juglab / cryoCARE_pip

PIP package of cryoCARE
BSD 3-Clause "New" or "Revised" License
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Output file not found after running training data preparation #62

Closed Amy1809 closed 2 months ago

Amy1809 commented 2 months ago

I am running cryoCARE_11 for my 5 tomograms, it seems run, but I cannot find the output file and it gives me an output saying :

2024-07-09 10:12:58.882483: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
Computing normalization parameters:
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 500/500 [00:00<00:00, 721.42it/s]
Output directory already exists. Please choose a new output directory or set 'overwrite' to 'true' in your configuration file.

Here is the command I run: cryoCARE_extract_train_data.py --conf train_data_config.json

And here is my 'train_data_config.json' file:

{
  "even": [
    "/home/tomograms/even/rec_Position_1_2_half2.mrc", "/home/tomograms/even/rec_Position_1_half2.mrc", "/home/tomograms/even/rec_Position_3_3_half2.mrc", "/home/tomograms/even/rec_Position_2_2_half2.mrc", "/home/tomograms/even/rec_Position_6_half2.mrc"
  ],
  "odd": [
    "/home/tomograms/odd/rec_Position_1_2_half1.mrc", "/home/tomograms/odd/rec_Position_1_half1.mrc", "/home/tomograms/odd/rec_Position_3_3_half1.mrc", "home/tomograms/odd/rec_Position_2_2_half1.mrc", "/home/tomograms/odd/rec_Position_6_half1.mrc"
  ],
  "patch_shape": [
    72,
    72,
    72
  ],
  "num_slices": 1200,
  "split": 0.9,
  "tilt_axis": "Y",
  "n_normalization_samples": 500,
  "path": "/home/cryocareTest"
}

Any suggestions or advice will be very helpful.

tibuch commented 2 months ago

Add the overwrite key to your config file. See predict_config.json.

Amy1809 commented 2 months ago

Add the overwrite key to your config file. See predict_config.json.

It worked, thanks so much!