Support private fields in header

medio/backends/itk_io.py

@@ -23,7 +23,7 @@ class ItkIO:
 
  @staticmethod
  def read_img(input_path, desired_axcodes=None, header=False, components_axis=None, pixel_type=pixel_type,
- fallback_only=True, series=None):
+ fallback_only=True, series=None, private_tags=False):
  """
  The main reader function, reads images and performs reorientation and unpacking
  :param input_path: path of image file or directory containing dicom series
@@ -36,11 +36,18 @@ def read_img(input_path, desired_axcodes=None, header=False, components_axis=Non
  :return: numpy image and metadata object which includes pixdim, affine, original orientation string and
  coordinates system
  """
+ if private_tags:
+ imageio = itk.GDCMImageIO.New()
+ imageio.LoadPrivateTagsOn()
+ # we need to set the imageio to the reader, but with fallback_only=True it will not set it unless it fails
+ fallback_only = False
+ else:
+ imageio = None
  input_path = Path(input_path)
  if input_path.is_dir():
  img = ItkIO.read_dir(str(input_path), pixel_type, fallback_only, series=series, header=header)
  elif input_path.is_file():
- img = ItkIO.read_img_file(str(input_path), pixel_type, fallback_only)
+ img = ItkIO.read_img_file(str(input_path), pixel_type, fallback_only, imageio)
  else:
  raise FileNotFoundError(f'No such file or directory: "{input_path}"')
 
@@ -130,14 +137,15 @@ def prepare_dcm_array(image_np, is_vector=False):
  'For negative values, try to save a dicom directory or use PdcmIO.save_arr2dcm_file')
 
  @staticmethod
- def read_img_file(filename, pixel_type=None, fallback_only=False):
+ def read_img_file(filename, pixel_type=None, fallback_only=False, imageio=None):
  """Common pixel types: itk.SS (int16), itk.US (uint16), itk.UC (uint8)"""
- return itk.imread(filename, pixel_type, fallback_only)
+ return itk.imread(filename, pixel_type, fallback_only, imageio)
 
  @staticmethod
  def read_img_file_long(filename, image_type=image_type):
  """Longer version of itk.imread that returns the itk image and io engine string"""
  reader = itk.ImageFileReader[image_type].New()
+ reader.LoadPrivateTagsOn()
  reader.SetFileName(filename)
  reader.Update()
  image_io = str(reader.GetImageIO()).split(' ')[0]