[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // ReadAndSearch.cc: Combining both the FITS reading and the searching. |
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| 3 | // ----------------------------------------------------------------------- |
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| 4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
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| 5 | // |
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| 6 | // This program is free software; you can redistribute it and/or modify it |
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| 7 | // under the terms of the GNU General Public License as published by the |
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| 8 | // Free Software Foundation; either version 2 of the License, or (at your |
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| 9 | // option) any later version. |
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| 10 | // |
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| 11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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| 12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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| 14 | // for more details. |
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| 15 | // |
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| 16 | // You should have received a copy of the GNU General Public License |
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| 17 | // along with Duchamp; if not, write to the Free Software Foundation, |
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| 18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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| 19 | // |
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| 20 | // Correspondence concerning Duchamp may be directed to: |
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| 21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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| 22 | // Postal address: Dr. Matthew Whiting |
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| 23 | // Australia Telescope National Facility, CSIRO |
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| 24 | // PO Box 76 |
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| 25 | // Epping NSW 1710 |
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| 26 | // AUSTRALIA |
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| 27 | // ----------------------------------------------------------------------- |
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[137] | 28 | #include <iostream> |
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| 29 | #include <iomanip> |
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| 30 | #include <string> |
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[394] | 31 | #include <wcslib/wcs.h> |
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| 32 | #include <wcslib/wcshdr.h> |
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[400] | 33 | #include <wcslib/fitshdr.h> |
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[394] | 34 | #include <wcslib/wcsfix.h> |
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| 35 | #include <wcslib/wcsunits.h> |
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[299] | 36 | #define WCSLIB_GETWCSTAB // define this so that we don't try and |
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| 37 | // redefine wtbarr (this is a problem when |
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| 38 | // using gcc v.4+ |
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[137] | 39 | #include <fitsio.h> |
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| 40 | #include <math.h> |
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[393] | 41 | #include <duchamp/duchamp.hh> |
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| 42 | #include <duchamp/param.hh> |
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| 43 | #include <duchamp/Cubes/cubes.hh> |
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| 44 | #include <duchamp/Detection/detection.hh> |
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| 45 | #include <duchamp/ATrous/atrous.hh> |
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| 46 | #include <duchamp/Utils/utils.hh> |
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[137] | 47 | |
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[232] | 48 | std::string imageType[4] = {"point", "spectrum", "image", "cube"}; |
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[137] | 49 | |
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| 50 | vector<Detection> readAndSearch(Param &par) |
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| 51 | { |
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| 52 | vector<Detection> outputList; |
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| 53 | |
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| 54 | short int maxdim=3; |
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| 55 | long *dimAxes = new long[maxdim]; |
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| 56 | for(int i=0;i<maxdim;i++) dimAxes[i]=1; |
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| 57 | long nelements; |
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| 58 | int bitpix,numAxes; |
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| 59 | int status = 0, nkeys; /* MUST initialize status */ |
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| 60 | fitsfile *fptr; |
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| 61 | |
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[232] | 62 | std::string fname = par.getImageFile(); |
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[137] | 63 | if(par.getFlagSubsection()){ |
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| 64 | par.parseSubsection(); |
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| 65 | fname+=par.getSubsection(); |
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| 66 | } |
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| 67 | |
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| 68 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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| 69 | fits_report_error(stderr, status); |
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| 70 | } |
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| 71 | |
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| 72 | status = 0; |
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| 73 | fits_get_img_param(fptr, maxdim, &bitpix, &numAxes, dimAxes, &status); |
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| 74 | if(status){ |
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| 75 | fits_report_error(stderr, status); |
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| 76 | } |
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| 77 | status = 0; |
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| 78 | fits_close_file(fptr, &status); |
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| 79 | if (status){ |
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| 80 | duchampWarning("readAndSearch","Error closing file: "); |
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| 81 | fits_report_error(stderr, status); |
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| 82 | } |
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| 83 | |
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| 84 | if(numAxes<=3) |
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| 85 | std::cout << "Dimensions of " << imageType[numAxes] << ": " << dimAxes[0]; |
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| 86 | else std::cout << "Dimensions of " << imageType[3] << ": " << dimAxes[0]; |
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| 87 | if(numAxes>1) std::cout << "x" << dimAxes[1]; |
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| 88 | if(numAxes>2) std::cout << "x" << dimAxes[2]; |
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| 89 | std::cout << std::endl; |
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| 90 | |
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| 91 | int anynul; |
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| 92 | long *fpixel = new long[numAxes]; |
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| 93 | long *lpixel = new long[numAxes]; |
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[160] | 94 | long *inc = new long[numAxes]; // the data-sampling increment |
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[137] | 95 | for(int i=0;i<numAxes;i++) inc[i]=1; |
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| 96 | |
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| 97 | //--------------------------------------------------------- |
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| 98 | // Read in spectra one at a time, reconstruct if necessary |
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| 99 | // and then search, adding found objects to cube's object list. |
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| 100 | |
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| 101 | fpixel[0] = 1; |
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| 102 | for(int i=2;i<numAxes;i++) fpixel[i] = 1; |
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| 103 | |
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| 104 | lpixel[0] = dimAxes[0]; |
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| 105 | lpixel[2] = dimAxes[2]; |
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| 106 | for(int i=3;i<numAxes;i++) lpixel[i] = 1; |
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| 107 | |
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| 108 | int numDetected = 0; |
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| 109 | |
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| 110 | std::cout << " 0: |"; |
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[175] | 111 | printSpace(50); |
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[137] | 112 | std::cout << "| " << std::setw(5) << numDetected << std::flush; |
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[175] | 113 | printBackSpace(64); |
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| 114 | std::cout << std::flush; |
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[137] | 115 | |
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| 116 | float *bigarray = new float[dimAxes[0] * dimAxes[2]]; |
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| 117 | float *array = new float[dimAxes[2]]; |
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| 118 | long *specdim = new long[2]; |
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| 119 | specdim[0] = dimAxes[2]; specdim[1]=1; |
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| 120 | |
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| 121 | float median,sigma; |
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| 122 | int pos,frac; |
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| 123 | |
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| 124 | Image *spectrum = new Image(specdim); |
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| 125 | spectrum->saveParam(par); |
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| 126 | spectrum->pars().setBeamSize(2.); // only neighbouring channels correlated |
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| 127 | |
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| 128 | for(int y=0;y<dimAxes[1];y++){ |
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| 129 | |
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| 130 | std::cout << std::setw(4) << y << ": " << std::flush; |
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| 131 | |
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| 132 | fpixel[1] = lpixel[1] = y+1; |
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| 133 | |
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| 134 | status = 0; |
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| 135 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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| 136 | duchampWarning("readAndSearch","Error opening file: "); |
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| 137 | fits_report_error(stderr, status); |
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| 138 | } |
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| 139 | status = 0; |
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| 140 | fits_read_subset(fptr, TFLOAT, fpixel, lpixel, inc, NULL, bigarray, &anynul, &status); |
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| 141 | if(status){ |
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| 142 | duchampError("readAndSearch","There was an error reading in the data array:"); |
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| 143 | fits_report_error(stderr, status); |
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| 144 | } |
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| 145 | status = 0; |
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| 146 | fits_close_file(fptr, &status); |
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| 147 | if (status){ |
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| 148 | duchampWarning("readAndSearch","Error closing file: "); |
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| 149 | fits_report_error(stderr, status); |
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| 150 | } |
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| 151 | |
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| 152 | for(int x=0;x<dimAxes[0];x++){ |
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| 153 | |
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| 154 | pos = y*dimAxes[0]+x; |
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| 155 | frac = 100*(pos+1)/(dimAxes[1]*dimAxes[0]); |
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| 156 | if(frac%2 == 0){ |
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| 157 | std::cout << "|"; |
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[175] | 158 | printHash(frac/2); |
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| 159 | printSpace(50-frac/2); |
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[137] | 160 | std::cout << "| " << std::setw(5) << numDetected; |
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[175] | 161 | printBackSpace(58); |
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[137] | 162 | std::cout << std::flush; |
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| 163 | } |
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| 164 | |
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| 165 | for(int z=0;z<dimAxes[2];z++) array[z] = bigarray[z*dimAxes[0] + x]; |
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| 166 | |
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| 167 | median = findMedian(array,dimAxes[2]); |
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| 168 | spectrum->clearDetectionList(); |
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| 169 | if(par.getFlagATrous()){ |
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| 170 | float *recon = new float[dimAxes[2]]; |
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| 171 | atrous1DReconstruct(dimAxes[2],array,recon,par); |
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| 172 | float *resid = new float[dimAxes[2]]; |
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| 173 | for(int i=0;i<dimAxes[2];i++) resid[i] = array[i] - recon[i]; |
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| 174 | sigma = findMADFM(recon,dimAxes[2])/correctionFactor; |
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| 175 | spectrum->saveArray(recon,dimAxes[2]); |
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[205] | 176 | delete [] recon; |
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| 177 | delete [] resid; |
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[137] | 178 | spectrum->removeMW(); // only works if flagMW is true |
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| 179 | spectrum->setStats(median,sigma,par.getCut()); |
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| 180 | if(par.getFlagFDR()) spectrum->setupFDR(); |
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| 181 | spectrum->setMinSize(par.getMinChannels()); |
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[582] | 182 | spectrum->findSources1D(); |
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[137] | 183 | } |
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| 184 | else{ |
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| 185 | sigma = findMADFM(array,dimAxes[2])/correctionFactor; |
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| 186 | spectrum->saveArray(array,dimAxes[2]); |
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| 187 | spectrum->removeMW(); // only works if flagMW is true |
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| 188 | spectrum->setStats(median,sigma,par.getCut()); |
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| 189 | if(par.getFlagFDR()) spectrum->setupFDR(); |
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| 190 | spectrum->setMinSize(par.getMinChannels()); |
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[582] | 191 | spectrum->findSources1D(); |
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[137] | 192 | } |
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| 193 | |
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| 194 | numDetected += spectrum->getNumObj(); |
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| 195 | for(int obj=0;obj<spectrum->getNumObj();obj++){ |
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| 196 | Detection *object = new Detection; |
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| 197 | *object = spectrum->getObject(obj); |
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| 198 | for(int pix=0;pix<object->getSize();pix++) { |
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| 199 | // Fix up coordinates of each pixel to match original array |
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| 200 | object->setZ(pix, object->getX(pix)); |
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| 201 | object->setX(pix, x); |
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| 202 | object->setY(pix, y); |
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| 203 | object->setF(pix, array[object->getZ(pix)]); |
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| 204 | // NB: set F to the original value, not the recon value. |
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| 205 | } |
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[221] | 206 | object->setOffsets(par); |
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[137] | 207 | object->calcParams(); |
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| 208 | mergeIntoList(*object,outputList,par); |
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| 209 | delete object; |
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| 210 | } |
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| 211 | |
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| 212 | |
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| 213 | } // end of loop over y |
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| 214 | |
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[175] | 215 | printBackSpace(6); |
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| 216 | std::cout << std::flush; |
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[137] | 217 | } // end of loop over x |
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| 218 | |
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| 219 | delete spectrum; |
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[205] | 220 | delete [] bigarray; |
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| 221 | delete [] array; |
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| 222 | delete [] fpixel; |
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| 223 | delete [] lpixel; |
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| 224 | delete [] inc; |
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| 225 | delete [] dimAxes; |
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| 226 | delete [] specdim; |
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[137] | 227 | |
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| 228 | return outputList; |
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| 229 | |
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| 230 | } |
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