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.evaluation.metric import dice set_determinism(123) import os from light_training.prediction import Predictor data_dir = "./data/fullres/train" env = "pytorch" max_epoch = 1000 batch_size = 2 val_every = 2 num_gpus = 1 device = "cuda:0" patch_size = [128, 128, 128] 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.patch_size = patch_size self.augmentation = False 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"] properties = batch["properties"] label = self.convert_labels(label) return image, label, properties def define_model_segmamba(self): from model_segmamba.segmamba import SegMamba model = SegMamba(in_chans=4, out_chans=4, depths=[2,2,2,2], feat_size=[48, 96, 192, 384]) model_path = "/home/xingzhaohu/dev/jiuding_code/brats23/logs/segmamba/model/final_model_0.9038.pt" new_sd = self.filte_state_dict(torch.load(model_path, map_location="cpu")) model.load_state_dict(new_sd) model.eval() window_infer = SlidingWindowInferer(roi_size=patch_size, sw_batch_size=2, overlap=0.5, progress=True, mode="gaussian") predictor = Predictor(window_infer=window_infer, mirror_axes=[0,1,2]) save_path = "./prediction_results/segmamba" os.makedirs(save_path, exist_ok=True) return model, predictor, save_path def validation_step(self, batch): image, label, properties = self.get_input(batch) ddim = False model, predictor, save_path = self.define_model_segmamba() model_output = predictor.maybe_mirror_and_predict(image, model, device=device) model_output = predictor.predict_raw_probability(model_output, properties=properties) model_output = model_output.argmax(dim=0)[None] model_output = self.convert_labels_dim0(model_output) label = label[0] c = 3 dices = [] for i in range(0, c): output_i = model_output[i].cpu().numpy() label_i = label[i].cpu().numpy() d = dice(output_i, label_i) dices.append(d) print(dices) model_output = predictor.predict_noncrop_probability(model_output, properties) predictor.save_to_nii(model_output, raw_spacing=[1,1,1], case_name = properties['name'][0], save_dir=save_path) return 0 def convert_labels_dim0(self, labels): ## TC, WT and ET result = [(labels == 1) | (labels == 3), (labels == 1) | (labels == 3) | (labels == 2), labels == 3] return torch.cat(result, dim=0).float() def filte_state_dict(self, sd): if "module" in sd : sd = sd["module"] new_sd = {} for k, v in sd.items(): k = str(k) new_k = k[7:] if k.startswith("module") else k new_sd[new_k] = v del sd return new_sd if __name__ == "__main__": trainer = BraTSTrainer(env_type=env, max_epochs=max_epoch, batch_size=batch_size, device=device, logdir="", val_every=val_every, num_gpus=num_gpus, master_port=17751, training_script=__file__) train_ds, val_ds, test_ds = get_train_val_test_loader_from_train(data_dir) trainer.validation_single_gpu(test_ds) # print(f"result is {v_mean}")