# ------------------------------------------------------------------------ # Libraries # ------------------------------------------------------------------------ # General libraries import os import sys import random from datetime import datetime import time import argparse import json # Deep learning libraries import torch from torch import nn from torch.utils.data import DataLoader from torch.optim.lr_scheduler import ReduceLROnPlateau # Custom libraries from utilities import * from landmarks_datasets import * from model.deep_learning import * from model.models import * # Set random seed random.seed(42) np.random.seed(42) torch.manual_seed(42) torch.cuda.manual_seed(42) # ------------------------------------------------------------------------ # MAIN # ------------------------------------------------------------------------ if __name__ == "__main__": # Parse arguments from command line parser = argparse.ArgumentParser() parser.add_argument( "-c", "--config", type=str, default="downstream_task/config/config.json", help="Path to the JSON config file." ) parser.add_argument( "-p", "--load_path", type=str, default=None, help="Path to the model to be loaded." ) args = parser.parse_args() config = json.load(open(args.config)) # Print system info print("----------------------------------------- SYSTEM INFO -----------------------------------------") print("Python version: {}".format(sys.version)) print("Pytorch version: {}".format(torch.__version__)) if "CUDA_VISIBLE_DEVICES" in os.environ: GPU = os.environ["CUDA_VISIBLE_DEVICES"] else: GPU = config["gpu"] os.environ["CUDA_VISIBLE_DEVICES"] = f"{GPU}" device = f"cuda" if torch.cuda.is_available() else "cpu" print(f"Torch GPU Name: {torch.cuda.get_device_name(0)}... Using GPU {GPU}" if device == "cuda" else "Torch GPU not available... Using CPU") print("------------------------------------------------------------------------------------------------") # -------------------------------------------- PATHS ------------- PREFIX = generate_path(config["experiment_path"]) log_file = f"{PREFIX}/experiments_results.txt" DATASET_NAME = config["dataset"]["name"] DATASET_PATH = os.path.join(config["dataset"]["path"], DATASET_NAME) # -------------------------------------------- PARAMETERS ------------- # Dataset parameters SIZE = tuple(config["dataset"]["image_size"]) NUM_CHANNELS = config["dataset"]["image_channels"] SIGMA = config["dataset"]["sigma"] TRAINING_SAMPLES = config["dataset"]["training_samples"] PIN_MEMORY = config["dataset"]["pin_memory"] NUM_WORKERS = 2 if config["dataset"]["num_workers"] == None else config["dataset"]["num_workers"] # Model parameters MODEL_NAME = config["model"]["name"] SSL_MODELS = ["moco", "mocov2", "mocov3", "simclr", "simclrv2", "dino", "barlow_twins", "byol"] if MODEL_NAME == "imagenet": MODEL_NAME = "smpUnet" elif MODEL_NAME == "ddpm": pass elif MODEL_NAME in SSL_MODELS: NUM_CHANNELS = 3 else: raise Exception("Model not found... Choose between: ddpm, imagenet, moco, mocov2, mocov3, simclr, simclrv2, dino, barlow_twins, byol") BACKBONE_NAME = config["model"]["encoder"] # Replace "efficientnet_b0" by "efficientnet-b0" and so on to match the model name BACKBONE_NAME = BACKBONE_NAME.replace("_", "-") if "efficientnet" in BACKBONE_NAME else BACKBONE_NAME PRETRAINED = config["training_protocol"]["scratch"]["apply"] == False NUM_EPOCHS = config["model"]["epochs"] BATCH_SIZE = config["dataset"]["batch_size"] GRAD_ACC = config["dataset"]["grad_accumulation"] LR = config["model"]["lr"] if PRETRAINED else config["model"]["lr"] / 0.1 OPTIMIZER = config["model"]["optimizer"] SCHEDULER = config["model"]["scheduler"] LOSS_FUNCTION = config["model"]["loss_function"] PATIENCE = GRAD_ACC + 5 EARLY_STOPPING = PATIENCE * 2 + 1 print(f"Pretrained: {PRETRAINED} -> the actual learning rate is {LR}") # ---------------------------------------------------------------- DATASET --------- if DATASET_NAME == "chest": train_dataset = Chest(prefix=DATASET_PATH, phase='train', size=SIZE, num_channels=NUM_CHANNELS, sigma=SIGMA) val_dataset = Chest(prefix=DATASET_PATH, phase='validate', size=SIZE, num_channels=NUM_CHANNELS, sigma=SIGMA) test_dataset = Chest(prefix=DATASET_PATH, phase='test', size=SIZE, num_channels=NUM_CHANNELS, sigma=SIGMA) elif DATASET_NAME == "hand": train_dataset = Hand(prefix=DATASET_PATH, phase='train', size=SIZE, num_channels=NUM_CHANNELS, sigma=SIGMA) val_dataset = Hand(prefix=DATASET_PATH, phase='validate', size=SIZE, num_channels=NUM_CHANNELS, sigma=SIGMA) test_dataset = Hand(prefix=DATASET_PATH, phase='test', size=SIZE, num_channels=NUM_CHANNELS, sigma=SIGMA) elif DATASET_NAME == "cephalo": train_dataset = Cephalo(prefix=DATASET_PATH, phase='train', size=SIZE, num_channels=NUM_CHANNELS, sigma=SIGMA) val_dataset = Cephalo(prefix=DATASET_PATH, phase='validate', size=SIZE, num_channels=NUM_CHANNELS, sigma=SIGMA) test_dataset = Cephalo(prefix=DATASET_PATH, phase='test', size=SIZE, num_channels=NUM_CHANNELS, sigma=SIGMA) else: raise Exception("Dataset not found") NUM_LANDMARKS = train_dataset.num_landmarks # ---------------------------------------------------------------- DATA LOADING --------- # Randomly exclude images to reduce the number of samples in the training dataset #random_indices = np.random.choice(len(train_dataset), TRAINING_SAMPLES, replace=False) #print(random_indices) #train_dataset.indexes = [train_dataset.indexes[i] for i in sorted(random_indices)] if TRAINING_SAMPLES == "all": pass else: assert len(train_dataset) >= int(TRAINING_SAMPLES), "The number of training samples is greater than the number of samples in the dataset" train_dataset.indexes = train_dataset.indexes[:int(TRAINING_SAMPLES)] # create dataloaders train_dataloader = DataLoader(train_dataset, batch_size=BATCH_SIZE, shuffle=True, pin_memory=PIN_MEMORY, num_workers=NUM_WORKERS, drop_last=False) val_dataloader = DataLoader(val_dataset, batch_size=BATCH_SIZE, shuffle=False, pin_memory=PIN_MEMORY, num_workers=NUM_WORKERS) test_dataloader = DataLoader(test_dataset, batch_size=BATCH_SIZE, shuffle=False, pin_memory=PIN_MEMORY, num_workers=NUM_WORKERS) # ---------------------------------------------------------------- LOG FILE --------- # Print dataset and experiment info in log file res_file = open(log_file, 'a') print(f"\n\n\n {datetime.now()} ---------------------- {DATASET_NAME} -------------------------------------------", file=res_file) print(f"SIZE: {SIZE} | BATCH: {BATCH_SIZE} | GRAD ACC: {GRAD_ACC} | SIGMA: {SIGMA} | LR: {LR} | CHANNELS: {NUM_CHANNELS} | Train Samples {TRAINING_SAMPLES}", file=res_file) print(f"samples -> Train: {len(train_dataset)} | Val: {len(val_dataset)} | Test: {len(test_dataset)}", file=res_file) print(f"dataloaders -> Train: {len(train_dataloader)} | Val: {len(val_dataloader)} | Test: {len(test_dataloader)}", file=res_file) res_file.close() print(f"\n\n\n {datetime.now()} ---------------------- {DATASET_NAME} -------------------------------------------") print(f"SIZE: {SIZE} | BATCH: {BATCH_SIZE} | GRAD ACC: {GRAD_ACC} | SIGMA: {SIGMA} | LR: {LR} | CHANNELS: {NUM_CHANNELS} | Train Samples {TRAINING_SAMPLES}") print(f"samples -> Train: {len(train_dataset)} | Val: {len(val_dataset)} | Test: {len(test_dataset)}") print(f"dataloaders -> Train: {len(train_dataloader)} | Val: {len(val_dataloader)} | Test: {len(test_dataloader)}") # ---------------------------------------------------------------- MODEL --------- if MODEL_NAME == "smpUnet" and BACKBONE_NAME is not None: if PRETRAINED == True and config["training_protocol"]["finetuning"]["resume"] == False: model = smpUnet( encoder_name=BACKBONE_NAME, encoder_weights="imagenet", in_channels=NUM_CHANNELS, classes=NUM_LANDMARKS ).to(device) model_name = f"{MODEL_NAME}/{model.encoder_name}/{model.encoder_weights}" else: model = smpUnet( encoder_name=BACKBONE_NAME, encoder_weights=None, in_channels=NUM_CHANNELS, classes=NUM_LANDMARKS ).to(device) model_name = f"{MODEL_NAME}/{model.encoder_name}/random" elif MODEL_NAME in SSL_MODELS and BACKBONE_NAME is not None: model = smpUnet( encoder_name=BACKBONE_NAME, encoder_weights=None, in_channels=NUM_CHANNELS, classes=NUM_LANDMARKS ).to(device) assert os.path.exists(f'{config["training_protocol"]["finetuning"]["path"]}'), f"{BACKBONE_NAME} pretrained model path not found" model.encoder.load_state_dict(torch.load(f'{config["training_protocol"]["finetuning"]["path"]}', map_location=device)) model_name = f"{MODEL_NAME}/{model.encoder_name}" elif MODEL_NAME == "ddpm": BACKBONE_NAME = "" model = Unet( dim=SIZE[0], channels=NUM_CHANNELS, dim_mults=[1,2,4,8], self_condition=True, resnet_block_groups=4, att_heads=4, att_res=32 ).to(device) if PRETRAINED == True and config["training_protocol"]["finetuning"]["resume"] == False: model_name = f"{MODEL_NAME}/pretrained" checkpoint = torch.load(config["training_protocol"]["finetuning"]["path"], map_location=device) model.load_state_dict(checkpoint["model_state_dict"]) pretrained_epoch = checkpoint.get("epoch", "undefined") #print(f"Loaded model weights from {checkpoint['epoch']} epoch with fid {checkpoint['fid']}") del checkpoint """ # freeze downsampling layers for name, param in model.named_parameters(): if 'downs' in name: param.requires_grad = False """ else: model_name = f"{MODEL_NAME}/random" # change the number of output channels of the final convolutional layer model.final_conv = nn.Conv2d(model.final_conv.in_channels, NUM_LANDMARKS, 1) # ---------------------------------------------------------------- COUNT PARAMS --------- table, total_params = count_parameters(model) res_file = open(log_file, 'a') #print(table, file=res_file) print(f"Total Trainable Params: {total_params}", file=res_file) res_file.close() # ---------------------------------------------------------------- LOSS FUNCTION --------- if LOSS_FUNCTION == "CrossEntropyLoss": loss_fn = nn.CrossEntropyLoss() else: raise Exception("Loss function not found... Choose between: CrossEntropyLoss") # ---------------------------------------------------------------- OPTIMIZER --------- if OPTIMIZER == "Adam": optimizer = torch.optim.Adam(params=model.parameters(), lr=LR) elif OPTIMIZER == "AdamW": optimizer = torch.optim.AdamW(params=model.parameters(), lr=LR) else: raise Exception("Optimizer not found... Choose between: Adam, AdamW") # ---------------------------------------------------------------- SCHEDULER --------- if SCHEDULER == "ReduceLROnPlateau": scheduler = ReduceLROnPlateau(optimizer, patience=PATIENCE, factor=0.5, verbose=True) else: raise Exception("Scheduler not found... Choose between: ReduceLROnPlateau") # ---------------------------------------------------------------- MODEL PATHS --------- save_model_path = f"{PREFIX}/{DATASET_NAME}/size{SIZE[0]}x{SIZE[1]}_ch{NUM_CHANNELS}_samples{TRAINING_SAMPLES}/{model_name}" use_validation_set_for_inference = True if config["inference_protocol"]["use_validation_set_for_inference"]=="true" else False if use_validation_set_for_inference==True and PRETRAINED == True and config["model"]["name"] == "ddpm" and config["training_protocol"]["finetuning"]["resume"] == False: save_model_path = f"{save_model_path}/val/epoch{pretrained_epoch}" print(save_model_path) save_model_path = generate_path(save_model_path) load_model_path = os.path.join(save_model_path, f"best_checkpoint.pt") # ---------------------------------------------------------------- TRAINING --------- start_time = time.time() if config["training_protocol"]["apply"] == True: # Assert if the model is being trained from scratch or if it is being fine-tuned assert config["training_protocol"]["scratch"]["apply"] != config["training_protocol"]["finetuning"]["apply"], "Choose only one training protocol (scratch or finetuning)" print(f"Training model on the {'validation' if use_validation_set_for_inference==True else 'test'} dataset") # Get the training protocol if config["training_protocol"]["scratch"]["apply"] == True: loss_results = train_and_validate(model, device, train_dataloader, val_dataloader, optimizer, scheduler, loss_fn, NUM_EPOCHS, save_model_path, patience=EARLY_STOPPING, useGradAcc=GRAD_ACC, continue_training=config["training_protocol"]["scratch"]["resume"]) elif config["training_protocol"]["finetuning"]["apply"] == True: DIFFERENT_DATASET = True if config["training_protocol"]["finetuning"]["different_dataset"] == "true" else False if DIFFERENT_DATASET == True: load_path = config["training_protocol"]["finetuning"]["path"] assert os.path.exists(load_path), "Pretrained model path not found" loss_results = fine_tune(model, device, train_dataloader, val_dataloader, optimizer, scheduler, loss_fn, NUM_EPOCHS, load_path, save_model_path, patience=EARLY_STOPPING, useGradAcc=GRAD_ACC) else: loss_results = train_and_validate(model, device, train_dataloader, val_dataloader, optimizer, scheduler, loss_fn, NUM_EPOCHS, save_model_path, patience=EARLY_STOPPING, useGradAcc=GRAD_ACC, continue_training=config["training_protocol"]["finetuning"]["resume"]) else: raise Exception("Training protocol not found... Choose between: scratch, finetuning") # ---------------------------------------------------------------- TESTING -------- end_time = time.time() if args.load_path is not None: load_model_path = args.load_path if config["inference_protocol"]["apply"] == True: print(f"Testing model on the {'validation' if use_validation_set_for_inference==True else 'test'} dataset") res_file = open(log_file, 'a') print(f"Testing model on the {'validation' if use_validation_set_for_inference==True else 'test'} dataset", file=res_file) res_file.close() if use_validation_set_for_inference == True: test_loss, results, mre, sdr, mse, mAP_heatmaps, mAP_keypoints, iou, epoch = evaluate(model, device, val_dataloader, loss_fn, load_model_path, NUM_LANDMARKS, sigma=SIGMA, res_file_path=log_file) else: test_loss, results, mre, sdr, mse, mAP_heatmaps, mAP_keypoints, iou, epoch = evaluate(model, device, test_dataloader, loss_fn, load_model_path, NUM_LANDMARKS, sigma=SIGMA, res_file_path=log_file) # ---------------------------------------------------------------- TELEGRAM --------- # Free GPU cache and RAM memory #free_gpu_cache() sdr_str = '\n'.join(f'\tThresholds {k}: {v*100:.2f}' for k, v in sorted(sdr.items())) message = ( f"{DATASET_NAME} | Train Samples: {TRAINING_SAMPLES} \n" f"Model: {model_name} \n" f"Shape:[{SIZE}, {SIZE}, {NUM_CHANNELS}] \n" f"Sigma: {SIGMA} \n" f"Batch: {BATCH_SIZE}x{GRAD_ACC} \n" f"Time: {time.strftime('%H:%M:%S', time.gmtime(end_time - start_time))} \n" f"MRE: {mre:.2f} \n\n" f"SDR: \n{sdr_str} \n" ) send_telegram_message(message) # Save the results in a file results_dir = f"outputs/{DATASET_NAME}_{MODEL_NAME}" os.makedirs(f'{results_dir}', exist_ok=True) if not os.path.exists(f'{results_dir}/outputs_{DATASET_NAME}_{MODEL_NAME}_{BACKBONE_NAME}_{TRAINING_SAMPLES}.txt'): with open(f'{results_dir}/outputs_{DATASET_NAME}_{MODEL_NAME}_{BACKBONE_NAME}_{TRAINING_SAMPLES}.txt', 'w') as f: print(f"\n\n{DATASET_NAME} | {MODEL_NAME} | {BACKBONE_NAME} | {TRAINING_SAMPLES}", file=f) print(f"Shape: [{SIZE}, {SIZE}, {NUM_CHANNELS}] | Sigma: {SIGMA} | Batch: {BATCH_SIZE}x{GRAD_ACC}", file=f) print(f"Time: {time.strftime('%H:%M:%S', time.gmtime(end_time - start_time))}", file=f) print(f"MRE: {mre:.2f}", file=f) print(f"SDR: \n{sdr_str}", file=f) print(f"MSE: {mse:.2f}", file=f) print(f"IOU: {iou:.2f}", file=f) print(f"mAP Heatmaps: {mAP_heatmaps:.2f}", file=f) print(f"mAP Keypoints: {mAP_keypoints:.2f}", file=f) print(f"Epoch: {epoch}", file=f) print(f"Test Loss: {test_loss:.2f}", file=f) print(f"Total Trainable Params: {total_params}", file=f) print(f"Model Path: {save_model_path}", file=f) else: with open(f'{results_dir}/outputs_{DATASET_NAME}_{MODEL_NAME}_{BACKBONE_NAME}_{TRAINING_SAMPLES}.txt', 'a') as f: print(f"\n\n{DATASET_NAME} | {MODEL_NAME} | {BACKBONE_NAME} | {TRAINING_SAMPLES}", file=f) print(f"Shape: [{SIZE}, {SIZE}, {NUM_CHANNELS}] | Sigma: {SIGMA} | Batch: {BATCH_SIZE}x{GRAD_ACC}", file=f) print(f"Time: {time.strftime('%H:%M:%S', time.gmtime(end_time - start_time))}", file=f) print(f"MRE: {mre:.2f}", file=f) print(f"SDR: \n{sdr_str}", file=f) print(f"MSE: {mse:.2f}", file=f) print(f"IOU: {iou:.2f}", file=f) print(f"mAP Heatmaps: {mAP_heatmaps:.2f}", file=f) print(f"mAP Keypoints: {mAP_keypoints:.2f}", file=f) print(f"Epoch: {epoch}", file=f) print(f"Test Loss: {test_loss:.2f}", file=f) print(f"Total Trainable Params: {total_params}", file=f) print(f"Model Path: {save_model_path}", file=f)