mosamatic2 2.0.8__py3-none-any.whl → 2.0.9__py3-none-any.whl

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/ui/resources/VERSION

@@ -1 +1 @@
-2.0.8 
+2.0.9 

{mosamatic2-2.0.8.dist-info → mosamatic2-2.0.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.8
+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)

{mosamatic2-2.0.8.dist-info → mosamatic2-2.0.9.dist-info}/RECORD

@@ -13,7 +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
@@ -25,14 +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
@@ -45,7 +45,7 @@ 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/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
@@ -53,7 +53,7 @@ mosamatic2/ui/resources/icons/mosamatic2.icns,sha256=OfhC-diJTIgaNMOezxKKilGsY7m
 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=f8DsaK2OdoYvUiYLs5HB9QOzREusf-ClX8iflIy2nY8,8
+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
@@ -85,7 +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
-mosamatic2-2.0.8.dist-info/entry_points.txt,sha256=MCUpKkgbej1clgp8EqlLQGs0BIKwGPcBPiVWLfGz9Gw,126
-mosamatic2-2.0.8.dist-info/METADATA,sha256=qTtZHQw_rcBOIVlCFKonPY9B2rygwNLf7-IVM8UJJzw,1467
-mosamatic2-2.0.8.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-mosamatic2-2.0.8.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,,