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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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#define INFO "Converts masked non-redundant tensor images to redundant" |
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static const char *_tend_expandInfoL = |
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(INFO |
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". For images of 3D tensors, this converts from a 7-value tensor " |
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"starting with the confidence/mask value " |
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"(conf, Dxx, Dxy, Dxz, Dyy, Dyz, Dzz) to " |
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"a 9-value tensor with the full matrix " |
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"(Dxx, Dxy, Dxz, Dxy, Dyy, Dyz, Dxz, Dyz, Dzz). " |
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"This is set to all zeros when the confidence is below the given " |
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"threshold. For images of 2D tensors, the conversion is from " |
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"(conf, Dxx, Dxy, Dyy) to (Dxx, Dxy, Dxy, Dyy). " ); |
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int |
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tend_expandMain(int argc, const char **argv, const char *me, |
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hestParm *hparm) { |
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int pret; |
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hestOpt *hopt = NULL; |
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char *perr, *err; |
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airArray *mop; |
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Nrrd *nin, *nout; |
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char *outS; |
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int orientRed, orientRedWithOrigin, mfRed; |
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float scale, thresh; |
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hestOptAdd(&hopt, "t", "thresh", airTypeFloat, 1, 1, &thresh, "0.5", |
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"confidence level to threshold output tensors at. Should " |
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"be between 0.0 and 1.0."); |
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hestOptAdd(&hopt, "s", "scale", airTypeFloat, 1, 1, &scale, "1.0", |
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"how to scale values before saving as 9-value tensor. Useful " |
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"for visualization tools which assume certain characteristic " |
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"ranges of eigenvalues"); |
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hestOptAdd(&hopt, "unmf", NULL, airTypeInt, 0, 0, &mfRed, NULL, |
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"apply and remove the measurement frame, if it exists"); |
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hestOptAdd(&hopt, "ro", NULL, airTypeInt, 0, 0, &orientRed, NULL, |
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"reduce general image orientation to axis-aligned spacings"); |
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hestOptAdd(&hopt, "roo", NULL, airTypeInt, 0, 0, |
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&orientRedWithOrigin, NULL, |
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"reduce general image orientation to axis-aligned spacings, " |
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"while also making some effort to set axis mins from " |
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"space origin"); |
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hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-", |
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"input diffusion tensor volume, with 7 values per sample", |
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NULL, NULL, nrrdHestNrrd); |
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hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, NULL, |
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"output tensor volume, with the 9 matrix components per sample"); |
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mop = airMopNew(); |
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airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways); |
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✓✗ |
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USAGE(_tend_expandInfoL); |
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PARSE(); |
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airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways); |
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nout = nrrdNew(); |
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airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways); |
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if (mfRed |
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&& 3 == nin->spaceDim |
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&& AIR_EXISTS(nin->measurementFrame[0][0])) { |
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if (tenMeasurementFrameReduce(nin, nin)) { |
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airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways); |
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fprintf(stderr, "%s: trouble with measurement frame:\n%s\n", me, err); |
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airMopError(mop); return 1; |
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} |
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} |
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if (4 == nin->axis[0].size |
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? tenExpand2D(nout, nin, scale, thresh) |
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: tenExpand(nout, nin, scale, thresh)) { |
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airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways); |
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fprintf(stderr, "%s: trouble expanding tensors:\n%s\n", me, err); |
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airMopError(mop); return 1; |
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} |
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if (orientRedWithOrigin || orientRed) { |
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if (nrrdOrientationReduce(nout, nout, |
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orientRedWithOrigin |
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? AIR_TRUE |
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: AIR_FALSE)) { |
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airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways); |
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fprintf(stderr, "%s: trouble unorienting:\n%s\n", me, err); |
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airMopError(mop); return 1; |
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} |
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} |
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if (nrrdSave(outS, nout, NULL)) { |
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airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways); |
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fprintf(stderr, "%s: trouble writing:\n%s\n", me, err); |
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airMopError(mop); return 1; |
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} |
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airMopOkay(mop); |
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return 0; |
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} |
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TEND_CMD(expand, INFO); |