Error in download_physionet.sh and prepare_physionet.sh

[s0536825]

Hi,

I get the following error if I write the command ./download_physionet.sh

./download_physionet.sh: line 1: wget: command not found
./download_physionet.sh: line 2: wget: command not found
...

and get also an error at the command python prepare_physionet.py --data_dir data --output_dir data/eeg_fpz_cz --select_ch 'EEG Fpz-Cz'

Traceback (most recent call last):
  File "prepare_physionet.py", line 13, in <module>
    import pandas as pd
ImportError: No module named pandas

What can be the Problem? Where is my mistake?

Thanks in advance.

[akaraspt]

Hi,

The first error might be solved by running the following command to install wget:
sudo apt-get install wget

For the second error, you can use the following command to install pandas Python package:
pip install pandas

Hope this can fix your errors.

Akara

[s0536825]

Hi,

thanks for your quick response.

I have tried your command to install wget, but got this answer:
Unable to locate an executable at "/Library/Java/JavaVirtualMachines/jdk1.8.0_91.jdk/Contents/Home/bin/apt" (-1)

I found out, that macOS Sierra doesn't support apt, so than I found this solution.
[https://stackoverflow.com/questions/33886917/how-to-install-wget-in-macos-capitan-sierra]
I have forgot to say that I use macOS Sierra.

The command pip install pandas also doesn't work on my mac.
So i use sudo pip install pandas, but get the following answer:
sudo: pip: command not found

[s0536825]

Hi,

i found out, that I should install pip at firs, so I use the command
pip install –U pip

But the command pip install pandas or sudo pip install pandas doesn't work still not

[akaraspt]

Hi,

It seems that this is the installation problem. I would suggest you to install miniconda2, which is used to create virtual environments for python.

After you have installed miniconda2, you should be able to create a virtual environment via:

conda create -n deepsleepnet python

Then you activate the virtual environment using:

source activate deepsleepnet
pip install numpy scipy pandas matplotlib scikit-learn
pip install <other python library>

Then following the instruction in this link to install Tensorflow r0.12

Once you finish with the experiment with deepsleepnet, you can exit the virtual environment via:

source deactivate

Hope this help

[s0536825]

Hi,

I have really problem with the installation, so I deleted all the stuffs that i downloaded and wanted to start at the begin.

Thanks for you suggest.

[s0536825]

Hi,

now, I get the following error of the command

python prepare_physionet.py --data_dir data --output_dir data/eeg_fpz_cz --select_ch 'EEG Fpz-Cz'

File "prepare_physionet.py", line 136
    print "Include onset:{}, duration:{}, label:{} ({})".format(
                                                                                  ^
SyntaxError: invalid syntax

It seems, there is a problem with the quotation marks or am I wrong?

[akaraspt]

Hi,

Which python version you are currently using?

My guess is that you are using Python 3, which requires brackets around the print command.

You can try to change from:
print "Include onset:{}, duration:{}, label:{} ({})".format(...)
to:
print("Include onset:{}, duration:{}, label:{} ({})".format(...))

[s0536825]

Hi,

yes I have Python 3.
The mistake was really the requires brackets. Thanks.
But it's better to switch to Python 2. Because there are other bugs that Python 3 doesn't support.

[s0536825]

Hi,

now I have a problem with the command:

python train.py --data_dir data/eeg_fpz_cz --output_dir output --n_folds 20 --fold_idx 0 --pretrain_epochs 100 --finetune_epochs 200 --resume False

I get the error:

File "train.py", line 6, in <module>
    import tensorflow as tf
  File "/Users/2B/anaconda2/envs/deepsleepnet/lib/python2.7/site-packages/tensorflow/__init__.py", line 24, in <module>
    from tensorflow.python import *
  File "/Users/2B/anaconda2/envs/deepsleepnet/lib/python2.7/site-packages/tensorflow/python/__init__.py", line 60, in <module>
    raise ImportError(msg)
ImportError: Traceback (most recent call last):
  File "/Users/2B/anaconda2/envs/deepsleepnet/lib/python2.7/site-packages/tensorflow/python/__init__.py", line 49, in <module>
    from tensorflow.python import pywrap_tensorflow
  File "/Users/2B/anaconda2/envs/deepsleepnet/lib/python2.7/site-packages/tensorflow/python/pywrap_tensorflow.py", line 28, in <module>
    _pywrap_tensorflow = swig_import_helper()
  File "/Users/2B/anaconda2/envs/deepsleepnet/lib/python2.7/site-packages/tensorflow/python/pywrap_tensorflow.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow', fp, pathname, description)
ImportError: dlopen(/Users/2B/anaconda2/envs/deepsleepnet/lib/python2.7/site-packages/tensorflow/python/_pywrap_tensorflow.so, 10): Library not loaded: @rpath/libcudart.8.0.dylib
  Referenced from: /Users/2B/anaconda2/envs/deepsleepnet/lib/python2.7/site-packages/tensorflow/python/_pywrap_tensorflow.so
  Reason: image not found


Error importing tensorflow.  Unless you are using bazel,
you should not try to import tensorflow from its source directory;
please exit the tensorflow source tree, and relaunch your python interpreter
from there.

I already install trensorflow, but i don't understand the error.

Thanks

[akaraspt]

It seems you have problem with the tensorflow installation. Try to reinstall Tensorflow v0.12 and try again.