GCC Code Coverage Report
Directory: ./ Exec Total Coverage
File: src/ten/tendBfit.c Lines: 19 49 38.8 %
Date: 2017-05-26 Branches: 1 30 3.3 %

Line Branch Exec Source
1
/*
2
  Teem: Tools to process and visualize scientific data and images             .
3
  Copyright (C) 2013, 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 "Non-linear least-squares fitting of b-value curves"
28
static const char *_tend_bfitInfoL =
29
  (INFO
30
   ". Axis 0 is replaced by three values: amp, dec, err, based on a "
31
   "non-linear least-squares fit of amp*exp(-b*dec) to the range of DWI "
32
   "values along input axis 0, as a function of changing b values.  ");
33
34
int
35
tend_bfitMain(int argc, const char **argv, const char *me,
36
              hestParm *hparm) {
37
  int pret;
38
2
  hestOpt *hopt = NULL;
39
1
  char *perr, *err;
40
  airArray *mop;
41
42
1
  Nrrd *nin, *nout;
43
1
  double *bb, *ww, *_ww, eps;
44
1
  unsigned int ii, bbLen, _wwLen;
45
1
  int iterMax;
46
1
  char *outS;
47
48
1
  hparm->respFileEnable = AIR_TRUE;
49
50
1
  hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
51
             "Input nrrd.  List of DWIs from different b-values must "
52
1
             "be along axis 0", NULL, NULL, nrrdHestNrrd);
53
1
  hestOptAdd(&hopt, "b", "b1 b2", airTypeDouble, 2, -1, &bb, NULL,
54
             "b values across axis 0 of input nrrd", &bbLen);
55
1
  hestOptAdd(&hopt, "w", "w1 w2", airTypeDouble, 2, -1, &_ww, "nan nan",
56
             "weights for samples in non-linear fitting", &_wwLen);
57
1
  hestOptAdd(&hopt, "imax", "# iter", airTypeInt, 1, 1, &iterMax, "10",
58
             "max number of iterations to use in non-linear fitting, or, "
59
             "use 0 to do only initial linear fit");
60
1
  hestOptAdd(&hopt, "eps", "epsilon", airTypeDouble, 1, 1, &eps, "1",
61
             "epsilon convergence threshold for non-linear fitting");
62
1
  hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
63
             "output tensor volume");
64
65
1
  mop = airMopNew();
66
1
  airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
67
2
  USAGE(_tend_bfitInfoL);
68
  PARSE();
69
  airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
70
71
  if (!( bbLen == nin->axis[0].size )) {
72
    char stmp[AIR_STRLEN_SMALL];
73
    fprintf(stderr, "%s: got %d b-values but axis 0 size is %s\n", me,
74
            bbLen, airSprintSize_t(stmp, nin->axis[0].size));
75
    airMopError(mop); return 1;
76
  }
77
  if (AIR_EXISTS(_ww[0])) {
78
    if (!( _wwLen == nin->axis[0].size )) {
79
      char stmp[AIR_STRLEN_SMALL];
80
      fprintf(stderr, "%s: got %d weights but axis 0 size is %s\n", me,
81
              _wwLen, airSprintSize_t(stmp, nin->axis[0].size));
82
      airMopError(mop); return 1;
83
    }
84
    ww = _ww;
85
  } else {
86
    /* no explicit weights specified */
87
    ww = (double*)calloc(nin->axis[0].size, sizeof(double));
88
    airMopAdd(mop, ww, airFree, airMopAlways);
89
    for (ii=0; ii<nin->axis[0].size; ii++) {
90
      ww[ii] = 1.0;
91
    }
92
  }
93
94
  nout = nrrdNew();
95
  airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
96
97
  if (tenBVecNonLinearFit(nout, nin, bb, ww, iterMax, eps)) {
98
    airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
99
    fprintf(stderr, "%s: trouble:\n%s\n", me, err);
100
    airMopError(mop); return 1;
101
  }
102
103
  if (nrrdSave(outS, nout, NULL)) {
104
    airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
105
    fprintf(stderr, "%s: trouble writing:\n%s\n", me, err);
106
    airMopError(mop); return 1;
107
  }
108
109
  airMopOkay(mop);
110
  return 0;
111
1
}
112
TEND_CMD(bfit, INFO);