1 /*
2 Teem: Tools to process and visualize scientific data and images .
3 Copyright (C) 2012, 2011, 2010, 2009 University of Chicago
4 Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
5 Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
6
7 This library is free software; you can redistribute it and/or
8 modify it under the terms of the GNU Lesser General Public License
9 (LGPL) as published by the Free Software Foundation; either
10 version 2.1 of the License, or (at your option) any later version.
11 The terms of redistributing and/or modifying this software also
12 include exceptions to the LGPL that facilitate static linking.
13
14 This library is distributed in the hope that it will be useful,
15 but WITHOUT ANY WARRANTY; without even the implied warranty of
16 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 Lesser General Public License for more details.
18
19 You should have received a copy of the GNU Lesser General Public License
20 along with this library; if not, write to Free Software Foundation, Inc.,
21 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
22 */
23
24 #include "unrrdu.h"
25 #include "privateUnrrdu.h"
26
27 #define INFO "Permute slices along one axis"
28 static const char *_unrrdu_shuffleInfoL =
29 (INFO
30 ". Slices along one axis are re-arranged as units "
31 "according to the given permutation (or its inverse). "
32 "The permutation tells which old slice to put at each "
33 "new position. For example, the shuffle "
34 "0->1,\t1->2,\t2->0 would be \"2 0 1\". Obviously, "
35 "if you have to rearrange the many slices of a large "
36 "dataset, you should probably store the permutation "
37 "in a plain text file and use it as a "
38 "\"response file\".\n "
39 "* Uses nrrdShuffle");
40
41 int
unrrdu_shuffleMain(int argc,const char ** argv,const char * me,hestParm * hparm)42 unrrdu_shuffleMain(int argc, const char **argv, const char *me,
43 hestParm *hparm) {
44 hestOpt *opt = NULL;
45 char *out, *err;
46 Nrrd *nin, *nout;
47 unsigned int di, axis, permLen, *perm, *iperm, *whichperm;
48 size_t *realperm;
49 int inverse, pret;
50 airArray *mop;
51
52 /* so that long permutations can be read from file */
53 hparm->respFileEnable = AIR_TRUE;
54
55 hestOptAdd(&opt, "p,permute", "slc0 slc1", airTypeUInt, 1, -1, &perm, NULL,
56 "new slice ordering", &permLen);
57 hestOptAdd(&opt, "inv,inverse", NULL, airTypeInt, 0, 0, &inverse, NULL,
58 "use inverse of given permutation");
59 OPT_ADD_AXIS(axis, "axis to shuffle along");
60 OPT_ADD_NIN(nin, "input nrrd");
61 OPT_ADD_NOUT(out, "output nrrd");
62
63 mop = airMopNew();
64 airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
65
66 USAGE(_unrrdu_shuffleInfoL);
67 PARSE();
68 airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
69
70 nout = nrrdNew();
71 airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
72
73 /* we have to do error checking on axis in order to do error
74 checking on length of permutation */
75 if (!( axis < nin->dim )) {
76 fprintf(stderr, "%s: axis %d not in valid range [0,%d]\n",
77 me, axis, nin->dim-1);
78 airMopError(mop);
79 return 1;
80 }
81 if (!( permLen == nin->axis[axis].size )) {
82 char stmp[AIR_STRLEN_SMALL];
83 fprintf(stderr, "%s: permutation length (%u) != axis %d's size (%s)\n",
84 me, permLen, axis,
85 airSprintSize_t(stmp, nin->axis[axis].size));
86 airMopError(mop);
87 return 1;
88 }
89 if (inverse) {
90 iperm = AIR_CALLOC(permLen, unsigned int);
91 airMopAdd(mop, iperm, airFree, airMopAlways);
92 if (nrrdInvertPerm(iperm, perm, permLen)) {
93 fprintf(stderr,
94 "%s: couldn't compute inverse of given permutation\n", me);
95 airMopError(mop);
96 return 1;
97 }
98 whichperm = iperm;
99 } else {
100 whichperm = perm;
101 }
102
103 realperm = AIR_CALLOC(permLen, size_t);
104 airMopAdd(mop, realperm, airFree, airMopAlways);
105 for (di=0; di<permLen; di++) {
106 realperm[di] = whichperm[di];
107 }
108 if (nrrdShuffle(nout, nin, axis, realperm)) {
109 airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
110 fprintf(stderr, "%s: error shuffling nrrd:\n%s", me, err);
111 airMopError(mop);
112 return 1;
113 }
114
115 SAVE(out, nout, NULL);
116
117 airMopOkay(mop);
118 return 0;
119 }
120
121 UNRRDU_CMD(shuffle, INFO);
122