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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 "unrrdu.h" |
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#include "privateUnrrdu.h" |
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#define INFO " Automatically crop axes based on given measure" |
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static const char *_unrrdu_acropInfoL = |
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(INFO ". For the axes that are to be cropped, the slices perpendicular " |
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"to that axis are projected down to a scalar with the specified measure. " |
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"The resulting 1D array is analyzed by determining what portions at the " |
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"beginning and end constitute less than some portion of the cumulative " |
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"array sum; these ends are cropped off. The cropping bounds determined " |
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"here can be saved and applied to other arrays via the \"-b\" option.\n " |
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"* Uses nrrdCropAuto"); |
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int |
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unrrdu_acropMain(int argc, const char **argv, const char *me, |
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hestParm *hparm) { |
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hestOpt *opt = NULL; |
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char *out, *err; |
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Nrrd *nin, *nout; |
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int pret; |
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airArray *mop; |
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size_t min[NRRD_DIM_MAX], max[NRRD_DIM_MAX]; |
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unsigned int *axes, axesLen; |
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double frac; |
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int measr, offset; |
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Nrrd *nbounds; |
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char *boundsSave; |
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hestOptAdd(&opt, "a,axes", "ax0", airTypeUInt, 0, -1, &axes, "", |
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"the axes (if any) that should NOT be cropped", &axesLen); |
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hestOptAdd(&opt, "m,measure", "measr", airTypeEnum, 1, 1, &measr, NULL, |
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"How to measure slices (along axes to crop) as scalars, " |
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"to form 1-D array analyzed to determine cropping extent. " |
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"All the measures from \"unu project\" can be used, but " |
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"those that make more sense here include:\n " |
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"\b\bo \"max\", \"mean\", \"median\", " |
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"\"variance\": (self-explanatory)\n " |
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"\b\bo \"stdv\": standard deviation\n " |
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"\b\bo \"cov\": coefficient of variation\n " |
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"\b\bo \"product\", \"sum\": product or sum of all values\n " |
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"\b\bo \"L1\", \"L2\", \"NL2\", \"RMS\", \"Linf\": " |
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"different norms.", NULL, nrrdMeasure); |
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hestOptAdd(&opt, "f,frac", "frac", airTypeDouble, 1, 1, &frac, "0.1", |
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"threshold of cumulative sum of 1-D array at which to crop. " |
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"Needs to be in interval [0.0,0.5)."); |
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hestOptAdd(&opt, "off,offset", "offset", airTypeInt, 1, 1, &offset, "1", |
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"how much to offset the numerically determined cropping; " |
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"positive offsets means expanding the interval of kept " |
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"indices (less cropping)"); |
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hestOptAdd(&opt, "b,bounds", "filename", airTypeString, 1, 1, |
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&boundsSave, "", |
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"if a filename is given here, the automatically determined " |
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"min and max bounds for cropping are saved to this file " |
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"as a 2-D array; first scanline is for -min, second is for -max. " |
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"Unfortunately nothing using the \"m\" and \"M\" semantics " |
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"(above) can currently be saved in the bounds file."); |
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OPT_ADD_NIN(nin, "input nrrd"); |
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OPT_ADD_NOUT(out, "output nrrd"); |
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mop = airMopNew(); |
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airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways); |
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✓✗ |
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USAGE(_unrrdu_acropInfoL); |
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PARSE(); |
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airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways); |
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nout = nrrdNew(); |
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airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways); |
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if (nrrdCropAuto(nout, nin, min, max, |
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axes, axesLen, |
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measr, frac, offset)) { |
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airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways); |
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fprintf(stderr, "%s: error cropping nrrd:\n%s", me, err); |
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airMopError(mop); |
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return 1; |
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} |
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if (airStrlen(boundsSave)) { |
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unsigned int axi; |
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airULLong *bounds; |
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nbounds = nrrdNew(); |
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airMopAdd(mop, nbounds, (airMopper)nrrdNuke, airMopAlways); |
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if (nrrdMaybeAlloc_va(nbounds, nrrdTypeULLong, 2, |
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AIR_CAST(airULLong, nin->dim), |
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AIR_CAST(airULLong, 2))) { |
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airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways); |
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fprintf(stderr, "%s: error allocating cropping bounds array:\n%s", |
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me, err); |
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airMopError(mop); |
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return 1; |
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} |
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bounds = AIR_CAST(airULLong*, nbounds->data); |
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for (axi=0; axi<nin->dim; axi++) { |
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bounds[axi + 0*(nin->dim)] = AIR_CAST(airULLong, min[axi]); |
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bounds[axi + 1*(nin->dim)] = AIR_CAST(airULLong, max[axi]); |
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} |
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if (nrrdSave(boundsSave, nbounds, NULL)) { |
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airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways); |
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fprintf(stderr, "%s: error saving cropping bounds array:\n%s", |
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me, err); |
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airMopError(mop); |
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return 1; |
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} |
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} |
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SAVE(out, nout, NULL); |
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airMopOkay(mop); |
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return 0; |
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} |
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UNRRDU_CMD(acrop, INFO); |