You are right, I was doing a bad conversion of the matrix to the numpy.array...
in fact the result of what you ask was:
Out[56]: ()
now everything works because I do:
mymatrixN = numpy.array(list(mymatrix))
and now if I run numpy.shape I have:
Out[56]: (50,50)
I got the hint from the author of the function I was using to produce
the matrix...
many thanks for the help,
simone
2009/1/15 Oliver Tomic <oliver.to...@nofima.no>:
> Looks like there is something wrong with your array.
>
> You said you matrix is a 50 x 50 matrix. What do you get when you try the
> following?
>
> numpy.shape(mymatrixNARRAY)
>
>
> Cheers
> Oliver
>
>
> "Simone Gabbriellini" <simone.gabbriell...@gmail.com> wrote on 15.01.2009
> 10:07:36:
>
>> mmmm... if I convert the matrix into array I have this new error:
>>
>> In [41]: mymatrixR = ro.conversion.py2ri(mymatrixNARRAY)
>>
>> ---------------------------------------------------------------------------
>> TypeError Traceback (most recent call
>> last)
>>
>> /Users/ogabbrie/Desktop/NetworkSimulatorTraits/<ipython console> in
>> <module>()
>>
>> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.
>> 5/site-packages/rpy2/robjects/numpy2ri.pyc
>> in numpy2ri(o)
>> 33 # Array-of-PyObject is treated like a Python list:
>> 34 elif o.dtype.kind == "O":
>> ---> 35 res = ro.conversion.py2ri(list(o))
>> 36 # Record arrays map onto R data frames:
>> 37 elif o.dtype.kind == "V":
>>
>> TypeError: iteration over a 0-d array
>>
>>
>> I cannot solve it..
>>
>> simone
>>
>>
>> 2009/1/15 Oliver Tomic <oliver.to...@nofima.no>:
>> > The conversion doesn't work for me with matrices either, but the output
>> > is
>> > different on my machine.
>> >
>> > This is what I get:
>> >
>> > [code START]
>> >>>> import numpy
>> >
>> >>>> b = [[1,2,3],[4,5,6]]
>> >
>> >>>>bb = numpy.matrix(b)
>> >
>> >>>> bb
>> > matrix([[1, 2, 3],
>> > [4, 5, 6]])
>> >
>> >>>> import rpy2.robjects as ro
>> >
>> >>>> import rpy2.robjects.numpy2ri
>> >
>> >>>> bR = ro.conversion.py2ri(bb)
>> >
>> >>>> bR
>> > <RArray - Python:0x014E7D00 / R:0x0211AFB0>
>> >
>> >>>> print bR
>> > [,1] [,2] [,3]
>> >
>> > [1,] NA NA NA
>> >
>> > [2,] NA NA NA
>> > [code END]
>> >
>> >
>> > If you convert the numpy matrix into an array prior to the
>> > RPy2-conversion
>> > it works fine.
>> > aa = numpy.array(bb)
>> >
>> > cheers
>> > Oliver
>> >
>> >
>> >
>> > "Simone Gabbriellini" <simone.gabbriell...@gmail.com> wrote on
>> > 15.01.2009
>> > 09:51:30:
>> >
>> >> Hi Oliver,
>> >>
>> >> yes this helps very much... anyway, this works with array or also with
>> >> matrix?
>> >>
>> >> I ask this because I have a matrix 50x50, and if I do:
>> >>
>> >> mymatrixNump = numpy.matrix(mymatrix)
>> >> mymatrixR = ro.conversion.py2ri(mymatrixNump)
>> >>
>> >> I have:
>> >>
>> >>
>> >> ---------------------------------------------------------------------------
>> >> RuntimeError Traceback (most recent call
>> >> last)
>> >>
>> >> /Users/ogabbrie/Desktop/NetworkSimulatorTraits/<ipython console> in
>> >> <module>()
>> >>
>> >> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.
>> >> 5/site-packages/rpy2/robjects/numpy2ri.pyc
>> >> in numpy2ri(o)
>> >> 33 # Array-of-PyObject is treated like a Python list:
>> >> 34 elif o.dtype.kind == "O":
>> >> ---> 35 res = ro.conversion.py2ri(list(o))
>> >> 36 # Record arrays map onto R data frames:
>> >> 37 elif o.dtype.kind == "V":
>> >>
>> >> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.
>> >> 5/site-packages/rpy2/robjects/numpy2ri.pyc
>> >> in numpy2ri(o)
>> >> 47 raise(ValueError("Unknown numpy array type."))
>> >> 48 else:
>> >> ---> 49 res = ro.default_py2ri(o)
>> >> 50 return res
>> >> 51
>> >>
>> >> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.
>> >> 5/site-packages/rpy2/robjects/__init__.pyc
>> >> in default_py2ri(o)
>> >> 87 res = rinterface.SexpVector([o, ], rinterface.STRSXP)
>> >> 88 elif isinstance(o, list):
>> >> ---> 89 res = r.list(*[conversion.ri2py(conversion.py2ri(x))
>> >> for x in o])
>> >> 90 elif isinstance(o, complex):
>> >> 91 res = rinterface.SexpVector([o, ], rinterface.CPLXSXP)
>> >>
>> >> RuntimeError: maximum recursion depth exceeded
>> >>
>> >>
>> >> 2009/1/15 Oliver Tomic <oliver.to...@nofima.no>:
>> >> > Hi Simone,
>> >> >
>> >> > maybe this helps:
>> >> >
>> >> > [code START]
>> >> >>>> import numpy
>> >> >
>> >> >>>> a = [[1,2,3],[4,5,6]]
>> >> >
>> >> >>>> aa = numpy.array(a)
>> >> >
>> >> >>>> aa
>> >> > array([[1, 2, 3],
>> >> > [4, 5, 6]])
>> >> >
>> >> >>>> import rpy2.robjects as ro
>> >> >
>> >> >>>> import rpy2.robjects.numpy2ri
>> >> >
>> >> >>>> aR = ro.conversion.py2ri(aa)
>> >> >
>> >> >>>> aR
>> >> > <RArray - Python:0x014E7D00 / R:0x0211AF98>
>> >> >
>> >> >>>> print aR
>> >> > [,1] [,2] [,3]
>> >> >
>> >> > [1,] 1 2 3
>> >> >
>> >> > [2,] 4 5 6
>> >> >
>> >> > [code END]
>> >> >
>> >> >
>> >> > cheers
>> >> > Oliver
>> >> >
>> >> >
>> >> >
>> >> > Laurent Gautier <lgaut...@gmail.com> wrote on 14.01.2009 23:11:28:
>> >> >
>> >> >> Simone Gabbriellini wrote:
>> >> >> > I would like to know if there is something like
>> >> >> > r.assign('ROBJECT',
>> >> >> > PYTHONOBJECT) in rpy2...
>> >> >>
>> >> >> http://rpy.sourceforge.net/rpy2/doc/html/robjects.html?
>> >> >> highlight=assign#environments
>> >> >>
>> >> >> Or "assign" as you write above:
>> >> >> r.assign("foo", 123)
>> >> >>
>> >> >>
>> >> >> > I don't want to use R function to evaluate an object IN Python, I
>> >> >> > want
>> >> >> > to assign a matrix made in python to an R object...
>> >> >> >
>> >> >> > simone
>> >> >> >
>> >> >> > 2009/1/14 Simone Gabbriellini <simone.gabbriell...@gmail.com>:
>> >> >> >> [so sorry but I just answer your mail... I write to the list and
>> >> >> >> you
>> >> >> >> answer to ME and to the list in CC... I have to remember to
>> >> >> >> answer
>> >> >> >> to
>> >> >> >> ALL to answer to the mailing list too... again, sorry for that, I
>> >> >> >> didn't mean to offend you]
>> >> >> >>
>> >> >> >> and thanks for the help
>> >> >> >> simone
>> >> >> >>
>> >> >> >> 2009/1/14 Laurent Gautier <lgaut...@gmail.com>:
>> >> >> >>> [why getting off the list ???]
>> >> >> >>>
>> >> >> >>> Simone Gabbriellini wrote:
>> >> >> >>>> please do you have an example?
>> >> >> >>>>
>> >> >> >>>> because when I read "That import alone is sufficient to switch
>> >> >> >>>> an
>> >> >> >>>> automatic conversion of numpy objects into rpy2 objects." I
>> >> >> >>>> suppose
>> >> >> >>>> that every numpy object is seen by R...
>> >> >> >>> Automatic conversion of a numpy object:
>> >> >> >>>
>> >> >> >>> rlen = robjects.r['length']
>> >> >> >>> print(rlen(gladj))
>> >> >> >>>
>> >> >> >>>
>> >> >> >>> You are otherwise giving a *string* to be evaluated as R code
>> >> >> >>> (and R not looking into the python namespace when trying
>> >> >> >>> resolvea
>> >> >> >>> symbol).
>> >> >> >>> More on evaluating strings here:
>> >> >> >>> http://rpy.sourceforge.net/rpy2/doc/html/robjects.html?
>> >> >> highlight=r_repr#strings-as-r-code
>> >> >> >>>
>> >> >> >>>> thank you,
>> >> >> >>>> simone
>> >> >> >>>>
>> >> >> >>>> 2009/1/14 Laurent Gautier <lgaut...@gmail.com>:
>> >> >> >>>>> Simone Gabbriellini wrote:
>> >> >> >>>>>> yes, like that...
>> >> >> >>>>>>
>> >> >> >>>>>> but simply importing:
>> >> >> >>>>>>
>> >> >> >>>>>> Import rpy2.robjects.numpy2ri
>> >> >> >>>>>>
>> >> >> >>>>>> when I do:
>> >> >> >>>>>>
>> >> >> >>>>>> g1adj = numpy.array(g1adj)
>> >> >> >>>>>>
>> >> >> >>>>>> robjects.r('QAPset[1,,]<-g1adj')
>> >> >> >>>>> R has no way to know your Python variable called "gladj"
>> >> >> >>>>> unless
>> >> >> >>>>> you
>> >> >> >>>>> indicate
>> >> >> >>>>> it.
>> >> >> >>>>>
>> >> >> >>>>> print(robjects.r('ls()'))
>> >> >> >>>>> should confirm that there is no variable 'gladj' in your
>> >> >> >>>>> globalEnv.
>> >> >> >>>>>
>> >> >> >>>>>
>> >> >> >>>>>> it says:
>> >> >> >>>>>>
>> >> >> >>>>>> Error in eval(expr, envir, enclos) : object "g1adj" not
>> >> >> >>>>>> found...
>> >> >> >>>>> The error message above is correct, I think.
>> >> >> >>>>>
>> >> >> >>>>>> while
>> >> >> >>>>>> in the docs it says that:
>> >> >> >>>>>> "That import alone is sufficient to switch an automatic
>> >> >> >>>>>> conversion
>> >> >> >>>>>> of
>> >> >> >>>>>> numpy objects into rpy2 objects."
>> >> >> >>>>>>
>> >> >> >>>>>> should I do something else?
>> >> >> >>>>>>
>> >> >> >>>>>> thank you,
>> >> >> >>>>>> simone
>> >> >> >>>>>>
>> >> >> >>>>>> 2009/1/14 Laurent Gautier <lgaut...@gmail.com>:
>> >> >> >>>>>>> Something like this
>> >> >> >>>>>>>
>> >> >> >>>>>>>
>> >> >> >>>>>>> http://rpy.sourceforge.net/rpy2/doc/html/numpy.html?
>> highlight=numpy
>> >> >> >>>>>>> ?
>> >> >> >>>>>>>
>> >> >> >>>>>>>
>> >> >> >>>>>>>
>> >> >> >>>>>>> Simone Gabbriellini wrote:
>> >> >> >>>>>>>> dear List,
>> >> >> >>>>>>>>
>> >> >> >>>>>>>> is it possible to pass a matrix I've built in python to R
>> >> >> >>>>>>>> via
>> >> >> >>>>>>>> rpy2?
>> >> >> >>>>>>>>
>> >> >> >>>>>>>> I'm sure I'm blind, but I cannot find example about how to
>> >> >> pass object
>> >> >> >>>>>>>> from python to r, while I see how to pass object from r to
>> >> >> >>>>>>>> python...
>> >> >> >>>>>>>>
>> >> >> >>>>>>>> best regards,
>> >> >> >>>>>>>> Simone Gabbriellini
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >>
>> >> >>
>> >>
>> >>
>>
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>> >> >>
>> >>
>> >>
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