DeepRegNet /
DeepReg
| @@ 242-258 (lines=17) @@ | ||
| 239 | for subfolder in tqdm(subfolders): |
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| 240 | files = os.listdir(os.path.join(data_dir, folder, subfolder)) |
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| 241 | for file in files: |
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| 242 | if file.startswith("case_020"): # this case did not laod correctly |
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| 243 | os.remove(os.path.join(data_dir, folder, subfolder, file)) |
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| 244 | else: |
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| 245 | im_data = np.asarray( |
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| 246 | nib.load(os.path.join(data_dir, folder, subfolder, file)).dataobj, |
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| 247 | dtype=np.float32, |
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| 248 | ) |
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| 249 | if np.max(im_data) > 255.0: |
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| 250 | im_data = ((im_data + 285) / (3770 + 285)) * 255.0 # rescale image |
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| 251 | img = nib.Nifti1Image(im_data, affine=None) |
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| 252 | nib.save(img, os.path.join(data_dir, folder, subfolder, file)) |
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| 253 | if np.max(img.dataobj) > 255.0: |
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| 254 | print( |
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| 255 | "Recheck the following file: ", |
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| 256 | os.path.join(data_dir, folder, subfolder, file), |
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| 257 | ) |
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| 258 | nib.save(img, os.path.join(data_dir, folder, subfolder, file)) |
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| 259 | ||
| 260 | ######## DOWNLOAD MODEL CKPT FROM MODEL ZOO ######## |
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| 261 | ||
| @@ 214-230 (lines=17) @@ | ||
| 211 | for subfolder in tqdm(subfolders): |
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| 212 | files = os.listdir(os.path.join(data_dir, folder, subfolder)) |
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| 213 | for file in files: |
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| 214 | if file.startswith("case_020"): # this case did not laod correctly |
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| 215 | os.remove(os.path.join(data_dir, folder, subfolder, file)) |
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| 216 | else: |
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| 217 | im_data = np.asarray( |
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| 218 | nib.load(os.path.join(data_dir, folder, subfolder, file)).dataobj, |
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| 219 | dtype=np.float32, |
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| 220 | ) |
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| 221 | if np.max(im_data) > 255.0: |
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| 222 | im_data = ((im_data + 285) / (3770 + 285)) * 255.0 # rescale image |
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| 223 | img = nib.Nifti1Image(im_data, affine=None) |
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| 224 | nib.save(img, os.path.join(data_dir, folder, subfolder, file)) |
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| 225 | if np.max(img.dataobj) > 255.0: |
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| 226 | print( |
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| 227 | "Recheck the following file: ", |
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| 228 | os.path.join(data_dir, folder, subfolder, file), |
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| 229 | ) |
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| 230 | nib.save(img, os.path.join(data_dir, folder, subfolder, file)) |
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| 231 | ||
| 232 | ######## DOWNLOAD MODEL CKPT FROM MODEL ZOO ######## |
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| 233 | ||
