adding roi from coordinates

rt_utils/ds_helper.py

@@ -1,4 +1,6 @@
 import datetime
+from typing import List
+
 from rt_utils.image_helper import get_contours_coords
 from rt_utils.utils import ROIData, SOPClassUID
 import numpy as np
@@ -157,7 +159,7 @@ def create_roi_contour(roi_data: ROIData, series_data) -> Dataset:
  return roi_contour
 
 
-def create_contour_sequence(roi_data: ROIData, series_data) -> Sequence:
+def create_contour_sequence(roi_data: ROIData, series_data: List[Dataset]) -> Sequence:
  """
  Iterate through each slice of the mask
  For each connected segment within a slice, create a contour
@@ -175,6 +177,62 @@ def create_contour_sequence(roi_data: ROIData, series_data) -> Sequence:
  return contour_sequence
 
 
+def create_roi_contour_from_coordinates(coordinates: List[List[float]], roi_data: ROIData, series_data) -> Dataset:
+ roi_contour = Dataset()
+ roi_contour.ROIDisplayColor = roi_data.color
+ roi_contour.ContourSequence = create_contour_sequence_from_coordinates(coordinates, series_data)
+ roi_contour.ReferencedROINumber = str(roi_data.number)
+
+ return roi_contour
+
+
+def _find_closest_slice(series_slices: List[Dataset], z_coord: float) -> Dataset:
+ return min(series_slices, key=lambda series_slice: abs(series_slice.SliceLocation - z_coord))
+
+
+def _flatten_lists(lists: List[List[float]]) -> List[float]:
+ """Flatten the list [[1, 2, 3], [1, 2, 3] -> [1, 2, 3, 1, 2, 3]"""
+ flatten_list = []
+ for l in lists:
+ flatten_list += l
+
+ return flatten_list
+
+
+def create_contour_sequence_from_coordinates(coordinates: List[List[List[float]]], series_data: List[Dataset]) -> Sequence:
+ """
+ Iterate through each slice of the mask
+ For each connected segment within a slice, create a contour
+ """
+ slice_position_to_contours_coords = {}
+
+ for contours_coords in coordinates:
+ # Find the closest slice from the provided z coordinates
+ closest_slice = _find_closest_slice(series_slices=series_data, z_coord=contours_coords[0][2])
+
+ # Format contour coordinates in DICOM format [x1,y1,z1,x2,y2,z2,x3,y3,z3]
+ contour = _flatten_lists(contours_coords)
+
+ # Add contour to
+ if closest_slice.SliceLocation not in slice_position_to_contours_coords:
+ slice_position_to_contours_coords[closest_slice.SliceLocation] = []
+
+ slice_position_to_contours_coords[closest_slice.SliceLocation].append(contour)
+
+ # Making the DICOM contour sequence
+ contour_sequence = Sequence()
+
+ for z_position, slice_contours in slice_position_to_contours_coords.items():
+ for series_slice in series_data:
+ if series_slice.SliceLocation == z_position:
+ for contour_data in slice_contours:
+ contour = create_contour(series_slice, contour_data)
+ contour_sequence.append(contour)
+ continue
+
+ return contour_sequence
+
+
 def create_contour(series_slice: Dataset, contour_data: np.ndarray) -> Dataset:
  contour_image = Dataset()
  contour_image.ReferencedSOPClassUID = series_slice.SOPClassUID

rt_utils/rtstruct.py

@@ -68,6 +68,39 @@ def add_roi(
  ds_helper.create_rtroi_observation(roi_data)
  )
 
+ def add_roi_from_coordinates(
+ self,
+ coordinates: List[List[List[float]]],
+ color: Union[str, List[int]] = None,
+ name: str = None,
+ description: str = "",
+ use_pin_hole: bool = False,
+ approximate_contours: bool = True,
+ roi_generation_algorithm: Union[str, int] = 0,
+ ):
+ roi_number = len(self.ds.StructureSetROISequence) + 1
+ roi_data = ROIData(
+ np.zeros(1), # Fake mask since we do not use it because we use coordinates
+ color,
+ roi_number,
+ name,
+ self.frame_of_reference_uid,
+ description,
+ use_pin_hole,
+ approximate_contours,
+ roi_generation_algorithm,
+ )
+
+ self.ds.ROIContourSequence.append(
+ ds_helper.create_roi_contour_from_coordinates(coordinates, 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)
+ )
+
  def validate_mask(self, mask: np.ndarray) -> bool:
  if mask.dtype != bool:
  raise RTStruct.ROIException(

rt_utils/utils.py

@@ -1,5 +1,7 @@
 from typing import List, Union
 from random import randrange
+
+import numpy as np
 from pydicom.uid import PYDICOM_IMPLEMENTATION_UID
 from dataclasses import dataclass
 
@@ -41,8 +43,7 @@ class SOPClassUID:
 @dataclass
 class ROIData:
  """Data class to easily pass ROI data to helper methods."""
-
- mask: str
+ mask: np.ndarray
  color: Union[str, List[int]]
  number: int
  name: str

tests/test_rtstruct_builder.py

@@ -81,6 +81,41 @@ def test_add_valid_roi(new_rtstruct: RTStruct):
  assert new_rtstruct.get_roi_names() == [NAME]
 
 
+def test_add_valid_roi_from_coordinates(new_rtstruct: RTStruct):
+ assert new_rtstruct.get_roi_names() == []
+ assert len(new_rtstruct.ds.ROIContourSequence) == 0
+ assert len(new_rtstruct.ds.StructureSetROISequence) == 0
+ assert len(new_rtstruct.ds.RTROIObservationsSequence) == 0
+
+ NAME = "Test ROI"
+ COLOR = [123, 123, 232]
+ coordinates = [
+ [
+ [-100, -100, 60],
+ [-100, -75, 60],
+ [-75, -75, 60],
+ [-75, -100, 60]
+ ],
+ [
+ [-90, -90, 65],
+ [-90, -65, 65],
+ [-65, -65, 65],
+ [-65, -90, 65],
+ ]
+ ]
+
+ new_rtstruct.add_roi_from_coordinates(coordinates, color=COLOR, name=NAME)
+
+ assert len(new_rtstruct.ds.ROIContourSequence) == 1
+ assert (
+ len(new_rtstruct.ds.ROIContourSequence[0].ContourSequence) == 2
+ ) # 2 contour on to slice were added
+ assert len(new_rtstruct.ds.StructureSetROISequence) == 1
+ assert len(new_rtstruct.ds.RTROIObservationsSequence) == 1
+ assert new_rtstruct.ds.ROIContourSequence[0].ROIDisplayColor == COLOR
+ assert new_rtstruct.get_roi_names() == [NAME]
+
+
 def test_get_invalid_roi_mask_by_name(new_rtstruct: RTStruct):
  assert new_rtstruct.get_roi_names() == []
  with pytest.raises(RTStruct.ROIException):