import numpy as np from light_training.dataloading.dataset import get_test_loader_from_test import torch import torch.nn as nn from monai.networks.nets.basic_unet import BasicUNet from monai.networks.nets.swin_unetr import SwinUNETR 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 models.uent3d import UNet3D from monai.networks.nets.segresnet import SegResNet from models.transbts.TransBTS_downsample8x_skipconnection import TransBTS from einops import rearrange from models.modelgenesis.unet3d import UNet3DModelGen from models.transvw.models.ynet3d import UNet3DTransVW from monai.networks.nets.basic_unet import BasicUNet from monai.networks.nets.attentionunet import AttentionUnet from light_training.loss.compound_losses import DC_and_CE_loss from light_training.loss.dice import MemoryEfficientSoftDiceLoss from light_training.evaluation.metric import dice set_determinism(123) from light_training.loss.compound_losses import DC_and_CE_loss import os from medpy import metric from light_training.prediction import Predictor data_dir = "./data/fullres/test" env = "pytorch" max_epoch = 1000 batch_size = 2 val_every = 2 num_gpus = 1 device = "cuda:2" 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 def get_input(self, batch): image = batch["data"] label = batch["seg"] properties = batch["properties"] # label = self.convert_labels(label) del batch return image, label, properties def define_model_diffunet(self): from models.nnunet_denoise_ddp_infer.get_unet3d_denoise_uncer_edge import DiffUNet model = DiffUNet(1, 10, 3, 1, bta=True) model_path = "/home/xingzhaohu/zongweizhou/logs_gpu4/diffunet/model/final_model_0.8384.pt" new_sd = self.filte_state_dict(torch.load(model_path, map_location="cpu")) model.load_state_dict(new_sd, strict=False) model.eval() window_infer = SlidingWindowInferer(roi_size=patch_size, sw_batch_size=2, overlap=0.3, progress=True, mode="gaussian") predictor = Predictor(window_infer=window_infer, mirror_axes=[0,1,2]) save_path = "./prediction_results/diffunet_ep1000_test" os.makedirs(save_path, exist_ok=True) return model, predictor, save_path def validation_step(self, batch): image, label, properties = self.get_input(batch) print(properties['spacing']) ddim = True model, predictor, save_path = self.define_model_diffunet() if ddim: model_output = predictor.maybe_mirror_and_predict(image, model, device=device, ddim=True) else : model_output = predictor.maybe_mirror_and_predict(image, model, device=device) model_output = predictor.predict_raw_probability(model_output, properties=properties).cpu() model_output = model_output.argmax(dim=0) model_output = predictor.predict_noncrop_probability(model_output, properties) print(f"save shape is {model_output.shape}") seg_list = ["aorta", "gall_bladder", "kidney_left", "kidney_right", "liver", "pancreas", "postcava", "spleen", "stomach"] save_path = os.path.join(save_path, properties['name'][0], "predictions") # print(f"save_path is {save_path}") os.makedirs(save_path, exist_ok=True) for i in range(1, len(seg_list) + 1): model_output_c = model_output == i predictor.save_to_nii(model_output_c, raw_spacing=properties['spacing'], case_name=seg_list[i-1], save_dir=save_path) return 0 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__) test_ds = get_test_loader_from_test(data_dir=data_dir) trainer.validation_single_gpu(test_ds)