I am running the code in CentOS Linux 7 which is based on RHEL.
How to see the visualization figures like the one you showed in your readme section of "6. Visualization" Deep Learning Model figures from B.i - B.iv?
py3) [SebliLo@tesla deepslide]$ python code/6_visualize.py
############### CONFIGURATION ###############
all_wsi: all_wsi
val_wsi_per_class: 20
test_wsi_per_class: 30
keep_orig_copy: True
num_workers: 8
patch_size: 224
wsi_train: wsi_train
wsi_val: wsi_val
wsi_test: wsi_test
labels_train: labels_train.csv
labels_val: labels_val.csv
labels_test: labels_test.csv
train_folder: train_folder
patches_eval_train: patches_eval_train
patches_eval_val: patches_eval_val
patches_eval_test: patches_eval_test
num_train_per_class: 8000
type_histopath: True
purple_threshold: 100
purple_scale_size: 15
slide_overlap: 3
gen_val_patches_overlap_factor: 1.5
image_ext: jpg
by_folder: True
color_jitter_brightness: 0.5
color_jitter_contrast: 0.5
color_jitter_saturation: 0.5
color_jitter_hue: 0.2
num_epochs: 20
num_layers: 18
learning_rate: 0.001
batch_size: 16
weight_decay: 0.0001
learning_rate_decay: 0.85
resume_checkpoint: False
save_interval: 1
checkpoints_folder: checkpoints
checkpoint_file: xyz.pt
pretrain: False
log_folder: logs
auto_select: True
preds_train: preds_train
preds_val: preds_val
preds_test: preds_test
inference_train: inference_train
inference_val: inference_val
inference_test: inference_test
vis_train: vis_train
vis_val: vis_val
vis_test: vis_test
device: cpu
classes: ['benign', 'tumor']
num_classes: 2
train_patches: train_folder/train
val_patches: train_folder/val
path_mean: [0.16684997, 0.16684997, 0.16684997]
path_std: [0.40847272, 0.40847272, 0.40847272]
resume_checkpoint_path: checkpoints/xyz.pt
log_csv: logs/log_2212022_231057.csv
eval_model: checkpoints/xyz.pt
threshold_search: (0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9)
colors: ('red', 'white', 'blue', 'green', 'purple', 'orange', 'black', 'pink', 'yellow')
#####################################################
+++++ Running 6_visualize.py +++++
----- Visualizing validation set -----
40 whole slides found from wsi_val
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_67_13_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_67_14_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_67_15_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_67_16_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_67_17_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_67_18_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_67_22_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_68_11_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_68_12_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_68_15_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_68_16_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_68_22_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_69_12_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_69_13_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_69_14_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_69_15_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_69_16_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_69_17_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_69_18_0.png of shape (256, 256, 3)
visualizing wsi_val/benign/Copy of 6 3412 2-L-1 HCC_69_19_0.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_104_65_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_104_66_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_105_62_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_105_63_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_105_64_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_105_65_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_105_66_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_105_67_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_105_68_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_49_58_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_50_56_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_51_56_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_52_55_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_59_68_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_59_69_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_60_43_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_60_44_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_60_45_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_60_67_1.png of shape (256, 256, 3)
visualizing wsi_val/tumor/Copy of 6 3412 2-L-1 HCC_61_44_1.png of shape (256, 256, 3)
find the visualizations in vis_val
----- Finished visualizing validation set -----
----- Visualizing test set -----
60 whole slides found from wsi_test
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_70_12_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_70_14_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_70_15_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_70_16_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_70_17_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_70_18_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_70_19_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_71_13_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_71_14_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_71_15_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_71_16_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_71_17_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_71_18_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_71_19_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_72_14_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_72_15_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_72_16_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_72_18_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_72_19_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_72_20_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_72_21_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_73_15_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_73_18_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_73_19_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_73_20_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_74_16_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_74_17_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_74_18_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_75_16_0.png of shape (256, 256, 3)
visualizing wsi_test/benign/Copy of 6 3412 2-L-1 HCC_75_17_0.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_61_45_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_61_46_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_61_66_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_62_42_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_62_43_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_62_46_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_63_41_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_63_42_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_63_44_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_63_45_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_64_40_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_64_43_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_65_42_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_65_51_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_65_52_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_66_50_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_66_51_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_66_52_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_67_50_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_75_8_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_75_9_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_76_6_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_77_7_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_77_8_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_89_64_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_91_64_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_92_62_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_92_63_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_92_64_1.png of shape (256, 256, 3)
visualizing wsi_test/tumor/Copy of 6 3412 2-L-1 HCC_93_65_1.png of shape (256, 256, 3)
find the visualizations in vis_test
----- Finished visualizing test set -----
+++++ Finished running 6_visualize.py +++++