added smoothing factor, which is just skipping every x coord. Also ad…

…ded adjustments for high res structure sets

rt_utils/image_helper.py

@@ -60,7 +60,10 @@ def get_contours_coords(roi_data: ROIData, series_data):
  mask_slice = create_pin_hole_mask(mask_slice, roi_data.approximate_contours)
 
  # Get contours from mask
- contours, _ = find_mask_contours(mask_slice, roi_data.approximate_contours)
+ contours, _ = find_mask_contours(mask_slice,
+ roi_data.approximate_contours,
+ smoothing_factor=roi_data.smoothing_factor,
+ scaling_factor=roi_data.scaling_factor)
  validate_contours(contours)
 
  # Format for DICOM
@@ -82,7 +85,7 @@ def get_contours_coords(roi_data: ROIData, series_data):
  return series_contours
 
 
-def find_mask_contours(mask: np.ndarray, approximate_contours: bool):
+def find_mask_contours(mask: np.ndarray, approximate_contours: bool, smoothing_factor=1, scaling_factor=1):
  approximation_method = (
  cv.CHAIN_APPROX_SIMPLE if approximate_contours else cv.CHAIN_APPROX_NONE
  )
@@ -93,8 +96,10 @@ def find_mask_contours(mask: np.ndarray, approximate_contours: bool):
  contours = list(
  contours
  ) # Open-CV updated contours to be a tuple so we convert it back into a list here
+
+ assert smoothing_factor > 0
  for i, contour in enumerate(contours):
- contours[i] = [[pos[0][0], pos[0][1]] for pos in contour]
+ contours[i] = [[(contour[i][0][0]/scaling_factor), (contour[i][0][1]/scaling_factor)] for i in range(0, len(contour), smoothing_factor)]
  hierarchy = hierarchy[0] # Format extra array out of data
 
  return contours, hierarchy

rt_utils/rtstruct.py

@@ -35,6 +35,7 @@ def add_roi(
  use_pin_hole: bool = False,
  approximate_contours: bool = True,
  roi_generation_algorithm: Union[str, int] = 0,
+ smoothing_factor: int = 1,
  ):
  """
  Add a ROI to the rtstruct given a 3D binary mask for the ROI's at each slice
@@ -43,6 +44,10 @@ def add_roi(
  If approximate_contours is set to False, no approximation will be done when generating contour data, leading to much larger amount of contour data
  """
 
+ ## If upscaled coords are given, they should be adjusted accordingly
+ rows = self.series_data[0][0x00280010].value
+ scaling_factor = int(mask.shape[0] / rows)
+
  # TODO test if name already exists
  self.validate_mask(mask)
  roi_number = len(self.ds.StructureSetROISequence) + 1
@@ -56,6 +61,8 @@ def add_roi(
  use_pin_hole,
  approximate_contours,
  roi_generation_algorithm,
+ smoothing_factor,
+ scaling_factor,
  )
 
  self.ds.ROIContourSequence.append(

rt_utils/utils.py

@@ -41,7 +41,6 @@ class SOPClassUID:
 @dataclass
 class ROIData:
  """Data class to easily pass ROI data to helper methods."""
-
  mask: str
  color: Union[str, List[int]]
  number: int
@@ -51,6 +50,11 @@ class ROIData:
  use_pin_hole: bool = False
  approximate_contours: bool = True
  roi_generation_algorithm: Union[str, int] = 0
+ smoothing_factor: int = 1
+ scaling_factor: int = 1
+
+
+
 
  def __post_init__(self):
  self.validate_color()