[463] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // spectraUtils.cc: Utility functions to obtain & manipulate spectra |
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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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| 28 | #include <iostream> |
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| 29 | #include <fstream> |
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| 30 | #include <iomanip> |
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| 31 | #include <sstream> |
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| 32 | #include <string> |
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[748] | 33 | #include <vector> |
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[463] | 34 | #include <math.h> |
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| 35 | #include <wcslib/wcs.h> |
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| 36 | #include <duchamp/Cubes/cubeUtils.hh> |
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| 37 | #include <duchamp/param.hh> |
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| 38 | #include <duchamp/duchamp.hh> |
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| 39 | #include <duchamp/fitsHeader.hh> |
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| 40 | #include <duchamp/PixelMap/Object3D.hh> |
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| 41 | #include <duchamp/Cubes/cubes.hh> |
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| 42 | #include <duchamp/Utils/utils.hh> |
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| 43 | |
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| 44 | using namespace PixelInfo; |
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| 45 | |
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| 46 | namespace duchamp |
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| 47 | { |
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| 48 | |
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[884] | 49 | void getSpecAbscissae(Detection &object, FitsHeader &head, size_t zdim, float *abscissae) |
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[463] | 50 | { |
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[528] | 51 | /// @details |
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| 52 | /// A function that returns an array of |
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| 53 | /// frequency/velocity/channel/etc values (that can be used as the |
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| 54 | /// abscissae on the spectral plot). |
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| 55 | /// \param object The object on which our spectrum is centered (in |
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| 56 | /// case the spectral value changes with x & y |
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| 57 | /// \param head The FitsHeader set of parameters that determine the coordinate transformation. |
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| 58 | /// \param zdim The length of the spectral axis |
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| 59 | /// \param abscissae The array of spectral values -- must be allocated first |
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| 60 | |
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[463] | 61 | getSpecAbscissae(head,object.getXcentre(),object.getYcentre(),zdim, abscissae); |
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| 62 | } |
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| 63 | |
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[884] | 64 | void getSpecAbscissae(FitsHeader &head, float xpt, float ypt, size_t zdim, float *abscissae) |
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[463] | 65 | { |
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[528] | 66 | /// @details |
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| 67 | /// A function that returns an array of |
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| 68 | /// frequency/velocity/channel/etc values (that can be used as the |
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| 69 | /// horizontal axis on the spectral plot). |
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| 70 | /// \param head The FitsHeader set of parameters that determine the coordinate transformation. |
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| 71 | /// \param xpt The x-value of the spatial position on which our spectrum is centred. |
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| 72 | /// \param ypt The y-value of the spatial position on which our spectrum is centred. |
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| 73 | /// \param zdim The length of the spectral axis |
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| 74 | /// \param abscissae The array of spectral values -- must be allocated first. |
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[463] | 75 | |
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| 76 | if(head.isWCS()){ |
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| 77 | double xval = double(xpt); |
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| 78 | double yval = double(ypt); |
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| 79 | for(double zval=0;zval<zdim;zval++) |
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| 80 | abscissae[int(zval)] = head.pixToVel(xval,yval,zval); |
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| 81 | } |
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| 82 | else |
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| 83 | for(double zval=0;zval<zdim;zval++) abscissae[int(zval)] = zval; |
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| 84 | |
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| 85 | } |
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| 86 | //-------------------------------------------------------------------- |
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| 87 | |
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[1393] | 88 | void getIntSpec(Detection &object, float *fluxArray, size_t *dimArray, std::vector<bool> mask, |
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[463] | 89 | float beamCorrection, float *spec) |
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| 90 | { |
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[528] | 91 | /// @details |
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| 92 | /// The base function that extracts an integrated spectrum for a |
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| 93 | /// given object from a pixel array. The spectrum is returned as |
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| 94 | /// the integrated flux, corrected for the beam using the given |
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| 95 | /// correction factor. |
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| 96 | /// \param object The Detection in question |
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| 97 | /// \param fluxArray The full array of pixel values. |
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| 98 | /// \param dimArray The axis dimensions for the fluxArray |
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| 99 | /// \param mask A mask array indicating whether given pixels are valid |
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| 100 | /// \param beamCorrection How much to divide the summed spectrum |
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| 101 | /// by to return the integrated flux. |
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| 102 | /// \param spec The integrated spectrum for the object -- must be allocated first. |
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[463] | 103 | |
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[894] | 104 | for(size_t i=0;i<dimArray[2];i++) spec[i] = 0.; |
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[884] | 105 | size_t xySize = dimArray[0]*dimArray[1]; |
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[1393] | 106 | std::vector<bool> done(xySize,false); |
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[570] | 107 | std::vector<Voxel> voxlist = object.getPixelSet(); |
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[623] | 108 | std::vector<Voxel>::iterator vox; |
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| 109 | for(vox=voxlist.begin();vox<voxlist.end();vox++){ |
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[894] | 110 | size_t pos = vox->getX() + dimArray[0] * vox->getY(); |
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[463] | 111 | if(!done[pos]){ |
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| 112 | done[pos] = true; |
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[894] | 113 | for(size_t z=0;z<dimArray[2];z++){ |
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[463] | 114 | if(mask[pos+z*xySize]){ |
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| 115 | spec[z] += fluxArray[pos + z*xySize] / beamCorrection; |
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| 116 | } |
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| 117 | } |
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| 118 | } |
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| 119 | } |
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| 120 | |
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| 121 | } |
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| 122 | //-------------------------------------------------------------------- |
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| 123 | |
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[1393] | 124 | void getPeakSpec(Detection &object, float *fluxArray, size_t *dimArray, std::vector<bool> mask, float *spec) |
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[463] | 125 | { |
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[528] | 126 | /// @details |
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| 127 | /// The base function that extracts an peak spectrum for a |
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| 128 | /// given object from a pixel array. The spectrum is returned as |
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| 129 | /// the integrated flux, corrected for the beam using the given |
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| 130 | /// correction factor. |
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| 131 | /// \param object The Detection in question |
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| 132 | /// \param fluxArray The full array of pixel values. |
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| 133 | /// \param dimArray The axis dimensions for the fluxArray |
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| 134 | /// \param mask A mask array indicating whether given pixels are valid |
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| 135 | /// \param spec The peak spectrum for the object -- must be allocated first |
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[463] | 136 | |
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[935] | 137 | if((object.getXPeak()<0 || object.getXPeak()>=int(dimArray[0])) || (object.getYPeak()<0 || object.getYPeak()>=int(dimArray[1]))){ |
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[921] | 138 | DUCHAMPWARN("getPeakSpec","Object peak outside array boundaries"); |
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| 139 | for (size_t z=0;z<dimArray[2];z++) spec[z]=0.; |
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[463] | 140 | } |
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[921] | 141 | else{ |
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| 142 | size_t xySize = dimArray[0]*dimArray[1]; |
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| 143 | size_t pos = object.getXPeak() + dimArray[0]*object.getYPeak(); |
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| 144 | for(size_t z=0;z<dimArray[2];z++){ |
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| 145 | if(mask[pos + z*xySize]) |
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| 146 | spec[z] = fluxArray[pos + z*xySize]; |
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| 147 | } |
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| 148 | } |
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[463] | 149 | } |
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| 150 | //-------------------------------------------------------------------- |
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| 151 | |
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| 152 | |
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| 153 | void Cube::getSpectralArrays(int objNum, float *specx, float *specy, |
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| 154 | float *specRecon, float *specBase) |
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| 155 | { |
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[528] | 156 | /// @details |
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| 157 | /// A utility function that goes and calculates, for a given |
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| 158 | /// Detection, the spectral arrays, according to whether we want |
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| 159 | /// the peak or integrated flux. The arrays can be used by |
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| 160 | /// Cube::plotSpectrum() and Cube::writeSpectralData(). The arrays |
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| 161 | /// calculated are listed below. Their length is given by the |
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| 162 | /// length of the Cube's spectral dimension. |
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| 163 | /// |
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| 164 | /// Note that the arrays need to be allocated prior to calling |
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| 165 | /// this function. |
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| 166 | /// |
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[985] | 167 | /// \param objNum The number of the object under |
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| 168 | /// consideration. If negative, we extract the single |
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| 169 | /// spectrum at (x,y)=(0,0) (useful for the 1D case). |
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[528] | 170 | /// \param specx The array of frequency/velocity/channel/etc |
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| 171 | /// values (the x-axis on the spectral plot). |
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| 172 | /// \param specy The array of flux values, matching the specx |
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| 173 | /// array. |
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| 174 | /// \param specRecon The reconstructed or smoothed array, done in |
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| 175 | /// the same way as specy. |
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| 176 | /// \param specBase The fitted baseline values, done in the same |
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| 177 | /// way as specy. |
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[463] | 178 | |
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[884] | 179 | size_t xdim = this->axisDim[0]; |
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| 180 | size_t ydim = this->axisDim[1]; |
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| 181 | size_t zdim = this->axisDim[2]; |
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[463] | 182 | |
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[935] | 183 | for(size_t i=0;i<zdim;i++){ |
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[894] | 184 | specy[i] = 0.; |
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| 185 | specRecon[i] = 0.; |
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| 186 | specBase[i] = 0.; |
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| 187 | } |
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| 188 | |
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[985] | 189 | double xloc,yloc; |
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| 190 | size_t spatpos=0; |
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| 191 | std::vector<Voxel> voxlist; |
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| 192 | if(objNum>=0){ |
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| 193 | if(this->par.getSpectralMethod()=="sum"){ |
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| 194 | xloc=double(this->objectList->at(objNum).getXcentre()); |
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| 195 | yloc=double(this->objectList->at(objNum).getYcentre()); |
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| 196 | voxlist = this->objectList->at(objNum).getPixelSet(); |
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| 197 | } |
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| 198 | else{ |
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| 199 | spatpos = this->objectList->at(objNum).getXPeak() + |
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| 200 | xdim*this->objectList->at(objNum).getYPeak(); |
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[1431] | 201 | xloc = spatpos % xdim; |
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| 202 | yloc = spatpos / xdim; |
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[985] | 203 | } |
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| 204 | } |
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| 205 | |
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[463] | 206 | if(this->head.isWCS()){ |
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| 207 | for(double zval=0;zval<zdim;zval++) |
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[985] | 208 | specx[int(zval)] = this->head.pixToVel(xloc,yloc,zval); |
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[463] | 209 | } |
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[1431] | 210 | else { |
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[463] | 211 | for(double zval=0;zval<zdim;zval++) specx[int(zval)] = zval; |
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[1431] | 212 | } |
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[463] | 213 | |
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| 214 | float beamCorrection; |
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| 215 | if(this->header().needBeamSize()) |
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[788] | 216 | beamCorrection = this->head.beam().area(); |
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[463] | 217 | else beamCorrection = 1.; |
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| 218 | |
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[985] | 219 | if(objNum>=0 && this->par.getSpectralMethod()=="sum"){ |
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[1393] | 220 | std::vector<bool> done(xdim*ydim,false); |
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[623] | 221 | std::vector<Voxel>::iterator vox; |
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| 222 | for(vox=voxlist.begin();vox<voxlist.end();vox++){ |
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[985] | 223 | spatpos = vox->getX() + xdim * vox->getY(); |
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| 224 | if(!done[spatpos]){ |
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| 225 | done[spatpos] = true; |
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[894] | 226 | for(size_t z=0;z<zdim;z++){ |
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[985] | 227 | if(!(this->isBlank(spatpos+z*xdim*ydim))){ |
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| 228 | specy[z] += this->array[spatpos + z*xdim*ydim] / beamCorrection; |
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[463] | 229 | if(this->reconExists) |
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[985] | 230 | specRecon[z] += this->recon[spatpos + z*xdim*ydim] / beamCorrection; |
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[463] | 231 | if(this->par.getFlagBaseline()) |
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[985] | 232 | specBase[z] += this->baseline[spatpos + z*xdim*ydim] / beamCorrection; |
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[463] | 233 | } |
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| 234 | } |
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| 235 | } |
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| 236 | } |
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| 237 | } |
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| 238 | else {// if(par.getSpectralMethod()=="peak"){ |
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[985] | 239 | // size_t spatpos = this->objectList->at(objNum).getXPeak() + |
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| 240 | // xdim*this->objectList->at(objNum).getYPeak(); |
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[894] | 241 | for(size_t z=0;z<zdim;z++){ |
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[985] | 242 | specy[z] = this->array[spatpos + z*xdim*ydim]; |
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[463] | 243 | if(this->reconExists) |
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[985] | 244 | specRecon[z] = this->recon[spatpos + z*xdim*ydim]; |
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[463] | 245 | if(this->par.getFlagBaseline()) |
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[985] | 246 | specBase[z] = this->baseline[spatpos + z*xdim*ydim]; |
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[463] | 247 | } |
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| 248 | } |
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| 249 | |
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[985] | 250 | } |
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| 251 | //-------------------------------------------------------------------- |
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[463] | 252 | |
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[985] | 253 | void getSmallVelRange(Detection &obj, FitsHeader &head, |
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| 254 | double *minvel, double *maxvel) |
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| 255 | { |
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| 256 | /// @details |
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| 257 | /// Routine to calculate the velocity range for the zoomed-in region. |
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| 258 | /// This range should be the maximum of 20 pixels, or 3x the wdith of |
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| 259 | /// the detection. |
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| 260 | /// Need to : |
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| 261 | /// Calculate pixel width of a 3x-detection-width region. |
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| 262 | /// If smaller than 20, calculate velocities of central vel +- 10 pixels |
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| 263 | /// If not, use the 3x-detection-width |
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| 264 | /// Range returned via "minvel" and "maxvel" parameters. |
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| 265 | /// \param obj Detection under examination. |
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| 266 | /// \param head FitsHeader, containing the WCS information. |
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| 267 | /// \param minvel Returned value of minimum velocity |
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| 268 | /// \param maxvel Returned value of maximum velocity |
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| 269 | |
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| 270 | double *pixcrd = new double[3]; |
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| 271 | double *world = new double[3]; |
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| 272 | float minpix,maxpix; |
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| 273 | // define new velocity extrema |
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| 274 | // -- make it 3x wider than the width of the detection. |
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| 275 | *minvel = 0.5*(obj.getVelMin()+obj.getVelMax()) - 1.5*obj.getVelWidth(); |
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| 276 | *maxvel = 0.5*(obj.getVelMin()+obj.getVelMax()) + 1.5*obj.getVelWidth(); |
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| 277 | // Find velocity range in number of pixels: |
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| 278 | world[0] = obj.getRA(); |
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| 279 | world[1] = obj.getDec(); |
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| 280 | world[2] = head.velToSpec(*minvel); |
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| 281 | head.wcsToPix(world,pixcrd); |
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| 282 | minpix = pixcrd[2]; |
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| 283 | world[2] = head.velToSpec(*maxvel); |
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| 284 | head.wcsToPix(world,pixcrd); |
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| 285 | maxpix = pixcrd[2]; |
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| 286 | if(maxpix<minpix) std::swap(maxpix,minpix); |
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| 287 | |
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| 288 | if((maxpix - minpix + 1) < 20){ |
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| 289 | pixcrd[0] = double(obj.getXcentre()); |
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| 290 | pixcrd[1] = double(obj.getYcentre()); |
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| 291 | pixcrd[2] = obj.getZcentre() - 10.; |
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| 292 | head.pixToWCS(pixcrd,world); |
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| 293 | // *minvel = setVel_kms(wcs,world[2]); |
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| 294 | *minvel = head.specToVel(world[2]); |
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| 295 | pixcrd[2] = obj.getZcentre() + 10.; |
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| 296 | head.pixToWCS(pixcrd,world); |
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| 297 | // *maxvel = setVel_kms(wcs,world[2]); |
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| 298 | *maxvel = head.specToVel(world[2]); |
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| 299 | if(*maxvel<*minvel) std::swap(*maxvel,*minvel); |
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| 300 | } |
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| 301 | delete [] pixcrd; |
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| 302 | delete [] world; |
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| 303 | |
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| 304 | } |
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[463] | 305 | //-------------------------------------------------------------------- |
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| 306 | |
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[985] | 307 | void getSmallZRange(Detection &obj, double *minz, double *maxz) |
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| 308 | { |
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| 309 | /// @details |
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| 310 | /// Routine to calculate the pixel range for the zoomed-in spectrum. |
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| 311 | /// This range should be the maximum of 20 pixels, or 3x the width |
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| 312 | /// of the detection. |
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| 313 | /// Need to : |
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| 314 | /// Calculate pixel width of a 3x-detection-width region. |
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| 315 | /// If smaller than 20, use central pixel +- 10 pixels |
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| 316 | /// Range returned via "minz" and "maxz" parameters. |
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| 317 | /// \param obj Detection under examination. |
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| 318 | /// \param minz Returned value of minimum z-pixel coordinate |
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| 319 | /// \param maxz Returned value of maximum z-pixel coordinate |
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| 320 | |
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| 321 | *minz = 2.*obj.getZmin() - obj.getZmax(); |
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| 322 | *maxz = 2.*obj.getZmax() - obj.getZmin(); |
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| 323 | |
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| 324 | if((*maxz - *minz + 1) < 20){ |
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| 325 | *minz = obj.getZcentre() - 10.; |
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| 326 | *maxz = obj.getZcentre() + 10.; |
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| 327 | } |
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| 328 | |
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| 329 | } |
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| 330 | //-------------------------------------------------------------------- |
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| 331 | |
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[463] | 332 | } |
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