Bring support for header in+private tags in series

medio/backends/itk_io.py

@@ -36,16 +36,17 @@ 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:
+ if header:
  imageio = itk.GDCMImageIO.New()
- imageio.LoadPrivateTagsOn()
+ if private_tags:
+ 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)
+ img = ItkIO.read_dir(str(input_path), pixel_type, fallback_only, series, imageio)
  elif input_path.is_file():
  img = ItkIO.read_img_file(str(input_path), pixel_type, fallback_only, imageio)
  else:
@@ -61,8 +62,7 @@ def read_img(input_path, desired_axcodes=None, header=False, components_axis=Non
  image_np, affine = ItkIO.unpack_img(img)
  metadata = MetaData(affine=affine, orig_ornt=orig_ornt, coord_sys=ItkIO.coord_sys)
  if header:
- # TODO: not implemented for a series (returns an empty dictionary), see ItkIO.read_dir
- metadict = img.GetMetaDataDictionary()
+ metadict = imageio.GetMetaDataDictionary()
  metadata.header = {key: metadict[key] for key in metadict.GetKeys() if not key.startswith('ITK_')}
 
  # TODO: consider unifying with PdcmIO.move_channels_axis
@@ -239,22 +239,15 @@ def reorient(img, desired_orientation: Union[int, tuple, str, None]):
  return reoriented_itk_img, original_orientation_code
 
  @staticmethod
- def read_dir(dirname, pixel_type=None, fallback_only=False, series=None, header=False):
+ def read_dir(dirname, pixel_type=None, fallback_only=False, series=None, imageio=None):
  """
  Read a dicom directory. If there is more than one series in the directory an error is raised
  (unless the series argument is used properly).
  Shorter option for a single series (provided the slices order is known):
  >>> itk.imread([filename0, filename1, ...])
  """
  filenames = ItkIO.extract_series(dirname, series)
- if header and isinstance(filenames, (tuple, list)):
- # TODO: to extract the metadata dictionary array use:
- # reader = itk.ImageSeriesReader.New(FileNames=filenames)
- # reader.Update()
- # metadict_arr = reader.GetMetaDataDictionaryArray()
- # (See also itk.imread source code)
- raise NotImplementedError("header=True is currently not supported for a series")
- return itk.imread(filenames, pixel_type, fallback_only)
+ return itk.imread(filenames, pixel_type, fallback_only, imageio)
 
  @staticmethod
  def extract_series(dirname, series=None):