Memory error while running points_extractor.py about digitalhistopath HOT 4 OPEN

Thank you for your continuous support. Below is the error message. The error raised in calling RandomUniformSample function from extract_tumor_patches_from_wsi function. It succeed in extracting 2000 normal patch coordinates (2000 lines in the generated text file) from the first svs image before the error.

from digitalhistopath.

I have pushed a hotfix, @heba9004 kindly let me know if that resolves the memory errors.

The error seemed to have originated when the script attempted to unnecessarily make a copy of the sample image.

from digitalhistopath.

Thank you for your fix. After it , it succeed in extracting the normal and tumor coordinates for the first svs image successfully and the normal patches of the second image with a total of 6000 lines in generated text file, then pycharm unexpectedly crashes. I am now inspecting the problem that caused this behavior, it gave another memory error that I am trying to understand but I posted since you asked so. Thank you again for your interest.

from digitalhistopath.

Ah damn, this script has not been optimised for memory. I'll try to find places where memory can be optimised like I had done in the previous fix.

Please feel free to look through the script and find places where you can optimised memory. A pull request from you would be most welcome.

from digitalhistopath.