snaphu_io.c

phase unwrapping algorithm for SAR interferometry

/*************************************************************************

  snaphu input/output source file

  Written by Curtis W. Chen
  Copyright 2002 Board of Trustees, Leland Stanford Jr. University
  Please see the supporting documentation for terms of use.
  No warranty.

*************************************************************************/

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <signal.h>
#include <limits.h>
#include <float.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include <fcntl.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <sys/wait.h>
#include <sys/time.h>
#include <sys/resource.h>

#include "snaphu.h"


/* function: SetDefaults()
 * -----------------------
 * Sets all parameters to their initial default values.
 */
void SetDefaults(infileT *infiles, outfileT *outfiles, paramT *params){

  /* input files */
  StrNCopy(infiles->weightfile,DEF_WEIGHTFILE,MAXSTRLEN);
  StrNCopy(infiles->corrfile,DEF_CORRFILE,MAXSTRLEN);
  StrNCopy(infiles->ampfile,DEF_AMPFILE,MAXSTRLEN);
  StrNCopy(infiles->ampfile2,DEF_AMPFILE2,MAXSTRLEN);
  StrNCopy(infiles->estfile,DEF_ESTFILE,MAXSTRLEN);  
  StrNCopy(infiles->magfile,DEF_MAGFILE,MAXSTRLEN);
  StrNCopy(infiles->costinfile,DEF_COSTINFILE,MAXSTRLEN);

  /* output and dump files */
  StrNCopy(outfiles->initfile,DEF_INITFILE,MAXSTRLEN);
  StrNCopy(outfiles->flowfile,DEF_FLOWFILE,MAXSTRLEN);
  StrNCopy(outfiles->eifile,DEF_EIFILE,MAXSTRLEN);
  StrNCopy(outfiles->rowcostfile,DEF_ROWCOSTFILE,MAXSTRLEN);
  StrNCopy(outfiles->colcostfile,DEF_COLCOSTFILE,MAXSTRLEN);
  StrNCopy(outfiles->mstrowcostfile,DEF_MSTROWCOSTFILE,MAXSTRLEN);
  StrNCopy(outfiles->mstcolcostfile,DEF_MSTCOLCOSTFILE,MAXSTRLEN);
  StrNCopy(outfiles->mstcostsfile,DEF_MSTCOSTSFILE,MAXSTRLEN);
  StrNCopy(outfiles->corrdumpfile,DEF_CORRDUMPFILE,MAXSTRLEN);
  StrNCopy(outfiles->rawcorrdumpfile,DEF_RAWCORRDUMPFILE,MAXSTRLEN);
  StrNCopy(outfiles->costoutfile,DEF_COSTOUTFILE,MAXSTRLEN);
  StrNCopy(outfiles->conncompfile,DEF_CONNCOMPFILE,MAXSTRLEN);
  StrNCopy(outfiles->outfile,DEF_OUTFILE,MAXSTRLEN);  
  StrNCopy(outfiles->logfile,DEF_LOGFILE,MAXSTRLEN);

  /* file formats */
  infiles->infileformat=DEF_INFILEFORMAT;
  infiles->unwrappedinfileformat=DEF_UNWRAPPEDINFILEFORMAT;
  infiles->magfileformat=DEF_MAGFILEFORMAT;
  infiles->corrfileformat=DEF_CORRFILEFORMAT;
  infiles->estfileformat=DEF_ESTFILEFORMAT;
  infiles->ampfileformat=DEF_AMPFILEFORMAT;
  outfiles->outfileformat=DEF_OUTFILEFORMAT;

  /* options and such */
  params->unwrapped=DEF_UNWRAPPED;
  params->regrowconncomps=DEF_REGROWCONNCOMPS;
  params->eval=DEF_EVAL;
  params->initonly=DEF_INITONLY;
  params->initmethod=DEF_INITMETHOD;
  params->costmode=DEF_COSTMODE;
  params->amplitude=DEF_AMPLITUDE;
  params->verbose=DEF_VERBOSE;

  /* SAR and geometry parameters */
  params->orbitradius=DEF_ORBITRADIUS;
  params->altitude=DEF_ALTITUDE;
  params->earthradius=DEF_EARTHRADIUS;
  params->bperp=DEF_BPERP; 
  params->transmitmode=DEF_TRANSMITMODE;
  params->baseline=DEF_BASELINE;
  params->baselineangle=DEF_BASELINEANGLE;
  params->nlooksrange=DEF_NLOOKSRANGE;
  params->nlooksaz=DEF_NLOOKSAZ;
  params->nlooksother=DEF_NLOOKSOTHER;
  params->ncorrlooks=DEF_NCORRLOOKS;           
  params->ncorrlooksrange=DEF_NCORRLOOKSRANGE;
  params->ncorrlooksaz=DEF_NCORRLOOKSAZ;
  params->nearrange=DEF_NEARRANGE;         
  params->dr=DEF_DR;               
  params->da=DEF_DA;               
  params->rangeres=DEF_RANGERES;         
  params->azres=DEF_AZRES;            
  params->lambda=DEF_LAMBDA;           

  /* scattering model parameters */
  params->kds=DEF_KDS;
  params->specularexp=DEF_SPECULAREXP;
  params->dzrcritfactor=DEF_DZRCRITFACTOR;
  params->shadow=DEF_SHADOW;
  params->dzeimin=DEF_DZEIMIN;
  params->laywidth=DEF_LAYWIDTH;
  params->layminei=DEF_LAYMINEI;
  params->sloperatiofactor=DEF_SLOPERATIOFACTOR;
  params->sigsqei=DEF_SIGSQEI;

  /* decorrelation model parameters */
  params->drho=DEF_DRHO;
  params->rhosconst1=DEF_RHOSCONST1;
  params->rhosconst2=DEF_RHOSCONST2;
  params->cstd1=DEF_CSTD1;
  params->cstd2=DEF_CSTD2;
  params->cstd3=DEF_CSTD3;
  params->defaultcorr=DEF_DEFAULTCORR;
  params->rhominfactor=DEF_RHOMINFACTOR;

  /* pdf model parameters */
  params->dzlaypeak=DEF_DZLAYPEAK;
  params->azdzfactor=DEF_AZDZFACTOR;
  params->dzeifactor=DEF_DZEIFACTOR;
  params->dzeiweight=DEF_DZEIWEIGHT;
  params->dzlayfactor=DEF_DZLAYFACTOR;
  params->layconst=DEF_LAYCONST;
  params->layfalloffconst=DEF_LAYFALLOFFCONST;
  params->sigsqshortmin=DEF_SIGSQSHORTMIN;
  params->sigsqlayfactor=DEF_SIGSQLAYFACTOR;
  
  /* deformation mode parameters */
  params->defoazdzfactor=DEF_DEFOAZDZFACTOR;
  params->defothreshfactor=DEF_DEFOTHRESHFACTOR;
  params->defomax=DEF_DEFOMAX;
  params->sigsqcorr=DEF_SIGSQCORR;
  params->defolayconst=DEF_DEFOLAYCONST;

  /* algorithm parameters */
  params->flipphasesign=DEF_FLIPPHASESIGN;
  params->initmaxflow=DEF_INITMAXFLOW;
  params->arcmaxflowconst=DEF_ARCMAXFLOWCONST;
  params->maxflow=DEF_MAXFLOW;
  params->krowei=DEF_KROWEI;
  params->kcolei=DEF_KCOLEI;   
  params->kperpdpsi=DEF_KPERPDPSI;
  params->kpardpsi=DEF_KPARDPSI;
  params->threshold=DEF_THRESHOLD;  
  params->initdzr=DEF_INITDZR;    
  params->initdzstep=DEF_INITDZSTEP;    
  params->maxcost=DEF_MAXCOST;
  params->costscale=DEF_COSTSCALE;      
  params->costscaleambight=DEF_COSTSCALEAMBIGHT;      
  params->dnomincangle=DEF_DNOMINCANGLE;
  params->srcrow=DEF_SRCROW;
  params->srccol=DEF_SRCCOL;
  params->p=DEF_P;
  params->nshortcycle=DEF_NSHORTCYCLE;
  params->maxnewnodeconst=DEF_MAXNEWNODECONST;
  params->maxcyclefraction=DEF_MAXCYCLEFRACTION;
  params->sourcemode=DEF_SOURCEMODE;
  params->maxnflowcycles=DEF_MAXNFLOWCYCLES;
  params->dumpall=DEF_DUMPALL;
  params->cs2scalefactor=DEF_CS2SCALEFACTOR;

  /* tile parameters */
  params->ntilerow=DEF_NTILEROW;
  params->ntilecol=DEF_NTILECOL;
  params->rowovrlp=DEF_ROWOVRLP;
  params->colovrlp=DEF_COLOVRLP;
  params->piecefirstrow=DEF_PIECEFIRSTROW;
  params->piecefirstcol=DEF_PIECEFIRSTCOL;
  params->piecenrow=DEF_PIECENROW;
  params->piecencol=DEF_PIECENCOL;
  params->tilecostthresh=DEF_TILECOSTTHRESH;
  params->minregionsize=DEF_MINREGIONSIZE;
  params->nthreads=DEF_NTHREADS;
  params->scndryarcflowmax=DEF_SCNDRYARCFLOWMAX;
  params->assembleonly=DEF_ASSEMBLEONLY;
  params->rmtmptile=DEF_RMTMPTILE;
  params->tileedgeweight=DEF_TILEEDGEWEIGHT;

  /* connected component parameters */
  params->minconncompfrac=DEF_MINCONNCOMPFRAC;
  params->conncompthresh=DEF_CONNCOMPTHRESH;
  params->maxncomps=DEF_MAXNCOMPS;

}


/* function: ProcessArgs()
 * -----------------------
 * Parses command line inputs passed to main().
 */
void ProcessArgs(int argc, char *argv[], infileT *infiles, outfileT *outfiles,
		 long *linelenptr, paramT *params){

  long i,j;
  signed char noarg_exit;

  /* required inputs */
  noarg_exit=FALSE;
  StrNCopy(infiles->infile,"",MAXSTRLEN);
  *linelenptr=0;

  /* loop over inputs */
  if(argc<2){                             /* catch zero arguments in */
    fprintf(sp1,OPTIONSHELPBRIEF);
    exit(ABNORMAL_EXIT);
  }
  for(i=1;i<argc;i++){                  
    /* if argument is an option */
    if(argv[i][0]=='-'){   
      if(strlen(argv[i])==1){
	fprintf(sp0,"invalid command line argument -\n");
	exit(ABNORMAL_EXIT);
      }else if(argv[i][1]!='-'){
	for(j=1;j<strlen(argv[i]);j++){
	  if(argv[i][j]=='h'){
	    fprintf(sp1,OPTIONSHELPFULL);
	    exit(ABNORMAL_EXIT);
	  }else if(argv[i][j]=='u'){
	    params->unwrapped=TRUE;
	  }else if(argv[i][j]=='t'){
	    params->costmode=TOPO;
	  }else if(argv[i][j]=='d'){
	    params->costmode=DEFO;
	  }else if(argv[i][j]=='s'){
	    params->costmode=SMOOTH;
	    params->defomax=0.0;
	  }else if(argv[i][j]=='q'){
	    params->eval=TRUE;
	    params->unwrapped=TRUE;
	  }else if(argv[i][j]=='f'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      
	      /* read user-supplied configuration file */
	      ReadConfigFile(argv[i],infiles,outfiles,linelenptr,params);
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='o'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(outfiles->outfile,argv[i],MAXSTRLEN);
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='c'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(infiles->corrfile,argv[i],MAXSTRLEN);
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='m'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(infiles->magfile,argv[i],MAXSTRLEN);
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='a'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(infiles->ampfile,argv[i],MAXSTRLEN);
	      params->amplitude=TRUE;
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='A'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(infiles->ampfile,argv[i],MAXSTRLEN);
	      params->amplitude=FALSE;
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='e'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(infiles->estfile,argv[i],MAXSTRLEN);
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='w'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(infiles->weightfile,argv[i],MAXSTRLEN);
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='g'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(outfiles->conncompfile,argv[i],MAXSTRLEN);
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='G'){
	    params->regrowconncomps=TRUE;
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(outfiles->conncompfile,argv[i],MAXSTRLEN);
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='b'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      if(StringToDouble(argv[i],&(params->bperp)) || !(params->bperp)){
		fprintf(sp0,"option -%c requires non-zero decimal argument\n",
			argv[i-1][j]);
		exit(ABNORMAL_EXIT);
	      }
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='p'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      if(StringToDouble(argv[i],&(params->p))){
		fprintf(sp0,"option -%c requires decimal argument\n",
			argv[i-1][j]);
		exit(ABNORMAL_EXIT);
	      }
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else if(argv[i][j]=='i'){
	    params->initonly=TRUE;
	  }else if(argv[i][j]=='n'){
	    params->costmode=NOSTATCOSTS;
	  }else if(argv[i][j]=='v'){
	    params->verbose=TRUE;
	  }else if(argv[i][j]=='l'){
	    if(++i<argc && j==strlen(argv[i-1])-1){
	      StrNCopy(outfiles->logfile,argv[i],MAXSTRLEN);
	      break;
	    }else{
	      noarg_exit=TRUE;
	    }
	  }else{
	    fprintf(sp0,"unrecognized option -%c\n",argv[i][j]);
	    exit(ABNORMAL_EXIT);
	  }
	  if(noarg_exit){
	    fprintf(sp0,"option -%c requires an argument\n",argv[i-1][j]);
	    exit(ABNORMAL_EXIT);
	  }
	}
      }else{
	/* argument is a "--" option */
	if(!strcmp(argv[i],"--costinfile")){
	  if(++i<argc){
	    StrNCopy(infiles->costinfile,argv[i],MAXSTRLEN);
	  }else{
	    noarg_exit=TRUE;
	  }
	}else if(!strcmp(argv[i],"--costoutfile")){
	  if(++i<argc){
	    StrNCopy(outfiles->costoutfile,argv[i],MAXSTRLEN);
	  }else{
	    noarg_exit=TRUE;
	  }
	}else if(!strcmp(argv[i],"--debug") || !strcmp(argv[i],"--dumpall")){
	  params->dumpall=TRUE;
	}else if(!strcmp(argv[i],"--mst")){