Tip of the day

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

Moderator: hines

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apdavison
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Tip of the day

Post by apdavison » Mon May 22, 2006 5:06 am

This will become obsolete as the functionality of the python interface increases, but I have created a class HocToPy, with a static method get(), to make getting variables from hoc into python easier:

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import hoc

class HocToPy:
    """Static class to simplify getting variables from hoc."""
    hocvar = None
    
    def get(name,return_type):
        """Return a variable from hoc.
           name can be a hoc variable (int, float, string) or a function/method
           that returns such a variable.
        """
        fmt_dict = {'int' : '%d', 'float' : '%g', 'string' : '\\"%s\\"'}
        hoc_commands = ['strdef cmd',
                        'sprint(cmd,"HocToPy.hocvar = %s",%s)' % (fmt_dict[return_type],name),
                        'nrnpython(cmd)']
        for cmd in hoc_commands:
            hoc.execute(cmd)
        return HocToPy.hocvar
    get = staticmethod(get)
    
hoc.execute("a = 2")
hoc.execute("pi = 3.14159")
hoc.execute("strdef hello")
hoc.execute('hello = "Hello World"')

a     = HocToPy.get('a','int')
pi    = HocToPy.get('pi','float')
hello = HocToPy.get('hello','string')

print "a = ", a
print "pi = ", pi
print hello

eacheon
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Post by eacheon » Mon Jul 10, 2006 6:58 pm

where can I get the "hoc" module, excuse me?

apdavison
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hoc python module

Post by apdavison » Tue Jul 11, 2006 4:38 am

To get the hoc module, you have to run

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nrniv -python
This starts NEURON with the python interpreter (assuming NEURON has been compiled with the --with-nrnpython configure option).

You should then be able to

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>>> import hoc
>>> import nrn
At the moment, the hoc module only provides one function: execute()

eacheon
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Joined: Wed Jan 18, 2006 2:20 pm

Post by eacheon » Tue Jul 11, 2006 6:05 pm

Ah, seems I have to get NEURON with cvs version. however, is cvs anonymous checkout avaiable now? I got the following error:

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$ cvs -d :ext:anonymous@www.neuron.yale.edu:/home/cvsroot checkout iv
Host key verification failed.
cvs [checkout aborted]: end of file from server (consult above messages if any)


ted
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Post by ted » Tue Jul 11, 2006 7:05 pm

The server (and host key) may have been changed since the last time that you got your
local copy of the repository. You might want to archive the copy you presently have,
then try setting up a new one.

eacheon
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Joined: Wed Jan 18, 2006 2:20 pm

Post by eacheon » Tue Jul 11, 2006 8:44 pm

ted wrote:The server (and host key) may have been changed since the last time that you got your
local copy of the repository. You might want to archive the copy you presently have,
then try setting up a new one.

I tried setting up a new one, but I got to be asked for password. I surely exported CVS_RSH, wierd. The error message is:

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anonymous@www.neuron.yale.edu's password:
anonymous@www.neuron.yale.edu's password:
anonymous@www.neuron.yale.edu's password:
Permission denied (publickey,gssapi-with-mic,password).
cvs [checkout aborted]: end of file from server (...)


apdavison
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nrnpython is in 5.8

Post by apdavison » Wed Jul 12, 2006 4:30 am

You don't need the CVS version for the example I posted above.
nrnpython was certainly in version 5.8, and I imagine it is in 5.9.

hines
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Post by hines » Wed Jul 12, 2006 7:21 am

Andrew is correct, all the python code fro NEURON is in the tar.gz file.
But to answer your question about CVS. Anonymous CVS broke when the old server
broke a month ago and I have not bothered to set it up on the temporary server since
I have switched to Subversion. I just have been remiss in updating the web pages to
explain how to checkout the sources. However, see the "View the Subversion Repository" link at http://www.neuron.yale.edu/neuron/install/install.html
The TRAC replacement for ViewCVS is much, much better.
To checkout the InterViews and NEURON main trunks you can temporarily use:
svn checkout http://miris.med.yale.edu/svn/neuron/iv/trunk iv
svn checkout http://miris.med.yale.edu/svn/neuron/nrn/trunk nrn

eacheon
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Post by eacheon » Tue May 08, 2007 6:33 pm

If I can get the Vectors into python efficiently, I'll switch to python. Do you have a good way to manage to getting hoc's Vectors into python?

hines
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Post by hines » Tue May 08, 2007 7:13 pm

Efficient? Probably not. But you can make it efficient if the idiom I mention below is not efficient enough.

First, all variables, objects, functions, etc in HOC --- built-in or user defined---- are available with almost identical syntax in Python.
e.g. grab the following and paste into the terminal after launching "nrniv -python"

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 import hoc
 h = hoc.HocObject() #access to everything in hoc
 #execute any hoc statement, Following creates a factory for hoc Vectors
 h('obfunc newvec() { return new Vector($1) }')
 #python and hoc object syntax is compatible
 vec = h.newvec(10)
 #now vec is a python object that knows everything about the new
 #hoc vector of size 10
 #can call any hoc method on the Vector
 vec.indgen().add(10) # set elements to 10, 11, 12, ... 19
 #and evaluate/assign any field
 print vec.x[5] #will print the number 15
the idiom i mentioned is

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px = vec.x
which thereafter can be used like px[index]. So now the problem becomes whether it is efficient enough for you to copy a hoc vector to a python vector from within python or whether you want to write some c code with a peak at nrn/src/nrnpython/nrnpy_hoc.cpp to get the double* pointer from

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// leave pointer on stack ready for get/set final
static void eval_component(PyHocObject* po, int ix) {
        int j;
        hoc_push_object(po->ho_);
        hocobj_pushtop(po, 0, ix);
        component(po);
}
The reason I did not do this myself is because I am confused about Python double vectors, how they are represented, and how they relate to the popular numpy extension. The latter I am trying to avoid as a requirement during linking.

eacheon
Posts: 97
Joined: Wed Jan 18, 2006 2:20 pm

Post by eacheon » Wed May 09, 2007 8:11 am

Nice job, Micheal! You did it so fast!

May I ask why you are reluctant to numpy dependency? My guess is every one is going to use numpy with NEURON so there should not be a dependency issue. At the same time I am not aware python has a way (with standard library) to represent a double vector. Numpy is a must when dealing with arrays.

I am rusty in C/C++ and do not quite understand the working of arrays in python, but people seem to be working on an nd-array interface which is destined to inclusion in Python core. In my understanding, for an object hocvector with this interface implemented we can construct a numpy array by

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pyarray = array(hocvector)
and gain all the strength of numpy. Is it what you are looking for?
http://numpy.scipy.org/array_interface.shtml


Again, very nice job. I am going to set out processing NEURON data directly in Python. Thanks a lot!

eacheon
Posts: 97
Joined: Wed Jan 18, 2006 2:20 pm

Post by eacheon » Sun May 13, 2007 3:02 pm

eacheon wrote:Nice job, Micheal! You did it so fast!

May I ask why you are reluctant to numpy dependency? My guess is every one is going to use numpy with NEURON so there should not be a dependency issue.
I am sorry, Micheal. I realized you meant the "build dependency"...

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