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