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# 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
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
__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:
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:
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:
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 []
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