mosamatic2 2.0.2__tar.gz → 2.0.4__tar.gz

{mosamatic2-2.0.2 → mosamatic2-2.0.4}/PKG-INFO

@@ -1,12 +1,15 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.2
+Version: 2.0.4
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl
 Requires-Python: >=3.11,<3.12
 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: flask (>=3.1.2)
 Requires-Dist: nibabel (>=5.3.2)
 Requires-Dist: numpy (>=1.26.4)
 Requires-Dist: openpyxl (>=3.1.5)
@@ -21,7 +24,8 @@ Requires-Dist: tensorboard (==2.15.2)
 Requires-Dist: tensorboard-data-server (==0.7.2)
 Requires-Dist: tensorflow (==2.15.*) ; platform_system == "Linux"
 Requires-Dist: tensorflow-intel (==2.15.0) ; platform_system == "Windows"
-Requires-Dist: tensorflow-io-gcs-filesystem (==0.31.0)
+Requires-Dist: tensorflow-io-gcs-filesystem (==0.31.0) ; platform_system == "Windows"
+Requires-Dist: tensorflow-io-gcs-filesystem (>=0.31.0) ; platform_system == "Darwin" and platform_machine == "arm64"
 Requires-Dist: tensorflow-macos (==2.15.0) ; platform_system == "Darwin" and platform_machine == "arm64"
 Requires-Dist: torch (>=2.8.0)
 Requires-Dist: torchvision (>=0.23.0)

{mosamatic2-2.0.2 → mosamatic2-2.0.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.2"
+version = "2.0.4"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}
@@ -10,6 +10,7 @@ requires-python = ">=3.11,<3.12"
 dependencies = [
     "pyside6-essentials>=6.9",
     "pydicom>=3.0.1",
+    "dicom2nifti>=2.6.2",
     "numpy>=1.26.4",
     "pandas>=2.3.2",
     "nibabel>=5.3.2",
@@ -25,8 +26,11 @@ dependencies = [
     "tensorflow-macos==2.15.0; platform_system == 'Darwin' and platform_machine == 'arm64'",
     "tensorboard==2.15.2",
     "tensorboard-data-server==0.7.2",
-    "tensorflow-io-gcs-filesystem==0.31.0",
+    "tensorflow-io-gcs-filesystem==0.31.0; platform_system == 'Windows'",
+    "tensorflow-io-gcs-filesystem>=0.31.0; platform_system == 'Darwin' and platform_machine == 'arm64'",
     "totalsegmentator>=2.11.0",
+    "flask>=3.1.2",
+    "antspyx>=0.5.4",
 ]
 
 [tool.poetry]
@@ -37,6 +41,7 @@ packages = [
 
 [tool.poetry.scripts]
 mosamatic2 = "mosamatic2.app:main"
+mosamatic2-cli = "mosamatic2.cli:main"
 mosamatic2-server = "mosamatic2.server:main"
 
 [tool.poetry.group.dev.dependencies]

{mosamatic2-2.0.2 → mosamatic2-2.0.4}/src/mosamatic2/app.py

@@ -9,6 +9,10 @@ from mosamatic2.ui.widgets.splashscreen import SplashScreen
 LOG = LogManager()
 
 
+def run_tests():
+    return 'PASSED'
+
+
 def main():
     settings = Settings()
     application_name = settings.get(constants.MOSAMATIC2_WINDOW_TITLE)

mosamatic2-2.0.4/src/mosamatic2/cli.py

@@ -0,0 +1,34 @@
+import click
+from mosamatic2.commands import (
+    calculatescores,
+    rescaledicomimages,
+    segmentmusclefatl3tensorflow,
+    createpngsfromsegmentations,
+    dicom2nifti,
+)
+from mosamatic2.core.utils import show_doc_command
+
+
+class CustomHelpGroup(click.Group):
+    def format_commands(self, ctx, formatter):
+        commands = self.list_commands(ctx)
+        with formatter.section('Commands'):
+            for command_name in commands:
+                command = self.get_command(ctx, command_name)
+                if command is None or command.hidden:
+                    continue
+                help_text = command.get_short_help_str()
+                formatter.write_text(f'{command_name:15} {help_text}')
+
+
+@click.group(cls=CustomHelpGroup)
+def main():
+    pass
+
+
+main.add_command(calculatescores.calculatescores)
+main.add_command(rescaledicomimages.rescaledicomimages)
+main.add_command(segmentmusclefatl3tensorflow.segmentmusclefatl3tensorflow)
+main.add_command(createpngsfromsegmentations.createpngsfromsegmentations)
+main.add_command(dicom2nifti.dicom2nifti)
+main.add_command(show_doc_command(main)) # Special command to show long description for command

mosamatic2-2.0.4/src/mosamatic2/commands/calculatescores.py

@@ -0,0 +1,73 @@
+import click
+
+from mosamatic2.core.tasks import CalculateScoresTask
+
+
+@click.command(help='Calculates body composition scores')
+@click.option(
+    '--images', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Directory with images',
+)
+@click.option(
+    '--segmentations',
+    required=True,
+    type=click.Path(exists=True), 
+    help='Directory with segmentations',
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--file_type',
+    default='npy',
+    help='Options: [npy, tag]'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def calculatescores(images, segmentations, output, file_type, overwrite):
+    """
+    Calculates the following body composition metrics from the muscle and fat 
+    images and segmentation files:
+
+    (1) Muscle area (cm^2)
+    (2) Mean muscle radiation attenuation (HU)
+    (3) Subcutaneous fat area (cm^2)
+    (4) Mean subcutaneous fat radiation attenuation (HU)
+    (5) Visceral fat area (cm^2)
+    (6) Mean visceral fat radiation attenuation (HU)
+    
+    Parameters
+    ----------
+    --images : str
+        Directory with input L3 images
+
+    --segmentations : str
+        Directory with L3 muscle and fat segmenation files. Must be output of 
+        "mosamatic2-cli segmentmusclefatl3tensorflow" OR a list of TAG files
+        corresponding to the input images
+
+    --output : str
+        Path to output directory
+
+    --file_type : str
+        Type of segmentation file to use. Can be either "npy" or "tag"
+    
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = CalculateScoresTask(
+        inputs={'images': images, 'segmentations': segmentations},
+        params={'file_type': file_type},
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2-2.0.4/src/mosamatic2/commands/createpngsfromsegmentations.py

@@ -0,0 +1,65 @@
+import click
+
+from mosamatic2.core.tasks import CreatePngsFromSegmentationsTask
+
+
+@click.command(help='Create PNG images from segmentation files')
+@click.option(
+    '--segmentations', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Input directory to segmentation files'
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory for PNG images'
+)
+@click.option(
+    '--fig_width', 
+    type=click.Path(), 
+    default=10,
+    help='Figure width (default: 10)'
+)
+@click.option(
+    '--fig_height', 
+    type=click.Path(), 
+    default=10,
+    help='Figure height (default: 10)'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def createpngsfromsegmentations(segmentations, output, fig_width, fig_height, overwrite):
+    """
+    Creates PNG images from L3 muscle and fat segmentation files
+    
+    Parameters
+    ----------
+    --segmentations : str
+        Directory with with input segmentation files. Must be L3 muscle and fat segmentations
+        (output of "mosamatic2-cli segmentmusclefatl3tensorflow")
+
+    --output : str
+        Path to output directory
+
+    --fig_width : int
+        Width of PNG image
+
+    --fig_height : int
+        Height of PNG image
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = CreatePngsFromSegmentationsTask(
+        inputs={'segmentations': segmentations},
+        params={'fig_width': fig_width, 'fig_height': fig_height},
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2-2.0.4/src/mosamatic2/commands/dicom2nifti.py

@@ -0,0 +1,46 @@
+import click
+
+from mosamatic2.core.tasks import Dicom2NiftiTask
+
+
+@click.command(help='Converts DICOM series to NIFTI')
+@click.option(
+    '--images', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Directory with images',
+)
+@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(images, output, overwrite):
+    """
+    Converts single DICOM series (scan) to NIFTI
+    
+    Parameters
+    ----------
+    --images : str
+        Directory with DICOM images of a single series
+
+    --output : str
+        Path to output directory
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = Dicom2NiftiTask(
+        inputs={'images': images},
+        params=None,
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2-2.0.4/src/mosamatic2/commands/rescaledicomimages.py

@@ -0,0 +1,54 @@
+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()

mosamatic2-2.0.4/src/mosamatic2/commands/segmentmusclefatl3tensorflow.py

@@ -0,0 +1,55 @@
+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()

{mosamatic2-2.0.2 → mosamatic2-2.0.4}/src/mosamatic2/constants.py

@@ -2,12 +2,15 @@ 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 = 'mosamaticdesktop/resources/ui/images/icons'
-MOSAMATIC2_APP_ICON_FILE_NAME_WIN = 'mosamaticdesktop.ico'
-MOSAMATIC2_APP_ICON_FILE_NAME_MAC = 'mosamaticdesktop.icns'
+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

mosamatic2-2.0.4/src/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

mosamatic2-2.0.4/src/mosamatic2/core/data/dicomimage.py

@@ -0,0 +1,18 @@
+from mosamatic2.core.data.filedata import FileData
+from mosamatic2.core.utils import (
+    is_dicom,
+    load_dicom,
+    is_jpeg2000_compressed,
+)
+
+
+class DicomImage(FileData):
+    def load(self):
+        if self.path():
+            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

mosamatic2-2.0.4/src/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

mosamatic2-2.0.4/src/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

mosamatic2-2.0.4/src/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()

mosamatic2-2.0.4/src/mosamatic2/core/data/multidicomimage.py

@@ -0,0 +1,30 @@
+import os
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.data.filedata import FileData
+from mosamatic2.core.data.dicomimage import DicomImage
+
+LOG = LogManager()
+
+
+class MultiDicomImage(FileData):
+    def __init__(self):
+        super(MultiDicomImage, self).__init__()
+        self._images = []
+
+    def images(self):
+        return self._images
+    
+    def load(self):
+        series_instance_uids = []
+        if self.path():
+            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():
+                    series_instance_uid = image.object().SeriesInstanceUID
+                    if series_instance_uid in series_instance_uids:
+                        RuntimeError('Cannot load DICOM images with identical series instance UID')
+                    self._images.append(image)
+            return True
+        return False

{mosamatic2-2.0.2 → mosamatic2-2.0.4}/src/mosamatic2/core/managers/logmanager.py

@@ -11,8 +11,6 @@ class LogManager:
         self._suppress_print = suppress_print
         self._listeners = []
         file_path = os.path.join(Path.home(), 'mosamatic2.log')
-        if os.path.isfile(file_path):
-            os.remove(file_path)
         self._file_handle = open(file_path, 'w', buffering=1)
         atexit.register(self.close_file)
 

mosamatic2-2.0.4/src/mosamatic2/core/pipelines/__init__.py

@@ -0,0 +1 @@
+from mosamatic2.core.pipelines.defaultpipeline import DefaultPipeline

mosamatic2-2.0.4/src/mosamatic2/core/pipelines/defaultpipeline.py

@@ -0,0 +1,79 @@
+import os
+
+from mosamatic2.core.pipelines.pipeline import Pipeline
+from mosamatic2.core.tasks import (
+    RescaleDicomImagesTask, 
+    SegmentMuscleFatL3TensorFlowTask,
+    SegmentMuscleFatL3TensorFlowTask,
+    CreatePngsFromSegmentationsTask,
+    CalculateScoresTask,
+)
+
+
+class DefaultPipeline(Pipeline):
+    INPUTS = [
+        'images',
+        'model_files',
+    ]
+    PARAMS = [
+        'target_size',
+        'file_type',
+        'fig_width',
+        'fig_height',
+        'model_type',
+        'model_version',
+    ]
+    def __init__(self, inputs, params, output, overwrite):
+        super(DefaultPipeline, self).__init__(inputs, params, output, overwrite)
+        model_type = self.param('model_type')
+        # segmentation_task_class = SegmentMuscleFatL3Task if model_type == 'pytorch' else SegmentMuscleFatL3TensorFlowTask
+        segmentation_task_class = SegmentMuscleFatL3TensorFlowTask
+        self.add_task(
+            RescaleDicomImagesTask(
+                inputs={'images': self.input('images')},
+                params={'target_size': self.param('target_size')},
+                output=self.output(),
+                overwrite=self.overwrite(),
+            )
+        )
+        self.add_task(
+            segmentation_task_class(
+                inputs={
+                    'images': os.path.join(self.output(), 'rescaledicomimagestask'),
+                    'model_files': self.input('model_files'),
+                },
+                params={'model_version': self.param('model_version')},
+                output=self.output(),
+                overwrite=self.overwrite(),
+            )
+        )
+        self.add_task(
+            CalculateScoresTask(
+                inputs={
+                    'images': os.path.join(self.output(), 'rescaledicomimagestask'),
+                    'segmentations': os.path.join(
+                        self.output(),
+                        'segmentmusclefatl3pytorchtask' if model_type == 'pytorch' else 'segmentmusclefatl3tensorflowtask',
+                    )
+                },
+                params={'file_type': self.param('file_type')},
+                output=self.output(),
+                overwrite=self.overwrite(),
+            )
+        )
+        self.add_task(
+            CreatePngsFromSegmentationsTask(
+                inputs={
+                    'segmentations': os.path.join(
+                        self.output(),
+                        'segmentmusclefatl3pytorchtask' if model_type == 'pytorch' else 'segmentmusclefatl3tensorflowtask',
+                    )
+                },
+                params={
+                    'fig_width': self.param('fig_width'),
+                    'fig_height': self.param('fig_height'),
+                },
+                output=self.output(),
+                overwrite=self.overwrite(),
+            )
+        )

mosamatic2-2.0.4/src/mosamatic2/core/pipelines/pipeline.py

@@ -0,0 +1,14 @@
+from mosamatic2.core.tasks.task import Task
+
+
+class Pipeline(Task):
+    def __init__(self, inputs, params, output, overwrite=False):
+        super(Pipeline, self).__init__(inputs, params, output, overwrite)
+        self._tasks = []
+
+    def add_task(self, task):
+        self._tasks.append(task)
+
+    def run(self):
+        for task in self._tasks:
+            task.run()

mosamatic2-2.0.4/src/mosamatic2/core/tasks/__init__.py

@@ -0,0 +1,5 @@
+from mosamatic2.core.tasks.rescaledicomimagestask.rescaledicomimagestask import RescaleDicomImagesTask
+from mosamatic2.core.tasks.segmentmusclefatl3tensorflowtask.segmentmusclefatl3tensorflowtask import SegmentMuscleFatL3TensorFlowTask
+from mosamatic2.core.tasks.calculatescorestask.calculatescorestask import CalculateScoresTask
+from mosamatic2.core.tasks.createpngsfromsegmentationstask.createpngsfromsegmentationstask import CreatePngsFromSegmentationsTask
+from mosamatic2.core.tasks.dicom2niftitask.dicom2niftitask import Dicom2NiftiTask