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 "ten.h"
25 #include "privateTen.h"
26
27 #define INFO "Converts masked non-redundant tensor images to redundant"
28 static const char *_tend_expandInfoL =
29 (INFO
30 ". For images of 3D tensors, this converts from a 7-value tensor "
31 "starting with the confidence/mask value "
32 "(conf, Dxx, Dxy, Dxz, Dyy, Dyz, Dzz) to "
33 "a 9-value tensor with the full matrix "
34 "(Dxx, Dxy, Dxz, Dxy, Dyy, Dyz, Dxz, Dyz, Dzz). "
35 "This is set to all zeros when the confidence is below the given "
36 "threshold. For images of 2D tensors, the conversion is from "
37 "(conf, Dxx, Dxy, Dyy) to (Dxx, Dxy, Dxy, Dyy). " );
38
39 int
tend_expandMain(int argc,const char ** argv,const char * me,hestParm * hparm)40 tend_expandMain(int argc, const char **argv, const char *me,
41 hestParm *hparm) {
42 int pret;
43 hestOpt *hopt = NULL;
44 char *perr, *err;
45 airArray *mop;
46
47 Nrrd *nin, *nout;
48 char *outS;
49 int orientRed, orientRedWithOrigin, mfRed;
50 float scale, thresh;
51
52 hestOptAdd(&hopt, "t", "thresh", airTypeFloat, 1, 1, &thresh, "0.5",
53 "confidence level to threshold output tensors at. Should "
54 "be between 0.0 and 1.0.");
55 hestOptAdd(&hopt, "s", "scale", airTypeFloat, 1, 1, &scale, "1.0",
56 "how to scale values before saving as 9-value tensor. Useful "
57 "for visualization tools which assume certain characteristic "
58 "ranges of eigenvalues");
59 hestOptAdd(&hopt, "unmf", NULL, airTypeInt, 0, 0, &mfRed, NULL,
60 "apply and remove the measurement frame, if it exists");
61 hestOptAdd(&hopt, "ro", NULL, airTypeInt, 0, 0, &orientRed, NULL,
62 "reduce general image orientation to axis-aligned spacings");
63 hestOptAdd(&hopt, "roo", NULL, airTypeInt, 0, 0,
64 &orientRedWithOrigin, NULL,
65 "reduce general image orientation to axis-aligned spacings, "
66 "while also making some effort to set axis mins from "
67 "space origin");
68 hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
69 "input diffusion tensor volume, with 7 values per sample",
70 NULL, NULL, nrrdHestNrrd);
71 hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, NULL,
72 "output tensor volume, with the 9 matrix components per sample");
73
74 mop = airMopNew();
75 airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
76 USAGE(_tend_expandInfoL);
77 PARSE();
78 airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
79
80 nout = nrrdNew();
81 airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
82 if (mfRed
83 && 3 == nin->spaceDim
84 && AIR_EXISTS(nin->measurementFrame[0][0])) {
85 if (tenMeasurementFrameReduce(nin, nin)) {
86 airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
87 fprintf(stderr, "%s: trouble with measurement frame:\n%s\n", me, err);
88 airMopError(mop); return 1;
89 }
90 }
91 if (4 == nin->axis[0].size
92 ? tenExpand2D(nout, nin, scale, thresh)
93 : tenExpand(nout, nin, scale, thresh)) {
94 airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
95 fprintf(stderr, "%s: trouble expanding tensors:\n%s\n", me, err);
96 airMopError(mop); return 1;
97 }
98 if (orientRedWithOrigin || orientRed) {
99 if (nrrdOrientationReduce(nout, nout,
100 orientRedWithOrigin
101 ? AIR_TRUE
102 : AIR_FALSE)) {
103 airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
104 fprintf(stderr, "%s: trouble unorienting:\n%s\n", me, err);
105 airMopError(mop); return 1;
106 }
107 }
108
109 if (nrrdSave(outS, nout, NULL)) {
110 airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
111 fprintf(stderr, "%s: trouble writing:\n%s\n", me, err);
112 airMopError(mop); return 1;
113 }
114
115 airMopOkay(mop);
116 return 0;
117 }
118 TEND_CMD(expand, INFO);
119