Faster conversion from numpy array to matrix mod 2

Author: user202729

src/sage/matrix/matrix_mod2_dense.pyx

@@ -108,7 +108,7 @@ from cysignals.memory cimport check_malloc, sig_free
 from cysignals.signals cimport sig_on, sig_str, sig_off
 
 cimport sage.matrix.matrix_dense as matrix_dense
-from sage.matrix.args cimport SparseEntry, MatrixArgs_init
+from sage.matrix.args cimport SparseEntry, MatrixArgs_init, MA_ENTRIES_NDARRAY
 from libc.stdio cimport *
 from sage.structure.element cimport (Matrix, Vector)
 from sage.modules.free_module_element cimport FreeModuleElement
@@ -257,8 +257,25 @@ cdef class Matrix_mod2_dense(matrix_dense.Matrix_dense):   # dense or sparse
             []
             sage: Matrix(GF(2),0,2)
             []
+
+        Make sure construction from numpy array is reasonably fast::
+
+            sage: # needs numpy
+            sage: import numpy as np
+            sage: n = 5000
+            sage: M = matrix(GF(2), np.random.randint(0, 2, (n, n)))  # around 700ms
+
+        Unsupported numpy data types (slower but still works)::
+
+            sage: # needs numpy
+            sage: n = 100
+            sage: M = matrix(GF(2), np.random.randint(0, 2, (n, n)).astype(np.float32))
         """
         ma = MatrixArgs_init(parent, entries)
+        if ma.get_type() == MA_ENTRIES_NDARRAY:
+            from ..modules.numpy_util import set_matrix_mod2_from_numpy
+            if set_matrix_mod2_from_numpy(self, ma.entries):
+                return
         for t in ma.iter(coerce, True):
             se = <SparseEntry>t
             mzd_write_bit(self._entries, se.i, se.j, se.entry)

src/sage/modules/numpy_util.pxd

@@ -1,5 +1,8 @@
 from libc.stdint cimport uintptr_t
 from sage.libs.m4ri cimport *
+from sage.matrix.matrix_mod2_dense cimport Matrix_mod2_dense
+
+cpdef int set_matrix_mod2_from_numpy(Matrix_mod2_dense a, b) except -1
 
 cpdef int set_mzd_from_numpy(uintptr_t entries_addr, Py_ssize_t degree, x) except -1
 # Note: we don't actually need ``cimport`` to work, which means this header file is not used in practice

src/sage/modules/numpy_util.pyx

@@ -1,12 +1,12 @@
 # sage.doctest: optional - numpy
+# cython: fast_getattr=False
+# https://github.com/cython/cython/issues/6442
 r"""
 Utility functions for numpy.
 """
 
 cimport numpy as np
 import numpy as np
-from sage.libs.m4ri cimport *
-from libc.stdint cimport uintptr_t
 
 
 ctypedef fused numpy_integral:
@@ -64,3 +64,32 @@ cpdef int set_mzd_from_numpy(uintptr_t entries_addr, Py_ssize_t degree, x) excep
                 mzd_write_bit(entries, 0, i, x_bool[i])
             return True
     return False
+
+
+cpdef int _set_matrix_mod2_from_numpy_helper(Matrix_mod2_dense a, np.ndarray[numpy_integral, ndim=2] b) except -1:
+    """
+    Internal function, helper for :func:`set_matrix_mod2_from_numpy`.
+    """
+    if not (a.nrows() == b.shape[0] and a.ncols() == b.shape[1]):
+        raise ValueError("shape mismatch")
+    for i in range(b.shape[0]):
+        for j in range(b.shape[1]):
+            a.set_unsafe_int(i, j, b[i, j] & 1)
+    return True
+
+
+cpdef int set_matrix_mod2_from_numpy(Matrix_mod2_dense a, b) except -1:
+    """
+    Try to set the entries of a matrix from a numpy array.
+
+    INPUT:
+
+    - ``a`` -- the destination matrix
+    - ``b`` -- a numpy array, must have dimension 2 and the same shape as ``a``
+
+    OUTPUT: ``True`` if successful, ``False`` otherwise. May throw ``ValueError``.
+    """
+    try:
+        return (<object>_set_matrix_mod2_from_numpy_helper)(a, b)  # https://github.com/cython/cython/issues/6588
+    except TypeError:
+        return False