rt-utils 1.3.1__tar.gz → 1.4.0__tar.gz

{rt_utils-1.3.1/rt_utils.egg-info → rt_utils-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rt-utils
-Version: 1.3.1
+Version: 1.4.0
 Summary: A small library for handling masks and RT-Structs
 Author-email: Asim Shrestha <asim.shrestha@hotmail.com>
 License-Expression: MIT

{rt_utils-1.3.1 → rt_utils-1.4.0}/rt_utils/_version.py

@@ -1,3 +1,3 @@
 """RT-Utils package version."""
 
-__version__ = "1.3.1"
+__version__ = "1.4.0"

{rt_utils-1.3.1 → rt_utils-1.4.0}/rt_utils/ds_helper.py

@@ -168,9 +168,11 @@ def create_contour_sequence(roi_data: ROIData, series_data) -> Sequence:
     contours_coords = get_contours_coords(roi_data, series_data)
 
     for series_slice, slice_contours in zip(series_data, contours_coords):
+
         for contour_data in slice_contours:
             contour = create_contour(series_slice, contour_data)
-            contour_sequence.append(contour)
+            if (contour.ContourGeometricType == 'CLOSED_PLANAR' and contour.NumberOfContourPoints > 2) or contour.ContourGeometricType != 'CLOSED_PLANAR':
+                contour_sequence.append(contour)
 
     return contour_sequence
 
@@ -184,14 +186,22 @@ def create_contour(series_slice: Dataset, contour_data: np.ndarray) -> Dataset:
     contour_image_sequence = Sequence()
     contour_image_sequence.append(contour_image)
 
+    number_of_points = len(contour_data) // 3  # Each point has an x, y and z value
+
+    # PS3.3 C.8.8.6.1: CLOSED_PLANAR requires at least three points. A contour
+    # of one or two points is a POINT or an OPEN_PLANAR, and labelling it
+    # CLOSED_PLANAR produces a dataset some treatment planning systems reject.
+    if number_of_points == 1:
+        geometric_type = "POINT"
+    elif number_of_points == 2:
+        geometric_type = "OPEN_PLANAR"
+    else:
+        geometric_type = "CLOSED_PLANAR"
+
     contour = Dataset()
     contour.ContourImageSequence = contour_image_sequence
-    contour.ContourGeometricType = (
-        "CLOSED_PLANAR"  # TODO figure out how to get this value
-    )
-    contour.NumberOfContourPoints = (
-        len(contour_data) / 3
-    )  # Each point has an x, y, and z value
+    contour.ContourGeometricType = geometric_type
+    contour.NumberOfContourPoints = number_of_points
 
     # Rounds ContourData to 10 decimal places to ensure it is <16 bytes length, as per NEMA DICOM standard guidelines.
     contour.ContourData = [round(val, 10) for val in contour_data]

{rt_utils-1.3.1 → rt_utils-1.4.0}/rt_utils/image_helper.py

@@ -370,15 +370,36 @@ def get_slice_mask_from_slice_contour_data(
 ):
     # Go through all contours in a slice, create polygons in correct space and with a correct format 
     # and append to polygons array (appropriate for fillPoly) 
+    slice_mask = create_empty_slice_mask(series_slice).astype(np.uint8)
     polygons = []
+    
     for contour_coords in slice_contour_data:
         reshaped_contour_data = np.reshape(contour_coords, [len(contour_coords) // 3, 3])
         translated_contour_data = apply_transformation_to_3d_points(reshaped_contour_data, transformation_matrix)
         polygon = [np.around([translated_contour_data[:, :2]]).astype(np.int32)]
         polygon = np.array(polygon).squeeze()
-        polygons.append(polygon)
-    slice_mask = create_empty_slice_mask(series_slice).astype(np.uint8)
-    cv.fillPoly(img=slice_mask, pts = polygons, color = 1)
+        
+        num_points = len(reshaped_contour_data)
+        
+        if num_points == 1:
+            # Single point contour - set exactly the one voxel it names.
+            # radius=0 paints a single pixel; radius=1 would paint five and
+            # inflate the smallest ROIs (fiducials, seeds, reference points).
+            point = tuple(polygon.flatten()[:2])
+            cv.circle(slice_mask, point, radius=0, color=1, thickness=-1)
+        elif num_points == 2:
+            # Two point contour - draw a line
+            pt1 = tuple(polygon[0])
+            pt2 = tuple(polygon[1])
+            cv.line(slice_mask, pt1, pt2, color=1, thickness=1)
+        else:
+            # Three or more points - use fillPoly
+            polygons.append(polygon)
+    
+    # Fill all valid polygons (3+ points) at once
+    if polygons:
+        cv.fillPoly(img=slice_mask, pts=polygons, color=1)
+    
     return slice_mask
 
 def create_empty_series_mask(series_data):

{rt_utils-1.3.1 → rt_utils-1.4.0}/rt_utils/rtstruct.py

@@ -139,13 +139,29 @@ class RTStruct:
             structure_roi.ROIName for structure_roi in self.ds.StructureSetROISequence
         ]
 
-    def get_roi_mask_by_name(self, name) -> np.ndarray:
+    def get_roi_mask_by_name(self, name, case_sensitive: bool = True) -> np.ndarray:
         """
-        Returns the 3D binary mask of the ROI with the given input name
+        Returns the 3D binary mask of the ROI with the given input name.
+
+        The name must match exactly by default. Pass case_sensitive=False to
+        match while ignoring case, which helps when ROI naming conventions
+        differ between treatment planning systems.
+
+        Matching exactly is the default because a structure set may contain
+        several ROIs whose names differ only in case, and those are distinct
+        structures. With case_sensitive=False the first one in
+        StructureSetROISequence wins and the others become unreachable.
         """
+        target = name
+        if not case_sensitive and isinstance(name, str):
+            target = name.casefold()
 
         for structure_roi in self.ds.StructureSetROISequence:
-            if structure_roi.ROIName == name:
+            roi_name = structure_roi.ROIName
+            if not case_sensitive and isinstance(roi_name, str):
+                roi_name = roi_name.casefold()
+
+            if roi_name == target:
                 contour_sequence = ds_helper.get_contour_sequence_by_roi_number(
                     self.ds, structure_roi.ROINumber
                 )

{rt_utils-1.3.1 → rt_utils-1.4.0/rt_utils.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rt-utils
-Version: 1.3.1
+Version: 1.4.0
 Summary: A small library for handling masks and RT-Structs
 Author-email: Asim Shrestha <asim.shrestha@hotmail.com>
 License-Expression: MIT