refactor: remove use_media_storage and use base attributes instead of…

… media header attributes

rt_utils/ds_helper.py

@@ -12,11 +12,11 @@
 """
 
 
-def create_rtstruct_dataset(series_data, use_media_storage: bool = True) -> FileDataset:
+def create_rtstruct_dataset(series_data) -> FileDataset:
  ds = generate_base_dataset()
  add_study_and_series_information(ds, series_data)
  add_patient_information(ds, series_data)
- add_refd_frame_of_ref_sequence(ds, series_data, use_media_storage)
+ add_refd_frame_of_ref_sequence(ds, series_data)
  return ds
 
 
@@ -94,21 +94,21 @@ def add_patient_information(ds: FileDataset, series_data):
  ds.PatientWeight = getattr(reference_ds, 'PatientWeight', '')
 
 
-def add_refd_frame_of_ref_sequence(ds: FileDataset, series_data, use_media_storage: bool = True):
+def add_refd_frame_of_ref_sequence(ds: FileDataset, series_data):
  refd_frame_of_ref = Dataset()
  refd_frame_of_ref.FrameOfReferenceUID = generate_uid() # TODO Find out if random generation is ok
- refd_frame_of_ref.RTReferencedStudySequence = create_frame_of_ref_study_sequence(series_data, use_media_storage)
+ refd_frame_of_ref.RTReferencedStudySequence = create_frame_of_ref_study_sequence(series_data)
 
  # Add to sequence
  ds.ReferencedFrameOfReferenceSequence = Sequence()
  ds.ReferencedFrameOfReferenceSequence.append(refd_frame_of_ref)
 
 
-def create_frame_of_ref_study_sequence(series_data, use_media_storage: bool = True) -> Sequence:
+def create_frame_of_ref_study_sequence(series_data) -> Sequence:
  reference_ds = series_data[0] # All elements in series should have the same data
  rt_refd_series = Dataset()
  rt_refd_series.SeriesInstanceUID = reference_ds.SeriesInstanceUID
- rt_refd_series.ContourImageSequence = create_contour_image_sequence(series_data, use_media_storage)
+ rt_refd_series.ContourImageSequence = create_contour_image_sequence(series_data)
 
  rt_refd_series_sequence = Sequence()
  rt_refd_series_sequence.append(rt_refd_series)
@@ -123,22 +123,15 @@ def create_frame_of_ref_study_sequence(series_data, use_media_storage: bool = Tr
  return rt_refd_study_sequence
 
 
-def create_contour_image_sequence(series_data, use_media_storage: bool = True) -> Sequence:
+def create_contour_image_sequence(series_data) -> Sequence:
  contour_image_sequence = Sequence()
 
  # Add each referenced image
- if use_media_storage:
- for series in series_data:
- contour_image = Dataset()
- contour_image.ReferencedSOPClassUID = series.file_meta.MediaStorageSOPClassUID
- contour_image.ReferencedSOPInstanceUID = series.file_meta.MediaStorageSOPInstanceUID
- contour_image_sequence.append(contour_image)
- else:
- for series in series_data:
- contour_image = Dataset()
- contour_image.ReferencedSOPClassUID = series.SOPClassUID
- contour_image.ReferencedSOPInstanceUID = series.SOPInstanceUID
- contour_image_sequence.append(contour_image)
+ for series in series_data:
+ contour_image = Dataset()
+ contour_image.ReferencedSOPClassUID = series.SOPClassUID
+ contour_image.ReferencedSOPInstanceUID = series.SOPInstanceUID
+ contour_image_sequence.append(contour_image)
 
  return contour_image_sequence
 
@@ -154,15 +147,15 @@ def create_structure_set_roi(roi_data: ROIData) -> Dataset:
  return structure_set_roi
 
 
-def create_roi_contour(roi_data: ROIData, series_data, use_media_storage: bool = True) -> Dataset:
+def create_roi_contour(roi_data: ROIData, series_data) -> Dataset:
  roi_contour = Dataset()
  roi_contour.ROIDisplayColor = roi_data.color
- roi_contour.ContourSequence = create_contour_sequence(roi_data, series_data, use_media_storage)
+ roi_contour.ContourSequence = create_contour_sequence(roi_data, series_data)
  roi_contour.ReferencedROINumber = str(roi_data.number)
  return roi_contour
 
 
-def create_contour_sequence(roi_data: ROIData, series_data, use_media_storage: bool = True) -> Sequence:
+def create_contour_sequence(roi_data: ROIData, series_data) -> Sequence:
  """
  Iterate through each slice of the mask
  For each connected segment within a slice, create a contour
@@ -174,20 +167,16 @@ def create_contour_sequence(roi_data: ROIData, series_data, use_media_storage: b
 
  for series_slice, slice_contours in zip(series_data, contours_coords):
  for contour_data in slice_contours:
- contour = create_contour(series_slice, contour_data, use_media_storage)
+ contour = create_contour(series_slice, contour_data)
  contour_sequence.append(contour)
 
  return contour_sequence
 
 
-def create_contour(series_slice: Dataset, contour_data: np.ndarray, use_media_storage: bool = True) -> Dataset:
+def create_contour(series_slice: Dataset, contour_data: np.ndarray) -> Dataset:
  contour_image = Dataset()
- if use_media_storage:
- contour_image.ReferencedSOPClassUID = series_slice.file_meta.MediaStorageSOPClassUID
- contour_image.ReferencedSOPInstanceUID = series_slice.file_meta.MediaStorageSOPInstanceUID
- else:
- contour_image.ReferencedSOPClassUID = series_slice.SOPClassUID
- contour_image.ReferencedSOPInstanceUID = series_slice.SOPInstanceUID
+ contour_image.ReferencedSOPClassUID = series_slice.SOPClassUID
+ contour_image.ReferencedSOPInstanceUID = series_slice.SOPInstanceUID
 
  # Contour Image Sequence
  contour_image_sequence = Sequence()

rt_utils/rtstruct.py

@@ -34,7 +34,7 @@ def add_roi(
  use_pin_hole: bool = False,
  approximate_contours: bool = True,
  roi_generation_algorithm: Union[str, int] = 0,
-  use_media_storage: bool = True):
+ ):
  """
  Add a ROI to the rtstruct given a 3D binary mask for the ROI's at each slice
  Optionally input a color or name for the ROI
@@ -57,7 +57,7 @@ def add_roi(
  roi_generation_algorithm
  )
 
- self.ds.ROIContourSequence.append(ds_helper.create_roi_contour(roi_data, self.series_data, use_media_storage))
+ self.ds.ROIContourSequence.append(ds_helper.create_roi_contour(roi_data, self.series_data))
  self.ds.StructureSetROISequence.append(ds_helper.create_structure_set_roi(roi_data))
  self.ds.RTROIObservationsSequence.append(ds_helper.create_rtroi_observation(roi_data))
 

rt_utils/rtstruct_builder.py

@@ -23,15 +23,15 @@ def create_new(dicom_series_path: str) -> RTStruct:
  return RTStruct(series_data, ds)
 
  @staticmethod
- def create_from(dicom_series_path: str, rt_struct_path: str, use_media_storage: bool = True) -> RTStruct:
+ def create_from(dicom_series_path: str, rt_struct_path: str) -> RTStruct:
  """
  Method to load an existing rt struct, given related DICOM series and existing rt struct
  """
 
  series_data = image_helper.load_sorted_image_series(dicom_series_path)
  ds = dcmread(rt_struct_path)
  RTStructBuilder.validate_rtstruct(ds)
- RTStructBuilder.validate_rtstruct_series_references(ds, series_data, use_media_storage)
+ RTStructBuilder.validate_rtstruct_series_references(ds, series_data)
 
  # TODO create new frame of reference? Right now we assume the last frame of reference created is suitable 
  return RTStruct(series_data, ds)
@@ -49,7 +49,7 @@ def validate_rtstruct(ds: Dataset):
  raise Exception("Please check that the existing RTStruct is valid")
 
  @staticmethod
- def validate_rtstruct_series_references(ds: Dataset, series_data: List[Dataset], use_media_storage: bool = True):
+ def validate_rtstruct_series_references(ds: Dataset, series_data: List[Dataset]):
  """
  Method to validate RTStruct only references dicom images found within the input series_data
  """
@@ -58,22 +58,16 @@ def validate_rtstruct_series_references(ds: Dataset, series_data: List[Dataset],
  for rt_refd_series in rt_refd_study.RTReferencedSeriesSequence:
  for contour_image in rt_refd_series.ContourImageSequence:
  RTStructBuilder.validate_contour_image_in_series_data(
- contour_image, series_data, use_media_storage)
+ contour_image, series_data)
 
  @staticmethod
- def validate_contour_image_in_series_data(contour_image: Dataset, series_data: List[Dataset],
- use_media_storage: bool = True):
+ def validate_contour_image_in_series_data(contour_image: Dataset, series_data: List[Dataset]):
  """
  Method to validate that the ReferencedSOPInstanceUID of a given contour image exists within the series data
  """
- if use_media_storage:
- for series in series_data:
- if contour_image.ReferencedSOPInstanceUID == series.file_meta.MediaStorageSOPInstanceUID:
- return
- else:
- for series in series_data:
- if contour_image.ReferencedSOPInstanceUID == series.SOPInstanceUID:
- return
+ for series in series_data:
+ if contour_image.ReferencedSOPInstanceUID == series.SOPInstanceUID:
+ return
 
  # ReferencedSOPInstanceUID is NOT available
  raise Exception(