Closed mahmoodn closed 1 year ago
Hi Is there any suggestion for the following error in 3d-unet preprocess?
$ docker run --ipc=host -it --rm --runtime=nvidia \ -v /disk1/scratch/data/KiTS19/kits19/data/:/raw_data -v /disk1/scratch/preprocessed_data/:/data \ -v /disk1/scratch/results/:/results unet3d:latest /bin/bash root@7c3f2d9f30da:/workspace/unet3d# python3 preprocess_dataset.py \ --data_dir /raw_data \ --results_dir /results/ Preprocessing /raw_data Saving case_00000 shape (1, 190, 392, 392) mean [-2.] std [0.85] Saving case_00001 shape (1, 188, 340, 340) mean [-1.82] std [0.94] ... Saving case_00208 shape (1, 278, 377, 377) mean [-1.88] std [0.99] Saving case_00209 shape (1, 318, 333, 333) mean [-1.65] std [1.11] Case 210. Skipped. Case 211. Skipped. ... Case 299. Skipped. Mean value: -1.850000023841858, std: 0.9800000190734863, d: 256.0, h: 333.0, w: 333.0 Traceback (most recent call last): File "preprocess_dataset.py", line 147, in <module> verify_dataset(args.results_dir) File "preprocess_dataset.py", line 127, in verify_dataset assert len(source) == len(os.listdir(results_dir)) AssertionError
The inference has no problem. The 209 and 210 folder are shown below:
root@7c3f2d9f30da:/workspace/unet3d# ls /data/KiTS19/ calibration/ etc/ inference/ reference/ # ls /raw_data/ LICENSE case_00027 case_00055 case_00083 case_00111 case_00139 case_00167 case_00195 case_00223 case_00251 case_00279 case_00000 case_00028 case_00056 case_00084 case_00112 case_00140 case_00168 case_00196 case_00224 case_00252 case_00280 case_00001 case_00029 case_00057 case_00085 case_00113 case_00141 case_00169 case_00197 case_00225 case_00253 case_00281 case_00002 case_00030 case_00058 case_00086 case_00114 case_00142 case_00170 case_00198 case_00226 case_00254 case_00282 case_00003 case_00031 case_00059 case_00087 case_00115 case_00143 case_00171 case_00199 case_00227 case_00255 case_00283 case_00004 case_00032 case_00060 case_00088 case_00116 case_00144 case_00172 case_00200 case_00228 case_00256 case_00284 case_00005 case_00033 case_00061 case_00089 case_00117 case_00145 case_00173 case_00201 case_00229 case_00257 case_00285 case_00006 case_00034 case_00062 case_00090 case_00118 case_00146 case_00174 case_00202 case_00230 case_00258 case_00286 case_00007 case_00035 case_00063 case_00091 case_00119 case_00147 case_00175 case_00203 case_00231 case_00259 case_00287 case_00008 case_00036 case_00064 case_00092 case_00120 case_00148 case_00176 case_00204 case_00232 case_00260 case_00288 case_00009 case_00037 case_00065 case_00093 case_00121 case_00149 case_00177 case_00205 case_00233 case_00261 case_00289 case_00010 case_00038 case_00066 case_00094 case_00122 case_00150 case_00178 case_00206 case_00234 case_00262 case_00290 case_00011 case_00039 case_00067 case_00095 case_00123 case_00151 case_00179 case_00207 case_00235 case_00263 case_00291 case_00012 case_00040 case_00068 case_00096 case_00124 case_00152 case_00180 case_00208 case_00236 case_00264 case_00292 case_00013 case_00041 case_00069 case_00097 case_00125 case_00153 case_00181 case_00209 case_00237 case_00265 case_00293 case_00014 case_00042 case_00070 case_00098 case_00126 case_00154 case_00182 case_00210 case_00238 case_00266 case_00294 case_00015 case_00043 case_00071 case_00099 case_00127 case_00155 case_00183 case_00211 case_00239 case_00267 case_00295 case_00016 case_00044 case_00072 case_00100 case_00128 case_00156 case_00184 case_00212 case_00240 case_00268 case_00296 case_00017 case_00045 case_00073 case_00101 case_00129 case_00157 case_00185 case_00213 case_00241 case_00269 case_00297 case_00018 case_00046 case_00074 case_00102 case_00130 case_00158 case_00186 case_00214 case_00242 case_00270 case_00298 case_00019 case_00047 case_00075 case_00103 case_00131 case_00159 case_00187 case_00215 case_00243 case_00271 case_00299 case_00020 case_00048 case_00076 case_00104 case_00132 case_00160 case_00188 case_00216 case_00244 case_00272 kits.json case_00021 case_00049 case_00077 case_00105 case_00133 case_00161 case_00189 case_00217 case_00245 case_00273 case_00022 case_00050 case_00078 case_00106 case_00134 case_00162 case_00190 case_00218 case_00246 case_00274 case_00023 case_00051 case_00079 case_00107 case_00135 case_00163 case_00191 case_00219 case_00247 case_00275 case_00024 case_00052 case_00080 case_00108 case_00136 case_00164 case_00192 case_00220 case_00248 case_00276 case_00025 case_00053 case_00081 case_00109 case_00137 case_00165 case_00193 case_00221 case_00249 case_00277 case_00026 case_00054 case_00082 case_00110 case_00138 case_00166 case_00194 case_00222 case_00250 case_00278 root@7c3f2d9f30da:/workspace/unet3d# ls /raw_data/case_00210/ imaging.nii.gz root@7c3f2d9f30da:/workspace/unet3d# ls /raw_data/case_00209/ imaging.nii.gz segmentation.nii.gz
Hi Is there any suggestion for the following error in 3d-unet preprocess?
The inference has no problem. The 209 and 210 folder are shown below: