[SciPy-user] sparse matrices - list assignment to rows and columns

josef.pktd@gmai... josef.pktd@gmai...
Thu Apr 9 04:05:29 CDT 2009


On Thu, Apr 9, 2009 at 4:51 AM,  <josef.pktd@gmail.com> wrote:
> On Wed, Apr 8, 2009 at 11:51 PM, Gergely Imreh <imrehg@gmail.com> wrote:
>> Hi,
>>
>>  I was trying figure out the scipy sparse matrix handling, but run
>> into some difficulties assigning a list of values to rows and columns.
>>  The scipy tutorial has the following example [1]:
>>
>> from scipy import sparse
>> Asp = sparse.lil_matrix((50000,50000))
>> Asp.setdiag(ones(50000))
>> Asp[20,100:250] = 10*random.rand(150)
>> Asp[200:250,30] = 10*random.rand(50)
>>
>>  That looks straightforward enough, make a large, diagonal sparse
>> matrix, and set some additional elements to non-zero. What I get,
>> however, is different:
>> Asp[20,100:250] = 10*random.rand(150)  sets the matrix elements at row
>> 20, column 100-249 to random values.
>> Asp[200:250,30] = 10*random.rand(50) sets the matrix element at row
>> 200, column 30 to a 50 element row vector with random values....
>> (elements at row 201-249, column 30 are still 0)
>>  If I reshape the results of random.rand(50) to be in a column
>> instead of row, the assignment will results in the elements of row
>> 200-249, column 30 to be set to a single element array values (So, for
>> exaple Asp[200,30] will be an array, which will have a single random
>> value at  [0,0])
>>
>>  I'm using Python 2.6 (that comes with my distro, or 2.4 for which
>> I'd have to recompile scipy) and scipy 0.7.0. Is this kind of
>> behaviour due to the changes (and incompatibilites) of 2.6 (since I
>> know scipy is writtend to be compatible up to 2.5) or something else?
>> The other sparse matrix types would handle this differently?
>>  A workaround is to do single element assignments but I'd think
>> that's probably slower in general.
>>
>>  Cheers!
>>      Greg
>> [1] http://www.scipy.org/SciPy_Tutorial
>
>
> There is an assignment error:
> Asp[200:250,30]  seems to assign all 50 elements to to the position Asp[200,30]
>
>>>> Asp[200,30]
> <1x50 sparse matrix of type '<type 'numpy.float64'>'
>        with 50 stored elements in LInked List format>
>>>> Aspc = Asp.tocrc()
> Traceback (most recent call last):
>  File "<pyshell#4>", line 1, in <module>
>    Aspc = Asp.tocrc()
>  File "c:\josef\_progs_scipy\scipy\sparse\base.py", line 429, in __getattr__
>    raise AttributeError, attr + " not found"
> AttributeError: tocrc not found

sorry, I copied the wrong traceback, it should be:

>>> Aspc = Asp.tocsr()
Traceback (most recent call last):
  File "<pyshell#7>", line 1, in <module>
    Aspc = Asp.tocsr()
  File "c:\josef\_progs_scipy\scipy\sparse\lil.py", line 427, in tocsr
    data = np.asarray(data, dtype=self.dtype)
  File "C:\Programs\Python25\Lib\site-packages\numpy\core\numeric.py",
line 230, in asarray
    return array(a, dtype, copy=False, order=order)
ValueError: setting an array element with a sequence.

>
> this is with
>>>> scipy.version.version
> '0.8.0.dev5551'
>
> there is a related assignment error that got fixed in trunk,
> http://thread.gmane.org/gmane.comp.python.scientific.user/19996
> I don't know if it also handles this case, a bug report might be
> useful to make sure this case is handled correctly
>
> I think, for this example dok format would be better to build the
> matrix, since column slices need to access many lists
>
> Asp = sparse.dok_matrix((50000,50000))
> Aspr = Asp.tocsr()
>
> works without problems
>
> I checked the history of the scipy tutorial that you linked to, the
> main editing has been done in 2006, and maybe it isn't up to date.
>
> The current docs are being written and are available at
> http://docs.scipy.org/doc/
>
> Josef
>


More information about the SciPy-user mailing list