mirror of
https://github.com/open-mmlab/mmclassification.git
synced 2025-06-03 21:53:55 +08:00
[Feature] Support K-fold cross-validation (#563)
* Support to use `indices` to specify which samples to evaluate. * Add KFoldDataset wrapper * Rename 'K' to 'num_splits' accroding to sklearn * Add `kfold-cross-valid.py` * Add unit tests * Add help doc and docstring
This commit is contained in:
parent
321ad09e6d
commit
b39885d953
@ -4,7 +4,7 @@ from .builder import (DATASETS, PIPELINES, SAMPLERS, build_dataloader,
|
|||||||
build_dataset, build_sampler)
|
build_dataset, build_sampler)
|
||||||
from .cifar import CIFAR10, CIFAR100
|
from .cifar import CIFAR10, CIFAR100
|
||||||
from .dataset_wrappers import (ClassBalancedDataset, ConcatDataset,
|
from .dataset_wrappers import (ClassBalancedDataset, ConcatDataset,
|
||||||
RepeatDataset)
|
KFoldDataset, RepeatDataset)
|
||||||
from .imagenet import ImageNet
|
from .imagenet import ImageNet
|
||||||
from .imagenet21k import ImageNet21k
|
from .imagenet21k import ImageNet21k
|
||||||
from .mnist import MNIST, FashionMNIST
|
from .mnist import MNIST, FashionMNIST
|
||||||
@ -17,5 +17,5 @@ __all__ = [
|
|||||||
'VOC', 'MultiLabelDataset', 'build_dataloader', 'build_dataset',
|
'VOC', 'MultiLabelDataset', 'build_dataloader', 'build_dataset',
|
||||||
'DistributedSampler', 'ConcatDataset', 'RepeatDataset',
|
'DistributedSampler', 'ConcatDataset', 'RepeatDataset',
|
||||||
'ClassBalancedDataset', 'DATASETS', 'PIPELINES', 'ImageNet21k', 'SAMPLERS',
|
'ClassBalancedDataset', 'DATASETS', 'PIPELINES', 'ImageNet21k', 'SAMPLERS',
|
||||||
'build_sampler', 'RepeatAugSampler'
|
'build_sampler', 'RepeatAugSampler', 'KFoldDataset'
|
||||||
]
|
]
|
||||||
|
@ -118,6 +118,7 @@ class BaseDataset(Dataset, metaclass=ABCMeta):
|
|||||||
results,
|
results,
|
||||||
metric='accuracy',
|
metric='accuracy',
|
||||||
metric_options=None,
|
metric_options=None,
|
||||||
|
indices=None,
|
||||||
logger=None):
|
logger=None):
|
||||||
"""Evaluate the dataset.
|
"""Evaluate the dataset.
|
||||||
|
|
||||||
@ -128,6 +129,8 @@ class BaseDataset(Dataset, metaclass=ABCMeta):
|
|||||||
metric_options (dict, optional): Options for calculating metrics.
|
metric_options (dict, optional): Options for calculating metrics.
|
||||||
Allowed keys are 'topk', 'thrs' and 'average_mode'.
|
Allowed keys are 'topk', 'thrs' and 'average_mode'.
|
||||||
Defaults to None.
|
Defaults to None.
|
||||||
|
indices (list, optional): The indices of samples corresponding to
|
||||||
|
the results. Defaults to None.
|
||||||
logger (logging.Logger | str, optional): Logger used for printing
|
logger (logging.Logger | str, optional): Logger used for printing
|
||||||
related information during evaluation. Defaults to None.
|
related information during evaluation. Defaults to None.
|
||||||
Returns:
|
Returns:
|
||||||
@ -145,6 +148,8 @@ class BaseDataset(Dataset, metaclass=ABCMeta):
|
|||||||
eval_results = {}
|
eval_results = {}
|
||||||
results = np.vstack(results)
|
results = np.vstack(results)
|
||||||
gt_labels = self.get_gt_labels()
|
gt_labels = self.get_gt_labels()
|
||||||
|
if indices is not None:
|
||||||
|
gt_labels = gt_labels[indices]
|
||||||
num_imgs = len(results)
|
num_imgs = len(results)
|
||||||
assert len(gt_labels) == num_imgs, 'dataset testing results should '\
|
assert len(gt_labels) == num_imgs, 'dataset testing results should '\
|
||||||
'be of the same length as gt_labels.'
|
'be of the same length as gt_labels.'
|
||||||
|
@ -1,4 +1,5 @@
|
|||||||
# Copyright (c) OpenMMLab. All rights reserved.
|
# Copyright (c) OpenMMLab. All rights reserved.
|
||||||
|
import copy
|
||||||
import platform
|
import platform
|
||||||
import random
|
import random
|
||||||
from functools import partial
|
from functools import partial
|
||||||
@ -25,7 +26,7 @@ SAMPLERS = Registry('sampler')
|
|||||||
|
|
||||||
def build_dataset(cfg, default_args=None):
|
def build_dataset(cfg, default_args=None):
|
||||||
from .dataset_wrappers import (ConcatDataset, RepeatDataset,
|
from .dataset_wrappers import (ConcatDataset, RepeatDataset,
|
||||||
ClassBalancedDataset)
|
ClassBalancedDataset, KFoldDataset)
|
||||||
if isinstance(cfg, (list, tuple)):
|
if isinstance(cfg, (list, tuple)):
|
||||||
dataset = ConcatDataset([build_dataset(c, default_args) for c in cfg])
|
dataset = ConcatDataset([build_dataset(c, default_args) for c in cfg])
|
||||||
elif cfg['type'] == 'RepeatDataset':
|
elif cfg['type'] == 'RepeatDataset':
|
||||||
@ -34,6 +35,13 @@ def build_dataset(cfg, default_args=None):
|
|||||||
elif cfg['type'] == 'ClassBalancedDataset':
|
elif cfg['type'] == 'ClassBalancedDataset':
|
||||||
dataset = ClassBalancedDataset(
|
dataset = ClassBalancedDataset(
|
||||||
build_dataset(cfg['dataset'], default_args), cfg['oversample_thr'])
|
build_dataset(cfg['dataset'], default_args), cfg['oversample_thr'])
|
||||||
|
elif cfg['type'] == 'KFoldDataset':
|
||||||
|
cp_cfg = copy.deepcopy(cfg)
|
||||||
|
if cp_cfg.get('test_mode', None) is None:
|
||||||
|
cp_cfg['test_mode'] = (default_args or {}).pop('test_mode', False)
|
||||||
|
cp_cfg['dataset'] = build_dataset(cp_cfg['dataset'], default_args)
|
||||||
|
cp_cfg.pop('type')
|
||||||
|
dataset = KFoldDataset(**cp_cfg)
|
||||||
else:
|
else:
|
||||||
dataset = build_from_cfg(cfg, DATASETS, default_args)
|
dataset = build_from_cfg(cfg, DATASETS, default_args)
|
||||||
|
|
||||||
|
@ -170,3 +170,56 @@ class ClassBalancedDataset(object):
|
|||||||
|
|
||||||
def __len__(self):
|
def __len__(self):
|
||||||
return len(self.repeat_indices)
|
return len(self.repeat_indices)
|
||||||
|
|
||||||
|
|
||||||
|
@DATASETS.register_module()
|
||||||
|
class KFoldDataset:
|
||||||
|
"""A wrapper of dataset for K-Fold cross-validation.
|
||||||
|
|
||||||
|
K-Fold cross-validation divides all the samples in groups of samples,
|
||||||
|
called folds, of almost equal sizes. And we use k-1 of folds to do training
|
||||||
|
and use the fold left to do validation.
|
||||||
|
|
||||||
|
Args:
|
||||||
|
dataset (:obj:`CustomDataset`): The dataset to be divided.
|
||||||
|
fold (int): The fold used to do validation. Defaults to 0.
|
||||||
|
num_splits (int): The number of all folds. Defaults to 5.
|
||||||
|
test_mode (bool): Use the training dataset or validation dataset.
|
||||||
|
Defaults to False.
|
||||||
|
seed (int, optional): The seed to shuffle the dataset before splitting.
|
||||||
|
If None, not shuffle the dataset. Defaults to None.
|
||||||
|
"""
|
||||||
|
|
||||||
|
def __init__(self,
|
||||||
|
dataset,
|
||||||
|
fold=0,
|
||||||
|
num_splits=5,
|
||||||
|
test_mode=False,
|
||||||
|
seed=None):
|
||||||
|
self.dataset = dataset
|
||||||
|
self.CLASSES = dataset.CLASSES
|
||||||
|
self.test_mode = test_mode
|
||||||
|
self.num_splits = num_splits
|
||||||
|
|
||||||
|
length = len(dataset)
|
||||||
|
indices = list(range(length))
|
||||||
|
if isinstance(seed, int):
|
||||||
|
rng = np.random.default_rng(seed)
|
||||||
|
rng.shuffle(indices)
|
||||||
|
|
||||||
|
test_start = length * fold // num_splits
|
||||||
|
test_end = length * (fold + 1) // num_splits
|
||||||
|
if test_mode:
|
||||||
|
self.indices = indices[test_start:test_end]
|
||||||
|
else:
|
||||||
|
self.indices = indices[:test_start] + indices[test_end:]
|
||||||
|
|
||||||
|
def __getitem__(self, idx):
|
||||||
|
return self.dataset[self.indices[idx]]
|
||||||
|
|
||||||
|
def __len__(self):
|
||||||
|
return len(self.indices)
|
||||||
|
|
||||||
|
def evaluate(self, *args, **kwargs):
|
||||||
|
kwargs['indices'] = self.indices
|
||||||
|
return self.dataset.evaluate(*args, **kwargs)
|
||||||
|
@ -28,6 +28,7 @@ class MultiLabelDataset(BaseDataset):
|
|||||||
results,
|
results,
|
||||||
metric='mAP',
|
metric='mAP',
|
||||||
metric_options=None,
|
metric_options=None,
|
||||||
|
indices=None,
|
||||||
logger=None,
|
logger=None,
|
||||||
**deprecated_kwargs):
|
**deprecated_kwargs):
|
||||||
"""Evaluate the dataset.
|
"""Evaluate the dataset.
|
||||||
@ -62,6 +63,8 @@ class MultiLabelDataset(BaseDataset):
|
|||||||
eval_results = {}
|
eval_results = {}
|
||||||
results = np.vstack(results)
|
results = np.vstack(results)
|
||||||
gt_labels = self.get_gt_labels()
|
gt_labels = self.get_gt_labels()
|
||||||
|
if indices is not None:
|
||||||
|
gt_labels = gt_labels[indices]
|
||||||
num_imgs = len(results)
|
num_imgs = len(results)
|
||||||
assert len(gt_labels) == num_imgs, 'dataset testing results should '\
|
assert len(gt_labels) == num_imgs, 'dataset testing results should '\
|
||||||
'be of the same length as gt_labels.'
|
'be of the same length as gt_labels.'
|
||||||
|
@ -1,9 +1,14 @@
|
|||||||
|
import os.path as osp
|
||||||
|
from copy import deepcopy
|
||||||
from unittest.mock import patch
|
from unittest.mock import patch
|
||||||
|
|
||||||
import torch
|
import torch
|
||||||
from mmcv.utils import digit_version
|
from mmcv.utils import digit_version
|
||||||
|
|
||||||
from mmcls.datasets import build_dataloader
|
from mmcls.datasets import ImageNet, build_dataloader, build_dataset
|
||||||
|
from mmcls.datasets.dataset_wrappers import (ClassBalancedDataset,
|
||||||
|
ConcatDataset, KFoldDataset,
|
||||||
|
RepeatDataset)
|
||||||
|
|
||||||
|
|
||||||
class TestDataloaderBuilder():
|
class TestDataloaderBuilder():
|
||||||
@ -119,3 +124,148 @@ class TestDataloaderBuilder():
|
|||||||
expect = torch.tensor(
|
expect = torch.tensor(
|
||||||
[0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6][1::2])
|
[0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6][1::2])
|
||||||
assert all(torch.cat(list(iter(dataloader))) == expect)
|
assert all(torch.cat(list(iter(dataloader))) == expect)
|
||||||
|
|
||||||
|
|
||||||
|
class TestDatasetBuilder():
|
||||||
|
|
||||||
|
@classmethod
|
||||||
|
def setup_class(cls):
|
||||||
|
data_prefix = osp.join(osp.dirname(__file__), '../data/dataset')
|
||||||
|
cls.dataset_cfg = dict(
|
||||||
|
type='ImageNet',
|
||||||
|
data_prefix=data_prefix,
|
||||||
|
ann_file=osp.join(data_prefix, 'ann.txt'),
|
||||||
|
pipeline=[],
|
||||||
|
test_mode=False,
|
||||||
|
)
|
||||||
|
|
||||||
|
def test_normal_dataset(self):
|
||||||
|
# Test build
|
||||||
|
dataset = build_dataset(self.dataset_cfg)
|
||||||
|
assert isinstance(dataset, ImageNet)
|
||||||
|
assert dataset.test_mode == self.dataset_cfg['test_mode']
|
||||||
|
|
||||||
|
# Test default_args
|
||||||
|
dataset = build_dataset(self.dataset_cfg, {'test_mode': True})
|
||||||
|
assert dataset.test_mode == self.dataset_cfg['test_mode']
|
||||||
|
|
||||||
|
cp_cfg = deepcopy(self.dataset_cfg)
|
||||||
|
cp_cfg.pop('test_mode')
|
||||||
|
dataset = build_dataset(cp_cfg, {'test_mode': True})
|
||||||
|
assert dataset.test_mode
|
||||||
|
|
||||||
|
def test_concat_dataset(self):
|
||||||
|
# Test build
|
||||||
|
dataset = build_dataset([self.dataset_cfg, self.dataset_cfg])
|
||||||
|
assert isinstance(dataset, ConcatDataset)
|
||||||
|
assert dataset.datasets[0].test_mode == self.dataset_cfg['test_mode']
|
||||||
|
|
||||||
|
# Test default_args
|
||||||
|
dataset = build_dataset([self.dataset_cfg, self.dataset_cfg],
|
||||||
|
{'test_mode': True})
|
||||||
|
assert dataset.datasets[0].test_mode == self.dataset_cfg['test_mode']
|
||||||
|
|
||||||
|
cp_cfg = deepcopy(self.dataset_cfg)
|
||||||
|
cp_cfg.pop('test_mode')
|
||||||
|
dataset = build_dataset([cp_cfg, cp_cfg], {'test_mode': True})
|
||||||
|
assert dataset.datasets[0].test_mode
|
||||||
|
|
||||||
|
def test_repeat_dataset(self):
|
||||||
|
# Test build
|
||||||
|
dataset = build_dataset(
|
||||||
|
dict(type='RepeatDataset', dataset=self.dataset_cfg, times=3))
|
||||||
|
assert isinstance(dataset, RepeatDataset)
|
||||||
|
assert dataset.dataset.test_mode == self.dataset_cfg['test_mode']
|
||||||
|
|
||||||
|
# Test default_args
|
||||||
|
dataset = build_dataset(
|
||||||
|
dict(type='RepeatDataset', dataset=self.dataset_cfg, times=3),
|
||||||
|
{'test_mode': True})
|
||||||
|
assert dataset.dataset.test_mode == self.dataset_cfg['test_mode']
|
||||||
|
|
||||||
|
cp_cfg = deepcopy(self.dataset_cfg)
|
||||||
|
cp_cfg.pop('test_mode')
|
||||||
|
dataset = build_dataset(
|
||||||
|
dict(type='RepeatDataset', dataset=cp_cfg, times=3),
|
||||||
|
{'test_mode': True})
|
||||||
|
assert dataset.dataset.test_mode
|
||||||
|
|
||||||
|
def test_class_balance_dataset(self):
|
||||||
|
# Test build
|
||||||
|
dataset = build_dataset(
|
||||||
|
dict(
|
||||||
|
type='ClassBalancedDataset',
|
||||||
|
dataset=self.dataset_cfg,
|
||||||
|
oversample_thr=1.,
|
||||||
|
))
|
||||||
|
assert isinstance(dataset, ClassBalancedDataset)
|
||||||
|
assert dataset.dataset.test_mode == self.dataset_cfg['test_mode']
|
||||||
|
|
||||||
|
# Test default_args
|
||||||
|
dataset = build_dataset(
|
||||||
|
dict(
|
||||||
|
type='ClassBalancedDataset',
|
||||||
|
dataset=self.dataset_cfg,
|
||||||
|
oversample_thr=1.,
|
||||||
|
), {'test_mode': True})
|
||||||
|
assert dataset.dataset.test_mode == self.dataset_cfg['test_mode']
|
||||||
|
|
||||||
|
cp_cfg = deepcopy(self.dataset_cfg)
|
||||||
|
cp_cfg.pop('test_mode')
|
||||||
|
dataset = build_dataset(
|
||||||
|
dict(
|
||||||
|
type='ClassBalancedDataset',
|
||||||
|
dataset=cp_cfg,
|
||||||
|
oversample_thr=1.,
|
||||||
|
), {'test_mode': True})
|
||||||
|
assert dataset.dataset.test_mode
|
||||||
|
|
||||||
|
def test_kfold_dataset(self):
|
||||||
|
# Test build
|
||||||
|
dataset = build_dataset(
|
||||||
|
dict(
|
||||||
|
type='KFoldDataset',
|
||||||
|
dataset=self.dataset_cfg,
|
||||||
|
fold=0,
|
||||||
|
num_splits=5,
|
||||||
|
test_mode=False,
|
||||||
|
))
|
||||||
|
assert isinstance(dataset, KFoldDataset)
|
||||||
|
assert not dataset.test_mode
|
||||||
|
assert dataset.dataset.test_mode == self.dataset_cfg['test_mode']
|
||||||
|
|
||||||
|
# Test default_args
|
||||||
|
dataset = build_dataset(
|
||||||
|
dict(
|
||||||
|
type='KFoldDataset',
|
||||||
|
dataset=self.dataset_cfg,
|
||||||
|
fold=0,
|
||||||
|
num_splits=5,
|
||||||
|
test_mode=False,
|
||||||
|
),
|
||||||
|
default_args={
|
||||||
|
'test_mode': True,
|
||||||
|
'classes': [1, 2, 3]
|
||||||
|
})
|
||||||
|
assert not dataset.test_mode
|
||||||
|
assert dataset.dataset.test_mode == self.dataset_cfg['test_mode']
|
||||||
|
assert dataset.dataset.CLASSES == [1, 2, 3]
|
||||||
|
|
||||||
|
cp_cfg = deepcopy(self.dataset_cfg)
|
||||||
|
cp_cfg.pop('test_mode')
|
||||||
|
dataset = build_dataset(
|
||||||
|
dict(
|
||||||
|
type='KFoldDataset',
|
||||||
|
dataset=self.dataset_cfg,
|
||||||
|
fold=0,
|
||||||
|
num_splits=5,
|
||||||
|
),
|
||||||
|
default_args={
|
||||||
|
'test_mode': True,
|
||||||
|
'classes': [1, 2, 3]
|
||||||
|
})
|
||||||
|
# The test_mode in default_args will be passed to KFoldDataset
|
||||||
|
assert dataset.test_mode
|
||||||
|
assert not dataset.dataset.test_mode
|
||||||
|
# Other default_args will be passed to child dataset.
|
||||||
|
assert dataset.dataset.CLASSES == [1, 2, 3]
|
||||||
|
@ -8,7 +8,20 @@ import numpy as np
|
|||||||
import pytest
|
import pytest
|
||||||
|
|
||||||
from mmcls.datasets import (BaseDataset, ClassBalancedDataset, ConcatDataset,
|
from mmcls.datasets import (BaseDataset, ClassBalancedDataset, ConcatDataset,
|
||||||
RepeatDataset)
|
KFoldDataset, RepeatDataset)
|
||||||
|
|
||||||
|
|
||||||
|
def mock_evaluate(results,
|
||||||
|
metric='accuracy',
|
||||||
|
metric_options=None,
|
||||||
|
indices=None,
|
||||||
|
logger=None):
|
||||||
|
return dict(
|
||||||
|
results=results,
|
||||||
|
metric=metric,
|
||||||
|
metric_options=metric_options,
|
||||||
|
indices=indices,
|
||||||
|
logger=logger)
|
||||||
|
|
||||||
|
|
||||||
@patch.multiple(BaseDataset, __abstractmethods__=set())
|
@patch.multiple(BaseDataset, __abstractmethods__=set())
|
||||||
@ -23,6 +36,8 @@ def construct_toy_multi_label_dataset(length):
|
|||||||
dataset.data_infos = MagicMock()
|
dataset.data_infos = MagicMock()
|
||||||
dataset.data_infos.__len__.return_value = length
|
dataset.data_infos.__len__.return_value = length
|
||||||
dataset.get_cat_ids = MagicMock(side_effect=lambda idx: cat_ids_list[idx])
|
dataset.get_cat_ids = MagicMock(side_effect=lambda idx: cat_ids_list[idx])
|
||||||
|
|
||||||
|
dataset.evaluate = MagicMock(side_effect=mock_evaluate)
|
||||||
return dataset, cat_ids_list
|
return dataset, cat_ids_list
|
||||||
|
|
||||||
|
|
||||||
@ -35,6 +50,7 @@ def construct_toy_single_label_dataset(length):
|
|||||||
dataset.data_infos = MagicMock()
|
dataset.data_infos = MagicMock()
|
||||||
dataset.data_infos.__len__.return_value = length
|
dataset.data_infos.__len__.return_value = length
|
||||||
dataset.get_cat_ids = MagicMock(side_effect=lambda idx: cat_ids_list[idx])
|
dataset.get_cat_ids = MagicMock(side_effect=lambda idx: cat_ids_list[idx])
|
||||||
|
dataset.evaluate = MagicMock(side_effect=mock_evaluate)
|
||||||
return dataset, cat_ids_list
|
return dataset, cat_ids_list
|
||||||
|
|
||||||
|
|
||||||
@ -107,3 +123,49 @@ def test_class_balanced_dataset(construct_dataset):
|
|||||||
for idx in np.random.randint(0, len(repeat_factor_dataset), 3):
|
for idx in np.random.randint(0, len(repeat_factor_dataset), 3):
|
||||||
assert repeat_factor_dataset[idx] == bisect.bisect_right(
|
assert repeat_factor_dataset[idx] == bisect.bisect_right(
|
||||||
repeat_factors_cumsum, idx)
|
repeat_factors_cumsum, idx)
|
||||||
|
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('construct_dataset', [
|
||||||
|
'construct_toy_multi_label_dataset', 'construct_toy_single_label_dataset'
|
||||||
|
])
|
||||||
|
def test_kfold_dataset(construct_dataset):
|
||||||
|
construct_toy_dataset = eval(construct_dataset)
|
||||||
|
dataset, _ = construct_toy_dataset(10)
|
||||||
|
|
||||||
|
# test without random seed
|
||||||
|
train_datasets = [
|
||||||
|
KFoldDataset(dataset, fold=i, num_splits=3, test_mode=False)
|
||||||
|
for i in range(5)
|
||||||
|
]
|
||||||
|
test_datasets = [
|
||||||
|
KFoldDataset(dataset, fold=i, num_splits=3, test_mode=True)
|
||||||
|
for i in range(5)
|
||||||
|
]
|
||||||
|
|
||||||
|
assert sum([i.indices for i in test_datasets], []) == list(range(10))
|
||||||
|
for train_set, test_set in zip(train_datasets, test_datasets):
|
||||||
|
train_samples = [train_set[i] for i in range(len(train_set))]
|
||||||
|
test_samples = [test_set[i] for i in range(len(test_set))]
|
||||||
|
assert set(train_samples + test_samples) == set(range(10))
|
||||||
|
|
||||||
|
# test with random seed
|
||||||
|
train_datasets = [
|
||||||
|
KFoldDataset(dataset, fold=i, num_splits=3, test_mode=False, seed=1)
|
||||||
|
for i in range(5)
|
||||||
|
]
|
||||||
|
test_datasets = [
|
||||||
|
KFoldDataset(dataset, fold=i, num_splits=3, test_mode=True, seed=1)
|
||||||
|
for i in range(5)
|
||||||
|
]
|
||||||
|
|
||||||
|
assert sum([i.indices for i in test_datasets], []) != list(range(10))
|
||||||
|
assert set(sum([i.indices for i in test_datasets], [])) == set(range(10))
|
||||||
|
for train_set, test_set in zip(train_datasets, test_datasets):
|
||||||
|
train_samples = [train_set[i] for i in range(len(train_set))]
|
||||||
|
test_samples = [test_set[i] for i in range(len(test_set))]
|
||||||
|
assert set(train_samples + test_samples) == set(range(10))
|
||||||
|
|
||||||
|
# test evaluate
|
||||||
|
for test_set in test_datasets:
|
||||||
|
eval_inputs = test_set.evaluate(None)
|
||||||
|
assert eval_inputs['indices'] == test_set.indices
|
||||||
|
355
tools/kfold-cross-valid.py
Normal file
355
tools/kfold-cross-valid.py
Normal file
@ -0,0 +1,355 @@
|
|||||||
|
# Copyright (c) OpenMMLab. All rights reserved.
|
||||||
|
import argparse
|
||||||
|
import copy
|
||||||
|
import os
|
||||||
|
import os.path as osp
|
||||||
|
import time
|
||||||
|
from datetime import datetime
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
import mmcv
|
||||||
|
import torch
|
||||||
|
from mmcv import Config, DictAction
|
||||||
|
from mmcv.runner import get_dist_info, init_dist
|
||||||
|
|
||||||
|
from mmcls import __version__
|
||||||
|
from mmcls.apis import init_random_seed, set_random_seed, train_model
|
||||||
|
from mmcls.datasets import build_dataset
|
||||||
|
from mmcls.models import build_classifier
|
||||||
|
from mmcls.utils import collect_env, get_root_logger, load_json_log
|
||||||
|
|
||||||
|
TEST_METRICS = ('precision', 'recall', 'f1_score', 'support', 'mAP', 'CP',
|
||||||
|
'CR', 'CF1', 'OP', 'OR', 'OF1', 'accuracy')
|
||||||
|
|
||||||
|
prog_description = """K-Fold cross-validation.
|
||||||
|
|
||||||
|
To start a 5-fold cross-validation experiment:
|
||||||
|
python tools/kfold-cross-valid.py $CONFIG --num-splits 5
|
||||||
|
|
||||||
|
To resume a 5-fold cross-validation from an interrupted experiment:
|
||||||
|
python tools/kfold-cross-valid.py $CONFIG --num-splits 5 --resume-from work_dirs/fold2/latest.pth
|
||||||
|
|
||||||
|
To summarize a 5-fold cross-validation:
|
||||||
|
python tools/kfold-cross-valid.py $CONFIG --num-splits 5 --summary
|
||||||
|
""" # noqa: E501
|
||||||
|
|
||||||
|
|
||||||
|
def parse_args():
|
||||||
|
parser = argparse.ArgumentParser(
|
||||||
|
formatter_class=argparse.RawDescriptionHelpFormatter,
|
||||||
|
description=prog_description)
|
||||||
|
parser.add_argument('config', help='train config file path')
|
||||||
|
parser.add_argument(
|
||||||
|
'--num-splits', type=int, help='The number of all folds.')
|
||||||
|
parser.add_argument(
|
||||||
|
'--fold',
|
||||||
|
type=int,
|
||||||
|
help='The fold used to do validation. '
|
||||||
|
'If specify, only do an experiment of the specified fold.')
|
||||||
|
parser.add_argument(
|
||||||
|
'--summary',
|
||||||
|
action='store_true',
|
||||||
|
help='Summarize the k-fold cross-validation results.')
|
||||||
|
parser.add_argument('--work-dir', help='the dir to save logs and models')
|
||||||
|
parser.add_argument(
|
||||||
|
'--resume-from', help='the checkpoint file to resume from')
|
||||||
|
parser.add_argument(
|
||||||
|
'--no-validate',
|
||||||
|
action='store_true',
|
||||||
|
help='whether not to evaluate the checkpoint during training')
|
||||||
|
group_gpus = parser.add_mutually_exclusive_group()
|
||||||
|
group_gpus.add_argument('--device', help='device used for training')
|
||||||
|
group_gpus.add_argument(
|
||||||
|
'--gpus',
|
||||||
|
type=int,
|
||||||
|
help='number of gpus to use '
|
||||||
|
'(only applicable to non-distributed training)')
|
||||||
|
group_gpus.add_argument(
|
||||||
|
'--gpu-ids',
|
||||||
|
type=int,
|
||||||
|
nargs='+',
|
||||||
|
help='ids of gpus to use '
|
||||||
|
'(only applicable to non-distributed training)')
|
||||||
|
parser.add_argument('--seed', type=int, default=None, help='random seed')
|
||||||
|
parser.add_argument(
|
||||||
|
'--deterministic',
|
||||||
|
action='store_true',
|
||||||
|
help='whether to set deterministic options for CUDNN backend.')
|
||||||
|
parser.add_argument(
|
||||||
|
'--cfg-options',
|
||||||
|
nargs='+',
|
||||||
|
action=DictAction,
|
||||||
|
help='override some settings in the used config, the key-value pair '
|
||||||
|
'in xxx=yyy format will be merged into config file. If the value to '
|
||||||
|
'be overwritten is a list, it should be like key="[a,b]" or key=a,b '
|
||||||
|
'It also allows nested list/tuple values, e.g. key="[(a,b),(c,d)]" '
|
||||||
|
'Note that the quotation marks are necessary and that no white space '
|
||||||
|
'is allowed.')
|
||||||
|
parser.add_argument(
|
||||||
|
'--launcher',
|
||||||
|
choices=['none', 'pytorch', 'slurm', 'mpi'],
|
||||||
|
default='none',
|
||||||
|
help='job launcher')
|
||||||
|
parser.add_argument('--local_rank', type=int, default=0)
|
||||||
|
args = parser.parse_args()
|
||||||
|
if 'LOCAL_RANK' not in os.environ:
|
||||||
|
os.environ['LOCAL_RANK'] = str(args.local_rank)
|
||||||
|
|
||||||
|
return args
|
||||||
|
|
||||||
|
|
||||||
|
def copy_config(old_cfg):
|
||||||
|
"""deepcopy a Config object."""
|
||||||
|
new_cfg = Config()
|
||||||
|
_cfg_dict = copy.deepcopy(old_cfg._cfg_dict)
|
||||||
|
_filename = copy.deepcopy(old_cfg._filename)
|
||||||
|
_text = copy.deepcopy(old_cfg._text)
|
||||||
|
super(Config, new_cfg).__setattr__('_cfg_dict', _cfg_dict)
|
||||||
|
super(Config, new_cfg).__setattr__('_filename', _filename)
|
||||||
|
super(Config, new_cfg).__setattr__('_text', _text)
|
||||||
|
return new_cfg
|
||||||
|
|
||||||
|
|
||||||
|
def train_single_fold(args, cfg, fold, distributed, seed):
|
||||||
|
# create the work_dir for the fold
|
||||||
|
work_dir = osp.join(cfg.work_dir, f'fold{fold}')
|
||||||
|
cfg.work_dir = work_dir
|
||||||
|
|
||||||
|
# create work_dir
|
||||||
|
mmcv.mkdir_or_exist(osp.abspath(cfg.work_dir))
|
||||||
|
|
||||||
|
# wrap the dataset cfg
|
||||||
|
train_dataset = dict(
|
||||||
|
type='KFoldDataset',
|
||||||
|
fold=fold,
|
||||||
|
dataset=cfg.data.train,
|
||||||
|
num_splits=args.num_splits,
|
||||||
|
seed=seed,
|
||||||
|
)
|
||||||
|
val_dataset = dict(
|
||||||
|
type='KFoldDataset',
|
||||||
|
fold=fold,
|
||||||
|
# Use the same dataset with training.
|
||||||
|
dataset=copy.deepcopy(cfg.data.train),
|
||||||
|
num_splits=args.num_splits,
|
||||||
|
seed=seed,
|
||||||
|
test_mode=True,
|
||||||
|
)
|
||||||
|
val_dataset['dataset']['pipeline'] = cfg.data.val.pipeline
|
||||||
|
cfg.data.train = train_dataset
|
||||||
|
cfg.data.val = val_dataset
|
||||||
|
cfg.data.test = val_dataset
|
||||||
|
|
||||||
|
# dump config
|
||||||
|
stem, suffix = osp.basename(args.config).rsplit('.', 1)
|
||||||
|
cfg.dump(osp.join(cfg.work_dir, f'{stem}_fold{fold}.{suffix}'))
|
||||||
|
# init the logger before other steps
|
||||||
|
timestamp = time.strftime('%Y%m%d_%H%M%S', time.localtime())
|
||||||
|
log_file = osp.join(cfg.work_dir, f'{timestamp}.log')
|
||||||
|
logger = get_root_logger(log_file=log_file, log_level=cfg.log_level)
|
||||||
|
|
||||||
|
# init the meta dict to record some important information such as
|
||||||
|
# environment info and seed, which will be logged
|
||||||
|
meta = dict()
|
||||||
|
# log env info
|
||||||
|
env_info_dict = collect_env()
|
||||||
|
env_info = '\n'.join([(f'{k}: {v}') for k, v in env_info_dict.items()])
|
||||||
|
dash_line = '-' * 60 + '\n'
|
||||||
|
logger.info('Environment info:\n' + dash_line + env_info + '\n' +
|
||||||
|
dash_line)
|
||||||
|
meta['env_info'] = env_info
|
||||||
|
|
||||||
|
# log some basic info
|
||||||
|
logger.info(f'Distributed training: {distributed}')
|
||||||
|
logger.info(f'Config:\n{cfg.pretty_text}')
|
||||||
|
logger.info(
|
||||||
|
f'-------- Cross-validation: [{fold+1}/{args.num_splits}] -------- ')
|
||||||
|
|
||||||
|
# set random seeds
|
||||||
|
# Use different seed in different folds
|
||||||
|
logger.info(f'Set random seed to {seed + fold}, '
|
||||||
|
f'deterministic: {args.deterministic}')
|
||||||
|
set_random_seed(seed + fold, deterministic=args.deterministic)
|
||||||
|
cfg.seed = seed + fold
|
||||||
|
meta['seed'] = seed + fold
|
||||||
|
|
||||||
|
model = build_classifier(cfg.model)
|
||||||
|
model.init_weights()
|
||||||
|
|
||||||
|
datasets = [build_dataset(cfg.data.train)]
|
||||||
|
if len(cfg.workflow) == 2:
|
||||||
|
val_dataset = copy.deepcopy(cfg.data.val)
|
||||||
|
val_dataset.pipeline = cfg.data.train.pipeline
|
||||||
|
datasets.append(build_dataset(val_dataset))
|
||||||
|
meta.update(
|
||||||
|
dict(
|
||||||
|
mmcls_version=__version__,
|
||||||
|
config=cfg.pretty_text,
|
||||||
|
CLASSES=datasets[0].CLASSES,
|
||||||
|
kfold=dict(fold=fold, num_splits=args.num_splits)))
|
||||||
|
# add an attribute for visualization convenience
|
||||||
|
train_model(
|
||||||
|
model,
|
||||||
|
datasets,
|
||||||
|
cfg,
|
||||||
|
distributed=distributed,
|
||||||
|
validate=(not args.no_validate),
|
||||||
|
timestamp=timestamp,
|
||||||
|
device='cpu' if args.device == 'cpu' else 'cuda',
|
||||||
|
meta=meta)
|
||||||
|
|
||||||
|
|
||||||
|
def summary(args, cfg):
|
||||||
|
summary = dict()
|
||||||
|
for fold in range(args.num_splits):
|
||||||
|
work_dir = Path(cfg.work_dir) / f'fold{fold}'
|
||||||
|
|
||||||
|
# Find the latest training log
|
||||||
|
log_files = list(work_dir.glob('*.log.json'))
|
||||||
|
if len(log_files) == 0:
|
||||||
|
continue
|
||||||
|
log_file = sorted(log_files)[-1]
|
||||||
|
|
||||||
|
date = datetime.fromtimestamp(log_file.lstat().st_mtime)
|
||||||
|
summary[fold] = {'date': date.strftime('%Y-%m-%d %H:%M:%S')}
|
||||||
|
|
||||||
|
# Find the latest eval log
|
||||||
|
json_log = load_json_log(log_file)
|
||||||
|
epochs = sorted(list(json_log.keys()))
|
||||||
|
eval_log = {}
|
||||||
|
|
||||||
|
def is_metric_key(key):
|
||||||
|
for metric in TEST_METRICS:
|
||||||
|
if metric in key:
|
||||||
|
return True
|
||||||
|
return False
|
||||||
|
|
||||||
|
for epoch in epochs[::-1]:
|
||||||
|
if any(is_metric_key(k) for k in json_log[epoch].keys()):
|
||||||
|
eval_log = json_log[epoch]
|
||||||
|
break
|
||||||
|
|
||||||
|
summary[fold]['epoch'] = epoch
|
||||||
|
summary[fold]['metric'] = {
|
||||||
|
k: v[0] # the value is a list with only one item.
|
||||||
|
for k, v in eval_log.items() if is_metric_key(k)
|
||||||
|
}
|
||||||
|
show_summary(args, summary)
|
||||||
|
|
||||||
|
|
||||||
|
def show_summary(args, summary_data):
|
||||||
|
try:
|
||||||
|
from rich.console import Console
|
||||||
|
from rich.table import Table
|
||||||
|
except ImportError:
|
||||||
|
raise ImportError('Please run `pip install rich` to install '
|
||||||
|
'package `rich` to draw the table.')
|
||||||
|
|
||||||
|
console = Console()
|
||||||
|
table = Table(title=f'{args.num_splits}-fold Cross-validation Summary')
|
||||||
|
table.add_column('Fold')
|
||||||
|
metrics = summary_data[0]['metric'].keys()
|
||||||
|
for metric in metrics:
|
||||||
|
table.add_column(metric)
|
||||||
|
table.add_column('Epoch')
|
||||||
|
table.add_column('Date')
|
||||||
|
|
||||||
|
for fold in range(args.num_splits):
|
||||||
|
row = [f'{fold+1}']
|
||||||
|
if fold not in summary_data:
|
||||||
|
table.add_row(*row)
|
||||||
|
continue
|
||||||
|
for metric in metrics:
|
||||||
|
metric_value = summary_data[fold]['metric'].get(metric, '')
|
||||||
|
|
||||||
|
def format_value(value):
|
||||||
|
if isinstance(value, float):
|
||||||
|
return f'{value:.2f}'
|
||||||
|
if isinstance(value, (list, tuple)):
|
||||||
|
return str([format_value(i) for i in value])
|
||||||
|
else:
|
||||||
|
return str(value)
|
||||||
|
|
||||||
|
row.append(format_value(metric_value))
|
||||||
|
row.append(str(summary_data[fold]['epoch']))
|
||||||
|
row.append(summary_data[fold]['date'])
|
||||||
|
table.add_row(*row)
|
||||||
|
|
||||||
|
console.print(table)
|
||||||
|
|
||||||
|
|
||||||
|
def main():
|
||||||
|
args = parse_args()
|
||||||
|
|
||||||
|
cfg = Config.fromfile(args.config)
|
||||||
|
if args.cfg_options is not None:
|
||||||
|
cfg.merge_from_dict(args.cfg_options)
|
||||||
|
# set cudnn_benchmark
|
||||||
|
if cfg.get('cudnn_benchmark', False):
|
||||||
|
torch.backends.cudnn.benchmark = True
|
||||||
|
|
||||||
|
# work_dir is determined in this priority: CLI > segment in file > filename
|
||||||
|
if args.work_dir is not None:
|
||||||
|
# update configs according to CLI args if args.work_dir is not None
|
||||||
|
cfg.work_dir = args.work_dir
|
||||||
|
elif cfg.get('work_dir', None) is None:
|
||||||
|
# use config filename as default work_dir if cfg.work_dir is None
|
||||||
|
cfg.work_dir = osp.join('./work_dirs',
|
||||||
|
osp.splitext(osp.basename(args.config))[0])
|
||||||
|
|
||||||
|
if args.summary:
|
||||||
|
summary(args, cfg)
|
||||||
|
return
|
||||||
|
|
||||||
|
# resume from the previous experiment
|
||||||
|
if args.resume_from is not None:
|
||||||
|
cfg.resume_from = args.resume_from
|
||||||
|
resume_kfold = torch.load(cfg.resume_from).get('meta',
|
||||||
|
{}).get('kfold', None)
|
||||||
|
if resume_kfold is None:
|
||||||
|
raise RuntimeError(
|
||||||
|
'No "meta" key in checkpoints or no "kfold" in the meta dict. '
|
||||||
|
'Please check if the resume checkpoint from a k-fold '
|
||||||
|
'cross-valid experiment.')
|
||||||
|
resume_fold = resume_kfold['fold']
|
||||||
|
assert args.num_splits == resume_kfold['num_splits']
|
||||||
|
else:
|
||||||
|
resume_fold = 0
|
||||||
|
|
||||||
|
if args.gpu_ids is not None:
|
||||||
|
cfg.gpu_ids = args.gpu_ids
|
||||||
|
else:
|
||||||
|
cfg.gpu_ids = range(1) if args.gpus is None else range(args.gpus)
|
||||||
|
|
||||||
|
# init distributed env first, since logger depends on the dist info.
|
||||||
|
if args.launcher == 'none':
|
||||||
|
distributed = False
|
||||||
|
else:
|
||||||
|
distributed = True
|
||||||
|
init_dist(args.launcher, **cfg.dist_params)
|
||||||
|
_, world_size = get_dist_info()
|
||||||
|
cfg.gpu_ids = range(world_size)
|
||||||
|
|
||||||
|
# init a unified random seed
|
||||||
|
seed = init_random_seed(args.seed)
|
||||||
|
|
||||||
|
# create work_dir
|
||||||
|
mmcv.mkdir_or_exist(osp.abspath(cfg.work_dir))
|
||||||
|
|
||||||
|
if args.fold is not None:
|
||||||
|
folds = [args.fold]
|
||||||
|
else:
|
||||||
|
folds = range(resume_fold, args.num_splits)
|
||||||
|
|
||||||
|
for fold in folds:
|
||||||
|
cfg_ = copy_config(cfg)
|
||||||
|
if fold != resume_fold:
|
||||||
|
cfg_.resume_from = None
|
||||||
|
train_single_fold(args, cfg_, fold, distributed, seed)
|
||||||
|
|
||||||
|
if args.fold is None:
|
||||||
|
summary(args, cfg)
|
||||||
|
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
main()
|
Loading…
x
Reference in New Issue
Block a user