rt-utils 1.3.1__tar.gz → 1.4.1__tar.gz

{rt_utils-1.3.1/rt_utils.egg-info → rt_utils-1.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rt-utils
-Version: 1.3.1
+Version: 1.4.1
 Summary: A small library for handling masks and RT-Structs
 Author-email: Asim Shrestha <asim.shrestha@hotmail.com>
 License-Expression: MIT
@@ -33,7 +33,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pydicom
 Requires-Dist: numpy
-Requires-Dist: opencv-python>=4.0.0
+Requires-Dist: opencv-python-headless>=4.0.0
 Provides-Extra: nifti
 Requires-Dist: SimpleITK; extra == "nifti"
 Provides-Extra: dev
@@ -71,18 +71,12 @@ RT-Utils provides a builder class to faciliate the creation and loading of an RT
 The format for the ROI mask is an nd numpy array of type bool. It is an array of 2d binary masks, one plane for each slice location within the DICOM series. The slices should be sorted in ascending order within the mask. Through these masks, we extract the contours of the regions of interest and place them within the RT Struct file. Note that there is currently only support for the use of one frame of reference UID and structered set ROI sequence. Also note that holes within the ROI may be handled poorly.
 
 ## Installation
-```
+```bash
 pip install rt_utils
 ```
-##
-**libGL**  
-   libGL is a required system dependency. Install it on Linux using:
-   ```
-   ```bash
-   sudo apt install libgl1
-```
+
 ## Installation in editable mode
-```
+```bash
 git clone https://github.com/qurit/rt-utils.git
 cd rt-utils
 pip install -e .

{rt_utils-1.3.1 → rt_utils-1.4.1}/README.md

@@ -26,18 +26,12 @@ RT-Utils provides a builder class to faciliate the creation and loading of an RT
 The format for the ROI mask is an nd numpy array of type bool. It is an array of 2d binary masks, one plane for each slice location within the DICOM series. The slices should be sorted in ascending order within the mask. Through these masks, we extract the contours of the regions of interest and place them within the RT Struct file. Note that there is currently only support for the use of one frame of reference UID and structered set ROI sequence. Also note that holes within the ROI may be handled poorly.
 
 ## Installation
-```
+```bash
 pip install rt_utils
 ```
-##
-**libGL**  
-   libGL is a required system dependency. Install it on Linux using:
-   ```
-   ```bash
-   sudo apt install libgl1
-```
+
 ## Installation in editable mode
-```
+```bash
 git clone https://github.com/qurit/rt-utils.git
 cd rt-utils
 pip install -e .

{rt_utils-1.3.1 → rt_utils-1.4.1}/pyproject.toml

@@ -38,7 +38,7 @@ classifiers = [
 dependencies = [
     "pydicom",
     "numpy",
-    "opencv-python>=4.0.0",
+    "opencv-python-headless>=4.0.0",
 ]
 dynamic = ["version"]
 

{rt_utils-1.3.1 → rt_utils-1.4.1}/rt_utils/_version.py

@@ -1,3 +1,3 @@
 """RT-Utils package version."""
 
-__version__ = "1.3.1"
+__version__ = "1.4.1"

{rt_utils-1.3.1 → rt_utils-1.4.1}/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-1.4.1}/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-1.4.1}/rt_utils/rtstruct.py

@@ -23,6 +23,26 @@ class RTStruct:
         """
         self.ds.SeriesDescription = description
 
+    def _next_roi_number(self) -> int:
+        """Return an ROINumber not already used in this structure set.
+
+        Counting the sequence is not enough. An ROI deleted in another
+        application leaves a gap, so len(StructureSetROISequence) + 1 can
+        collide with an ROINumber that is still in use. ROINumber is the key
+        that ties StructureSetROISequence to ROIContourSequence, so a
+        duplicate silently associates two ROIs with the same contours.
+
+        DICOM numbers ROIs from 1, so an empty structure set yields 1.
+        """
+        used = []
+        for structure_roi in self.ds.StructureSetROISequence:
+            try:
+                used.append(int(structure_roi.ROINumber))
+            except (AttributeError, TypeError, ValueError):
+                continue
+
+        return max(used, default=0) + 1
+
     def add_roi(
         self,
         mask: np.ndarray,
@@ -83,7 +103,7 @@ class RTStruct:
         """
         # TODO: test if name already exists
         self.validate_mask(mask)
-        roi_number = len(self.ds.StructureSetROISequence) + 1
+        roi_number = self._next_roi_number()
         roi_data = ROIData(
             mask,
             color,
@@ -139,13 +159,29 @@ 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-1.4.1/rt_utils.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rt-utils
-Version: 1.3.1
+Version: 1.4.1
 Summary: A small library for handling masks and RT-Structs
 Author-email: Asim Shrestha <asim.shrestha@hotmail.com>
 License-Expression: MIT
@@ -33,7 +33,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pydicom
 Requires-Dist: numpy
-Requires-Dist: opencv-python>=4.0.0
+Requires-Dist: opencv-python-headless>=4.0.0
 Provides-Extra: nifti
 Requires-Dist: SimpleITK; extra == "nifti"
 Provides-Extra: dev
@@ -71,18 +71,12 @@ RT-Utils provides a builder class to faciliate the creation and loading of an RT
 The format for the ROI mask is an nd numpy array of type bool. It is an array of 2d binary masks, one plane for each slice location within the DICOM series. The slices should be sorted in ascending order within the mask. Through these masks, we extract the contours of the regions of interest and place them within the RT Struct file. Note that there is currently only support for the use of one frame of reference UID and structered set ROI sequence. Also note that holes within the ROI may be handled poorly.
 
 ## Installation
-```
+```bash
 pip install rt_utils
 ```
-##
-**libGL**  
-   libGL is a required system dependency. Install it on Linux using:
-   ```
-   ```bash
-   sudo apt install libgl1
-```
+
 ## Installation in editable mode
-```
+```bash
 git clone https://github.com/qurit/rt-utils.git
 cd rt-utils
 pip install -e .

{rt_utils-1.3.1 → rt_utils-1.4.1}/rt_utils.egg-info/requires.txt

@@ -1,6 +1,6 @@
 pydicom
 numpy
-opencv-python>=4.0.0
+opencv-python-headless>=4.0.0
 
 [dev]
 pytest