add code for convert refuge datasets

tools/dataset_converters/refuge.py

@@ -0,0 +1,171 @@
+# Copyright (c) OpenMMLab. All rights reserved.
+import argparse
+import os
+from glob import glob
+import os.path as osp
+import tempfile
+import zipfile
+import numpy as np
+import matplotlib.pyplot as plt
+
+import mmcv
+from mmengine.utils import mkdir_or_exist
+
+HRF_LEN = 15
+TRAINING_LEN = 5
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description='Convert HRF dataset to mmsegmentation format')
+    parser.add_argument('--raw_data_root', help='the root path of raw data')
+
+    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 extract_img(root: str,cur_dir: str,out_dir: str,mode: str='train',file_type: str='img')-> None:
+    """_summary_
+
+    Args:
+       Args:
+        root (str): root where the extracted data is saved
+        cur_dir (cur_dir): dir where the zip_file exists
+        out_dir (str): root dir where the data is saved
+
+        mode (str, optional): _description_. Defaults to 'train'.
+        file_type (str, optional): _description_. Defaults to 'img',else to 'mask'.
+    """
+    print('mode',mode)
+    zip_file = zipfile.ZipFile(cur_dir)
+    zip_file.extractall(root)
+    for cur_dir,dirs,files in os.walk(root):
+        #filter child dirs and directories with "Illustration" and "MACOSX"
+        if len(dirs) == 0 and cur_dir.split('\\')[-1].find('Illustration') == -1 \
+        and cur_dir.find('MACOSX') == -1:
+
+            file_names = [file for  file in files if file.endswith('.jpg') or file.endswith('.bmp') ]
+            for filename in sorted(file_names):
+                img = mmcv.imread(osp.join(cur_dir, filename))
+
+                if file_type == 'annotations':
+                    img = img[:,:,0]
+                    img[np.where(img==0)] = 1
+                    img[np.where(img==128)] = 2
+                    img[np.where(img==255)] = 0
+                mmcv.imwrite(
+                    img,
+                    osp.join(out_dir, file_type, mode,
+                             osp.splitext(filename)[0] + '.png'))    
+
+def main():
+    args = parse_args()
+
+    raw_data_root = args.raw_data_root
+    if args.out_dir is None:
+        out_dir = osp.join('./data', 'REFUGE')
+        print('out_dir:',out_dir)
+    else:
+        out_dir = args.out_dir
+
+    print('Making directories...')
+    mkdir_or_exist(out_dir)
+    mkdir_or_exist(osp.join(out_dir, 'images'))
+    mkdir_or_exist(osp.join(out_dir, 'images', 'training'))
+    mkdir_or_exist(osp.join(out_dir, 'images', 'validation'))
+    mkdir_or_exist(osp.join(out_dir, 'images', 'test'))
+    mkdir_or_exist(osp.join(out_dir, 'annotations'))
+    mkdir_or_exist(osp.join(out_dir, 'annotations', 'training'))
+    mkdir_or_exist(osp.join(out_dir, 'annotations', 'validation'))
+    mkdir_or_exist(osp.join(out_dir, 'annotations', 'test'))
+
+    print('Generating images and annotations...')
+    cur_dir,dirs,files = list(os.walk(raw_data_root))[0]
+    print("====================")
+
+
+    files = list(filter(lambda x: x.endswith('.zip'),files))
+    files.remove('Disc_Cup_Masks.zip')
+    print(files)
+
+
+    with tempfile.TemporaryDirectory(dir=args.tmp_dir) as tmp_dir:
+        for file in files:
+            mode = list(filter(lambda x:file.lower().find(x)!= -1,['training','test','validation']))[0]
+            file_root = osp.join(tmp_dir,file[:-4])
+            file_type = 'images' if file.find('Anno') == -1 and file.find('GT')== -1 else 'annotations'
+            # if file_type == 'annotations':
+            extract_img(file_root,osp.join(cur_dir,file),out_dir,mode,file_type)
+
+
+    print('Done!')
+
+
+
+
+if __name__ == '__main__':
+    main()
+    # raw_data_root = 'D:\OpenMMlab\Refuge'
+    # print(os.listdir('../../'))
+    # tmp_dir = '../mmsegmentation/data/refuge'
+    # print(os.listdir(tmp_dir))
+    # print(glob(tmp_dir))
+    # # for cur_dir,dirs,files in list(os.walk(raw_data_root))[:1]:
+    # cur_dir,dirs,files = list(os.walk(raw_data_root))[0]
+    # print("====================")
+
+    # # print('cur:',cur_dir,dirs,files)
+    # # for cur_dir,dirs,files in list(os.walk(raw_data_root)):
+    # #     child_dir = cur_dir.split('\\')[-1]
+    # #     if child_dir not in ['Glaucoma','Non-Glaucoma']:
+    # #         print(child_dir)
+    # #         print("现在的目录：" + cur_dir)
+    # #         print("该目录下包含的子目录：" + str(dirs))
+    # #         print("该目录下包含的文件：" + str(files))
+    # files = list(filter(lambda x: x.endswith('.zip'),files))
+    # print(files)
+
+    # # print(cur_dir)
+    # # print(child_dir)
+    # with tempfile.TemporaryDirectory(dir=tmp_dir) as tmp_dir:
+    #     for file in files:
+    #         mode = list(filter(lambda x:file.lower().find(x)!= -1,['training','test','validation']))[0]
+    #         file_root = osp.join(tmp_dir,file[:-4])
+    #         file_type = 'img' if file.find('Anno') == -1 and file.find('GT')== -1 else 'annotations'
+    #         if file_type == 'annotations':
+    #             extract_img(file_root,osp.join(cur_dir,file),mode,file_type)
+            # if file.lower().find('train') != -1:
+            #     train_root = osp.join(tmp_dir,file[:-4])
+            #     file_type = 'img' if file.find('Anno') == -1 and file.find('GT')== -1 else 'mask'
+            #     zip_file = zipfile.ZipFile(osp.join(cur_dir,file))
+            #     zip_file.extractall(train_root)
+
+
+        # if child_dir in ['Glaucoma','Non-Glaucoma']:
+        #     print(child_dir)
+        #     print("现在的目录：" + cur_dir)
+        #     print("该目录下包含的子目录：" + str(dirs))
+        #     print("该目录下包含的文件：" + str(files))
+    # mmcv.mkdir_or_exist(tmp_dir)
+    # print(os.listdir(tmp_dir))
+    # now_path = os.path.join(raw_data_root,'REFUGE-Validation400.zip')
+    # out_dir = osp.join('data', 'HRF')
+
+    # print('Making directories...')
+    # mkdir_or_exist(out_dir)
+    # mkdir_or_exist(osp.join(out_dir, 'images'))
+    # mkdir_or_exist(osp.join(out_dir, 'images', 'training'))
+    # mkdir_or_exist(osp.join(out_dir, 'images', 'validation'))
+    # mkdir_or_exist(osp.join(out_dir, 'annotations'))
+    # mkdir_or_exist(osp.join(out_dir, 'annotations', 'training'))
+    # mkdir_or_exist(osp.join(out_dir, 'annotations', 'validation'))
+
+    # with tempfile.TemporaryDirectory(dir=tmp_dir) as tmp_dir:
+    #         print(tmp_dir)
+    #         zip_file = zipfile.ZipFile(now_path)
+    #         zip_file.extractall(tmp_dir)
+    #         for filename in sorted(os.listdir(tmp_dir)):
+    #             img = mmcv.imread(osp.join(tmp_dir, filename))