import torch import requests from tqdm import tqdm import zipfile import shutil from pathlib import Path import os from functools import partial from total.model import Unet_TS_CT from total_mr.model import Unet_TS_MR import json def convert_torchScript_full(model_name: str, model: torch.nn.Module, task: str, type: int, mri: bool, url: str) -> None: state_dict = download(url, model_name, mri) tmp = {} with open("Destination_Unet_{}.txt".format(type)) as f2: it = iter(state_dict.keys()) for l1 in f2: print(l1) key = next(it) print(key) while "decoder.seg_layers" in key: if type == 1: if "decoder.seg_layers.4" in key : break if type == 2: if "decoder.seg_layers.3" in key: break if type == 3: if "decoder.seg_layers.2" in key: break key = next(it) while "all_modules" in key or "decoder.encoder" in key: key = next(it) tmp[l1.replace("\n", "")] = state_dict[key] if not mri: tmp["ClipAndNormalize.mean"] = state_dict["mean"] tmp["ClipAndNormalize.std"] = state_dict["std"] tmp["ClipAndNormalize.clip_min"] = state_dict["percentile_00_5"] tmp["ClipAndNormalize.clip_max"] = state_dict["percentile_99_5"] state_dict = {"Model" : {model.name : tmp}} model.load(state_dict) dest_path = Path(f"./{task}") dest_path.mkdir(exist_ok=True) torch.save(state_dict, str(dest_path/f"{model_name}.pt")) def download(url: str, model_name: str, mri: bool) -> dict[str, torch.Tensor]: with open(url.split("/")[-1], 'wb') as f: with requests.get(url, stream=True) as r: r.raise_for_status() total_size = int(r.headers.get('content-length', 0)) progress_bar = tqdm(total=total_size, unit='B', unit_scale=True, desc=f"Downloading {model_name}") for chunk in r.iter_content(chunk_size=8192 * 16): progress_bar.update(len(chunk)) f.write(chunk) progress_bar.close() with zipfile.ZipFile(url.split("/")[-1], 'r') as zip_f: zip_f.extractall(url.split("/")[-1].replace(".zip", "")) os.remove(url.split("/")[-1]) zip_path = Path(url.split("/")[-1].replace(".zip", "")) state_dict = torch.load(next(zip_path.rglob("checkpoint_final.pth"), None), map_location="cpu", weights_only=False)["network_weights"] if not mri: dataset_fingerprint_path = next(zip_path.rglob("dataset_fingerprint.json"), None) with open(dataset_fingerprint_path, "r") as f: data = json.load(f) ch0 = data["foreground_intensity_properties_per_channel"]["0"] state_dict["mean"] = torch.tensor([ch0["mean"]]) state_dict["std"] = torch.tensor([ch0["std"]]) state_dict["percentile_00_5"] = torch.tensor([ch0["percentile_00_5"]]) state_dict["percentile_99_5"] = torch.tensor([ch0["percentile_99_5"]]) shutil.rmtree(zip_path) return state_dict url = "https://github.com/wasserth/TotalSegmentator/releases/download/" UnetCPP_1_CT = partial(Unet_TS_CT, channels = [1,32,64,128,256,320,320]) UnetCPP_2_CT = partial(Unet_TS_CT, channels = [1,32,64,128,256,320]) UnetCPP_3_CT = partial(Unet_TS_CT, channels = [1,32,64,128,256]) UnetCPP_1_MR = partial(Unet_TS_MR, channels = [1,32,64,128,256,320,320]) UnetCPP_2_MR = partial(Unet_TS_MR, channels = [1,32,64,128,256,320]) UnetCPP_3_MR = partial(Unet_TS_MR, channels = [1,32,64,128,256]) models = { "M291" : (UnetCPP_1_CT(), "total", 1, False, url+"v2.0.0-weights/Dataset291_TotalSegmentator_part1_organs_1559subj.zip"), "M292" : (UnetCPP_1_CT(), "total", 1, False, url+"v2.0.0-weights/Dataset292_TotalSegmentator_part2_vertebrae_1532subj.zip"), "M293" : (UnetCPP_1_CT(), "total", 1, False, url+"v2.0.0-weights/Dataset293_TotalSegmentator_part3_cardiac_1559subj.zip"), "M294" : (UnetCPP_1_CT(), "total", 1, False, url+"v2.0.0-weights/Dataset294_TotalSegmentator_part4_muscles_1559subj.zip"), "M295" : (UnetCPP_1_CT(), "total", 1, False, url+"v2.0.0-weights/Dataset295_TotalSegmentator_part5_ribs_1559subj.zip"), "M297" : (UnetCPP_2_CT(), "total-3mm", 2, False, url+"v2.0.4-weights/Dataset297_TotalSegmentator_total_3mm_1559subj_v204.zip"), #"M298" : (UnetCPP_2_CT(), 2, False, url+"v2.0.0-weights/Dataset298_TotalSegmentator_total_6mm_1559subj.zip"), #"M730" : (UnetCPP_1_MR(), True, 1, url+"v2.2.0-weights/Dataset730_TotalSegmentatorMRI_part1_organs_495subj.zip"), #"M731" : (UnetCPP_1_MR(), True, 1, url+"v2.2.0-weights/Dataset731_TotalSegmentatorMRI_part2_muscles_495subj.zip"), #"M732" : (UnetCPP_2_MR(), False, 2, url+"v2.2.0-weights/Dataset732_TotalSegmentatorMRI_total_3mm_495subj.zip"), #"M733" : (UnetCPP_3_MR(), False, 3, url+"v2.2.0-weights/Dataset733_TotalSegmentatorMRI_total_6mm_495subj.zip"), "M850" : (UnetCPP_1_MR(), "total_mr", 1, True, url+"v2.5.0-weights/Dataset850_TotalSegMRI_part1_organs_1088subj.zip"), "M851" : (UnetCPP_1_MR(), "total_mr", 1, True, url+"v2.5.0-weights/Dataset851_TotalSegMRI_part2_muscles_1088subj.zip"), "M852" : (UnetCPP_2_MR(), "total_mr-3mm", 2, True, url+"v2.5.0-weights/Dataset852_TotalSegMRI_total_3mm_1088subj.zip"), #"M853" : (UnetCPP_3_MR(), False, 3, url+"v2.5.0-weights/Dataset853_TotalSegMRI_total_6mm_1088subj.zip") } if __name__ == "__main__": for name, model in models.items(): convert_torchScript_full(name, *model)