I might be going down the wrong path, but is seems like I would want
to add a
copy_mpz_vector_init
function to vector_integer_sparse_c.pxi that would make a copy of an
mpz_vector. Is that overkill?
My first idea was to use add_mpz_vector_init(sum, v, w, mul), which
sets sum equal to v + mul*w, but let mul = 0. However
add_mpz_vector_init returns the zero vector when mul = 0 !
Dave
On Jun 2, 9:06 pm, William Stein <wst...@gmail.com> wrote:
> On Tue, Jun 2, 2009 at 8:45 PM, davidp <dav...@reed.edu> wrote:
>
> > I can't figure out how to create a new sparse matrix (see below).
>
> > Sorry,
> > Dave
>
> You can make a new matrix with the analogous parent but a different
> shape using the new_matrix method.
>
> sage: a = random_matrix(ZZ,3,4,sparse=True)
> sage: a.new_matrix(2,4)
> [0 0 0 0]
> [0 0 0 0]
>
> In your cython code you would write something like
>
> cdef Matrix_integer_sparse M = a.new_matrix(2,4)
>
> William
>
>
>
>
>
> > M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
> > sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
> > sparse=True), None, None, None)
>
> > -------------------
> > ...
> > def _delete_row_(self, Py_ssize_t row_number):
> > cdef Py_ssize_t i
> > cdef mpz_vector* self_row, *M_row
> > cdef Matrix_integer_sparse M
>
> > M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
> > sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
> > sparse=True), None, None, None)
>
> > ^
> > ------------------------------------------------------------
>
> > /usr/local/sage-devel/devel/sage-devel/sage/matrix/
> > matrix_integer_sparse.pyx:221:101: Compiler crash in
> > AnalyseExpressionsTransform
>
> > ModuleNode.body = StatListNode(matrix_integer_sparse.pyx:23:0)
> > StatListNode.stats[13] = StatListNode(matrix_integer_sparse.pyx:43:5)
> > StatListNode.stats[0] = CClassDefNode(matrix_integer_sparse.pyx:43:5,
> > as_name = u'Matrix_integer_sparse',
> > base_class_module = u'matrix_sparse',
> > base_class_name = u'Matrix_sparse',
> > class_name = u'Matrix_integer_sparse',
> > module_name = '',
> > visibility = 'private')
> > CClassDefNode.body = StatListNode(matrix_integer_sparse.pyx:55:4)
> > StatListNode.stats[9] = DefNode(matrix_integer_sparse.pyx:216:4,
> > name = u'_delete_row_',
> > num_required_args = 2,
> > reqd_kw_flags_cname = '0')
> > File 'Nodes.py', line 360, in analyse_expressions: StatListNode
> > (matrix_integer_sparse.pyx:217:8)
> > File 'Nodes.py', line 2835, in analyse_expressions:
> > SingleAssignmentNode(matrix_integer_sparse.pyx:221:41)
> > File 'Nodes.py', line 2928, in analyse_types: SingleAssignmentNode
> > (matrix_integer_sparse.pyx:221:41)
> > File 'ExprNodes.py', line 2281, in analyse_types: SimpleCallNode
> > (matrix_integer_sparse.pyx:221:41)
> > File 'ExprNodes.py', line 3105, in analyse_types: TupleNode
> > (matrix_integer_sparse.pyx:221:41,
> > is_sequence_constructor = 1)
> > File 'ExprNodes.py', line 2972, in analyse_types: TupleNode
> > (matrix_integer_sparse.pyx:221:41,
> > is_sequence_constructor = 1)
> > File 'ExprNodes.py', line 2522, in analyse_types: GeneralCallNode
> > (matrix_integer_sparse.pyx:221:101)
>
> > Compiler crash traceback from this point on:
> > File "/usr/local/sage-devel/local/lib/python2.5/site-packages/Cython/
> > Compiler/ExprNodes.py", line 2532, in analyse_types
> > if hasattr(self.function, 'entry') and not
> > self.function.entry.as_variable:
> > AttributeError: 'NoneType' object has no attribute 'as_variable'
> > Error running command, failed with status 256.
> > sage: There was an error installing modified sage library code.
>
> > On Jun 2, 7:28 pm, William Stein <wst...@gmail.com> wrote:
> >> On Tue, Jun 2, 2009 at 7:22 PM, davidp <dav...@reed.edu> wrote:
>
> >> > I tried adding a delete_row method to matrix_integer_sparse.pyx but
> >> > stopped after getting the error message:
>
> >> Just def your method -- do not cpdef it. You can still use Cython
> >> code in a cpdef's method and it will be just as fast.
>
> >> Make sure that your "delete row" method returns a *new* matrix by the
> >> way...
>
> >> William
>
> >> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> > Error converting Pyrex file to C:
> >> > ------------------------------------------------------------
> >> > ...
> >> > add_mpz_vector_init(&M._matrix[i], &self._matrix[i], &
> >> > (<Matrix_integer_sparse>right)._matrix[i], mul)
> >> > mpz_clear(mul)
> >> > return M
>
> >> > # added by David Perkinson
> >> > cpdef ModuleElement _delete_row_(self, Py_ssize_t row_number):
> >> > ^
> >> > ------------------------------------------------------------
>
> >> > /usr/local/sage-devel/devel/sage-devel/sage/matrix/
> >> > matrix_integer_sparse.pyx:216:10: C method '_delete_row_' not
> >> > previously declared in definition part of extension type
> >> > Error running command, failed with status 256.
> >> > sage: There was an error installing modified sage library code.
>
> >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> >> > I might have to actually read the Cython documentation!
>
> >> > Dave
>
> >> > On Jun 2, 5:43 pm, Jason Grout <jason-s...@creativetrax.com> wrote:
> >> >> William Stein wrote:
> >> >> > On Mon, Jun 1, 2009 at 5:16 PM, davidp <dav...@reed.edu> wrote:
> >> >> >> Is there a fast way to create a submatrix?
>
> >> >> >> -------------------------------------------------
>
> >> >> >> sage: version()
> >> >> >> 'Sage Version 4.0.alpha0, Release Date: 2009-05-15'
> >> >> >> sage: G = graphs.GridGraph([100,100])
> >> >> >> sage: L = G.laplacian_matrix()
> >> >> >> sage: L
> >> >> >> 10000 x 10000 sparse matrix over Integer Ring
> >> >> >> sage: time M = L[1:9999,1:9999]
> >> >> >> CPU times: user 24.93 s, sys: 0.04 s, total: 24.97 s
> >> >> >> Wall time: 25.27 s
>
> >> >> >> ----------------------------------------------------
>
> >> >> >> I am just interested in deleting a single row and column of the
> >> >> >> matrix
> >> >> >> (not necessarily the first).
>
> >> >> >> Thanks,
>
> >> >> > There is no fast way to do that right now. One could easily add code
> >> >> > to SAGE_ROOT/devel/sage/sage/matrix/matrix_integer_sparse.pyx that
> >> >> > would provide blazingly fast deletion of a row, and reasonably fast
> >> >> > deletion of a column. Of course it would be better to implement
> >> >> > arbitrary slicing in some optimized way in matrix_integer_sparse.pyx.
> >> >> > I hope somebody does so.
>
> >> >> Just looking at the generic code, it seems that it goes through each and
> >> >> every index position in the slice, setting the new matrix entry to the
> >> >> old one. This is obviously the wrong thing to do for sparse matrices,
> >> >> and can likely trivially be made faster. I think all you may have to do
> >> >> is override the matrix_from_rows_and_columns for sparse matrices.
>
> >> >> Jason
>
> >> --
> >> William Stein
> >> Associate Professor of Mathematics
> >> University of Washingtonhttp://wstein.org
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
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