update to allow latest version of pydicom which changed read_file to …

…dcmread

requirements.txt

@@ -4,7 +4,7 @@ opencv-python
 openpyxl
 pandas
 Pillow
-pydicom==2.4.4
+pydicom
 scikit-image
 scipy
 SimpleITK

setup.py

@@ -13,7 +13,7 @@
     name='DicomRTTool',
     author='Brian Mark Anderson',
     author_email='b5anderson@health.ucsd.edu',
-    version='2.1.9',
+    version='2.2.0',
     description='Services for reading dicom files, RT structures, and dose files, as well as tools for '
                 'converting numpy prediction masks back to an RT structure',
     long_description=long_description,

src/DicomRTTool/ReaderWriter.py

@@ -11,6 +11,10 @@
 import pydicom
 import numpy as np
 from pydicom.tag import Tag
+if hasattr(pydicom, 'read_file'):
+    dcmread_function = pydicom.read_file
+else:
+    dcmread_function = pydicom.dcmread
 import SimpleITK as sitk
 from skimage.measure import label, regionprops, find_contours
 from threading import Thread
@@ -258,7 +262,7 @@ def add_dicom_to_dictionary_from_path(self, dicom_path, images_dictionary: Dict[
         rt_files = [file for file in file_list if file not in all_names]
         for i in rt_files:
             lstRSFile = os.path.join(dicom_path, i)
-            rt = pydicom.read_file(lstRSFile)
+            rt = dcmread_function(lstRSFile)
             modality = rt.Modality
             if modality.lower().find('struct') != -1:
                 add_rt_to_dictionary(ds=rt, path=lstRSFile, rt_dictionary=rt_dictionary)
@@ -1122,7 +1126,7 @@ def get_images(self) -> None:
                 print('Loading images for {} at \n {}\n'.format(self.series_instances_dictionary[index].Description,
                                                                 self.series_instances_dictionary[index].path))
             dicom_names = self.series_instances_dictionary[index].files
-            self.ds = pydicom.read_file(dicom_names[0])
+            self.ds = dcmread_function(dicom_names[0])
             self.reader.SetFileNames(dicom_names)
             self.dicom_handle = self.reader.Execute()
             if self.verbose:
@@ -1194,7 +1198,7 @@ def get_dose(self, dose_type="PLAN") -> None:
     def __characterize_RT__(self, RT: RTBase):
         if self.RS_struct_uid != RT.SeriesInstanceUID:
             self.structure_references = {}
-            self.RS_struct = pydicom.read_file(RT.path)
+            self.RS_struct = dcmread_function(RT.path)
             self.RS_struct_uid = RT.SeriesInstanceUID
             for contour_number in range(len(self.RS_struct.ROIContourSequence)):
                 self.structure_references[
@@ -1348,7 +1352,7 @@ def use_template(self) -> None:
             if not os.path.exists(self.template_dir):
                 self.template_dir = os.path.join('..', '..', 'Shared_Drive', 'Auto_Contour_Sites', 'template_RS.dcm')
         self.key_list = self.template_dir.replace('template_RS.dcm', 'key_list.txt')
-        self.RS_struct = pydicom.read_file(self.template_dir)
+        self.RS_struct = dcmread_function(self.template_dir)
         print('Running off a template')
         self.change_template()
 
@@ -1401,7 +1405,7 @@ def prediction_array_to_RT(self, prediction_array: np.array, output_dir: typing.
         elif self.RS_struct_uid != self.series_instances_dictionary[index].SeriesInstanceUID:
             rt_structures = self.series_instances_dictionary[index].RTs
             for uid_key in rt_structures:
-                self.RS_struct = pydicom.read_file(rt_structures[uid_key].path)
+                self.RS_struct = dcmread_function(rt_structures[uid_key].path)
                 self.RS_struct_uid = self.series_instances_dictionary[index].SeriesInstanceUID
                 break
 
@@ -1607,7 +1611,7 @@ def change_template(self):
 
     def rewrite_RT(self, lstRSFile: typing.Union[str, bytes, os.PathLike] = None):
         if lstRSFile is not None:
-            self.RS_struct = pydicom.read_file(lstRSFile)
+            self.RS_struct = dcmread_function(lstRSFile)
         if Tag((0x3006, 0x020)) in self.RS_struct.keys():
             self.ROI_Structure = self.RS_struct.StructureSetROISequence
         else:

src/DicomRTTool/Services/DicomBases.py

@@ -1,5 +1,9 @@
 import typing
 import pydicom
+if hasattr(pydicom, 'read_file'):
+    dcmread_function = pydicom.read_file
+else:
+    dcmread_function = pydicom.dcmread
 from pydicom.tag import Tag, BaseTag
 import SimpleITK as sitk
 from typing import List, Dict
@@ -41,7 +45,7 @@ def __init__(self):
 
     def load_info(self, sitk_dicom_reader, sitk_string_keys: SitkDicomKeys = None):
         file_name = sitk_dicom_reader.GetFileName()
-        ds = pydicom.read_file(file_name)
+        ds = dcmread_function(file_name)
         self.SeriesInstanceUID = ds.SeriesInstanceUID
         self.DoseType = ds.DoseType
         self.DoseUnits = ds.DoseUnits
@@ -68,7 +72,7 @@ def load_info(self, sitk_dicom_reader, sitk_string_keys: SitkDicomKeys = None):
 
     def add_beam(self, sitk_dicom_reader):
         file_name = sitk_dicom_reader.GetFileName()
-        ds = pydicom.read_file(file_name)
+        ds = dcmread_function(file_name)
         if self.SeriesInstanceUID == ds.SeriesInstanceUID:
             """
             Means these are compatible beams