Error with single page PDF at the get_mask_center function

[Iagea]

Hi,

the following error appears with the attached PDF document, do you know why?

Best,
Isa.

Traceback (most recent call last): File "/Users/mag/UCMI/DECIMER-Image-Segmentation/segment_structures_in_document.py", line 45, in <module> main() File "/Users/mag/UCMI/DECIMER-Image-Segmentation/segment_structures_in_document.py", line 22, in main raw_segments = segment_chemical_structures_from_file(sys.argv[1]) File "/Users/mag/UCMI/DECIMER-Image-Segmentation/decimer_segmentation/decimer_segmentation.py", line 75, in segment_chemical_structures_from_file segments = segment_chemical_structures(images[0]) File "/Users/mag/UCMI/DECIMER-Image-Segmentation/decimer_segmentation/decimer_segmentation.py", line 100, in segment_chemical_structures masks = get_expanded_masks(image) File "/Users/mag/UCMI/DECIMER-Image-Segmentation/decimer_segmentation/decimer_segmentation.py", line 157, in get_expanded_masks expanded_masks = complete_structure_mask(image_array=image, mask_array=masks) File "/Users/mag/UCMI/DECIMER-Image-Segmentation/decimer_segmentation/complete_structure.py", line 451, in complete_structure_mask mask_array = np.stack(expanded_split_mask_arrays, -1) File "<__array_function__ internals>", line 180, in stack File "/Users/mag/opt/anaconda3/envs/DECIMER_IMGSEG/lib/python3.10/site-packages/numpy/core/shape_base.py", line 420, in stack arrays = [asanyarray(arr) for arr in arrays] File "/Users/mag/opt/anaconda3/envs/DECIMER_IMGSEG/lib/python3.10/site-packages/numpy/core/shape_base.py", line 420, in <listcomp> arrays = [asanyarray(arr) for arr in arrays] File "/Users/mag/UCMI/DECIMER-Image-Segmentation/decimer_segmentation/complete_structure.py", line 399, in expansion_coordination seed_pixels = get_seeds(image_array, mask_array) File "/Users/mag/UCMI/DECIMER-Image-Segmentation/decimer_segmentation/complete_structure.py", line 297, in get_seeds x_center, y_center = get_mask_center(mask_array) File "/Users/mag/UCMI/DECIMER-Image-Segmentation/decimer_segmentation/complete_structure.py", line 280, in get_mask_center x_center = np.where(mask_array[y_center] == True)[0][0] IndexError: index 0 is out of bounds for axis 0 with size 0

105.pdf

[Kohulan]

This PDF also crashes decimer.ai

[OBrink]

Oh wow, sorry, I somehow forgot about this issue existing. I am on it now and will send a PR soon.

The problem seems to be that an empty mask is returned by the model and there are no seed pixels to be determined. This problem is not handled properly.

[OBrink]

PR #78 fixes this. Thank you @Iagea for reporting this problem, and sorry again for the late response!