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/* |
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Teem: Tools to process and visualize scientific data and images . |
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Copyright (C) 2013, 2012, 2011, 2010, 2009 University of Chicago |
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Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann |
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Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah |
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This library is free software; you can redistribute it and/or |
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modify it under the terms of the GNU Lesser General Public License |
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(LGPL) as published by the Free Software Foundation; either |
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version 2.1 of the License, or (at your option) any later version. |
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The terms of redistributing and/or modifying this software also |
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include exceptions to the LGPL that facilitate static linking. |
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This library is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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Lesser General Public License for more details. |
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You should have received a copy of the GNU Lesser General Public License |
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along with this library; if not, write to Free Software Foundation, Inc., |
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51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA |
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*/ |
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#include "unrrdu.h" |
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#include "privateUnrrdu.h" |
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#define INFO "Merge CCs with their neighbors, under various constraints" |
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static const char *_unrrdu_ccmergeInfoL = |
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(INFO |
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". This operates on the output of \"ccfind\". " |
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"Merging of a CC is always done into its largest neighbor. " |
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"Whether or not to merge can be constrained by one or more of: " |
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"CC size (\"-s\"), original CC value being brighter or darker (\"-d\"), " |
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"and number of neighbors (\"-n\").\n " |
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"* Uses nrrdCCMerge"); |
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int |
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unrrdu_ccmergeMain(int argc, const char **argv, const char *me, |
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hestParm *hparm) { |
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hestOpt *opt = NULL; |
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char *out, *err; |
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Nrrd *nin, *nout, *nout2, *nval; |
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airArray *mop; |
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int pret, maxSize, dir, maxNeigh, revalue; |
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unsigned int conny; |
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hestOptAdd(&opt, "d,directed", "dir", airTypeInt, 1, 1, &dir, "0", |
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"do value-driven merging. Using (positive) \"1\" says that " |
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"dark islands get merged with bright surrounds, while \"-1\" " |
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"says the opposite. By default, merging can go either way. "); |
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hestOptAdd(&opt, "s,size", "max size", airTypeInt, 1, 1, &maxSize, "0", |
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"a cap on the CC size that will be absorbed into its " |
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"surround. CCs larger than this are deemed too significant " |
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"to mess with. Or, use \"0\" to remove any such restriction " |
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"on merging."); |
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hestOptAdd(&opt, "n,neighbor", "max # neigh", airTypeInt, 1, 1, |
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&maxNeigh, "1", |
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"a cap on the number of neighbors that a CC may have if it is " |
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"to be be merged. \"1\" allows only islands to be merged, " |
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"\"2\" does merging with bigger of two neighbors, etc, while " |
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"\"0\" says that number of neighbors is no constraint"); |
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hestOptAdd(&opt, "c,connect", "connectivity", airTypeUInt, 1, 1, |
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&conny, NULL, |
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"what kind of connectivity to use: the number of coordinates " |
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"that vary in order to traverse the neighborhood of a given " |
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"sample. In 2D: \"1\": 4-connected, \"2\": 8-connected"); |
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hestOptAdd(&opt, "revalue", NULL, airTypeInt, 0, 0, &revalue, NULL, |
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"If this option is given, then after the merging, the CCs " |
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"are re-assigned their original datavalues, as given by " |
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"the \"-v\" option"); |
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OPT_ADD_NIN(nin, "input nrrd"); |
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hestOptAdd(&opt, "v,values", "values", airTypeOther, 1, 1, &nval, "", |
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"result of using \"ccfind -v\", the record of which values " |
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"were originally associated with each CC. This is required " |
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"for value-directed merging (with non-zero \"-d\" option), " |
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"or if the \"-revalue\" option is given, " |
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"but is not needed otherwise", |
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NULL, NULL, nrrdHestNrrd); |
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OPT_ADD_NOUT(out, "output nrrd"); |
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mop = airMopNew(); |
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airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways); |
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✓✗ |
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USAGE(_unrrdu_ccmergeInfoL); |
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PARSE(); |
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airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways); |
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airMopAdd(mop, nout=nrrdNew(), (airMopper)nrrdNuke, airMopAlways); |
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airMopAdd(mop, nout2=nrrdNew(), (airMopper)nrrdNuke, airMopAlways); |
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if (nrrdCCMerge(nout, nin, nval, dir, maxSize, maxNeigh, conny)) { |
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airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways); |
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fprintf(stderr, "%s: error doing merging:\n%s", me, err); |
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airMopError(mop); |
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return 1; |
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} |
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if (revalue && nrrdCCRevalue(nout2, nout, nval)) { |
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airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways); |
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fprintf(stderr, "%s: error doing CC revalue:\n%s", me, err); |
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airMopError(mop); |
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return 1; |
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} |
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SAVE(out, revalue ? nout2 : nout, NULL); |
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airMopOkay(mop); |
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return 0; |
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} |
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UNRRDU_CMD(ccmerge, INFO); |