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Diffstat (limited to 'src/Gudhi_stat/include/gudhi/fill_in_missing_data.h')
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diff --git a/src/Gudhi_stat/include/gudhi/fill_in_missing_data.h b/src/Gudhi_stat/include/gudhi/fill_in_missing_data.h deleted file mode 100644 index a9997aa2..00000000 --- a/src/Gudhi_stat/include/gudhi/fill_in_missing_data.h +++ /dev/null @@ -1,144 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2015 INRIA (France) - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#ifndef FILL_IN_MISSING_DATA_H -#define FILL_IN_MISSING_DATA_H - -namespace Gudhi -{ -namespace Gudhi_stat -{ - -/** - * Quite often in biological sciences we are facing a problem of missing data. We may have for instance a number of sequences of observations made in between times A and B in a discrete - * collection of times A = t1, t2,...,tn = B. But quite typically some of the observations may be missing. Then quite often it is hard to estimate the values in the missing times. - * The procedure below assumes that we compute some topological descriptor of the observations we are given. Most typically this will be some type of persistence homology representation. - * The the values in the missing points are filled in by linear interpolation and extrapolation. The procedure below have minimal requirements: it assumes that we have two elements that - * filled in. The rest will be filled in by using them. - * The fill-in process is done based on the idea of linear approximation. Let us assume that we have two positions A and B which are filled in with proper objects of a type Representation_of_topology. - * Any intermediate time step can be interpolated by taking a linear combination t*A + (1-t)*B, where t \in [0,1]. - * If the missing data are located at the beginning of at the end of vector of Representation_of_topology, then we use the following extrapolation scheme: - * First we make sure that there are no missing data except at the very beginning and at the very end of a vector of data. Then, we pick two constitutive closest filled-in data A and B and we extrapolate - * by using a formula: t*A-(t-1)*B, where t is a natural number > 1. - * Note that both vector of data and the vector is_the_position_filled_in are modified by this procedure. Upon successful termination of the procedure, the vector is_the_position_filled_in has only 'true' entries, - * and the vector data do not have missing data. -**/ - -template < typename Representation_of_topology > -void fill_in_missing_data( std::vector< Representation_of_topology* >& data , std::vector< bool >& is_the_position_filled_in ) -{ - bool dbg = false; - - //first check if at least two positions are filled in: - size_t number_of_positions_that_are_filled_in = 0; - for ( size_t i = 0 ; i != is_the_position_filled_in.size() ; ++i ) - { - if ( is_the_position_filled_in[i] )++number_of_positions_that_are_filled_in; - } - - if ( number_of_positions_that_are_filled_in < 2 ) - { - std::cerr << "There are too few positions filled in to do extrapolation / interpolation. The program will now terminate.\n"; - throw "There are too few positions filled in to do extrapolation / interpolation. The program will now terminate.\n"; - } - - for ( size_t i = 0 ; i != data.size() ; ++i ) - { - if ( !is_the_position_filled_in[i] ) - { - //This position is not filled in. Find the next position which is nonzero. - size_t j = 1; - while ( (is_the_position_filled_in[i+j] == false) && ( i+j != data.size() ) )++j; - if ( dbg ) - { - std::cout << "The position number : " << i << " is not filled in. The next filled-in position is : " << i+j << std::endl; - } - if ( i != 0 ) - { - //this is not the first position of the data: - if ( i + j != data.size() ) - { - //this is not the last position of the data either - for ( size_t k = 0 ; k != j ; ++k ) - { - double weight1 = double(j-k)/(double)(j+1); - double weight2 = double(k+1)/(double)(j+1); - data[i+k] = new Representation_of_topology(weight1*(*data[i-1]) + weight2*(*data[i+j])); - is_the_position_filled_in[i+k] = true; - if ( dbg ) - { - std::cerr << "We fill in a position : " << i+k << " with: position " << i-1 << " with weight " << weight1 << " and position " << i+j << " with weight " << weight2 << std::endl; - } - } - } - } - else - { - //this is the first position of the data, i.e. i == 0. - while ( is_the_position_filled_in[i] == 0 )++i; - } - - } - } - - - if ( is_the_position_filled_in[0] == false ) - { - //find the first nonzero (then, we know that the second one will be nonzero too, since we filled it in above): - size_t i = 0; - while ( is_the_position_filled_in[i] == false )++i; - //the data at position i is declared. Since, we made sure that all other positions, except maybe a few first and a few last, are declared too. Therefore, if we find a - //first declared, then the next one will be declared too. So, we can do a telescopic declaration backward and forward. - - for ( size_t j = i ; j != 0 ; --j ) - { - data[j-1] = new Representation_of_topology(2*(*data[j]) + (-1)*(*data[j+1])); - is_the_position_filled_in[j-1] = true; - if ( dbg ) - { - std::cerr << "Filling in a position : " << j-1 << " by using: " << j << " and " << j+1 <<std::endl; - } - } - } - - if ( is_the_position_filled_in[ is_the_position_filled_in.size()-1 ] == false ) - { - //first the first nonzero (then, we know that the second one will be nonzero too): - size_t i = is_the_position_filled_in.size()-1; - while ( is_the_position_filled_in[i] == false )--i; - - for ( size_t j = i+1 ; j != data.size() ; ++j ) - { - data[j] = new Representation_of_topology(2*(*data[j-1]) + (-1)*(*data[j-2])); - is_the_position_filled_in[j] = true; - if ( dbg ) - { - std::cerr << "Filling in a position : " << j << " by using: " << j-1 << " and " << j-2 <<std::endl; - } - } - } -}//fill_in_missing_data - -}//namespace Gudhi_stat -}//namespace Gudhi - -#endif |