[Tutor] Trouble using bioread to convert files from .acq to .mat

Discussion:

Ila Kumar

2015-06-01 19:50:26 UTC

Hello,

I am a new Python user attempting to use bioread (
https://pypi.python.org/pypi/bioread/0.9.5) to convert files from
aqknowledge to matlab. I am using a 64-bit PC, and I have downloaded
Matlab, Python, numpy, scipy and bioread. Can someone walk me through the
installation process for this package? I can't seem to get it to work.

Thank you so much for your help!!
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Alan Gauld

2015-06-01 22:50:33 UTC

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Post by Ila Kumar
Hello,
I am a new Python user attempting to use bioread (
https://pypi.python.org/pypi/bioread/0.9.5) to convert files from
aqknowledge to matlab. I am using a 64-bit PC, and I have downloaded
Matlab, Python, numpy, scipy and bioread. Can someone walk me through the
installation process for this package? I can't seem to get it to work.

This list is really for questions about core Python and its
standard library. None of the packages you mention fall into
that category so you will likely get better support on their
dedicated fora. The SciPy packages in particular have an
active community.

That having been said, if you are struggling with installation,
try getting one of the SciPy bundles such as Anaconda or
Canopy which install all (or most) of the modules you mention
as default.

However, if you do have questions about core python feel
free to ask those here.
--
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
http://www.amazon.com/author/alan_gauld
Follow my photo-blog on Flickr at:
http://www.flickr.com/photos/alangauldphotos

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Mark Lawrence

2015-06-01 23:01:38 UTC

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Post by Alan Gauld

If the OP comes back please provide your OS and Python versions and a
specific problem. For all we know "I can't seem to get it to work"
might mean that everything is going along beautifully but you just can't
see the output because your monitor has failed :)
--
My fellow Pythonistas, ask not what our language can do for you, ask
what you can do for our language.

Mark Lawrence

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Laura Creighton

2015-06-02 08:45:29 UTC

Permalink

You are getting something like:
Command python setup.py egg_info failed with error code 1 in /tmp/pip-build-T3JieI/bioread
Storing debug log for failure in /home/lac/.pip/pip.log

when you run pip, correct?

So you go read the package documentation and discover that bioread
uses easy_install (which you are beginning to learn to hate) instead of pip.

So then you try that and you get crud like this:
....
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 43, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-PGpger/bioread-0.9.5/setup.py", line 3, in <module>
ImportError: No module named ez_setup

Correct?

If this is your problem, go install this package:

https://pypi.python.org/pypi/ez_setup

And then install bioread, still with easy_install

If this isn't your problem,
write back with more of what is not working, please.

Hope this is it :)
Laura

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Ila Kumar

2015-06-03 12:57:38 UTC

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Laura, that was it! Thank you so much.

However, now I am confused about what I need to type into the Command
prompt window (on a 64-bit windows computer, using python 2.7) in order to
convert a folder of data files. Does anyone know the proper code to do this?

Post by Laura Creighton

Command python setup.py egg_info failed with error code 1 in
/tmp/pip-build-T3JieI/bioread
Storing debug log for failure in /home/lac/.pip/pip.log
when you run pip, correct?
So you go read the package documentation and discover that bioread
uses easy_install (which you are beginning to learn to hate) instead of pip.
....
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 43, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-PGpger/bioread-0.9.5/setup.py", line 3, in <module>
ImportError: No module named ez_setup
Correct?
https://pypi.python.org/pypi/ez_setup
And then install bioread, still with easy_install
If this isn't your problem,
write back with more of what is not working, please.
Hope this is it :)
Laura

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Alan Gauld

2015-06-03 16:18:06 UTC

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Post by Ila Kumar
However, now I am confused about what I need to type into the Command
prompt window (on a 64-bit windows computer, using python 2.7) in order to
convert a folder of data files. Does anyone know the proper code to do this?

You will need to give us a lot more detail than that to help you.
Convert what kind of data file? To what kind of output file?

Also for most such tasks you won;t be typing it at the prompt
you will be writing a script and executing that. Do you have any
experience of Python scripting/programming? If not you should find a
tutorial and follow that. If you know how to program in another language
then the official web site tutorial should be just fine.

If you are a complete beginner to programming try one of these:

https://wiki.python.org/moin/BeginnersGuide/NonProgrammers

Or try mine (see link below)...

The code you need could be as simple as

#################
import os

def convertFile(fname):
# your code to do the conversion goes here

dir = /your/folder/path/here
for fileName in os.listdir(dir):
convertFile(fileName)

##################

But if there are subfolders to consider, or errors to
handle, then it all gets more messy quite quickly.
--
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
http://www.amazon.com/author/alan_gauld
Follow my photo-blog on Flickr at:
http://www.flickr.com/photos/alangauldphotos

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