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Daniel Galbraith
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deepslide
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[dd9da8]: / code / 2_process_patches.py

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import config



from utils_processing import (balance_classes, gen_train_patches,

                              gen_val_patches, produce_patches)



###########################################

#                  MAIN                   #

###########################################

print("\n\n+++++ Running 2_process_patches.py +++++")

print("\n----- Generating training patches -----")

# Generate training patches.

gen_train_patches(input_folder=config.args.wsi_train,

                  output_folder=config.train_patches,

                  num_train_per_class=config.args.num_train_per_class,

                  num_workers=config.args.num_workers,

                  patch_size=config.args.patch_size,

                  purple_threshold=config.args.purple_threshold,

                  purple_scale_size=config.args.purple_scale_size,

                  image_ext=config.args.image_ext,

                  type_histopath=config.args.type_histopath)

print("----- Finished generating training patches -----\n")

print("----- Balancing the training patches -----")

# Balance the training patches.

balance_classes(training_folder=config.train_patches)

print("----- Finished balancing the training patches -----\n")

print("----- Generating validation patches -----")

# Generate validation patches.

gen_val_patches(input_folder=config.args.wsi_val,

                output_folder=config.val_patches,

                overlap_factor=config.args.gen_val_patches_overlap_factor,

                num_workers=config.args.num_workers,

                patch_size=config.args.patch_size,

                purple_threshold=config.args.purple_threshold,

                purple_scale_size=config.args.purple_scale_size,

                image_ext=config.args.image_ext,

                type_histopath=config.args.type_histopath)

print("----- Finished generating validation patches -----\n")

print("----- Generating validation evaluation patches -----")

# Generate validation evaluation patches.

produce_patches(input_folder=config.args.wsi_val,

                output_folder=config.args.patches_eval_val,

                inverse_overlap_factor=config.args.slide_overlap,

                by_folder=config.args.by_folder,

                num_workers=config.args.num_workers,

                patch_size=config.args.patch_size,

                purple_threshold=config.args.purple_threshold,

                purple_scale_size=config.args.purple_scale_size,

                image_ext=config.args.image_ext,

                type_histopath=config.args.type_histopath)

print("----- Finished generating validation evaluation patches -----\n")

print("----- Generating test evaluation patches -----")

# Generate test evaluation patches.

produce_patches(input_folder=config.args.wsi_test,

                output_folder=config.args.patches_eval_test,

                inverse_overlap_factor=config.args.slide_overlap,

                by_folder=config.args.by_folder,

                num_workers=config.args.num_workers,

                patch_size=config.args.patch_size,

                purple_threshold=config.args.purple_threshold,

                purple_scale_size=config.args.purple_scale_size,

                image_ext=config.args.image_ext,

                type_histopath=config.args.type_histopath)

print("----- Finished generating test evaluation patches -----\n")

print("+++++ Finished running 2_process_patches.py +++++\n\n")