[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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| 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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[947] | 83 | this->specType = ""; |
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[570] | 84 | this->fluxUnits = ""; |
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| 85 | this->intFluxUnits = ""; |
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| 86 | this->lngtype = "RA"; |
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| 87 | this->lattype = "DEC"; |
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| 88 | this->vel = 0.; |
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| 89 | this->velWidth = 0.; |
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| 90 | this->velMin = 0.; |
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| 91 | this->velMax = 0.; |
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| 92 | this->w20 = 0.; |
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| 93 | this->v20min = 0.; |
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| 94 | this->v20max = 0.; |
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| 95 | this->w50 = 0.; |
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| 96 | this->v50min = 0.; |
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| 97 | this->v50max = 0.; |
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[1061] | 98 | this->posPrec = Catalogues::prPOS; |
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| 99 | this->xyzPrec = Catalogues::prXYZ; |
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| 100 | this->fintPrec = Catalogues::prFLUX; |
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| 101 | this->fpeakPrec = Catalogues::prFLUX; |
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| 102 | this->velPrec = Catalogues::prVEL; |
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| 103 | this->snrPrec = Catalogues::prSNR; |
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[378] | 104 | } |
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[218] | 105 | |
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[570] | 106 | Detection::Detection(): |
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| 107 | Object3D() |
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[378] | 108 | { |
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[570] | 109 | this->defaultDetection(); |
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| 110 | } |
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| 111 | |
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| 112 | Detection::Detection(const Object3D& o): |
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| 113 | Object3D(o) |
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| 114 | { |
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| 115 | this->defaultDetection(); |
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| 116 | } |
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| 117 | |
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| 118 | Detection::Detection(const Detection& d): |
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| 119 | Object3D(d) |
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| 120 | { |
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[378] | 121 | operator=(d); |
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| 122 | } |
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[218] | 123 | |
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[378] | 124 | Detection& Detection::operator= (const Detection& d) |
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| 125 | { |
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[570] | 126 | ((Object3D &) *this) = d; |
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[378] | 127 | this->xSubOffset = d.xSubOffset; |
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| 128 | this->ySubOffset = d.ySubOffset; |
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| 129 | this->zSubOffset = d.zSubOffset; |
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[681] | 130 | this->haveParams = d.haveParams; |
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[378] | 131 | this->totalFlux = d.totalFlux; |
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[461] | 132 | this->intFlux = d.intFlux; |
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[378] | 133 | this->peakFlux = d.peakFlux; |
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| 134 | this->xpeak = d.xpeak; |
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| 135 | this->ypeak = d.ypeak; |
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| 136 | this->zpeak = d.zpeak; |
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| 137 | this->peakSNR = d.peakSNR; |
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| 138 | this->xCentroid = d.xCentroid; |
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| 139 | this->yCentroid = d.yCentroid; |
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| 140 | this->zCentroid = d.zCentroid; |
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| 141 | this->centreType = d.centreType; |
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| 142 | this->negSource = d.negSource; |
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| 143 | this->flagText = d.flagText; |
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| 144 | this->id = d.id; |
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| 145 | this->name = d.name; |
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| 146 | this->flagWCS = d.flagWCS; |
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| 147 | this->specOK = d.specOK; |
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| 148 | this->raS = d.raS; |
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| 149 | this->decS = d.decS; |
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| 150 | this->ra = d.ra; |
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[461] | 151 | this->dec = d.dec; |
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| 152 | this->raWidth = d.raWidth; |
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[378] | 153 | this->decWidth = d.decWidth; |
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[473] | 154 | this->majorAxis = d.majorAxis; |
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| 155 | this->minorAxis = d.minorAxis; |
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| 156 | this->posang = d.posang; |
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[378] | 157 | this->specUnits = d.specUnits; |
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[947] | 158 | this->specType = d.specType; |
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[378] | 159 | this->fluxUnits = d.fluxUnits; |
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| 160 | this->intFluxUnits = d.intFluxUnits; |
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[461] | 161 | this->lngtype = d.lngtype; |
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| 162 | this->lattype = d.lattype; |
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[378] | 163 | this->vel = d.vel; |
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| 164 | this->velWidth = d.velWidth; |
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| 165 | this->velMin = d.velMin; |
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| 166 | this->velMax = d.velMax; |
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[463] | 167 | this->w20 = d.w20; |
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| 168 | this->v20min = d.v20min; |
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| 169 | this->v20max = d.v20max; |
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| 170 | this->w50 = d.w50; |
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| 171 | this->v50min = d.v50min; |
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| 172 | this->v50max = d.v50max; |
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[378] | 173 | this->posPrec = d.posPrec; |
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| 174 | this->xyzPrec = d.xyzPrec; |
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| 175 | this->fintPrec = d.fintPrec; |
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| 176 | this->fpeakPrec = d.fpeakPrec; |
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[461] | 177 | this->velPrec = d.velPrec; |
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[378] | 178 | this->snrPrec = d.snrPrec; |
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| 179 | return *this; |
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| 180 | } |
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[3] | 181 | |
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[378] | 182 | //-------------------------------------------------------------------- |
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[570] | 183 | float Detection::getXcentre() |
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| 184 | { |
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| 185 | if(this->centreType=="peak") return this->xpeak; |
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| 186 | else if(this->centreType=="average") return this->getXaverage(); |
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| 187 | else return this->xCentroid; |
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| 188 | } |
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[258] | 189 | |
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[570] | 190 | float Detection::getYcentre() |
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| 191 | { |
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| 192 | if(this->centreType=="peak") return this->ypeak; |
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| 193 | else if(this->centreType=="average") return this->getYaverage(); |
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| 194 | else return this->yCentroid; |
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| 195 | } |
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| 196 | |
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| 197 | float Detection::getZcentre() |
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| 198 | { |
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| 199 | if(this->centreType=="peak") return this->zpeak; |
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| 200 | else if(this->centreType=="average") return this->getZaverage(); |
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| 201 | else return this->zCentroid; |
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| 202 | } |
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| 203 | |
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| 204 | //-------------------------------------------------------------------- |
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| 205 | |
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[417] | 206 | bool Detection::voxelListsMatch(std::vector<Voxel> voxelList) |
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| 207 | { |
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[528] | 208 | /// @details |
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| 209 | /// A test to see whether there is a 1-1 correspondence between |
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| 210 | /// the given list of Voxels and the voxel positions contained in |
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| 211 | /// this Detection's pixel list. No testing of the fluxes of the |
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| 212 | /// Voxels is done. |
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| 213 | /// |
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| 214 | /// \param voxelList The std::vector list of Voxels to be tested. |
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[417] | 215 | |
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| 216 | bool listsMatch = true; |
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| 217 | // compare sizes |
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| 218 | listsMatch = listsMatch && (voxelList.size() == this->getSize()); |
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| 219 | if(!listsMatch) return listsMatch; |
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| 220 | |
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[463] | 221 | // make sure all Detection pixels are in voxel list |
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| 222 | listsMatch = listsMatch && this->voxelListCovered(voxelList); |
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| 223 | |
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[417] | 224 | // make sure all voxels are in Detection |
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[623] | 225 | std::vector<Voxel>::iterator vox; |
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| 226 | for(vox=voxelList.begin();vox<voxelList.end();vox++) |
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| 227 | listsMatch = listsMatch && this->isInObject(*vox); |
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[463] | 228 | |
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| 229 | return listsMatch; |
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| 230 | |
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| 231 | } |
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| 232 | //-------------------------------------------------------------------- |
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| 233 | |
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| 234 | bool Detection::voxelListCovered(std::vector<Voxel> voxelList) |
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| 235 | { |
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[528] | 236 | /// @details |
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| 237 | /// A test to see whether the given list of Voxels contains each |
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| 238 | /// position in this Detection's pixel list. It does not look for |
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| 239 | /// a 1-1 correspondence: the given list can be a super-set of the |
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| 240 | /// Detection. No testing of the fluxes of the Voxels is done. |
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| 241 | /// |
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| 242 | /// \param voxelList The std::vector list of Voxels to be tested. |
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[463] | 243 | |
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| 244 | bool listsMatch = true; |
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| 245 | |
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[417] | 246 | // make sure all Detection pixels are in voxel list |
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[623] | 247 | size_t v1=0; |
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[570] | 248 | std::vector<Voxel> detpixlist = this->getPixelSet(); |
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| 249 | while(listsMatch && v1<detpixlist.size()){ |
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[417] | 250 | bool inList = false; |
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[623] | 251 | size_t v2=0; |
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[417] | 252 | while(!inList && v2<voxelList.size()){ |
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[570] | 253 | inList = inList || detpixlist[v1].match(voxelList[v2]); |
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[417] | 254 | v2++; |
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| 255 | } |
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| 256 | listsMatch = listsMatch && inList; |
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[418] | 257 | v1++; |
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[417] | 258 | } |
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| 259 | |
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| 260 | return listsMatch; |
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| 261 | |
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| 262 | } |
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| 263 | //-------------------------------------------------------------------- |
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| 264 | |
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| 265 | void Detection::calcFluxes(std::vector<Voxel> voxelList) |
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| 266 | { |
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[528] | 267 | /// @details |
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| 268 | /// A function that calculates total & peak fluxes (and the location |
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| 269 | /// of the peak flux) for a Detection. |
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| 270 | /// |
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| 271 | /// \param fluxArray The array of flux values to calculate the |
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| 272 | /// flux parameters from. |
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| 273 | /// \param dim The dimensions of the flux array. |
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[681] | 274 | |
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| 275 | // this->haveParams = true; |
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[417] | 276 | |
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| 277 | this->totalFlux = this->peakFlux = 0; |
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| 278 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 279 | |
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| 280 | // first check that the voxel list and the Detection's pixel list |
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| 281 | // have a 1-1 correspondence |
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| 282 | |
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[463] | 283 | if(!this->voxelListCovered(voxelList)){ |
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[913] | 284 | DUCHAMPERROR("Detection::calcFluxes","Voxel list provided does not match"); |
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[417] | 285 | return; |
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| 286 | } |
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| 287 | |
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[623] | 288 | std::vector<Voxel>::iterator vox; |
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| 289 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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| 290 | if(this->isInObject(*vox)){ |
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| 291 | long x = vox->getX(); |
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| 292 | long y = vox->getY(); |
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| 293 | long z = vox->getZ(); |
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| 294 | float f = vox->getF(); |
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[463] | 295 | this->totalFlux += f; |
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| 296 | this->xCentroid += x*f; |
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| 297 | this->yCentroid += y*f; |
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| 298 | this->zCentroid += z*f; |
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[623] | 299 | if( (vox==voxelList.begin()) || //first time round |
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[463] | 300 | (this->negSource&&(f<this->peakFlux)) || |
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| 301 | (!this->negSource&&(f>this->peakFlux)) ) |
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| 302 | { |
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| 303 | this->peakFlux = f; |
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| 304 | this->xpeak = x; |
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| 305 | this->ypeak = y; |
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| 306 | this->zpeak = z; |
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| 307 | } |
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| 308 | } |
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[417] | 309 | } |
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| 310 | |
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| 311 | this->xCentroid /= this->totalFlux; |
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| 312 | this->yCentroid /= this->totalFlux; |
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| 313 | this->zCentroid /= this->totalFlux; |
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| 314 | } |
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| 315 | //-------------------------------------------------------------------- |
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| 316 | |
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[863] | 317 | void Detection::calcFluxes(std::map<Voxel,float> &voxelMap) |
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| 318 | { |
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| 319 | /// @details |
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| 320 | /// A function that calculates total & peak fluxes (and the location |
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| 321 | /// of the peak flux) for a Detection. |
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| 322 | /// |
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| 323 | /// \param fluxArray The array of flux values to calculate the |
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| 324 | /// flux parameters from. |
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| 325 | /// \param dim The dimensions of the flux array. |
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| 326 | |
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| 327 | // this->haveParams = true; |
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| 328 | |
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| 329 | this->totalFlux = this->peakFlux = 0; |
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| 330 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 331 | |
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| 332 | std::vector<Voxel> voxelList = this->getPixelSet(); |
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| 333 | std::vector<Voxel>::iterator vox; |
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| 334 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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| 335 | if(voxelMap.find(*vox) == voxelMap.end()){ |
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[913] | 336 | DUCHAMPERROR("Detection::calcFluxes","Voxel list provided does not match"); |
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[863] | 337 | return; |
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| 338 | } |
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| 339 | else { |
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| 340 | long x = vox->getX(); |
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| 341 | long y = vox->getY(); |
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| 342 | long z = vox->getZ(); |
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| 343 | float f = voxelMap[*vox]; |
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| 344 | this->totalFlux += f; |
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| 345 | this->xCentroid += x*f; |
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| 346 | this->yCentroid += y*f; |
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| 347 | this->zCentroid += z*f; |
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| 348 | if( (vox==voxelList.begin()) || //first time round |
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| 349 | (this->negSource&&(f<this->peakFlux)) || |
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| 350 | (!this->negSource&&(f>this->peakFlux)) ) |
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| 351 | { |
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| 352 | this->peakFlux = f; |
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| 353 | this->xpeak = x; |
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| 354 | this->ypeak = y; |
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| 355 | this->zpeak = z; |
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| 356 | } |
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| 357 | } |
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| 358 | } |
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| 359 | |
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| 360 | this->xCentroid /= this->totalFlux; |
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| 361 | this->yCentroid /= this->totalFlux; |
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| 362 | this->zCentroid /= this->totalFlux; |
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| 363 | } |
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| 364 | //-------------------------------------------------------------------- |
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| 365 | |
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[884] | 366 | void Detection::calcFluxes(float *fluxArray, size_t *dim) |
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[378] | 367 | { |
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[528] | 368 | /// @details |
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| 369 | /// A function that calculates total & peak fluxes (and the location |
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| 370 | /// of the peak flux) for a Detection. |
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| 371 | /// |
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| 372 | /// \param fluxArray The array of flux values to calculate the |
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| 373 | /// flux parameters from. |
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| 374 | /// \param dim The dimensions of the flux array. |
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[258] | 375 | |
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[681] | 376 | // this->haveParams = true; |
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| 377 | |
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[378] | 378 | this->totalFlux = this->peakFlux = 0; |
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| 379 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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| 380 | |
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[570] | 381 | std::vector<Voxel> voxList = this->getPixelSet(); |
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[473] | 382 | std::vector<Voxel>::iterator vox=voxList.begin(); |
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| 383 | for(;vox<voxList.end();vox++){ |
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[378] | 384 | |
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[473] | 385 | long x=vox->getX(); |
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| 386 | long y=vox->getY(); |
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| 387 | long z=vox->getZ(); |
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[884] | 388 | size_t ind = vox->arrayIndex(dim); |
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[473] | 389 | float f = fluxArray[ind]; |
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| 390 | this->totalFlux += f; |
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| 391 | this->xCentroid += x*f; |
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| 392 | this->yCentroid += y*f; |
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| 393 | this->zCentroid += z*f; |
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| 394 | if( (vox==voxList.begin()) || |
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| 395 | (this->negSource&&(f<this->peakFlux)) || |
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| 396 | (!this->negSource&&(f>this->peakFlux)) ) |
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| 397 | { |
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| 398 | this->peakFlux = f; |
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| 399 | this->xpeak = x; |
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| 400 | this->ypeak = y; |
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| 401 | this->zpeak = z; |
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[378] | 402 | } |
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[473] | 403 | |
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[45] | 404 | } |
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[378] | 405 | |
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| 406 | this->xCentroid /= this->totalFlux; |
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| 407 | this->yCentroid /= this->totalFlux; |
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| 408 | this->zCentroid /= this->totalFlux; |
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[263] | 409 | } |
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[378] | 410 | //-------------------------------------------------------------------- |
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[263] | 411 | |
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[417] | 412 | void Detection::calcWCSparams(FitsHeader &head) |
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[378] | 413 | { |
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[528] | 414 | /// @details |
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| 415 | /// Use the input wcs to calculate the position and velocity |
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| 416 | /// information for the Detection. |
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| 417 | /// Quantities calculated: |
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| 418 | /// <ul><li> RA: ra [deg], ra (string), ra width. |
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| 419 | /// <li> Dec: dec [deg], dec (string), dec width. |
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| 420 | /// <li> Vel: vel [km/s], min & max vel, vel width. |
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| 421 | /// <li> coord type for all three axes, nuRest, |
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| 422 | /// <li> name (IAU-style, in equatorial or Galactic) |
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| 423 | /// </ul> |
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| 424 | /// |
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| 425 | /// Note that the regular parameters are NOT recalculated! |
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| 426 | /// |
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| 427 | /// \param head FitsHeader object that contains the WCS information. |
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[3] | 428 | |
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[378] | 429 | if(head.isWCS()){ |
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[3] | 430 | |
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[378] | 431 | double *pixcrd = new double[15]; |
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| 432 | double *world = new double[15]; |
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| 433 | /* |
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| 434 | define a five-point array in 3D: |
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| 435 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
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| 436 | [note: x = central point, x1 = minimum x, x2 = maximum x etc.] |
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| 437 | and convert to world coordinates. |
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| 438 | */ |
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| 439 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->getXcentre(); |
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| 440 | pixcrd[9] = this->getXmin()-0.5; |
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| 441 | pixcrd[12] = this->getXmax()+0.5; |
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| 442 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->getYcentre(); |
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| 443 | pixcrd[10] = this->getYmin()-0.5; |
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| 444 | pixcrd[13] = this->getYmax()+0.5; |
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| 445 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->getZcentre(); |
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| 446 | pixcrd[5] = this->getZmin(); |
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| 447 | pixcrd[8] = this->getZmax(); |
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| 448 | int flag = head.pixToWCS(pixcrd, world, 5); |
---|
| 449 | delete [] pixcrd; |
---|
[913] | 450 | if(flag!=0) { |
---|
| 451 | DUCHAMPERROR("calcWCSparams", "Error in calculating the WCS for this object."); |
---|
| 452 | } |
---|
[378] | 453 | else{ |
---|
[913] | 454 | |
---|
[378] | 455 | // world now has the WCS coords for the five points |
---|
| 456 | // -- use this to work out WCS params |
---|
[22] | 457 | |
---|
[681] | 458 | this->haveParams = true; |
---|
| 459 | |
---|
[378] | 460 | this->specOK = head.canUseThirdAxis(); |
---|
[963] | 461 | this->lngtype = head.lngtype(); |
---|
| 462 | this->lattype = head.lattype(); |
---|
[378] | 463 | this->specUnits = head.getSpectralUnits(); |
---|
[947] | 464 | this->specType = head.getSpectralType(); |
---|
[378] | 465 | this->fluxUnits = head.getFluxUnits(); |
---|
| 466 | // if fluxUnits are eg. Jy/beam, make intFluxUnits = Jy km/s |
---|
| 467 | this->intFluxUnits = head.getIntFluxUnits(); |
---|
| 468 | this->ra = world[0]; |
---|
| 469 | this->dec = world[1]; |
---|
[907] | 470 | int precision = -int(log10(fabs(head.WCS().cdelt[head.WCS().lng]*3600./10.))); |
---|
| 471 | this->raS = decToDMS(this->ra, this->lngtype,precision); |
---|
| 472 | this->decS = decToDMS(this->dec,this->lattype,precision); |
---|
[378] | 473 | this->raWidth = angularSeparation(world[9],world[1], |
---|
| 474 | world[12],world[1]) * 60.; |
---|
| 475 | this->decWidth = angularSeparation(world[0],world[10], |
---|
| 476 | world[0],world[13]) * 60.; |
---|
[473] | 477 | |
---|
[570] | 478 | Object2D spatMap = this->getSpatialMap(); |
---|
[473] | 479 | std::pair<double,double> axes = spatMap.getPrincipleAxes(); |
---|
| 480 | this->majorAxis = std::max(axes.first,axes.second) * head.getAvPixScale(); |
---|
| 481 | this->minorAxis = std::min(axes.first,axes.second) * head.getAvPixScale(); |
---|
| 482 | this->posang = spatMap.getPositionAngle() * 180. / M_PI; |
---|
[1130] | 483 | // std::cerr << majorAxis << " " << minorAxis << " " << posang << " " << majorAxis/head.getAvPixScale() << " " << minorAxis/head.getAvPixScale() << " " << posang*M_PI/180.<<"\n"; |
---|
[473] | 484 | |
---|
[378] | 485 | this->name = head.getIAUName(this->ra, this->dec); |
---|
| 486 | this->vel = head.specToVel(world[2]); |
---|
| 487 | this->velMin = head.specToVel(world[5]); |
---|
| 488 | this->velMax = head.specToVel(world[8]); |
---|
| 489 | this->velWidth = fabs(this->velMax - this->velMin); |
---|
[3] | 490 | |
---|
[378] | 491 | this->flagWCS = true; |
---|
| 492 | } |
---|
| 493 | delete [] world; |
---|
| 494 | |
---|
[270] | 495 | } |
---|
[982] | 496 | else { |
---|
| 497 | double x=this->getXcentre(),y=this->getYcentre(),z=this->getZmin(); |
---|
| 498 | this->velMin = head.pixToVel(x,y,z); |
---|
| 499 | z=this->getZmax(); |
---|
| 500 | this->velMax = head.pixToVel(x,y,z); |
---|
| 501 | this->velWidth = fabs(this->velMax - this->velMin); |
---|
| 502 | } |
---|
| 503 | |
---|
| 504 | |
---|
[103] | 505 | } |
---|
[378] | 506 | //-------------------------------------------------------------------- |
---|
[3] | 507 | |
---|
[884] | 508 | void Detection::calcIntegFlux(size_t zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
[417] | 509 | { |
---|
[528] | 510 | /// @details |
---|
| 511 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
| 512 | /// putting velocity in units of km/s. |
---|
| 513 | /// The fluxes used are taken from the Voxels, rather than an |
---|
| 514 | /// array of flux values. |
---|
| 515 | /// Integrates over full spatial and velocity range as given |
---|
| 516 | /// by the extrema calculated by calcWCSparams. |
---|
| 517 | /// |
---|
| 518 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
| 519 | /// corrected by the beam size (in pixels). This is done by |
---|
| 520 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
| 521 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
| 522 | /// pix/beam --> Jy) |
---|
| 523 | /// |
---|
[719] | 524 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
[528] | 525 | /// \param voxelList The list of Voxels with flux information |
---|
| 526 | /// \param head FitsHeader object that contains the WCS information. |
---|
[417] | 527 | |
---|
[463] | 528 | if(!this->voxelListCovered(voxelList)){ |
---|
[913] | 529 | DUCHAMPERROR("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
[417] | 530 | return; |
---|
| 531 | } |
---|
| 532 | |
---|
[513] | 533 | if(!head.is2D()){ |
---|
[417] | 534 | |
---|
[681] | 535 | this->haveParams = true; |
---|
| 536 | |
---|
[982] | 537 | const int border = 1; // include one pixel either side in each direction |
---|
[983] | 538 | size_t xsize = size_t(this->xmax-this->xmin+2*border+1); |
---|
| 539 | size_t ysize = size_t(this->ymax-this->ymin+2*border+1); |
---|
| 540 | size_t zsize = size_t(this->zmax-this->zmin+2*border+1); |
---|
[982] | 541 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
| 542 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
| 543 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
[884] | 544 | size_t spatsize=xsize*ysize; |
---|
| 545 | size_t size = xsize*ysize*zsize; |
---|
[473] | 546 | std::vector <bool> isObj(size,false); |
---|
[463] | 547 | double *localFlux = new double[size]; |
---|
[884] | 548 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
[417] | 549 | |
---|
[623] | 550 | std::vector<Voxel>::iterator vox; |
---|
| 551 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 552 | if(this->isInObject(*vox)){ |
---|
[983] | 553 | size_t pos=(vox->getX()-xzero) + (vox->getY()-yzero)*xsize + (vox->getZ()-zzero)*spatsize; |
---|
[623] | 554 | localFlux[pos] = vox->getF(); |
---|
[463] | 555 | isObj[pos] = true; |
---|
| 556 | } |
---|
[417] | 557 | } |
---|
| 558 | |
---|
| 559 | // work out the WCS coords for each pixel |
---|
[463] | 560 | double *world = new double[size]; |
---|
[417] | 561 | double xpt,ypt,zpt; |
---|
[924] | 562 | for(size_t i=0;i<size;i++){ |
---|
[463] | 563 | xpt = double( this->getXmin() - border + i%xsize ); |
---|
| 564 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
---|
| 565 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
---|
[417] | 566 | world[i] = head.pixToVel(xpt,ypt,zpt); |
---|
| 567 | } |
---|
| 568 | |
---|
| 569 | double integrated = 0.; |
---|
[884] | 570 | for(size_t pix=0; pix<spatsize; pix++){ // loop over each spatial pixel. |
---|
| 571 | for(size_t z=0; z<zsize; z++){ |
---|
[921] | 572 | size_t pos = z*xsize*ysize + pix; |
---|
[417] | 573 | if(isObj[pos]){ // if it's an object pixel... |
---|
| 574 | double deltaVel; |
---|
| 575 | if(z==0) |
---|
| 576 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
| 577 | else if(z==(zsize-1)) |
---|
| 578 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
| 579 | else |
---|
| 580 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
| 581 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
| 582 | } |
---|
| 583 | } |
---|
| 584 | } |
---|
| 585 | this->intFlux = integrated; |
---|
| 586 | |
---|
| 587 | delete [] world; |
---|
| 588 | delete [] localFlux; |
---|
| 589 | |
---|
[719] | 590 | calcVelWidths(zdim,voxelList,head); |
---|
[464] | 591 | |
---|
[417] | 592 | } |
---|
| 593 | else // in this case there is just a 2D image. |
---|
| 594 | this->intFlux = this->totalFlux; |
---|
| 595 | |
---|
| 596 | if(head.isWCS()){ |
---|
| 597 | // correct for the beam size if the flux units string ends in "/beam" |
---|
[788] | 598 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
[417] | 599 | } |
---|
| 600 | |
---|
| 601 | } |
---|
| 602 | //-------------------------------------------------------------------- |
---|
| 603 | |
---|
[884] | 604 | void Detection::calcIntegFlux(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
[863] | 605 | { |
---|
| 606 | /// @details |
---|
| 607 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
| 608 | /// putting velocity in units of km/s. |
---|
| 609 | /// The fluxes used are taken from the Voxels, rather than an |
---|
| 610 | /// array of flux values. |
---|
| 611 | /// Integrates over full spatial and velocity range as given |
---|
| 612 | /// by the extrema calculated by calcWCSparams. |
---|
| 613 | /// |
---|
| 614 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
| 615 | /// corrected by the beam size (in pixels). This is done by |
---|
| 616 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
| 617 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
| 618 | /// pix/beam --> Jy) |
---|
| 619 | /// |
---|
| 620 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
| 621 | /// \param voxelList The list of Voxels with flux information |
---|
| 622 | /// \param head FitsHeader object that contains the WCS information. |
---|
| 623 | |
---|
| 624 | if(!head.is2D()){ |
---|
| 625 | |
---|
| 626 | this->haveParams = true; |
---|
| 627 | |
---|
[982] | 628 | const int border = 1; // include one pixel either side in each direction |
---|
[983] | 629 | size_t xsize = size_t(this->xmax-this->xmin+2*border+1); |
---|
| 630 | size_t ysize = size_t(this->ymax-this->ymin+2*border+1); |
---|
| 631 | size_t zsize = size_t(this->zmax-this->zmin+2*border+1); |
---|
[982] | 632 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
| 633 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
| 634 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
[884] | 635 | size_t spatsize=xsize*ysize; |
---|
| 636 | size_t size = xsize*ysize*zsize; |
---|
[863] | 637 | std::vector <bool> isObj(size,false); |
---|
| 638 | double *localFlux = new double[size]; |
---|
[884] | 639 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
[863] | 640 | |
---|
| 641 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
| 642 | std::vector<Voxel>::iterator vox; |
---|
| 643 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 644 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
[913] | 645 | DUCHAMPERROR("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
[863] | 646 | return; |
---|
| 647 | } |
---|
| 648 | else { |
---|
[983] | 649 | size_t pos=(vox->getX()-xzero) + (vox->getY()-yzero)*xsize + (vox->getZ()-zzero)*spatsize; |
---|
[863] | 650 | localFlux[pos] = voxelMap[*vox]; |
---|
| 651 | isObj[pos] = true; |
---|
| 652 | } |
---|
| 653 | } |
---|
| 654 | |
---|
| 655 | // work out the WCS coords for each pixel |
---|
| 656 | double *world = new double[size]; |
---|
| 657 | double xpt,ypt,zpt; |
---|
[884] | 658 | for(size_t i=0;i<xsize*ysize*zsize;i++){ |
---|
[863] | 659 | xpt = double( this->getXmin() - border + i%xsize ); |
---|
| 660 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
---|
| 661 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
---|
| 662 | world[i] = head.pixToVel(xpt,ypt,zpt); |
---|
| 663 | } |
---|
| 664 | |
---|
| 665 | double integrated = 0.; |
---|
[884] | 666 | for(size_t pix=0; pix<spatsize; pix++){ // loop over each spatial pixel. |
---|
| 667 | for(size_t z=0; z<zsize; z++){ |
---|
[921] | 668 | size_t pos = z*xsize*ysize + pix; |
---|
[863] | 669 | if(isObj[pos]){ // if it's an object pixel... |
---|
| 670 | double deltaVel; |
---|
| 671 | if(z==0) |
---|
| 672 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
| 673 | else if(z==(zsize-1)) |
---|
| 674 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
| 675 | else |
---|
| 676 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
| 677 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
| 678 | } |
---|
| 679 | } |
---|
| 680 | } |
---|
| 681 | this->intFlux = integrated; |
---|
| 682 | |
---|
| 683 | delete [] world; |
---|
| 684 | delete [] localFlux; |
---|
| 685 | |
---|
| 686 | calcVelWidths(zdim,voxelMap,head); |
---|
| 687 | |
---|
| 688 | } |
---|
| 689 | else // in this case there is just a 2D image. |
---|
| 690 | this->intFlux = this->totalFlux; |
---|
| 691 | |
---|
| 692 | if(head.isWCS()){ |
---|
| 693 | // correct for the beam size if the flux units string ends in "/beam" |
---|
| 694 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
| 695 | } |
---|
| 696 | |
---|
| 697 | } |
---|
| 698 | //-------------------------------------------------------------------- |
---|
| 699 | |
---|
[884] | 700 | void Detection::calcIntegFlux(float *fluxArray, size_t *dim, FitsHeader &head) |
---|
[378] | 701 | { |
---|
[528] | 702 | /// @details |
---|
| 703 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
| 704 | /// putting velocity in units of km/s. |
---|
| 705 | /// Integrates over full spatial and velocity range as given |
---|
| 706 | /// by the extrema calculated by calcWCSparams. |
---|
| 707 | /// |
---|
| 708 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
| 709 | /// corrected by the beam size (in pixels). This is done by |
---|
| 710 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
| 711 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
| 712 | /// pix/beam --> Jy) |
---|
| 713 | /// |
---|
| 714 | /// \param fluxArray The array of flux values. |
---|
| 715 | /// \param dim The dimensions of the flux array. |
---|
| 716 | /// \param head FitsHeader object that contains the WCS information. |
---|
[3] | 717 | |
---|
[513] | 718 | if(!head.is2D()){ |
---|
[271] | 719 | |
---|
[681] | 720 | this->haveParams = true; |
---|
| 721 | |
---|
[982] | 722 | const int border=1; // include one pixel either side in each direction |
---|
| 723 | size_t xsize = std::min(size_t(this->xmax-this->xmin+2*border+1),dim[0]); |
---|
| 724 | size_t ysize = std::min(size_t(this->ymax-this->ymin+2*border+1),dim[1]); |
---|
| 725 | size_t zsize = std::min(size_t(this->zmax-this->zmin+2*border+1),dim[2]); |
---|
| 726 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
| 727 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
| 728 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
[884] | 729 | size_t spatsize = xsize*ysize; |
---|
| 730 | size_t size = xsize*ysize*zsize; |
---|
[473] | 731 | std::vector <bool> isObj(size,false); |
---|
[463] | 732 | double *localFlux = new double[size]; |
---|
[894] | 733 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
[1130] | 734 | float *momMap = new float[spatsize]; |
---|
| 735 | for(size_t i=0;i<spatsize;i++) momMap[i]=0.; |
---|
[378] | 736 | // work out which pixels are object pixels |
---|
[774] | 737 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
| 738 | for(std::vector<Voxel>::iterator v=voxlist.begin();v<voxlist.end();v++){ |
---|
[1130] | 739 | size_t spatpos=(v->getX()-xzero) + (v->getY()-yzero)*xsize; |
---|
| 740 | size_t pos= spatpos + (v->getZ()-zzero)*spatsize; |
---|
[778] | 741 | localFlux[pos] = fluxArray[v->arrayIndex(dim)]; |
---|
[1130] | 742 | momMap[spatpos] += fluxArray[v->arrayIndex(dim)]; |
---|
[774] | 743 | isObj[pos] = true; |
---|
[258] | 744 | } |
---|
[22] | 745 | |
---|
[378] | 746 | // work out the WCS coords for each pixel |
---|
[463] | 747 | double *world = new double[size]; |
---|
[378] | 748 | double xpt,ypt,zpt; |
---|
[884] | 749 | size_t i=0; |
---|
[986] | 750 | for(size_t z=zzero;z<zzero+zsize;z++){ |
---|
| 751 | for(size_t y=yzero;y<yzero+ysize;y++){ |
---|
| 752 | for(size_t x=xzero;x<xzero+xsize;x++){ |
---|
| 753 | xpt=double(x); |
---|
| 754 | ypt=double(y); |
---|
| 755 | zpt=double(z); |
---|
[781] | 756 | world[i++] = head.pixToVel(xpt,ypt,zpt); |
---|
| 757 | } |
---|
| 758 | } |
---|
[378] | 759 | } |
---|
[3] | 760 | |
---|
[378] | 761 | double integrated = 0.; |
---|
[884] | 762 | for(size_t pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
---|
| 763 | for(size_t z=0; z<zsize; z++){ |
---|
[921] | 764 | size_t pos = z*xsize*ysize + pix; |
---|
[378] | 765 | if(isObj[pos]){ // if it's an object pixel... |
---|
| 766 | double deltaVel; |
---|
| 767 | if(z==0) |
---|
| 768 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
| 769 | else if(z==(zsize-1)) |
---|
| 770 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
| 771 | else |
---|
| 772 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
| 773 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
| 774 | } |
---|
[271] | 775 | } |
---|
[3] | 776 | } |
---|
[378] | 777 | this->intFlux = integrated; |
---|
| 778 | |
---|
[1130] | 779 | bool ellipseGood=this->spatialMap.findEllipse(true,momMap,xsize,ysize,xzero,yzero); // try first by weighting the pixels by their flux |
---|
| 780 | if(!ellipseGood) ellipseGood=this->spatialMap.findEllipse(false,momMap,xsize,ysize,xzero,yzero); // if that fails, remove the flux weighting |
---|
| 781 | if(ellipseGood){ |
---|
| 782 | this->majorAxis = this->spatialMap.major() * head.getAvPixScale(); |
---|
| 783 | this->minorAxis = this->spatialMap.minor() * head.getAvPixScale(); |
---|
| 784 | this->posang = this->spatialMap.posAng() * 180. / M_PI; |
---|
| 785 | } |
---|
| 786 | |
---|
[464] | 787 | delete [] world; |
---|
| 788 | delete [] localFlux; |
---|
[1130] | 789 | delete [] momMap; |
---|
[463] | 790 | |
---|
[464] | 791 | calcVelWidths(fluxArray, dim, head); |
---|
[463] | 792 | |
---|
[464] | 793 | } |
---|
| 794 | else // in this case there is just a 2D image. |
---|
| 795 | this->intFlux = this->totalFlux; |
---|
[463] | 796 | |
---|
[464] | 797 | if(head.isWCS()){ |
---|
[789] | 798 | // correct for the beam size if the flux units string ends in "/beam" and we have beam info |
---|
[788] | 799 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
[464] | 800 | } |
---|
[463] | 801 | |
---|
[464] | 802 | } |
---|
| 803 | //-------------------------------------------------------------------- |
---|
| 804 | |
---|
[884] | 805 | void Detection::calcVelWidths(size_t zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
[464] | 806 | { |
---|
[528] | 807 | /// @details |
---|
| 808 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
| 809 | /// peak integrated flux. The procedure is as follows: first |
---|
| 810 | /// generate an integrated flux spectrum (using all given voxels |
---|
| 811 | /// that lie in the object's spatial map); find the peak; starting |
---|
| 812 | /// at the spectral edges of the detection, move in or out until |
---|
| 813 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
| 814 | /// between points is done. |
---|
| 815 | /// |
---|
[719] | 816 | /// \param zdim The size of the spectral axis in the cube |
---|
[528] | 817 | /// \param voxelList The list of Voxels with flux information |
---|
| 818 | /// \param head FitsHeader object that contains the WCS information. |
---|
[464] | 819 | |
---|
[719] | 820 | float *intSpec = new float[zdim]; |
---|
[894] | 821 | for(size_t i=0;i<zdim;i++) intSpec[i]=0; |
---|
[464] | 822 | |
---|
[570] | 823 | Object2D spatMap = this->getSpatialMap(); |
---|
[464] | 824 | for(int s=0;s<spatMap.getNumScan();s++){ |
---|
[623] | 825 | std::vector<Voxel>::iterator vox; |
---|
| 826 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 827 | if(spatMap.isInObject(*vox)){ |
---|
[719] | 828 | intSpec[vox->getZ()] += vox->getF(); |
---|
[464] | 829 | } |
---|
[463] | 830 | } |
---|
[464] | 831 | } |
---|
| 832 | |
---|
[719] | 833 | calcVelWidths(zdim, intSpec, head); |
---|
| 834 | |
---|
| 835 | delete [] intSpec; |
---|
| 836 | |
---|
| 837 | } |
---|
| 838 | |
---|
| 839 | //-------------------------------------------------------------------- |
---|
| 840 | |
---|
[884] | 841 | void Detection::calcVelWidths(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
[863] | 842 | { |
---|
| 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 | /// |
---|
| 852 | /// \param zdim The size of the spectral axis in the cube |
---|
| 853 | /// \param voxelList The list of Voxels with flux information |
---|
| 854 | /// \param head FitsHeader object that contains the WCS information. |
---|
| 855 | |
---|
| 856 | float *intSpec = new float[zdim]; |
---|
[894] | 857 | for(size_t i=0;i<zdim;i++) intSpec[i]=0; |
---|
[863] | 858 | |
---|
| 859 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
| 860 | std::vector<Voxel>::iterator vox; |
---|
| 861 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
| 862 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
[913] | 863 | DUCHAMPERROR("Detection::calcVelWidths","Voxel list provided does not match"); |
---|
[863] | 864 | return; |
---|
| 865 | } |
---|
| 866 | else { |
---|
| 867 | intSpec[vox->getZ()] += voxelMap[*vox]; |
---|
| 868 | } |
---|
| 869 | } |
---|
| 870 | |
---|
| 871 | calcVelWidths(zdim, intSpec, head); |
---|
| 872 | |
---|
| 873 | delete [] intSpec; |
---|
| 874 | |
---|
| 875 | } |
---|
| 876 | |
---|
| 877 | //-------------------------------------------------------------------- |
---|
| 878 | |
---|
[884] | 879 | void Detection::calcVelWidths(size_t zdim, float *intSpec, FitsHeader &head) |
---|
[719] | 880 | { |
---|
| 881 | |
---|
[913] | 882 | // finding the 20% & 50% points. Start at the velmin & velmax |
---|
| 883 | // points. Then, if the int flux there is above the 20%/50% |
---|
| 884 | // limit, go out, otherwise go in. This is to deal with the |
---|
| 885 | // problems from double- (or multi-) peaked sources. |
---|
[719] | 886 | |
---|
| 887 | this->haveParams = true; |
---|
| 888 | |
---|
[924] | 889 | double zpt,xpt=double(this->getXcentre()),ypt=double(this->getYcentre()); |
---|
[719] | 890 | bool goLeft; |
---|
| 891 | |
---|
[1054] | 892 | if(this->negSource){ |
---|
| 893 | // if we've inverted the source, need to make the feature |
---|
| 894 | // positive for the interpolation/extrapolation to work |
---|
| 895 | for(size_t i=0;i<zdim;i++) intSpec[i] *= -1.; |
---|
| 896 | } |
---|
| 897 | |
---|
[634] | 898 | float peak=0.; |
---|
[894] | 899 | size_t peakLoc=0; |
---|
| 900 | for(size_t z=this->getZmin();z<=size_t(this->getZmax());z++) { |
---|
[464] | 901 | if(z==0 || peak<intSpec[z]){ |
---|
| 902 | peak = intSpec[z]; |
---|
| 903 | peakLoc = z; |
---|
[463] | 904 | } |
---|
[464] | 905 | } |
---|
[719] | 906 | |
---|
[894] | 907 | size_t z=this->getZmin(); |
---|
[464] | 908 | goLeft = intSpec[z]>peak*0.5; |
---|
| 909 | if(goLeft) while(z>0 && intSpec[z]>peak*0.5) z--; |
---|
| 910 | else while(z<peakLoc && intSpec[z]<peak*0.5) z++; |
---|
| 911 | if(z==0) this->v50min = this->velMin; |
---|
| 912 | else{ |
---|
[719] | 913 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 914 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
[464] | 915 | this->v50min = head.pixToVel(xpt,ypt,zpt); |
---|
| 916 | } |
---|
[719] | 917 | z=this->getZmax(); |
---|
[464] | 918 | goLeft = intSpec[z]<peak*0.5; |
---|
| 919 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.5) z--; |
---|
[719] | 920 | else while(z<zdim && intSpec[z]>peak*0.5) z++; |
---|
| 921 | if(z==zdim) this->v50max = this->velMax; |
---|
[464] | 922 | else{ |
---|
[719] | 923 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 924 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
[464] | 925 | this->v50max = head.pixToVel(xpt,ypt,zpt); |
---|
| 926 | } |
---|
[719] | 927 | z=this->getZmin(); |
---|
[588] | 928 | goLeft = intSpec[z]>peak*0.2; |
---|
[464] | 929 | if(goLeft) while(z>0 && intSpec[z]>peak*0.2) z--; |
---|
| 930 | else while(z<peakLoc && intSpec[z]<peak*0.2) z++; |
---|
| 931 | if(z==0) this->v20min = this->velMin; |
---|
| 932 | else{ |
---|
[719] | 933 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 934 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
[464] | 935 | this->v20min = head.pixToVel(xpt,ypt,zpt); |
---|
| 936 | } |
---|
[719] | 937 | z=this->getZmax(); |
---|
[588] | 938 | goLeft = intSpec[z]<peak*0.2; |
---|
[464] | 939 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.2) z--; |
---|
[719] | 940 | else while(z<zdim && intSpec[z]>peak*0.2) z++; |
---|
| 941 | if(z==zdim) this->v20max = this->velMax; |
---|
[464] | 942 | else{ |
---|
[719] | 943 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
| 944 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
[464] | 945 | this->v20max = head.pixToVel(xpt,ypt,zpt); |
---|
| 946 | } |
---|
[463] | 947 | |
---|
[464] | 948 | this->w20 = fabs(this->v20min - this->v20max); |
---|
| 949 | this->w50 = fabs(this->v50min - this->v50max); |
---|
[982] | 950 | |
---|
[1054] | 951 | if(this->negSource){ |
---|
| 952 | // un-do the inversion, in case intSpec is needed elsewhere |
---|
| 953 | for(size_t i=0;i<zdim;i++) intSpec[i] *= -1.; |
---|
| 954 | } |
---|
| 955 | |
---|
| 956 | |
---|
[464] | 957 | } |
---|
[781] | 958 | //-------------------------------------------------------------------- |
---|
[464] | 959 | |
---|
[884] | 960 | void Detection::calcVelWidths(float *fluxArray, size_t *dim, FitsHeader &head) |
---|
[464] | 961 | { |
---|
[528] | 962 | /// @details |
---|
| 963 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
| 964 | /// peak integrated flux. The procedure is as follows: first |
---|
| 965 | /// generate an integrated flux spectrum (summing each spatial |
---|
| 966 | /// pixel's spectrum); find the peak; starting at the spectral |
---|
| 967 | /// edges of the detection, move in or out until you reach the 20% |
---|
| 968 | /// or 50% peak flux level. Linear interpolation between points is |
---|
| 969 | /// done. |
---|
| 970 | /// |
---|
| 971 | /// \param fluxArray The array of flux values. |
---|
| 972 | /// \param dim The dimensions of the flux array. |
---|
| 973 | /// \param head FitsHeader object that contains the WCS information. |
---|
[464] | 974 | |
---|
[465] | 975 | if(dim[2] > 2){ |
---|
[464] | 976 | |
---|
[465] | 977 | float *intSpec = new float[dim[2]]; |
---|
[884] | 978 | size_t size=dim[0]*dim[1]*dim[2]; |
---|
[748] | 979 | std::vector<bool> mask(size,true); |
---|
[465] | 980 | getIntSpec(*this,fluxArray,dim,mask,1.,intSpec); |
---|
| 981 | |
---|
[719] | 982 | this->calcVelWidths(dim[2],intSpec,head); |
---|
| 983 | |
---|
[465] | 984 | delete [] intSpec; |
---|
| 985 | |
---|
[378] | 986 | } |
---|
[464] | 987 | else{ |
---|
[465] | 988 | this->v50min = this->v20min = this->velMin; |
---|
| 989 | this->v50max = this->v20max = this->velMax; |
---|
[719] | 990 | this->w20 = fabs(this->v20min - this->v20max); |
---|
| 991 | this->w50 = fabs(this->v50min - this->v50max); |
---|
[464] | 992 | } |
---|
[300] | 993 | |
---|
| 994 | } |
---|
[378] | 995 | //-------------------------------------------------------------------- |
---|
[300] | 996 | |
---|
[378] | 997 | void Detection::setOffsets(Param &par) |
---|
| 998 | { |
---|
[528] | 999 | /// @details |
---|
| 1000 | /// This function stores the values of the offsets for each cube axis. |
---|
| 1001 | /// The offsets are the starting values of the cube axes that may differ from |
---|
| 1002 | /// the default value of 0 (for instance, if a subsection is being used). |
---|
| 1003 | /// The values will be used when the detection is outputted. |
---|
| 1004 | |
---|
[378] | 1005 | this->xSubOffset = par.getXOffset(); |
---|
| 1006 | this->ySubOffset = par.getYOffset(); |
---|
| 1007 | this->zSubOffset = par.getZOffset(); |
---|
| 1008 | } |
---|
| 1009 | //-------------------------------------------------------------------- |
---|
[3] | 1010 | |
---|
[378] | 1011 | bool Detection::hasEnoughChannels(int minNumber) |
---|
| 1012 | { |
---|
[528] | 1013 | /// @details |
---|
| 1014 | /// A function to determine if the Detection has enough |
---|
| 1015 | /// contiguous channels to meet the minimum requirement |
---|
| 1016 | /// given as the argument. |
---|
| 1017 | /// \param minNumber How many channels is the minimum acceptable number? |
---|
| 1018 | /// \return True if there is at least one occurence of minNumber consecutive |
---|
| 1019 | /// channels present to return true. False otherwise. |
---|
[3] | 1020 | |
---|
[378] | 1021 | // Preferred method -- need a set of minNumber consecutive channels present. |
---|
[3] | 1022 | |
---|
[570] | 1023 | int numChan = this->getMaxAdjacentChannels(); |
---|
| 1024 | bool result = (numChan >= minNumber); |
---|
| 1025 | |
---|
[378] | 1026 | return result; |
---|
| 1027 | |
---|
| 1028 | } |
---|
| 1029 | //-------------------------------------------------------------------- |
---|
[3] | 1030 | |
---|
[452] | 1031 | std::vector<int> Detection::getVertexSet() |
---|
| 1032 | { |
---|
[528] | 1033 | /// @details |
---|
| 1034 | /// Gets a list of points being the end-points of 1-pixel long |
---|
| 1035 | /// segments drawing a border around the spatial extend of a |
---|
| 1036 | /// detection. The vector is a series of 4 integers, being: x_0, |
---|
| 1037 | /// y_0, x_1, y_1. |
---|
| 1038 | /// \return The vector of vertex positions. |
---|
| 1039 | |
---|
[452] | 1040 | std::vector<int> vertexSet; |
---|
| 1041 | |
---|
| 1042 | int xmin = this->getXmin() - 1; |
---|
| 1043 | int xmax = this->getXmax() + 1; |
---|
| 1044 | int ymin = this->getYmin() - 1; |
---|
| 1045 | int ymax = this->getYmax() + 1; |
---|
| 1046 | int xsize = xmax - xmin + 1; |
---|
| 1047 | int ysize = ymax - ymin + 1; |
---|
| 1048 | |
---|
[570] | 1049 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
[452] | 1050 | std::vector<bool> isObj(xsize*ysize,false); |
---|
[623] | 1051 | std::vector<Voxel>::iterator vox; |
---|
| 1052 | for(vox=voxlist.begin();vox<voxlist.end();vox++){ |
---|
[921] | 1053 | size_t pos = (vox->getX()-xmin) + |
---|
[623] | 1054 | (vox->getY()-ymin)*xsize; |
---|
[452] | 1055 | isObj[pos] = true; |
---|
| 1056 | } |
---|
| 1057 | voxlist.clear(); |
---|
| 1058 | |
---|
| 1059 | for(int x=xmin; x<=xmax; x++){ |
---|
| 1060 | // for each column... |
---|
| 1061 | for(int y=ymin+1;y<=ymax;y++){ |
---|
| 1062 | int current = (y-ymin)*xsize + x-xmin; |
---|
| 1063 | int previous = (y-ymin-1)*xsize + x-xmin; |
---|
| 1064 | if((isObj[current]&&!isObj[previous]) || |
---|
| 1065 | (!isObj[current]&&isObj[previous])){ |
---|
| 1066 | vertexSet.push_back(x); |
---|
| 1067 | vertexSet.push_back(y); |
---|
| 1068 | vertexSet.push_back(x+1); |
---|
| 1069 | vertexSet.push_back(y); |
---|
| 1070 | } |
---|
| 1071 | } |
---|
| 1072 | } |
---|
| 1073 | for(int y=ymin; y<=ymax; y++){ |
---|
| 1074 | // now for each row... |
---|
| 1075 | for(int x=xmin+1;x<=xmax;x++){ |
---|
| 1076 | int current = (y-ymin)*xsize + x-xmin; |
---|
| 1077 | int previous = (y-ymin)*xsize + x-xmin - 1; |
---|
| 1078 | if((isObj[current]&&!isObj[previous]) || |
---|
| 1079 | (!isObj[current]&&isObj[previous])){ |
---|
| 1080 | vertexSet.push_back(x); |
---|
| 1081 | vertexSet.push_back(y); |
---|
| 1082 | vertexSet.push_back(x); |
---|
| 1083 | vertexSet.push_back(y+1); |
---|
| 1084 | } |
---|
| 1085 | } |
---|
| 1086 | } |
---|
| 1087 | |
---|
| 1088 | return vertexSet; |
---|
| 1089 | |
---|
| 1090 | } |
---|
| 1091 | |
---|
[747] | 1092 | |
---|
[770] | 1093 | void Detection::addDetection(Detection &other) |
---|
[747] | 1094 | { |
---|
| 1095 | for(std::map<long, Object2D>::iterator it = other.chanlist.begin(); it!=other.chanlist.end();it++) |
---|
[770] | 1096 | // this->addChannel(*it); |
---|
[747] | 1097 | this->addChannel(it->first, it->second); |
---|
| 1098 | this->haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
| 1099 | } |
---|
[624] | 1100 | |
---|
[770] | 1101 | Detection operator+ (Detection &lhs, Detection &rhs) |
---|
[624] | 1102 | { |
---|
| 1103 | Detection output = lhs; |
---|
| 1104 | for(std::map<long, Object2D>::iterator it = rhs.chanlist.begin(); it!=rhs.chanlist.end();it++) |
---|
| 1105 | output.addChannel(it->first, it->second); |
---|
[681] | 1106 | output.haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
[624] | 1107 | return output; |
---|
| 1108 | } |
---|
| 1109 | |
---|
| 1110 | |
---|
[770] | 1111 | bool Detection::canMerge(Detection &other, Param &par) |
---|
| 1112 | { |
---|
| 1113 | bool near = this->isNear(other,par); |
---|
| 1114 | if(near) return this->isClose(other,par); |
---|
| 1115 | else return near; |
---|
| 1116 | } |
---|
[624] | 1117 | |
---|
[770] | 1118 | bool Detection::isNear(Detection &other, Param &par) |
---|
| 1119 | { |
---|
[624] | 1120 | |
---|
[770] | 1121 | bool flagAdj = par.getFlagAdjacent(); |
---|
| 1122 | float threshS = par.getThreshS(); |
---|
| 1123 | float threshV = par.getThreshV(); |
---|
| 1124 | |
---|
| 1125 | long gap; |
---|
| 1126 | if(flagAdj) gap = 1; |
---|
| 1127 | else gap = long( ceil(threshS) ); |
---|
| 1128 | |
---|
| 1129 | bool areNear; |
---|
| 1130 | // Test X ranges |
---|
| 1131 | if((this->xmin-gap)<other.xmin) areNear=((this->xmax+gap)>=other.xmin); |
---|
| 1132 | else areNear=(other.xmax>=(this->xmin-gap)); |
---|
| 1133 | // Test Y ranges |
---|
| 1134 | if(areNear){ |
---|
| 1135 | if((this->ymin-gap)<other.ymin) areNear=areNear&&((this->ymax+gap)>=other.ymin); |
---|
| 1136 | else areNear=areNear&&(other.ymax>=(this->ymin-gap)); |
---|
| 1137 | } |
---|
| 1138 | // Test Z ranges |
---|
| 1139 | if(areNear){ |
---|
| 1140 | gap = long(ceil(threshV)); |
---|
| 1141 | if((this->zmin-gap)<other.zmin) areNear=areNear&&((this->zmax+gap)>=other.zmin); |
---|
| 1142 | else areNear=areNear&&(other.zmax>=(this->zmin-gap)); |
---|
| 1143 | } |
---|
| 1144 | |
---|
| 1145 | return areNear; |
---|
| 1146 | |
---|
| 1147 | } |
---|
| 1148 | |
---|
| 1149 | bool Detection::isClose(Detection &other, Param &par) |
---|
| 1150 | { |
---|
| 1151 | bool close = false; // this will be the value returned |
---|
| 1152 | |
---|
| 1153 | bool flagAdj = par.getFlagAdjacent(); |
---|
| 1154 | float threshS = par.getThreshS(); |
---|
| 1155 | float threshV = par.getThreshV(); |
---|
| 1156 | |
---|
| 1157 | // |
---|
| 1158 | // If we get to here, the pixel ranges overlap -- so we do a |
---|
| 1159 | // pixel-by-pixel comparison to make sure they are actually |
---|
| 1160 | // "close" according to the thresholds. Otherwise, close=false, |
---|
| 1161 | // and so don't need to do anything else before returning. |
---|
| 1162 | // |
---|
| 1163 | |
---|
| 1164 | std::vector<long> zlist1 = this->getChannelList(); |
---|
| 1165 | std::vector<long> zlist2 = other.getChannelList(); |
---|
| 1166 | Scan test1,test2; |
---|
| 1167 | |
---|
| 1168 | for(size_t ct1=0; (!close && (ct1<zlist1.size())); ct1++){ |
---|
| 1169 | for(size_t ct2=0; (!close && (ct2<zlist2.size())); ct2++){ |
---|
| 1170 | |
---|
| 1171 | if(abs(zlist1[ct1]-zlist2[ct2])<=threshV){ |
---|
| 1172 | |
---|
| 1173 | Object2D temp1 = this->getChanMap(zlist1[ct1]); |
---|
| 1174 | Object2D temp2 = other.getChanMap(zlist2[ct2]); |
---|
| 1175 | |
---|
| 1176 | close = temp1.canMerge(temp2,threshS,flagAdj); |
---|
| 1177 | |
---|
| 1178 | } |
---|
| 1179 | |
---|
| 1180 | } |
---|
| 1181 | } |
---|
| 1182 | |
---|
| 1183 | return close; |
---|
| 1184 | |
---|
| 1185 | } |
---|
| 1186 | |
---|
| 1187 | |
---|
| 1188 | |
---|
[3] | 1189 | } |
---|