+++ /dev/null
-/*
- * This file is part of TISEAN
- *
- * Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
- *
- * TISEAN 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 2 of the License, or
- * (at your option) any later version.
- *
- * TISEAN 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 TISEAN; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-/*Author: Rainer Hegger Last modified: Sep 16, 2004 */
-/* Sep 16, 2004: Change of index in output. before 0->N-1 now 1->N
- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include <limits.h>
-#include "routines/tsa.h"
-
-#define WID_STR "This programs makes a recurrence plot for the data."
-
-#define BOX 1024
-
-unsigned long length=ULONG_MAX,exclude=0;
-unsigned int embed=2,dim=1,delay=1;
-unsigned int verbosity=0xff;
-double eps=1.e-3,fraction=1.0;
-char dimset=0;
-char *columns;
-char *outfile=NULL,stdo=1;
-char *infile=NULL;
-char epsset=0;
-
-double **series;
-long **box,*list;
-
-void show_options(char *progname)
-{
- what_i_do(progname,WID_STR);
- fprintf(stderr,"Usage: %s [options]\n",progname);
- fprintf(stderr,"Options:\n");
- fprintf(stderr,"Everything not being a valid option will be interpreted"
- " as a possible"
- " datafile.\nIf no datafile is given stdin is read. Just - also"
- " means stdin\n");
- fprintf(stderr,"\t-l # of data to use [Default: whole file]\n");
- fprintf(stderr,"\t-x # of lines to be ignored [Default: 0]\n");
- fprintf(stderr,"\t-c columns to read [Default: 1]\n");
- fprintf(stderr,"\t-m # of components,embedding dimension [Default: 1,2]\n");
- fprintf(stderr,"\t-d delay [Default: 1]\n");
- fprintf(stderr,"\t-r size of the neighbourhood "
- "[Default: (data interval)/1000]\n");
- fprintf(stderr,"\t-%% print only a percentage of points found [Default: "
- " 100.0]\n");
- fprintf(stderr,"\t-o output file name [Default: 'datafile'.rec\n"
- "\t\twithout -o: stdout]\n");
- fprintf(stderr,"\t-V verbosity level [Default: 1]\n\t\t"
- "0='only panic messages'\n\t\t"
- "1='+ input/output messages'\n");
- fprintf(stderr,"\t-h show these options\n");
- exit(0);
-}
-
-void scan_options(int n,char **in)
-{
- char *out;
-
- if ((out=check_option(in,n,'l','u')) != NULL)
- sscanf(out,"%lu",&length);
- if ((out=check_option(in,n,'x','u')) != NULL)
- sscanf(out,"%lu",&exclude);
- if ((out=check_option(in,n,'c','s')) != NULL)
- columns=out;
- if ((out=check_option(in,n,'m','2')) != NULL) {
- sscanf(out,"%u,%u",&dim,&embed);
- dimset=1;
- }
- if ((out=check_option(in,n,'d','u')) != NULL)
- sscanf(out,"%u",&delay);
- if ((out=check_option(in,n,'V','u')) != NULL)
- sscanf(out,"%u",&verbosity);
- if ((out=check_option(in,n,'r','f')) != NULL) {
- epsset=1;
- sscanf(out,"%lf",&eps);
- }
- if ((out=check_option(in,n,'%','f')) != NULL) {
- sscanf(out,"%lf",&fraction);
- fraction /= 100.0;
- }
- if ((out=check_option(in,n,'o','o')) != NULL) {
- stdo=0;
- if (strlen(out) > 0)
- outfile=out;
- }
-}
-
-void lfind_neighbors(void)
-{
- int i,i1,i2,j,j1,ke,ked,kd;
- int ibox=BOX-1;
- long n,element;
- double dx,epsinv;
- char toolarge;
- FILE *fout=NULL;
-
- epsinv=1./eps;
- rnd_init(0x9834725L);
-
- if (!stdo) {
- fout=fopen(outfile,"w");
- if (verbosity&VER_INPUT)
- fprintf(stderr,"Opened %s for writing\n",outfile);
- }
- else {
- if (verbosity&VER_INPUT)
- fprintf(stderr,"Writing to stdout\n");
- }
-
- for (n=(embed-1)*delay;n<length;n++) {
- i=(int)(series[0][n]*epsinv)&ibox;
- j=(int)(series[dim-1][n]*epsinv)&ibox;
- for (i1=i-1;i1<=i+1;i1++) {
- i2=i1&ibox;
- for (j1=j-1;j1<=j+1;j1++) {
- element=box[i2][j1&ibox];
- while (element > n) {
- toolarge=0;
- for (ke=0;ke<embed;ke++) {
- ked=ke*delay;
- for (kd=0;kd<dim;kd++) {
- dx=fabs(series[kd][n-ked]-series[kd][element-ked]);
- if (dx >= eps) {
- toolarge=1;
- break;
- }
- }
- if (toolarge)
- break;
- }
- if (!toolarge)
- if (((double)rnd69069()/ULONG_MAX) <= fraction) {
- if (!stdo)
- fprintf(fout,"%ld %ld\n",n+1,element+1);
- else
- fprintf(stdout,"%ld %ld\n",n+1,element+1);
- }
- element=list[element];
- }
- }
- }
- }
- if (!stdo)
- fclose(fout);
-}
-
-int main(int argc,char **argv)
-{
- long i;
- char stdi=0;
- double min,max,maxmax;
-
- if (scan_help(argc,argv))
- show_options(argv[0]);
-
- scan_options(argc,argv);
-#ifndef OMIT_WHAT_I_DO
- if (verbosity&VER_INPUT)
- what_i_do(argv[0],WID_STR);
-#endif
-
- infile=search_datafile(argc,argv,NULL,verbosity);
- if (infile == NULL)
- stdi=1;
-
- if (outfile == NULL) {
- if (!stdi) {
- check_alloc(outfile=(char*)calloc(strlen(infile)+5,(size_t)1));
- strcpy(outfile,infile);
- strcat(outfile,".rec");
- }
- else {
- check_alloc(outfile=(char*)calloc((size_t)10,(size_t)1));
- strcpy(outfile,"stdin.rec");
- }
- }
- if (!stdo)
- test_outfile(outfile);
-
- if (columns == NULL)
- series=(double**)get_multi_series(infile,&length,exclude,&dim,"",dimset,
- verbosity);
- else
- series=(double**)get_multi_series(infile,&length,exclude,&dim,columns,
- dimset,verbosity);
-
- maxmax=0.0;
- for (i=0;i<dim;i++) {
- rescale_data(series[i],length,&min,&max);
- if (max > maxmax)
- maxmax=max;
- }
-
- if (epsset)
- eps /= maxmax;
-
- check_alloc(list=(long*)malloc(sizeof(long)*length));
- check_alloc(box=(long**)malloc(sizeof(long*)*BOX));
- for (i=0;i<BOX;i++)
- check_alloc(box[i]=(long*)malloc(sizeof(long)*BOX));
-
- make_multi_box(series,box,list,length,BOX,dim,embed,delay,eps);
- lfind_neighbors();
-
- return 0;
-}
git://source.jalview.org / jabaws.git / blobdiff