mosamatic2 2.0.24__py3-none-any.whl

mosamatic2/commands/defaultdockerpipeline.py

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+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(
+    '--version', 
+    required=True, 
+    help='Docker image version'
+)
+@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, version, 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!
+
+    --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!)
+
+    --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,
+            'version': version,
+        },
+        output=output,
+        overwrite=overwrite,
+    )
+    pipeline.run()

mosamatic2/commands/defaultpipeline.py

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+import click
+
+from mosamatic2.core.pipelines import DefaultPipeline
+
+
+@click.command(help='Runs default L3 analysis pipeline')
+@click.option(
+    '--images', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Directory with L3 images',
+)
+@click.option(
+    '--model_files', 
+    required=True, 
+    type=click.Path(), 
+    help='Input directory with AI model files'
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def defaultpipeline(images, model_files, output, overwrite):
+    """
+    Runs default L3 analysis pipeline
+    
+    Parameters
+    ----------
+    --images : str
+        Directory with L3 images
+
+    --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/
+
+    --output : str
+        Path to output directory
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    pipeline = DefaultPipeline(
+        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

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+import click
+
+from mosamatic2.core.tasks import Dicom2NiftiTask
+
+
+@click.command(help='Converts root directory with DICOM series to NIFTI format')
+@click.option(
+    '--scans', 
+    required=True, 
+    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, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def dicom2nifti(scans, compressed, output, overwrite):
+    """
+    Converts DICOM scans to NIFTI format.
+    
+    Parameters
+    ----------
+    --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
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = Dicom2NiftiTask(
+        inputs={'scans': scans},
+        params={'compressed': compressed},
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2/commands/liveranalysispipeline.py

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+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/commands/rescaledicomimages.py

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+import click
+
+from mosamatic2.core.tasks import RescaleDicomImagesTask
+
+
+@click.command(help='Rescale DICOM files to target size')
+@click.option(
+    '--images', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Input directory with images'
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--target_size', 
+    default=512,
+    help='Target size of rescaled images (default: 512)'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def rescaledicomimages(images, output, target_size, overwrite):
+    """
+    Rescales DICOM images to given (square) target size
+
+    Parameters
+    ----------
+    --images : str
+        Directory with input DICOM images
+
+    --output : str
+        Path to output directory
+
+    --target_size : int
+        Target size for rescaled images (default: 512)
+    
+    --overwrite : bool
+        Overwrite contents output directory: [true|false]
+    """
+    task = RescaleDicomImagesTask(
+        inputs={'images': images}, 
+        params={'target_size': target_size}, 
+        output=output, 
+        overwrite=overwrite
+    )
+    task.run()

mosamatic2/commands/segmentmusclefatl3tensorflow.py

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+import click
+
+from mosamatic2.core.tasks import SegmentMuscleFatL3TensorFlowTask
+
+
+@click.command(help='Extracts muscle and fat regions from CT images at L3 (uses PyTorch)')
+@click.option(
+    '--images', 
+    required=True, 
+    type=click.Path(), 
+    help='Input directory with images'
+)
+@click.option(
+    '--model_files', 
+    required=True, 
+    type=click.Path(), 
+    help='Input directory with AI model files'
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--overwrite', 
+    default=False, 
+    type=click.BOOL, 
+    help='Overwrite [true|false]'
+)
+def segmentmusclefatl3tensorflow(images, model_files, output, overwrite):
+    """
+    Automatically segments muscle and fat tissue in CT images at L3 level.
+    
+    Parameters
+    ----------
+    --images : str
+        Directory with input L3 images
+
+    --model_files : str
+        Directory with AI model files (model-1.0.zip, contour_model-1.0.zip, params-1.0.json)
+
+    --output : str
+        Path to output directory
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = SegmentMuscleFatL3TensorFlowTask(
+        inputs={'images': images, 'model_files': model_files},
+        params={'model_version': 1.0},
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2/commands/selectslicefromscans.py

@@ -0,0 +1,66 @@
+import click
+
+from mosamatic2.core.tasks import SelectSliceFromScansTask
+
+
+@click.command(help='Selects specific slice from 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(
+    '--vertebra', 
+    required=True,
+    default='L3',
+    help='Vertebral level for selecting slice (default: "L3")'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=True, 
+    help='Overwrite [true|false] (default: true)'
+)
+def selectslicefromscans(scans, vertebra, output, overwrite):
+    """
+    Selects specific slice from list of CT scans
+    
+    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.
+
+    --vertebra : str
+        Vertebral level where to take slice [L3|T4] (default: L3)
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false] (default: true)
+    """
+    task = SelectSliceFromScansTask(
+        inputs={'scans': scans},
+        params={'vertebra': vertebra},
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2/commands/totalsegmentator.py

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+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(
+    '--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, 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.
+    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!)
+
+    --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, 'format': format},
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2/constants.py

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+MOSAMATIC2_BUNDLE_IDENTIFIER = 'org.mumc'
+MOSAMATIC2_APP_NAME = 'mosamatic2'
+MOSAMATIC2_VERSION_FILE = 'mosamatic2/ui/resources/VERSION'
+MOSAMATIC2_IMAGES_DIR_PATH = 'mosamatic2/ui/resources/images'
+MOSAMATIC2_ICONS_DIR_PATH = 'mosamatic2/ui/resources/icons'
+MOSAMATIC2_APP_ICON_FILE_NAME_WIN = 'mosamatic2.ico'
+MOSAMATIC2_APP_ICON_FILE_NAME_MAC = 'mosamatic2.icns'
+MOSAMATIC2_BACKGROUND_IMAGE_FILE_NAME = 'body-composition.jpg'
+MOSAMATIC2_BACKGROUND_IMAGE_OPACITY = 0.4
+
+MOSAMATIC2_SERVER_PORT = 8000
+MOSAMATIC2_SERVER_DEBUG = True
+
+MOSAMATIC2_WINDOW_TITLE = 'Mosamatic'
+MOSAMATIC2_WINDOW_W = 1000
+MOSAMATIC2_WINDOW_H = 600
+MOSAMATIC2_WINDOW_GEOMETRY_KEY = 'mainwindow/geometry'
+MOSAMATIC2_WINDOW_STATE_KEY = 'mainwindow/state'
+
+MOSAMATIC2_SPLASH_SCREEN_TITLE = MOSAMATIC2_WINDOW_TITLE
+MOSAMATIC2_SPLASH_SCREEN_TITLE_STYLESHEET = 'color: rgb(64, 64, 64); font-weight: bold; font-size: 32pt;'
+MOSAMATIC2_SPLASH_SCREEN_SUB_TEXT = 'This software is for research only'
+MOSAMATIC2_SPLASH_SCREEN_SUB_TEXT_STYLE_SHEET = 'color: rgb(64, 64, 64); font-style: italic; font-size: 10pt;'
+MOSAMATIC2_SPLASH_SCREEN_START_BUTTON_TEXT = 'Start Application'
+MOSAMATIC2_SPLASH_SCREEN_QUIT_BUTTON_TEXT = 'Quit'
+MOSAMATIC2_SPLASH_SCREEN_W = 600
+MOSAMATIC2_SPLASH_SCREEN_H = 300

mosamatic2/core/data/__init__.py

@@ -0,0 +1,5 @@
+from mosamatic2.core.data.filedata import FileData
+from mosamatic2.core.data.dicomimage import DicomImage
+from mosamatic2.core.data.dicomimageseries import DicomImageSeries
+from mosamatic2.core.data.multidicomimage import MultiDicomImage
+from mosamatic2.core.data.dixonseries import DixonSeries

mosamatic2/core/data/dicomimage.py

@@ -0,0 +1,27 @@
+from mosamatic2.core.data.filedata import FileData
+from mosamatic2.core.utils import (
+    is_dicom,
+    load_dicom,
+    is_jpeg2000_compressed,
+)
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
+
+
+class DicomImage(FileData):
+    def load(self):
+        if self.path():
+            p = load_dicom(self.path())
+            if p:
+                if is_jpeg2000_compressed(p):
+                    p.decompress()
+                self.set_object(p)
+                return True
+            # if is_dicom(self.path()):
+            #     p = load_dicom(self.path())
+            #     if is_jpeg2000_compressed(p):
+            #         p.decompress()
+            #     self.set_object(p)
+            #     return True
+        return False

mosamatic2/core/data/dicomimageseries.py

@@ -0,0 +1,26 @@
+import os
+from mosamatic2.core.data.filedata import FileData
+from mosamatic2.core.data.dicomimage import DicomImage
+
+
+class DicomImageSeries(FileData):
+    def __init__(self):
+        super(DicomImageSeries, self).__init__()
+        self._images = []
+
+    def images(self):
+        return self._images
+    
+    def load(self):
+        if self.path():
+            images = []
+            for f in os.listdir(self.path()):
+                f_path = os.path.join(self.path(), f)
+                image = DicomImage()
+                image.set_path(f_path)
+                if image.load():
+                    images.append(image)
+            # Sort DICOM objects by instance number
+            self._images = sorted(images, key=lambda image: int(image.object().get('InstanceNumber')))
+            return True
+        return False

mosamatic2/core/data/dixonseries.py

@@ -0,0 +1,22 @@
+from mosamatic2.core.data.filedata import FileData
+
+
+class DixonSeries(FileData):
+    def __init__(self):
+        super(DixonSeries, self).__init__()
+        self._series = {'ip': None, 'op': None, 'water': None, 'fat': None}
+
+    def ip(self):
+        return self._series['ip']
+    
+    def op(self):
+        return self._series['op']
+    
+    def water(self):
+        return self._series['water']
+    
+    def fat(self):
+        return self._series['fat']
+    
+    def load(self):
+        pass

mosamatic2/core/data/filedata.py

@@ -0,0 +1,26 @@
+import os
+
+
+class FileData:
+    def __init__(self):
+        self._path = None
+        self._name = None
+        self._object = None
+
+    def path(self):
+        return self._path
+    
+    def set_path(self, path):
+        self._path = path
+
+    def name(self):
+        return os.path.split(self.path())[1]
+    
+    def object(self):
+        return self._object
+    
+    def set_object(self, object):
+        self._object = object
+    
+    def load(self):
+        raise NotImplementedError()