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mm_write.cpp
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mm_write.cpp
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/** \file mm_write.cpp
*\author Weilei Zeng
* revised from Matrix Market I/O example program
* (See http://math.nist.gov/MatrixMarket for details.)
*/
//recomend file format for Matrix Market file is .mm or .mtx
//the segmentation fault is finally solved by reserve memory for I,J and Vval. May 2018
//trouble shooting: segmentation fault: directory not exist; wrong folder name
#include "mmio.h"
//#include <stdio.h>
//#include <stdlib.h>
//#include <fstream> //ofstream ifstream
#include <itpp/itbase.h>
//int GF2mat_to_MM(GF2mat G, char* file_name="mm_temp.dat")
int GF2mat_to_MM(itpp::GF2mat G, char* file_name, int debug)
{
int M=G.rows(),N=G.cols(),nt=M*N;//nt is the total number of elements, will find nz later. nz is the number of non-zero elements
//make nt smaller; the size of int[] should be less than about 2000000+; otherwise it creat segmentation fault
//this could be fixed by seperate int[] into smaller ones, but in this case the matrix is already too bigfor any calculation
// std::cout<<"density of GF2mat: "<<G.density()<<endl;
nt=floor(1+nt*(G.density()+0.001) ); //minimize total number of entry "nt" to reduce memery usage
int *I, *J;
I = (int *) malloc(nt * sizeof(int));
J = (int *) malloc(nt * sizeof(int));
int * val;
val = (int *) malloc(nt * sizeof(int));
// int I[nt],J[nt];//the location of nonzero elements
//usually nt is much larger than nz, where nz/nt is the density of the code. There is some wasted memory here.
// double val[nt];//have to use double to save the binary value in order to match the format of the file, didn't affect the result so far
int pos=0;
for(int m=0;m<M;m++){
// std::cout<<"\t m="<<m<<",";
for(int n=0;n<N;n++){
if(G.get(m,n)){//if it is nonzero
I[pos]=m;
J[pos]=n;
val[pos]=1;//we know it is one. so dont use G.get(m,n)
pos++;
}
}
}
int nz=pos;//number of nonzero elements
//std::cout<<"number of ones in the matrix is nz= "<<nz<<std::endl;
MM_typecode matcode;
mm_initialize_typecode(&matcode);
mm_set_matrix(&matcode);
mm_set_coordinate(&matcode);
// mm_set_real(&matcode);
mm_set_integer(&matcode);
mm_set_sparse(&matcode);
//create a file and wrote into it.
FILE *fout;
fout=fopen(file_name,"w");
mm_write_banner(fout, matcode);
mm_write_mtx_crd_size(fout, M, N, nz);
/* NOTE: matrix market files use 1-based indices, i.e. first element
of a vector has index 1, not 0. */
//it is not necessary to seperate the reading and writing in 2 loops
for (int i=0; i<nz; i++)
fprintf(fout, "%d %d %d\n", I[i]+1, J[i]+1, val[i]);
fclose(fout);
if ( debug ) std::cout<<"wrote the matrix (density:"<<G.density()<<") into file "<<file_name<<std::endl;
return 0;
}
//int mat_to_MM(mat G, char* filename="mm_temp.dat")
int mat_to_MM(itpp::mat G, char * filename){//use this when G is not a binary matrix
//dose not work sometimes and not sure why. Segmentation fault in line: mm_write_banner(fout, matcode);
int M=G.rows(),N=G.cols(),nt=M*N;//nt is the total number of elements, will find nz later. nz is the number of non-zero elements
//make nt smaller; the size of int[] should be less than about 2000000+
//nt=floor(1+nt*G.density());//design to be not sparse and small size
MM_typecode matcode;
int I[nt],J[nt];//the location of nonzero elements
//usually nt is much larger than nz, where nz/nt is the density of the code. There is some wasted memory here.
double val[nt];//have to use double to save the binary value in order to match the format of the file, didn't affect the result so far
int pos=0;
for(int m=0;m<M;m++){
for(int n=0;n<N;n++){
if(G.get(m,n)){//if it is nonzero
I[pos]=m;
J[pos]=n;
val[pos]=G.get(m,n);
pos++;
}
}
}
int nz=pos;//number of nonzero elements
mm_initialize_typecode(&matcode);
mm_set_matrix(&matcode);
mm_set_coordinate(&matcode);
mm_set_real(&matcode);
//create a file and wrote into it.
// std::cout<<filename<<", "<<M<<", "<<N<<", "<<nz<<std::endl;
FILE *fout;
fout=fopen(filename,"w");
mm_write_banner(fout, matcode);
mm_write_mtx_crd_size(fout, M, N, nz);
/* NOTE: matrix market files use 1-based indices, i.e. first element
of a vector has index 1, not 0. */
//it is not necessary to seperate the reading and writing in 2 loops
for (int i=0; i<nz; i++){
fprintf(fout, "%d %d %g\n", I[i]+1, J[i]+1, val[i]);
//originally use %10.3g, now use %g
}
fclose(fout);
std::cout<<"wrote the matrix into file "<<filename<<std::endl;
return 0;
}
int GF2mat_to_MM(itpp::mat G, std::string file_name){
char temp[file_name.length()+1];
strcpy(temp, file_name.c_str());
return GF2mat_to_MM(G, temp);
}
int mat_to_MM(itpp::mat G, std::string file_name){
char temp[file_name.length()+1];
strcpy(temp, file_name.c_str());
return mat_to_MM(G, temp);
}