Support for SNAPHU v2.0.6

[comma-never-coma]

I just replaced the source code from snaphu-v2.0.6 and made a few modifications based on the compilation format of snaphu-v1.4.2 to ensure that it can be successfully compiled. I haven't added any new parameters for snaphu-v2.0.6 yet.
I would be immensely grateful if someone could help with improvements or corrections.

[forrestfwilliams]

Hey @comma-never-coma, which changes here are due to replacing the SNAPHU source code, and which are to ensure you can successfully compile? Are the changes in the include directory the compilation changes?

[comma-never-coma]

OK. First, obtain the source code for SNAPHU, which contains 8 *.c files and 2 *.h files in the src folder. Just replace them in the corresponding src and include folders of ISCE2. Next, u only need to modify snaphu.c – mainly replacing the main function located in line 69 with snaphu function reference to ISCE2, as shown below.

/***************************/
/* main program for snaphu */
/***************************/

int snaphu(infileT *infiles,outfileT *outfiles, paramT *params,long linelen) {

  /* variable declarations
  infileT infiles[1];
  outfileT outfiles[1];
  paramT params[1];
  time_t tstart;
  double cputimestart;
  long linelen, nlines;*/
	long nlines;


  /* get current wall clock and CPU time
  StartTimers(&tstart,&cputimestart);*/

  /* set output stream pointers (may be reset after inputs parsed) */
  SetStreamPointers();

  /* print greeting */
  fprintf(sp1,"\n%s v%s\n",PROGRAMNAME,VERSION);

  /* set default parameters */
  /*SetDefaults(infiles,outfiles,params);
  ReadConfigFile(DEF_SYSCONFFILE,infiles,outfiles,&linelen,params);*/

  /* parse the command line inputs */
  /*ProcessArgs(argc,argv,infiles,outfiles,&linelen,params);*/

  /* set verbose output if specified */
  SetVerboseOut(params);

  /* set names of dump files if necessary */
  SetDumpAll(outfiles,params);

  /* get number of lines in file */
  nlines=GetNLines(infiles,linelen,params);

  /* check validity of parameters */
  CheckParams(infiles,outfiles,linelen,nlines,params);

  /* log the runtime parameters */
  /*WriteConfigLogFile(argc,argv,infiles,outfiles,linelen,params);*/

  /* unwrap, forming tiles and reassembling if necessary */
  Unwrap(infiles,outfiles,params,linelen,nlines);

  /* finish up
  fprintf(sp1,"Program %s done\n",PROGRAMNAME);
  DisplayElapsedTime(tstart,cputimestart);
  exit(NORMAL_EXIT);*/

  return EXIT_SUCCESS;

} /* end of main() */

[yuankailiu]

Hi, is this still under review/development? I wonder if there are any updates. Thanks.

[comma-never-coma]

I apologize, but due to a change in my research focus, I have not been following this line of work for over half a year now.

[hfattahi]

Sorry for getting to this so late. In the meantime we have a stand alone thin Snaphu wrapper here developed by @gmgunter which one could call in different isce2 workflows. I'm wondering if the better approach at this point will be to add dependency to snaphu_py and with a thin wrapper inside isce2, transform to latest snpahu? @rtburns-jpl @gmgunter what do you think?