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    nk53
    @nk53
    Do you want the sima directory from my github clone?
    ROI.py init.pyc imaging.py misc sequence.py
    ROI.pyc extract.py imaging.pyc motion sequence.pyc
    init.py extract.pyc imaging_parameters.py segment tests
    Patrick Kaifosh
    @pkaifosh
    ok, and the sima/motion directory?
    nk53
    @nk53
    and in motion:
    _init_.py
    _init_.pyc
    _motion.c
    _motion.pyx
    frame_align.py
    hmm.py
    motion.py
    motion.pyc
    tests
    tests/test_frame_align.py
    tests/test_hmm.py
    tests/test_motion.py
    transform.py
    Patrick Kaifosh
    @pkaifosh
    What operating system are you on?
    nk53
    @nk53
    Mac OS X, version 10.9.5
    although now that I think of it, I wonder if my Cython is bound to the correct Python version (or if it even matters)
    do you know how I would check for that?
    Patrick Kaifosh
    @pkaifosh
    I don't think that's the issue, or it would have given you an error. It seems you have the .c file generated fine.
    You could try deleting the .c file and then rerunning install to generate it, but I'd be surprised if that's the problem.
    What if you do this:
    ```import sima
    import sima
    sima.__file__
    nk53
    @nk53
    well, the problem is I can't currently import sima, so checking the file would be impossible
    oh wait
    what
    well nevermind, now it imports
    not really sure why
    Patrick Kaifosh
    @pkaifosh
    So is everything fixed?
    nk53
    @nk53
    let me check
    Yes, it seems to work now. I'm not really sure where this bizarre error came from.
    In fact, I didn't even re-run setup.py
    all I did was type Cython into the console
    ok, perhaps I merely ran from the wrong directory or something
    anyway, thanks for your help!
    Patrick Kaifosh
    @pkaifosh
    Glad it's working. Just out of curiosity (if you don't mind me asking), what are you using the software for?
    Vijay Mohan K Namboodiri
    @vjlbym
    Hey SIMA people, I have written a code that will launch an Amazon EC2 instance and set it up for running SIMA. I happened to just tweak the [Thunder project's] (http://thunder-project.org/) code to write my own launch script. I also then copy another file over that sets up SIMA analysis on multiple files that are stored on S3 in parallel. This file is custom modifiable to run whatever SIMA analysis needs to be run. Do you guys think making this public would be useful to the SIMA user base?
    Nathan Danielson
    @nbdanielson
    absolutely, this sounds like great functionality
    perhaps you could write a well-documented script that could live in the /examples directory and make a pull-request we could merge into the main repository?
    Vijay Mohan K Namboodiri
    @vjlbym
    Great. I'll do that. There are a couple more bugs that I am trying to fix right now. Once that's done, I'll upload it. Thanks!
    Nathan Danielson
    @nbdanielson
    sounds great man, thanks for the contribution!
    HE Chong
    @Ron89
    A question, on your github page, you said SIMA works on Python2. But for some reason, I can also install it with Python3's pip. Does it also support Python3 now? Or am I to expect some exceptions?
    Nathan Danielson
    @nbdanielson
    Hello,
    Yes sima should work with Python 3, though we use 2.7 in the lab, so this is the most thoroughly tested
    HE Chong
    @Ron89
    Thanks for the reply. I'll use it on python3. And report if there are exceptions. Python2 support will end after less than four years. So I'm currently transiting everything to Py3...
    HE Chong
    @Ron89
    Oh... And, if it doesn't do anything, prompting nothing, it's possible that completefunc is overwritten by youcompleteme. I recently installed it on my working computer. And this happens too.
    Nathan Danielson
    @nbdanielson
    sounds good, we'd certainly appreciate any python3-related bug reports