'Spot_radius' value; the parameter `image` is an empty array

[celluwee]

While using image batch mode and setting 'Spot_radius' to 0.5, I keep getting an empty spot_img array (spot_mask.shape: (1, 1), spot_img.shape: (0, 1, 3)) and the ValueError:

ERROR::: File "/home/SPROD/sprod.py", line 312, in ERROR:::_ = extract_img_features(input_path, img_type, input_path) ERROR::: File "/home/feature_extraction.py", line 135, in extract_img_features ERROR:::normed=False, ERROR::: File "/home/skimage/feature/texture.py", line 106, in greycomatrix ERROR:::check_nD(image, 2) ERROR::: File "/home/skimage/_shared/utils.py", line 276, in check_nD ERROR:::raise ValueError(msg_empty_array % (arg_name)) ERROR:::ValueError ERROR:::The parameter image cannot be an empty array.

Otherwise, setting 'Spot_radius' to bigger integer values (such as 3, 6, 14) returns (for 'Spot_radius' set to 6) spot_mask.shape: (13, 13), spot_img.shape: (5, 13, 3), and has another error:

ERROR::: File "/home/SPROD/sprod.py", line 312, in ERROR:::_ = extract_img_features(input_path, img_type, input_path) ERROR::: File "/home/SPROD/sprod/feature_extraction.py", line 120, in extract_img_features ERROR:::spot_img = np.einsum("ij,ijk->ijk", spot_mask, spot_img) ERROR::: File "<__array_function__ internals>", line 6, in einsum ERROR::: File "/home/numpy/core/einsumfunc.py", line 1359, in einsum ERROR:::return c_einsum(*operands, **kwargs) ERROR:::ValueError ERROR:::operands could not be broadcast together with remapped shapes [original->remapped]: (13,13)->(13,13,newaxis) (5,13,3)->(5,13,3)

My 'Spot_metadata.csv' file has the shape of (1459, 1475, 3)

By the way, do you plan on adding an alternative input to the .tif image such as an RGB numpy.ndarray for example?

[wtwt5237]

Hello @celluwee

Please contact Yunguan Wang, [yunguan.wang@cchmc.org] directly for your question. I believe he wrote this part of the codes

Thanks!

Tao