debug = 0 from pathlib import Path import numpy as np import matplotlib.pyplot as plt from utils import sample_prompt , main_prompt from collections import defaultdict import torchvision.transforms as transforms import torch from torch import nn import torch.nn.functional as F from segment_anything.utils.transforms import ResizeLongestSide import albumentations as A from albumentations.pytorch import ToTensorV2 import numpy as np from einops import rearrange import random from tqdm import tqdm from time import sleep from data import * from time import time from PIL import Image from sklearn.model_selection import KFold from shutil import copyfile from args import get_arguments args = get_arguments() def save_img(img, dir): img = img.clone().cpu().numpy() + 100 if len(img.shape) == 3: img = rearrange(img, "c h w -> h w c") img_min = np.amin(img, axis=(0, 1), keepdims=True) img = img - img_min img_max = np.amax(img, axis=(0, 1), keepdims=True) img = (img / img_max * 255).astype(np.uint8) # grey_img = Image.fromarray(img[:, :, 0]) img = Image.fromarray(img) else: img_min = img.min() img = img - img_min img_max = img.max() if img_max != 0: img = img / img_max * 255 img = Image.fromarray(img).convert("L") img.save(dir) class loss_fn(torch.nn.Module): def __init__(self, alpha=0.7, gamma=2.0, epsilon=1e-5): super(loss_fn, self).__init__() self.alpha = alpha self.gamma = gamma self.epsilon = epsilon def tversky_loss(self, y_pred, y_true, alpha=0.8, beta=0.2, smooth=1e-2): y_pred = torch.sigmoid(y_pred) y_true_pos = torch.flatten(y_true) y_pred_pos = torch.flatten(y_pred) true_pos = torch.sum(y_true_pos * y_pred_pos) false_neg = torch.sum(y_true_pos * (1 - y_pred_pos)) false_pos = torch.sum((1 - y_true_pos) * y_pred_pos) tversky_index = (true_pos + smooth) / ( true_pos + alpha * false_neg + beta * false_pos + smooth ) return 1 - tversky_index def focal_tversky(self, y_pred, y_true, gamma=0.75): pt_1 = self.tversky_loss(y_pred, y_true) return torch.pow((1 - pt_1), gamma) def dice_loss(self, logits, gt, eps=1): # Convert logits to probabilities # Flatten the tensorsx probs = torch.sigmoid(logits) probs = probs.view(-1) gt = gt.view(-1) # Compute Dice coefficient intersection = (probs * gt).sum() dice_coeff = (2.0 * intersection + eps) / (probs.sum() + gt.sum() + eps) # Compute Dice Los[s loss = 1 - dice_coeff return loss def focal_loss(self, logits, gt, gamma=2): logits = logits.reshape(-1, 1) gt = gt.reshape(-1, 1) logits = torch.cat((1 - logits, logits), dim=1) probs = torch.sigmoid(logits) pt = probs.gather(1, gt.long()) modulating_factor = (1 - pt) ** gamma # pt_false= pt<=0.5 # modulating_factor[pt_false] *= 2 focal_loss = -modulating_factor * torch.log(pt + 1e-12) # Compute the mean focal loss loss = focal_loss.mean() return loss # Store as a Python number to save memory def forward(self, logits, target): logits = logits.squeeze(1) target = target.squeeze(1) # Dice Loss # prob = F.softmax(logits, dim=1)[:, 1, ...] dice_loss = self.dice_loss(logits, target) tversky_loss = self.tversky_loss(logits, target) # Focal Loss focal_loss = self.focal_loss(logits, target.squeeze(-1)) alpha = 20.0 # Combined Loss combined_loss = alpha * focal_loss + dice_loss return combined_loss def img_enhance(img2, coef=0.2): img_mean = np.mean(img2) img_max = np.max(img2) val = (img_max - img_mean) * coef + img_mean img2[img2 < img_mean * 0.7] = img_mean * 0.7 img2[img2 > val] = val return img2 def dice_coefficient(logits, gt): eps=1 binary_mask = logits>0 intersection = (binary_mask * gt).sum(dim=(-2,-1)) dice_scores = (2.0 * intersection + eps) / (binary_mask.sum(dim=(-2,-1)) + gt.sum(dim=(-2,-1)) + eps) return dice_scores.mean() def what_the_f(low_res_masks,label): low_res_label = F.interpolate(label, low_res_masks.shape[-2:]) dice = dice_coefficient( low_res_masks, low_res_label ) return dice image_size = args.image_size exp_id = 0 found = 0 if debug: user_input='debug' else: user_input = input("Related changes: ") while found == 0: try: os.makedirs(f"exps/{exp_id}-{user_input}") found = 1 except: exp_id = exp_id + 1 copyfile(os.path.realpath(__file__), f"exps/{exp_id}-{user_input}/code.py") layer_n = 4 L = layer_n a = np.full(L, layer_n) params = {"M": 255, "a": a, "p": 0.35} device = "cuda:1" from segment_anything import SamPredictor, sam_model_registry class panc_sam(nn.Module): def __init__(self, *args, **kwargs) -> None: super().__init__(*args, **kwargs) #Promptless sam = torch.load(args.promptprovider) self.prompt_encoder = sam.prompt_encoder self.mask_decoder = sam.mask_decoder for param in self.prompt_encoder.parameters(): param.requires_grad = False for param in self.mask_decoder.parameters(): param.requires_grad = False #with Prompt sam=sam_model_registry[args.model_type](args.checkpoint) self.image_encoder = sam.image_encoder self.prompt_encoder2 = sam.prompt_encoder self.mask_decoder2 = sam.mask_decoder for param in self.image_encoder.parameters(): param.requires_grad = False for param in self.prompt_encoder2.parameters(): param.requires_grad = False def forward(self, input_images,box=None): # input_images = torch.stack([x["image"] for x in batched_input], dim=0) with torch.no_grad(): image_embeddings = self.image_encoder(input_images).detach() outputs_prompt = [] outputs = [] for curr_embedding in image_embeddings: with torch.no_grad(): sparse_embeddings, dense_embeddings = self.prompt_encoder( points=None, boxes=None, masks=None, ) low_res_masks, _ = self.mask_decoder( image_embeddings=curr_embedding, image_pe=self.prompt_encoder.get_dense_pe().detach(), sparse_prompt_embeddings=sparse_embeddings.detach(), dense_prompt_embeddings=dense_embeddings.detach(), multimask_output=False, ) outputs_prompt.append(low_res_masks) points, point_labels = main_prompt(low_res_masks) points_sconed, point_labels_sconed = sample_prompt(low_res_masks) points = torch.cat([points, points_sconed], dim=1) # Adjust dimensions as necessary point_labels = torch.cat([point_labels, point_labels_sconed], dim=1) points = points * 4 points = (points, point_labels) with torch.no_grad(): sparse_embeddings, dense_embeddings = self.prompt_encoder2( points=points, boxes=None, masks=None, ) low_res_masks, _ = self.mask_decoder2( image_embeddings=curr_embedding, image_pe=self.prompt_encoder2.get_dense_pe().detach(), sparse_prompt_embeddings=sparse_embeddings.detach(), dense_prompt_embeddings=dense_embeddings.detach(), multimask_output=False, ) outputs.append(low_res_masks) low_res_masks_promtp = torch.cat(outputs_prompt, dim=0) low_res_masks = torch.cat(outputs, dim=0) return low_res_masks, low_res_masks_promtp augmentation = A.Compose( [ A.Rotate(limit=30, p=0.5), A.RandomBrightnessContrast(brightness_limit=0.3, contrast_limit=0.3, p=1), A.RandomResizedCrop(1024, 1024, scale=(0.9, 1.0), p=1), A.HorizontalFlip(p=0.5), A.CLAHE(clip_limit=2.0, tile_grid_size=(8, 8), p=0.5), A.CoarseDropout( max_holes=8, max_height=16, max_width=16, min_height=8, min_width=8, fill_value=0, p=0.5, ), A.RandomScale(scale_limit=0.3, p=0.5), ] ) panc_sam_instance = panc_sam() panc_sam_instance.to(device) panc_sam_instance.train() train_dataset = PanDataset( [args.dir_train], [args.dir_labels], [["NIH_PNG",1]], args.image_size, slice_per_image=args.slice_per_image, train=True, augmentation=augmentation, ) val_dataset = PanDataset( [args.dir_train], [args.dir_labels], [["NIH_PNG",1]], image_size, slice_per_image=args.slice_per_image, train=False, ) train_loader = DataLoader( train_dataset, batch_size=args.batch_size, collate_fn=train_dataset.collate_fn, shuffle=True, drop_last=False, num_workers=args.num_workers, ) val_loader = DataLoader( val_dataset, batch_size=args.batch_size, collate_fn=val_dataset.collate_fn, shuffle=True, drop_last=False, num_workers=args.num_workers, ) lr = 1e-4 #1e-3 max_lr = 3e-4 wd = 5e-4 optimizer_main = torch.optim.Adam( # parameters, list(panc_sam_instance.mask_decoder2.parameters()), lr=lr, weight_decay=wd, ) scheduler_main = torch.optim.lr_scheduler.OneCycleLR( optimizer_main, max_lr=max_lr, epochs=args.num_epochs, steps_per_epoch=args.sample_size // (args.accumulative_batch_size // args.batch_size), ) ##################################################### from statistics import mean from tqdm import tqdm from torch.nn.functional import threshold, normalize loss_function = loss_fn(alpha=0.5, gamma=4.0) loss_function.to(device) from time import time import time as s_time log_file = open(f"exps/{exp_id}-{user_input}/log.txt", "a") def process_model(main_model , data_loader, train=0, save_output=0): epoch_losses = [] index = 0 results = torch.zeros((2, 0, 256, 256)) total_dice = 0.0 num_samples = 0 total_dice_main =0.0 counterb = 0 for image, label,raw_data in tqdm(data_loader, total=args.sample_size): num_samples += 1 counterb += 1 index += 1 image = image.to(device) label = label.to(device).float() ############################promt######################################## box = torch.tensor([[200, 200, 750, 800]]).to(device) low_res_masks_main,low_res_masks_prompt = main_model(image,box) low_res_label = F.interpolate(label, low_res_masks_main.shape[-2:]) dice_prompt = what_the_f(low_res_masks_prompt,low_res_label) dice_main = what_the_f(low_res_masks_main,low_res_label) binary_mask = normalize(threshold(low_res_masks_main, 0.0,0)) total_dice += dice_prompt total_dice_main+=dice_main average_dice = total_dice / num_samples average_dice_main = total_dice_main / num_samples log_file.write(str(average_dice) + "\n") log_file.flush() loss = loss_function.forward(low_res_masks_main, low_res_label) loss /= args.accumulative_batch_size / args.batch_size if train: loss.backward() if index % (args.accumulative_batch_size / args.batch_size) == 0: # print(loss) optimizer_main.step() scheduler_main.step() optimizer_main.zero_grad() index = 0 else: result = torch.cat( ( low_res_masks_main[0].detach().cpu().reshape(1, 1, 256, 256), binary_mask[0].detach().cpu().reshape(1, 1, 256, 256), ), dim=0, ) results = torch.cat((results, result), dim=1) if index % (args.accumulative_batch_size / args.batch_size) == 0: epoch_losses.append(loss.item()) if counterb == args.sample_size and train: break elif counterb == args.sample_size //2 and not train: break return epoch_losses, results, average_dice ,average_dice_main def train_model(train_loader, val_loader, K_fold=False, N_fold=7, epoch_num_start=7): print("Train model started.") train_losses = [] train_epochs = [] val_losses = [] val_epochs = [] dice = [] dice_main = [] dice_val = [] dice_val_main =[] results = [] #########################save image################################## index = 0 if debug==0: for image, label , raw_data in tqdm(val_loader): if index < 100: if not os.path.exists(f"ims/batch_{index}"): os.mkdir(f"ims/batch_{index}") save_img( image[0], f"ims/batch_{index}/img_0.png", ) save_img(0.2 * image[0][0] + label[0][0], f"ims/batch_{index}/gt_0.png") index += 1 if index == 100: break # In each epoch we will train the model and the val it # training without k_fold cross validation: last_best_dice = 0 if K_fold == False: for epoch in range(args.num_epochs): print(f"=====================EPOCH: {epoch + 1}=====================") log_file.write( f"=====================EPOCH: {epoch + 1}===================\n" ) print("Training:") train_epoch_losses, epoch_results, average_dice ,average_dice_main = process_model(panc_sam_instance,train_loader, train=1) dice.append(average_dice) dice_main.append(average_dice_main) train_losses.append(train_epoch_losses) if (average_dice) > 0.5: print("validating:") val_epoch_losses, epoch_results, average_dice_val,average_dice_val_main = process_model( panc_sam_instance,val_loader ) val_losses.append(val_epoch_losses) for i in tqdm(range(len(epoch_results[0]))): if not os.path.exists(f"ims/batch_{i}"): os.mkdir(f"ims/batch_{i}") save_img( epoch_results[0, i].clone(), f"ims/batch_{i}/prob_epoch_{epoch}.png", ) save_img( epoch_results[1, i].clone(), f"ims/batch_{i}/pred_epoch_{epoch}.png", ) train_mean_losses = [mean(x) for x in train_losses] val_mean_losses = [mean(x) for x in val_losses] np.save("train_losses.npy", train_mean_losses) np.save("val_losses.npy", val_mean_losses) print(f"Train Dice: {average_dice}") print(f"Train Dice main: {average_dice_main}") print(f"Mean train loss: {mean(train_epoch_losses)}") try: dice_val.append(average_dice_val) dice_val_main.append(average_dice_val_main) print(f"val Dice : {average_dice_val}") print(f"val Dice main : {average_dice_val_main}") print(f"Mean val loss: {mean(val_epoch_losses)}") results.append(epoch_results) val_epochs.append(epoch) train_epochs.append(epoch) plt.plot(val_epochs, val_mean_losses, train_epochs, train_mean_losses) if average_dice_val_main > last_best_dice: torch.save( panc_sam_instance, f"exps/{exp_id}-{user_input}/sam_tuned_save.pth", ) last_best_dice = average_dice_val del epoch_results del average_dice_val except: train_epochs.append(epoch) plt.plot(train_epochs, train_mean_losses) print(f"=================End of EPOCH: {epoch}==================\n") plt.yscale("log") plt.title("Mean epoch loss") plt.xlabel("Epoch Number") plt.ylabel("Loss") plt.savefig("result") ## training with k-fold cross validation: return train_losses, val_losses, results train_losses, val_losses, results = train_model(train_loader, val_loader) log_file.close()