feat: add controllable param for approximation method

rt_utils/ds_helper.py

@@ -160,7 +160,7 @@ def create_contour_sequence(roi_data: ROIData, series_data) -> Sequence:
  print("Skipping empty mask layer")
  continue
 
- contour_coords = get_contours_coords(mask_slice, series_slice, roi_data.use_pin_hole)
+ contour_coords = get_contours_coords(mask_slice, series_slice, roi_data)
  for contour_data in contour_coords:
  contour = create_contour(series_slice, contour_data)
  contour_sequence.append(contour)

rt_utils/image_helper.py

@@ -8,7 +8,7 @@
 from pydicom.dataset import Dataset
 from pydicom.sequence import Sequence
 
-from rt_utils.utils import SOPClassUID
+from rt_utils.utils import ROIData, SOPClassUID
 
 
 def load_sorted_image_series(dicom_series_path: str):
@@ -43,13 +43,13 @@ def load_dcm_images_from_path(dicom_series_path: str) -> List[Dataset]:
  return series_data
 
 
-def get_contours_coords(mask_slice: np.ndarray, series_slice: Dataset, use_pin_hole: bool):
+def get_contours_coords(mask_slice: np.ndarray, series_slice: Dataset, roi_data: ROIData):
  # Create pin hole mask if specified
- if use_pin_hole:
- mask_slice = create_pin_hole_mask(mask_slice)
+ if roi_data.use_pin_hole:
+ mask_slice = create_pin_hole_mask(mask_slice, roi_data.approximate_contours)
 
  # Get contours from mask
- contours, _ = find_mask_contours(mask_slice)
+ contours, _ = find_mask_contours(mask_slice, roi_data.approximate_contours)
  validate_contours(contours)
 
  # Format for DICOM
@@ -63,8 +63,9 @@ def get_contours_coords(mask_slice: np.ndarray, series_slice: Dataset, use_pin_h
  return formatted_contours 
 
 
-def find_mask_contours(mask):
- contours, hierarchy = cv.findContours(mask.astype(np.uint8), cv.RETR_TREE, cv.CHAIN_APPROX_SIMPLE)
+def find_mask_contours(mask: np.ndarray, approximate_contours: bool):
+ approximation_method = cv.CHAIN_APPROX_SIMPLE if approximate_contours else cv.CHAIN_APPROX_NONE 
+ contours, hierarchy = cv.findContours(mask.astype(np.uint8), cv.RETR_TREE, approximation_method)
  # Format extra array out of data
  for i, contour in enumerate(contours):
  contours[i] = [[pos[0][0], pos[0][1]] for pos in contour]
@@ -74,13 +75,13 @@ def find_mask_contours(mask):
 
 
 
-def create_pin_hole_mask(mask):
+def create_pin_hole_mask(mask: np.ndarray, approximate_contours: bool):
  """
  Creates masks with pin holes added to contour regions with holes.
  This is done so that a given region can be represented by a single contour.
  """
 
- contours, hierarchy = find_mask_contours(mask)
+ contours, hierarchy = find_mask_contours(mask, approximate_contours)
  pin_hole_mask = mask.copy()
 
  # Iterate through the hierarchy, for child nodes, draw a line upwards from the first point

rt_utils/rtstruct.py

@@ -24,7 +24,15 @@ def set_series_description(self, description: str):
 
  self.ds.SeriesDescription = description
 
- def add_roi(self, mask: np.ndarray, color: Union[str, List[int]] = None, name: str = None, description: str = '', use_pin_hole: bool = False):
+ def add_roi(
+ self,
+ mask: np.ndarray,
+ color: Union[str, List[int]] = None,
+ name: str = None,
+ description: str = '', 
+ use_pin_hole: bool = False,
+ approximate_contours: 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
@@ -34,7 +42,16 @@ def add_roi(self, mask: np.ndarray, color: Union[str, List[int]] = None, name: s
  # TODO test if name already exists
  self.validate_mask(mask)
  roi_number = len(self.ds.StructureSetROISequence) + 1
- roi_data = ROIData(mask, color, roi_number, name, self.frame_of_reference_uid, description, use_pin_hole)
+ roi_data = ROIData(
+ mask,
+ color,
+ roi_number,
+ name,
+ self.frame_of_reference_uid,
+ description,
+ use_pin_hole,
+ approximate_contours
+ )
 
  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))

rt_utils/utils.py

@@ -43,6 +43,7 @@ class ROIData:
  frame_of_reference_uid: int
  description: str = ''
  use_pin_hole: bool = False
+ approximate_contours: bool = True
 
  def __post_init__(self):
  self.validate_color()

setup.py

@@ -1,6 +1,6 @@
 import setuptools
 
-VERSION = '1.1.1'
+VERSION = '1.1.2'
 with open("README.md", "r", encoding="utf-8") as fh:
  long_description = fh.read()
 with open('requirements.txt') as f:

tests/conftest.py

@@ -17,4 +17,4 @@ def get_and_test_series_path() -> str:
  series_path = os.path.join(os.path.dirname(__file__), 'mock_data/')
  assert os.path.exists(series_path)
  return series_path
-
+

tests/test_rtstruct_builder.py

@@ -121,7 +121,7 @@ def test_loaded_mask_iou(new_rtstruct: RTStruct):
  mask[50:100, 50:100, 0] = 1
  mask[60:150, 40:120, 0] = 1
 
- IOU_threshold = 0.95 # Expect 95% accuracy for this mask 
+ IOU_threshold = 0.95 # Expected accuracy
  run_mask_iou_test(new_rtstruct, mask, IOU_threshold)
 
 
@@ -131,8 +131,8 @@ def test_mask_with_holes_iou(new_rtstruct: RTStruct):
  mask[50:100, 50:100, 0] = 1
  mask[65:85, 65:85, 0] = 0
 
- IOU_threshold = 0.85 # Expect lower accuracy holes lose information
- run_mask_iou_test(new_rtstruct, mask,  IOU_threshold)
+ IOU_threshold = 0.85 # Expect lower accuracy since holes lose information
+ run_mask_iou_test(new_rtstruct, mask, IOU_threshold)
 
 
 def test_pin_hole_iou(new_rtstruct: RTStruct):
@@ -142,13 +142,21 @@ def test_pin_hole_iou(new_rtstruct: RTStruct):
  mask[65:85, 65:85, 0] = 0
 
  IOU_threshold = 0.85 # Expect lower accuracy holes lose information
- run_mask_iou_test(new_rtstruct, mask,  IOU_threshold, True)
+ run_mask_iou_test(new_rtstruct, mask, IOU_threshold, use_pin_hole=True)
 
+def test_no_approximation_iou(new_rtstruct: RTStruct):
+ mask = get_empty_mask(new_rtstruct)
+ mask[50:100, 50:100, 0] = 1
+ mask[60:150, 40:120, 0] = 1
+
+ IOU_threshold = 0.95 # Expected accuracy
+ run_mask_iou_test(new_rtstruct, mask, IOU_threshold, approximate_contours=False)
+
 
-def run_mask_iou_test(rtstruct:RTStruct, mask, IOU_threshold, use_pin_hole=False):
+def run_mask_iou_test(rtstruct:RTStruct, mask, IOU_threshold, use_pin_hole=False, approximate_contours=True):
  # Save and load mask
  mask_name = "test"
- rtstruct.add_roi(mask, name=mask_name, use_pin_hole=use_pin_hole)
+ rtstruct.add_roi(mask, name=mask_name, use_pin_hole=use_pin_hole, approximate_contours=approximate_contours)
  loaded_mask = rtstruct.get_roi_mask_by_name(mask_name)
 
  # Use IOU to test accuracy of loaded mask