Merge pull request #8 from RSIP-Vision/elazarcoh/issue5

Support private fields in header

medio/backends/itk_io.py

@@ -30,6 +30,7 @@ def read_img(
  pixel_type=pixel_type,
  fallback_only=True,
  series=None,
+ private_tags=False,
  ):
  """
  The main reader function, reads images and performs reorientation and unpacking
@@ -43,13 +44,33 @@ def read_img(
  :return: numpy image and metadata object which includes pixdim, affine, original orientation string and
  coordinates system
  """
+ if header:
+ # Currently, only DICOM will use imageio (GDCM). For NIfTI, we'll use ITK default reader.
+ imageio = itk.GDCMImageIO.New()
+ if private_tags:
+ imageio.LoadPrivateTagsOn()
+ else:
+ imageio = None
  input_path = Path(input_path)
  if input_path.is_dir():
+ # We assume that the directory contains dicom series, do imageio will work, if used.
+ if imageio is not None:
+ # 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
  img = ItkIO.read_dir(
- str(input_path), pixel_type, fallback_only, series=series, header=header
+ 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)
+ # If the input file is not a dicom (e.g. NIfTI), fallback to not use imageio.
+ use_dicom_imageio = imageio.CanReadFile(str(input_path))
+ if use_dicom_imageio:
+ # 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
+ img = ItkIO.read_img_file(
+ str(input_path), pixel_type, fallback_only, imageio
+ )
  else:
  raise FileNotFoundError(f'No such file or directory: "{input_path}"')
 
@@ -65,8 +86,10 @@ def read_img(
  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()
+ if imageio:
+ metadict = imageio.GetMetaDataDictionary()
+ else:
+ metadict = img.GetMetaDataDictionary()
  metadata.header = {
  key: metadict[key]
  for key in metadict.GetKeys()
@@ -174,14 +197,15 @@ def prepare_dcm_array(image_np, is_vector=False):
  )
 
  @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]
@@ -285,7 +309,7 @@ def reorient(img, desired_orientation: Union[int, tuple, str, None]):
 
  @staticmethod
  def read_dir(
- dirname, pixel_type=None, fallback_only=False, series=None, header=False
+ 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
@@ -294,16 +318,7 @@ def read_dir(
  >>> 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):