dbdicom 0.3.0__py3-none-any.whl → 0.3.1__py3-none-any.whl

dbdicom/api.py

@@ -24,6 +24,7 @@ def print(path):
     """
     dbd = open(path)
     dbd.print()
+    dbd.close()
 
 
 def summary(path) -> dict:
@@ -36,7 +37,9 @@ def summary(path) -> dict:
         dict: Nested dictionary with summary information on the database.
     """
     dbd = open(path)
-    return dbd.summary()
+    s = dbd.summary()
+    dbd.close()
+    return s
 
 
 def patients(path, name:str=None, contains:str=None, isin:list=None)->list:
@@ -56,7 +59,9 @@ def patients(path, name:str=None, contains:str=None, isin:list=None)->list:
         list: list of patients fulfilling the criteria.
     """
     dbd = open(path)
-    return dbd.patients(name, contains, isin)
+    p = dbd.patients(name, contains, isin)
+    dbd.close()
+    return p
 
 
 def studies(entity:str | list, name:str=None, contains:str=None, isin:list=None)->list:
@@ -79,10 +84,14 @@ def studies(entity:str | list, name:str=None, contains:str=None, isin:list=None)
     """
     if isinstance(entity, str): # path = folder
         dbd = open(entity)
-        return dbd.studies(entity, name, contains, isin)
+        s = dbd.studies(entity, name, contains, isin)
+        dbd.close()
+        return s
     elif len(entity)==2: # path = patient
         dbd = open(entity[0])
-        return dbd.studies(entity, name, contains, isin)
+        s = dbd.studies(entity, name, contains, isin)
+        dbd.close()
+        return s
     else:
         raise ValueError(
             "The path must be a folder or a 2-element list "
@@ -110,10 +119,14 @@ def series(entity:str | list, name:str=None, contains:str=None, isin:list=None)-
     """
     if isinstance(entity, str): # path = folder
         dbd = open(entity)
-        return dbd.series(entity, name, contains, isin)
+        s = dbd.series(entity, name, contains, isin)
+        dbd.close()
+        return s
     elif len(entity) in [2,3]:
         dbd = open(entity[0])
-        return dbd.series(entity, name, contains, isin)
+        s = dbd.series(entity, name, contains, isin)
+        dbd.close()
+        return s
     else:
         raise ValueError(
             "To retrieve a series, the entity must be a database, patient or study."
@@ -168,7 +181,9 @@ def volume(series:list, dims:list=None, multislice=False) -> vreg.Volume3D:
         vreg.Volume3D: vole read from the series.
     """
     dbd = open(series[0])
-    return dbd.volume(series, dims, multislice)
+    vol = dbd.volume(series, dims, multislice)
+    dbd.close()
+    return vol
 
 def write_volume(vol:vreg.Volume3D, series:list, ref:list=None, 
                  multislice=False):
@@ -200,6 +215,7 @@ def to_nifti(series:list, file:str, dims:list=None, multislice=False):
     """
     dbd = open(series[0])
     dbd.to_nifti(series, file, dims, multislice)
+    dbd.close()
 
 def from_nifti(file:str, series:list, ref:list=None, multislice=False):
     """Create a DICOM series from a nifti file.
@@ -232,7 +248,9 @@ def pixel_data(series:list, dims:list=None, include:list=None) -> tuple:
             return value.
     """
     dbd = open(series[0])
-    return dbd.pixel_data(series, dims, include)
+    array = dbd.pixel_data(series, dims, include)
+    dbd.close()
+    return array
 
 # write_pixel_data()
 # values()
@@ -255,7 +273,9 @@ def unique(pars:list, entity:list) -> dict:
         dict: dictionary with unique values for each attribute.
     """
     dbd = open(entity[0])
-    return dbd.unique(pars, entity)
+    u = dbd.unique(pars, entity)
+    dbd.close()
+    return u
 
 
 

dbdicom/dataset.py

@@ -1,3 +1,6 @@
+# Test data
+# https://www.aliza-dicom-viewer.com/download/datasets
+
 import os
 from datetime import datetime
 import struct
@@ -712,41 +715,7 @@ def set_signal_type(ds, value):
 
 
 
+if __name__=='__main__':
 
-# def _initialize(ds, UID=None, ref=None): # ds is pydicom dataset
-
-#     # Date and Time of Creation
-#     dt = datetime.now()
-#     timeStr = dt.strftime('%H%M%S')  # long format with micro seconds
-
-#     ds.ContentDate = dt.strftime('%Y%m%d')
-#     ds.ContentTime = timeStr
-#     ds.AcquisitionDate = dt.strftime('%Y%m%d')
-#     ds.AcquisitionTime = timeStr
-#     ds.SeriesDate = dt.strftime('%Y%m%d')
-#     ds.SeriesTime = timeStr
-#     ds.InstanceCreationDate = dt.strftime('%Y%m%d')
-#     ds.InstanceCreationTime = timeStr
-
-#     if UID is not None:
-
-#         # overwrite UIDs
-#         ds.PatientID = UID[0]
-#         ds.StudyInstanceUID = UID[1]
-#         ds.SeriesInstanceUID = UID[2]
-#         ds.SOPInstanceUID = UID[3]
-
-#     if ref is not None: 
-
-#         # Series, Instance and Class for Reference
-#         refd_instance = Dataset()
-#         refd_instance.ReferencedSOPClassUID = ref.SOPClassUID
-#         refd_instance.ReferencedSOPInstanceUID = ref.SOPInstanceUID
-
-#         refd_series = Dataset()
-#         refd_series.ReferencedInstanceSequence = Sequence([refd_instance])
-#         refd_series.SeriesInstanceUID = ds.SeriesInstanceUID
-
-#         ds.ReferencedSeriesSequence = Sequence([refd_series])
-
-#     return ds
+    pass
+    #codify('C:\\Users\\md1spsx\\Documents\\f32bit.dcm', 'C:\\Users\\md1spsx\\Documents\\f32bit.py')

dbdicom/dbd.py

@@ -343,26 +343,38 @@ class DataBaseDicom():
         self.write_volume(vol, series, ref, multislice)
         return self
     
-    def pixel_data(self, series:list, dims:list=None, include=None) -> np.ndarray:
+    def pixel_data(self, series:list, dims:list=None, coords=False, include=None) -> np.ndarray:
         """Read the pixel data from a DICOM series
 
         Args:
             series (list): DICOM series to read
             dims (list, optional): Dimensions of the array.
+            coords (bool): If set to Trye, the coordinates of the 
+                arrays are returned alongside the pixel data
             include (list, optional): list of DICOM attributes that are 
                 read on the fly to avoid reading the data twice.
 
         Returns:
-            tuple: numpy array with pixel values and an array with 
+            numpy.ndarray or tuple: numpy array with pixel values, with 
+                at least 3 dimensions (x,y,z). If 
+                coords is set these are returned too as an array with 
                 coordinates of the slices according to dims. If include 
-                is provide these are returned as a dictionary in a third 
+                is provide the values are returned as a dictionary in the last 
                 return value.
         """
+        if coords:
+            if dims is None:
+                raise ValueError(
+                    "Coordinates can only be returned if dimensions are specified."
+                )
 
-        if np.isscalar(dims):
+        if dims is None:
+            dims = []
+        elif np.isscalar(dims):
             dims = [dims]
         else:
             dims = list(dims)
+        dims = ['SliceLocation'] + dims
 
         # Ensure return_vals is a list
         if include is None:
@@ -375,34 +387,40 @@ class DataBaseDicom():
         files = register.files(self.register, series)
         
         # Read dicom files
-        coords = []
+        coords_array = []
         arrays = np.empty(len(files), dtype=dict)
         if include is not None:
             values = np.empty(len(files), dtype=dict)
         for i, f in tqdm(enumerate(files), desc='Reading pixel data..'):
             ds = dbdataset.read_dataset(f)  
-            coords.append(dbdataset.get_values(ds, dims))
+            coords_array.append(dbdataset.get_values(ds, dims))
             # save as dict so numpy does not stack as arrays
             arrays[i] = {'pixel_data': dbdataset.pixel_data(ds)}
             if include is not None:
                 values[i] = {'values': dbdataset.get_values(ds, params)}
 
         # Format as mesh
-        coords = np.stack([v for v in coords], axis=-1)
-        coords, inds = dbdicom.utils.arrays.meshvals(coords)
+        coords_array = np.stack([v for v in coords_array], axis=-1)
+        coords_array, inds = dbdicom.utils.arrays.meshvals(coords_array)
 
-        arrays = arrays[inds].reshape(coords.shape[1:])
+        arrays = arrays[inds].reshape(coords_array.shape[1:])
         arrays = np.stack([a['pixel_data'] for a in arrays.reshape(-1)], axis=-1)
-        arrays = arrays.reshape(arrays.shape[:2] + coords.shape[1:])
+        arrays = arrays.reshape(arrays.shape[:2] + coords_array.shape[1:])
 
         if include is None:
-            return arrays, coords
+            if coords:
+                return arrays, coords_array[1:,...]
+            else:
+                return arrays
         
-        values = values[inds].reshape(coords.shape[1:])
+        values = values[inds].reshape(coords_array.shape[1:])
         values = np.stack([a['values'] for a in values.reshape(-1)], axis=-1)
-        values = values.reshape((len(params), ) + coords.shape[1:])
+        values = values.reshape((len(params), ) + coords_array.shape[1:])
 
-        return arrays, coords, values
+        if coords:
+            return arrays, coords_array[1:,...], values
+        else:
+            return arrays, values
     
     
     def unique(self, pars:list, entity:list) -> dict:
@@ -695,8 +713,7 @@ class DataBaseDicom():
         """
         # For each series, check if there are multiple
         # SOP Classes in the series and split them if yes.
-        all_series = self.series()
-        for series in tqdm(all_series, desc='Splitting series with multiple SOP Classes.'):
+        for series in self.series():
             series_index = register.index(self.register, series)
             df_series = self.register.loc[series_index]
             sop_classes = df_series.SOPClassUID.unique()
@@ -704,7 +721,7 @@ class DataBaseDicom():
                 # For each sop_class, create a new series and move all
                 # instances of that sop_class to the new series
                 desc = series[-1] if isinstance(series, str) else series[0]
-                for i, sop_class in enumerate(sop_classes[1:]):
+                for i, sop_class in tqdm(enumerate(sop_classes[1:]), desc='Splitting series with multiple SOP Classes.'):
                     df_sop_class = df_series[df_series.SOPClassUID == sop_class]
                     relpaths = df_sop_class.index.tolist()
                     sop_class_files = [os.path.join(self.path, p) for p in relpaths]

dbdicom/sop_classes/parametric_map.py

@@ -6,6 +6,9 @@ from pydicom.uid import generate_uid, ParametricMapStorage
 from datetime import datetime
 
 
+def from_volume(vol):
+    pass
+
 
 def create_parametric_map(rows=64, cols=64, frames=1):
     # Create dummy pixel data (floating point)
@@ -57,7 +60,7 @@ def create_parametric_map(rows=64, cols=64, frames=1):
     ds.HighBit = 31
     ds.PixelRepresentation = 1  # 1 = signed, 0 = unsigned
     ds.FloatPixelData = pixel_array.astype(np.float32).tobytes()
-    ds.PixelData = b''  # Actual data goes in FloatPixelData
+    ds.PixelData = b"\0" * rows * cols * frames  # Actual data goes in FloatPixelData
 
     # Functional Group Sequences (minimal dummy values)
     ds.SharedFunctionalGroupsSequence = [Dataset()]

{dbdicom-0.3.0.dist-info → dbdicom-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dbdicom
-Version: 0.3.0
+Version: 0.3.1
 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-0.3.0.dist-info → dbdicom-0.3.1.dist-info}/RECORD

@@ -1,20 +1,20 @@
 dbdicom/__init__.py,sha256=DyogeTraV6o-FgWdBCbtVEaMmdkMQHkYkraDIE0t8OA,25
-dbdicom/api.py,sha256=_baV2dR9Szay4z2_JY-QmTB9gTTc_PB7OzzgqRwmYHg,8945
+dbdicom/api.py,sha256=sxQYjNu4q0gGAQ5jcE2yCpMKJnMjniTGsqwrGSQdMsU,9275
 dbdicom/const.py,sha256=BqBiRRjeiSqDr1W6YvaayD8WKCjG4Cny2NT0GeLM6bI,4269
-dbdicom/dataset.py,sha256=IVTLq4pTydwKjS9-xCQAqiSd0Xm63JxCxos4HemtuVs,23945
-dbdicom/dbd.py,sha256=MKZDnQu1R0s1RlJ5VAKcty4UFmtMg6aXz9epjLilYzc,29001
+dbdicom/dataset.py,sha256=fPKemmsJSaoyZHO-xdxvVtd4Rlh5m6rR63YkKuIFYAo,22874
+dbdicom/dbd.py,sha256=Y4BMR9QATz1Y4HhvPOw-pB8ps4D7Z8584PKOJQE9tzM,29768
 dbdicom/register.py,sha256=Nt-Q3Nvb72qRqSL1ervuunp2LBuOZEs-K8YUqihR_oQ,21210
 dbdicom/external/__init__.py,sha256=XNQqfspyf6vFGedXlRKZsUB8k8E-0W19Uamwn8Aioxo,316
-dbdicom/external/__pycache__/__init__.cpython-311.pyc,sha256=tvFkDCXniSXAqkZTFggZPxaPTVgaRmpeGYZlZw0Ibhc,534
+dbdicom/external/__pycache__/__init__.cpython-311.pyc,sha256=cIySrImYKo1fJP3-0ZMV-5ZKcZEEDX-uwfZ7I4U-jRs,534
 dbdicom/external/dcm4che/README.md,sha256=0aAGRs36W3_0s5LzWHRGf_tqariS_JP4iJggaxnD4Xw,8987
 dbdicom/external/dcm4che/__init__.py,sha256=YwpeMCLrxffGOkchsGjgAuB6ia3VX_tx9Y7ru9EWtoY,35
-dbdicom/external/dcm4che/__pycache__/__init__.cpython-311.pyc,sha256=qbKEVGsXw9bmCxsR6KssmR3ZoGJAkkVv5LQ2eFVhs5M,248
+dbdicom/external/dcm4che/__pycache__/__init__.cpython-311.pyc,sha256=QsnVh0zH1ZSOoNwtTqiirWH8CB0b2eJ0DEvgVoVhZ0Y,248
 dbdicom/external/dcm4che/bin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dbdicom/external/dcm4che/bin/deidentify,sha256=64MNIEpp-CWzFSb6TV0KtyCBvD7XyEsovRjBeyxDqSc,1698
 dbdicom/external/dcm4che/bin/deidentify.bat,sha256=kVXUkcy1C4Y3KjC2NJwmmR0pufSJWmaof_LR5CTAxMg,1455
 dbdicom/external/dcm4che/bin/emf2sf,sha256=svCzkZ-QhdVTV0NNHOpBiwNBMODVWZHJIFA7cWaN2bM,1622
 dbdicom/external/dcm4che/bin/emf2sf.bat,sha256=Vh0ry9KNJX_WXcyCrLSxbJ_6Crot9rjmwi__u2GZqLY,1375
-dbdicom/external/dcm4che/bin/__pycache__/__init__.cpython-311.pyc,sha256=NnB9_qHwjxDZrdid-_YGOWCzkEy8p9ka3FHiCUtFX-M,195
+dbdicom/external/dcm4che/bin/__pycache__/__init__.cpython-311.pyc,sha256=M2mla4vNW1gSUWQps3dx4g8NRd4BaQJLP1OKQHmi6Sk,195
 dbdicom/external/dcm4che/etc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dbdicom/external/dcm4che/etc/emf2sf/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dbdicom/external/dcm4che/etc/emf2sf/log4j.properties,sha256=3hHcBFt2oNRjvHtix5bfuEsnKfdv5IYOkbsyoY9g7cM,223
@@ -36,7 +36,7 @@ dbdicom/external/dcm4che/lib/windows-x86-64/opencv_java.dll,sha256=TmjW2SbG4MR3G
 dbdicom/sop_classes/ct_image.py,sha256=16PNv_0e1_7cfxE12JWlx5YQeaTAQVzwtXTjxs3aonk,2812
 dbdicom/sop_classes/enhanced_mr_image.py,sha256=13j4EGXniBpJxpzzL3Xa4y3g5OKhMd5Ct7cjPGOYQY4,35496
 dbdicom/sop_classes/mr_image.py,sha256=6V2OyjwkaZxoljImNREU0Du4NJLHHsY_GgOe2XQsmNg,10683
-dbdicom/sop_classes/parametric_map.py,sha256=eyJdHUxh9KUI7qPaGANU2H3R1Br4CH0XHmRIGvrsKY8,10220
+dbdicom/sop_classes/parametric_map.py,sha256=ayNMpeBbc-neVGDjEAe5ww_UYJvbRmk46rHa_CjwZao,10280
 dbdicom/sop_classes/secondary_capture.py,sha256=wgNRX8qyhV7HR7Jq2tQWPPuGpiRzYl6qPOgK6qFbPUc,4541
 dbdicom/sop_classes/segmentation.py,sha256=I8-PciIoIz27_-dZ4esBZSw0TBBbO8KbNYTiTmVe62g,11465
 dbdicom/sop_classes/ultrasound_multiframe_image.py,sha256=j3KN5R90j6WwPMy01hAN2_XSum5TvksF2MYoNGfX_yE,2797
@@ -46,8 +46,8 @@ dbdicom/utils/dcm4che.py,sha256=Vxq8NYWWK3BuqJkzhBQ89oMqzJlnxqTxgsgTo_Frznc,2317
 dbdicom/utils/files.py,sha256=qhWNJqeWnRjDNbERpC6Mz962_TW9mFdvd2lnBbK3xt4,2259
 dbdicom/utils/image.py,sha256=s1P8m-s64ygKSh_X4DdV96LC4DvCe3KO3_71l72zWoU,4057
 dbdicom/utils/variables.py,sha256=vUh5cDnmCft5hoXDYXUvfkg5Cy5WlgMAogU38Y_BKRo,5753
-dbdicom-0.3.0.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
-dbdicom-0.3.0.dist-info/METADATA,sha256=0NHxTTJitzp6e80Ly6NFWNsAepbjRTQWsBk0L-FqsbE,1075
-dbdicom-0.3.0.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
-dbdicom-0.3.0.dist-info/top_level.txt,sha256=nJWxXg4YjD6QblfmhrzTMXcr8FSKNc0Yk-CAIDUsYkQ,8
-dbdicom-0.3.0.dist-info/RECORD,,
+dbdicom-0.3.1.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
+dbdicom-0.3.1.dist-info/METADATA,sha256=97Xgzc6BE9N3ygBO59psUqmVs9TTZ9iw7o2dUMJSFfQ,1075
+dbdicom-0.3.1.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
+dbdicom-0.3.1.dist-info/top_level.txt,sha256=nJWxXg4YjD6QblfmhrzTMXcr8FSKNc0Yk-CAIDUsYkQ,8
+dbdicom-0.3.1.dist-info/RECORD,,