/*
  Teem: Tools to process and visualize scientific data and images
  Copyright (C) 2005  Gordon Kindlmann
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998  University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public License
  (LGPL) as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
  The terms of redistributing and/or modifying this software also
  include exceptions to the LGPL that facilitate static linking.

  This library 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
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

#include "unrrdu.h"
#include "privateUnrrdu.h"

#define INFO "Find connected components (CCs)"
char *_unrrdu_ccfindInfoL =
(INFO
 ". This works on 1-byte and 2-byte integral values, as well as "
 "4-byte ints.");

int
unrrdu_ccfindMain(int argc, char **argv, char *me, hestParm *hparm) {
  hestOpt *opt = NULL;
  char *out, *err, *valS;
  Nrrd *nin, *nout, *nval=NULL;
  airArray *mop;
  int type, pret;
  unsigned int conny;

  hestOptAdd(&opt, "v,values", "filename", airTypeString, 1, 1, &valS, "",
             "Giving a filename here allows you to save out the values "
             "associated with each connect component.  This can be used "
             "later with \"ccmerge -d\".  By default, no record of the "
             "original CC values is kept.");
  hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &type, "default",
             "type to use for output, to store the CC ID values.  By default "
             "(not using this option), the type used will be the smallest of "
             "uchar, ushort, or int, that can represent all the CC ID values. "
             "Using this option allows one to specify the integral type to "
             "be used.",
             NULL, NULL, &unrrduHestMaybeTypeCB);
  hestOptAdd(&opt, "c,connect", "connectivity", airTypeUInt, 1, 1,
             &conny, NULL,
             "what kind of connectivity to use: the number of coordinates "
             "that vary in order to traverse the neighborhood of a given "
             "sample.  In 2D: \"1\": 4-connected, \"2\": 8-connected");
  OPT_ADD_NIN(nin, "input nrrd");
  OPT_ADD_NOUT(out, "output nrrd");

  mop = airMopNew();
  airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);

  USAGE(_unrrdu_ccfindInfoL);
  PARSE();
  airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);

  nout = nrrdNew();
  airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);

  if (nrrdCCFind(nout, airStrlen(valS) ? &nval : NULL, nin, type, conny)) {
    if (nval) nrrdNuke(nval); // Delete the memory if allocated.
    airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
    fprintf(stderr, "%s: error doing connected components:\n%s", me, err);
    airMopError(mop);
    return 1;
  }
  if (nval) {
    airMopAdd(mop, nval, (airMopper)nrrdNuke, airMopAlways);
  }

  if (airStrlen(valS)) {
    SAVE(valS, nval, NULL);
  }
  SAVE(out, nout, NULL);

  airMopOkay(mop);
  return 0;
}

UNRRDU_CMD(ccfind, INFO);
