[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // param.cc: Dealing with the set of parameters for Duchamp. |
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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 <fstream> |
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| 31 | #include <sstream> |
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| 32 | #include <string> |
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[534] | 33 | #include <algorithm> |
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[205] | 34 | #include <stdlib.h> |
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[269] | 35 | #include <ctype.h> |
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[3] | 36 | #include <math.h> |
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[410] | 37 | #include <unistd.h> |
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[393] | 38 | #include <duchamp/param.hh> |
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| 39 | #include <duchamp/fitsHeader.hh> |
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| 40 | #include <duchamp/duchamp.hh> |
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[420] | 41 | #include <duchamp/pgheader.hh> |
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[393] | 42 | #include <duchamp/ATrous/filter.hh> |
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[1339] | 43 | #include <duchamp/ATrous/FilterFactory.hh> |
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[393] | 44 | #include <duchamp/Utils/utils.hh> |
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| 45 | #include <duchamp/Utils/Section.hh> |
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[916] | 46 | #include <duchamp/Utils/VOParam.hh> |
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[1061] | 47 | #include <duchamp/Outputs/columns.hh> |
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[3] | 48 | |
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[378] | 49 | namespace duchamp |
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[309] | 50 | { |
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[882] | 51 | const std::string defaultSection = "[*,*,*]"; |
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[309] | 52 | |
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[378] | 53 | /****************************************************************/ |
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| 54 | /////////////////////////////////////////////////// |
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| 55 | //// Accessor Functions for Parameter class: |
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| 56 | /////////////////////////////////////////////////// |
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| 57 | Param::~Param() |
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| 58 | { |
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[528] | 59 | /// Deletes the offsets array if the sizeOffsets parameter is |
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| 60 | /// positive. |
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[1450] | 61 | if(this->sizeOffsets>0){ |
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| 62 | delete [] this->offsets; |
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| 63 | } |
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| 64 | if (this->reconFilter){ |
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| 65 | delete this->reconFilter; |
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| 66 | } |
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[378] | 67 | } |
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[309] | 68 | |
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[378] | 69 | Param::Param() |
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| 70 | { |
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| 71 | this->defaultValues(); |
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| 72 | } |
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[3] | 73 | |
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[378] | 74 | void Param::defaultValues() |
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| 75 | { |
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[528] | 76 | /// Provides default intial values for the parameters. Note that |
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| 77 | /// imageFile has no default value! |
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| 78 | |
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[378] | 79 | // Input files |
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| 80 | this->imageFile = ""; |
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| 81 | this->flagSubsection = false; |
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[1190] | 82 | this->pixelSec = Section(); |
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[378] | 83 | this->flagReconExists = false; |
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| 84 | this->reconFile = ""; |
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| 85 | this->flagSmoothExists = false; |
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| 86 | this->smoothFile = ""; |
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[475] | 87 | this->usePrevious = false; |
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| 88 | this->objectList = ""; |
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[378] | 89 | // Output files |
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| 90 | this->flagLog = false; |
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| 91 | this->logFile = "duchamp-Logfile.txt"; |
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| 92 | this->outFile = "duchamp-Results.txt"; |
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| 93 | this->flagSeparateHeader= false; |
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| 94 | this->headerFile = "duchamp-Results.hdr"; |
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[1146] | 95 | this->flagWriteBinaryCatalogue = true; |
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| 96 | this->binaryCatalogue = "duchamp-Catalogue.dpc"; |
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[831] | 97 | this->flagPlotSpectra = true; |
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[378] | 98 | this->spectraFile = "duchamp-Spectra.ps"; |
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[1148] | 99 | this->flagPlotIndividualSpectra = false; |
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[424] | 100 | this->flagTextSpectra = false; |
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| 101 | this->spectraTextFile = "duchamp-Spectra.txt"; |
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[1120] | 102 | this->flagOutputBaseline = false; |
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| 103 | this->fileOutputBaseline = ""; |
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[670] | 104 | this->flagOutputMomentMap = false; |
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| 105 | this->fileOutputMomentMap = ""; |
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[1142] | 106 | this->flagOutputMomentMask = false; |
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| 107 | this->fileOutputMomentMask = ""; |
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[379] | 108 | this->flagOutputMask = false; |
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[525] | 109 | this->fileOutputMask = ""; |
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[521] | 110 | this->flagMaskWithObjectNum = false; |
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[378] | 111 | this->flagOutputSmooth = false; |
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[525] | 112 | this->fileOutputSmooth = ""; |
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[378] | 113 | this->flagOutputRecon = false; |
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[525] | 114 | this->fileOutputRecon = ""; |
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[378] | 115 | this->flagOutputResid = false; |
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[525] | 116 | this->fileOutputResid = ""; |
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[378] | 117 | this->flagVOT = false; |
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| 118 | this->votFile = "duchamp-Results.xml"; |
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| 119 | this->flagKarma = false; |
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| 120 | this->karmaFile = "duchamp-Results.ann"; |
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[1077] | 121 | this->flagDS9 = false; |
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| 122 | this->ds9File = "duchamp-Results.reg"; |
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[1126] | 123 | this->flagCasa = false; |
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| 124 | this->casaFile = "duchamp-Results.crf"; |
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[446] | 125 | this->annotationType = "borders"; |
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[378] | 126 | this->flagMaps = true; |
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| 127 | this->detectionMap = "duchamp-DetectionMap.ps"; |
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| 128 | this->momentMap = "duchamp-MomentMap.ps"; |
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| 129 | this->flagXOutput = true; |
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[1061] | 130 | this->precFlux = Catalogues::prFLUX; |
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| 131 | this->precVel = Catalogues::prVEL; |
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| 132 | this->precSNR = Catalogues::prSNR; |
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[378] | 133 | // Cube related parameters |
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[845] | 134 | this->flagBlankPix = false; |
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[378] | 135 | this->blankPixValue = -8.00061; |
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| 136 | this->blankKeyword = 1; |
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| 137 | this->bscaleKeyword = -8.00061; |
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| 138 | this->bzeroKeyword = 0.; |
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[434] | 139 | this->newFluxUnits = ""; |
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[1259] | 140 | // Flagged channel parameters |
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[1240] | 141 | this->flaggedChannelList = ""; |
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[1247] | 142 | this->flaggedChannels = std::vector<int>(); |
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| 143 | this->flaggedChannelMask= std::vector<bool>(); |
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[1259] | 144 | // Beam |
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[788] | 145 | this->areaBeam = 0.; |
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| 146 | this->fwhmBeam = 0.; |
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[791] | 147 | this->beamAsUsed.empty(); |
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[686] | 148 | this->searchType = "spatial"; |
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[378] | 149 | // Trim-related |
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| 150 | this->flagTrim = false; |
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| 151 | this->hasBeenTrimmed = false; |
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| 152 | this->borderLeft = 0; |
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| 153 | this->borderRight = 0; |
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| 154 | this->borderBottom = 0; |
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| 155 | this->borderTop = 0; |
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| 156 | // Subsection offsets |
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| 157 | this->sizeOffsets = 0; |
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| 158 | this->xSubOffset = 0; |
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| 159 | this->ySubOffset = 0; |
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| 160 | this->zSubOffset = 0; |
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| 161 | // Baseline related |
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| 162 | this->flagBaseline = false; |
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[1259] | 163 | this->baselineType = "atrous"; |
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| 164 | this->baselineBoxWidth = 51; |
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[378] | 165 | // Detection-related |
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| 166 | this->flagNegative = false; |
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| 167 | // Object growth |
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| 168 | this->flagGrowth = false; |
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[458] | 169 | this->growthCut = 3.; |
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[461] | 170 | this->flagUserGrowthThreshold = false; |
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| 171 | this->growthThreshold = 0.; |
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[378] | 172 | // FDR analysis |
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| 173 | this->flagFDR = false; |
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| 174 | this->alphaFDR = 0.01; |
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[543] | 175 | this->FDRnumCorChan = 2; |
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[378] | 176 | // Other detection |
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| 177 | this->flagStatSec = false; |
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[1190] | 178 | this->statSec = Section(); |
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[385] | 179 | this->flagRobustStats = true; |
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[1025] | 180 | this->snrCut = 5.; |
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[378] | 181 | this->threshold = 0.; |
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| 182 | this->flagUserThreshold = false; |
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| 183 | // Smoothing |
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| 184 | this->flagSmooth = false; |
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| 185 | this->smoothType = "spectral"; |
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| 186 | this->hanningWidth = 5; |
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| 187 | this->kernMaj = 3.; |
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| 188 | this->kernMin = -1.; |
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| 189 | this->kernPA = 0.; |
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[1279] | 190 | this->smoothEdgeMethod = "equal"; |
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| 191 | this->spatialSmoothCutoff = 1.e-10; |
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[378] | 192 | // A trous reconstruction parameters |
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| 193 | this->flagATrous = false; |
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| 194 | this->reconDim = 1; |
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| 195 | this->scaleMin = 1; |
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| 196 | this->scaleMax = 0; |
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| 197 | this->snrRecon = 4.; |
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[1026] | 198 | this->reconConvergence = 0.005; |
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[378] | 199 | this->filterCode = 1; |
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[1428] | 200 | FilterFactory filtFac; |
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| 201 | this->reconFilter = filtFac.getFilter(this->filterCode); |
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[1450] | 202 | |
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[378] | 203 | // Volume-merging parameters |
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| 204 | this->flagAdjacent = true; |
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| 205 | this->threshSpatial = 3.; |
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| 206 | this->threshVelocity = 7.; |
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| 207 | this->minChannels = 3; |
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| 208 | this->minPix = 2; |
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[720] | 209 | this->minVoxels = 4; |
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[1261] | 210 | this->maxChannels = -1; |
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| 211 | this->maxPix = -1; |
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| 212 | this->maxVoxels = -1; |
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[672] | 213 | this->flagRejectBeforeMerge = false; |
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[691] | 214 | this->flagTwoStageMerging = true; |
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[378] | 215 | // Input-Output related |
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| 216 | this->spectralMethod = "peak"; |
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[948] | 217 | this->spectralType = ""; |
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| 218 | this->restFrequency = -1.; |
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| 219 | this->restFrequencyUsed = false; |
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[949] | 220 | this->spectralUnits = ""; |
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[378] | 221 | this->pixelCentre = "centroid"; |
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[571] | 222 | this->sortingParam = "vel"; |
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[378] | 223 | this->borders = true; |
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| 224 | this->blankEdge = true; |
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| 225 | this->verbose = true; |
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[1140] | 226 | this->commentStr = ""; |
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[419] | 227 | } |
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[204] | 228 | |
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[378] | 229 | Param::Param (const Param& p) |
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| 230 | { |
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| 231 | operator=(p); |
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[309] | 232 | } |
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[137] | 233 | |
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[378] | 234 | Param& Param::operator= (const Param& p) |
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| 235 | { |
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| 236 | if(this == &p) return *this; |
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| 237 | this->imageFile = p.imageFile; |
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| 238 | this->flagSubsection = p.flagSubsection; |
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| 239 | this->pixelSec = p.pixelSec; |
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| 240 | this->flagReconExists = p.flagReconExists; |
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| 241 | this->reconFile = p.reconFile; |
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| 242 | this->flagSmoothExists = p.flagSmoothExists; |
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[475] | 243 | this->smoothFile = p.smoothFile; |
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| 244 | this->usePrevious = p.usePrevious; |
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| 245 | this->objectList = p.objectList; |
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[378] | 246 | this->flagLog = p.flagLog; |
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| 247 | this->logFile = p.logFile; |
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| 248 | this->outFile = p.outFile; |
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| 249 | this->flagSeparateHeader= p.flagSeparateHeader; |
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| 250 | this->headerFile = p.headerFile; |
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[1146] | 251 | this->flagWriteBinaryCatalogue = p.flagWriteBinaryCatalogue; |
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| 252 | this->binaryCatalogue = p.binaryCatalogue; |
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[882] | 253 | this->flagPlotSpectra = p.flagPlotSpectra; |
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[378] | 254 | this->spectraFile = p.spectraFile; |
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[1148] | 255 | this->flagPlotIndividualSpectra = p.flagPlotIndividualSpectra; |
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[424] | 256 | this->flagTextSpectra = p.flagTextSpectra; |
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| 257 | this->spectraTextFile = p.spectraTextFile; |
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[1120] | 258 | this->flagOutputBaseline = p.flagOutputBaseline; |
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| 259 | this->fileOutputBaseline = p.fileOutputBaseline; |
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[670] | 260 | this->flagOutputMomentMap = p.flagOutputMomentMap; |
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| 261 | this->fileOutputMomentMap = p.fileOutputMomentMap; |
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[1142] | 262 | this->flagOutputMomentMask = p.flagOutputMomentMask; |
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| 263 | this->fileOutputMomentMask = p.fileOutputMomentMask; |
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[379] | 264 | this->flagOutputMask = p.flagOutputMask; |
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[525] | 265 | this->fileOutputMask = p.fileOutputMask; |
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[521] | 266 | this->flagMaskWithObjectNum = p.flagMaskWithObjectNum; |
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[378] | 267 | this->flagOutputSmooth = p.flagOutputSmooth; |
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[525] | 268 | this->fileOutputSmooth = p.fileOutputSmooth; |
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[378] | 269 | this->flagOutputRecon = p.flagOutputRecon; |
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[525] | 270 | this->fileOutputRecon = p.fileOutputRecon; |
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[378] | 271 | this->flagOutputResid = p.flagOutputResid; |
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[525] | 272 | this->fileOutputResid = p.fileOutputResid; |
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[378] | 273 | this->flagVOT = p.flagVOT; |
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| 274 | this->votFile = p.votFile; |
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| 275 | this->flagKarma = p.flagKarma; |
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| 276 | this->karmaFile = p.karmaFile; |
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[1077] | 277 | this->flagDS9 = p.flagDS9; |
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| 278 | this->ds9File = p.ds9File; |
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[1126] | 279 | this->flagCasa = p.flagCasa; |
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| 280 | this->casaFile = p.casaFile; |
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[446] | 281 | this->annotationType = p.annotationType; |
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[378] | 282 | this->flagMaps = p.flagMaps; |
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| 283 | this->detectionMap = p.detectionMap; |
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| 284 | this->momentMap = p.momentMap; |
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| 285 | this->flagXOutput = p.flagXOutput; |
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[438] | 286 | this->precFlux = p.precFlux; |
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| 287 | this->precVel = p.precVel; |
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| 288 | this->precSNR = p.precSNR; |
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[882] | 289 | this->flagNegative = p.flagNegative; |
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[378] | 290 | this->flagBlankPix = p.flagBlankPix; |
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| 291 | this->blankPixValue = p.blankPixValue; |
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| 292 | this->blankKeyword = p.blankKeyword; |
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| 293 | this->bscaleKeyword = p.bscaleKeyword; |
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| 294 | this->bzeroKeyword = p.bzeroKeyword; |
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[434] | 295 | this->newFluxUnits = p.newFluxUnits; |
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[1240] | 296 | this->flaggedChannelList = p.flaggedChannelList; |
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| 297 | this->flaggedChannels = p.flaggedChannels; |
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[1242] | 298 | this->flaggedChannelMask= p.flaggedChannelMask; |
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[662] | 299 | this->areaBeam = p.areaBeam; |
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| 300 | this->fwhmBeam = p.fwhmBeam; |
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[791] | 301 | this->beamAsUsed = p.beamAsUsed; |
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[686] | 302 | this->searchType = p.searchType; |
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[378] | 303 | this->flagTrim = p.flagTrim; |
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| 304 | this->hasBeenTrimmed = p.hasBeenTrimmed; |
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| 305 | this->borderLeft = p.borderLeft; |
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| 306 | this->borderRight = p.borderRight; |
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| 307 | this->borderBottom = p.borderBottom; |
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| 308 | this->borderTop = p.borderTop; |
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| 309 | if(this->sizeOffsets>0) delete [] this->offsets; |
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| 310 | this->sizeOffsets = p.sizeOffsets; |
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| 311 | if(this->sizeOffsets>0){ |
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| 312 | this->offsets = new long[this->sizeOffsets]; |
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| 313 | for(int i=0;i<this->sizeOffsets;i++) this->offsets[i] = p.offsets[i]; |
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| 314 | } |
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| 315 | this->xSubOffset = p.xSubOffset; |
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| 316 | this->ySubOffset = p.ySubOffset; |
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| 317 | this->zSubOffset = p.zSubOffset; |
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| 318 | this->flagBaseline = p.flagBaseline; |
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[1259] | 319 | this->baselineType = p.baselineType; |
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| 320 | this->baselineBoxWidth = p.baselineBoxWidth; |
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[378] | 321 | this->flagGrowth = p.flagGrowth; |
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| 322 | this->growthCut = p.growthCut; |
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[503] | 323 | this->growthThreshold = p.growthThreshold; |
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| 324 | this->flagUserGrowthThreshold = p.flagUserGrowthThreshold; |
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[378] | 325 | this->flagFDR = p.flagFDR; |
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| 326 | this->alphaFDR = p.alphaFDR; |
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[543] | 327 | this->FDRnumCorChan = p.FDRnumCorChan; |
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[378] | 328 | this->flagStatSec = p.flagStatSec; |
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[385] | 329 | this->statSec = p.statSec; |
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| 330 | this->flagRobustStats = p.flagRobustStats; |
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[378] | 331 | this->snrCut = p.snrCut; |
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| 332 | this->threshold = p.threshold; |
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| 333 | this->flagUserThreshold = p.flagUserThreshold; |
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| 334 | this->flagSmooth = p.flagSmooth; |
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| 335 | this->smoothType = p.smoothType; |
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| 336 | this->hanningWidth = p.hanningWidth; |
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| 337 | this->kernMaj = p.kernMaj; |
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| 338 | this->kernMin = p.kernMin; |
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| 339 | this->kernPA = p.kernPA; |
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[1279] | 340 | this->smoothEdgeMethod = p.smoothEdgeMethod; |
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| 341 | this->spatialSmoothCutoff = p.spatialSmoothCutoff; |
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[378] | 342 | this->flagATrous = p.flagATrous; |
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| 343 | this->reconDim = p.reconDim; |
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| 344 | this->scaleMin = p.scaleMin; |
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| 345 | this->scaleMax = p.scaleMax; |
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| 346 | this->snrRecon = p.snrRecon; |
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[1026] | 347 | this->reconConvergence = p.reconConvergence; |
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[378] | 348 | this->filterCode = p.filterCode; |
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[1450] | 349 | FilterFactory filtFac; |
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| 350 | this->reconFilter = filtFac.getFilter(this->filterCode); |
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[378] | 351 | this->flagAdjacent = p.flagAdjacent; |
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| 352 | this->threshSpatial = p.threshSpatial; |
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| 353 | this->threshVelocity = p.threshVelocity; |
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| 354 | this->minChannels = p.minChannels; |
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| 355 | this->minPix = p.minPix; |
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[720] | 356 | this->minVoxels = p.minVoxels; |
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[1261] | 357 | this->maxChannels = p.maxChannels; |
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| 358 | this->maxPix = p.maxPix; |
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| 359 | this->maxVoxels = p.maxVoxels; |
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[691] | 360 | this->flagRejectBeforeMerge = p.flagRejectBeforeMerge; |
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| 361 | this->flagTwoStageMerging = p.flagTwoStageMerging; |
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[378] | 362 | this->spectralMethod = p.spectralMethod; |
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[948] | 363 | this->spectralType = p.spectralType; |
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| 364 | this->restFrequency = p.restFrequency; |
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| 365 | this->restFrequencyUsed = p.restFrequencyUsed; |
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[378] | 366 | this->spectralUnits = p.spectralUnits; |
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| 367 | this->pixelCentre = p.pixelCentre; |
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[571] | 368 | this->sortingParam = p.sortingParam; |
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[378] | 369 | this->borders = p.borders; |
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[571] | 370 | this->blankEdge = p.blankEdge; |
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[378] | 371 | this->verbose = p.verbose; |
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[1140] | 372 | this->commentStr = p.commentStr; |
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[378] | 373 | return *this; |
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| 374 | } |
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| 375 | //-------------------------------------------------------------------- |
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[266] | 376 | |
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[698] | 377 | OUTCOME Param::getopts(int argc, char ** argv, std::string progname) |
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[378] | 378 | { |
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[528] | 379 | /// A function that reads in the command-line options, in a manner |
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| 380 | /// tailored for use with the main Duchamp program. |
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| 381 | /// |
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| 382 | /// \param argc The number of command line arguments. |
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| 383 | /// \param argv The array of command line arguments. |
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[378] | 384 | |
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[698] | 385 | OUTCOME returnValue = FAILURE; |
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[378] | 386 | if(argc==1){ |
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[1149] | 387 | std::cout << ERR_USAGE_MSG; |
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[378] | 388 | returnValue = FAILURE; |
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| 389 | } |
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| 390 | else { |
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| 391 | std::string file; |
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[1149] | 392 | float thresh; |
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| 393 | bool changeX = false, changeThresh=false; |
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[378] | 394 | this->defaultValues(); |
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| 395 | char c; |
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[1149] | 396 | while( ( c = getopt(argc,argv,"p:f:t:hvx") )!=-1){ |
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[378] | 397 | switch(c) { |
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| 398 | case 'p': |
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| 399 | file = optarg; |
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| 400 | if(this->readParams(file)==FAILURE){ |
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[913] | 401 | DUCHAMPERROR(progname,"Could not open parameter file " << file); |
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[378] | 402 | } |
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| 403 | else returnValue = SUCCESS; |
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| 404 | break; |
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| 405 | case 'f': |
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| 406 | file = optarg; |
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| 407 | this->imageFile = file; |
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| 408 | returnValue = SUCCESS; |
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| 409 | break; |
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| 410 | case 'v': |
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| 411 | std::cout << PROGNAME << " version " << VERSION << std::endl; |
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| 412 | break; |
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| 413 | case 'x': |
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| 414 | changeX = true; |
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| 415 | break; |
---|
[1149] | 416 | case 't': |
---|
| 417 | thresh = atof(optarg); |
---|
| 418 | changeThresh = true; |
---|
| 419 | break; |
---|
[378] | 420 | case 'h': |
---|
| 421 | default : |
---|
[1149] | 422 | std::cout << ERR_USAGE_MSG; |
---|
[378] | 423 | break; |
---|
[266] | 424 | } |
---|
| 425 | } |
---|
[378] | 426 | if(changeX){ |
---|
| 427 | if(returnValue == SUCCESS) this->setFlagXOutput(false); |
---|
| 428 | else { |
---|
[913] | 429 | DUCHAMPERROR(progname, "You need to specify either a parameter file or FITS image.\n"); |
---|
[378] | 430 | std::cout << "\n" << ERR_USAGE_MSG; |
---|
| 431 | } |
---|
[294] | 432 | } |
---|
[1149] | 433 | if(changeThresh){ |
---|
| 434 | this->threshold = thresh; |
---|
| 435 | this->flagUserThreshold = true; |
---|
| 436 | this->checkPars(); |
---|
| 437 | } |
---|
[294] | 438 | } |
---|
[378] | 439 | return returnValue; |
---|
[266] | 440 | } |
---|
[378] | 441 | //-------------------------------------------------------------------- |
---|
[266] | 442 | |
---|
[378] | 443 | bool Param::isBlank(float &value) |
---|
| 444 | { |
---|
[528] | 445 | /// Tests whether the value passed as the argument is BLANK or not. |
---|
| 446 | /// \param value Pixel value to be tested. |
---|
| 447 | /// \return False if flagBlankPix is false. Else, compare to the |
---|
| 448 | /// relevant FITS keywords, using integer comparison. |
---|
| 449 | |
---|
[378] | 450 | return this->flagBlankPix && |
---|
| 451 | (this->blankKeyword == int((value-this->bzeroKeyword)/this->bscaleKeyword)); |
---|
[419] | 452 | } |
---|
[266] | 453 | |
---|
[1393] | 454 | std::vector<bool> Param::makeBlankMask(float *array, size_t size) |
---|
[378] | 455 | { |
---|
[528] | 456 | /// This returns an array of bools, saying whether each pixel in the |
---|
| 457 | /// given array is BLANK or not. If the pixel is BLANK, set mask to |
---|
| 458 | /// false, else set to true. The array is allocated by the function. |
---|
| 459 | |
---|
[1393] | 460 | std::vector<bool> mask(size); |
---|
| 461 | for(size_t i=0;i<size;i++) mask[i] = !this->isBlank(array[i]); |
---|
| 462 | return mask; |
---|
[378] | 463 | } |
---|
[275] | 464 | |
---|
| 465 | |
---|
[1393] | 466 | std::vector<bool> Param::makeStatMask(float *array, size_t *dim) |
---|
[506] | 467 | { |
---|
[528] | 468 | /// This returns an array of bools, saying whether each pixel in |
---|
| 469 | /// the given array is suitable for a stats calculation. It needs |
---|
[1246] | 470 | /// to be in the StatSec (if defined), not blank and not a flagged |
---|
[528] | 471 | /// channel. The array is allocated by the function with a 'new' call. |
---|
| 472 | |
---|
[1393] | 473 | std::vector<bool> mask(dim[0]*dim[1]*dim[2]); |
---|
[1242] | 474 | std::vector<bool> flaggedChans = this->getChannelFlags(dim[2]); |
---|
[1000] | 475 | for(size_t x=0;x<dim[0];x++) { |
---|
| 476 | for(size_t y=0;y<dim[1];y++) { |
---|
| 477 | for(size_t z=0;z<dim[2];z++) { |
---|
| 478 | size_t i = x+y*dim[0]+z*dim[0]*dim[1]; |
---|
[1242] | 479 | mask[i] = !this->isBlank(array[i]) && !flaggedChans[z] && this->isStatOK(x,y,z); |
---|
[506] | 480 | } |
---|
| 481 | } |
---|
| 482 | } |
---|
| 483 | return mask; |
---|
| 484 | } |
---|
| 485 | |
---|
[1242] | 486 | bool Param::isFlaggedChannel(int z) |
---|
| 487 | { |
---|
| 488 | /// Tests whether a given channel has been flagged by the user |
---|
| 489 | |
---|
| 490 | // bool isFlagged=false; |
---|
| 491 | // for(size_t i=0;i<this->flaggedChannels.size()&&!isFlagged;i++) |
---|
| 492 | // isFlagged=(z==this->flaggedChannels[i]); |
---|
| 493 | // return isFlagged; |
---|
| 494 | |
---|
[1244] | 495 | if(this->flaggedChannelMask.size()==0) return false; |
---|
[1261] | 496 | else if(z>int(this->flaggedChannelMask.size()) || z<0) return false; |
---|
[1242] | 497 | else return this->flaggedChannelMask[z]; |
---|
| 498 | |
---|
| 499 | } |
---|
| 500 | |
---|
| 501 | std::vector<bool> Param::getChannelFlags(int numChannels) |
---|
| 502 | { |
---|
| 503 | |
---|
| 504 | std::vector<bool> flags(numChannels,false); |
---|
| 505 | for(std::vector<int>::iterator chan = this->flaggedChannels.begin(); chan!=this->flaggedChannels.end(); chan++){ |
---|
| 506 | // channels are zero-based, but channel-specification is 1-based |
---|
| 507 | if(*chan<=numChannels && *chan>-1) flags[*chan-1] = true; |
---|
| 508 | } |
---|
| 509 | return flags; |
---|
| 510 | } |
---|
| 511 | |
---|
| 512 | |
---|
[378] | 513 | bool Param::isStatOK(int x, int y, int z) |
---|
| 514 | { |
---|
[913] | 515 | /// Test whether a given pixel position lies within the subsection |
---|
| 516 | /// given by the statSec parameter. Only tested if the flagSubsection |
---|
| 517 | /// parameter is true -- if it isn't, we just return true since all |
---|
| 518 | /// pixels are therefore available for statstical calculations. |
---|
| 519 | /// \param x X-value of pixel being tested. |
---|
| 520 | /// \param y Y-value of pixel being tested. |
---|
| 521 | /// \param z Z-value of pixel being tested. |
---|
| 522 | /// \return True if pixel is able to be used for statistical |
---|
| 523 | /// calculations. False otherwise. |
---|
[528] | 524 | |
---|
[272] | 525 | int xval=x,yval=y,zval=z; |
---|
| 526 | if(flagSubsection){ |
---|
| 527 | xval += pixelSec.getStart(0); |
---|
| 528 | yval += pixelSec.getStart(1); |
---|
| 529 | zval += pixelSec.getStart(2); |
---|
| 530 | } |
---|
| 531 | return !flagStatSec || statSec.isInside(xval,yval,zval); |
---|
[419] | 532 | } |
---|
[266] | 533 | |
---|
[475] | 534 | std::vector<bool> Param::getObjectChoices() |
---|
| 535 | { |
---|
[528] | 536 | /// Returns a list of bool values, indicating whether a given |
---|
| 537 | /// object was requested or not. The size of the vector is |
---|
| 538 | /// determined by the maximum value in objectList. For instance, |
---|
| 539 | /// if objectList="2,3,5-8", then the returned vector will be |
---|
| 540 | /// [0,1,1,0,1,1,1,1]. |
---|
| 541 | /// \return Vector of bool values. |
---|
| 542 | |
---|
[1242] | 543 | if(this->objectListVector.size()==0) return std::vector<bool>(0); |
---|
[1240] | 544 | else { |
---|
[1242] | 545 | int maxNum = *std::max_element(this->objectListVector.begin(), this->objectListVector.end()); |
---|
[1240] | 546 | std::vector<bool> choices(maxNum,false); |
---|
[1242] | 547 | for(std::vector<int>::iterator obj = objectListVector.begin();obj!=objectListVector.end();obj++) |
---|
[1240] | 548 | choices[*obj-1] = true; |
---|
| 549 | return choices; |
---|
| 550 | } |
---|
[475] | 551 | } |
---|
| 552 | |
---|
| 553 | std::vector<bool> Param::getObjectChoices(int numObjects) |
---|
| 554 | { |
---|
[528] | 555 | /// Returns a list of bool values, indicating whether a given |
---|
| 556 | /// object was requested or not. The size of the vector is given |
---|
| 557 | /// by the numObjects parameter. So, if objectList="2,3,5-8", then |
---|
| 558 | /// the returned vector from a getObjectChoices(10) call will be |
---|
| 559 | /// [0,1,1,0,1,1,1,1,0,0]. |
---|
| 560 | /// \param numObjects How many objects there are in total. |
---|
| 561 | /// \return Vector of bool values. |
---|
| 562 | |
---|
[475] | 563 | if(this->objectList==""){ |
---|
| 564 | std::vector<bool> choices(numObjects,true); |
---|
| 565 | return choices; |
---|
| 566 | } |
---|
| 567 | else{ |
---|
| 568 | std::vector<bool> choices(numObjects,false); |
---|
[1240] | 569 | std::vector<int> duds,goodlist; |
---|
[1242] | 570 | for(std::vector<int>::iterator obj = this->objectListVector.begin();obj!=this->objectListVector.end();obj++){ |
---|
| 571 | if(*obj<=numObjects) { |
---|
| 572 | choices[*obj-1] = true; |
---|
| 573 | goodlist.push_back(*obj); |
---|
| 574 | } |
---|
| 575 | else duds.push_back(*obj); |
---|
[1240] | 576 | } |
---|
| 577 | if(duds.size()>0){ |
---|
[1242] | 578 | this->objectListVector = goodlist; |
---|
| 579 | std::stringstream dudlist; |
---|
| 580 | dudlist << duds[0]; |
---|
| 581 | for(size_t i=1;i<duds.size();i++) dudlist << ","<<duds[i]; |
---|
| 582 | std::string obj="object"; |
---|
| 583 | if(duds.size()>1) obj+= "s"; |
---|
| 584 | DUCHAMPWARN("Object Selection", "You have only detected " << numObjects << " objects, so the requested " |
---|
| 585 | << obj << " '" << dudlist.str() << "' cannot be returned. Please check your request, as it doesn't match the results."); |
---|
[1240] | 586 | } |
---|
[475] | 587 | return choices; |
---|
| 588 | } |
---|
[1242] | 589 | |
---|
[475] | 590 | } |
---|
| 591 | |
---|
[378] | 592 | /****************************************************************/ |
---|
[528] | 593 | /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// |
---|
| 594 | /// / Other Functions using the Parameter class: |
---|
| 595 | /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// |
---|
[3] | 596 | |
---|
[698] | 597 | OUTCOME Param::readParams(std::string paramfile) |
---|
[378] | 598 | { |
---|
[528] | 599 | /// The parameters are read in from a disk file, on the assumption that each |
---|
| 600 | /// line of the file has the format "parameter value" (eg. alphafdr 0.1) |
---|
| 601 | /// |
---|
| 602 | /// The case of the parameter name does not matter, nor does the |
---|
| 603 | /// formatting of the spaces (it can be any amount of whitespace or |
---|
| 604 | /// tabs). |
---|
| 605 | /// |
---|
| 606 | /// \param paramfile A std::string containing the parameter filename. |
---|
| 607 | /// |
---|
| 608 | /// \return FAILURE if the parameter file does not exist. SUCCESS if |
---|
| 609 | /// it is able to read it. |
---|
| 610 | |
---|
[839] | 611 | if(!USE_PGPLOT){ |
---|
| 612 | // Change default values for these parameters when we don't use PGPlot |
---|
| 613 | this->flagXOutput = false; |
---|
| 614 | this->flagMaps = false; |
---|
| 615 | this->flagPlotSpectra = false; |
---|
| 616 | } |
---|
| 617 | |
---|
[378] | 618 | std::ifstream fin(paramfile.c_str()); |
---|
| 619 | if(!fin.is_open()) return FAILURE; |
---|
| 620 | std::string line; |
---|
| 621 | while( !std::getline(fin,line,'\n').eof()){ |
---|
[3] | 622 | |
---|
[378] | 623 | if(line[0]!='#'){ |
---|
| 624 | std::stringstream ss; |
---|
| 625 | ss.str(line); |
---|
| 626 | std::string arg; |
---|
| 627 | ss >> arg; |
---|
| 628 | arg = makelower(arg); |
---|
[733] | 629 | if(arg=="imagefile") this->imageFile = readFilename(ss); |
---|
[378] | 630 | if(arg=="flagsubsection") this->flagSubsection = readFlag(ss); |
---|
| 631 | if(arg=="subsection") this->pixelSec.setSection(readSval(ss)); |
---|
| 632 | if(arg=="flagreconexists") this->flagReconExists = readFlag(ss); |
---|
| 633 | if(arg=="reconfile") this->reconFile = readSval(ss); |
---|
| 634 | if(arg=="flagsmoothexists")this->flagSmoothExists = readFlag(ss); |
---|
| 635 | if(arg=="smoothfile") this->smoothFile = readSval(ss); |
---|
[839] | 636 | if(arg=="beamarea") this->areaBeam = readFval(ss); |
---|
| 637 | if(arg=="beamfwhm") this->fwhmBeam = readFval(ss); |
---|
[475] | 638 | if(arg=="useprevious") this->usePrevious = readFlag(ss); |
---|
| 639 | if(arg=="objectlist") this->objectList = readSval(ss); |
---|
[71] | 640 | |
---|
[378] | 641 | if(arg=="flaglog") this->flagLog = readFlag(ss); |
---|
| 642 | if(arg=="logfile") this->logFile = readSval(ss); |
---|
| 643 | if(arg=="outfile") this->outFile = readSval(ss); |
---|
| 644 | if(arg=="flagseparateheader") this->flagSeparateHeader = readFlag(ss); |
---|
[733] | 645 | if(arg=="headerfile") this->headerFile = readFilename(ss); |
---|
[1146] | 646 | if(arg=="flagwritebinarycatalogue") this->flagWriteBinaryCatalogue = readFlag(ss); |
---|
| 647 | if(arg=="binarycatalogue") this->binaryCatalogue = readFilename(ss); |
---|
[831] | 648 | if(arg=="flagplotspectra") this->flagPlotSpectra = readFlag(ss); |
---|
[733] | 649 | if(arg=="spectrafile") this->spectraFile = readFilename(ss); |
---|
[1148] | 650 | if(arg=="flagplotindividualspectra") this->flagPlotIndividualSpectra = readFlag(ss); |
---|
[424] | 651 | if(arg=="flagtextspectra") this->flagTextSpectra = readFlag(ss); |
---|
[733] | 652 | if(arg=="spectratextfile") this->spectraTextFile = readFilename(ss); |
---|
[1120] | 653 | if(arg=="flagoutputbaseline") this->flagOutputBaseline = readFlag(ss); |
---|
| 654 | if(arg=="fileoutputbaseline") this->fileOutputBaseline = readFilename(ss); |
---|
[670] | 655 | if(arg=="flagoutputmomentmap") this->flagOutputMomentMap = readFlag(ss); |
---|
[733] | 656 | if(arg=="fileoutputmomentmap") this->fileOutputMomentMap = readFilename(ss); |
---|
[1142] | 657 | if(arg=="flagoutputmomentmask") this->flagOutputMomentMask = readFlag(ss); |
---|
| 658 | if(arg=="fileoutputmomentmask") this->fileOutputMomentMask = readFilename(ss); |
---|
[379] | 659 | if(arg=="flagoutputmask") this->flagOutputMask = readFlag(ss); |
---|
[733] | 660 | if(arg=="fileoutputmask") this->fileOutputMask = readFilename(ss); |
---|
[521] | 661 | if(arg=="flagmaskwithobjectnum") this->flagMaskWithObjectNum = readFlag(ss); |
---|
[378] | 662 | if(arg=="flagoutputsmooth")this->flagOutputSmooth = readFlag(ss); |
---|
[733] | 663 | if(arg=="fileoutputsmooth")this->fileOutputSmooth = readFilename(ss); |
---|
[378] | 664 | if(arg=="flagoutputrecon") this->flagOutputRecon = readFlag(ss); |
---|
[733] | 665 | if(arg=="fileoutputrecon") this->fileOutputRecon = readFilename(ss); |
---|
[378] | 666 | if(arg=="flagoutputresid") this->flagOutputResid = readFlag(ss); |
---|
[733] | 667 | if(arg=="fileoutputresid") this->fileOutputResid = readFilename(ss); |
---|
[378] | 668 | if(arg=="flagvot") this->flagVOT = readFlag(ss); |
---|
[733] | 669 | if(arg=="votfile") this->votFile = readFilename(ss); |
---|
[378] | 670 | if(arg=="flagkarma") this->flagKarma = readFlag(ss); |
---|
[733] | 671 | if(arg=="karmafile") this->karmaFile = readFilename(ss); |
---|
[1077] | 672 | if(arg=="flagds9") this->flagDS9 = readFlag(ss); |
---|
| 673 | if(arg=="ds9file") this->ds9File = readFilename(ss); |
---|
[1126] | 674 | if(arg=="flagcasa") this->flagCasa = readFlag(ss); |
---|
| 675 | if(arg=="casafile") this->casaFile = readFilename(ss); |
---|
[446] | 676 | if(arg=="annotationtype") this->annotationType = readSval(ss); |
---|
[378] | 677 | if(arg=="flagmaps") this->flagMaps = readFlag(ss); |
---|
[733] | 678 | if(arg=="detectionmap") this->detectionMap = readFilename(ss); |
---|
| 679 | if(arg=="momentmap") this->momentMap = readFilename(ss); |
---|
[378] | 680 | if(arg=="flagxoutput") this->flagXOutput = readFlag(ss); |
---|
[434] | 681 | if(arg=="newfluxunits") this->newFluxUnits = readSval(ss); |
---|
[438] | 682 | if(arg=="precflux") this->precFlux = readIval(ss); |
---|
| 683 | if(arg=="precvel") this->precVel = readIval(ss); |
---|
| 684 | if(arg=="precsnr") this->precSNR = readIval(ss); |
---|
[3] | 685 | |
---|
[378] | 686 | if(arg=="flagtrim") this->flagTrim = readFlag(ss); |
---|
[1240] | 687 | if(arg=="flaggedchannels") this->flaggedChannelList = readSval(ss); |
---|
[442] | 688 | if(arg=="flagbaseline") this->flagBaseline = readFlag(ss); |
---|
[1259] | 689 | if(arg=="baselinetype") this->baselineType = readSval(ss); |
---|
| 690 | if(arg=="baselineboxwidth") this->baselineBoxWidth = readIval(ss); |
---|
[691] | 691 | if(arg=="searchtype") this->searchType = readSval(ss); |
---|
[71] | 692 | |
---|
[442] | 693 | if(arg=="flagnegative") this->flagNegative = readFlag(ss); |
---|
[378] | 694 | if(arg=="flaggrowth") this->flagGrowth = readFlag(ss); |
---|
| 695 | if(arg=="growthcut") this->growthCut = readFval(ss); |
---|
[461] | 696 | if(arg=="growththreshold"){ |
---|
| 697 | this->growthThreshold = readFval(ss); |
---|
| 698 | this->flagUserGrowthThreshold = true; |
---|
| 699 | } |
---|
[71] | 700 | |
---|
[378] | 701 | if(arg=="flagfdr") this->flagFDR = readFlag(ss); |
---|
| 702 | if(arg=="alphafdr") this->alphaFDR = readFval(ss); |
---|
[543] | 703 | if(arg=="fdrnumcorchan") this->FDRnumCorChan = readIval(ss); |
---|
[378] | 704 | if(arg=="flagstatsec") this->flagStatSec = readFlag(ss); |
---|
| 705 | if(arg=="statsec") this->statSec.setSection(readSval(ss)); |
---|
[385] | 706 | if(arg=="flagrobuststats") this->flagRobustStats = readFlag(ss); |
---|
[378] | 707 | if(arg=="snrcut") this->snrCut = readFval(ss); |
---|
| 708 | if(arg=="threshold"){ |
---|
| 709 | this->threshold = readFval(ss); |
---|
| 710 | this->flagUserThreshold = true; |
---|
| 711 | } |
---|
[201] | 712 | |
---|
[378] | 713 | if(arg=="flagsmooth") this->flagSmooth = readFlag(ss); |
---|
| 714 | if(arg=="smoothtype") this->smoothType = readSval(ss); |
---|
| 715 | if(arg=="hanningwidth") this->hanningWidth = readIval(ss); |
---|
| 716 | if(arg=="kernmaj") this->kernMaj = readFval(ss); |
---|
| 717 | if(arg=="kernmin") this->kernMin = readFval(ss); |
---|
| 718 | if(arg=="kernpa") this->kernPA = readFval(ss); |
---|
[1279] | 719 | if(arg=="smoothedgemethod") this->smoothEdgeMethod = readSval(ss); |
---|
| 720 | if(arg=="spatialsmoothcutoff") this->spatialSmoothCutoff = readFval(ss); |
---|
[103] | 721 | |
---|
[378] | 722 | if(arg=="flagatrous") this->flagATrous = readFlag(ss); |
---|
| 723 | if(arg=="recondim") this->reconDim = readIval(ss); |
---|
| 724 | if(arg=="scalemin") this->scaleMin = readIval(ss); |
---|
| 725 | if(arg=="scalemax") this->scaleMax = readIval(ss); |
---|
| 726 | if(arg=="snrrecon") this->snrRecon = readFval(ss); |
---|
[1026] | 727 | if(arg=="reconconvergence") this->reconConvergence = readFval(ss); |
---|
| 728 | if(arg=="filtercode") this->filterCode = readIval(ss); |
---|
[71] | 729 | |
---|
[378] | 730 | if(arg=="flagadjacent") this->flagAdjacent = readFlag(ss); |
---|
| 731 | if(arg=="threshspatial") this->threshSpatial = readFval(ss); |
---|
| 732 | if(arg=="threshvelocity") this->threshVelocity = readFval(ss); |
---|
[1261] | 733 | if(arg=="minpix") this->minPix = readIval(ss); |
---|
[378] | 734 | if(arg=="minchannels") this->minChannels = readIval(ss); |
---|
[720] | 735 | if(arg=="minvoxels") this->minVoxels = readIval(ss); |
---|
[1261] | 736 | if(arg=="maxpix") this->maxPix = readIval(ss); |
---|
| 737 | if(arg=="maxchannels") this->maxChannels = readIval(ss); |
---|
| 738 | if(arg=="maxvoxels") this->maxVoxels = readIval(ss); |
---|
[691] | 739 | if(arg=="flagrejectbeforemerge") this->flagRejectBeforeMerge = readFlag(ss); |
---|
| 740 | if(arg=="flagtwostagemerging") this->flagTwoStageMerging = readFlag(ss); |
---|
[71] | 741 | |
---|
[378] | 742 | if(arg=="spectralmethod") this->spectralMethod=makelower(readSval(ss)); |
---|
[948] | 743 | if(arg=="spectraltype") this->spectralType = readSval(ss); |
---|
| 744 | if(arg=="restfrequency") this->restFrequency = readFval(ss); |
---|
[949] | 745 | if(arg=="spectralunits") this->spectralUnits = readSval(ss); |
---|
[378] | 746 | if(arg=="pixelcentre") this->pixelCentre = makelower(readSval(ss)); |
---|
[571] | 747 | if(arg=="sortingparam") this->sortingParam = makelower(readSval(ss)); |
---|
[378] | 748 | if(arg=="drawborders") this->borders = readFlag(ss); |
---|
| 749 | if(arg=="drawblankedges") this->blankEdge = readFlag(ss); |
---|
| 750 | if(arg=="verbose") this->verbose = readFlag(ss); |
---|
[295] | 751 | |
---|
[378] | 752 | // Dealing with deprecated parameters. |
---|
| 753 | if(arg=="flagblankpix"){ |
---|
| 754 | this->flagTrim = readFlag(ss); |
---|
[913] | 755 | DUCHAMPWARN("Reading parameters","The parameter flagBlankPix is deprecated. Please use the flagTrim parameter in future."); |
---|
[1248] | 756 | DUCHAMPWARN("Reading parameters"," Setting flagTrim = " << stringize(this->flagTrim)); |
---|
[378] | 757 | } |
---|
| 758 | if(arg=="blankpixvalue"){ |
---|
[913] | 759 | DUCHAMPWARN("Reading parameters","The parameter blankPixValue is deprecated. This value is only taken from the FITS header."); |
---|
[378] | 760 | } |
---|
[662] | 761 | if(arg=="beamsize"){ |
---|
[675] | 762 | this->areaBeam = readFval(ss); |
---|
[913] | 763 | DUCHAMPWARN("Reading parameters","The parameter beamSize is deprecated. You can specify the beam size by beamArea or beamFWHM."); |
---|
[1248] | 764 | DUCHAMPWARN("Reading parameters"," Setting beamArea = " << this->areaBeam); |
---|
[662] | 765 | } |
---|
[1248] | 766 | if(arg=="flagmw"){ |
---|
| 767 | DUCHAMPWARN("Reading parameters", "The parameters flagMW, minMW and maxMW have been deprecated."); |
---|
| 768 | DUCHAMPWARN("Reading parameters", " Instead, use the parameter flaggedChannels to indicate channels & channel ranges to be excluded from detection."); |
---|
| 769 | } |
---|
[295] | 770 | } |
---|
[378] | 771 | } |
---|
[295] | 772 | |
---|
[506] | 773 | this->checkPars(); |
---|
| 774 | |
---|
| 775 | return SUCCESS; |
---|
| 776 | |
---|
| 777 | } |
---|
| 778 | |
---|
| 779 | void Param::checkPars() |
---|
| 780 | { |
---|
| 781 | |
---|
[882] | 782 | // If flagSubsection is false, but the parset had a subsection string in it, we want to set this back to the default. |
---|
| 783 | if(!this->flagSubsection){ |
---|
| 784 | this->pixelSec.setSection(defaultSection); |
---|
| 785 | } |
---|
| 786 | if(!this->flagStatSec){ |
---|
| 787 | this->statSec.setSection(defaultSection); |
---|
| 788 | } |
---|
| 789 | |
---|
[1240] | 790 | // If we have usePrevious=false, set the objectlist to blank so that we use all of them. Otherwise, define the vector list of choices. |
---|
[475] | 791 | if(!this->usePrevious) this->objectList = ""; |
---|
[1242] | 792 | else this->objectListVector = selectionToIntVec(this->objectList); |
---|
[475] | 793 | |
---|
[1240] | 794 | // Defining the vector list of flagged channels |
---|
[1247] | 795 | if(this->flaggedChannelList.size()>0){ |
---|
| 796 | this->flaggedChannels = selectionToIntVec(this->flaggedChannelList); |
---|
| 797 | this->flaggedChannelMask = std::vector<bool>(*std::max_element(this->flaggedChannels.begin(),this->flaggedChannels.end()),false); |
---|
| 798 | for(size_t i=0;i<this->flaggedChannels.size();i++) this->flaggedChannelMask[ this->flaggedChannels[i] ] = true; |
---|
| 799 | } |
---|
[1240] | 800 | |
---|
[420] | 801 | // If pgplot was not included in the compilation, need to set flagXOutput to false |
---|
[831] | 802 | if(!USE_PGPLOT){ |
---|
[1148] | 803 | if(this->flagXOutput || this->flagMaps || this->flagPlotSpectra || this->flagPlotIndividualSpectra) |
---|
| 804 | DUCHAMPWARN("Reading parameters","PGPlot has not been enabled, so setting flagXOutput, flagMaps, flagPlotSpectra and flagPlotIndividualSpectra to false."); |
---|
[831] | 805 | this->flagXOutput = false; |
---|
| 806 | this->flagMaps = false; |
---|
| 807 | this->flagPlotSpectra = false; |
---|
[1148] | 808 | this->flagPlotIndividualSpectra = false; |
---|
[831] | 809 | } |
---|
[420] | 810 | |
---|
[1148] | 811 | if(!this->flagPlotSpectra && this->flagPlotIndividualSpectra){ |
---|
| 812 | DUCHAMPWARN("Reading parameters","flagPlotSpectra is false, so setting flagPlotIndividualSpectra to false as well."); |
---|
| 813 | this->flagPlotIndividualSpectra = false; |
---|
| 814 | } |
---|
| 815 | |
---|
[438] | 816 | // Correcting bad precision values -- if negative, set to 0 |
---|
| 817 | if(this->precFlux<0) this->precFlux = 0; |
---|
| 818 | if(this->precVel<0) this->precVel = 0; |
---|
| 819 | if(this->precSNR<0) this->precSNR = 0; |
---|
| 820 | |
---|
[686] | 821 | // Can only have "spatial" or "spectral" as search types |
---|
| 822 | if(this->searchType != "spatial" && this->searchType != "spectral"){ |
---|
[913] | 823 | DUCHAMPWARN("Reading parameters","You have requested a search type of \""<<this->searchType<<"\" -- Only \"spectral\" and \"spatial\" are accepted, so setting to \"spatial\"."); |
---|
[686] | 824 | this->searchType = "spatial"; |
---|
| 825 | } |
---|
| 826 | |
---|
[378] | 827 | // The wavelet reconstruction takes precendence over the smoothing. |
---|
| 828 | if(this->flagATrous) this->flagSmooth = false; |
---|
| 829 | |
---|
[1026] | 830 | // Check validity of recon parameters |
---|
| 831 | if(this->flagATrous){ |
---|
| 832 | if(this->reconConvergence < 0.){ |
---|
| 833 | DUCHAMPWARN("Reading Parameters","Your reconConvergence value is negative ("<<this->reconConvergence<<") - setting to " << -this->reconConvergence <<"."); |
---|
| 834 | this->reconConvergence *= -1.; |
---|
| 835 | } |
---|
| 836 | |
---|
[1448] | 837 | if (this->reconFilter){ |
---|
| 838 | delete this->reconFilter; |
---|
| 839 | } |
---|
[1339] | 840 | FilterFactory filtFac; |
---|
| 841 | this->reconFilter = filtFac.getFilter(this->filterCode); |
---|
[1026] | 842 | |
---|
| 843 | if((this->scaleMax) > 0 && (this->scaleMax < this->scaleMin)){ |
---|
| 844 | DUCHAMPWARN("Reading Parameters","Reconstruction scaleMax ("<<this->scaleMax<<") is less than scaleMin ("<<this->scaleMin<<"): setting both to "<<this->scaleMin); |
---|
| 845 | this->scaleMax = this->scaleMin; |
---|
| 846 | } |
---|
| 847 | |
---|
| 848 | if( (this->reconDim < 1) || (this->reconDim > 3) ){ |
---|
| 849 | DUCHAMPWARN("Reading Parameters", "You requested a " << this->reconDim << " dimensional reconstruction. Setting reconDim to 1"); |
---|
| 850 | this->reconDim = 1; |
---|
| 851 | } |
---|
| 852 | |
---|
| 853 | if( this->snrRecon < 0.){ |
---|
| 854 | DUCHAMPWARN("Reading Parameters", "Your snrRecon value is negative (" << this->snrRecon<<"). Turning reconstruction off -- fix your parameter file!"); |
---|
| 855 | this->flagATrous = false; |
---|
| 856 | } |
---|
| 857 | |
---|
| 858 | } |
---|
| 859 | |
---|
[1279] | 860 | // Check validity of smoothing parameters |
---|
| 861 | if(this->flagSmooth){ |
---|
| 862 | |
---|
| 863 | // Make sure smoothType is an acceptable type -- default is "spectral" |
---|
| 864 | if((this->smoothType!="spectral")&& |
---|
| 865 | (this->smoothType!="spatial")){ |
---|
| 866 | DUCHAMPWARN("Reading parameters","The requested value of the parameter smoothType, \"" << this->smoothType << "\", is invalid -- changing to \"spectral\"."); |
---|
| 867 | this->smoothType = "spectral"; |
---|
| 868 | } |
---|
| 869 | |
---|
| 870 | // If kernMin has not been given, or is negative, make it equal to kernMaj |
---|
| 871 | if(this->kernMin < 0) this->kernMin = this->kernMaj; |
---|
| 872 | |
---|
| 873 | // Check the smoothEdgeMethod and spatialSmoothCutoff parameters. |
---|
| 874 | if(this->smoothType=="spatial"){ |
---|
| 875 | if((this->smoothEdgeMethod != "equal") && (this->smoothEdgeMethod!="truncate") && (this->smoothEdgeMethod!="scale")){ |
---|
| 876 | DUCHAMPWARN("Reading parameters","The requested value of the parameter smoothEdgeMethod, \""<< this->smoothEdgeMethod << "\", is invalid - changing to \"equal\"."); |
---|
| 877 | this->smoothEdgeMethod = "equal"; |
---|
| 878 | } |
---|
| 879 | if(this->spatialSmoothCutoff<0.){ |
---|
| 880 | this->spatialSmoothCutoff *= -1.; |
---|
| 881 | DUCHAMPWARN("Reading parameters","The value of spatialSmoothCutoff is negative. Changing to "<<this->spatialSmoothCutoff); |
---|
| 882 | } |
---|
| 883 | } |
---|
| 884 | |
---|
| 885 | } |
---|
| 886 | |
---|
[461] | 887 | if(this->flagUserThreshold){ |
---|
| 888 | |
---|
| 889 | // If we specify a manual threshold, need to also specify a manual growth threshold |
---|
| 890 | // If we haven't done so, turn growing off |
---|
| 891 | if(this->flagGrowth && !this->flagUserGrowthThreshold){ |
---|
[913] | 892 | DUCHAMPWARN("Reading parameters","You have specified a manual search threshold, but not a manual growth threshold. You need to do so using the \"growthThreshold\" parameter."); |
---|
| 893 | DUCHAMPWARN("Reading parameters","The growth function is being turned off."); |
---|
[461] | 894 | this->flagGrowth = false; |
---|
| 895 | } |
---|
| 896 | |
---|
| 897 | // If we specify a manual threshold, we don't need the FDR method, so turn it off if requested. |
---|
| 898 | if(this->flagFDR){ |
---|
[913] | 899 | DUCHAMPWARN("Reading parameters","You have specified a manual search threshold, so we don't need to use the FDR method. Setting \"flagFDR=false\"."); |
---|
[461] | 900 | this->flagFDR = false; |
---|
| 901 | } |
---|
| 902 | |
---|
| 903 | } |
---|
| 904 | |
---|
[537] | 905 | // Make sure the growth level is less than the detection level. Else turn off growing. |
---|
| 906 | if(this->flagGrowth){ |
---|
| 907 | std::stringstream errmsg; |
---|
| 908 | bool doWarn = false; |
---|
| 909 | if(this->flagUserThreshold && |
---|
| 910 | ( (this->threshold < this->growthThreshold) |
---|
| 911 | || (this->snrCut < this->growthCut) ) ){ |
---|
[913] | 912 | errmsg << "Your \"growthThreshold\" parameter" << this->growthThreshold <<" is larger than your \"threshold\"" << this->threshold; |
---|
[537] | 913 | doWarn = true; |
---|
| 914 | } |
---|
| 915 | |
---|
| 916 | if(!this->flagUserThreshold && |
---|
| 917 | (this->snrCut < this->growthCut)) { |
---|
[913] | 918 | errmsg << "Your \"growthCut\" parameter " << this->growthCut << " is larger than your \"snrCut\"" << this->snrCut; |
---|
[537] | 919 | doWarn = true; |
---|
| 920 | } |
---|
| 921 | |
---|
[913] | 922 | if(doWarn){ |
---|
[1427] | 923 | DUCHAMPWARN("Reading parameters",errmsg.str()); |
---|
[913] | 924 | DUCHAMPWARN("Reading parameters","The growth function is being turned off."); |
---|
[537] | 925 | |
---|
[913] | 926 | } |
---|
[537] | 927 | } |
---|
| 928 | |
---|
[446] | 929 | // Make sure the annnotationType is an acceptable option -- default is "borders" |
---|
[1130] | 930 | if((this->annotationType != "borders") && (this->annotationType!="circles") && (this->annotationType!="ellipses")){ |
---|
[913] | 931 | DUCHAMPWARN("Reading parameters","The requested value of the parameter annotationType, \"" << this->annotationType << "\", is invalid -- changing to \"borders\"."); |
---|
[446] | 932 | this->annotationType = "borders"; |
---|
| 933 | } |
---|
| 934 | |
---|
[272] | 935 | |
---|
[378] | 936 | // Make sure spectralMethod is an acceptable type -- default is "peak" |
---|
| 937 | if((this->spectralMethod!="peak")&& |
---|
| 938 | (this->spectralMethod!="sum")){ |
---|
[913] | 939 | DUCHAMPWARN("Reading parameters","The requested value of the parameter spectralMethod, \"" << this->spectralMethod << "\", is invalid -- changing to \"peak\"."); |
---|
[378] | 940 | this->spectralMethod = "peak"; |
---|
| 941 | } |
---|
[232] | 942 | |
---|
[913] | 943 | // make sure pixelCentre is an acceptable type -- default is "peak" |
---|
[378] | 944 | if((this->pixelCentre!="centroid")&& |
---|
| 945 | (this->pixelCentre!="average") && |
---|
| 946 | (this->pixelCentre!="peak") ){ |
---|
[913] | 947 | DUCHAMPWARN("Reading parameters","The requested value of the parameter pixelCentre, \"" << this->pixelCentre << "\", is invalid -- changing to \"centroid\"."); |
---|
[378] | 948 | this->pixelCentre = "centroid"; |
---|
| 949 | } |
---|
[275] | 950 | |
---|
[571] | 951 | // Make sure sortingParam is an acceptable type -- default is "vel" |
---|
| 952 | bool OK = false; |
---|
[955] | 953 | int loc=(this->sortingParam[0]=='-') ? 1 : 0; |
---|
[571] | 954 | for(int i=0;i<numSortingParamOptions;i++) |
---|
[955] | 955 | OK = OK || this->sortingParam.substr(loc)==sortingParamOptions[i]; |
---|
[571] | 956 | if(!OK){ |
---|
[913] | 957 | DUCHAMPWARN("Reading parameters","The requested value of the parameter sortingParam, \"" << this->sortingParam << "\", is invalid. -- changing to \"vel\"."); |
---|
[571] | 958 | this->sortingParam = "vel"; |
---|
| 959 | } |
---|
[942] | 960 | |
---|
| 961 | // Make sure minVoxels is appropriate given minChannels & minPixels |
---|
| 962 | if(this->minVoxels < (this->minPix + this->minChannels - 1) ){ |
---|
| 963 | DUCHAMPWARN("Reading parameters","Changing minVoxels to " << this->minPix + this->minChannels - 1 << " given minPix="<<this->minPix << " and minChannels="<<this->minChannels); |
---|
| 964 | this->minVoxels = this->minPix + this->minChannels - 1; |
---|
| 965 | } |
---|
[1261] | 966 | |
---|
[1146] | 967 | // check that baselines are being calculated if we want to save them to a FITS file |
---|
| 968 | if(this->flagOutputBaseline && !this->flagBaseline){ |
---|
| 969 | DUCHAMPWARN("Reading parameters","Saving of baseline values to a FITS file has been requested, but baselines are not being calculated. Turning off saving of baseline values."); |
---|
| 970 | this->flagOutputBaseline = false; |
---|
| 971 | } |
---|
[1259] | 972 | |
---|
| 973 | // check that the baseline option is valid |
---|
| 974 | if(this->flagBaseline){ |
---|
| 975 | if (this->baselineType != "atrous" && this->baselineType != "median"){ |
---|
| 976 | DUCHAMPWARN("Reading parameters", "The only types of baseline subtraction available are 'atrous' or 'median' - you provided '"<<this->baselineType <<"'. Setting to 'atrous'."); |
---|
| 977 | this->baselineType = "atrous"; |
---|
| 978 | } |
---|
| 979 | if(this->baselineType == "median" && this->baselineBoxWidth%2 == 0){ |
---|
| 980 | DUCHAMPWARN("Reading parameters", "The baseline box width needs to be odd. Changing from " << this->baselineBoxWidth << " to " << this->baselineBoxWidth+1 <<"."); |
---|
| 981 | this->baselineBoxWidth++; |
---|
| 982 | } |
---|
| 983 | } |
---|
[571] | 984 | |
---|
[265] | 985 | } |
---|
| 986 | |
---|
[910] | 987 | OUTCOME Param::checkImageExists() |
---|
| 988 | { |
---|
| 989 | /// A simple check to see whether the image actually exists or not, using the cfitsio interface. |
---|
| 990 | /// If it does, we return SUCCESS, otherwise we throw an exception. |
---|
| 991 | |
---|
| 992 | int exists,status = 0; /* MUST initialize status */ |
---|
| 993 | fits_file_exists(this->imageFile.c_str(),&exists,&status); |
---|
| 994 | if(exists<=0){ |
---|
| 995 | fits_report_error(stderr, status); |
---|
| 996 | DUCHAMPTHROW("Cube Reader","Requested image " << this->imageFile << " does not exist!"); |
---|
| 997 | return FAILURE; |
---|
| 998 | } |
---|
| 999 | return SUCCESS; |
---|
| 1000 | } |
---|
| 1001 | |
---|
| 1002 | |
---|
[1137] | 1003 | void recordParameters(std::ostream& theStream, Param &par, std::string paramName, std::string paramDesc, std::string paramValue) |
---|
[664] | 1004 | { |
---|
| 1005 | |
---|
[1142] | 1006 | const int width = 60; |
---|
[716] | 1007 | int widthText = width - paramName.size(); |
---|
[265] | 1008 | |
---|
[1137] | 1009 | theStream << par.commentString() |
---|
| 1010 | << std::setw(widthText) << paramDesc |
---|
[1346] | 1011 | << std::setiosflags(std::ios::right) << paramName |
---|
[1348] | 1012 | << " = " << std::resetiosflags(std::ios::right) << paramValue |
---|
[664] | 1013 | <<std::endl; |
---|
| 1014 | } |
---|
| 1015 | |
---|
| 1016 | std::string fileOption(bool flag, std::string file) |
---|
| 1017 | { |
---|
| 1018 | std::ostringstream ss; |
---|
| 1019 | ss << stringize(flag); |
---|
| 1020 | if(flag) ss << " --> " << file; |
---|
| 1021 | return ss.str(); |
---|
| 1022 | |
---|
| 1023 | } |
---|
| 1024 | |
---|
[378] | 1025 | std::ostream& operator<< ( std::ostream& theStream, Param& par) |
---|
| 1026 | { |
---|
[528] | 1027 | /// Print out the parameter set in a formatted, easy to read style. |
---|
| 1028 | /// Lists the parameters, a description of them, and their value. |
---|
[3] | 1029 | |
---|
[378] | 1030 | // BUG -- can get error: `boolalpha' is not a member of type `ios' -- old compilers: gcc 2.95.3? |
---|
| 1031 | // theStream.setf(std::ios::boolalpha); |
---|
| 1032 | theStream.setf(std::ios::left); |
---|
[1137] | 1033 | theStream <<par.commentString()<<"\n"<<par.commentString()<<"---- Parameters ----"<<std::endl; |
---|
[378] | 1034 | theStream << std::setfill('.'); |
---|
| 1035 | if(par.getFlagSubsection()) |
---|
[1137] | 1036 | recordParam(theStream, par, "[imageFile]", "Image to be analysed", par.getImageFile()<<par.getSubsection()); |
---|
[378] | 1037 | else |
---|
[1137] | 1038 | recordParam(theStream, par, "[imageFile]", "Image to be analysed", par.getImageFile()); |
---|
[948] | 1039 | if(par.getFlagRestFrequencyUsed()){ |
---|
[1137] | 1040 | recordParam(theStream, par, "[restFrequency]","Rest frequency as used", par.getRestFrequency()); |
---|
[948] | 1041 | } |
---|
[378] | 1042 | if(par.getFlagReconExists() && par.getFlagATrous()){ |
---|
[1137] | 1043 | recordParam(theStream, par, "[reconExists]", "Reconstructed array exists?", stringize(par.getFlagReconExists())); |
---|
| 1044 | recordParam(theStream, par, "[reconFile]", "FITS file containing reconstruction", par.getReconFile()); |
---|
[378] | 1045 | } |
---|
| 1046 | if(par.getFlagSmoothExists() && par.getFlagSmooth()){ |
---|
[1137] | 1047 | recordParam(theStream, par, "[smoothExists]", "Smoothed array exists?", stringize(par.getFlagSmoothExists())); |
---|
| 1048 | recordParam(theStream, par, "[smoothFile]", "FITS file containing smoothed array", par.getSmoothFile()); |
---|
[378] | 1049 | } |
---|
[1419] | 1050 | if(par.getFlagLog()){ |
---|
| 1051 | recordParam(theStream, par, "[logFile]", "Intermediate Logfile", par.logFile); |
---|
| 1052 | } |
---|
[1137] | 1053 | recordParam(theStream, par, "[outFile]", "Final Results file", par.getOutFile()); |
---|
[664] | 1054 | if(par.getFlagSeparateHeader()){ |
---|
[1137] | 1055 | recordParam(theStream, par, "[headerFile]", "Header for results file", par.getHeaderFile()); |
---|
[664] | 1056 | } |
---|
[831] | 1057 | if(USE_PGPLOT && par.getFlagPlotSpectra()){ |
---|
[1148] | 1058 | std::string label=par.getSpectraFile(); |
---|
| 1059 | if(par.getFlagPlotIndividualSpectra()) label += ", with individual spectra too"; |
---|
| 1060 | recordParam(theStream, par, "[spectraFile]", "Spectrum file", label); |
---|
[831] | 1061 | } |
---|
[424] | 1062 | if(par.getFlagTextSpectra()){ |
---|
[1137] | 1063 | recordParam(theStream, par, "[spectraTextFile]", "Text file with ascii spectral data", par.getSpectraTextFile()); |
---|
[424] | 1064 | } |
---|
[378] | 1065 | if(par.getFlagVOT()){ |
---|
[1137] | 1066 | recordParam(theStream, par, "[votFile]", "VOTable file", par.getVOTFile()); |
---|
[378] | 1067 | } |
---|
| 1068 | if(par.getFlagKarma()){ |
---|
[1137] | 1069 | recordParam(theStream, par, "[karmaFile]", "Karma annotation file" , par.getKarmaFile()); |
---|
[378] | 1070 | } |
---|
[1077] | 1071 | if(par.getFlagDS9()){ |
---|
[1137] | 1072 | recordParam(theStream, par, "[ds9File]", "DS9 annotation file" , par.getDS9File()); |
---|
[1077] | 1073 | } |
---|
[1126] | 1074 | if(par.getFlagCasa()){ |
---|
[1137] | 1075 | recordParam(theStream, par, "[casaFile]", "CASA annotation file" , par.getCasaFile()); |
---|
[1126] | 1076 | } |
---|
[831] | 1077 | if(USE_PGPLOT && par.getFlagMaps()){ |
---|
[1137] | 1078 | recordParam(theStream, par, "[momentMap]", "0th Moment Map", par.getMomentMap()); |
---|
| 1079 | recordParam(theStream, par, "[detectionMap]", "Detection Map", par.getDetectionMap()); |
---|
[378] | 1080 | } |
---|
[831] | 1081 | if(USE_PGPLOT){ |
---|
[1137] | 1082 | recordParam(theStream, par, "[flagXOutput]", "Display a map in a pgplot xwindow?", stringize(par.getFlagXOutput())); |
---|
[831] | 1083 | } |
---|
[664] | 1084 | if(par.getFlagATrous()){ |
---|
[1137] | 1085 | recordParam(theStream, par, "[flagOutputRecon]", "Saving reconstructed cube?", fileOption(par.getFlagOutputRecon(),par.outputReconFile())); |
---|
| 1086 | recordParam(theStream, par, "[flagOutputResid]", "Saving residuals from reconstruction?", fileOption(par.getFlagOutputResid(),par.outputResidFile())); |
---|
[378] | 1087 | } |
---|
[664] | 1088 | if(par.getFlagSmooth()){ |
---|
[1137] | 1089 | recordParam(theStream, par, "[flagOutputSmooth]", "Saving smoothed cube?", fileOption(par.getFlagOutputSmooth(),par.outputSmoothFile())); |
---|
[378] | 1090 | } |
---|
[1137] | 1091 | recordParam(theStream, par, "[flagOutputMask]", "Saving mask cube?", fileOption(par.getFlagOutputMask(),par.outputMaskFile())); |
---|
| 1092 | recordParam(theStream, par, "[flagOutputMomentMap]", "Saving 0th moment to FITS file?", fileOption(par.getFlagOutputMomentMap(),par.outputMomentMapFile())); |
---|
[1142] | 1093 | recordParam(theStream, par, "[flagOutputMomentMask]", "Saving 0th moment mask to FITS file?", fileOption(par.getFlagOutputMomentMask(),par.outputMomentMaskFile())); |
---|
[1137] | 1094 | recordParam(theStream, par, "[flagOutputBaseline]", "Saving baseline values to FITS file?", fileOption(par.getFlagOutputBaseline(),par.outputBaselineFile())); |
---|
[664] | 1095 | |
---|
[1137] | 1096 | theStream << par.commentString() <<"------"<<std::endl; |
---|
[664] | 1097 | |
---|
[1137] | 1098 | recordParam(theStream, par, "[searchType]", "Type of searching performed", par.getSearchType()); |
---|
[378] | 1099 | if(par.getFlagBlankPix()){ |
---|
[1137] | 1100 | recordParam(theStream, par, "", "Blank Pixel Value", par.getBlankPixVal()); |
---|
[275] | 1101 | } |
---|
[1137] | 1102 | recordParam(theStream, par, "[flagTrim]", "Trimming Blank Pixels?", stringize(par.getFlagTrim())); |
---|
| 1103 | recordParam(theStream, par, "[flagNegative]", "Searching for Negative features?", stringize(par.getFlagNegative())); |
---|
[1242] | 1104 | if(par.getFlaggedChannelList().size()>0){ |
---|
| 1105 | recordParam(theStream, par, "[flaggedChannels]", "Channels flagged by user", par.getFlaggedChannelList()); |
---|
| 1106 | } |
---|
[791] | 1107 | if(par.beamAsUsed.origin()==EMPTY){ // No beam in FITS file and no information provided |
---|
[1137] | 1108 | recordParam(theStream, par, "", "Area of Beam", "No beam"); |
---|
[675] | 1109 | } |
---|
[791] | 1110 | else if(par.beamAsUsed.origin()==HEADER){ // Report beam size from FITS file |
---|
[1137] | 1111 | recordParam(theStream, par, "", "Area of Beam (pixels)", par.beamAsUsed.area() << " (beam: " << par.beamAsUsed.maj() << " x " << par.beamAsUsed.min() <<" pixels)"); |
---|
[675] | 1112 | } |
---|
[791] | 1113 | else if(par.beamAsUsed.origin()==PARAM){ // Report beam size requested in parameter set input |
---|
[1137] | 1114 | if(par.fwhmBeam>0.) recordParam(theStream, par, "[beamFWHM]", "FWHM of Beam (pixels)", par.beamAsUsed.maj() << " (beam area = " << par.beamAsUsed.area() <<" pixels)"); |
---|
| 1115 | else recordParam(theStream, par, "[beamArea]", "Area of Beam (pixels)", par.beamAsUsed.area()); |
---|
[788] | 1116 | } |
---|
| 1117 | else{ |
---|
[1137] | 1118 | recordParam(theStream, par, "[beam info]", "Size & shape of beam", "No information available!"); |
---|
[788] | 1119 | } |
---|
[1137] | 1120 | recordParam(theStream, par, "[flagBaseline]", "Removing baselines before search?", stringize(par.getFlagBaseline())); |
---|
[1260] | 1121 | if(par.getFlagBaseline()){ |
---|
| 1122 | recordParam(theStream, par, "[baselineType]", "Baseline removal algorithm", par.getBaselineType()); |
---|
| 1123 | if(par.getBaselineType()=="median") |
---|
| 1124 | recordParam(theStream, par, "[baselineBoxWidth]", "Box width for median baseline estimation", par.getBaselineBoxWidth()); |
---|
| 1125 | } |
---|
[1137] | 1126 | recordParam(theStream, par, "[flagSmooth]", "Smoothing data prior to searching?", stringize(par.getFlagSmooth())); |
---|
[378] | 1127 | if(par.getFlagSmooth()){ |
---|
[1137] | 1128 | recordParam(theStream, par, "[smoothType]", "Type of smoothing", par.getSmoothType()); |
---|
[378] | 1129 | if(par.getSmoothType()=="spectral") |
---|
[1137] | 1130 | recordParam(theStream, par, "[hanningWidth]", "Width of hanning filter", par.getHanningWidth()); |
---|
[378] | 1131 | else{ |
---|
[1279] | 1132 | recordParam(theStream, par, "[kernMaj]", "Gaussian kernel major axis FWHM [pix]", par.getKernMaj()); |
---|
| 1133 | recordParam(theStream, par, "[kernMin]", "Gaussian kernel minor axis FWHM [pix]", par.getKernMin()); |
---|
[1137] | 1134 | recordParam(theStream, par, "[kernPA]", "Gaussian kernel position angle [deg]", par.getKernPA()); |
---|
[1279] | 1135 | recordParam(theStream, par, "[smoothEdgeMethod]","Method for treating edge pixels", par.getSmoothEdgeMethod()); |
---|
| 1136 | recordParam(theStream, par, "[spatialSmoothCutoff]","Cutoff value for determining kernel", par.getSpatialSmoothCutoff()); |
---|
[378] | 1137 | } |
---|
[348] | 1138 | } |
---|
[1137] | 1139 | recordParam(theStream, par, "[flagATrous]", "Using A Trous reconstruction?", stringize(par.getFlagATrous())); |
---|
[378] | 1140 | if(par.getFlagATrous()){ |
---|
[1137] | 1141 | recordParam(theStream, par, "[reconDim]", "Number of dimensions in reconstruction", par.getReconDim()); |
---|
[378] | 1142 | if(par.getMaxScale()>0){ |
---|
[1137] | 1143 | recordParam(theStream, par, "[scaleMin-scaleMax]", "Scales used in reconstruction", par.getMinScale()<<"-"<<par.getMaxScale()); |
---|
[378] | 1144 | } |
---|
| 1145 | else{ |
---|
[1137] | 1146 | recordParam(theStream, par, "[scaleMin]", "Minimum scale in reconstruction", par.getMinScale()); |
---|
[378] | 1147 | } |
---|
[1137] | 1148 | recordParam(theStream, par, "[snrRecon]", "SNR Threshold within reconstruction", par.getAtrousCut()); |
---|
| 1149 | recordParam(theStream, par, "[reconConvergence]", "Residual convergence criterion", par.getReconConvergence()); |
---|
| 1150 | recordParam(theStream, par, "[filterCode]", "Filter being used for reconstruction", par.getFilterCode()<<" ("<<par.getFilterName()<<")"); |
---|
[378] | 1151 | } |
---|
[1137] | 1152 | recordParam(theStream, par, "[flagRobustStats]", "Using Robust statistics?", stringize(par.getFlagRobustStats())); |
---|
[378] | 1153 | if(par.getFlagStatSec()){ |
---|
[1137] | 1154 | recordParam(theStream, par, "[statSec]", "Section used by statistics calculation", par.statSec.getSection()); |
---|
[189] | 1155 | } |
---|
[1137] | 1156 | recordParam(theStream, par, "[flagFDR]", "Using FDR analysis?", stringize(par.getFlagFDR())); |
---|
[378] | 1157 | if(par.getFlagFDR()){ |
---|
[1137] | 1158 | recordParam(theStream, par, "[alphaFDR]", "Alpha value for FDR analysis", par.getAlpha()); |
---|
| 1159 | recordParam(theStream, par, "[FDRnumCorChan]", "Number of correlated channels for FDR", par.getFDRnumCorChan()); |
---|
[378] | 1160 | } |
---|
| 1161 | else { |
---|
| 1162 | if(par.getFlagUserThreshold()){ |
---|
[1137] | 1163 | recordParam(theStream, par, "[threshold]", "Detection Threshold", par.getThreshold()); |
---|
[378] | 1164 | } |
---|
| 1165 | else{ |
---|
[1137] | 1166 | recordParam(theStream, par, "[snrCut]", "SNR Threshold (in sigma)", par.getCut()); |
---|
[378] | 1167 | } |
---|
[189] | 1168 | } |
---|
[1137] | 1169 | recordParam(theStream, par, "[minPix]", "Minimum # Pixels in a detection", par.getMinPix()); |
---|
| 1170 | recordParam(theStream, par, "[minChannels]", "Minimum # Channels in a detection", par.getMinChannels()); |
---|
| 1171 | recordParam(theStream, par, "[minVoxels]", "Minimum # Voxels in a detection", par.getMinVoxels()); |
---|
[1261] | 1172 | if(par.getMaxPix()>0) recordParam(theStream, par, "[maxPix]", "Maximum # Pixels in a detection", par.getMaxPix()); |
---|
| 1173 | if(par.getMaxChannels()>0) recordParam(theStream, par, "[maxChannels]", "Maximum # Channels in a detection", par.getMaxChannels()); |
---|
| 1174 | if(par.getMaxVoxels()>0) recordParam(theStream, par, "[maxVoxels]", "Maximum # Voxels in a detection", par.getMaxVoxels()); |
---|
[1137] | 1175 | recordParam(theStream, par, "[flagGrowth]", "Growing objects after detection?", stringize(par.getFlagGrowth())); |
---|
[378] | 1176 | if(par.getFlagGrowth()) { |
---|
[503] | 1177 | if(par.getFlagUserGrowthThreshold()){ |
---|
[1137] | 1178 | recordParam(theStream, par, "[growthThreshold]", "Threshold for growth", par.getGrowthThreshold()); |
---|
[503] | 1179 | } |
---|
| 1180 | else{ |
---|
[1137] | 1181 | recordParam(theStream, par, "[growthCut]", "SNR Threshold for growth", par.getGrowthCut()); |
---|
[503] | 1182 | } |
---|
[378] | 1183 | } |
---|
[1137] | 1184 | recordParam(theStream, par, "[flagAdjacent]", "Using Adjacent-pixel criterion?", stringize(par.getFlagAdjacent())); |
---|
[378] | 1185 | if(!par.getFlagAdjacent()){ |
---|
[1137] | 1186 | recordParam(theStream, par, "[threshSpatial]", "Max. spatial separation for merging", par.getThreshS()); |
---|
[378] | 1187 | } |
---|
[1137] | 1188 | recordParam(theStream, par, "[threshVelocity]", "Max. velocity separation for merging", par.getThreshV()); |
---|
| 1189 | recordParam(theStream, par, "[flagRejectBeforeMerge]", "Reject objects before merging?", stringize(par.getFlagRejectBeforeMerge())); |
---|
| 1190 | recordParam(theStream, par, "[flagTwoStageMerging]", "Merge objects in two stages?", stringize(par.getFlagTwoStageMerging())); |
---|
| 1191 | recordParam(theStream, par, "[spectralMethod]", "Method of spectral plotting", par.getSpectralMethod()); |
---|
| 1192 | recordParam(theStream, par, "[pixelCentre]", "Type of object centre used in results", par.getPixelCentre()); |
---|
[664] | 1193 | |
---|
[1137] | 1194 | theStream << par.commentString() <<"--------------------\n"; |
---|
[378] | 1195 | theStream << std::setfill(' '); |
---|
| 1196 | theStream.unsetf(std::ios::left); |
---|
| 1197 | // theStream.unsetf(std::ios::boolalpha); |
---|
| 1198 | return theStream; |
---|
[3] | 1199 | } |
---|
| 1200 | |
---|
[916] | 1201 | std::vector<VOParam> Param::getVOParams() |
---|
| 1202 | { |
---|
| 1203 | std::vector<VOParam> vopars; |
---|
| 1204 | vopars.push_back(VOParam("imageFile","meta.file;meta.fits","char",this->imageFile,this->imageFile.size(),"")); |
---|
[958] | 1205 | vopars.push_back(VOParam("flagSubsection","meta.code","boolean",this->flagSubsection,0,"")); |
---|
[916] | 1206 | if(this->flagSubsection) |
---|
| 1207 | vopars.push_back(VOParam("subsection","","char",this->pixelSec.getSection(),this->pixelSec.getSection().size(),"")); |
---|
[958] | 1208 | vopars.push_back(VOParam("flagStatSec","meta.code","boolean",this->flagStatSec,0,"")); |
---|
[916] | 1209 | if(this->flagSubsection) |
---|
| 1210 | vopars.push_back(VOParam("StatSec","","char",this->statSec.getSection(),this->statSec.getSection().size(),"")); |
---|
| 1211 | if(this->flagReconExists) |
---|
| 1212 | vopars.push_back(VOParam("reconfile","meta.file;meta.fits","char",this->reconFile, this->reconFile.size(),"")); |
---|
| 1213 | if(this->flagSmoothExists) |
---|
| 1214 | vopars.push_back(VOParam("smoothfile","meta.file;meta.fits","char",this->smoothFile, this->smoothFile.size(),"")); |
---|
| 1215 | if(this->usePrevious) |
---|
| 1216 | vopars.push_back(VOParam("objectlist","","char",this->objectList,this->objectList.size(),"")); |
---|
[120] | 1217 | |
---|
[916] | 1218 | vopars.push_back(VOParam("searchType","meta.note","char",this->searchType,this->searchType.size(),"")); |
---|
[958] | 1219 | vopars.push_back(VOParam("flagNegative","meta.code","boolean",this->flagNegative,0,"")); |
---|
| 1220 | vopars.push_back(VOParam("flagBaseline","meta.code","boolean",this->flagBaseline,0,"")); |
---|
[1260] | 1221 | if(this->flagBaseline){ |
---|
| 1222 | vopars.push_back(VOParam("baselineType","meta.note","char",this->baselineType,this->baselineType.size(),"")); |
---|
| 1223 | if(this->baselineType=="median") |
---|
| 1224 | vopars.push_back(VOParam("baselineBoxWidth","","int",this->baselineBoxWidth,0,"")); |
---|
| 1225 | } |
---|
[958] | 1226 | vopars.push_back(VOParam("flagRobustStats","meta.code","boolean",this->flagRobustStats,0,"")); |
---|
| 1227 | vopars.push_back(VOParam("flagFDR","meta.code","boolean",this->flagFDR,0,"")); |
---|
[916] | 1228 | if(this->flagFDR){ |
---|
| 1229 | vopars.push_back(VOParam("alphaFDR","stat.param","float",this->alphaFDR,0,"")); |
---|
| 1230 | vopars.push_back(VOParam("FDRnumCorChan","stat.param","int",this->FDRnumCorChan,0,"")); |
---|
| 1231 | } |
---|
| 1232 | else{ |
---|
| 1233 | if(this->flagUserThreshold) |
---|
| 1234 | vopars.push_back(VOParam("threshold","phot.flux;stat.min","float",this->threshold,0,"")); |
---|
| 1235 | else |
---|
| 1236 | vopars.push_back(VOParam("snrCut","stat.snr;phot;stat.min","float",this->snrCut,0,"")); |
---|
| 1237 | } |
---|
[958] | 1238 | vopars.push_back(VOParam("flagGrowth","meta.code","boolean",this->flagGrowth,0,"")); |
---|
[916] | 1239 | if(this->flagGrowth){ |
---|
| 1240 | if(this->flagUserGrowthThreshold) |
---|
| 1241 | vopars.push_back(VOParam("growthThreshold","phot.flux;stat.min","float",this->growthThreshold,0,"")); |
---|
| 1242 | else |
---|
| 1243 | vopars.push_back(VOParam("growthCut","stat.snr;phot;stat.min","float",this->growthCut,0,"")); |
---|
| 1244 | } |
---|
[1261] | 1245 | vopars.push_back(VOParam("minPix","","int",this->minPix,0,"")); |
---|
| 1246 | vopars.push_back(VOParam("minChannels","","int",this->minChannels,0,"")); |
---|
| 1247 | vopars.push_back(VOParam("minVoxels","","int",this->minVoxels,0,"")); |
---|
| 1248 | if(this->maxPix>0) vopars.push_back(VOParam("maxPix","","int",this->maxPix,0,"")); |
---|
| 1249 | if(this->maxChannels>0) vopars.push_back(VOParam("maxChannels","","int",this->maxChannels,0,"")); |
---|
| 1250 | if(this->maxVoxels>0) vopars.push_back(VOParam("maxVoxels","","int",this->maxVoxels,0,"")); |
---|
[958] | 1251 | vopars.push_back(VOParam("flagAdjacent","meta.code","boolean",this->flagAdjacent,0,"")); |
---|
[916] | 1252 | if(!this->flagAdjacent) |
---|
| 1253 | vopars.push_back(VOParam("threshSpatial","","float",this->threshSpatial,0,"")); |
---|
[1145] | 1254 | vopars.push_back(VOParam("threshVelocity","","float",this->threshVelocity,0,"")); |
---|
[958] | 1255 | vopars.push_back(VOParam("flagRejectBeforeMerge","","boolean",this->flagRejectBeforeMerge,0,"")); |
---|
| 1256 | vopars.push_back(VOParam("flagTwoStageMerging","","boolean",this->flagTwoStageMerging,0,"")); |
---|
[916] | 1257 | vopars.push_back(VOParam("pixelCentre","","char",this->pixelCentre,this->pixelCentre.size(),"")); |
---|
[958] | 1258 | vopars.push_back(VOParam("flagSmooth","meta.code","boolean",this->flagSmooth,0,"")); |
---|
[916] | 1259 | if(this->flagSmooth){ |
---|
| 1260 | vopars.push_back(VOParam("smoothType","","char",this->smoothType,this->smoothType.size(),"")); |
---|
| 1261 | if(this->smoothType=="spectral") |
---|
| 1262 | vopars.push_back(VOParam("hanningWidth","","int",this->hanningWidth,0,"")); |
---|
| 1263 | else{ |
---|
| 1264 | vopars.push_back(VOParam("kernMaj","","float",this->kernMaj,0,"")); |
---|
| 1265 | vopars.push_back(VOParam("kernMin","","float",this->kernMin,0,"")); |
---|
| 1266 | vopars.push_back(VOParam("kernPA","","float",this->kernPA,0,"")); |
---|
[1279] | 1267 | vopars.push_back(VOParam("smoothEdgeMethod","","char",this->smoothEdgeMethod,this->smoothEdgeMethod.size(),"")); |
---|
| 1268 | vopars.push_back(VOParam("spatialSmoothCutoff","","float", this->spatialSmoothCutoff,0,"")); |
---|
[916] | 1269 | } |
---|
| 1270 | } |
---|
[958] | 1271 | vopars.push_back(VOParam("flagATrous","meta.code","boolean",this->flagATrous,0,"")); |
---|
[916] | 1272 | if(this->flagATrous){ |
---|
| 1273 | vopars.push_back(VOParam("reconDim","","int",this->reconDim,0,"")); |
---|
| 1274 | vopars.push_back(VOParam("scaleMin","","int",this->scaleMin,0,"")); |
---|
| 1275 | if(this->scaleMax>0) |
---|
| 1276 | vopars.push_back(VOParam("scaleMax","","int",this->scaleMax,0,"")); |
---|
| 1277 | vopars.push_back(VOParam("snrRecon","","float",this->snrRecon,0,"")); |
---|
[1026] | 1278 | vopars.push_back(VOParam("reconConvergence","","float",this->reconConvergence,0,"")); |
---|
[916] | 1279 | vopars.push_back(VOParam("filterCode","","int",this->filterCode,0,"")); |
---|
| 1280 | } |
---|
| 1281 | if(this->beamAsUsed.origin()==PARAM){ |
---|
| 1282 | if(this->fwhmBeam>0) |
---|
| 1283 | vopars.push_back(VOParam("beamFWHM","","float",this->fwhmBeam,0,"")); |
---|
| 1284 | else |
---|
| 1285 | vopars.push_back(VOParam("beamArea","","float",this->areaBeam,0,"")); |
---|
| 1286 | } |
---|
[948] | 1287 | if(this->restFrequencyUsed){ |
---|
| 1288 | vopars.push_back(VOParam("restFrequency","em.freq","float",this->restFrequency,0,"Hz")); |
---|
| 1289 | } |
---|
[916] | 1290 | |
---|
| 1291 | return vopars; |
---|
| 1292 | |
---|
| 1293 | } |
---|
| 1294 | |
---|
[1145] | 1295 | void Param::writeToBinaryFile(std::string &filename) |
---|
| 1296 | { |
---|
| 1297 | std::ofstream outfile(filename.c_str(), std::ios::out | std::ios::binary | std::ios::app); |
---|
| 1298 | writeStringToBinaryFile(outfile,this->imageFile); |
---|
| 1299 | outfile.write(reinterpret_cast<const char*>(&this->flagSubsection), sizeof this->flagSubsection); |
---|
| 1300 | if(this->flagSubsection) writeStringToBinaryFile(outfile,this->pixelSec.getSection()); |
---|
| 1301 | outfile.write(reinterpret_cast<const char*>(&this->flagStatSec), sizeof this->flagStatSec); |
---|
| 1302 | if(this->flagStatSec) writeStringToBinaryFile(outfile,this->statSec.getSection()); |
---|
| 1303 | outfile.write(reinterpret_cast<const char*>(&this->flagReconExists), sizeof this->flagReconExists); |
---|
| 1304 | if(this->flagReconExists) writeStringToBinaryFile(outfile,this->reconFile); |
---|
| 1305 | outfile.write(reinterpret_cast<const char*>(&this->flagSmoothExists), sizeof this->flagSmoothExists); |
---|
| 1306 | if(this->flagSmoothExists) writeStringToBinaryFile(outfile,this->smoothFile); |
---|
| 1307 | // |
---|
| 1308 | writeStringToBinaryFile(outfile,this->searchType); |
---|
| 1309 | outfile.write(reinterpret_cast<const char*>(&this->flagNegative), sizeof this->flagNegative); |
---|
| 1310 | outfile.write(reinterpret_cast<const char*>(&this->flagBaseline), sizeof this->flagBaseline); |
---|
[1260] | 1311 | if(this->flagBaseline){ |
---|
| 1312 | writeStringToBinaryFile(outfile,this->baselineType); |
---|
| 1313 | if(this->baselineType=="median") |
---|
| 1314 | outfile.write(reinterpret_cast<const char*>(&this->baselineBoxWidth), sizeof this->baselineBoxWidth); |
---|
| 1315 | } |
---|
[1145] | 1316 | outfile.write(reinterpret_cast<const char*>(&this->flagRobustStats), sizeof this->flagRobustStats); |
---|
| 1317 | outfile.write(reinterpret_cast<const char*>(&this->flagFDR), sizeof this->flagFDR); |
---|
| 1318 | if(this->flagFDR){ |
---|
| 1319 | outfile.write(reinterpret_cast<const char*>(&this->alphaFDR), sizeof this->alphaFDR); |
---|
| 1320 | outfile.write(reinterpret_cast<const char*>(&this->FDRnumCorChan), sizeof this->FDRnumCorChan); |
---|
[1345] | 1321 | bool beamFromParam=(this->beamAsUsed.origin() == PARAM); |
---|
| 1322 | outfile.write(reinterpret_cast<const char*>(&beamFromParam), sizeof beamFromParam); |
---|
| 1323 | if(beamFromParam){ |
---|
[1145] | 1324 | outfile.write(reinterpret_cast<const char*>(&this->fwhmBeam), sizeof this->fwhmBeam); |
---|
| 1325 | outfile.write(reinterpret_cast<const char*>(&this->areaBeam), sizeof this->areaBeam); |
---|
| 1326 | } |
---|
| 1327 | } |
---|
| 1328 | else{ |
---|
| 1329 | outfile.write(reinterpret_cast<const char*>(&this->flagUserThreshold), sizeof this->flagUserThreshold); |
---|
| 1330 | if(this->flagUserThreshold) |
---|
| 1331 | outfile.write(reinterpret_cast<const char*>(&this->threshold), sizeof this->threshold); |
---|
| 1332 | else |
---|
| 1333 | outfile.write(reinterpret_cast<const char*>(&this->snrCut), sizeof this->snrCut); |
---|
| 1334 | } |
---|
| 1335 | outfile.write(reinterpret_cast<const char*>(&this->flagGrowth), sizeof this->flagGrowth); |
---|
| 1336 | if(this->flagGrowth){ |
---|
[1345] | 1337 | outfile.write(reinterpret_cast<const char*>(&this->flagUserGrowthThreshold), sizeof this->flagUserGrowthThreshold); |
---|
[1145] | 1338 | if(this->flagUserGrowthThreshold) |
---|
| 1339 | outfile.write(reinterpret_cast<const char*>(&this->growthThreshold), sizeof this->growthThreshold); |
---|
| 1340 | else |
---|
| 1341 | outfile.write(reinterpret_cast<const char*>(&this->growthCut), sizeof this->growthCut); |
---|
| 1342 | } |
---|
| 1343 | outfile.write(reinterpret_cast<const char*>(&this->minPix), sizeof this->minPix); |
---|
| 1344 | outfile.write(reinterpret_cast<const char*>(&this->minChannels), sizeof this->minChannels); |
---|
[1261] | 1345 | outfile.write(reinterpret_cast<const char*>(&this->minVoxels), sizeof this->minVoxels); |
---|
| 1346 | outfile.write(reinterpret_cast<const char*>(&this->maxPix), sizeof this->maxPix); |
---|
| 1347 | outfile.write(reinterpret_cast<const char*>(&this->maxChannels), sizeof this->maxChannels); |
---|
| 1348 | outfile.write(reinterpret_cast<const char*>(&this->maxVoxels), sizeof this->maxVoxels); |
---|
[1145] | 1349 | outfile.write(reinterpret_cast<const char*>(&this->flagAdjacent), sizeof this->flagAdjacent); |
---|
| 1350 | if(!this->flagAdjacent) |
---|
| 1351 | outfile.write(reinterpret_cast<const char*>(&this->threshSpatial), sizeof this->threshSpatial); |
---|
| 1352 | outfile.write(reinterpret_cast<const char*>(&this->threshVelocity), sizeof this->threshVelocity); |
---|
| 1353 | outfile.write(reinterpret_cast<const char*>(&this->flagRejectBeforeMerge), sizeof this->flagRejectBeforeMerge); |
---|
| 1354 | outfile.write(reinterpret_cast<const char*>(&this->flagTwoStageMerging), sizeof this->flagTwoStageMerging); |
---|
| 1355 | outfile.write(reinterpret_cast<const char*>(&this->flagSmooth), sizeof this->flagSmooth); |
---|
| 1356 | if(this->flagSmooth){ |
---|
| 1357 | bool type=(this->smoothType=="spectral"); |
---|
| 1358 | outfile.write(reinterpret_cast<const char*>(&type), sizeof type); |
---|
| 1359 | if(type) |
---|
| 1360 | outfile.write(reinterpret_cast<const char*>(&this->hanningWidth), sizeof this->hanningWidth); |
---|
| 1361 | else{ |
---|
| 1362 | outfile.write(reinterpret_cast<const char*>(&this->kernMaj), sizeof this->kernMaj); |
---|
| 1363 | outfile.write(reinterpret_cast<const char*>(&this->kernMin), sizeof this->kernMin); |
---|
| 1364 | outfile.write(reinterpret_cast<const char*>(&this->kernPA), sizeof this->kernPA); |
---|
[1279] | 1365 | outfile.write(reinterpret_cast<const char*>(&this->smoothEdgeMethod), sizeof this->smoothEdgeMethod); |
---|
| 1366 | outfile.write(reinterpret_cast<const char*>(&this->spatialSmoothCutoff), sizeof this->spatialSmoothCutoff); |
---|
[1145] | 1367 | } |
---|
| 1368 | } |
---|
| 1369 | outfile.write(reinterpret_cast<const char*>(&this->flagATrous), sizeof this->flagATrous); |
---|
| 1370 | if(this->flagATrous){ |
---|
| 1371 | outfile.write(reinterpret_cast<const char*>(&this->reconDim), sizeof this->reconDim); |
---|
| 1372 | outfile.write(reinterpret_cast<const char*>(&this->scaleMin), sizeof this->scaleMin); |
---|
| 1373 | outfile.write(reinterpret_cast<const char*>(&this->scaleMax), sizeof this->scaleMax); |
---|
| 1374 | outfile.write(reinterpret_cast<const char*>(&this->snrRecon), sizeof this->snrRecon); |
---|
| 1375 | outfile.write(reinterpret_cast<const char*>(&this->reconConvergence), sizeof this->reconConvergence); |
---|
| 1376 | outfile.write(reinterpret_cast<const char*>(&this->filterCode), sizeof this->filterCode); |
---|
| 1377 | } |
---|
[1242] | 1378 | writeStringToBinaryFile(outfile,this->flaggedChannelList); |
---|
| 1379 | |
---|
[1145] | 1380 | outfile.close(); |
---|
| 1381 | } |
---|
| 1382 | |
---|
[1146] | 1383 | std::streampos Param::readFromBinaryFile(std::string &filename, std::streampos loc) |
---|
[1145] | 1384 | { |
---|
[1146] | 1385 | std::ifstream infile(filename.c_str(), std::ios::in | std::ios::binary); |
---|
| 1386 | if(!infile.is_open()){ |
---|
| 1387 | DUCHAMPERROR("read binary parameters","Could not open binary catalogue \""<<filename <<"\""); |
---|
| 1388 | return -1; |
---|
| 1389 | } |
---|
| 1390 | infile.seekg(loc); |
---|
[1145] | 1391 | this->imageFile = readStringFromBinaryFile(infile); |
---|
| 1392 | infile.read(reinterpret_cast<char*>(&this->flagSubsection), sizeof this->flagSubsection); |
---|
| 1393 | if(this->flagSubsection){ |
---|
| 1394 | std::string sec=readStringFromBinaryFile(infile); |
---|
| 1395 | this->pixelSec.setSection(sec); |
---|
| 1396 | } |
---|
| 1397 | infile.read(reinterpret_cast<char*>(&this->flagStatSec), sizeof this->flagStatSec); |
---|
| 1398 | if(this->flagStatSec){ |
---|
| 1399 | std::string sec=readStringFromBinaryFile(infile); |
---|
| 1400 | this->statSec.setSection(sec); |
---|
| 1401 | } |
---|
| 1402 | infile.read(reinterpret_cast<char*>(&this->flagReconExists), sizeof this->flagReconExists); |
---|
| 1403 | if(this->flagReconExists) this->reconFile=readStringFromBinaryFile(infile); |
---|
| 1404 | infile.read(reinterpret_cast<char*>(&this->flagSmoothExists), sizeof this->flagSmoothExists); |
---|
| 1405 | if(this->flagSmoothExists) this->smoothFile=readStringFromBinaryFile(infile); |
---|
| 1406 | // |
---|
| 1407 | this->searchType=readStringFromBinaryFile(infile); |
---|
| 1408 | infile.read(reinterpret_cast<char*>(&this->flagNegative), sizeof this->flagNegative); |
---|
| 1409 | infile.read(reinterpret_cast<char*>(&this->flagBaseline), sizeof this->flagBaseline); |
---|
[1260] | 1410 | if(this->flagBaseline){ |
---|
| 1411 | this->baselineType = readStringFromBinaryFile(infile); |
---|
| 1412 | if(this->baselineType == "median") |
---|
| 1413 | infile.read(reinterpret_cast<char*>(&this->baselineBoxWidth), sizeof this->baselineBoxWidth); |
---|
| 1414 | } |
---|
[1145] | 1415 | infile.read(reinterpret_cast<char*>(&this->flagRobustStats), sizeof this->flagRobustStats); |
---|
| 1416 | infile.read(reinterpret_cast<char*>(&this->flagFDR), sizeof this->flagFDR); |
---|
| 1417 | if(this->flagFDR){ |
---|
| 1418 | infile.read(reinterpret_cast<char*>(&this->alphaFDR), sizeof this->alphaFDR); |
---|
| 1419 | infile.read(reinterpret_cast<char*>(&this->FDRnumCorChan), sizeof this->FDRnumCorChan); |
---|
[1345] | 1420 | bool beamFromParam; |
---|
| 1421 | infile.read(reinterpret_cast<char*>(&beamFromParam), sizeof beamFromParam); |
---|
| 1422 | if(beamFromParam){ |
---|
[1145] | 1423 | infile.read(reinterpret_cast<char*>(&this->fwhmBeam), sizeof this->fwhmBeam); |
---|
| 1424 | infile.read(reinterpret_cast<char*>(&this->areaBeam), sizeof this->areaBeam); |
---|
| 1425 | } |
---|
| 1426 | } |
---|
| 1427 | else{ |
---|
| 1428 | infile.read(reinterpret_cast<char*>(&this->flagUserThreshold), sizeof this->flagUserThreshold); |
---|
| 1429 | if(this->flagUserThreshold) |
---|
| 1430 | infile.read(reinterpret_cast<char*>(&this->threshold), sizeof this->threshold); |
---|
| 1431 | else |
---|
| 1432 | infile.read(reinterpret_cast<char*>(&this->snrCut), sizeof this->snrCut); |
---|
| 1433 | } |
---|
| 1434 | infile.read(reinterpret_cast<char*>(&this->flagGrowth), sizeof this->flagGrowth); |
---|
| 1435 | if(this->flagGrowth){ |
---|
[1345] | 1436 | infile.read(reinterpret_cast<char*>(&this->flagUserGrowthThreshold), sizeof this->flagUserGrowthThreshold); |
---|
[1145] | 1437 | if(this->flagUserGrowthThreshold) |
---|
| 1438 | infile.read(reinterpret_cast<char*>(&this->growthThreshold), sizeof this->growthThreshold); |
---|
| 1439 | else |
---|
| 1440 | infile.read(reinterpret_cast<char*>(&this->growthCut), sizeof this->growthCut); |
---|
| 1441 | } |
---|
| 1442 | infile.read(reinterpret_cast<char*>(&this->minPix), sizeof this->minPix); |
---|
| 1443 | infile.read(reinterpret_cast<char*>(&this->minChannels), sizeof this->minChannels); |
---|
[1261] | 1444 | infile.read(reinterpret_cast<char*>(&this->minVoxels), sizeof this->minVoxels); |
---|
| 1445 | infile.read(reinterpret_cast<char*>(&this->maxPix), sizeof this->maxPix); |
---|
| 1446 | infile.read(reinterpret_cast<char*>(&this->maxChannels), sizeof this->maxChannels); |
---|
| 1447 | infile.read(reinterpret_cast<char*>(&this->maxVoxels), sizeof this->maxVoxels); |
---|
[1145] | 1448 | infile.read(reinterpret_cast<char*>(&this->flagAdjacent), sizeof this->flagAdjacent); |
---|
| 1449 | if(!this->flagAdjacent) |
---|
| 1450 | infile.read(reinterpret_cast<char*>(&this->threshSpatial), sizeof this->threshSpatial); |
---|
| 1451 | infile.read(reinterpret_cast<char*>(&this->threshVelocity), sizeof this->threshVelocity); |
---|
| 1452 | infile.read(reinterpret_cast<char*>(&this->flagRejectBeforeMerge), sizeof this->flagRejectBeforeMerge); |
---|
| 1453 | infile.read(reinterpret_cast<char*>(&this->flagTwoStageMerging), sizeof this->flagTwoStageMerging); |
---|
| 1454 | infile.read(reinterpret_cast<char*>(&this->flagSmooth), sizeof this->flagSmooth); |
---|
| 1455 | if(this->flagSmooth){ |
---|
| 1456 | bool type; |
---|
| 1457 | infile.read(reinterpret_cast<char*>(&type), sizeof type); |
---|
| 1458 | this->smoothType = type ? "spectral" : "spatial"; |
---|
| 1459 | if(type) |
---|
| 1460 | infile.read(reinterpret_cast<char*>(&this->hanningWidth), sizeof this->hanningWidth); |
---|
| 1461 | else{ |
---|
| 1462 | infile.read(reinterpret_cast<char*>(&this->kernMaj), sizeof this->kernMaj); |
---|
| 1463 | infile.read(reinterpret_cast<char*>(&this->kernMin), sizeof this->kernMin); |
---|
| 1464 | infile.read(reinterpret_cast<char*>(&this->kernPA), sizeof this->kernPA); |
---|
[1279] | 1465 | infile.read(reinterpret_cast<char*>(&this->smoothEdgeMethod), sizeof this->smoothEdgeMethod); |
---|
| 1466 | infile.read(reinterpret_cast<char*>(&this->spatialSmoothCutoff), sizeof this->spatialSmoothCutoff); |
---|
[1145] | 1467 | } |
---|
| 1468 | } |
---|
| 1469 | infile.read(reinterpret_cast<char*>(&this->flagATrous), sizeof this->flagATrous); |
---|
| 1470 | if(this->flagATrous){ |
---|
| 1471 | infile.read(reinterpret_cast<char*>(&this->reconDim), sizeof this->reconDim); |
---|
| 1472 | infile.read(reinterpret_cast<char*>(&this->scaleMin), sizeof this->scaleMin); |
---|
| 1473 | infile.read(reinterpret_cast<char*>(&this->scaleMax), sizeof this->scaleMax); |
---|
| 1474 | infile.read(reinterpret_cast<char*>(&this->snrRecon), sizeof this->snrRecon); |
---|
| 1475 | infile.read(reinterpret_cast<char*>(&this->reconConvergence), sizeof this->reconConvergence); |
---|
| 1476 | infile.read(reinterpret_cast<char*>(&this->filterCode), sizeof this->filterCode); |
---|
| 1477 | } |
---|
[1242] | 1478 | this->flaggedChannelList=readStringFromBinaryFile(infile); |
---|
| 1479 | |
---|
[1146] | 1480 | std::streampos newloc = infile.tellg(); |
---|
[1145] | 1481 | infile.close(); |
---|
[1146] | 1482 | return newloc; |
---|
[1145] | 1483 | |
---|
| 1484 | } |
---|
| 1485 | |
---|
| 1486 | |
---|
| 1487 | |
---|
| 1488 | |
---|
[378] | 1489 | void Param::copyHeaderInfo(FitsHeader &head) |
---|
| 1490 | { |
---|
[528] | 1491 | /// A function to copy across relevant header keywords from the |
---|
| 1492 | /// FitsHeader class to the Param class, as they are needed by |
---|
| 1493 | /// functions in the Param class. |
---|
| 1494 | /// The parameters are the keywords BLANK, BSCALE, BZERO, and the beam size. |
---|
[112] | 1495 | |
---|
[378] | 1496 | this->blankKeyword = head.getBlankKeyword(); |
---|
| 1497 | this->bscaleKeyword = head.getBscaleKeyword(); |
---|
| 1498 | this->bzeroKeyword = head.getBzeroKeyword(); |
---|
| 1499 | this->blankPixValue = this->blankKeyword * this->bscaleKeyword + |
---|
| 1500 | this->bzeroKeyword; |
---|
| 1501 | } |
---|
[112] | 1502 | |
---|
[1364] | 1503 | std::string Param::inputWithoutExtension() |
---|
| 1504 | { |
---|
| 1505 | /// This function takes the input filename and returns a string |
---|
| 1506 | /// that doesn't have its .fits extension. It will also remove a |
---|
| 1507 | /// .fits.gz extension. If no such extension exists, then the full |
---|
| 1508 | /// filename is returned. |
---|
| 1509 | |
---|
| 1510 | std::string inputName = this->imageFile; |
---|
| 1511 | std::string outputName; |
---|
| 1512 | size_t size=inputName.size(); |
---|
| 1513 | if(size>5 && inputName.substr(size-5,5)==".fits") |
---|
| 1514 | outputName = inputName.substr(0,size-5); |
---|
| 1515 | else if(size>8 && inputName.substr(size-8,8)==".fits.gz") |
---|
| 1516 | outputName = inputName.substr(0,size-8); |
---|
| 1517 | else |
---|
| 1518 | outputName = inputName; |
---|
| 1519 | return outputName; |
---|
| 1520 | } |
---|
| 1521 | |
---|
[379] | 1522 | std::string Param::outputMaskFile() |
---|
| 1523 | { |
---|
[528] | 1524 | /// This function produces the required filename in which to save |
---|
| 1525 | /// the mask image, indicating which pixels have been detected as |
---|
| 1526 | /// part of an object. If the input image is image.fits, then the |
---|
| 1527 | /// output will be image.MASK.fits. |
---|
| 1528 | |
---|
[525] | 1529 | if(this->fileOutputMask==""){ |
---|
[1364] | 1530 | std::string outputName = this->inputWithoutExtension(); |
---|
[1092] | 1531 | outputName += ".MASK.fits"; |
---|
| 1532 | return outputName; |
---|
[525] | 1533 | } |
---|
| 1534 | else return this->fileOutputMask; |
---|
[379] | 1535 | } |
---|
| 1536 | |
---|
[670] | 1537 | std::string Param::outputMomentMapFile() |
---|
| 1538 | { |
---|
| 1539 | /// This function produces the required filename in which to save |
---|
| 1540 | /// the moment-0 FITS image. If the input image is image.fits, then the |
---|
| 1541 | /// output will be image.MOM0.fits. |
---|
| 1542 | |
---|
| 1543 | if(this->fileOutputMomentMap==""){ |
---|
[1364] | 1544 | std::string outputName = this->inputWithoutExtension(); |
---|
[1092] | 1545 | outputName += ".MOM0.fits"; |
---|
| 1546 | return outputName; |
---|
[670] | 1547 | } |
---|
| 1548 | else return this->fileOutputMomentMap; |
---|
| 1549 | } |
---|
| 1550 | |
---|
[1142] | 1551 | std::string Param::outputMomentMaskFile() |
---|
| 1552 | { |
---|
| 1553 | /// This function produces the required filename in which to save |
---|
| 1554 | /// the moment-0 FITS image. If the input image is image.fits, then the |
---|
| 1555 | /// output will be image.MOM0.fits. |
---|
| 1556 | |
---|
| 1557 | if(this->fileOutputMomentMask==""){ |
---|
[1364] | 1558 | std::string outputName = this->inputWithoutExtension(); |
---|
[1142] | 1559 | outputName += ".MOM0MASK.fits"; |
---|
| 1560 | return outputName; |
---|
| 1561 | } |
---|
| 1562 | else return this->fileOutputMomentMask; |
---|
| 1563 | } |
---|
| 1564 | |
---|
[1120] | 1565 | std::string Param::outputBaselineFile() |
---|
| 1566 | { |
---|
| 1567 | /// This function produces the required filename in which to save |
---|
| 1568 | /// the baseline FITS image. If the input image is image.fits, then the |
---|
| 1569 | /// output will be image.BASE.fits. |
---|
| 1570 | |
---|
[1121] | 1571 | if(this->fileOutputBaseline==""){ |
---|
[1364] | 1572 | std::string outputName = this->inputWithoutExtension(); |
---|
[1120] | 1573 | outputName += ".BASE.fits"; |
---|
| 1574 | return outputName; |
---|
| 1575 | } |
---|
[1121] | 1576 | else return this->fileOutputBaseline; |
---|
[1120] | 1577 | } |
---|
| 1578 | |
---|
[378] | 1579 | std::string Param::outputSmoothFile() |
---|
| 1580 | { |
---|
[528] | 1581 | /// This function produces the required filename in which to save |
---|
| 1582 | /// the smoothed array. If the input image is image.fits, then |
---|
| 1583 | /// the output will be: |
---|
| 1584 | /// <ul><li> Spectral smoothing: image.SMOOTH-1D-3.fits, where the |
---|
| 1585 | /// width of the Hanning filter was 3 pixels. |
---|
[1279] | 1586 | /// <li> Spatial smoothing : image.SMOOTH-2D-3-2-20-E-10.fits, where |
---|
| 1587 | /// kernMaj=3, kernMin=2 and kernPA=20 degrees, EQUAL edge method, and cutoff of 1.e-10. |
---|
[528] | 1588 | /// </ul> |
---|
| 1589 | |
---|
[525] | 1590 | if(this->fileOutputSmooth==""){ |
---|
| 1591 | std::stringstream ss; |
---|
[1364] | 1592 | ss << this->inputWithoutExtension(); |
---|
[525] | 1593 | if(this->flagSubsection) ss<<".sub"; |
---|
| 1594 | if(this->smoothType=="spectral") |
---|
| 1595 | ss << ".SMOOTH-1D-" << this->hanningWidth << ".fits"; |
---|
[1279] | 1596 | else if(this->smoothType=="spatial"){ |
---|
| 1597 | char method='X'; |
---|
| 1598 | if(this->smoothEdgeMethod=="equal") method='E'; |
---|
| 1599 | else if (this->smoothEdgeMethod=="truncate") method='T'; |
---|
| 1600 | else if (this->smoothEdgeMethod=="scale") method='S'; |
---|
| 1601 | ss << ".SMOOTH-2D-" |
---|
| 1602 | << this->kernMaj << "-" |
---|
| 1603 | << this->kernMin << "-" |
---|
| 1604 | << this->kernPA << "-" |
---|
| 1605 | << method << "-" |
---|
| 1606 | << -log10(this->spatialSmoothCutoff) |
---|
| 1607 | << ".fits"; |
---|
| 1608 | } |
---|
[525] | 1609 | return ss.str(); |
---|
| 1610 | } |
---|
| 1611 | else return this->fileOutputSmooth; |
---|
[378] | 1612 | } |
---|
[208] | 1613 | |
---|
[378] | 1614 | std::string Param::outputReconFile() |
---|
| 1615 | { |
---|
[528] | 1616 | /// This function produces the required filename in which to save |
---|
| 1617 | /// the reconstructed array. If the input image is image.fits, then |
---|
| 1618 | /// the output will be eg. image.RECON-3-2-4-1.fits, where the numbers are |
---|
| 1619 | /// 3=reconDim, 2=filterCode, 4=snrRecon, 1=minScale |
---|
| 1620 | |
---|
[525] | 1621 | if(this->fileOutputRecon==""){ |
---|
| 1622 | std::stringstream ss; |
---|
[1364] | 1623 | ss << this->inputWithoutExtension(); |
---|
[525] | 1624 | if(this->flagSubsection) ss<<".sub"; |
---|
| 1625 | ss << ".RECON-" << this->reconDim |
---|
| 1626 | << "-" << this->filterCode |
---|
| 1627 | << "-" << this->snrRecon |
---|
| 1628 | << "-" << this->scaleMin |
---|
[1027] | 1629 | << "-" << this->scaleMax |
---|
[1026] | 1630 | << "-" << this->reconConvergence |
---|
[525] | 1631 | << ".fits"; |
---|
| 1632 | return ss.str(); |
---|
| 1633 | } |
---|
| 1634 | else return this->fileOutputRecon; |
---|
[378] | 1635 | } |
---|
[103] | 1636 | |
---|
[378] | 1637 | std::string Param::outputResidFile() |
---|
| 1638 | { |
---|
[528] | 1639 | /// This function produces the required filename in which to save |
---|
| 1640 | /// the reconstructed array. If the input image is image.fits, then |
---|
| 1641 | /// the output will be eg. image.RESID-3-2-4-1.fits, where the numbers are |
---|
| 1642 | /// 3=reconDim, 2=filterCode, 4=snrRecon, 1=scaleMin |
---|
| 1643 | |
---|
[525] | 1644 | if(this->fileOutputResid==""){ |
---|
| 1645 | std::stringstream ss; |
---|
[1364] | 1646 | ss << this->inputWithoutExtension(); |
---|
[525] | 1647 | if(this->flagSubsection) ss<<".sub"; |
---|
| 1648 | ss << ".RESID-" << this->reconDim |
---|
| 1649 | << "-" << this->filterCode |
---|
| 1650 | << "-" << this->snrRecon |
---|
| 1651 | << "-" << this->scaleMin |
---|
[1027] | 1652 | << "-" << this->scaleMax |
---|
[1026] | 1653 | << "-" << this->reconConvergence |
---|
[525] | 1654 | << ".fits"; |
---|
| 1655 | return ss.str(); |
---|
| 1656 | } |
---|
| 1657 | else return this->fileOutputResid; |
---|
[378] | 1658 | } |
---|
| 1659 | |
---|
[103] | 1660 | } |
---|