Python 操作系统：[Errno 13] 权限被拒绝

Question

I am trying to get a deep learning network ( https://github.com/MIC-DKFZ/nnUNet ) to work with my own dataset and I am having trouble with the paths. I have used several approaches to define my paths. The authors import the following packages for this issue:

import os

from batchgenerators.utilities.file_and_folder_operations import maybe_mkdir_p, join

With this, I have tried the following lines, separately:

base = os.environ["nnUNet_base"]

base = join("Tortuosity", "nnUNet_base")

base = "Tortuosity/nnUNet_base"

I have the nnUNet_base directory inside the Tortuosity directory. With the first approach it seems that it is not registering the directory correctly (I ask for print("base =", base) and in return I get None . For the second and third approaches, I obtain the following error:

Traceback (most recent call last):
  File "experiment_planning/plan_and_preprocess_task.py", line 18, in <module>
    from nnunet.paths import base,splitted_4d_output_dir, cropped_output_dir, preprocessing_output_dir, raw_dataset_dir, network_training_output_dir
  File "/home/pere/anaconda3/envs/nnunet_env/nnUNet/nnunet/paths.py", line 51, in <module>
    maybe_mkdir_p(splitted_4d_output_dir)
  File "/home/pere/anaconda3/envs/nnunet_env/lib/python3.6/site-packages/batchgenerators/utilities/file_and_folder_operations.py", line 40, in maybe_mkdir_p
    os.mkdir(os.path.join("/", *splits[:i+1]))
PermissionError: [Errno 13] Permission denied: '/nnUNet_base'

I do not know how to habilitate permissions in this case. Please help, what should I do to effectively define the paths for my case? I am running a VM with Ubuntu 16.04 in a Mac.

Thank you!

Answer 1

The error says this:

os.mkdir(os.path.join("/", *splits[:i+1]))

That means, tht the path is under / and not in your home Directory. The fix that just use the absolute path at it is written in the comments of nunet.

base = "/home/pere/Tortuosity/nnUNet_base"

If Tortuosity is directly in your home folder.