Implementation of Full PREP and Python3 compatability about pyprep HOT 8 CLOSED

Thanks a lot @adam2392 :-)

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Are there any updates on this?

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This was closed with #6

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@neerajww I streamlined that inclusion a bit and updated the docs. You can check out the bottom part of the examples page:https://pyprep.readthedocs.io/en/latest/examples.html

it now links to: https://nbviewer.jupyter.org/github/sappelhoff/pyprep/blob/master/examples/prep_demo.ipynb

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@sappelhoff Thank you very much. I am eager to try this out on my dataset. As I installed, I am faced the following issues which hints something is missing in my installation. Can you help me on this.
``
Step 1: pip install pyprep
This threw error:
ERROR: Cannot uninstall 'psutil'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
Step 2: sudo pip install --ignore-installed pyprep
This gave the message:
Successfully installed mne-0.19.2 numpy-1.18.1 pandas-1.0.1 patsy-0.5.1 psutil-5.6.7 pyprep-0.2.3 python-dateutil-2.8.1 pytz-2019.3 scipy-1.4.1 six-1.14.0 statsmodels-0.11.0
Step 3: I typed the following in Jupyter Notebook:
import pyprep
dir(pyprep)
This gives the following output:
['builtins',
'cached',
'doc',
'file',
'loader',
'name',
'package',
'path',
'spec']

Step 4: I guess something is missing in the installation because
from pyprep.prep_pipeline import PrepPipeline
This gives the following output:

ModuleNotFoundError Traceback (most recent call last)
in
----> 1 from pyprep.prep_pipeline import PrepPipeline

ModuleNotFoundError: No module named 'pyprep.prep_pipeline'
``

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Hi @neerajww - I have updated the installation instructions. please check out: https://github.com/sappelhoff/pyprep/blob/master/README.md#installation

regarding using pyprep, please check out the examples: https://pyprep.readthedocs.io/en/latest/examples.html

You tried to use pyprep.prep_pipeline --> this module is only available in the development version of the package. That is, it has not yet been released. I have made a comment to the example covering pyprep.prep_pipeline that you need to install the development version in order to use it. See here: https://github.com/sappelhoff/pyprep/blob/master/examples/prep_demo.ipynb

By using pip install pyprep you can only use the features included in the stable version that has been released on pypi.

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Thank you @sappelhoff . It seems to take the raw MNE object as input. Is this necessary requirement for bad channel detection? Can it not work on epoch object as well.

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Yes, pyprep works only on raw data. Not sure if it could be extended to work on epochs, feel free to look into that and let me know.

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