Raise error when header=True for a series

Author: jond01

medio/backends/itk_io.py

@@ -38,7 +38,7 @@ def read_img(input_path, desired_axcodes=None, header=False, components_axis=Non
         """
         input_path = Path(input_path)
         if input_path.is_dir():
-            img = ItkIO.read_dir(str(input_path), pixel_type, fallback_only, series=series)
+            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)
         else:
@@ -54,6 +54,7 @@ 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()
             metadata.header = {key: metadict[key] for key in metadict.GetKeys() if not key.startswith('ITK_')}
 
@@ -230,14 +231,21 @@ 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):
+    def read_dir(dirname, pixel_type=None, fallback_only=False, series=None, header=False):
         """
         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)
 
     @staticmethod

medio/backends/pdcm_io.py

@@ -39,9 +39,8 @@ def read_img(input_path, desired_ornt=None, header=False, channels_axis=None, gl
         input_path = Path(input_path)
         temp_channels_axis = -1  # if there are channels, they must be in the last axis for the reorientation
         if input_path.is_dir():
-            # TODO: add header support
-            img, metadata, channeled = PdcmIO.read_dcm_dir(input_path, globber, channels_axis=temp_channels_axis,
-                                                           series=series)
+            img, metadata, channeled = PdcmIO.read_dcm_dir(input_path, header, globber,
+                                                           channels_axis=temp_channels_axis, series=series)
         else:
             img, metadata, channeled = PdcmIO.read_dcm_file(
                 input_path, header, allow_default_affine=allow_default_affine, channels_axis=temp_channels_axis)
@@ -73,7 +72,7 @@ def read_dcm_file(filename, header=False, allow_default_affine=False, channels_a
         return img, metadata, samples_per_pixel > 1
 
     @staticmethod
-    def read_dcm_dir(input_dir, globber='*', channels_axis=None, series=None):
+    def read_dcm_dir(input_dir, header=False, globber='*', channels_axis=None, series=None):
         """
         Reads a 3D dicom image: input path can be a file or directory (DICOM series).
         Return the image array, metadata, and whether it has channels
@@ -82,6 +81,10 @@ def read_dcm_dir(input_dir, globber='*', channels_axis=None, series=None):
         slices = PdcmIO.extract_slices(input_dir, globber=globber, series=series)
         img, affine = combine_slices(slices)
         metadata = PdcmIO.aff2meta(affine)
+        if header:
+            # TODO: add header support, something like
+            #  metdata.header = [{str(key): ds[key] for key in ds.keys()} for ds in slices]
+            raise NotImplementedError("header=True is currently not supported for a series")
         samples_per_pixel = slices[0].SamplesPerPixel
         img = PdcmIO.move_channels_axis(img, samples_per_pixel=samples_per_pixel, channels_axis=channels_axis,
                                         planar_configuration=slices[0].get('PlanarConfiguration', None),