[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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| 40 | #include <duchamp/ATrous/filter.hh> |
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| 41 | #include <duchamp/Utils/utils.hh> |
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| 42 | #include <duchamp/Utils/Section.hh> |
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[3] | 43 | |
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[378] | 44 | namespace duchamp |
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[309] | 45 | { |
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| 46 | |
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[378] | 47 | /****************************************************************/ |
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| 48 | /////////////////////////////////////////////////// |
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| 49 | //// Accessor Functions for Parameter class: |
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| 50 | /////////////////////////////////////////////////// |
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| 51 | Param::~Param() |
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| 52 | { |
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| 53 | /** |
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| 54 | * Deletes the offsets array if the sizeOffsets parameter is |
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| 55 | * positive. |
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| 56 | */ |
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| 57 | if(this->sizeOffsets>0) delete [] this->offsets; |
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| 58 | } |
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[309] | 59 | |
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[378] | 60 | Param::Param() |
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| 61 | { |
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| 62 | this->defaultValues(); |
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| 63 | } |
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[3] | 64 | |
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[378] | 65 | void Param::defaultValues() |
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| 66 | { |
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| 67 | /** |
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| 68 | * Provides default intial values for the parameters. Note that |
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| 69 | * imageFile has no default value! |
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| 70 | */ |
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| 71 | std::string baseSection = "[*,*,*]"; |
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| 72 | // Input files |
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| 73 | this->imageFile = ""; |
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| 74 | this->flagSubsection = false; |
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| 75 | this->pixelSec.setSection(baseSection); |
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| 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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| 80 | // Output files |
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| 81 | this->flagLog = false; |
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| 82 | this->logFile = "duchamp-Logfile.txt"; |
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| 83 | this->outFile = "duchamp-Results.txt"; |
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| 84 | this->flagSeparateHeader= false; |
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| 85 | this->headerFile = "duchamp-Results.hdr"; |
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| 86 | this->spectraFile = "duchamp-Spectra.ps"; |
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[379] | 87 | this->flagOutputMask = false; |
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[378] | 88 | this->flagOutputSmooth = false; |
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| 89 | this->flagOutputRecon = false; |
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| 90 | this->flagOutputResid = false; |
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| 91 | this->flagVOT = false; |
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| 92 | this->votFile = "duchamp-Results.xml"; |
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| 93 | this->flagKarma = false; |
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| 94 | this->karmaFile = "duchamp-Results.ann"; |
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| 95 | this->flagMaps = true; |
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| 96 | this->detectionMap = "duchamp-DetectionMap.ps"; |
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| 97 | this->momentMap = "duchamp-MomentMap.ps"; |
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| 98 | this->flagXOutput = true; |
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| 99 | // Cube related parameters |
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| 100 | this->flagBlankPix = true; |
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| 101 | this->blankPixValue = -8.00061; |
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| 102 | this->blankKeyword = 1; |
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| 103 | this->bscaleKeyword = -8.00061; |
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| 104 | this->bzeroKeyword = 0.; |
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| 105 | // Milky-Way parameters |
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| 106 | this->flagMW = false; |
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| 107 | this->maxMW = 112; |
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| 108 | this->minMW = 75; |
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| 109 | this->numPixBeam = 10.; |
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| 110 | this->flagUsingBeam = false; |
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| 111 | // Trim-related |
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| 112 | this->flagTrim = false; |
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| 113 | this->hasBeenTrimmed = false; |
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| 114 | this->borderLeft = 0; |
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| 115 | this->borderRight = 0; |
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| 116 | this->borderBottom = 0; |
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| 117 | this->borderTop = 0; |
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| 118 | // Subsection offsets |
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| 119 | this->sizeOffsets = 0; |
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| 120 | this->xSubOffset = 0; |
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| 121 | this->ySubOffset = 0; |
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| 122 | this->zSubOffset = 0; |
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| 123 | // Baseline related |
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| 124 | this->flagBaseline = false; |
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| 125 | // Detection-related |
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| 126 | this->flagNegative = false; |
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| 127 | // Object growth |
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| 128 | this->flagGrowth = false; |
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| 129 | this->growthCut = 2.; |
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| 130 | // FDR analysis |
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| 131 | this->flagFDR = false; |
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| 132 | this->alphaFDR = 0.01; |
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| 133 | // Other detection |
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| 134 | this->flagStatSec = false; |
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| 135 | this->statSec.setSection(baseSection); |
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[385] | 136 | this->flagRobustStats = true; |
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[378] | 137 | this->snrCut = 3.; |
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| 138 | this->threshold = 0.; |
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| 139 | this->flagUserThreshold = false; |
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| 140 | // Smoothing |
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| 141 | this->flagSmooth = false; |
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| 142 | this->smoothType = "spectral"; |
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| 143 | this->hanningWidth = 5; |
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| 144 | this->kernMaj = 3.; |
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| 145 | this->kernMin = -1.; |
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| 146 | this->kernPA = 0.; |
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| 147 | // A trous reconstruction parameters |
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| 148 | this->flagATrous = false; |
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| 149 | this->reconDim = 1; |
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| 150 | this->scaleMin = 1; |
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| 151 | this->scaleMax = 0; |
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| 152 | this->snrRecon = 4.; |
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| 153 | this->filterCode = 1; |
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| 154 | this->reconFilter.define(this->filterCode); |
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| 155 | // Volume-merging parameters |
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| 156 | this->flagAdjacent = true; |
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| 157 | this->threshSpatial = 3.; |
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| 158 | this->threshVelocity = 7.; |
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| 159 | this->minChannels = 3; |
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| 160 | this->minPix = 2; |
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| 161 | // Input-Output related |
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| 162 | this->spectralMethod = "peak"; |
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| 163 | this->spectralUnits = "km/s"; |
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| 164 | this->pixelCentre = "centroid"; |
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| 165 | this->borders = true; |
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| 166 | this->blankEdge = true; |
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| 167 | this->verbose = true; |
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[419] | 168 | } |
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[204] | 169 | |
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[378] | 170 | Param::Param (const Param& p) |
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| 171 | { |
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| 172 | operator=(p); |
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[309] | 173 | } |
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[137] | 174 | |
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[378] | 175 | Param& Param::operator= (const Param& p) |
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| 176 | { |
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| 177 | if(this == &p) return *this; |
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| 178 | this->imageFile = p.imageFile; |
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| 179 | this->flagSubsection = p.flagSubsection; |
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| 180 | this->pixelSec = p.pixelSec; |
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| 181 | this->flagReconExists = p.flagReconExists; |
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| 182 | this->reconFile = p.reconFile; |
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| 183 | this->flagSmoothExists = p.flagSmoothExists; |
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| 184 | this->smoothFile = p.smoothFile; |
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| 185 | this->flagLog = p.flagLog; |
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| 186 | this->logFile = p.logFile; |
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| 187 | this->outFile = p.outFile; |
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| 188 | this->flagSeparateHeader= p.flagSeparateHeader; |
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| 189 | this->headerFile = p.headerFile; |
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| 190 | this->spectraFile = p.spectraFile; |
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[379] | 191 | this->flagOutputMask = p.flagOutputMask; |
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[378] | 192 | this->flagOutputSmooth = p.flagOutputSmooth; |
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| 193 | this->flagOutputRecon = p.flagOutputRecon; |
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| 194 | this->flagOutputResid = p.flagOutputResid; |
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| 195 | this->flagVOT = p.flagVOT; |
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| 196 | this->votFile = p.votFile; |
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| 197 | this->flagKarma = p.flagKarma; |
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| 198 | this->karmaFile = p.karmaFile; |
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| 199 | this->flagMaps = p.flagMaps; |
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| 200 | this->detectionMap = p.detectionMap; |
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| 201 | this->momentMap = p.momentMap; |
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| 202 | this->flagXOutput = p.flagXOutput; |
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| 203 | this->flagBlankPix = p.flagBlankPix; |
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| 204 | this->blankPixValue = p.blankPixValue; |
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| 205 | this->blankKeyword = p.blankKeyword; |
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| 206 | this->bscaleKeyword = p.bscaleKeyword; |
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| 207 | this->bzeroKeyword = p.bzeroKeyword; |
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| 208 | this->flagMW = p.flagMW; |
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| 209 | this->maxMW = p.maxMW; |
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| 210 | this->minMW = p.minMW; |
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| 211 | this->numPixBeam = p.numPixBeam; |
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| 212 | this->flagTrim = p.flagTrim; |
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| 213 | this->hasBeenTrimmed = p.hasBeenTrimmed; |
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| 214 | this->borderLeft = p.borderLeft; |
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| 215 | this->borderRight = p.borderRight; |
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| 216 | this->borderBottom = p.borderBottom; |
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| 217 | this->borderTop = p.borderTop; |
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| 218 | if(this->sizeOffsets>0) delete [] this->offsets; |
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| 219 | this->sizeOffsets = p.sizeOffsets; |
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| 220 | if(this->sizeOffsets>0){ |
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| 221 | this->offsets = new long[this->sizeOffsets]; |
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| 222 | for(int i=0;i<this->sizeOffsets;i++) this->offsets[i] = p.offsets[i]; |
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| 223 | } |
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| 224 | this->xSubOffset = p.xSubOffset; |
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| 225 | this->ySubOffset = p.ySubOffset; |
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| 226 | this->zSubOffset = p.zSubOffset; |
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| 227 | this->flagBaseline = p.flagBaseline; |
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| 228 | this->flagNegative = p.flagNegative; |
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| 229 | this->flagGrowth = p.flagGrowth; |
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| 230 | this->growthCut = p.growthCut; |
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| 231 | this->flagFDR = p.flagFDR; |
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| 232 | this->alphaFDR = p.alphaFDR; |
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| 233 | this->flagStatSec = p.flagStatSec; |
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[385] | 234 | this->statSec = p.statSec; |
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| 235 | this->flagRobustStats = p.flagRobustStats; |
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[378] | 236 | this->snrCut = p.snrCut; |
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| 237 | this->threshold = p.threshold; |
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| 238 | this->flagUserThreshold = p.flagUserThreshold; |
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| 239 | this->flagSmooth = p.flagSmooth; |
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| 240 | this->smoothType = p.smoothType; |
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| 241 | this->hanningWidth = p.hanningWidth; |
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| 242 | this->kernMaj = p.kernMaj; |
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| 243 | this->kernMin = p.kernMin; |
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| 244 | this->kernPA = p.kernPA; |
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| 245 | this->flagATrous = p.flagATrous; |
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| 246 | this->reconDim = p.reconDim; |
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| 247 | this->scaleMin = p.scaleMin; |
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| 248 | this->scaleMax = p.scaleMax; |
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| 249 | this->snrRecon = p.snrRecon; |
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| 250 | this->filterCode = p.filterCode; |
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| 251 | this->reconFilter = p.reconFilter; |
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| 252 | this->flagAdjacent = p.flagAdjacent; |
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| 253 | this->threshSpatial = p.threshSpatial; |
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| 254 | this->threshVelocity = p.threshVelocity; |
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| 255 | this->minChannels = p.minChannels; |
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| 256 | this->minPix = p.minPix; |
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| 257 | this->spectralMethod = p.spectralMethod; |
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| 258 | this->spectralUnits = p.spectralUnits; |
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| 259 | this->pixelCentre = p.pixelCentre; |
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| 260 | this->borders = p.borders; |
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| 261 | this->verbose = p.verbose; |
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| 262 | return *this; |
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| 263 | } |
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| 264 | //-------------------------------------------------------------------- |
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[266] | 265 | |
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[378] | 266 | int Param::getopts(int argc, char ** argv) |
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| 267 | { |
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| 268 | /** |
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| 269 | * A function that reads in the command-line options, in a manner |
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| 270 | * tailored for use with the main Duchamp program. |
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| 271 | * |
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| 272 | * \param argc The number of command line arguments. |
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| 273 | * \param argv The array of command line arguments. |
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| 274 | */ |
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| 275 | |
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| 276 | int returnValue = FAILURE; |
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| 277 | if(argc==1){ |
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| 278 | std::cout << ERR_USAGE_MSG; |
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| 279 | returnValue = FAILURE; |
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| 280 | } |
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| 281 | else { |
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| 282 | std::string file; |
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| 283 | bool changeX = false; |
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| 284 | this->defaultValues(); |
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| 285 | char c; |
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| 286 | while( ( c = getopt(argc,argv,"p:f:hvx") )!=-1){ |
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| 287 | switch(c) { |
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| 288 | case 'p': |
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| 289 | file = optarg; |
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| 290 | if(this->readParams(file)==FAILURE){ |
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| 291 | std::stringstream errmsg; |
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| 292 | errmsg << "Could not open parameter file " << file << ".\n"; |
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| 293 | duchampError("Duchamp",errmsg.str()); |
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| 294 | } |
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| 295 | else returnValue = SUCCESS; |
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| 296 | break; |
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| 297 | case 'f': |
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| 298 | file = optarg; |
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| 299 | this->imageFile = file; |
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| 300 | returnValue = SUCCESS; |
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| 301 | break; |
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| 302 | case 'v': |
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| 303 | std::cout << PROGNAME << " version " << VERSION << std::endl; |
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| 304 | break; |
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| 305 | case 'x': |
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| 306 | changeX = true; |
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| 307 | break; |
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| 308 | case 'h': |
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| 309 | default : |
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| 310 | std::cout << ERR_USAGE_MSG; |
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| 311 | break; |
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[266] | 312 | } |
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| 313 | } |
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[378] | 314 | if(changeX){ |
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| 315 | if(returnValue == SUCCESS) this->setFlagXOutput(false); |
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| 316 | else { |
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| 317 | duchampError("Duchamp", |
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| 318 | "You need to specify either a parameter file or FITS image.\n"); |
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| 319 | std::cout << "\n" << ERR_USAGE_MSG; |
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| 320 | } |
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[294] | 321 | } |
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| 322 | } |
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[378] | 323 | return returnValue; |
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[266] | 324 | } |
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[378] | 325 | //-------------------------------------------------------------------- |
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[266] | 326 | |
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[378] | 327 | bool Param::isBlank(float &value) |
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| 328 | { |
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| 329 | /** |
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| 330 | * Tests whether the value passed as the argument is BLANK or not. |
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| 331 | * \param value Pixel value to be tested. |
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| 332 | * \return False if flagBlankPix is false. Else, compare to the |
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| 333 | * relevant FITS keywords, using integer comparison. |
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| 334 | */ |
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| 335 | return this->flagBlankPix && |
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| 336 | (this->blankKeyword == int((value-this->bzeroKeyword)/this->bscaleKeyword)); |
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[419] | 337 | } |
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[266] | 338 | |
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[378] | 339 | bool *Param::makeBlankMask(float *array, int size) |
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| 340 | { |
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| 341 | /** |
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| 342 | * This returns an array of bools, saying whether each pixel in the |
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| 343 | * given array is BLANK or not. If the pixel is BLANK, set mask to |
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| 344 | * false, else set to true. The array is allocated by the function. |
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| 345 | */ |
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| 346 | bool *mask = new bool[size]; |
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| 347 | for(int i=0;i<size;i++) mask[i] = !this->isBlank(array[i]); |
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| 348 | return mask; |
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| 349 | } |
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[275] | 350 | |
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| 351 | |
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[378] | 352 | bool Param::isInMW(int z) |
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| 353 | { |
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| 354 | /** |
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| 355 | * Tests whether we are flagging Milky Way channels, and if so |
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| 356 | * whether the given channel number is in the Milky Way range. The |
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| 357 | * channels are assumed to start at number 0. |
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| 358 | * \param z The channel number |
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| 359 | * \return True if we are flagging Milky Way channels and z is in |
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| 360 | * the range. |
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| 361 | */ |
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| 362 | return ( flagMW && (z>=minMW) && (z<=maxMW) ); |
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| 363 | } |
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[266] | 364 | |
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[378] | 365 | bool Param::isStatOK(int x, int y, int z) |
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| 366 | { |
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| 367 | /** |
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| 368 | * Test whether a given pixel position lies within the subsection |
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| 369 | * given by the statSec parameter. Only tested if the flagSubsection |
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| 370 | * parameter is true -- if it isn't, we just return true since all |
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| 371 | * pixels are therefore available for statstical calculations. |
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| 372 | * \param x X-value of pixel being tested. |
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| 373 | * \param y Y-value of pixel being tested. |
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| 374 | * \param z Z-value of pixel being tested. |
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| 375 | * \return True if pixel is able to be used for statistical |
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| 376 | * calculations. False otherwise. |
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| 377 | */ |
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[272] | 378 | int xval=x,yval=y,zval=z; |
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| 379 | if(flagSubsection){ |
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| 380 | xval += pixelSec.getStart(0); |
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| 381 | yval += pixelSec.getStart(1); |
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| 382 | zval += pixelSec.getStart(2); |
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| 383 | } |
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| 384 | return !flagStatSec || statSec.isInside(xval,yval,zval); |
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[419] | 385 | } |
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[266] | 386 | |
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[378] | 387 | /****************************************************************/ |
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| 388 | /////////////////////////////////////////////////// |
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| 389 | //// Other Functions using the Parameter class: |
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| 390 | /////////////////////////////////////////////////// |
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[3] | 391 | |
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[378] | 392 | std::string makelower( std::string s ) |
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| 393 | { |
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| 394 | // "borrowed" from Matt Howlett's 'fred' |
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| 395 | std::string out = ""; |
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| 396 | for( int i=0; i<s.size(); ++i ) { |
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| 397 | out += tolower(s[i]); |
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| 398 | } |
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| 399 | return out; |
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[3] | 400 | } |
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| 401 | |
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[378] | 402 | inline std::string stringize(bool b) |
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| 403 | { |
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| 404 | /** |
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| 405 | * Convert a bool variable to the textual equivalent. |
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| 406 | * \return A std::string with the english equivalent of the bool. |
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| 407 | */ |
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| 408 | std::string output; |
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| 409 | if(b) output="true"; |
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| 410 | else output="false"; |
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| 411 | return output; |
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| 412 | } |
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[274] | 413 | |
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[378] | 414 | inline bool boolify( std::string s ) |
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| 415 | { |
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| 416 | /** |
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| 417 | * Convert a std::string to a bool variable: |
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| 418 | * "1" and "true" get converted to true; |
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| 419 | * "0" and "false" (and anything else) get converted to false. |
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| 420 | * \return The bool equivalent of the string. |
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| 421 | */ |
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| 422 | if((s=="1") || (makelower(s)=="true")) return true; |
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| 423 | else if((s=="0") || (makelower(s)=="false")) return false; |
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| 424 | else return false; |
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| 425 | } |
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[132] | 426 | |
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[378] | 427 | inline std::string readSval(std::stringstream& ss) |
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| 428 | { |
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| 429 | std::string val; ss >> val; return val; |
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| 430 | } |
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[163] | 431 | |
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[378] | 432 | inline bool readFlag(std::stringstream& ss) |
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| 433 | { |
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| 434 | std::string val; ss >> val; return boolify(val); |
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| 435 | } |
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[163] | 436 | |
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[378] | 437 | inline float readFval(std::stringstream& ss) |
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| 438 | { |
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| 439 | float val; ss >> val; return val; |
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| 440 | } |
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[163] | 441 | |
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[378] | 442 | inline int readIval(std::stringstream& ss) |
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| 443 | { |
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| 444 | int val; ss >> val; return val; |
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| 445 | } |
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[163] | 446 | |
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[378] | 447 | int Param::readParams(std::string paramfile) |
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| 448 | { |
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| 449 | /** |
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| 450 | * The parameters are read in from a disk file, on the assumption that each |
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| 451 | * line of the file has the format "parameter value" (eg. alphafdr 0.1) |
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| 452 | * |
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| 453 | * The case of the parameter name does not matter, nor does the |
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| 454 | * formatting of the spaces (it can be any amount of whitespace or |
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| 455 | * tabs). |
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| 456 | * |
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| 457 | * \param paramfile A std::string containing the parameter filename. |
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| 458 | * |
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| 459 | * \return FAILURE if the parameter file does not exist. SUCCESS if |
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| 460 | * it is able to read it. |
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| 461 | */ |
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| 462 | std::ifstream fin(paramfile.c_str()); |
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| 463 | if(!fin.is_open()) return FAILURE; |
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| 464 | std::string line; |
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| 465 | while( !std::getline(fin,line,'\n').eof()){ |
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[3] | 466 | |
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[378] | 467 | if(line[0]!='#'){ |
---|
| 468 | std::stringstream ss; |
---|
| 469 | ss.str(line); |
---|
| 470 | std::string arg; |
---|
| 471 | ss >> arg; |
---|
| 472 | arg = makelower(arg); |
---|
| 473 | if(arg=="imagefile") this->imageFile = readSval(ss); |
---|
| 474 | if(arg=="flagsubsection") this->flagSubsection = readFlag(ss); |
---|
| 475 | if(arg=="subsection") this->pixelSec.setSection(readSval(ss)); |
---|
| 476 | if(arg=="flagreconexists") this->flagReconExists = readFlag(ss); |
---|
| 477 | if(arg=="reconfile") this->reconFile = readSval(ss); |
---|
| 478 | if(arg=="flagsmoothexists")this->flagSmoothExists = readFlag(ss); |
---|
| 479 | if(arg=="smoothfile") this->smoothFile = readSval(ss); |
---|
[71] | 480 | |
---|
[378] | 481 | if(arg=="flaglog") this->flagLog = readFlag(ss); |
---|
| 482 | if(arg=="logfile") this->logFile = readSval(ss); |
---|
| 483 | if(arg=="outfile") this->outFile = readSval(ss); |
---|
| 484 | if(arg=="flagseparateheader") this->flagSeparateHeader = readFlag(ss); |
---|
| 485 | if(arg=="headerfile") this->headerFile = readSval(ss); |
---|
| 486 | if(arg=="spectrafile") this->spectraFile = readSval(ss); |
---|
[379] | 487 | if(arg=="flagoutputmask") this->flagOutputMask = readFlag(ss); |
---|
[378] | 488 | if(arg=="flagoutputsmooth")this->flagOutputSmooth = readFlag(ss); |
---|
| 489 | if(arg=="flagoutputrecon") this->flagOutputRecon = readFlag(ss); |
---|
| 490 | if(arg=="flagoutputresid") this->flagOutputResid = readFlag(ss); |
---|
| 491 | if(arg=="flagvot") this->flagVOT = readFlag(ss); |
---|
| 492 | if(arg=="votfile") this->votFile = readSval(ss); |
---|
| 493 | if(arg=="flagkarma") this->flagKarma = readFlag(ss); |
---|
| 494 | if(arg=="karmafile") this->karmaFile = readSval(ss); |
---|
| 495 | if(arg=="flagmaps") this->flagMaps = readFlag(ss); |
---|
| 496 | if(arg=="detectionmap") this->detectionMap = readSval(ss); |
---|
| 497 | if(arg=="momentmap") this->momentMap = readSval(ss); |
---|
| 498 | if(arg=="flagxoutput") this->flagXOutput = readFlag(ss); |
---|
[3] | 499 | |
---|
[378] | 500 | if(arg=="flagnegative") this->flagNegative = readFlag(ss); |
---|
| 501 | if(arg=="flagtrim") this->flagTrim = readFlag(ss); |
---|
| 502 | if(arg=="flagmw") this->flagMW = readFlag(ss); |
---|
| 503 | if(arg=="maxmw") this->maxMW = readIval(ss); |
---|
| 504 | if(arg=="minmw") this->minMW = readIval(ss); |
---|
| 505 | if(arg=="beamsize") this->numPixBeam = readFval(ss); |
---|
[71] | 506 | |
---|
[378] | 507 | if(arg=="flagbaseline") this->flagBaseline = readFlag(ss); |
---|
| 508 | if(arg=="minpix") this->minPix = readIval(ss); |
---|
| 509 | if(arg=="flaggrowth") this->flagGrowth = readFlag(ss); |
---|
| 510 | if(arg=="growthcut") this->growthCut = readFval(ss); |
---|
[71] | 511 | |
---|
[378] | 512 | if(arg=="flagfdr") this->flagFDR = readFlag(ss); |
---|
| 513 | if(arg=="alphafdr") this->alphaFDR = readFval(ss); |
---|
[103] | 514 | |
---|
[378] | 515 | if(arg=="flagstatsec") this->flagStatSec = readFlag(ss); |
---|
| 516 | if(arg=="statsec") this->statSec.setSection(readSval(ss)); |
---|
[385] | 517 | if(arg=="flagrobuststats") this->flagRobustStats = readFlag(ss); |
---|
[378] | 518 | if(arg=="snrcut") this->snrCut = readFval(ss); |
---|
| 519 | if(arg=="threshold"){ |
---|
| 520 | this->threshold = readFval(ss); |
---|
| 521 | this->flagUserThreshold = true; |
---|
| 522 | } |
---|
[201] | 523 | |
---|
[378] | 524 | if(arg=="flagsmooth") this->flagSmooth = readFlag(ss); |
---|
| 525 | if(arg=="smoothtype") this->smoothType = readSval(ss); |
---|
| 526 | if(arg=="hanningwidth") this->hanningWidth = readIval(ss); |
---|
| 527 | if(arg=="kernmaj") this->kernMaj = readFval(ss); |
---|
| 528 | if(arg=="kernmin") this->kernMin = readFval(ss); |
---|
| 529 | if(arg=="kernpa") this->kernPA = readFval(ss); |
---|
[103] | 530 | |
---|
[378] | 531 | if(arg=="flagatrous") this->flagATrous = readFlag(ss); |
---|
| 532 | if(arg=="recondim") this->reconDim = readIval(ss); |
---|
| 533 | if(arg=="scalemin") this->scaleMin = readIval(ss); |
---|
| 534 | if(arg=="scalemax") this->scaleMax = readIval(ss); |
---|
| 535 | if(arg=="snrrecon") this->snrRecon = readFval(ss); |
---|
| 536 | if(arg=="filtercode"){ |
---|
| 537 | this->filterCode = readIval(ss); |
---|
| 538 | this->reconFilter.define(this->filterCode); |
---|
| 539 | } |
---|
[71] | 540 | |
---|
[378] | 541 | if(arg=="flagadjacent") this->flagAdjacent = readFlag(ss); |
---|
| 542 | if(arg=="threshspatial") this->threshSpatial = readFval(ss); |
---|
| 543 | if(arg=="threshvelocity") this->threshVelocity = readFval(ss); |
---|
| 544 | if(arg=="minchannels") this->minChannels = readIval(ss); |
---|
[71] | 545 | |
---|
[378] | 546 | if(arg=="spectralmethod") this->spectralMethod=makelower(readSval(ss)); |
---|
| 547 | if(arg=="spectralunits") this->spectralUnits = makelower(readSval(ss)); |
---|
| 548 | if(arg=="pixelcentre") this->pixelCentre = makelower(readSval(ss)); |
---|
| 549 | if(arg=="drawborders") this->borders = readFlag(ss); |
---|
| 550 | if(arg=="drawblankedges") this->blankEdge = readFlag(ss); |
---|
| 551 | if(arg=="verbose") this->verbose = readFlag(ss); |
---|
[295] | 552 | |
---|
[378] | 553 | // Dealing with deprecated parameters. |
---|
| 554 | if(arg=="flagblankpix"){ |
---|
| 555 | this->flagTrim = readFlag(ss); |
---|
| 556 | std::stringstream errmsg; |
---|
| 557 | errmsg <<"The parameter flagBlankPix is deprecated. " |
---|
| 558 | <<"Please use the flagTrim parameter in future.\n" |
---|
| 559 | <<"Setting flagTrim = " << stringize(this->flagTrim) << ".\n"; |
---|
| 560 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 561 | } |
---|
| 562 | if(arg=="blankpixvalue"){ |
---|
| 563 | std::stringstream errmsg; |
---|
| 564 | errmsg <<"The parameter blankPixValue is deprecated.\n" |
---|
| 565 | <<"This value is only taken from the FITS header.\n"; |
---|
| 566 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 567 | } |
---|
| 568 | |
---|
[295] | 569 | } |
---|
[378] | 570 | } |
---|
[295] | 571 | |
---|
[378] | 572 | // The wavelet reconstruction takes precendence over the smoothing. |
---|
| 573 | if(this->flagATrous) this->flagSmooth = false; |
---|
| 574 | |
---|
| 575 | // Make sure smoothType is an acceptable type -- default is "spectral" |
---|
| 576 | if((this->smoothType!="spectral")&& |
---|
| 577 | (this->smoothType!="spatial")){ |
---|
| 578 | std::stringstream errmsg; |
---|
| 579 | errmsg << "The requested value of the parameter smoothType, \"" |
---|
| 580 | << this->smoothType << "\" is invalid.\n" |
---|
| 581 | << "Changing to \"spectral\".\n"; |
---|
| 582 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 583 | this->smoothType = "spectral"; |
---|
[3] | 584 | } |
---|
[378] | 585 | // If kernMin has not been given, or is negative, make it equal to kernMaj |
---|
| 586 | if(this->kernMin < 0) this->kernMin = this->kernMaj; |
---|
[272] | 587 | |
---|
[378] | 588 | // Make sure spectralMethod is an acceptable type -- default is "peak" |
---|
| 589 | if((this->spectralMethod!="peak")&& |
---|
| 590 | (this->spectralMethod!="sum")){ |
---|
| 591 | std::stringstream errmsg; |
---|
| 592 | errmsg << "The requested value of the parameter spectralMethod, \"" |
---|
| 593 | << this->spectralMethod << "\" is invalid.\n" |
---|
| 594 | << "Changing to \"peak\".\n"; |
---|
| 595 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 596 | this->spectralMethod = "peak"; |
---|
| 597 | } |
---|
[232] | 598 | |
---|
[378] | 599 | // Make sure pixelCentre is an acceptable type -- default is "peak" |
---|
| 600 | if((this->pixelCentre!="centroid")&& |
---|
| 601 | (this->pixelCentre!="average") && |
---|
| 602 | (this->pixelCentre!="peak") ){ |
---|
| 603 | std::stringstream errmsg; |
---|
| 604 | errmsg << "The requested value of the parameter pixelCentre, \"" |
---|
| 605 | << this->pixelCentre << "\" is invalid.\n" |
---|
| 606 | << "Changing to \"centroid\".\n"; |
---|
| 607 | duchampWarning("Reading parameters",errmsg.str()); |
---|
| 608 | this->pixelCentre = "centroid"; |
---|
| 609 | } |
---|
[275] | 610 | |
---|
[378] | 611 | return SUCCESS; |
---|
[265] | 612 | } |
---|
| 613 | |
---|
| 614 | |
---|
[378] | 615 | std::ostream& operator<< ( std::ostream& theStream, Param& par) |
---|
| 616 | { |
---|
| 617 | /** |
---|
| 618 | * Print out the parameter set in a formatted, easy to read style. |
---|
| 619 | * Lists the parameters, a description of them, and their value. |
---|
| 620 | */ |
---|
[3] | 621 | |
---|
[378] | 622 | // Only show the [beamSize] bit if we are using the parameter |
---|
| 623 | // otherwise we have read it from the FITS header. |
---|
| 624 | std::string beamParam = ""; |
---|
| 625 | if(par.getFlagUsingBeam()) beamParam = "[beamSize]"; |
---|
[3] | 626 | |
---|
[378] | 627 | // BUG -- can get error: `boolalpha' is not a member of type `ios' -- old compilers: gcc 2.95.3? |
---|
| 628 | // theStream.setf(std::ios::boolalpha); |
---|
| 629 | theStream.setf(std::ios::left); |
---|
| 630 | theStream <<"\n---- Parameters ----"<<std::endl; |
---|
| 631 | theStream << std::setfill('.'); |
---|
| 632 | const int widthText = 38; |
---|
| 633 | const int widthPar = 18; |
---|
| 634 | if(par.getFlagSubsection()) |
---|
| 635 | theStream<<std::setw(widthText)<<"Image to be analysed" |
---|
| 636 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[imageFile]" |
---|
| 637 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 638 | <<(par.getImageFile()+par.getSubsection()) <<std::endl; |
---|
| 639 | else |
---|
| 640 | theStream<<std::setw(widthText)<<"Image to be analysed" |
---|
| 641 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[imageFile]" |
---|
| 642 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 643 | <<par.getImageFile() <<std::endl; |
---|
| 644 | if(par.getFlagReconExists() && par.getFlagATrous()){ |
---|
| 645 | theStream<<std::setw(widthText)<<"Reconstructed array exists?" |
---|
| 646 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[reconExists]" |
---|
| 647 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 648 | <<stringize(par.getFlagReconExists())<<std::endl; |
---|
| 649 | theStream<<std::setw(widthText)<<"FITS file containing reconstruction" |
---|
| 650 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[reconFile]" |
---|
| 651 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 652 | <<par.getReconFile() <<std::endl; |
---|
| 653 | } |
---|
| 654 | if(par.getFlagSmoothExists() && par.getFlagSmooth()){ |
---|
| 655 | theStream<<std::setw(widthText)<<"Smoothed array exists?" |
---|
| 656 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[smoothExists]" |
---|
| 657 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 658 | <<stringize(par.getFlagSmoothExists())<<std::endl; |
---|
| 659 | theStream<<std::setw(widthText)<<"FITS file containing smoothed array" |
---|
| 660 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[smoothFile]" |
---|
| 661 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 662 | <<par.getSmoothFile() <<std::endl; |
---|
| 663 | } |
---|
| 664 | theStream <<std::setw(widthText)<<"Intermediate Logfile" |
---|
| 665 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[logFile]" |
---|
| 666 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 667 | <<par.getLogFile() <<std::endl; |
---|
| 668 | theStream <<std::setw(widthText)<<"Final Results file" |
---|
| 669 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[outFile]" |
---|
| 670 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 671 | <<par.getOutFile() <<std::endl; |
---|
| 672 | if(par.getFlagSeparateHeader()) |
---|
| 673 | theStream <<std::setw(widthText)<<"Header for results file" |
---|
| 674 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[headerFile]" |
---|
| 675 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 676 | <<par.getHeaderFile() <<std::endl; |
---|
| 677 | theStream <<std::setw(widthText)<<"Spectrum file" |
---|
| 678 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[spectraFile]" |
---|
| 679 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 680 | <<par.getSpectraFile() <<std::endl; |
---|
| 681 | if(par.getFlagVOT()){ |
---|
| 682 | theStream<<std::setw(widthText)<<"VOTable file" |
---|
| 683 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[votFile]" |
---|
| 684 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 685 | <<par.getVOTFile() <<std::endl; |
---|
| 686 | } |
---|
| 687 | if(par.getFlagKarma()){ |
---|
| 688 | theStream<<std::setw(widthText)<<"Karma annotation file" |
---|
| 689 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[karmaFile]" |
---|
| 690 | <<" = " <<resetiosflags(std::ios::right) |
---|
[172] | 691 | |
---|
[378] | 692 | <<par.getKarmaFile() <<std::endl; |
---|
| 693 | } |
---|
| 694 | if(par.getFlagMaps()){ |
---|
| 695 | theStream<<std::setw(widthText)<<"0th Moment Map" |
---|
| 696 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[momentMap]" |
---|
[275] | 697 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 698 | <<par.getMomentMap() <<std::endl; |
---|
| 699 | theStream<<std::setw(widthText)<<"Detection Map" |
---|
| 700 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[detectionMap]" |
---|
[275] | 701 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 702 | <<par.getDetectionMap() <<std::endl; |
---|
| 703 | } |
---|
| 704 | theStream <<std::setw(widthText)<<"Display a map in a pgplot xwindow?" |
---|
| 705 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagXOutput]" |
---|
[275] | 706 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 707 | <<stringize(par.getFlagXOutput()) <<std::endl; |
---|
| 708 | if(par.getFlagATrous()){ |
---|
| 709 | theStream<<std::setw(widthText)<<"Saving reconstructed cube?" |
---|
| 710 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagOutputRecon]" |
---|
[275] | 711 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 712 | <<stringize(par.getFlagOutputRecon())<<std::endl; |
---|
| 713 | theStream<<std::setw(widthText)<<"Saving residuals from reconstruction?" |
---|
| 714 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagOutputResid]" |
---|
| 715 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 716 | <<stringize(par.getFlagOutputResid())<<std::endl; |
---|
| 717 | } |
---|
| 718 | if(par.getFlagSmooth()){ |
---|
| 719 | theStream<<std::setw(widthText)<<"Saving smoothed cube?" |
---|
| 720 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagOutputSmooth]" |
---|
| 721 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 722 | <<stringize(par.getFlagOutputSmooth())<<std::endl; |
---|
| 723 | } |
---|
[379] | 724 | theStream<<std::setw(widthText)<<"Saving mask cube?" |
---|
| 725 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagOutputMask]" |
---|
| 726 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 727 | <<stringize(par.getFlagOutputMask())<<std::endl; |
---|
[378] | 728 | theStream <<"------"<<std::endl; |
---|
| 729 | if(par.getFlagBlankPix()){ |
---|
| 730 | theStream<<std::setw(widthText)<<"Blank Pixel Value" |
---|
| 731 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<< "" |
---|
| 732 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 733 | <<par.getBlankPixVal() <<std::endl; |
---|
[275] | 734 | } |
---|
[378] | 735 | theStream <<std::setw(widthText)<<"Trimming Blank Pixels?" |
---|
| 736 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagTrim]" |
---|
[348] | 737 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 738 | <<stringize(par.getFlagTrim()) <<std::endl; |
---|
| 739 | theStream <<std::setw(widthText)<<"Searching for Negative features?" |
---|
| 740 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagNegative]" |
---|
| 741 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 742 | <<stringize(par.getFlagNegative()) <<std::endl; |
---|
| 743 | theStream <<std::setw(widthText)<<"Removing Milky Way channels?" |
---|
| 744 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagMW]" |
---|
| 745 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 746 | <<stringize(par.getFlagMW()) <<std::endl; |
---|
| 747 | if(par.getFlagMW()){ |
---|
| 748 | theStream<<std::setw(widthText)<<"Milky Way Channels" |
---|
| 749 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[minMW - maxMW]" |
---|
| 750 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 751 | <<par.getMinMW() |
---|
| 752 | <<"-" <<par.getMaxMW() <<std::endl; |
---|
[348] | 753 | } |
---|
[378] | 754 | theStream <<std::setw(widthText)<<"Beam Size (pixels)" |
---|
| 755 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<< beamParam |
---|
[348] | 756 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 757 | <<par.getBeamSize() <<std::endl; |
---|
| 758 | theStream <<std::setw(widthText)<<"Removing baselines before search?" |
---|
| 759 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagBaseline]" |
---|
| 760 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 761 | <<stringize(par.getFlagBaseline()) <<std::endl; |
---|
| 762 | theStream <<std::setw(widthText)<<"Smoothing each spectrum first?" |
---|
| 763 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagSmooth]" |
---|
| 764 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 765 | <<stringize(par.getFlagSmooth()) <<std::endl; |
---|
| 766 | if(par.getFlagSmooth()){ |
---|
| 767 | theStream<<std::setw(widthText)<<"Type of smoothing" |
---|
| 768 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[smoothType]" |
---|
| 769 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 770 | <<par.getSmoothType() <<std::endl; |
---|
| 771 | if(par.getSmoothType()=="spectral") |
---|
| 772 | theStream<<std::setw(widthText)<<"Width of hanning filter" |
---|
| 773 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[hanningWidth]" |
---|
| 774 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 775 | <<par.getHanningWidth() <<std::endl; |
---|
| 776 | else{ |
---|
| 777 | theStream<<std::setw(widthText)<<"Gaussian kernel semi-major axis [pix]" |
---|
| 778 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[kernMaj]" |
---|
| 779 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 780 | <<par.getKernMaj() << std::endl; |
---|
| 781 | theStream<<std::setw(widthText)<<"Gaussian kernel semi-minor axis [pix]" |
---|
| 782 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[kernMin]" |
---|
| 783 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 784 | <<par.getKernMin() << std::endl; |
---|
| 785 | theStream<<std::setw(widthText)<<"Gaussian kernel position angle [deg]" |
---|
| 786 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[kernPA]" |
---|
| 787 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 788 | <<par.getKernPA() << std::endl; |
---|
| 789 | } |
---|
[348] | 790 | } |
---|
[378] | 791 | theStream <<std::setw(widthText)<<"Using A Trous reconstruction?" |
---|
| 792 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagATrous]" |
---|
[189] | 793 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 794 | <<stringize(par.getFlagATrous()) <<std::endl; |
---|
| 795 | if(par.getFlagATrous()){ |
---|
| 796 | theStream<<std::setw(widthText)<<"Number of dimensions in reconstruction" |
---|
| 797 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[reconDim]" |
---|
| 798 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 799 | <<par.getReconDim() <<std::endl; |
---|
| 800 | if(par.getMaxScale()>0){ |
---|
| 801 | theStream<<std::setw(widthText-1)<<"Scales used in reconstruction" |
---|
| 802 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[scaleMin-scaleMax]" |
---|
| 803 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 804 | <<par.getMinScale() << "-" << par.getMaxScale() <<std::endl; |
---|
| 805 | } |
---|
| 806 | else{ |
---|
| 807 | theStream<<std::setw(widthText)<<"Minimum scale in reconstruction" |
---|
| 808 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[scaleMin]" |
---|
| 809 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 810 | <<par.getMinScale() <<std::endl; |
---|
| 811 | } |
---|
| 812 | theStream<<std::setw(widthText)<<"SNR Threshold within reconstruction" |
---|
| 813 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[snrRecon]" |
---|
| 814 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 815 | <<par.getAtrousCut() <<std::endl; |
---|
| 816 | theStream<<std::setw(widthText)<<"Filter being used for reconstruction" |
---|
| 817 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[filterCode]" |
---|
| 818 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 819 | <<par.getFilterCode() |
---|
| 820 | << " (" << par.getFilterName() << ")" <<std::endl; |
---|
| 821 | } |
---|
[385] | 822 | theStream <<std::setw(widthText)<<"Using Robust statistics?" |
---|
| 823 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagRobustStats]" |
---|
| 824 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 825 | <<stringize(par.getFlagRobustStats()) <<std::endl; |
---|
[378] | 826 | if(par.getFlagStatSec()){ |
---|
| 827 | theStream<<std::setw(widthText)<<"Section used by statistics calculation" |
---|
| 828 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[statSec]" |
---|
| 829 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 830 | <<par.statSec.getSection() <<std::endl; |
---|
[189] | 831 | } |
---|
[378] | 832 | theStream <<std::setw(widthText)<<"Using FDR analysis?" |
---|
| 833 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagFDR]" |
---|
[189] | 834 | <<" = " <<resetiosflags(std::ios::right) |
---|
[378] | 835 | <<stringize(par.getFlagFDR()) <<std::endl; |
---|
| 836 | if(par.getFlagFDR()){ |
---|
| 837 | theStream<<std::setw(widthText)<<"Alpha value for FDR analysis" |
---|
| 838 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[alphaFDR]" |
---|
| 839 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 840 | <<par.getAlpha() <<std::endl; |
---|
| 841 | } |
---|
| 842 | else { |
---|
| 843 | if(par.getFlagUserThreshold()){ |
---|
| 844 | theStream<<std::setw(widthText)<<"Detection Threshold" |
---|
| 845 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[threshold]" |
---|
| 846 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 847 | <<par.getThreshold() <<std::endl; |
---|
| 848 | } |
---|
| 849 | else{ |
---|
| 850 | theStream<<std::setw(widthText)<<"SNR Threshold (in sigma)" |
---|
| 851 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[snrCut]" |
---|
| 852 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 853 | <<par.getCut() <<std::endl; |
---|
| 854 | } |
---|
[189] | 855 | } |
---|
[378] | 856 | theStream <<std::setw(widthText)<<"Minimum # Pixels in a detection" |
---|
| 857 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[minPix]" |
---|
| 858 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 859 | <<par.getMinPix() <<std::endl; |
---|
| 860 | theStream <<std::setw(widthText)<<"Minimum # Channels in a detection" |
---|
| 861 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[minChannels]" |
---|
| 862 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 863 | <<par.getMinChannels() <<std::endl; |
---|
| 864 | theStream <<std::setw(widthText)<<"Growing objects after detection?" |
---|
| 865 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagGrowth]" |
---|
| 866 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 867 | <<stringize(par.getFlagGrowth()) <<std::endl; |
---|
| 868 | if(par.getFlagGrowth()) { |
---|
| 869 | theStream<<std::setw(widthText)<<"SNR Threshold for growth" |
---|
| 870 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[growthCut]" |
---|
| 871 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 872 | <<par.getGrowthCut() <<std::endl; |
---|
| 873 | } |
---|
| 874 | theStream <<std::setw(widthText)<<"Using Adjacent-pixel criterion?" |
---|
| 875 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[flagAdjacent]" |
---|
| 876 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 877 | <<stringize(par.getFlagAdjacent()) <<std::endl; |
---|
| 878 | if(!par.getFlagAdjacent()){ |
---|
| 879 | theStream<<std::setw(widthText)<<"Max. spatial separation for merging" |
---|
| 880 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[threshSpatial]" |
---|
| 881 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 882 | <<par.getThreshS() <<std::endl; |
---|
| 883 | } |
---|
| 884 | theStream <<std::setw(widthText)<<"Max. velocity separation for merging" |
---|
| 885 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[threshVelocity]" |
---|
| 886 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 887 | <<par.getThreshV() <<std::endl; |
---|
| 888 | theStream <<std::setw(widthText)<<"Method of spectral plotting" |
---|
| 889 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[spectralMethod]" |
---|
| 890 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 891 | <<par.getSpectralMethod() <<std::endl; |
---|
| 892 | theStream <<std::setw(widthText)<<"Type of object centre used in results" |
---|
| 893 | <<std::setw(widthPar)<<setiosflags(std::ios::right)<<"[pixelCentre]" |
---|
| 894 | <<" = " <<resetiosflags(std::ios::right) |
---|
| 895 | <<par.getPixelCentre() <<std::endl; |
---|
| 896 | theStream <<"--------------------\n\n"; |
---|
| 897 | theStream << std::setfill(' '); |
---|
| 898 | theStream.unsetf(std::ios::left); |
---|
| 899 | // theStream.unsetf(std::ios::boolalpha); |
---|
| 900 | return theStream; |
---|
[3] | 901 | } |
---|
| 902 | |
---|
[120] | 903 | |
---|
[378] | 904 | void Param::copyHeaderInfo(FitsHeader &head) |
---|
| 905 | { |
---|
| 906 | /** |
---|
| 907 | * A function to copy across relevant header keywords from the |
---|
| 908 | * FitsHeader class to the Param class, as they are needed by |
---|
| 909 | * functions in the Param class. |
---|
| 910 | * The parameters are the keywords BLANK, BSCALE, BZERO, and the beam size. |
---|
| 911 | */ |
---|
[112] | 912 | |
---|
[378] | 913 | this->blankKeyword = head.getBlankKeyword(); |
---|
| 914 | this->bscaleKeyword = head.getBscaleKeyword(); |
---|
| 915 | this->bzeroKeyword = head.getBzeroKeyword(); |
---|
| 916 | this->blankPixValue = this->blankKeyword * this->bscaleKeyword + |
---|
| 917 | this->bzeroKeyword; |
---|
[112] | 918 | |
---|
[378] | 919 | this->numPixBeam = head.getBeamSize(); |
---|
| 920 | } |
---|
[112] | 921 | |
---|
[379] | 922 | std::string Param::outputMaskFile() |
---|
| 923 | { |
---|
| 924 | /** |
---|
| 925 | * This function produces the required filename in which to save |
---|
| 926 | * the mask image, indicating which pixels have been detected as |
---|
| 927 | * part of an object. If the input image is image.fits, then the |
---|
| 928 | * output will be image.MASK.fits. |
---|
| 929 | */ |
---|
| 930 | std::string inputName = this->imageFile; |
---|
| 931 | std::stringstream ss; |
---|
| 932 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 933 | // remove the ".fits" on the end. |
---|
| 934 | ss << ".MASK.fits"; |
---|
| 935 | return ss.str(); |
---|
| 936 | } |
---|
| 937 | |
---|
[378] | 938 | std::string Param::outputSmoothFile() |
---|
| 939 | { |
---|
| 940 | /** |
---|
| 941 | * This function produces the required filename in which to save |
---|
| 942 | * the smoothed array. If the input image is image.fits, then |
---|
| 943 | * the output will be: |
---|
| 944 | * <ul><li> Spectral smoothing: image.SMOOTH-1D-3.fits, where the |
---|
| 945 | * width of the Hanning filter was 3 pixels. |
---|
| 946 | * <li> Spatial smoothing : image.SMOOTH-2D-3-2-20.fits, where |
---|
| 947 | * kernMaj=3, kernMin=2 and kernPA=20 degrees. |
---|
| 948 | * </ul> |
---|
| 949 | */ |
---|
| 950 | std::string inputName = this->imageFile; |
---|
| 951 | std::stringstream ss; |
---|
| 952 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 953 | // remove the ".fits" on the end. |
---|
| 954 | if(this->flagSubsection) ss<<".sub"; |
---|
| 955 | if(this->smoothType=="spectral") |
---|
| 956 | ss << ".SMOOTH-1D-" << this->hanningWidth << ".fits"; |
---|
| 957 | else if(this->smoothType=="spatial") |
---|
| 958 | ss << ".SMOOTH-2D-" |
---|
| 959 | << this->kernMaj << "-" |
---|
| 960 | << this->kernMin << "-" |
---|
| 961 | << this->kernPA << ".fits"; |
---|
| 962 | return ss.str(); |
---|
| 963 | } |
---|
[208] | 964 | |
---|
[378] | 965 | std::string Param::outputReconFile() |
---|
| 966 | { |
---|
| 967 | /** |
---|
| 968 | * This function produces the required filename in which to save |
---|
| 969 | * the reconstructed array. If the input image is image.fits, then |
---|
| 970 | * the output will be eg. image.RECON-3-2-4-1.fits, where the numbers are |
---|
| 971 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=minScale |
---|
| 972 | */ |
---|
| 973 | std::string inputName = this->imageFile; |
---|
| 974 | std::stringstream ss; |
---|
| 975 | // First we remove the ".fits" from the end of the filename. |
---|
| 976 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 977 | if(this->flagSubsection) ss<<".sub"; |
---|
| 978 | ss << ".RECON-" << this->reconDim |
---|
| 979 | << "-" << this->filterCode |
---|
| 980 | << "-" << this->snrRecon |
---|
| 981 | << "-" << this->scaleMin |
---|
| 982 | << ".fits"; |
---|
| 983 | return ss.str(); |
---|
| 984 | } |
---|
[103] | 985 | |
---|
[378] | 986 | std::string Param::outputResidFile() |
---|
| 987 | { |
---|
| 988 | /** |
---|
| 989 | * This function produces the required filename in which to save |
---|
| 990 | * the reconstructed array. If the input image is image.fits, then |
---|
| 991 | * the output will be eg. image.RESID-3-2-4-1.fits, where the numbers are |
---|
| 992 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=scaleMin |
---|
| 993 | */ |
---|
| 994 | std::string inputName = this->imageFile; |
---|
| 995 | std::stringstream ss; |
---|
| 996 | // First we remove the ".fits" from the end of the filename. |
---|
| 997 | ss << inputName.substr(0,inputName.size()-5); |
---|
| 998 | if(this->flagSubsection) ss<<".sub"; |
---|
| 999 | ss << ".RESID-" << this->reconDim |
---|
| 1000 | << "-" << this->filterCode |
---|
| 1001 | << "-" << this->snrRecon |
---|
| 1002 | << "-" << this->scaleMin |
---|
| 1003 | << ".fits"; |
---|
| 1004 | return ss.str(); |
---|
| 1005 | } |
---|
| 1006 | |
---|
[103] | 1007 | } |
---|