mosamatic2 2.0.8__tar.gz → 2.0.10__tar.gz

{mosamatic2-2.0.8 → mosamatic2-2.0.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.8
+Version: 2.0.10
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl
@@ -10,6 +10,7 @@ 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: moosez
 Requires-Dist: nibabel (>=5.3.2)
 Requires-Dist: numpy (>=1.26.4)
 Requires-Dist: openpyxl (>=3.1.5)
@@ -28,8 +29,8 @@ Requires-Dist: tensorflow-intel (==2.15.0) ; platform_system == "Windows"
 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)
+Requires-Dist: torch (==2.5.1)
+Requires-Dist: torchvision (>=0.20.1)
 Requires-Dist: totalsegmentator (>=2.11.0)
 Requires-Dist: vtk (>=9.5.1)
 Description-Content-Type: text/markdown

{mosamatic2-2.0.8 → mosamatic2-2.0.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.8"
+version = "2.0.10"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}
@@ -19,8 +19,8 @@ dependencies = [
     "pillow>=11.3.0",
     "python-gdcm>=3.0.26",
     "scipy>=1.15.3",
-    "torch>=2.8.0",
-    "torchvision>=0.23.0",
+    "torch==2.5.1",
+    "torchvision>=0.20.1",
     "tensorflow==2.15.*; platform_system == 'Linux'",
     "tensorflow-intel==2.15.0; platform_system == 'Windows'",
     "tensorflow-macos==2.15.0; platform_system == 'Darwin' and platform_machine == 'arm64'",
@@ -33,6 +33,7 @@ dependencies = [
     "antspyx>=0.5.4",
     "vtk>=9.5.1",
     "pyqtgraph>=0.13.7",
+    "moosez",
 ]
 
 [tool.poetry]

{mosamatic2-2.0.8 → mosamatic2-2.0.10}/src/mosamatic2/cli.py

@@ -7,6 +7,7 @@ from mosamatic2.commands import (
     dicom2nifti,
     selectslicefromscans,
     createdicomsummary,
+    defaultpipeline,
 )
 from mosamatic2.core.utils import show_doc_command
 
@@ -35,4 +36,5 @@ main.add_command(createpngsfromsegmentations.createpngsfromsegmentations)
 main.add_command(dicom2nifti.dicom2nifti)
 main.add_command(selectslicefromscans.selectslicefromscans)
 main.add_command(createdicomsummary.createdicomsummary)
+main.add_command(defaultpipeline.defaultpipeline)
 main.add_command(show_doc_command(main)) # Special command to show long description for command

mosamatic2-2.0.10/src/mosamatic2/commands/defaultpipeline.py

@@ -0,0 +1,70 @@
+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()

mosamatic2-2.0.10/src/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

{mosamatic2-2.0.8 → mosamatic2-2.0.10}/src/mosamatic2/core/pipelines/defaultpipeline/defaultpipeline.py

@@ -8,6 +8,9 @@ from mosamatic2.core.tasks import (
     CreatePngsFromSegmentationsTask,
     CalculateScoresTask,
 )
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
 
 
 class DefaultPipeline(Pipeline):
@@ -25,6 +28,7 @@ class DefaultPipeline(Pipeline):
     ]
     def __init__(self, inputs, params, output, overwrite):
         super(DefaultPipeline, self).__init__(inputs, params, output, overwrite)
+        LOG.info('Found {} images to process'.format(len(os.listdir(self.input('images')))))
         model_type = self.param('model_type')
         # segmentation_task_class = SegmentMuscleFatL3Task if model_type == 'pytorch' else SegmentMuscleFatL3TensorFlowTask
         segmentation_task_class = SegmentMuscleFatL3TensorFlowTask

{mosamatic2-2.0.8 → mosamatic2-2.0.10}/src/mosamatic2/core/tasks/createdicomsummarytask/createdicomsummarytask.py

@@ -25,8 +25,9 @@ class CreateDicomSummaryTask(Task):
             for root, dirs, files in os.walk(patient_dir_path):
                 for f in files:
                     f_path = os.path.join(root, f)
-                    if is_dicom(f_path):
-                        p = load_dicom(f_path, stop_before_pixels=True)
+                    # if is_dicom(f_path):
+                    p = load_dicom(f_path, stop_before_pixels=True)
+                    if p:
                         series_instance_uid = p.SeriesInstanceUID
                         if not series_instance_uid in data[patient_dir_name].keys():
                             data[patient_dir_name][series_instance_uid] = []

{mosamatic2-2.0.8 → mosamatic2-2.0.10}/src/mosamatic2/core/tasks/selectslicefromscanstask/selectslicefromscanstask.py

@@ -97,7 +97,12 @@ class SelectSliceFromScansTask(Task):
         for step in range(nr_steps):
             scan_dir = scan_dirs[step]
             scan_name = os.path.split(scan_dir)[1]
-            self.extract_masks(scan_dir)
+            try:
+                self.extract_masks(scan_dir)
+            except Exception as e:
+                LOG.warning(f'Could not extract masks from {scan_dir} [{str(e)}]')
+                self.set_progress(step, nr_steps)
+                continue
             file_path = self.find_slice(scan_dir, vertebra)
             if file_path is not None:
                 extension = '' if file_path.endswith('.dcm') else '.dcm'

{mosamatic2-2.0.8 → mosamatic2-2.0.10}/src/mosamatic2/core/utils.py

@@ -14,10 +14,12 @@ from pydicom.uid import (
     ExplicitVRLittleEndian, ImplicitVRLittleEndian, ExplicitVRBigEndian
 )
 from PIL import Image
+from mosamatic2.core.managers.logmanager import LogManager
 
 warnings.filterwarnings("ignore", message="Invalid value for VR UI:", category=UserWarning)
 
 MUSCLE, VAT, SAT = 1, 5, 7
+LOG = LogManager()
 
 
 def create_name_with_timestamp(prefix: str='') -> str:
@@ -102,17 +104,34 @@ def is_dicom(f):
         pydicom.dcmread(f, stop_before_pixels=True)
         return True
     except pydicom.errors.InvalidDicomError:
-        return False
+        try:
+            pydicom.dcmread(f, stop_before_pixels=True, force=True)
+            return True
+        except pydicom.errors.InvalidDicomError:
+            pass
+    return False
     
 
 def load_dicom(f, stop_before_pixels=False):
-    if is_dicom(f):
+    try:
         return pydicom.dcmread(f, stop_before_pixels=stop_before_pixels)
+    except pydicom.errors.InvalidDicomError:
+        try:
+            p = pydicom.dcmread(f, stop_before_pixels=stop_before_pixels, force=True)
+            if hasattr(p, 'SOPClassUID'):
+                if not hasattr(p.file_meta, 'TransferSyntaxUID'):
+                    LOG.warning(f'DICOM file {f} does not have FileMetaData/TransferSyntaxUID, trying to fix...')
+                    p.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
+                return p
+        except pydicom.errors.InvalidDicomError:
+            pass
     return None
 
 
 def is_jpeg2000_compressed(p):
-    return p.file_meta.TransferSyntaxUID not in [ExplicitVRLittleEndian, ImplicitVRLittleEndian, ExplicitVRBigEndian]
+    if hasattr(p.file_meta, 'TransferSyntaxUID'):
+        return p.file_meta.TransferSyntaxUID not in [ExplicitVRLittleEndian, ImplicitVRLittleEndian, ExplicitVRBigEndian]
+    return False
 
 
 def is_numpy_array(value):

mosamatic2-2.0.10/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.10 

mosamatic2-2.0.8/src/mosamatic2/core/data/dicomimage.py

@@ -1,18 +0,0 @@
-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

mosamatic2-2.0.8/src/mosamatic2/ui/resources/VERSION

@@ -1 +0,0 @@
-2.0.8