diff options
Diffstat (limited to 'src/python/gudhi/simplex_tree.pyx')
| -rw-r--r-- | src/python/gudhi/simplex_tree.pyx | 11 |
1 files changed, 8 insertions, 3 deletions
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 18215d2f..4cf176f5 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -12,6 +12,7 @@ from libc.stdint cimport intptr_t, int32_t, int64_t import numpy as np cimport gudhi.simplex_tree cimport cython +from numpy.math cimport INFINITY __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" @@ -239,7 +240,7 @@ cdef class SimplexTree: @staticmethod @cython.boundscheck(False) - def create_from_array(filtrations, double max_filtration=np.inf): + def create_from_array(filtrations, double max_filtration=INFINITY): """Creates a new, empty complex and inserts vertices and edges. The vertices are numbered from 0 to n-1, and the filtration values are encoded in the array, with the diagonal representing the vertices. It is the caller's responsibility to ensure that this defines a filtration, which can be achieved with either:: @@ -281,6 +282,8 @@ cdef class SimplexTree: .. seealso:: :func:`insert_batch` """ + # Without this, it could be slow if we end up inserting vertices in a bad order (flat_map). + self.get_ptr().insert_batch_vertices(np.unique(np.stack((edges.row, edges.col))), INFINITY) # TODO: optimize this? for edge in zip(edges.row, edges.col, edges.data): self.get_ptr().insert((edge[0], edge[1]), edge[2]) @@ -303,8 +306,7 @@ cdef class SimplexTree: :param filtrations: the filtration values. :type filtrations: numpy.array of shape (n,) """ - # This may be slow if we end up inserting vertices in a bad order (flat_map). - # We could first insert the vertices from np.unique(vertex_array), or leave it to the caller. + cdef vector[int] vertices = np.unique(vertex_array) cdef Py_ssize_t k = vertex_array.shape[0] cdef Py_ssize_t n = vertex_array.shape[1] assert filtrations.shape[0] == n, 'inconsistent sizes for vertex_array and filtrations' @@ -312,6 +314,9 @@ cdef class SimplexTree: cdef Py_ssize_t j cdef vector[int] v with nogil: + # Without this, it could be slow if we end up inserting vertices in a bad order (flat_map). + # NaN currently does the wrong thing + self.get_ptr().insert_batch_vertices(vertices, INFINITY) for i in range(n): for j in range(k): v.push_back(vertex_array[j, i]) |