fixed graphs

.gitignore

 logs/*
 lightning_logs/*
 test/*
+DeepGraft_Project_Plan_12.7.22.pdf
+monai_test.json

DeepGraft/Resnet50.yaml → DeepGraft/Inception_norm_rest.yaml

@@ -4,46 +4,52 @@ General:
     fp16: True
     amp_level: O2
     precision: 16
-    multi_gpu_mode: dp
-    gpus: [0]
-    epochs: &epoch 200 
+    multi_gpu_mode: ddp
+    gpus: [0, 1]
+    epochs: &epoch 500 
     grad_acc: 2
     frozen_bn: False
-    patience: 200
-    server: test #train #test
-    log_path: logs/
+    patience: 50
+    server: train #train #test
+    log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/
 
 Data:
     dataset_name: custom
     data_shuffle: False
-    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
-    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_bin.json'
-    fold: 0
-    nfold: 4
+    mixup: False
+    aug: True
+    cache: False
+    data_dir: '/home/ylan/data/DeepGraft/224_256uM_annotated/'
+    label_file: '/home/ylan/data/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rest_val_1.json'
+    fold: 1
+    nfold: 3
+    cross_val: False
 
     train_dataloader:
-        batch_size: 1 
-        num_workers: 8
+        batch_size: 500 
+        num_workers: 4
 
     test_dataloader:
         batch_size: 1
-        num_workers: 8
-
-        
+        num_workers: 4
 
 Model:
-    name: resnet50
+    name: inception
     n_classes: 2
+    backbone: inception
+    in_features: 2048
+    out_features: 1024
 
 
 Optimizer:
-    opt: lookahead_radam
+    opt: adam
     lr: 0.0002
     opt_eps: null 
     opt_betas: null
     momentum: null 
-    weight_decay: 0.00001
+    weight_decay: 0.01
 
 Loss:
     base_loss: CrossEntropyLoss
     
+

DeepGraft/Resnet18_img_norm_rest.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16
+    multi_gpu_mode: ddp
+    gpus: [0, 1]
+    epochs: &epoch 500 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 50
+    server: train #train #test
+    log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    mixup: True
+    aug: True
+    cache: False
+    data_dir: '/home/ylan/data/DeepGraft/224_256uM_annotated/'
+    label_file: '/home/ylan/data/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rest_val_1.json'
+    fold: 1
+    nfold: 3
+    cross_val: False
+
+    train_dataloader:
+        batch_size: 1000 
+        num_workers: 4
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 4
+
+Model:
+    name: resnet18
+    n_classes: 2
+    backbone: resnet18
+    in_features: 2048
+    out_features: 1024
+
+
+Optimizer:
+    opt: Adam
+    lr: 0.0001
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.01
+
+Loss:
+    base_loss: CrossEntropyLoss
+    
+

DeepGraft/TransMIL_feat_norm_rej_rest.yaml

@@ -3,27 +3,30 @@ General:
     seed: 2021
     fp16: True
     amp_level: O2
-    precision: 16 
-    multi_gpu_mode: dp
-    gpus: [0]
+    precision: 32
+    multi_gpu_mode: ddp
+    gpus: [0, 1]
     epochs: &epoch 1000 
     grad_acc: 2
     frozen_bn: False
-    patience: 100
-    server: test #train #test
+    patience: 300
+    server: train #train #test
     log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/
 
 Data:
     dataset_name: custom
     data_shuffle: False
-    data_dir: '/home/ylan/data/DeepGraft/224_128um_v2/'
-    label_file: '/home/ylan/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rej_rest.json'
+    mixup: True
+    aug: True
+    cache: False
+    data_dir: '/home/ylan/data/DeepGraft/224_256uM_annotated/'
+    label_file: '/home/ylan/data/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rej_rest_val_1.json'
     fold: 1
     nfold: 3
     cross_val: False
 
     train_dataloader:
-        batch_size: 1 
+        batch_size: 100
         num_workers: 4
 
     test_dataloader:
@@ -34,13 +37,13 @@ Model:
     name: TransMIL
     n_classes: 3
     backbone: features
-    in_features: 512
+    in_features: 2048
     out_features: 512
 
 
 Optimizer:
     opt: lookahead_radam
-    lr: 0.0002
+    lr: 0.002
     opt_eps: null 
     opt_betas: null
     momentum: null 

DeepGraft/TransMIL_feat_norm_rest.yaml

@@ -4,9 +4,9 @@ General:
     fp16: True
     amp_level: O2
     precision: 16
-    multi_gpu_mode: dp
+    multi_gpu_mode: ddp
     gpus: [0, 1]
-    epochs: &epoch 500 
+    epochs: &epoch 1000 
     grad_acc: 2
     frozen_bn: False
     patience: 50
@@ -16,16 +16,17 @@ General:
 Data:
     dataset_name: custom
     data_shuffle: False
-    mixup: False
+    mixup: True
     aug: True
-    data_dir: '/home/ylan/data/DeepGraft/224_128uM_annotated/'
-    label_file: '/home/ylan/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rest.json'
+    cache: False
+    data_dir: '/home/ylan/data/DeepGraft/224_256uM_annotated/'
+    label_file: '/home/ylan/data/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rest_val_1.json'
     fold: 1
     nfold: 3
     cross_val: False
 
     train_dataloader:
-        batch_size: 1 
+        batch_size: 100
         num_workers: 4
 
     test_dataloader:
@@ -37,12 +38,12 @@ Model:
     n_classes: 2
     backbone: features
     in_features: 2048
-    out_features: 1024
+    out_features: 512
 
 
 Optimizer:
-    opt: Adam
-    lr: 0.0001
+    opt: lookahead_radam
+    lr: 0.002
     opt_eps: null 
     opt_betas: null
     momentum: null 

DeepGraft/TransMIL_feat_rej_rest.yaml

@@ -4,43 +4,46 @@ General:
     fp16: True
     amp_level: O2
     precision: 16
-    multi_gpu_mode: dp
-    gpus: [0]
-    epochs: &epoch 500 
+    multi_gpu_mode: ddp
+    gpus: [0, 1]
+    epochs: &epoch 1000 
     grad_acc: 2
     frozen_bn: False
     patience: 50
-    server: test #train #test
+    server: train #train #test
     log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/
 
 Data:
     dataset_name: custom
     data_shuffle: False
-    data_dir: '/home/ylan/data/DeepGraft/224_128um_v2/'
-    label_file: '/home/ylan/DeepGraft/training_tables/dg_split_PAS_HE_Jones_rej_rest.json'
+    mixup: True
+    aug: True
+    cache: False
+    data_dir: '/home/ylan/data/DeepGraft/224_256uM_annotated/'
+    label_file: '/home/ylan/data/DeepGraft/training_tables/dg_split_PAS_HE_Jones_rej_rest_val_1.json'
     fold: 1
     nfold: 3
     cross_val: False
 
     train_dataloader:
-        batch_size: 1 
-        num_workers: 8
+        batch_size: 100
+        num_workers: 4
 
     test_dataloader:
         batch_size: 1
-        num_workers: 8
+        num_workers: 4
 
 Model:
     name: TransMIL
     n_classes: 2
     backbone: features
-    in_features: 1024
+    in_features: 2048
     out_features: 512
 
 
 Optimizer:
     opt: lookahead_radam
-    lr: 0.0002
+    lr: 0.002
     opt_eps: null 
     opt_betas: null
     momentum: null 

DeepGraft/TransMIL_retccl_norm_rest.yaml

@@ -16,14 +16,14 @@ General:
 Data:
     dataset_name: custom
     data_shuffle: False
-    data_dir: '/home/ylan/data/DeepGraft/224_128um_v2/'
-    label_file: '/home/ylan/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rest.json'
+    data_dir: '/home/ylan/data/DeepGraft/224_256uM_annotated/'
+    label_file: '/home/ylan/data/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rest_img_val_1.json'
     fold: 1
     nfold: 3
     cross_val: False
 
     train_dataloader:
-        batch_size: 1 
+        batch_size: 5 
         num_workers: 4
 
     test_dataloader:
@@ -34,8 +34,8 @@ Model:
     name: TransMIL
     n_classes: 2
     backbone: retccl
-    in_features: 512
-    out_features: 1024
+    in_features: 2048
+    out_features: 512
 
 
 Optimizer:

DeepGraft/TransformerMIL_feat_norm_rest.yaml

@@ -10,14 +10,14 @@ General:
     grad_acc: 2
     frozen_bn: False
     patience: 100
-    server: test #train #test
+    server: train #train #test
     log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/
 
 Data:
     dataset_name: custom
     data_shuffle: False
-    data_dir: '/home/ylan/data/DeepGraft/224_128um_v2/'
-    label_file: '/home/ylan/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rest.json'
+    data_dir: '/home/ylan/data/DeepGraft/224_256uM_annotated/'
+    label_file: '/home/ylan/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rest_val_1.json'
     fold: 1
     nfold: 3
     cross_val: False
@@ -34,8 +34,8 @@ Model:
     name: TransformerMIL
     n_classes: 2
     backbone: features
-    in_features: 512
-    out_features: 1024
+    in_features: 2048
+    out_features: 512
 
 
 Optimizer:

DeepGraft/Vit_norm_rest.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16
+    multi_gpu_mode: ddp
+    gpus: [0, 1]
+    epochs: &epoch 500 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 50
+    server: train #train #test
+    log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    mixup: True
+    aug: True
+    cache: False
+    data_dir: '/home/ylan/data/DeepGraft/224_128uM_annotated/'
+    label_file: '/home/ylan/DeepGraft/training_tables/dg_split_PAS_HE_Jones_norm_rest_val_1.json'
+    fold: 1
+    nfold: 3
+    cross_val: False
+
+    train_dataloader:
+        batch_size: 500 
+        num_workers: 4
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 4
+
+Model:
+    name: vit
+    n_classes: 2
+    backbone: vit
+    in_features: 2048
+    out_features: 1024
+
+
+Optimizer:
+    opt: Adam
+    lr: 0.0001
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.01
+
+Loss:
+    base_loss: CrossEntropyLoss
+    
+

code/MyLoss/loss_factory.py

@@ -27,10 +27,10 @@ def create_loss(args, n_classes, w1=1.0, w2=0.5):
     ### MulticlassJaccardLoss(classes=np.arange(11)
     # mode = args.base_loss #BINARY_MODE \MULTICLASS_MODE \MULTILABEL_MODE 
     loss = None
-    print(conf_loss)
+    # print(conf_loss)
     if hasattr(nn, conf_loss): 
         loss = getattr(nn, conf_loss)()
-        # loss = getattr(nn, conf_loss)(label_smoothing=0.5) 
+        # loss = getattr(nn, conf_loss)(label_smoothing=0.1) 
     #binary loss
     elif conf_loss == "focal":
         loss = FocalLoss_Ori(n_classes)

code/cufile.log

+ 21-12-2022 16:48:14:373 [pid=1690629 tid=1690629] NOTICE  cufio-drv:625 running in compatible mode
+ 22-12-2022 10:31:41:400 [pid=1904890 tid=1904890] NOTICE  cufio-drv:625 running in compatible mode
+ 22-12-2022 10:52:13:216 [pid=1909914 tid=1909914] NOTICE  cufio-drv:625 running in compatible mode
+ 22-12-2022 11:02:15:996 [pid=1912278 tid=1912278] NOTICE  cufio-drv:625 running in compatible mode
+ 22-12-2022 11:15:17:212 [pid=1915495 tid=1915495] NOTICE  cufio-drv:625 running in compatible mode
+ 02-01-2023 00:11:43:868 [pid=931838 tid=931838] NOTICE  cufio-drv:625 running in compatible mode

code/datasets/__init__.py

-
-from .custom_jpg_dataloader import JPGMILDataloader
+# from .custom_jpg_dataloader import JPGMILDataloader
+from .jpg_dataloader import JPGMILDataloader
 from .data_interface import MILDataModule
 from .fast_tensor_dl import FastTensorDataLoader