fix finetuning

config/config_cspca_train.yaml

@@ -7,10 +7,10 @@ tile_size: !!int 64
 depth: !!int 3
 use_heatmap: !!bool True
 workers: !!int 6
-checkpoint_pirads: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/models/pirads.pt
+checkpoint_pirads: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/logs/pirads_training/model_47.pt
 epochs: !!int 80
 batch_size: !!int 8
-optim_lr: !!float 2e-4
+optim_lr: !!float 2e-5
 
 
 

job_scripts/train_cspca.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
-#SBATCH --job-name=cspca_training       # Specify job name
+#SBATCH --job-name=cspca_train_47      # Specify job name
 #SBATCH --partition=gpu               # Specify partition name
 #SBATCH --mem=128G   
 #SBATCH --gres=gpu:1             
 #SBATCH --time=48:00:00               # Set a limit on the total run time
-#SBATCH --output=/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/git_updated/Prostate-Foundation/MIL/logs/%x/log.o%j      # File name for standard output
-#SBATCH --error=/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/git_updated/Prostate-Foundation/MIL/logs/%x/log.e%j       # File name for standard error output
+#SBATCH --output=/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/logs/%x/log.o%j      # File name for standard output
+#SBATCH --error=/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/logs/%x/log.e%j        # File name for standard error output
 #SBATCH --mail-user=anirudh.balaraman@charite.de
 #SBATCH --mail-type=END,FAIL
 
@@ -13,7 +13,7 @@
 source /etc/profile.d/conda.sh
 conda activate foundation
 
-RUNDIR="/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/git_updated/Prostate-Foundation"
+RUNDIR="/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate"
 
 
-srun python -u $RUNDIR/MIL/new_folder/run_cspca.py --mode train --config $RUNDIR/MIL/new_folder/config/config_cspca_train.yaml
+srun python -u $RUNDIR/run_cspca.py --mode train --config $RUNDIR/config/config_cspca_train.yaml

requirements.txt

@@ -14,6 +14,7 @@ triton==3.1.0
 
 # ---- MONAI / medical imaging ----
 monai==1.4.0
+itk>=5.3.0
 SimpleITK==2.4.0
 pynrrd==1.1.1
 nibabel==5.3.2
@@ -35,7 +36,6 @@ tensorboard==2.18.0
 
 # ---- Utilities ----
 tqdm==4.67.1
-gdown==5.2.0
 requests
 filelock
 packaging
@@ -44,7 +44,4 @@ packaging
 streamlit==1.50.0
 
 # ---- Grad-CAM ----
-grad-cam @ git+https://github.com/jacobgil/pytorch-grad-cam.git@781dbc0d16ffa95b6d18b96b7b829840a82d93d1
-
-# ---- Your external dependency ----
--e git+https://github.com/ai-assisted-healthcare/AIAH_utility.git@368233822b057b6bfef88f9e4b23c2967ae7bb35#egg=AIAH_utility
+grad-cam @ git+https://github.com/jacobgil/pytorch-grad-cam.git@781dbc0d16ffa95b6d18b96b7b829840a82d93d1

run_pirads.py

@@ -75,7 +75,7 @@ def main_worker(args):
         val_loss_min = float("inf")
         epochs_no_improve = 0
         for epoch in range(start_epoch, n_epochs):
-            logging.info(time.ctime(), "Epoch:", epoch)
+            logging.info(f"{time.ctime()} | Epoch: {epoch}")
             epoch_time = time.time()
             train_loss, train_acc, train_att_loss, batch_norm = train_epoch(
                 model, train_loader, optimizer, scaler=scaler, epoch=epoch, args=args

src/utils.py

@@ -35,7 +35,6 @@ def save_cspca_checkpoint(model, val_metric, model_dir):
         "auc": val_metric["auc"],
         "sensitivity": val_metric["sensitivity"],
         "specificity": val_metric["specificity"],
-        "state": val_metric["state"],
         "state_dict": state_dict,
     }
     torch.save(save_dict, os.path.join(model_dir, "cspca_model.pth"))