Add blood vessel dataset processing script (#184)
* Add blood vessel dataset processing script * Fix syntax error * Fix syntax error * Fix syntax error * Fix bugs * Fix bugs * Fix bugs * Use safe functions and expand more apis * Use safe functions and expand more apis * Fix hard code and verify dataset integritypull/202/head
yamengxi
GitHub
parent
5a76a715f1
commit
cb2e0d3cb1
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@ -46,6 +46,34 @@ mmsegmentation
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│ │ │ ├── images
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│ │ │ │ ├── training
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│ │ │ │ ├── validation
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│ ├── CHASE_DB1
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│ │ ├── images
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│ │ │ ├── training
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│ │ │ ├── validation
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│ │ ├── annotations
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│ │ │ ├── training
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│ │ │ ├── validation
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│ ├── DRIVE
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│ │ ├── images
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│ │ │ ├── training
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│ │ │ ├── validation
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│ │ ├── annotations
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│ │ │ ├── training
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│ │ │ ├── validation
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│ ├── HRF
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│ │ ├── images
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│ │ │ ├── training
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│ │ │ ├── validation
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│ │ ├── annotations
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│ │ │ ├── training
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│ │ │ ├── validation
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│ ├── STARE
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│ │ ├── images
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│ │ │ ├── training
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│ │ │ ├── validation
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│ │ ├── annotations
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│ │ │ ├── training
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│ │ │ ├── validation
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```
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@ -93,6 +121,54 @@ If you would like to use Pascal Context dataset, please install [Detail](https:/
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python tools/convert_datasets/pascal_context.py data/VOCdevkit data/VOCdevkit/VOC2010/trainval_merged.json
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```
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### CHASE DB1
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The training and validation set of CHASE DB1 could be download from [here](https://staffnet.kingston.ac.uk/~ku15565/CHASE_DB1/assets/CHASEDB1.zip).
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To convert CHASE DB1 dataset to MMSegmentation format, you should run the following command:
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```shell
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python tools/convert_datasets/chase_db1.py /path/to/CHASEDB1.zip
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```
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The script will make directory structure automatically.
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### DRIVE
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The training and validation set of DRIVE could be download from [here](https://drive.grand-challenge.org/). Before that, you should register an account. Currently '1st_manual' is not provided officially.
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To convert DRIVE dataset to MMSegmentation format, you should run the following command:
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```shell
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python tools/convert_datasets/drive.py /path/to/training.zip /path/to/test.zip
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```
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The script will make directory structure automatically.
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### HRF
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First, download [healthy.zip](https://www5.cs.fau.de/fileadmin/research/datasets/fundus-images/healthy.zip), [glaucoma.zip](https://www5.cs.fau.de/fileadmin/research/datasets/fundus-images/glaucoma.zip), [diabetic_retinopathy.zip](https://www5.cs.fau.de/fileadmin/research/datasets/fundus-images/diabetic_retinopathy.zip), [healthy_manualsegm.zip](https://www5.cs.fau.de/fileadmin/research/datasets/fundus-images/healthy_manualsegm.zip), [glaucoma_manualsegm.zip](https://www5.cs.fau.de/fileadmin/research/datasets/fundus-images/glaucoma_manualsegm.zip) and [diabetic_retinopathy_manualsegm.zip](https://www5.cs.fau.de/fileadmin/research/datasets/fundus-images/diabetic_retinopathy_manualsegm.zip).
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To convert HRF dataset to MMSegmentation format, you should run the following command:
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```shell
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python tools/convert_datasets/hrf.py /path/to/healthy.zip /path/to/healthy_manualsegm.zip /path/to/glaucoma.zip /path/to/glaucoma_manualsegm.zip /path/to/diabetic_retinopathy.zip /path/to/diabetic_retinopathy_manualsegm.zip
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```
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The script will make directory structure automatically.
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### STARE
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First, download [stare-images.tar](http://cecas.clemson.edu/~ahoover/stare/probing/stare-images.tar), [labels-ah.tar](http://cecas.clemson.edu/~ahoover/stare/probing/labels-ah.tar) and [labels-vk.tar](http://cecas.clemson.edu/~ahoover/stare/probing/labels-vk.tar).
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To convert STARE dataset to MMSegmentation format, you should run the following command:
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```shell
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python tools/convert_datasets/stare.py /path/to/stare-images.tar /path/to/labels-ah.tar /path/to/labels-vk.tar
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```
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The script will make directory structure automatically.
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## Inference with pretrained models
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We provide testing scripts to evaluate a whole dataset (Cityscapes, PASCAL VOC, ADE20k, etc.),
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@ -8,6 +8,6 @@ line_length = 79
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multi_line_output = 0
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known_standard_library = setuptools
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known_first_party = mmseg
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known_third_party = PIL,cityscapesscripts,detail,matplotlib,mmcv,numpy,onnxruntime,oss2,pytest,scipy,torch
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known_third_party = PIL,cityscapesscripts,cv2,detail,matplotlib,mmcv,numpy,onnxruntime,oss2,pytest,scipy,torch
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no_lines_before = STDLIB,LOCALFOLDER
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default_section = THIRDPARTY
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@ -0,0 +1,83 @@
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import argparse
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import os
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import os.path as osp
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import tempfile
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import zipfile
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import mmcv
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CHASE_DB1_LEN = 28 * 3
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TRAINING_LEN = 60
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def parse_args():
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parser = argparse.ArgumentParser(
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description='Convert CHASE_DB1 dataset to mmsegmentation format')
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parser.add_argument('dataset_path', help='path of CHASEDB1.zip')
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parser.add_argument('--tmp_dir', help='path of the temporary directory')
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parser.add_argument('-o', '--out_dir', help='output path')
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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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dataset_path = args.dataset_path
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if args.out_dir is None:
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out_dir = osp.join('data', 'CHASE_DB1')
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else:
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out_dir = args.out_dir
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print('Making directories...')
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mmcv.mkdir_or_exist(out_dir)
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mmcv.mkdir_or_exist(osp.join(out_dir, 'images'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'images', 'training'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'images', 'validation'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations', 'training'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations', 'validation'))
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with tempfile.TemporaryDirectory(dir=args.tmp_dir) as tmp_dir:
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print('Extracting CHASEDB1.zip...')
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zip_file = zipfile.ZipFile(dataset_path)
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zip_file.extractall(tmp_dir)
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print('Generating training dataset...')
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assert len(os.listdir(tmp_dir)) == CHASE_DB1_LEN, \
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'len(os.listdir(tmp_dir)) != {}'.format(CHASE_DB1_LEN)
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for img_name in sorted(os.listdir(tmp_dir))[:TRAINING_LEN]:
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img = mmcv.imread(osp.join(tmp_dir, img_name))
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if osp.splitext(img_name)[1] == '.jpg':
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mmcv.imwrite(img,
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osp.join(out_dir, 'images', 'training', img_name))
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else:
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# The annotation img should be divided by 128, because some of
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# the annotation imgs are not standard. We should set a
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# threshold to convert the nonstandard annotation imgs. The
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# value divided by 128 is equivalent to '1 if value >= 128
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# else 0'
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mmcv.imwrite(
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img[:, :, 0] // 128,
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osp.join(out_dir, 'annotations', 'training',
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osp.splitext(img_name)[0] + '.jpg'))
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for img_name in sorted(os.listdir(tmp_dir))[TRAINING_LEN:]:
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img = mmcv.imread(osp.join(tmp_dir, img_name))
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if osp.splitext(img_name)[1] == '.jpg':
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mmcv.imwrite(
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img, osp.join(out_dir, 'images', 'validation', img_name))
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else:
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mmcv.imwrite(
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img[:, :, 0] // 128,
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osp.join(out_dir, 'annotations', 'validation',
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osp.splitext(img_name)[0] + '.jpg'))
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print('Removing the temporary files...')
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print('Done!')
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if __name__ == '__main__':
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main()
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@ -0,0 +1,109 @@
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import argparse
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import os
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import os.path as osp
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import tempfile
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import zipfile
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import cv2
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import mmcv
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def parse_args():
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parser = argparse.ArgumentParser(
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description='Convert DRIVE dataset to mmsegmentation format')
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parser.add_argument(
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'training_path', help='the training part of DRIVE dataset')
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parser.add_argument(
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'testing_path', help='the testing part of DRIVE dataset')
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parser.add_argument('--tmp_dir', help='path of the temporary directory')
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parser.add_argument('-o', '--out_dir', help='output path')
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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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training_path = args.training_path
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testing_path = args.testing_path
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if args.out_dir is None:
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out_dir = osp.join('data', 'DRIVE')
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else:
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out_dir = args.out_dir
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print('Making directories...')
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mmcv.mkdir_or_exist(out_dir)
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mmcv.mkdir_or_exist(osp.join(out_dir, 'images'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'images', 'training'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'images', 'validation'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations', 'training'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations', 'validation'))
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with tempfile.TemporaryDirectory(dir=args.tmp_dir) as tmp_dir:
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print('Extracting training.zip...')
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zip_file = zipfile.ZipFile(training_path)
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zip_file.extractall(tmp_dir)
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print('Generating training dataset...')
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now_dir = osp.join(tmp_dir, 'training', 'images')
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for img_name in os.listdir(now_dir):
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img = mmcv.imread(osp.join(now_dir, img_name))
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mmcv.imwrite(
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img,
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osp.join(out_dir, 'images', 'training',
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osp.splitext(img_name)[0] + '.jpg'))
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now_dir = osp.join(tmp_dir, 'training', '1st_manual')
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for img_name in os.listdir(now_dir):
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cap = cv2.VideoCapture(osp.join(now_dir, img_name))
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ret, img = cap.read()
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mmcv.imwrite(
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img[:, :, 0] // 128,
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osp.join(out_dir, 'annotations', 'training',
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osp.splitext(img_name)[0] + '.jpg'))
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print('Extracting test.zip...')
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zip_file = zipfile.ZipFile(testing_path)
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zip_file.extractall(tmp_dir)
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print('Generating validation dataset...')
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now_dir = osp.join(tmp_dir, 'test', 'images')
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for img_name in os.listdir(now_dir):
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img = mmcv.imread(osp.join(now_dir, img_name))
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mmcv.imwrite(
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img,
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osp.join(out_dir, 'images', 'validation',
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osp.splitext(img_name)[0] + '.jpg'))
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now_dir = osp.join(tmp_dir, 'test', '1st_manual')
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if osp.exists(now_dir):
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for img_name in os.listdir(now_dir):
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cap = cv2.VideoCapture(osp.join(now_dir, img_name))
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ret, img = cap.read()
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# The annotation img should be divided by 128, because some of
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# the annotation imgs are not standard. We should set a
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# threshold to convert the nonstandard annotation imgs. The
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# value divided by 128 is equivalent to '1 if value >= 128
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# else 0'
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mmcv.imwrite(
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img[:, :, 0] // 128,
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osp.join(out_dir, 'annotations', 'validation',
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osp.splitext(img_name)[0] + '.jpg'))
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now_dir = osp.join(tmp_dir, 'test', '2nd_manual')
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if osp.exists(now_dir):
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for img_name in os.listdir(now_dir):
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cap = cv2.VideoCapture(osp.join(now_dir, img_name))
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ret, img = cap.read()
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mmcv.imwrite(
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img[:, :, 0] // 128,
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osp.join(out_dir, 'annotations', 'validation',
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osp.splitext(img_name)[0] + '.jpg'))
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print('Removing the temporary files...')
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print('Done!')
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if __name__ == '__main__':
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main()
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@ -0,0 +1,110 @@
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import argparse
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import os
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import os.path as osp
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import tempfile
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import zipfile
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import mmcv
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HRF_LEN = 15
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TRAINING_LEN = 5
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def parse_args():
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parser = argparse.ArgumentParser(
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description='Convert HRF dataset to mmsegmentation format')
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parser.add_argument('healthy_path', help='the path of healthy.zip')
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parser.add_argument(
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'healthy_manualsegm_path', help='the path of healthy_manualsegm.zip')
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parser.add_argument('glaucoma_path', help='the path of glaucoma.zip')
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parser.add_argument(
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'glaucoma_manualsegm_path', help='the path of glaucoma_manualsegm.zip')
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parser.add_argument(
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'diabetic_retinopathy_path',
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help='the path of diabetic_retinopathy.zip')
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parser.add_argument(
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'diabetic_retinopathy_manualsegm_path',
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help='the path of diabetic_retinopathy_manualsegm.zip')
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parser.add_argument('--tmp_dir', help='path of the temporary directory')
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parser.add_argument('-o', '--out_dir', help='output path')
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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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images_path = [
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args.healthy_path, args.glaucoma_path, args.diabetic_retinopathy_path
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]
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annotations_path = [
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args.healthy_manualsegm_path, args.glaucoma_manualsegm_path,
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args.diabetic_retinopathy_manualsegm_path
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]
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if args.out_dir is None:
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out_dir = osp.join('data', 'HRF')
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else:
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out_dir = args.out_dir
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print('Making directories...')
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mmcv.mkdir_or_exist(out_dir)
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mmcv.mkdir_or_exist(osp.join(out_dir, 'images'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'images', 'training'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'images', 'validation'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations', 'training'))
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mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations', 'validation'))
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print('Generating images...')
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for now_path in images_path:
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with tempfile.TemporaryDirectory(dir=args.tmp_dir) as tmp_dir:
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zip_file = zipfile.ZipFile(now_path)
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zip_file.extractall(tmp_dir)
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assert len(os.listdir(tmp_dir)) == HRF_LEN, \
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'len(os.listdir(tmp_dir)) != {}'.format(HRF_LEN)
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for filename in sorted(os.listdir(tmp_dir))[:TRAINING_LEN]:
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img = mmcv.imread(osp.join(tmp_dir, filename))
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mmcv.imwrite(
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img,
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osp.join(out_dir, 'images', 'training',
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osp.splitext(filename)[0] + '.jpg'))
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for filename in sorted(os.listdir(tmp_dir))[TRAINING_LEN:]:
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img = mmcv.imread(osp.join(tmp_dir, filename))
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mmcv.imwrite(
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img,
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osp.join(out_dir, 'images', 'validation',
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osp.splitext(filename)[0] + '.jpg'))
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print('Generating annotations...')
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for now_path in annotations_path:
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with tempfile.TemporaryDirectory(dir=args.tmp_dir) as tmp_dir:
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zip_file = zipfile.ZipFile(now_path)
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zip_file.extractall(tmp_dir)
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assert len(os.listdir(tmp_dir)) == HRF_LEN, \
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'len(os.listdir(tmp_dir)) != {}'.format(HRF_LEN)
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for filename in sorted(os.listdir(tmp_dir))[:TRAINING_LEN]:
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img = mmcv.imread(osp.join(tmp_dir, filename))
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# The annotation img should be divided by 128, because some of
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# the annotation imgs are not standard. We should set a
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# threshold to convert the nonstandard annotation imgs. The
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# value divided by 128 is equivalent to '1 if value >= 128
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# else 0'
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mmcv.imwrite(
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img[:, :, 0] // 128,
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osp.join(out_dir, 'annotations', 'training',
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osp.splitext(filename)[0] + '.jpg'))
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for filename in sorted(os.listdir(tmp_dir))[TRAINING_LEN:]:
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img = mmcv.imread(osp.join(tmp_dir, filename))
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mmcv.imwrite(
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img[:, :, 0] // 128,
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osp.join(out_dir, 'annotations', 'validation',
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osp.splitext(filename)[0] + '.jpg'))
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print('Done!')
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if __name__ == '__main__':
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main()
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@ -0,0 +1,165 @@
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import argparse
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import gzip
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import os
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import os.path as osp
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import tarfile
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import tempfile
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import mmcv
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STARE_LEN = 20
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TRAINING_LEN = 10
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def un_gz(src, dst):
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g_file = gzip.GzipFile(src)
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||||
with open(dst, 'wb+') as f:
|
||||
f.write(g_file.read())
|
||||
g_file.close()
|
||||
|
||||
|
||||
def parse_args():
|
||||
parser = argparse.ArgumentParser(
|
||||
description='Convert STARE dataset to mmsegmentation format')
|
||||
parser.add_argument('image_path', help='the path of stare-images.tar')
|
||||
parser.add_argument('labels_ah', help='the path of labels-ah.tar')
|
||||
parser.add_argument('labels_vk', help='the path of labels-vk.tar')
|
||||
parser.add_argument('--tmp_dir', help='path of the temporary directory')
|
||||
parser.add_argument('-o', '--out_dir', help='output path')
|
||||
args = parser.parse_args()
|
||||
return args
|
||||
|
||||
|
||||
def main():
|
||||
args = parse_args()
|
||||
image_path = args.image_path
|
||||
labels_ah = args.labels_ah
|
||||
labels_vk = args.labels_vk
|
||||
if args.out_dir is None:
|
||||
out_dir = osp.join('data', 'STARE')
|
||||
else:
|
||||
out_dir = args.out_dir
|
||||
|
||||
print('Making directories...')
|
||||
mmcv.mkdir_or_exist(out_dir)
|
||||
mmcv.mkdir_or_exist(osp.join(out_dir, 'images'))
|
||||
mmcv.mkdir_or_exist(osp.join(out_dir, 'images', 'training'))
|
||||
mmcv.mkdir_or_exist(osp.join(out_dir, 'images', 'validation'))
|
||||
mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations'))
|
||||
mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations', 'training'))
|
||||
mmcv.mkdir_or_exist(osp.join(out_dir, 'annotations', 'validation'))
|
||||
|
||||
with tempfile.TemporaryDirectory(dir=args.tmp_dir) as tmp_dir:
|
||||
mmcv.mkdir_or_exist(osp.join(tmp_dir, 'gz'))
|
||||
mmcv.mkdir_or_exist(osp.join(tmp_dir, 'files'))
|
||||
|
||||
print('Extracting stare-images.tar...')
|
||||
with tarfile.open(image_path) as f:
|
||||
f.extractall(osp.join(tmp_dir, 'gz'))
|
||||
|
||||
for filename in os.listdir(osp.join(tmp_dir, 'gz')):
|
||||
un_gz(
|
||||
osp.join(tmp_dir, 'gz', filename),
|
||||
osp.join(tmp_dir, 'files',
|
||||
osp.splitext(filename)[0]))
|
||||
|
||||
now_dir = osp.join(tmp_dir, 'files')
|
||||
|
||||
assert len(os.listdir(now_dir)) == STARE_LEN, \
|
||||
'len(os.listdir(now_dir)) != {}'.format(STARE_LEN)
|
||||
|
||||
for filename in sorted(os.listdir(now_dir))[:TRAINING_LEN]:
|
||||
img = mmcv.imread(osp.join(now_dir, filename))
|
||||
mmcv.imwrite(
|
||||
img,
|
||||
osp.join(out_dir, 'images', 'training',
|
||||
osp.splitext(filename)[0] + '.jpg'))
|
||||
|
||||
for filename in sorted(os.listdir(now_dir))[TRAINING_LEN:]:
|
||||
img = mmcv.imread(osp.join(now_dir, filename))
|
||||
mmcv.imwrite(
|
||||
img,
|
||||
osp.join(out_dir, 'images', 'validation',
|
||||
osp.splitext(filename)[0] + '.jpg'))
|
||||
|
||||
print('Removing the temporary files...')
|
||||
|
||||
with tempfile.TemporaryDirectory(dir=args.tmp_dir) as tmp_dir:
|
||||
mmcv.mkdir_or_exist(osp.join(tmp_dir, 'gz'))
|
||||
mmcv.mkdir_or_exist(osp.join(tmp_dir, 'files'))
|
||||
|
||||
print('Extracting labels-ah.tar...')
|
||||
with tarfile.open(labels_ah) as f:
|
||||
f.extractall(osp.join(tmp_dir, 'gz'))
|
||||
|
||||
for filename in os.listdir(osp.join(tmp_dir, 'gz')):
|
||||
un_gz(
|
||||
osp.join(tmp_dir, 'gz', filename),
|
||||
osp.join(tmp_dir, 'files',
|
||||
osp.splitext(filename)[0]))
|
||||
|
||||
now_dir = osp.join(tmp_dir, 'files')
|
||||
|
||||
assert len(os.listdir(now_dir)) == STARE_LEN, \
|
||||
'len(os.listdir(now_dir)) != {}'.format(STARE_LEN)
|
||||
|
||||
for filename in sorted(os.listdir(now_dir))[:TRAINING_LEN]:
|
||||
img = mmcv.imread(osp.join(now_dir, filename))
|
||||
# The annotation img should be divided by 128, because some of
|
||||
# the annotation imgs are not standard. We should set a threshold
|
||||
# to convert the nonstandard annotation imgs. The value divided by
|
||||
# 128 equivalent to '1 if value >= 128 else 0'
|
||||
mmcv.imwrite(
|
||||
img[:, :, 0] // 128,
|
||||
osp.join(out_dir, 'annotations', 'training',
|
||||
osp.splitext(filename)[0] + '.jpg'))
|
||||
|
||||
for filename in sorted(os.listdir(now_dir))[TRAINING_LEN:]:
|
||||
img = mmcv.imread(osp.join(now_dir, filename))
|
||||
mmcv.imwrite(
|
||||
img[:, :, 0] // 128,
|
||||
osp.join(out_dir, 'annotations', 'validation',
|
||||
osp.splitext(filename)[0] + '.jpg'))
|
||||
|
||||
print('Removing the temporary files...')
|
||||
|
||||
with tempfile.TemporaryDirectory(dir=args.tmp_dir) as tmp_dir:
|
||||
mmcv.mkdir_or_exist(osp.join(tmp_dir, 'gz'))
|
||||
mmcv.mkdir_or_exist(osp.join(tmp_dir, 'files'))
|
||||
|
||||
print('Extracting labels-vk.tar...')
|
||||
with tarfile.open(labels_vk) as f:
|
||||
f.extractall(osp.join(tmp_dir, 'gz'))
|
||||
|
||||
for filename in os.listdir(osp.join(tmp_dir, 'gz')):
|
||||
un_gz(
|
||||
osp.join(tmp_dir, 'gz', filename),
|
||||
osp.join(tmp_dir, 'files',
|
||||
osp.splitext(filename)[0]))
|
||||
|
||||
now_dir = osp.join(tmp_dir, 'files')
|
||||
|
||||
assert len(os.listdir(now_dir)) == STARE_LEN, \
|
||||
'len(os.listdir(now_dir)) != {}'.format(STARE_LEN)
|
||||
|
||||
for filename in sorted(os.listdir(now_dir))[:TRAINING_LEN]:
|
||||
img = mmcv.imread(osp.join(now_dir, filename))
|
||||
mmcv.imwrite(
|
||||
img[:, :, 0] // 128,
|
||||
osp.join(out_dir, 'annotations', 'training',
|
||||
osp.splitext(filename)[0] + '.jpg'))
|
||||
|
||||
for filename in sorted(os.listdir(now_dir))[TRAINING_LEN:]:
|
||||
img = mmcv.imread(osp.join(now_dir, filename))
|
||||
mmcv.imwrite(
|
||||
img[:, :, 0] // 128,
|
||||
osp.join(out_dir, 'annotations', 'validation',
|
||||
osp.splitext(filename)[0] + '.jpg'))
|
||||
|
||||
print('Removing the temporary files...')
|
||||
|
||||
print('Done!')
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
Loading…
Reference in New Issue