[Bug] Patches truncated for 16 bit images

Likely due to this line: https://github.com/neuropoly/axondeepseg/blob/57047da51781c12d06c1b5d59dcb705bf4adc376/AxonDeepSeg/data_management/dataset_building.py#L44

Combining preserve_range plus asint may be what’s truncating the patches (all white).

The solution may be as simple as removing the asint call.

@maxwab you wrote that line; do you see any issues with removing the asint call? I’ll double check the rest of the code to make sure it’s not assumed to be an 8bit int anywhere else. I guess it means that if I remove this, the data size will be much larger… Otherwise, removing the perserve_range could also possibly be a solution.

[maxwab]

Hi @mathieuboudreau, At first glance I don’t see any problem with removing the .astype(int) call. The most likely reason I added this call at the time was to ensure the type of img. As far as I can tell, the reason was not memory usage.

[mathieuboudreau]

It may also be the “L” mode: https://github.com/python-pillow/Pillow/issues/3011

L mode is 8bit pixel (black and white): https://docs.scipy.org/doc/scipy/reference/generated/scipy.misc.imread.html