refactoring the way warn_only is passed qurit#64

rt_utils/rtstruct_builder.py

@@ -13,7 +13,7 @@ class RTStructBuilder:
  """
 
  @staticmethod
- def create_new(dicom_series_path: str, warn_only: bool = False) -> RTStruct:
+ def create_new(dicom_series_path: str) -> RTStruct:
  """
  Method to generate a new rt struct from a DICOM series
  """
@@ -23,15 +23,15 @@ def create_new(dicom_series_path: str, warn_only: bool = False) -> RTStruct:
  return RTStruct(series_data, ds, warn_only=warn_only)
 
  @staticmethod
- def create_from(dicom_series_path: str, rt_struct_path: str) -> RTStruct:
+ def create_from(dicom_series_path: str, rt_struct_path: str, warn_only: bool = False) -> 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)
+ RTStructBuilder.validate_rtstruct_series_references(ds, series_data, warn_only)
 
  # TODO create new frame of reference? Right now we assume the last frame of reference created is suitable
  return RTStruct(series_data, ds)
@@ -51,7 +51,7 @@ 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]):
+ def validate_rtstruct_series_references(ds: Dataset, series_data: List[Dataset], warn_only: bool = False):
  """
  Method to validate RTStruct only references dicom images found within the input series_data
  """
@@ -64,7 +64,7 @@ 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
+ contour_image, series_data, warn_only
  )
 
  @staticmethod
@@ -79,8 +79,8 @@ def validate_contour_image_in_series_data(
  return
 
  # ReferencedSOPInstanceUID is NOT available
- msg = f"Loaded RTStruct references image(s) that are not contained in input series data. "
-  + f"Problematic image has SOP Instance Id: {contour_image.ReferencedSOPInstanceUID}"
+ msg = f"Loaded RTStruct references image(s) that are not contained in input series data. " \
+ f"Problematic image has SOP Instance Id: {contour_image.ReferencedSOPInstanceUID}"
  if warning_only:
  warnings.warn(msg)
  else: