#148:

Make compatible with pydicom >= 3.0.0

dicom2nifti/common.py

@@ -11,6 +11,7 @@
 
 import numpy
 import pydicom
+from pydicom import dcmread
 from pydicom.tag import Tag
 
 import dicom2nifti.settings
@@ -36,7 +37,7 @@ def read_dicom_directory(dicom_directory, stop_before_pixels=False):
         for dicom_file in files:
             file_path = os.path.join(root, dicom_file)
             if is_dicom_file(file_path):
-                dicom_headers = pydicom.read_file(file_path,
+                dicom_headers = dcmread(file_path,
                                                   defer_size="1 KB",
                                                   stop_before_pixels=stop_before_pixels,
                                                   force=dicom2nifti.settings.pydicom_read_force)
@@ -1161,7 +1162,7 @@ def is_dicom_file(filename):
         return True
     if dicom2nifti.settings.pydicom_read_force:
         try:
-            dicom_headers = pydicom.read_file(filename, defer_size="1 KB", stop_before_pixels=True, force=True)
+            dicom_headers = dcmread(filename, defer_size="1 KB", stop_before_pixels=True, force=True)
             if dicom_headers is not None:
                 return True
         except:

dicom2nifti/convert_dicom.py

@@ -11,6 +11,7 @@
 import tempfile
 
 import pydicom
+from pydicom import dcmread
 from pydicom.tag import Tag
 
 import dicom2nifti.common as common
@@ -199,7 +200,7 @@ def _get_first_header(dicom_directory):
             if not common.is_dicom_file(file_path):
                 continue
             # read the headers
-            return pydicom.read_file(file_path,
+            return dcmread(file_path,
                                      stop_before_pixels=True,
                                      force=dicom2nifti.settings.pydicom_read_force)
     # no dicom files found

dicom2nifti/convert_dir.py

@@ -12,6 +12,7 @@
 import unicodedata
 
 import pydicom
+from pydicom import dcmread
 from pydicom.tag import Tag
 
 import dicom2nifti.common as common
@@ -41,7 +42,7 @@ def convert_directory(dicom_directory, output_folder, compression=True, reorient
                     # read the dicom as fast as possible
                     # (max length for SeriesInstanceUID is 64 so defer_size 100 should be ok)
 
-                    dicom_headers = pydicom.read_file(file_path,
+                    dicom_headers = dcmread(file_path,
                                                       defer_size="1 KB",
                                                       stop_before_pixels=False,
                                                       force=dicom2nifti.settings.pydicom_read_force)

scripts/anonymize_testdata.py

@@ -12,6 +12,7 @@
 import pydicom
 import pydicom.dataset
 import pydicom.uid
+from pydicom import dcmread
 
 import common
 from dicom2nifti.common import read_dicom_directory, is_philips, is_siemens, is_ge
@@ -132,7 +133,7 @@ def _anonymize_file(dicom_file_in, dicom_file_out, fields_to_keep):
                    'ImplementationClassUID']
 
     # Load dicom_file_in
-    dicom_in = pydicom.read_file(dicom_file_in)
+    dicom_in = dcmread(dicom_file_in)
 
     # Create new dicom file
     # Set new file meta information

scripts/debug_directory.py

@@ -34,7 +34,7 @@ def run_convert_directory2():
     tmp_output_dir = tempfile.mkdtemp()
     try:
         import pydicom
-        # headers = pydicom.read_file("/Users/abrys/Downloads/failing_cases/test.dcm")
+        # headers = dcmread("/Users/abrys/Downloads/failing_cases/test.dcm")
         convert_directory.convert_directory("/Users/abrys/Downloads/dti",
                                             "/Users/abrys/Downloads/dti")
 

scripts/dicomdiff.py

@@ -7,6 +7,7 @@
 import sys
 
 import pydicom
+from pydicom import dcmread
 
 
 def dicom_diff(file1, file2):
@@ -15,7 +16,7 @@ def dicom_diff(file1, file2):
     Inspired by https://code.google.com/p/pydicom/source/browse/source/dicom/examples/DicomDiff.py
     """
 
-    datasets = pydicom.read_file(file1), pydicom.read_file(file2)
+    datasets = dcmread(file1), dcmread(file2)
 
     rep = []
 

scripts/shrink_multiframe.py

@@ -9,6 +9,7 @@
 
 import numpy
 import pydicom
+from pydicom import dcmread
 
 import dicom2nifti.common as common
 from dicom2nifti.convert_philips import _is_multiframe_diffusion_imaging, _is_multiframe_4d
@@ -19,7 +20,7 @@ def shrink_multiframe(input_file, output_file=None, slice_count=8, timepoint_cou
         output_file = input_file
 
     # Load dicom_file_in
-    dicom_in = pydicom.read_file(input_file)
+    dicom_in = dcmread(input_file)
 
     if _is_multiframe_diffusion_imaging([dicom_in]) or _is_multiframe_4d([dicom_in]):
 

scripts/shrink_singleframe.py

@@ -9,6 +9,7 @@
 
 import pydicom
 import pydicom.dataset
+from pydicom import dcmread
 
 
 def _shrink_file(dicom_file_in, subsample_factor):
@@ -24,7 +25,7 @@ def _shrink_file(dicom_file_in, subsample_factor):
     dicom_file_out = dicom_file_in
 
     # Load dicom_file_in
-    dicom_in = pydicom.read_file(dicom_file_in)
+    dicom_in = dcmread(dicom_file_in)
 
     # Create new dicom file
     # Set new file meta information

tests/test_siemens.py

@@ -12,6 +12,7 @@
 import nibabel
 import numpy
 import pydicom
+from pydicom import dcmread
 
 import dicom2nifti.common as common
 import dicom2nifti.convert_siemens as convert_siemens
@@ -199,7 +200,7 @@ def test_is_siemens(self):
         assert not common.is_siemens(read_dicom_directory(test_data.HITACHI_ANATOMICAL))
 
     def test_get_asconv_headers(self):
-        mosaic = pydicom.read_file(os.path.join(test_data.SIEMENS_FMRI, 'IM-0001-0001.dcm'))
+        mosaic = dcmread(os.path.join(test_data.SIEMENS_FMRI, 'IM-0001-0001.dcm'))
         asconv_headers = convert_siemens._get_asconv_headers(mosaic)
         assert len(asconv_headers) == 64022