[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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[1061] | 43 | #include <duchamp/Outputs/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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[1153] | 57 | this->eTotalFlux = 0.; |
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[570] | 58 | this->peakFlux = 0.; |
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| 59 | this->intFlux = 0.; |
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[1152] | 60 | this->eIntFlux = 0.; |
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[570] | 61 | this->xpeak = 0; |
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| 62 | this->ypeak = 0; |
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| 63 | this->zpeak = 0; |
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| 64 | this->peakSNR = 0.; |
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| 65 | this->xCentroid = 0.; |
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| 66 | this->yCentroid = 0.; |
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| 67 | this->zCentroid = 0.; |
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| 68 | this->centreType="centroid"; |
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[378] | 69 | this->negSource = false; |
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| 70 | this->flagText=""; |
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[468] | 71 | this->id = -1; |
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[570] | 72 | this->name = ""; |
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| 73 | this->flagWCS=false; |
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| 74 | this->specOK = true; |
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| 75 | this->raS = ""; |
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| 76 | this->decS = ""; |
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| 77 | this->ra = 0.; |
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| 78 | this->dec = 0.; |
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| 79 | this->raWidth = 0.; |
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| 80 | this->decWidth = 0.; |
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| 81 | this->majorAxis = 0.; |
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| 82 | this->minorAxis = 0.; |
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| 83 | this->posang = 0.; |
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| 84 | this->specUnits = ""; |
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[947] | 85 | this->specType = ""; |
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[570] | 86 | this->fluxUnits = ""; |
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| 87 | this->intFluxUnits = ""; |
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| 88 | this->lngtype = "RA"; |
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| 89 | this->lattype = "DEC"; |
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| 90 | this->vel = 0.; |
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| 91 | this->velWidth = 0.; |
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| 92 | this->velMin = 0.; |
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| 93 | this->velMax = 0.; |
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[1425] | 94 | this->z50min = 0.; |
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| 95 | this->z50max = 0.; |
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| 96 | this->z20min = 0.; |
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| 97 | this->z20max = 0.; |
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[570] | 98 | this->w20 = 0.; |
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| 99 | this->v20min = 0.; |
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| 100 | this->v20max = 0.; |
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| 101 | this->w50 = 0.; |
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| 102 | this->v50min = 0.; |
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| 103 | this->v50max = 0.; |
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[1061] | 104 | this->posPrec = Catalogues::prPOS; |
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| 105 | this->xyzPrec = Catalogues::prXYZ; |
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| 106 | this->fintPrec = Catalogues::prFLUX; |
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| 107 | this->fpeakPrec = Catalogues::prFLUX; |
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| 108 | this->velPrec = Catalogues::prVEL; |
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| 109 | this->snrPrec = Catalogues::prSNR; |
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[378] | 110 | } |
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[218] | 111 | |
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[570] | 112 | Detection::Detection(): |
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| 113 | Object3D() |
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[378] | 114 | { |
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[570] | 115 | this->defaultDetection(); |
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| 116 | } |
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| 117 | |
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| 118 | Detection::Detection(const Object3D& o): |
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| 119 | Object3D(o) |
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| 120 | { |
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| 121 | this->defaultDetection(); |
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| 122 | } |
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| 123 | |
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| 124 | Detection::Detection(const Detection& d): |
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| 125 | Object3D(d) |
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| 126 | { |
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[378] | 127 | operator=(d); |
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| 128 | } |
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[218] | 129 | |
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[378] | 130 | Detection& Detection::operator= (const Detection& d) |
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| 131 | { |
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[570] | 132 | ((Object3D &) *this) = d; |
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[378] | 133 | this->xSubOffset = d.xSubOffset; |
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| 134 | this->ySubOffset = d.ySubOffset; |
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| 135 | this->zSubOffset = d.zSubOffset; |
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[681] | 136 | this->haveParams = d.haveParams; |
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[378] | 137 | this->totalFlux = d.totalFlux; |
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[1153] | 138 | this->eTotalFlux = d.eTotalFlux; |
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[461] | 139 | this->intFlux = d.intFlux; |
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[1152] | 140 | this->eIntFlux = d.eIntFlux; |
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[378] | 141 | this->peakFlux = d.peakFlux; |
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| 142 | this->xpeak = d.xpeak; |
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| 143 | this->ypeak = d.ypeak; |
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| 144 | this->zpeak = d.zpeak; |
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| 145 | this->peakSNR = d.peakSNR; |
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| 146 | this->xCentroid = d.xCentroid; |
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| 147 | this->yCentroid = d.yCentroid; |
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| 148 | this->zCentroid = d.zCentroid; |
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| 149 | this->centreType = d.centreType; |
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| 150 | this->negSource = d.negSource; |
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| 151 | this->flagText = d.flagText; |
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| 152 | this->id = d.id; |
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| 153 | this->name = d.name; |
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| 154 | this->flagWCS = d.flagWCS; |
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| 155 | this->specOK = d.specOK; |
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| 156 | this->raS = d.raS; |
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| 157 | this->decS = d.decS; |
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| 158 | this->ra = d.ra; |
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[461] | 159 | this->dec = d.dec; |
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| 160 | this->raWidth = d.raWidth; |
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[378] | 161 | this->decWidth = d.decWidth; |
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[473] | 162 | this->majorAxis = d.majorAxis; |
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| 163 | this->minorAxis = d.minorAxis; |
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| 164 | this->posang = d.posang; |
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[378] | 165 | this->specUnits = d.specUnits; |
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[947] | 166 | this->specType = d.specType; |
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[378] | 167 | this->fluxUnits = d.fluxUnits; |
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| 168 | this->intFluxUnits = d.intFluxUnits; |
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[461] | 169 | this->lngtype = d.lngtype; |
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| 170 | this->lattype = d.lattype; |
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[378] | 171 | this->vel = d.vel; |
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| 172 | this->velWidth = d.velWidth; |
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| 173 | this->velMin = d.velMin; |
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| 174 | this->velMax = d.velMax; |
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[1425] | 175 | this->z50min = d.z50min; |
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| 176 | this->z50max = d.z50max; |
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| 177 | this->z20min = d.z20min; |
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| 178 | this->z20max = d.z20max; |
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[463] | 179 | this->w20 = d.w20; |
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| 180 | this->v20min = d.v20min; |
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| 181 | this->v20max = d.v20max; |
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| 182 | this->w50 = d.w50; |
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| 183 | this->v50min = d.v50min; |
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| 184 | this->v50max = d.v50max; |
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[378] | 185 | this->posPrec = d.posPrec; |
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| 186 | this->xyzPrec = d.xyzPrec; |
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| 187 | this->fintPrec = d.fintPrec; |
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| 188 | this->fpeakPrec = d.fpeakPrec; |
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[461] | 189 | this->velPrec = d.velPrec; |
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[378] | 190 | this->snrPrec = d.snrPrec; |
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| 191 | return *this; |
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| 192 | } |
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[3] | 193 | |
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[378] | 194 | //-------------------------------------------------------------------- |
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[570] | 195 | float Detection::getXcentre() |
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| 196 | { |
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| 197 | if(this->centreType=="peak") return this->xpeak; |
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| 198 | else if(this->centreType=="average") return this->getXaverage(); |
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| 199 | else return this->xCentroid; |
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| 200 | } |
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[258] | 201 | |
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[570] | 202 | float Detection::getYcentre() |
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| 203 | { |
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| 204 | if(this->centreType=="peak") return this->ypeak; |
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| 205 | else if(this->centreType=="average") return this->getYaverage(); |
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| 206 | else return this->yCentroid; |
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| 207 | } |
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| 208 | |
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| 209 | float Detection::getZcentre() |
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| 210 | { |
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| 211 | if(this->centreType=="peak") return this->zpeak; |
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| 212 | else if(this->centreType=="average") return this->getZaverage(); |
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| 213 | else return this->zCentroid; |
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| 214 | } |
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| 215 | |
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| 216 | //-------------------------------------------------------------------- |
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| 217 | |
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[417] | 218 | bool Detection::voxelListsMatch(std::vector<Voxel> voxelList) |
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| 219 | { |
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[528] | 220 | /// @details |
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| 221 | /// A test to see whether there is a 1-1 correspondence between |
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| 222 | /// the given list of Voxels and the voxel positions contained in |
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| 223 | /// this Detection's pixel list. No testing of the fluxes of the |
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| 224 | /// Voxels is done. |
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| 225 | /// |
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| 226 | /// \param voxelList The std::vector list of Voxels to be tested. |
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[417] | 227 | |
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| 228 | bool listsMatch = true; |
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| 229 | // compare sizes |
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| 230 | listsMatch = listsMatch && (voxelList.size() == this->getSize()); |
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| 231 | if(!listsMatch) return listsMatch; |
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| 232 | |
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[463] | 233 | // make sure all Detection pixels are in voxel list |
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| 234 | listsMatch = listsMatch && this->voxelListCovered(voxelList); |
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| 235 | |
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[417] | 236 | // make sure all voxels are in Detection |
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[623] | 237 | std::vector<Voxel>::iterator vox; |
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| 238 | for(vox=voxelList.begin();vox<voxelList.end();vox++) |
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| 239 | listsMatch = listsMatch && this->isInObject(*vox); |
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[463] | 240 | |
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| 241 | return listsMatch; |
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| 242 | |
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| 243 | } |
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| 244 | //-------------------------------------------------------------------- |
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| 245 | |
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| 246 | bool Detection::voxelListCovered(std::vector<Voxel> voxelList) |
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| 247 | { |
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[528] | 248 | /// @details |
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| 249 | /// A test to see whether the given list of Voxels contains each |
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| 250 | /// position in this Detection's pixel list. It does not look for |
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| 251 | /// a 1-1 correspondence: the given list can be a super-set of the |
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| 252 | /// Detection. No testing of the fluxes of the Voxels is done. |
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| 253 | /// |
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| 254 | /// \param voxelList The std::vector list of Voxels to be tested. |
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[463] | 255 | |
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| 256 | bool listsMatch = true; |
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| 257 | |
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[417] | 258 | // make sure all Detection pixels are in voxel list |
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[623] | 259 | size_t v1=0; |
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[570] | 260 | std::vector<Voxel> detpixlist = this->getPixelSet(); |
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| 261 | while(listsMatch && v1<detpixlist.size()){ |
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[417] | 262 | bool inList = false; |
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[623] | 263 | size_t v2=0; |
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[417] | 264 | while(!inList && v2<voxelList.size()){ |
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[570] | 265 | inList = inList || detpixlist[v1].match(voxelList[v2]); |
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[417] | 266 | v2++; |
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| 267 | } |
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| 268 | listsMatch = listsMatch && inList; |
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[418] | 269 | v1++; |
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[417] | 270 | } |
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| 271 | |
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| 272 | return listsMatch; |
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| 273 | |
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| 274 | } |
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| 275 | //-------------------------------------------------------------------- |
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| 276 | |
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[1207] | 277 | void Detection::invert() |
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| 278 | { |
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| 279 | /// @details |
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| 280 | /// A front-end to simplify the inversion that is done at the Cube level. |
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| 281 | /// The fluxes are made negative, and the negSource flag is flipped. |
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| 282 | /// This can be used at any time - it doesn't matter which way the inversion is happening. |
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| 283 | |
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[1361] | 284 | this->negSource = true; |
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[1207] | 285 | this->totalFlux = -1. * this->totalFlux; |
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| 286 | this->intFlux = -1. * this->intFlux; |
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| 287 | this->peakFlux = -1. * this->peakFlux; |
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| 288 | |
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| 289 | } |
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| 290 | |
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| 291 | //-------------------------------------------------------------------- |
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| 292 | |
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[417] | 293 | void Detection::calcFluxes(std::vector<Voxel> voxelList) |
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| 294 | { |
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[528] | 295 | /// @details |
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| 296 | /// A function that calculates total & peak fluxes (and the location |
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| 297 | /// of the peak flux) for a Detection. |
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| 298 | /// |
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| 299 | /// \param fluxArray The array of flux values to calculate the |
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| 300 | /// flux parameters from. |
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| 301 | /// \param dim The dimensions of the flux array. |
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[681] | 302 | |
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| 303 | // this->haveParams = true; |
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[417] | 304 | |
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| 305 | this->totalFlux = this->peakFlux = 0; |
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| 306 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 307 | |
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| 308 | // first check that the voxel list and the Detection's pixel list |
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| 309 | // have a 1-1 correspondence |
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| 310 | |
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[463] | 311 | if(!this->voxelListCovered(voxelList)){ |
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[913] | 312 | DUCHAMPERROR("Detection::calcFluxes","Voxel list provided does not match"); |
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[417] | 313 | return; |
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| 314 | } |
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| 315 | |
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[623] | 316 | std::vector<Voxel>::iterator vox; |
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| 317 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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| 318 | if(this->isInObject(*vox)){ |
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| 319 | long x = vox->getX(); |
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| 320 | long y = vox->getY(); |
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| 321 | long z = vox->getZ(); |
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| 322 | float f = vox->getF(); |
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[463] | 323 | this->totalFlux += f; |
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| 324 | this->xCentroid += x*f; |
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| 325 | this->yCentroid += y*f; |
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| 326 | this->zCentroid += z*f; |
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[623] | 327 | if( (vox==voxelList.begin()) || //first time round |
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[1361] | 328 | (f>this->peakFlux) ) |
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[463] | 329 | { |
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| 330 | this->peakFlux = f; |
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| 331 | this->xpeak = x; |
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| 332 | this->ypeak = y; |
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| 333 | this->zpeak = z; |
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| 334 | } |
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| 335 | } |
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[417] | 336 | } |
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| 337 | |
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| 338 | this->xCentroid /= this->totalFlux; |
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| 339 | this->yCentroid /= this->totalFlux; |
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| 340 | this->zCentroid /= this->totalFlux; |
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| 341 | } |
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| 342 | //-------------------------------------------------------------------- |
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| 343 | |
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[863] | 344 | void Detection::calcFluxes(std::map<Voxel,float> &voxelMap) |
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| 345 | { |
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| 346 | /// @details |
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| 347 | /// A function that calculates total & peak fluxes (and the location |
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| 348 | /// of the peak flux) for a Detection. |
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| 349 | /// |
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| 350 | /// \param fluxArray The array of flux values to calculate the |
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| 351 | /// flux parameters from. |
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| 352 | /// \param dim The dimensions of the flux array. |
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| 353 | |
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| 354 | // this->haveParams = true; |
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| 355 | |
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| 356 | this->totalFlux = this->peakFlux = 0; |
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| 357 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 358 | |
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| 359 | std::vector<Voxel> voxelList = this->getPixelSet(); |
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| 360 | std::vector<Voxel>::iterator vox; |
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| 361 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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| 362 | if(voxelMap.find(*vox) == voxelMap.end()){ |
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[913] | 363 | DUCHAMPERROR("Detection::calcFluxes","Voxel list provided does not match"); |
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[863] | 364 | return; |
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| 365 | } |
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| 366 | else { |
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| 367 | long x = vox->getX(); |
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| 368 | long y = vox->getY(); |
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| 369 | long z = vox->getZ(); |
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| 370 | float f = voxelMap[*vox]; |
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| 371 | this->totalFlux += f; |
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| 372 | this->xCentroid += x*f; |
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| 373 | this->yCentroid += y*f; |
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| 374 | this->zCentroid += z*f; |
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| 375 | if( (vox==voxelList.begin()) || //first time round |
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[1361] | 376 | (f>this->peakFlux) ) |
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[863] | 377 | { |
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| 378 | this->peakFlux = f; |
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| 379 | this->xpeak = x; |
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| 380 | this->ypeak = y; |
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| 381 | this->zpeak = z; |
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| 382 | } |
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| 383 | } |
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| 384 | } |
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| 385 | |
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| 386 | this->xCentroid /= this->totalFlux; |
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| 387 | this->yCentroid /= this->totalFlux; |
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| 388 | this->zCentroid /= this->totalFlux; |
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| 389 | } |
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| 390 | //-------------------------------------------------------------------- |
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| 391 | |
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[884] | 392 | void Detection::calcFluxes(float *fluxArray, size_t *dim) |
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[378] | 393 | { |
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[528] | 394 | /// @details |
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| 395 | /// A function that calculates total & peak fluxes (and the location |
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| 396 | /// of the peak flux) for a Detection. |
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| 397 | /// |
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| 398 | /// \param fluxArray The array of flux values to calculate the |
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| 399 | /// flux parameters from. |
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| 400 | /// \param dim The dimensions of the flux array. |
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[258] | 401 | |
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[681] | 402 | // this->haveParams = true; |
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| 403 | |
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[378] | 404 | this->totalFlux = this->peakFlux = 0; |
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| 405 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 406 | |
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[570] | 407 | std::vector<Voxel> voxList = this->getPixelSet(); |
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[473] | 408 | std::vector<Voxel>::iterator vox=voxList.begin(); |
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| 409 | for(;vox<voxList.end();vox++){ |
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[378] | 410 | |
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[473] | 411 | long x=vox->getX(); |
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| 412 | long y=vox->getY(); |
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| 413 | long z=vox->getZ(); |
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[884] | 414 | size_t ind = vox->arrayIndex(dim); |
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[473] | 415 | float f = fluxArray[ind]; |
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| 416 | this->totalFlux += f; |
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| 417 | this->xCentroid += x*f; |
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| 418 | this->yCentroid += y*f; |
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| 419 | this->zCentroid += z*f; |
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[1361] | 420 | if( (vox==voxList.begin()) || (f > this->peakFlux) ) |
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[473] | 421 | { |
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| 422 | this->peakFlux = f; |
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| 423 | this->xpeak = x; |
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| 424 | this->ypeak = y; |
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| 425 | this->zpeak = z; |
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[378] | 426 | } |
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[473] | 427 | |
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[45] | 428 | } |
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[378] | 429 | |
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| 430 | this->xCentroid /= this->totalFlux; |
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| 431 | this->yCentroid /= this->totalFlux; |
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| 432 | this->zCentroid /= this->totalFlux; |
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[263] | 433 | } |
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[378] | 434 | //-------------------------------------------------------------------- |
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[263] | 435 | |
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[417] | 436 | void Detection::calcWCSparams(FitsHeader &head) |
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[378] | 437 | { |
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[528] | 438 | /// @details |
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| 439 | /// Use the input wcs to calculate the position and velocity |
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| 440 | /// information for the Detection. |
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| 441 | /// Quantities calculated: |
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| 442 | /// <ul><li> RA: ra [deg], ra (string), ra width. |
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| 443 | /// <li> Dec: dec [deg], dec (string), dec width. |
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| 444 | /// <li> Vel: vel [km/s], min & max vel, vel width. |
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| 445 | /// <li> coord type for all three axes, nuRest, |
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| 446 | /// <li> name (IAU-style, in equatorial or Galactic) |
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| 447 | /// </ul> |
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| 448 | /// |
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| 449 | /// Note that the regular parameters are NOT recalculated! |
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| 450 | /// |
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| 451 | /// \param head FitsHeader object that contains the WCS information. |
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[3] | 452 | |
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[378] | 453 | if(head.isWCS()){ |
---|
[3] | 454 | |
---|
[378] | 455 | double *pixcrd = new double[15]; |
---|
| 456 | double *world = new double[15]; |
---|
| 457 | /* |
---|
| 458 | define a five-point array in 3D: |
---|
| 459 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
---|
| 460 | [note: x = central point, x1 = minimum x, x2 = maximum x etc.] |
---|
| 461 | and convert to world coordinates. |
---|
| 462 | */ |
---|
| 463 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->getXcentre(); |
---|
| 464 | pixcrd[9] = this->getXmin()-0.5; |
---|
| 465 | pixcrd[12] = this->getXmax()+0.5; |
---|
| 466 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->getYcentre(); |
---|
| 467 | pixcrd[10] = this->getYmin()-0.5; |
---|
| 468 | pixcrd[13] = this->getYmax()+0.5; |
---|
| 469 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->getZcentre(); |
---|
| 470 | pixcrd[5] = this->getZmin(); |
---|
| 471 | pixcrd[8] = this->getZmax(); |
---|
| 472 | int flag = head.pixToWCS(pixcrd, world, 5); |
---|
| 473 | delete [] pixcrd; |
---|
[913] | 474 | if(flag!=0) { |
---|
| 475 | DUCHAMPERROR("calcWCSparams", "Error in calculating the WCS for this object."); |
---|
| 476 | } |
---|
[378] | 477 | else{ |
---|
[913] | 478 | |
---|
[378] | 479 | // world now has the WCS coords for the five points |
---|
| 480 | // -- use this to work out WCS params |
---|
[22] | 481 | |
---|
[681] | 482 | this->haveParams = true; |
---|
| 483 | |
---|
[378] | 484 | this->specOK = head.canUseThirdAxis(); |
---|
[963] | 485 | this->lngtype = head.lngtype(); |
---|
| 486 | this->lattype = head.lattype(); |
---|
[378] | 487 | this->specUnits = head.getSpectralUnits(); |
---|
[947] | 488 | this->specType = head.getSpectralType(); |
---|
[378] | 489 | this->fluxUnits = head.getFluxUnits(); |
---|
| 490 | // if fluxUnits are eg. Jy/beam, make intFluxUnits = Jy km/s |
---|
| 491 | this->intFluxUnits = head.getIntFluxUnits(); |
---|
| 492 | this->ra = world[0]; |
---|
| 493 | this->dec = world[1]; |
---|
[907] | 494 | int precision = -int(log10(fabs(head.WCS().cdelt[head.WCS().lng]*3600./10.))); |
---|
| 495 | this->raS = decToDMS(this->ra, this->lngtype,precision); |
---|
| 496 | this->decS = decToDMS(this->dec,this->lattype,precision); |
---|
[378] | 497 | this->raWidth = angularSeparation(world[9],world[1], |
---|
| 498 | world[12],world[1]) * 60.; |
---|
| 499 | this->decWidth = angularSeparation(world[0],world[10], |
---|
| 500 | world[0],world[13]) * 60.; |
---|
[473] | 501 | |
---|
[378] | 502 | this->name = head.getIAUName(this->ra, this->dec); |
---|
| 503 | this->vel = head.specToVel(world[2]); |
---|
| 504 | this->velMin = head.specToVel(world[5]); |
---|
| 505 | this->velMax = head.specToVel(world[8]); |
---|
| 506 | this->velWidth = fabs(this->velMax - this->velMin); |
---|
[3] | 507 | |
---|
[378] | 508 | this->flagWCS = true; |
---|
| 509 | } |
---|
| 510 | delete [] world; |
---|
| 511 | |
---|
[270] | 512 | } |
---|
[982] | 513 | else { |
---|
| 514 | double x=this->getXcentre(),y=this->getYcentre(),z=this->getZmin(); |
---|
| 515 | this->velMin = head.pixToVel(x,y,z); |
---|
| 516 | z=this->getZmax(); |
---|
| 517 | this->velMax = head.pixToVel(x,y,z); |
---|
| 518 | this->velWidth = fabs(this->velMax - this->velMin); |
---|
| 519 | } |
---|
| 520 | |
---|
| 521 | |
---|
[103] | 522 | } |
---|
[378] | 523 | //-------------------------------------------------------------------- |
---|
[3] | 524 | |
---|
[884] | 525 | void Detection::calcIntegFlux(size_t zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
[417] | 526 | { |
---|
[528] | 527 | /// @details |
---|
| 528 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
| 529 | /// putting velocity in units of km/s. |
---|
| 530 | /// The fluxes used are taken from the Voxels, rather than an |
---|
| 531 | /// array of flux values. |
---|
| 532 | /// Integrates over full spatial and velocity range as given |
---|
| 533 | /// by the extrema calculated by calcWCSparams. |
---|
| 534 | /// |
---|
| 535 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
| 536 | /// corrected by the beam size (in pixels). This is done by |
---|
| 537 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
| 538 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
| 539 | /// pix/beam --> Jy) |
---|
| 540 | /// |
---|
[719] | 541 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
[528] | 542 | /// \param voxelList The list of Voxels with flux information |
---|
| 543 | /// \param head FitsHeader object that contains the WCS information. |
---|
[417] | 544 | |
---|
[463] | 545 | if(!this->voxelListCovered(voxelList)){ |
---|
[913] | 546 | DUCHAMPERROR("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
[417] | 547 | return; |
---|
| 548 | } |
---|
| 549 | |
---|
[513] | 550 | if(!head.is2D()){ |
---|
[417] | 551 | |
---|
[681] | 552 | this->haveParams = true; |
---|
| 553 | |
---|
[982] | 554 | const int border = 1; // include one pixel either side in each direction |
---|
[983] | 555 | size_t xsize = size_t(this->xmax-this->xmin+2*border+1); |
---|
| 556 | size_t ysize = size_t(this->ymax-this->ymin+2*border+1); |
---|
| 557 | size_t zsize = size_t(this->zmax-this->zmin+2*border+1); |
---|
[982] | 558 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
| 559 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
| 560 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
[884] | 561 | size_t spatsize=xsize*ysize; |
---|
| 562 | size_t size = xsize*ysize*zsize; |
---|
[473] | 563 | std::vector <bool> isObj(size,false); |
---|
[463] | 564 | double *localFlux = new double[size]; |
---|
[884] | 565 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
[417] | 566 | |
---|
[623] | 567 | std::vector<Voxel>::iterator vox; |
---|
| 568 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 569 | if(this->isInObject(*vox)){ |
---|
[983] | 570 | size_t pos=(vox->getX()-xzero) + (vox->getY()-yzero)*xsize + (vox->getZ()-zzero)*spatsize; |
---|
[623] | 571 | localFlux[pos] = vox->getF(); |
---|
[463] | 572 | isObj[pos] = true; |
---|
| 573 | } |
---|
[417] | 574 | } |
---|
| 575 | |
---|
| 576 | // work out the WCS coords for each pixel |
---|
[463] | 577 | double *world = new double[size]; |
---|
[417] | 578 | double xpt,ypt,zpt; |
---|
[924] | 579 | for(size_t i=0;i<size;i++){ |
---|
[463] | 580 | xpt = double( this->getXmin() - border + i%xsize ); |
---|
| 581 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
---|
| 582 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
---|
[417] | 583 | world[i] = head.pixToVel(xpt,ypt,zpt); |
---|
| 584 | } |
---|
| 585 | |
---|
| 586 | double integrated = 0.; |
---|
[884] | 587 | for(size_t pix=0; pix<spatsize; pix++){ // loop over each spatial pixel. |
---|
| 588 | for(size_t z=0; z<zsize; z++){ |
---|
[921] | 589 | size_t pos = z*xsize*ysize + pix; |
---|
[417] | 590 | if(isObj[pos]){ // if it's an object pixel... |
---|
| 591 | double deltaVel; |
---|
| 592 | if(z==0) |
---|
| 593 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
| 594 | else if(z==(zsize-1)) |
---|
| 595 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
| 596 | else |
---|
| 597 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
| 598 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
| 599 | } |
---|
| 600 | } |
---|
| 601 | } |
---|
| 602 | this->intFlux = integrated; |
---|
| 603 | |
---|
| 604 | delete [] world; |
---|
| 605 | delete [] localFlux; |
---|
| 606 | |
---|
[719] | 607 | calcVelWidths(zdim,voxelList,head); |
---|
[464] | 608 | |
---|
[417] | 609 | } |
---|
| 610 | else // in this case there is just a 2D image. |
---|
| 611 | this->intFlux = this->totalFlux; |
---|
| 612 | |
---|
| 613 | if(head.isWCS()){ |
---|
| 614 | // correct for the beam size if the flux units string ends in "/beam" |
---|
[788] | 615 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
[417] | 616 | } |
---|
| 617 | |
---|
| 618 | } |
---|
| 619 | //-------------------------------------------------------------------- |
---|
| 620 | |
---|
[884] | 621 | void Detection::calcIntegFlux(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
[863] | 622 | { |
---|
| 623 | /// @details |
---|
| 624 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
| 625 | /// putting velocity in units of km/s. |
---|
| 626 | /// The fluxes used are taken from the Voxels, rather than an |
---|
| 627 | /// array of flux values. |
---|
| 628 | /// Integrates over full spatial and velocity range as given |
---|
| 629 | /// by the extrema calculated by calcWCSparams. |
---|
| 630 | /// |
---|
| 631 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
| 632 | /// corrected by the beam size (in pixels). This is done by |
---|
| 633 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
| 634 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
| 635 | /// pix/beam --> Jy) |
---|
| 636 | /// |
---|
| 637 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
| 638 | /// \param voxelList The list of Voxels with flux information |
---|
| 639 | /// \param head FitsHeader object that contains the WCS information. |
---|
| 640 | |
---|
| 641 | if(!head.is2D()){ |
---|
| 642 | |
---|
| 643 | this->haveParams = true; |
---|
| 644 | |
---|
[1269] | 645 | this->intFlux = 0.; |
---|
[863] | 646 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
| 647 | std::vector<Voxel>::iterator vox; |
---|
| 648 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
[1269] | 649 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
| 650 | DUCHAMPERROR("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
| 651 | return; |
---|
| 652 | } |
---|
| 653 | else { |
---|
| 654 | this->intFlux += voxelMap[*vox]; |
---|
[863] | 655 | } |
---|
| 656 | } |
---|
[1269] | 657 | this->intFlux *= fabs(head.WCS().cdelt[head.WCS().spec]); |
---|
[863] | 658 | |
---|
| 659 | calcVelWidths(zdim,voxelMap,head); |
---|
| 660 | |
---|
| 661 | } |
---|
| 662 | else // in this case there is just a 2D image. |
---|
| 663 | this->intFlux = this->totalFlux; |
---|
| 664 | |
---|
| 665 | if(head.isWCS()){ |
---|
| 666 | // correct for the beam size if the flux units string ends in "/beam" |
---|
| 667 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
| 668 | } |
---|
| 669 | |
---|
| 670 | } |
---|
| 671 | //-------------------------------------------------------------------- |
---|
| 672 | |
---|
[1269] | 673 | void Detection::calcIntegFlux(float *fluxArray, size_t *dim, FitsHeader &head, Param &par) |
---|
[378] | 674 | { |
---|
[528] | 675 | /// @details |
---|
| 676 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
| 677 | /// putting velocity in units of km/s. |
---|
| 678 | /// Integrates over full spatial and velocity range as given |
---|
| 679 | /// by the extrema calculated by calcWCSparams. |
---|
| 680 | /// |
---|
| 681 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
| 682 | /// corrected by the beam size (in pixels). This is done by |
---|
| 683 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
| 684 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
| 685 | /// pix/beam --> Jy) |
---|
| 686 | /// |
---|
| 687 | /// \param fluxArray The array of flux values. |
---|
| 688 | /// \param dim The dimensions of the flux array. |
---|
| 689 | /// \param head FitsHeader object that contains the WCS information. |
---|
[3] | 690 | |
---|
[1133] | 691 | this->haveParams = true; |
---|
[271] | 692 | |
---|
[1369] | 693 | if (head.is2D() ){ |
---|
| 694 | // in this case there is just a 2D image. |
---|
| 695 | this->intFlux = this->totalFlux; |
---|
[1133] | 696 | } |
---|
[1369] | 697 | else { |
---|
| 698 | |
---|
| 699 | const int border=1; // include one pixel either side in each direction |
---|
| 700 | size_t xsize = std::min(size_t(this->xmax-this->xmin+2*border+1),dim[0]); |
---|
| 701 | size_t ysize = std::min(size_t(this->ymax-this->ymin+2*border+1),dim[1]); |
---|
| 702 | size_t zsize = std::min(size_t(this->zmax-this->zmin+2*border+1),dim[2]); |
---|
| 703 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
| 704 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
| 705 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
| 706 | size_t spatsize = xsize*ysize; |
---|
| 707 | size_t size = xsize*ysize*zsize; |
---|
| 708 | std::vector <bool> isObj(size,false); |
---|
| 709 | double *localFlux = new double[size]; |
---|
| 710 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
| 711 | float *momMap = new float[spatsize]; |
---|
| 712 | for(size_t i=0;i<spatsize;i++) momMap[i]=0.; |
---|
| 713 | // work out which pixels are object pixels |
---|
| 714 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
| 715 | for(std::vector<Voxel>::iterator v=voxlist.begin();v<voxlist.end();v++){ |
---|
| 716 | size_t spatpos=(v->getX()-xzero) + (v->getY()-yzero)*xsize; |
---|
| 717 | size_t pos= spatpos + (v->getZ()-zzero)*spatsize; |
---|
| 718 | localFlux[pos] = fluxArray[v->arrayIndex(dim)]; |
---|
| 719 | momMap[spatpos] += fluxArray[v->arrayIndex(dim)]*head.WCS().cdelt[head.WCS().spec]; |
---|
| 720 | isObj[pos] = true; |
---|
| 721 | } |
---|
[1133] | 722 | |
---|
[1369] | 723 | // work out the WCS coords for each pixel |
---|
[463] | 724 | double *world = new double[size]; |
---|
[378] | 725 | double xpt,ypt,zpt; |
---|
[884] | 726 | size_t i=0; |
---|
[986] | 727 | for(size_t z=zzero;z<zzero+zsize;z++){ |
---|
| 728 | for(size_t y=yzero;y<yzero+ysize;y++){ |
---|
| 729 | for(size_t x=xzero;x<xzero+xsize;x++){ |
---|
| 730 | xpt=double(x); |
---|
| 731 | ypt=double(y); |
---|
| 732 | zpt=double(z); |
---|
[781] | 733 | world[i++] = head.pixToVel(xpt,ypt,zpt); |
---|
| 734 | } |
---|
| 735 | } |
---|
[378] | 736 | } |
---|
[3] | 737 | |
---|
[378] | 738 | double integrated = 0.; |
---|
[884] | 739 | for(size_t pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
---|
| 740 | for(size_t z=0; z<zsize; z++){ |
---|
[921] | 741 | size_t pos = z*xsize*ysize + pix; |
---|
[378] | 742 | if(isObj[pos]){ // if it's an object pixel... |
---|
| 743 | double deltaVel; |
---|
| 744 | if(z==0) |
---|
| 745 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
| 746 | else if(z==(zsize-1)) |
---|
| 747 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
| 748 | else |
---|
| 749 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
| 750 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
| 751 | } |
---|
[271] | 752 | } |
---|
[3] | 753 | } |
---|
[378] | 754 | |
---|
[464] | 755 | delete [] world; |
---|
[1133] | 756 | |
---|
| 757 | this->intFlux = integrated; |
---|
| 758 | |
---|
[1269] | 759 | calcVelWidths(fluxArray, dim, head, par); |
---|
[1369] | 760 | |
---|
| 761 | delete [] localFlux; |
---|
| 762 | delete [] momMap; |
---|
[463] | 763 | |
---|
[1369] | 764 | } |
---|
[1133] | 765 | |
---|
[464] | 766 | if(head.isWCS()){ |
---|
[789] | 767 | // correct for the beam size if the flux units string ends in "/beam" and we have beam info |
---|
[788] | 768 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
[464] | 769 | } |
---|
[463] | 770 | |
---|
[464] | 771 | } |
---|
| 772 | //-------------------------------------------------------------------- |
---|
| 773 | |
---|
[1155] | 774 | void Detection::findShape(const float *fluxArray, const size_t *dim, FitsHeader &head) |
---|
[1133] | 775 | { |
---|
[1175] | 776 | const long border=1; // include one pixel either side in each direction |
---|
| 777 | size_t x1 = size_t(std::max(long(0),this->xmin-border)); |
---|
| 778 | size_t y1 = size_t(std::max(long(0),this->ymin-border)); |
---|
| 779 | size_t x2 = size_t(std::min(long(dim[0])-1,this->xmax+border)); |
---|
| 780 | size_t y2 = size_t(std::min(long(dim[1])-1,this->ymax+border)); |
---|
[1174] | 781 | size_t xsize = x2-x1+1; |
---|
| 782 | size_t ysize = y2-y1+1; |
---|
[1155] | 783 | size_t spatsize = xsize*ysize; |
---|
[1133] | 784 | |
---|
[1154] | 785 | float *momentMap = new float[spatsize]; |
---|
| 786 | for(size_t i=0;i<spatsize;i++) momentMap[i]=0.; |
---|
| 787 | // work out which pixels are object pixels |
---|
| 788 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
[1211] | 789 | float delta = (head.isWCS() && head.getWCS()->spec>=0) ? fabs(head.WCS().cdelt[head.WCS().spec]) : 1.; |
---|
| 790 | float sign = this->negSource ? -1. : 1.; |
---|
[1154] | 791 | for(std::vector<Voxel>::iterator v=voxlist.begin();v<voxlist.end();v++){ |
---|
[1174] | 792 | size_t spatpos=(v->getX()-x1) + (v->getY()-y1)*xsize; |
---|
[1297] | 793 | if(spatpos<spatsize) |
---|
[1211] | 794 | momentMap[spatpos] += fluxArray[v->arrayIndex(dim)] * delta * sign; |
---|
[1269] | 795 | else DUCHAMPTHROW("findShape","Memory overflow - accessing spatpos="<<spatpos<<" when spatsize="<<spatsize <<". Pixel is (x,y)=("<<v->getX() <<","<<v->getY()<<") and (x1,y1)="<<x1<<","<<y1<<"), (x2,y2)="<<x2<<","<<y2<<"), xsize="<<xsize); |
---|
[1154] | 796 | } |
---|
[1361] | 797 | if(this->negSource) |
---|
| 798 | for(size_t i=0;i<spatsize;i++) momentMap[i]*=-1.; |
---|
[1154] | 799 | |
---|
[1155] | 800 | size_t smldim[2]; smldim[0]=xsize; smldim[1]=ysize; |
---|
| 801 | Image *smlIm = new Image(smldim); |
---|
| 802 | smlIm->saveArray(momentMap,spatsize); |
---|
[1133] | 803 | smlIm->setMinSize(1); |
---|
[1155] | 804 | float max = *std::max_element(momentMap,momentMap+spatsize); |
---|
[1133] | 805 | smlIm->stats().setThreshold(max/2.); |
---|
| 806 | std::vector<Object2D> objlist=smlIm->findSources2D(); |
---|
| 807 | |
---|
| 808 | Object2D combined; |
---|
| 809 | for(size_t i=0;i<objlist.size();i++) combined = combined + objlist[i]; |
---|
[1211] | 810 | std::string extraFlag=""; |
---|
[1174] | 811 | bool ellipseGood = combined.findEllipse(true, momentMap, xsize, ysize, 0,0, this->getXcentre()-x1, this->getYcentre()-y1); // try first by weighting the pixels by their flux |
---|
[1133] | 812 | if(!ellipseGood) { |
---|
[1174] | 813 | ellipseGood = combined.findEllipse(false, momentMap, xsize, ysize, 0,0, this->getXcentre()-x1, this->getYcentre()-y1); // if that fails, remove the flux weighting |
---|
[1211] | 814 | extraFlag="W"; |
---|
[1133] | 815 | } |
---|
[1211] | 816 | float scale=head.getShapeScale(); |
---|
[1133] | 817 | if(ellipseGood){ |
---|
[1155] | 818 | // multiply axes by 2 to go from semi-major to FWHM... |
---|
| 819 | this->majorAxis = combined.major() * head.getAvPixScale() * 2. * scale; |
---|
| 820 | this->minorAxis = combined.minor() * head.getAvPixScale() * 2. * scale; |
---|
| 821 | this->posang = combined.posAng() * 180. / M_PI; |
---|
[1211] | 822 | // std::cerr << "*** " << combined.getSize()<< " " << majorAxis<<" " << minorAxis << " " << posang<< " " << scale <<"\n"; |
---|
[1133] | 823 | } |
---|
[1155] | 824 | else { |
---|
[1211] | 825 | extraFlag="w"; |
---|
[1212] | 826 | std::pair<double,double> axes = combined.getPrincipalAxes(); |
---|
[1211] | 827 | this->majorAxis = std::max(axes.first,axes.second) * head.getAvPixScale() * scale; |
---|
| 828 | this->minorAxis = std::min(axes.first,axes.second) * head.getAvPixScale() * scale; |
---|
[1212] | 829 | this->posang = combined.getPositionAngle() * 180. / M_PI; |
---|
[1211] | 830 | // std::cerr << "** " << combined.getSize()<< " " << majorAxis<<" " << minorAxis << " " << posang<< " " << scale <<"\n"; |
---|
| 831 | } |
---|
| 832 | this->flagText += extraFlag; |
---|
[1155] | 833 | |
---|
[1133] | 834 | |
---|
| 835 | delete smlIm; |
---|
[1155] | 836 | delete [] momentMap; |
---|
[1133] | 837 | } |
---|
| 838 | |
---|
| 839 | //-------------------------------------------------------------------- |
---|
| 840 | |
---|
[884] | 841 | void Detection::calcVelWidths(size_t zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
[464] | 842 | { |
---|
[528] | 843 | /// @details |
---|
| 844 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
| 845 | /// peak integrated flux. The procedure is as follows: first |
---|
| 846 | /// generate an integrated flux spectrum (using all given voxels |
---|
| 847 | /// that lie in the object's spatial map); find the peak; starting |
---|
| 848 | /// at the spectral edges of the detection, move in or out until |
---|
| 849 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
| 850 | /// between points is done. |
---|
| 851 | /// |
---|
[719] | 852 | /// \param zdim The size of the spectral axis in the cube |
---|
[528] | 853 | /// \param voxelList The list of Voxels with flux information |
---|
| 854 | /// \param head FitsHeader object that contains the WCS information. |
---|
[464] | 855 | |
---|
[719] | 856 | float *intSpec = new float[zdim]; |
---|
[894] | 857 | for(size_t i=0;i<zdim;i++) intSpec[i]=0; |
---|
[464] | 858 | |
---|
[570] | 859 | Object2D spatMap = this->getSpatialMap(); |
---|
[464] | 860 | for(int s=0;s<spatMap.getNumScan();s++){ |
---|
[623] | 861 | std::vector<Voxel>::iterator vox; |
---|
| 862 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 863 | if(spatMap.isInObject(*vox)){ |
---|
[719] | 864 | intSpec[vox->getZ()] += vox->getF(); |
---|
[464] | 865 | } |
---|
[463] | 866 | } |
---|
[464] | 867 | } |
---|
| 868 | |
---|
[719] | 869 | calcVelWidths(zdim, intSpec, head); |
---|
| 870 | |
---|
| 871 | delete [] intSpec; |
---|
| 872 | |
---|
| 873 | } |
---|
| 874 | |
---|
| 875 | //-------------------------------------------------------------------- |
---|
| 876 | |
---|
[884] | 877 | void Detection::calcVelWidths(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
[863] | 878 | { |
---|
| 879 | /// @details |
---|
| 880 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
| 881 | /// peak integrated flux. The procedure is as follows: first |
---|
| 882 | /// generate an integrated flux spectrum (using all given voxels |
---|
| 883 | /// that lie in the object's spatial map); find the peak; starting |
---|
| 884 | /// at the spectral edges of the detection, move in or out until |
---|
| 885 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
| 886 | /// between points is done. |
---|
| 887 | /// |
---|
| 888 | /// \param zdim The size of the spectral axis in the cube |
---|
| 889 | /// \param voxelList The list of Voxels with flux information |
---|
| 890 | /// \param head FitsHeader object that contains the WCS information. |
---|
| 891 | |
---|
| 892 | float *intSpec = new float[zdim]; |
---|
[894] | 893 | for(size_t i=0;i<zdim;i++) intSpec[i]=0; |
---|
[863] | 894 | |
---|
| 895 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
| 896 | std::vector<Voxel>::iterator vox; |
---|
| 897 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 898 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
[913] | 899 | DUCHAMPERROR("Detection::calcVelWidths","Voxel list provided does not match"); |
---|
[863] | 900 | return; |
---|
| 901 | } |
---|
| 902 | else { |
---|
| 903 | intSpec[vox->getZ()] += voxelMap[*vox]; |
---|
| 904 | } |
---|
| 905 | } |
---|
| 906 | |
---|
| 907 | calcVelWidths(zdim, intSpec, head); |
---|
| 908 | |
---|
| 909 | delete [] intSpec; |
---|
| 910 | |
---|
| 911 | } |
---|
| 912 | |
---|
| 913 | //-------------------------------------------------------------------- |
---|
| 914 | |
---|
[884] | 915 | void Detection::calcVelWidths(size_t zdim, float *intSpec, FitsHeader &head) |
---|
[719] | 916 | { |
---|
| 917 | |
---|
[913] | 918 | // finding the 20% & 50% points. Start at the velmin & velmax |
---|
| 919 | // points. Then, if the int flux there is above the 20%/50% |
---|
| 920 | // limit, go out, otherwise go in. This is to deal with the |
---|
| 921 | // problems from double- (or multi-) peaked sources. |
---|
[719] | 922 | |
---|
| 923 | this->haveParams = true; |
---|
| 924 | |
---|
[924] | 925 | double zpt,xpt=double(this->getXcentre()),ypt=double(this->getYcentre()); |
---|
[719] | 926 | bool goLeft; |
---|
| 927 | |
---|
[1425] | 928 | // if(this->negSource){ |
---|
| 929 | // // if we've inverted the source, need to make the feature |
---|
| 930 | // // positive for the interpolation/extrapolation to work |
---|
| 931 | // for(size_t i=0;i<zdim;i++) intSpec[i] *= -1.; |
---|
| 932 | // } |
---|
[1054] | 933 | |
---|
[634] | 934 | float peak=0.; |
---|
[894] | 935 | size_t peakLoc=0; |
---|
| 936 | for(size_t z=this->getZmin();z<=size_t(this->getZmax());z++) { |
---|
[464] | 937 | if(z==0 || peak<intSpec[z]){ |
---|
| 938 | peak = intSpec[z]; |
---|
| 939 | peakLoc = z; |
---|
[463] | 940 | } |
---|
[464] | 941 | } |
---|
[1425] | 942 | zpt=double(peakLoc); |
---|
| 943 | float level20=peak*0.2; |
---|
| 944 | float level50=peak*0.5; |
---|
[719] | 945 | |
---|
[894] | 946 | size_t z=this->getZmin(); |
---|
[1425] | 947 | goLeft = intSpec[z]>level50; |
---|
| 948 | if(goLeft) while(z>0 && intSpec[z]>level50) z--; |
---|
| 949 | else while(z<peakLoc && intSpec[z]<level50) z++; |
---|
| 950 | if(z==0) { |
---|
| 951 | this->z50min = this->getZmin(); |
---|
| 952 | this->v50min = this->velMin; |
---|
| 953 | } |
---|
[464] | 954 | else{ |
---|
[1425] | 955 | if(goLeft) this->z50min = z + (level50-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 956 | else this->z50min = z - (level50-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
| 957 | this->v50min = head.pixToVel(xpt,ypt,this->z50min); |
---|
[464] | 958 | } |
---|
[1425] | 959 | |
---|
[719] | 960 | z=this->getZmax(); |
---|
[1425] | 961 | goLeft = intSpec[z]<level50; |
---|
| 962 | if(goLeft) while(z>peakLoc && intSpec[z]<level50) z--; |
---|
| 963 | else while(z<zdim && intSpec[z]>level50) z++; |
---|
| 964 | if(z==zdim){ |
---|
| 965 | this->z50max = this->getZmax(); |
---|
| 966 | this->v50max = this->velMax; |
---|
| 967 | } |
---|
[464] | 968 | else{ |
---|
[1425] | 969 | if(goLeft) this->z50max = z + (level50-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 970 | else this->z50max = z - (level50-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
| 971 | this->v50max = head.pixToVel(xpt,ypt,this->z50max); |
---|
[464] | 972 | } |
---|
[1425] | 973 | |
---|
| 974 | if (z50min > z50max){ |
---|
| 975 | std::swap(z50min,z50max); |
---|
| 976 | } |
---|
| 977 | if (v50min > v50max){ |
---|
| 978 | std::swap(v50min,v50max); |
---|
| 979 | } |
---|
| 980 | |
---|
[719] | 981 | z=this->getZmin(); |
---|
[1425] | 982 | goLeft = intSpec[z]>level20; |
---|
| 983 | if(goLeft) while(z>0 && intSpec[z]>level20) z--; |
---|
| 984 | else while(z<peakLoc && intSpec[z]<level20) z++; |
---|
| 985 | if(z==0){ |
---|
| 986 | this->z20min = this->getZmin(); |
---|
| 987 | this->v20min = this->velMin; |
---|
| 988 | } |
---|
[464] | 989 | else{ |
---|
[1425] | 990 | if(goLeft) this->z20min = z + (level20-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 991 | else this->z20min = z - (level20-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
| 992 | this->v20min = head.pixToVel(xpt,ypt,this->z20min); |
---|
[464] | 993 | } |
---|
[1425] | 994 | |
---|
[719] | 995 | z=this->getZmax(); |
---|
[1425] | 996 | goLeft = intSpec[z]<level20; |
---|
| 997 | if(goLeft) while(z>peakLoc && intSpec[z]<level20) z--; |
---|
| 998 | else while(z<zdim && intSpec[z]>level20) z++; |
---|
| 999 | if(z==zdim){ |
---|
| 1000 | this->z50max = this->getZmax(); |
---|
| 1001 | this->v20max = this->velMax; |
---|
| 1002 | } |
---|
[464] | 1003 | else{ |
---|
[1425] | 1004 | if(goLeft) this->z20max = z + (level20-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 1005 | else this->z20max = z - (level20-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
| 1006 | this->v20max = head.pixToVel(xpt,ypt,this->z20max); |
---|
[464] | 1007 | } |
---|
[463] | 1008 | |
---|
[1425] | 1009 | if (z20min > z20max){ |
---|
| 1010 | std::swap(z20min,z20max); |
---|
| 1011 | } |
---|
| 1012 | if (v20min > v20max){ |
---|
| 1013 | std::swap(v20min,v20max); |
---|
| 1014 | } |
---|
| 1015 | |
---|
| 1016 | |
---|
[464] | 1017 | this->w20 = fabs(this->v20min - this->v20max); |
---|
| 1018 | this->w50 = fabs(this->v50min - this->v50max); |
---|
[982] | 1019 | |
---|
[1425] | 1020 | // if(this->negSource){ |
---|
| 1021 | // // un-do the inversion, in case intSpec is needed elsewhere |
---|
| 1022 | // for(size_t i=0;i<zdim;i++) intSpec[i] *= -1.; |
---|
| 1023 | // } |
---|
[1054] | 1024 | |
---|
| 1025 | |
---|
[464] | 1026 | } |
---|
[781] | 1027 | //-------------------------------------------------------------------- |
---|
[464] | 1028 | |
---|
[1269] | 1029 | void Detection::calcVelWidths(float *fluxArray, size_t *dim, FitsHeader &head, Param &par) |
---|
[464] | 1030 | { |
---|
[528] | 1031 | /// @details |
---|
| 1032 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
| 1033 | /// peak integrated flux. The procedure is as follows: first |
---|
| 1034 | /// generate an integrated flux spectrum (summing each spatial |
---|
| 1035 | /// pixel's spectrum); find the peak; starting at the spectral |
---|
| 1036 | /// edges of the detection, move in or out until you reach the 20% |
---|
| 1037 | /// or 50% peak flux level. Linear interpolation between points is |
---|
| 1038 | /// done. |
---|
| 1039 | /// |
---|
| 1040 | /// \param fluxArray The array of flux values. |
---|
| 1041 | /// \param dim The dimensions of the flux array. |
---|
| 1042 | /// \param head FitsHeader object that contains the WCS information. |
---|
[464] | 1043 | |
---|
[465] | 1044 | if(dim[2] > 2){ |
---|
[464] | 1045 | |
---|
[465] | 1046 | float *intSpec = new float[dim[2]]; |
---|
[884] | 1047 | size_t size=dim[0]*dim[1]*dim[2]; |
---|
[1393] | 1048 | std::vector<bool> mask = par.makeBlankMask(fluxArray,size); |
---|
[465] | 1049 | getIntSpec(*this,fluxArray,dim,mask,1.,intSpec); |
---|
| 1050 | |
---|
[719] | 1051 | this->calcVelWidths(dim[2],intSpec,head); |
---|
| 1052 | |
---|
[465] | 1053 | delete [] intSpec; |
---|
| 1054 | |
---|
[378] | 1055 | } |
---|
[464] | 1056 | else{ |
---|
[465] | 1057 | this->v50min = this->v20min = this->velMin; |
---|
| 1058 | this->v50max = this->v20max = this->velMax; |
---|
[719] | 1059 | this->w20 = fabs(this->v20min - this->v20max); |
---|
| 1060 | this->w50 = fabs(this->v50min - this->v50max); |
---|
[464] | 1061 | } |
---|
[300] | 1062 | |
---|
| 1063 | } |
---|
[378] | 1064 | //-------------------------------------------------------------------- |
---|
[300] | 1065 | |
---|
[1425] | 1066 | std::string Detection::boundingSection(std::vector<size_t> dim, FitsHeader *header, unsigned int padsize) |
---|
| 1067 | { |
---|
| 1068 | /// @details This function returns a subsection string that shows the bounding box for the object. This will be in a suitable format for use with the subsection string in the input parameter set. It uses the FitsHeader object to know which axis belongs where. |
---|
| 1069 | |
---|
| 1070 | std::vector<std::string> sectionlist(dim.size(),"1:1"); |
---|
| 1071 | std::stringstream ss; |
---|
| 1072 | // ra - x-dim range |
---|
| 1073 | int axis=header->getWCS()->lng; |
---|
[1443] | 1074 | long start=1; |
---|
| 1075 | long end=dim[axis]; |
---|
[1425] | 1076 | if(axis>=0){ |
---|
[1444] | 1077 | // Force these to be long, rather than unsigned long - some compilers complain if we include in the std::max etc |
---|
| 1078 | long xminpad=this->xmin-padsize+1; |
---|
| 1079 | long xmaxpad=this->xmax+padsize+1; |
---|
[1425] | 1080 | ss.str(""); |
---|
[1444] | 1081 | ss << std::max(start,xminpad) <<":"<<std::min(end,xmaxpad); |
---|
[1425] | 1082 | sectionlist[axis]=ss.str(); |
---|
| 1083 | } |
---|
| 1084 | // dec - y-dim range |
---|
| 1085 | axis=header->getWCS()->lat; |
---|
| 1086 | if(axis>=0){ |
---|
[1444] | 1087 | long yminpad=this->ymin-padsize+1; |
---|
| 1088 | long ymaxpad=this->ymax+padsize+1; |
---|
[1425] | 1089 | ss.str(""); |
---|
[1444] | 1090 | ss << std::max(start,yminpad) <<":"<<std::min(end,ymaxpad); |
---|
[1425] | 1091 | sectionlist[axis]=ss.str(); |
---|
| 1092 | } |
---|
| 1093 | // ra - x-dim range |
---|
| 1094 | axis=header->getWCS()->spec; |
---|
| 1095 | if(axis>=0){ |
---|
[1444] | 1096 | long zminpad=this->zmin-padsize+1; |
---|
| 1097 | long zmaxpad=this->zmax+padsize+1; |
---|
[1425] | 1098 | ss.str(""); |
---|
[1444] | 1099 | ss << std::max(start,zminpad) <<":"<<std::min(end,zmaxpad); |
---|
[1425] | 1100 | sectionlist[axis]=ss.str(); |
---|
| 1101 | } |
---|
| 1102 | ss.str(""); |
---|
| 1103 | ss << "[ " << sectionlist[0]; |
---|
| 1104 | for(size_t i=1;i<dim.size();i++) ss << "," << sectionlist[i]; |
---|
| 1105 | ss << "]"; |
---|
| 1106 | return ss.str(); |
---|
| 1107 | } |
---|
| 1108 | |
---|
| 1109 | //-------------------------------------------------------------------- |
---|
| 1110 | |
---|
[378] | 1111 | void Detection::setOffsets(Param &par) |
---|
| 1112 | { |
---|
[1417] | 1113 | /// @details This function stores the values of the offsets for |
---|
| 1114 | /// each cube axis. The offsets are the starting values of the |
---|
| 1115 | /// cube axes that may differ from the default value of 0 (for |
---|
| 1116 | /// instance, if a subsection is being used). The values will be |
---|
| 1117 | /// used when the detection is outputted. NB - this function |
---|
| 1118 | /// merely sets the values of the offset parameters, it *does not* |
---|
| 1119 | /// apply them to the pixels & parameters (that is the |
---|
| 1120 | /// applyOffsets() function). |
---|
[528] | 1121 | |
---|
[378] | 1122 | this->xSubOffset = par.getXOffset(); |
---|
| 1123 | this->ySubOffset = par.getYOffset(); |
---|
| 1124 | this->zSubOffset = par.getZOffset(); |
---|
| 1125 | } |
---|
| 1126 | //-------------------------------------------------------------------- |
---|
[3] | 1127 | |
---|
[378] | 1128 | bool Detection::hasEnoughChannels(int minNumber) |
---|
| 1129 | { |
---|
[528] | 1130 | /// @details |
---|
| 1131 | /// A function to determine if the Detection has enough |
---|
| 1132 | /// contiguous channels to meet the minimum requirement |
---|
| 1133 | /// given as the argument. |
---|
| 1134 | /// \param minNumber How many channels is the minimum acceptable number? |
---|
| 1135 | /// \return True if there is at least one occurence of minNumber consecutive |
---|
| 1136 | /// channels present to return true. False otherwise. |
---|
[3] | 1137 | |
---|
[378] | 1138 | // Preferred method -- need a set of minNumber consecutive channels present. |
---|
[3] | 1139 | |
---|
[570] | 1140 | int numChan = this->getMaxAdjacentChannels(); |
---|
| 1141 | bool result = (numChan >= minNumber); |
---|
| 1142 | |
---|
[378] | 1143 | return result; |
---|
| 1144 | |
---|
| 1145 | } |
---|
| 1146 | //-------------------------------------------------------------------- |
---|
[452] | 1147 | |
---|
[770] | 1148 | void Detection::addDetection(Detection &other) |
---|
[747] | 1149 | { |
---|
| 1150 | for(std::map<long, Object2D>::iterator it = other.chanlist.begin(); it!=other.chanlist.end();it++) |
---|
[770] | 1151 | // this->addChannel(*it); |
---|
[747] | 1152 | this->addChannel(it->first, it->second); |
---|
| 1153 | this->haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
| 1154 | } |
---|
[624] | 1155 | |
---|
[770] | 1156 | Detection operator+ (Detection &lhs, Detection &rhs) |
---|
[624] | 1157 | { |
---|
| 1158 | Detection output = lhs; |
---|
| 1159 | for(std::map<long, Object2D>::iterator it = rhs.chanlist.begin(); it!=rhs.chanlist.end();it++) |
---|
| 1160 | output.addChannel(it->first, it->second); |
---|
[681] | 1161 | output.haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
[624] | 1162 | return output; |
---|
| 1163 | } |
---|
| 1164 | |
---|
| 1165 | |
---|
[770] | 1166 | bool Detection::canMerge(Detection &other, Param &par) |
---|
| 1167 | { |
---|
| 1168 | bool near = this->isNear(other,par); |
---|
| 1169 | if(near) return this->isClose(other,par); |
---|
| 1170 | else return near; |
---|
| 1171 | } |
---|
[624] | 1172 | |
---|
[770] | 1173 | bool Detection::isNear(Detection &other, Param &par) |
---|
| 1174 | { |
---|
[624] | 1175 | |
---|
[770] | 1176 | bool flagAdj = par.getFlagAdjacent(); |
---|
| 1177 | float threshS = par.getThreshS(); |
---|
| 1178 | float threshV = par.getThreshV(); |
---|
| 1179 | |
---|
| 1180 | long gap; |
---|
| 1181 | if(flagAdj) gap = 1; |
---|
| 1182 | else gap = long( ceil(threshS) ); |
---|
| 1183 | |
---|
| 1184 | bool areNear; |
---|
| 1185 | // Test X ranges |
---|
| 1186 | if((this->xmin-gap)<other.xmin) areNear=((this->xmax+gap)>=other.xmin); |
---|
| 1187 | else areNear=(other.xmax>=(this->xmin-gap)); |
---|
| 1188 | // Test Y ranges |
---|
| 1189 | if(areNear){ |
---|
| 1190 | if((this->ymin-gap)<other.ymin) areNear=areNear&&((this->ymax+gap)>=other.ymin); |
---|
| 1191 | else areNear=areNear&&(other.ymax>=(this->ymin-gap)); |
---|
| 1192 | } |
---|
| 1193 | // Test Z ranges |
---|
| 1194 | if(areNear){ |
---|
| 1195 | gap = long(ceil(threshV)); |
---|
| 1196 | if((this->zmin-gap)<other.zmin) areNear=areNear&&((this->zmax+gap)>=other.zmin); |
---|
| 1197 | else areNear=areNear&&(other.zmax>=(this->zmin-gap)); |
---|
| 1198 | } |
---|
| 1199 | |
---|
| 1200 | return areNear; |
---|
| 1201 | |
---|
| 1202 | } |
---|
| 1203 | |
---|
| 1204 | bool Detection::isClose(Detection &other, Param &par) |
---|
| 1205 | { |
---|
| 1206 | bool close = false; // this will be the value returned |
---|
| 1207 | |
---|
| 1208 | bool flagAdj = par.getFlagAdjacent(); |
---|
| 1209 | float threshS = par.getThreshS(); |
---|
| 1210 | float threshV = par.getThreshV(); |
---|
| 1211 | |
---|
| 1212 | // |
---|
| 1213 | // If we get to here, the pixel ranges overlap -- so we do a |
---|
| 1214 | // pixel-by-pixel comparison to make sure they are actually |
---|
| 1215 | // "close" according to the thresholds. Otherwise, close=false, |
---|
| 1216 | // and so don't need to do anything else before returning. |
---|
| 1217 | // |
---|
| 1218 | |
---|
| 1219 | std::vector<long> zlist1 = this->getChannelList(); |
---|
| 1220 | std::vector<long> zlist2 = other.getChannelList(); |
---|
| 1221 | Scan test1,test2; |
---|
| 1222 | |
---|
| 1223 | for(size_t ct1=0; (!close && (ct1<zlist1.size())); ct1++){ |
---|
| 1224 | for(size_t ct2=0; (!close && (ct2<zlist2.size())); ct2++){ |
---|
| 1225 | |
---|
[1443] | 1226 | if(abs(zlist1[ct1]-zlist2[ct2])<=threshV){ |
---|
[770] | 1227 | |
---|
| 1228 | Object2D temp1 = this->getChanMap(zlist1[ct1]); |
---|
| 1229 | Object2D temp2 = other.getChanMap(zlist2[ct2]); |
---|
| 1230 | |
---|
| 1231 | close = temp1.canMerge(temp2,threshS,flagAdj); |
---|
| 1232 | |
---|
| 1233 | } |
---|
| 1234 | |
---|
| 1235 | } |
---|
| 1236 | } |
---|
| 1237 | |
---|
| 1238 | return close; |
---|
| 1239 | |
---|
| 1240 | } |
---|
| 1241 | |
---|
| 1242 | |
---|
| 1243 | |
---|
[3] | 1244 | } |
---|