[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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[863] | 31 | #include <map> |
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[3] | 32 | #include <string> |
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[394] | 33 | #include <wcslib/wcs.h> |
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[69] | 34 | #include <math.h> |
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[393] | 35 | #include <duchamp/duchamp.hh> |
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| 36 | #include <duchamp/param.hh> |
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| 37 | #include <duchamp/fitsHeader.hh> |
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| 38 | #include <duchamp/Utils/utils.hh> |
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| 39 | #include <duchamp/PixelMap/Voxel.hh> |
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| 40 | #include <duchamp/PixelMap/Object3D.hh> |
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| 41 | #include <duchamp/Detection/detection.hh> |
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[463] | 42 | #include <duchamp/Cubes/cubeUtils.hh> |
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[570] | 43 | #include <duchamp/Detection/columns.hh> |
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[3] | 44 | |
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[258] | 45 | using namespace PixelInfo; |
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| 46 | |
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[378] | 47 | namespace duchamp |
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[365] | 48 | { |
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| 49 | |
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[570] | 50 | void Detection::defaultDetection() |
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[378] | 51 | { |
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[570] | 52 | this->xSubOffset = 0; |
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| 53 | this->ySubOffset = 0; |
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| 54 | this->zSubOffset = 0; |
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[681] | 55 | this->haveParams = false; |
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[570] | 56 | this->totalFlux = 0.; |
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| 57 | this->peakFlux = 0.; |
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| 58 | this->intFlux = 0.; |
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| 59 | this->xpeak = 0; |
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| 60 | this->ypeak = 0; |
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| 61 | this->zpeak = 0; |
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| 62 | this->peakSNR = 0.; |
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| 63 | this->xCentroid = 0.; |
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| 64 | this->yCentroid = 0.; |
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| 65 | this->zCentroid = 0.; |
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| 66 | this->centreType="centroid"; |
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[378] | 67 | this->negSource = false; |
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| 68 | this->flagText=""; |
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[468] | 69 | this->id = -1; |
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[570] | 70 | this->name = ""; |
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| 71 | this->flagWCS=false; |
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| 72 | this->specOK = true; |
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| 73 | this->raS = ""; |
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| 74 | this->decS = ""; |
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| 75 | this->ra = 0.; |
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| 76 | this->dec = 0.; |
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| 77 | this->raWidth = 0.; |
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| 78 | this->decWidth = 0.; |
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| 79 | this->majorAxis = 0.; |
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| 80 | this->minorAxis = 0.; |
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| 81 | this->posang = 0.; |
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| 82 | this->specUnits = ""; |
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| 83 | this->fluxUnits = ""; |
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| 84 | this->intFluxUnits = ""; |
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| 85 | this->lngtype = "RA"; |
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| 86 | this->lattype = "DEC"; |
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| 87 | this->vel = 0.; |
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| 88 | this->velWidth = 0.; |
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| 89 | this->velMin = 0.; |
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| 90 | this->velMax = 0.; |
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| 91 | this->w20 = 0.; |
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| 92 | this->v20min = 0.; |
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| 93 | this->v20max = 0.; |
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| 94 | this->w50 = 0.; |
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| 95 | this->v50min = 0.; |
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| 96 | this->v50max = 0.; |
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| 97 | this->posPrec = Column::prPOS; |
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| 98 | this->xyzPrec = Column::prXYZ; |
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| 99 | this->fintPrec = Column::prFLUX; |
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| 100 | this->fpeakPrec = Column::prFLUX; |
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| 101 | this->velPrec = Column::prVEL; |
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| 102 | this->snrPrec = Column::prSNR; |
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[378] | 103 | } |
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[218] | 104 | |
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[570] | 105 | Detection::Detection(): |
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| 106 | Object3D() |
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[378] | 107 | { |
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[570] | 108 | this->defaultDetection(); |
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| 109 | } |
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| 110 | |
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| 111 | Detection::Detection(const Object3D& o): |
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| 112 | Object3D(o) |
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| 113 | { |
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| 114 | this->defaultDetection(); |
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| 115 | } |
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| 116 | |
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| 117 | Detection::Detection(const Detection& d): |
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| 118 | Object3D(d) |
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| 119 | { |
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[378] | 120 | operator=(d); |
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| 121 | } |
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[218] | 122 | |
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[378] | 123 | Detection& Detection::operator= (const Detection& d) |
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| 124 | { |
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[570] | 125 | ((Object3D &) *this) = d; |
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[378] | 126 | this->xSubOffset = d.xSubOffset; |
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| 127 | this->ySubOffset = d.ySubOffset; |
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| 128 | this->zSubOffset = d.zSubOffset; |
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[681] | 129 | this->haveParams = d.haveParams; |
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[378] | 130 | this->totalFlux = d.totalFlux; |
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[461] | 131 | this->intFlux = d.intFlux; |
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[378] | 132 | this->peakFlux = d.peakFlux; |
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| 133 | this->xpeak = d.xpeak; |
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| 134 | this->ypeak = d.ypeak; |
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| 135 | this->zpeak = d.zpeak; |
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| 136 | this->peakSNR = d.peakSNR; |
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| 137 | this->xCentroid = d.xCentroid; |
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| 138 | this->yCentroid = d.yCentroid; |
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| 139 | this->zCentroid = d.zCentroid; |
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| 140 | this->centreType = d.centreType; |
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| 141 | this->negSource = d.negSource; |
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| 142 | this->flagText = d.flagText; |
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| 143 | this->id = d.id; |
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| 144 | this->name = d.name; |
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| 145 | this->flagWCS = d.flagWCS; |
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| 146 | this->specOK = d.specOK; |
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| 147 | this->raS = d.raS; |
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| 148 | this->decS = d.decS; |
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| 149 | this->ra = d.ra; |
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[461] | 150 | this->dec = d.dec; |
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| 151 | this->raWidth = d.raWidth; |
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[378] | 152 | this->decWidth = d.decWidth; |
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[473] | 153 | this->majorAxis = d.majorAxis; |
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| 154 | this->minorAxis = d.minorAxis; |
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| 155 | this->posang = d.posang; |
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[378] | 156 | this->specUnits = d.specUnits; |
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| 157 | this->fluxUnits = d.fluxUnits; |
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| 158 | this->intFluxUnits = d.intFluxUnits; |
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[461] | 159 | this->lngtype = d.lngtype; |
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| 160 | this->lattype = d.lattype; |
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[378] | 161 | this->vel = d.vel; |
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| 162 | this->velWidth = d.velWidth; |
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| 163 | this->velMin = d.velMin; |
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| 164 | this->velMax = d.velMax; |
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[463] | 165 | this->w20 = d.w20; |
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| 166 | this->v20min = d.v20min; |
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| 167 | this->v20max = d.v20max; |
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| 168 | this->w50 = d.w50; |
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| 169 | this->v50min = d.v50min; |
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| 170 | this->v50max = d.v50max; |
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[378] | 171 | this->posPrec = d.posPrec; |
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| 172 | this->xyzPrec = d.xyzPrec; |
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| 173 | this->fintPrec = d.fintPrec; |
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| 174 | this->fpeakPrec = d.fpeakPrec; |
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[461] | 175 | this->velPrec = d.velPrec; |
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[378] | 176 | this->snrPrec = d.snrPrec; |
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| 177 | return *this; |
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| 178 | } |
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[3] | 179 | |
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[378] | 180 | //-------------------------------------------------------------------- |
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[570] | 181 | float Detection::getXcentre() |
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| 182 | { |
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| 183 | if(this->centreType=="peak") return this->xpeak; |
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| 184 | else if(this->centreType=="average") return this->getXaverage(); |
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| 185 | else return this->xCentroid; |
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| 186 | } |
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[258] | 187 | |
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[570] | 188 | float Detection::getYcentre() |
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| 189 | { |
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| 190 | if(this->centreType=="peak") return this->ypeak; |
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| 191 | else if(this->centreType=="average") return this->getYaverage(); |
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| 192 | else return this->yCentroid; |
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| 193 | } |
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| 194 | |
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| 195 | float Detection::getZcentre() |
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| 196 | { |
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| 197 | if(this->centreType=="peak") return this->zpeak; |
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| 198 | else if(this->centreType=="average") return this->getZaverage(); |
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| 199 | else return this->zCentroid; |
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| 200 | } |
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| 201 | |
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| 202 | //-------------------------------------------------------------------- |
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| 203 | |
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[417] | 204 | bool Detection::voxelListsMatch(std::vector<Voxel> voxelList) |
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| 205 | { |
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[528] | 206 | /// @details |
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| 207 | /// A test to see whether there is a 1-1 correspondence between |
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| 208 | /// the given list of Voxels and the voxel positions contained in |
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| 209 | /// this Detection's pixel list. No testing of the fluxes of the |
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| 210 | /// Voxels is done. |
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| 211 | /// |
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| 212 | /// \param voxelList The std::vector list of Voxels to be tested. |
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[417] | 213 | |
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| 214 | bool listsMatch = true; |
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| 215 | // compare sizes |
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| 216 | listsMatch = listsMatch && (voxelList.size() == this->getSize()); |
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| 217 | if(!listsMatch) return listsMatch; |
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| 218 | |
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[463] | 219 | // make sure all Detection pixels are in voxel list |
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| 220 | listsMatch = listsMatch && this->voxelListCovered(voxelList); |
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| 221 | |
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[417] | 222 | // make sure all voxels are in Detection |
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[623] | 223 | std::vector<Voxel>::iterator vox; |
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| 224 | for(vox=voxelList.begin();vox<voxelList.end();vox++) |
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| 225 | listsMatch = listsMatch && this->isInObject(*vox); |
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[463] | 226 | |
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| 227 | return listsMatch; |
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| 228 | |
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| 229 | } |
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| 230 | //-------------------------------------------------------------------- |
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| 231 | |
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| 232 | bool Detection::voxelListCovered(std::vector<Voxel> voxelList) |
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| 233 | { |
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[528] | 234 | /// @details |
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| 235 | /// A test to see whether the given list of Voxels contains each |
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| 236 | /// position in this Detection's pixel list. It does not look for |
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| 237 | /// a 1-1 correspondence: the given list can be a super-set of the |
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| 238 | /// Detection. No testing of the fluxes of the Voxels is done. |
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| 239 | /// |
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| 240 | /// \param voxelList The std::vector list of Voxels to be tested. |
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[463] | 241 | |
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| 242 | bool listsMatch = true; |
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| 243 | |
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[417] | 244 | // make sure all Detection pixels are in voxel list |
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[623] | 245 | size_t v1=0; |
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[570] | 246 | std::vector<Voxel> detpixlist = this->getPixelSet(); |
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| 247 | while(listsMatch && v1<detpixlist.size()){ |
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[417] | 248 | bool inList = false; |
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[623] | 249 | size_t v2=0; |
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[417] | 250 | while(!inList && v2<voxelList.size()){ |
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[570] | 251 | inList = inList || detpixlist[v1].match(voxelList[v2]); |
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[417] | 252 | v2++; |
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| 253 | } |
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| 254 | listsMatch = listsMatch && inList; |
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[418] | 255 | v1++; |
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[417] | 256 | } |
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| 257 | |
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| 258 | return listsMatch; |
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| 259 | |
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| 260 | } |
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| 261 | //-------------------------------------------------------------------- |
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| 262 | |
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| 263 | void Detection::calcFluxes(std::vector<Voxel> voxelList) |
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| 264 | { |
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[528] | 265 | /// @details |
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| 266 | /// A function that calculates total & peak fluxes (and the location |
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| 267 | /// of the peak flux) for a Detection. |
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| 268 | /// |
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| 269 | /// \param fluxArray The array of flux values to calculate the |
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| 270 | /// flux parameters from. |
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| 271 | /// \param dim The dimensions of the flux array. |
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[681] | 272 | |
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| 273 | // this->haveParams = true; |
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[417] | 274 | |
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| 275 | this->totalFlux = this->peakFlux = 0; |
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| 276 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 277 | |
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| 278 | // first check that the voxel list and the Detection's pixel list |
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| 279 | // have a 1-1 correspondence |
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| 280 | |
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[463] | 281 | if(!this->voxelListCovered(voxelList)){ |
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[417] | 282 | duchampError("Detection::calcFluxes","Voxel list provided does not match"); |
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| 283 | return; |
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| 284 | } |
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| 285 | |
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[623] | 286 | std::vector<Voxel>::iterator vox; |
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| 287 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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| 288 | if(this->isInObject(*vox)){ |
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| 289 | long x = vox->getX(); |
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| 290 | long y = vox->getY(); |
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| 291 | long z = vox->getZ(); |
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| 292 | float f = vox->getF(); |
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[463] | 293 | this->totalFlux += f; |
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| 294 | this->xCentroid += x*f; |
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| 295 | this->yCentroid += y*f; |
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| 296 | this->zCentroid += z*f; |
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[623] | 297 | if( (vox==voxelList.begin()) || //first time round |
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[463] | 298 | (this->negSource&&(f<this->peakFlux)) || |
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| 299 | (!this->negSource&&(f>this->peakFlux)) ) |
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| 300 | { |
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| 301 | this->peakFlux = f; |
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| 302 | this->xpeak = x; |
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| 303 | this->ypeak = y; |
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| 304 | this->zpeak = z; |
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| 305 | } |
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| 306 | } |
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[417] | 307 | } |
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| 308 | |
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| 309 | this->xCentroid /= this->totalFlux; |
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| 310 | this->yCentroid /= this->totalFlux; |
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| 311 | this->zCentroid /= this->totalFlux; |
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| 312 | } |
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| 313 | //-------------------------------------------------------------------- |
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| 314 | |
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[863] | 315 | void Detection::calcFluxes(std::map<Voxel,float> &voxelMap) |
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| 316 | { |
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| 317 | /// @details |
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| 318 | /// A function that calculates total & peak fluxes (and the location |
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| 319 | /// of the peak flux) for a Detection. |
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| 320 | /// |
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| 321 | /// \param fluxArray The array of flux values to calculate the |
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| 322 | /// flux parameters from. |
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| 323 | /// \param dim The dimensions of the flux array. |
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| 324 | |
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| 325 | // this->haveParams = true; |
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| 326 | |
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| 327 | this->totalFlux = this->peakFlux = 0; |
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| 328 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 329 | |
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| 330 | std::vector<Voxel> voxelList = this->getPixelSet(); |
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| 331 | std::vector<Voxel>::iterator vox; |
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| 332 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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| 333 | if(voxelMap.find(*vox) == voxelMap.end()){ |
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| 334 | duchampError("Detection::calcFluxes","Voxel list provided does not match"); |
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| 335 | return; |
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| 336 | } |
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| 337 | else { |
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| 338 | long x = vox->getX(); |
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| 339 | long y = vox->getY(); |
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| 340 | long z = vox->getZ(); |
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| 341 | float f = voxelMap[*vox]; |
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| 342 | this->totalFlux += f; |
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| 343 | this->xCentroid += x*f; |
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| 344 | this->yCentroid += y*f; |
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| 345 | this->zCentroid += z*f; |
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| 346 | if( (vox==voxelList.begin()) || //first time round |
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| 347 | (this->negSource&&(f<this->peakFlux)) || |
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| 348 | (!this->negSource&&(f>this->peakFlux)) ) |
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| 349 | { |
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| 350 | this->peakFlux = f; |
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| 351 | this->xpeak = x; |
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| 352 | this->ypeak = y; |
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| 353 | this->zpeak = z; |
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| 354 | } |
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| 355 | } |
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| 356 | } |
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| 357 | |
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| 358 | this->xCentroid /= this->totalFlux; |
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| 359 | this->yCentroid /= this->totalFlux; |
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| 360 | this->zCentroid /= this->totalFlux; |
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| 361 | } |
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| 362 | //-------------------------------------------------------------------- |
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| 363 | |
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[378] | 364 | void Detection::calcFluxes(float *fluxArray, long *dim) |
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| 365 | { |
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[528] | 366 | /// @details |
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| 367 | /// A function that calculates total & peak fluxes (and the location |
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| 368 | /// of the peak flux) for a Detection. |
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| 369 | /// |
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| 370 | /// \param fluxArray The array of flux values to calculate the |
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| 371 | /// flux parameters from. |
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| 372 | /// \param dim The dimensions of the flux array. |
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[258] | 373 | |
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[681] | 374 | // this->haveParams = true; |
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| 375 | |
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[378] | 376 | this->totalFlux = this->peakFlux = 0; |
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| 377 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 378 | |
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[570] | 379 | std::vector<Voxel> voxList = this->getPixelSet(); |
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[473] | 380 | std::vector<Voxel>::iterator vox=voxList.begin(); |
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| 381 | for(;vox<voxList.end();vox++){ |
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[378] | 382 | |
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[473] | 383 | long x=vox->getX(); |
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| 384 | long y=vox->getY(); |
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| 385 | long z=vox->getZ(); |
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| 386 | long ind = vox->arrayIndex(dim); |
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| 387 | float f = fluxArray[ind]; |
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| 388 | this->totalFlux += f; |
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| 389 | this->xCentroid += x*f; |
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| 390 | this->yCentroid += y*f; |
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| 391 | this->zCentroid += z*f; |
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| 392 | if( (vox==voxList.begin()) || |
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| 393 | (this->negSource&&(f<this->peakFlux)) || |
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| 394 | (!this->negSource&&(f>this->peakFlux)) ) |
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| 395 | { |
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| 396 | this->peakFlux = f; |
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| 397 | this->xpeak = x; |
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| 398 | this->ypeak = y; |
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| 399 | this->zpeak = z; |
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[378] | 400 | } |
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[473] | 401 | |
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[45] | 402 | } |
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[378] | 403 | |
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| 404 | this->xCentroid /= this->totalFlux; |
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| 405 | this->yCentroid /= this->totalFlux; |
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| 406 | this->zCentroid /= this->totalFlux; |
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[263] | 407 | } |
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[378] | 408 | //-------------------------------------------------------------------- |
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[263] | 409 | |
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[417] | 410 | void Detection::calcWCSparams(FitsHeader &head) |
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[378] | 411 | { |
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[528] | 412 | /// @details |
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| 413 | /// Use the input wcs to calculate the position and velocity |
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| 414 | /// information for the Detection. |
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| 415 | /// Quantities calculated: |
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| 416 | /// <ul><li> RA: ra [deg], ra (string), ra width. |
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| 417 | /// <li> Dec: dec [deg], dec (string), dec width. |
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| 418 | /// <li> Vel: vel [km/s], min & max vel, vel width. |
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| 419 | /// <li> coord type for all three axes, nuRest, |
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| 420 | /// <li> name (IAU-style, in equatorial or Galactic) |
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| 421 | /// </ul> |
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| 422 | /// |
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| 423 | /// Note that the regular parameters are NOT recalculated! |
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| 424 | /// |
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| 425 | /// \param head FitsHeader object that contains the WCS information. |
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[3] | 426 | |
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[378] | 427 | if(head.isWCS()){ |
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[3] | 428 | |
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[378] | 429 | double *pixcrd = new double[15]; |
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| 430 | double *world = new double[15]; |
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| 431 | /* |
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| 432 | define a five-point array in 3D: |
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| 433 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
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| 434 | [note: x = central point, x1 = minimum x, x2 = maximum x etc.] |
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| 435 | and convert to world coordinates. |
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| 436 | */ |
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| 437 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->getXcentre(); |
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| 438 | pixcrd[9] = this->getXmin()-0.5; |
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| 439 | pixcrd[12] = this->getXmax()+0.5; |
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| 440 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->getYcentre(); |
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| 441 | pixcrd[10] = this->getYmin()-0.5; |
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| 442 | pixcrd[13] = this->getYmax()+0.5; |
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| 443 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->getZcentre(); |
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| 444 | pixcrd[5] = this->getZmin(); |
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| 445 | pixcrd[8] = this->getZmax(); |
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| 446 | int flag = head.pixToWCS(pixcrd, world, 5); |
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| 447 | delete [] pixcrd; |
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| 448 | if(flag!=0) duchampError("calcWCSparams", |
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| 449 | "Error in calculating the WCS for this object.\n"); |
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| 450 | else{ |
---|
[60] | 451 | |
---|
[378] | 452 | // world now has the WCS coords for the five points |
---|
| 453 | // -- use this to work out WCS params |
---|
[22] | 454 | |
---|
[681] | 455 | this->haveParams = true; |
---|
| 456 | |
---|
[378] | 457 | this->specOK = head.canUseThirdAxis(); |
---|
| 458 | this->lngtype = head.WCS().lngtyp; |
---|
| 459 | this->lattype = head.WCS().lattyp; |
---|
| 460 | this->specUnits = head.getSpectralUnits(); |
---|
| 461 | this->fluxUnits = head.getFluxUnits(); |
---|
| 462 | // if fluxUnits are eg. Jy/beam, make intFluxUnits = Jy km/s |
---|
| 463 | this->intFluxUnits = head.getIntFluxUnits(); |
---|
| 464 | this->ra = world[0]; |
---|
| 465 | this->dec = world[1]; |
---|
| 466 | this->raS = decToDMS(this->ra, this->lngtype); |
---|
| 467 | this->decS = decToDMS(this->dec,this->lattype); |
---|
| 468 | this->raWidth = angularSeparation(world[9],world[1], |
---|
| 469 | world[12],world[1]) * 60.; |
---|
| 470 | this->decWidth = angularSeparation(world[0],world[10], |
---|
| 471 | world[0],world[13]) * 60.; |
---|
[473] | 472 | |
---|
[570] | 473 | Object2D spatMap = this->getSpatialMap(); |
---|
[473] | 474 | std::pair<double,double> axes = spatMap.getPrincipleAxes(); |
---|
| 475 | this->majorAxis = std::max(axes.first,axes.second) * head.getAvPixScale(); |
---|
| 476 | this->minorAxis = std::min(axes.first,axes.second) * head.getAvPixScale(); |
---|
| 477 | this->posang = spatMap.getPositionAngle() * 180. / M_PI; |
---|
| 478 | |
---|
[378] | 479 | this->name = head.getIAUName(this->ra, this->dec); |
---|
| 480 | this->vel = head.specToVel(world[2]); |
---|
| 481 | this->velMin = head.specToVel(world[5]); |
---|
| 482 | this->velMax = head.specToVel(world[8]); |
---|
| 483 | this->velWidth = fabs(this->velMax - this->velMin); |
---|
[3] | 484 | |
---|
[378] | 485 | this->flagWCS = true; |
---|
| 486 | } |
---|
| 487 | delete [] world; |
---|
| 488 | |
---|
[270] | 489 | } |
---|
[103] | 490 | } |
---|
[378] | 491 | //-------------------------------------------------------------------- |
---|
[3] | 492 | |
---|
[719] | 493 | void Detection::calcIntegFlux(long zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
[417] | 494 | { |
---|
[528] | 495 | /// @details |
---|
| 496 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
| 497 | /// putting velocity in units of km/s. |
---|
| 498 | /// The fluxes used are taken from the Voxels, rather than an |
---|
| 499 | /// array of flux values. |
---|
| 500 | /// Integrates over full spatial and velocity range as given |
---|
| 501 | /// by the extrema calculated by calcWCSparams. |
---|
| 502 | /// |
---|
| 503 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
| 504 | /// corrected by the beam size (in pixels). This is done by |
---|
| 505 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
| 506 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
| 507 | /// pix/beam --> Jy) |
---|
| 508 | /// |
---|
[719] | 509 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
[528] | 510 | /// \param voxelList The list of Voxels with flux information |
---|
| 511 | /// \param head FitsHeader object that contains the WCS information. |
---|
[417] | 512 | |
---|
[463] | 513 | const int border = 1; |
---|
| 514 | |
---|
| 515 | if(!this->voxelListCovered(voxelList)){ |
---|
[417] | 516 | duchampError("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
| 517 | return; |
---|
| 518 | } |
---|
| 519 | |
---|
[513] | 520 | if(!head.is2D()){ |
---|
[417] | 521 | |
---|
[681] | 522 | this->haveParams = true; |
---|
| 523 | |
---|
[417] | 524 | // include one pixel either side in each direction |
---|
[463] | 525 | long xsize = (this->getXmax()-this->getXmin()+border*2+1); |
---|
| 526 | long ysize = (this->getYmax()-this->getYmin()+border*2+1); |
---|
| 527 | long zsize = (this->getZmax()-this->getZmin()+border*2+1); |
---|
| 528 | long size = xsize*ysize*zsize; |
---|
[473] | 529 | std::vector <bool> isObj(size,false); |
---|
[463] | 530 | double *localFlux = new double[size]; |
---|
| 531 | for(int i=0;i<size;i++) localFlux[i]=0.; |
---|
[417] | 532 | |
---|
[623] | 533 | std::vector<Voxel>::iterator vox; |
---|
| 534 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 535 | if(this->isInObject(*vox)){ |
---|
| 536 | long x = vox->getX(); |
---|
| 537 | long y = vox->getY(); |
---|
| 538 | long z = vox->getZ(); |
---|
[463] | 539 | long pos = (x-this->getXmin()+border) + (y-this->getYmin()+border)*xsize |
---|
| 540 | + (z-this->getZmin()+border)*xsize*ysize; |
---|
[623] | 541 | localFlux[pos] = vox->getF(); |
---|
[463] | 542 | isObj[pos] = true; |
---|
| 543 | } |
---|
[417] | 544 | } |
---|
| 545 | |
---|
| 546 | // work out the WCS coords for each pixel |
---|
[463] | 547 | double *world = new double[size]; |
---|
[417] | 548 | double xpt,ypt,zpt; |
---|
| 549 | for(int i=0;i<xsize*ysize*zsize;i++){ |
---|
[463] | 550 | xpt = double( this->getXmin() - border + i%xsize ); |
---|
| 551 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
---|
| 552 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
---|
[417] | 553 | world[i] = head.pixToVel(xpt,ypt,zpt); |
---|
| 554 | } |
---|
| 555 | |
---|
| 556 | double integrated = 0.; |
---|
| 557 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
---|
| 558 | for(int z=0; z<zsize; z++){ |
---|
| 559 | int pos = z*xsize*ysize + pix; |
---|
| 560 | if(isObj[pos]){ // if it's an object pixel... |
---|
| 561 | double deltaVel; |
---|
| 562 | if(z==0) |
---|
| 563 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
| 564 | else if(z==(zsize-1)) |
---|
| 565 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
| 566 | else |
---|
| 567 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
| 568 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
| 569 | } |
---|
| 570 | } |
---|
| 571 | } |
---|
| 572 | this->intFlux = integrated; |
---|
| 573 | |
---|
| 574 | delete [] world; |
---|
| 575 | delete [] localFlux; |
---|
| 576 | |
---|
[719] | 577 | calcVelWidths(zdim,voxelList,head); |
---|
[464] | 578 | |
---|
[417] | 579 | } |
---|
| 580 | else // in this case there is just a 2D image. |
---|
| 581 | this->intFlux = this->totalFlux; |
---|
| 582 | |
---|
| 583 | if(head.isWCS()){ |
---|
| 584 | // correct for the beam size if the flux units string ends in "/beam" |
---|
[788] | 585 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
[417] | 586 | } |
---|
| 587 | |
---|
| 588 | } |
---|
| 589 | //-------------------------------------------------------------------- |
---|
| 590 | |
---|
[863] | 591 | void Detection::calcIntegFlux(long zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
| 592 | { |
---|
| 593 | /// @details |
---|
| 594 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
| 595 | /// putting velocity in units of km/s. |
---|
| 596 | /// The fluxes used are taken from the Voxels, rather than an |
---|
| 597 | /// array of flux values. |
---|
| 598 | /// Integrates over full spatial and velocity range as given |
---|
| 599 | /// by the extrema calculated by calcWCSparams. |
---|
| 600 | /// |
---|
| 601 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
| 602 | /// corrected by the beam size (in pixels). This is done by |
---|
| 603 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
| 604 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
| 605 | /// pix/beam --> Jy) |
---|
| 606 | /// |
---|
| 607 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
| 608 | /// \param voxelList The list of Voxels with flux information |
---|
| 609 | /// \param head FitsHeader object that contains the WCS information. |
---|
| 610 | |
---|
| 611 | const int border = 1; |
---|
| 612 | |
---|
| 613 | if(!head.is2D()){ |
---|
| 614 | |
---|
| 615 | this->haveParams = true; |
---|
| 616 | |
---|
| 617 | // include one pixel either side in each direction |
---|
| 618 | long xsize = (this->getXmax()-this->getXmin()+border*2+1); |
---|
| 619 | long ysize = (this->getYmax()-this->getYmin()+border*2+1); |
---|
| 620 | long zsize = (this->getZmax()-this->getZmin()+border*2+1); |
---|
| 621 | long size = xsize*ysize*zsize; |
---|
| 622 | std::vector <bool> isObj(size,false); |
---|
| 623 | double *localFlux = new double[size]; |
---|
| 624 | for(int i=0;i<size;i++) localFlux[i]=0.; |
---|
| 625 | |
---|
| 626 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
| 627 | std::vector<Voxel>::iterator vox; |
---|
| 628 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 629 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
| 630 | duchampError("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
| 631 | return; |
---|
| 632 | } |
---|
| 633 | else { |
---|
| 634 | long x = vox->getX(); |
---|
| 635 | long y = vox->getY(); |
---|
| 636 | long z = vox->getZ(); |
---|
| 637 | long pos = (x-this->getXmin()+border) + (y-this->getYmin()+border)*xsize |
---|
| 638 | + (z-this->getZmin()+border)*xsize*ysize; |
---|
| 639 | localFlux[pos] = voxelMap[*vox]; |
---|
| 640 | isObj[pos] = true; |
---|
| 641 | } |
---|
| 642 | } |
---|
| 643 | |
---|
| 644 | // work out the WCS coords for each pixel |
---|
| 645 | double *world = new double[size]; |
---|
| 646 | double xpt,ypt,zpt; |
---|
| 647 | for(int i=0;i<xsize*ysize*zsize;i++){ |
---|
| 648 | xpt = double( this->getXmin() - border + i%xsize ); |
---|
| 649 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
---|
| 650 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
---|
| 651 | world[i] = head.pixToVel(xpt,ypt,zpt); |
---|
| 652 | } |
---|
| 653 | |
---|
| 654 | double integrated = 0.; |
---|
| 655 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
---|
| 656 | for(int z=0; z<zsize; z++){ |
---|
| 657 | int pos = z*xsize*ysize + pix; |
---|
| 658 | if(isObj[pos]){ // if it's an object pixel... |
---|
| 659 | double deltaVel; |
---|
| 660 | if(z==0) |
---|
| 661 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
| 662 | else if(z==(zsize-1)) |
---|
| 663 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
| 664 | else |
---|
| 665 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
| 666 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
| 667 | } |
---|
| 668 | } |
---|
| 669 | } |
---|
| 670 | this->intFlux = integrated; |
---|
| 671 | |
---|
| 672 | delete [] world; |
---|
| 673 | delete [] localFlux; |
---|
| 674 | |
---|
| 675 | calcVelWidths(zdim,voxelMap,head); |
---|
| 676 | |
---|
| 677 | } |
---|
| 678 | else // in this case there is just a 2D image. |
---|
| 679 | this->intFlux = this->totalFlux; |
---|
| 680 | |
---|
| 681 | if(head.isWCS()){ |
---|
| 682 | // correct for the beam size if the flux units string ends in "/beam" |
---|
| 683 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
| 684 | } |
---|
| 685 | |
---|
| 686 | } |
---|
| 687 | //-------------------------------------------------------------------- |
---|
| 688 | |
---|
[378] | 689 | void Detection::calcIntegFlux(float *fluxArray, long *dim, FitsHeader &head) |
---|
| 690 | { |
---|
[528] | 691 | /// @details |
---|
| 692 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
| 693 | /// putting velocity in units of km/s. |
---|
| 694 | /// Integrates over full spatial and velocity range as given |
---|
| 695 | /// by the extrema calculated by calcWCSparams. |
---|
| 696 | /// |
---|
| 697 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
| 698 | /// corrected by the beam size (in pixels). This is done by |
---|
| 699 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
| 700 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
| 701 | /// pix/beam --> Jy) |
---|
| 702 | /// |
---|
| 703 | /// \param fluxArray The array of flux values. |
---|
| 704 | /// \param dim The dimensions of the flux array. |
---|
| 705 | /// \param head FitsHeader object that contains the WCS information. |
---|
[3] | 706 | |
---|
[513] | 707 | if(!head.is2D()){ |
---|
[271] | 708 | |
---|
[681] | 709 | this->haveParams = true; |
---|
| 710 | |
---|
[378] | 711 | // include one pixel either side in each direction |
---|
[570] | 712 | long xsize = (this->xmax-this->xmin+3); |
---|
| 713 | long ysize = (this->ymax-this->ymin+3); |
---|
| 714 | long zsize = (this->zmax-this->zmin+3); |
---|
[463] | 715 | long size = xsize*ysize*zsize; |
---|
[473] | 716 | std::vector <bool> isObj(size,false); |
---|
[463] | 717 | double *localFlux = new double[size]; |
---|
| 718 | for(int i=0;i<size;i++) localFlux[i]=0.; |
---|
[378] | 719 | // work out which pixels are object pixels |
---|
[774] | 720 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
| 721 | for(std::vector<Voxel>::iterator v=voxlist.begin();v<voxlist.end();v++){ |
---|
| 722 | long pos=(v->getX()-this->xmin+1) + (v->getY()-this->ymin+1)*xsize |
---|
| 723 | + (v->getZ()-this->zmin+1)*xsize*ysize; |
---|
[778] | 724 | localFlux[pos] = fluxArray[v->arrayIndex(dim)]; |
---|
[774] | 725 | isObj[pos] = true; |
---|
[258] | 726 | } |
---|
[22] | 727 | |
---|
[378] | 728 | // work out the WCS coords for each pixel |
---|
[463] | 729 | double *world = new double[size]; |
---|
[378] | 730 | double xpt,ypt,zpt; |
---|
[781] | 731 | int i=0; |
---|
| 732 | for(int z=0;z<zsize;z++){ |
---|
| 733 | for(int y=0;y<ysize;y++){ |
---|
| 734 | for(int x=0;x<xsize;x++){ |
---|
| 735 | xpt=double(this->xmin - 1 + x); |
---|
| 736 | ypt=double(this->ymin - 1 + y); |
---|
| 737 | zpt=double(this->zmin - 1 + z); |
---|
| 738 | world[i++] = head.pixToVel(xpt,ypt,zpt); |
---|
| 739 | } |
---|
| 740 | } |
---|
[378] | 741 | } |
---|
[3] | 742 | |
---|
[378] | 743 | double integrated = 0.; |
---|
| 744 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
---|
| 745 | for(int z=0; z<zsize; z++){ |
---|
| 746 | int pos = z*xsize*ysize + pix; |
---|
| 747 | if(isObj[pos]){ // if it's an object pixel... |
---|
| 748 | double deltaVel; |
---|
| 749 | if(z==0) |
---|
| 750 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
| 751 | else if(z==(zsize-1)) |
---|
| 752 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
| 753 | else |
---|
| 754 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
| 755 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
| 756 | } |
---|
[271] | 757 | } |
---|
[3] | 758 | } |
---|
[378] | 759 | this->intFlux = integrated; |
---|
| 760 | |
---|
[464] | 761 | delete [] world; |
---|
| 762 | delete [] localFlux; |
---|
[463] | 763 | |
---|
[464] | 764 | calcVelWidths(fluxArray, dim, head); |
---|
[463] | 765 | |
---|
[464] | 766 | } |
---|
| 767 | else // in this case there is just a 2D image. |
---|
| 768 | this->intFlux = this->totalFlux; |
---|
[463] | 769 | |
---|
[464] | 770 | if(head.isWCS()){ |
---|
[789] | 771 | // correct for the beam size if the flux units string ends in "/beam" and we have beam info |
---|
[788] | 772 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
[464] | 773 | } |
---|
[463] | 774 | |
---|
[464] | 775 | } |
---|
| 776 | //-------------------------------------------------------------------- |
---|
| 777 | |
---|
[719] | 778 | void Detection::calcVelWidths(long zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
[464] | 779 | { |
---|
[528] | 780 | /// @details |
---|
| 781 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
| 782 | /// peak integrated flux. The procedure is as follows: first |
---|
| 783 | /// generate an integrated flux spectrum (using all given voxels |
---|
| 784 | /// that lie in the object's spatial map); find the peak; starting |
---|
| 785 | /// at the spectral edges of the detection, move in or out until |
---|
| 786 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
| 787 | /// between points is done. |
---|
| 788 | /// |
---|
[719] | 789 | /// \param zdim The size of the spectral axis in the cube |
---|
[528] | 790 | /// \param voxelList The list of Voxels with flux information |
---|
| 791 | /// \param head FitsHeader object that contains the WCS information. |
---|
[464] | 792 | |
---|
[719] | 793 | float *intSpec = new float[zdim]; |
---|
| 794 | for(int i=0;i<zdim;i++) intSpec[i]=0; |
---|
[464] | 795 | |
---|
[570] | 796 | Object2D spatMap = this->getSpatialMap(); |
---|
[464] | 797 | for(int s=0;s<spatMap.getNumScan();s++){ |
---|
[623] | 798 | std::vector<Voxel>::iterator vox; |
---|
| 799 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 800 | if(spatMap.isInObject(*vox)){ |
---|
[719] | 801 | intSpec[vox->getZ()] += vox->getF(); |
---|
[464] | 802 | } |
---|
[463] | 803 | } |
---|
[464] | 804 | } |
---|
| 805 | |
---|
[719] | 806 | calcVelWidths(zdim, intSpec, head); |
---|
| 807 | |
---|
| 808 | delete [] intSpec; |
---|
| 809 | |
---|
| 810 | } |
---|
| 811 | |
---|
| 812 | //-------------------------------------------------------------------- |
---|
| 813 | |
---|
[863] | 814 | void Detection::calcVelWidths(long zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
| 815 | { |
---|
| 816 | /// @details |
---|
| 817 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
| 818 | /// peak integrated flux. The procedure is as follows: first |
---|
| 819 | /// generate an integrated flux spectrum (using all given voxels |
---|
| 820 | /// that lie in the object's spatial map); find the peak; starting |
---|
| 821 | /// at the spectral edges of the detection, move in or out until |
---|
| 822 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
| 823 | /// between points is done. |
---|
| 824 | /// |
---|
| 825 | /// \param zdim The size of the spectral axis in the cube |
---|
| 826 | /// \param voxelList The list of Voxels with flux information |
---|
| 827 | /// \param head FitsHeader object that contains the WCS information. |
---|
| 828 | |
---|
| 829 | float *intSpec = new float[zdim]; |
---|
| 830 | for(int i=0;i<zdim;i++) intSpec[i]=0; |
---|
| 831 | |
---|
| 832 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
| 833 | std::vector<Voxel>::iterator vox; |
---|
| 834 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 835 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
| 836 | duchampError("Detection::calcVelWidths","Voxel list provided does not match"); |
---|
| 837 | return; |
---|
| 838 | } |
---|
| 839 | else { |
---|
| 840 | intSpec[vox->getZ()] += voxelMap[*vox]; |
---|
| 841 | } |
---|
| 842 | } |
---|
| 843 | |
---|
| 844 | calcVelWidths(zdim, intSpec, head); |
---|
| 845 | |
---|
| 846 | delete [] intSpec; |
---|
| 847 | |
---|
| 848 | } |
---|
| 849 | |
---|
| 850 | //-------------------------------------------------------------------- |
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| 851 | |
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[719] | 852 | void Detection::calcVelWidths(long zdim, float *intSpec, FitsHeader &head) |
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| 853 | { |
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| 854 | |
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| 855 | // finding the 20% & 50% points. Start at the velmin & velmax |
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| 856 | // points. Then, if the int flux there is above the 20%/50% |
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| 857 | // limit, go out, otherwise go in. This is to deal with the |
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| 858 | // problems from double- (or multi-) peaked sources. |
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| 859 | |
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| 860 | this->haveParams = true; |
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| 861 | |
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| 862 | double zpt,xpt=double(this->getXcentre()),ypt=double(this->getXcentre()); |
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| 863 | bool goLeft; |
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| 864 | |
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[634] | 865 | float peak=0.; |
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| 866 | int peakLoc=0; |
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[835] | 867 | for(int z=this->getZmin();z<=this->getZmax();z++) { |
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[464] | 868 | if(z==0 || peak<intSpec[z]){ |
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| 869 | peak = intSpec[z]; |
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| 870 | peakLoc = z; |
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[463] | 871 | } |
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[464] | 872 | } |
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[719] | 873 | |
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[863] | 874 | int z=this->getZmin(); |
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[464] | 875 | goLeft = intSpec[z]>peak*0.5; |
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| 876 | if(goLeft) while(z>0 && intSpec[z]>peak*0.5) z--; |
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| 877 | else while(z<peakLoc && intSpec[z]<peak*0.5) z++; |
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| 878 | if(z==0) this->v50min = this->velMin; |
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| 879 | else{ |
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[719] | 880 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
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| 881 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
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[464] | 882 | this->v50min = head.pixToVel(xpt,ypt,zpt); |
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| 883 | } |
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[719] | 884 | z=this->getZmax(); |
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[464] | 885 | goLeft = intSpec[z]<peak*0.5; |
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| 886 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.5) z--; |
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[719] | 887 | else while(z<zdim && intSpec[z]>peak*0.5) z++; |
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| 888 | if(z==zdim) this->v50max = this->velMax; |
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[464] | 889 | else{ |
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[719] | 890 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
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| 891 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
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[464] | 892 | this->v50max = head.pixToVel(xpt,ypt,zpt); |
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| 893 | } |
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[719] | 894 | z=this->getZmin(); |
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[588] | 895 | goLeft = intSpec[z]>peak*0.2; |
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[464] | 896 | if(goLeft) while(z>0 && intSpec[z]>peak*0.2) z--; |
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| 897 | else while(z<peakLoc && intSpec[z]<peak*0.2) z++; |
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| 898 | if(z==0) this->v20min = this->velMin; |
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| 899 | else{ |
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[719] | 900 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
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| 901 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
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[464] | 902 | this->v20min = head.pixToVel(xpt,ypt,zpt); |
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| 903 | } |
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[719] | 904 | z=this->getZmax(); |
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[588] | 905 | goLeft = intSpec[z]<peak*0.2; |
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[464] | 906 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.2) z--; |
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[719] | 907 | else while(z<zdim && intSpec[z]>peak*0.2) z++; |
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| 908 | if(z==zdim) this->v20max = this->velMax; |
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[464] | 909 | else{ |
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[719] | 910 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
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| 911 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
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[464] | 912 | this->v20max = head.pixToVel(xpt,ypt,zpt); |
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| 913 | } |
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[463] | 914 | |
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[464] | 915 | this->w20 = fabs(this->v20min - this->v20max); |
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| 916 | this->w50 = fabs(this->v50min - this->v50max); |
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[463] | 917 | |
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[378] | 918 | |
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[464] | 919 | } |
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[781] | 920 | //-------------------------------------------------------------------- |
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[464] | 921 | |
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| 922 | void Detection::calcVelWidths(float *fluxArray, long *dim, FitsHeader &head) |
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| 923 | { |
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[528] | 924 | /// @details |
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| 925 | /// Calculates the widths of the detection at 20% and 50% of the |
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| 926 | /// peak integrated flux. The procedure is as follows: first |
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| 927 | /// generate an integrated flux spectrum (summing each spatial |
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| 928 | /// pixel's spectrum); find the peak; starting at the spectral |
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| 929 | /// edges of the detection, move in or out until you reach the 20% |
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| 930 | /// or 50% peak flux level. Linear interpolation between points is |
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| 931 | /// done. |
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| 932 | /// |
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| 933 | /// \param fluxArray The array of flux values. |
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| 934 | /// \param dim The dimensions of the flux array. |
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| 935 | /// \param head FitsHeader object that contains the WCS information. |
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[464] | 936 | |
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[465] | 937 | if(dim[2] > 2){ |
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[464] | 938 | |
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[465] | 939 | float *intSpec = new float[dim[2]]; |
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[748] | 940 | long size=dim[0]*dim[1]*dim[2]; |
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| 941 | std::vector<bool> mask(size,true); |
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[465] | 942 | getIntSpec(*this,fluxArray,dim,mask,1.,intSpec); |
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| 943 | |
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[719] | 944 | this->calcVelWidths(dim[2],intSpec,head); |
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| 945 | |
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[465] | 946 | delete [] intSpec; |
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| 947 | |
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[378] | 948 | } |
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[464] | 949 | else{ |
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[465] | 950 | this->v50min = this->v20min = this->velMin; |
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| 951 | this->v50max = this->v20max = this->velMax; |
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[719] | 952 | this->w20 = fabs(this->v20min - this->v20max); |
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| 953 | this->w50 = fabs(this->v50min - this->v50max); |
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[464] | 954 | } |
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[300] | 955 | |
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| 956 | } |
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[378] | 957 | //-------------------------------------------------------------------- |
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[300] | 958 | |
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[378] | 959 | void Detection::setOffsets(Param &par) |
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| 960 | { |
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[528] | 961 | /// @details |
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| 962 | /// This function stores the values of the offsets for each cube axis. |
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| 963 | /// The offsets are the starting values of the cube axes that may differ from |
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| 964 | /// the default value of 0 (for instance, if a subsection is being used). |
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| 965 | /// The values will be used when the detection is outputted. |
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| 966 | |
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[378] | 967 | this->xSubOffset = par.getXOffset(); |
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| 968 | this->ySubOffset = par.getYOffset(); |
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| 969 | this->zSubOffset = par.getZOffset(); |
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| 970 | } |
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| 971 | //-------------------------------------------------------------------- |
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[3] | 972 | |
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[378] | 973 | bool Detection::hasEnoughChannels(int minNumber) |
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| 974 | { |
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[528] | 975 | /// @details |
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| 976 | /// A function to determine if the Detection has enough |
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| 977 | /// contiguous channels to meet the minimum requirement |
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| 978 | /// given as the argument. |
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| 979 | /// \param minNumber How many channels is the minimum acceptable number? |
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| 980 | /// \return True if there is at least one occurence of minNumber consecutive |
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| 981 | /// channels present to return true. False otherwise. |
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[3] | 982 | |
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[378] | 983 | // Preferred method -- need a set of minNumber consecutive channels present. |
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[3] | 984 | |
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[570] | 985 | int numChan = this->getMaxAdjacentChannels(); |
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| 986 | bool result = (numChan >= minNumber); |
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| 987 | |
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[378] | 988 | return result; |
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| 989 | |
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| 990 | } |
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| 991 | //-------------------------------------------------------------------- |
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[3] | 992 | |
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[452] | 993 | std::vector<int> Detection::getVertexSet() |
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| 994 | { |
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[528] | 995 | /// @details |
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| 996 | /// Gets a list of points being the end-points of 1-pixel long |
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| 997 | /// segments drawing a border around the spatial extend of a |
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| 998 | /// detection. The vector is a series of 4 integers, being: x_0, |
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| 999 | /// y_0, x_1, y_1. |
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| 1000 | /// \return The vector of vertex positions. |
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| 1001 | |
---|
[452] | 1002 | std::vector<int> vertexSet; |
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| 1003 | |
---|
| 1004 | int xmin = this->getXmin() - 1; |
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| 1005 | int xmax = this->getXmax() + 1; |
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| 1006 | int ymin = this->getYmin() - 1; |
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| 1007 | int ymax = this->getYmax() + 1; |
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| 1008 | int xsize = xmax - xmin + 1; |
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| 1009 | int ysize = ymax - ymin + 1; |
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| 1010 | |
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[570] | 1011 | std::vector<Voxel> voxlist = this->getPixelSet(); |
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[452] | 1012 | std::vector<bool> isObj(xsize*ysize,false); |
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[623] | 1013 | std::vector<Voxel>::iterator vox; |
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| 1014 | for(vox=voxlist.begin();vox<voxlist.end();vox++){ |
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| 1015 | int pos = (vox->getX()-xmin) + |
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| 1016 | (vox->getY()-ymin)*xsize; |
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[452] | 1017 | isObj[pos] = true; |
---|
| 1018 | } |
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| 1019 | voxlist.clear(); |
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| 1020 | |
---|
| 1021 | for(int x=xmin; x<=xmax; x++){ |
---|
| 1022 | // for each column... |
---|
| 1023 | for(int y=ymin+1;y<=ymax;y++){ |
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| 1024 | int current = (y-ymin)*xsize + x-xmin; |
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| 1025 | int previous = (y-ymin-1)*xsize + x-xmin; |
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| 1026 | if((isObj[current]&&!isObj[previous]) || |
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| 1027 | (!isObj[current]&&isObj[previous])){ |
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| 1028 | vertexSet.push_back(x); |
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| 1029 | vertexSet.push_back(y); |
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| 1030 | vertexSet.push_back(x+1); |
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| 1031 | vertexSet.push_back(y); |
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| 1032 | } |
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| 1033 | } |
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| 1034 | } |
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| 1035 | for(int y=ymin; y<=ymax; y++){ |
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| 1036 | // now for each row... |
---|
| 1037 | for(int x=xmin+1;x<=xmax;x++){ |
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| 1038 | int current = (y-ymin)*xsize + x-xmin; |
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| 1039 | int previous = (y-ymin)*xsize + x-xmin - 1; |
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| 1040 | if((isObj[current]&&!isObj[previous]) || |
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| 1041 | (!isObj[current]&&isObj[previous])){ |
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| 1042 | vertexSet.push_back(x); |
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| 1043 | vertexSet.push_back(y); |
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| 1044 | vertexSet.push_back(x); |
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| 1045 | vertexSet.push_back(y+1); |
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| 1046 | } |
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| 1047 | } |
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| 1048 | } |
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| 1049 | |
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| 1050 | return vertexSet; |
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| 1051 | |
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| 1052 | } |
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| 1053 | |
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[747] | 1054 | |
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[770] | 1055 | void Detection::addDetection(Detection &other) |
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[747] | 1056 | { |
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| 1057 | for(std::map<long, Object2D>::iterator it = other.chanlist.begin(); it!=other.chanlist.end();it++) |
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[770] | 1058 | // this->addChannel(*it); |
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[747] | 1059 | this->addChannel(it->first, it->second); |
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| 1060 | this->haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
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| 1061 | } |
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[624] | 1062 | |
---|
[770] | 1063 | Detection operator+ (Detection &lhs, Detection &rhs) |
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[624] | 1064 | { |
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| 1065 | Detection output = lhs; |
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| 1066 | for(std::map<long, Object2D>::iterator it = rhs.chanlist.begin(); it!=rhs.chanlist.end();it++) |
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| 1067 | output.addChannel(it->first, it->second); |
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[681] | 1068 | output.haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
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[624] | 1069 | return output; |
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| 1070 | } |
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| 1071 | |
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| 1072 | |
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[770] | 1073 | bool Detection::canMerge(Detection &other, Param &par) |
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| 1074 | { |
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| 1075 | bool near = this->isNear(other,par); |
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| 1076 | if(near) return this->isClose(other,par); |
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| 1077 | else return near; |
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| 1078 | } |
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[624] | 1079 | |
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[770] | 1080 | bool Detection::isNear(Detection &other, Param &par) |
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| 1081 | { |
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[624] | 1082 | |
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[770] | 1083 | bool flagAdj = par.getFlagAdjacent(); |
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| 1084 | float threshS = par.getThreshS(); |
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| 1085 | float threshV = par.getThreshV(); |
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| 1086 | |
---|
| 1087 | long gap; |
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| 1088 | if(flagAdj) gap = 1; |
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| 1089 | else gap = long( ceil(threshS) ); |
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| 1090 | |
---|
| 1091 | bool areNear; |
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| 1092 | // Test X ranges |
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| 1093 | if((this->xmin-gap)<other.xmin) areNear=((this->xmax+gap)>=other.xmin); |
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| 1094 | else areNear=(other.xmax>=(this->xmin-gap)); |
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| 1095 | // Test Y ranges |
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| 1096 | if(areNear){ |
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| 1097 | if((this->ymin-gap)<other.ymin) areNear=areNear&&((this->ymax+gap)>=other.ymin); |
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| 1098 | else areNear=areNear&&(other.ymax>=(this->ymin-gap)); |
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| 1099 | } |
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| 1100 | // Test Z ranges |
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| 1101 | if(areNear){ |
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| 1102 | gap = long(ceil(threshV)); |
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| 1103 | if((this->zmin-gap)<other.zmin) areNear=areNear&&((this->zmax+gap)>=other.zmin); |
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| 1104 | else areNear=areNear&&(other.zmax>=(this->zmin-gap)); |
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| 1105 | } |
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| 1106 | |
---|
| 1107 | return areNear; |
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| 1108 | |
---|
| 1109 | } |
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| 1110 | |
---|
| 1111 | bool Detection::isClose(Detection &other, Param &par) |
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| 1112 | { |
---|
| 1113 | bool close = false; // this will be the value returned |
---|
| 1114 | |
---|
| 1115 | bool flagAdj = par.getFlagAdjacent(); |
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| 1116 | float threshS = par.getThreshS(); |
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| 1117 | float threshV = par.getThreshV(); |
---|
| 1118 | |
---|
| 1119 | // |
---|
| 1120 | // If we get to here, the pixel ranges overlap -- so we do a |
---|
| 1121 | // pixel-by-pixel comparison to make sure they are actually |
---|
| 1122 | // "close" according to the thresholds. Otherwise, close=false, |
---|
| 1123 | // and so don't need to do anything else before returning. |
---|
| 1124 | // |
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| 1125 | |
---|
| 1126 | std::vector<long> zlist1 = this->getChannelList(); |
---|
| 1127 | std::vector<long> zlist2 = other.getChannelList(); |
---|
| 1128 | Scan test1,test2; |
---|
| 1129 | |
---|
| 1130 | for(size_t ct1=0; (!close && (ct1<zlist1.size())); ct1++){ |
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| 1131 | for(size_t ct2=0; (!close && (ct2<zlist2.size())); ct2++){ |
---|
| 1132 | |
---|
| 1133 | if(abs(zlist1[ct1]-zlist2[ct2])<=threshV){ |
---|
| 1134 | |
---|
| 1135 | Object2D temp1 = this->getChanMap(zlist1[ct1]); |
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| 1136 | Object2D temp2 = other.getChanMap(zlist2[ct2]); |
---|
| 1137 | |
---|
| 1138 | close = temp1.canMerge(temp2,threshS,flagAdj); |
---|
| 1139 | |
---|
| 1140 | } |
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| 1141 | |
---|
| 1142 | } |
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| 1143 | } |
---|
| 1144 | |
---|
| 1145 | return close; |
---|
| 1146 | |
---|
| 1147 | } |
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| 1148 | |
---|
| 1149 | |
---|
| 1150 | |
---|
[3] | 1151 | } |
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