dbdicom 0.3.12__tar.gz → 0.3.13__tar.gz

{dbdicom-0.3.12/src/dbdicom.egg-info → dbdicom-0.3.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dbdicom
-Version: 0.3.12
+Version: 0.3.13
 Summary: A pythonic interface for reading and writing DICOM databases
 Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>, Ebony Gunwhy <e.gunwhy@sheffield.ac.uk>
 Project-URL: Homepage, https://openmiblab.github.io/dbdicom/

{dbdicom-0.3.12 → dbdicom-0.3.13}/pyproject.toml

@@ -7,7 +7,7 @@ requires = ['setuptools>=61.2']
 
 [project]
 name = "dbdicom"
-version = "0.3.12"
+version = "0.3.13"
 dependencies = [ 
     "tqdm",
     "importlib-resources",

{dbdicom-0.3.12 → dbdicom-0.3.13}/src/dbdicom/dataset.py

@@ -85,8 +85,8 @@ def write(ds, file, status=None):
     dir = os.path.dirname(file)
     if not os.path.exists(dir):
         os.makedirs(dir)
-    ds.save_as(file, write_like_original=False) # deprecated
-    # ds.save_as(file, enforce_file_format=True)
+    # ds.save_as(file, write_like_original=False) # deprecated
+    pydicom.dcmwrite(file, ds, enforce_file_format=True)
 
 
 def codify(source_file, save_file, **kwargs):

{dbdicom-0.3.12 → dbdicom-0.3.13}/src/dbdicom/dbd.py

@@ -70,8 +70,6 @@ class DataBaseDicom():
         # self._split_series()
         return self
 
-    
-
     def delete(self, entity, not_exists_ok=False):
         """Delete a DICOM entity from the database
 
@@ -729,7 +727,7 @@ class DataBaseDicom():
                 else:
                     to_entity[-1] = (to_entity[-1] + '_copy', 0)
                 while to_entity in self.series():
-                    to_entity[-1][1] += 1
+                    to_entity[-1] = (to_entity[-1][0], to_entity[-1][1] + 1)
             if len(to_entity) != 4:
                 raise ValueError(
                     f"Cannot copy series {from_entity} to series {to_entity}. "

{dbdicom-0.3.12 → dbdicom-0.3.13}/src/dbdicom/register.py

@@ -79,6 +79,7 @@ def index(dbtree, entity):
                     for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']):
                         idx += list(sr['instances'].values())
                 return idx
+        raise ValueError(f'Patient {patient_id} not found')
     elif len(entity)==3:
         study_uid = uid(dbtree, entity)
         idx = []
@@ -88,6 +89,7 @@ def index(dbtree, entity):
                     for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']):
                         idx += list(sr['instances'].values())
                     return idx
+        raise ValueError(f'Study {study_uid} not found')
     elif len(entity)==4:
         series_uid = uid(dbtree, entity)
         for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
@@ -95,6 +97,7 @@ def index(dbtree, entity):
                 for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']):
                     if sr['SeriesInstanceUID'] == series_uid:
                         return list(sr['instances'].values())
+        raise ValueError(f'Series {series_uid} not found')
                     
 def remove(dbtree, entity):
     if len(entity)==2:

{dbdicom-0.3.12 → dbdicom-0.3.13/src/dbdicom.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dbdicom
-Version: 0.3.12
+Version: 0.3.13
 Summary: A pythonic interface for reading and writing DICOM databases
 Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>, Ebony Gunwhy <e.gunwhy@sheffield.ac.uk>
 Project-URL: Homepage, https://openmiblab.github.io/dbdicom/

{dbdicom-0.3.12 → dbdicom-0.3.13}/src/dbdicom.egg-info/SOURCES.txt

@@ -58,5 +58,6 @@ src/dbdicom/utils/image.py
 src/dbdicom/utils/pydicom_dataset.py
 tests/test_api.py
 tests/test_dcm4che.py
+tests/test_mt.py
 tests/test_sop_classes.py
 tests/test_utils.py

dbdicom-0.3.13/tests/test_mt.py

@@ -0,0 +1,39 @@
+import os
+import shutil
+import numpy as np
+import dbdicom as db
+import vreg
+
+
+tmp = os.path.join(os.getcwd(), 'tests', 'tmp')
+os.makedirs(tmp, exist_ok=True)
+shutil.rmtree(tmp)
+os.makedirs(tmp, exist_ok=True)
+
+
+def test_write():
+
+    # Currently works as expected
+    values = 100*np.random.rand(256, 256, 16, 2).astype(np.float32)
+    dims = ['ScanOptions']
+    coords = (['PFP', 'PFP'], )
+    vol = vreg.volume(values, dims=dims, coords=coords, orient='coronal')
+    series = [tmp, '007', 'dbdicom_test', 'mt1']
+    db.write_volume(vol, series)
+    
+    # # Currently does not work
+    # values = 100*np.random.rand(256, 256, 16, 2).astype(np.float32)
+    # dims = ['ScanOptions']
+    # coords = (['PFP', ['PFP', 'MT']], )
+    # vol = vreg.volume(values, dims=dims, coords=coords, orient='coronal')
+    # series = [tmp, '007', 'dbdicom_test', 'mt2']
+    # db.write_volume(vol, series)
+
+    shutil.rmtree(tmp)
+
+
+if __name__ == '__main__':
+
+    test_write()
+
+    print('All mt tests have passed!!!')