mosamatic2 2.0.7__py3-none-any.whl → 2.0.9__py3-none-any.whl

mosamatic2/cli.py

@@ -6,6 +6,7 @@ from mosamatic2.commands import (
     createpngsfromsegmentations,
     dicom2nifti,
     selectslicefromscans,
+    createdicomsummary,
 )
 from mosamatic2.core.utils import show_doc_command
 
@@ -33,4 +34,5 @@ main.add_command(segmentmusclefatl3tensorflow.segmentmusclefatl3tensorflow)
 main.add_command(createpngsfromsegmentations.createpngsfromsegmentations)
 main.add_command(dicom2nifti.dicom2nifti)
 main.add_command(selectslicefromscans.selectslicefromscans)
+main.add_command(createdicomsummary.createdicomsummary)
 main.add_command(show_doc_command(main)) # Special command to show long description for command

mosamatic2/commands/createdicomsummary.py

@@ -0,0 +1,61 @@
+import click
+
+from mosamatic2.core.tasks import CreateDicomSummaryTask
+
+
+@click.command(help='Creates a DICOM summary inside a root directory')
+@click.option(
+    '--directory', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Root directory with DICOM images (can be multiple scans)',
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def createdicomsummary(directory, output, overwrite):
+    """
+    Creates a DICOM summary inside a root directory. Each patient should have
+    its own directory. Inside each patient's directory, there can be multiple
+    scans (called series) and multiple DICOM files per scan. The output of this
+    command is a file summary.txt (stored in the output directory) that contains
+    the following information:
+
+    - A list of patient directory names with the number of scans inside each
+      patient directory
+    - For each patient directory and scan directory the following information:
+        - Nr. of DICOM images in the scan
+        - Modality (e.g., CT or MRI)
+        - Image type (e.g., for Dixon scans can be in-phase, opposite-phase, 
+          water or fat images)
+        - Rows/columns (size of the images)
+        - Pixel spacing (size of each pixel in mm^2)
+        - Slice thickness: (thickness of each image slice)
+
+    Parameters
+    ----------
+    --directory : str
+        Root directory with patient directories, scans and DICOM images
+
+    --output : str
+        Path to output directory
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = CreateDicomSummaryTask(
+        inputs={'directory': directory},
+        params=None,
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2/core/data/dicomimage.py

@@ -4,15 +4,24 @@ from mosamatic2.core.utils import (
     load_dicom,
     is_jpeg2000_compressed,
 )
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
 
 
 class DicomImage(FileData):
     def load(self):
         if self.path():
-            if is_dicom(self.path()):
-                p = load_dicom(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/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/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/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/server.py

@@ -7,6 +7,7 @@ from mosamatic2.core.tasks import CalculateScoresTask
 from mosamatic2.core.tasks import CreatePngsFromSegmentationsTask
 from mosamatic2.core.tasks import Dicom2NiftiTask
 from mosamatic2.core.tasks import SelectSliceFromScansTask
+from mosamatic2.core.tasks import CreateDicomSummaryTask
 
 app = Flask(__name__)
 
@@ -122,6 +123,21 @@ def run_selectslicefromscans():
     return 'PASSED'
 
 
+@app.route('/createdicomsummary')
+def run_createdicomsummary():
+    directory = request.args.get('directory')
+    output = request.args.get('output')
+    overwrite = request.args.get('overwrite', default=True, type=bool)
+    task = CreateDicomSummaryTask(
+        inputs={'directory': directory},
+        params=None,
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()
+    return 'PASSED'
+
+
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('--port', type=int, default=constants.MOSAMATIC2_SERVER_PORT)

mosamatic2/ui/resources/VERSION

@@ -1 +1 @@
-2.0.7 
+2.0.9 

{mosamatic2-2.0.7.dist-info → mosamatic2-2.0.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.7
+Version: 2.0.9
 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)

{mosamatic2-2.0.7.dist-info → mosamatic2-2.0.9.dist-info}/RECORD

@@ -1,9 +1,10 @@
 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=RTogXBXiYW_EDTmnX7TXx2T22Yth_1AwLFiJP2IUDMc,1289
+mosamatic2/cli.py,sha256=kqLdLCZCA7-xxgOOWohsCCrD6Jz3MamslmCl-41R2rA,1371
 mosamatic2/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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/dicom2nifti.py,sha256=4hMvglxdOid7p7P_Jc-Tudsf93JRMlYaQsEQctLq2d4,1015
 mosamatic2/commands/rescaledicomimages.py,sha256=25QdCzB5s0sRwkTb3o5zco2bIwy6LttNf7i97kGBDYQ,1280
@@ -12,7 +13,7 @@ mosamatic2/commands/selectslicefromscans.py,sha256=3398PM2uBcxF6wpb0-c-Itp_qxoAx
 mosamatic2/constants.py,sha256=MVYMwO-x2jQSN37o3zNkRseVQ1nYRA3mLv3v_Q0Mlds,1284
 mosamatic2/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/core/data/__init__.py,sha256=j9iGqUTJlGF0N0gPrzzpe_Dhv0Bj9c6FdQ1g7U-_j2g,298
-mosamatic2/core/data/dicomimage.py,sha256=jv1KIZBgN3SFjqgjXcPG_cx23RPauJ2TF1CzA9vj3Z8,484
+mosamatic2/core/data/dicomimage.py,sha256=e4n-xw5FP_bmvjgPUSg_wPDkByYscaEm3TWAzjd935Y,786
 mosamatic2/core/data/dicomimageseries.py,sha256=OZkNi15crL8nEA-PGYsM0k9NMi2mMHRvDRePr_-czvA,849
 mosamatic2/core/data/dixonseries.py,sha256=kq9fy65MSM2XwiScqp7b3rQ09JmpyGwbG6ldZsuPRrM,516
 mosamatic2/core/data/filedata.py,sha256=hCnpizGqOpxzIADJkDS2_NSmKVLL1u49TYjSJE5UXQo,515
@@ -24,14 +25,14 @@ mosamatic2/core/managers/logmanager.py,sha256=NEaXvhl0aILjBbK710GaWanVuuNvB51HpH
 mosamatic2/core/managers/logmanagerlistener.py,sha256=Gaig07yjBnyQq9I8sN85olTEeDCDyCFQnEJdwzvmgvc,99
 mosamatic2/core/pipelines/__init__.py,sha256=Esb4TQFvY2soU2dfQPgVlhfTx1LdxYrPBiuAKDosHqA,85
 mosamatic2/core/pipelines/defaultpipeline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mosamatic2/core/pipelines/defaultpipeline/defaultpipeline.py,sha256=EUblRhLZXhslz9bdBmx8v9yjpgOdsHviqQZ5elK8gNQ,2901
+mosamatic2/core/pipelines/defaultpipeline/defaultpipeline.py,sha256=Bme0r_shnrllWYCYDNc6cLM2fQC2yD8RJKpRdoh_6Uc,3077
 mosamatic2/core/pipelines/pipeline.py,sha256=mRxKXLKwgKDpc8R9mCI6gDKGJ2lKVxRQ__Sf0Mfn_Qc,384
 mosamatic2/core/singleton.py,sha256=FV0k_LlOCmFhlWN6gf1c2x7YXWyd8-7DsIMvOKrI6NY,224
 mosamatic2/core/tasks/__init__.py,sha256=w03AyCk2BQ6gGPBEKhtad6lt9WuwHC-nMztv7wQNwb4,759
 mosamatic2/core/tasks/calculatescorestask/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/core/tasks/calculatescorestask/calculatescorestask.py,sha256=jEbogrEnEtMbmfQ8KOGSUdGMhdeX69Bv01-82faRIlY,6617
 mosamatic2/core/tasks/createdicomsummarytask/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mosamatic2/core/tasks/createdicomsummarytask/createdicomsummarytask.py,sha256=TebP3bI_TAUa93mp5XtnPW5NSVFMvbvb-CQAQnh6RfY,2932
+mosamatic2/core/tasks/createdicomsummarytask/createdicomsummarytask.py,sha256=kcdwIBnoAXexok2j6_tF_s6gwvn2DvjLwe_VhdODpbM,2957
 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
@@ -44,15 +45,15 @@ mosamatic2/core/tasks/segmentmusclefatl3tensorflowtask/segmentmusclefatl3tensorf
 mosamatic2/core/tasks/selectslicefromscanstask/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/core/tasks/selectslicefromscanstask/selectslicefromscanstask.py,sha256=1a_QHcIdS4VB39cNEBniaaDzUx3k8DcR0wCtdr8G1d0,4586
 mosamatic2/core/tasks/task.py,sha256=APPnid6dpSGkPuDqU1vm2RIMR5vkpvbP1CPHUMjympg,1691
-mosamatic2/core/utils.py,sha256=zh44FNOWxNKuZ4FcM7VIfMvdlzOr4AA8_PJ1r-6_83k,10855
-mosamatic2/server.py,sha256=jiUc7-aFaDMSY2hg6BhMC9C2FU4V2OrMBSoiIAP8Zcs,4158
+mosamatic2/core/utils.py,sha256=iib_o_dD4hnqGIgOxLOfvMFOqLZOpt0iT_8Oarkmdjs,11723
+mosamatic2/server.py,sha256=-cZ9BPsZUXoINKqwhCHN8c59mlvzzDXzTVxsYt9au70,4644
 mosamatic2/ui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/ui/mainwindow.py,sha256=nV9RqqSZVoVbU2opJIk7E3n4GvZWtuDETxmzwzmx4mg,13099
 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=KwH-299m3oBSV3-QDLRQdLqL7fYkxUJhV8qlxIIJb74,8
+mosamatic2/ui/resources/VERSION,sha256=GK-SWujODPcbTcVr82R22iPUlrjhCG6gyHU--L4NyBQ,8
 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
@@ -84,7 +85,7 @@ 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
-mosamatic2-2.0.7.dist-info/entry_points.txt,sha256=MCUpKkgbej1clgp8EqlLQGs0BIKwGPcBPiVWLfGz9Gw,126
-mosamatic2-2.0.7.dist-info/METADATA,sha256=aX9U18Z7h4eR4CR3bRliqeGp8VIwSiBGvw9d42MpowU,1467
-mosamatic2-2.0.7.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-mosamatic2-2.0.7.dist-info/RECORD,,
+mosamatic2-2.0.9.dist-info/entry_points.txt,sha256=MCUpKkgbej1clgp8EqlLQGs0BIKwGPcBPiVWLfGz9Gw,126
+mosamatic2-2.0.9.dist-info/METADATA,sha256=ghYgnAGDjhsgKeX6PpcMuQ_Dr2ZkEI4HMXkMXBRpLW8,1489
+mosamatic2-2.0.9.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+mosamatic2-2.0.9.dist-info/RECORD,,