diff --git a/config.yaml b/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..81cca28c64d6770dffb25480ce3e2bfc8838e997 --- /dev/null +++ b/config.yaml @@ -0,0 +1,70 @@ +#General: +gpu_ids: '0' +phase: train +verbose: False +update_TB_images_freq: 5000 +grid_search: False +n_min_layers: 4 +n_max_layers: 7 +run_dev_mode: False + +#Data: +########### +# Update! # +########### +stain: HE +stainB: PAS +pathStainA: /path/to/A +pathStainB: /path/to/B +resultsPath: /train/result/path +testResultsPath: /test/result/path +dataStage: Train +########### + +suffix: '' +dataset_mode: unaligned +preload: True +direction: BtoA +serial_batches: 4 +num_threads: 4 +batch_size: 3 +load_size: 640 +crop_size: 640 +max_dataset_size: inf +preprocess: none +no_flip: False + +#Model: +model: cycle_gan +input_nc: 3 +output_nc: 3 +ngf: 32 # # of gen filters in the last conv layer +ndf: 32 # # of disc filters in the first conv layer +netD: n_layers +netG: unet +n_layers_D: 4 +n_layers_G: 7 +norm: instance +init_type: normal +init_gain: 0.02 +no_dropout: False +use_MC: False + +#SegModel +use_segm_model: True +segm_model_path: /path/to/flash/model/ + +#Training: +niters: 30000 +niters_init: 0 +beta1: 0.5 +lambda_id: 1 +lr: 0.0001 +gan_mode: lsgan +pool_size: 50 +lr_policy: linear +niters_linDecay: 100 +niters_stepDecay: 50 +validation_freq: 1000 +saveModelEachNIteration: 10000 +print_memory_usage_freq: 5000 \ No newline at end of file diff --git a/workflow.md b/workflow.md index a8e3bb26e09cfc8f64b2c892f76c6d34932493c5..e738e1ede3cc5cc64c31ba5b131eacfb2ad76f69 100644 --- a/workflow.md +++ b/workflow.md @@ -15,20 +15,26 @@ `CUDA_VISIBLE_DEVICES=0 python train.py --config config.yaml --gridsearch` Directory output should look like this: +``` ├── somewhere │ ├── StainA_StainB │ │ ├── cycle_gan_gen_unet_4_32_dis_n_layers_4_32_batch... │ │ ├── cycle_gan_gen_unet_4_32_dis_n_layers_5_32_batch... │ │ │ ├── Models +``` + 4. Run test_gridseach.py to generate visual_check images to decide which model is best `CUDA_VISIBLE_DEVICES=0 python test_gridsearch.py --config config.yaml` - +``` ├── somewhere │ ├── StainA_StainB │ │ ├── gridsearch_visual_check_4_8.png │ │ ├── cycle_gan_gen_unet_4_32_dis_n_layers_4_32_batch... │ │ ├── cycle_gan_gen_unet_4_32_dis_n_layers_5_32_batch... │ │ │ ├── Models +``` + +5. Copy best model with directory to `somewhere/StainA_StainB/best/ -5. Copy best model with directory to `somewhere/StainA_StainB/best/ \ No newline at end of file +6. run `test.py` and the best model should be found automatically. \ No newline at end of file