File rsna_test_patients_normal.npy not found

[spohngellert-o]

Description

I am getting an issue that was previously posted about then closed: https://github.com/lindawangg/COVID-Net/issues/118

Steps to Reproduce

1. Download the datasets as described in https://github.com/lindawangg/COVID-Net/blob/master/docs/COVIDx.md
2. Run the file create_COVIDx_binary.ipynb (is this recommended, or create_COVIDx.ipynb).
3. File structure as follows:
   • Actualmed-COVID-chestxray-dataset
   • COVID-19-Radiography-Database
   • covid-chestxray-dataset
   • Figure1-COVID-chestxray-dataset
   • rsna-pneumonia-detection-challenge
   • datamaker
     • create_COVIDx_binary.ipynb
     • data
     • test
     • train

Expected behavior

Dataset created

Actual behavior

The following error:

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-15-1658f091297f> in <module>
     19     num_diff_patients = len(np.unique(arr))
     20     # num_test = max(1, round(split*num_diff_patients))
---> 21     test_patients = np.load('rsna_test_patients_{}.npy'.format(key)) # random.sample(list(arr), num_test), download the .npy files from the repo.
     22     # np.save('rsna_test_patients_{}.npy'.format(key), np.array(test_patients))
     23     for patient in arr:

~/anaconda3/envs/ds5500/lib/python3.7/site-packages/numpy/lib/npyio.py in load(file, mmap_mode, allow_pickle, fix_imports, encoding)
    414             own_fid = False
    415         else:
--> 416             fid = stack.enter_context(open(os_fspath(file), "rb"))
    417             own_fid = True
    418 

FileNotFoundError: [Errno 2] No such file or directory: 'rsna_test_patients_normal.npy'

Environment

• Ubuntu 18.04 LTS
• conda, python 3.7

[spohngellert-o]

I have managed to resolve this issue with the following steps:

1. Download the file here: https://github.com/lindawangg/COVID-Net/blob/master/rsna_test_patients_normal.npy
2. Save it in datamaker dir