# Copyright (c) 2017-present, Facebook, Inc. # All rights reserved. # # This source code is licensed under the license found in the # LICENSE file in the root directory of this source tree. # import os import pickle import numpy as np import re from scipy.ndimage import distance_transform_edt as distance from skimage import segmentation as skimage_seg import torch from torch.utils.data.sampler import Sampler import torch.distributed as dist import networks # many issues with this function def load_model(path): """Loads model and return it without DataParallel table.""" if os.path.isfile(path): print("=> loading checkpoint '{}'".format(path)) checkpoint = torch.load(path) for key in checkpoint["state_dict"]: print(key) # size of the top layer N = checkpoint["state_dict"]["decoder.out_conv.bias"].size() # build skeleton of the model sob = "sobel.0.weight" in checkpoint["state_dict"].keys() model = models.__dict__[checkpoint["arch"]](sobel=sob, out=int(N[0])) # deal with a dataparallel table def rename_key(key): if not "module" in key: return key return "".join(key.split(".module")) checkpoint["state_dict"] = { rename_key(key): val for key, val in checkpoint["state_dict"].items() } # load weights model.load_state_dict(checkpoint["state_dict"]) print("Loaded") else: model = None print("=> no checkpoint found at '{}'".format(path)) return model def load_checkpoint(path, model, optimizer, from_ddp=False): """loads previous checkpoint Args: path (str): path to checkpoint model (model): model to restore checkpoint to optimizer (optimizer): torch optimizer to load optimizer state_dict to from_ddp (bool, optional): load DistributedDataParallel checkpoint to regular model. Defaults to False. Returns: model, optimizer, epoch_num, loss """ # load checkpoint checkpoint = torch.load(path) # transfer state_dict from checkpoint to model model.load_state_dict(checkpoint["state_dict"]) # transfer optimizer state_dict from checkpoint to model optimizer.load_state_dict(checkpoint["optimizer_state_dict"]) # track loss loss = checkpoint["loss"] return model, optimizer, checkpoint["epoch"], loss.item() def restore_model(logger, snapshot_path, model_num=None): """wrapper function to read log dir and load restore a previous checkpoint Args: logger (Logger): logger object (for info output to console) snapshot_path (str): path to checkpoint directory Returns: model, optimizer, start_epoch, performance """ try: # check if there is previous progress to be restored: logger.info(f"Snapshot path: {snapshot_path}") iter_num = [] name = "model_iter" if model_num: name = model_num for filename in os.listdir(snapshot_path): if name in filename: basename, extension = os.path.splitext(filename) iter_num.append(int(basename.split("_")[2])) iter_num = max(iter_num) for filename in os.listdir(snapshot_path): if name in filename and str(iter_num) in filename: model_checkpoint = filename except Exception as e: logger.warning(f"Error finding previous checkpoints: {e}") try: logger.info(f"Restoring model checkpoint: {model_checkpoint}") model, optimizer, start_epoch, performance = load_checkpoint( snapshot_path + "/" + model_checkpoint, model, optimizer ) logger.info(f"Models restored from iteration {iter_num}") return model, optimizer, start_epoch, performance except Exception as e: logger.warning(f"Unable to restore model checkpoint: {e}, using new model") def save_checkpoint(epoch, model, optimizer, loss, path): """Saves model as checkpoint""" torch.save( { "epoch": epoch, "state_dict": model.state_dict(), "optimizer_state_dict": optimizer.state_dict(), "loss": loss, }, path, ) class UnifLabelSampler(Sampler): """Samples elements uniformely accross pseudolabels. Args: N (int): size of returned iterator. images_lists: dict of key (target), value (list of data with this target) """ def __init__(self, N, images_lists): self.N = N self.images_lists = images_lists self.indexes = self.generate_indexes_epoch() def generate_indexes_epoch(self): size_per_pseudolabel = int(self.N / len(self.images_lists)) + 1 res = np.zeros(size_per_pseudolabel * len(self.images_lists)) for i in range(len(self.images_lists)): indexes = np.random.choice( self.images_lists[i], size_per_pseudolabel, replace=(len(self.images_lists[i]) <= size_per_pseudolabel), ) res[i * size_per_pseudolabel : (i + 1) * size_per_pseudolabel] = indexes np.random.shuffle(res) return res[: self.N].astype("int") def __iter__(self): return iter(self.indexes) def __len__(self): return self.N class AverageMeter(object): """Computes and stores the average and current value""" def __init__(self): self.reset() def reset(self): self.val = 0 self.avg = 0 self.sum = 0 self.count = 0 def update(self, val, n=1): self.val = val self.sum += val * n self.count += n self.avg = self.sum / self.count def learning_rate_decay(optimizer, t, lr_0): for param_group in optimizer.param_groups: lr = lr_0 / np.sqrt(1 + lr_0 * param_group["weight_decay"] * t) param_group["lr"] = lr class Logger: """Class to update every epoch to keep trace of the results Methods: - log() log and save """ def __init__(self, path): self.path = path self.data = [] def log(self, train_point): self.data.append(train_point) with open(os.path.join(self.path), "wb") as fp: pickle.dump(self.data, fp, -1) def compute_sdf(img_gt, out_shape): """ compute the signed distance map of binary mask input: segmentation, shape = (batch_size, x, y, z) output: the Signed Distance Map (SDM) sdf(x) = 0; x in segmentation boundary -inf|x-y|; x in segmentation +inf|x-y|; x out of segmentation normalize sdf to [-1,1] """ img_gt = img_gt.astype(np.uint8) normalized_sdf = np.zeros(out_shape) for b in range(out_shape[0]): # batch size posmask = img_gt[b].astype(np.bool) if posmask.any(): negmask = ~posmask posdis = distance(posmask) negdis = distance(negmask) boundary = skimage_seg.find_boundaries(posmask, mode="inner").astype( np.uint8 ) sdf = (negdis - np.min(negdis)) / (np.max(negdis) - np.min(negdis)) - ( posdis - np.min(posdis) ) / (np.max(posdis) - np.min(posdis)) sdf[boundary == 1] = 0 normalized_sdf[b] = sdf # assert np.min(sdf) == -1.0, print(np.min(posdis), np.max(posdis), np.min(negdis), np.max(negdis)) # assert np.max(sdf) == 1.0, print(np.min(posdis), np.min(negdis), np.max(posdis), np.max(negdis)) return normalized_sdf # set up process group for distributed computing def distributed_setup(rank, world_size): os.environ["MASTER_ADDR"] = "localhost" os.environ["MASTER_PORT"] = "12355" print("setting up dist process group now") dist.init_process_group("nccl", rank=rank, world_size=world_size) def load_ddp_to_nddp(state_dict): pattern = re.compile("module") for k, v in state_dict.items(): if re.search("module", k): model_dict[re.sub(pattern, "", k)] = v else: model_dict = state_dict return model_dict