[300] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // detection.cc : Member functions for the Detection class. |
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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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[3] | 28 | #include <iostream> |
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| 29 | #include <iomanip> |
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| 30 | #include <vector> |
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| 31 | #include <string> |
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[394] | 32 | #include <wcslib/wcs.h> |
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[69] | 33 | #include <math.h> |
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[393] | 34 | #include <duchamp/duchamp.hh> |
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| 35 | #include <duchamp/param.hh> |
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| 36 | #include <duchamp/fitsHeader.hh> |
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| 37 | #include <duchamp/Utils/utils.hh> |
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| 38 | #include <duchamp/PixelMap/Voxel.hh> |
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| 39 | #include <duchamp/PixelMap/Object3D.hh> |
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| 40 | #include <duchamp/Detection/detection.hh> |
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[3] | 41 | |
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| 42 | using std::setw; |
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| 43 | using std::setprecision; |
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| 44 | using std::endl; |
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[232] | 45 | using std::vector; |
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[3] | 46 | |
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[258] | 47 | using namespace PixelInfo; |
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| 48 | |
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[378] | 49 | namespace duchamp |
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[365] | 50 | { |
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| 51 | |
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[218] | 52 | |
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[378] | 53 | Detection::Detection() |
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| 54 | { |
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| 55 | this->flagWCS=false; |
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| 56 | this->negSource = false; |
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| 57 | this->flagText=""; |
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| 58 | this->totalFlux = peakFlux = 0.; |
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| 59 | this->centreType="centroid"; |
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| 60 | } |
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[218] | 61 | |
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[378] | 62 | Detection::Detection(const Detection& d) |
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| 63 | { |
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| 64 | operator=(d); |
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| 65 | } |
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[218] | 66 | |
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[378] | 67 | Detection& Detection::operator= (const Detection& d) |
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| 68 | { |
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| 69 | if(this == &d) return *this; |
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| 70 | this->pixelArray = d.pixelArray; |
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| 71 | this->xSubOffset = d.xSubOffset; |
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| 72 | this->ySubOffset = d.ySubOffset; |
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| 73 | this->zSubOffset = d.zSubOffset; |
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| 74 | this->totalFlux = d.totalFlux; |
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| 75 | this->intFlux = d.intFlux; |
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| 76 | this->peakFlux = d.peakFlux; |
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| 77 | this->xpeak = d.xpeak; |
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| 78 | this->ypeak = d.ypeak; |
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| 79 | this->zpeak = d.zpeak; |
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| 80 | this->peakSNR = d.peakSNR; |
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| 81 | this->xCentroid = d.xCentroid; |
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| 82 | this->yCentroid = d.yCentroid; |
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| 83 | this->zCentroid = d.zCentroid; |
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| 84 | this->centreType = d.centreType; |
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| 85 | this->negSource = d.negSource; |
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| 86 | this->flagText = d.flagText; |
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| 87 | this->id = d.id; |
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| 88 | this->name = d.name; |
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| 89 | this->flagWCS = d.flagWCS; |
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| 90 | this->specOK = d.specOK; |
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| 91 | this->raS = d.raS; |
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| 92 | this->decS = d.decS; |
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| 93 | this->ra = d.ra; |
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| 94 | this->dec = d.dec; |
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| 95 | this->raWidth = d.raWidth; |
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| 96 | this->decWidth = d.decWidth; |
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| 97 | this->specUnits = d.specUnits; |
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| 98 | this->fluxUnits = d.fluxUnits; |
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| 99 | this->intFluxUnits = d.intFluxUnits; |
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| 100 | this->lngtype = d.lngtype; |
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| 101 | this->lattype = d.lattype; |
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| 102 | this->vel = d.vel; |
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| 103 | this->velWidth = d.velWidth; |
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| 104 | this->velMin = d.velMin; |
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| 105 | this->velMax = d.velMax; |
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| 106 | this->posPrec = d.posPrec; |
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| 107 | this->xyzPrec = d.xyzPrec; |
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| 108 | this->fintPrec = d.fintPrec; |
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| 109 | this->fpeakPrec = d.fpeakPrec; |
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| 110 | this->velPrec = d.velPrec; |
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| 111 | this->snrPrec = d.snrPrec; |
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| 112 | return *this; |
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| 113 | } |
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[3] | 114 | |
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[378] | 115 | //-------------------------------------------------------------------- |
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[258] | 116 | |
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[378] | 117 | void Detection::calcFluxes(float *fluxArray, long *dim) |
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| 118 | { |
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| 119 | /** |
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| 120 | * A function that calculates total & peak fluxes (and the location |
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| 121 | * of the peak flux) for a Detection. |
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| 122 | * |
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| 123 | * \param fluxArray The array of flux values to calculate the |
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| 124 | * flux parameters from. |
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| 125 | * \param dim The dimensions of the flux array. |
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| 126 | */ |
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[258] | 127 | |
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[378] | 128 | this->totalFlux = this->peakFlux = 0; |
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| 129 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 130 | long y,z,count=0; |
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| 131 | |
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| 132 | for(int m=0; m<this->pixelArray.getNumChanMap(); m++){ |
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| 133 | ChanMap *tempmap = new ChanMap; |
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| 134 | *tempmap = this->pixelArray.getChanMap(m); |
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| 135 | z = tempmap->getZ(); |
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| 136 | for(int s=0; s<tempmap->getNumScan(); s++){ |
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| 137 | Scan *tempscan = new Scan; |
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| 138 | *tempscan = tempmap->getScan(s); |
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| 139 | y = tempscan->getY(); |
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| 140 | for(long x=tempscan->getX(); x<=tempscan->getXmax(); x++){ |
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| 141 | |
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| 142 | float f = fluxArray[x + y*dim[0] + z*dim[0]*dim[1]]; |
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| 143 | this->totalFlux += f; |
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| 144 | this->xCentroid += x*f; |
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| 145 | this->yCentroid += y*f; |
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| 146 | this->zCentroid += z*f; |
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| 147 | if( (count==0) || //first time round |
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| 148 | (this->negSource&&(f<this->peakFlux)) || |
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| 149 | (!this->negSource&&(f>this->peakFlux)) ) |
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| 150 | { |
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| 151 | this->peakFlux = f; |
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| 152 | this->xpeak = x; |
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| 153 | this->ypeak = y; |
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| 154 | this->zpeak = z; |
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| 155 | } |
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| 156 | count++; |
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| 157 | } |
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| 158 | delete tempscan; |
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[263] | 159 | } |
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[378] | 160 | delete tempmap; |
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[45] | 161 | } |
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[378] | 162 | |
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| 163 | this->xCentroid /= this->totalFlux; |
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| 164 | this->yCentroid /= this->totalFlux; |
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| 165 | this->zCentroid /= this->totalFlux; |
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[263] | 166 | } |
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[378] | 167 | //-------------------------------------------------------------------- |
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[263] | 168 | |
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[378] | 169 | void Detection::calcWCSparams(float *fluxArray, long *dim, FitsHeader &head) |
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| 170 | { |
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| 171 | /** |
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| 172 | * Use the input wcs to calculate the position and velocity |
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| 173 | * information for the Detection. |
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| 174 | * Quantities calculated: |
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| 175 | * <ul><li> RA: ra [deg], ra (string), ra width. |
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| 176 | * <li> Dec: dec [deg], dec (string), dec width. |
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| 177 | * <li> Vel: vel [km/s], min & max vel, vel width. |
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| 178 | * <li> coord type for all three axes, nuRest, |
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| 179 | * <li> name (IAU-style, in equatorial or Galactic) |
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| 180 | * </ul> |
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| 181 | * Uses Detection::calcIntegFlux() to calculate the |
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| 182 | * integrated flux in (say) [Jy km/s] |
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| 183 | * |
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| 184 | * Note that the regular parameters are NOT recalculated! |
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| 185 | * |
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| 186 | * \param fluxArray The array of flux values to calculate the |
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| 187 | * integrated flux from. |
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| 188 | * \param dim The dimensions of the flux array. |
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| 189 | * \param head FitsHeader object that contains the WCS information. |
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| 190 | */ |
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[3] | 191 | |
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[378] | 192 | if(head.isWCS()){ |
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[3] | 193 | |
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[378] | 194 | double *pixcrd = new double[15]; |
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| 195 | double *world = new double[15]; |
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| 196 | /* |
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| 197 | define a five-point array in 3D: |
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| 198 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
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| 199 | [note: x = central point, x1 = minimum x, x2 = maximum x etc.] |
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| 200 | and convert to world coordinates. |
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| 201 | */ |
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| 202 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->getXcentre(); |
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| 203 | pixcrd[9] = this->getXmin()-0.5; |
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| 204 | pixcrd[12] = this->getXmax()+0.5; |
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| 205 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->getYcentre(); |
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| 206 | pixcrd[10] = this->getYmin()-0.5; |
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| 207 | pixcrd[13] = this->getYmax()+0.5; |
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| 208 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->getZcentre(); |
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| 209 | pixcrd[5] = this->getZmin(); |
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| 210 | pixcrd[8] = this->getZmax(); |
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| 211 | int flag = head.pixToWCS(pixcrd, world, 5); |
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| 212 | delete [] pixcrd; |
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| 213 | if(flag!=0) duchampError("calcWCSparams", |
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| 214 | "Error in calculating the WCS for this object.\n"); |
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| 215 | else{ |
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[60] | 216 | |
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[378] | 217 | // world now has the WCS coords for the five points |
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| 218 | // -- use this to work out WCS params |
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[22] | 219 | |
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[378] | 220 | // this->specOK = ((head.WCS().spec >= 0); |
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| 221 | this->specOK = head.canUseThirdAxis(); |
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| 222 | this->lngtype = head.WCS().lngtyp; |
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| 223 | this->lattype = head.WCS().lattyp; |
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| 224 | this->specUnits = head.getSpectralUnits(); |
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| 225 | this->fluxUnits = head.getFluxUnits(); |
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| 226 | // if fluxUnits are eg. Jy/beam, make intFluxUnits = Jy km/s |
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| 227 | this->intFluxUnits = head.getIntFluxUnits(); |
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| 228 | this->ra = world[0]; |
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| 229 | this->dec = world[1]; |
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| 230 | this->raS = decToDMS(this->ra, this->lngtype); |
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| 231 | this->decS = decToDMS(this->dec,this->lattype); |
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| 232 | this->raWidth = angularSeparation(world[9],world[1], |
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| 233 | world[12],world[1]) * 60.; |
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| 234 | this->decWidth = angularSeparation(world[0],world[10], |
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| 235 | world[0],world[13]) * 60.; |
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| 236 | this->name = head.getIAUName(this->ra, this->dec); |
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| 237 | this->vel = head.specToVel(world[2]); |
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| 238 | this->velMin = head.specToVel(world[5]); |
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| 239 | this->velMax = head.specToVel(world[8]); |
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| 240 | this->velWidth = fabs(this->velMax - this->velMin); |
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[3] | 241 | |
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[378] | 242 | this->calcIntegFlux(fluxArray,dim,head); |
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[129] | 243 | |
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[378] | 244 | this->flagWCS = true; |
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| 245 | } |
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| 246 | delete [] world; |
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| 247 | |
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[270] | 248 | } |
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[103] | 249 | } |
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[378] | 250 | //-------------------------------------------------------------------- |
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[3] | 251 | |
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[378] | 252 | void Detection::calcIntegFlux(float *fluxArray, long *dim, FitsHeader &head) |
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| 253 | { |
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| 254 | /** |
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| 255 | * Uses the input WCS to calculate the velocity-integrated flux, |
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| 256 | * putting velocity in units of km/s. |
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| 257 | * Integrates over full spatial and velocity range as given |
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| 258 | * by the extrema calculated by calcWCSparams. |
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| 259 | * |
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| 260 | * If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
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| 261 | * corrected by the beam size (in pixels). This is done by |
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| 262 | * multiplying the integrated flux by the number of spatial pixels, |
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| 263 | * and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
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| 264 | * pix/beam --> Jy) |
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| 265 | * |
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| 266 | * \param fluxArray The array of flux values. |
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| 267 | * \param dim The dimensions of the flux array. |
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| 268 | * \param head FitsHeader object that contains the WCS information. |
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| 269 | */ |
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[3] | 270 | |
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[378] | 271 | if(head.getNumAxes() > 2) { |
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[271] | 272 | |
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[378] | 273 | // include one pixel either side in each direction |
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| 274 | long xsize = (this->getXmax()-this->getXmin()+3); |
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| 275 | long ysize = (this->getYmax()-this->getYmin()+3); |
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| 276 | long zsize = (this->getZmax()-this->getZmin()+3); |
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| 277 | vector <bool> isObj(xsize*ysize*zsize,false); |
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| 278 | double *localFlux = new double[xsize*ysize*zsize]; |
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| 279 | for(int i=0;i<xsize*ysize*zsize;i++) localFlux[i]=0.; |
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| 280 | // work out which pixels are object pixels |
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| 281 | for(int m=0; m<this->pixelArray.getNumChanMap(); m++){ |
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| 282 | ChanMap tempmap = this->pixelArray.getChanMap(m); |
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| 283 | long z = this->pixelArray.getChanMap(m).getZ(); |
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| 284 | for(int s=0; s<this->pixelArray.getChanMap(m).getNumScan(); s++){ |
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| 285 | long y = this->pixelArray.getChanMap(m).getScan(s).getY(); |
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| 286 | for(long x=this->pixelArray.getChanMap(m).getScan(s).getX(); |
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| 287 | x<=this->pixelArray.getChanMap(m).getScan(s).getXmax(); |
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| 288 | x++){ |
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| 289 | long pos = (x-this->getXmin()+1) + (y-this->getYmin()+1)*xsize |
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| 290 | + (z-this->getZmin()+1)*xsize*ysize; |
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| 291 | localFlux[pos] = fluxArray[x + y*dim[0] + z*dim[0]*dim[1]]; |
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| 292 | isObj[pos] = true; |
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| 293 | } |
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[271] | 294 | } |
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[258] | 295 | } |
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[22] | 296 | |
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[378] | 297 | // work out the WCS coords for each pixel |
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| 298 | double *world = new double[xsize*ysize*zsize]; |
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| 299 | double xpt,ypt,zpt; |
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| 300 | for(int i=0;i<xsize*ysize*zsize;i++){ |
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| 301 | xpt = double( this->getXmin() -1 + i%xsize ); |
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| 302 | ypt = double( this->getYmin() -1 + (i/xsize)%ysize ); |
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| 303 | zpt = double( this->getZmin() -1 + i/(xsize*ysize) ); |
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| 304 | world[i] = head.pixToVel(xpt,ypt,zpt); |
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| 305 | } |
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[3] | 306 | |
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[378] | 307 | double integrated = 0.; |
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| 308 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
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| 309 | for(int z=0; z<zsize; z++){ |
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| 310 | int pos = z*xsize*ysize + pix; |
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| 311 | if(isObj[pos]){ // if it's an object pixel... |
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| 312 | double deltaVel; |
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| 313 | if(z==0) |
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| 314 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
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| 315 | else if(z==(zsize-1)) |
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| 316 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
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| 317 | else |
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| 318 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
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| 319 | integrated += localFlux[pos] * fabs(deltaVel); |
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| 320 | } |
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[271] | 321 | } |
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[3] | 322 | } |
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[378] | 323 | this->intFlux = integrated; |
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| 324 | |
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| 325 | delete [] world; |
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| 326 | delete [] localFlux; |
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| 327 | |
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[3] | 328 | } |
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[378] | 329 | else // in this case there is just a 2D image. |
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| 330 | this->intFlux = this->totalFlux; |
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[103] | 331 | |
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[378] | 332 | if(head.isWCS()){ |
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| 333 | // correct for the beam size if the flux units string ends in "/beam" |
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| 334 | if(head.needBeamSize()) |
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| 335 | this->intFlux *= double(this->getSpatialSize())/head.getBeamSize(); |
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| 336 | } |
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[300] | 337 | |
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| 338 | } |
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[378] | 339 | //-------------------------------------------------------------------- |
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[300] | 340 | |
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[378] | 341 | Detection operator+ (Detection lhs, Detection rhs) |
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| 342 | { |
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| 343 | /** |
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| 344 | * Combines two objects by adding all the pixels using the Object3D |
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| 345 | * operator. |
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| 346 | * |
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| 347 | * The pixel parameters are recalculated in the process (equivalent |
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| 348 | * to calling pixels().calcParams()), but WCS parameters are not. |
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| 349 | */ |
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| 350 | Detection output = lhs; |
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| 351 | output.pixelArray = lhs.pixelArray + rhs.pixelArray; |
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| 352 | return output; |
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[300] | 353 | } |
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[378] | 354 | //-------------------------------------------------------------------- |
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[103] | 355 | |
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[378] | 356 | void Detection::setOffsets(Param &par) |
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| 357 | { |
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| 358 | /** |
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| 359 | * This function stores the values of the offsets for each cube axis. |
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| 360 | * The offsets are the starting values of the cube axes that may differ from |
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| 361 | * the default value of 0 (for instance, if a subsection is being used). |
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| 362 | * The values will be used when the detection is outputted. |
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| 363 | */ |
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| 364 | this->xSubOffset = par.getXOffset(); |
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| 365 | this->ySubOffset = par.getYOffset(); |
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| 366 | this->zSubOffset = par.getZOffset(); |
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| 367 | } |
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| 368 | //-------------------------------------------------------------------- |
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[3] | 369 | |
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[378] | 370 | bool Detection::hasEnoughChannels(int minNumber) |
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| 371 | { |
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| 372 | /** |
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| 373 | * A function to determine if the Detection has enough |
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| 374 | * contiguous channels to meet the minimum requirement |
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| 375 | * given as the argument. |
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| 376 | * \param minNumber How many channels is the minimum acceptable number? |
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| 377 | * \return True if there is at least one occurence of minNumber consecutive |
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| 378 | * channels present to return true. False otherwise. |
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| 379 | */ |
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[3] | 380 | |
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[378] | 381 | // Preferred method -- need a set of minNumber consecutive channels present. |
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| 382 | this->pixelArray.order(); |
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| 383 | int numChannels = 0; |
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| 384 | bool result = false; |
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| 385 | int size = this->pixelArray.getNumChanMap(); |
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| 386 | if(size>0) numChannels++; |
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| 387 | if( numChannels >= minNumber) result = true; |
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| 388 | for(int i=1;(i<size && !result);i++) { |
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| 389 | if( (this->pixelArray.getZ(i) - this->pixelArray.getZ(i-1)) == 1) |
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| 390 | numChannels++; |
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| 391 | else if( (this->pixelArray.getZ(i) - this->pixelArray.getZ(i-1)) >= 2) |
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| 392 | numChannels = 1; |
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[3] | 393 | |
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[378] | 394 | if( numChannels >= minNumber) result = true; |
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| 395 | } |
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| 396 | return result; |
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| 397 | |
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| 398 | } |
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| 399 | //-------------------------------------------------------------------- |
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[3] | 400 | |
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[378] | 401 | std::ostream& operator<< ( std::ostream& theStream, Detection& obj) |
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| 402 | { |
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| 403 | /** |
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| 404 | * A convenient way of printing the coordinate values for each |
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| 405 | * pixel in the Detection. |
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| 406 | * |
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| 407 | * NOTE THAT THERE IS CURRENTLY NO FLUX INFORMATION BEING PRINTED! |
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| 408 | * |
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| 409 | * Use as front end to the Object3D::operator<< function. |
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| 410 | */ |
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[3] | 411 | |
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[378] | 412 | theStream << obj.pixelArray << "---\n"; |
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| 413 | return theStream; |
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[3] | 414 | } |
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[378] | 415 | //-------------------------------------------------------------------- |
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[3] | 416 | |
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| 417 | } |
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