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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 "ten.h" |
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#include "privateTen.h" |
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static int |
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_experAlloc(tenExperSpec* espec, unsigned int num) { |
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static char me[]="_experAlloc"; |
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airFree(espec->bval); espec->bval = NULL; |
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airFree(espec->grad); espec->grad = NULL; |
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/* espec->wght = airFree(espec->wght); */ |
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✗✓ |
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if (!num) { |
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biffAddf(TEN, "%s: need a non-zero number of images", me); |
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return 1; |
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} |
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espec->imgNum = num; |
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espec->bval = AIR_CALLOC(num, double); |
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espec->grad = AIR_CALLOC(3*num, double); |
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/* espec->wght = AIR_CALLOC(num, double); */ |
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✓✗✗✓
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if (!( espec->bval && espec->grad /* && espec->wght */ )) { |
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biffAddf(TEN, "%s: couldn't allocate for %u images", me, num); |
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return 1; |
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} |
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return 0; |
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} |
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tenExperSpec* |
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tenExperSpecNew(void) { |
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tenExperSpec* espec; |
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espec = AIR_CALLOC(1, tenExperSpec); |
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espec->set = AIR_FALSE; |
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espec->imgNum = 0; |
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espec->bval = NULL; |
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espec->grad = NULL; |
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/* espec->wght = NULL; */ |
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return espec; |
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} |
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int |
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tenExperSpecGradSingleBValSet(tenExperSpec *espec, |
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int insertB0, |
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double bval, |
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const double *grad, |
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unsigned int gradNum) { |
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static const char me[]="tenExperSpecGradSingleBValSet"; |
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unsigned int ii, imgNum, ei; |
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✗✓ |
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if (!espec) { |
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biffAddf(TEN, "%s: got NULL pointer", me); |
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return 1; |
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} |
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✗✓✗✗
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if (insertB0 && !ELL_3V_LEN(grad + 3*0)) { |
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biffAddf(TEN, "%s: wanted insertB0 but gradients " |
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"already start with (0,0,0)", me); |
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return 1; |
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} |
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imgNum = gradNum + !!insertB0; |
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✗✓ |
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if (_experAlloc(espec, imgNum)) { |
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biffAddf(TEN, "%s: couldn't allocate", me); |
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return 1; |
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} |
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✗✓ |
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if (insertB0) { |
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espec->bval[0] = 0; |
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ELL_3V_SET(espec->grad + 3*0, 1, 0, 0); |
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ei = 1; |
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} else { |
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ei = 0; |
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} |
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✓✓ |
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for (ii=0; ii<gradNum; ei++, ii++) { |
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espec->bval[ei] = bval; |
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ELL_3V_COPY(espec->grad + 3*ei, grad + 3*ii); |
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/* espec->wght[ii] = 1.0; */ |
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} |
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return 0; |
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} |
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int |
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tenExperSpecGradBValSet(tenExperSpec *espec, |
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int insertB0, |
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const double *bval, |
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const double *grad, |
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unsigned int bgNum) { |
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static const char me[]="tenExperSpecGradBValSet"; |
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unsigned int ii, imgNum, ei; |
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if (!espec) { |
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biffAddf(TEN, "%s: got NULL pointer", me); |
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return 1; |
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} |
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if (insertB0 && (!ELL_3V_LEN(grad + 3*0) || !bval[0])) { |
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biffAddf(TEN, "%s: wanted insertB0 but gradients " |
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"already start with (0,0,0) or bvals start with 0", me); |
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return 1; |
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} |
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imgNum = bgNum + !!insertB0; |
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if (_experAlloc(espec, imgNum)) { |
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biffAddf(TEN, "%s: couldn't allocate", me); |
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return 1; |
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} |
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if (insertB0) { |
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espec->bval[0] = 0; |
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ELL_3V_SET(espec->grad + 3*0, 0, 0, 0); |
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ei = 1; |
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} else { |
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ei = 0; |
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} |
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for (ii=0; ii<bgNum; ei++, ii++) { |
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espec->bval[ei] = bval[ii]; |
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ELL_3V_COPY(espec->grad + 3*ei, grad + 3*ii); |
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/* espec->wght[ii] = 1.0; */ |
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} |
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return 0; |
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} |
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/* |
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int |
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tenExperSpecGradBValWghtSet(tenExperSpec *espec, |
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unsigned int imgNum, |
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const double *bval, |
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const double *grad, |
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const double *wght) { |
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static const char me[]="tenExperSpecGradBValWghtSet"; |
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unsigned int ii; |
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if (!espec) { |
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biffAddf(TEN, "%s: got NULL pointer", me); |
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return 1; |
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} |
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if (_experAlloc(espec, imgNum)) { |
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biffAddf(TEN, "%s: couldn't allocate", me); |
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return 1; |
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} |
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for (ii=0; ii<imgNum; ii++) { |
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espec->bval[ii] = bval[ii]; |
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ELL_3V_COPY(espec->grad + 3*ii, grad + 3*ii); |
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espec->wght[ii] = wght[ii]; |
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} |
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return 0; |
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} |
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*/ |
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int |
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tenExperSpecFromKeyValueSet(tenExperSpec *espec, const Nrrd *ndwi) { |
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static const char me[]="tenExperSpecFromKeyValueSet"; |
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unsigned int *skip, skipNum, ii, imgNum, dwiax; |
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Nrrd *ngrad, *nbmat; |
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airArray *mop; |
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double len, singleBval, *bval, *grad; |
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for (dwiax=0; dwiax<ndwi->dim; dwiax++) { |
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if (nrrdKindList == ndwi->axis[dwiax].kind |
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|| nrrdKindVector == ndwi->axis[dwiax].kind) { |
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break; |
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} |
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} |
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if (ndwi->dim == dwiax) { |
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biffAddf(TEN, "%s: need dwis to have a kind %s or %s axis", me, |
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airEnumStr(nrrdKind, nrrdKindList), |
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airEnumStr(nrrdKind, nrrdKindVector)); |
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return 1; |
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} else { |
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if (0 != dwiax) { |
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biffAddf(TEN, "%s: need dwis (kind %s or %s) along axis 0, not %u", me, |
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airEnumStr(nrrdKind, nrrdKindList), |
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airEnumStr(nrrdKind, nrrdKindVector), dwiax); |
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return 1; |
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} |
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} |
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for (ii=dwiax+1; ii<ndwi->dim; ii++) { |
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if (nrrdKindList == ndwi->axis[ii].kind |
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|| nrrdKindVector == ndwi->axis[ii].kind) { |
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break; |
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} |
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} |
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if (ii < ndwi->dim) { |
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biffAddf(TEN, "%s: saw on %u another %s or %s kind axis, after 0", me, |
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ii, airEnumStr(nrrdKind, nrrdKindList), |
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airEnumStr(nrrdKind, nrrdKindVector)); |
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return 1; |
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} |
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if (tenDWMRIKeyValueParse(&ngrad, &nbmat, &singleBval, |
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&skip, &skipNum, ndwi)) { |
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biffAddf(TEN, "%s: trouble parsing DWI info from key/value pairs", me); |
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return 1; |
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} |
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mop = airMopNew(); |
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if (ngrad) { |
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airMopAdd(mop, ngrad, (airMopper)nrrdNuke, airMopAlways); |
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} |
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if (nbmat) { |
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airMopAdd(mop, nbmat, (airMopper)nrrdNuke, airMopAlways); |
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} |
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if (skip) { |
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airMopAdd(mop, skip, airFree, airMopAlways); |
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} |
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if (nbmat) { |
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biffAddf(TEN, "%s: sorry, currently can't handle B-matrices here", me); |
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airMopError(mop); return 1; |
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} |
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if (skipNum) { |
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biffAddf(TEN, "%s: sorry, currently can't handle skipping (%u) here", me, |
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skipNum); |
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airMopError(mop); return 1; |
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} |
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imgNum = ngrad->axis[1].size; |
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bval = AIR_CALLOC(imgNum, double); |
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airMopAdd(mop, bval, airFree, airMopAlways); |
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grad = AIR_CAST(double *, ngrad->data); |
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for (ii=0; ii<imgNum; ii++) { |
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len = ELL_3V_LEN(grad + 3*ii); |
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bval[ii] = singleBval*len*len; |
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if (len) { |
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ELL_3V_SCALE(grad + 3*ii, 1/len, grad + 3*ii); |
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} else { |
243 |
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ELL_3V_SET(grad + 3*ii, 0, 0, -1); |
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} |
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} |
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if (tenExperSpecGradBValSet(espec, AIR_FALSE, bval, grad, imgNum)) { |
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biffAddf(TEN, "%s: trouble", me); |
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airMopError(mop); return 1; |
249 |
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} |
250 |
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airMopOkay(mop); |
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return 0; |
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} |
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254 |
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tenExperSpec* |
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tenExperSpecNix(tenExperSpec *espec) { |
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257 |
✓✗ |
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if (espec) { |
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airFree(espec->bval); |
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airFree(espec->grad); |
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/* espec->wght = airFree(espec->wght); */ |
261 |
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airFree(espec); |
262 |
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} |
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return NULL; |
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} |
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double |
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_tenExperSpec_sqe(const double *dwiMeas, const double *dwiSim, |
268 |
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const tenExperSpec *espec, int knownB0) { |
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unsigned int ii; |
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double sqe; |
271 |
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272 |
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sqe = 0; |
273 |
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if (knownB0) { |
274 |
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for (ii=0; ii<espec->imgNum; ii++) { |
275 |
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double dd; |
276 |
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if (!espec->bval[ii]) { |
277 |
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continue; |
278 |
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} |
279 |
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dd = dwiMeas[ii] - dwiSim[ii]; |
280 |
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sqe += dd*dd; |
281 |
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/* |
282 |
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fprintf(stderr, "!%s: dwi[%u]: %g - %g -> %g\n", "_tenExperSpec_sqe", |
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ii, dwiMeas[ii], dwiSim[ii], sqe); |
284 |
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*/ |
285 |
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} |
286 |
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} else { |
287 |
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for (ii=0; ii<espec->imgNum; ii++) { |
288 |
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double dd; |
289 |
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dd = dwiMeas[ii] - dwiSim[ii]; |
290 |
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sqe += dd*dd; |
291 |
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} |
292 |
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} |
293 |
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return sqe; |
294 |
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} |
295 |
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296 |
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double |
297 |
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_tenExperSpec_nll(const double *dwiMeas, const double *dwiSim, |
298 |
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const tenExperSpec *espec, |
299 |
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int rician, double sigma, int knownB0) { |
300 |
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double nll; |
301 |
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unsigned int ii; |
302 |
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303 |
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nll = 0; |
304 |
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if (rician) { |
305 |
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for (ii=0; ii<espec->imgNum; ii++) { |
306 |
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if (knownB0 && !espec->bval[ii]) { |
307 |
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continue; |
308 |
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} |
309 |
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nll += -airLogRician(dwiMeas[ii], dwiSim[ii], sigma); |
310 |
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} |
311 |
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} else { |
312 |
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double dd, ladd, denom; |
313 |
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ladd = log(sigma*sqrt(2*AIR_PI)); |
314 |
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denom = 1.0/(2*sigma*sigma); |
315 |
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for (ii=0; ii<espec->imgNum; ii++) { |
316 |
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if (knownB0 && !espec->bval[ii]) { |
317 |
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continue; |
318 |
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} |
319 |
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dd = dwiMeas[ii] - dwiSim[ii]; |
320 |
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nll += dd*dd*denom + ladd; |
321 |
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} |
322 |
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} |
323 |
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return nll; |
324 |
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} |
325 |
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326 |
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int |
327 |
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tenDWMRIKeyValueFromExperSpecSet(Nrrd *ndwi, const tenExperSpec *espec) { |
328 |
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static char me[]="tenDWMRIKeyValueFromExperSpecSet"; |
329 |
|
16 |
char keystr[AIR_STRLEN_MED], valstr[AIR_STRLEN_MED]; |
330 |
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double maxb, bb; |
331 |
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unsigned int ii; |
332 |
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|
333 |
✗✓ |
8 |
if (!(ndwi && espec)) { |
334 |
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biffAddf(TEN, "%s: got NULL pointer", me); |
335 |
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return 1; |
336 |
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} |
337 |
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|
338 |
|
8 |
nrrdKeyValueAdd(ndwi, tenDWMRIModalityKey, tenDWMRIModalityVal); |
339 |
|
8 |
maxb = tenExperSpecMaxBGet(espec); |
340 |
|
8 |
sprintf(valstr, "%.17g", maxb); |
341 |
|
8 |
nrrdKeyValueAdd(ndwi, tenDWMRIBValueKey, valstr); |
342 |
✓✓ |
192 |
for (ii=0; ii<espec->imgNum; ii++) { |
343 |
|
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double vec[3]; |
344 |
|
88 |
sprintf(keystr, tenDWMRIGradKeyFmt, ii); |
345 |
|
88 |
ELL_3V_COPY(vec, espec->grad + 3*ii); |
346 |
|
88 |
bb = espec->bval[ii]; |
347 |
|
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/* Thu Dec 20 03:25:20 CST 2012 this rescaling is not, btw, |
348 |
|
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what is causing the small discrepency between ngrad before |
349 |
|
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and after saving to KVPs */ |
350 |
|
88 |
ELL_3V_SCALE(vec, sqrt(bb/maxb), vec); |
351 |
|
88 |
sprintf(valstr, "%.17g %.17g %.17g", vec[0], vec[1], vec[2]); |
352 |
|
88 |
nrrdKeyValueAdd(ndwi, keystr, valstr); |
353 |
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} |
354 |
|
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/* HEY what if its a full B-matrix? */ |
355 |
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|
356 |
|
8 |
return 0; |
357 |
|
8 |
} |
358 |
|
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|
359 |
|
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/* |
360 |
|
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** learns B0 from DWIs by simple averaging of all the dwi[ii] |
361 |
|
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** without any diffusion weighting, as indicated by espec->bval[ii], |
362 |
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** or, returns AIR_NAN when there are no such dwi[ii] |
363 |
|
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*/ |
364 |
|
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double |
365 |
|
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tenExperSpecKnownB0Get(const tenExperSpec *espec, const double *dwi) { |
366 |
|
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unsigned int ii, nb; |
367 |
|
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double ret, b0; |
368 |
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|
369 |
|
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if (!( dwi && espec )) { |
370 |
|
|
return AIR_NAN; |
371 |
|
|
} |
372 |
|
|
|
373 |
|
|
nb = 0; |
374 |
|
|
b0 = 0.0; |
375 |
|
|
for (ii=0; ii<espec->imgNum; ii++) { |
376 |
|
|
if (0 == espec->bval[ii]) { |
377 |
|
|
b0 += dwi[ii]; |
378 |
|
|
++nb; |
379 |
|
|
} |
380 |
|
|
} |
381 |
|
|
if (nb) { |
382 |
|
|
ret = b0/nb; |
383 |
|
|
} else { |
384 |
|
|
ret = AIR_NAN; |
385 |
|
|
} |
386 |
|
|
return ret; |
387 |
|
|
} |
388 |
|
|
|
389 |
|
|
double |
390 |
|
|
tenExperSpecMaxBGet(const tenExperSpec *espec) { |
391 |
|
|
unsigned int ii; |
392 |
|
|
double bval; |
393 |
|
|
|
394 |
✗✓ |
16 |
if (!( espec )) { |
395 |
|
|
return AIR_NAN; |
396 |
|
|
} |
397 |
|
|
|
398 |
|
|
bval = -1; |
399 |
✓✓ |
192 |
for (ii=0; ii<espec->imgNum; ii++) { |
400 |
✗✓ |
264 |
bval = AIR_MAX(bval, espec->bval[ii]); |
401 |
|
|
} |
402 |
|
8 |
return bval; |
403 |
|
8 |
} |