save

Zero-shot_classification/configs/chexray_mavl.yaml

@@ -1,9 +1,9 @@
-test_file: '/data/data/xray14/test.csv'
+test_file: '/data/VLM/data/xray14/test.csv'
 disease_book: 'observation explanation.json'
 concept_book: '../Pretrain/concept_gen/gpt4_mimic.json'
 
 dataset: 'chexray'
-root: '/data/data/xray14/cxr'
+root: '/data/VLM/data/xray14/cxr'
 model: mavl
 model_path: '../checkpoints/checkpoint_full_40.pth'
 
@@ -21,4 +21,4 @@ H: 4
 self_attention: True
 text_encoder: 'emilyalsentzer/Bio_ClinicalBERT'
 pretrained: True
-mode: feature
+mode: text

Zero-shot_classification/configs/covid_mavl.yaml

@@ -1,9 +1,9 @@
-test_file: '/data/data/covidx-cxr2/test_split.csv'
+test_file: '/data/VLM/data/covidx-cxr2/test_split.csv'
 disease_book: 'observation explanation.json'
 concept_book: '../Pretrain/concept_gen/gpt4_mimic.json'
 
 dataset: 'covid-cxr2'
-root: '/data/data/covidx-cxr2/train'
+root: '/data/VLM/data/covidx-cxr2/train'
 model: 'mavl'
 model_path: '../checkpoints/checkpoint_full_40.pth'
 

Zero-shot_classification/configs/padchest_rare_mavl.yaml

@@ -1,10 +1,10 @@
-test_file: '/data/data/PadChest/test.csv'
+test_file: '/data/VLM/data/PadChest/test.csv'
 disease_book: 'observation explanation_padchest_rare.json'
 # concept_book: '../Pretrain/concept_gen/gpt4_mimic_padchest_rare.json'
 concept_book: '../Pretrain/concept_gen/gpt4_mimic_padchest_rare.json'
 
 dataset: 'padchest'
-root: '/data/data/PadChest/'
+root: '/data/VLM/data/PadChest/'
 model: 'mavl'
 model_path: '../checkpoints/checkpoint_full_40.pth'
 
@@ -22,5 +22,5 @@ H: 4
 text_encoder: 'emilyalsentzer/Bio_ClinicalBERT'
 self_attention: True
 pretrained: True
-mode: text
+mode: feature
 class: rare

Zero-shot_classification/configs/padchest_seen_mavl.yaml

@@ -1,17 +1,15 @@
 test_file: '/data/VLM/data/PadChest/test.csv'
 disease_book: 'observation explanation_padchest_rare.json'
-# concept_book: '../Pretrain/concept_gen/gpt4_mimic_padchest_rare.json'
 concept_book: '../Pretrain/concept_gen/gpt4_mimic_padchest_rare.json'
 
 dataset: 'padchest'
 root: '/data/VLM/data/PadChest/'
 model: 'mavl'
-# model_path: '../checkpoints/checkpoint_short_37.pth'
-model_path: '../../medslip/checkpoints/cl_global_1e-1_true/checkpoint_40.pth'
+model_path: '../checkpoints/checkpoint_37.pth'
 
 
 image_res: 224
-test_batch_size: 512
+test_batch_size: 1024
 
 d_model: 256
 base_model: 'resnet50'

Zero-shot_classification/configs/padchest_unseen_mavl.yaml

@@ -1,10 +1,10 @@
-test_file: '/data/data/PadChest/test.csv'
+test_file: '/data/VLM/data/PadChest/test.csv'
 disease_book: 'observation explanation_padchest_rare.json'
 # concept_book: '../Pretrain/concept_gen/gpt4_mimic_padchest_rare.json'
 concept_book: '../Pretrain/concept_gen/gpt4_mimic_padchest_rare.json'
 
 dataset: 'padchest'
-root: '/data/data/PadChest/'
+root: '/data/VLM/data/PadChest/'
 model: 'mavl'
 model_path: '../checkpoints/checkpoint_full_40.pth'
 
@@ -22,5 +22,5 @@ H: 4
 text_encoder: 'emilyalsentzer/Bio_ClinicalBERT'
 self_attention: True
 pretrained: True
-mode: text
+mode: feature
 class: unseen

Zero-shot_classification/configs/rsna_mavl.yaml

@@ -5,7 +5,7 @@ concept_book: '../Pretrain/concept_gen/gpt4_mimic.json'
 dataset: 'rsna'
 root: '/data/VLM/data/rsna'
 model: mavl
-model_path: '../checkpoints/checkpoint_full_46.pth'
+model_path: '../checkpoints/checkpoint_full_40.pth'
 
 
 image_res: 224

Zero-shot_classification/configs/siim_mavl.yaml

@@ -1,9 +1,9 @@
-test_file: '/data/data/siimacr/test.csv'
+test_file: '/data/VLM/data/siimacr/test.csv'
 disease_book: 'observation explanation.json'
 concept_book: '../Pretrain/concept_gen/gpt4_mimic.json'
 
 dataset: 'siim'
-root: '/data/data/siimacr'
+root: '/data/VLM/data/siimacr'
 model: mavl
 model_path: '../checkpoints/checkpoint_full_40.pth'
 

Zero-shot_classification/test.py

@@ -146,6 +146,16 @@ def get_tokenizer(tokenizer,target_text):
 
     return target_tokenizer
 
+def log_to_csv(filename, data, firstrow=None):
+    file_exists = os.path.isfile(filename)
+    with open(filename, 'a', newline='') as csvfile:
+        writer = csv.writer(csvfile)
+        if not file_exists:
+            # Write header if file doesn't exist
+            writer.writerow(firstrow)  # Example header
+        writer.writerow(data)
+
+
 def test(config):
     device = accelerator.device
     print("Total CUDA devices: ", torch.cuda.device_count())
@@ -452,7 +462,10 @@ def test(config):
 
         # Write the data rows
         csv_writer.writerows(table_data)
+<<<<<<< HEAD
 
+=======
+>>>>>>> c7e9f45 (update result logs)
     print(table)
     log_csv = True
     if log_csv:
@@ -466,12 +479,17 @@ def test(config):
         header = ['Dataset',  "Accuracy", "Max F1", "AUC ROC", "Precision", "Recall"]
         log_to_csv(csv_filename, data, header)
 
+<<<<<<< HEAD
     # print('The average f1 is {F1_avg:.4f}'.format(F1_avg=f1_avg))
     # print('The average ACC is {ACC_avg:.4f}'.format(ACC_avg=acc_avg))
     # for i in range(len(target_class)):
     #     print('F1 of {} is {}'.format(target_class[i], max_f1s[i]))
     #     print('ACC of {} is {}'.format(target_class[i], accs[i]))
 
+=======
+    # Print the table
+
+>>>>>>> c7e9f45 (update result logs)
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
@@ -485,7 +503,11 @@ def test(config):
     accelerator = Accelerator()
     if args.model_path:
         config['model_path'] = args.model_path
+<<<<<<< HEAD
 
+=======
+
+>>>>>>> c7e9f45 (update result logs)
     os.environ["CUDA_VISIBLE_DEVICES"] = args.gpu
     if args.gpu != '-1':
         torch.cuda.current_device()

Zero-shot_classification/test.sh

@@ -1,3 +1,4 @@
+<<<<<<< HEAD
 filenames=(chexpert_mavl chexray_mavl covid_mavl rsna_mavl siim_mavl padchest_rare_mavl padchest_seen_mavl padchest_unseen_mavl)
 ckpts=(25 28 31 34 37 state)
 # model_name=output_masked_text5e-1
@@ -6,4 +7,22 @@ for filename in "${filenames[@]}"; do
     for ckpt in "${ckpts[@]}"; do
         CUDA_VISIBLE_DEVICES=0 python test.py --config configs/${filename}.yaml --model_path ../checkpoints/${model_name}/checkpoint_${ckpt}.pth
     done
-done
+done
+=======
+# filenames=(chexpert_mavl chexray_mavl covid_mavl rsna_mavl siim_mavl padchest_rare_mavl padchest_seen_mavl padchest_unseen_mavl)
+filenames=(padchest_unseen_mavl)
+# model_name=output_masked_text5e-1
+for filename in "${filenames[@]}"; do
+    CUDA_VISIBLE_DEVICES=0 python test.py --config configs/${filename}.yaml --model_path ../checkpoints/checkpoint_full_40.pth
+done
+
+for filename in "${filenames[@]}"; do
+    CUDA_VISIBLE_DEVICES=0 python test.py --config configs/${filename}.yaml --model_path ../checkpoints/checkpoint_full_46.pth
+done
+
+# for filename in "${filenames[@]}"; do
+#     CUDA_VISIBLE_DEVICES=0 python test.py --config configs/${filename}.yaml --model_path ../checkpoints/checkpoint_short_37.pth
+# done
+
+
+>>>>>>> c7e9f45 (update result logs)