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ncoudray / DeepPATH

Classification of Lung cancer slide images using deep-learning
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0f_HeatMap_nClasses.py parameterization #31

Closed bcli4d closed 5 years ago

bcli4d commented 5 years ago

Hello, I'm trying to run 03_postprocessing/0f_HeatMap_nClasses.py. The --image_file parameter is presumably the output directory of the tiling stage. In that directory, I find subdirectories named "TCGA_xxx_files". It looks like 0f_HeatMap_nClasses.py expects to find jpegs in those subdirectories. However those subdirectories only contain magnification specific subdirectories, e.g. "5.0" or "20.0". It's the magnification specific supdirectories that hold the jpegs. As a result, the code in lines 347-356 doesn't find the file that corresponds to each tile.

Am I missing something here? It's easy enough to change the code, but before I do that I thought I should ask if I'm not understanding something. Thanks.

bcli4d commented 5 years ago

Ah, it appears that I need to pass the directory of sorted tiles. Nevermind!