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author | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-09-09 16:03:40 +0200 |
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committer | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-09-09 16:03:40 +0200 |
commit | 68753b3c28321e28eedd5829c94234da84e25c8d (patch) | |
tree | 36003a30309b3203b41092ad4d7ee8fa78551452 /src/python/gudhi/reader_utils.pyx | |
parent | dcbdaa0dc00eb069d1a13575f22c0a2f7d63dcc8 (diff) |
Code review: rename cython as python (make target and directory
Diffstat (limited to 'src/python/gudhi/reader_utils.pyx')
-rw-r--r-- | src/python/gudhi/reader_utils.pyx | 87 |
1 files changed, 87 insertions, 0 deletions
diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx new file mode 100644 index 00000000..147fae71 --- /dev/null +++ b/src/python/gudhi/reader_utils.pyx @@ -0,0 +1,87 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.string cimport string +from libcpp.map cimport map +from libcpp.pair cimport pair + +from os import path +from numpy import array as np_array + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2017 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2017 Inria" +__license__ = "MIT" + +cdef extern from "Reader_utils_interface.h" namespace "Gudhi": + vector[vector[double]] read_matrix_from_csv_file(string off_file, char separator) + map[int, vector[pair[double, double]]] read_pers_intervals_grouped_by_dimension(string filename) + vector[pair[double, double]] read_pers_intervals_in_dimension(string filename, int only_this_dim) + +def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'): + """Read lower triangular matrix from a CSV style file. + + :param csv_file: A CSV file style name. + :type csv_file: string + :param separator: The value separator in the CSV file. Default value is ';' + :type separator: char + + :returns: The lower triangular matrix. + :rtype: vector[vector[double]] + """ + if csv_file is not '': + if path.isfile(csv_file): + return read_matrix_from_csv_file(str.encode(csv_file), ord(separator[0])) + print("file " + csv_file + " not set or not found.") + return [] + +def read_persistence_intervals_grouped_by_dimension(persistence_file=''): + """Reads a file containing persistence intervals. + Each line might contain 2, 3 or 4 values: [[field] dimension] birth death + The return value is an `map[dim, vector[pair[birth, death]]]` + where `dim` is an `int`, `birth` a `double`, and `death` a `double`. + Note: the function does not check that birth <= death. + + :param persistence_file: A persistence file style name. + :type persistence_file: string + + :returns: The persistence pairs grouped by dimension. + :rtype: map[int, vector[pair[double, double]]] + """ + if persistence_file is not '': + if path.isfile(persistence_file): + return read_pers_intervals_grouped_by_dimension(str.encode(persistence_file)) + print("file " + persistence_file + " not set or not found.") + return [] + +def read_persistence_intervals_in_dimension(persistence_file='', only_this_dim=-1): + """Reads a file containing persistence intervals. + Each line of persistence_file might contain 2, 3 or 4 values: + [[field] dimension] birth death + Note: the function does not check that birth <= death. + + :param persistence_file: A persistence file style name. + :type persistence_file: string + :param only_this_dim: The specific dimension. Default value is -1. + If `only_this_dim` = -1, dimension is ignored and all lines are returned. + If `only_this_dim` is >= 0, only the lines where dimension = + `only_this_dim` (or where dimension is not specified) are returned. + :type only_this_dim: int. + + :returns: The persistence intervals. + :rtype: numpy array of dimension 2 + """ + if persistence_file is not '': + if path.isfile(persistence_file): + return np_array(read_pers_intervals_in_dimension(str.encode( + persistence_file), only_this_dim)) + print("file " + persistence_file + " not set or not found.") + return [] |