Error when segmentation consists of only one pixel

[ThomasBudd]

Hi together,

I've encontered an openCV error in one case where only one voxel was annotated in a slice (full error log below).

I found the root of the error in the file image_helper.py in the function get_slice_mask_from_slice_contour_data. When there is only one annotated pixel, the line 275

polygon = np.array(polygon).squeeze()

reduces the polygon array to an array of size 2, but the cv.fillPoly needs the array to be of size n x 2 where n is the number of countour points in this slice (in this case n=1). I fixed this by adding

if polygon.ndim == 1:
        polygon = polygon[None]

just in the line below and now it works for me. Would you mind adding this to your repo?

Many thanks!

here is the full error log:

File ~/miniconda3/envs/torch_env/lib/python3.12/site-packages/spyder_kernels/py3compat.py:356 in compat_exec
exec(code, globals, locals)

File /import/H-HH-Laufwerk/thomas/lungenprojekte/Python/visual_eval/NILS/try_read_rtstruct.py:21
ccs += (i+1) * rtstruct.get_roi_mask_by_name(roi_name)

File ~/miniconda3/envs/torch_env/lib/python3.12/site-packages/rt_utils/rtstruct.py:113 in get_roi_mask_by_name
return image_helper.create_series_mask_from_contour_sequence(

File ~/miniconda3/envs/torch_env/lib/python3.12/site-packages/rt_utils/image_helper.py:247 in create_series_mask_from_contour_sequence
mask[:, :, i] = get_slice_mask_from_slice_contour_data(

File ~/miniconda3/envs/torch_env/lib/python3.12/site-packages/rt_utils/image_helper.py:280 in get_slice_mask_from_slice_contour_data
cv.fillPoly(img=slice_mask, pts = polygons, color = 1)

error: OpenCV(4.9.0) /io/opencv/modules/imgproc/src/drawing.cpp:2432: error: (-215:Assertion failed) p.checkVector(2, CV_32S) >= 0 in function 'fillPoly'

[PereGinebra]

you might want to take a look at this previous issue, there's some relevant code to fix it that hasn't yet been implemented.