[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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[463] | 41 | #include <duchamp/Cubes/cubeUtils.hh> |
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[570] | 42 | #include <duchamp/Detection/columns.hh> |
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[3] | 43 | |
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[258] | 44 | using namespace PixelInfo; |
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| 45 | |
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[378] | 46 | namespace duchamp |
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[365] | 47 | { |
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| 48 | |
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[570] | 49 | void Detection::defaultDetection() |
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[378] | 50 | { |
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[570] | 51 | this->xSubOffset = 0; |
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| 52 | this->ySubOffset = 0; |
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| 53 | this->zSubOffset = 0; |
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[681] | 54 | this->haveParams = false; |
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[570] | 55 | this->totalFlux = 0.; |
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| 56 | this->peakFlux = 0.; |
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| 57 | this->intFlux = 0.; |
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| 58 | this->xpeak = 0; |
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| 59 | this->ypeak = 0; |
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| 60 | this->zpeak = 0; |
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| 61 | this->peakSNR = 0.; |
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| 62 | this->xCentroid = 0.; |
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| 63 | this->yCentroid = 0.; |
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| 64 | this->zCentroid = 0.; |
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| 65 | this->centreType="centroid"; |
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[378] | 66 | this->negSource = false; |
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| 67 | this->flagText=""; |
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[468] | 68 | this->id = -1; |
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[570] | 69 | this->name = ""; |
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| 70 | this->flagWCS=false; |
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| 71 | this->specOK = true; |
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| 72 | this->raS = ""; |
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| 73 | this->decS = ""; |
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| 74 | this->ra = 0.; |
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| 75 | this->dec = 0.; |
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| 76 | this->raWidth = 0.; |
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| 77 | this->decWidth = 0.; |
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| 78 | this->majorAxis = 0.; |
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| 79 | this->minorAxis = 0.; |
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| 80 | this->posang = 0.; |
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| 81 | this->specUnits = ""; |
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| 82 | this->fluxUnits = ""; |
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| 83 | this->intFluxUnits = ""; |
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| 84 | this->lngtype = "RA"; |
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| 85 | this->lattype = "DEC"; |
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| 86 | this->vel = 0.; |
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| 87 | this->velWidth = 0.; |
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| 88 | this->velMin = 0.; |
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| 89 | this->velMax = 0.; |
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| 90 | this->w20 = 0.; |
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| 91 | this->v20min = 0.; |
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| 92 | this->v20max = 0.; |
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| 93 | this->w50 = 0.; |
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| 94 | this->v50min = 0.; |
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| 95 | this->v50max = 0.; |
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| 96 | this->posPrec = Column::prPOS; |
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| 97 | this->xyzPrec = Column::prXYZ; |
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| 98 | this->fintPrec = Column::prFLUX; |
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| 99 | this->fpeakPrec = Column::prFLUX; |
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| 100 | this->velPrec = Column::prVEL; |
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| 101 | this->snrPrec = Column::prSNR; |
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[378] | 102 | } |
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[218] | 103 | |
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[570] | 104 | Detection::Detection(): |
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| 105 | Object3D() |
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[378] | 106 | { |
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[570] | 107 | this->defaultDetection(); |
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| 108 | } |
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| 109 | |
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| 110 | Detection::Detection(const Object3D& o): |
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| 111 | Object3D(o) |
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| 112 | { |
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| 113 | this->defaultDetection(); |
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| 114 | } |
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| 115 | |
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| 116 | Detection::Detection(const Detection& d): |
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| 117 | Object3D(d) |
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| 118 | { |
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[378] | 119 | operator=(d); |
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| 120 | } |
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[218] | 121 | |
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[378] | 122 | Detection& Detection::operator= (const Detection& d) |
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| 123 | { |
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[570] | 124 | ((Object3D &) *this) = d; |
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[378] | 125 | this->xSubOffset = d.xSubOffset; |
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| 126 | this->ySubOffset = d.ySubOffset; |
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| 127 | this->zSubOffset = d.zSubOffset; |
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[681] | 128 | this->haveParams = d.haveParams; |
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[378] | 129 | this->totalFlux = d.totalFlux; |
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[461] | 130 | this->intFlux = d.intFlux; |
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[378] | 131 | this->peakFlux = d.peakFlux; |
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| 132 | this->xpeak = d.xpeak; |
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| 133 | this->ypeak = d.ypeak; |
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| 134 | this->zpeak = d.zpeak; |
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| 135 | this->peakSNR = d.peakSNR; |
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| 136 | this->xCentroid = d.xCentroid; |
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| 137 | this->yCentroid = d.yCentroid; |
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| 138 | this->zCentroid = d.zCentroid; |
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| 139 | this->centreType = d.centreType; |
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| 140 | this->negSource = d.negSource; |
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| 141 | this->flagText = d.flagText; |
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| 142 | this->id = d.id; |
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| 143 | this->name = d.name; |
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| 144 | this->flagWCS = d.flagWCS; |
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| 145 | this->specOK = d.specOK; |
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| 146 | this->raS = d.raS; |
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| 147 | this->decS = d.decS; |
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| 148 | this->ra = d.ra; |
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[461] | 149 | this->dec = d.dec; |
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| 150 | this->raWidth = d.raWidth; |
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[378] | 151 | this->decWidth = d.decWidth; |
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[473] | 152 | this->majorAxis = d.majorAxis; |
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| 153 | this->minorAxis = d.minorAxis; |
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| 154 | this->posang = d.posang; |
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[378] | 155 | this->specUnits = d.specUnits; |
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| 156 | this->fluxUnits = d.fluxUnits; |
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| 157 | this->intFluxUnits = d.intFluxUnits; |
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[461] | 158 | this->lngtype = d.lngtype; |
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| 159 | this->lattype = d.lattype; |
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[378] | 160 | this->vel = d.vel; |
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| 161 | this->velWidth = d.velWidth; |
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| 162 | this->velMin = d.velMin; |
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| 163 | this->velMax = d.velMax; |
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[463] | 164 | this->w20 = d.w20; |
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| 165 | this->v20min = d.v20min; |
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| 166 | this->v20max = d.v20max; |
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| 167 | this->w50 = d.w50; |
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| 168 | this->v50min = d.v50min; |
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| 169 | this->v50max = d.v50max; |
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[378] | 170 | this->posPrec = d.posPrec; |
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| 171 | this->xyzPrec = d.xyzPrec; |
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| 172 | this->fintPrec = d.fintPrec; |
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| 173 | this->fpeakPrec = d.fpeakPrec; |
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[461] | 174 | this->velPrec = d.velPrec; |
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[378] | 175 | this->snrPrec = d.snrPrec; |
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| 176 | return *this; |
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| 177 | } |
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[3] | 178 | |
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[378] | 179 | //-------------------------------------------------------------------- |
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[570] | 180 | float Detection::getXcentre() |
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| 181 | { |
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| 182 | if(this->centreType=="peak") return this->xpeak; |
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| 183 | else if(this->centreType=="average") return this->getXaverage(); |
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| 184 | else return this->xCentroid; |
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| 185 | } |
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[258] | 186 | |
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[570] | 187 | float Detection::getYcentre() |
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| 188 | { |
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| 189 | if(this->centreType=="peak") return this->ypeak; |
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| 190 | else if(this->centreType=="average") return this->getYaverage(); |
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| 191 | else return this->yCentroid; |
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| 192 | } |
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| 193 | |
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| 194 | float Detection::getZcentre() |
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| 195 | { |
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| 196 | if(this->centreType=="peak") return this->zpeak; |
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| 197 | else if(this->centreType=="average") return this->getZaverage(); |
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| 198 | else return this->zCentroid; |
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| 199 | } |
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| 200 | |
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| 201 | //-------------------------------------------------------------------- |
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| 202 | |
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[417] | 203 | bool Detection::voxelListsMatch(std::vector<Voxel> voxelList) |
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| 204 | { |
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[528] | 205 | /// @details |
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| 206 | /// A test to see whether there is a 1-1 correspondence between |
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| 207 | /// the given list of Voxels and the voxel positions contained in |
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| 208 | /// this Detection's pixel list. No testing of the fluxes of the |
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| 209 | /// Voxels is done. |
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| 210 | /// |
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| 211 | /// \param voxelList The std::vector list of Voxels to be tested. |
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[417] | 212 | |
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| 213 | bool listsMatch = true; |
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| 214 | // compare sizes |
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| 215 | listsMatch = listsMatch && (voxelList.size() == this->getSize()); |
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| 216 | if(!listsMatch) return listsMatch; |
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| 217 | |
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[463] | 218 | // make sure all Detection pixels are in voxel list |
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| 219 | listsMatch = listsMatch && this->voxelListCovered(voxelList); |
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| 220 | |
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[417] | 221 | // make sure all voxels are in Detection |
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[623] | 222 | std::vector<Voxel>::iterator vox; |
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| 223 | for(vox=voxelList.begin();vox<voxelList.end();vox++) |
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| 224 | listsMatch = listsMatch && this->isInObject(*vox); |
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[463] | 225 | |
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| 226 | return listsMatch; |
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| 227 | |
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| 228 | } |
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| 229 | //-------------------------------------------------------------------- |
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| 230 | |
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| 231 | bool Detection::voxelListCovered(std::vector<Voxel> voxelList) |
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| 232 | { |
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[528] | 233 | /// @details |
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| 234 | /// A test to see whether the given list of Voxels contains each |
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| 235 | /// position in this Detection's pixel list. It does not look for |
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| 236 | /// a 1-1 correspondence: the given list can be a super-set of the |
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| 237 | /// Detection. No testing of the fluxes of the Voxels is done. |
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| 238 | /// |
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| 239 | /// \param voxelList The std::vector list of Voxels to be tested. |
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[463] | 240 | |
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| 241 | bool listsMatch = true; |
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| 242 | |
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[417] | 243 | // make sure all Detection pixels are in voxel list |
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[623] | 244 | size_t v1=0; |
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[570] | 245 | std::vector<Voxel> detpixlist = this->getPixelSet(); |
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| 246 | while(listsMatch && v1<detpixlist.size()){ |
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[417] | 247 | bool inList = false; |
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[623] | 248 | size_t v2=0; |
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[417] | 249 | while(!inList && v2<voxelList.size()){ |
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[570] | 250 | inList = inList || detpixlist[v1].match(voxelList[v2]); |
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[417] | 251 | v2++; |
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| 252 | } |
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| 253 | listsMatch = listsMatch && inList; |
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[418] | 254 | v1++; |
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[417] | 255 | } |
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| 256 | |
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| 257 | return listsMatch; |
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| 258 | |
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| 259 | } |
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| 260 | //-------------------------------------------------------------------- |
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| 261 | |
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| 262 | void Detection::calcFluxes(std::vector<Voxel> voxelList) |
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| 263 | { |
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[528] | 264 | /// @details |
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| 265 | /// A function that calculates total & peak fluxes (and the location |
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| 266 | /// of the peak flux) for a Detection. |
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| 267 | /// |
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| 268 | /// \param fluxArray The array of flux values to calculate the |
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| 269 | /// flux parameters from. |
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| 270 | /// \param dim The dimensions of the flux array. |
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[681] | 271 | |
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| 272 | // this->haveParams = true; |
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[417] | 273 | |
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| 274 | this->totalFlux = this->peakFlux = 0; |
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| 275 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 276 | |
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| 277 | // first check that the voxel list and the Detection's pixel list |
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| 278 | // have a 1-1 correspondence |
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| 279 | |
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[463] | 280 | if(!this->voxelListCovered(voxelList)){ |
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[417] | 281 | duchampError("Detection::calcFluxes","Voxel list provided does not match"); |
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| 282 | return; |
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| 283 | } |
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| 284 | |
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[623] | 285 | std::vector<Voxel>::iterator vox; |
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| 286 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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| 287 | if(this->isInObject(*vox)){ |
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| 288 | long x = vox->getX(); |
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| 289 | long y = vox->getY(); |
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| 290 | long z = vox->getZ(); |
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| 291 | float f = vox->getF(); |
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[463] | 292 | this->totalFlux += f; |
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| 293 | this->xCentroid += x*f; |
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| 294 | this->yCentroid += y*f; |
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| 295 | this->zCentroid += z*f; |
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[623] | 296 | if( (vox==voxelList.begin()) || //first time round |
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[463] | 297 | (this->negSource&&(f<this->peakFlux)) || |
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| 298 | (!this->negSource&&(f>this->peakFlux)) ) |
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| 299 | { |
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| 300 | this->peakFlux = f; |
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| 301 | this->xpeak = x; |
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| 302 | this->ypeak = y; |
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| 303 | this->zpeak = z; |
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| 304 | } |
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| 305 | } |
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[417] | 306 | } |
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| 307 | |
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| 308 | this->xCentroid /= this->totalFlux; |
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| 309 | this->yCentroid /= this->totalFlux; |
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| 310 | this->zCentroid /= this->totalFlux; |
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| 311 | } |
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| 312 | //-------------------------------------------------------------------- |
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| 313 | |
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[378] | 314 | void Detection::calcFluxes(float *fluxArray, long *dim) |
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| 315 | { |
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[528] | 316 | /// @details |
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| 317 | /// A function that calculates total & peak fluxes (and the location |
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| 318 | /// of the peak flux) for a Detection. |
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| 319 | /// |
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| 320 | /// \param fluxArray The array of flux values to calculate the |
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| 321 | /// flux parameters from. |
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| 322 | /// \param dim The dimensions of the flux array. |
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[258] | 323 | |
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[681] | 324 | // this->haveParams = true; |
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| 325 | |
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[378] | 326 | this->totalFlux = this->peakFlux = 0; |
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| 327 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 328 | |
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[570] | 329 | std::vector<Voxel> voxList = this->getPixelSet(); |
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[473] | 330 | std::vector<Voxel>::iterator vox=voxList.begin(); |
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| 331 | for(;vox<voxList.end();vox++){ |
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[378] | 332 | |
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[473] | 333 | long x=vox->getX(); |
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| 334 | long y=vox->getY(); |
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| 335 | long z=vox->getZ(); |
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| 336 | long ind = vox->arrayIndex(dim); |
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| 337 | float f = fluxArray[ind]; |
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| 338 | this->totalFlux += f; |
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| 339 | this->xCentroid += x*f; |
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| 340 | this->yCentroid += y*f; |
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| 341 | this->zCentroid += z*f; |
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| 342 | if( (vox==voxList.begin()) || |
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| 343 | (this->negSource&&(f<this->peakFlux)) || |
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| 344 | (!this->negSource&&(f>this->peakFlux)) ) |
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| 345 | { |
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| 346 | this->peakFlux = f; |
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| 347 | this->xpeak = x; |
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| 348 | this->ypeak = y; |
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| 349 | this->zpeak = z; |
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[378] | 350 | } |
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[473] | 351 | |
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[45] | 352 | } |
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[378] | 353 | |
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| 354 | this->xCentroid /= this->totalFlux; |
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| 355 | this->yCentroid /= this->totalFlux; |
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| 356 | this->zCentroid /= this->totalFlux; |
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[263] | 357 | } |
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[378] | 358 | //-------------------------------------------------------------------- |
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[263] | 359 | |
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[417] | 360 | void Detection::calcWCSparams(FitsHeader &head) |
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[378] | 361 | { |
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[528] | 362 | /// @details |
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| 363 | /// Use the input wcs to calculate the position and velocity |
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| 364 | /// information for the Detection. |
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| 365 | /// Quantities calculated: |
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| 366 | /// <ul><li> RA: ra [deg], ra (string), ra width. |
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| 367 | /// <li> Dec: dec [deg], dec (string), dec width. |
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| 368 | /// <li> Vel: vel [km/s], min & max vel, vel width. |
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| 369 | /// <li> coord type for all three axes, nuRest, |
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| 370 | /// <li> name (IAU-style, in equatorial or Galactic) |
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| 371 | /// </ul> |
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| 372 | /// |
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| 373 | /// Note that the regular parameters are NOT recalculated! |
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| 374 | /// |
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| 375 | /// \param head FitsHeader object that contains the WCS information. |
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[3] | 376 | |
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[378] | 377 | if(head.isWCS()){ |
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[3] | 378 | |
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[378] | 379 | double *pixcrd = new double[15]; |
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| 380 | double *world = new double[15]; |
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| 381 | /* |
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| 382 | define a five-point array in 3D: |
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| 383 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
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| 384 | [note: x = central point, x1 = minimum x, x2 = maximum x etc.] |
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| 385 | and convert to world coordinates. |
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| 386 | */ |
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| 387 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->getXcentre(); |
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| 388 | pixcrd[9] = this->getXmin()-0.5; |
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| 389 | pixcrd[12] = this->getXmax()+0.5; |
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| 390 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->getYcentre(); |
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| 391 | pixcrd[10] = this->getYmin()-0.5; |
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| 392 | pixcrd[13] = this->getYmax()+0.5; |
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| 393 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->getZcentre(); |
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| 394 | pixcrd[5] = this->getZmin(); |
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| 395 | pixcrd[8] = this->getZmax(); |
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| 396 | int flag = head.pixToWCS(pixcrd, world, 5); |
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| 397 | delete [] pixcrd; |
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| 398 | if(flag!=0) duchampError("calcWCSparams", |
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| 399 | "Error in calculating the WCS for this object.\n"); |
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| 400 | else{ |
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[60] | 401 | |
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[378] | 402 | // world now has the WCS coords for the five points |
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| 403 | // -- use this to work out WCS params |
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[22] | 404 | |
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[681] | 405 | this->haveParams = true; |
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| 406 | |
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[378] | 407 | this->specOK = head.canUseThirdAxis(); |
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| 408 | this->lngtype = head.WCS().lngtyp; |
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| 409 | this->lattype = head.WCS().lattyp; |
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| 410 | this->specUnits = head.getSpectralUnits(); |
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| 411 | this->fluxUnits = head.getFluxUnits(); |
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| 412 | // if fluxUnits are eg. Jy/beam, make intFluxUnits = Jy km/s |
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| 413 | this->intFluxUnits = head.getIntFluxUnits(); |
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| 414 | this->ra = world[0]; |
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| 415 | this->dec = world[1]; |
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| 416 | this->raS = decToDMS(this->ra, this->lngtype); |
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| 417 | this->decS = decToDMS(this->dec,this->lattype); |
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| 418 | this->raWidth = angularSeparation(world[9],world[1], |
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| 419 | world[12],world[1]) * 60.; |
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| 420 | this->decWidth = angularSeparation(world[0],world[10], |
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| 421 | world[0],world[13]) * 60.; |
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[473] | 422 | |
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[570] | 423 | Object2D spatMap = this->getSpatialMap(); |
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[473] | 424 | std::pair<double,double> axes = spatMap.getPrincipleAxes(); |
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| 425 | this->majorAxis = std::max(axes.first,axes.second) * head.getAvPixScale(); |
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| 426 | this->minorAxis = std::min(axes.first,axes.second) * head.getAvPixScale(); |
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| 427 | this->posang = spatMap.getPositionAngle() * 180. / M_PI; |
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| 428 | |
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[378] | 429 | this->name = head.getIAUName(this->ra, this->dec); |
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| 430 | this->vel = head.specToVel(world[2]); |
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| 431 | this->velMin = head.specToVel(world[5]); |
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| 432 | this->velMax = head.specToVel(world[8]); |
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| 433 | this->velWidth = fabs(this->velMax - this->velMin); |
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[3] | 434 | |
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[378] | 435 | this->flagWCS = true; |
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| 436 | } |
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| 437 | delete [] world; |
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| 438 | |
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[270] | 439 | } |
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[103] | 440 | } |
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[378] | 441 | //-------------------------------------------------------------------- |
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[3] | 442 | |
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[719] | 443 | void Detection::calcIntegFlux(long zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
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[417] | 444 | { |
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[528] | 445 | /// @details |
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| 446 | /// Uses the input WCS to calculate the velocity-integrated flux, |
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| 447 | /// putting velocity in units of km/s. |
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| 448 | /// The fluxes used are taken from the Voxels, rather than an |
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| 449 | /// array of flux values. |
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| 450 | /// Integrates over full spatial and velocity range as given |
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| 451 | /// by the extrema calculated by calcWCSparams. |
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| 452 | /// |
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| 453 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
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| 454 | /// corrected by the beam size (in pixels). This is done by |
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| 455 | /// multiplying the integrated flux by the number of spatial pixels, |
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| 456 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
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| 457 | /// pix/beam --> Jy) |
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| 458 | /// |
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[719] | 459 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
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[528] | 460 | /// \param voxelList The list of Voxels with flux information |
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| 461 | /// \param head FitsHeader object that contains the WCS information. |
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[417] | 462 | |
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[463] | 463 | const int border = 1; |
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| 464 | |
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| 465 | if(!this->voxelListCovered(voxelList)){ |
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[417] | 466 | duchampError("Detection::calcIntegFlux","Voxel list provided does not match"); |
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| 467 | return; |
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| 468 | } |
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| 469 | |
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[513] | 470 | if(!head.is2D()){ |
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[417] | 471 | |
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[681] | 472 | this->haveParams = true; |
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| 473 | |
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[417] | 474 | // include one pixel either side in each direction |
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[463] | 475 | long xsize = (this->getXmax()-this->getXmin()+border*2+1); |
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| 476 | long ysize = (this->getYmax()-this->getYmin()+border*2+1); |
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| 477 | long zsize = (this->getZmax()-this->getZmin()+border*2+1); |
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| 478 | long size = xsize*ysize*zsize; |
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[473] | 479 | std::vector <bool> isObj(size,false); |
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[463] | 480 | double *localFlux = new double[size]; |
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| 481 | for(int i=0;i<size;i++) localFlux[i]=0.; |
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[417] | 482 | |
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[623] | 483 | std::vector<Voxel>::iterator vox; |
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| 484 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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| 485 | if(this->isInObject(*vox)){ |
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| 486 | long x = vox->getX(); |
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| 487 | long y = vox->getY(); |
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| 488 | long z = vox->getZ(); |
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[463] | 489 | long pos = (x-this->getXmin()+border) + (y-this->getYmin()+border)*xsize |
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| 490 | + (z-this->getZmin()+border)*xsize*ysize; |
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[623] | 491 | localFlux[pos] = vox->getF(); |
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[463] | 492 | isObj[pos] = true; |
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| 493 | } |
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[417] | 494 | } |
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| 495 | |
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| 496 | // work out the WCS coords for each pixel |
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[463] | 497 | double *world = new double[size]; |
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[417] | 498 | double xpt,ypt,zpt; |
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| 499 | for(int i=0;i<xsize*ysize*zsize;i++){ |
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[463] | 500 | xpt = double( this->getXmin() - border + i%xsize ); |
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| 501 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
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| 502 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
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[417] | 503 | world[i] = head.pixToVel(xpt,ypt,zpt); |
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| 504 | } |
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| 505 | |
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| 506 | double integrated = 0.; |
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| 507 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
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| 508 | for(int z=0; z<zsize; z++){ |
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| 509 | int pos = z*xsize*ysize + pix; |
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| 510 | if(isObj[pos]){ // if it's an object pixel... |
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| 511 | double deltaVel; |
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| 512 | if(z==0) |
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| 513 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
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| 514 | else if(z==(zsize-1)) |
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| 515 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
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| 516 | else |
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| 517 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
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| 518 | integrated += localFlux[pos] * fabs(deltaVel); |
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| 519 | } |
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| 520 | } |
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| 521 | } |
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| 522 | this->intFlux = integrated; |
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| 523 | |
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| 524 | delete [] world; |
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| 525 | delete [] localFlux; |
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| 526 | |
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[719] | 527 | calcVelWidths(zdim,voxelList,head); |
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[464] | 528 | |
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[417] | 529 | } |
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| 530 | else // in this case there is just a 2D image. |
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| 531 | this->intFlux = this->totalFlux; |
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| 532 | |
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| 533 | if(head.isWCS()){ |
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| 534 | // correct for the beam size if the flux units string ends in "/beam" |
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[429] | 535 | if(head.needBeamSize()) this->intFlux /= head.getBeamSize(); |
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[417] | 536 | } |
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| 537 | |
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| 538 | } |
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| 539 | //-------------------------------------------------------------------- |
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| 540 | |
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[378] | 541 | void Detection::calcIntegFlux(float *fluxArray, long *dim, FitsHeader &head) |
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| 542 | { |
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[528] | 543 | /// @details |
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| 544 | /// Uses the input WCS to calculate the velocity-integrated flux, |
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| 545 | /// putting velocity in units of km/s. |
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| 546 | /// Integrates over full spatial and velocity range as given |
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| 547 | /// by the extrema calculated by calcWCSparams. |
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| 548 | /// |
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| 549 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
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| 550 | /// corrected by the beam size (in pixels). This is done by |
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| 551 | /// multiplying the integrated flux by the number of spatial pixels, |
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| 552 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
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| 553 | /// pix/beam --> Jy) |
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| 554 | /// |
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| 555 | /// \param fluxArray The array of flux values. |
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| 556 | /// \param dim The dimensions of the flux array. |
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| 557 | /// \param head FitsHeader object that contains the WCS information. |
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[3] | 558 | |
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[513] | 559 | if(!head.is2D()){ |
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[271] | 560 | |
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[681] | 561 | this->haveParams = true; |
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| 562 | |
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[378] | 563 | // include one pixel either side in each direction |
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[570] | 564 | long xsize = (this->xmax-this->xmin+3); |
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| 565 | long ysize = (this->ymax-this->ymin+3); |
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| 566 | long zsize = (this->zmax-this->zmin+3); |
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[463] | 567 | long size = xsize*ysize*zsize; |
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[473] | 568 | std::vector <bool> isObj(size,false); |
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[463] | 569 | double *localFlux = new double[size]; |
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| 570 | for(int i=0;i<size;i++) localFlux[i]=0.; |
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[378] | 571 | // work out which pixels are object pixels |
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[570] | 572 | for(std::map<long,Object2D>::iterator it=this->chanlist.begin(); |
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| 573 | it!=this->chanlist.end(); it++){ |
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| 574 | long z = it->first; |
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| 575 | for(int s=0; s<it->second.getNumScan();s++){ |
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| 576 | long y = it->second.getScan(s).getY(); |
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| 577 | for(long x=it->second.getScan(s).getX(); |
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| 578 | x<=it->second.getScan(s).getXmax(); |
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[378] | 579 | x++){ |
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[570] | 580 | long pos = (x-this->xmin+1) + (y-this->ymin+1)*xsize |
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| 581 | + (z-this->zmin+1)*xsize*ysize; |
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[378] | 582 | localFlux[pos] = fluxArray[x + y*dim[0] + z*dim[0]*dim[1]]; |
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| 583 | isObj[pos] = true; |
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| 584 | } |
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[271] | 585 | } |
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[258] | 586 | } |
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[570] | 587 | |
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[22] | 588 | |
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[378] | 589 | // work out the WCS coords for each pixel |
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[463] | 590 | double *world = new double[size]; |
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[378] | 591 | double xpt,ypt,zpt; |
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| 592 | for(int i=0;i<xsize*ysize*zsize;i++){ |
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| 593 | xpt = double( this->getXmin() -1 + i%xsize ); |
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| 594 | ypt = double( this->getYmin() -1 + (i/xsize)%ysize ); |
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| 595 | zpt = double( this->getZmin() -1 + i/(xsize*ysize) ); |
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| 596 | world[i] = head.pixToVel(xpt,ypt,zpt); |
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| 597 | } |
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[3] | 598 | |
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[378] | 599 | double integrated = 0.; |
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| 600 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
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| 601 | for(int z=0; z<zsize; z++){ |
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| 602 | int pos = z*xsize*ysize + pix; |
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| 603 | if(isObj[pos]){ // if it's an object pixel... |
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| 604 | double deltaVel; |
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| 605 | if(z==0) |
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| 606 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
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| 607 | else if(z==(zsize-1)) |
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| 608 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
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| 609 | else |
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| 610 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
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| 611 | integrated += localFlux[pos] * fabs(deltaVel); |
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| 612 | } |
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[271] | 613 | } |
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[3] | 614 | } |
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[378] | 615 | this->intFlux = integrated; |
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| 616 | |
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[464] | 617 | delete [] world; |
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| 618 | delete [] localFlux; |
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[463] | 619 | |
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[464] | 620 | calcVelWidths(fluxArray, dim, head); |
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[463] | 621 | |
---|
[464] | 622 | } |
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| 623 | else // in this case there is just a 2D image. |
---|
| 624 | this->intFlux = this->totalFlux; |
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[463] | 625 | |
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[464] | 626 | if(head.isWCS()){ |
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| 627 | // correct for the beam size if the flux units string ends in "/beam" |
---|
| 628 | if(head.needBeamSize()) this->intFlux /= head.getBeamSize(); |
---|
| 629 | } |
---|
[463] | 630 | |
---|
[464] | 631 | } |
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| 632 | //-------------------------------------------------------------------- |
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| 633 | |
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[719] | 634 | void Detection::calcVelWidths(long zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
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[464] | 635 | { |
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[528] | 636 | /// @details |
---|
| 637 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
| 638 | /// peak integrated flux. The procedure is as follows: first |
---|
| 639 | /// generate an integrated flux spectrum (using all given voxels |
---|
| 640 | /// that lie in the object's spatial map); find the peak; starting |
---|
| 641 | /// at the spectral edges of the detection, move in or out until |
---|
| 642 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
| 643 | /// between points is done. |
---|
| 644 | /// |
---|
[719] | 645 | /// \param zdim The size of the spectral axis in the cube |
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[528] | 646 | /// \param voxelList The list of Voxels with flux information |
---|
| 647 | /// \param head FitsHeader object that contains the WCS information. |
---|
[464] | 648 | |
---|
[719] | 649 | // this->haveParams = true; |
---|
[681] | 650 | |
---|
[719] | 651 | // const int border = 1; |
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| 652 | // // long zsize = (this->getZmax()-this->getZmin()+border*2+1); |
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| 653 | // double xpt = double(this->getXcentre()); |
---|
| 654 | // double ypt = double(this->getYcentre()); |
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| 655 | // double zpt; |
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[464] | 656 | |
---|
[719] | 657 | // float *intSpec = new float[zsize]; |
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| 658 | // for(int i=0;i<zsize;i++) intSpec[i]=0; |
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| 659 | float *intSpec = new float[zdim]; |
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| 660 | for(int i=0;i<zdim;i++) intSpec[i]=0; |
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[464] | 661 | |
---|
[570] | 662 | Object2D spatMap = this->getSpatialMap(); |
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[464] | 663 | for(int s=0;s<spatMap.getNumScan();s++){ |
---|
[623] | 664 | std::vector<Voxel>::iterator vox; |
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| 665 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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| 666 | if(spatMap.isInObject(*vox)){ |
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[719] | 667 | // if(vox->getZ()>=this->getZmin()-border && |
---|
| 668 | // vox->getZ()<=this->getZmax()+border) |
---|
| 669 | // intSpec[vox->getZ()-this->getZmin()+1] += vox->getF(); |
---|
| 670 | intSpec[vox->getZ()] += vox->getF(); |
---|
[464] | 671 | } |
---|
[463] | 672 | } |
---|
[464] | 673 | } |
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| 674 | |
---|
[719] | 675 | // std::vector<std::pair<int,float> > goodPix; |
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| 676 | // float peak=0.; |
---|
| 677 | // int peakLoc=0; |
---|
| 678 | // // for(int z=0;z<zsize;z++) { |
---|
| 679 | // for(int z=0;z<zdim;z++) { |
---|
| 680 | // if(z==0 || peak<intSpec[z]){ |
---|
| 681 | // peak = intSpec[z]; |
---|
| 682 | // peakLoc = z; |
---|
| 683 | // } |
---|
| 684 | // goodPix.push_back(std::pair<int,float>(z,intSpec[z])); |
---|
| 685 | // } |
---|
| 686 | |
---|
| 687 | // // finding the 20% & 50% points. Start at the velmin & velmax |
---|
| 688 | // // points. Then, if the int flux there is above the 20%/50% |
---|
| 689 | // // limit, go out, otherwise go in. This is to deal with the |
---|
| 690 | // // problems from double peaked sources. |
---|
| 691 | |
---|
| 692 | // int z; |
---|
| 693 | // bool goLeft; |
---|
| 694 | // z=border; |
---|
| 695 | // goLeft = intSpec[z]>peak*0.5; |
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| 696 | // if(goLeft) while(z>0 && intSpec[z]>peak*0.5) z--; |
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| 697 | // else while(z<peakLoc && intSpec[z]<peak*0.5) z++; |
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| 698 | // if(z==0) this->v50min = this->velMin; |
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| 699 | // else{ |
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| 700 | // if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]) + this->getZmin() - border; |
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| 701 | // else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]) + this->getZmin() - border; |
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| 702 | // this->v50min = head.pixToVel(xpt,ypt,zpt); |
---|
| 703 | // } |
---|
| 704 | // z=this->getZmax()-this->getZmin(); |
---|
| 705 | // goLeft = intSpec[z]<peak*0.5; |
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| 706 | // if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.5) z--; |
---|
| 707 | // else while(z<zsize && intSpec[z]>peak*0.5) z++; |
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| 708 | // if(z==zsize) this->v50max = this->velMax; |
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| 709 | // else{ |
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| 710 | // if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]) + this->getZmin() - border; |
---|
| 711 | // else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]) + this->getZmin() - border; |
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| 712 | // this->v50max = head.pixToVel(xpt,ypt,zpt); |
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| 713 | // } |
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| 714 | // z=border; |
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| 715 | // goLeft = intSpec[z]>peak*0.2; |
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| 716 | // if(goLeft) while(z>0 && intSpec[z]>peak*0.2) z--; |
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| 717 | // else while(z<peakLoc && intSpec[z]<peak*0.2) z++; |
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| 718 | // if(z==0) this->v20min = this->velMin; |
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| 719 | // else{ |
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| 720 | // if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]) + this->getZmin() - border; |
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| 721 | // else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]) + this->getZmin() - border; |
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| 722 | // this->v20min = head.pixToVel(xpt,ypt,zpt); |
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| 723 | // } |
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| 724 | // z=this->getZmax()-this->getZmin(); |
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| 725 | // goLeft = intSpec[z]<peak*0.2; |
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| 726 | // if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.2) z--; |
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| 727 | // else while(z<zsize && intSpec[z]>peak*0.2) z++; |
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| 728 | // if(z==zsize) this->v20max = this->velMax; |
---|
| 729 | // else{ |
---|
| 730 | // if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]) + this->getZmin() - border; |
---|
| 731 | // else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]) + this->getZmin() - border; |
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| 732 | // this->v20max = head.pixToVel(xpt,ypt,zpt); |
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| 733 | // } |
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| 734 | |
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| 735 | // this->w20 = fabs(this->v20min - this->v20max); |
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| 736 | // this->w50 = fabs(this->v50min - this->v50max); |
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| 737 | |
---|
| 738 | calcVelWidths(zdim, intSpec, head); |
---|
| 739 | |
---|
| 740 | delete [] intSpec; |
---|
| 741 | |
---|
| 742 | } |
---|
| 743 | |
---|
| 744 | //-------------------------------------------------------------------- |
---|
| 745 | |
---|
| 746 | void Detection::calcVelWidths(long zdim, float *intSpec, FitsHeader &head) |
---|
| 747 | { |
---|
| 748 | |
---|
| 749 | // finding the 20% & 50% points. Start at the velmin & velmax |
---|
| 750 | // points. Then, if the int flux there is above the 20%/50% |
---|
| 751 | // limit, go out, otherwise go in. This is to deal with the |
---|
| 752 | // problems from double- (or multi-) peaked sources. |
---|
| 753 | |
---|
| 754 | this->haveParams = true; |
---|
| 755 | |
---|
| 756 | int z=this->getZmin(); |
---|
| 757 | double zpt,xpt=double(this->getXcentre()),ypt=double(this->getXcentre()); |
---|
| 758 | bool goLeft; |
---|
| 759 | |
---|
| 760 | // std::vector<std::pair<int,float> > goodPix; |
---|
[634] | 761 | float peak=0.; |
---|
| 762 | int peakLoc=0; |
---|
[719] | 763 | for(int z=0;z<zdim;z++) { |
---|
[464] | 764 | if(z==0 || peak<intSpec[z]){ |
---|
| 765 | peak = intSpec[z]; |
---|
| 766 | peakLoc = z; |
---|
[463] | 767 | } |
---|
[719] | 768 | // goodPix.push_back(std::pair<int,float>(z,intSpec[z])); |
---|
[464] | 769 | } |
---|
[719] | 770 | |
---|
[464] | 771 | goLeft = intSpec[z]>peak*0.5; |
---|
| 772 | if(goLeft) while(z>0 && intSpec[z]>peak*0.5) z--; |
---|
| 773 | else while(z<peakLoc && intSpec[z]<peak*0.5) z++; |
---|
| 774 | if(z==0) this->v50min = this->velMin; |
---|
| 775 | else{ |
---|
[719] | 776 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 777 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
[464] | 778 | this->v50min = head.pixToVel(xpt,ypt,zpt); |
---|
| 779 | } |
---|
[719] | 780 | z=this->getZmax(); |
---|
[464] | 781 | goLeft = intSpec[z]<peak*0.5; |
---|
| 782 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.5) z--; |
---|
[719] | 783 | else while(z<zdim && intSpec[z]>peak*0.5) z++; |
---|
| 784 | if(z==zdim) this->v50max = this->velMax; |
---|
[464] | 785 | else{ |
---|
[719] | 786 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 787 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
[464] | 788 | this->v50max = head.pixToVel(xpt,ypt,zpt); |
---|
| 789 | } |
---|
[719] | 790 | z=this->getZmin(); |
---|
[588] | 791 | goLeft = intSpec[z]>peak*0.2; |
---|
[464] | 792 | if(goLeft) while(z>0 && intSpec[z]>peak*0.2) z--; |
---|
| 793 | else while(z<peakLoc && intSpec[z]<peak*0.2) z++; |
---|
| 794 | if(z==0) this->v20min = this->velMin; |
---|
| 795 | else{ |
---|
[719] | 796 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 797 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
[464] | 798 | this->v20min = head.pixToVel(xpt,ypt,zpt); |
---|
| 799 | } |
---|
[719] | 800 | z=this->getZmax(); |
---|
[588] | 801 | goLeft = intSpec[z]<peak*0.2; |
---|
[464] | 802 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.2) z--; |
---|
[719] | 803 | else while(z<zdim && intSpec[z]>peak*0.2) z++; |
---|
| 804 | if(z==zdim) this->v20max = this->velMax; |
---|
[464] | 805 | else{ |
---|
[719] | 806 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 807 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
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[464] | 808 | this->v20max = head.pixToVel(xpt,ypt,zpt); |
---|
| 809 | } |
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[463] | 810 | |
---|
[464] | 811 | this->w20 = fabs(this->v20min - this->v20max); |
---|
| 812 | this->w50 = fabs(this->v50min - this->v50max); |
---|
[463] | 813 | |
---|
[378] | 814 | |
---|
[464] | 815 | } |
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| 816 | |
---|
| 817 | |
---|
[719] | 818 | |
---|
[464] | 819 | void Detection::calcVelWidths(float *fluxArray, long *dim, FitsHeader &head) |
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| 820 | { |
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[528] | 821 | /// @details |
---|
| 822 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
| 823 | /// peak integrated flux. The procedure is as follows: first |
---|
| 824 | /// generate an integrated flux spectrum (summing each spatial |
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| 825 | /// pixel's spectrum); find the peak; starting at the spectral |
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| 826 | /// edges of the detection, move in or out until you reach the 20% |
---|
| 827 | /// or 50% peak flux level. Linear interpolation between points is |
---|
| 828 | /// done. |
---|
| 829 | /// |
---|
| 830 | /// \param fluxArray The array of flux values. |
---|
| 831 | /// \param dim The dimensions of the flux array. |
---|
| 832 | /// \param head FitsHeader object that contains the WCS information. |
---|
[464] | 833 | |
---|
[465] | 834 | if(dim[2] > 2){ |
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[464] | 835 | |
---|
[719] | 836 | // this->haveParams = true; |
---|
[681] | 837 | |
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[719] | 838 | // double xpt = double(this->getXcentre()); |
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| 839 | // double ypt = double(this->getYcentre()); |
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| 840 | // double zpt; |
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[464] | 841 | |
---|
[465] | 842 | float *intSpec = new float[dim[2]]; |
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[748] | 843 | long size=dim[0]*dim[1]*dim[2]; |
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| 844 | std::vector<bool> mask(size,true); |
---|
[465] | 845 | getIntSpec(*this,fluxArray,dim,mask,1.,intSpec); |
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| 846 | |
---|
[719] | 847 | // std::vector<std::pair<int,float> > goodPix; |
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| 848 | // float peak=0.; |
---|
| 849 | // int peakLoc=0; |
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| 850 | // for(int z=this->getZmin();z<=this->getZmax();z++) { |
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| 851 | // if(z==this->getZmin() || peak<intSpec[z]){ |
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| 852 | // peak = intSpec[z]; |
---|
| 853 | // peakLoc = z; |
---|
| 854 | // } |
---|
| 855 | // goodPix.push_back(std::pair<int,float>(z,intSpec[z])); |
---|
| 856 | // } |
---|
[103] | 857 | |
---|
[719] | 858 | // // finding the 20% & 50% points. Start at the velmin & velmax |
---|
| 859 | // // points. Then, if the int flux there is above the 20%/50% |
---|
| 860 | // // limit, go out, otherwise go in. This is to deal with the |
---|
| 861 | // // problems from double- (or multi-) peaked sources. |
---|
[464] | 862 | |
---|
[719] | 863 | // int z; |
---|
| 864 | // bool goLeft; |
---|
| 865 | // z=this->getZmin(); |
---|
| 866 | // goLeft = intSpec[z]>peak*0.5; |
---|
| 867 | // if(goLeft) while(z>0 && intSpec[z]>peak*0.5) z--; |
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| 868 | // else while(z<peakLoc && intSpec[z]<peak*0.5) z++; |
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| 869 | // if(z==0) this->v50min = this->velMin; |
---|
| 870 | // else{ |
---|
| 871 | // if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 872 | // else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
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| 873 | // this->v50min = head.pixToVel(xpt,ypt,zpt); |
---|
| 874 | // } |
---|
| 875 | // z=this->getZmax(); |
---|
| 876 | // goLeft = intSpec[z]<peak*0.5; |
---|
| 877 | // if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.5) z--; |
---|
| 878 | // else while(z<dim[2] && intSpec[z]>peak*0.5) z++; |
---|
| 879 | // if(z==dim[2]) this->v50max = this->velMax; |
---|
| 880 | // else{ |
---|
| 881 | // if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 882 | // else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
| 883 | // this->v50max = head.pixToVel(xpt,ypt,zpt); |
---|
| 884 | // } |
---|
| 885 | // z=this->getZmin(); |
---|
| 886 | // goLeft = intSpec[z]>peak*0.2; |
---|
| 887 | // if(goLeft) while(z>0 && intSpec[z]>peak*0.2) z--; |
---|
| 888 | // else while(z<peakLoc && intSpec[z]<peak*0.2) z++; |
---|
| 889 | // if(z==0) this->v20min = this->velMin; |
---|
| 890 | // else{ |
---|
| 891 | // if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 892 | // else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
| 893 | // this->v20min = head.pixToVel(xpt,ypt,zpt); |
---|
| 894 | // } |
---|
| 895 | // z=this->getZmax(); |
---|
| 896 | // goLeft = intSpec[z]<peak*0.2; |
---|
| 897 | // if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.2) z--; |
---|
| 898 | // else while(z<dim[2] && intSpec[z]>peak*0.2) z++; |
---|
| 899 | // if(z==dim[2]) this->v20max = this->velMax; |
---|
| 900 | // else{ |
---|
| 901 | // if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 902 | // else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
| 903 | // this->v20max = head.pixToVel(xpt,ypt,zpt); |
---|
| 904 | // } |
---|
[465] | 905 | |
---|
[719] | 906 | this->calcVelWidths(dim[2],intSpec,head); |
---|
| 907 | |
---|
[465] | 908 | delete [] intSpec; |
---|
| 909 | |
---|
[378] | 910 | } |
---|
[464] | 911 | else{ |
---|
[465] | 912 | this->v50min = this->v20min = this->velMin; |
---|
| 913 | this->v50max = this->v20max = this->velMax; |
---|
[719] | 914 | this->w20 = fabs(this->v20min - this->v20max); |
---|
| 915 | this->w50 = fabs(this->v50min - this->v50max); |
---|
[464] | 916 | } |
---|
[300] | 917 | |
---|
[719] | 918 | // this->w20 = fabs(this->v20min - this->v20max); |
---|
| 919 | // this->w50 = fabs(this->v50min - this->v50max); |
---|
[464] | 920 | |
---|
[300] | 921 | } |
---|
[378] | 922 | //-------------------------------------------------------------------- |
---|
[300] | 923 | |
---|
[378] | 924 | void Detection::setOffsets(Param &par) |
---|
| 925 | { |
---|
[528] | 926 | /// @details |
---|
| 927 | /// This function stores the values of the offsets for each cube axis. |
---|
| 928 | /// The offsets are the starting values of the cube axes that may differ from |
---|
| 929 | /// the default value of 0 (for instance, if a subsection is being used). |
---|
| 930 | /// The values will be used when the detection is outputted. |
---|
| 931 | |
---|
[378] | 932 | this->xSubOffset = par.getXOffset(); |
---|
| 933 | this->ySubOffset = par.getYOffset(); |
---|
| 934 | this->zSubOffset = par.getZOffset(); |
---|
| 935 | } |
---|
| 936 | //-------------------------------------------------------------------- |
---|
[3] | 937 | |
---|
[378] | 938 | bool Detection::hasEnoughChannels(int minNumber) |
---|
| 939 | { |
---|
[528] | 940 | /// @details |
---|
| 941 | /// A function to determine if the Detection has enough |
---|
| 942 | /// contiguous channels to meet the minimum requirement |
---|
| 943 | /// given as the argument. |
---|
| 944 | /// \param minNumber How many channels is the minimum acceptable number? |
---|
| 945 | /// \return True if there is at least one occurence of minNumber consecutive |
---|
| 946 | /// channels present to return true. False otherwise. |
---|
[3] | 947 | |
---|
[378] | 948 | // Preferred method -- need a set of minNumber consecutive channels present. |
---|
[3] | 949 | |
---|
[570] | 950 | int numChan = this->getMaxAdjacentChannels(); |
---|
| 951 | bool result = (numChan >= minNumber); |
---|
| 952 | |
---|
[378] | 953 | return result; |
---|
| 954 | |
---|
| 955 | } |
---|
| 956 | //-------------------------------------------------------------------- |
---|
[3] | 957 | |
---|
[452] | 958 | std::vector<int> Detection::getVertexSet() |
---|
| 959 | { |
---|
[528] | 960 | /// @details |
---|
| 961 | /// Gets a list of points being the end-points of 1-pixel long |
---|
| 962 | /// segments drawing a border around the spatial extend of a |
---|
| 963 | /// detection. The vector is a series of 4 integers, being: x_0, |
---|
| 964 | /// y_0, x_1, y_1. |
---|
| 965 | /// \return The vector of vertex positions. |
---|
| 966 | |
---|
[452] | 967 | std::vector<int> vertexSet; |
---|
| 968 | |
---|
| 969 | int xmin = this->getXmin() - 1; |
---|
| 970 | int xmax = this->getXmax() + 1; |
---|
| 971 | int ymin = this->getYmin() - 1; |
---|
| 972 | int ymax = this->getYmax() + 1; |
---|
| 973 | int xsize = xmax - xmin + 1; |
---|
| 974 | int ysize = ymax - ymin + 1; |
---|
| 975 | |
---|
[570] | 976 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
[452] | 977 | std::vector<bool> isObj(xsize*ysize,false); |
---|
[623] | 978 | std::vector<Voxel>::iterator vox; |
---|
| 979 | for(vox=voxlist.begin();vox<voxlist.end();vox++){ |
---|
| 980 | int pos = (vox->getX()-xmin) + |
---|
| 981 | (vox->getY()-ymin)*xsize; |
---|
[452] | 982 | isObj[pos] = true; |
---|
| 983 | } |
---|
| 984 | voxlist.clear(); |
---|
| 985 | |
---|
| 986 | for(int x=xmin; x<=xmax; x++){ |
---|
| 987 | // for each column... |
---|
| 988 | for(int y=ymin+1;y<=ymax;y++){ |
---|
| 989 | int current = (y-ymin)*xsize + x-xmin; |
---|
| 990 | int previous = (y-ymin-1)*xsize + x-xmin; |
---|
| 991 | if((isObj[current]&&!isObj[previous]) || |
---|
| 992 | (!isObj[current]&&isObj[previous])){ |
---|
| 993 | vertexSet.push_back(x); |
---|
| 994 | vertexSet.push_back(y); |
---|
| 995 | vertexSet.push_back(x+1); |
---|
| 996 | vertexSet.push_back(y); |
---|
| 997 | } |
---|
| 998 | } |
---|
| 999 | } |
---|
| 1000 | for(int y=ymin; y<=ymax; y++){ |
---|
| 1001 | // now for each row... |
---|
| 1002 | for(int x=xmin+1;x<=xmax;x++){ |
---|
| 1003 | int current = (y-ymin)*xsize + x-xmin; |
---|
| 1004 | int previous = (y-ymin)*xsize + x-xmin - 1; |
---|
| 1005 | if((isObj[current]&&!isObj[previous]) || |
---|
| 1006 | (!isObj[current]&&isObj[previous])){ |
---|
| 1007 | vertexSet.push_back(x); |
---|
| 1008 | vertexSet.push_back(y); |
---|
| 1009 | vertexSet.push_back(x); |
---|
| 1010 | vertexSet.push_back(y+1); |
---|
| 1011 | } |
---|
| 1012 | } |
---|
| 1013 | } |
---|
| 1014 | |
---|
| 1015 | return vertexSet; |
---|
| 1016 | |
---|
| 1017 | } |
---|
| 1018 | |
---|
[747] | 1019 | |
---|
| 1020 | void Detection::addDetection(Detection other) |
---|
| 1021 | { |
---|
| 1022 | for(std::map<long, Object2D>::iterator it = other.chanlist.begin(); it!=other.chanlist.end();it++) |
---|
| 1023 | this->addChannel(it->first, it->second); |
---|
| 1024 | this->haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
| 1025 | } |
---|
[624] | 1026 | |
---|
| 1027 | Detection operator+ (Detection lhs, Detection rhs) |
---|
| 1028 | { |
---|
| 1029 | Detection output = lhs; |
---|
| 1030 | for(std::map<long, Object2D>::iterator it = rhs.chanlist.begin(); it!=rhs.chanlist.end();it++) |
---|
| 1031 | output.addChannel(it->first, it->second); |
---|
[681] | 1032 | output.haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
[624] | 1033 | return output; |
---|
| 1034 | } |
---|
| 1035 | |
---|
| 1036 | |
---|
| 1037 | |
---|
| 1038 | |
---|
[3] | 1039 | } |
---|