import numpy as np from light_training.dataloading.dataset import get_train_val_test_loader_from_train import torch import torch.nn as nn from monai.inferers import SlidingWindowInferer from light_training.evaluation.metric import dice from light_training.trainer import Trainer from monai.utils import set_determinism from light_training.utils.files_helper import save_new_model_and_delete_last from monai.losses.dice import DiceLoss set_determinism(123) import os data_dir = "./data/fullres/train" logdir = f"./logs/segmamba" model_save_path = os.path.join(logdir, "model") # augmentation = "nomirror" augmentation = True env = "pytorch" max_epoch = 1000 batch_size = 2 val_every = 2 num_gpus = 1 device = "cuda:0" roi_size = [128, 128, 128] def func(m, epochs): return np.exp(-10*(1- m / epochs)**2) class BraTSTrainer(Trainer): def __init__(self, env_type, max_epochs, batch_size, device="cpu", val_every=1, num_gpus=1, logdir="./logs/", master_ip='localhost', master_port=17750, training_script="train.py"): super().__init__(env_type, max_epochs, batch_size, device, val_every, num_gpus, logdir, master_ip, master_port, training_script) self.window_infer = SlidingWindowInferer(roi_size=roi_size, sw_batch_size=1, overlap=0.5) self.augmentation = augmentation from model_segmamba.segmamba import SegMamba self.model = SegMamba(in_chans=4, out_chans=4, depths=[2,2,2,2], feat_size=[48, 96, 192, 384]) self.patch_size = roi_size self.best_mean_dice = 0.0 self.ce = nn.CrossEntropyLoss() self.mse = nn.MSELoss() self.train_process = 18 self.optimizer = torch.optim.SGD(self.model.parameters(), lr=1e-2, weight_decay=3e-5, momentum=0.99, nesterov=True) self.scheduler_type = "poly" self.cross = nn.CrossEntropyLoss() def training_step(self, batch): image, label = self.get_input(batch) pred = self.model(image) loss = self.cross(pred, label) self.log("training_loss", loss, step=self.global_step) return loss def convert_labels(self, labels): ## TC, WT and ET result = [(labels == 1) | (labels == 3), (labels == 1) | (labels == 3) | (labels == 2), labels == 3] return torch.cat(result, dim=1).float() def get_input(self, batch): image = batch["data"] label = batch["seg"] label = label[:, 0].long() return image, label def cal_metric(self, gt, pred, voxel_spacing=[1.0, 1.0, 1.0]): if pred.sum() > 0 and gt.sum() > 0: d = dice(pred, gt) return np.array([d, 50]) elif gt.sum() == 0 and pred.sum() == 0: return np.array([1.0, 50]) else: return np.array([0.0, 50]) def validation_step(self, batch): image, label = self.get_input(batch) output = self.model(image) output = output.argmax(dim=1) output = output[:, None] output = self.convert_labels(output) label = label[:, None] label = self.convert_labels(label) output = output.cpu().numpy() target = label.cpu().numpy() dices = [] c = 3 for i in range(0, c): pred_c = output[:, i] target_c = target[:, i] cal_dice, _ = self.cal_metric(target_c, pred_c) dices.append(cal_dice) return dices def validation_end(self, val_outputs): dices = val_outputs tc, wt, et = dices[0].mean(), dices[1].mean(), dices[2].mean() print(f"dices is {tc, wt, et}") mean_dice = (tc + wt + et) / 3 self.log("tc", tc, step=self.epoch) self.log("wt", wt, step=self.epoch) self.log("et", et, step=self.epoch) self.log("mean_dice", mean_dice, step=self.epoch) if mean_dice > self.best_mean_dice: self.best_mean_dice = mean_dice save_new_model_and_delete_last(self.model, os.path.join(model_save_path, f"best_model_{mean_dice:.4f}.pt"), delete_symbol="best_model") save_new_model_and_delete_last(self.model, os.path.join(model_save_path, f"final_model_{mean_dice:.4f}.pt"), delete_symbol="final_model") if (self.epoch + 1) % 100 == 0: torch.save(self.model.state_dict(), os.path.join(model_save_path, f"tmp_model_ep{self.epoch}_{mean_dice:.4f}.pt")) print(f"mean_dice is {mean_dice}") if __name__ == "__main__": trainer = BraTSTrainer(env_type=env, max_epochs=max_epoch, batch_size=batch_size, device=device, logdir=logdir, val_every=val_every, num_gpus=num_gpus, master_port=17759, training_script=__file__) train_ds, val_ds, test_ds = get_train_val_test_loader_from_train(data_dir) trainer.train(train_dataset=train_ds, val_dataset=val_ds)