[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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[205] | 33 | #include <stdlib.h> |
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[269] | 34 | #include <ctype.h> |
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[3] | 35 | #include <math.h> |
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[410] | 36 | #include <unistd.h> |
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[393] | 37 | #include <duchamp/param.hh> |
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| 38 | #include <duchamp/fitsHeader.hh> |
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| 39 | #include <duchamp/duchamp.hh> |
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[420] | 40 | #include <duchamp/pgheader.hh> |
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[393] | 41 | #include <duchamp/ATrous/filter.hh> |
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| 42 | #include <duchamp/Utils/utils.hh> |
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| 43 | #include <duchamp/Utils/Section.hh> |
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[438] | 44 | #include <duchamp/Detection/columns.hh> |
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[3] | 45 | |
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[378] | 46 | namespace duchamp |
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[309] | 47 | { |
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| 48 | |
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[378] | 49 | /****************************************************************/ |
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| 50 | /////////////////////////////////////////////////// |
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| 51 | //// Accessor Functions for Parameter class: |
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| 52 | /////////////////////////////////////////////////// |
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| 53 | Param::~Param() |
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| 54 | { |
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| 55 | /** |
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| 56 | * Deletes the offsets array if the sizeOffsets parameter is |
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| 57 | * positive. |
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| 58 | */ |
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| 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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| 69 | /** |
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| 70 | * Provides default intial values for the parameters. Note that |
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| 71 | * imageFile has no default value! |
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| 72 | */ |
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| 73 | std::string baseSection = "[*,*,*]"; |
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| 74 | // Input files |
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| 75 | this->imageFile = ""; |
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| 76 | this->flagSubsection = false; |
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| 77 | this->pixelSec.setSection(baseSection); |
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| 78 | this->flagReconExists = false; |
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| 79 | this->reconFile = ""; |
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| 80 | this->flagSmoothExists = false; |
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| 81 | this->smoothFile = ""; |
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[475] | 82 | this->usePrevious = false; |
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| 83 | this->objectList = ""; |
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[378] | 84 | // Output files |
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| 85 | this->flagLog = false; |
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| 86 | this->logFile = "duchamp-Logfile.txt"; |
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| 87 | this->outFile = "duchamp-Results.txt"; |
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| 88 | this->flagSeparateHeader= false; |
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| 89 | this->headerFile = "duchamp-Results.hdr"; |
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| 90 | this->spectraFile = "duchamp-Spectra.ps"; |
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[424] | 91 | this->flagTextSpectra = false; |
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| 92 | this->spectraTextFile = "duchamp-Spectra.txt"; |
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[379] | 93 | this->flagOutputMask = false; |
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[378] | 94 | this->flagOutputSmooth = false; |
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| 95 | this->flagOutputRecon = false; |
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| 96 | this->flagOutputResid = false; |
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| 97 | this->flagVOT = false; |
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| 98 | this->votFile = "duchamp-Results.xml"; |
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| 99 | this->flagKarma = false; |
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| 100 | this->karmaFile = "duchamp-Results.ann"; |
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[446] | 101 | this->annotationType = "borders"; |
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[378] | 102 | this->flagMaps = true; |
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| 103 | this->detectionMap = "duchamp-DetectionMap.ps"; |
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| 104 | this->momentMap = "duchamp-MomentMap.ps"; |
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| 105 | this->flagXOutput = true; |
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[439] | 106 | this->precFlux = Column::prFLUX; |
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| 107 | this->precVel = Column::prVEL; |
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| 108 | this->precSNR = Column::prSNR; |
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[378] | 109 | // Cube related parameters |
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| 110 | this->flagBlankPix = true; |
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| 111 | this->blankPixValue = -8.00061; |
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| 112 | this->blankKeyword = 1; |
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| 113 | this->bscaleKeyword = -8.00061; |
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| 114 | this->bzeroKeyword = 0.; |
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[434] | 115 | this->newFluxUnits = ""; |
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[378] | 116 | // Milky-Way parameters |
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| 117 | this->flagMW = false; |
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| 118 | this->maxMW = 112; |
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| 119 | this->minMW = 75; |
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| 120 | this->numPixBeam = 10.; |
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| 121 | this->flagUsingBeam = false; |
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| 122 | // Trim-related |
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| 123 | this->flagTrim = false; |
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| 124 | this->hasBeenTrimmed = false; |
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| 125 | this->borderLeft = 0; |
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| 126 | this->borderRight = 0; |
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| 127 | this->borderBottom = 0; |
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| 128 | this->borderTop = 0; |
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| 129 | // Subsection offsets |
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| 130 | this->sizeOffsets = 0; |
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| 131 | this->xSubOffset = 0; |
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| 132 | this->ySubOffset = 0; |
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| 133 | this->zSubOffset = 0; |
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| 134 | // Baseline related |
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| 135 | this->flagBaseline = false; |
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| 136 | // Detection-related |
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| 137 | this->flagNegative = false; |
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| 138 | // Object growth |
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| 139 | this->flagGrowth = false; |
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[458] | 140 | this->growthCut = 3.; |
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[461] | 141 | this->flagUserGrowthThreshold = false; |
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| 142 | this->growthThreshold = 0.; |
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[378] | 143 | // FDR analysis |
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| 144 | this->flagFDR = false; |
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| 145 | this->alphaFDR = 0.01; |
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| 146 | // Other detection |
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| 147 | this->flagStatSec = false; |
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| 148 | this->statSec.setSection(baseSection); |
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[385] | 149 | this->flagRobustStats = true; |
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[378] | 150 | this->snrCut = 3.; |
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| 151 | this->threshold = 0.; |
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| 152 | this->flagUserThreshold = false; |
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| 153 | // Smoothing |
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| 154 | this->flagSmooth = false; |
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| 155 | this->smoothType = "spectral"; |
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| 156 | this->hanningWidth = 5; |
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| 157 | this->kernMaj = 3.; |
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| 158 | this->kernMin = -1.; |
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| 159 | this->kernPA = 0.; |
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| 160 | // A trous reconstruction parameters |
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| 161 | this->flagATrous = false; |
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| 162 | this->reconDim = 1; |
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| 163 | this->scaleMin = 1; |
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| 164 | this->scaleMax = 0; |
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| 165 | this->snrRecon = 4.; |
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| 166 | this->filterCode = 1; |
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| 167 | this->reconFilter.define(this->filterCode); |
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| 168 | // Volume-merging parameters |
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| 169 | this->flagAdjacent = true; |
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| 170 | this->threshSpatial = 3.; |
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| 171 | this->threshVelocity = 7.; |
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| 172 | this->minChannels = 3; |
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| 173 | this->minPix = 2; |
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| 174 | // Input-Output related |
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| 175 | this->spectralMethod = "peak"; |
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| 176 | this->spectralUnits = "km/s"; |
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| 177 | this->pixelCentre = "centroid"; |
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| 178 | this->borders = true; |
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| 179 | this->blankEdge = true; |
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| 180 | this->verbose = true; |
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[419] | 181 | } |
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[204] | 182 | |
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[378] | 183 | Param::Param (const Param& p) |
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| 184 | { |
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| 185 | operator=(p); |
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[309] | 186 | } |
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[137] | 187 | |
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[378] | 188 | Param& Param::operator= (const Param& p) |
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| 189 | { |
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| 190 | if(this == &p) return *this; |
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| 191 | this->imageFile = p.imageFile; |
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| 192 | this->flagSubsection = p.flagSubsection; |
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| 193 | this->pixelSec = p.pixelSec; |
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| 194 | this->flagReconExists = p.flagReconExists; |
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| 195 | this->reconFile = p.reconFile; |
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| 196 | this->flagSmoothExists = p.flagSmoothExists; |
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[475] | 197 | this->smoothFile = p.smoothFile; |
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| 198 | this->usePrevious = p.usePrevious; |
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| 199 | this->objectList = p.objectList; |
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[378] | 200 | this->flagLog = p.flagLog; |
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| 201 | this->logFile = p.logFile; |
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| 202 | this->outFile = p.outFile; |
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| 203 | this->flagSeparateHeader= p.flagSeparateHeader; |
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| 204 | this->headerFile = p.headerFile; |
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| 205 | this->spectraFile = p.spectraFile; |
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[424] | 206 | this->flagTextSpectra = p.flagTextSpectra; |
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| 207 | this->spectraTextFile = p.spectraTextFile; |
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[379] | 208 | this->flagOutputMask = p.flagOutputMask; |
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[378] | 209 | this->flagOutputSmooth = p.flagOutputSmooth; |
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| 210 | this->flagOutputRecon = p.flagOutputRecon; |
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| 211 | this->flagOutputResid = p.flagOutputResid; |
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| 212 | this->flagVOT = p.flagVOT; |
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| 213 | this->votFile = p.votFile; |
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| 214 | this->flagKarma = p.flagKarma; |
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| 215 | this->karmaFile = p.karmaFile; |
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[446] | 216 | this->annotationType = p.annotationType; |
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[378] | 217 | this->flagMaps = p.flagMaps; |
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| 218 | this->detectionMap = p.detectionMap; |
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| 219 | this->momentMap = p.momentMap; |
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| 220 | this->flagXOutput = p.flagXOutput; |
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[438] | 221 | this->precFlux = p.precFlux; |
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| 222 | this->precVel = p.precVel; |
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| 223 | this->precSNR = p.precSNR; |
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[378] | 224 | this->flagBlankPix = p.flagBlankPix; |
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| 225 | this->blankPixValue = p.blankPixValue; |
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| 226 | this->blankKeyword = p.blankKeyword; |
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| 227 | this->bscaleKeyword = p.bscaleKeyword; |
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| 228 | this->bzeroKeyword = p.bzeroKeyword; |
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[434] | 229 | this->newFluxUnits = p.newFluxUnits; |
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[378] | 230 | this->flagMW = p.flagMW; |
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| 231 | this->maxMW = p.maxMW; |
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| 232 | this->minMW = p.minMW; |
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| 233 | this->numPixBeam = p.numPixBeam; |
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| 234 | this->flagTrim = p.flagTrim; |
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| 235 | this->hasBeenTrimmed = p.hasBeenTrimmed; |
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| 236 | this->borderLeft = p.borderLeft; |
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| 237 | this->borderRight = p.borderRight; |
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| 238 | this->borderBottom = p.borderBottom; |
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| 239 | this->borderTop = p.borderTop; |
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| 240 | if(this->sizeOffsets>0) delete [] this->offsets; |
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| 241 | this->sizeOffsets = p.sizeOffsets; |
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| 242 | if(this->sizeOffsets>0){ |
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| 243 | this->offsets = new long[this->sizeOffsets]; |
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| 244 | for(int i=0;i<this->sizeOffsets;i++) this->offsets[i] = p.offsets[i]; |
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| 245 | } |
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| 246 | this->xSubOffset = p.xSubOffset; |
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| 247 | this->ySubOffset = p.ySubOffset; |
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| 248 | this->zSubOffset = p.zSubOffset; |
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| 249 | this->flagBaseline = p.flagBaseline; |
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| 250 | this->flagNegative = p.flagNegative; |
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| 251 | this->flagGrowth = p.flagGrowth; |
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| 252 | this->growthCut = p.growthCut; |
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[461] | 253 | this->growthThreshold = p.threshold; |
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| 254 | this->flagUserGrowthThreshold = p.flagUserThreshold; |
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[378] | 255 | this->flagFDR = p.flagFDR; |
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| 256 | this->alphaFDR = p.alphaFDR; |
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| 257 | this->flagStatSec = p.flagStatSec; |
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[385] | 258 | this->statSec = p.statSec; |
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| 259 | this->flagRobustStats = p.flagRobustStats; |
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[378] | 260 | this->snrCut = p.snrCut; |
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| 261 | this->threshold = p.threshold; |
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| 262 | this->flagUserThreshold = p.flagUserThreshold; |
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| 263 | this->flagSmooth = p.flagSmooth; |
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| 264 | this->smoothType = p.smoothType; |
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| 265 | this->hanningWidth = p.hanningWidth; |
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| 266 | this->kernMaj = p.kernMaj; |
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| 267 | this->kernMin = p.kernMin; |
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| 268 | this->kernPA = p.kernPA; |
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| 269 | this->flagATrous = p.flagATrous; |
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| 270 | this->reconDim = p.reconDim; |
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| 271 | this->scaleMin = p.scaleMin; |
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| 272 | this->scaleMax = p.scaleMax; |
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| 273 | this->snrRecon = p.snrRecon; |
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| 274 | this->filterCode = p.filterCode; |
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| 275 | this->reconFilter = p.reconFilter; |
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| 276 | this->flagAdjacent = p.flagAdjacent; |
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| 277 | this->threshSpatial = p.threshSpatial; |
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| 278 | this->threshVelocity = p.threshVelocity; |
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| 279 | this->minChannels = p.minChannels; |
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| 280 | this->minPix = p.minPix; |
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| 281 | this->spectralMethod = p.spectralMethod; |
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| 282 | this->spectralUnits = p.spectralUnits; |
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| 283 | this->pixelCentre = p.pixelCentre; |
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| 284 | this->borders = p.borders; |
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| 285 | this->verbose = p.verbose; |
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| 286 | return *this; |
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| 287 | } |
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| 288 | //-------------------------------------------------------------------- |
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[266] | 289 | |
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[474] | 290 | int Param::getopts(int argc, char ** argv, std::string progname) |
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[378] | 291 | { |
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| 292 | /** |
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| 293 | * A function that reads in the command-line options, in a manner |
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| 294 | * tailored for use with the main Duchamp program. |
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| 295 | * |
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| 296 | * \param argc The number of command line arguments. |
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| 297 | * \param argv The array of command line arguments. |
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| 298 | */ |
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| 299 | |
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| 300 | int returnValue = FAILURE; |
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| 301 | if(argc==1){ |
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[474] | 302 | if(progname=="Selavy") std::cout << SELAVY_ERR_USAGE_MSG; |
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| 303 | else if(progname=="Duchamp") std::cout << ERR_USAGE_MSG; |
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| 304 | else std::cout << ERR_USAGE_MSG; |
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[378] | 305 | returnValue = FAILURE; |
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| 306 | } |
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| 307 | else { |
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| 308 | std::string file; |
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| 309 | bool changeX = false; |
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| 310 | this->defaultValues(); |
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| 311 | char c; |
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| 312 | while( ( c = getopt(argc,argv,"p:f:hvx") )!=-1){ |
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| 313 | switch(c) { |
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| 314 | case 'p': |
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| 315 | file = optarg; |
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| 316 | if(this->readParams(file)==FAILURE){ |
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| 317 | std::stringstream errmsg; |
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| 318 | errmsg << "Could not open parameter file " << file << ".\n"; |
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[474] | 319 | duchampError(progname,errmsg.str()); |
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[378] | 320 | } |
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| 321 | else returnValue = SUCCESS; |
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| 322 | break; |
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| 323 | case 'f': |
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| 324 | file = optarg; |
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| 325 | this->imageFile = file; |
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| 326 | returnValue = SUCCESS; |
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| 327 | break; |
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| 328 | case 'v': |
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| 329 | std::cout << PROGNAME << " version " << VERSION << std::endl; |
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| 330 | break; |
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| 331 | case 'x': |
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| 332 | changeX = true; |
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| 333 | break; |
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| 334 | case 'h': |
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| 335 | default : |
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[474] | 336 | if(progname=="Selavy") std::cout << SELAVY_ERR_USAGE_MSG; |
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| 337 | else if(progname=="Duchamp") std::cout << ERR_USAGE_MSG; |
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| 338 | else std::cout << ERR_USAGE_MSG; |
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[378] | 339 | break; |
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[266] | 340 | } |
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| 341 | } |
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[378] | 342 | if(changeX){ |
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| 343 | if(returnValue == SUCCESS) this->setFlagXOutput(false); |
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| 344 | else { |
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[474] | 345 | duchampError(progname, |
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[378] | 346 | "You need to specify either a parameter file or FITS image.\n"); |
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| 347 | std::cout << "\n" << ERR_USAGE_MSG; |
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| 348 | } |
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[294] | 349 | } |
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| 350 | } |
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[378] | 351 | return returnValue; |
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[266] | 352 | } |
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[378] | 353 | //-------------------------------------------------------------------- |
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[266] | 354 | |
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[378] | 355 | bool Param::isBlank(float &value) |
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| 356 | { |
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| 357 | /** |
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| 358 | * Tests whether the value passed as the argument is BLANK or not. |
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| 359 | * \param value Pixel value to be tested. |
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| 360 | * \return False if flagBlankPix is false. Else, compare to the |
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| 361 | * relevant FITS keywords, using integer comparison. |
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| 362 | */ |
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| 363 | return this->flagBlankPix && |
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| 364 | (this->blankKeyword == int((value-this->bzeroKeyword)/this->bscaleKeyword)); |
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[419] | 365 | } |
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[266] | 366 | |
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[378] | 367 | bool *Param::makeBlankMask(float *array, int size) |
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| 368 | { |
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| 369 | /** |
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| 370 | * This returns an array of bools, saying whether each pixel in the |
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| 371 | * given array is BLANK or not. If the pixel is BLANK, set mask to |
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| 372 | * false, else set to true. The array is allocated by the function. |
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| 373 | */ |
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| 374 | bool *mask = new bool[size]; |
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| 375 | for(int i=0;i<size;i++) mask[i] = !this->isBlank(array[i]); |
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| 376 | return mask; |
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| 377 | } |
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[275] | 378 | |
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| 379 | |
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[378] | 380 | bool Param::isInMW(int z) |
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| 381 | { |
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| 382 | /** |
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| 383 | * Tests whether we are flagging Milky Way channels, and if so |
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| 384 | * whether the given channel number is in the Milky Way range. The |
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| 385 | * channels are assumed to start at number 0. |
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| 386 | * \param z The channel number |
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| 387 | * \return True if we are flagging Milky Way channels and z is in |
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| 388 | * the range. |
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| 389 | */ |
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| 390 | return ( flagMW && (z>=minMW) && (z<=maxMW) ); |
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| 391 | } |
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[266] | 392 | |
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[378] | 393 | bool Param::isStatOK(int x, int y, int z) |
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| 394 | { |
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| 395 | /** |
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| 396 | * Test whether a given pixel position lies within the subsection |
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| 397 | * given by the statSec parameter. Only tested if the flagSubsection |
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| 398 | * parameter is true -- if it isn't, we just return true since all |
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| 399 | * pixels are therefore available for statstical calculations. |
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| 400 | * \param x X-value of pixel being tested. |
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| 401 | * \param y Y-value of pixel being tested. |
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| 402 | * \param z Z-value of pixel being tested. |
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| 403 | * \return True if pixel is able to be used for statistical |
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| 404 | * calculations. False otherwise. |
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| 405 | */ |
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[272] | 406 | int xval=x,yval=y,zval=z; |
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| 407 | if(flagSubsection){ |
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| 408 | xval += pixelSec.getStart(0); |
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| 409 | yval += pixelSec.getStart(1); |
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| 410 | zval += pixelSec.getStart(2); |
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| 411 | } |
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| 412 | return !flagStatSec || statSec.isInside(xval,yval,zval); |
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[419] | 413 | } |
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[266] | 414 | |
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[475] | 415 | std::vector<int> Param::getObjectRequest() |
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| 416 | { |
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| 417 | /** |
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| 418 | * Returns a list of the object numbers requested via the objectList parameter. |
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| 419 | * \return a vector of integers, one for each number in the objectList set. |
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| 420 | */ |
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| 421 | std::stringstream ss1; |
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| 422 | std::string tmp; |
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| 423 | std::vector<int> tmplist; |
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| 424 | ss1.str(this->objectList); |
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| 425 | while(!ss1.eof()){ |
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| 426 | getline(ss1,tmp,','); |
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| 427 | for(int i=0;i<tmp.size();i++) if(tmp[i]=='-') tmp[i]=' '; |
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| 428 | int a,b; |
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| 429 | std::stringstream ss2; |
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| 430 | ss2.str(tmp); |
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| 431 | ss2 >>a; |
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| 432 | if(!ss2.eof()) ss2 >> b; |
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| 433 | else b=a; |
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| 434 | for(int n=a;n<=b;n++){ |
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| 435 | tmplist.push_back(n); |
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| 436 | } |
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| 437 | } |
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| 438 | return tmplist; |
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| 439 | } |
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| 440 | |
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| 441 | std::vector<bool> Param::getObjectChoices() |
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| 442 | { |
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| 443 | /** |
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| 444 | * Returns a list of bool values, indicating whether a given |
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| 445 | * object was requested or not. The size of the vector is |
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| 446 | * determined by the maximum value in objectList. For instance, |
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| 447 | * if objectList="2,3,5-8", then the returned vector will be |
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| 448 | * [0,1,1,0,1,1,1,1]. |
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| 449 | * \return Vector of bool values. |
---|
| 450 | */ |
---|
| 451 | std::vector<int> objectChoices = this->getObjectRequest(); |
---|
| 452 | int maxNum = *std::max_element(objectChoices.begin(), objectChoices.end()); |
---|
| 453 | std::vector<bool> choices(maxNum,false); |
---|
| 454 | for(int i=0;i<objectChoices.size();i++) choices[objectChoices[i]-1] = true; |
---|
| 455 | return choices; |
---|
| 456 | } |
---|
| 457 | |
---|
| 458 | std::vector<bool> Param::getObjectChoices(int numObjects) |
---|
| 459 | { |
---|
| 460 | /** |
---|
| 461 | * Returns a list of bool values, indicating whether a given |
---|
| 462 | * object was requested or not. The size of the vector is given |
---|
| 463 | * by the numObjects parameter. So, if objectList="2,3,5-8", then |
---|
| 464 | * the returned vector from a getObjectChoices(10) call will be |
---|
| 465 | * [0,1,1,0,1,1,1,1,0,0]. |
---|
| 466 | * \param numObjects How many objects there are in total. |
---|
| 467 | * \return Vector of bool values. |
---|
| 468 | */ |
---|
| 469 | if(this->objectList==""){ |
---|
| 470 | std::vector<bool> choices(numObjects,true); |
---|
| 471 | return choices; |
---|
| 472 | } |
---|
| 473 | else{ |
---|
| 474 | std::vector<int> objectChoices = this->getObjectRequest(); |
---|
| 475 | std::vector<bool> choices(numObjects,false); |
---|
| 476 | for(int i=0;i<objectChoices.size();i++) |
---|
| 477 | if(objectChoices[i]<=numObjects) choices[objectChoices[i]-1] = true; |
---|
| 478 | return choices; |
---|
| 479 | } |
---|
| 480 | } |
---|
| 481 | |
---|
[378] | 482 | /****************************************************************/ |
---|
| 483 | /////////////////////////////////////////////////// |
---|
| 484 | //// Other Functions using the Parameter class: |
---|
| 485 | /////////////////////////////////////////////////// |
---|
[3] | 486 | |
---|
[378] | 487 | std::string makelower( std::string s ) |
---|
| 488 | { |
---|
| 489 | // "borrowed" from Matt Howlett's 'fred' |
---|
| 490 | std::string out = ""; |
---|
| 491 | for( int i=0; i<s.size(); ++i ) { |
---|
| 492 | out += tolower(s[i]); |
---|
| 493 | } |
---|
| 494 | return out; |
---|
[3] | 495 | } |
---|
| 496 | |
---|
[378] | 497 | inline std::string stringize(bool b) |
---|
| 498 | { |
---|
| 499 | /** |
---|
| 500 | * Convert a bool variable to the textual equivalent. |
---|
| 501 | * \return A std::string with the english equivalent of the bool. |
---|
| 502 | */ |
---|
| 503 | std::string output; |
---|
| 504 | if(b) output="true"; |
---|
| 505 | else output="false"; |
---|
| 506 | return output; |
---|
| 507 | } |
---|
[274] | 508 | |
---|
[378] | 509 | inline bool boolify( std::string s ) |
---|
| 510 | { |
---|
| 511 | /** |
---|
| 512 | * Convert a std::string to a bool variable: |
---|
| 513 | * "1" and "true" get converted to true; |
---|
| 514 | * "0" and "false" (and anything else) get converted to false. |
---|
| 515 | * \return The bool equivalent of the string. |
---|
| 516 | */ |
---|
| 517 | if((s=="1") || (makelower(s)=="true")) return true; |
---|
| 518 | else if((s=="0") || (makelower(s)=="false")) return false; |
---|
| 519 | else return false; |
---|
| 520 | } |
---|
[132] | 521 | |
---|
[378] | 522 | inline std::string readSval(std::stringstream& ss) |
---|
| 523 | { |
---|
| 524 | std::string val; ss >> val; return val; |
---|
| 525 | } |
---|
[163] | 526 | |
---|
[378] | 527 | inline bool readFlag(std::stringstream& ss) |
---|
| 528 | { |
---|
| 529 | std::string val; ss >> val; return boolify(val); |
---|
| 530 | } |
---|
[163] | 531 | |
---|
[378] | 532 | inline float readFval(std::stringstream& ss) |
---|
| 533 | { |
---|
| 534 | float val; ss >> val; return val; |
---|
| 535 | } |
---|
[163] | 536 | |
---|
[378] | 537 | inline int readIval(std::stringstream& ss) |
---|
| 538 | { |
---|
| 539 | int val; ss >> val; return val; |
---|
| 540 | } |
---|
[163] | 541 | |
---|
[378] | 542 | int Param::readParams(std::string paramfile) |
---|
| 543 | { |
---|
| 544 | /** |
---|
| 545 | * The parameters are read in from a disk file, on the assumption that each |
---|
| 546 | * line of the file has the format "parameter value" (eg. alphafdr 0.1) |
---|
| 547 | * |
---|
| 548 | * The case of the parameter name does not matter, nor does the |
---|
| 549 | * formatting of the spaces (it can be any amount of whitespace or |
---|
| 550 | * tabs). |
---|
| 551 | * |
---|
| 552 | * \param paramfile A std::string containing the parameter filename. |
---|
| 553 | * |
---|
| 554 | * \return FAILURE if the parameter file does not exist. SUCCESS if |
---|
| 555 | * it is able to read it. |
---|
| 556 | */ |
---|
| 557 | std::ifstream fin(paramfile.c_str()); |
---|
| 558 | if(!fin.is_open()) return FAILURE; |
---|
| 559 | std::string line; |
---|
| 560 | while( !std::getline(fin,line,'\n').eof()){ |
---|
[3] | 561 | |
---|
[378] | 562 | if(line[0]!='#'){ |
---|
| 563 | std::stringstream ss; |
---|
| 564 | ss.str(line); |
---|
| 565 | std::string arg; |
---|
| 566 | ss >> arg; |
---|
| 567 | arg = makelower(arg); |
---|
| 568 | if(arg=="imagefile") this->imageFile = readSval(ss); |
---|
| 569 | if(arg=="flagsubsection") this->flagSubsection = readFlag(ss); |
---|
| 570 | if(arg=="subsection") this->pixelSec.setSection(readSval(ss)); |
---|
| 571 | if(arg=="flagreconexists") this->flagReconExists = readFlag(ss); |
---|
| 572 | if(arg=="reconfile") this->reconFile = readSval(ss); |
---|
| 573 | if(arg=="flagsmoothexists")this->flagSmoothExists = readFlag(ss); |
---|
| 574 | if(arg=="smoothfile") this->smoothFile = readSval(ss); |
---|
[442] | 575 | if(arg=="beamsize") this->numPixBeam = readFval(ss); |
---|
[475] | 576 | if(arg=="useprevious") this->usePrevious = readFlag(ss); |
---|
| 577 | if(arg=="objectlist") this->objectList = readSval(ss); |
---|
[71] | 578 | |
---|
[378] | 579 | if(arg=="flaglog") this->flagLog = readFlag(ss); |
---|
| 580 | if(arg=="logfile") this->logFile = readSval(ss); |
---|
| 581 | if(arg=="outfile") this->outFile = readSval(ss); |
---|
| 582 | if(arg=="flagseparateheader") this->flagSeparateHeader = readFlag(ss); |
---|
| 583 | if(arg=="headerfile") this->headerFile = readSval(ss); |
---|
| 584 | if(arg=="spectrafile") this->spectraFile = readSval(ss); |
---|
[424] | 585 | if(arg=="flagtextspectra") this->flagTextSpectra = readFlag(ss); |
---|
| 586 | if(arg=="spectraTextfile") this->spectraTextFile = readSval(ss); |
---|
[379] | 587 | if(arg=="flagoutputmask") this->flagOutputMask = readFlag(ss); |
---|
[378] | 588 | if(arg=="flagoutputsmooth")this->flagOutputSmooth = readFlag(ss); |
---|
| 589 | if(arg=="flagoutputrecon") this->flagOutputRecon = readFlag(ss); |
---|
| 590 | if(arg=="flagoutputresid") this->flagOutputResid = readFlag(ss); |
---|
| 591 | if(arg=="flagvot") this->flagVOT = readFlag(ss); |
---|
| 592 | if(arg=="votfile") this->votFile = readSval(ss); |
---|
| 593 | if(arg=="flagkarma") this->flagKarma = readFlag(ss); |
---|
| 594 | if(arg=="karmafile") this->karmaFile = readSval(ss); |
---|
[446] | 595 | if(arg=="annotationtype") this->annotationType = readSval(ss); |
---|
[378] | 596 | if(arg=="flagmaps") this->flagMaps = readFlag(ss); |
---|
| 597 | if(arg=="detectionmap") this->detectionMap = readSval(ss); |
---|
| 598 | if(arg=="momentmap") this->momentMap = readSval(ss); |
---|
| 599 | if(arg=="flagxoutput") this->flagXOutput = readFlag(ss); |
---|
[434] | 600 | if(arg=="newfluxunits") this->newFluxUnits = readSval(ss); |
---|
[438] | 601 | if(arg=="precflux") this->precFlux = readIval(ss); |
---|
| 602 | if(arg=="precvel") this->precVel = readIval(ss); |
---|
| 603 | if(arg=="precsnr") this->precSNR = readIval(ss); |
---|
[3] | 604 | |
---|
[378] | 605 | if(arg=="flagtrim") this->flagTrim = readFlag(ss); |
---|
| 606 | if(arg=="flagmw") this->flagMW = readFlag(ss); |
---|
| 607 | if(arg=="maxmw") this->maxMW = readIval(ss); |
---|
| 608 | if(arg=="minmw") this->minMW = readIval(ss); |
---|
[442] | 609 | if(arg=="flagbaseline") this->flagBaseline = readFlag(ss); |
---|
[71] | 610 | |
---|
[442] | 611 | if(arg=="flagnegative") this->flagNegative = readFlag(ss); |
---|
[378] | 612 | if(arg=="minpix") this->minPix = readIval(ss); |
---|
| 613 | if(arg=="flaggrowth") this->flagGrowth = readFlag(ss); |
---|
| 614 | if(arg=="growthcut") this->growthCut = readFval(ss); |
---|
[461] | 615 | if(arg=="growththreshold"){ |
---|
| 616 | this->growthThreshold = readFval(ss); |
---|
| 617 | this->flagUserGrowthThreshold = true; |
---|
| 618 | } |
---|
[71] | 619 | |
---|
[378] | 620 | if(arg=="flagfdr") this->flagFDR = readFlag(ss); |
---|
| 621 | if(arg=="alphafdr") this->alphaFDR = readFval(ss); |
---|
[103] | 622 | |
---|
[378] | 623 | if(arg=="flagstatsec") this->flagStatSec = readFlag(ss); |
---|
| 624 | if(arg=="statsec") this->statSec.setSection(readSval(ss)); |
---|
[385] | 625 | if(arg=="flagrobuststats") this->flagRobustStats = readFlag(ss); |
---|
[378] | 626 | if(arg=="snrcut") this->snrCut = readFval(ss); |
---|
| 627 | if(arg=="threshold"){ |
---|
| 628 | this->threshold = readFval(ss); |
---|
| 629 | this->flagUserThreshold = true; |
---|
| 630 | } |
---|
[201] | 631 | |
---|
[378] | 632 | if(arg=="flagsmooth") this->flagSmooth = readFlag(ss); |
---|
| 633 | if(arg=="smoothtype") this->smoothType = readSval(ss); |
---|
| 634 | if(arg=="hanningwidth") this->hanningWidth = readIval(ss); |
---|
| 635 | if(arg=="kernmaj") this->kernMaj = readFval(ss); |
---|
| 636 | if(arg=="kernmin") this->kernMin = readFval(ss); |
---|
| 637 | if(arg=="kernpa") this->kernPA = readFval(ss); |
---|
[103] | 638 | |
---|
[378] | 639 | if(arg=="flagatrous") this->flagATrous = readFlag(ss); |
---|
| 640 | if(arg=="recondim") this->reconDim = readIval(ss); |
---|
| 641 | if(arg=="scalemin") this->scaleMin = readIval(ss); |
---|
| 642 | if(arg=="scalemax") this->scaleMax = readIval(ss); |
---|
| 643 | if(arg=="snrrecon") this->snrRecon = readFval(ss); |
---|
| 644 | if(arg=="filtercode"){ |
---|
| 645 | this->filterCode = readIval(ss); |
---|
| 646 | this->reconFilter.define(this->filterCode); |
---|
| 647 | } |
---|
[71] | 648 | |
---|
[378] | 649 | if(arg=="flagadjacent") this->flagAdjacent = readFlag(ss); |
---|
| 650 | if(arg=="threshspatial") this->threshSpatial = readFval(ss); |
---|
| 651 | if(arg=="threshvelocity") this->threshVelocity = readFval(ss); |
---|
| 652 | if(arg=="minchannels") this->minChannels = readIval(ss); |
---|
[71] | 653 | |
---|
[378] | 654 | if(arg=="spectralmethod") this->spectralMethod=makelower(readSval(ss)); |
---|
| 655 | if(arg=="spectralunits") this->spectralUnits = makelower(readSval(ss)); |
---|
| 656 | if(arg=="pixelcentre") this->pixelCentre = makelower(readSval(ss)); |
---|
| 657 | if(arg=="drawborders") this->borders = readFlag(ss); |
---|
| 658 | if(arg=="drawblankedges") this->blankEdge = readFlag(ss); |
---|
| 659 | if(arg=="verbose") this->verbose = readFlag(ss); |
---|
[295] | 660 | |
---|
[378] | 661 | // Dealing with deprecated parameters. |
---|
| 662 | if(arg=="flagblankpix"){ |
---|
| 663 | this->flagTrim = readFlag(ss); |
---|
| 664 | std::stringstream errmsg; |
---|
| 665 | errmsg <<"The parameter flagBlankPix is deprecated. " |
---|
| 666 | <<"Please use the flagTrim parameter in future.\n" |
---|
| 667 | <<"Setting flagTrim = " << stringize(this->flagTrim) << ".\n"; |
---|
| 668 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 669 | } |
---|
| 670 | if(arg=="blankpixvalue"){ |
---|
| 671 | std::stringstream errmsg; |
---|
| 672 | errmsg <<"The parameter blankPixValue is deprecated.\n" |
---|
| 673 | <<"This value is only taken from the FITS header.\n"; |
---|
| 674 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 675 | } |
---|
| 676 | |
---|
[295] | 677 | } |
---|
[378] | 678 | } |
---|
[295] | 679 | |
---|
[475] | 680 | // If we have usePrevious=false, set the objectlist to blank so that we use all of them |
---|
| 681 | if(!this->usePrevious) this->objectList = ""; |
---|
| 682 | |
---|
[420] | 683 | // If pgplot was not included in the compilation, need to set flagXOutput to false |
---|
| 684 | if(!USE_PGPLOT) this->flagXOutput = false; |
---|
| 685 | |
---|
[438] | 686 | // Correcting bad precision values -- if negative, set to 0 |
---|
| 687 | if(this->precFlux<0) this->precFlux = 0; |
---|
| 688 | if(this->precVel<0) this->precVel = 0; |
---|
| 689 | if(this->precSNR<0) this->precSNR = 0; |
---|
| 690 | |
---|
[378] | 691 | // The wavelet reconstruction takes precendence over the smoothing. |
---|
| 692 | if(this->flagATrous) this->flagSmooth = false; |
---|
| 693 | |
---|
[461] | 694 | if(this->flagUserThreshold){ |
---|
| 695 | |
---|
| 696 | // If we specify a manual threshold, need to also specify a manual growth threshold |
---|
| 697 | // If we haven't done so, turn growing off |
---|
| 698 | if(this->flagGrowth && !this->flagUserGrowthThreshold){ |
---|
| 699 | std::stringstream errmsg; |
---|
| 700 | errmsg << "You have specified a manual search threshold, but not a manual growth threshold.\n" |
---|
| 701 | << "You need to do so using the \"growthThreshold\" parameter.\n" |
---|
| 702 | << "The growth function is being turned off.\n"; |
---|
| 703 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 704 | this->flagGrowth = false; |
---|
| 705 | } |
---|
| 706 | |
---|
| 707 | // If we specify a manual threshold, we don't need the FDR method, so turn it off if requested. |
---|
| 708 | if(this->flagFDR){ |
---|
| 709 | std::stringstream errmsg; |
---|
| 710 | errmsg << "You have specified a manual search threshold, so we don't need to use the FDR method.\n" |
---|
| 711 | << "Setting \"flagFDR=false\".\n"; |
---|
| 712 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 713 | this->flagFDR = false; |
---|
| 714 | } |
---|
| 715 | |
---|
| 716 | } |
---|
| 717 | |
---|
| 718 | |
---|
[446] | 719 | // Make sure the annnotationType is an acceptable option -- default is "borders" |
---|
| 720 | if((this->annotationType != "borders") && (this->annotationType!="circles")){ |
---|
| 721 | std::stringstream errmsg; |
---|
| 722 | errmsg << "The requested value of the parameter annotationType, \"" |
---|
| 723 | << this->annotationType << "\" is invalid.\n" |
---|
| 724 | << "Changing to \"borders\".\n"; |
---|
| 725 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 726 | this->annotationType = "borders"; |
---|
| 727 | } |
---|
| 728 | |
---|
[378] | 729 | // Make sure smoothType is an acceptable type -- default is "spectral" |
---|
| 730 | if((this->smoothType!="spectral")&& |
---|
| 731 | (this->smoothType!="spatial")){ |
---|
| 732 | std::stringstream errmsg; |
---|
| 733 | errmsg << "The requested value of the parameter smoothType, \"" |
---|
| 734 | << this->smoothType << "\" is invalid.\n" |
---|
| 735 | << "Changing to \"spectral\".\n"; |
---|
| 736 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 737 | this->smoothType = "spectral"; |
---|
[3] | 738 | } |
---|
[378] | 739 | // If kernMin has not been given, or is negative, make it equal to kernMaj |
---|
| 740 | if(this->kernMin < 0) this->kernMin = this->kernMaj; |
---|
[272] | 741 | |
---|
[378] | 742 | // Make sure spectralMethod is an acceptable type -- default is "peak" |
---|
| 743 | if((this->spectralMethod!="peak")&& |
---|
| 744 | (this->spectralMethod!="sum")){ |
---|
| 745 | std::stringstream errmsg; |
---|
| 746 | errmsg << "The requested value of the parameter spectralMethod, \"" |
---|
| 747 | << this->spectralMethod << "\" is invalid.\n" |
---|
| 748 | << "Changing to \"peak\".\n"; |
---|
| 749 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 750 | this->spectralMethod = "peak"; |
---|
| 751 | } |
---|
[232] | 752 | |
---|
[378] | 753 | // Make sure pixelCentre is an acceptable type -- default is "peak" |
---|
| 754 | if((this->pixelCentre!="centroid")&& |
---|
| 755 | (this->pixelCentre!="average") && |
---|
| 756 | (this->pixelCentre!="peak") ){ |
---|
| 757 | std::stringstream errmsg; |
---|
| 758 | errmsg << "The requested value of the parameter pixelCentre, \"" |
---|
| 759 | << this->pixelCentre << "\" is invalid.\n" |
---|
| 760 | << "Changing to \"centroid\".\n"; |
---|
| 761 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 762 | this->pixelCentre = "centroid"; |
---|
| 763 | } |
---|
[275] | 764 | |
---|
[378] | 765 | return SUCCESS; |
---|
[265] | 766 | } |
---|
| 767 | |
---|
| 768 | |
---|
[378] | 769 | std::ostream& operator<< ( std::ostream& theStream, Param& par) |
---|
| 770 | { |
---|
| 771 | /** |
---|
| 772 | * Print out the parameter set in a formatted, easy to read style. |
---|
| 773 | * Lists the parameters, a description of them, and their value. |
---|
| 774 | */ |
---|
[3] | 775 | |
---|
[378] | 776 | // Only show the [beamSize] bit if we are using the parameter |
---|
| 777 | // otherwise we have read it from the FITS header. |
---|
| 778 | std::string beamParam = ""; |
---|
| 779 | if(par.getFlagUsingBeam()) beamParam = "[beamSize]"; |
---|
[3] | 780 | |
---|
[378] | 781 | // BUG -- can get error: `boolalpha' is not a member of type `ios' -- old compilers: gcc 2.95.3? |
---|
| 782 | // theStream.setf(std::ios::boolalpha); |
---|
| 783 | theStream.setf(std::ios::left); |
---|
| 784 | theStream <<"\n---- Parameters ----"<<std::endl; |
---|
| 785 | theStream << std::setfill('.'); |
---|
| 786 | const int widthText = 38; |
---|
| 787 | const int widthPar = 18; |
---|
| 788 | if(par.getFlagSubsection()) |
---|
| 789 | theStream<<std::setw(widthText)<<"Image to be analysed" |
---|
| 790 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[imageFile]" |
---|
| 791 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 792 | <<(par.getImageFile()+par.getSubsection()) <<std::endl; |
---|
| 793 | else |
---|
| 794 | theStream<<std::setw(widthText)<<"Image to be analysed" |
---|
| 795 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[imageFile]" |
---|
| 796 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 797 | <<par.getImageFile() <<std::endl; |
---|
| 798 | if(par.getFlagReconExists() && par.getFlagATrous()){ |
---|
| 799 | theStream<<std::setw(widthText)<<"Reconstructed array exists?" |
---|
| 800 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[reconExists]" |
---|
| 801 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 802 | <<stringize(par.getFlagReconExists())<<std::endl; |
---|
| 803 | theStream<<std::setw(widthText)<<"FITS file containing reconstruction" |
---|
| 804 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[reconFile]" |
---|
| 805 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 806 | <<par.getReconFile() <<std::endl; |
---|
| 807 | } |
---|
| 808 | if(par.getFlagSmoothExists() && par.getFlagSmooth()){ |
---|
| 809 | theStream<<std::setw(widthText)<<"Smoothed array exists?" |
---|
| 810 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[smoothExists]" |
---|
| 811 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 812 | <<stringize(par.getFlagSmoothExists())<<std::endl; |
---|
| 813 | theStream<<std::setw(widthText)<<"FITS file containing smoothed array" |
---|
| 814 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[smoothFile]" |
---|
| 815 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 816 | <<par.getSmoothFile() <<std::endl; |
---|
| 817 | } |
---|
| 818 | theStream <<std::setw(widthText)<<"Intermediate Logfile" |
---|
| 819 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[logFile]" |
---|
| 820 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 821 | <<par.getLogFile() <<std::endl; |
---|
| 822 | theStream <<std::setw(widthText)<<"Final Results file" |
---|
| 823 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[outFile]" |
---|
| 824 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 825 | <<par.getOutFile() <<std::endl; |
---|
| 826 | if(par.getFlagSeparateHeader()) |
---|
| 827 | theStream <<std::setw(widthText)<<"Header for results file" |
---|
| 828 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[headerFile]" |
---|
| 829 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 830 | <<par.getHeaderFile() <<std::endl; |
---|
| 831 | theStream <<std::setw(widthText)<<"Spectrum file" |
---|
| 832 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[spectraFile]" |
---|
| 833 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 834 | <<par.getSpectraFile() <<std::endl; |
---|
[424] | 835 | if(par.getFlagTextSpectra()){ |
---|
| 836 | theStream<<std::setw(widthText)<<"Text file with ascii spectral data" |
---|
| 837 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[spectraTextFile]" |
---|
| 838 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 839 | <<par.getSpectraTextFile()<<std::endl; |
---|
| 840 | } |
---|
[378] | 841 | if(par.getFlagVOT()){ |
---|
| 842 | theStream<<std::setw(widthText)<<"VOTable file" |
---|
| 843 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[votFile]" |
---|
| 844 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 845 | <<par.getVOTFile() <<std::endl; |
---|
| 846 | } |
---|
| 847 | if(par.getFlagKarma()){ |
---|
| 848 | theStream<<std::setw(widthText)<<"Karma annotation file" |
---|
| 849 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[karmaFile]" |
---|
| 850 | <<" = " <<resetiosflags(std::ios::right) |
---|
[172] | 851 | |
---|
[378] | 852 | <<par.getKarmaFile() <<std::endl; |
---|
| 853 | } |
---|
| 854 | if(par.getFlagMaps()){ |
---|
| 855 | theStream<<std::setw(widthText)<<"0th Moment Map" |
---|
| 856 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[momentMap]" |
---|
[275] | 857 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 858 | <<par.getMomentMap() <<std::endl; |
---|
| 859 | theStream<<std::setw(widthText)<<"Detection Map" |
---|
| 860 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[detectionMap]" |
---|
[275] | 861 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 862 | <<par.getDetectionMap() <<std::endl; |
---|
| 863 | } |
---|
| 864 | theStream <<std::setw(widthText)<<"Display a map in a pgplot xwindow?" |
---|
| 865 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagXOutput]" |
---|
[275] | 866 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 867 | <<stringize(par.getFlagXOutput()) <<std::endl; |
---|
| 868 | if(par.getFlagATrous()){ |
---|
| 869 | theStream<<std::setw(widthText)<<"Saving reconstructed cube?" |
---|
| 870 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagOutputRecon]" |
---|
[275] | 871 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 872 | <<stringize(par.getFlagOutputRecon())<<std::endl; |
---|
| 873 | theStream<<std::setw(widthText)<<"Saving residuals from reconstruction?" |
---|
| 874 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagOutputResid]" |
---|
| 875 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 876 | <<stringize(par.getFlagOutputResid())<<std::endl; |
---|
| 877 | } |
---|
| 878 | if(par.getFlagSmooth()){ |
---|
| 879 | theStream<<std::setw(widthText)<<"Saving smoothed cube?" |
---|
| 880 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagOutputSmooth]" |
---|
| 881 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 882 | <<stringize(par.getFlagOutputSmooth())<<std::endl; |
---|
| 883 | } |
---|
[379] | 884 | theStream<<std::setw(widthText)<<"Saving mask cube?" |
---|
| 885 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagOutputMask]" |
---|
| 886 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 887 | <<stringize(par.getFlagOutputMask())<<std::endl; |
---|
[378] | 888 | theStream <<"------"<<std::endl; |
---|
| 889 | if(par.getFlagBlankPix()){ |
---|
| 890 | theStream<<std::setw(widthText)<<"Blank Pixel Value" |
---|
| 891 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<< "" |
---|
| 892 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 893 | <<par.getBlankPixVal() <<std::endl; |
---|
[275] | 894 | } |
---|
[378] | 895 | theStream <<std::setw(widthText)<<"Trimming Blank Pixels?" |
---|
| 896 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagTrim]" |
---|
[348] | 897 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 898 | <<stringize(par.getFlagTrim()) <<std::endl; |
---|
| 899 | theStream <<std::setw(widthText)<<"Searching for Negative features?" |
---|
| 900 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagNegative]" |
---|
| 901 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 902 | <<stringize(par.getFlagNegative()) <<std::endl; |
---|
| 903 | theStream <<std::setw(widthText)<<"Removing Milky Way channels?" |
---|
| 904 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagMW]" |
---|
| 905 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 906 | <<stringize(par.getFlagMW()) <<std::endl; |
---|
| 907 | if(par.getFlagMW()){ |
---|
| 908 | theStream<<std::setw(widthText)<<"Milky Way Channels" |
---|
| 909 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[minMW - maxMW]" |
---|
| 910 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 911 | <<par.getMinMW() |
---|
| 912 | <<"-" <<par.getMaxMW() <<std::endl; |
---|
[348] | 913 | } |
---|
[378] | 914 | theStream <<std::setw(widthText)<<"Beam Size (pixels)" |
---|
| 915 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<< beamParam |
---|
[348] | 916 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 917 | <<par.getBeamSize() <<std::endl; |
---|
| 918 | theStream <<std::setw(widthText)<<"Removing baselines before search?" |
---|
| 919 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagBaseline]" |
---|
| 920 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 921 | <<stringize(par.getFlagBaseline()) <<std::endl; |
---|
| 922 | theStream <<std::setw(widthText)<<"Smoothing each spectrum first?" |
---|
| 923 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagSmooth]" |
---|
| 924 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 925 | <<stringize(par.getFlagSmooth()) <<std::endl; |
---|
| 926 | if(par.getFlagSmooth()){ |
---|
| 927 | theStream<<std::setw(widthText)<<"Type of smoothing" |
---|
| 928 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[smoothType]" |
---|
| 929 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 930 | <<par.getSmoothType() <<std::endl; |
---|
| 931 | if(par.getSmoothType()=="spectral") |
---|
| 932 | theStream<<std::setw(widthText)<<"Width of hanning filter" |
---|
| 933 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[hanningWidth]" |
---|
| 934 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 935 | <<par.getHanningWidth() <<std::endl; |
---|
| 936 | else{ |
---|
| 937 | theStream<<std::setw(widthText)<<"Gaussian kernel semi-major axis [pix]" |
---|
| 938 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[kernMaj]" |
---|
| 939 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 940 | <<par.getKernMaj() << std::endl; |
---|
| 941 | theStream<<std::setw(widthText)<<"Gaussian kernel semi-minor axis [pix]" |
---|
| 942 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[kernMin]" |
---|
| 943 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 944 | <<par.getKernMin() << std::endl; |
---|
| 945 | theStream<<std::setw(widthText)<<"Gaussian kernel position angle [deg]" |
---|
| 946 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[kernPA]" |
---|
| 947 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 948 | <<par.getKernPA() << std::endl; |
---|
| 949 | } |
---|
[348] | 950 | } |
---|
[378] | 951 | theStream <<std::setw(widthText)<<"Using A Trous reconstruction?" |
---|
| 952 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagATrous]" |
---|
[189] | 953 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 954 | <<stringize(par.getFlagATrous()) <<std::endl; |
---|
| 955 | if(par.getFlagATrous()){ |
---|
| 956 | theStream<<std::setw(widthText)<<"Number of dimensions in reconstruction" |
---|
| 957 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[reconDim]" |
---|
| 958 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 959 | <<par.getReconDim() <<std::endl; |
---|
| 960 | if(par.getMaxScale()>0){ |
---|
| 961 | theStream<<std::setw(widthText-1)<<"Scales used in reconstruction" |
---|
| 962 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[scaleMin-scaleMax]" |
---|
| 963 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 964 | <<par.getMinScale() << "-" << par.getMaxScale() <<std::endl; |
---|
| 965 | } |
---|
| 966 | else{ |
---|
| 967 | theStream<<std::setw(widthText)<<"Minimum scale in reconstruction" |
---|
| 968 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[scaleMin]" |
---|
| 969 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 970 | <<par.getMinScale() <<std::endl; |
---|
| 971 | } |
---|
| 972 | theStream<<std::setw(widthText)<<"SNR Threshold within reconstruction" |
---|
| 973 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[snrRecon]" |
---|
| 974 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 975 | <<par.getAtrousCut() <<std::endl; |
---|
| 976 | theStream<<std::setw(widthText)<<"Filter being used for reconstruction" |
---|
| 977 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[filterCode]" |
---|
| 978 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 979 | <<par.getFilterCode() |
---|
| 980 | << " (" << par.getFilterName() << ")" <<std::endl; |
---|
| 981 | } |
---|
[385] | 982 | theStream <<std::setw(widthText)<<"Using Robust statistics?" |
---|
| 983 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagRobustStats]" |
---|
| 984 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 985 | <<stringize(par.getFlagRobustStats()) <<std::endl; |
---|
[378] | 986 | if(par.getFlagStatSec()){ |
---|
| 987 | theStream<<std::setw(widthText)<<"Section used by statistics calculation" |
---|
| 988 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[statSec]" |
---|
| 989 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 990 | <<par.statSec.getSection() <<std::endl; |
---|
[189] | 991 | } |
---|
[378] | 992 | theStream <<std::setw(widthText)<<"Using FDR analysis?" |
---|
| 993 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagFDR]" |
---|
[189] | 994 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 995 | <<stringize(par.getFlagFDR()) <<std::endl; |
---|
| 996 | if(par.getFlagFDR()){ |
---|
| 997 | theStream<<std::setw(widthText)<<"Alpha value for FDR analysis" |
---|
| 998 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[alphaFDR]" |
---|
| 999 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1000 | <<par.getAlpha() <<std::endl; |
---|
| 1001 | } |
---|
| 1002 | else { |
---|
| 1003 | if(par.getFlagUserThreshold()){ |
---|
| 1004 | theStream<<std::setw(widthText)<<"Detection Threshold" |
---|
| 1005 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[threshold]" |
---|
| 1006 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1007 | <<par.getThreshold() <<std::endl; |
---|
| 1008 | } |
---|
| 1009 | else{ |
---|
| 1010 | theStream<<std::setw(widthText)<<"SNR Threshold (in sigma)" |
---|
| 1011 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[snrCut]" |
---|
| 1012 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1013 | <<par.getCut() <<std::endl; |
---|
| 1014 | } |
---|
[189] | 1015 | } |
---|
[378] | 1016 | theStream <<std::setw(widthText)<<"Minimum # Pixels in a detection" |
---|
| 1017 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[minPix]" |
---|
| 1018 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1019 | <<par.getMinPix() <<std::endl; |
---|
| 1020 | theStream <<std::setw(widthText)<<"Minimum # Channels in a detection" |
---|
| 1021 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[minChannels]" |
---|
| 1022 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1023 | <<par.getMinChannels() <<std::endl; |
---|
| 1024 | theStream <<std::setw(widthText)<<"Growing objects after detection?" |
---|
| 1025 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagGrowth]" |
---|
| 1026 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1027 | <<stringize(par.getFlagGrowth()) <<std::endl; |
---|
| 1028 | if(par.getFlagGrowth()) { |
---|
| 1029 | theStream<<std::setw(widthText)<<"SNR Threshold for growth" |
---|
| 1030 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[growthCut]" |
---|
| 1031 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1032 | <<par.getGrowthCut() <<std::endl; |
---|
| 1033 | } |
---|
| 1034 | theStream <<std::setw(widthText)<<"Using Adjacent-pixel criterion?" |
---|
| 1035 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagAdjacent]" |
---|
| 1036 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1037 | <<stringize(par.getFlagAdjacent()) <<std::endl; |
---|
| 1038 | if(!par.getFlagAdjacent()){ |
---|
| 1039 | theStream<<std::setw(widthText)<<"Max. spatial separation for merging" |
---|
| 1040 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[threshSpatial]" |
---|
| 1041 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1042 | <<par.getThreshS() <<std::endl; |
---|
| 1043 | } |
---|
| 1044 | theStream <<std::setw(widthText)<<"Max. velocity separation for merging" |
---|
| 1045 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[threshVelocity]" |
---|
| 1046 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1047 | <<par.getThreshV() <<std::endl; |
---|
| 1048 | theStream <<std::setw(widthText)<<"Method of spectral plotting" |
---|
| 1049 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[spectralMethod]" |
---|
| 1050 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1051 | <<par.getSpectralMethod() <<std::endl; |
---|
| 1052 | theStream <<std::setw(widthText)<<"Type of object centre used in results" |
---|
| 1053 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[pixelCentre]" |
---|
| 1054 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 1055 | <<par.getPixelCentre() <<std::endl; |
---|
| 1056 | theStream <<"--------------------\n\n"; |
---|
| 1057 | theStream << std::setfill(' '); |
---|
| 1058 | theStream.unsetf(std::ios::left); |
---|
| 1059 | // theStream.unsetf(std::ios::boolalpha); |
---|
| 1060 | return theStream; |
---|
[3] | 1061 | } |
---|
| 1062 | |
---|
[120] | 1063 | |
---|
[378] | 1064 | void Param::copyHeaderInfo(FitsHeader &head) |
---|
| 1065 | { |
---|
| 1066 | /** |
---|
| 1067 | * A function to copy across relevant header keywords from the |
---|
| 1068 | * FitsHeader class to the Param class, as they are needed by |
---|
| 1069 | * functions in the Param class. |
---|
| 1070 | * The parameters are the keywords BLANK, BSCALE, BZERO, and the beam size. |
---|
| 1071 | */ |
---|
[112] | 1072 | |
---|
[378] | 1073 | this->blankKeyword = head.getBlankKeyword(); |
---|
| 1074 | this->bscaleKeyword = head.getBscaleKeyword(); |
---|
| 1075 | this->bzeroKeyword = head.getBzeroKeyword(); |
---|
| 1076 | this->blankPixValue = this->blankKeyword * this->bscaleKeyword + |
---|
| 1077 | this->bzeroKeyword; |
---|
[112] | 1078 | |
---|
[378] | 1079 | this->numPixBeam = head.getBeamSize(); |
---|
| 1080 | } |
---|
[112] | 1081 | |
---|
[379] | 1082 | std::string Param::outputMaskFile() |
---|
| 1083 | { |
---|
| 1084 | /** |
---|
| 1085 | * This function produces the required filename in which to save |
---|
| 1086 | * the mask image, indicating which pixels have been detected as |
---|
| 1087 | * part of an object. If the input image is image.fits, then the |
---|
| 1088 | * output will be image.MASK.fits. |
---|
| 1089 | */ |
---|
| 1090 | std::string inputName = this->imageFile; |
---|
| 1091 | std::stringstream ss; |
---|
| 1092 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 1093 | // remove the ".fits" on the end. |
---|
| 1094 | ss << ".MASK.fits"; |
---|
| 1095 | return ss.str(); |
---|
| 1096 | } |
---|
| 1097 | |
---|
[378] | 1098 | std::string Param::outputSmoothFile() |
---|
| 1099 | { |
---|
| 1100 | /** |
---|
| 1101 | * This function produces the required filename in which to save |
---|
| 1102 | * the smoothed array. If the input image is image.fits, then |
---|
| 1103 | * the output will be: |
---|
| 1104 | * <ul><li> Spectral smoothing: image.SMOOTH-1D-3.fits, where the |
---|
| 1105 | * width of the Hanning filter was 3 pixels. |
---|
| 1106 | * <li> Spatial smoothing : image.SMOOTH-2D-3-2-20.fits, where |
---|
| 1107 | * kernMaj=3, kernMin=2 and kernPA=20 degrees. |
---|
| 1108 | * </ul> |
---|
| 1109 | */ |
---|
| 1110 | std::string inputName = this->imageFile; |
---|
| 1111 | std::stringstream ss; |
---|
| 1112 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 1113 | // remove the ".fits" on the end. |
---|
| 1114 | if(this->flagSubsection) ss<<".sub"; |
---|
| 1115 | if(this->smoothType=="spectral") |
---|
| 1116 | ss << ".SMOOTH-1D-" << this->hanningWidth << ".fits"; |
---|
| 1117 | else if(this->smoothType=="spatial") |
---|
| 1118 | ss << ".SMOOTH-2D-" |
---|
| 1119 | << this->kernMaj << "-" |
---|
| 1120 | << this->kernMin << "-" |
---|
| 1121 | << this->kernPA << ".fits"; |
---|
| 1122 | return ss.str(); |
---|
| 1123 | } |
---|
[208] | 1124 | |
---|
[378] | 1125 | std::string Param::outputReconFile() |
---|
| 1126 | { |
---|
| 1127 | /** |
---|
| 1128 | * This function produces the required filename in which to save |
---|
| 1129 | * the reconstructed array. If the input image is image.fits, then |
---|
| 1130 | * the output will be eg. image.RECON-3-2-4-1.fits, where the numbers are |
---|
| 1131 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=minScale |
---|
| 1132 | */ |
---|
| 1133 | std::string inputName = this->imageFile; |
---|
| 1134 | std::stringstream ss; |
---|
| 1135 | // First we remove the ".fits" from the end of the filename. |
---|
| 1136 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 1137 | if(this->flagSubsection) ss<<".sub"; |
---|
| 1138 | ss << ".RECON-" << this->reconDim |
---|
| 1139 | << "-" << this->filterCode |
---|
| 1140 | << "-" << this->snrRecon |
---|
| 1141 | << "-" << this->scaleMin |
---|
| 1142 | << ".fits"; |
---|
| 1143 | return ss.str(); |
---|
| 1144 | } |
---|
[103] | 1145 | |
---|
[378] | 1146 | std::string Param::outputResidFile() |
---|
| 1147 | { |
---|
| 1148 | /** |
---|
| 1149 | * This function produces the required filename in which to save |
---|
| 1150 | * the reconstructed array. If the input image is image.fits, then |
---|
| 1151 | * the output will be eg. image.RESID-3-2-4-1.fits, where the numbers are |
---|
| 1152 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=scaleMin |
---|
| 1153 | */ |
---|
| 1154 | std::string inputName = this->imageFile; |
---|
| 1155 | std::stringstream ss; |
---|
| 1156 | // First we remove the ".fits" from the end of the filename. |
---|
| 1157 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 1158 | if(this->flagSubsection) ss<<".sub"; |
---|
| 1159 | ss << ".RESID-" << this->reconDim |
---|
| 1160 | << "-" << this->filterCode |
---|
| 1161 | << "-" << this->snrRecon |
---|
| 1162 | << "-" << this->scaleMin |
---|
| 1163 | << ".fits"; |
---|
| 1164 | return ss.str(); |
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| 1165 | } |
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| 1166 | |
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[103] | 1167 | } |
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