268 lines
9.7 KiB
Python
268 lines
9.7 KiB
Python
# Copyright (c) OpenMMLab. All rights reserved.
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import argparse
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import os.path as osp
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import time
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from collections import defaultdict
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import matplotlib.pyplot as plt
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import numpy as np
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import rich.progress as progress
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import torch
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import torch.nn.functional as F
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from mmengine.config import Config, DictAction
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from mmengine.device import get_device
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from mmengine.logging import MMLogger
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from mmengine.runner import Runner
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from mmengine.utils import mkdir_or_exist
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from mmpretrain.apis import get_model
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from mmpretrain.registry import DATASETS
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try:
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from sklearn.manifold import TSNE
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except ImportError as e:
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raise ImportError('Please install `sklearn` to calculate '
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'TSNE by `pip install scikit-learn`') from e
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def parse_args():
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parser = argparse.ArgumentParser(description='t-SNE visualization')
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parser.add_argument('config', help='tsne config file path')
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parser.add_argument('--checkpoint', default=None, help='checkpoint file')
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parser.add_argument('--work-dir', help='the dir to save logs and models')
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parser.add_argument(
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'--test-cfg',
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help='tsne config file path to load config of test dataloader.')
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parser.add_argument(
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'--vis-stage',
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choices=['backbone', 'neck', 'pre_logits'],
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help='The visualization stage of the model')
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parser.add_argument(
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'--class-idx',
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nargs='+',
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type=int,
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help='The categories used to calculate t-SNE.')
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parser.add_argument(
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'--max-num-class',
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type=int,
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default=20,
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help='The first N categories to apply t-SNE algorithms. '
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'Defaults to 20.')
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parser.add_argument(
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'--max-num-samples',
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type=int,
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default=100,
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help='The maximum number of samples per category. '
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'Higher number need longer time to calculate. Defaults to 100.')
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parser.add_argument(
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'--cfg-options',
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nargs='+',
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action=DictAction,
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help='override some settings in the used config, the key-value pair '
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'in xxx=yyy format will be merged into config file. If the value to '
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'be overwritten is a list, it should be like key="[a,b]" or key=a,b '
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'It also allows nested list/tuple values, e.g. key="[(a,b),(c,d)]" '
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'Note that the quotation marks are necessary and that no white space '
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'is allowed.')
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parser.add_argument('--device', help='Device used for inference')
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parser.add_argument(
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'--legend',
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action='store_true',
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help='Show the legend of all categories.')
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parser.add_argument(
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'--show',
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action='store_true',
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help='Display the result in a graphical window.')
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# t-SNE settings
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parser.add_argument(
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'--n-components', type=int, default=2, help='the dimension of results')
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parser.add_argument(
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'--perplexity',
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type=float,
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default=30.0,
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help='The perplexity is related to the number of nearest neighbors'
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'that is used in other manifold learning algorithms.')
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parser.add_argument(
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'--early-exaggeration',
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type=float,
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default=12.0,
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help='Controls how tight natural clusters in the original space are in'
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'the embedded space and how much space will be between them.')
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parser.add_argument(
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'--learning-rate',
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type=float,
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default=200.0,
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help='The learning rate for t-SNE is usually in the range'
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'[10.0, 1000.0]. If the learning rate is too high, the data may look'
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'like a ball with any point approximately equidistant from its nearest'
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'neighbours. If the learning rate is too low, most points may look'
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'compressed in a dense cloud with few outliers.')
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parser.add_argument(
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'--n-iter',
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type=int,
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default=1000,
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help='Maximum number of iterations for the optimization. Should be at'
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'least 250.')
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parser.add_argument(
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'--n-iter-without-progress',
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type=int,
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default=300,
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help='Maximum number of iterations without progress before we abort'
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'the optimization.')
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parser.add_argument(
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'--init', type=str, default='random', help='The init method')
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args = parser.parse_args()
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return args
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def main():
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args = parse_args()
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cfg = Config.fromfile(args.config)
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if args.cfg_options is not None:
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cfg.merge_from_dict(args.cfg_options)
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# work_dir is determined in this priority: CLI > segment in file > filename
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if args.work_dir is not None:
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# update configs according to CLI args if args.work_dir is not None
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cfg.work_dir = args.work_dir
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elif cfg.get('work_dir', None) is None:
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# use config filename as default work_dir if cfg.work_dir is None
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work_type = args.config.split('/')[1]
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cfg.work_dir = osp.join('./work_dirs', work_type,
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osp.splitext(osp.basename(args.config))[0])
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# create work_dir
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timestamp = time.strftime('%Y%m%d_%H%M%S', time.localtime())
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tsne_work_dir = osp.join(cfg.work_dir, f'tsne_{timestamp}/')
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mkdir_or_exist(osp.abspath(tsne_work_dir))
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# init the logger before other steps
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log_file = osp.join(tsne_work_dir, 'tsne.log')
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logger = MMLogger.get_instance(
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'mmpretrain',
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logger_name='mmpretrain',
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log_file=log_file,
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log_level=cfg.log_level)
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# build the model from a config file and a checkpoint file
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device = args.device or get_device()
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model = get_model(cfg, args.checkpoint, device=device)
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logger.info('Model loaded.')
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# build the dataset
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if args.test_cfg is not None:
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dataloader_cfg = Config.fromfile(args.test_cfg).get('test_dataloader')
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elif 'test_dataloader' not in cfg:
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raise ValueError('No `test_dataloader` in the config, you can '
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'specify another config file that includes test '
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'dataloader settings by the `--test-cfg` option.')
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else:
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dataloader_cfg = cfg.get('test_dataloader')
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dataset = DATASETS.build(dataloader_cfg.pop('dataset'))
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classes = dataset.metainfo.get('classes')
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if args.class_idx is None:
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num_classes = args.max_num_class if classes is None else len(classes)
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args.class_idx = list(range(num_classes))[:args.max_num_class]
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if classes is not None:
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classes = [classes[idx] for idx in args.class_idx]
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else:
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classes = args.class_idx
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# compress dataset, select that the label is less then max_num_class
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subset_idx_list = []
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counter = defaultdict(int)
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for i in range(len(dataset)):
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gt_label = dataset.get_data_info(i)['gt_label']
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if (gt_label in args.class_idx
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and counter[gt_label] < args.max_num_samples):
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subset_idx_list.append(i)
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counter[gt_label] += 1
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dataset.get_subset_(subset_idx_list)
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logger.info(f'Apply t-SNE to visualize {len(subset_idx_list)} samples.')
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dataloader_cfg.dataset = dataset
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dataloader_cfg.setdefault('collate_fn', dict(type='default_collate'))
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dataloader = Runner.build_dataloader(dataloader_cfg)
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results = dict()
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features = []
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labels = []
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for data in progress.track(dataloader, description='Calculating...'):
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with torch.no_grad():
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# preprocess data
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data = model.data_preprocessor(data)
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batch_inputs, batch_data_samples = \
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data['inputs'], data['data_samples']
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batch_labels = torch.cat([i.gt_label for i in batch_data_samples])
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# extract backbone features
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extract_args = {}
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if args.vis_stage:
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extract_args['stage'] = args.vis_stage
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batch_features = model.extract_feat(batch_inputs, **extract_args)
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# post process
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if batch_features[0].ndim == 4:
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# For (N, C, H, W) feature
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batch_features = [
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F.adaptive_avg_pool2d(inputs, 1).squeeze()
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for inputs in batch_features
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]
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elif batch_features[0].ndim == 3:
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# For (N, L, C) feature
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batch_features = [inputs.mean(1) for inputs in batch_features]
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# save batch features
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features.append(batch_features)
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labels.extend(batch_labels.cpu().numpy())
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for i in range(len(features[0])):
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key = 'feat_' + str(model.backbone.out_indices[i])
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results[key] = np.concatenate(
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[batch[i].cpu().numpy() for batch in features], axis=0)
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# save features
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for key, val in results.items():
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output_file = f'{tsne_work_dir}{key}.npy'
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np.save(output_file, val)
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# build t-SNE model
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tsne_model = TSNE(
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n_components=args.n_components,
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perplexity=args.perplexity,
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early_exaggeration=args.early_exaggeration,
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learning_rate=args.learning_rate,
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n_iter=args.n_iter,
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n_iter_without_progress=args.n_iter_without_progress,
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init=args.init)
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# run and get results
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logger.info('Running t-SNE.')
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for key, val in results.items():
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result = tsne_model.fit_transform(val)
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res_min, res_max = result.min(0), result.max(0)
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res_norm = (result - res_min) / (res_max - res_min)
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_, ax = plt.subplots(figsize=(10, 10))
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scatter = ax.scatter(
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res_norm[:, 0],
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res_norm[:, 1],
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alpha=1.0,
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s=15,
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c=labels,
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cmap='tab20')
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if args.legend:
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legend = ax.legend(scatter.legend_elements()[0], classes)
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ax.add_artist(legend)
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plt.savefig(f'{tsne_work_dir}{key}.png')
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if args.show:
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plt.show()
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logger.info(f'Save features and results to {tsne_work_dir}')
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if __name__ == '__main__':
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main()
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