[3] | 1 | #include <iostream> |
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| 2 | #include <iomanip> |
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| 3 | #include <fstream> |
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| 4 | #include <sstream> |
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| 5 | #include <string> |
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| 6 | #include <math.h> |
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| 7 | #include <param.hh> |
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| 8 | |
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| 9 | using std::setw; |
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| 10 | using std::endl; |
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| 11 | |
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| 12 | /****************************************************************/ |
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| 13 | /////////////////////////////////////////////////// |
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| 14 | //// Accessor Functions for Parameter class: |
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| 15 | /////////////////////////////////////////////////// |
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| 16 | Param::Param(){ |
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| 17 | /** |
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| 18 | * Param() |
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| 19 | * Default intial values for the parameters. |
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| 20 | * imageFile has no default value! |
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| 21 | */ |
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| 22 | // Input files |
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| 23 | this->imageFile = ""; |
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| 24 | this->flagSubsection = false; |
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| 25 | this->subsection = "[*,*,*]"; |
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| 26 | // Output files |
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| 27 | this->flagLog = true; |
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| 28 | this->logFile = "./duchamp-Logfile"; |
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| 29 | this->outFile = "./duchamp-Results"; |
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| 30 | this->spectraFile = "./duchamp-Spectra.ps"; |
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| 31 | this->flagOutputRecon = false; |
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| 32 | this->flagOutputResid = false; |
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| 33 | this->flagVOT = false; |
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| 34 | this->votFile = "./duchamp-Results.xml"; |
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[20] | 35 | this->flagKarma = false; |
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| 36 | this->karmaFile = "./duchamp-Results.ann"; |
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[3] | 37 | this->flagMaps = true; |
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| 38 | this->detectionMap = "./latest-detection-map.ps"; |
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| 39 | this->momentMap = "./latest-moment-map.ps"; |
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| 40 | // Cube related parameters |
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| 41 | this->flagBlankPix = true; |
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| 42 | this->blankPixValue = -8.00061; |
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| 43 | this->blankKeyword = 1; |
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| 44 | this->bscaleKeyword = -8.00061; |
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| 45 | this->bzeroKeyword = 0.; |
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| 46 | this->nanAsBlank = false; |
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| 47 | this->flagMW = true; |
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| 48 | this->maxMW = 112; |
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| 49 | this->minMW = 75; |
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| 50 | this->numPixBeam = 0.; |
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| 51 | // Trim-related |
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| 52 | this->flagTrimmed = false; |
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| 53 | this->borderLeft = 0; |
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| 54 | this->borderRight = 0; |
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| 55 | this->borderBottom = 0; |
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| 56 | this->borderTop = 0; |
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| 57 | // Subsection offsets |
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| 58 | this->xSubOffset = 0; |
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| 59 | this->ySubOffset = 0; |
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| 60 | this->zSubOffset = 0; |
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| 61 | // Baseline related |
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| 62 | this->flagBaseline = false; |
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| 63 | // Detection-related |
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[13] | 64 | this->minPix = 2; |
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[3] | 65 | // Object growth |
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| 66 | this->flagGrowth = true; |
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| 67 | this->growthCut = 1.5; |
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| 68 | // FDR analysis |
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| 69 | this->flagFDR = false; |
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| 70 | this->alphaFDR = 0.01; |
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| 71 | // Other detection |
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| 72 | this->snrCut = 3.; |
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| 73 | // A trous reconstruction parameters |
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| 74 | this->flagATrous = true; |
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| 75 | this->scaleMin = 1; |
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| 76 | this->snrRecon = 4.; |
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| 77 | this->filterCode = 2; |
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| 78 | // Volume-merging parameters |
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| 79 | this->flagAdjacent = true; |
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| 80 | this->threshSpatial = 3.; |
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| 81 | this->threshVelocity = 7.; |
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| 82 | this->minChannels = 3; |
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| 83 | // Input-Output related |
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| 84 | this->borders = true; |
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| 85 | this->verbose = true; |
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| 86 | }; |
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| 87 | |
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| 88 | /****************************************************************/ |
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| 89 | /////////////////////////////////////////////////// |
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| 90 | //// Other Functions using the Parameter class: |
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| 91 | /////////////////////////////////////////////////// |
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| 92 | |
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| 93 | string makelower( string s ) |
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| 94 | { |
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| 95 | // "borrowed" from Matt Howlett's 'fred' |
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| 96 | string out = ""; |
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| 97 | for( int i=0; i<s.size(); ++i ) { |
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| 98 | out += tolower(s[i]); |
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| 99 | } |
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| 100 | return out; |
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| 101 | } |
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| 102 | |
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| 103 | void Param::readParams(string ¶mfile) |
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| 104 | { |
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| 105 | |
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| 106 | std::ifstream fin(paramfile.c_str()); |
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| 107 | string line; |
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| 108 | string sval; |
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| 109 | float fval; |
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| 110 | int ival; |
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| 111 | bool bval; |
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| 112 | while( !std::getline(fin,line,'\n').eof()){ |
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| 113 | |
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| 114 | if(line[0]!='#'){ |
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| 115 | std::stringstream ss; |
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| 116 | ss.str(line); |
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| 117 | string arg; |
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| 118 | ss >> arg; |
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| 119 | if(makelower(arg)=="imagefile"){ ss >> sval; this->imageFile = sval;} |
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| 120 | if(makelower(arg)=="flaglog"){ ss >> bval; this->flagLog = bval; } |
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| 121 | if(makelower(arg)=="logfile"){ ss >> sval; this->logFile = sval; } |
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| 122 | if(makelower(arg)=="outfile"){ ss >> sval; this->outFile = sval; } |
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| 123 | if(makelower(arg)=="spectrafile"){ ss >> sval; this->spectraFile = sval; } |
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| 124 | if(makelower(arg)=="flagoutputrecon"){ ss >> bval; this->flagOutputRecon = bval; } |
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| 125 | if(makelower(arg)=="flagoutputresid"){ ss >> bval; this->flagOutputResid = bval; } |
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| 126 | if(makelower(arg)=="flagvot"){ ss >> bval; this->flagVOT = bval; } |
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| 127 | if(makelower(arg)=="votfile"){ ss >> sval; this->votFile = sval; } |
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[20] | 128 | if(makelower(arg)=="flagkarma"){ ss >> bval; this->flagKarma = bval; } |
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| 129 | if(makelower(arg)=="karmafile"){ ss >> sval; this->karmaFile = sval; } |
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[3] | 130 | if(makelower(arg)=="flagmaps"){ ss >> bval; this->flagMaps = bval; } |
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| 131 | if(makelower(arg)=="detectionmap"){ ss >> sval; this->detectionMap = sval; } |
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| 132 | if(makelower(arg)=="momentmap"){ ss >> sval; this->momentMap = sval; } |
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| 133 | |
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| 134 | if(makelower(arg)=="flagblankpix"){ ss >> bval; this->flagBlankPix = bval; } |
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| 135 | if(makelower(arg)=="blankpixvalue"){ ss >> fval; this->blankPixValue = fval; } |
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| 136 | if(makelower(arg)=="flagmw"){ ss >> bval; this->flagMW = bval; } |
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| 137 | if(makelower(arg)=="maxmw"){ ss >> ival; this->maxMW = ival; } |
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| 138 | if(makelower(arg)=="minmw"){ ss >> ival; this->minMW = ival; } |
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| 139 | if(makelower(arg)=="minpix"){ ss >> ival; this->minPix = ival; } |
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| 140 | if(makelower(arg)=="flagfdr"){ ss >> bval; this->flagFDR = bval; } |
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| 141 | if(makelower(arg)=="alphafdr"){ ss >> fval; this->alphaFDR = fval; } |
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| 142 | if(makelower(arg)=="flagbaseline"){ ss >> bval; this->flagBaseline = bval; } |
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| 143 | if(makelower(arg)=="snrcut"){ ss >> fval; this->snrCut = fval; } |
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| 144 | if(makelower(arg)=="flaggrowth"){ ss >> bval; this->flagGrowth = bval; } |
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| 145 | if(makelower(arg)=="growthcut"){ ss >> fval; this->growthCut = fval; } |
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| 146 | if(makelower(arg)=="flagatrous"){ ss >> bval; this->flagATrous = bval; } |
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| 147 | if(makelower(arg)=="scalemin"){ ss >> ival; this->scaleMin = ival; } |
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| 148 | if(makelower(arg)=="snrrecon"){ ss >> fval; this->snrRecon = fval; } |
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| 149 | if(makelower(arg)=="filtercode"){ ss >> ival; this->filterCode = ival; } |
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| 150 | if(makelower(arg)=="flagadjacent"){ ss >> bval; this->flagAdjacent = bval; } |
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| 151 | if(makelower(arg)=="threshspatial"){ ss >> fval; this->threshSpatial = fval; } |
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| 152 | if(makelower(arg)=="threshvelocity"){ ss >> fval; this->threshVelocity = fval; } |
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| 153 | if(makelower(arg)=="minchannels"){ ss >> ival; this->minChannels = ival; } |
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| 154 | if(makelower(arg)=="flagsubsection"){ ss >> bval; this->flagSubsection = bval; } |
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| 155 | if(makelower(arg)=="subsection"){ ss >> sval; this->subsection = sval; } |
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| 156 | if(makelower(arg)=="drawborders"){ ss >> bval; this->borders = bval; } |
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| 157 | if(makelower(arg)=="verbose"){ ss >> bval; this->verbose = bval; } |
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| 158 | } |
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| 159 | } |
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| 160 | } |
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| 161 | |
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| 162 | |
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| 163 | std::ostream& operator<< ( std::ostream& theStream, Param& par) |
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| 164 | { |
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| 165 | theStream.setf(std::ios::boolalpha); |
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| 166 | theStream.setf(std::ios::left); |
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| 167 | theStream <<"---- Parameters ----"<<endl; |
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| 168 | if(par.getFlagSubsection()) |
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| 169 | theStream<<setw(40)<<"Image to be analysed" <<"= "<<(par.getImageFile()+ |
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| 170 | par.getSubsection()) <<endl; |
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| 171 | else |
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| 172 | theStream<<setw(40)<<"Image to be analysed" <<"= "<<par.getImageFile() <<endl; |
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| 173 | theStream <<setw(40)<<"Intermediate Logfile" <<"= "<<par.getLogFile() <<endl; |
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| 174 | theStream <<setw(40)<<"Final Results file" <<"= "<<par.getOutFile() <<endl; |
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| 175 | theStream <<setw(40)<<"Spectrum file" <<"= "<<par.getSpectraFile() <<endl; |
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| 176 | if(par.getFlagVOT()){ |
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| 177 | theStream<<setw(40)<<"VOTable file" <<"= "<<par.getVOTFile() <<endl; |
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| 178 | } |
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[20] | 179 | if(par.getFlagKarma()){ |
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| 180 | theStream<<setw(40)<<"Karma annotation file" <<"= "<<par.getKarmaFile() <<endl; |
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| 181 | } |
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[3] | 182 | if(par.getFlagMaps()){ |
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[17] | 183 | theStream<<setw(40)<<"0th Moment Map" <<"= "<<par.getMomentMap() <<endl; |
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[3] | 184 | theStream<<setw(40)<<"Detection Map" <<"= "<<par.getDetectionMap() <<endl; |
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| 185 | } |
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| 186 | if(par.getFlagATrous()){ |
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| 187 | theStream<<setw(40)<<"Saving reconstructed cube?" <<"= "<<par.getFlagOutputRecon()<<endl; |
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| 188 | theStream<<setw(40)<<"Saving residuals from reconstruction?"<<"= "<<par.getFlagOutputResid()<<endl; |
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| 189 | } |
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| 190 | theStream <<"------"<<endl; |
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| 191 | theStream <<setw(40)<<"Fixing Blank Pixels?" <<"= "<<par.getFlagBlankPix() <<endl; |
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| 192 | if(par.getFlagBlankPix()){ |
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| 193 | theStream<<setw(40)<<"Blank Pixel Value" <<"= "<<par.getBlankPixVal() <<endl; |
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| 194 | } |
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| 195 | theStream <<setw(40)<<"Removing Milky Way channels?" <<"= "<<par.getFlagMW() <<endl; |
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| 196 | if(par.getFlagMW()){ |
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| 197 | theStream<<setw(40)<<"Milky Way Channels" <<"= "<<par.getMinMW() |
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| 198 | <<"-" <<par.getMaxMW() <<endl; |
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| 199 | } |
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| 200 | theStream <<setw(40)<<"Beam Size (pixels)" <<"= "<<par.getBeamSize() <<endl; |
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| 201 | theStream <<setw(40)<<"Removing baselines before search?" <<"= "<<par.getFlagBaseline() <<endl; |
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| 202 | theStream <<setw(40)<<"Minimum # Pixels in a detection" <<"= "<<par.getMinPix() <<endl; |
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| 203 | theStream <<setw(40)<<"Growing objects after detection?" <<"= "<<par.getFlagGrowth() <<endl; |
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| 204 | if(par.getFlagGrowth()) { |
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| 205 | theStream<<setw(40)<<"SNR Threshold for growth" <<"= "<<par.getGrowthCut() <<endl; |
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| 206 | } |
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| 207 | theStream <<setw(40)<<"Using A Trous reconstruction?" <<"= "<<par.getFlagATrous() <<endl; |
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| 208 | if(par.getFlagATrous()){ |
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| 209 | theStream<<setw(40)<<"Minimum scale in reconstruction" <<"= "<<par.getMinScale() <<endl; |
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| 210 | theStream<<setw(40)<<"SNR Threshold within reconstruction" <<"= "<<par.getAtrousCut() <<endl; |
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| 211 | theStream<<setw(40)<<"Filter being used for reconstruction" <<"= "<<par.getFilterName() <<endl; |
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| 212 | } |
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| 213 | theStream <<setw(40)<<"Using FDR analysis?" <<"= "<<par.getFlagFDR() <<endl; |
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| 214 | if(par.getFlagFDR()){ |
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| 215 | theStream<<setw(40)<<"Alpha value for FDR analysis" <<"= "<<par.getAlpha() <<endl; |
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| 216 | } |
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| 217 | else { |
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| 218 | theStream<<setw(40)<<"SNR Threshold" <<"= "<<par.getCut() <<endl; |
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| 219 | } |
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| 220 | theStream <<setw(40)<<"Using Adjacent-pixel criterion?" <<"= "<<par.getFlagAdjacent() <<endl; |
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| 221 | if(!par.getFlagAdjacent()){ |
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| 222 | theStream<<setw(40)<<"Max. spatial separation for merging" <<"= "<<par.getThreshS() <<endl; |
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| 223 | } |
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[42] | 224 | theStream <<setw(40)<<"Max. velocity separation for merging" <<"= "<<par.getThreshV() <<endl; |
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[3] | 225 | theStream <<setw(40)<<"Min. # channels for merging" <<"= "<<par.getMinChannels() <<endl; |
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| 226 | theStream <<"--------------------"<<endl; |
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| 227 | theStream.unsetf(std::ios::left); |
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| 228 | theStream.unsetf(std::ios::boolalpha); |
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| 229 | } |
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| 230 | |
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| 231 | void Param::parseSubsection() |
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| 232 | { |
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| 233 | std::stringstream ss; |
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| 234 | ss.str(this->subsection); |
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| 235 | bool removeStep = false; |
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| 236 | string x,y,z; |
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| 237 | getline(ss,x,'['); |
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| 238 | getline(ss,x,','); |
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| 239 | getline(ss,y,','); |
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| 240 | getline(ss,z,']'); |
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| 241 | char *end; |
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| 242 | if(x!="*") { |
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| 243 | int x1,x2,dx; |
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| 244 | int a = x.find(':'); // first occurence of ':' in x-subsection string |
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| 245 | int b = x.find(':',a+1); // location of second ':' -- will be -1 if there is no second occurence. |
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| 246 | x1 = atoi( x.substr(0,a).c_str() ); // minimum x in subsection |
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| 247 | this->xSubOffset = x1 - 1; |
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| 248 | if(b>0){ // there is a dx component |
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| 249 | x2 = atoi( x.substr(a+1,b-a-1).c_str() ); // maximum x in subsection |
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| 250 | dx = atoi( x.substr(b+1,x.size()).c_str() ); // delta x in subsection |
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| 251 | x = x.substr(0,b); // rewrite x without the delta-x part. |
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| 252 | removeStep = true; |
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| 253 | } |
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| 254 | } |
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| 255 | if(y!="*") { |
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| 256 | int y1,y2,dy; |
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| 257 | int a = y.find(':'); // first occurence of ':' in y-subsection string |
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| 258 | int b = y.find(':',a+1); // location of second ':' -- will be -1 if there is no second occurence. |
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| 259 | y1 = atoi( y.substr(0,a).c_str() ); // minimum y in subsection |
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| 260 | this->ySubOffset = y1 - 1; |
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| 261 | if(b>0){ // there is a dy component |
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| 262 | y2 = atoi( y.substr(a+1,b-a-1).c_str() ); // maximum y in subsection |
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| 263 | dy = atoi( y.substr(b+1,y.size()).c_str() ); // delta y in subsection |
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| 264 | y = y.substr(0,b); // rewrite y without the delta-y part. |
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| 265 | removeStep = true; |
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| 266 | } |
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| 267 | } |
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| 268 | if(z!="*") { |
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| 269 | int z1,z2,dz; |
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| 270 | int a = z.find(':'); // first occurence of ':' in z-subsection string |
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| 271 | int b = z.find(':',a+1); // location of second ':' -- will be -1 if there is no second occurence. |
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| 272 | z1 = atoi( z.substr(0,a).c_str() ); // minimum z in subsection |
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| 273 | this->zSubOffset = z1 - 1; |
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| 274 | if(b>0){ // there is a dz component |
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| 275 | z2 = atoi( z.substr(a+1,b-a-1).c_str() ); // maximum z in subsection |
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| 276 | dz = atoi( z.substr(b+1,z.size()).c_str() ); // delta z in subsection |
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| 277 | z = z.substr(0,b); // rewrite z without the delta-z part. |
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| 278 | removeStep = true; |
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| 279 | } |
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| 280 | } |
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| 281 | |
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| 282 | if(removeStep){ |
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| 283 | std::cerr << "\a\tThe subsection given is " << this->subsection <<".\n"; |
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| 284 | std::cerr << "\tDuchamp is currently unable to deal with pixel steps in the subsection.\n"; |
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| 285 | std::cerr << "\tThese have been ignored, and so the subection used is "; |
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| 286 | this->subsection = "[" + x + "," + y + "," + z + "]"; // rewrite subsection without any step sizes. |
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| 287 | std::cerr << this->subsection << std::endl; |
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| 288 | } |
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| 289 | |
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| 290 | // if(x!="*") this->xSubOffset = strtol(x.c_str(),&end,10) - 1; |
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| 291 | // if(y!="*") this->ySubOffset = strtol(y.c_str(),&end,10) - 1; |
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| 292 | // if(z!="*") this->zSubOffset = strtol(z.c_str(),&end,10) - 1; |
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| 293 | } |
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| 294 | |
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| 295 | bool Param::isBlank(float &val) |
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| 296 | { |
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| 297 | // std::cerr << "val = " << val << " " << int((val-this->bzeroKeyword)/this->bscaleKeyword) |
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| 298 | // <<" " <<this->blankKeyword << std::endl; |
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| 299 | if(this->flagBlankPix){ |
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| 300 | if(this->nanAsBlank) return bool(isnan(val)); |
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| 301 | else// return (val == this->blankPixValue); |
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| 302 | return ( this->blankKeyword == int((val-this->bzeroKeyword)/this->bscaleKeyword) ); |
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| 303 | } |
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| 304 | else return false; |
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| 305 | } |
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