1 | //
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2 | // C++ Implementation: Scantable
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3 | //
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4 | // Description:
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5 | //
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6 | //
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7 | // Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005
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8 | //
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9 | // Copyright: See COPYING file that comes with this distribution
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10 | //
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11 | //
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12 | #include <map>
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13 |
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14 | #include <atnf/PKSIO/SrcType.h>
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15 |
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16 | #include <casa/aips.h>
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17 | #include <casa/iomanip.h>
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18 | #include <casa/iostream.h>
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19 | #include <casa/OS/File.h>
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20 | #include <casa/OS/Path.h>
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21 | #include <casa/Arrays/Array.h>
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22 | #include <casa/Arrays/ArrayAccessor.h>
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23 | #include <casa/Arrays/ArrayLogical.h>
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24 | #include <casa/Arrays/ArrayMath.h>
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25 | #include <casa/Arrays/MaskArrMath.h>
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26 | #include <casa/Arrays/Slice.h>
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27 | #include <casa/Arrays/Vector.h>
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28 | #include <casa/Arrays/VectorSTLIterator.h>
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29 | #include <casa/BasicMath/Math.h>
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30 | #include <casa/BasicSL/Constants.h>
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31 | #include <casa/Containers/RecordField.h>
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32 | #include <casa/Logging/LogIO.h>
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33 | #include <casa/Quanta/MVAngle.h>
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34 | #include <casa/Quanta/MVTime.h>
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35 | #include <casa/Utilities/GenSort.h>
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36 |
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37 | #include <coordinates/Coordinates/CoordinateUtil.h>
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38 |
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39 | // needed to avoid error in .tcc
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40 | #include <measures/Measures/MCDirection.h>
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41 | //
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42 | #include <measures/Measures/MDirection.h>
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43 | #include <measures/Measures/MEpoch.h>
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44 | #include <measures/Measures/MFrequency.h>
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45 | #include <measures/Measures/MeasRef.h>
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46 | #include <measures/Measures/MeasTable.h>
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47 | #include <measures/TableMeasures/ScalarMeasColumn.h>
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48 | #include <measures/TableMeasures/TableMeasDesc.h>
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49 | #include <measures/TableMeasures/TableMeasRefDesc.h>
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50 | #include <measures/TableMeasures/TableMeasValueDesc.h>
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51 |
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52 | #include <tables/Tables/ArrColDesc.h>
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53 | #include <tables/Tables/ExprNode.h>
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54 | #include <tables/Tables/ScaColDesc.h>
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55 | #include <tables/Tables/SetupNewTab.h>
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56 | #include <tables/Tables/TableCopy.h>
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57 | #include <tables/Tables/TableDesc.h>
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58 | #include <tables/Tables/TableIter.h>
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59 | #include <tables/Tables/TableParse.h>
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60 | #include <tables/Tables/TableRecord.h>
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61 | #include <tables/Tables/TableRow.h>
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62 | #include <tables/Tables/TableVector.h>
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63 |
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64 | #include "MathUtils.h"
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65 | #include "STAttr.h"
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66 | #include "STLineFinder.h"
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67 | #include "STPolCircular.h"
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68 | #include "STPolLinear.h"
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69 | #include "STPolStokes.h"
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70 | #include "STUpgrade.h"
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71 | #include "Scantable.h"
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72 |
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73 | using namespace casa;
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74 |
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75 | namespace asap {
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76 |
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77 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_;
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78 |
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79 | void Scantable::initFactories() {
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80 | if ( factories_.empty() ) {
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81 | Scantable::factories_["linear"] = &STPolLinear::myFactory;
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82 | Scantable::factories_["circular"] = &STPolCircular::myFactory;
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83 | Scantable::factories_["stokes"] = &STPolStokes::myFactory;
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84 | }
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85 | }
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86 |
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87 | Scantable::Scantable(Table::TableType ttype) :
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88 | type_(ttype)
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89 | {
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90 | initFactories();
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91 | setupMainTable();
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92 | freqTable_ = STFrequencies(*this);
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93 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
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94 | weatherTable_ = STWeather(*this);
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95 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
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96 | focusTable_ = STFocus(*this);
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97 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
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98 | tcalTable_ = STTcal(*this);
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99 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
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100 | moleculeTable_ = STMolecules(*this);
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101 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
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102 | historyTable_ = STHistory(*this);
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103 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table());
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104 | fitTable_ = STFit(*this);
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105 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table());
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106 | table_.tableInfo().setType( "Scantable" ) ;
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107 | originalTable_ = table_;
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108 | attach();
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109 | }
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110 |
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111 | Scantable::Scantable(const std::string& name, Table::TableType ttype) :
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112 | type_(ttype)
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113 | {
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114 | initFactories();
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115 |
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116 | Table tab(name, Table::Update);
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117 | uInt version = tab.keywordSet().asuInt("VERSION");
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118 | if (version != version_) {
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119 | STUpgrade upgrader(version_);
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120 | LogIO os( LogOrigin( "Scantable" ) ) ;
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121 | os << LogIO::WARN
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122 | << name << " data format version " << version
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123 | << " is deprecated" << endl
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124 | << "Running upgrade."<< endl
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125 | << LogIO::POST ;
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126 | std::string outname = upgrader.upgrade(name);
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127 | if ( outname != name ) {
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128 | os << LogIO::WARN
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129 | << "Data will be loaded from " << outname << " instead of "
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130 | << name << LogIO::POST ;
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131 | tab = Table(outname, Table::Update ) ;
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132 | }
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133 | }
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134 | if ( type_ == Table::Memory ) {
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135 | table_ = tab.copyToMemoryTable(generateName());
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136 | } else {
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137 | table_ = tab;
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138 | }
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139 | table_.tableInfo().setType( "Scantable" ) ;
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140 |
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141 | attachSubtables();
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142 | originalTable_ = table_;
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143 | attach();
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144 | }
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145 | /*
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146 | Scantable::Scantable(const std::string& name, Table::TableType ttype) :
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147 | type_(ttype)
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148 | {
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149 | initFactories();
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150 | Table tab(name, Table::Update);
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151 | uInt version = tab.keywordSet().asuInt("VERSION");
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152 | if (version != version_) {
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153 | throw(AipsError("Unsupported version of ASAP file."));
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154 | }
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155 | if ( type_ == Table::Memory ) {
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156 | table_ = tab.copyToMemoryTable(generateName());
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157 | } else {
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158 | table_ = tab;
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159 | }
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160 |
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161 | attachSubtables();
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162 | originalTable_ = table_;
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163 | attach();
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164 | }
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165 | */
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166 |
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167 | Scantable::Scantable( const Scantable& other, bool clear ):
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168 | Logger()
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169 | {
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170 | // with or without data
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171 | String newname = String(generateName());
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172 | type_ = other.table_.tableType();
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173 | if ( other.table_.tableType() == Table::Memory ) {
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174 | if ( clear ) {
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175 | table_ = TableCopy::makeEmptyMemoryTable(newname,
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176 | other.table_, True);
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177 | } else
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178 | table_ = other.table_.copyToMemoryTable(newname);
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179 | } else {
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180 | other.table_.deepCopy(newname, Table::New, False,
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181 | other.table_.endianFormat(),
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182 | Bool(clear));
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183 | table_ = Table(newname, Table::Update);
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184 | table_.markForDelete();
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185 | }
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186 | table_.tableInfo().setType( "Scantable" ) ;
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187 | /// @todo reindex SCANNO, recompute nbeam, nif, npol
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188 | if ( clear ) copySubtables(other);
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189 | attachSubtables();
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190 | originalTable_ = table_;
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191 | attach();
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192 | }
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193 |
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194 | void Scantable::copySubtables(const Scantable& other) {
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195 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
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196 | TableCopy::copyRows(t, other.freqTable_.table());
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197 | t = table_.rwKeywordSet().asTable("FOCUS");
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198 | TableCopy::copyRows(t, other.focusTable_.table());
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199 | t = table_.rwKeywordSet().asTable("WEATHER");
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200 | TableCopy::copyRows(t, other.weatherTable_.table());
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201 | t = table_.rwKeywordSet().asTable("TCAL");
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202 | TableCopy::copyRows(t, other.tcalTable_.table());
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203 | t = table_.rwKeywordSet().asTable("MOLECULES");
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204 | TableCopy::copyRows(t, other.moleculeTable_.table());
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205 | t = table_.rwKeywordSet().asTable("HISTORY");
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206 | TableCopy::copyRows(t, other.historyTable_.table());
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207 | t = table_.rwKeywordSet().asTable("FIT");
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208 | TableCopy::copyRows(t, other.fitTable_.table());
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209 | }
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210 |
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211 | void Scantable::attachSubtables()
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212 | {
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213 | freqTable_ = STFrequencies(table_);
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214 | focusTable_ = STFocus(table_);
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215 | weatherTable_ = STWeather(table_);
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216 | tcalTable_ = STTcal(table_);
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217 | moleculeTable_ = STMolecules(table_);
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218 | historyTable_ = STHistory(table_);
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219 | fitTable_ = STFit(table_);
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220 | }
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221 |
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222 | Scantable::~Scantable()
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223 | {
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224 | //cout << "~Scantable() " << this << endl;
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225 | }
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226 |
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227 | void Scantable::setupMainTable()
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228 | {
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229 | TableDesc td("", "1", TableDesc::Scratch);
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230 | td.comment() = "An ASAP Scantable";
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231 | td.rwKeywordSet().define("VERSION", uInt(version_));
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232 |
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233 | // n Cycles
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234 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
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235 | // new index every nBeam x nIF x nPol
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236 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
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237 |
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238 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
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239 | td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
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240 | // linear, circular, stokes
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241 | td.rwKeywordSet().define("POLTYPE", String("linear"));
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242 | td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
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243 |
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244 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
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245 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
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246 |
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247 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
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248 | refbeamnoColumn.setDefault(Int(-1));
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249 | td.addColumn(refbeamnoColumn);
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250 |
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251 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
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252 | flagrowColumn.setDefault(uInt(0));
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253 | td.addColumn(flagrowColumn);
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254 |
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255 | td.addColumn(ScalarColumnDesc<Double>("TIME"));
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256 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
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257 | TableMeasValueDesc measVal(td, "TIME");
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258 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
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259 | mepochCol.write(td);
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260 |
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261 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
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262 |
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263 | td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
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264 | // Type of source (on=0, off=1, other=-1)
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265 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE");
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266 | stypeColumn.setDefault(Int(-1));
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267 | td.addColumn(stypeColumn);
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268 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
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269 |
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270 | //The actual Data Vectors
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271 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
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272 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
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273 | td.addColumn(ArrayColumnDesc<Float>("TSYS"));
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274 |
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275 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
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276 | IPosition(1,2),
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277 | ColumnDesc::Direct));
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278 | TableMeasRefDesc mdirRef(MDirection::J2000); // default
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279 | TableMeasValueDesc tmvdMDir(td, "DIRECTION");
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280 | // the TableMeasDesc gives the column a type
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281 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
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282 | // a uder set table type e.g. GALCTIC, B1950 ...
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283 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000"));
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284 | // writing create the measure column
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285 | mdirCol.write(td);
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286 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
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287 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
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288 | td.addColumn(ScalarColumnDesc<Float>("OPACITY"));
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289 |
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290 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
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291 | ScalarColumnDesc<Int> fitColumn("FIT_ID");
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292 | fitColumn.setDefault(Int(-1));
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293 | td.addColumn(fitColumn);
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294 |
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295 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
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296 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
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297 |
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298 | // columns which just get dragged along, as they aren't used in asap
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299 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY"));
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300 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION"));
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301 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION"));
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302 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE"));
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303 |
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304 | td.rwKeywordSet().define("OBSMODE", String(""));
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305 |
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306 | // Now create Table SetUp from the description.
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307 | SetupNewTable aNewTab(generateName(), td, Table::Scratch);
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308 | table_ = Table(aNewTab, type_, 0);
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309 | originalTable_ = table_;
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310 | }
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311 |
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312 | void Scantable::attach()
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313 | {
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314 | timeCol_.attach(table_, "TIME");
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315 | srcnCol_.attach(table_, "SRCNAME");
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316 | srctCol_.attach(table_, "SRCTYPE");
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317 | specCol_.attach(table_, "SPECTRA");
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318 | flagsCol_.attach(table_, "FLAGTRA");
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319 | tsysCol_.attach(table_, "TSYS");
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320 | cycleCol_.attach(table_,"CYCLENO");
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321 | scanCol_.attach(table_, "SCANNO");
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322 | beamCol_.attach(table_, "BEAMNO");
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323 | ifCol_.attach(table_, "IFNO");
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324 | polCol_.attach(table_, "POLNO");
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325 | integrCol_.attach(table_, "INTERVAL");
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326 | azCol_.attach(table_, "AZIMUTH");
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327 | elCol_.attach(table_, "ELEVATION");
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328 | dirCol_.attach(table_, "DIRECTION");
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329 | fldnCol_.attach(table_, "FIELDNAME");
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330 | rbeamCol_.attach(table_, "REFBEAMNO");
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331 |
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332 | mweatheridCol_.attach(table_,"WEATHER_ID");
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333 | mfitidCol_.attach(table_,"FIT_ID");
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334 | mfreqidCol_.attach(table_, "FREQ_ID");
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335 | mtcalidCol_.attach(table_, "TCAL_ID");
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336 | mfocusidCol_.attach(table_, "FOCUS_ID");
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337 | mmolidCol_.attach(table_, "MOLECULE_ID");
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338 |
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339 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki)
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340 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0);
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341 |
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342 | }
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343 |
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344 | template<class T, class T2>
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345 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col,
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346 | const String& colName,
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347 | const T2& defValue)
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348 | {
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349 | try {
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350 | col.attach(table_, colName);
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351 | } catch (TableError& err) {
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352 | String errMesg = err.getMesg();
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353 | if (errMesg == "Table column " + colName + " is unknown") {
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354 | table_.addColumn(ScalarColumnDesc<T>(colName));
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355 | col.attach(table_, colName);
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356 | col.fillColumn(static_cast<T>(defValue));
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357 | } else {
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358 | throw;
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359 | }
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360 | } catch (...) {
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361 | throw;
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362 | }
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363 | }
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364 |
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365 | template<class T, class T2>
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366 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
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367 | const String& colName,
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368 | const Array<T2>& defValue)
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369 | {
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370 | try {
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371 | col.attach(table_, colName);
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372 | } catch (TableError& err) {
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373 | String errMesg = err.getMesg();
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374 | if (errMesg == "Table column " + colName + " is unknown") {
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375 | table_.addColumn(ArrayColumnDesc<T>(colName));
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376 | col.attach(table_, colName);
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377 |
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378 | int size = 0;
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379 | ArrayIterator<T2>& it = defValue.begin();
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380 | while (it != defValue.end()) {
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381 | ++size;
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382 | ++it;
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383 | }
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384 | IPosition ip(1, size);
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385 | Array<T>& arr(ip);
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386 | for (int i = 0; i < size; ++i)
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387 | arr[i] = static_cast<T>(defValue[i]);
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388 |
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389 | col.fillColumn(arr);
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390 | } else {
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391 | throw;
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392 | }
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393 | } catch (...) {
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394 | throw;
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395 | }
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396 | }
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397 |
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398 | void Scantable::setHeader(const STHeader& sdh)
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399 | {
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400 | table_.rwKeywordSet().define("nIF", sdh.nif);
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401 | table_.rwKeywordSet().define("nBeam", sdh.nbeam);
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402 | table_.rwKeywordSet().define("nPol", sdh.npol);
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403 | table_.rwKeywordSet().define("nChan", sdh.nchan);
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404 | table_.rwKeywordSet().define("Observer", sdh.observer);
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405 | table_.rwKeywordSet().define("Project", sdh.project);
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406 | table_.rwKeywordSet().define("Obstype", sdh.obstype);
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407 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
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408 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
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409 | table_.rwKeywordSet().define("Equinox", sdh.equinox);
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410 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
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411 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
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412 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
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413 | table_.rwKeywordSet().define("UTC", sdh.utc);
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414 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
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415 | table_.rwKeywordSet().define("Epoch", sdh.epoch);
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416 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
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417 | }
|
---|
418 |
|
---|
419 | STHeader Scantable::getHeader() const
|
---|
420 | {
|
---|
421 | STHeader sdh;
|
---|
422 | table_.keywordSet().get("nBeam",sdh.nbeam);
|
---|
423 | table_.keywordSet().get("nIF",sdh.nif);
|
---|
424 | table_.keywordSet().get("nPol",sdh.npol);
|
---|
425 | table_.keywordSet().get("nChan",sdh.nchan);
|
---|
426 | table_.keywordSet().get("Observer", sdh.observer);
|
---|
427 | table_.keywordSet().get("Project", sdh.project);
|
---|
428 | table_.keywordSet().get("Obstype", sdh.obstype);
|
---|
429 | table_.keywordSet().get("AntennaName", sdh.antennaname);
|
---|
430 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
|
---|
431 | table_.keywordSet().get("Equinox", sdh.equinox);
|
---|
432 | table_.keywordSet().get("FreqRefFrame", sdh.freqref);
|
---|
433 | table_.keywordSet().get("FreqRefVal", sdh.reffreq);
|
---|
434 | table_.keywordSet().get("Bandwidth", sdh.bandwidth);
|
---|
435 | table_.keywordSet().get("UTC", sdh.utc);
|
---|
436 | table_.keywordSet().get("FluxUnit", sdh.fluxunit);
|
---|
437 | table_.keywordSet().get("Epoch", sdh.epoch);
|
---|
438 | table_.keywordSet().get("POLTYPE", sdh.poltype);
|
---|
439 | return sdh;
|
---|
440 | }
|
---|
441 |
|
---|
442 | void Scantable::setSourceType( int stype )
|
---|
443 | {
|
---|
444 | if ( stype < 0 || stype > 1 )
|
---|
445 | throw(AipsError("Illegal sourcetype."));
|
---|
446 | TableVector<Int> tabvec(table_, "SRCTYPE");
|
---|
447 | tabvec = Int(stype);
|
---|
448 | }
|
---|
449 |
|
---|
450 | bool Scantable::conformant( const Scantable& other )
|
---|
451 | {
|
---|
452 | return this->getHeader().conformant(other.getHeader());
|
---|
453 | }
|
---|
454 |
|
---|
455 |
|
---|
456 |
|
---|
457 | std::string Scantable::formatSec(Double x) const
|
---|
458 | {
|
---|
459 | Double xcop = x;
|
---|
460 | MVTime mvt(xcop/24./3600.); // make days
|
---|
461 |
|
---|
462 | if (x < 59.95)
|
---|
463 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
|
---|
464 | else if (x < 3599.95)
|
---|
465 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
|
---|
466 | else {
|
---|
467 | ostringstream oss;
|
---|
468 | oss << setw(2) << std::right << setprecision(1) << mvt.hour();
|
---|
469 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
|
---|
470 | return String(oss);
|
---|
471 | }
|
---|
472 | };
|
---|
473 |
|
---|
474 | std::string Scantable::formatDirection(const MDirection& md) const
|
---|
475 | {
|
---|
476 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
|
---|
477 | Int prec = 7;
|
---|
478 |
|
---|
479 | MVAngle mvLon(t[0]);
|
---|
480 | String sLon = mvLon.string(MVAngle::TIME,prec);
|
---|
481 | uInt tp = md.getRef().getType();
|
---|
482 | if (tp == MDirection::GALACTIC ||
|
---|
483 | tp == MDirection::SUPERGAL ) {
|
---|
484 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
|
---|
485 | }
|
---|
486 | MVAngle mvLat(t[1]);
|
---|
487 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
|
---|
488 | return sLon + String(" ") + sLat;
|
---|
489 | }
|
---|
490 |
|
---|
491 |
|
---|
492 | std::string Scantable::getFluxUnit() const
|
---|
493 | {
|
---|
494 | return table_.keywordSet().asString("FluxUnit");
|
---|
495 | }
|
---|
496 |
|
---|
497 | void Scantable::setFluxUnit(const std::string& unit)
|
---|
498 | {
|
---|
499 | String tmp(unit);
|
---|
500 | Unit tU(tmp);
|
---|
501 | if (tU==Unit("K") || tU==Unit("Jy")) {
|
---|
502 | table_.rwKeywordSet().define(String("FluxUnit"), tmp);
|
---|
503 | } else {
|
---|
504 | throw AipsError("Illegal unit - must be compatible with Jy or K");
|
---|
505 | }
|
---|
506 | }
|
---|
507 |
|
---|
508 | void Scantable::setInstrument(const std::string& name)
|
---|
509 | {
|
---|
510 | bool throwIt = true;
|
---|
511 | // create an Instrument to see if this is valid
|
---|
512 | STAttr::convertInstrument(name, throwIt);
|
---|
513 | String nameU(name);
|
---|
514 | nameU.upcase();
|
---|
515 | table_.rwKeywordSet().define(String("AntennaName"), nameU);
|
---|
516 | }
|
---|
517 |
|
---|
518 | void Scantable::setFeedType(const std::string& feedtype)
|
---|
519 | {
|
---|
520 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
|
---|
521 | std::string msg = "Illegal feed type "+ feedtype;
|
---|
522 | throw(casa::AipsError(msg));
|
---|
523 | }
|
---|
524 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
|
---|
525 | }
|
---|
526 |
|
---|
527 | MPosition Scantable::getAntennaPosition() const
|
---|
528 | {
|
---|
529 | Vector<Double> antpos;
|
---|
530 | table_.keywordSet().get("AntennaPosition", antpos);
|
---|
531 | MVPosition mvpos(antpos(0),antpos(1),antpos(2));
|
---|
532 | return MPosition(mvpos);
|
---|
533 | }
|
---|
534 |
|
---|
535 | void Scantable::makePersistent(const std::string& filename)
|
---|
536 | {
|
---|
537 | String inname(filename);
|
---|
538 | Path path(inname);
|
---|
539 | /// @todo reindex SCANNO, recompute nbeam, nif, npol
|
---|
540 | inname = path.expandedName();
|
---|
541 | // 2011/03/04 TN
|
---|
542 | // We can comment out this workaround since the essential bug is
|
---|
543 | // fixed in casacore (r20889 in google code).
|
---|
544 | table_.deepCopy(inname, Table::New);
|
---|
545 | // // WORKAROUND !!! for Table bug
|
---|
546 | // // Remove when fixed in casacore
|
---|
547 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) {
|
---|
548 | // Table tab = table_.copyToMemoryTable(generateName());
|
---|
549 | // tab.deepCopy(inname, Table::New);
|
---|
550 | // tab.markForDelete();
|
---|
551 | //
|
---|
552 | // } else {
|
---|
553 | // table_.deepCopy(inname, Table::New);
|
---|
554 | // }
|
---|
555 | }
|
---|
556 |
|
---|
557 | int Scantable::nbeam( int scanno ) const
|
---|
558 | {
|
---|
559 | if ( scanno < 0 ) {
|
---|
560 | Int n;
|
---|
561 | table_.keywordSet().get("nBeam",n);
|
---|
562 | return int(n);
|
---|
563 | } else {
|
---|
564 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
|
---|
565 | Table t = table_(table_.col("SCANNO") == scanno);
|
---|
566 | ROTableRow row(t);
|
---|
567 | const TableRecord& rec = row.get(0);
|
---|
568 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO"))
|
---|
569 | && t.col("POLNO") == Int(rec.asuInt("POLNO"))
|
---|
570 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
|
---|
571 | ROTableVector<uInt> v(subt, "BEAMNO");
|
---|
572 | return int(v.nelements());
|
---|
573 | }
|
---|
574 | return 0;
|
---|
575 | }
|
---|
576 |
|
---|
577 | int Scantable::nif( int scanno ) const
|
---|
578 | {
|
---|
579 | if ( scanno < 0 ) {
|
---|
580 | Int n;
|
---|
581 | table_.keywordSet().get("nIF",n);
|
---|
582 | return int(n);
|
---|
583 | } else {
|
---|
584 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
|
---|
585 | Table t = table_(table_.col("SCANNO") == scanno);
|
---|
586 | ROTableRow row(t);
|
---|
587 | const TableRecord& rec = row.get(0);
|
---|
588 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
|
---|
589 | && t.col("POLNO") == Int(rec.asuInt("POLNO"))
|
---|
590 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
|
---|
591 | if ( subt.nrow() == 0 ) return 0;
|
---|
592 | ROTableVector<uInt> v(subt, "IFNO");
|
---|
593 | return int(v.nelements());
|
---|
594 | }
|
---|
595 | return 0;
|
---|
596 | }
|
---|
597 |
|
---|
598 | int Scantable::npol( int scanno ) const
|
---|
599 | {
|
---|
600 | if ( scanno < 0 ) {
|
---|
601 | Int n;
|
---|
602 | table_.keywordSet().get("nPol",n);
|
---|
603 | return n;
|
---|
604 | } else {
|
---|
605 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
|
---|
606 | Table t = table_(table_.col("SCANNO") == scanno);
|
---|
607 | ROTableRow row(t);
|
---|
608 | const TableRecord& rec = row.get(0);
|
---|
609 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
|
---|
610 | && t.col("IFNO") == Int(rec.asuInt("IFNO"))
|
---|
611 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
|
---|
612 | if ( subt.nrow() == 0 ) return 0;
|
---|
613 | ROTableVector<uInt> v(subt, "POLNO");
|
---|
614 | return int(v.nelements());
|
---|
615 | }
|
---|
616 | return 0;
|
---|
617 | }
|
---|
618 |
|
---|
619 | int Scantable::ncycle( int scanno ) const
|
---|
620 | {
|
---|
621 | if ( scanno < 0 ) {
|
---|
622 | Block<String> cols(2);
|
---|
623 | cols[0] = "SCANNO";
|
---|
624 | cols[1] = "CYCLENO";
|
---|
625 | TableIterator it(table_, cols);
|
---|
626 | int n = 0;
|
---|
627 | while ( !it.pastEnd() ) {
|
---|
628 | ++n;
|
---|
629 | ++it;
|
---|
630 | }
|
---|
631 | return n;
|
---|
632 | } else {
|
---|
633 | Table t = table_(table_.col("SCANNO") == scanno);
|
---|
634 | ROTableRow row(t);
|
---|
635 | const TableRecord& rec = row.get(0);
|
---|
636 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
|
---|
637 | && t.col("POLNO") == Int(rec.asuInt("POLNO"))
|
---|
638 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) );
|
---|
639 | if ( subt.nrow() == 0 ) return 0;
|
---|
640 | return int(subt.nrow());
|
---|
641 | }
|
---|
642 | return 0;
|
---|
643 | }
|
---|
644 |
|
---|
645 |
|
---|
646 | int Scantable::nrow( int scanno ) const
|
---|
647 | {
|
---|
648 | return int(table_.nrow());
|
---|
649 | }
|
---|
650 |
|
---|
651 | int Scantable::nchan( int ifno ) const
|
---|
652 | {
|
---|
653 | if ( ifno < 0 ) {
|
---|
654 | Int n;
|
---|
655 | table_.keywordSet().get("nChan",n);
|
---|
656 | return int(n);
|
---|
657 | } else {
|
---|
658 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't
|
---|
659 | // vary with these
|
---|
660 | Table t = table_(table_.col("IFNO") == ifno, 1);
|
---|
661 | if ( t.nrow() == 0 ) return 0;
|
---|
662 | ROArrayColumn<Float> v(t, "SPECTRA");
|
---|
663 | return v.shape(0)(0);
|
---|
664 | }
|
---|
665 | return 0;
|
---|
666 | }
|
---|
667 |
|
---|
668 | int Scantable::nscan() const {
|
---|
669 | Vector<uInt> scannos(scanCol_.getColumn());
|
---|
670 | uInt nout = genSort( scannos, Sort::Ascending,
|
---|
671 | Sort::QuickSort|Sort::NoDuplicates );
|
---|
672 | return int(nout);
|
---|
673 | }
|
---|
674 |
|
---|
675 | int Scantable::getChannels(int whichrow) const
|
---|
676 | {
|
---|
677 | return specCol_.shape(whichrow)(0);
|
---|
678 | }
|
---|
679 |
|
---|
680 | int Scantable::getBeam(int whichrow) const
|
---|
681 | {
|
---|
682 | return beamCol_(whichrow);
|
---|
683 | }
|
---|
684 |
|
---|
685 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const
|
---|
686 | {
|
---|
687 | Vector<uInt> nos(col.getColumn());
|
---|
688 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates );
|
---|
689 | nos.resize(n, True);
|
---|
690 | std::vector<uint> stlout;
|
---|
691 | nos.tovector(stlout);
|
---|
692 | return stlout;
|
---|
693 | }
|
---|
694 |
|
---|
695 | int Scantable::getIF(int whichrow) const
|
---|
696 | {
|
---|
697 | return ifCol_(whichrow);
|
---|
698 | }
|
---|
699 |
|
---|
700 | int Scantable::getPol(int whichrow) const
|
---|
701 | {
|
---|
702 | return polCol_(whichrow);
|
---|
703 | }
|
---|
704 |
|
---|
705 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
|
---|
706 | {
|
---|
707 | return formatTime(me, showdate, 0);
|
---|
708 | }
|
---|
709 |
|
---|
710 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const
|
---|
711 | {
|
---|
712 | MVTime mvt(me.getValue());
|
---|
713 | if (showdate)
|
---|
714 | //mvt.setFormat(MVTime::YMD);
|
---|
715 | mvt.setFormat(MVTime::YMD, prec);
|
---|
716 | else
|
---|
717 | //mvt.setFormat(MVTime::TIME);
|
---|
718 | mvt.setFormat(MVTime::TIME, prec);
|
---|
719 | ostringstream oss;
|
---|
720 | oss << mvt;
|
---|
721 | return String(oss);
|
---|
722 | }
|
---|
723 |
|
---|
724 | void Scantable::calculateAZEL()
|
---|
725 | {
|
---|
726 | MPosition mp = getAntennaPosition();
|
---|
727 | MEpoch::ROScalarColumn timeCol(table_, "TIME");
|
---|
728 | ostringstream oss;
|
---|
729 | oss << "Computed azimuth/elevation using " << endl
|
---|
730 | << mp << endl;
|
---|
731 | for (Int i=0; i<nrow(); ++i) {
|
---|
732 | MEpoch me = timeCol(i);
|
---|
733 | MDirection md = getDirection(i);
|
---|
734 | oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md)
|
---|
735 | << endl << " => ";
|
---|
736 | MeasFrame frame(mp, me);
|
---|
737 | Vector<Double> azel =
|
---|
738 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
|
---|
739 | frame)
|
---|
740 | )().getAngle("rad").getValue();
|
---|
741 | azCol_.put(i,Float(azel[0]));
|
---|
742 | elCol_.put(i,Float(azel[1]));
|
---|
743 | oss << "azel: " << azel[0]/C::pi*180.0 << " "
|
---|
744 | << azel[1]/C::pi*180.0 << " (deg)" << endl;
|
---|
745 | }
|
---|
746 | pushLog(String(oss));
|
---|
747 | }
|
---|
748 |
|
---|
749 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag)
|
---|
750 | {
|
---|
751 | for (uInt i=0; i<table_.nrow(); ++i) {
|
---|
752 | Vector<uChar> flgs = flagsCol_(i);
|
---|
753 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs);
|
---|
754 | flagsCol_.put(i, flgs);
|
---|
755 | }
|
---|
756 | }
|
---|
757 |
|
---|
758 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag)
|
---|
759 | {
|
---|
760 | Vector<uChar> flags;
|
---|
761 | flagsCol_.get(uInt(whichrow), flags);
|
---|
762 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags);
|
---|
763 | Vector<Bool> bflag(flags.shape());
|
---|
764 | convertArray(bflag, flags);
|
---|
765 | //bflag = !bflag;
|
---|
766 |
|
---|
767 | std::vector<bool> mask;
|
---|
768 | bflag.tovector(mask);
|
---|
769 | return mask;
|
---|
770 | }
|
---|
771 |
|
---|
772 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag,
|
---|
773 | Vector<uChar> flgs)
|
---|
774 | {
|
---|
775 | Vector<Float> spcs = specCol_(whichrow);
|
---|
776 | uInt nchannel = nchan();
|
---|
777 | if (spcs.nelements() != nchannel) {
|
---|
778 | throw(AipsError("Data has incorrect number of channels"));
|
---|
779 | }
|
---|
780 | uChar userflag = 1 << 7;
|
---|
781 | if (unflag) {
|
---|
782 | userflag = 0 << 7;
|
---|
783 | }
|
---|
784 | if (clipoutside) {
|
---|
785 | for (uInt j = 0; j < nchannel; ++j) {
|
---|
786 | Float spc = spcs(j);
|
---|
787 | if ((spc >= uthres) || (spc <= dthres)) {
|
---|
788 | flgs(j) = userflag;
|
---|
789 | }
|
---|
790 | }
|
---|
791 | } else {
|
---|
792 | for (uInt j = 0; j < nchannel; ++j) {
|
---|
793 | Float spc = spcs(j);
|
---|
794 | if ((spc < uthres) && (spc > dthres)) {
|
---|
795 | flgs(j) = userflag;
|
---|
796 | }
|
---|
797 | }
|
---|
798 | }
|
---|
799 | }
|
---|
800 |
|
---|
801 |
|
---|
802 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) {
|
---|
803 | std::vector<bool>::const_iterator it;
|
---|
804 | uInt ntrue = 0;
|
---|
805 | if (whichrow >= int(table_.nrow()) ) {
|
---|
806 | throw(AipsError("Invalid row number"));
|
---|
807 | }
|
---|
808 | for (it = msk.begin(); it != msk.end(); ++it) {
|
---|
809 | if ( *it ) {
|
---|
810 | ntrue++;
|
---|
811 | }
|
---|
812 | }
|
---|
813 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
|
---|
814 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
|
---|
815 | throw(AipsError("Trying to flag whole scantable."));
|
---|
816 | uChar userflag = 1 << 7;
|
---|
817 | if ( unflag ) {
|
---|
818 | userflag = 0 << 7;
|
---|
819 | }
|
---|
820 | if (whichrow > -1 ) {
|
---|
821 | applyChanFlag(uInt(whichrow), msk, userflag);
|
---|
822 | } else {
|
---|
823 | for ( uInt i=0; i<table_.nrow(); ++i) {
|
---|
824 | applyChanFlag(i, msk, userflag);
|
---|
825 | }
|
---|
826 | }
|
---|
827 | }
|
---|
828 |
|
---|
829 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval )
|
---|
830 | {
|
---|
831 | if (whichrow >= table_.nrow() ) {
|
---|
832 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) );
|
---|
833 | }
|
---|
834 | Vector<uChar> flgs = flagsCol_(whichrow);
|
---|
835 | if ( msk.size() == 0 ) {
|
---|
836 | flgs = flagval;
|
---|
837 | flagsCol_.put(whichrow, flgs);
|
---|
838 | return;
|
---|
839 | }
|
---|
840 | if ( int(msk.size()) != nchan() ) {
|
---|
841 | throw(AipsError("Mask has incorrect number of channels."));
|
---|
842 | }
|
---|
843 | if ( flgs.nelements() != msk.size() ) {
|
---|
844 | throw(AipsError("Mask has incorrect number of channels."
|
---|
845 | " Probably varying with IF. Please flag per IF"));
|
---|
846 | }
|
---|
847 | std::vector<bool>::const_iterator it;
|
---|
848 | uInt j = 0;
|
---|
849 | for (it = msk.begin(); it != msk.end(); ++it) {
|
---|
850 | if ( *it ) {
|
---|
851 | flgs(j) = flagval;
|
---|
852 | }
|
---|
853 | ++j;
|
---|
854 | }
|
---|
855 | flagsCol_.put(whichrow, flgs);
|
---|
856 | }
|
---|
857 |
|
---|
858 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag)
|
---|
859 | {
|
---|
860 | if ( selector_.empty() && (rows.size() == table_.nrow()) )
|
---|
861 | throw(AipsError("Trying to flag whole scantable."));
|
---|
862 |
|
---|
863 | uInt rowflag = (unflag ? 0 : 1);
|
---|
864 | std::vector<uInt>::const_iterator it;
|
---|
865 | for (it = rows.begin(); it != rows.end(); ++it)
|
---|
866 | flagrowCol_.put(*it, rowflag);
|
---|
867 | }
|
---|
868 |
|
---|
869 | std::vector<bool> Scantable::getMask(int whichrow) const
|
---|
870 | {
|
---|
871 | Vector<uChar> flags;
|
---|
872 | flagsCol_.get(uInt(whichrow), flags);
|
---|
873 | Vector<Bool> bflag(flags.shape());
|
---|
874 | convertArray(bflag, flags);
|
---|
875 | bflag = !bflag;
|
---|
876 | std::vector<bool> mask;
|
---|
877 | bflag.tovector(mask);
|
---|
878 | return mask;
|
---|
879 | }
|
---|
880 |
|
---|
881 | std::vector<float> Scantable::getSpectrum( int whichrow,
|
---|
882 | const std::string& poltype ) const
|
---|
883 | {
|
---|
884 | String ptype = poltype;
|
---|
885 | if (poltype == "" ) ptype = getPolType();
|
---|
886 | if ( whichrow < 0 || whichrow >= nrow() )
|
---|
887 | throw(AipsError("Illegal row number."));
|
---|
888 | std::vector<float> out;
|
---|
889 | Vector<Float> arr;
|
---|
890 | uInt requestedpol = polCol_(whichrow);
|
---|
891 | String basetype = getPolType();
|
---|
892 | if ( ptype == basetype ) {
|
---|
893 | specCol_.get(whichrow, arr);
|
---|
894 | } else {
|
---|
895 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_,
|
---|
896 | basetype));
|
---|
897 | uInt row = uInt(whichrow);
|
---|
898 | stpol->setSpectra(getPolMatrix(row));
|
---|
899 | Float fang,fhand;
|
---|
900 | fang = focusTable_.getTotalAngle(mfocusidCol_(row));
|
---|
901 | fhand = focusTable_.getFeedHand(mfocusidCol_(row));
|
---|
902 | stpol->setPhaseCorrections(fang, fhand);
|
---|
903 | arr = stpol->getSpectrum(requestedpol, ptype);
|
---|
904 | }
|
---|
905 | if ( arr.nelements() == 0 )
|
---|
906 | pushLog("Not enough polarisations present to do the conversion.");
|
---|
907 | arr.tovector(out);
|
---|
908 | return out;
|
---|
909 | }
|
---|
910 |
|
---|
911 | void Scantable::setSpectrum( const std::vector<float>& spec,
|
---|
912 | int whichrow )
|
---|
913 | {
|
---|
914 | Vector<Float> spectrum(spec);
|
---|
915 | Vector<Float> arr;
|
---|
916 | specCol_.get(whichrow, arr);
|
---|
917 | if ( spectrum.nelements() != arr.nelements() )
|
---|
918 | throw AipsError("The spectrum has incorrect number of channels.");
|
---|
919 | specCol_.put(whichrow, spectrum);
|
---|
920 | }
|
---|
921 |
|
---|
922 |
|
---|
923 | String Scantable::generateName()
|
---|
924 | {
|
---|
925 | return (File::newUniqueName("./","temp")).baseName();
|
---|
926 | }
|
---|
927 |
|
---|
928 | const casa::Table& Scantable::table( ) const
|
---|
929 | {
|
---|
930 | return table_;
|
---|
931 | }
|
---|
932 |
|
---|
933 | casa::Table& Scantable::table( )
|
---|
934 | {
|
---|
935 | return table_;
|
---|
936 | }
|
---|
937 |
|
---|
938 | std::string Scantable::getPolType() const
|
---|
939 | {
|
---|
940 | return table_.keywordSet().asString("POLTYPE");
|
---|
941 | }
|
---|
942 |
|
---|
943 | void Scantable::unsetSelection()
|
---|
944 | {
|
---|
945 | table_ = originalTable_;
|
---|
946 | attach();
|
---|
947 | selector_.reset();
|
---|
948 | }
|
---|
949 |
|
---|
950 | void Scantable::setSelection( const STSelector& selection )
|
---|
951 | {
|
---|
952 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
|
---|
953 | if ( tab.nrow() == 0 ) {
|
---|
954 | throw(AipsError("Selection contains no data. Not applying it."));
|
---|
955 | }
|
---|
956 | table_ = tab;
|
---|
957 | attach();
|
---|
958 | // tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ;
|
---|
959 | // vector<uint> selectedIFs = getIFNos() ;
|
---|
960 | // Int newnIF = selectedIFs.size() ;
|
---|
961 | // tab.rwKeywordSet().define("nIF",newnIF) ;
|
---|
962 | // if ( newnIF != 0 ) {
|
---|
963 | // Int newnChan = 0 ;
|
---|
964 | // for ( Int i = 0 ; i < newnIF ; i++ ) {
|
---|
965 | // Int nChan = nchan( selectedIFs[i] ) ;
|
---|
966 | // if ( newnChan > nChan )
|
---|
967 | // newnChan = nChan ;
|
---|
968 | // }
|
---|
969 | // tab.rwKeywordSet().define("nChan",newnChan) ;
|
---|
970 | // }
|
---|
971 | // tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ;
|
---|
972 | selector_ = selection;
|
---|
973 | }
|
---|
974 |
|
---|
975 |
|
---|
976 | std::string Scantable::headerSummary()
|
---|
977 | {
|
---|
978 | // Format header info
|
---|
979 | // STHeader sdh;
|
---|
980 | // sdh = getHeader();
|
---|
981 | // sdh.print();
|
---|
982 | ostringstream oss;
|
---|
983 | oss.flags(std::ios_base::left);
|
---|
984 | String tmp;
|
---|
985 | // Project
|
---|
986 | table_.keywordSet().get("Project", tmp);
|
---|
987 | oss << setw(15) << "Project:" << tmp << endl;
|
---|
988 | // Observation date
|
---|
989 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
|
---|
990 | // Observer
|
---|
991 | oss << setw(15) << "Observer:"
|
---|
992 | << table_.keywordSet().asString("Observer") << endl;
|
---|
993 | // Antenna Name
|
---|
994 | table_.keywordSet().get("AntennaName", tmp);
|
---|
995 | oss << setw(15) << "Antenna Name:" << tmp << endl;
|
---|
996 | // Obs type
|
---|
997 | table_.keywordSet().get("Obstype", tmp);
|
---|
998 | // Records (nrow)
|
---|
999 | oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl;
|
---|
1000 | oss << setw(15) << "Obs. Type:" << tmp << endl;
|
---|
1001 | // Beams, IFs, Polarizations, and Channels
|
---|
1002 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
|
---|
1003 | << setw(15) << "IFs:" << setw(4) << nif() << endl
|
---|
1004 | << setw(15) << "Polarisations:" << setw(4) << npol()
|
---|
1005 | << "(" << getPolType() << ")" << endl
|
---|
1006 | << setw(15) << "Channels:" << nchan() << endl;
|
---|
1007 | // Flux unit
|
---|
1008 | table_.keywordSet().get("FluxUnit", tmp);
|
---|
1009 | oss << setw(15) << "Flux Unit:" << tmp << endl;
|
---|
1010 | // Abscissa Unit
|
---|
1011 | oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl;
|
---|
1012 | // Selection
|
---|
1013 | oss << selector_.print() << endl;
|
---|
1014 |
|
---|
1015 | return String(oss);
|
---|
1016 | }
|
---|
1017 |
|
---|
1018 | void Scantable::summary( const std::string& filename )
|
---|
1019 | {
|
---|
1020 | ostringstream oss;
|
---|
1021 | ofstream ofs;
|
---|
1022 | LogIO ols(LogOrigin("Scantable", "summary", WHERE));
|
---|
1023 |
|
---|
1024 | if (filename != "")
|
---|
1025 | ofs.open( filename.c_str(), ios::out );
|
---|
1026 |
|
---|
1027 | oss << endl;
|
---|
1028 | oss << asap::SEPERATOR << endl;
|
---|
1029 | oss << " Scan Table Summary" << endl;
|
---|
1030 | oss << asap::SEPERATOR << endl;
|
---|
1031 |
|
---|
1032 | // Format header info
|
---|
1033 | oss << headerSummary();
|
---|
1034 | oss << endl;
|
---|
1035 |
|
---|
1036 | if (table_.nrow() <= 0){
|
---|
1037 | oss << asap::SEPERATOR << endl;
|
---|
1038 | oss << "The MAIN table is empty: there are no data!!!" << endl;
|
---|
1039 | oss << asap::SEPERATOR << endl;
|
---|
1040 |
|
---|
1041 | ols << String(oss) << LogIO::POST;
|
---|
1042 | if (ofs) {
|
---|
1043 | ofs << String(oss) << flush;
|
---|
1044 | ofs.close();
|
---|
1045 | }
|
---|
1046 | return;
|
---|
1047 | }
|
---|
1048 |
|
---|
1049 |
|
---|
1050 |
|
---|
1051 | // main table
|
---|
1052 | String dirtype = "Position ("
|
---|
1053 | + getDirectionRefString()
|
---|
1054 | + ")";
|
---|
1055 | oss.flags(std::ios_base::left);
|
---|
1056 | oss << setw(5) << "Scan"
|
---|
1057 | << setw(15) << "Source"
|
---|
1058 | << setw(35) << "Time range"
|
---|
1059 | << setw(2) << "" << setw(7) << "Int[s]"
|
---|
1060 | << setw(7) << "Record"
|
---|
1061 | << setw(8) << "SrcType"
|
---|
1062 | << setw(8) << "FreqIDs"
|
---|
1063 | << setw(7) << "MolIDs" << endl;
|
---|
1064 | oss << setw(7)<< "" << setw(6) << "Beam"
|
---|
1065 | << setw(23) << dirtype << endl;
|
---|
1066 |
|
---|
1067 | oss << asap::SEPERATOR << endl;
|
---|
1068 |
|
---|
1069 | // Flush summary and clear up the string
|
---|
1070 | ols << String(oss) << LogIO::POST;
|
---|
1071 | if (ofs) ofs << String(oss) << flush;
|
---|
1072 | oss.str("");
|
---|
1073 | oss.clear();
|
---|
1074 |
|
---|
1075 |
|
---|
1076 | // Get Freq_ID map
|
---|
1077 | ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID");
|
---|
1078 | Int nfid = ftabIds.nrow();
|
---|
1079 | if (nfid <= 0){
|
---|
1080 | oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl;
|
---|
1081 | oss << asap::SEPERATOR << endl;
|
---|
1082 |
|
---|
1083 | ols << String(oss) << LogIO::POST;
|
---|
1084 | if (ofs) {
|
---|
1085 | ofs << String(oss) << flush;
|
---|
1086 | ofs.close();
|
---|
1087 | }
|
---|
1088 | return;
|
---|
1089 | }
|
---|
1090 | // Storages of overall IFNO, POLNO, and nchan per FREQ_ID
|
---|
1091 | // the orders are identical to ID in FREQ subtable
|
---|
1092 | Block< Vector<uInt> > ifNos(nfid), polNos(nfid);
|
---|
1093 | Vector<Int> fIdchans(nfid,-1);
|
---|
1094 | map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair
|
---|
1095 | for (Int i=0; i < nfid; i++){
|
---|
1096 | // fidMap[freqId] returns row number in FREQ subtable
|
---|
1097 | fidMap.insert(pair<uInt, Int>(ftabIds(i),i));
|
---|
1098 | ifNos[i] = Vector<uInt>();
|
---|
1099 | polNos[i] = Vector<uInt>();
|
---|
1100 | }
|
---|
1101 |
|
---|
1102 | TableIterator iter(table_, "SCANNO");
|
---|
1103 |
|
---|
1104 | // Vars for keeping track of time, freqids, molIds in a SCANNO
|
---|
1105 | Vector<uInt> freqids;
|
---|
1106 | Vector<uInt> molids;
|
---|
1107 | Vector<uInt> beamids(1,0);
|
---|
1108 | Vector<MDirection> beamDirs;
|
---|
1109 | Vector<Int> stypeids(1,0);
|
---|
1110 | Vector<String> stypestrs;
|
---|
1111 | Int nfreq(1);
|
---|
1112 | Int nmol(1);
|
---|
1113 | uInt nbeam(1);
|
---|
1114 | uInt nstype(1);
|
---|
1115 |
|
---|
1116 | Double btime(0.0), etime(0.0);
|
---|
1117 | Double meanIntTim(0.0);
|
---|
1118 |
|
---|
1119 | uInt currFreqId(0), ftabRow(0);
|
---|
1120 | Int iflen(0), pollen(0);
|
---|
1121 |
|
---|
1122 | while (!iter.pastEnd()) {
|
---|
1123 | Table subt = iter.table();
|
---|
1124 | uInt snrow = subt.nrow();
|
---|
1125 | ROTableRow row(subt);
|
---|
1126 | const TableRecord& rec = row.get(0);
|
---|
1127 |
|
---|
1128 | // relevant columns
|
---|
1129 | ROScalarColumn<Double> mjdCol(subt,"TIME");
|
---|
1130 | ROScalarColumn<Double> intervalCol(subt,"INTERVAL");
|
---|
1131 | MDirection::ROScalarColumn dirCol(subt,"DIRECTION");
|
---|
1132 |
|
---|
1133 | ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID");
|
---|
1134 | ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID");
|
---|
1135 | ROScalarColumn<uInt> beamCol(subt,"BEAMNO");
|
---|
1136 | ROScalarColumn<Int> stypeCol(subt,"SRCTYPE");
|
---|
1137 |
|
---|
1138 | ROScalarColumn<uInt> ifNoCol(subt,"IFNO");
|
---|
1139 | ROScalarColumn<uInt> polNoCol(subt,"POLNO");
|
---|
1140 |
|
---|
1141 |
|
---|
1142 | // Times
|
---|
1143 | meanIntTim = sum(intervalCol.getColumn()) / (double) snrow;
|
---|
1144 | minMax(btime, etime, mjdCol.getColumn());
|
---|
1145 | etime += meanIntTim/C::day;
|
---|
1146 |
|
---|
1147 | // MOLECULE_ID and FREQ_ID
|
---|
1148 | molids = getNumbers(molIdCol);
|
---|
1149 | molids.shape(nmol);
|
---|
1150 |
|
---|
1151 | freqids = getNumbers(freqIdCol);
|
---|
1152 | freqids.shape(nfreq);
|
---|
1153 |
|
---|
1154 | // Add first beamid, and srcNames
|
---|
1155 | beamids.resize(1,False);
|
---|
1156 | beamDirs.resize(1,False);
|
---|
1157 | beamids(0)=beamCol(0);
|
---|
1158 | beamDirs(0)=dirCol(0);
|
---|
1159 | nbeam = 1;
|
---|
1160 |
|
---|
1161 | stypeids.resize(1,False);
|
---|
1162 | stypeids(0)=stypeCol(0);
|
---|
1163 | nstype = 1;
|
---|
1164 |
|
---|
1165 | // Global listings of nchan/IFNO/POLNO per FREQ_ID
|
---|
1166 | currFreqId=freqIdCol(0);
|
---|
1167 | ftabRow = fidMap[currFreqId];
|
---|
1168 | // Assumes an identical number of channels per FREQ_ID
|
---|
1169 | if (fIdchans(ftabRow) < 0 ) {
|
---|
1170 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
|
---|
1171 | fIdchans(ftabRow)=(*spec).shape()(0);
|
---|
1172 | }
|
---|
1173 | // Should keep ifNos and polNos form the previous SCANNO
|
---|
1174 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) {
|
---|
1175 | ifNos[ftabRow].shape(iflen);
|
---|
1176 | iflen++;
|
---|
1177 | ifNos[ftabRow].resize(iflen,True);
|
---|
1178 | ifNos[ftabRow](iflen-1) = ifNoCol(0);
|
---|
1179 | }
|
---|
1180 | if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) {
|
---|
1181 | polNos[ftabRow].shape(pollen);
|
---|
1182 | pollen++;
|
---|
1183 | polNos[ftabRow].resize(pollen,True);
|
---|
1184 | polNos[ftabRow](pollen-1) = polNoCol(0);
|
---|
1185 | }
|
---|
1186 |
|
---|
1187 | for (uInt i=1; i < snrow; i++){
|
---|
1188 | // Need to list BEAMNO and DIRECTION in the same order
|
---|
1189 | if ( !anyEQ(beamids,beamCol(i)) ) {
|
---|
1190 | nbeam++;
|
---|
1191 | beamids.resize(nbeam,True);
|
---|
1192 | beamids(nbeam-1)=beamCol(i);
|
---|
1193 | beamDirs.resize(nbeam,True);
|
---|
1194 | beamDirs(nbeam-1)=dirCol(i);
|
---|
1195 | }
|
---|
1196 |
|
---|
1197 | // SRCTYPE is Int (getNumber takes only uInt)
|
---|
1198 | if ( !anyEQ(stypeids,stypeCol(i)) ) {
|
---|
1199 | nstype++;
|
---|
1200 | stypeids.resize(nstype,True);
|
---|
1201 | stypeids(nstype-1)=stypeCol(i);
|
---|
1202 | }
|
---|
1203 |
|
---|
1204 | // Global listings of nchan/IFNO/POLNO per FREQ_ID
|
---|
1205 | currFreqId=freqIdCol(i);
|
---|
1206 | ftabRow = fidMap[currFreqId];
|
---|
1207 | if (fIdchans(ftabRow) < 0 ) {
|
---|
1208 | const TableRecord& rec = row.get(i);
|
---|
1209 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
|
---|
1210 | fIdchans(ftabRow) = (*spec).shape()(0);
|
---|
1211 | }
|
---|
1212 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) {
|
---|
1213 | ifNos[ftabRow].shape(iflen);
|
---|
1214 | iflen++;
|
---|
1215 | ifNos[ftabRow].resize(iflen,True);
|
---|
1216 | ifNos[ftabRow](iflen-1) = ifNoCol(i);
|
---|
1217 | }
|
---|
1218 | if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) {
|
---|
1219 | polNos[ftabRow].shape(pollen);
|
---|
1220 | pollen++;
|
---|
1221 | polNos[ftabRow].resize(pollen,True);
|
---|
1222 | polNos[ftabRow](pollen-1) = polNoCol(i);
|
---|
1223 | }
|
---|
1224 | } // end of row iteration
|
---|
1225 |
|
---|
1226 | stypestrs.resize(nstype,False);
|
---|
1227 | for (uInt j=0; j < nstype; j++)
|
---|
1228 | stypestrs(j) = SrcType::getName(stypeids(j));
|
---|
1229 |
|
---|
1230 | // Format Scan summary
|
---|
1231 | oss << setw(4) << std::right << rec.asuInt("SCANNO")
|
---|
1232 | << std::left << setw(1) << ""
|
---|
1233 | << setw(15) << rec.asString("SRCNAME")
|
---|
1234 | << setw(21) << MVTime(btime).string(MVTime::YMD,7)
|
---|
1235 | << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7)
|
---|
1236 | << setw(3) << "" << setw(6) << meanIntTim << setw(1) << ""
|
---|
1237 | << std::right << setw(5) << snrow << setw(2) << ""
|
---|
1238 | << std::left << stypestrs << setw(1) << ""
|
---|
1239 | << freqids << setw(1) << ""
|
---|
1240 | << molids << endl;
|
---|
1241 | // Format Beam summary
|
---|
1242 | for (uInt j=0; j < nbeam; j++) {
|
---|
1243 | oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << ""
|
---|
1244 | << formatDirection(beamDirs(j)) << endl;
|
---|
1245 | }
|
---|
1246 | // Flush summary every scan and clear up the string
|
---|
1247 | ols << String(oss) << LogIO::POST;
|
---|
1248 | if (ofs) ofs << String(oss) << flush;
|
---|
1249 | oss.str("");
|
---|
1250 | oss.clear();
|
---|
1251 |
|
---|
1252 | ++iter;
|
---|
1253 | } // end of scan iteration
|
---|
1254 | oss << asap::SEPERATOR << endl;
|
---|
1255 |
|
---|
1256 | // List FRECUENCIES Table (using STFrequencies.print may be slow)
|
---|
1257 | oss << "FREQUENCIES: " << nfreq << endl;
|
---|
1258 | oss << std::right << setw(5) << "ID" << setw(2) << ""
|
---|
1259 | << std::left << setw(5) << "IFNO" << setw(2) << ""
|
---|
1260 | << setw(8) << "Frame"
|
---|
1261 | << setw(16) << "RefVal"
|
---|
1262 | << setw(7) << "RefPix"
|
---|
1263 | << setw(15) << "Increment"
|
---|
1264 | << setw(9) << "Channels"
|
---|
1265 | << setw(6) << "POLNOs" << endl;
|
---|
1266 | Int tmplen;
|
---|
1267 | for (Int i=0; i < nfid; i++){
|
---|
1268 | // List row=i of FREQUENCIES subtable
|
---|
1269 | ifNos[i].shape(tmplen);
|
---|
1270 | if (tmplen == 1) {
|
---|
1271 | oss << std::right << setw(5) << ftabIds(i) << setw(2) << ""
|
---|
1272 | << setw(3) << ifNos[i](0) << setw(1) << ""
|
---|
1273 | << std::left << setw(46) << frequencies().print(ftabIds(i))
|
---|
1274 | << setw(2) << ""
|
---|
1275 | << std::right << setw(8) << fIdchans[i] << setw(2) << ""
|
---|
1276 | << std::left << polNos[i] << endl;
|
---|
1277 | } else if (tmplen > 0 ) {
|
---|
1278 | // You shouldn't come here
|
---|
1279 | oss << std::left
|
---|
1280 | << "Multiple IFNOs in FREQ_ID = " << ftabIds(i)
|
---|
1281 | << " !!!" << endl;
|
---|
1282 | }
|
---|
1283 | }
|
---|
1284 | oss << asap::SEPERATOR << endl;
|
---|
1285 |
|
---|
1286 | // List MOLECULES Table (currently lists all rows)
|
---|
1287 | oss << "MOLECULES: " << endl;
|
---|
1288 | if (molecules().nrow() <= 0) {
|
---|
1289 | oss << " MOLECULES subtable is empty: there are no data" << endl;
|
---|
1290 | } else {
|
---|
1291 | ROTableRow row(molecules().table());
|
---|
1292 | oss << std::right << setw(5) << "ID"
|
---|
1293 | << std::left << setw(3) << ""
|
---|
1294 | << setw(18) << "RestFreq"
|
---|
1295 | << setw(15) << "Name" << endl;
|
---|
1296 | for (Int i=0; i < molecules().nrow(); i++){
|
---|
1297 | const TableRecord& rec=row.get(i);
|
---|
1298 | oss << std::right << setw(5) << rec.asuInt("ID")
|
---|
1299 | << std::left << setw(3) << ""
|
---|
1300 | << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << ""
|
---|
1301 | << rec.asArrayString("NAME") << endl;
|
---|
1302 | }
|
---|
1303 | }
|
---|
1304 | oss << asap::SEPERATOR << endl;
|
---|
1305 | ols << String(oss) << LogIO::POST;
|
---|
1306 | if (ofs) {
|
---|
1307 | ofs << String(oss) << flush;
|
---|
1308 | ofs.close();
|
---|
1309 | }
|
---|
1310 | // return String(oss);
|
---|
1311 | }
|
---|
1312 |
|
---|
1313 |
|
---|
1314 | std::string Scantable::oldheaderSummary()
|
---|
1315 | {
|
---|
1316 | // Format header info
|
---|
1317 | // STHeader sdh;
|
---|
1318 | // sdh = getHeader();
|
---|
1319 | // sdh.print();
|
---|
1320 | ostringstream oss;
|
---|
1321 | oss.flags(std::ios_base::left);
|
---|
1322 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
|
---|
1323 | << setw(15) << "IFs:" << setw(4) << nif() << endl
|
---|
1324 | << setw(15) << "Polarisations:" << setw(4) << npol()
|
---|
1325 | << "(" << getPolType() << ")" << endl
|
---|
1326 | << setw(15) << "Channels:" << nchan() << endl;
|
---|
1327 | String tmp;
|
---|
1328 | oss << setw(15) << "Observer:"
|
---|
1329 | << table_.keywordSet().asString("Observer") << endl;
|
---|
1330 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
|
---|
1331 | table_.keywordSet().get("Project", tmp);
|
---|
1332 | oss << setw(15) << "Project:" << tmp << endl;
|
---|
1333 | table_.keywordSet().get("Obstype", tmp);
|
---|
1334 | oss << setw(15) << "Obs. Type:" << tmp << endl;
|
---|
1335 | table_.keywordSet().get("AntennaName", tmp);
|
---|
1336 | oss << setw(15) << "Antenna Name:" << tmp << endl;
|
---|
1337 | table_.keywordSet().get("FluxUnit", tmp);
|
---|
1338 | oss << setw(15) << "Flux Unit:" << tmp << endl;
|
---|
1339 | int nid = moleculeTable_.nrow();
|
---|
1340 | Bool firstline = True;
|
---|
1341 | oss << setw(15) << "Rest Freqs:";
|
---|
1342 | for (int i=0; i<nid; i++) {
|
---|
1343 | Table t = table_(table_.col("MOLECULE_ID") == i, 1);
|
---|
1344 | if (t.nrow() > 0) {
|
---|
1345 | Vector<Double> vec(moleculeTable_.getRestFrequency(i));
|
---|
1346 | if (vec.nelements() > 0) {
|
---|
1347 | if (firstline) {
|
---|
1348 | oss << setprecision(10) << vec << " [Hz]" << endl;
|
---|
1349 | firstline=False;
|
---|
1350 | }
|
---|
1351 | else{
|
---|
1352 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
|
---|
1353 | }
|
---|
1354 | } else {
|
---|
1355 | oss << "none" << endl;
|
---|
1356 | }
|
---|
1357 | }
|
---|
1358 | }
|
---|
1359 |
|
---|
1360 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
|
---|
1361 | oss << selector_.print() << endl;
|
---|
1362 | return String(oss);
|
---|
1363 | }
|
---|
1364 |
|
---|
1365 | //std::string Scantable::summary( const std::string& filename )
|
---|
1366 | void Scantable::oldsummary( const std::string& filename )
|
---|
1367 | {
|
---|
1368 | ostringstream oss;
|
---|
1369 | ofstream ofs;
|
---|
1370 | LogIO ols(LogOrigin("Scantable", "summary", WHERE));
|
---|
1371 |
|
---|
1372 | if (filename != "")
|
---|
1373 | ofs.open( filename.c_str(), ios::out );
|
---|
1374 |
|
---|
1375 | oss << endl;
|
---|
1376 | oss << asap::SEPERATOR << endl;
|
---|
1377 | oss << " Scan Table Summary" << endl;
|
---|
1378 | oss << asap::SEPERATOR << endl;
|
---|
1379 |
|
---|
1380 | // Format header info
|
---|
1381 | oss << oldheaderSummary();
|
---|
1382 | oss << endl;
|
---|
1383 |
|
---|
1384 | // main table
|
---|
1385 | String dirtype = "Position ("
|
---|
1386 | + getDirectionRefString()
|
---|
1387 | + ")";
|
---|
1388 | oss.flags(std::ios_base::left);
|
---|
1389 | oss << setw(5) << "Scan" << setw(15) << "Source"
|
---|
1390 | << setw(10) << "Time" << setw(18) << "Integration"
|
---|
1391 | << setw(15) << "Source Type" << endl;
|
---|
1392 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
|
---|
1393 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
|
---|
1394 | << setw(8) << "Frame" << setw(16)
|
---|
1395 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
|
---|
1396 | << setw(7) << "Channels"
|
---|
1397 | << endl;
|
---|
1398 | oss << asap::SEPERATOR << endl;
|
---|
1399 |
|
---|
1400 | // Flush summary and clear up the string
|
---|
1401 | ols << String(oss) << LogIO::POST;
|
---|
1402 | if (ofs) ofs << String(oss) << flush;
|
---|
1403 | oss.str("");
|
---|
1404 | oss.clear();
|
---|
1405 |
|
---|
1406 | TableIterator iter(table_, "SCANNO");
|
---|
1407 | while (!iter.pastEnd()) {
|
---|
1408 | Table subt = iter.table();
|
---|
1409 | ROTableRow row(subt);
|
---|
1410 | MEpoch::ROScalarColumn timeCol(subt,"TIME");
|
---|
1411 | const TableRecord& rec = row.get(0);
|
---|
1412 | oss << setw(4) << std::right << rec.asuInt("SCANNO")
|
---|
1413 | << std::left << setw(1) << ""
|
---|
1414 | << setw(15) << rec.asString("SRCNAME")
|
---|
1415 | << setw(10) << formatTime(timeCol(0), false);
|
---|
1416 | // count the cycles in the scan
|
---|
1417 | TableIterator cyciter(subt, "CYCLENO");
|
---|
1418 | int nint = 0;
|
---|
1419 | while (!cyciter.pastEnd()) {
|
---|
1420 | ++nint;
|
---|
1421 | ++cyciter;
|
---|
1422 | }
|
---|
1423 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
|
---|
1424 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
|
---|
1425 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
|
---|
1426 |
|
---|
1427 | TableIterator biter(subt, "BEAMNO");
|
---|
1428 | while (!biter.pastEnd()) {
|
---|
1429 | Table bsubt = biter.table();
|
---|
1430 | ROTableRow brow(bsubt);
|
---|
1431 | const TableRecord& brec = brow.get(0);
|
---|
1432 | uInt row0 = bsubt.rowNumbers(table_)[0];
|
---|
1433 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
|
---|
1434 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
|
---|
1435 | TableIterator iiter(bsubt, "IFNO");
|
---|
1436 | while (!iiter.pastEnd()) {
|
---|
1437 | Table isubt = iiter.table();
|
---|
1438 | ROTableRow irow(isubt);
|
---|
1439 | const TableRecord& irec = irow.get(0);
|
---|
1440 | oss << setw(9) << "";
|
---|
1441 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
|
---|
1442 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
|
---|
1443 | << setw(3) << "" << nchan(irec.asuInt("IFNO"))
|
---|
1444 | << endl;
|
---|
1445 |
|
---|
1446 | ++iiter;
|
---|
1447 | }
|
---|
1448 | ++biter;
|
---|
1449 | }
|
---|
1450 | // Flush summary every scan and clear up the string
|
---|
1451 | ols << String(oss) << LogIO::POST;
|
---|
1452 | if (ofs) ofs << String(oss) << flush;
|
---|
1453 | oss.str("");
|
---|
1454 | oss.clear();
|
---|
1455 |
|
---|
1456 | ++iter;
|
---|
1457 | }
|
---|
1458 | oss << asap::SEPERATOR << endl;
|
---|
1459 | ols << String(oss) << LogIO::POST;
|
---|
1460 | if (ofs) {
|
---|
1461 | ofs << String(oss) << flush;
|
---|
1462 | ofs.close();
|
---|
1463 | }
|
---|
1464 | // return String(oss);
|
---|
1465 | }
|
---|
1466 |
|
---|
1467 | // std::string Scantable::getTime(int whichrow, bool showdate) const
|
---|
1468 | // {
|
---|
1469 | // MEpoch::ROScalarColumn timeCol(table_, "TIME");
|
---|
1470 | // MEpoch me;
|
---|
1471 | // if (whichrow > -1) {
|
---|
1472 | // me = timeCol(uInt(whichrow));
|
---|
1473 | // } else {
|
---|
1474 | // Double tm;
|
---|
1475 | // table_.keywordSet().get("UTC",tm);
|
---|
1476 | // me = MEpoch(MVEpoch(tm));
|
---|
1477 | // }
|
---|
1478 | // return formatTime(me, showdate);
|
---|
1479 | // }
|
---|
1480 |
|
---|
1481 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
|
---|
1482 | {
|
---|
1483 | MEpoch me;
|
---|
1484 | me = getEpoch(whichrow);
|
---|
1485 | return formatTime(me, showdate, prec);
|
---|
1486 | }
|
---|
1487 |
|
---|
1488 | MEpoch Scantable::getEpoch(int whichrow) const
|
---|
1489 | {
|
---|
1490 | if (whichrow > -1) {
|
---|
1491 | return timeCol_(uInt(whichrow));
|
---|
1492 | } else {
|
---|
1493 | Double tm;
|
---|
1494 | table_.keywordSet().get("UTC",tm);
|
---|
1495 | return MEpoch(MVEpoch(tm));
|
---|
1496 | }
|
---|
1497 | }
|
---|
1498 |
|
---|
1499 | std::string Scantable::getDirectionString(int whichrow) const
|
---|
1500 | {
|
---|
1501 | return formatDirection(getDirection(uInt(whichrow)));
|
---|
1502 | }
|
---|
1503 |
|
---|
1504 |
|
---|
1505 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
|
---|
1506 | const MPosition& mp = getAntennaPosition();
|
---|
1507 | const MDirection& md = getDirection(whichrow);
|
---|
1508 | const MEpoch& me = timeCol_(whichrow);
|
---|
1509 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
|
---|
1510 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
|
---|
1511 | return freqTable_.getSpectralCoordinate(md, mp, me, rf,
|
---|
1512 | mfreqidCol_(whichrow));
|
---|
1513 | }
|
---|
1514 |
|
---|
1515 | std::vector< double > Scantable::getAbcissa( int whichrow ) const
|
---|
1516 | {
|
---|
1517 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
|
---|
1518 | std::vector<double> stlout;
|
---|
1519 | int nchan = specCol_(whichrow).nelements();
|
---|
1520 | String us = freqTable_.getUnitString();
|
---|
1521 | if ( us == "" || us == "pixel" || us == "channel" ) {
|
---|
1522 | for (int i=0; i<nchan; ++i) {
|
---|
1523 | stlout.push_back(double(i));
|
---|
1524 | }
|
---|
1525 | return stlout;
|
---|
1526 | }
|
---|
1527 | SpectralCoordinate spc = getSpectralCoordinate(whichrow);
|
---|
1528 | Vector<Double> pixel(nchan);
|
---|
1529 | Vector<Double> world;
|
---|
1530 | indgen(pixel);
|
---|
1531 | if ( Unit(us) == Unit("Hz") ) {
|
---|
1532 | for ( int i=0; i < nchan; ++i) {
|
---|
1533 | Double world;
|
---|
1534 | spc.toWorld(world, pixel[i]);
|
---|
1535 | stlout.push_back(double(world));
|
---|
1536 | }
|
---|
1537 | } else if ( Unit(us) == Unit("km/s") ) {
|
---|
1538 | Vector<Double> world;
|
---|
1539 | spc.pixelToVelocity(world, pixel);
|
---|
1540 | world.tovector(stlout);
|
---|
1541 | }
|
---|
1542 | return stlout;
|
---|
1543 | }
|
---|
1544 | void Scantable::setDirectionRefString( const std::string & refstr )
|
---|
1545 | {
|
---|
1546 | MDirection::Types mdt;
|
---|
1547 | if (refstr != "" && !MDirection::getType(mdt, refstr)) {
|
---|
1548 | throw(AipsError("Illegal Direction frame."));
|
---|
1549 | }
|
---|
1550 | if ( refstr == "" ) {
|
---|
1551 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
|
---|
1552 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
|
---|
1553 | } else {
|
---|
1554 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
|
---|
1555 | }
|
---|
1556 | }
|
---|
1557 |
|
---|
1558 | std::string Scantable::getDirectionRefString( ) const
|
---|
1559 | {
|
---|
1560 | return table_.keywordSet().asString("DIRECTIONREF");
|
---|
1561 | }
|
---|
1562 |
|
---|
1563 | MDirection Scantable::getDirection(int whichrow ) const
|
---|
1564 | {
|
---|
1565 | String usertype = table_.keywordSet().asString("DIRECTIONREF");
|
---|
1566 | String type = MDirection::showType(dirCol_.getMeasRef().getType());
|
---|
1567 | if ( usertype != type ) {
|
---|
1568 | MDirection::Types mdt;
|
---|
1569 | if (!MDirection::getType(mdt, usertype)) {
|
---|
1570 | throw(AipsError("Illegal Direction frame."));
|
---|
1571 | }
|
---|
1572 | return dirCol_.convert(uInt(whichrow), mdt);
|
---|
1573 | } else {
|
---|
1574 | return dirCol_(uInt(whichrow));
|
---|
1575 | }
|
---|
1576 | }
|
---|
1577 |
|
---|
1578 | std::string Scantable::getAbcissaLabel( int whichrow ) const
|
---|
1579 | {
|
---|
1580 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
|
---|
1581 | const MPosition& mp = getAntennaPosition();
|
---|
1582 | const MDirection& md = getDirection(whichrow);
|
---|
1583 | const MEpoch& me = timeCol_(whichrow);
|
---|
1584 | //const Double& rf = mmolidCol_(whichrow);
|
---|
1585 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
|
---|
1586 | SpectralCoordinate spc =
|
---|
1587 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
|
---|
1588 |
|
---|
1589 | String s = "Channel";
|
---|
1590 | Unit u = Unit(freqTable_.getUnitString());
|
---|
1591 | if (u == Unit("km/s")) {
|
---|
1592 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
|
---|
1593 | } else if (u == Unit("Hz")) {
|
---|
1594 | Vector<String> wau(1);wau = u.getName();
|
---|
1595 | spc.setWorldAxisUnits(wau);
|
---|
1596 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
|
---|
1597 | }
|
---|
1598 | return s;
|
---|
1599 |
|
---|
1600 | }
|
---|
1601 |
|
---|
1602 | /**
|
---|
1603 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
|
---|
1604 | const std::string& unit )
|
---|
1605 | **/
|
---|
1606 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
|
---|
1607 | const std::string& unit )
|
---|
1608 |
|
---|
1609 | {
|
---|
1610 | ///@todo lookup in line table to fill in name and formattedname
|
---|
1611 | Unit u(unit);
|
---|
1612 | //Quantum<Double> urf(rf, u);
|
---|
1613 | Quantum<Vector<Double> >urf(rf, u);
|
---|
1614 | Vector<String> formattedname(0);
|
---|
1615 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
|
---|
1616 |
|
---|
1617 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
|
---|
1618 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
|
---|
1619 | TableVector<uInt> tabvec(table_, "MOLECULE_ID");
|
---|
1620 | tabvec = id;
|
---|
1621 | }
|
---|
1622 |
|
---|
1623 | /**
|
---|
1624 | void asap::Scantable::setRestFrequencies( const std::string& name )
|
---|
1625 | {
|
---|
1626 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
|
---|
1627 | ///@todo implement
|
---|
1628 | }
|
---|
1629 | **/
|
---|
1630 |
|
---|
1631 | void Scantable::setRestFrequencies( const vector<std::string>& name )
|
---|
1632 | {
|
---|
1633 | (void) name; // suppress unused warning
|
---|
1634 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
|
---|
1635 | ///@todo implement
|
---|
1636 | }
|
---|
1637 |
|
---|
1638 | std::vector< unsigned int > Scantable::rownumbers( ) const
|
---|
1639 | {
|
---|
1640 | std::vector<unsigned int> stlout;
|
---|
1641 | Vector<uInt> vec = table_.rowNumbers();
|
---|
1642 | vec.tovector(stlout);
|
---|
1643 | return stlout;
|
---|
1644 | }
|
---|
1645 |
|
---|
1646 |
|
---|
1647 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
|
---|
1648 | {
|
---|
1649 | ROTableRow row(table_);
|
---|
1650 | const TableRecord& rec = row.get(whichrow);
|
---|
1651 | Table t =
|
---|
1652 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
|
---|
1653 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
|
---|
1654 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
|
---|
1655 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
|
---|
1656 | ROArrayColumn<Float> speccol(t, "SPECTRA");
|
---|
1657 | return speccol.getColumn();
|
---|
1658 | }
|
---|
1659 |
|
---|
1660 | std::vector< std::string > Scantable::columnNames( ) const
|
---|
1661 | {
|
---|
1662 | Vector<String> vec = table_.tableDesc().columnNames();
|
---|
1663 | return mathutil::tovectorstring(vec);
|
---|
1664 | }
|
---|
1665 |
|
---|
1666 | MEpoch::Types Scantable::getTimeReference( ) const
|
---|
1667 | {
|
---|
1668 | return MEpoch::castType(timeCol_.getMeasRef().getType());
|
---|
1669 | }
|
---|
1670 |
|
---|
1671 | void Scantable::addFit( const STFitEntry& fit, int row )
|
---|
1672 | {
|
---|
1673 | //cout << mfitidCol_(uInt(row)) << endl;
|
---|
1674 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
|
---|
1675 | os << mfitidCol_(uInt(row)) << LogIO::POST ;
|
---|
1676 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
|
---|
1677 | mfitidCol_.put(uInt(row), id);
|
---|
1678 | }
|
---|
1679 |
|
---|
1680 | void Scantable::shift(int npix)
|
---|
1681 | {
|
---|
1682 | Vector<uInt> fids(mfreqidCol_.getColumn());
|
---|
1683 | genSort( fids, Sort::Ascending,
|
---|
1684 | Sort::QuickSort|Sort::NoDuplicates );
|
---|
1685 | for (uInt i=0; i<fids.nelements(); ++i) {
|
---|
1686 | frequencies().shiftRefPix(npix, fids[i]);
|
---|
1687 | }
|
---|
1688 | }
|
---|
1689 |
|
---|
1690 | String Scantable::getAntennaName() const
|
---|
1691 | {
|
---|
1692 | String out;
|
---|
1693 | table_.keywordSet().get("AntennaName", out);
|
---|
1694 | String::size_type pos1 = out.find("@") ;
|
---|
1695 | String::size_type pos2 = out.find("//") ;
|
---|
1696 | if ( pos2 != String::npos )
|
---|
1697 | out = out.substr(pos2+2,pos1-pos2-2) ;
|
---|
1698 | else if ( pos1 != String::npos )
|
---|
1699 | out = out.substr(0,pos1) ;
|
---|
1700 | return out;
|
---|
1701 | }
|
---|
1702 |
|
---|
1703 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
|
---|
1704 | {
|
---|
1705 | String tbpath;
|
---|
1706 | int ret = 0;
|
---|
1707 | if ( table_.keywordSet().isDefined("GBT_GO") ) {
|
---|
1708 | table_.keywordSet().get("GBT_GO", tbpath);
|
---|
1709 | Table t(tbpath,Table::Old);
|
---|
1710 | // check each scan if other scan of the pair exist
|
---|
1711 | int nscan = scanlist.size();
|
---|
1712 | for (int i = 0; i < nscan; i++) {
|
---|
1713 | Table subt = t( t.col("SCAN") == scanlist[i]+1 );
|
---|
1714 | if (subt.nrow()==0) {
|
---|
1715 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
|
---|
1716 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
1717 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
|
---|
1718 | ret = 1;
|
---|
1719 | break;
|
---|
1720 | }
|
---|
1721 | ROTableRow row(subt);
|
---|
1722 | const TableRecord& rec = row.get(0);
|
---|
1723 | int scan1seqn = rec.asuInt("PROCSEQN");
|
---|
1724 | int laston1 = rec.asuInt("LASTON");
|
---|
1725 | if ( rec.asuInt("PROCSIZE")==2 ) {
|
---|
1726 | if ( i < nscan-1 ) {
|
---|
1727 | Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 );
|
---|
1728 | if ( subt2.nrow() == 0) {
|
---|
1729 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
1730 |
|
---|
1731 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
|
---|
1732 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
|
---|
1733 | ret = 1;
|
---|
1734 | break;
|
---|
1735 | }
|
---|
1736 | ROTableRow row2(subt2);
|
---|
1737 | const TableRecord& rec2 = row2.get(0);
|
---|
1738 | int scan2seqn = rec2.asuInt("PROCSEQN");
|
---|
1739 | int laston2 = rec2.asuInt("LASTON");
|
---|
1740 | if (scan1seqn == 1 && scan2seqn == 2) {
|
---|
1741 | if (laston1 == laston2) {
|
---|
1742 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
1743 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
|
---|
1744 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
|
---|
1745 | i +=1;
|
---|
1746 | }
|
---|
1747 | else {
|
---|
1748 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
1749 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
|
---|
1750 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
|
---|
1751 | }
|
---|
1752 | }
|
---|
1753 | else if (scan1seqn==2 && scan2seqn == 1) {
|
---|
1754 | if (laston1 == laston2) {
|
---|
1755 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
1756 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
|
---|
1757 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
|
---|
1758 | ret = 1;
|
---|
1759 | break;
|
---|
1760 | }
|
---|
1761 | }
|
---|
1762 | else {
|
---|
1763 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
1764 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
|
---|
1765 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
|
---|
1766 | ret = 1;
|
---|
1767 | break;
|
---|
1768 | }
|
---|
1769 | }
|
---|
1770 | }
|
---|
1771 | else {
|
---|
1772 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
1773 | //cerr<<"The scan does not appear to be standard obsevation."<<endl;
|
---|
1774 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
|
---|
1775 | }
|
---|
1776 | //if ( i >= nscan ) break;
|
---|
1777 | }
|
---|
1778 | }
|
---|
1779 | else {
|
---|
1780 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
1781 | //cerr<<"No reference to GBT_GO table."<<endl;
|
---|
1782 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
|
---|
1783 | ret = 1;
|
---|
1784 | }
|
---|
1785 | return ret;
|
---|
1786 | }
|
---|
1787 |
|
---|
1788 | std::vector<double> Scantable::getDirectionVector(int whichrow) const
|
---|
1789 | {
|
---|
1790 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
|
---|
1791 | std::vector<double> dir;
|
---|
1792 | Dir.tovector(dir);
|
---|
1793 | return dir;
|
---|
1794 | }
|
---|
1795 |
|
---|
1796 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
|
---|
1797 | throw( casa::AipsError )
|
---|
1798 | {
|
---|
1799 | // assumed that all rows have same nChan
|
---|
1800 | Vector<Float> arr = specCol_( 0 ) ;
|
---|
1801 | int nChan = arr.nelements() ;
|
---|
1802 |
|
---|
1803 | // if nmin < 0 or nmax < 0, nothing to do
|
---|
1804 | if ( nmin < 0 ) {
|
---|
1805 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
|
---|
1806 | }
|
---|
1807 | if ( nmax < 0 ) {
|
---|
1808 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
|
---|
1809 | }
|
---|
1810 |
|
---|
1811 | // if nmin > nmax, exchange values
|
---|
1812 | if ( nmin > nmax ) {
|
---|
1813 | int tmp = nmax ;
|
---|
1814 | nmax = nmin ;
|
---|
1815 | nmin = tmp ;
|
---|
1816 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
|
---|
1817 | os << "Swap values. Applied range is ["
|
---|
1818 | << nmin << ", " << nmax << "]" << LogIO::POST ;
|
---|
1819 | }
|
---|
1820 |
|
---|
1821 | // if nmin exceeds nChan, nothing to do
|
---|
1822 | if ( nmin >= nChan ) {
|
---|
1823 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
|
---|
1824 | }
|
---|
1825 |
|
---|
1826 | // if nmax exceeds nChan, reset nmax to nChan
|
---|
1827 | if ( nmax >= nChan ) {
|
---|
1828 | if ( nmin == 0 ) {
|
---|
1829 | // nothing to do
|
---|
1830 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
|
---|
1831 | os << "Whole range is selected. Nothing to do." << LogIO::POST ;
|
---|
1832 | return ;
|
---|
1833 | }
|
---|
1834 | else {
|
---|
1835 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
|
---|
1836 | os << "Specified maximum exceeds nChan. Applied range is ["
|
---|
1837 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
|
---|
1838 | nmax = nChan - 1 ;
|
---|
1839 | }
|
---|
1840 | }
|
---|
1841 |
|
---|
1842 | // reshape specCol_ and flagCol_
|
---|
1843 | for ( int irow = 0 ; irow < nrow() ; irow++ ) {
|
---|
1844 | reshapeSpectrum( nmin, nmax, irow ) ;
|
---|
1845 | }
|
---|
1846 |
|
---|
1847 | // update FREQUENCIES subtable
|
---|
1848 | Double refpix ;
|
---|
1849 | Double refval ;
|
---|
1850 | Double increment ;
|
---|
1851 | int freqnrow = freqTable_.table().nrow() ;
|
---|
1852 | Vector<uInt> oldId( freqnrow ) ;
|
---|
1853 | Vector<uInt> newId( freqnrow ) ;
|
---|
1854 | for ( int irow = 0 ; irow < freqnrow ; irow++ ) {
|
---|
1855 | freqTable_.getEntry( refpix, refval, increment, irow ) ;
|
---|
1856 | /***
|
---|
1857 | * need to shift refpix to nmin
|
---|
1858 | * note that channel nmin in old index will be channel 0 in new one
|
---|
1859 | ***/
|
---|
1860 | refval = refval - ( refpix - nmin ) * increment ;
|
---|
1861 | refpix = 0 ;
|
---|
1862 | freqTable_.setEntry( refpix, refval, increment, irow ) ;
|
---|
1863 | }
|
---|
1864 |
|
---|
1865 | // update nchan
|
---|
1866 | int newsize = nmax - nmin + 1 ;
|
---|
1867 | table_.rwKeywordSet().define( "nChan", newsize ) ;
|
---|
1868 |
|
---|
1869 | // update bandwidth
|
---|
1870 | // assumed all spectra in the scantable have same bandwidth
|
---|
1871 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
|
---|
1872 |
|
---|
1873 | return ;
|
---|
1874 | }
|
---|
1875 |
|
---|
1876 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
|
---|
1877 | {
|
---|
1878 | // reshape specCol_ and flagCol_
|
---|
1879 | Vector<Float> oldspec = specCol_( irow ) ;
|
---|
1880 | Vector<uChar> oldflag = flagsCol_( irow ) ;
|
---|
1881 | uInt newsize = nmax - nmin + 1 ;
|
---|
1882 | specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ;
|
---|
1883 | flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ;
|
---|
1884 |
|
---|
1885 | return ;
|
---|
1886 | }
|
---|
1887 |
|
---|
1888 | void asap::Scantable::regridChannel( int nChan, double dnu )
|
---|
1889 | {
|
---|
1890 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
|
---|
1891 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
|
---|
1892 | // assumed that all rows have same nChan
|
---|
1893 | Vector<Float> arr = specCol_( 0 ) ;
|
---|
1894 | int oldsize = arr.nelements() ;
|
---|
1895 |
|
---|
1896 | // if oldsize == nChan, nothing to do
|
---|
1897 | if ( oldsize == nChan ) {
|
---|
1898 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
|
---|
1899 | return ;
|
---|
1900 | }
|
---|
1901 |
|
---|
1902 | // if oldChan < nChan, unphysical operation
|
---|
1903 | if ( oldsize < nChan ) {
|
---|
1904 | os << "Unphysical operation. Nothing to do." << LogIO::POST ;
|
---|
1905 | return ;
|
---|
1906 | }
|
---|
1907 |
|
---|
1908 | // change channel number for specCol_ and flagCol_
|
---|
1909 | Vector<Float> newspec( nChan, 0 ) ;
|
---|
1910 | Vector<uChar> newflag( nChan, false ) ;
|
---|
1911 | vector<string> coordinfo = getCoordInfo() ;
|
---|
1912 | string oldinfo = coordinfo[0] ;
|
---|
1913 | coordinfo[0] = "Hz" ;
|
---|
1914 | setCoordInfo( coordinfo ) ;
|
---|
1915 | for ( int irow = 0 ; irow < nrow() ; irow++ ) {
|
---|
1916 | regridChannel( nChan, dnu, irow ) ;
|
---|
1917 | }
|
---|
1918 | coordinfo[0] = oldinfo ;
|
---|
1919 | setCoordInfo( coordinfo ) ;
|
---|
1920 |
|
---|
1921 |
|
---|
1922 | // NOTE: this method does not update metadata such as
|
---|
1923 | // FREQUENCIES subtable, nChan, Bandwidth, etc.
|
---|
1924 |
|
---|
1925 | return ;
|
---|
1926 | }
|
---|
1927 |
|
---|
1928 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
|
---|
1929 | {
|
---|
1930 | // logging
|
---|
1931 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
|
---|
1932 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
|
---|
1933 |
|
---|
1934 | Vector<Float> oldspec = specCol_( irow ) ;
|
---|
1935 | Vector<uChar> oldflag = flagsCol_( irow ) ;
|
---|
1936 | Vector<Float> newspec( nChan, 0 ) ;
|
---|
1937 | Vector<uChar> newflag( nChan, false ) ;
|
---|
1938 |
|
---|
1939 | // regrid
|
---|
1940 | vector<double> abcissa = getAbcissa( irow ) ;
|
---|
1941 | int oldsize = abcissa.size() ;
|
---|
1942 | double olddnu = abcissa[1] - abcissa[0] ;
|
---|
1943 | //int refChan = 0 ;
|
---|
1944 | //double frac = 0.0 ;
|
---|
1945 | //double wedge = 0.0 ;
|
---|
1946 | //double pile = 0.0 ;
|
---|
1947 | int ichan = 0 ;
|
---|
1948 | double wsum = 0.0 ;
|
---|
1949 | Vector<Float> zi( nChan+1 ) ;
|
---|
1950 | Vector<Float> yi( oldsize + 1 ) ;
|
---|
1951 | zi[0] = abcissa[0] - 0.5 * olddnu ;
|
---|
1952 | zi[1] = zi[1] + dnu ;
|
---|
1953 | for ( int ii = 2 ; ii < nChan ; ii++ )
|
---|
1954 | zi[ii] = zi[0] + dnu * ii ;
|
---|
1955 | zi[nChan] = zi[nChan-1] + dnu ;
|
---|
1956 | yi[0] = abcissa[0] - 0.5 * olddnu ;
|
---|
1957 | yi[1] = abcissa[1] + 0.5 * olddnu ;
|
---|
1958 | for ( int ii = 2 ; ii < oldsize ; ii++ )
|
---|
1959 | yi[ii] = abcissa[ii-1] + olddnu ;
|
---|
1960 | yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ;
|
---|
1961 | if ( dnu > 0.0 ) {
|
---|
1962 | for ( int ii = 0 ; ii < nChan ; ii++ ) {
|
---|
1963 | double zl = zi[ii] ;
|
---|
1964 | double zr = zi[ii+1] ;
|
---|
1965 | for ( int j = ichan ; j < oldsize ; j++ ) {
|
---|
1966 | double yl = yi[j] ;
|
---|
1967 | double yr = yi[j+1] ;
|
---|
1968 | if ( yl <= zl ) {
|
---|
1969 | if ( yr <= zl ) {
|
---|
1970 | continue ;
|
---|
1971 | }
|
---|
1972 | else if ( yr <= zr ) {
|
---|
1973 | newspec[ii] += oldspec[j] * ( yr - zl ) ;
|
---|
1974 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
1975 | wsum += ( yr - zl ) ;
|
---|
1976 | }
|
---|
1977 | else {
|
---|
1978 | newspec[ii] += oldspec[j] * dnu ;
|
---|
1979 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
1980 | wsum += dnu ;
|
---|
1981 | ichan = j ;
|
---|
1982 | break ;
|
---|
1983 | }
|
---|
1984 | }
|
---|
1985 | else if ( yl < zr ) {
|
---|
1986 | if ( yr <= zr ) {
|
---|
1987 | newspec[ii] += oldspec[j] * ( yr - yl ) ;
|
---|
1988 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
1989 | wsum += ( yr - yl ) ;
|
---|
1990 | }
|
---|
1991 | else {
|
---|
1992 | newspec[ii] += oldspec[j] * ( zr - yl ) ;
|
---|
1993 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
1994 | wsum += ( zr - yl ) ;
|
---|
1995 | ichan = j ;
|
---|
1996 | break ;
|
---|
1997 | }
|
---|
1998 | }
|
---|
1999 | else {
|
---|
2000 | ichan = j - 1 ;
|
---|
2001 | break ;
|
---|
2002 | }
|
---|
2003 | }
|
---|
2004 | if ( wsum != 0.0 )
|
---|
2005 | newspec[ii] /= wsum ;
|
---|
2006 | wsum = 0.0 ;
|
---|
2007 | }
|
---|
2008 | }
|
---|
2009 | else if ( dnu < 0.0 ) {
|
---|
2010 | for ( int ii = 0 ; ii < nChan ; ii++ ) {
|
---|
2011 | double zl = zi[ii] ;
|
---|
2012 | double zr = zi[ii+1] ;
|
---|
2013 | for ( int j = ichan ; j < oldsize ; j++ ) {
|
---|
2014 | double yl = yi[j] ;
|
---|
2015 | double yr = yi[j+1] ;
|
---|
2016 | if ( yl >= zl ) {
|
---|
2017 | if ( yr >= zl ) {
|
---|
2018 | continue ;
|
---|
2019 | }
|
---|
2020 | else if ( yr >= zr ) {
|
---|
2021 | newspec[ii] += oldspec[j] * abs( yr - zl ) ;
|
---|
2022 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
2023 | wsum += abs( yr - zl ) ;
|
---|
2024 | }
|
---|
2025 | else {
|
---|
2026 | newspec[ii] += oldspec[j] * abs( dnu ) ;
|
---|
2027 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
2028 | wsum += abs( dnu ) ;
|
---|
2029 | ichan = j ;
|
---|
2030 | break ;
|
---|
2031 | }
|
---|
2032 | }
|
---|
2033 | else if ( yl > zr ) {
|
---|
2034 | if ( yr >= zr ) {
|
---|
2035 | newspec[ii] += oldspec[j] * abs( yr - yl ) ;
|
---|
2036 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
2037 | wsum += abs( yr - yl ) ;
|
---|
2038 | }
|
---|
2039 | else {
|
---|
2040 | newspec[ii] += oldspec[j] * abs( zr - yl ) ;
|
---|
2041 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
2042 | wsum += abs( zr - yl ) ;
|
---|
2043 | ichan = j ;
|
---|
2044 | break ;
|
---|
2045 | }
|
---|
2046 | }
|
---|
2047 | else {
|
---|
2048 | ichan = j - 1 ;
|
---|
2049 | break ;
|
---|
2050 | }
|
---|
2051 | }
|
---|
2052 | if ( wsum != 0.0 )
|
---|
2053 | newspec[ii] /= wsum ;
|
---|
2054 | wsum = 0.0 ;
|
---|
2055 | }
|
---|
2056 | }
|
---|
2057 | // * ichan = 0
|
---|
2058 | // ***/
|
---|
2059 | // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
|
---|
2060 | // pile += dnu ;
|
---|
2061 | // wedge = olddnu * ( refChan + 1 ) ;
|
---|
2062 | // while ( wedge < pile ) {
|
---|
2063 | // newspec[0] += olddnu * oldspec[refChan] ;
|
---|
2064 | // newflag[0] = newflag[0] || oldflag[refChan] ;
|
---|
2065 | // //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
|
---|
2066 | // refChan++ ;
|
---|
2067 | // wedge += olddnu ;
|
---|
2068 | // wsum += olddnu ;
|
---|
2069 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
|
---|
2070 | // }
|
---|
2071 | // frac = ( wedge - pile ) / olddnu ;
|
---|
2072 | // wsum += ( 1.0 - frac ) * olddnu ;
|
---|
2073 | // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
|
---|
2074 | // newflag[0] = newflag[0] || oldflag[refChan] ;
|
---|
2075 | // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
|
---|
2076 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
|
---|
2077 | // newspec[0] /= wsum ;
|
---|
2078 | // //ofs << "newspec[0] = " << newspec[0] << endl ;
|
---|
2079 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
|
---|
2080 |
|
---|
2081 | // /***
|
---|
2082 | // * ichan = 1 - nChan-2
|
---|
2083 | // ***/
|
---|
2084 | // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
|
---|
2085 | // pile += dnu ;
|
---|
2086 | // newspec[ichan] += frac * olddnu * oldspec[refChan] ;
|
---|
2087 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
|
---|
2088 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
|
---|
2089 | // refChan++ ;
|
---|
2090 | // wedge += olddnu ;
|
---|
2091 | // wsum = frac * olddnu ;
|
---|
2092 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
|
---|
2093 | // while ( wedge < pile ) {
|
---|
2094 | // newspec[ichan] += olddnu * oldspec[refChan] ;
|
---|
2095 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
|
---|
2096 | // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
|
---|
2097 | // refChan++ ;
|
---|
2098 | // wedge += olddnu ;
|
---|
2099 | // wsum += olddnu ;
|
---|
2100 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
|
---|
2101 | // }
|
---|
2102 | // frac = ( wedge - pile ) / olddnu ;
|
---|
2103 | // wsum += ( 1.0 - frac ) * olddnu ;
|
---|
2104 | // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
|
---|
2105 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
|
---|
2106 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
|
---|
2107 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
|
---|
2108 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
|
---|
2109 | // newspec[ichan] /= wsum ;
|
---|
2110 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
|
---|
2111 | // }
|
---|
2112 |
|
---|
2113 | // /***
|
---|
2114 | // * ichan = nChan-1
|
---|
2115 | // ***/
|
---|
2116 | // // NOTE: Assumed that all spectra have the same bandwidth
|
---|
2117 | // pile += dnu ;
|
---|
2118 | // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
|
---|
2119 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
|
---|
2120 | // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
|
---|
2121 | // refChan++ ;
|
---|
2122 | // wedge += olddnu ;
|
---|
2123 | // wsum = frac * olddnu ;
|
---|
2124 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
|
---|
2125 | // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
|
---|
2126 | // newspec[nChan-1] += olddnu * oldspec[jchan] ;
|
---|
2127 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
|
---|
2128 | // wsum += olddnu ;
|
---|
2129 | // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
|
---|
2130 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
|
---|
2131 | // }
|
---|
2132 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
|
---|
2133 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
|
---|
2134 | // newspec[nChan-1] /= wsum ;
|
---|
2135 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
|
---|
2136 |
|
---|
2137 | // // ofs.close() ;
|
---|
2138 |
|
---|
2139 | specCol_.put( irow, newspec ) ;
|
---|
2140 | flagsCol_.put( irow, newflag ) ;
|
---|
2141 |
|
---|
2142 | return ;
|
---|
2143 | }
|
---|
2144 |
|
---|
2145 | std::vector<float> Scantable::getWeather(int whichrow) const
|
---|
2146 | {
|
---|
2147 | std::vector<float> out(5);
|
---|
2148 | //Float temperature, pressure, humidity, windspeed, windaz;
|
---|
2149 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
|
---|
2150 | mweatheridCol_(uInt(whichrow)));
|
---|
2151 |
|
---|
2152 |
|
---|
2153 | return out;
|
---|
2154 | }
|
---|
2155 |
|
---|
2156 | bool Scantable::getFlagtraFast(uInt whichrow)
|
---|
2157 | {
|
---|
2158 | uChar flag;
|
---|
2159 | Vector<uChar> flags;
|
---|
2160 | flagsCol_.get(whichrow, flags);
|
---|
2161 | flag = flags[0];
|
---|
2162 | for (uInt i = 1; i < flags.size(); ++i) {
|
---|
2163 | flag &= flags[i];
|
---|
2164 | }
|
---|
2165 | return ((flag >> 7) == 1);
|
---|
2166 | }
|
---|
2167 |
|
---|
2168 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
|
---|
2169 | {
|
---|
2170 | try {
|
---|
2171 | ofstream ofs;
|
---|
2172 | String coordInfo = "";
|
---|
2173 | bool hasSameNchan = true;
|
---|
2174 | bool outTextFile = false;
|
---|
2175 |
|
---|
2176 | if (blfile != "") {
|
---|
2177 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
2178 | if (ofs) outTextFile = true;
|
---|
2179 | }
|
---|
2180 |
|
---|
2181 | if (outLogger || outTextFile) {
|
---|
2182 | coordInfo = getCoordInfo()[0];
|
---|
2183 | if (coordInfo == "") coordInfo = "channel";
|
---|
2184 | hasSameNchan = hasSameNchanOverIFs();
|
---|
2185 | }
|
---|
2186 |
|
---|
2187 | Fitter fitter = Fitter();
|
---|
2188 | fitter.setExpression("poly", order);
|
---|
2189 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
2190 |
|
---|
2191 | int nRow = nrow();
|
---|
2192 | std::vector<bool> chanMask;
|
---|
2193 | bool showProgress;
|
---|
2194 | int minNRow;
|
---|
2195 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
2196 |
|
---|
2197 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
2198 | chanMask = getCompositeChanMask(whichrow, mask);
|
---|
2199 | fitBaseline(chanMask, whichrow, fitter);
|
---|
2200 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
2201 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter);
|
---|
2202 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
2203 | }
|
---|
2204 |
|
---|
2205 | if (outTextFile) ofs.close();
|
---|
2206 |
|
---|
2207 | } catch (...) {
|
---|
2208 | throw;
|
---|
2209 | }
|
---|
2210 | }
|
---|
2211 |
|
---|
2212 | void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
|
---|
2213 | {
|
---|
2214 | try {
|
---|
2215 | ofstream ofs;
|
---|
2216 | String coordInfo = "";
|
---|
2217 | bool hasSameNchan = true;
|
---|
2218 | bool outTextFile = false;
|
---|
2219 |
|
---|
2220 | if (blfile != "") {
|
---|
2221 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
2222 | if (ofs) outTextFile = true;
|
---|
2223 | }
|
---|
2224 |
|
---|
2225 | if (outLogger || outTextFile) {
|
---|
2226 | coordInfo = getCoordInfo()[0];
|
---|
2227 | if (coordInfo == "") coordInfo = "channel";
|
---|
2228 | hasSameNchan = hasSameNchanOverIFs();
|
---|
2229 | }
|
---|
2230 |
|
---|
2231 | Fitter fitter = Fitter();
|
---|
2232 | fitter.setExpression("poly", order);
|
---|
2233 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
2234 |
|
---|
2235 | int nRow = nrow();
|
---|
2236 | std::vector<bool> chanMask;
|
---|
2237 | int minEdgeSize = getIFNos().size()*2;
|
---|
2238 | STLineFinder lineFinder = STLineFinder();
|
---|
2239 | lineFinder.setOptions(threshold, 3, chanAvgLimit);
|
---|
2240 |
|
---|
2241 | bool showProgress;
|
---|
2242 | int minNRow;
|
---|
2243 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
2244 |
|
---|
2245 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
2246 |
|
---|
2247 | //-------------------------------------------------------
|
---|
2248 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
|
---|
2249 | //-------------------------------------------------------
|
---|
2250 | int edgeSize = edge.size();
|
---|
2251 | std::vector<int> currentEdge;
|
---|
2252 | if (edgeSize >= 2) {
|
---|
2253 | int idx = 0;
|
---|
2254 | if (edgeSize > 2) {
|
---|
2255 | if (edgeSize < minEdgeSize) {
|
---|
2256 | throw(AipsError("Length of edge element info is less than that of IFs"));
|
---|
2257 | }
|
---|
2258 | idx = 2 * getIF(whichrow);
|
---|
2259 | }
|
---|
2260 | currentEdge.push_back(edge[idx]);
|
---|
2261 | currentEdge.push_back(edge[idx+1]);
|
---|
2262 | } else {
|
---|
2263 | throw(AipsError("Wrong length of edge element"));
|
---|
2264 | }
|
---|
2265 | lineFinder.setData(getSpectrum(whichrow));
|
---|
2266 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
|
---|
2267 | chanMask = lineFinder.getMask();
|
---|
2268 | //-------------------------------------------------------
|
---|
2269 |
|
---|
2270 | fitBaseline(chanMask, whichrow, fitter);
|
---|
2271 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
2272 |
|
---|
2273 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter);
|
---|
2274 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
2275 | }
|
---|
2276 |
|
---|
2277 | if (outTextFile) ofs.close();
|
---|
2278 |
|
---|
2279 | } catch (...) {
|
---|
2280 | throw;
|
---|
2281 | }
|
---|
2282 | }
|
---|
2283 |
|
---|
2284 | void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
|
---|
2285 | {
|
---|
2286 | try {
|
---|
2287 | ofstream ofs;
|
---|
2288 | String coordInfo = "";
|
---|
2289 | bool hasSameNchan = true;
|
---|
2290 | bool outTextFile = false;
|
---|
2291 |
|
---|
2292 | if (blfile != "") {
|
---|
2293 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
2294 | if (ofs) outTextFile = true;
|
---|
2295 | }
|
---|
2296 |
|
---|
2297 | if (outLogger || outTextFile) {
|
---|
2298 | coordInfo = getCoordInfo()[0];
|
---|
2299 | if (coordInfo == "") coordInfo = "channel";
|
---|
2300 | hasSameNchan = hasSameNchanOverIFs();
|
---|
2301 | }
|
---|
2302 |
|
---|
2303 | //Fitter fitter = Fitter();
|
---|
2304 | //fitter.setExpression("cspline", nPiece);
|
---|
2305 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
2306 |
|
---|
2307 | int nRow = nrow();
|
---|
2308 | std::vector<bool> chanMask;
|
---|
2309 | bool showProgress;
|
---|
2310 | int minNRow;
|
---|
2311 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
2312 |
|
---|
2313 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
2314 | chanMask = getCompositeChanMask(whichrow, mask);
|
---|
2315 | //fitBaseline(chanMask, whichrow, fitter);
|
---|
2316 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
2317 | std::vector<int> pieceEdges;
|
---|
2318 | std::vector<float> params;
|
---|
2319 | int nClipped = 0;
|
---|
2320 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
|
---|
2321 | setSpectrum(res, whichrow);
|
---|
2322 | //
|
---|
2323 |
|
---|
2324 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped);
|
---|
2325 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
2326 | }
|
---|
2327 |
|
---|
2328 | if (outTextFile) ofs.close();
|
---|
2329 |
|
---|
2330 | } catch (...) {
|
---|
2331 | throw;
|
---|
2332 | }
|
---|
2333 | }
|
---|
2334 |
|
---|
2335 | void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
|
---|
2336 | {
|
---|
2337 | try {
|
---|
2338 | ofstream ofs;
|
---|
2339 | String coordInfo = "";
|
---|
2340 | bool hasSameNchan = true;
|
---|
2341 | bool outTextFile = false;
|
---|
2342 |
|
---|
2343 | if (blfile != "") {
|
---|
2344 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
2345 | if (ofs) outTextFile = true;
|
---|
2346 | }
|
---|
2347 |
|
---|
2348 | if (outLogger || outTextFile) {
|
---|
2349 | coordInfo = getCoordInfo()[0];
|
---|
2350 | if (coordInfo == "") coordInfo = "channel";
|
---|
2351 | hasSameNchan = hasSameNchanOverIFs();
|
---|
2352 | }
|
---|
2353 |
|
---|
2354 | //Fitter fitter = Fitter();
|
---|
2355 | //fitter.setExpression("cspline", nPiece);
|
---|
2356 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
2357 |
|
---|
2358 | int nRow = nrow();
|
---|
2359 | std::vector<bool> chanMask;
|
---|
2360 | int minEdgeSize = getIFNos().size()*2;
|
---|
2361 | STLineFinder lineFinder = STLineFinder();
|
---|
2362 | lineFinder.setOptions(threshold, 3, chanAvgLimit);
|
---|
2363 |
|
---|
2364 | bool showProgress;
|
---|
2365 | int minNRow;
|
---|
2366 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
2367 |
|
---|
2368 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
2369 |
|
---|
2370 | //-------------------------------------------------------
|
---|
2371 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
|
---|
2372 | //-------------------------------------------------------
|
---|
2373 | int edgeSize = edge.size();
|
---|
2374 | std::vector<int> currentEdge;
|
---|
2375 | if (edgeSize >= 2) {
|
---|
2376 | int idx = 0;
|
---|
2377 | if (edgeSize > 2) {
|
---|
2378 | if (edgeSize < minEdgeSize) {
|
---|
2379 | throw(AipsError("Length of edge element info is less than that of IFs"));
|
---|
2380 | }
|
---|
2381 | idx = 2 * getIF(whichrow);
|
---|
2382 | }
|
---|
2383 | currentEdge.push_back(edge[idx]);
|
---|
2384 | currentEdge.push_back(edge[idx+1]);
|
---|
2385 | } else {
|
---|
2386 | throw(AipsError("Wrong length of edge element"));
|
---|
2387 | }
|
---|
2388 | lineFinder.setData(getSpectrum(whichrow));
|
---|
2389 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
|
---|
2390 | chanMask = lineFinder.getMask();
|
---|
2391 | //-------------------------------------------------------
|
---|
2392 |
|
---|
2393 |
|
---|
2394 | //fitBaseline(chanMask, whichrow, fitter);
|
---|
2395 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
2396 | std::vector<int> pieceEdges;
|
---|
2397 | std::vector<float> params;
|
---|
2398 | int nClipped = 0;
|
---|
2399 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
|
---|
2400 | setSpectrum(res, whichrow);
|
---|
2401 | //
|
---|
2402 |
|
---|
2403 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped);
|
---|
2404 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
2405 | }
|
---|
2406 |
|
---|
2407 | if (outTextFile) ofs.close();
|
---|
2408 |
|
---|
2409 | } catch (...) {
|
---|
2410 | throw;
|
---|
2411 | }
|
---|
2412 | }
|
---|
2413 |
|
---|
2414 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, std::vector<int>& idxEdge, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual)
|
---|
2415 | {
|
---|
2416 | if (data.size() != mask.size()) {
|
---|
2417 | throw(AipsError("data and mask sizes are not identical"));
|
---|
2418 | }
|
---|
2419 | if (nPiece < 1) {
|
---|
2420 | throw(AipsError("number of the sections must be one or more"));
|
---|
2421 | }
|
---|
2422 |
|
---|
2423 | int nChan = data.size();
|
---|
2424 | std::vector<int> maskArray;
|
---|
2425 | std::vector<int> x;
|
---|
2426 | for (int i = 0; i < nChan; ++i) {
|
---|
2427 | maskArray.push_back(mask[i] ? 1 : 0);
|
---|
2428 | if (mask[i]) {
|
---|
2429 | x.push_back(i);
|
---|
2430 | }
|
---|
2431 | }
|
---|
2432 |
|
---|
2433 | int initNData = x.size();
|
---|
2434 | if (initNData < nPiece) {
|
---|
2435 | throw(AipsError("too few non-flagged channels"));
|
---|
2436 | }
|
---|
2437 |
|
---|
2438 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
|
---|
2439 | std::vector<double> invEdge;
|
---|
2440 | idxEdge.clear();
|
---|
2441 | idxEdge.push_back(x[0]);
|
---|
2442 | for (int i = 1; i < nPiece; ++i) {
|
---|
2443 | int valX = x[nElement*i];
|
---|
2444 | idxEdge.push_back(valX);
|
---|
2445 | invEdge.push_back(1.0/(double)valX);
|
---|
2446 | }
|
---|
2447 | idxEdge.push_back(x[x.size()-1]+1);
|
---|
2448 |
|
---|
2449 | int nData = initNData;
|
---|
2450 | int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1).
|
---|
2451 |
|
---|
2452 | std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1, residual;
|
---|
2453 | for (int i = 0; i < nChan; ++i) {
|
---|
2454 | double di = (double)i;
|
---|
2455 | double dD = (double)data[i];
|
---|
2456 | x1.push_back(di);
|
---|
2457 | x2.push_back(di*di);
|
---|
2458 | x3.push_back(di*di*di);
|
---|
2459 | z1.push_back(dD);
|
---|
2460 | x1z1.push_back(dD*di);
|
---|
2461 | x2z1.push_back(dD*di*di);
|
---|
2462 | x3z1.push_back(dD*di*di*di);
|
---|
2463 | r1.push_back(0.0);
|
---|
2464 | residual.push_back(0.0);
|
---|
2465 | }
|
---|
2466 |
|
---|
2467 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
|
---|
2468 | // xMatrix : horizontal concatenation of
|
---|
2469 | // the least-sq. matrix (left) and an
|
---|
2470 | // identity matrix (right).
|
---|
2471 | // the right part is used to calculate the inverse matrix of the left part.
|
---|
2472 | double xMatrix[nDOF][2*nDOF];
|
---|
2473 | double zMatrix[nDOF];
|
---|
2474 | for (int i = 0; i < nDOF; ++i) {
|
---|
2475 | for (int j = 0; j < 2*nDOF; ++j) {
|
---|
2476 | xMatrix[i][j] = 0.0;
|
---|
2477 | }
|
---|
2478 | xMatrix[i][nDOF+i] = 1.0;
|
---|
2479 | zMatrix[i] = 0.0;
|
---|
2480 | }
|
---|
2481 |
|
---|
2482 | for (int n = 0; n < nPiece; ++n) {
|
---|
2483 | int nUseDataInPiece = 0;
|
---|
2484 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
|
---|
2485 |
|
---|
2486 | if (maskArray[i] == 0) continue;
|
---|
2487 |
|
---|
2488 | xMatrix[0][0] += 1.0;
|
---|
2489 | xMatrix[0][1] += x1[i];
|
---|
2490 | xMatrix[0][2] += x2[i];
|
---|
2491 | xMatrix[0][3] += x3[i];
|
---|
2492 | xMatrix[1][1] += x2[i];
|
---|
2493 | xMatrix[1][2] += x3[i];
|
---|
2494 | xMatrix[1][3] += x2[i]*x2[i];
|
---|
2495 | xMatrix[2][2] += x2[i]*x2[i];
|
---|
2496 | xMatrix[2][3] += x3[i]*x2[i];
|
---|
2497 | xMatrix[3][3] += x3[i]*x3[i];
|
---|
2498 | zMatrix[0] += z1[i];
|
---|
2499 | zMatrix[1] += x1z1[i];
|
---|
2500 | zMatrix[2] += x2z1[i];
|
---|
2501 | zMatrix[3] += x3z1[i];
|
---|
2502 |
|
---|
2503 | for (int j = 0; j < n; ++j) {
|
---|
2504 | double q = 1.0 - x1[i]*invEdge[j];
|
---|
2505 | q = q*q*q;
|
---|
2506 | xMatrix[0][j+4] += q;
|
---|
2507 | xMatrix[1][j+4] += q*x1[i];
|
---|
2508 | xMatrix[2][j+4] += q*x2[i];
|
---|
2509 | xMatrix[3][j+4] += q*x3[i];
|
---|
2510 | for (int k = 0; k < j; ++k) {
|
---|
2511 | double r = 1.0 - x1[i]*invEdge[k];
|
---|
2512 | r = r*r*r;
|
---|
2513 | xMatrix[k+4][j+4] += r*q;
|
---|
2514 | }
|
---|
2515 | xMatrix[j+4][j+4] += q*q;
|
---|
2516 | zMatrix[j+4] += q*z1[i];
|
---|
2517 | }
|
---|
2518 |
|
---|
2519 | nUseDataInPiece++;
|
---|
2520 | }
|
---|
2521 |
|
---|
2522 | if (nUseDataInPiece < 1) {
|
---|
2523 | std::vector<string> suffixOfPieceNumber(4);
|
---|
2524 | suffixOfPieceNumber[0] = "th";
|
---|
2525 | suffixOfPieceNumber[1] = "st";
|
---|
2526 | suffixOfPieceNumber[2] = "nd";
|
---|
2527 | suffixOfPieceNumber[3] = "rd";
|
---|
2528 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
|
---|
2529 | ostringstream oss;
|
---|
2530 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
|
---|
2531 | oss << " piece of the spectrum. can't execute fitting anymore.";
|
---|
2532 | throw(AipsError(String(oss)));
|
---|
2533 | }
|
---|
2534 | }
|
---|
2535 |
|
---|
2536 | for (int i = 0; i < nDOF; ++i) {
|
---|
2537 | for (int j = 0; j < i; ++j) {
|
---|
2538 | xMatrix[i][j] = xMatrix[j][i];
|
---|
2539 | }
|
---|
2540 | }
|
---|
2541 |
|
---|
2542 | std::vector<double> invDiag;
|
---|
2543 | for (int i = 0; i < nDOF; ++i) {
|
---|
2544 | invDiag.push_back(1.0/xMatrix[i][i]);
|
---|
2545 | for (int j = 0; j < nDOF; ++j) {
|
---|
2546 | xMatrix[i][j] *= invDiag[i];
|
---|
2547 | }
|
---|
2548 | }
|
---|
2549 |
|
---|
2550 | for (int k = 0; k < nDOF; ++k) {
|
---|
2551 | for (int i = 0; i < nDOF; ++i) {
|
---|
2552 | if (i != k) {
|
---|
2553 | double factor1 = xMatrix[k][k];
|
---|
2554 | double factor2 = xMatrix[i][k];
|
---|
2555 | for (int j = k; j < 2*nDOF; ++j) {
|
---|
2556 | xMatrix[i][j] *= factor1;
|
---|
2557 | xMatrix[i][j] -= xMatrix[k][j]*factor2;
|
---|
2558 | xMatrix[i][j] /= factor1;
|
---|
2559 | }
|
---|
2560 | }
|
---|
2561 | }
|
---|
2562 | double xDiag = xMatrix[k][k];
|
---|
2563 | for (int j = k; j < 2*nDOF; ++j) {
|
---|
2564 | xMatrix[k][j] /= xDiag;
|
---|
2565 | }
|
---|
2566 | }
|
---|
2567 |
|
---|
2568 | for (int i = 0; i < nDOF; ++i) {
|
---|
2569 | for (int j = 0; j < nDOF; ++j) {
|
---|
2570 | xMatrix[i][nDOF+j] *= invDiag[j];
|
---|
2571 | }
|
---|
2572 | }
|
---|
2573 | //compute a vector y which consists of the coefficients of the best-fit spline curves
|
---|
2574 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
|
---|
2575 | //cubic terms for the other pieces (in case nPiece>1).
|
---|
2576 | std::vector<double> y;
|
---|
2577 | y.clear();
|
---|
2578 | for (int i = 0; i < nDOF; ++i) {
|
---|
2579 | y.push_back(0.0);
|
---|
2580 | for (int j = 0; j < nDOF; ++j) {
|
---|
2581 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
|
---|
2582 | }
|
---|
2583 | }
|
---|
2584 |
|
---|
2585 | double a0 = y[0];
|
---|
2586 | double a1 = y[1];
|
---|
2587 | double a2 = y[2];
|
---|
2588 | double a3 = y[3];
|
---|
2589 | params.clear();
|
---|
2590 |
|
---|
2591 | for (int n = 0; n < nPiece; ++n) {
|
---|
2592 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
|
---|
2593 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
|
---|
2594 | residual[i] = z1[i] - r1[i];
|
---|
2595 | }
|
---|
2596 | params.push_back(a0);
|
---|
2597 | params.push_back(a1);
|
---|
2598 | params.push_back(a2);
|
---|
2599 | params.push_back(a3);
|
---|
2600 |
|
---|
2601 | if (n == nPiece-1) break;
|
---|
2602 |
|
---|
2603 | double d = y[4+n];
|
---|
2604 | double iE = invEdge[n];
|
---|
2605 | a0 += d;
|
---|
2606 | a1 -= 3.0*d*iE;
|
---|
2607 | a2 += 3.0*d*iE*iE;
|
---|
2608 | a3 -= d*iE*iE*iE;
|
---|
2609 | }
|
---|
2610 |
|
---|
2611 | if ((nClip == nIterClip) || (thresClip <= 0.0)) {
|
---|
2612 | break;
|
---|
2613 | } else {
|
---|
2614 | double stdDev = 0.0;
|
---|
2615 | for (int i = 0; i < nChan; ++i) {
|
---|
2616 | stdDev += residual[i]*residual[i]*(double)maskArray[i];
|
---|
2617 | }
|
---|
2618 | stdDev = sqrt(stdDev/(double)nData);
|
---|
2619 |
|
---|
2620 | double thres = stdDev * thresClip;
|
---|
2621 | int newNData = 0;
|
---|
2622 | for (int i = 0; i < nChan; ++i) {
|
---|
2623 | if (abs(residual[i]) >= thres) {
|
---|
2624 | maskArray[i] = 0;
|
---|
2625 | }
|
---|
2626 | if (maskArray[i] > 0) {
|
---|
2627 | newNData++;
|
---|
2628 | }
|
---|
2629 | }
|
---|
2630 | if (newNData == nData) {
|
---|
2631 | break; //no more flag to add. iteration stops.
|
---|
2632 | } else {
|
---|
2633 | nData = newNData;
|
---|
2634 | }
|
---|
2635 | }
|
---|
2636 | }
|
---|
2637 |
|
---|
2638 | nClipped = initNData - nData;
|
---|
2639 |
|
---|
2640 | std::vector<float> result;
|
---|
2641 | if (getResidual) {
|
---|
2642 | for (int i = 0; i < nChan; ++i) {
|
---|
2643 | result.push_back((float)residual[i]);
|
---|
2644 | }
|
---|
2645 | } else {
|
---|
2646 | for (int i = 0; i < nChan; ++i) {
|
---|
2647 | result.push_back((float)r1[i]);
|
---|
2648 | }
|
---|
2649 | }
|
---|
2650 |
|
---|
2651 | return result;
|
---|
2652 | }
|
---|
2653 |
|
---|
2654 | void Scantable::selectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
|
---|
2655 | {
|
---|
2656 | nWaves.clear();
|
---|
2657 |
|
---|
2658 | if (applyFFT) {
|
---|
2659 | string fftThAttr;
|
---|
2660 | float fftThSigma;
|
---|
2661 | int fftThTop;
|
---|
2662 | parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop);
|
---|
2663 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
|
---|
2664 | }
|
---|
2665 |
|
---|
2666 | addAuxWaveNumbers(addNWaves, rejectNWaves, nWaves);
|
---|
2667 | }
|
---|
2668 |
|
---|
2669 | void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
|
---|
2670 | {
|
---|
2671 | uInt idxSigma = fftThresh.find("sigma");
|
---|
2672 | uInt idxTop = fftThresh.find("top");
|
---|
2673 |
|
---|
2674 | if (idxSigma == fftThresh.size() - 5) {
|
---|
2675 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
|
---|
2676 | is >> fftThSigma;
|
---|
2677 | fftThAttr = "sigma";
|
---|
2678 | } else if (idxTop == 0) {
|
---|
2679 | std::istringstream is(fftThresh.substr(3));
|
---|
2680 | is >> fftThTop;
|
---|
2681 | fftThAttr = "top";
|
---|
2682 | } else {
|
---|
2683 | bool isNumber = true;
|
---|
2684 | for (uInt i = 0; i < fftThresh.size()-1; ++i) {
|
---|
2685 | char ch = (fftThresh.substr(i, 1).c_str())[0];
|
---|
2686 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
|
---|
2687 | isNumber = false;
|
---|
2688 | break;
|
---|
2689 | }
|
---|
2690 | }
|
---|
2691 | if (isNumber) {
|
---|
2692 | std::istringstream is(fftThresh);
|
---|
2693 | is >> fftThSigma;
|
---|
2694 | fftThAttr = "sigma";
|
---|
2695 | } else {
|
---|
2696 | throw(AipsError("fftthresh has a wrong value"));
|
---|
2697 | }
|
---|
2698 | }
|
---|
2699 | }
|
---|
2700 |
|
---|
2701 | void Scantable::doSelectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const std::string& fftMethod, const float fftThSigma, const int fftThTop, const std::string& fftThAttr, std::vector<int>& nWaves)
|
---|
2702 | {
|
---|
2703 | std::vector<float> fspec;
|
---|
2704 | if (fftMethod == "fft") {
|
---|
2705 | fspec = execFFT(whichrow, chanMask, false, true);
|
---|
2706 | //} else if (fftMethod == "lsp") {
|
---|
2707 | // fspec = lombScarglePeriodogram(whichrow);
|
---|
2708 | }
|
---|
2709 |
|
---|
2710 | if (fftThAttr == "sigma") {
|
---|
2711 | float mean = 0.0;
|
---|
2712 | float mean2 = 0.0;
|
---|
2713 | for (uInt i = 0; i < fspec.size(); ++i) {
|
---|
2714 | mean += fspec[i];
|
---|
2715 | mean2 += fspec[i]*fspec[i];
|
---|
2716 | }
|
---|
2717 | mean /= float(fspec.size());
|
---|
2718 | mean2 /= float(fspec.size());
|
---|
2719 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
|
---|
2720 |
|
---|
2721 | for (uInt i = 0; i < fspec.size(); ++i) {
|
---|
2722 | if (fspec[i] >= thres) {
|
---|
2723 | nWaves.push_back(i);
|
---|
2724 | }
|
---|
2725 | }
|
---|
2726 |
|
---|
2727 | } else if (fftThAttr == "top") {
|
---|
2728 | for (int i = 0; i < fftThTop; ++i) {
|
---|
2729 | float max = 0.0;
|
---|
2730 | int maxIdx = 0;
|
---|
2731 | for (uInt j = 0; j < fspec.size(); ++j) {
|
---|
2732 | if (fspec[j] > max) {
|
---|
2733 | max = fspec[j];
|
---|
2734 | maxIdx = j;
|
---|
2735 | }
|
---|
2736 | }
|
---|
2737 | nWaves.push_back(maxIdx);
|
---|
2738 | fspec[maxIdx] = 0.0;
|
---|
2739 | }
|
---|
2740 |
|
---|
2741 | }
|
---|
2742 |
|
---|
2743 | if (nWaves.size() > 1) {
|
---|
2744 | sort(nWaves.begin(), nWaves.end());
|
---|
2745 | }
|
---|
2746 | }
|
---|
2747 |
|
---|
2748 | void Scantable::addAuxWaveNumbers(const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
|
---|
2749 | {
|
---|
2750 | for (uInt i = 0; i < addNWaves.size(); ++i) {
|
---|
2751 | bool found = false;
|
---|
2752 | for (uInt j = 0; j < nWaves.size(); ++j) {
|
---|
2753 | if (nWaves[j] == addNWaves[i]) {
|
---|
2754 | found = true;
|
---|
2755 | break;
|
---|
2756 | }
|
---|
2757 | }
|
---|
2758 | if (!found) nWaves.push_back(addNWaves[i]);
|
---|
2759 | }
|
---|
2760 |
|
---|
2761 | for (uInt i = 0; i < rejectNWaves.size(); ++i) {
|
---|
2762 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
|
---|
2763 | if (*j == rejectNWaves[i]) {
|
---|
2764 | j = nWaves.erase(j);
|
---|
2765 | } else {
|
---|
2766 | ++j;
|
---|
2767 | }
|
---|
2768 | }
|
---|
2769 | }
|
---|
2770 |
|
---|
2771 | if (nWaves.size() > 1) {
|
---|
2772 | sort(nWaves.begin(), nWaves.end());
|
---|
2773 | unique(nWaves.begin(), nWaves.end());
|
---|
2774 | }
|
---|
2775 | }
|
---|
2776 |
|
---|
2777 | void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
|
---|
2778 | {
|
---|
2779 | try {
|
---|
2780 | ofstream ofs;
|
---|
2781 | String coordInfo = "";
|
---|
2782 | bool hasSameNchan = true;
|
---|
2783 | bool outTextFile = false;
|
---|
2784 |
|
---|
2785 | if (blfile != "") {
|
---|
2786 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
2787 | if (ofs) outTextFile = true;
|
---|
2788 | }
|
---|
2789 |
|
---|
2790 | if (outLogger || outTextFile) {
|
---|
2791 | coordInfo = getCoordInfo()[0];
|
---|
2792 | if (coordInfo == "") coordInfo = "channel";
|
---|
2793 | hasSameNchan = hasSameNchanOverIFs();
|
---|
2794 | }
|
---|
2795 |
|
---|
2796 | //Fitter fitter = Fitter();
|
---|
2797 | //fitter.setExpression("sinusoid", nWaves);
|
---|
2798 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
2799 |
|
---|
2800 | int nRow = nrow();
|
---|
2801 | std::vector<bool> chanMask;
|
---|
2802 | std::vector<int> nWaves;
|
---|
2803 |
|
---|
2804 | bool showProgress;
|
---|
2805 | int minNRow;
|
---|
2806 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
2807 |
|
---|
2808 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
2809 | chanMask = getCompositeChanMask(whichrow, mask);
|
---|
2810 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
|
---|
2811 |
|
---|
2812 | //FOR DEBUGGING------------
|
---|
2813 | if (whichrow < 0) {// == nRow -1) {
|
---|
2814 | cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow);
|
---|
2815 | if (applyFFT) {
|
---|
2816 | cout << "[ ";
|
---|
2817 | for (uInt j = 0; j < nWaves.size(); ++j) {
|
---|
2818 | cout << nWaves[j] << ", ";
|
---|
2819 | }
|
---|
2820 | cout << " ] " << endl;
|
---|
2821 | }
|
---|
2822 | cout << flush;
|
---|
2823 | }
|
---|
2824 | //-------------------------
|
---|
2825 |
|
---|
2826 | //fitBaseline(chanMask, whichrow, fitter);
|
---|
2827 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
2828 | std::vector<float> params;
|
---|
2829 | int nClipped = 0;
|
---|
2830 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
|
---|
2831 | setSpectrum(res, whichrow);
|
---|
2832 | //
|
---|
2833 |
|
---|
2834 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped);
|
---|
2835 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
2836 | }
|
---|
2837 |
|
---|
2838 | if (outTextFile) ofs.close();
|
---|
2839 |
|
---|
2840 | } catch (...) {
|
---|
2841 | throw;
|
---|
2842 | }
|
---|
2843 | }
|
---|
2844 |
|
---|
2845 | void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
|
---|
2846 | {
|
---|
2847 | try {
|
---|
2848 | ofstream ofs;
|
---|
2849 | String coordInfo = "";
|
---|
2850 | bool hasSameNchan = true;
|
---|
2851 | bool outTextFile = false;
|
---|
2852 |
|
---|
2853 | if (blfile != "") {
|
---|
2854 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
2855 | if (ofs) outTextFile = true;
|
---|
2856 | }
|
---|
2857 |
|
---|
2858 | if (outLogger || outTextFile) {
|
---|
2859 | coordInfo = getCoordInfo()[0];
|
---|
2860 | if (coordInfo == "") coordInfo = "channel";
|
---|
2861 | hasSameNchan = hasSameNchanOverIFs();
|
---|
2862 | }
|
---|
2863 |
|
---|
2864 | //Fitter fitter = Fitter();
|
---|
2865 | //fitter.setExpression("sinusoid", nWaves);
|
---|
2866 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
2867 |
|
---|
2868 | int nRow = nrow();
|
---|
2869 | std::vector<bool> chanMask;
|
---|
2870 | std::vector<int> nWaves;
|
---|
2871 |
|
---|
2872 | int minEdgeSize = getIFNos().size()*2;
|
---|
2873 | STLineFinder lineFinder = STLineFinder();
|
---|
2874 | lineFinder.setOptions(threshold, 3, chanAvgLimit);
|
---|
2875 |
|
---|
2876 | bool showProgress;
|
---|
2877 | int minNRow;
|
---|
2878 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
2879 |
|
---|
2880 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
2881 |
|
---|
2882 | //-------------------------------------------------------
|
---|
2883 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
|
---|
2884 | //-------------------------------------------------------
|
---|
2885 | int edgeSize = edge.size();
|
---|
2886 | std::vector<int> currentEdge;
|
---|
2887 | if (edgeSize >= 2) {
|
---|
2888 | int idx = 0;
|
---|
2889 | if (edgeSize > 2) {
|
---|
2890 | if (edgeSize < minEdgeSize) {
|
---|
2891 | throw(AipsError("Length of edge element info is less than that of IFs"));
|
---|
2892 | }
|
---|
2893 | idx = 2 * getIF(whichrow);
|
---|
2894 | }
|
---|
2895 | currentEdge.push_back(edge[idx]);
|
---|
2896 | currentEdge.push_back(edge[idx+1]);
|
---|
2897 | } else {
|
---|
2898 | throw(AipsError("Wrong length of edge element"));
|
---|
2899 | }
|
---|
2900 | lineFinder.setData(getSpectrum(whichrow));
|
---|
2901 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
|
---|
2902 | chanMask = lineFinder.getMask();
|
---|
2903 | //-------------------------------------------------------
|
---|
2904 |
|
---|
2905 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
|
---|
2906 |
|
---|
2907 | //fitBaseline(chanMask, whichrow, fitter);
|
---|
2908 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
2909 | std::vector<float> params;
|
---|
2910 | int nClipped = 0;
|
---|
2911 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
|
---|
2912 | setSpectrum(res, whichrow);
|
---|
2913 | //
|
---|
2914 |
|
---|
2915 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped);
|
---|
2916 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
2917 | }
|
---|
2918 |
|
---|
2919 | if (outTextFile) ofs.close();
|
---|
2920 |
|
---|
2921 | } catch (...) {
|
---|
2922 | throw;
|
---|
2923 | }
|
---|
2924 | }
|
---|
2925 |
|
---|
2926 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual)
|
---|
2927 | {
|
---|
2928 | if (data.size() != mask.size()) {
|
---|
2929 | throw(AipsError("data and mask sizes are not identical"));
|
---|
2930 | }
|
---|
2931 | if (data.size() < 2) {
|
---|
2932 | throw(AipsError("data size is too short"));
|
---|
2933 | }
|
---|
2934 | if (waveNumbers.size() == 0) {
|
---|
2935 | throw(AipsError("no wave numbers given"));
|
---|
2936 | }
|
---|
2937 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers
|
---|
2938 | nWaves.reserve(waveNumbers.size());
|
---|
2939 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
|
---|
2940 | sort(nWaves.begin(), nWaves.end());
|
---|
2941 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
|
---|
2942 | nWaves.erase(end_it, nWaves.end());
|
---|
2943 |
|
---|
2944 | int minNWaves = nWaves[0];
|
---|
2945 | if (minNWaves < 0) {
|
---|
2946 | throw(AipsError("wave number must be positive or zero (i.e. constant)"));
|
---|
2947 | }
|
---|
2948 | bool hasConstantTerm = (minNWaves == 0);
|
---|
2949 |
|
---|
2950 | int nChan = data.size();
|
---|
2951 | std::vector<int> maskArray;
|
---|
2952 | std::vector<int> x;
|
---|
2953 | for (int i = 0; i < nChan; ++i) {
|
---|
2954 | maskArray.push_back(mask[i] ? 1 : 0);
|
---|
2955 | if (mask[i]) {
|
---|
2956 | x.push_back(i);
|
---|
2957 | }
|
---|
2958 | }
|
---|
2959 |
|
---|
2960 | int initNData = x.size();
|
---|
2961 |
|
---|
2962 | int nData = initNData;
|
---|
2963 | int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
|
---|
2964 |
|
---|
2965 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
|
---|
2966 | double baseXFactor = 2.0*PI/(double)(nChan-1); //the denominator (nChan-1) should be changed to (xdata[nChan-1]-xdata[0]) for accepting x-values given in velocity or frequency when this function is moved to fitter. (2011/03/30 WK)
|
---|
2967 |
|
---|
2968 | // xArray : contains elemental values for computing the least-square matrix.
|
---|
2969 | // xArray.size() is nDOF and xArray[*].size() is nChan.
|
---|
2970 | // Each xArray element are as follows:
|
---|
2971 | // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0},
|
---|
2972 | // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])},
|
---|
2973 | // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])},
|
---|
2974 | // where (1 <= n <= nMaxWavesInSW),
|
---|
2975 | // or,
|
---|
2976 | // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])},
|
---|
2977 | // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])},
|
---|
2978 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
|
---|
2979 | std::vector<std::vector<double> > xArray;
|
---|
2980 | if (hasConstantTerm) {
|
---|
2981 | std::vector<double> xu;
|
---|
2982 | for (int j = 0; j < nChan; ++j) {
|
---|
2983 | xu.push_back(1.0);
|
---|
2984 | }
|
---|
2985 | xArray.push_back(xu);
|
---|
2986 | }
|
---|
2987 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
|
---|
2988 | double xFactor = baseXFactor*(double)nWaves[i];
|
---|
2989 | std::vector<double> xs, xc;
|
---|
2990 | xs.clear();
|
---|
2991 | xc.clear();
|
---|
2992 | for (int j = 0; j < nChan; ++j) {
|
---|
2993 | xs.push_back(sin(xFactor*(double)j));
|
---|
2994 | xc.push_back(cos(xFactor*(double)j));
|
---|
2995 | }
|
---|
2996 | xArray.push_back(xs);
|
---|
2997 | xArray.push_back(xc);
|
---|
2998 | }
|
---|
2999 |
|
---|
3000 | std::vector<double> z1, r1, residual;
|
---|
3001 | for (int i = 0; i < nChan; ++i) {
|
---|
3002 | z1.push_back((double)data[i]);
|
---|
3003 | r1.push_back(0.0);
|
---|
3004 | residual.push_back(0.0);
|
---|
3005 | }
|
---|
3006 |
|
---|
3007 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
|
---|
3008 | // xMatrix : horizontal concatenation of
|
---|
3009 | // the least-sq. matrix (left) and an
|
---|
3010 | // identity matrix (right).
|
---|
3011 | // the right part is used to calculate the inverse matrix of the left part.
|
---|
3012 | double xMatrix[nDOF][2*nDOF];
|
---|
3013 | double zMatrix[nDOF];
|
---|
3014 | for (int i = 0; i < nDOF; ++i) {
|
---|
3015 | for (int j = 0; j < 2*nDOF; ++j) {
|
---|
3016 | xMatrix[i][j] = 0.0;
|
---|
3017 | }
|
---|
3018 | xMatrix[i][nDOF+i] = 1.0;
|
---|
3019 | zMatrix[i] = 0.0;
|
---|
3020 | }
|
---|
3021 |
|
---|
3022 | int nUseData = 0;
|
---|
3023 | for (int k = 0; k < nChan; ++k) {
|
---|
3024 | if (maskArray[k] == 0) continue;
|
---|
3025 |
|
---|
3026 | for (int i = 0; i < nDOF; ++i) {
|
---|
3027 | for (int j = i; j < nDOF; ++j) {
|
---|
3028 | xMatrix[i][j] += xArray[i][k] * xArray[j][k];
|
---|
3029 | }
|
---|
3030 | zMatrix[i] += z1[k] * xArray[i][k];
|
---|
3031 | }
|
---|
3032 |
|
---|
3033 | nUseData++;
|
---|
3034 | }
|
---|
3035 |
|
---|
3036 | if (nUseData < 1) {
|
---|
3037 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
|
---|
3038 | }
|
---|
3039 |
|
---|
3040 | for (int i = 0; i < nDOF; ++i) {
|
---|
3041 | for (int j = 0; j < i; ++j) {
|
---|
3042 | xMatrix[i][j] = xMatrix[j][i];
|
---|
3043 | }
|
---|
3044 | }
|
---|
3045 |
|
---|
3046 | std::vector<double> invDiag;
|
---|
3047 | for (int i = 0; i < nDOF; ++i) {
|
---|
3048 | invDiag.push_back(1.0/xMatrix[i][i]);
|
---|
3049 | for (int j = 0; j < nDOF; ++j) {
|
---|
3050 | xMatrix[i][j] *= invDiag[i];
|
---|
3051 | }
|
---|
3052 | }
|
---|
3053 |
|
---|
3054 | for (int k = 0; k < nDOF; ++k) {
|
---|
3055 | for (int i = 0; i < nDOF; ++i) {
|
---|
3056 | if (i != k) {
|
---|
3057 | double factor1 = xMatrix[k][k];
|
---|
3058 | double factor2 = xMatrix[i][k];
|
---|
3059 | for (int j = k; j < 2*nDOF; ++j) {
|
---|
3060 | xMatrix[i][j] *= factor1;
|
---|
3061 | xMatrix[i][j] -= xMatrix[k][j]*factor2;
|
---|
3062 | xMatrix[i][j] /= factor1;
|
---|
3063 | }
|
---|
3064 | }
|
---|
3065 | }
|
---|
3066 | double xDiag = xMatrix[k][k];
|
---|
3067 | for (int j = k; j < 2*nDOF; ++j) {
|
---|
3068 | xMatrix[k][j] /= xDiag;
|
---|
3069 | }
|
---|
3070 | }
|
---|
3071 |
|
---|
3072 | for (int i = 0; i < nDOF; ++i) {
|
---|
3073 | for (int j = 0; j < nDOF; ++j) {
|
---|
3074 | xMatrix[i][nDOF+j] *= invDiag[j];
|
---|
3075 | }
|
---|
3076 | }
|
---|
3077 | //compute a vector y which consists of the coefficients of the sinusoids forming the
|
---|
3078 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine
|
---|
3079 | //and cosine functions, respectively.
|
---|
3080 | std::vector<double> y;
|
---|
3081 | params.clear();
|
---|
3082 | for (int i = 0; i < nDOF; ++i) {
|
---|
3083 | y.push_back(0.0);
|
---|
3084 | for (int j = 0; j < nDOF; ++j) {
|
---|
3085 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
|
---|
3086 | }
|
---|
3087 | params.push_back(y[i]);
|
---|
3088 | }
|
---|
3089 |
|
---|
3090 | for (int i = 0; i < nChan; ++i) {
|
---|
3091 | r1[i] = y[0];
|
---|
3092 | for (int j = 1; j < nDOF; ++j) {
|
---|
3093 | r1[i] += y[j]*xArray[j][i];
|
---|
3094 | }
|
---|
3095 | residual[i] = z1[i] - r1[i];
|
---|
3096 | }
|
---|
3097 |
|
---|
3098 | if ((nClip == nIterClip) || (thresClip <= 0.0)) {
|
---|
3099 | break;
|
---|
3100 | } else {
|
---|
3101 | double stdDev = 0.0;
|
---|
3102 | for (int i = 0; i < nChan; ++i) {
|
---|
3103 | stdDev += residual[i]*residual[i]*(double)maskArray[i];
|
---|
3104 | }
|
---|
3105 | stdDev = sqrt(stdDev/(double)nData);
|
---|
3106 |
|
---|
3107 | double thres = stdDev * thresClip;
|
---|
3108 | int newNData = 0;
|
---|
3109 | for (int i = 0; i < nChan; ++i) {
|
---|
3110 | if (abs(residual[i]) >= thres) {
|
---|
3111 | maskArray[i] = 0;
|
---|
3112 | }
|
---|
3113 | if (maskArray[i] > 0) {
|
---|
3114 | newNData++;
|
---|
3115 | }
|
---|
3116 | }
|
---|
3117 | if (newNData == nData) {
|
---|
3118 | break; //no more flag to add. iteration stops.
|
---|
3119 | } else {
|
---|
3120 | nData = newNData;
|
---|
3121 | }
|
---|
3122 | }
|
---|
3123 | }
|
---|
3124 |
|
---|
3125 | nClipped = initNData - nData;
|
---|
3126 |
|
---|
3127 | std::vector<float> result;
|
---|
3128 | if (getResidual) {
|
---|
3129 | for (int i = 0; i < nChan; ++i) {
|
---|
3130 | result.push_back((float)residual[i]);
|
---|
3131 | }
|
---|
3132 | } else {
|
---|
3133 | for (int i = 0; i < nChan; ++i) {
|
---|
3134 | result.push_back((float)r1[i]);
|
---|
3135 | }
|
---|
3136 | }
|
---|
3137 |
|
---|
3138 | return result;
|
---|
3139 | }
|
---|
3140 |
|
---|
3141 | void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter)
|
---|
3142 | {
|
---|
3143 | std::vector<double> dAbcissa = getAbcissa(whichrow);
|
---|
3144 | std::vector<float> abcissa;
|
---|
3145 | for (uInt i = 0; i < dAbcissa.size(); ++i) {
|
---|
3146 | abcissa.push_back((float)dAbcissa[i]);
|
---|
3147 | }
|
---|
3148 | std::vector<float> spec = getSpectrum(whichrow);
|
---|
3149 |
|
---|
3150 | fitter.setData(abcissa, spec, mask);
|
---|
3151 | fitter.lfit();
|
---|
3152 | }
|
---|
3153 |
|
---|
3154 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask)
|
---|
3155 | {
|
---|
3156 | std::vector<bool> mask = getMask(whichrow);
|
---|
3157 | uInt maskSize = mask.size();
|
---|
3158 | if (maskSize != inMask.size()) {
|
---|
3159 | throw(AipsError("mask sizes are not the same."));
|
---|
3160 | }
|
---|
3161 | for (uInt i = 0; i < maskSize; ++i) {
|
---|
3162 | mask[i] = mask[i] && inMask[i];
|
---|
3163 | }
|
---|
3164 |
|
---|
3165 | return mask;
|
---|
3166 | }
|
---|
3167 |
|
---|
3168 | /*
|
---|
3169 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder)
|
---|
3170 | {
|
---|
3171 | int edgeSize = edge.size();
|
---|
3172 | std::vector<int> currentEdge;
|
---|
3173 | if (edgeSize >= 2) {
|
---|
3174 | int idx = 0;
|
---|
3175 | if (edgeSize > 2) {
|
---|
3176 | if (edgeSize < minEdgeSize) {
|
---|
3177 | throw(AipsError("Length of edge element info is less than that of IFs"));
|
---|
3178 | }
|
---|
3179 | idx = 2 * getIF(whichrow);
|
---|
3180 | }
|
---|
3181 | currentEdge.push_back(edge[idx]);
|
---|
3182 | currentEdge.push_back(edge[idx+1]);
|
---|
3183 | } else {
|
---|
3184 | throw(AipsError("Wrong length of edge element"));
|
---|
3185 | }
|
---|
3186 |
|
---|
3187 | lineFinder.setData(getSpectrum(whichrow));
|
---|
3188 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
|
---|
3189 |
|
---|
3190 | return lineFinder.getMask();
|
---|
3191 | }
|
---|
3192 | */
|
---|
3193 |
|
---|
3194 | /* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */
|
---|
3195 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter)
|
---|
3196 | {
|
---|
3197 | if (outLogger || outTextFile) {
|
---|
3198 | std::vector<float> params = fitter.getParameters();
|
---|
3199 | std::vector<bool> fixed = fitter.getFixedParameters();
|
---|
3200 | float rms = getRms(chanMask, whichrow);
|
---|
3201 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
|
---|
3202 |
|
---|
3203 | if (outLogger) {
|
---|
3204 | LogIO ols(LogOrigin("Scantable", funcName, WHERE));
|
---|
3205 | ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false) << LogIO::POST ;
|
---|
3206 | }
|
---|
3207 | if (outTextFile) {
|
---|
3208 | ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true) << flush;
|
---|
3209 | }
|
---|
3210 | }
|
---|
3211 | }
|
---|
3212 |
|
---|
3213 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
|
---|
3214 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped)
|
---|
3215 | {
|
---|
3216 | if (outLogger || outTextFile) {
|
---|
3217 | float rms = getRms(chanMask, whichrow);
|
---|
3218 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
|
---|
3219 | std::vector<bool> fixed;
|
---|
3220 | fixed.clear();
|
---|
3221 |
|
---|
3222 | if (outLogger) {
|
---|
3223 | LogIO ols(LogOrigin("Scantable", funcName, WHERE));
|
---|
3224 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
|
---|
3225 | }
|
---|
3226 | if (outTextFile) {
|
---|
3227 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
|
---|
3228 | }
|
---|
3229 | }
|
---|
3230 | }
|
---|
3231 |
|
---|
3232 | /* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */
|
---|
3233 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped)
|
---|
3234 | {
|
---|
3235 | if (outLogger || outTextFile) {
|
---|
3236 | float rms = getRms(chanMask, whichrow);
|
---|
3237 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
|
---|
3238 | std::vector<bool> fixed;
|
---|
3239 | fixed.clear();
|
---|
3240 |
|
---|
3241 | if (outLogger) {
|
---|
3242 | LogIO ols(LogOrigin("Scantable", funcName, WHERE));
|
---|
3243 | ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
|
---|
3244 | }
|
---|
3245 | if (outTextFile) {
|
---|
3246 | ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
|
---|
3247 | }
|
---|
3248 | }
|
---|
3249 | }
|
---|
3250 |
|
---|
3251 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
|
---|
3252 | {
|
---|
3253 | int idxDelimiter = progressInfo.find(",");
|
---|
3254 | if (idxDelimiter < 0) {
|
---|
3255 | throw(AipsError("wrong value in 'showprogress' parameter")) ;
|
---|
3256 | }
|
---|
3257 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
|
---|
3258 | std::istringstream is(progressInfo.substr(idxDelimiter+1));
|
---|
3259 | is >> minNRow;
|
---|
3260 | }
|
---|
3261 |
|
---|
3262 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
|
---|
3263 | {
|
---|
3264 | if (showProgress && (nTotal >= nTotalThreshold)) {
|
---|
3265 | int nInterval = int(floor(double(nTotal)/100.0));
|
---|
3266 | if (nInterval == 0) nInterval++;
|
---|
3267 |
|
---|
3268 | if (nProcessed % nInterval == 0) {
|
---|
3269 | printf("\r"); //go to the head of line
|
---|
3270 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted
|
---|
3271 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
|
---|
3272 | printf("\x1b[39m\x1b[0m"); //set default attributes
|
---|
3273 | fflush(NULL);
|
---|
3274 | }
|
---|
3275 |
|
---|
3276 | if (nProcessed == nTotal - 1) {
|
---|
3277 | printf("\r\x1b[K"); //clear
|
---|
3278 | fflush(NULL);
|
---|
3279 | }
|
---|
3280 |
|
---|
3281 | }
|
---|
3282 | }
|
---|
3283 |
|
---|
3284 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
|
---|
3285 | {
|
---|
3286 | std::vector<bool> mask = getMask(whichrow);
|
---|
3287 |
|
---|
3288 | if (inMask.size() > 0) {
|
---|
3289 | uInt maskSize = mask.size();
|
---|
3290 | if (maskSize != inMask.size()) {
|
---|
3291 | throw(AipsError("mask sizes are not the same."));
|
---|
3292 | }
|
---|
3293 | for (uInt i = 0; i < maskSize; ++i) {
|
---|
3294 | mask[i] = mask[i] && inMask[i];
|
---|
3295 | }
|
---|
3296 | }
|
---|
3297 |
|
---|
3298 | Vector<Float> spec = getSpectrum(whichrow);
|
---|
3299 | mathutil::doZeroOrderInterpolation(spec, mask);
|
---|
3300 |
|
---|
3301 | FFTServer<Float,Complex> ffts;
|
---|
3302 | Vector<Complex> fftres;
|
---|
3303 | ffts.fft0(fftres, spec);
|
---|
3304 |
|
---|
3305 | std::vector<float> res;
|
---|
3306 | float norm = float(2.0/double(spec.size()));
|
---|
3307 |
|
---|
3308 | if (getRealImag) {
|
---|
3309 | for (uInt i = 0; i < fftres.size(); ++i) {
|
---|
3310 | res.push_back(real(fftres[i])*norm);
|
---|
3311 | res.push_back(imag(fftres[i])*norm);
|
---|
3312 | }
|
---|
3313 | } else {
|
---|
3314 | for (uInt i = 0; i < fftres.size(); ++i) {
|
---|
3315 | res.push_back(abs(fftres[i])*norm);
|
---|
3316 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
|
---|
3317 | }
|
---|
3318 | }
|
---|
3319 |
|
---|
3320 | return res;
|
---|
3321 | }
|
---|
3322 |
|
---|
3323 |
|
---|
3324 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
|
---|
3325 | {
|
---|
3326 | Vector<Float> spec;
|
---|
3327 | specCol_.get(whichrow, spec);
|
---|
3328 |
|
---|
3329 | float mean = 0.0;
|
---|
3330 | float smean = 0.0;
|
---|
3331 | int n = 0;
|
---|
3332 | for (uInt i = 0; i < spec.nelements(); ++i) {
|
---|
3333 | if (mask[i]) {
|
---|
3334 | mean += spec[i];
|
---|
3335 | smean += spec[i]*spec[i];
|
---|
3336 | n++;
|
---|
3337 | }
|
---|
3338 | }
|
---|
3339 |
|
---|
3340 | mean /= (float)n;
|
---|
3341 | smean /= (float)n;
|
---|
3342 |
|
---|
3343 | return sqrt(smean - mean*mean);
|
---|
3344 | }
|
---|
3345 |
|
---|
3346 |
|
---|
3347 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const
|
---|
3348 | {
|
---|
3349 | ostringstream oss;
|
---|
3350 |
|
---|
3351 | if (verbose) {
|
---|
3352 | oss << " Scan[" << getScan(whichrow) << "]";
|
---|
3353 | oss << " Beam[" << getBeam(whichrow) << "]";
|
---|
3354 | oss << " IF[" << getIF(whichrow) << "]";
|
---|
3355 | oss << " Pol[" << getPol(whichrow) << "]";
|
---|
3356 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
|
---|
3357 | oss << "Fitter range = " << masklist << endl;
|
---|
3358 | oss << "Baseline parameters" << endl;
|
---|
3359 | oss << flush;
|
---|
3360 | }
|
---|
3361 |
|
---|
3362 | return String(oss);
|
---|
3363 | }
|
---|
3364 |
|
---|
3365 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const
|
---|
3366 | {
|
---|
3367 | ostringstream oss;
|
---|
3368 |
|
---|
3369 | if (verbose) {
|
---|
3370 | oss << "Results of baseline fit" << endl;
|
---|
3371 | oss << " rms = " << setprecision(6) << rms << endl;
|
---|
3372 | if (nClipped >= 0) {
|
---|
3373 | oss << " Number of clipped channels = " << nClipped << endl;
|
---|
3374 | }
|
---|
3375 | for (int i = 0; i < 60; ++i) {
|
---|
3376 | oss << "-";
|
---|
3377 | }
|
---|
3378 | oss << endl;
|
---|
3379 | oss << flush;
|
---|
3380 | }
|
---|
3381 |
|
---|
3382 | return String(oss);
|
---|
3383 | }
|
---|
3384 |
|
---|
3385 | std::string Scantable::formatBaselineParams(const std::vector<float>& params,
|
---|
3386 | const std::vector<bool>& fixed,
|
---|
3387 | float rms,
|
---|
3388 | int nClipped,
|
---|
3389 | const std::string& masklist,
|
---|
3390 | int whichrow,
|
---|
3391 | bool verbose,
|
---|
3392 | int start, int count,
|
---|
3393 | bool resetparamid) const
|
---|
3394 | {
|
---|
3395 | int nParam = (int)(params.size());
|
---|
3396 |
|
---|
3397 | if (nParam < 1) {
|
---|
3398 | return(" Not fitted");
|
---|
3399 | } else {
|
---|
3400 |
|
---|
3401 | ostringstream oss;
|
---|
3402 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
|
---|
3403 |
|
---|
3404 | if (start < 0) start = 0;
|
---|
3405 | if (count < 0) count = nParam;
|
---|
3406 | int end = start + count;
|
---|
3407 | if (end > nParam) end = nParam;
|
---|
3408 | int paramidoffset = (resetparamid) ? (-start) : 0;
|
---|
3409 |
|
---|
3410 | for (int i = start; i < end; ++i) {
|
---|
3411 | if (i > start) {
|
---|
3412 | oss << ",";
|
---|
3413 | }
|
---|
3414 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
|
---|
3415 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
|
---|
3416 | }
|
---|
3417 |
|
---|
3418 | oss << endl;
|
---|
3419 | oss << formatBaselineParamsFooter(rms, nClipped, verbose);
|
---|
3420 |
|
---|
3421 | return String(oss);
|
---|
3422 | }
|
---|
3423 |
|
---|
3424 | }
|
---|
3425 |
|
---|
3426 | std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, int nClipped, const std::string& masklist, int whichrow, bool verbose) const
|
---|
3427 | {
|
---|
3428 | int nOutParam = (int)(params.size());
|
---|
3429 | int nPiece = (int)(ranges.size()) - 1;
|
---|
3430 |
|
---|
3431 | if (nOutParam < 1) {
|
---|
3432 | return(" Not fitted");
|
---|
3433 | } else if (nPiece < 0) {
|
---|
3434 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose);
|
---|
3435 | } else if (nPiece < 1) {
|
---|
3436 | return(" Bad count of the piece edge info");
|
---|
3437 | } else if (nOutParam % nPiece != 0) {
|
---|
3438 | return(" Bad count of the output baseline parameters");
|
---|
3439 | } else {
|
---|
3440 |
|
---|
3441 | int nParam = nOutParam / nPiece;
|
---|
3442 |
|
---|
3443 | ostringstream oss;
|
---|
3444 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
|
---|
3445 |
|
---|
3446 | stringstream ss;
|
---|
3447 | ss << ranges[nPiece] << flush;
|
---|
3448 | int wRange = ss.str().size() * 2 + 5;
|
---|
3449 |
|
---|
3450 | for (int i = 0; i < nPiece; ++i) {
|
---|
3451 | ss.str("");
|
---|
3452 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
|
---|
3453 | oss << left << setw(wRange) << ss.str();
|
---|
3454 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, i*nParam, nParam, true);
|
---|
3455 | }
|
---|
3456 |
|
---|
3457 | oss << formatBaselineParamsFooter(rms, nClipped, verbose);
|
---|
3458 |
|
---|
3459 | return String(oss);
|
---|
3460 | }
|
---|
3461 |
|
---|
3462 | }
|
---|
3463 |
|
---|
3464 | bool Scantable::hasSameNchanOverIFs()
|
---|
3465 | {
|
---|
3466 | int nIF = nif(-1);
|
---|
3467 | int nCh;
|
---|
3468 | int totalPositiveNChan = 0;
|
---|
3469 | int nPositiveNChan = 0;
|
---|
3470 |
|
---|
3471 | for (int i = 0; i < nIF; ++i) {
|
---|
3472 | nCh = nchan(i);
|
---|
3473 | if (nCh > 0) {
|
---|
3474 | totalPositiveNChan += nCh;
|
---|
3475 | nPositiveNChan++;
|
---|
3476 | }
|
---|
3477 | }
|
---|
3478 |
|
---|
3479 | return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
|
---|
3480 | }
|
---|
3481 |
|
---|
3482 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
|
---|
3483 | {
|
---|
3484 | if (mask.size() < 2) {
|
---|
3485 | throw(AipsError("The mask elements should be > 1"));
|
---|
3486 | }
|
---|
3487 | int IF = getIF(whichrow);
|
---|
3488 | if (mask.size() != (uInt)nchan(IF)) {
|
---|
3489 | throw(AipsError("Number of channels in scantable != number of mask elements"));
|
---|
3490 | }
|
---|
3491 |
|
---|
3492 | if (verbose) {
|
---|
3493 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
|
---|
3494 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
|
---|
3495 | if (!hasSameNchan) {
|
---|
3496 | logOs << endl << "This mask is only valid for IF=" << IF;
|
---|
3497 | }
|
---|
3498 | logOs << LogIO::POST;
|
---|
3499 | }
|
---|
3500 |
|
---|
3501 | std::vector<double> abcissa = getAbcissa(whichrow);
|
---|
3502 | std::vector<int> edge = getMaskEdgeIndices(mask);
|
---|
3503 |
|
---|
3504 | ostringstream oss;
|
---|
3505 | oss.setf(ios::fixed);
|
---|
3506 | oss << setprecision(1) << "[";
|
---|
3507 | for (uInt i = 0; i < edge.size(); i+=2) {
|
---|
3508 | if (i > 0) oss << ",";
|
---|
3509 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
|
---|
3510 | }
|
---|
3511 | oss << "]" << flush;
|
---|
3512 |
|
---|
3513 | return String(oss);
|
---|
3514 | }
|
---|
3515 |
|
---|
3516 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
|
---|
3517 | {
|
---|
3518 | if (mask.size() < 2) {
|
---|
3519 | throw(AipsError("The mask elements should be > 1"));
|
---|
3520 | }
|
---|
3521 |
|
---|
3522 | std::vector<int> out, startIndices, endIndices;
|
---|
3523 | int maskSize = mask.size();
|
---|
3524 |
|
---|
3525 | startIndices.clear();
|
---|
3526 | endIndices.clear();
|
---|
3527 |
|
---|
3528 | if (mask[0]) {
|
---|
3529 | startIndices.push_back(0);
|
---|
3530 | }
|
---|
3531 | for (int i = 1; i < maskSize; ++i) {
|
---|
3532 | if ((!mask[i-1]) && mask[i]) {
|
---|
3533 | startIndices.push_back(i);
|
---|
3534 | } else if (mask[i-1] && (!mask[i])) {
|
---|
3535 | endIndices.push_back(i-1);
|
---|
3536 | }
|
---|
3537 | }
|
---|
3538 | if (mask[maskSize-1]) {
|
---|
3539 | endIndices.push_back(maskSize-1);
|
---|
3540 | }
|
---|
3541 |
|
---|
3542 | if (startIndices.size() != endIndices.size()) {
|
---|
3543 | throw(AipsError("Inconsistent Mask Size: bad data?"));
|
---|
3544 | }
|
---|
3545 | for (uInt i = 0; i < startIndices.size(); ++i) {
|
---|
3546 | if (startIndices[i] > endIndices[i]) {
|
---|
3547 | throw(AipsError("Mask start index > mask end index"));
|
---|
3548 | }
|
---|
3549 | }
|
---|
3550 |
|
---|
3551 | out.clear();
|
---|
3552 | for (uInt i = 0; i < startIndices.size(); ++i) {
|
---|
3553 | out.push_back(startIndices[i]);
|
---|
3554 | out.push_back(endIndices[i]);
|
---|
3555 | }
|
---|
3556 |
|
---|
3557 | return out;
|
---|
3558 | }
|
---|
3559 |
|
---|
3560 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const
|
---|
3561 | {
|
---|
3562 | Vector<Float> tsys( tsysCol_(whichrow) ) ;
|
---|
3563 | vector<float> stlTsys ;
|
---|
3564 | tsys.tovector( stlTsys ) ;
|
---|
3565 | return stlTsys ;
|
---|
3566 | }
|
---|
3567 |
|
---|
3568 |
|
---|
3569 | }
|
---|
3570 | //namespace asap
|
---|