panel(self):
+        if not self._liver_analysis_pipeline_panel:
+            self._liver_analysis_pipeline_panel = LiverAnalysisPipelinePanel()
+        return self._liver_analysis_pipeline_panel
+    
     def slice_visualization(self):
         if not self._slice_visualization:
             self._slice_visualization = SliceVisualization()
@@ -249,6 +271,9 @@ class MainWindow(QMainWindow):
     def handle_total_segmentator_task_action(self):
         self.main_panel().select_panel('totalsegmentatortaskpanel')
 
+    def handle_calculate_mask_statistics_task_action(self):
+        self.main_panel().select_panel('calculatemaskstatisticstaskpanel')
+
     def handle_default_pipeline_action(self):
         self.main_panel().select_panel('defaultpipelinepanel')
 
@@ -258,6 +283,9 @@ class MainWindow(QMainWindow):
     def handle_boa_docker_pipeline_action(self):
         self.main_panel().select_panel('boadockerpipelinepanel')
 
+    def handle_liver_analysis_pipeline_action(self):
+        self.main_panel().select_panel('liveranalysispipelinepanel')
+
     def handle_slice_visualization_action(self):
         self.main_panel().select_panel('slicevisualization')
 
@@ -275,9 +303,11 @@ 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.total_segmentator_task_panel().save_inputs_and_parameters()
+        self.calculate_mask_statistics_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.liver_analysis_pipeline_panel().save_inputs_and_parameters()
         self.slice_visualization().save_inputs_and_parameters()
         return super().closeEvent(event)
 

mosamatic2-2.0.18/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.18