[SciPy-user] sparse matrices - list assignment to rows and columns
Gergely Imreh
imrehg@gmail....
Thu Apr 9 04:17:35 CDT 2009
2009/4/9 <josef.pktd@gmail.com>:
> 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
>>
Yes, I think is the same, I got a ValueError as well, having upgraded
to the latest (r5655) version.
Traceback (most recent call last):
File "sp2.py", line 6, in <module>
Asp[200:250,30] = 10*random.rand(50)
File "/usr/lib/python2.6/site-packages/scipy/sparse/lil.py", line
329, in __setitem__
self._insertat3(row, data, j, xx)
File "/usr/lib/python2.6/site-packages/scipy/sparse/lil.py", line
285, in _insertat3
self._insertat2(row, data, j, x)
File "/usr/lib/python2.6/site-packages/scipy/sparse/lil.py", line
246, in _insertat2
raise ValueError('setting an array element with a sequence')
ValueError: setting an array element with a sequence
Checked out the new documentation you referenced[1] and there is only
same-row assignment (e.g. A[0, :100] = rand(100) ) but no same-column
assignment...
So still, my question is that is there something inherently different
between array -> row and array -> column assigment in this case?
Cheers,
Greg
[1] http://docs.scipy.org/doc/scipy/reference/sparse.html
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