[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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| 43 | #include <duchamp/Utils/utils.hh> |
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| 44 | #include <duchamp/Utils/Section.hh> |
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[438] | 45 | #include <duchamp/Detection/columns.hh> |
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[3] | 46 | |
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[378] | 47 | namespace duchamp |
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[309] | 48 | { |
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[882] | 49 | const std::string defaultSection = "[*,*,*]"; |
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[309] | 50 | |
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[378] | 51 | /****************************************************************/ |
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| 52 | /////////////////////////////////////////////////// |
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| 53 | //// Accessor Functions for Parameter class: |
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| 54 | /////////////////////////////////////////////////// |
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| 55 | Param::~Param() |
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| 56 | { |
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[528] | 57 | /// Deletes the offsets array if the sizeOffsets parameter is |
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| 58 | /// positive. |
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[378] | 59 | if(this->sizeOffsets>0) delete [] this->offsets; |
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| 60 | } |
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[309] | 61 | |
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[378] | 62 | Param::Param() |
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| 63 | { |
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| 64 | this->defaultValues(); |
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| 65 | } |
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[3] | 66 | |
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[378] | 67 | void Param::defaultValues() |
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| 68 | { |
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[528] | 69 | /// Provides default intial values for the parameters. Note that |
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| 70 | /// imageFile has no default value! |
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| 71 | |
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[378] | 72 | // Input files |
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| 73 | this->imageFile = ""; |
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| 74 | this->flagSubsection = false; |
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[882] | 75 | this->pixelSec.setSection(defaultSection); |
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[378] | 76 | this->flagReconExists = false; |
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| 77 | this->reconFile = ""; |
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| 78 | this->flagSmoothExists = false; |
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| 79 | this->smoothFile = ""; |
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[475] | 80 | this->usePrevious = false; |
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| 81 | this->objectList = ""; |
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[378] | 82 | // Output files |
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| 83 | this->flagLog = false; |
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| 84 | this->logFile = "duchamp-Logfile.txt"; |
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| 85 | this->outFile = "duchamp-Results.txt"; |
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| 86 | this->flagSeparateHeader= false; |
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| 87 | this->headerFile = "duchamp-Results.hdr"; |
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[831] | 88 | this->flagPlotSpectra = true; |
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[378] | 89 | this->spectraFile = "duchamp-Spectra.ps"; |
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[424] | 90 | this->flagTextSpectra = false; |
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| 91 | this->spectraTextFile = "duchamp-Spectra.txt"; |
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[670] | 92 | this->flagOutputMomentMap = false; |
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| 93 | this->fileOutputMomentMap = ""; |
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[379] | 94 | this->flagOutputMask = false; |
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[525] | 95 | this->fileOutputMask = ""; |
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[521] | 96 | this->flagMaskWithObjectNum = false; |
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[378] | 97 | this->flagOutputSmooth = false; |
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[525] | 98 | this->fileOutputSmooth = ""; |
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[378] | 99 | this->flagOutputRecon = false; |
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[525] | 100 | this->fileOutputRecon = ""; |
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[378] | 101 | this->flagOutputResid = false; |
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[525] | 102 | this->fileOutputResid = ""; |
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[378] | 103 | this->flagVOT = false; |
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| 104 | this->votFile = "duchamp-Results.xml"; |
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| 105 | this->flagKarma = false; |
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| 106 | this->karmaFile = "duchamp-Results.ann"; |
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[446] | 107 | this->annotationType = "borders"; |
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[378] | 108 | this->flagMaps = true; |
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| 109 | this->detectionMap = "duchamp-DetectionMap.ps"; |
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| 110 | this->momentMap = "duchamp-MomentMap.ps"; |
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| 111 | this->flagXOutput = true; |
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[439] | 112 | this->precFlux = Column::prFLUX; |
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| 113 | this->precVel = Column::prVEL; |
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| 114 | this->precSNR = Column::prSNR; |
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[378] | 115 | // Cube related parameters |
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[845] | 116 | this->flagBlankPix = false; |
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[378] | 117 | this->blankPixValue = -8.00061; |
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| 118 | this->blankKeyword = 1; |
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| 119 | this->bscaleKeyword = -8.00061; |
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| 120 | this->bzeroKeyword = 0.; |
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[434] | 121 | this->newFluxUnits = ""; |
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[378] | 122 | // Milky-Way parameters |
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| 123 | this->flagMW = false; |
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| 124 | this->maxMW = 112; |
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| 125 | this->minMW = 75; |
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[788] | 126 | this->areaBeam = 0.; |
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| 127 | this->fwhmBeam = 0.; |
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[791] | 128 | this->beamAsUsed.empty(); |
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[686] | 129 | this->searchType = "spatial"; |
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[378] | 130 | // Trim-related |
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| 131 | this->flagTrim = false; |
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| 132 | this->hasBeenTrimmed = false; |
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| 133 | this->borderLeft = 0; |
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| 134 | this->borderRight = 0; |
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| 135 | this->borderBottom = 0; |
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| 136 | this->borderTop = 0; |
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| 137 | // Subsection offsets |
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| 138 | this->sizeOffsets = 0; |
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| 139 | this->xSubOffset = 0; |
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| 140 | this->ySubOffset = 0; |
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| 141 | this->zSubOffset = 0; |
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| 142 | // Baseline related |
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| 143 | this->flagBaseline = false; |
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| 144 | // Detection-related |
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| 145 | this->flagNegative = false; |
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| 146 | // Object growth |
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| 147 | this->flagGrowth = false; |
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[458] | 148 | this->growthCut = 3.; |
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[461] | 149 | this->flagUserGrowthThreshold = false; |
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| 150 | this->growthThreshold = 0.; |
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[378] | 151 | // FDR analysis |
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| 152 | this->flagFDR = false; |
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| 153 | this->alphaFDR = 0.01; |
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[543] | 154 | this->FDRnumCorChan = 2; |
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[378] | 155 | // Other detection |
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| 156 | this->flagStatSec = false; |
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[882] | 157 | this->statSec.setSection(defaultSection); |
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[385] | 158 | this->flagRobustStats = true; |
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[378] | 159 | this->snrCut = 3.; |
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| 160 | this->threshold = 0.; |
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| 161 | this->flagUserThreshold = false; |
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| 162 | // Smoothing |
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| 163 | this->flagSmooth = false; |
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| 164 | this->smoothType = "spectral"; |
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| 165 | this->hanningWidth = 5; |
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| 166 | this->kernMaj = 3.; |
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| 167 | this->kernMin = -1.; |
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| 168 | this->kernPA = 0.; |
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| 169 | // A trous reconstruction parameters |
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| 170 | this->flagATrous = false; |
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| 171 | this->reconDim = 1; |
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| 172 | this->scaleMin = 1; |
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| 173 | this->scaleMax = 0; |
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| 174 | this->snrRecon = 4.; |
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| 175 | this->filterCode = 1; |
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| 176 | this->reconFilter.define(this->filterCode); |
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| 177 | // Volume-merging parameters |
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| 178 | this->flagAdjacent = true; |
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| 179 | this->threshSpatial = 3.; |
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| 180 | this->threshVelocity = 7.; |
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| 181 | this->minChannels = 3; |
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| 182 | this->minPix = 2; |
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[720] | 183 | this->minVoxels = 4; |
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[672] | 184 | this->flagRejectBeforeMerge = false; |
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[691] | 185 | this->flagTwoStageMerging = true; |
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[378] | 186 | // Input-Output related |
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| 187 | this->spectralMethod = "peak"; |
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| 188 | this->spectralUnits = "km/s"; |
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| 189 | this->pixelCentre = "centroid"; |
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[571] | 190 | this->sortingParam = "vel"; |
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[378] | 191 | this->borders = true; |
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| 192 | this->blankEdge = true; |
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| 193 | this->verbose = true; |
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[419] | 194 | } |
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[204] | 195 | |
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[378] | 196 | Param::Param (const Param& p) |
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| 197 | { |
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| 198 | operator=(p); |
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[309] | 199 | } |
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[137] | 200 | |
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[378] | 201 | Param& Param::operator= (const Param& p) |
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| 202 | { |
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| 203 | if(this == &p) return *this; |
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| 204 | this->imageFile = p.imageFile; |
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| 205 | this->flagSubsection = p.flagSubsection; |
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| 206 | this->pixelSec = p.pixelSec; |
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| 207 | this->flagReconExists = p.flagReconExists; |
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| 208 | this->reconFile = p.reconFile; |
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| 209 | this->flagSmoothExists = p.flagSmoothExists; |
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[475] | 210 | this->smoothFile = p.smoothFile; |
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| 211 | this->usePrevious = p.usePrevious; |
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| 212 | this->objectList = p.objectList; |
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[378] | 213 | this->flagLog = p.flagLog; |
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| 214 | this->logFile = p.logFile; |
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| 215 | this->outFile = p.outFile; |
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| 216 | this->flagSeparateHeader= p.flagSeparateHeader; |
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| 217 | this->headerFile = p.headerFile; |
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[882] | 218 | this->flagPlotSpectra = p.flagPlotSpectra; |
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[378] | 219 | this->spectraFile = p.spectraFile; |
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[424] | 220 | this->flagTextSpectra = p.flagTextSpectra; |
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| 221 | this->spectraTextFile = p.spectraTextFile; |
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[670] | 222 | this->flagOutputMomentMap = p.flagOutputMomentMap; |
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| 223 | this->fileOutputMomentMap = p.fileOutputMomentMap; |
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[379] | 224 | this->flagOutputMask = p.flagOutputMask; |
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[525] | 225 | this->fileOutputMask = p.fileOutputMask; |
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[521] | 226 | this->flagMaskWithObjectNum = p.flagMaskWithObjectNum; |
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[378] | 227 | this->flagOutputSmooth = p.flagOutputSmooth; |
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[525] | 228 | this->fileOutputSmooth = p.fileOutputSmooth; |
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[378] | 229 | this->flagOutputRecon = p.flagOutputRecon; |
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[525] | 230 | this->fileOutputRecon = p.fileOutputRecon; |
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[378] | 231 | this->flagOutputResid = p.flagOutputResid; |
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[525] | 232 | this->fileOutputResid = p.fileOutputResid; |
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[378] | 233 | this->flagVOT = p.flagVOT; |
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| 234 | this->votFile = p.votFile; |
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| 235 | this->flagKarma = p.flagKarma; |
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| 236 | this->karmaFile = p.karmaFile; |
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[446] | 237 | this->annotationType = p.annotationType; |
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[378] | 238 | this->flagMaps = p.flagMaps; |
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| 239 | this->detectionMap = p.detectionMap; |
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| 240 | this->momentMap = p.momentMap; |
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| 241 | this->flagXOutput = p.flagXOutput; |
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[438] | 242 | this->precFlux = p.precFlux; |
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| 243 | this->precVel = p.precVel; |
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| 244 | this->precSNR = p.precSNR; |
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[882] | 245 | this->flagNegative = p.flagNegative; |
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[378] | 246 | this->flagBlankPix = p.flagBlankPix; |
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| 247 | this->blankPixValue = p.blankPixValue; |
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| 248 | this->blankKeyword = p.blankKeyword; |
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| 249 | this->bscaleKeyword = p.bscaleKeyword; |
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| 250 | this->bzeroKeyword = p.bzeroKeyword; |
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[434] | 251 | this->newFluxUnits = p.newFluxUnits; |
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[378] | 252 | this->flagMW = p.flagMW; |
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| 253 | this->maxMW = p.maxMW; |
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| 254 | this->minMW = p.minMW; |
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[662] | 255 | this->areaBeam = p.areaBeam; |
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| 256 | this->fwhmBeam = p.fwhmBeam; |
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[791] | 257 | this->beamAsUsed = p.beamAsUsed; |
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[686] | 258 | this->searchType = p.searchType; |
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[378] | 259 | this->flagTrim = p.flagTrim; |
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| 260 | this->hasBeenTrimmed = p.hasBeenTrimmed; |
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| 261 | this->borderLeft = p.borderLeft; |
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| 262 | this->borderRight = p.borderRight; |
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| 263 | this->borderBottom = p.borderBottom; |
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| 264 | this->borderTop = p.borderTop; |
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| 265 | if(this->sizeOffsets>0) delete [] this->offsets; |
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| 266 | this->sizeOffsets = p.sizeOffsets; |
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| 267 | if(this->sizeOffsets>0){ |
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| 268 | this->offsets = new long[this->sizeOffsets]; |
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| 269 | for(int i=0;i<this->sizeOffsets;i++) this->offsets[i] = p.offsets[i]; |
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| 270 | } |
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| 271 | this->xSubOffset = p.xSubOffset; |
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| 272 | this->ySubOffset = p.ySubOffset; |
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| 273 | this->zSubOffset = p.zSubOffset; |
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| 274 | this->flagBaseline = p.flagBaseline; |
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| 275 | this->flagGrowth = p.flagGrowth; |
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| 276 | this->growthCut = p.growthCut; |
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[503] | 277 | this->growthThreshold = p.growthThreshold; |
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| 278 | this->flagUserGrowthThreshold = p.flagUserGrowthThreshold; |
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[378] | 279 | this->flagFDR = p.flagFDR; |
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| 280 | this->alphaFDR = p.alphaFDR; |
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[543] | 281 | this->FDRnumCorChan = p.FDRnumCorChan; |
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[378] | 282 | this->flagStatSec = p.flagStatSec; |
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[385] | 283 | this->statSec = p.statSec; |
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| 284 | this->flagRobustStats = p.flagRobustStats; |
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[378] | 285 | this->snrCut = p.snrCut; |
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| 286 | this->threshold = p.threshold; |
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| 287 | this->flagUserThreshold = p.flagUserThreshold; |
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| 288 | this->flagSmooth = p.flagSmooth; |
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| 289 | this->smoothType = p.smoothType; |
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| 290 | this->hanningWidth = p.hanningWidth; |
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| 291 | this->kernMaj = p.kernMaj; |
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| 292 | this->kernMin = p.kernMin; |
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| 293 | this->kernPA = p.kernPA; |
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| 294 | this->flagATrous = p.flagATrous; |
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| 295 | this->reconDim = p.reconDim; |
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| 296 | this->scaleMin = p.scaleMin; |
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| 297 | this->scaleMax = p.scaleMax; |
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| 298 | this->snrRecon = p.snrRecon; |
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| 299 | this->filterCode = p.filterCode; |
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| 300 | this->reconFilter = p.reconFilter; |
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| 301 | this->flagAdjacent = p.flagAdjacent; |
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| 302 | this->threshSpatial = p.threshSpatial; |
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| 303 | this->threshVelocity = p.threshVelocity; |
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| 304 | this->minChannels = p.minChannels; |
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| 305 | this->minPix = p.minPix; |
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[720] | 306 | this->minVoxels = p.minVoxels; |
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[691] | 307 | this->flagRejectBeforeMerge = p.flagRejectBeforeMerge; |
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| 308 | this->flagTwoStageMerging = p.flagTwoStageMerging; |
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[378] | 309 | this->spectralMethod = p.spectralMethod; |
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| 310 | this->spectralUnits = p.spectralUnits; |
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| 311 | this->pixelCentre = p.pixelCentre; |
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[571] | 312 | this->sortingParam = p.sortingParam; |
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[378] | 313 | this->borders = p.borders; |
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[571] | 314 | this->blankEdge = p.blankEdge; |
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[378] | 315 | this->verbose = p.verbose; |
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| 316 | return *this; |
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| 317 | } |
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| 318 | //-------------------------------------------------------------------- |
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[266] | 319 | |
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[698] | 320 | OUTCOME Param::getopts(int argc, char ** argv, std::string progname) |
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[378] | 321 | { |
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[528] | 322 | /// A function that reads in the command-line options, in a manner |
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| 323 | /// tailored for use with the main Duchamp program. |
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| 324 | /// |
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| 325 | /// \param argc The number of command line arguments. |
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| 326 | /// \param argv The array of command line arguments. |
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[378] | 327 | |
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[698] | 328 | OUTCOME returnValue = FAILURE; |
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[378] | 329 | if(argc==1){ |
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[474] | 330 | if(progname=="Selavy") std::cout << SELAVY_ERR_USAGE_MSG; |
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| 331 | else if(progname=="Duchamp") std::cout << ERR_USAGE_MSG; |
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| 332 | else std::cout << ERR_USAGE_MSG; |
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[378] | 333 | returnValue = FAILURE; |
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| 334 | } |
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| 335 | else { |
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| 336 | std::string file; |
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| 337 | bool changeX = false; |
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| 338 | this->defaultValues(); |
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| 339 | char c; |
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| 340 | while( ( c = getopt(argc,argv,"p:f:hvx") )!=-1){ |
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| 341 | switch(c) { |
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| 342 | case 'p': |
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| 343 | file = optarg; |
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| 344 | if(this->readParams(file)==FAILURE){ |
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| 345 | std::stringstream errmsg; |
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| 346 | errmsg << "Could not open parameter file " << file << ".\n"; |
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[474] | 347 | duchampError(progname,errmsg.str()); |
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[378] | 348 | } |
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| 349 | else returnValue = SUCCESS; |
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| 350 | break; |
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| 351 | case 'f': |
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| 352 | file = optarg; |
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| 353 | this->imageFile = file; |
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| 354 | returnValue = SUCCESS; |
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| 355 | break; |
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| 356 | case 'v': |
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| 357 | std::cout << PROGNAME << " version " << VERSION << std::endl; |
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| 358 | break; |
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| 359 | case 'x': |
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| 360 | changeX = true; |
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| 361 | break; |
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| 362 | case 'h': |
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| 363 | default : |
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[474] | 364 | if(progname=="Selavy") std::cout << SELAVY_ERR_USAGE_MSG; |
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| 365 | else if(progname=="Duchamp") std::cout << ERR_USAGE_MSG; |
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| 366 | else std::cout << ERR_USAGE_MSG; |
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[378] | 367 | break; |
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[266] | 368 | } |
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| 369 | } |
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[378] | 370 | if(changeX){ |
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| 371 | if(returnValue == SUCCESS) this->setFlagXOutput(false); |
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| 372 | else { |
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[474] | 373 | duchampError(progname, |
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[378] | 374 | "You need to specify either a parameter file or FITS image.\n"); |
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| 375 | std::cout << "\n" << ERR_USAGE_MSG; |
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| 376 | } |
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[294] | 377 | } |
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| 378 | } |
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[378] | 379 | return returnValue; |
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[266] | 380 | } |
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[378] | 381 | //-------------------------------------------------------------------- |
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[266] | 382 | |
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[378] | 383 | bool Param::isBlank(float &value) |
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| 384 | { |
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[528] | 385 | /// Tests whether the value passed as the argument is BLANK or not. |
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| 386 | /// \param value Pixel value to be tested. |
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| 387 | /// \return False if flagBlankPix is false. Else, compare to the |
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| 388 | /// relevant FITS keywords, using integer comparison. |
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| 389 | |
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[378] | 390 | return this->flagBlankPix && |
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| 391 | (this->blankKeyword == int((value-this->bzeroKeyword)/this->bscaleKeyword)); |
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[419] | 392 | } |
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[266] | 393 | |
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[378] | 394 | bool *Param::makeBlankMask(float *array, int size) |
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| 395 | { |
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[528] | 396 | /// This returns an array of bools, saying whether each pixel in the |
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| 397 | /// given array is BLANK or not. If the pixel is BLANK, set mask to |
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| 398 | /// false, else set to true. The array is allocated by the function. |
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| 399 | |
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[378] | 400 | bool *mask = new bool[size]; |
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| 401 | for(int i=0;i<size;i++) mask[i] = !this->isBlank(array[i]); |
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| 402 | return mask; |
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| 403 | } |
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[275] | 404 | |
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| 405 | |
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[506] | 406 | bool *Param::makeStatMask(float *array, long *dim) |
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| 407 | { |
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[528] | 408 | /// This returns an array of bools, saying whether each pixel in |
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| 409 | /// the given array is suitable for a stats calculation. It needs |
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| 410 | /// to be in the StatSec (if defined), not blank and not a MW |
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| 411 | /// channel. The array is allocated by the function with a 'new' call. |
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| 412 | |
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[506] | 413 | bool *mask = new bool[dim[0]*dim[1]*dim[2]]; |
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| 414 | for(int x=0;x<dim[0];x++) { |
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| 415 | for(int y=0;y<dim[1];y++) { |
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| 416 | for(int z=0;z<dim[2];z++) { |
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| 417 | int i = x+y*dim[0]+z*dim[0]*dim[1]; |
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| 418 | mask[i] = !this->isBlank(array[i]) && !this->isInMW(z) && this->isStatOK(x,y,z); |
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| 419 | } |
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| 420 | } |
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| 421 | } |
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| 422 | return mask; |
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| 423 | } |
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| 424 | |
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| 425 | |
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[378] | 426 | bool Param::isInMW(int z) |
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| 427 | { |
---|
[528] | 428 | /// Tests whether we are flagging Milky Way channels, and if so |
---|
| 429 | /// whether the given channel number is in the Milky Way range. The |
---|
| 430 | /// channels are assumed to start at number 0. |
---|
| 431 | /// \param z The channel number |
---|
| 432 | /// \return True if we are flagging Milky Way channels and z is in |
---|
| 433 | /// the range. |
---|
| 434 | |
---|
[673] | 435 | return ( this->flagMW && (z>=this->getMinMW()) && (z<=this->getMaxMW()) ); |
---|
[378] | 436 | } |
---|
[266] | 437 | |
---|
[378] | 438 | bool Param::isStatOK(int x, int y, int z) |
---|
| 439 | { |
---|
[528] | 440 | /// Test whether a given pixel position lies within the subsection |
---|
| 441 | /// given by the statSec parameter. Only tested if the flagSubsection |
---|
| 442 | /// parameter is true -- if it isn't, we just return true since all |
---|
| 443 | /// pixels are therefore available for statstical calculations. |
---|
| 444 | /// \param x X-value of pixel being tested. |
---|
| 445 | /// \param y Y-value of pixel being tested. |
---|
| 446 | /// \param z Z-value of pixel being tested. |
---|
| 447 | /// \return True if pixel is able to be used for statistical |
---|
| 448 | /// calculations. False otherwise. |
---|
| 449 | |
---|
[272] | 450 | int xval=x,yval=y,zval=z; |
---|
| 451 | if(flagSubsection){ |
---|
| 452 | xval += pixelSec.getStart(0); |
---|
| 453 | yval += pixelSec.getStart(1); |
---|
| 454 | zval += pixelSec.getStart(2); |
---|
| 455 | } |
---|
| 456 | return !flagStatSec || statSec.isInside(xval,yval,zval); |
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[419] | 457 | } |
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[266] | 458 | |
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[475] | 459 | std::vector<int> Param::getObjectRequest() |
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| 460 | { |
---|
[528] | 461 | /// Returns a list of the object numbers requested via the objectList parameter. |
---|
| 462 | /// \return a vector of integers, one for each number in the objectList set. |
---|
| 463 | |
---|
[475] | 464 | std::stringstream ss1; |
---|
| 465 | std::string tmp; |
---|
| 466 | std::vector<int> tmplist; |
---|
| 467 | ss1.str(this->objectList); |
---|
| 468 | while(!ss1.eof()){ |
---|
| 469 | getline(ss1,tmp,','); |
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[623] | 470 | for(size_t i=0;i<tmp.size();i++) if(tmp[i]=='-') tmp[i]=' '; |
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[475] | 471 | int a,b; |
---|
| 472 | std::stringstream ss2; |
---|
| 473 | ss2.str(tmp); |
---|
| 474 | ss2 >>a; |
---|
| 475 | if(!ss2.eof()) ss2 >> b; |
---|
| 476 | else b=a; |
---|
| 477 | for(int n=a;n<=b;n++){ |
---|
| 478 | tmplist.push_back(n); |
---|
| 479 | } |
---|
| 480 | } |
---|
| 481 | return tmplist; |
---|
| 482 | } |
---|
| 483 | |
---|
| 484 | std::vector<bool> Param::getObjectChoices() |
---|
| 485 | { |
---|
[528] | 486 | /// Returns a list of bool values, indicating whether a given |
---|
| 487 | /// object was requested or not. The size of the vector is |
---|
| 488 | /// determined by the maximum value in objectList. For instance, |
---|
| 489 | /// if objectList="2,3,5-8", then the returned vector will be |
---|
| 490 | /// [0,1,1,0,1,1,1,1]. |
---|
| 491 | /// \return Vector of bool values. |
---|
| 492 | |
---|
[475] | 493 | std::vector<int> objectChoices = this->getObjectRequest(); |
---|
| 494 | int maxNum = *std::max_element(objectChoices.begin(), objectChoices.end()); |
---|
| 495 | std::vector<bool> choices(maxNum,false); |
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[623] | 496 | for(std::vector<int>::iterator obj = objectChoices.begin();obj!=objectChoices.end();obj++) |
---|
| 497 | choices[*obj-1] = true; |
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[475] | 498 | return choices; |
---|
| 499 | } |
---|
| 500 | |
---|
| 501 | std::vector<bool> Param::getObjectChoices(int numObjects) |
---|
| 502 | { |
---|
[528] | 503 | /// Returns a list of bool values, indicating whether a given |
---|
| 504 | /// object was requested or not. The size of the vector is given |
---|
| 505 | /// by the numObjects parameter. So, if objectList="2,3,5-8", then |
---|
| 506 | /// the returned vector from a getObjectChoices(10) call will be |
---|
| 507 | /// [0,1,1,0,1,1,1,1,0,0]. |
---|
| 508 | /// \param numObjects How many objects there are in total. |
---|
| 509 | /// \return Vector of bool values. |
---|
| 510 | |
---|
[475] | 511 | if(this->objectList==""){ |
---|
| 512 | std::vector<bool> choices(numObjects,true); |
---|
| 513 | return choices; |
---|
| 514 | } |
---|
| 515 | else{ |
---|
| 516 | std::vector<int> objectChoices = this->getObjectRequest(); |
---|
| 517 | std::vector<bool> choices(numObjects,false); |
---|
[623] | 518 | for(std::vector<int>::iterator obj = objectChoices.begin();obj!=objectChoices.end();obj++) |
---|
| 519 | if(*obj<=numObjects) choices[*obj-1] = true; |
---|
[475] | 520 | return choices; |
---|
| 521 | } |
---|
| 522 | } |
---|
| 523 | |
---|
[378] | 524 | /****************************************************************/ |
---|
[528] | 525 | /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// |
---|
| 526 | /// / Other Functions using the Parameter class: |
---|
| 527 | /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// |
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[3] | 528 | |
---|
[698] | 529 | OUTCOME Param::readParams(std::string paramfile) |
---|
[378] | 530 | { |
---|
[528] | 531 | /// The parameters are read in from a disk file, on the assumption that each |
---|
| 532 | /// line of the file has the format "parameter value" (eg. alphafdr 0.1) |
---|
| 533 | /// |
---|
| 534 | /// The case of the parameter name does not matter, nor does the |
---|
| 535 | /// formatting of the spaces (it can be any amount of whitespace or |
---|
| 536 | /// tabs). |
---|
| 537 | /// |
---|
| 538 | /// \param paramfile A std::string containing the parameter filename. |
---|
| 539 | /// |
---|
| 540 | /// \return FAILURE if the parameter file does not exist. SUCCESS if |
---|
| 541 | /// it is able to read it. |
---|
| 542 | |
---|
[839] | 543 | if(!USE_PGPLOT){ |
---|
| 544 | // Change default values for these parameters when we don't use PGPlot |
---|
| 545 | this->flagXOutput = false; |
---|
| 546 | this->flagMaps = false; |
---|
| 547 | this->flagPlotSpectra = false; |
---|
| 548 | } |
---|
| 549 | |
---|
[378] | 550 | std::ifstream fin(paramfile.c_str()); |
---|
| 551 | if(!fin.is_open()) return FAILURE; |
---|
| 552 | std::string line; |
---|
| 553 | while( !std::getline(fin,line,'\n').eof()){ |
---|
[3] | 554 | |
---|
[378] | 555 | if(line[0]!='#'){ |
---|
| 556 | std::stringstream ss; |
---|
| 557 | ss.str(line); |
---|
| 558 | std::string arg; |
---|
| 559 | ss >> arg; |
---|
| 560 | arg = makelower(arg); |
---|
[733] | 561 | if(arg=="imagefile") this->imageFile = readFilename(ss); |
---|
[378] | 562 | if(arg=="flagsubsection") this->flagSubsection = readFlag(ss); |
---|
| 563 | if(arg=="subsection") this->pixelSec.setSection(readSval(ss)); |
---|
| 564 | if(arg=="flagreconexists") this->flagReconExists = readFlag(ss); |
---|
| 565 | if(arg=="reconfile") this->reconFile = readSval(ss); |
---|
| 566 | if(arg=="flagsmoothexists")this->flagSmoothExists = readFlag(ss); |
---|
| 567 | if(arg=="smoothfile") this->smoothFile = readSval(ss); |
---|
[839] | 568 | if(arg=="beamarea") this->areaBeam = readFval(ss); |
---|
| 569 | if(arg=="beamfwhm") this->fwhmBeam = readFval(ss); |
---|
[475] | 570 | if(arg=="useprevious") this->usePrevious = readFlag(ss); |
---|
| 571 | if(arg=="objectlist") this->objectList = readSval(ss); |
---|
[71] | 572 | |
---|
[378] | 573 | if(arg=="flaglog") this->flagLog = readFlag(ss); |
---|
| 574 | if(arg=="logfile") this->logFile = readSval(ss); |
---|
| 575 | if(arg=="outfile") this->outFile = readSval(ss); |
---|
| 576 | if(arg=="flagseparateheader") this->flagSeparateHeader = readFlag(ss); |
---|
[733] | 577 | if(arg=="headerfile") this->headerFile = readFilename(ss); |
---|
[831] | 578 | if(arg=="flagplotspectra") this->flagPlotSpectra = readFlag(ss); |
---|
[733] | 579 | if(arg=="spectrafile") this->spectraFile = readFilename(ss); |
---|
[424] | 580 | if(arg=="flagtextspectra") this->flagTextSpectra = readFlag(ss); |
---|
[733] | 581 | if(arg=="spectratextfile") this->spectraTextFile = readFilename(ss); |
---|
[670] | 582 | if(arg=="flagoutputmomentmap") this->flagOutputMomentMap = readFlag(ss); |
---|
[733] | 583 | if(arg=="fileoutputmomentmap") this->fileOutputMomentMap = readFilename(ss); |
---|
[379] | 584 | if(arg=="flagoutputmask") this->flagOutputMask = readFlag(ss); |
---|
[733] | 585 | if(arg=="fileoutputmask") this->fileOutputMask = readFilename(ss); |
---|
[521] | 586 | if(arg=="flagmaskwithobjectnum") this->flagMaskWithObjectNum = readFlag(ss); |
---|
[378] | 587 | if(arg=="flagoutputsmooth")this->flagOutputSmooth = readFlag(ss); |
---|
[733] | 588 | if(arg=="fileoutputsmooth")this->fileOutputSmooth = readFilename(ss); |
---|
[378] | 589 | if(arg=="flagoutputrecon") this->flagOutputRecon = readFlag(ss); |
---|
[733] | 590 | if(arg=="fileoutputrecon") this->fileOutputRecon = readFilename(ss); |
---|
[378] | 591 | if(arg=="flagoutputresid") this->flagOutputResid = readFlag(ss); |
---|
[733] | 592 | if(arg=="fileoutputresid") this->fileOutputResid = readFilename(ss); |
---|
[378] | 593 | if(arg=="flagvot") this->flagVOT = readFlag(ss); |
---|
[733] | 594 | if(arg=="votfile") this->votFile = readFilename(ss); |
---|
[378] | 595 | if(arg=="flagkarma") this->flagKarma = readFlag(ss); |
---|
[733] | 596 | if(arg=="karmafile") this->karmaFile = readFilename(ss); |
---|
[446] | 597 | if(arg=="annotationtype") this->annotationType = readSval(ss); |
---|
[378] | 598 | if(arg=="flagmaps") this->flagMaps = readFlag(ss); |
---|
[733] | 599 | if(arg=="detectionmap") this->detectionMap = readFilename(ss); |
---|
| 600 | if(arg=="momentmap") this->momentMap = readFilename(ss); |
---|
[378] | 601 | if(arg=="flagxoutput") this->flagXOutput = readFlag(ss); |
---|
[434] | 602 | if(arg=="newfluxunits") this->newFluxUnits = readSval(ss); |
---|
[438] | 603 | if(arg=="precflux") this->precFlux = readIval(ss); |
---|
| 604 | if(arg=="precvel") this->precVel = readIval(ss); |
---|
| 605 | if(arg=="precsnr") this->precSNR = readIval(ss); |
---|
[3] | 606 | |
---|
[378] | 607 | if(arg=="flagtrim") this->flagTrim = readFlag(ss); |
---|
| 608 | if(arg=="flagmw") this->flagMW = readFlag(ss); |
---|
| 609 | if(arg=="maxmw") this->maxMW = readIval(ss); |
---|
| 610 | if(arg=="minmw") this->minMW = readIval(ss); |
---|
[442] | 611 | if(arg=="flagbaseline") this->flagBaseline = readFlag(ss); |
---|
[691] | 612 | if(arg=="searchtype") this->searchType = readSval(ss); |
---|
[71] | 613 | |
---|
[442] | 614 | if(arg=="flagnegative") this->flagNegative = readFlag(ss); |
---|
[378] | 615 | if(arg=="minpix") this->minPix = readIval(ss); |
---|
| 616 | if(arg=="flaggrowth") this->flagGrowth = readFlag(ss); |
---|
| 617 | if(arg=="growthcut") this->growthCut = readFval(ss); |
---|
[461] | 618 | if(arg=="growththreshold"){ |
---|
| 619 | this->growthThreshold = readFval(ss); |
---|
| 620 | this->flagUserGrowthThreshold = true; |
---|
| 621 | } |
---|
[71] | 622 | |
---|
[378] | 623 | if(arg=="flagfdr") this->flagFDR = readFlag(ss); |
---|
| 624 | if(arg=="alphafdr") this->alphaFDR = readFval(ss); |
---|
[543] | 625 | if(arg=="fdrnumcorchan") this->FDRnumCorChan = readIval(ss); |
---|
[378] | 626 | if(arg=="flagstatsec") this->flagStatSec = readFlag(ss); |
---|
| 627 | if(arg=="statsec") this->statSec.setSection(readSval(ss)); |
---|
[385] | 628 | if(arg=="flagrobuststats") this->flagRobustStats = readFlag(ss); |
---|
[378] | 629 | if(arg=="snrcut") this->snrCut = readFval(ss); |
---|
| 630 | if(arg=="threshold"){ |
---|
| 631 | this->threshold = readFval(ss); |
---|
| 632 | this->flagUserThreshold = true; |
---|
| 633 | } |
---|
[201] | 634 | |
---|
[378] | 635 | if(arg=="flagsmooth") this->flagSmooth = readFlag(ss); |
---|
| 636 | if(arg=="smoothtype") this->smoothType = readSval(ss); |
---|
| 637 | if(arg=="hanningwidth") this->hanningWidth = readIval(ss); |
---|
| 638 | if(arg=="kernmaj") this->kernMaj = readFval(ss); |
---|
| 639 | if(arg=="kernmin") this->kernMin = readFval(ss); |
---|
| 640 | if(arg=="kernpa") this->kernPA = readFval(ss); |
---|
[103] | 641 | |
---|
[378] | 642 | if(arg=="flagatrous") this->flagATrous = readFlag(ss); |
---|
| 643 | if(arg=="recondim") this->reconDim = readIval(ss); |
---|
| 644 | if(arg=="scalemin") this->scaleMin = readIval(ss); |
---|
| 645 | if(arg=="scalemax") this->scaleMax = readIval(ss); |
---|
| 646 | if(arg=="snrrecon") this->snrRecon = readFval(ss); |
---|
| 647 | if(arg=="filtercode"){ |
---|
| 648 | this->filterCode = readIval(ss); |
---|
| 649 | this->reconFilter.define(this->filterCode); |
---|
| 650 | } |
---|
[71] | 651 | |
---|
[378] | 652 | if(arg=="flagadjacent") this->flagAdjacent = readFlag(ss); |
---|
| 653 | if(arg=="threshspatial") this->threshSpatial = readFval(ss); |
---|
| 654 | if(arg=="threshvelocity") this->threshVelocity = readFval(ss); |
---|
| 655 | if(arg=="minchannels") this->minChannels = readIval(ss); |
---|
[720] | 656 | if(arg=="minvoxels") this->minVoxels = readIval(ss); |
---|
[691] | 657 | if(arg=="flagrejectbeforemerge") this->flagRejectBeforeMerge = readFlag(ss); |
---|
| 658 | if(arg=="flagtwostagemerging") this->flagTwoStageMerging = readFlag(ss); |
---|
[71] | 659 | |
---|
[378] | 660 | if(arg=="spectralmethod") this->spectralMethod=makelower(readSval(ss)); |
---|
| 661 | if(arg=="spectralunits") this->spectralUnits = makelower(readSval(ss)); |
---|
| 662 | if(arg=="pixelcentre") this->pixelCentre = makelower(readSval(ss)); |
---|
[571] | 663 | if(arg=="sortingparam") this->sortingParam = makelower(readSval(ss)); |
---|
[378] | 664 | if(arg=="drawborders") this->borders = readFlag(ss); |
---|
| 665 | if(arg=="drawblankedges") this->blankEdge = readFlag(ss); |
---|
| 666 | if(arg=="verbose") this->verbose = readFlag(ss); |
---|
[295] | 667 | |
---|
[378] | 668 | // Dealing with deprecated parameters. |
---|
| 669 | if(arg=="flagblankpix"){ |
---|
| 670 | this->flagTrim = readFlag(ss); |
---|
| 671 | std::stringstream errmsg; |
---|
| 672 | errmsg <<"The parameter flagBlankPix is deprecated. " |
---|
| 673 | <<"Please use the flagTrim parameter in future.\n" |
---|
| 674 | <<"Setting flagTrim = " << stringize(this->flagTrim) << ".\n"; |
---|
| 675 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 676 | } |
---|
| 677 | if(arg=="blankpixvalue"){ |
---|
| 678 | std::stringstream errmsg; |
---|
| 679 | errmsg <<"The parameter blankPixValue is deprecated.\n" |
---|
| 680 | <<"This value is only taken from the FITS header.\n"; |
---|
| 681 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 682 | } |
---|
[662] | 683 | if(arg=="beamsize"){ |
---|
[675] | 684 | this->areaBeam = readFval(ss); |
---|
[662] | 685 | std::stringstream errmsg; |
---|
| 686 | errmsg <<"The parameter beamSize is deprecated.\n" |
---|
| 687 | <<"You can specify the beam size by beamArea or beamFWHM.\n" |
---|
[675] | 688 | <<"Setting beamArea = " << this->areaBeam << ".\n"; |
---|
[662] | 689 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 690 | } |
---|
[378] | 691 | |
---|
[295] | 692 | } |
---|
[378] | 693 | } |
---|
[295] | 694 | |
---|
[506] | 695 | this->checkPars(); |
---|
| 696 | |
---|
| 697 | return SUCCESS; |
---|
| 698 | |
---|
| 699 | } |
---|
| 700 | |
---|
| 701 | void Param::checkPars() |
---|
| 702 | { |
---|
| 703 | |
---|
[882] | 704 | // If flagSubsection is false, but the parset had a subsection string in it, we want to set this back to the default. |
---|
| 705 | if(!this->flagSubsection){ |
---|
| 706 | this->pixelSec.setSection(defaultSection); |
---|
| 707 | } |
---|
| 708 | if(!this->flagStatSec){ |
---|
| 709 | this->statSec.setSection(defaultSection); |
---|
| 710 | } |
---|
| 711 | |
---|
[475] | 712 | // If we have usePrevious=false, set the objectlist to blank so that we use all of them |
---|
| 713 | if(!this->usePrevious) this->objectList = ""; |
---|
| 714 | |
---|
[420] | 715 | // If pgplot was not included in the compilation, need to set flagXOutput to false |
---|
[831] | 716 | if(!USE_PGPLOT){ |
---|
| 717 | if(this->flagXOutput || this->flagMaps || this->flagPlotSpectra) |
---|
| 718 | duchampWarning("Reading parameters","PGPlot has not been enabled, so setting flagXOutput, flagMaps and flagPlotSpectra to false.\n"); |
---|
| 719 | this->flagXOutput = false; |
---|
| 720 | this->flagMaps = false; |
---|
| 721 | this->flagPlotSpectra = false; |
---|
| 722 | } |
---|
[420] | 723 | |
---|
[438] | 724 | // Correcting bad precision values -- if negative, set to 0 |
---|
| 725 | if(this->precFlux<0) this->precFlux = 0; |
---|
| 726 | if(this->precVel<0) this->precVel = 0; |
---|
| 727 | if(this->precSNR<0) this->precSNR = 0; |
---|
| 728 | |
---|
[686] | 729 | // Can only have "spatial" or "spectral" as search types |
---|
| 730 | if(this->searchType != "spatial" && this->searchType != "spectral"){ |
---|
| 731 | std::stringstream errmsg; |
---|
| 732 | errmsg << "You have requested a search type of \""<<this->searchType<<"\".\n" |
---|
| 733 | << "Only \"spectral\" and \"spatial\" are accepted. Setting to \"spatial\".\n"; |
---|
| 734 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 735 | this->searchType = "spatial"; |
---|
| 736 | } |
---|
| 737 | |
---|
[378] | 738 | // The wavelet reconstruction takes precendence over the smoothing. |
---|
| 739 | if(this->flagATrous) this->flagSmooth = false; |
---|
| 740 | |
---|
[461] | 741 | if(this->flagUserThreshold){ |
---|
| 742 | |
---|
| 743 | // If we specify a manual threshold, need to also specify a manual growth threshold |
---|
| 744 | // If we haven't done so, turn growing off |
---|
| 745 | if(this->flagGrowth && !this->flagUserGrowthThreshold){ |
---|
| 746 | std::stringstream errmsg; |
---|
| 747 | errmsg << "You have specified a manual search threshold, but not a manual growth threshold.\n" |
---|
| 748 | << "You need to do so using the \"growthThreshold\" parameter.\n" |
---|
| 749 | << "The growth function is being turned off.\n"; |
---|
| 750 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 751 | this->flagGrowth = false; |
---|
| 752 | } |
---|
| 753 | |
---|
| 754 | // If we specify a manual threshold, we don't need the FDR method, so turn it off if requested. |
---|
| 755 | if(this->flagFDR){ |
---|
| 756 | std::stringstream errmsg; |
---|
| 757 | errmsg << "You have specified a manual search threshold, so we don't need to use the FDR method.\n" |
---|
| 758 | << "Setting \"flagFDR=false\".\n"; |
---|
| 759 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 760 | this->flagFDR = false; |
---|
| 761 | } |
---|
| 762 | |
---|
| 763 | } |
---|
| 764 | |
---|
[537] | 765 | // Make sure the growth level is less than the detection level. Else turn off growing. |
---|
| 766 | if(this->flagGrowth){ |
---|
| 767 | std::stringstream errmsg; |
---|
| 768 | bool doWarn = false; |
---|
| 769 | if(this->flagUserThreshold && |
---|
| 770 | ( (this->threshold < this->growthThreshold) |
---|
| 771 | || (this->snrCut < this->growthCut) ) ){ |
---|
| 772 | errmsg << "Your \"growthThreshold\" parameter is larger than your \"threshold\".\n" |
---|
| 773 | << "The growth function is being turned off.\n"; |
---|
| 774 | doWarn = true; |
---|
| 775 | } |
---|
| 776 | |
---|
| 777 | if(!this->flagUserThreshold && |
---|
| 778 | (this->snrCut < this->growthCut)) { |
---|
| 779 | errmsg << "Your \"growthCut\" parameter is larger than your \"snrCut\".\n" |
---|
| 780 | << "The growth function is being turned off.\n"; |
---|
| 781 | doWarn = true; |
---|
| 782 | } |
---|
| 783 | |
---|
| 784 | if(doWarn) duchampWarning("Reading parameters",errmsg.str()); |
---|
| 785 | |
---|
| 786 | } |
---|
| 787 | |
---|
[446] | 788 | // Make sure the annnotationType is an acceptable option -- default is "borders" |
---|
| 789 | if((this->annotationType != "borders") && (this->annotationType!="circles")){ |
---|
| 790 | std::stringstream errmsg; |
---|
| 791 | errmsg << "The requested value of the parameter annotationType, \"" |
---|
[571] | 792 | << this->annotationType << "\", is invalid.\n" |
---|
[446] | 793 | << "Changing to \"borders\".\n"; |
---|
| 794 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 795 | this->annotationType = "borders"; |
---|
| 796 | } |
---|
| 797 | |
---|
[378] | 798 | // Make sure smoothType is an acceptable type -- default is "spectral" |
---|
| 799 | if((this->smoothType!="spectral")&& |
---|
| 800 | (this->smoothType!="spatial")){ |
---|
| 801 | std::stringstream errmsg; |
---|
| 802 | errmsg << "The requested value of the parameter smoothType, \"" |
---|
[571] | 803 | << this->smoothType << "\", is invalid.\n" |
---|
[378] | 804 | << "Changing to \"spectral\".\n"; |
---|
| 805 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 806 | this->smoothType = "spectral"; |
---|
[3] | 807 | } |
---|
[378] | 808 | // If kernMin has not been given, or is negative, make it equal to kernMaj |
---|
| 809 | if(this->kernMin < 0) this->kernMin = this->kernMaj; |
---|
[272] | 810 | |
---|
[378] | 811 | // Make sure spectralMethod is an acceptable type -- default is "peak" |
---|
| 812 | if((this->spectralMethod!="peak")&& |
---|
| 813 | (this->spectralMethod!="sum")){ |
---|
| 814 | std::stringstream errmsg; |
---|
| 815 | errmsg << "The requested value of the parameter spectralMethod, \"" |
---|
[571] | 816 | << this->spectralMethod << "\", is invalid.\n" |
---|
[378] | 817 | << "Changing to \"peak\".\n"; |
---|
| 818 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 819 | this->spectralMethod = "peak"; |
---|
| 820 | } |
---|
[232] | 821 | |
---|
[378] | 822 | // Make sure pixelCentre is an acceptable type -- default is "peak" |
---|
| 823 | if((this->pixelCentre!="centroid")&& |
---|
| 824 | (this->pixelCentre!="average") && |
---|
| 825 | (this->pixelCentre!="peak") ){ |
---|
| 826 | std::stringstream errmsg; |
---|
| 827 | errmsg << "The requested value of the parameter pixelCentre, \"" |
---|
[571] | 828 | << this->pixelCentre << "\", is invalid.\n" |
---|
[378] | 829 | << "Changing to \"centroid\".\n"; |
---|
| 830 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 831 | this->pixelCentre = "centroid"; |
---|
| 832 | } |
---|
[275] | 833 | |
---|
[571] | 834 | // Make sure sortingParam is an acceptable type -- default is "vel" |
---|
| 835 | bool OK = false; |
---|
| 836 | for(int i=0;i<numSortingParamOptions;i++) |
---|
| 837 | OK = OK || this->sortingParam==sortingParamOptions[i]; |
---|
| 838 | if(!OK){ |
---|
| 839 | std::stringstream errmsg; |
---|
| 840 | errmsg << "The requested value of the parameter sortingParam, \"" |
---|
| 841 | << this->sortingParam << "\", is invalid.\n" |
---|
| 842 | << "Changing to \"vel\".\n"; |
---|
| 843 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 844 | this->sortingParam = "vel"; |
---|
| 845 | } |
---|
| 846 | |
---|
[265] | 847 | } |
---|
| 848 | |
---|
[664] | 849 | void recordParameters(std::ostream& theStream, std::string paramName, std::string paramDesc, std::string paramValue) |
---|
| 850 | { |
---|
| 851 | |
---|
[716] | 852 | const int width = 56; |
---|
| 853 | int widthText = width - paramName.size(); |
---|
[265] | 854 | |
---|
[664] | 855 | theStream << std::setw(widthText) << paramDesc |
---|
[716] | 856 | << setiosflags(std::ios::right) << paramName |
---|
[664] | 857 | << " = " << resetiosflags(std::ios::right) << paramValue |
---|
| 858 | <<std::endl; |
---|
| 859 | } |
---|
| 860 | |
---|
| 861 | std::string fileOption(bool flag, std::string file) |
---|
| 862 | { |
---|
| 863 | std::ostringstream ss; |
---|
| 864 | ss << stringize(flag); |
---|
| 865 | if(flag) ss << " --> " << file; |
---|
| 866 | return ss.str(); |
---|
| 867 | |
---|
| 868 | } |
---|
| 869 | |
---|
[378] | 870 | std::ostream& operator<< ( std::ostream& theStream, Param& par) |
---|
| 871 | { |
---|
[528] | 872 | /// Print out the parameter set in a formatted, easy to read style. |
---|
| 873 | /// Lists the parameters, a description of them, and their value. |
---|
[3] | 874 | |
---|
[378] | 875 | // BUG -- can get error: `boolalpha' is not a member of type `ios' -- old compilers: gcc 2.95.3? |
---|
| 876 | // theStream.setf(std::ios::boolalpha); |
---|
| 877 | theStream.setf(std::ios::left); |
---|
| 878 | theStream <<"\n---- Parameters ----"<<std::endl; |
---|
| 879 | theStream << std::setfill('.'); |
---|
| 880 | if(par.getFlagSubsection()) |
---|
[664] | 881 | recordParam(theStream, "[imageFile]", "Image to be analysed", par.getImageFile()<<par.getSubsection()); |
---|
[378] | 882 | else |
---|
[664] | 883 | recordParam(theStream, "[imageFile]", "Image to be analysed", par.getImageFile()); |
---|
[378] | 884 | if(par.getFlagReconExists() && par.getFlagATrous()){ |
---|
[664] | 885 | recordParam(theStream, "[reconExists]", "Reconstructed array exists?", stringize(par.getFlagReconExists())); |
---|
| 886 | recordParam(theStream, "[reconFile]", "FITS file containing reconstruction", par.getReconFile()); |
---|
[378] | 887 | } |
---|
| 888 | if(par.getFlagSmoothExists() && par.getFlagSmooth()){ |
---|
[664] | 889 | recordParam(theStream, "[smoothExists]", "Smoothed array exists?", stringize(par.getFlagSmoothExists())); |
---|
| 890 | recordParam(theStream, "[smoothFile]", "FITS file containing smoothed array", par.getSmoothFile()); |
---|
[378] | 891 | } |
---|
[788] | 892 | recordParam(theStream, "[logFile]", "Intermediate Logfile", par.logFile); |
---|
[664] | 893 | recordParam(theStream, "[outFile]", "Final Results file", par.getOutFile()); |
---|
| 894 | if(par.getFlagSeparateHeader()){ |
---|
| 895 | recordParam(theStream, "[headerFile]", "Header for results file", par.getHeaderFile()); |
---|
| 896 | } |
---|
[831] | 897 | if(USE_PGPLOT && par.getFlagPlotSpectra()){ |
---|
| 898 | recordParam(theStream, "[spectraFile]", "Spectrum file", par.getSpectraFile()); |
---|
| 899 | } |
---|
[424] | 900 | if(par.getFlagTextSpectra()){ |
---|
[664] | 901 | recordParam(theStream, "[spectraTextFile]", "Text file with ascii spectral data", par.getSpectraTextFile()); |
---|
[424] | 902 | } |
---|
[378] | 903 | if(par.getFlagVOT()){ |
---|
[664] | 904 | recordParam(theStream, "[votFile]", "VOTable file", par.getVOTFile()); |
---|
[378] | 905 | } |
---|
| 906 | if(par.getFlagKarma()){ |
---|
[664] | 907 | recordParam(theStream, "[karmaFile]", "Karma annotation file" , par.getKarmaFile()); |
---|
[378] | 908 | } |
---|
[831] | 909 | if(USE_PGPLOT && par.getFlagMaps()){ |
---|
[664] | 910 | recordParam(theStream, "[momentMap]", "0th Moment Map", par.getMomentMap()); |
---|
| 911 | recordParam(theStream, "[detectionMap]", "Detection Map", par.getDetectionMap()); |
---|
[378] | 912 | } |
---|
[831] | 913 | if(USE_PGPLOT){ |
---|
| 914 | recordParam(theStream, "[flagXOutput]", "Display a map in a pgplot xwindow?", stringize(par.getFlagXOutput())); |
---|
| 915 | } |
---|
[664] | 916 | if(par.getFlagATrous()){ |
---|
| 917 | recordParam(theStream, "[flagOutputRecon]", "Saving reconstructed cube?", fileOption(par.getFlagOutputRecon(),par.outputReconFile())); |
---|
| 918 | recordParam(theStream, "[flagOutputResid]", "Saving residuals from reconstruction?", fileOption(par.getFlagOutputResid(),par.outputResidFile())); |
---|
[378] | 919 | } |
---|
[664] | 920 | if(par.getFlagSmooth()){ |
---|
| 921 | recordParam(theStream, "[flagOutputSmooth]", "Saving smoothed cube?", fileOption(par.getFlagOutputSmooth(),par.outputSmoothFile())); |
---|
[378] | 922 | } |
---|
[664] | 923 | recordParam(theStream, "[flagOutputMask]", "Saving mask cube?", fileOption(par.getFlagOutputMask(),par.outputMaskFile())); |
---|
[670] | 924 | recordParam(theStream, "[flagOutputMask]", "Saving 0th moment to FITS file?", fileOption(par.getFlagOutputMomentMap(),par.outputMomentMapFile())); |
---|
[664] | 925 | |
---|
[378] | 926 | theStream <<"------"<<std::endl; |
---|
[664] | 927 | |
---|
[686] | 928 | recordParam(theStream, "[searchType]", "Type of searching performed", par.getSearchType()); |
---|
[378] | 929 | if(par.getFlagBlankPix()){ |
---|
[664] | 930 | recordParam(theStream, "", "Blank Pixel Value", par.getBlankPixVal()); |
---|
[275] | 931 | } |
---|
[664] | 932 | recordParam(theStream, "[flagTrim]", "Trimming Blank Pixels?", stringize(par.getFlagTrim())); |
---|
| 933 | recordParam(theStream, "[flagNegative]", "Searching for Negative features?", stringize(par.getFlagNegative())); |
---|
| 934 | recordParam(theStream, "[flagMW]", "Removing Milky Way channels?", stringize(par.getFlagMW())); |
---|
[378] | 935 | if(par.getFlagMW()){ |
---|
[673] | 936 | // need to remove the offset correction, as we want to report the parameters actually entered |
---|
| 937 | recordParam(theStream, "[minMW - maxMW]", "Milky Way Channels", par.getMinMW()+par.getZOffset()<<"-"<<par.getMaxMW()+par.getZOffset()); |
---|
[348] | 938 | } |
---|
[791] | 939 | if(par.beamAsUsed.origin()==EMPTY){ // No beam in FITS file and no information provided |
---|
[788] | 940 | recordParam(theStream, "", "Area of Beam", "No beam"); |
---|
[675] | 941 | } |
---|
[791] | 942 | else if(par.beamAsUsed.origin()==HEADER){ // Report beam size from FITS file |
---|
[795] | 943 | recordParam(theStream, "", "Area of Beam (pixels)", par.beamAsUsed.area() << " (beam: " << par.beamAsUsed.maj() << " x " << par.beamAsUsed.min() <<" pixels)"); |
---|
[675] | 944 | } |
---|
[791] | 945 | else if(par.beamAsUsed.origin()==PARAM){ // Report beam size requested in parameter set input |
---|
[788] | 946 | if(par.fwhmBeam>0.) recordParam(theStream, "[beamFWHM]", "FWHM of Beam (pixels)", par.beamAsUsed.maj() << " (beam area = " << par.beamAsUsed.area() <<" pixels)"); |
---|
| 947 | else recordParam(theStream, "[beamArea]", "Area of Beam (pixels)", par.beamAsUsed.area()); |
---|
| 948 | } |
---|
| 949 | else{ |
---|
| 950 | duchampError("Parameter output","Unknown value for origin of beam"); |
---|
| 951 | } |
---|
[664] | 952 | recordParam(theStream, "[flagBaseline]", "Removing baselines before search?", stringize(par.getFlagBaseline())); |
---|
| 953 | recordParam(theStream, "[flagSmooth]", "Smoothing data prior to searching?", stringize(par.getFlagSmooth())); |
---|
[378] | 954 | if(par.getFlagSmooth()){ |
---|
[664] | 955 | recordParam(theStream, "[smoothType]", "Type of smoothing", par.getSmoothType()); |
---|
[378] | 956 | if(par.getSmoothType()=="spectral") |
---|
[664] | 957 | recordParam(theStream, "[hanningWidth]", "Width of hanning filter", par.getHanningWidth()); |
---|
[378] | 958 | else{ |
---|
[664] | 959 | recordParam(theStream, "[kernMaj]", "Gaussian kernel semi-major axis [pix]", par.getKernMaj()); |
---|
| 960 | recordParam(theStream, "[kernMin]", "Gaussian kernel semi-minor axis [pix]", par.getKernMin()); |
---|
| 961 | recordParam(theStream, "[kernPA]", "Gaussian kernel position angle [deg]", par.getKernPA()); |
---|
[378] | 962 | } |
---|
[348] | 963 | } |
---|
[664] | 964 | recordParam(theStream, "[flagATrous]", "Using A Trous reconstruction?", stringize(par.getFlagATrous())); |
---|
[378] | 965 | if(par.getFlagATrous()){ |
---|
[664] | 966 | recordParam(theStream, "[reconDim]", "Number of dimensions in reconstruction", par.getReconDim()); |
---|
[378] | 967 | if(par.getMaxScale()>0){ |
---|
[664] | 968 | recordParam(theStream, "[scaleMin-scaleMax]", "Scales used in reconstruction", par.getMinScale()<<"-"<<par.getMaxScale()); |
---|
[378] | 969 | } |
---|
| 970 | else{ |
---|
[664] | 971 | recordParam(theStream, "[scaleMin]", "Minimum scale in reconstruction", par.getMinScale()); |
---|
[378] | 972 | } |
---|
[664] | 973 | recordParam(theStream, "[snrRecon]", "SNR Threshold within reconstruction", par.getAtrousCut()); |
---|
| 974 | recordParam(theStream, "[filterCode]", "Filter being used for reconstruction", par.getFilterCode()<<" ("<<par.getFilterName()<<")"); |
---|
[378] | 975 | } |
---|
[664] | 976 | recordParam(theStream, "[flagRobustStats]", "Using Robust statistics?", stringize(par.getFlagRobustStats())); |
---|
[378] | 977 | if(par.getFlagStatSec()){ |
---|
[664] | 978 | recordParam(theStream, "[statSec]", "Section used by statistics calculation", par.statSec.getSection()); |
---|
[189] | 979 | } |
---|
[664] | 980 | recordParam(theStream, "[flagFDR]", "Using FDR analysis?", stringize(par.getFlagFDR())); |
---|
[378] | 981 | if(par.getFlagFDR()){ |
---|
[664] | 982 | recordParam(theStream, "[alphaFDR]", "Alpha value for FDR analysis", par.getAlpha()); |
---|
| 983 | recordParam(theStream, "[FDRnumCorChan]", "Number of correlated channels for FDR", par.getFDRnumCorChan()); |
---|
[378] | 984 | } |
---|
| 985 | else { |
---|
| 986 | if(par.getFlagUserThreshold()){ |
---|
[664] | 987 | recordParam(theStream, "[threshold]", "Detection Threshold", par.getThreshold()); |
---|
[378] | 988 | } |
---|
| 989 | else{ |
---|
[664] | 990 | recordParam(theStream, "[snrCut]", "SNR Threshold (in sigma)", par.getCut()); |
---|
[378] | 991 | } |
---|
[189] | 992 | } |
---|
[664] | 993 | recordParam(theStream, "[minPix]", "Minimum # Pixels in a detection", par.getMinPix()); |
---|
| 994 | recordParam(theStream, "[minChannels]", "Minimum # Channels in a detection", par.getMinChannels()); |
---|
[720] | 995 | recordParam(theStream, "[minVoxels]", "Minimum # Voxels in a detection", par.getMinVoxels()); |
---|
[664] | 996 | recordParam(theStream, "[flagGrowth]", "Growing objects after detection?", stringize(par.getFlagGrowth())); |
---|
[378] | 997 | if(par.getFlagGrowth()) { |
---|
[503] | 998 | if(par.getFlagUserGrowthThreshold()){ |
---|
[664] | 999 | recordParam(theStream, "[growthThreshold]", "Threshold for growth", par.getGrowthThreshold()); |
---|
[503] | 1000 | } |
---|
| 1001 | else{ |
---|
[664] | 1002 | recordParam(theStream, "[growthCut]", "SNR Threshold for growth", par.getGrowthCut()); |
---|
[503] | 1003 | } |
---|
[378] | 1004 | } |
---|
[664] | 1005 | recordParam(theStream, "[flagAdjacent]", "Using Adjacent-pixel criterion?", stringize(par.getFlagAdjacent())); |
---|
[378] | 1006 | if(!par.getFlagAdjacent()){ |
---|
[664] | 1007 | recordParam(theStream, "[threshSpatial]", "Max. spatial separation for merging", par.getThreshS()); |
---|
[378] | 1008 | } |
---|
[664] | 1009 | recordParam(theStream, "[threshVelocity]", "Max. velocity separation for merging", par.getThreshV()); |
---|
[672] | 1010 | recordParam(theStream, "[flagRejectBeforeMerge]", "Reject objects before merging?", stringize(par.getFlagRejectBeforeMerge())); |
---|
[691] | 1011 | recordParam(theStream, "[flagTwoStageMerging]", "Merge objects in two stages?", stringize(par.getFlagTwoStageMerging())); |
---|
[664] | 1012 | recordParam(theStream, "[spectralMethod]", "Method of spectral plotting", par.getSpectralMethod()); |
---|
| 1013 | recordParam(theStream, "[pixelCentre]", "Type of object centre used in results", par.getPixelCentre()); |
---|
| 1014 | |
---|
[378] | 1015 | theStream <<"--------------------\n\n"; |
---|
| 1016 | theStream << std::setfill(' '); |
---|
| 1017 | theStream.unsetf(std::ios::left); |
---|
| 1018 | // theStream.unsetf(std::ios::boolalpha); |
---|
| 1019 | return theStream; |
---|
[3] | 1020 | } |
---|
| 1021 | |
---|
[120] | 1022 | |
---|
[378] | 1023 | void Param::copyHeaderInfo(FitsHeader &head) |
---|
| 1024 | { |
---|
[528] | 1025 | /// A function to copy across relevant header keywords from the |
---|
| 1026 | /// FitsHeader class to the Param class, as they are needed by |
---|
| 1027 | /// functions in the Param class. |
---|
| 1028 | /// The parameters are the keywords BLANK, BSCALE, BZERO, and the beam size. |
---|
[112] | 1029 | |
---|
[378] | 1030 | this->blankKeyword = head.getBlankKeyword(); |
---|
| 1031 | this->bscaleKeyword = head.getBscaleKeyword(); |
---|
| 1032 | this->bzeroKeyword = head.getBzeroKeyword(); |
---|
| 1033 | this->blankPixValue = this->blankKeyword * this->bscaleKeyword + |
---|
| 1034 | this->bzeroKeyword; |
---|
| 1035 | } |
---|
[112] | 1036 | |
---|
[379] | 1037 | std::string Param::outputMaskFile() |
---|
| 1038 | { |
---|
[528] | 1039 | /// This function produces the required filename in which to save |
---|
| 1040 | /// the mask image, indicating which pixels have been detected as |
---|
| 1041 | /// part of an object. If the input image is image.fits, then the |
---|
| 1042 | /// output will be image.MASK.fits. |
---|
| 1043 | |
---|
[525] | 1044 | if(this->fileOutputMask==""){ |
---|
| 1045 | std::string inputName = this->imageFile; |
---|
| 1046 | std::stringstream ss; |
---|
| 1047 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 1048 | // remove the ".fits" on the end. |
---|
| 1049 | ss << ".MASK.fits"; |
---|
| 1050 | return ss.str(); |
---|
| 1051 | } |
---|
| 1052 | else return this->fileOutputMask; |
---|
[379] | 1053 | } |
---|
| 1054 | |
---|
[670] | 1055 | std::string Param::outputMomentMapFile() |
---|
| 1056 | { |
---|
| 1057 | /// This function produces the required filename in which to save |
---|
| 1058 | /// the moment-0 FITS image. If the input image is image.fits, then the |
---|
| 1059 | /// output will be image.MOM0.fits. |
---|
| 1060 | |
---|
| 1061 | if(this->fileOutputMomentMap==""){ |
---|
| 1062 | std::string inputName = this->imageFile; |
---|
| 1063 | std::stringstream ss; |
---|
| 1064 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 1065 | // remove the ".fits" on the end. |
---|
| 1066 | ss << ".MOM0.fits"; |
---|
| 1067 | return ss.str(); |
---|
| 1068 | } |
---|
| 1069 | else return this->fileOutputMomentMap; |
---|
| 1070 | } |
---|
| 1071 | |
---|
[378] | 1072 | std::string Param::outputSmoothFile() |
---|
| 1073 | { |
---|
[528] | 1074 | /// This function produces the required filename in which to save |
---|
| 1075 | /// the smoothed array. If the input image is image.fits, then |
---|
| 1076 | /// the output will be: |
---|
| 1077 | /// <ul><li> Spectral smoothing: image.SMOOTH-1D-3.fits, where the |
---|
| 1078 | /// width of the Hanning filter was 3 pixels. |
---|
| 1079 | /// <li> Spatial smoothing : image.SMOOTH-2D-3-2-20.fits, where |
---|
| 1080 | /// kernMaj=3, kernMin=2 and kernPA=20 degrees. |
---|
| 1081 | /// </ul> |
---|
| 1082 | |
---|
[525] | 1083 | if(this->fileOutputSmooth==""){ |
---|
| 1084 | std::string inputName = this->imageFile; |
---|
| 1085 | std::stringstream ss; |
---|
| 1086 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 1087 | // remove the ".fits" on the end. |
---|
| 1088 | if(this->flagSubsection) ss<<".sub"; |
---|
| 1089 | if(this->smoothType=="spectral") |
---|
| 1090 | ss << ".SMOOTH-1D-" << this->hanningWidth << ".fits"; |
---|
| 1091 | else if(this->smoothType=="spatial") |
---|
| 1092 | ss << ".SMOOTH-2D-" |
---|
| 1093 | << this->kernMaj << "-" |
---|
| 1094 | << this->kernMin << "-" |
---|
| 1095 | << this->kernPA << ".fits"; |
---|
| 1096 | return ss.str(); |
---|
| 1097 | } |
---|
| 1098 | else return this->fileOutputSmooth; |
---|
[378] | 1099 | } |
---|
[208] | 1100 | |
---|
[378] | 1101 | std::string Param::outputReconFile() |
---|
| 1102 | { |
---|
[528] | 1103 | /// This function produces the required filename in which to save |
---|
| 1104 | /// the reconstructed array. If the input image is image.fits, then |
---|
| 1105 | /// the output will be eg. image.RECON-3-2-4-1.fits, where the numbers are |
---|
| 1106 | /// 3=reconDim, 2=filterCode, 4=snrRecon, 1=minScale |
---|
| 1107 | |
---|
[525] | 1108 | if(this->fileOutputRecon==""){ |
---|
| 1109 | std::string inputName = this->imageFile; |
---|
| 1110 | std::stringstream ss; |
---|
| 1111 | // First we remove the ".fits" from the end of the filename. |
---|
| 1112 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 1113 | if(this->flagSubsection) ss<<".sub"; |
---|
| 1114 | ss << ".RECON-" << this->reconDim |
---|
| 1115 | << "-" << this->filterCode |
---|
| 1116 | << "-" << this->snrRecon |
---|
| 1117 | << "-" << this->scaleMin |
---|
| 1118 | << ".fits"; |
---|
| 1119 | return ss.str(); |
---|
| 1120 | } |
---|
| 1121 | else return this->fileOutputRecon; |
---|
[378] | 1122 | } |
---|
[103] | 1123 | |
---|
[378] | 1124 | std::string Param::outputResidFile() |
---|
| 1125 | { |
---|
[528] | 1126 | /// This function produces the required filename in which to save |
---|
| 1127 | /// the reconstructed array. If the input image is image.fits, then |
---|
| 1128 | /// the output will be eg. image.RESID-3-2-4-1.fits, where the numbers are |
---|
| 1129 | /// 3=reconDim, 2=filterCode, 4=snrRecon, 1=scaleMin |
---|
| 1130 | |
---|
[525] | 1131 | if(this->fileOutputResid==""){ |
---|
| 1132 | std::string inputName = this->imageFile; |
---|
| 1133 | std::stringstream ss; |
---|
| 1134 | // First we remove the ".fits" from the end of the filename. |
---|
| 1135 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 1136 | if(this->flagSubsection) ss<<".sub"; |
---|
| 1137 | ss << ".RESID-" << this->reconDim |
---|
| 1138 | << "-" << this->filterCode |
---|
| 1139 | << "-" << this->snrRecon |
---|
| 1140 | << "-" << this->scaleMin |
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| 1141 | << ".fits"; |
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| 1142 | return ss.str(); |
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| 1143 | } |
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| 1144 | else return this->fileOutputResid; |
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[378] | 1145 | } |
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| 1146 | |
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[103] | 1147 | } |
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