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 "Scantable.h" |
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71 | |
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72 | using namespace casa; |
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73 | |
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74 | namespace asap { |
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75 | |
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76 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_; |
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77 | |
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78 | void Scantable::initFactories() { |
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79 | if ( factories_.empty() ) { |
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80 | Scantable::factories_["linear"] = &STPolLinear::myFactory; |
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81 | Scantable::factories_["circular"] = &STPolCircular::myFactory; |
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82 | Scantable::factories_["stokes"] = &STPolStokes::myFactory; |
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83 | } |
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84 | } |
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85 | |
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86 | Scantable::Scantable(Table::TableType ttype) : |
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87 | type_(ttype) |
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88 | { |
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89 | initFactories(); |
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90 | setupMainTable(); |
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91 | freqTable_ = STFrequencies(*this); |
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92 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table()); |
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93 | weatherTable_ = STWeather(*this); |
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94 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table()); |
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95 | focusTable_ = STFocus(*this); |
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96 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table()); |
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97 | tcalTable_ = STTcal(*this); |
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98 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table()); |
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99 | moleculeTable_ = STMolecules(*this); |
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100 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table()); |
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101 | historyTable_ = STHistory(*this); |
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102 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table()); |
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103 | fitTable_ = STFit(*this); |
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104 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table()); |
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105 | table_.tableInfo().setType( "Scantable" ) ; |
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106 | originalTable_ = table_; |
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107 | attach(); |
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108 | } |
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109 | |
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110 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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111 | type_(ttype) |
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112 | { |
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113 | initFactories(); |
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114 | |
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115 | Table tab(name, Table::Update); |
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116 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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117 | if (version != version_) { |
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118 | if ( version == 2 && version_ == 3 ) { |
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119 | // run asap2to3 command |
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120 | LogIO os( LogOrigin( "Scantable" ) ) ; |
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121 | string command="asap2to3" ; |
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122 | string exec=command+" in="+name ; |
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123 | string outname=name ; |
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124 | if ( name.at(name.length()-1) == '/' ) |
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125 | outname = outname.substr( 0, name.length()-1 ) ; |
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126 | outname += ".asap3" ; |
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127 | os << LogIO::WARN |
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128 | << name << " is incompatible data format (Scantable v2)." << endl |
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129 | << "Running " << command << " to create " << outname << ", " << endl |
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130 | << "which is identical to " << name << " but compatible " << endl |
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131 | << "data format with current software version (Scantable v3)." |
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132 | << LogIO::POST ; |
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133 | int ret = system( string("which "+command+" > /dev/null 2>&1").c_str() ) ; |
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134 | if ( ret != 0 ) |
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135 | throw(AipsError(command+" is not installed")) ; |
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136 | os << LogIO::WARN |
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137 | << "Data will be loaded from " << outname << " instead of " |
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138 | << name << LogIO::POST ; |
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139 | int tmp = system( exec.c_str() ) ; |
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140 | (void) tmp; |
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141 | tab = Table(outname, Table::Update ) ; |
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142 | //os << "tab.tableName()=" << tab.tableName() << LogIO::POST ; |
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143 | } |
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144 | else { |
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145 | throw(AipsError("Unsupported version of ASAP file.")); |
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146 | } |
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147 | } |
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148 | if ( type_ == Table::Memory ) { |
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149 | table_ = tab.copyToMemoryTable(generateName()); |
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150 | } else { |
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151 | table_ = tab; |
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152 | } |
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153 | table_.tableInfo().setType( "Scantable" ) ; |
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154 | |
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155 | attachSubtables(); |
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156 | originalTable_ = table_; |
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157 | attach(); |
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158 | } |
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159 | /* |
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160 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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161 | type_(ttype) |
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162 | { |
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163 | initFactories(); |
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164 | Table tab(name, Table::Update); |
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165 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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166 | if (version != version_) { |
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167 | throw(AipsError("Unsupported version of ASAP file.")); |
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168 | } |
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169 | if ( type_ == Table::Memory ) { |
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170 | table_ = tab.copyToMemoryTable(generateName()); |
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171 | } else { |
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172 | table_ = tab; |
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173 | } |
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174 | |
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175 | attachSubtables(); |
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176 | originalTable_ = table_; |
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177 | attach(); |
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178 | } |
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179 | */ |
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180 | |
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181 | Scantable::Scantable( const Scantable& other, bool clear ): |
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182 | Logger() |
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183 | { |
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184 | // with or without data |
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185 | String newname = String(generateName()); |
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186 | type_ = other.table_.tableType(); |
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187 | if ( other.table_.tableType() == Table::Memory ) { |
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188 | if ( clear ) { |
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189 | table_ = TableCopy::makeEmptyMemoryTable(newname, |
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190 | other.table_, True); |
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191 | } else |
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192 | table_ = other.table_.copyToMemoryTable(newname); |
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193 | } else { |
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194 | other.table_.deepCopy(newname, Table::New, False, |
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195 | other.table_.endianFormat(), |
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196 | Bool(clear)); |
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197 | table_ = Table(newname, Table::Update); |
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198 | table_.markForDelete(); |
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199 | } |
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200 | table_.tableInfo().setType( "Scantable" ) ; |
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201 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
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202 | if ( clear ) copySubtables(other); |
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203 | attachSubtables(); |
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204 | originalTable_ = table_; |
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205 | attach(); |
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206 | } |
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207 | |
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208 | void Scantable::copySubtables(const Scantable& other) { |
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209 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES"); |
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210 | TableCopy::copyRows(t, other.freqTable_.table()); |
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211 | t = table_.rwKeywordSet().asTable("FOCUS"); |
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212 | TableCopy::copyRows(t, other.focusTable_.table()); |
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213 | t = table_.rwKeywordSet().asTable("WEATHER"); |
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214 | TableCopy::copyRows(t, other.weatherTable_.table()); |
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215 | t = table_.rwKeywordSet().asTable("TCAL"); |
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216 | TableCopy::copyRows(t, other.tcalTable_.table()); |
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217 | t = table_.rwKeywordSet().asTable("MOLECULES"); |
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218 | TableCopy::copyRows(t, other.moleculeTable_.table()); |
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219 | t = table_.rwKeywordSet().asTable("HISTORY"); |
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220 | TableCopy::copyRows(t, other.historyTable_.table()); |
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221 | t = table_.rwKeywordSet().asTable("FIT"); |
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222 | TableCopy::copyRows(t, other.fitTable_.table()); |
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223 | } |
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224 | |
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225 | void Scantable::attachSubtables() |
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226 | { |
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227 | freqTable_ = STFrequencies(table_); |
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228 | focusTable_ = STFocus(table_); |
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229 | weatherTable_ = STWeather(table_); |
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230 | tcalTable_ = STTcal(table_); |
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231 | moleculeTable_ = STMolecules(table_); |
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232 | historyTable_ = STHistory(table_); |
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233 | fitTable_ = STFit(table_); |
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234 | } |
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235 | |
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236 | Scantable::~Scantable() |
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237 | { |
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238 | //cout << "~Scantable() " << this << endl; |
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239 | } |
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240 | |
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241 | void Scantable::setupMainTable() |
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242 | { |
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243 | TableDesc td("", "1", TableDesc::Scratch); |
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244 | td.comment() = "An ASAP Scantable"; |
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245 | td.rwKeywordSet().define("VERSION", uInt(version_)); |
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246 | |
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247 | // n Cycles |
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248 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO")); |
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249 | // new index every nBeam x nIF x nPol |
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250 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO")); |
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251 | |
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252 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO")); |
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253 | td.addColumn(ScalarColumnDesc<uInt>("IFNO")); |
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254 | // linear, circular, stokes |
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255 | td.rwKeywordSet().define("POLTYPE", String("linear")); |
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256 | td.addColumn(ScalarColumnDesc<uInt>("POLNO")); |
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257 | |
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258 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID")); |
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259 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID")); |
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260 | |
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261 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO"); |
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262 | refbeamnoColumn.setDefault(Int(-1)); |
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263 | td.addColumn(refbeamnoColumn); |
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264 | |
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265 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW"); |
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266 | flagrowColumn.setDefault(uInt(0)); |
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267 | td.addColumn(flagrowColumn); |
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268 | |
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269 | td.addColumn(ScalarColumnDesc<Double>("TIME")); |
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270 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default |
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271 | TableMeasValueDesc measVal(td, "TIME"); |
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272 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef); |
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273 | mepochCol.write(td); |
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274 | |
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275 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL")); |
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276 | |
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277 | td.addColumn(ScalarColumnDesc<String>("SRCNAME")); |
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278 | // Type of source (on=0, off=1, other=-1) |
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279 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE"); |
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280 | stypeColumn.setDefault(Int(-1)); |
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281 | td.addColumn(stypeColumn); |
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282 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME")); |
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283 | |
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284 | //The actual Data Vectors |
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285 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA")); |
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286 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA")); |
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287 | td.addColumn(ArrayColumnDesc<Float>("TSYS")); |
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288 | |
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289 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION", |
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290 | IPosition(1,2), |
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291 | ColumnDesc::Direct)); |
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292 | TableMeasRefDesc mdirRef(MDirection::J2000); // default |
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293 | TableMeasValueDesc tmvdMDir(td, "DIRECTION"); |
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294 | // the TableMeasDesc gives the column a type |
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295 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef); |
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296 | // a uder set table type e.g. GALCTIC, B1950 ... |
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297 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000")); |
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298 | // writing create the measure column |
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299 | mdirCol.write(td); |
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300 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH")); |
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301 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION")); |
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302 | td.addColumn(ScalarColumnDesc<Float>("OPACITY")); |
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303 | |
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304 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID")); |
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305 | ScalarColumnDesc<Int> fitColumn("FIT_ID"); |
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306 | fitColumn.setDefault(Int(-1)); |
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307 | td.addColumn(fitColumn); |
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308 | |
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309 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID")); |
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310 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID")); |
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311 | |
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312 | // columns which just get dragged along, as they aren't used in asap |
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313 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY")); |
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314 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION")); |
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315 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION")); |
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316 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE")); |
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317 | |
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318 | td.rwKeywordSet().define("OBSMODE", String("")); |
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319 | |
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320 | // Now create Table SetUp from the description. |
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321 | SetupNewTable aNewTab(generateName(), td, Table::Scratch); |
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322 | table_ = Table(aNewTab, type_, 0); |
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323 | originalTable_ = table_; |
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324 | } |
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325 | |
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326 | void Scantable::attach() |
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327 | { |
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328 | timeCol_.attach(table_, "TIME"); |
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329 | srcnCol_.attach(table_, "SRCNAME"); |
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330 | srctCol_.attach(table_, "SRCTYPE"); |
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331 | specCol_.attach(table_, "SPECTRA"); |
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332 | flagsCol_.attach(table_, "FLAGTRA"); |
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333 | tsysCol_.attach(table_, "TSYS"); |
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334 | cycleCol_.attach(table_,"CYCLENO"); |
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335 | scanCol_.attach(table_, "SCANNO"); |
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336 | beamCol_.attach(table_, "BEAMNO"); |
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337 | ifCol_.attach(table_, "IFNO"); |
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338 | polCol_.attach(table_, "POLNO"); |
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339 | integrCol_.attach(table_, "INTERVAL"); |
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340 | azCol_.attach(table_, "AZIMUTH"); |
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341 | elCol_.attach(table_, "ELEVATION"); |
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342 | dirCol_.attach(table_, "DIRECTION"); |
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343 | fldnCol_.attach(table_, "FIELDNAME"); |
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344 | rbeamCol_.attach(table_, "REFBEAMNO"); |
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345 | |
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346 | mweatheridCol_.attach(table_,"WEATHER_ID"); |
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347 | mfitidCol_.attach(table_,"FIT_ID"); |
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348 | mfreqidCol_.attach(table_, "FREQ_ID"); |
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349 | mtcalidCol_.attach(table_, "TCAL_ID"); |
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350 | mfocusidCol_.attach(table_, "FOCUS_ID"); |
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351 | mmolidCol_.attach(table_, "MOLECULE_ID"); |
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352 | |
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353 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki) |
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354 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0); |
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355 | |
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356 | } |
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357 | |
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358 | template<class T, class T2> |
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359 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col, |
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360 | const String& colName, |
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361 | const T2& defValue) |
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362 | { |
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363 | try { |
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364 | col.attach(table_, colName); |
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365 | } catch (TableError& err) { |
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366 | String errMesg = err.getMesg(); |
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367 | if (errMesg == "Table column " + colName + " is unknown") { |
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368 | table_.addColumn(ScalarColumnDesc<T>(colName)); |
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369 | col.attach(table_, colName); |
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370 | col.fillColumn(static_cast<T>(defValue)); |
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371 | } else { |
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372 | throw; |
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373 | } |
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374 | } catch (...) { |
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375 | throw; |
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376 | } |
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377 | } |
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378 | |
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379 | template<class T, class T2> |
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380 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col, |
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381 | const String& colName, |
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382 | const Array<T2>& defValue) |
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383 | { |
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384 | try { |
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385 | col.attach(table_, colName); |
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386 | } catch (TableError& err) { |
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387 | String errMesg = err.getMesg(); |
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388 | if (errMesg == "Table column " + colName + " is unknown") { |
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389 | table_.addColumn(ArrayColumnDesc<T>(colName)); |
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390 | col.attach(table_, colName); |
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391 | |
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392 | int size = 0; |
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393 | ArrayIterator<T2>& it = defValue.begin(); |
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394 | while (it != defValue.end()) { |
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395 | ++size; |
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396 | ++it; |
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397 | } |
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398 | IPosition ip(1, size); |
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399 | Array<T>& arr(ip); |
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400 | for (int i = 0; i < size; ++i) |
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401 | arr[i] = static_cast<T>(defValue[i]); |
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402 | |
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403 | col.fillColumn(arr); |
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404 | } else { |
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405 | throw; |
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406 | } |
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407 | } catch (...) { |
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408 | throw; |
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409 | } |
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410 | } |
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411 | |
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412 | void Scantable::setHeader(const STHeader& sdh) |
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413 | { |
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414 | table_.rwKeywordSet().define("nIF", sdh.nif); |
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415 | table_.rwKeywordSet().define("nBeam", sdh.nbeam); |
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416 | table_.rwKeywordSet().define("nPol", sdh.npol); |
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417 | table_.rwKeywordSet().define("nChan", sdh.nchan); |
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418 | table_.rwKeywordSet().define("Observer", sdh.observer); |
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419 | table_.rwKeywordSet().define("Project", sdh.project); |
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420 | table_.rwKeywordSet().define("Obstype", sdh.obstype); |
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421 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname); |
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422 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition); |
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423 | table_.rwKeywordSet().define("Equinox", sdh.equinox); |
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424 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref); |
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425 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq); |
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426 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth); |
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427 | table_.rwKeywordSet().define("UTC", sdh.utc); |
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428 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit); |
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429 | table_.rwKeywordSet().define("Epoch", sdh.epoch); |
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430 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype); |
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431 | } |
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432 | |
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433 | STHeader Scantable::getHeader() const |
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434 | { |
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435 | STHeader sdh; |
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436 | table_.keywordSet().get("nBeam",sdh.nbeam); |
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437 | table_.keywordSet().get("nIF",sdh.nif); |
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438 | table_.keywordSet().get("nPol",sdh.npol); |
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439 | table_.keywordSet().get("nChan",sdh.nchan); |
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440 | table_.keywordSet().get("Observer", sdh.observer); |
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441 | table_.keywordSet().get("Project", sdh.project); |
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442 | table_.keywordSet().get("Obstype", sdh.obstype); |
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443 | table_.keywordSet().get("AntennaName", sdh.antennaname); |
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444 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition); |
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445 | table_.keywordSet().get("Equinox", sdh.equinox); |
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446 | table_.keywordSet().get("FreqRefFrame", sdh.freqref); |
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447 | table_.keywordSet().get("FreqRefVal", sdh.reffreq); |
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448 | table_.keywordSet().get("Bandwidth", sdh.bandwidth); |
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449 | table_.keywordSet().get("UTC", sdh.utc); |
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450 | table_.keywordSet().get("FluxUnit", sdh.fluxunit); |
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451 | table_.keywordSet().get("Epoch", sdh.epoch); |
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452 | table_.keywordSet().get("POLTYPE", sdh.poltype); |
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453 | return sdh; |
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454 | } |
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455 | |
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456 | void Scantable::setSourceType( int stype ) |
---|
457 | { |
---|
458 | if ( stype < 0 || stype > 1 ) |
---|
459 | throw(AipsError("Illegal sourcetype.")); |
---|
460 | TableVector<Int> tabvec(table_, "SRCTYPE"); |
---|
461 | tabvec = Int(stype); |
---|
462 | } |
---|
463 | |
---|
464 | bool Scantable::conformant( const Scantable& other ) |
---|
465 | { |
---|
466 | return this->getHeader().conformant(other.getHeader()); |
---|
467 | } |
---|
468 | |
---|
469 | |
---|
470 | |
---|
471 | std::string Scantable::formatSec(Double x) const |
---|
472 | { |
---|
473 | Double xcop = x; |
---|
474 | MVTime mvt(xcop/24./3600.); // make days |
---|
475 | |
---|
476 | if (x < 59.95) |
---|
477 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s"; |
---|
478 | else if (x < 3599.95) |
---|
479 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" "; |
---|
480 | else { |
---|
481 | ostringstream oss; |
---|
482 | oss << setw(2) << std::right << setprecision(1) << mvt.hour(); |
---|
483 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " "; |
---|
484 | return String(oss); |
---|
485 | } |
---|
486 | }; |
---|
487 | |
---|
488 | std::string Scantable::formatDirection(const MDirection& md) const |
---|
489 | { |
---|
490 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue(); |
---|
491 | Int prec = 7; |
---|
492 | |
---|
493 | MVAngle mvLon(t[0]); |
---|
494 | String sLon = mvLon.string(MVAngle::TIME,prec); |
---|
495 | uInt tp = md.getRef().getType(); |
---|
496 | if (tp == MDirection::GALACTIC || |
---|
497 | tp == MDirection::SUPERGAL ) { |
---|
498 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec); |
---|
499 | } |
---|
500 | MVAngle mvLat(t[1]); |
---|
501 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec); |
---|
502 | return sLon + String(" ") + sLat; |
---|
503 | } |
---|
504 | |
---|
505 | |
---|
506 | std::string Scantable::getFluxUnit() const |
---|
507 | { |
---|
508 | return table_.keywordSet().asString("FluxUnit"); |
---|
509 | } |
---|
510 | |
---|
511 | void Scantable::setFluxUnit(const std::string& unit) |
---|
512 | { |
---|
513 | String tmp(unit); |
---|
514 | Unit tU(tmp); |
---|
515 | if (tU==Unit("K") || tU==Unit("Jy")) { |
---|
516 | table_.rwKeywordSet().define(String("FluxUnit"), tmp); |
---|
517 | } else { |
---|
518 | throw AipsError("Illegal unit - must be compatible with Jy or K"); |
---|
519 | } |
---|
520 | } |
---|
521 | |
---|
522 | void Scantable::setInstrument(const std::string& name) |
---|
523 | { |
---|
524 | bool throwIt = true; |
---|
525 | // create an Instrument to see if this is valid |
---|
526 | STAttr::convertInstrument(name, throwIt); |
---|
527 | String nameU(name); |
---|
528 | nameU.upcase(); |
---|
529 | table_.rwKeywordSet().define(String("AntennaName"), nameU); |
---|
530 | } |
---|
531 | |
---|
532 | void Scantable::setFeedType(const std::string& feedtype) |
---|
533 | { |
---|
534 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) { |
---|
535 | std::string msg = "Illegal feed type "+ feedtype; |
---|
536 | throw(casa::AipsError(msg)); |
---|
537 | } |
---|
538 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype); |
---|
539 | } |
---|
540 | |
---|
541 | MPosition Scantable::getAntennaPosition() const |
---|
542 | { |
---|
543 | Vector<Double> antpos; |
---|
544 | table_.keywordSet().get("AntennaPosition", antpos); |
---|
545 | MVPosition mvpos(antpos(0),antpos(1),antpos(2)); |
---|
546 | return MPosition(mvpos); |
---|
547 | } |
---|
548 | |
---|
549 | void Scantable::makePersistent(const std::string& filename) |
---|
550 | { |
---|
551 | String inname(filename); |
---|
552 | Path path(inname); |
---|
553 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
---|
554 | inname = path.expandedName(); |
---|
555 | // 2011/03/04 TN |
---|
556 | // We can comment out this workaround since the essential bug is |
---|
557 | // fixed in casacore (r20889 in google code). |
---|
558 | table_.deepCopy(inname, Table::New); |
---|
559 | // // WORKAROUND !!! for Table bug |
---|
560 | // // Remove when fixed in casacore |
---|
561 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) { |
---|
562 | // Table tab = table_.copyToMemoryTable(generateName()); |
---|
563 | // tab.deepCopy(inname, Table::New); |
---|
564 | // tab.markForDelete(); |
---|
565 | // |
---|
566 | // } else { |
---|
567 | // table_.deepCopy(inname, Table::New); |
---|
568 | // } |
---|
569 | } |
---|
570 | |
---|
571 | int Scantable::nbeam( int scanno ) const |
---|
572 | { |
---|
573 | if ( scanno < 0 ) { |
---|
574 | Int n; |
---|
575 | table_.keywordSet().get("nBeam",n); |
---|
576 | return int(n); |
---|
577 | } else { |
---|
578 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
579 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
580 | ROTableRow row(t); |
---|
581 | const TableRecord& rec = row.get(0); |
---|
582 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
583 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
584 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
585 | ROTableVector<uInt> v(subt, "BEAMNO"); |
---|
586 | return int(v.nelements()); |
---|
587 | } |
---|
588 | return 0; |
---|
589 | } |
---|
590 | |
---|
591 | int Scantable::nif( int scanno ) const |
---|
592 | { |
---|
593 | if ( scanno < 0 ) { |
---|
594 | Int n; |
---|
595 | table_.keywordSet().get("nIF",n); |
---|
596 | return int(n); |
---|
597 | } else { |
---|
598 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these |
---|
599 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
600 | ROTableRow row(t); |
---|
601 | const TableRecord& rec = row.get(0); |
---|
602 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
603 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
604 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
605 | if ( subt.nrow() == 0 ) return 0; |
---|
606 | ROTableVector<uInt> v(subt, "IFNO"); |
---|
607 | return int(v.nelements()); |
---|
608 | } |
---|
609 | return 0; |
---|
610 | } |
---|
611 | |
---|
612 | int Scantable::npol( int scanno ) const |
---|
613 | { |
---|
614 | if ( scanno < 0 ) { |
---|
615 | Int n; |
---|
616 | table_.keywordSet().get("nPol",n); |
---|
617 | return n; |
---|
618 | } else { |
---|
619 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
620 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
621 | ROTableRow row(t); |
---|
622 | const TableRecord& rec = row.get(0); |
---|
623 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
624 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
625 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
626 | if ( subt.nrow() == 0 ) return 0; |
---|
627 | ROTableVector<uInt> v(subt, "POLNO"); |
---|
628 | return int(v.nelements()); |
---|
629 | } |
---|
630 | return 0; |
---|
631 | } |
---|
632 | |
---|
633 | int Scantable::ncycle( int scanno ) const |
---|
634 | { |
---|
635 | if ( scanno < 0 ) { |
---|
636 | Block<String> cols(2); |
---|
637 | cols[0] = "SCANNO"; |
---|
638 | cols[1] = "CYCLENO"; |
---|
639 | TableIterator it(table_, cols); |
---|
640 | int n = 0; |
---|
641 | while ( !it.pastEnd() ) { |
---|
642 | ++n; |
---|
643 | ++it; |
---|
644 | } |
---|
645 | return n; |
---|
646 | } else { |
---|
647 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
648 | ROTableRow row(t); |
---|
649 | const TableRecord& rec = row.get(0); |
---|
650 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
651 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
652 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) ); |
---|
653 | if ( subt.nrow() == 0 ) return 0; |
---|
654 | return int(subt.nrow()); |
---|
655 | } |
---|
656 | return 0; |
---|
657 | } |
---|
658 | |
---|
659 | |
---|
660 | int Scantable::nrow( int scanno ) const |
---|
661 | { |
---|
662 | return int(table_.nrow()); |
---|
663 | } |
---|
664 | |
---|
665 | int Scantable::nchan( int ifno ) const |
---|
666 | { |
---|
667 | if ( ifno < 0 ) { |
---|
668 | Int n; |
---|
669 | table_.keywordSet().get("nChan",n); |
---|
670 | return int(n); |
---|
671 | } else { |
---|
672 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't |
---|
673 | // vary with these |
---|
674 | Table t = table_(table_.col("IFNO") == ifno, 1); |
---|
675 | if ( t.nrow() == 0 ) return 0; |
---|
676 | ROArrayColumn<Float> v(t, "SPECTRA"); |
---|
677 | return v.shape(0)(0); |
---|
678 | } |
---|
679 | return 0; |
---|
680 | } |
---|
681 | |
---|
682 | int Scantable::nscan() const { |
---|
683 | Vector<uInt> scannos(scanCol_.getColumn()); |
---|
684 | uInt nout = genSort( scannos, Sort::Ascending, |
---|
685 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
686 | return int(nout); |
---|
687 | } |
---|
688 | |
---|
689 | int Scantable::getChannels(int whichrow) const |
---|
690 | { |
---|
691 | return specCol_.shape(whichrow)(0); |
---|
692 | } |
---|
693 | |
---|
694 | int Scantable::getBeam(int whichrow) const |
---|
695 | { |
---|
696 | return beamCol_(whichrow); |
---|
697 | } |
---|
698 | |
---|
699 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const |
---|
700 | { |
---|
701 | Vector<uInt> nos(col.getColumn()); |
---|
702 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates ); |
---|
703 | nos.resize(n, True); |
---|
704 | std::vector<uint> stlout; |
---|
705 | nos.tovector(stlout); |
---|
706 | return stlout; |
---|
707 | } |
---|
708 | |
---|
709 | int Scantable::getIF(int whichrow) const |
---|
710 | { |
---|
711 | return ifCol_(whichrow); |
---|
712 | } |
---|
713 | |
---|
714 | int Scantable::getPol(int whichrow) const |
---|
715 | { |
---|
716 | return polCol_(whichrow); |
---|
717 | } |
---|
718 | |
---|
719 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const |
---|
720 | { |
---|
721 | return formatTime(me, showdate, 0); |
---|
722 | } |
---|
723 | |
---|
724 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const |
---|
725 | { |
---|
726 | MVTime mvt(me.getValue()); |
---|
727 | if (showdate) |
---|
728 | //mvt.setFormat(MVTime::YMD); |
---|
729 | mvt.setFormat(MVTime::YMD, prec); |
---|
730 | else |
---|
731 | //mvt.setFormat(MVTime::TIME); |
---|
732 | mvt.setFormat(MVTime::TIME, prec); |
---|
733 | ostringstream oss; |
---|
734 | oss << mvt; |
---|
735 | return String(oss); |
---|
736 | } |
---|
737 | |
---|
738 | void Scantable::calculateAZEL() |
---|
739 | { |
---|
740 | MPosition mp = getAntennaPosition(); |
---|
741 | MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
742 | ostringstream oss; |
---|
743 | oss << "Computed azimuth/elevation using " << endl |
---|
744 | << mp << endl; |
---|
745 | for (Int i=0; i<nrow(); ++i) { |
---|
746 | MEpoch me = timeCol(i); |
---|
747 | MDirection md = getDirection(i); |
---|
748 | oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md) |
---|
749 | << endl << " => "; |
---|
750 | MeasFrame frame(mp, me); |
---|
751 | Vector<Double> azel = |
---|
752 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL, |
---|
753 | frame) |
---|
754 | )().getAngle("rad").getValue(); |
---|
755 | azCol_.put(i,Float(azel[0])); |
---|
756 | elCol_.put(i,Float(azel[1])); |
---|
757 | oss << "azel: " << azel[0]/C::pi*180.0 << " " |
---|
758 | << azel[1]/C::pi*180.0 << " (deg)" << endl; |
---|
759 | } |
---|
760 | pushLog(String(oss)); |
---|
761 | } |
---|
762 | |
---|
763 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
764 | { |
---|
765 | for (uInt i=0; i<table_.nrow(); ++i) { |
---|
766 | Vector<uChar> flgs = flagsCol_(i); |
---|
767 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs); |
---|
768 | flagsCol_.put(i, flgs); |
---|
769 | } |
---|
770 | } |
---|
771 | |
---|
772 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
773 | { |
---|
774 | Vector<uChar> flags; |
---|
775 | flagsCol_.get(uInt(whichrow), flags); |
---|
776 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags); |
---|
777 | Vector<Bool> bflag(flags.shape()); |
---|
778 | convertArray(bflag, flags); |
---|
779 | //bflag = !bflag; |
---|
780 | |
---|
781 | std::vector<bool> mask; |
---|
782 | bflag.tovector(mask); |
---|
783 | return mask; |
---|
784 | } |
---|
785 | |
---|
786 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag, |
---|
787 | Vector<uChar> flgs) |
---|
788 | { |
---|
789 | Vector<Float> spcs = specCol_(whichrow); |
---|
790 | uInt nchannel = nchan(); |
---|
791 | if (spcs.nelements() != nchannel) { |
---|
792 | throw(AipsError("Data has incorrect number of channels")); |
---|
793 | } |
---|
794 | uChar userflag = 1 << 7; |
---|
795 | if (unflag) { |
---|
796 | userflag = 0 << 7; |
---|
797 | } |
---|
798 | if (clipoutside) { |
---|
799 | for (uInt j = 0; j < nchannel; ++j) { |
---|
800 | Float spc = spcs(j); |
---|
801 | if ((spc >= uthres) || (spc <= dthres)) { |
---|
802 | flgs(j) = userflag; |
---|
803 | } |
---|
804 | } |
---|
805 | } else { |
---|
806 | for (uInt j = 0; j < nchannel; ++j) { |
---|
807 | Float spc = spcs(j); |
---|
808 | if ((spc < uthres) && (spc > dthres)) { |
---|
809 | flgs(j) = userflag; |
---|
810 | } |
---|
811 | } |
---|
812 | } |
---|
813 | } |
---|
814 | |
---|
815 | |
---|
816 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) { |
---|
817 | std::vector<bool>::const_iterator it; |
---|
818 | uInt ntrue = 0; |
---|
819 | if (whichrow >= int(table_.nrow()) ) { |
---|
820 | throw(AipsError("Invalid row number")); |
---|
821 | } |
---|
822 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
823 | if ( *it ) { |
---|
824 | ntrue++; |
---|
825 | } |
---|
826 | } |
---|
827 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
828 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
829 | throw(AipsError("Trying to flag whole scantable.")); |
---|
830 | uChar userflag = 1 << 7; |
---|
831 | if ( unflag ) { |
---|
832 | userflag = 0 << 7; |
---|
833 | } |
---|
834 | if (whichrow > -1 ) { |
---|
835 | applyChanFlag(uInt(whichrow), msk, userflag); |
---|
836 | } else { |
---|
837 | for ( uInt i=0; i<table_.nrow(); ++i) { |
---|
838 | applyChanFlag(i, msk, userflag); |
---|
839 | } |
---|
840 | } |
---|
841 | } |
---|
842 | |
---|
843 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval ) |
---|
844 | { |
---|
845 | if (whichrow >= table_.nrow() ) { |
---|
846 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) ); |
---|
847 | } |
---|
848 | Vector<uChar> flgs = flagsCol_(whichrow); |
---|
849 | if ( msk.size() == 0 ) { |
---|
850 | flgs = flagval; |
---|
851 | flagsCol_.put(whichrow, flgs); |
---|
852 | return; |
---|
853 | } |
---|
854 | if ( int(msk.size()) != nchan() ) { |
---|
855 | throw(AipsError("Mask has incorrect number of channels.")); |
---|
856 | } |
---|
857 | if ( flgs.nelements() != msk.size() ) { |
---|
858 | throw(AipsError("Mask has incorrect number of channels." |
---|
859 | " Probably varying with IF. Please flag per IF")); |
---|
860 | } |
---|
861 | std::vector<bool>::const_iterator it; |
---|
862 | uInt j = 0; |
---|
863 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
864 | if ( *it ) { |
---|
865 | flgs(j) = flagval; |
---|
866 | } |
---|
867 | ++j; |
---|
868 | } |
---|
869 | flagsCol_.put(whichrow, flgs); |
---|
870 | } |
---|
871 | |
---|
872 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag) |
---|
873 | { |
---|
874 | if ( selector_.empty() && (rows.size() == table_.nrow()) ) |
---|
875 | throw(AipsError("Trying to flag whole scantable.")); |
---|
876 | |
---|
877 | uInt rowflag = (unflag ? 0 : 1); |
---|
878 | std::vector<uInt>::const_iterator it; |
---|
879 | for (it = rows.begin(); it != rows.end(); ++it) |
---|
880 | flagrowCol_.put(*it, rowflag); |
---|
881 | } |
---|
882 | |
---|
883 | std::vector<bool> Scantable::getMask(int whichrow) const |
---|
884 | { |
---|
885 | Vector<uChar> flags; |
---|
886 | flagsCol_.get(uInt(whichrow), flags); |
---|
887 | Vector<Bool> bflag(flags.shape()); |
---|
888 | convertArray(bflag, flags); |
---|
889 | bflag = !bflag; |
---|
890 | std::vector<bool> mask; |
---|
891 | bflag.tovector(mask); |
---|
892 | return mask; |
---|
893 | } |
---|
894 | |
---|
895 | std::vector<float> Scantable::getSpectrum( int whichrow, |
---|
896 | const std::string& poltype ) const |
---|
897 | { |
---|
898 | String ptype = poltype; |
---|
899 | if (poltype == "" ) ptype = getPolType(); |
---|
900 | if ( whichrow < 0 || whichrow >= nrow() ) |
---|
901 | throw(AipsError("Illegal row number.")); |
---|
902 | std::vector<float> out; |
---|
903 | Vector<Float> arr; |
---|
904 | uInt requestedpol = polCol_(whichrow); |
---|
905 | String basetype = getPolType(); |
---|
906 | if ( ptype == basetype ) { |
---|
907 | specCol_.get(whichrow, arr); |
---|
908 | } else { |
---|
909 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_, |
---|
910 | basetype)); |
---|
911 | uInt row = uInt(whichrow); |
---|
912 | stpol->setSpectra(getPolMatrix(row)); |
---|
913 | Float fang,fhand; |
---|
914 | fang = focusTable_.getTotalAngle(mfocusidCol_(row)); |
---|
915 | fhand = focusTable_.getFeedHand(mfocusidCol_(row)); |
---|
916 | stpol->setPhaseCorrections(fang, fhand); |
---|
917 | arr = stpol->getSpectrum(requestedpol, ptype); |
---|
918 | } |
---|
919 | if ( arr.nelements() == 0 ) |
---|
920 | pushLog("Not enough polarisations present to do the conversion."); |
---|
921 | arr.tovector(out); |
---|
922 | return out; |
---|
923 | } |
---|
924 | |
---|
925 | void Scantable::setSpectrum( const std::vector<float>& spec, |
---|
926 | int whichrow ) |
---|
927 | { |
---|
928 | Vector<Float> spectrum(spec); |
---|
929 | Vector<Float> arr; |
---|
930 | specCol_.get(whichrow, arr); |
---|
931 | if ( spectrum.nelements() != arr.nelements() ) |
---|
932 | throw AipsError("The spectrum has incorrect number of channels."); |
---|
933 | specCol_.put(whichrow, spectrum); |
---|
934 | } |
---|
935 | |
---|
936 | |
---|
937 | String Scantable::generateName() |
---|
938 | { |
---|
939 | return (File::newUniqueName("./","temp")).baseName(); |
---|
940 | } |
---|
941 | |
---|
942 | const casa::Table& Scantable::table( ) const |
---|
943 | { |
---|
944 | return table_; |
---|
945 | } |
---|
946 | |
---|
947 | casa::Table& Scantable::table( ) |
---|
948 | { |
---|
949 | return table_; |
---|
950 | } |
---|
951 | |
---|
952 | std::string Scantable::getPolType() const |
---|
953 | { |
---|
954 | return table_.keywordSet().asString("POLTYPE"); |
---|
955 | } |
---|
956 | |
---|
957 | void Scantable::unsetSelection() |
---|
958 | { |
---|
959 | table_ = originalTable_; |
---|
960 | attach(); |
---|
961 | selector_.reset(); |
---|
962 | } |
---|
963 | |
---|
964 | void Scantable::setSelection( const STSelector& selection ) |
---|
965 | { |
---|
966 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_); |
---|
967 | if ( tab.nrow() == 0 ) { |
---|
968 | throw(AipsError("Selection contains no data. Not applying it.")); |
---|
969 | } |
---|
970 | table_ = tab; |
---|
971 | attach(); |
---|
972 | // tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ; |
---|
973 | // vector<uint> selectedIFs = getIFNos() ; |
---|
974 | // Int newnIF = selectedIFs.size() ; |
---|
975 | // tab.rwKeywordSet().define("nIF",newnIF) ; |
---|
976 | // if ( newnIF != 0 ) { |
---|
977 | // Int newnChan = 0 ; |
---|
978 | // for ( Int i = 0 ; i < newnIF ; i++ ) { |
---|
979 | // Int nChan = nchan( selectedIFs[i] ) ; |
---|
980 | // if ( newnChan > nChan ) |
---|
981 | // newnChan = nChan ; |
---|
982 | // } |
---|
983 | // tab.rwKeywordSet().define("nChan",newnChan) ; |
---|
984 | // } |
---|
985 | // tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ; |
---|
986 | selector_ = selection; |
---|
987 | } |
---|
988 | |
---|
989 | |
---|
990 | std::string Scantable::headerSummary() |
---|
991 | { |
---|
992 | // Format header info |
---|
993 | // STHeader sdh; |
---|
994 | // sdh = getHeader(); |
---|
995 | // sdh.print(); |
---|
996 | ostringstream oss; |
---|
997 | oss.flags(std::ios_base::left); |
---|
998 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
999 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
1000 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
1001 | << "(" << getPolType() << ")" << endl |
---|
1002 | << setw(15) << "Channels:" << nchan() << endl; |
---|
1003 | String tmp; |
---|
1004 | oss << setw(15) << "Observer:" |
---|
1005 | << table_.keywordSet().asString("Observer") << endl; |
---|
1006 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
1007 | table_.keywordSet().get("Project", tmp); |
---|
1008 | oss << setw(15) << "Project:" << tmp << endl; |
---|
1009 | table_.keywordSet().get("Obstype", tmp); |
---|
1010 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
1011 | table_.keywordSet().get("AntennaName", tmp); |
---|
1012 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
1013 | table_.keywordSet().get("FluxUnit", tmp); |
---|
1014 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
1015 | //Vector<Double> vec(moleculeTable_.getRestFrequencies()); |
---|
1016 | int nid = moleculeTable_.nrow(); |
---|
1017 | Bool firstline = True; |
---|
1018 | oss << setw(15) << "Rest Freqs:"; |
---|
1019 | for (int i=0; i<nid; i++) { |
---|
1020 | Table t = table_(table_.col("MOLECULE_ID") == i, 1); |
---|
1021 | if (t.nrow() > 0) { |
---|
1022 | Vector<Double> vec(moleculeTable_.getRestFrequency(i)); |
---|
1023 | if (vec.nelements() > 0) { |
---|
1024 | if (firstline) { |
---|
1025 | oss << setprecision(10) << vec << " [Hz]" << endl; |
---|
1026 | firstline=False; |
---|
1027 | } |
---|
1028 | else{ |
---|
1029 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl; |
---|
1030 | } |
---|
1031 | } else { |
---|
1032 | oss << "none" << endl; |
---|
1033 | } |
---|
1034 | } |
---|
1035 | } |
---|
1036 | |
---|
1037 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl; |
---|
1038 | oss << selector_.print() << endl; |
---|
1039 | return String(oss); |
---|
1040 | } |
---|
1041 | |
---|
1042 | std::string Scantable::summary() |
---|
1043 | { |
---|
1044 | ostringstream oss; |
---|
1045 | oss << endl; |
---|
1046 | oss << asap::SEPERATOR << endl; |
---|
1047 | oss << " Scan Table Summary" << endl; |
---|
1048 | oss << asap::SEPERATOR << endl; |
---|
1049 | |
---|
1050 | // Format header info |
---|
1051 | oss << headerSummary(); |
---|
1052 | oss << endl; |
---|
1053 | |
---|
1054 | // main table |
---|
1055 | String dirtype = "Position (" |
---|
1056 | + getDirectionRefString() |
---|
1057 | + ")"; |
---|
1058 | oss.flags(std::ios_base::left); |
---|
1059 | oss << setw(5) << "Scan" << setw(15) << "Source" |
---|
1060 | << setw(10) << "Time" << setw(18) << "Integration" |
---|
1061 | << setw(15) << "Source Type" << endl; |
---|
1062 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl; |
---|
1063 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << "" |
---|
1064 | << setw(8) << "Frame" << setw(16) |
---|
1065 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" |
---|
1066 | << setw(7) << "Channels" |
---|
1067 | << endl; |
---|
1068 | oss << asap::SEPERATOR << endl; |
---|
1069 | TableIterator iter(table_, "SCANNO"); |
---|
1070 | while (!iter.pastEnd()) { |
---|
1071 | Table subt = iter.table(); |
---|
1072 | ROTableRow row(subt); |
---|
1073 | MEpoch::ROScalarColumn timeCol(subt,"TIME"); |
---|
1074 | const TableRecord& rec = row.get(0); |
---|
1075 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
1076 | << std::left << setw(1) << "" |
---|
1077 | << setw(15) << rec.asString("SRCNAME") |
---|
1078 | << setw(10) << formatTime(timeCol(0), false); |
---|
1079 | // count the cycles in the scan |
---|
1080 | TableIterator cyciter(subt, "CYCLENO"); |
---|
1081 | int nint = 0; |
---|
1082 | while (!cyciter.pastEnd()) { |
---|
1083 | ++nint; |
---|
1084 | ++cyciter; |
---|
1085 | } |
---|
1086 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left |
---|
1087 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << "" |
---|
1088 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl; |
---|
1089 | |
---|
1090 | TableIterator biter(subt, "BEAMNO"); |
---|
1091 | while (!biter.pastEnd()) { |
---|
1092 | Table bsubt = biter.table(); |
---|
1093 | ROTableRow brow(bsubt); |
---|
1094 | const TableRecord& brec = brow.get(0); |
---|
1095 | uInt row0 = bsubt.rowNumbers(table_)[0]; |
---|
1096 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left; |
---|
1097 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl; |
---|
1098 | TableIterator iiter(bsubt, "IFNO"); |
---|
1099 | while (!iiter.pastEnd()) { |
---|
1100 | Table isubt = iiter.table(); |
---|
1101 | ROTableRow irow(isubt); |
---|
1102 | const TableRecord& irec = irow.get(0); |
---|
1103 | oss << setw(9) << ""; |
---|
1104 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left |
---|
1105 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID")) |
---|
1106 | << setw(3) << "" << nchan(irec.asuInt("IFNO")) |
---|
1107 | << endl; |
---|
1108 | |
---|
1109 | ++iiter; |
---|
1110 | } |
---|
1111 | ++biter; |
---|
1112 | } |
---|
1113 | ++iter; |
---|
1114 | } |
---|
1115 | return String(oss); |
---|
1116 | } |
---|
1117 | |
---|
1118 | // std::string Scantable::getTime(int whichrow, bool showdate) const |
---|
1119 | // { |
---|
1120 | // MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
1121 | // MEpoch me; |
---|
1122 | // if (whichrow > -1) { |
---|
1123 | // me = timeCol(uInt(whichrow)); |
---|
1124 | // } else { |
---|
1125 | // Double tm; |
---|
1126 | // table_.keywordSet().get("UTC",tm); |
---|
1127 | // me = MEpoch(MVEpoch(tm)); |
---|
1128 | // } |
---|
1129 | // return formatTime(me, showdate); |
---|
1130 | // } |
---|
1131 | |
---|
1132 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const |
---|
1133 | { |
---|
1134 | MEpoch me; |
---|
1135 | me = getEpoch(whichrow); |
---|
1136 | return formatTime(me, showdate, prec); |
---|
1137 | } |
---|
1138 | |
---|
1139 | MEpoch Scantable::getEpoch(int whichrow) const |
---|
1140 | { |
---|
1141 | if (whichrow > -1) { |
---|
1142 | return timeCol_(uInt(whichrow)); |
---|
1143 | } else { |
---|
1144 | Double tm; |
---|
1145 | table_.keywordSet().get("UTC",tm); |
---|
1146 | return MEpoch(MVEpoch(tm)); |
---|
1147 | } |
---|
1148 | } |
---|
1149 | |
---|
1150 | std::string Scantable::getDirectionString(int whichrow) const |
---|
1151 | { |
---|
1152 | return formatDirection(getDirection(uInt(whichrow))); |
---|
1153 | } |
---|
1154 | |
---|
1155 | |
---|
1156 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const { |
---|
1157 | const MPosition& mp = getAntennaPosition(); |
---|
1158 | const MDirection& md = getDirection(whichrow); |
---|
1159 | const MEpoch& me = timeCol_(whichrow); |
---|
1160 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
1161 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
1162 | return freqTable_.getSpectralCoordinate(md, mp, me, rf, |
---|
1163 | mfreqidCol_(whichrow)); |
---|
1164 | } |
---|
1165 | |
---|
1166 | std::vector< double > Scantable::getAbcissa( int whichrow ) const |
---|
1167 | { |
---|
1168 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number")); |
---|
1169 | std::vector<double> stlout; |
---|
1170 | int nchan = specCol_(whichrow).nelements(); |
---|
1171 | String us = freqTable_.getUnitString(); |
---|
1172 | if ( us == "" || us == "pixel" || us == "channel" ) { |
---|
1173 | for (int i=0; i<nchan; ++i) { |
---|
1174 | stlout.push_back(double(i)); |
---|
1175 | } |
---|
1176 | return stlout; |
---|
1177 | } |
---|
1178 | SpectralCoordinate spc = getSpectralCoordinate(whichrow); |
---|
1179 | Vector<Double> pixel(nchan); |
---|
1180 | Vector<Double> world; |
---|
1181 | indgen(pixel); |
---|
1182 | if ( Unit(us) == Unit("Hz") ) { |
---|
1183 | for ( int i=0; i < nchan; ++i) { |
---|
1184 | Double world; |
---|
1185 | spc.toWorld(world, pixel[i]); |
---|
1186 | stlout.push_back(double(world)); |
---|
1187 | } |
---|
1188 | } else if ( Unit(us) == Unit("km/s") ) { |
---|
1189 | Vector<Double> world; |
---|
1190 | spc.pixelToVelocity(world, pixel); |
---|
1191 | world.tovector(stlout); |
---|
1192 | } |
---|
1193 | return stlout; |
---|
1194 | } |
---|
1195 | void Scantable::setDirectionRefString( const std::string & refstr ) |
---|
1196 | { |
---|
1197 | MDirection::Types mdt; |
---|
1198 | if (refstr != "" && !MDirection::getType(mdt, refstr)) { |
---|
1199 | throw(AipsError("Illegal Direction frame.")); |
---|
1200 | } |
---|
1201 | if ( refstr == "" ) { |
---|
1202 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
1203 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr); |
---|
1204 | } else { |
---|
1205 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr)); |
---|
1206 | } |
---|
1207 | } |
---|
1208 | |
---|
1209 | std::string Scantable::getDirectionRefString( ) const |
---|
1210 | { |
---|
1211 | return table_.keywordSet().asString("DIRECTIONREF"); |
---|
1212 | } |
---|
1213 | |
---|
1214 | MDirection Scantable::getDirection(int whichrow ) const |
---|
1215 | { |
---|
1216 | String usertype = table_.keywordSet().asString("DIRECTIONREF"); |
---|
1217 | String type = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
1218 | if ( usertype != type ) { |
---|
1219 | MDirection::Types mdt; |
---|
1220 | if (!MDirection::getType(mdt, usertype)) { |
---|
1221 | throw(AipsError("Illegal Direction frame.")); |
---|
1222 | } |
---|
1223 | return dirCol_.convert(uInt(whichrow), mdt); |
---|
1224 | } else { |
---|
1225 | return dirCol_(uInt(whichrow)); |
---|
1226 | } |
---|
1227 | } |
---|
1228 | |
---|
1229 | std::string Scantable::getAbcissaLabel( int whichrow ) const |
---|
1230 | { |
---|
1231 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number")); |
---|
1232 | const MPosition& mp = getAntennaPosition(); |
---|
1233 | const MDirection& md = getDirection(whichrow); |
---|
1234 | const MEpoch& me = timeCol_(whichrow); |
---|
1235 | //const Double& rf = mmolidCol_(whichrow); |
---|
1236 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
1237 | SpectralCoordinate spc = |
---|
1238 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow)); |
---|
1239 | |
---|
1240 | String s = "Channel"; |
---|
1241 | Unit u = Unit(freqTable_.getUnitString()); |
---|
1242 | if (u == Unit("km/s")) { |
---|
1243 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True); |
---|
1244 | } else if (u == Unit("Hz")) { |
---|
1245 | Vector<String> wau(1);wau = u.getName(); |
---|
1246 | spc.setWorldAxisUnits(wau); |
---|
1247 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False); |
---|
1248 | } |
---|
1249 | return s; |
---|
1250 | |
---|
1251 | } |
---|
1252 | |
---|
1253 | /** |
---|
1254 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name, |
---|
1255 | const std::string& unit ) |
---|
1256 | **/ |
---|
1257 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name, |
---|
1258 | const std::string& unit ) |
---|
1259 | |
---|
1260 | { |
---|
1261 | ///@todo lookup in line table to fill in name and formattedname |
---|
1262 | Unit u(unit); |
---|
1263 | //Quantum<Double> urf(rf, u); |
---|
1264 | Quantum<Vector<Double> >urf(rf, u); |
---|
1265 | Vector<String> formattedname(0); |
---|
1266 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl; |
---|
1267 | |
---|
1268 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, ""); |
---|
1269 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname); |
---|
1270 | TableVector<uInt> tabvec(table_, "MOLECULE_ID"); |
---|
1271 | tabvec = id; |
---|
1272 | } |
---|
1273 | |
---|
1274 | /** |
---|
1275 | void asap::Scantable::setRestFrequencies( const std::string& name ) |
---|
1276 | { |
---|
1277 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI")); |
---|
1278 | ///@todo implement |
---|
1279 | } |
---|
1280 | **/ |
---|
1281 | |
---|
1282 | void Scantable::setRestFrequencies( const vector<std::string>& name ) |
---|
1283 | { |
---|
1284 | (void) name; // suppress unused warning |
---|
1285 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI")); |
---|
1286 | ///@todo implement |
---|
1287 | } |
---|
1288 | |
---|
1289 | std::vector< unsigned int > Scantable::rownumbers( ) const |
---|
1290 | { |
---|
1291 | std::vector<unsigned int> stlout; |
---|
1292 | Vector<uInt> vec = table_.rowNumbers(); |
---|
1293 | vec.tovector(stlout); |
---|
1294 | return stlout; |
---|
1295 | } |
---|
1296 | |
---|
1297 | |
---|
1298 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const |
---|
1299 | { |
---|
1300 | ROTableRow row(table_); |
---|
1301 | const TableRecord& rec = row.get(whichrow); |
---|
1302 | Table t = |
---|
1303 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO")) |
---|
1304 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
1305 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
1306 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
1307 | ROArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
1308 | return speccol.getColumn(); |
---|
1309 | } |
---|
1310 | |
---|
1311 | std::vector< std::string > Scantable::columnNames( ) const |
---|
1312 | { |
---|
1313 | Vector<String> vec = table_.tableDesc().columnNames(); |
---|
1314 | return mathutil::tovectorstring(vec); |
---|
1315 | } |
---|
1316 | |
---|
1317 | MEpoch::Types Scantable::getTimeReference( ) const |
---|
1318 | { |
---|
1319 | return MEpoch::castType(timeCol_.getMeasRef().getType()); |
---|
1320 | } |
---|
1321 | |
---|
1322 | void Scantable::addFit( const STFitEntry& fit, int row ) |
---|
1323 | { |
---|
1324 | //cout << mfitidCol_(uInt(row)) << endl; |
---|
1325 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ; |
---|
1326 | os << mfitidCol_(uInt(row)) << LogIO::POST ; |
---|
1327 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row))); |
---|
1328 | mfitidCol_.put(uInt(row), id); |
---|
1329 | } |
---|
1330 | |
---|
1331 | void Scantable::shift(int npix) |
---|
1332 | { |
---|
1333 | Vector<uInt> fids(mfreqidCol_.getColumn()); |
---|
1334 | genSort( fids, Sort::Ascending, |
---|
1335 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
1336 | for (uInt i=0; i<fids.nelements(); ++i) { |
---|
1337 | frequencies().shiftRefPix(npix, fids[i]); |
---|
1338 | } |
---|
1339 | } |
---|
1340 | |
---|
1341 | String Scantable::getAntennaName() const |
---|
1342 | { |
---|
1343 | String out; |
---|
1344 | table_.keywordSet().get("AntennaName", out); |
---|
1345 | String::size_type pos1 = out.find("@") ; |
---|
1346 | String::size_type pos2 = out.find("//") ; |
---|
1347 | if ( pos2 != String::npos ) |
---|
1348 | out = out.substr(pos2+2,pos1-pos2-2) ; |
---|
1349 | else if ( pos1 != String::npos ) |
---|
1350 | out = out.substr(0,pos1) ; |
---|
1351 | return out; |
---|
1352 | } |
---|
1353 | |
---|
1354 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const |
---|
1355 | { |
---|
1356 | String tbpath; |
---|
1357 | int ret = 0; |
---|
1358 | if ( table_.keywordSet().isDefined("GBT_GO") ) { |
---|
1359 | table_.keywordSet().get("GBT_GO", tbpath); |
---|
1360 | Table t(tbpath,Table::Old); |
---|
1361 | // check each scan if other scan of the pair exist |
---|
1362 | int nscan = scanlist.size(); |
---|
1363 | for (int i = 0; i < nscan; i++) { |
---|
1364 | Table subt = t( t.col("SCAN") == scanlist[i]+1 ); |
---|
1365 | if (subt.nrow()==0) { |
---|
1366 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl; |
---|
1367 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1368 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
1369 | ret = 1; |
---|
1370 | break; |
---|
1371 | } |
---|
1372 | ROTableRow row(subt); |
---|
1373 | const TableRecord& rec = row.get(0); |
---|
1374 | int scan1seqn = rec.asuInt("PROCSEQN"); |
---|
1375 | int laston1 = rec.asuInt("LASTON"); |
---|
1376 | if ( rec.asuInt("PROCSIZE")==2 ) { |
---|
1377 | if ( i < nscan-1 ) { |
---|
1378 | Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 ); |
---|
1379 | if ( subt2.nrow() == 0) { |
---|
1380 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1381 | |
---|
1382 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl; |
---|
1383 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
1384 | ret = 1; |
---|
1385 | break; |
---|
1386 | } |
---|
1387 | ROTableRow row2(subt2); |
---|
1388 | const TableRecord& rec2 = row2.get(0); |
---|
1389 | int scan2seqn = rec2.asuInt("PROCSEQN"); |
---|
1390 | int laston2 = rec2.asuInt("LASTON"); |
---|
1391 | if (scan1seqn == 1 && scan2seqn == 2) { |
---|
1392 | if (laston1 == laston2) { |
---|
1393 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1394 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
1395 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
1396 | i +=1; |
---|
1397 | } |
---|
1398 | else { |
---|
1399 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1400 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
1401 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
1402 | } |
---|
1403 | } |
---|
1404 | else if (scan1seqn==2 && scan2seqn == 1) { |
---|
1405 | if (laston1 == laston2) { |
---|
1406 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1407 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl; |
---|
1408 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST; |
---|
1409 | ret = 1; |
---|
1410 | break; |
---|
1411 | } |
---|
1412 | } |
---|
1413 | else { |
---|
1414 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1415 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl; |
---|
1416 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST; |
---|
1417 | ret = 1; |
---|
1418 | break; |
---|
1419 | } |
---|
1420 | } |
---|
1421 | } |
---|
1422 | else { |
---|
1423 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1424 | //cerr<<"The scan does not appear to be standard obsevation."<<endl; |
---|
1425 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST; |
---|
1426 | } |
---|
1427 | //if ( i >= nscan ) break; |
---|
1428 | } |
---|
1429 | } |
---|
1430 | else { |
---|
1431 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1432 | //cerr<<"No reference to GBT_GO table."<<endl; |
---|
1433 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST; |
---|
1434 | ret = 1; |
---|
1435 | } |
---|
1436 | return ret; |
---|
1437 | } |
---|
1438 | |
---|
1439 | std::vector<double> Scantable::getDirectionVector(int whichrow) const |
---|
1440 | { |
---|
1441 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue(); |
---|
1442 | std::vector<double> dir; |
---|
1443 | Dir.tovector(dir); |
---|
1444 | return dir; |
---|
1445 | } |
---|
1446 | |
---|
1447 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax ) |
---|
1448 | throw( casa::AipsError ) |
---|
1449 | { |
---|
1450 | // assumed that all rows have same nChan |
---|
1451 | Vector<Float> arr = specCol_( 0 ) ; |
---|
1452 | int nChan = arr.nelements() ; |
---|
1453 | |
---|
1454 | // if nmin < 0 or nmax < 0, nothing to do |
---|
1455 | if ( nmin < 0 ) { |
---|
1456 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
1457 | } |
---|
1458 | if ( nmax < 0 ) { |
---|
1459 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
1460 | } |
---|
1461 | |
---|
1462 | // if nmin > nmax, exchange values |
---|
1463 | if ( nmin > nmax ) { |
---|
1464 | int tmp = nmax ; |
---|
1465 | nmax = nmin ; |
---|
1466 | nmin = tmp ; |
---|
1467 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
1468 | os << "Swap values. Applied range is [" |
---|
1469 | << nmin << ", " << nmax << "]" << LogIO::POST ; |
---|
1470 | } |
---|
1471 | |
---|
1472 | // if nmin exceeds nChan, nothing to do |
---|
1473 | if ( nmin >= nChan ) { |
---|
1474 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ; |
---|
1475 | } |
---|
1476 | |
---|
1477 | // if nmax exceeds nChan, reset nmax to nChan |
---|
1478 | if ( nmax >= nChan ) { |
---|
1479 | if ( nmin == 0 ) { |
---|
1480 | // nothing to do |
---|
1481 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
1482 | os << "Whole range is selected. Nothing to do." << LogIO::POST ; |
---|
1483 | return ; |
---|
1484 | } |
---|
1485 | else { |
---|
1486 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
1487 | os << "Specified maximum exceeds nChan. Applied range is [" |
---|
1488 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ; |
---|
1489 | nmax = nChan - 1 ; |
---|
1490 | } |
---|
1491 | } |
---|
1492 | |
---|
1493 | // reshape specCol_ and flagCol_ |
---|
1494 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
1495 | reshapeSpectrum( nmin, nmax, irow ) ; |
---|
1496 | } |
---|
1497 | |
---|
1498 | // update FREQUENCIES subtable |
---|
1499 | Double refpix ; |
---|
1500 | Double refval ; |
---|
1501 | Double increment ; |
---|
1502 | int freqnrow = freqTable_.table().nrow() ; |
---|
1503 | Vector<uInt> oldId( freqnrow ) ; |
---|
1504 | Vector<uInt> newId( freqnrow ) ; |
---|
1505 | for ( int irow = 0 ; irow < freqnrow ; irow++ ) { |
---|
1506 | freqTable_.getEntry( refpix, refval, increment, irow ) ; |
---|
1507 | /*** |
---|
1508 | * need to shift refpix to nmin |
---|
1509 | * note that channel nmin in old index will be channel 0 in new one |
---|
1510 | ***/ |
---|
1511 | refval = refval - ( refpix - nmin ) * increment ; |
---|
1512 | refpix = 0 ; |
---|
1513 | freqTable_.setEntry( refpix, refval, increment, irow ) ; |
---|
1514 | } |
---|
1515 | |
---|
1516 | // update nchan |
---|
1517 | int newsize = nmax - nmin + 1 ; |
---|
1518 | table_.rwKeywordSet().define( "nChan", newsize ) ; |
---|
1519 | |
---|
1520 | // update bandwidth |
---|
1521 | // assumed all spectra in the scantable have same bandwidth |
---|
1522 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ; |
---|
1523 | |
---|
1524 | return ; |
---|
1525 | } |
---|
1526 | |
---|
1527 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) |
---|
1528 | { |
---|
1529 | // reshape specCol_ and flagCol_ |
---|
1530 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
1531 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
1532 | uInt newsize = nmax - nmin + 1 ; |
---|
1533 | specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ; |
---|
1534 | flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ; |
---|
1535 | |
---|
1536 | return ; |
---|
1537 | } |
---|
1538 | |
---|
1539 | void asap::Scantable::regridChannel( int nChan, double dnu ) |
---|
1540 | { |
---|
1541 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
1542 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ; |
---|
1543 | // assumed that all rows have same nChan |
---|
1544 | Vector<Float> arr = specCol_( 0 ) ; |
---|
1545 | int oldsize = arr.nelements() ; |
---|
1546 | |
---|
1547 | // if oldsize == nChan, nothing to do |
---|
1548 | if ( oldsize == nChan ) { |
---|
1549 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ; |
---|
1550 | return ; |
---|
1551 | } |
---|
1552 | |
---|
1553 | // if oldChan < nChan, unphysical operation |
---|
1554 | if ( oldsize < nChan ) { |
---|
1555 | os << "Unphysical operation. Nothing to do." << LogIO::POST ; |
---|
1556 | return ; |
---|
1557 | } |
---|
1558 | |
---|
1559 | // change channel number for specCol_ and flagCol_ |
---|
1560 | Vector<Float> newspec( nChan, 0 ) ; |
---|
1561 | Vector<uChar> newflag( nChan, false ) ; |
---|
1562 | vector<string> coordinfo = getCoordInfo() ; |
---|
1563 | string oldinfo = coordinfo[0] ; |
---|
1564 | coordinfo[0] = "Hz" ; |
---|
1565 | setCoordInfo( coordinfo ) ; |
---|
1566 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
1567 | regridChannel( nChan, dnu, irow ) ; |
---|
1568 | } |
---|
1569 | coordinfo[0] = oldinfo ; |
---|
1570 | setCoordInfo( coordinfo ) ; |
---|
1571 | |
---|
1572 | |
---|
1573 | // NOTE: this method does not update metadata such as |
---|
1574 | // FREQUENCIES subtable, nChan, Bandwidth, etc. |
---|
1575 | |
---|
1576 | return ; |
---|
1577 | } |
---|
1578 | |
---|
1579 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) |
---|
1580 | { |
---|
1581 | // logging |
---|
1582 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ; |
---|
1583 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ; |
---|
1584 | |
---|
1585 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
1586 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
1587 | Vector<Float> newspec( nChan, 0 ) ; |
---|
1588 | Vector<uChar> newflag( nChan, false ) ; |
---|
1589 | |
---|
1590 | // regrid |
---|
1591 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
1592 | int oldsize = abcissa.size() ; |
---|
1593 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
1594 | //int refChan = 0 ; |
---|
1595 | //double frac = 0.0 ; |
---|
1596 | //double wedge = 0.0 ; |
---|
1597 | //double pile = 0.0 ; |
---|
1598 | int ichan = 0 ; |
---|
1599 | double wsum = 0.0 ; |
---|
1600 | Vector<Float> zi( nChan+1 ) ; |
---|
1601 | Vector<Float> yi( oldsize + 1 ) ; |
---|
1602 | zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
1603 | zi[1] = zi[1] + dnu ; |
---|
1604 | for ( int ii = 2 ; ii < nChan ; ii++ ) |
---|
1605 | zi[ii] = zi[0] + dnu * ii ; |
---|
1606 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
1607 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
1608 | yi[1] = abcissa[1] + 0.5 * olddnu ; |
---|
1609 | for ( int ii = 2 ; ii < oldsize ; ii++ ) |
---|
1610 | yi[ii] = abcissa[ii-1] + olddnu ; |
---|
1611 | yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ; |
---|
1612 | if ( dnu > 0.0 ) { |
---|
1613 | for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
1614 | double zl = zi[ii] ; |
---|
1615 | double zr = zi[ii+1] ; |
---|
1616 | for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
1617 | double yl = yi[j] ; |
---|
1618 | double yr = yi[j+1] ; |
---|
1619 | if ( yl <= zl ) { |
---|
1620 | if ( yr <= zl ) { |
---|
1621 | continue ; |
---|
1622 | } |
---|
1623 | else if ( yr <= zr ) { |
---|
1624 | newspec[ii] += oldspec[j] * ( yr - zl ) ; |
---|
1625 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
1626 | wsum += ( yr - zl ) ; |
---|
1627 | } |
---|
1628 | else { |
---|
1629 | newspec[ii] += oldspec[j] * dnu ; |
---|
1630 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
1631 | wsum += dnu ; |
---|
1632 | ichan = j ; |
---|
1633 | break ; |
---|
1634 | } |
---|
1635 | } |
---|
1636 | else if ( yl < zr ) { |
---|
1637 | if ( yr <= zr ) { |
---|
1638 | newspec[ii] += oldspec[j] * ( yr - yl ) ; |
---|
1639 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
1640 | wsum += ( yr - yl ) ; |
---|
1641 | } |
---|
1642 | else { |
---|
1643 | newspec[ii] += oldspec[j] * ( zr - yl ) ; |
---|
1644 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
1645 | wsum += ( zr - yl ) ; |
---|
1646 | ichan = j ; |
---|
1647 | break ; |
---|
1648 | } |
---|
1649 | } |
---|
1650 | else { |
---|
1651 | ichan = j - 1 ; |
---|
1652 | break ; |
---|
1653 | } |
---|
1654 | } |
---|
1655 | if ( wsum != 0.0 ) |
---|
1656 | newspec[ii] /= wsum ; |
---|
1657 | wsum = 0.0 ; |
---|
1658 | } |
---|
1659 | } |
---|
1660 | else if ( dnu < 0.0 ) { |
---|
1661 | for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
1662 | double zl = zi[ii] ; |
---|
1663 | double zr = zi[ii+1] ; |
---|
1664 | for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
1665 | double yl = yi[j] ; |
---|
1666 | double yr = yi[j+1] ; |
---|
1667 | if ( yl >= zl ) { |
---|
1668 | if ( yr >= zl ) { |
---|
1669 | continue ; |
---|
1670 | } |
---|
1671 | else if ( yr >= zr ) { |
---|
1672 | newspec[ii] += oldspec[j] * abs( yr - zl ) ; |
---|
1673 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
1674 | wsum += abs( yr - zl ) ; |
---|
1675 | } |
---|
1676 | else { |
---|
1677 | newspec[ii] += oldspec[j] * abs( dnu ) ; |
---|
1678 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
1679 | wsum += abs( dnu ) ; |
---|
1680 | ichan = j ; |
---|
1681 | break ; |
---|
1682 | } |
---|
1683 | } |
---|
1684 | else if ( yl > zr ) { |
---|
1685 | if ( yr >= zr ) { |
---|
1686 | newspec[ii] += oldspec[j] * abs( yr - yl ) ; |
---|
1687 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
1688 | wsum += abs( yr - yl ) ; |
---|
1689 | } |
---|
1690 | else { |
---|
1691 | newspec[ii] += oldspec[j] * abs( zr - yl ) ; |
---|
1692 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
1693 | wsum += abs( zr - yl ) ; |
---|
1694 | ichan = j ; |
---|
1695 | break ; |
---|
1696 | } |
---|
1697 | } |
---|
1698 | else { |
---|
1699 | ichan = j - 1 ; |
---|
1700 | break ; |
---|
1701 | } |
---|
1702 | } |
---|
1703 | if ( wsum != 0.0 ) |
---|
1704 | newspec[ii] /= wsum ; |
---|
1705 | wsum = 0.0 ; |
---|
1706 | } |
---|
1707 | } |
---|
1708 | // * ichan = 0 |
---|
1709 | // ***/ |
---|
1710 | // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ; |
---|
1711 | // pile += dnu ; |
---|
1712 | // wedge = olddnu * ( refChan + 1 ) ; |
---|
1713 | // while ( wedge < pile ) { |
---|
1714 | // newspec[0] += olddnu * oldspec[refChan] ; |
---|
1715 | // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
1716 | // //ofs << "channel " << refChan << " is included in new channel 0" << endl ; |
---|
1717 | // refChan++ ; |
---|
1718 | // wedge += olddnu ; |
---|
1719 | // wsum += olddnu ; |
---|
1720 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
1721 | // } |
---|
1722 | // frac = ( wedge - pile ) / olddnu ; |
---|
1723 | // wsum += ( 1.0 - frac ) * olddnu ; |
---|
1724 | // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
1725 | // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
1726 | // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
1727 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
1728 | // newspec[0] /= wsum ; |
---|
1729 | // //ofs << "newspec[0] = " << newspec[0] << endl ; |
---|
1730 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
1731 | |
---|
1732 | // /*** |
---|
1733 | // * ichan = 1 - nChan-2 |
---|
1734 | // ***/ |
---|
1735 | // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) { |
---|
1736 | // pile += dnu ; |
---|
1737 | // newspec[ichan] += frac * olddnu * oldspec[refChan] ; |
---|
1738 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
1739 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ; |
---|
1740 | // refChan++ ; |
---|
1741 | // wedge += olddnu ; |
---|
1742 | // wsum = frac * olddnu ; |
---|
1743 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
1744 | // while ( wedge < pile ) { |
---|
1745 | // newspec[ichan] += olddnu * oldspec[refChan] ; |
---|
1746 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
1747 | // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ; |
---|
1748 | // refChan++ ; |
---|
1749 | // wedge += olddnu ; |
---|
1750 | // wsum += olddnu ; |
---|
1751 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
1752 | // } |
---|
1753 | // frac = ( wedge - pile ) / olddnu ; |
---|
1754 | // wsum += ( 1.0 - frac ) * olddnu ; |
---|
1755 | // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
1756 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
1757 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
1758 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
1759 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
1760 | // newspec[ichan] /= wsum ; |
---|
1761 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ; |
---|
1762 | // } |
---|
1763 | |
---|
1764 | // /*** |
---|
1765 | // * ichan = nChan-1 |
---|
1766 | // ***/ |
---|
1767 | // // NOTE: Assumed that all spectra have the same bandwidth |
---|
1768 | // pile += dnu ; |
---|
1769 | // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ; |
---|
1770 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ; |
---|
1771 | // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
1772 | // refChan++ ; |
---|
1773 | // wedge += olddnu ; |
---|
1774 | // wsum = frac * olddnu ; |
---|
1775 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
1776 | // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) { |
---|
1777 | // newspec[nChan-1] += olddnu * oldspec[jchan] ; |
---|
1778 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ; |
---|
1779 | // wsum += olddnu ; |
---|
1780 | // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
1781 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
1782 | // } |
---|
1783 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
1784 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
1785 | // newspec[nChan-1] /= wsum ; |
---|
1786 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ; |
---|
1787 | |
---|
1788 | // // ofs.close() ; |
---|
1789 | |
---|
1790 | specCol_.put( irow, newspec ) ; |
---|
1791 | flagsCol_.put( irow, newflag ) ; |
---|
1792 | |
---|
1793 | return ; |
---|
1794 | } |
---|
1795 | |
---|
1796 | std::vector<float> Scantable::getWeather(int whichrow) const |
---|
1797 | { |
---|
1798 | std::vector<float> out(5); |
---|
1799 | //Float temperature, pressure, humidity, windspeed, windaz; |
---|
1800 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4], |
---|
1801 | mweatheridCol_(uInt(whichrow))); |
---|
1802 | |
---|
1803 | |
---|
1804 | return out; |
---|
1805 | } |
---|
1806 | |
---|
1807 | bool Scantable::getFlagtraFast(uInt whichrow) |
---|
1808 | { |
---|
1809 | uChar flag; |
---|
1810 | Vector<uChar> flags; |
---|
1811 | flagsCol_.get(whichrow, flags); |
---|
1812 | flag = flags[0]; |
---|
1813 | for (uInt i = 1; i < flags.size(); ++i) { |
---|
1814 | flag &= flags[i]; |
---|
1815 | } |
---|
1816 | return ((flag >> 7) == 1); |
---|
1817 | } |
---|
1818 | |
---|
1819 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
1820 | { |
---|
1821 | try { |
---|
1822 | ofstream ofs; |
---|
1823 | String coordInfo = ""; |
---|
1824 | bool hasSameNchan = true; |
---|
1825 | bool outTextFile = false; |
---|
1826 | |
---|
1827 | if (blfile != "") { |
---|
1828 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
1829 | if (ofs) outTextFile = true; |
---|
1830 | } |
---|
1831 | |
---|
1832 | if (outLogger || outTextFile) { |
---|
1833 | coordInfo = getCoordInfo()[0]; |
---|
1834 | if (coordInfo == "") coordInfo = "channel"; |
---|
1835 | hasSameNchan = hasSameNchanOverIFs(); |
---|
1836 | } |
---|
1837 | |
---|
1838 | Fitter fitter = Fitter(); |
---|
1839 | fitter.setExpression("poly", order); |
---|
1840 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
1841 | |
---|
1842 | int nRow = nrow(); |
---|
1843 | std::vector<bool> chanMask; |
---|
1844 | bool showProgress; |
---|
1845 | int minNRow; |
---|
1846 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
1847 | |
---|
1848 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
1849 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
1850 | fitBaseline(chanMask, whichrow, fitter); |
---|
1851 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
1852 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter); |
---|
1853 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
1854 | } |
---|
1855 | |
---|
1856 | if (outTextFile) ofs.close(); |
---|
1857 | |
---|
1858 | } catch (...) { |
---|
1859 | throw; |
---|
1860 | } |
---|
1861 | } |
---|
1862 | |
---|
1863 | 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) |
---|
1864 | { |
---|
1865 | try { |
---|
1866 | ofstream ofs; |
---|
1867 | String coordInfo = ""; |
---|
1868 | bool hasSameNchan = true; |
---|
1869 | bool outTextFile = false; |
---|
1870 | |
---|
1871 | if (blfile != "") { |
---|
1872 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
1873 | if (ofs) outTextFile = true; |
---|
1874 | } |
---|
1875 | |
---|
1876 | if (outLogger || outTextFile) { |
---|
1877 | coordInfo = getCoordInfo()[0]; |
---|
1878 | if (coordInfo == "") coordInfo = "channel"; |
---|
1879 | hasSameNchan = hasSameNchanOverIFs(); |
---|
1880 | } |
---|
1881 | |
---|
1882 | Fitter fitter = Fitter(); |
---|
1883 | fitter.setExpression("poly", order); |
---|
1884 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
1885 | |
---|
1886 | int nRow = nrow(); |
---|
1887 | std::vector<bool> chanMask; |
---|
1888 | int minEdgeSize = getIFNos().size()*2; |
---|
1889 | STLineFinder lineFinder = STLineFinder(); |
---|
1890 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
1891 | |
---|
1892 | bool showProgress; |
---|
1893 | int minNRow; |
---|
1894 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
1895 | |
---|
1896 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
1897 | |
---|
1898 | //------------------------------------------------------- |
---|
1899 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
1900 | //------------------------------------------------------- |
---|
1901 | int edgeSize = edge.size(); |
---|
1902 | std::vector<int> currentEdge; |
---|
1903 | if (edgeSize >= 2) { |
---|
1904 | int idx = 0; |
---|
1905 | if (edgeSize > 2) { |
---|
1906 | if (edgeSize < minEdgeSize) { |
---|
1907 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
1908 | } |
---|
1909 | idx = 2 * getIF(whichrow); |
---|
1910 | } |
---|
1911 | currentEdge.push_back(edge[idx]); |
---|
1912 | currentEdge.push_back(edge[idx+1]); |
---|
1913 | } else { |
---|
1914 | throw(AipsError("Wrong length of edge element")); |
---|
1915 | } |
---|
1916 | lineFinder.setData(getSpectrum(whichrow)); |
---|
1917 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
1918 | chanMask = lineFinder.getMask(); |
---|
1919 | //------------------------------------------------------- |
---|
1920 | |
---|
1921 | fitBaseline(chanMask, whichrow, fitter); |
---|
1922 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
1923 | |
---|
1924 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter); |
---|
1925 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
1926 | } |
---|
1927 | |
---|
1928 | if (outTextFile) ofs.close(); |
---|
1929 | |
---|
1930 | } catch (...) { |
---|
1931 | throw; |
---|
1932 | } |
---|
1933 | } |
---|
1934 | |
---|
1935 | 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) |
---|
1936 | { |
---|
1937 | try { |
---|
1938 | ofstream ofs; |
---|
1939 | String coordInfo = ""; |
---|
1940 | bool hasSameNchan = true; |
---|
1941 | bool outTextFile = false; |
---|
1942 | |
---|
1943 | if (blfile != "") { |
---|
1944 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
1945 | if (ofs) outTextFile = true; |
---|
1946 | } |
---|
1947 | |
---|
1948 | if (outLogger || outTextFile) { |
---|
1949 | coordInfo = getCoordInfo()[0]; |
---|
1950 | if (coordInfo == "") coordInfo = "channel"; |
---|
1951 | hasSameNchan = hasSameNchanOverIFs(); |
---|
1952 | } |
---|
1953 | |
---|
1954 | //Fitter fitter = Fitter(); |
---|
1955 | //fitter.setExpression("cspline", nPiece); |
---|
1956 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
1957 | |
---|
1958 | int nRow = nrow(); |
---|
1959 | std::vector<bool> chanMask; |
---|
1960 | bool showProgress; |
---|
1961 | int minNRow; |
---|
1962 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
1963 | |
---|
1964 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
1965 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
1966 | //fitBaseline(chanMask, whichrow, fitter); |
---|
1967 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
1968 | std::vector<int> pieceEdges; |
---|
1969 | std::vector<float> params; |
---|
1970 | int nClipped = 0; |
---|
1971 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
1972 | setSpectrum(res, whichrow); |
---|
1973 | // |
---|
1974 | |
---|
1975 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
1976 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
1977 | } |
---|
1978 | |
---|
1979 | if (outTextFile) ofs.close(); |
---|
1980 | |
---|
1981 | } catch (...) { |
---|
1982 | throw; |
---|
1983 | } |
---|
1984 | } |
---|
1985 | |
---|
1986 | 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) |
---|
1987 | { |
---|
1988 | try { |
---|
1989 | ofstream ofs; |
---|
1990 | String coordInfo = ""; |
---|
1991 | bool hasSameNchan = true; |
---|
1992 | bool outTextFile = false; |
---|
1993 | |
---|
1994 | if (blfile != "") { |
---|
1995 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
1996 | if (ofs) outTextFile = true; |
---|
1997 | } |
---|
1998 | |
---|
1999 | if (outLogger || outTextFile) { |
---|
2000 | coordInfo = getCoordInfo()[0]; |
---|
2001 | if (coordInfo == "") coordInfo = "channel"; |
---|
2002 | hasSameNchan = hasSameNchanOverIFs(); |
---|
2003 | } |
---|
2004 | |
---|
2005 | //Fitter fitter = Fitter(); |
---|
2006 | //fitter.setExpression("cspline", nPiece); |
---|
2007 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
2008 | |
---|
2009 | int nRow = nrow(); |
---|
2010 | std::vector<bool> chanMask; |
---|
2011 | int minEdgeSize = getIFNos().size()*2; |
---|
2012 | STLineFinder lineFinder = STLineFinder(); |
---|
2013 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
2014 | |
---|
2015 | bool showProgress; |
---|
2016 | int minNRow; |
---|
2017 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
2018 | |
---|
2019 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
2020 | |
---|
2021 | //------------------------------------------------------- |
---|
2022 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
2023 | //------------------------------------------------------- |
---|
2024 | int edgeSize = edge.size(); |
---|
2025 | std::vector<int> currentEdge; |
---|
2026 | if (edgeSize >= 2) { |
---|
2027 | int idx = 0; |
---|
2028 | if (edgeSize > 2) { |
---|
2029 | if (edgeSize < minEdgeSize) { |
---|
2030 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
2031 | } |
---|
2032 | idx = 2 * getIF(whichrow); |
---|
2033 | } |
---|
2034 | currentEdge.push_back(edge[idx]); |
---|
2035 | currentEdge.push_back(edge[idx+1]); |
---|
2036 | } else { |
---|
2037 | throw(AipsError("Wrong length of edge element")); |
---|
2038 | } |
---|
2039 | lineFinder.setData(getSpectrum(whichrow)); |
---|
2040 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
2041 | chanMask = lineFinder.getMask(); |
---|
2042 | //------------------------------------------------------- |
---|
2043 | |
---|
2044 | |
---|
2045 | //fitBaseline(chanMask, whichrow, fitter); |
---|
2046 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
2047 | std::vector<int> pieceEdges; |
---|
2048 | std::vector<float> params; |
---|
2049 | int nClipped = 0; |
---|
2050 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
2051 | setSpectrum(res, whichrow); |
---|
2052 | // |
---|
2053 | |
---|
2054 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
2055 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
2056 | } |
---|
2057 | |
---|
2058 | if (outTextFile) ofs.close(); |
---|
2059 | |
---|
2060 | } catch (...) { |
---|
2061 | throw; |
---|
2062 | } |
---|
2063 | } |
---|
2064 | |
---|
2065 | 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) |
---|
2066 | { |
---|
2067 | if (data.size() != mask.size()) { |
---|
2068 | throw(AipsError("data and mask sizes are not identical")); |
---|
2069 | } |
---|
2070 | if (nPiece < 1) { |
---|
2071 | throw(AipsError("number of the sections must be one or more")); |
---|
2072 | } |
---|
2073 | |
---|
2074 | int nChan = data.size(); |
---|
2075 | std::vector<int> maskArray; |
---|
2076 | std::vector<int> x; |
---|
2077 | for (int i = 0; i < nChan; ++i) { |
---|
2078 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
2079 | if (mask[i]) { |
---|
2080 | x.push_back(i); |
---|
2081 | } |
---|
2082 | } |
---|
2083 | |
---|
2084 | int initNData = x.size(); |
---|
2085 | if (initNData < nPiece) { |
---|
2086 | throw(AipsError("too few non-flagged channels")); |
---|
2087 | } |
---|
2088 | |
---|
2089 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5)); |
---|
2090 | std::vector<double> invEdge; |
---|
2091 | idxEdge.clear(); |
---|
2092 | idxEdge.push_back(x[0]); |
---|
2093 | for (int i = 1; i < nPiece; ++i) { |
---|
2094 | int valX = x[nElement*i]; |
---|
2095 | idxEdge.push_back(valX); |
---|
2096 | invEdge.push_back(1.0/(double)valX); |
---|
2097 | } |
---|
2098 | idxEdge.push_back(x[x.size()-1]+1); |
---|
2099 | |
---|
2100 | int nData = initNData; |
---|
2101 | int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1). |
---|
2102 | |
---|
2103 | std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1, residual; |
---|
2104 | for (int i = 0; i < nChan; ++i) { |
---|
2105 | double di = (double)i; |
---|
2106 | double dD = (double)data[i]; |
---|
2107 | x1.push_back(di); |
---|
2108 | x2.push_back(di*di); |
---|
2109 | x3.push_back(di*di*di); |
---|
2110 | z1.push_back(dD); |
---|
2111 | x1z1.push_back(dD*di); |
---|
2112 | x2z1.push_back(dD*di*di); |
---|
2113 | x3z1.push_back(dD*di*di*di); |
---|
2114 | r1.push_back(0.0); |
---|
2115 | residual.push_back(0.0); |
---|
2116 | } |
---|
2117 | |
---|
2118 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
2119 | // xMatrix : horizontal concatenation of |
---|
2120 | // the least-sq. matrix (left) and an |
---|
2121 | // identity matrix (right). |
---|
2122 | // the right part is used to calculate the inverse matrix of the left part. |
---|
2123 | double xMatrix[nDOF][2*nDOF]; |
---|
2124 | double zMatrix[nDOF]; |
---|
2125 | for (int i = 0; i < nDOF; ++i) { |
---|
2126 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
2127 | xMatrix[i][j] = 0.0; |
---|
2128 | } |
---|
2129 | xMatrix[i][nDOF+i] = 1.0; |
---|
2130 | zMatrix[i] = 0.0; |
---|
2131 | } |
---|
2132 | |
---|
2133 | for (int n = 0; n < nPiece; ++n) { |
---|
2134 | int nUseDataInPiece = 0; |
---|
2135 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
2136 | |
---|
2137 | if (maskArray[i] == 0) continue; |
---|
2138 | |
---|
2139 | xMatrix[0][0] += 1.0; |
---|
2140 | xMatrix[0][1] += x1[i]; |
---|
2141 | xMatrix[0][2] += x2[i]; |
---|
2142 | xMatrix[0][3] += x3[i]; |
---|
2143 | xMatrix[1][1] += x2[i]; |
---|
2144 | xMatrix[1][2] += x3[i]; |
---|
2145 | xMatrix[1][3] += x2[i]*x2[i]; |
---|
2146 | xMatrix[2][2] += x2[i]*x2[i]; |
---|
2147 | xMatrix[2][3] += x3[i]*x2[i]; |
---|
2148 | xMatrix[3][3] += x3[i]*x3[i]; |
---|
2149 | zMatrix[0] += z1[i]; |
---|
2150 | zMatrix[1] += x1z1[i]; |
---|
2151 | zMatrix[2] += x2z1[i]; |
---|
2152 | zMatrix[3] += x3z1[i]; |
---|
2153 | |
---|
2154 | for (int j = 0; j < n; ++j) { |
---|
2155 | double q = 1.0 - x1[i]*invEdge[j]; |
---|
2156 | q = q*q*q; |
---|
2157 | xMatrix[0][j+4] += q; |
---|
2158 | xMatrix[1][j+4] += q*x1[i]; |
---|
2159 | xMatrix[2][j+4] += q*x2[i]; |
---|
2160 | xMatrix[3][j+4] += q*x3[i]; |
---|
2161 | for (int k = 0; k < j; ++k) { |
---|
2162 | double r = 1.0 - x1[i]*invEdge[k]; |
---|
2163 | r = r*r*r; |
---|
2164 | xMatrix[k+4][j+4] += r*q; |
---|
2165 | } |
---|
2166 | xMatrix[j+4][j+4] += q*q; |
---|
2167 | zMatrix[j+4] += q*z1[i]; |
---|
2168 | } |
---|
2169 | |
---|
2170 | nUseDataInPiece++; |
---|
2171 | } |
---|
2172 | |
---|
2173 | if (nUseDataInPiece < 1) { |
---|
2174 | std::vector<string> suffixOfPieceNumber(4); |
---|
2175 | suffixOfPieceNumber[0] = "th"; |
---|
2176 | suffixOfPieceNumber[1] = "st"; |
---|
2177 | suffixOfPieceNumber[2] = "nd"; |
---|
2178 | suffixOfPieceNumber[3] = "rd"; |
---|
2179 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0; |
---|
2180 | ostringstream oss; |
---|
2181 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece]; |
---|
2182 | oss << " piece of the spectrum. can't execute fitting anymore."; |
---|
2183 | throw(AipsError(String(oss))); |
---|
2184 | } |
---|
2185 | } |
---|
2186 | |
---|
2187 | for (int i = 0; i < nDOF; ++i) { |
---|
2188 | for (int j = 0; j < i; ++j) { |
---|
2189 | xMatrix[i][j] = xMatrix[j][i]; |
---|
2190 | } |
---|
2191 | } |
---|
2192 | |
---|
2193 | std::vector<double> invDiag; |
---|
2194 | for (int i = 0; i < nDOF; ++i) { |
---|
2195 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
2196 | for (int j = 0; j < nDOF; ++j) { |
---|
2197 | xMatrix[i][j] *= invDiag[i]; |
---|
2198 | } |
---|
2199 | } |
---|
2200 | |
---|
2201 | for (int k = 0; k < nDOF; ++k) { |
---|
2202 | for (int i = 0; i < nDOF; ++i) { |
---|
2203 | if (i != k) { |
---|
2204 | double factor1 = xMatrix[k][k]; |
---|
2205 | double factor2 = xMatrix[i][k]; |
---|
2206 | for (int j = k; j < 2*nDOF; ++j) { |
---|
2207 | xMatrix[i][j] *= factor1; |
---|
2208 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
2209 | xMatrix[i][j] /= factor1; |
---|
2210 | } |
---|
2211 | } |
---|
2212 | } |
---|
2213 | double xDiag = xMatrix[k][k]; |
---|
2214 | for (int j = k; j < 2*nDOF; ++j) { |
---|
2215 | xMatrix[k][j] /= xDiag; |
---|
2216 | } |
---|
2217 | } |
---|
2218 | |
---|
2219 | for (int i = 0; i < nDOF; ++i) { |
---|
2220 | for (int j = 0; j < nDOF; ++j) { |
---|
2221 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
2222 | } |
---|
2223 | } |
---|
2224 | //compute a vector y which consists of the coefficients of the best-fit spline curves |
---|
2225 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of |
---|
2226 | //cubic terms for the other pieces (in case nPiece>1). |
---|
2227 | std::vector<double> y; |
---|
2228 | y.clear(); |
---|
2229 | for (int i = 0; i < nDOF; ++i) { |
---|
2230 | y.push_back(0.0); |
---|
2231 | for (int j = 0; j < nDOF; ++j) { |
---|
2232 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
2233 | } |
---|
2234 | } |
---|
2235 | |
---|
2236 | double a0 = y[0]; |
---|
2237 | double a1 = y[1]; |
---|
2238 | double a2 = y[2]; |
---|
2239 | double a3 = y[3]; |
---|
2240 | params.clear(); |
---|
2241 | |
---|
2242 | for (int n = 0; n < nPiece; ++n) { |
---|
2243 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
2244 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i]; |
---|
2245 | residual[i] = z1[i] - r1[i]; |
---|
2246 | } |
---|
2247 | params.push_back(a0); |
---|
2248 | params.push_back(a1); |
---|
2249 | params.push_back(a2); |
---|
2250 | params.push_back(a3); |
---|
2251 | |
---|
2252 | if (n == nPiece-1) break; |
---|
2253 | |
---|
2254 | double d = y[4+n]; |
---|
2255 | double iE = invEdge[n]; |
---|
2256 | a0 += d; |
---|
2257 | a1 -= 3.0*d*iE; |
---|
2258 | a2 += 3.0*d*iE*iE; |
---|
2259 | a3 -= d*iE*iE*iE; |
---|
2260 | } |
---|
2261 | |
---|
2262 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
2263 | break; |
---|
2264 | } else { |
---|
2265 | double stdDev = 0.0; |
---|
2266 | for (int i = 0; i < nChan; ++i) { |
---|
2267 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
2268 | } |
---|
2269 | stdDev = sqrt(stdDev/(double)nData); |
---|
2270 | |
---|
2271 | double thres = stdDev * thresClip; |
---|
2272 | int newNData = 0; |
---|
2273 | for (int i = 0; i < nChan; ++i) { |
---|
2274 | if (abs(residual[i]) >= thres) { |
---|
2275 | maskArray[i] = 0; |
---|
2276 | } |
---|
2277 | if (maskArray[i] > 0) { |
---|
2278 | newNData++; |
---|
2279 | } |
---|
2280 | } |
---|
2281 | if (newNData == nData) { |
---|
2282 | break; //no more flag to add. iteration stops. |
---|
2283 | } else { |
---|
2284 | nData = newNData; |
---|
2285 | } |
---|
2286 | } |
---|
2287 | } |
---|
2288 | |
---|
2289 | nClipped = initNData - nData; |
---|
2290 | |
---|
2291 | std::vector<float> result; |
---|
2292 | if (getResidual) { |
---|
2293 | for (int i = 0; i < nChan; ++i) { |
---|
2294 | result.push_back((float)residual[i]); |
---|
2295 | } |
---|
2296 | } else { |
---|
2297 | for (int i = 0; i < nChan; ++i) { |
---|
2298 | result.push_back((float)r1[i]); |
---|
2299 | } |
---|
2300 | } |
---|
2301 | |
---|
2302 | return result; |
---|
2303 | } |
---|
2304 | |
---|
2305 | 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) |
---|
2306 | { |
---|
2307 | nWaves.clear(); |
---|
2308 | |
---|
2309 | if (applyFFT) { |
---|
2310 | string fftThAttr; |
---|
2311 | float fftThSigma; |
---|
2312 | int fftThTop; |
---|
2313 | parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop); |
---|
2314 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves); |
---|
2315 | } |
---|
2316 | |
---|
2317 | addAuxWaveNumbers(addNWaves, rejectNWaves, nWaves); |
---|
2318 | } |
---|
2319 | |
---|
2320 | void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop) |
---|
2321 | { |
---|
2322 | uInt idxSigma = fftThresh.find("sigma"); |
---|
2323 | uInt idxTop = fftThresh.find("top"); |
---|
2324 | |
---|
2325 | if (idxSigma == fftThresh.size() - 5) { |
---|
2326 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5)); |
---|
2327 | is >> fftThSigma; |
---|
2328 | fftThAttr = "sigma"; |
---|
2329 | } else if (idxTop == 0) { |
---|
2330 | std::istringstream is(fftThresh.substr(3)); |
---|
2331 | is >> fftThTop; |
---|
2332 | fftThAttr = "top"; |
---|
2333 | } else { |
---|
2334 | bool isNumber = true; |
---|
2335 | for (uInt i = 0; i < fftThresh.size()-1; ++i) { |
---|
2336 | char ch = (fftThresh.substr(i, 1).c_str())[0]; |
---|
2337 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) { |
---|
2338 | isNumber = false; |
---|
2339 | break; |
---|
2340 | } |
---|
2341 | } |
---|
2342 | if (isNumber) { |
---|
2343 | std::istringstream is(fftThresh); |
---|
2344 | is >> fftThSigma; |
---|
2345 | fftThAttr = "sigma"; |
---|
2346 | } else { |
---|
2347 | throw(AipsError("fftthresh has a wrong value")); |
---|
2348 | } |
---|
2349 | } |
---|
2350 | } |
---|
2351 | |
---|
2352 | 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) |
---|
2353 | { |
---|
2354 | std::vector<float> fspec; |
---|
2355 | if (fftMethod == "fft") { |
---|
2356 | fspec = execFFT(whichrow, chanMask, false, true); |
---|
2357 | //} else if (fftMethod == "lsp") { |
---|
2358 | // fspec = lombScarglePeriodogram(whichrow); |
---|
2359 | } |
---|
2360 | |
---|
2361 | if (fftThAttr == "sigma") { |
---|
2362 | float mean = 0.0; |
---|
2363 | float mean2 = 0.0; |
---|
2364 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
2365 | mean += fspec[i]; |
---|
2366 | mean2 += fspec[i]*fspec[i]; |
---|
2367 | } |
---|
2368 | mean /= float(fspec.size()); |
---|
2369 | mean2 /= float(fspec.size()); |
---|
2370 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean)); |
---|
2371 | |
---|
2372 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
2373 | if (fspec[i] >= thres) { |
---|
2374 | nWaves.push_back(i); |
---|
2375 | } |
---|
2376 | } |
---|
2377 | |
---|
2378 | } else if (fftThAttr == "top") { |
---|
2379 | for (int i = 0; i < fftThTop; ++i) { |
---|
2380 | float max = 0.0; |
---|
2381 | int maxIdx = 0; |
---|
2382 | for (uInt j = 0; j < fspec.size(); ++j) { |
---|
2383 | if (fspec[j] > max) { |
---|
2384 | max = fspec[j]; |
---|
2385 | maxIdx = j; |
---|
2386 | } |
---|
2387 | } |
---|
2388 | nWaves.push_back(maxIdx); |
---|
2389 | fspec[maxIdx] = 0.0; |
---|
2390 | } |
---|
2391 | |
---|
2392 | } |
---|
2393 | |
---|
2394 | if (nWaves.size() > 1) { |
---|
2395 | sort(nWaves.begin(), nWaves.end()); |
---|
2396 | } |
---|
2397 | } |
---|
2398 | |
---|
2399 | void Scantable::addAuxWaveNumbers(const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
2400 | { |
---|
2401 | for (uInt i = 0; i < addNWaves.size(); ++i) { |
---|
2402 | bool found = false; |
---|
2403 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
2404 | if (nWaves[j] == addNWaves[i]) { |
---|
2405 | found = true; |
---|
2406 | break; |
---|
2407 | } |
---|
2408 | } |
---|
2409 | if (!found) nWaves.push_back(addNWaves[i]); |
---|
2410 | } |
---|
2411 | |
---|
2412 | for (uInt i = 0; i < rejectNWaves.size(); ++i) { |
---|
2413 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) { |
---|
2414 | if (*j == rejectNWaves[i]) { |
---|
2415 | j = nWaves.erase(j); |
---|
2416 | } else { |
---|
2417 | ++j; |
---|
2418 | } |
---|
2419 | } |
---|
2420 | } |
---|
2421 | |
---|
2422 | if (nWaves.size() > 1) { |
---|
2423 | sort(nWaves.begin(), nWaves.end()); |
---|
2424 | unique(nWaves.begin(), nWaves.end()); |
---|
2425 | } |
---|
2426 | } |
---|
2427 | |
---|
2428 | 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) |
---|
2429 | { |
---|
2430 | try { |
---|
2431 | ofstream ofs; |
---|
2432 | String coordInfo = ""; |
---|
2433 | bool hasSameNchan = true; |
---|
2434 | bool outTextFile = false; |
---|
2435 | |
---|
2436 | if (blfile != "") { |
---|
2437 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
2438 | if (ofs) outTextFile = true; |
---|
2439 | } |
---|
2440 | |
---|
2441 | if (outLogger || outTextFile) { |
---|
2442 | coordInfo = getCoordInfo()[0]; |
---|
2443 | if (coordInfo == "") coordInfo = "channel"; |
---|
2444 | hasSameNchan = hasSameNchanOverIFs(); |
---|
2445 | } |
---|
2446 | |
---|
2447 | //Fitter fitter = Fitter(); |
---|
2448 | //fitter.setExpression("sinusoid", nWaves); |
---|
2449 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
2450 | |
---|
2451 | int nRow = nrow(); |
---|
2452 | std::vector<bool> chanMask; |
---|
2453 | std::vector<int> nWaves; |
---|
2454 | |
---|
2455 | bool showProgress; |
---|
2456 | int minNRow; |
---|
2457 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
2458 | |
---|
2459 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
2460 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
2461 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
2462 | |
---|
2463 | //FOR DEBUGGING------------ |
---|
2464 | if (whichrow < 0) {// == nRow -1) { |
---|
2465 | cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow); |
---|
2466 | if (applyFFT) { |
---|
2467 | cout << "[ "; |
---|
2468 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
2469 | cout << nWaves[j] << ", "; |
---|
2470 | } |
---|
2471 | cout << " ] " << endl; |
---|
2472 | } |
---|
2473 | cout << flush; |
---|
2474 | } |
---|
2475 | //------------------------- |
---|
2476 | |
---|
2477 | //fitBaseline(chanMask, whichrow, fitter); |
---|
2478 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
2479 | std::vector<float> params; |
---|
2480 | int nClipped = 0; |
---|
2481 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
2482 | setSpectrum(res, whichrow); |
---|
2483 | // |
---|
2484 | |
---|
2485 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped); |
---|
2486 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
2487 | } |
---|
2488 | |
---|
2489 | if (outTextFile) ofs.close(); |
---|
2490 | |
---|
2491 | } catch (...) { |
---|
2492 | throw; |
---|
2493 | } |
---|
2494 | } |
---|
2495 | |
---|
2496 | 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) |
---|
2497 | { |
---|
2498 | try { |
---|
2499 | ofstream ofs; |
---|
2500 | String coordInfo = ""; |
---|
2501 | bool hasSameNchan = true; |
---|
2502 | bool outTextFile = false; |
---|
2503 | |
---|
2504 | if (blfile != "") { |
---|
2505 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
2506 | if (ofs) outTextFile = true; |
---|
2507 | } |
---|
2508 | |
---|
2509 | if (outLogger || outTextFile) { |
---|
2510 | coordInfo = getCoordInfo()[0]; |
---|
2511 | if (coordInfo == "") coordInfo = "channel"; |
---|
2512 | hasSameNchan = hasSameNchanOverIFs(); |
---|
2513 | } |
---|
2514 | |
---|
2515 | //Fitter fitter = Fitter(); |
---|
2516 | //fitter.setExpression("sinusoid", nWaves); |
---|
2517 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
2518 | |
---|
2519 | int nRow = nrow(); |
---|
2520 | std::vector<bool> chanMask; |
---|
2521 | std::vector<int> nWaves; |
---|
2522 | |
---|
2523 | int minEdgeSize = getIFNos().size()*2; |
---|
2524 | STLineFinder lineFinder = STLineFinder(); |
---|
2525 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
2526 | |
---|
2527 | bool showProgress; |
---|
2528 | int minNRow; |
---|
2529 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
2530 | |
---|
2531 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
2532 | |
---|
2533 | //------------------------------------------------------- |
---|
2534 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
2535 | //------------------------------------------------------- |
---|
2536 | int edgeSize = edge.size(); |
---|
2537 | std::vector<int> currentEdge; |
---|
2538 | if (edgeSize >= 2) { |
---|
2539 | int idx = 0; |
---|
2540 | if (edgeSize > 2) { |
---|
2541 | if (edgeSize < minEdgeSize) { |
---|
2542 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
2543 | } |
---|
2544 | idx = 2 * getIF(whichrow); |
---|
2545 | } |
---|
2546 | currentEdge.push_back(edge[idx]); |
---|
2547 | currentEdge.push_back(edge[idx+1]); |
---|
2548 | } else { |
---|
2549 | throw(AipsError("Wrong length of edge element")); |
---|
2550 | } |
---|
2551 | lineFinder.setData(getSpectrum(whichrow)); |
---|
2552 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
2553 | chanMask = lineFinder.getMask(); |
---|
2554 | //------------------------------------------------------- |
---|
2555 | |
---|
2556 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
2557 | |
---|
2558 | //fitBaseline(chanMask, whichrow, fitter); |
---|
2559 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
2560 | std::vector<float> params; |
---|
2561 | int nClipped = 0; |
---|
2562 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
2563 | setSpectrum(res, whichrow); |
---|
2564 | // |
---|
2565 | |
---|
2566 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped); |
---|
2567 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
2568 | } |
---|
2569 | |
---|
2570 | if (outTextFile) ofs.close(); |
---|
2571 | |
---|
2572 | } catch (...) { |
---|
2573 | throw; |
---|
2574 | } |
---|
2575 | } |
---|
2576 | |
---|
2577 | 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) |
---|
2578 | { |
---|
2579 | if (data.size() != mask.size()) { |
---|
2580 | throw(AipsError("data and mask sizes are not identical")); |
---|
2581 | } |
---|
2582 | if (data.size() < 2) { |
---|
2583 | throw(AipsError("data size is too short")); |
---|
2584 | } |
---|
2585 | if (waveNumbers.size() == 0) { |
---|
2586 | throw(AipsError("no wave numbers given")); |
---|
2587 | } |
---|
2588 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers |
---|
2589 | nWaves.reserve(waveNumbers.size()); |
---|
2590 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves)); |
---|
2591 | sort(nWaves.begin(), nWaves.end()); |
---|
2592 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end()); |
---|
2593 | nWaves.erase(end_it, nWaves.end()); |
---|
2594 | |
---|
2595 | int minNWaves = nWaves[0]; |
---|
2596 | if (minNWaves < 0) { |
---|
2597 | throw(AipsError("wave number must be positive or zero (i.e. constant)")); |
---|
2598 | } |
---|
2599 | bool hasConstantTerm = (minNWaves == 0); |
---|
2600 | |
---|
2601 | int nChan = data.size(); |
---|
2602 | std::vector<int> maskArray; |
---|
2603 | std::vector<int> x; |
---|
2604 | for (int i = 0; i < nChan; ++i) { |
---|
2605 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
2606 | if (mask[i]) { |
---|
2607 | x.push_back(i); |
---|
2608 | } |
---|
2609 | } |
---|
2610 | |
---|
2611 | int initNData = x.size(); |
---|
2612 | |
---|
2613 | int nData = initNData; |
---|
2614 | int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve. |
---|
2615 | |
---|
2616 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
2617 | 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) |
---|
2618 | |
---|
2619 | // xArray : contains elemental values for computing the least-square matrix. |
---|
2620 | // xArray.size() is nDOF and xArray[*].size() is nChan. |
---|
2621 | // Each xArray element are as follows: |
---|
2622 | // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
2623 | // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])}, |
---|
2624 | // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])}, |
---|
2625 | // where (1 <= n <= nMaxWavesInSW), |
---|
2626 | // or, |
---|
2627 | // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])}, |
---|
2628 | // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])}, |
---|
2629 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()). |
---|
2630 | std::vector<std::vector<double> > xArray; |
---|
2631 | if (hasConstantTerm) { |
---|
2632 | std::vector<double> xu; |
---|
2633 | for (int j = 0; j < nChan; ++j) { |
---|
2634 | xu.push_back(1.0); |
---|
2635 | } |
---|
2636 | xArray.push_back(xu); |
---|
2637 | } |
---|
2638 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) { |
---|
2639 | double xFactor = baseXFactor*(double)nWaves[i]; |
---|
2640 | std::vector<double> xs, xc; |
---|
2641 | xs.clear(); |
---|
2642 | xc.clear(); |
---|
2643 | for (int j = 0; j < nChan; ++j) { |
---|
2644 | xs.push_back(sin(xFactor*(double)j)); |
---|
2645 | xc.push_back(cos(xFactor*(double)j)); |
---|
2646 | } |
---|
2647 | xArray.push_back(xs); |
---|
2648 | xArray.push_back(xc); |
---|
2649 | } |
---|
2650 | |
---|
2651 | std::vector<double> z1, r1, residual; |
---|
2652 | for (int i = 0; i < nChan; ++i) { |
---|
2653 | z1.push_back((double)data[i]); |
---|
2654 | r1.push_back(0.0); |
---|
2655 | residual.push_back(0.0); |
---|
2656 | } |
---|
2657 | |
---|
2658 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
2659 | // xMatrix : horizontal concatenation of |
---|
2660 | // the least-sq. matrix (left) and an |
---|
2661 | // identity matrix (right). |
---|
2662 | // the right part is used to calculate the inverse matrix of the left part. |
---|
2663 | double xMatrix[nDOF][2*nDOF]; |
---|
2664 | double zMatrix[nDOF]; |
---|
2665 | for (int i = 0; i < nDOF; ++i) { |
---|
2666 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
2667 | xMatrix[i][j] = 0.0; |
---|
2668 | } |
---|
2669 | xMatrix[i][nDOF+i] = 1.0; |
---|
2670 | zMatrix[i] = 0.0; |
---|
2671 | } |
---|
2672 | |
---|
2673 | int nUseData = 0; |
---|
2674 | for (int k = 0; k < nChan; ++k) { |
---|
2675 | if (maskArray[k] == 0) continue; |
---|
2676 | |
---|
2677 | for (int i = 0; i < nDOF; ++i) { |
---|
2678 | for (int j = i; j < nDOF; ++j) { |
---|
2679 | xMatrix[i][j] += xArray[i][k] * xArray[j][k]; |
---|
2680 | } |
---|
2681 | zMatrix[i] += z1[k] * xArray[i][k]; |
---|
2682 | } |
---|
2683 | |
---|
2684 | nUseData++; |
---|
2685 | } |
---|
2686 | |
---|
2687 | if (nUseData < 1) { |
---|
2688 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
2689 | } |
---|
2690 | |
---|
2691 | for (int i = 0; i < nDOF; ++i) { |
---|
2692 | for (int j = 0; j < i; ++j) { |
---|
2693 | xMatrix[i][j] = xMatrix[j][i]; |
---|
2694 | } |
---|
2695 | } |
---|
2696 | |
---|
2697 | std::vector<double> invDiag; |
---|
2698 | for (int i = 0; i < nDOF; ++i) { |
---|
2699 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
2700 | for (int j = 0; j < nDOF; ++j) { |
---|
2701 | xMatrix[i][j] *= invDiag[i]; |
---|
2702 | } |
---|
2703 | } |
---|
2704 | |
---|
2705 | for (int k = 0; k < nDOF; ++k) { |
---|
2706 | for (int i = 0; i < nDOF; ++i) { |
---|
2707 | if (i != k) { |
---|
2708 | double factor1 = xMatrix[k][k]; |
---|
2709 | double factor2 = xMatrix[i][k]; |
---|
2710 | for (int j = k; j < 2*nDOF; ++j) { |
---|
2711 | xMatrix[i][j] *= factor1; |
---|
2712 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
2713 | xMatrix[i][j] /= factor1; |
---|
2714 | } |
---|
2715 | } |
---|
2716 | } |
---|
2717 | double xDiag = xMatrix[k][k]; |
---|
2718 | for (int j = k; j < 2*nDOF; ++j) { |
---|
2719 | xMatrix[k][j] /= xDiag; |
---|
2720 | } |
---|
2721 | } |
---|
2722 | |
---|
2723 | for (int i = 0; i < nDOF; ++i) { |
---|
2724 | for (int j = 0; j < nDOF; ++j) { |
---|
2725 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
2726 | } |
---|
2727 | } |
---|
2728 | //compute a vector y which consists of the coefficients of the sinusoids forming the |
---|
2729 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine |
---|
2730 | //and cosine functions, respectively. |
---|
2731 | std::vector<double> y; |
---|
2732 | params.clear(); |
---|
2733 | for (int i = 0; i < nDOF; ++i) { |
---|
2734 | y.push_back(0.0); |
---|
2735 | for (int j = 0; j < nDOF; ++j) { |
---|
2736 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
2737 | } |
---|
2738 | params.push_back(y[i]); |
---|
2739 | } |
---|
2740 | |
---|
2741 | for (int i = 0; i < nChan; ++i) { |
---|
2742 | r1[i] = y[0]; |
---|
2743 | for (int j = 1; j < nDOF; ++j) { |
---|
2744 | r1[i] += y[j]*xArray[j][i]; |
---|
2745 | } |
---|
2746 | residual[i] = z1[i] - r1[i]; |
---|
2747 | } |
---|
2748 | |
---|
2749 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
2750 | break; |
---|
2751 | } else { |
---|
2752 | double stdDev = 0.0; |
---|
2753 | for (int i = 0; i < nChan; ++i) { |
---|
2754 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
2755 | } |
---|
2756 | stdDev = sqrt(stdDev/(double)nData); |
---|
2757 | |
---|
2758 | double thres = stdDev * thresClip; |
---|
2759 | int newNData = 0; |
---|
2760 | for (int i = 0; i < nChan; ++i) { |
---|
2761 | if (abs(residual[i]) >= thres) { |
---|
2762 | maskArray[i] = 0; |
---|
2763 | } |
---|
2764 | if (maskArray[i] > 0) { |
---|
2765 | newNData++; |
---|
2766 | } |
---|
2767 | } |
---|
2768 | if (newNData == nData) { |
---|
2769 | break; //no more flag to add. iteration stops. |
---|
2770 | } else { |
---|
2771 | nData = newNData; |
---|
2772 | } |
---|
2773 | } |
---|
2774 | } |
---|
2775 | |
---|
2776 | nClipped = initNData - nData; |
---|
2777 | |
---|
2778 | std::vector<float> result; |
---|
2779 | if (getResidual) { |
---|
2780 | for (int i = 0; i < nChan; ++i) { |
---|
2781 | result.push_back((float)residual[i]); |
---|
2782 | } |
---|
2783 | } else { |
---|
2784 | for (int i = 0; i < nChan; ++i) { |
---|
2785 | result.push_back((float)r1[i]); |
---|
2786 | } |
---|
2787 | } |
---|
2788 | |
---|
2789 | return result; |
---|
2790 | } |
---|
2791 | |
---|
2792 | void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter) |
---|
2793 | { |
---|
2794 | std::vector<double> dAbcissa = getAbcissa(whichrow); |
---|
2795 | std::vector<float> abcissa; |
---|
2796 | for (uInt i = 0; i < dAbcissa.size(); ++i) { |
---|
2797 | abcissa.push_back((float)dAbcissa[i]); |
---|
2798 | } |
---|
2799 | std::vector<float> spec = getSpectrum(whichrow); |
---|
2800 | |
---|
2801 | fitter.setData(abcissa, spec, mask); |
---|
2802 | fitter.lfit(); |
---|
2803 | } |
---|
2804 | |
---|
2805 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask) |
---|
2806 | { |
---|
2807 | std::vector<bool> mask = getMask(whichrow); |
---|
2808 | uInt maskSize = mask.size(); |
---|
2809 | if (maskSize != inMask.size()) { |
---|
2810 | throw(AipsError("mask sizes are not the same.")); |
---|
2811 | } |
---|
2812 | for (uInt i = 0; i < maskSize; ++i) { |
---|
2813 | mask[i] = mask[i] && inMask[i]; |
---|
2814 | } |
---|
2815 | |
---|
2816 | return mask; |
---|
2817 | } |
---|
2818 | |
---|
2819 | /* |
---|
2820 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder) |
---|
2821 | { |
---|
2822 | int edgeSize = edge.size(); |
---|
2823 | std::vector<int> currentEdge; |
---|
2824 | if (edgeSize >= 2) { |
---|
2825 | int idx = 0; |
---|
2826 | if (edgeSize > 2) { |
---|
2827 | if (edgeSize < minEdgeSize) { |
---|
2828 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
2829 | } |
---|
2830 | idx = 2 * getIF(whichrow); |
---|
2831 | } |
---|
2832 | currentEdge.push_back(edge[idx]); |
---|
2833 | currentEdge.push_back(edge[idx+1]); |
---|
2834 | } else { |
---|
2835 | throw(AipsError("Wrong length of edge element")); |
---|
2836 | } |
---|
2837 | |
---|
2838 | lineFinder.setData(getSpectrum(whichrow)); |
---|
2839 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow); |
---|
2840 | |
---|
2841 | return lineFinder.getMask(); |
---|
2842 | } |
---|
2843 | */ |
---|
2844 | |
---|
2845 | /* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */ |
---|
2846 | 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) |
---|
2847 | { |
---|
2848 | if (outLogger || outTextFile) { |
---|
2849 | std::vector<float> params = fitter.getParameters(); |
---|
2850 | std::vector<bool> fixed = fitter.getFixedParameters(); |
---|
2851 | float rms = getRms(chanMask, whichrow); |
---|
2852 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
2853 | |
---|
2854 | if (outLogger) { |
---|
2855 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
2856 | ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false) << LogIO::POST ; |
---|
2857 | } |
---|
2858 | if (outTextFile) { |
---|
2859 | ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true) << flush; |
---|
2860 | } |
---|
2861 | } |
---|
2862 | } |
---|
2863 | |
---|
2864 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */ |
---|
2865 | 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) |
---|
2866 | { |
---|
2867 | if (outLogger || outTextFile) { |
---|
2868 | float rms = getRms(chanMask, whichrow); |
---|
2869 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
2870 | std::vector<bool> fixed; |
---|
2871 | fixed.clear(); |
---|
2872 | |
---|
2873 | if (outLogger) { |
---|
2874 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
2875 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ; |
---|
2876 | } |
---|
2877 | if (outTextFile) { |
---|
2878 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true) << flush; |
---|
2879 | } |
---|
2880 | } |
---|
2881 | } |
---|
2882 | |
---|
2883 | /* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */ |
---|
2884 | 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) |
---|
2885 | { |
---|
2886 | if (outLogger || outTextFile) { |
---|
2887 | float rms = getRms(chanMask, whichrow); |
---|
2888 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
2889 | std::vector<bool> fixed; |
---|
2890 | fixed.clear(); |
---|
2891 | |
---|
2892 | if (outLogger) { |
---|
2893 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
2894 | ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ; |
---|
2895 | } |
---|
2896 | if (outTextFile) { |
---|
2897 | ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true) << flush; |
---|
2898 | } |
---|
2899 | } |
---|
2900 | } |
---|
2901 | |
---|
2902 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow) |
---|
2903 | { |
---|
2904 | int idxDelimiter = progressInfo.find(","); |
---|
2905 | if (idxDelimiter < 0) { |
---|
2906 | throw(AipsError("wrong value in 'showprogress' parameter")) ; |
---|
2907 | } |
---|
2908 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true"); |
---|
2909 | std::istringstream is(progressInfo.substr(idxDelimiter+1)); |
---|
2910 | is >> minNRow; |
---|
2911 | } |
---|
2912 | |
---|
2913 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold) |
---|
2914 | { |
---|
2915 | if (showProgress && (nTotal >= nTotalThreshold)) { |
---|
2916 | int nInterval = int(floor(double(nTotal)/100.0)); |
---|
2917 | if (nInterval == 0) nInterval++; |
---|
2918 | |
---|
2919 | if (nProcessed % nInterval == 0) { |
---|
2920 | printf("\r"); //go to the head of line |
---|
2921 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted |
---|
2922 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) ); |
---|
2923 | printf("\x1b[39m\x1b[0m"); //set default attributes |
---|
2924 | fflush(NULL); |
---|
2925 | } |
---|
2926 | |
---|
2927 | if (nProcessed == nTotal - 1) { |
---|
2928 | printf("\r\x1b[K"); //clear |
---|
2929 | fflush(NULL); |
---|
2930 | } |
---|
2931 | |
---|
2932 | } |
---|
2933 | } |
---|
2934 | |
---|
2935 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly) |
---|
2936 | { |
---|
2937 | std::vector<bool> mask = getMask(whichrow); |
---|
2938 | |
---|
2939 | if (inMask.size() > 0) { |
---|
2940 | uInt maskSize = mask.size(); |
---|
2941 | if (maskSize != inMask.size()) { |
---|
2942 | throw(AipsError("mask sizes are not the same.")); |
---|
2943 | } |
---|
2944 | for (uInt i = 0; i < maskSize; ++i) { |
---|
2945 | mask[i] = mask[i] && inMask[i]; |
---|
2946 | } |
---|
2947 | } |
---|
2948 | |
---|
2949 | Vector<Float> spec = getSpectrum(whichrow); |
---|
2950 | mathutil::doZeroOrderInterpolation(spec, mask); |
---|
2951 | |
---|
2952 | FFTServer<Float,Complex> ffts; |
---|
2953 | Vector<Complex> fftres; |
---|
2954 | ffts.fft0(fftres, spec); |
---|
2955 | |
---|
2956 | std::vector<float> res; |
---|
2957 | float norm = float(2.0/double(spec.size())); |
---|
2958 | |
---|
2959 | if (getRealImag) { |
---|
2960 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
2961 | res.push_back(real(fftres[i])*norm); |
---|
2962 | res.push_back(imag(fftres[i])*norm); |
---|
2963 | } |
---|
2964 | } else { |
---|
2965 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
2966 | res.push_back(abs(fftres[i])*norm); |
---|
2967 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i])); |
---|
2968 | } |
---|
2969 | } |
---|
2970 | |
---|
2971 | return res; |
---|
2972 | } |
---|
2973 | |
---|
2974 | |
---|
2975 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow) |
---|
2976 | { |
---|
2977 | Vector<Float> spec; |
---|
2978 | specCol_.get(whichrow, spec); |
---|
2979 | |
---|
2980 | float mean = 0.0; |
---|
2981 | float smean = 0.0; |
---|
2982 | int n = 0; |
---|
2983 | for (uInt i = 0; i < spec.nelements(); ++i) { |
---|
2984 | if (mask[i]) { |
---|
2985 | mean += spec[i]; |
---|
2986 | smean += spec[i]*spec[i]; |
---|
2987 | n++; |
---|
2988 | } |
---|
2989 | } |
---|
2990 | |
---|
2991 | mean /= (float)n; |
---|
2992 | smean /= (float)n; |
---|
2993 | |
---|
2994 | return sqrt(smean - mean*mean); |
---|
2995 | } |
---|
2996 | |
---|
2997 | |
---|
2998 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const |
---|
2999 | { |
---|
3000 | ostringstream oss; |
---|
3001 | |
---|
3002 | if (verbose) { |
---|
3003 | oss << " Scan[" << getScan(whichrow) << "]"; |
---|
3004 | oss << " Beam[" << getBeam(whichrow) << "]"; |
---|
3005 | oss << " IF[" << getIF(whichrow) << "]"; |
---|
3006 | oss << " Pol[" << getPol(whichrow) << "]"; |
---|
3007 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl; |
---|
3008 | oss << "Fitter range = " << masklist << endl; |
---|
3009 | oss << "Baseline parameters" << endl; |
---|
3010 | oss << flush; |
---|
3011 | } |
---|
3012 | |
---|
3013 | return String(oss); |
---|
3014 | } |
---|
3015 | |
---|
3016 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const |
---|
3017 | { |
---|
3018 | ostringstream oss; |
---|
3019 | |
---|
3020 | if (verbose) { |
---|
3021 | oss << "Results of baseline fit" << endl; |
---|
3022 | oss << " rms = " << setprecision(6) << rms << endl; |
---|
3023 | if (nClipped >= 0) { |
---|
3024 | oss << " Number of clipped channels = " << nClipped << endl; |
---|
3025 | } |
---|
3026 | for (int i = 0; i < 60; ++i) { |
---|
3027 | oss << "-"; |
---|
3028 | } |
---|
3029 | oss << endl; |
---|
3030 | oss << flush; |
---|
3031 | } |
---|
3032 | |
---|
3033 | return String(oss); |
---|
3034 | } |
---|
3035 | |
---|
3036 | std::string Scantable::formatBaselineParams(const std::vector<float>& params, |
---|
3037 | const std::vector<bool>& fixed, |
---|
3038 | float rms, |
---|
3039 | int nClipped, |
---|
3040 | const std::string& masklist, |
---|
3041 | int whichrow, |
---|
3042 | bool verbose, |
---|
3043 | int start, int count, |
---|
3044 | bool resetparamid) const |
---|
3045 | { |
---|
3046 | int nParam = (int)(params.size()); |
---|
3047 | |
---|
3048 | if (nParam < 1) { |
---|
3049 | return(" Not fitted"); |
---|
3050 | } else { |
---|
3051 | |
---|
3052 | ostringstream oss; |
---|
3053 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose); |
---|
3054 | |
---|
3055 | if (start < 0) start = 0; |
---|
3056 | if (count < 0) count = nParam; |
---|
3057 | int end = start + count; |
---|
3058 | if (end > nParam) end = nParam; |
---|
3059 | int paramidoffset = (resetparamid) ? (-start) : 0; |
---|
3060 | |
---|
3061 | for (int i = start; i < end; ++i) { |
---|
3062 | if (i > start) { |
---|
3063 | oss << ","; |
---|
3064 | } |
---|
3065 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : ""; |
---|
3066 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i]; |
---|
3067 | } |
---|
3068 | |
---|
3069 | oss << endl; |
---|
3070 | oss << formatBaselineParamsFooter(rms, nClipped, verbose); |
---|
3071 | |
---|
3072 | return String(oss); |
---|
3073 | } |
---|
3074 | |
---|
3075 | } |
---|
3076 | |
---|
3077 | 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 |
---|
3078 | { |
---|
3079 | int nOutParam = (int)(params.size()); |
---|
3080 | int nPiece = (int)(ranges.size()) - 1; |
---|
3081 | |
---|
3082 | if (nOutParam < 1) { |
---|
3083 | return(" Not fitted"); |
---|
3084 | } else if (nPiece < 0) { |
---|
3085 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose); |
---|
3086 | } else if (nPiece < 1) { |
---|
3087 | return(" Bad count of the piece edge info"); |
---|
3088 | } else if (nOutParam % nPiece != 0) { |
---|
3089 | return(" Bad count of the output baseline parameters"); |
---|
3090 | } else { |
---|
3091 | |
---|
3092 | int nParam = nOutParam / nPiece; |
---|
3093 | |
---|
3094 | ostringstream oss; |
---|
3095 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose); |
---|
3096 | |
---|
3097 | stringstream ss; |
---|
3098 | ss << ranges[nPiece] << flush; |
---|
3099 | int wRange = ss.str().size() * 2 + 5; |
---|
3100 | |
---|
3101 | for (int i = 0; i < nPiece; ++i) { |
---|
3102 | ss.str(""); |
---|
3103 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]"; |
---|
3104 | oss << left << setw(wRange) << ss.str(); |
---|
3105 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, i*nParam, nParam, true); |
---|
3106 | } |
---|
3107 | |
---|
3108 | oss << formatBaselineParamsFooter(rms, nClipped, verbose); |
---|
3109 | |
---|
3110 | return String(oss); |
---|
3111 | } |
---|
3112 | |
---|
3113 | } |
---|
3114 | |
---|
3115 | bool Scantable::hasSameNchanOverIFs() |
---|
3116 | { |
---|
3117 | int nIF = nif(-1); |
---|
3118 | int nCh; |
---|
3119 | int totalPositiveNChan = 0; |
---|
3120 | int nPositiveNChan = 0; |
---|
3121 | |
---|
3122 | for (int i = 0; i < nIF; ++i) { |
---|
3123 | nCh = nchan(i); |
---|
3124 | if (nCh > 0) { |
---|
3125 | totalPositiveNChan += nCh; |
---|
3126 | nPositiveNChan++; |
---|
3127 | } |
---|
3128 | } |
---|
3129 | |
---|
3130 | return (totalPositiveNChan == (nPositiveNChan * nchan(0))); |
---|
3131 | } |
---|
3132 | |
---|
3133 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose) |
---|
3134 | { |
---|
3135 | if (mask.size() < 2) { |
---|
3136 | throw(AipsError("The mask elements should be > 1")); |
---|
3137 | } |
---|
3138 | int IF = getIF(whichrow); |
---|
3139 | if (mask.size() != (uInt)nchan(IF)) { |
---|
3140 | throw(AipsError("Number of channels in scantable != number of mask elements")); |
---|
3141 | } |
---|
3142 | |
---|
3143 | if (verbose) { |
---|
3144 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE)); |
---|
3145 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo; |
---|
3146 | if (!hasSameNchan) { |
---|
3147 | logOs << endl << "This mask is only valid for IF=" << IF; |
---|
3148 | } |
---|
3149 | logOs << LogIO::POST; |
---|
3150 | } |
---|
3151 | |
---|
3152 | std::vector<double> abcissa = getAbcissa(whichrow); |
---|
3153 | std::vector<int> edge = getMaskEdgeIndices(mask); |
---|
3154 | |
---|
3155 | ostringstream oss; |
---|
3156 | oss.setf(ios::fixed); |
---|
3157 | oss << setprecision(1) << "["; |
---|
3158 | for (uInt i = 0; i < edge.size(); i+=2) { |
---|
3159 | if (i > 0) oss << ","; |
---|
3160 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]"; |
---|
3161 | } |
---|
3162 | oss << "]" << flush; |
---|
3163 | |
---|
3164 | return String(oss); |
---|
3165 | } |
---|
3166 | |
---|
3167 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask) |
---|
3168 | { |
---|
3169 | if (mask.size() < 2) { |
---|
3170 | throw(AipsError("The mask elements should be > 1")); |
---|
3171 | } |
---|
3172 | |
---|
3173 | std::vector<int> out, startIndices, endIndices; |
---|
3174 | int maskSize = mask.size(); |
---|
3175 | |
---|
3176 | startIndices.clear(); |
---|
3177 | endIndices.clear(); |
---|
3178 | |
---|
3179 | if (mask[0]) { |
---|
3180 | startIndices.push_back(0); |
---|
3181 | } |
---|
3182 | for (int i = 1; i < maskSize; ++i) { |
---|
3183 | if ((!mask[i-1]) && mask[i]) { |
---|
3184 | startIndices.push_back(i); |
---|
3185 | } else if (mask[i-1] && (!mask[i])) { |
---|
3186 | endIndices.push_back(i-1); |
---|
3187 | } |
---|
3188 | } |
---|
3189 | if (mask[maskSize-1]) { |
---|
3190 | endIndices.push_back(maskSize-1); |
---|
3191 | } |
---|
3192 | |
---|
3193 | if (startIndices.size() != endIndices.size()) { |
---|
3194 | throw(AipsError("Inconsistent Mask Size: bad data?")); |
---|
3195 | } |
---|
3196 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
3197 | if (startIndices[i] > endIndices[i]) { |
---|
3198 | throw(AipsError("Mask start index > mask end index")); |
---|
3199 | } |
---|
3200 | } |
---|
3201 | |
---|
3202 | out.clear(); |
---|
3203 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
3204 | out.push_back(startIndices[i]); |
---|
3205 | out.push_back(endIndices[i]); |
---|
3206 | } |
---|
3207 | |
---|
3208 | return out; |
---|
3209 | } |
---|
3210 | |
---|
3211 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const |
---|
3212 | { |
---|
3213 | Vector<Float> tsys( tsysCol_(whichrow) ) ; |
---|
3214 | vector<float> stlTsys ; |
---|
3215 | tsys.tovector( stlTsys ) ; |
---|
3216 | return stlTsys ; |
---|
3217 | } |
---|
3218 | |
---|
3219 | |
---|
3220 | } |
---|
3221 | //namespace asap |
---|