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 | #include <sys/time.h> |
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14 | |
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15 | #include <atnf/PKSIO/SrcType.h> |
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16 | |
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17 | #include <casa/aips.h> |
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18 | #include <casa/iomanip.h> |
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19 | #include <casa/iostream.h> |
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20 | #include <casa/OS/File.h> |
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21 | #include <casa/OS/Path.h> |
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22 | #include <casa/Logging/LogIO.h> |
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23 | #include <casa/Arrays/Array.h> |
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24 | #include <casa/Arrays/ArrayAccessor.h> |
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25 | #include <casa/Arrays/ArrayLogical.h> |
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26 | #include <casa/Arrays/ArrayMath.h> |
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27 | #include <casa/Arrays/MaskArrMath.h> |
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28 | #include <casa/Arrays/Slice.h> |
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29 | #include <casa/Arrays/Vector.h> |
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30 | #include <casa/Arrays/VectorSTLIterator.h> |
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31 | #include <casa/BasicMath/Math.h> |
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32 | #include <casa/BasicSL/Constants.h> |
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33 | #include <casa/Containers/RecordField.h> |
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34 | #include <casa/Logging/LogIO.h> |
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35 | #include <casa/Quanta/MVAngle.h> |
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36 | #include <casa/Quanta/MVTime.h> |
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37 | #include <casa/Utilities/GenSort.h> |
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38 | |
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39 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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40 | |
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41 | // needed to avoid error in .tcc |
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42 | #include <measures/Measures/MCDirection.h> |
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43 | // |
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44 | #include <measures/Measures/MDirection.h> |
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45 | #include <measures/Measures/MEpoch.h> |
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46 | #include <measures/Measures/MFrequency.h> |
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47 | #include <measures/Measures/MeasRef.h> |
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48 | #include <measures/Measures/MeasTable.h> |
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49 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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50 | #include <measures/TableMeasures/TableMeasDesc.h> |
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51 | #include <measures/TableMeasures/TableMeasRefDesc.h> |
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52 | #include <measures/TableMeasures/TableMeasValueDesc.h> |
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53 | |
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54 | #include <tables/Tables/ArrColDesc.h> |
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55 | #include <tables/Tables/ExprNode.h> |
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56 | #include <tables/Tables/ScaColDesc.h> |
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57 | #include <tables/Tables/SetupNewTab.h> |
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58 | #include <tables/Tables/TableCopy.h> |
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59 | #include <tables/Tables/TableDesc.h> |
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60 | #include <tables/Tables/TableIter.h> |
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61 | #include <tables/Tables/TableParse.h> |
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62 | #include <tables/Tables/TableRecord.h> |
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63 | #include <tables/Tables/TableRow.h> |
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64 | #include <tables/Tables/TableVector.h> |
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65 | |
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66 | #include "MathUtils.h" |
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67 | #include "STAttr.h" |
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68 | #include "STLineFinder.h" |
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69 | #include "STPolCircular.h" |
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70 | #include "STPolLinear.h" |
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71 | #include "STPolStokes.h" |
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72 | #include "STUpgrade.h" |
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73 | #include "STFitter.h" |
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74 | #include "Scantable.h" |
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75 | |
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76 | #define debug 1 |
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77 | |
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78 | using namespace casa; |
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79 | |
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80 | namespace asap { |
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81 | |
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82 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_; |
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83 | |
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84 | void Scantable::initFactories() { |
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85 | if ( factories_.empty() ) { |
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86 | Scantable::factories_["linear"] = &STPolLinear::myFactory; |
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87 | Scantable::factories_["circular"] = &STPolCircular::myFactory; |
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88 | Scantable::factories_["stokes"] = &STPolStokes::myFactory; |
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89 | } |
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90 | } |
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91 | |
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92 | Scantable::Scantable(Table::TableType ttype) : |
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93 | type_(ttype) |
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94 | { |
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95 | initFactories(); |
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96 | setupMainTable(); |
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97 | freqTable_ = STFrequencies(*this); |
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98 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table()); |
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99 | weatherTable_ = STWeather(*this); |
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100 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table()); |
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101 | focusTable_ = STFocus(*this); |
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102 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table()); |
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103 | tcalTable_ = STTcal(*this); |
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104 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table()); |
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105 | moleculeTable_ = STMolecules(*this); |
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106 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table()); |
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107 | historyTable_ = STHistory(*this); |
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108 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table()); |
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109 | fitTable_ = STFit(*this); |
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110 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table()); |
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111 | table_.tableInfo().setType( "Scantable" ) ; |
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112 | originalTable_ = table_; |
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113 | attach(); |
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114 | } |
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115 | |
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116 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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117 | type_(ttype) |
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118 | { |
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119 | initFactories(); |
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120 | |
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121 | Table tab(name, Table::Update); |
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122 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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123 | if (version != version_) { |
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124 | STUpgrade upgrader(version_); |
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125 | LogIO os( LogOrigin( "Scantable" ) ) ; |
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126 | os << LogIO::WARN |
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127 | << name << " data format version " << version |
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128 | << " is deprecated" << endl |
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129 | << "Running upgrade."<< endl |
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130 | << LogIO::POST ; |
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131 | std::string outname = upgrader.upgrade(name); |
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132 | if ( outname != name ) { |
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133 | os << LogIO::WARN |
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134 | << "Data will be loaded from " << outname << " instead of " |
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135 | << name << LogIO::POST ; |
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136 | tab = Table(outname, Table::Update ) ; |
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137 | } |
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138 | } |
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139 | if ( type_ == Table::Memory ) { |
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140 | table_ = tab.copyToMemoryTable(generateName()); |
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141 | } else { |
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142 | table_ = tab; |
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143 | } |
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144 | table_.tableInfo().setType( "Scantable" ) ; |
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145 | |
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146 | attachSubtables(); |
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147 | originalTable_ = table_; |
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148 | attach(); |
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149 | } |
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150 | /* |
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151 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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152 | type_(ttype) |
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153 | { |
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154 | initFactories(); |
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155 | Table tab(name, Table::Update); |
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156 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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157 | if (version != version_) { |
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158 | throw(AipsError("Unsupported version of ASAP file.")); |
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159 | } |
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160 | if ( type_ == Table::Memory ) { |
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161 | table_ = tab.copyToMemoryTable(generateName()); |
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162 | } else { |
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163 | table_ = tab; |
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164 | } |
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165 | |
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166 | attachSubtables(); |
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167 | originalTable_ = table_; |
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168 | attach(); |
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169 | } |
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170 | */ |
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171 | |
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172 | Scantable::Scantable( const Scantable& other, bool clear ) |
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173 | { |
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174 | // with or without data |
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175 | String newname = String(generateName()); |
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176 | type_ = other.table_.tableType(); |
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177 | if ( other.table_.tableType() == Table::Memory ) { |
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178 | if ( clear ) { |
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179 | table_ = TableCopy::makeEmptyMemoryTable(newname, |
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180 | other.table_, True); |
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181 | } else |
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182 | table_ = other.table_.copyToMemoryTable(newname); |
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183 | } else { |
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184 | other.table_.deepCopy(newname, Table::New, False, |
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185 | other.table_.endianFormat(), |
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186 | Bool(clear)); |
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187 | table_ = Table(newname, Table::Update); |
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188 | table_.markForDelete(); |
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189 | } |
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190 | table_.tableInfo().setType( "Scantable" ) ; |
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191 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
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192 | if ( clear ) copySubtables(other); |
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193 | attachSubtables(); |
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194 | originalTable_ = table_; |
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195 | attach(); |
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196 | } |
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197 | |
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198 | void Scantable::copySubtables(const Scantable& other) { |
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199 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES"); |
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200 | TableCopy::copyRows(t, other.freqTable_.table()); |
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201 | t = table_.rwKeywordSet().asTable("FOCUS"); |
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202 | TableCopy::copyRows(t, other.focusTable_.table()); |
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203 | t = table_.rwKeywordSet().asTable("WEATHER"); |
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204 | TableCopy::copyRows(t, other.weatherTable_.table()); |
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205 | t = table_.rwKeywordSet().asTable("TCAL"); |
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206 | TableCopy::copyRows(t, other.tcalTable_.table()); |
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207 | t = table_.rwKeywordSet().asTable("MOLECULES"); |
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208 | TableCopy::copyRows(t, other.moleculeTable_.table()); |
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209 | t = table_.rwKeywordSet().asTable("HISTORY"); |
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210 | TableCopy::copyRows(t, other.historyTable_.table()); |
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211 | t = table_.rwKeywordSet().asTable("FIT"); |
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212 | TableCopy::copyRows(t, other.fitTable_.table()); |
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213 | } |
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214 | |
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215 | void Scantable::attachSubtables() |
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216 | { |
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217 | freqTable_ = STFrequencies(table_); |
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218 | focusTable_ = STFocus(table_); |
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219 | weatherTable_ = STWeather(table_); |
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220 | tcalTable_ = STTcal(table_); |
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221 | moleculeTable_ = STMolecules(table_); |
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222 | historyTable_ = STHistory(table_); |
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223 | fitTable_ = STFit(table_); |
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224 | } |
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225 | |
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226 | Scantable::~Scantable() |
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227 | { |
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228 | } |
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229 | |
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230 | void Scantable::setupMainTable() |
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231 | { |
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232 | TableDesc td("", "1", TableDesc::Scratch); |
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233 | td.comment() = "An ASAP Scantable"; |
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234 | td.rwKeywordSet().define("VERSION", uInt(version_)); |
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235 | |
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236 | // n Cycles |
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237 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO")); |
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238 | // new index every nBeam x nIF x nPol |
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239 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO")); |
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240 | |
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241 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO")); |
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242 | td.addColumn(ScalarColumnDesc<uInt>("IFNO")); |
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243 | // linear, circular, stokes |
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244 | td.rwKeywordSet().define("POLTYPE", String("linear")); |
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245 | td.addColumn(ScalarColumnDesc<uInt>("POLNO")); |
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246 | |
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247 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID")); |
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248 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID")); |
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249 | |
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250 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO"); |
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251 | refbeamnoColumn.setDefault(Int(-1)); |
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252 | td.addColumn(refbeamnoColumn); |
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253 | |
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254 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW"); |
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255 | flagrowColumn.setDefault(uInt(0)); |
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256 | td.addColumn(flagrowColumn); |
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257 | |
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258 | td.addColumn(ScalarColumnDesc<Double>("TIME")); |
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259 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default |
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260 | TableMeasValueDesc measVal(td, "TIME"); |
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261 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef); |
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262 | mepochCol.write(td); |
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263 | |
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264 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL")); |
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265 | |
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266 | td.addColumn(ScalarColumnDesc<String>("SRCNAME")); |
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267 | // Type of source (on=0, off=1, other=-1) |
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268 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE"); |
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269 | stypeColumn.setDefault(Int(-1)); |
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270 | td.addColumn(stypeColumn); |
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271 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME")); |
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272 | |
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273 | //The actual Data Vectors |
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274 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA")); |
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275 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA")); |
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276 | td.addColumn(ArrayColumnDesc<Float>("TSYS")); |
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277 | |
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278 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION", |
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279 | IPosition(1,2), |
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280 | ColumnDesc::Direct)); |
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281 | TableMeasRefDesc mdirRef(MDirection::J2000); // default |
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282 | TableMeasValueDesc tmvdMDir(td, "DIRECTION"); |
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283 | // the TableMeasDesc gives the column a type |
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284 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef); |
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285 | // a uder set table type e.g. GALCTIC, B1950 ... |
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286 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000")); |
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287 | // writing create the measure column |
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288 | mdirCol.write(td); |
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289 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH")); |
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290 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION")); |
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291 | td.addColumn(ScalarColumnDesc<Float>("OPACITY")); |
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292 | |
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293 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID")); |
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294 | ScalarColumnDesc<Int> fitColumn("FIT_ID"); |
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295 | fitColumn.setDefault(Int(-1)); |
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296 | td.addColumn(fitColumn); |
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297 | |
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298 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID")); |
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299 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID")); |
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300 | |
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301 | // columns which just get dragged along, as they aren't used in asap |
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302 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY")); |
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303 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION")); |
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304 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION")); |
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305 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE")); |
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306 | |
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307 | td.rwKeywordSet().define("OBSMODE", String("")); |
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308 | |
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309 | // Now create Table SetUp from the description. |
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310 | SetupNewTable aNewTab(generateName(), td, Table::Scratch); |
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311 | table_ = Table(aNewTab, type_, 0); |
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312 | originalTable_ = table_; |
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313 | } |
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314 | |
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315 | void Scantable::attach() |
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316 | { |
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317 | timeCol_.attach(table_, "TIME"); |
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318 | srcnCol_.attach(table_, "SRCNAME"); |
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319 | srctCol_.attach(table_, "SRCTYPE"); |
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320 | specCol_.attach(table_, "SPECTRA"); |
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321 | flagsCol_.attach(table_, "FLAGTRA"); |
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322 | tsysCol_.attach(table_, "TSYS"); |
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323 | cycleCol_.attach(table_,"CYCLENO"); |
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324 | scanCol_.attach(table_, "SCANNO"); |
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325 | beamCol_.attach(table_, "BEAMNO"); |
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326 | ifCol_.attach(table_, "IFNO"); |
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327 | polCol_.attach(table_, "POLNO"); |
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328 | integrCol_.attach(table_, "INTERVAL"); |
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329 | azCol_.attach(table_, "AZIMUTH"); |
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330 | elCol_.attach(table_, "ELEVATION"); |
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331 | dirCol_.attach(table_, "DIRECTION"); |
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332 | fldnCol_.attach(table_, "FIELDNAME"); |
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333 | rbeamCol_.attach(table_, "REFBEAMNO"); |
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334 | |
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335 | mweatheridCol_.attach(table_,"WEATHER_ID"); |
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336 | mfitidCol_.attach(table_,"FIT_ID"); |
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337 | mfreqidCol_.attach(table_, "FREQ_ID"); |
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338 | mtcalidCol_.attach(table_, "TCAL_ID"); |
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339 | mfocusidCol_.attach(table_, "FOCUS_ID"); |
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340 | mmolidCol_.attach(table_, "MOLECULE_ID"); |
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341 | |
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342 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki) |
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343 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0); |
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344 | |
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345 | } |
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346 | |
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347 | template<class T, class T2> |
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348 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col, |
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349 | const String& colName, |
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350 | const T2& defValue) |
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351 | { |
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352 | try { |
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353 | col.attach(table_, colName); |
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354 | } catch (TableError& err) { |
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355 | String errMesg = err.getMesg(); |
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356 | if (errMesg == "Table column " + colName + " is unknown") { |
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357 | table_.addColumn(ScalarColumnDesc<T>(colName)); |
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358 | col.attach(table_, colName); |
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359 | col.fillColumn(static_cast<T>(defValue)); |
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360 | } else { |
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361 | throw; |
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362 | } |
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363 | } catch (...) { |
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364 | throw; |
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365 | } |
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366 | } |
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367 | |
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368 | template<class T, class T2> |
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369 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col, |
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370 | const String& colName, |
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371 | const Array<T2>& defValue) |
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372 | { |
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373 | try { |
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374 | col.attach(table_, colName); |
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375 | } catch (TableError& err) { |
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376 | String errMesg = err.getMesg(); |
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377 | if (errMesg == "Table column " + colName + " is unknown") { |
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378 | table_.addColumn(ArrayColumnDesc<T>(colName)); |
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379 | col.attach(table_, colName); |
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380 | |
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381 | int size = 0; |
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382 | ArrayIterator<T2>& it = defValue.begin(); |
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383 | while (it != defValue.end()) { |
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384 | ++size; |
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385 | ++it; |
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386 | } |
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387 | IPosition ip(1, size); |
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388 | Array<T>& arr(ip); |
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389 | for (int i = 0; i < size; ++i) |
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390 | arr[i] = static_cast<T>(defValue[i]); |
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391 | |
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392 | col.fillColumn(arr); |
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393 | } else { |
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394 | throw; |
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395 | } |
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396 | } catch (...) { |
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397 | throw; |
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398 | } |
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399 | } |
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400 | |
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401 | void Scantable::setHeader(const STHeader& sdh) |
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402 | { |
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403 | table_.rwKeywordSet().define("nIF", sdh.nif); |
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404 | table_.rwKeywordSet().define("nBeam", sdh.nbeam); |
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405 | table_.rwKeywordSet().define("nPol", sdh.npol); |
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406 | table_.rwKeywordSet().define("nChan", sdh.nchan); |
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407 | table_.rwKeywordSet().define("Observer", sdh.observer); |
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408 | table_.rwKeywordSet().define("Project", sdh.project); |
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409 | table_.rwKeywordSet().define("Obstype", sdh.obstype); |
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410 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname); |
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411 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition); |
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412 | table_.rwKeywordSet().define("Equinox", sdh.equinox); |
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413 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref); |
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414 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq); |
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415 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth); |
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416 | table_.rwKeywordSet().define("UTC", sdh.utc); |
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417 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit); |
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418 | table_.rwKeywordSet().define("Epoch", sdh.epoch); |
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419 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype); |
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420 | } |
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421 | |
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422 | STHeader Scantable::getHeader() const |
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423 | { |
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424 | STHeader sdh; |
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425 | table_.keywordSet().get("nBeam",sdh.nbeam); |
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426 | table_.keywordSet().get("nIF",sdh.nif); |
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427 | table_.keywordSet().get("nPol",sdh.npol); |
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428 | table_.keywordSet().get("nChan",sdh.nchan); |
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429 | table_.keywordSet().get("Observer", sdh.observer); |
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430 | table_.keywordSet().get("Project", sdh.project); |
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431 | table_.keywordSet().get("Obstype", sdh.obstype); |
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432 | table_.keywordSet().get("AntennaName", sdh.antennaname); |
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433 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition); |
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434 | table_.keywordSet().get("Equinox", sdh.equinox); |
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435 | table_.keywordSet().get("FreqRefFrame", sdh.freqref); |
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436 | table_.keywordSet().get("FreqRefVal", sdh.reffreq); |
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437 | table_.keywordSet().get("Bandwidth", sdh.bandwidth); |
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438 | table_.keywordSet().get("UTC", sdh.utc); |
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439 | table_.keywordSet().get("FluxUnit", sdh.fluxunit); |
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440 | table_.keywordSet().get("Epoch", sdh.epoch); |
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441 | table_.keywordSet().get("POLTYPE", sdh.poltype); |
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442 | return sdh; |
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443 | } |
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444 | |
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445 | void Scantable::setSourceType( int stype ) |
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446 | { |
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447 | if ( stype < 0 || stype > 1 ) |
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448 | throw(AipsError("Illegal sourcetype.")); |
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449 | TableVector<Int> tabvec(table_, "SRCTYPE"); |
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450 | tabvec = Int(stype); |
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451 | } |
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452 | |
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453 | bool Scantable::conformant( const Scantable& other ) |
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454 | { |
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455 | return this->getHeader().conformant(other.getHeader()); |
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456 | } |
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457 | |
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458 | |
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459 | |
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460 | std::string Scantable::formatSec(Double x) const |
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461 | { |
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462 | Double xcop = x; |
---|
463 | MVTime mvt(xcop/24./3600.); // make days |
---|
464 | |
---|
465 | if (x < 59.95) |
---|
466 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s"; |
---|
467 | else if (x < 3599.95) |
---|
468 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" "; |
---|
469 | else { |
---|
470 | ostringstream oss; |
---|
471 | oss << setw(2) << std::right << setprecision(1) << mvt.hour(); |
---|
472 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " "; |
---|
473 | return String(oss); |
---|
474 | } |
---|
475 | }; |
---|
476 | |
---|
477 | std::string Scantable::formatDirection(const MDirection& md) const |
---|
478 | { |
---|
479 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue(); |
---|
480 | Int prec = 7; |
---|
481 | |
---|
482 | String ref = md.getRefString(); |
---|
483 | MVAngle mvLon(t[0]); |
---|
484 | String sLon = mvLon.string(MVAngle::TIME,prec); |
---|
485 | uInt tp = md.getRef().getType(); |
---|
486 | if (tp == MDirection::GALACTIC || |
---|
487 | tp == MDirection::SUPERGAL ) { |
---|
488 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec); |
---|
489 | } |
---|
490 | MVAngle mvLat(t[1]); |
---|
491 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec); |
---|
492 | return ref + String(" ") + sLon + String(" ") + sLat; |
---|
493 | } |
---|
494 | |
---|
495 | |
---|
496 | std::string Scantable::getFluxUnit() const |
---|
497 | { |
---|
498 | return table_.keywordSet().asString("FluxUnit"); |
---|
499 | } |
---|
500 | |
---|
501 | void Scantable::setFluxUnit(const std::string& unit) |
---|
502 | { |
---|
503 | String tmp(unit); |
---|
504 | Unit tU(tmp); |
---|
505 | if (tU==Unit("K") || tU==Unit("Jy")) { |
---|
506 | table_.rwKeywordSet().define(String("FluxUnit"), tmp); |
---|
507 | } else { |
---|
508 | throw AipsError("Illegal unit - must be compatible with Jy or K"); |
---|
509 | } |
---|
510 | } |
---|
511 | |
---|
512 | void Scantable::setInstrument(const std::string& name) |
---|
513 | { |
---|
514 | bool throwIt = true; |
---|
515 | // create an Instrument to see if this is valid |
---|
516 | STAttr::convertInstrument(name, throwIt); |
---|
517 | String nameU(name); |
---|
518 | nameU.upcase(); |
---|
519 | table_.rwKeywordSet().define(String("AntennaName"), nameU); |
---|
520 | } |
---|
521 | |
---|
522 | void Scantable::setFeedType(const std::string& feedtype) |
---|
523 | { |
---|
524 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) { |
---|
525 | std::string msg = "Illegal feed type "+ feedtype; |
---|
526 | throw(casa::AipsError(msg)); |
---|
527 | } |
---|
528 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype); |
---|
529 | } |
---|
530 | |
---|
531 | MPosition Scantable::getAntennaPosition() const |
---|
532 | { |
---|
533 | Vector<Double> antpos; |
---|
534 | table_.keywordSet().get("AntennaPosition", antpos); |
---|
535 | MVPosition mvpos(antpos(0),antpos(1),antpos(2)); |
---|
536 | return MPosition(mvpos); |
---|
537 | } |
---|
538 | |
---|
539 | void Scantable::makePersistent(const std::string& filename) |
---|
540 | { |
---|
541 | String inname(filename); |
---|
542 | Path path(inname); |
---|
543 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
---|
544 | inname = path.expandedName(); |
---|
545 | // 2011/03/04 TN |
---|
546 | // We can comment out this workaround since the essential bug is |
---|
547 | // fixed in casacore (r20889 in google code). |
---|
548 | table_.deepCopy(inname, Table::New); |
---|
549 | // // WORKAROUND !!! for Table bug |
---|
550 | // // Remove when fixed in casacore |
---|
551 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) { |
---|
552 | // Table tab = table_.copyToMemoryTable(generateName()); |
---|
553 | // tab.deepCopy(inname, Table::New); |
---|
554 | // tab.markForDelete(); |
---|
555 | // |
---|
556 | // } else { |
---|
557 | // table_.deepCopy(inname, Table::New); |
---|
558 | // } |
---|
559 | } |
---|
560 | |
---|
561 | int Scantable::nbeam( int scanno ) const |
---|
562 | { |
---|
563 | if ( scanno < 0 ) { |
---|
564 | Int n; |
---|
565 | table_.keywordSet().get("nBeam",n); |
---|
566 | return int(n); |
---|
567 | } else { |
---|
568 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
569 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
570 | ROTableRow row(t); |
---|
571 | const TableRecord& rec = row.get(0); |
---|
572 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
573 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
574 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
575 | ROTableVector<uInt> v(subt, "BEAMNO"); |
---|
576 | return int(v.nelements()); |
---|
577 | } |
---|
578 | return 0; |
---|
579 | } |
---|
580 | |
---|
581 | int Scantable::nif( int scanno ) const |
---|
582 | { |
---|
583 | if ( scanno < 0 ) { |
---|
584 | Int n; |
---|
585 | table_.keywordSet().get("nIF",n); |
---|
586 | return int(n); |
---|
587 | } else { |
---|
588 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these |
---|
589 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
590 | ROTableRow row(t); |
---|
591 | const TableRecord& rec = row.get(0); |
---|
592 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
593 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
594 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
595 | if ( subt.nrow() == 0 ) return 0; |
---|
596 | ROTableVector<uInt> v(subt, "IFNO"); |
---|
597 | return int(v.nelements()); |
---|
598 | } |
---|
599 | return 0; |
---|
600 | } |
---|
601 | |
---|
602 | int Scantable::npol( int scanno ) const |
---|
603 | { |
---|
604 | if ( scanno < 0 ) { |
---|
605 | Int n; |
---|
606 | table_.keywordSet().get("nPol",n); |
---|
607 | return n; |
---|
608 | } else { |
---|
609 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
610 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
611 | ROTableRow row(t); |
---|
612 | const TableRecord& rec = row.get(0); |
---|
613 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
614 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
615 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
616 | if ( subt.nrow() == 0 ) return 0; |
---|
617 | ROTableVector<uInt> v(subt, "POLNO"); |
---|
618 | return int(v.nelements()); |
---|
619 | } |
---|
620 | return 0; |
---|
621 | } |
---|
622 | |
---|
623 | int Scantable::ncycle( int scanno ) const |
---|
624 | { |
---|
625 | if ( scanno < 0 ) { |
---|
626 | Block<String> cols(2); |
---|
627 | cols[0] = "SCANNO"; |
---|
628 | cols[1] = "CYCLENO"; |
---|
629 | TableIterator it(table_, cols); |
---|
630 | int n = 0; |
---|
631 | while ( !it.pastEnd() ) { |
---|
632 | ++n; |
---|
633 | ++it; |
---|
634 | } |
---|
635 | return n; |
---|
636 | } else { |
---|
637 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
638 | ROTableRow row(t); |
---|
639 | const TableRecord& rec = row.get(0); |
---|
640 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
641 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
642 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) ); |
---|
643 | if ( subt.nrow() == 0 ) return 0; |
---|
644 | return int(subt.nrow()); |
---|
645 | } |
---|
646 | return 0; |
---|
647 | } |
---|
648 | |
---|
649 | |
---|
650 | int Scantable::nrow( int scanno ) const |
---|
651 | { |
---|
652 | return int(table_.nrow()); |
---|
653 | } |
---|
654 | |
---|
655 | int Scantable::nchan( int ifno ) const |
---|
656 | { |
---|
657 | if ( ifno < 0 ) { |
---|
658 | Int n; |
---|
659 | table_.keywordSet().get("nChan",n); |
---|
660 | return int(n); |
---|
661 | } else { |
---|
662 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't |
---|
663 | // vary with these |
---|
664 | Table t = table_(table_.col("IFNO") == ifno, 1); |
---|
665 | if ( t.nrow() == 0 ) return 0; |
---|
666 | ROArrayColumn<Float> v(t, "SPECTRA"); |
---|
667 | return v.shape(0)(0); |
---|
668 | } |
---|
669 | return 0; |
---|
670 | } |
---|
671 | |
---|
672 | int Scantable::nscan() const { |
---|
673 | Vector<uInt> scannos(scanCol_.getColumn()); |
---|
674 | uInt nout = genSort( scannos, Sort::Ascending, |
---|
675 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
676 | return int(nout); |
---|
677 | } |
---|
678 | |
---|
679 | int Scantable::getChannels(int whichrow) const |
---|
680 | { |
---|
681 | return specCol_.shape(whichrow)(0); |
---|
682 | } |
---|
683 | |
---|
684 | int Scantable::getBeam(int whichrow) const |
---|
685 | { |
---|
686 | return beamCol_(whichrow); |
---|
687 | } |
---|
688 | |
---|
689 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const |
---|
690 | { |
---|
691 | Vector<uInt> nos(col.getColumn()); |
---|
692 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates ); |
---|
693 | nos.resize(n, True); |
---|
694 | std::vector<uint> stlout; |
---|
695 | nos.tovector(stlout); |
---|
696 | return stlout; |
---|
697 | } |
---|
698 | |
---|
699 | int Scantable::getIF(int whichrow) const |
---|
700 | { |
---|
701 | return ifCol_(whichrow); |
---|
702 | } |
---|
703 | |
---|
704 | int Scantable::getPol(int whichrow) const |
---|
705 | { |
---|
706 | return polCol_(whichrow); |
---|
707 | } |
---|
708 | |
---|
709 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const |
---|
710 | { |
---|
711 | return formatTime(me, showdate, 0); |
---|
712 | } |
---|
713 | |
---|
714 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const |
---|
715 | { |
---|
716 | MVTime mvt(me.getValue()); |
---|
717 | if (showdate) |
---|
718 | //mvt.setFormat(MVTime::YMD); |
---|
719 | mvt.setFormat(MVTime::YMD, prec); |
---|
720 | else |
---|
721 | //mvt.setFormat(MVTime::TIME); |
---|
722 | mvt.setFormat(MVTime::TIME, prec); |
---|
723 | ostringstream oss; |
---|
724 | oss << mvt; |
---|
725 | return String(oss); |
---|
726 | } |
---|
727 | |
---|
728 | void Scantable::calculateAZEL() |
---|
729 | { |
---|
730 | LogIO os( LogOrigin( "Scantable", "calculateAZEL()", WHERE ) ) ; |
---|
731 | MPosition mp = getAntennaPosition(); |
---|
732 | MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
733 | ostringstream oss; |
---|
734 | oss << mp; |
---|
735 | os << "Computed azimuth/elevation using " << endl |
---|
736 | << String(oss) << endl; |
---|
737 | for (Int i=0; i<nrow(); ++i) { |
---|
738 | MEpoch me = timeCol(i); |
---|
739 | MDirection md = getDirection(i); |
---|
740 | os << " Time: " << formatTime(me,False) |
---|
741 | << " Direction: " << formatDirection(md) |
---|
742 | << endl << " => "; |
---|
743 | MeasFrame frame(mp, me); |
---|
744 | Vector<Double> azel = |
---|
745 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL, |
---|
746 | frame) |
---|
747 | )().getAngle("rad").getValue(); |
---|
748 | azCol_.put(i,Float(azel[0])); |
---|
749 | elCol_.put(i,Float(azel[1])); |
---|
750 | os << "azel: " << azel[0]/C::pi*180.0 << " " |
---|
751 | << azel[1]/C::pi*180.0 << " (deg)" << LogIO::POST; |
---|
752 | } |
---|
753 | } |
---|
754 | |
---|
755 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
756 | { |
---|
757 | for (uInt i=0; i<table_.nrow(); ++i) { |
---|
758 | Vector<uChar> flgs = flagsCol_(i); |
---|
759 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs); |
---|
760 | flagsCol_.put(i, flgs); |
---|
761 | } |
---|
762 | } |
---|
763 | |
---|
764 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
765 | { |
---|
766 | Vector<uChar> flags; |
---|
767 | flagsCol_.get(uInt(whichrow), flags); |
---|
768 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags); |
---|
769 | Vector<Bool> bflag(flags.shape()); |
---|
770 | convertArray(bflag, flags); |
---|
771 | //bflag = !bflag; |
---|
772 | |
---|
773 | std::vector<bool> mask; |
---|
774 | bflag.tovector(mask); |
---|
775 | return mask; |
---|
776 | } |
---|
777 | |
---|
778 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag, |
---|
779 | Vector<uChar> flgs) |
---|
780 | { |
---|
781 | Vector<Float> spcs = specCol_(whichrow); |
---|
782 | uInt nchannel = spcs.nelements(); |
---|
783 | if (spcs.nelements() != nchannel) { |
---|
784 | throw(AipsError("Data has incorrect number of channels")); |
---|
785 | } |
---|
786 | uChar userflag = 1 << 7; |
---|
787 | if (unflag) { |
---|
788 | userflag = 0 << 7; |
---|
789 | } |
---|
790 | if (clipoutside) { |
---|
791 | for (uInt j = 0; j < nchannel; ++j) { |
---|
792 | Float spc = spcs(j); |
---|
793 | if ((spc >= uthres) || (spc <= dthres)) { |
---|
794 | flgs(j) = userflag; |
---|
795 | } |
---|
796 | } |
---|
797 | } else { |
---|
798 | for (uInt j = 0; j < nchannel; ++j) { |
---|
799 | Float spc = spcs(j); |
---|
800 | if ((spc < uthres) && (spc > dthres)) { |
---|
801 | flgs(j) = userflag; |
---|
802 | } |
---|
803 | } |
---|
804 | } |
---|
805 | } |
---|
806 | |
---|
807 | |
---|
808 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) { |
---|
809 | std::vector<bool>::const_iterator it; |
---|
810 | uInt ntrue = 0; |
---|
811 | if (whichrow >= int(table_.nrow()) ) { |
---|
812 | throw(AipsError("Invalid row number")); |
---|
813 | } |
---|
814 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
815 | if ( *it ) { |
---|
816 | ntrue++; |
---|
817 | } |
---|
818 | } |
---|
819 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
820 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
821 | throw(AipsError("Trying to flag whole scantable.")); |
---|
822 | uChar userflag = 1 << 7; |
---|
823 | if ( unflag ) { |
---|
824 | userflag = 0 << 7; |
---|
825 | } |
---|
826 | if (whichrow > -1 ) { |
---|
827 | applyChanFlag(uInt(whichrow), msk, userflag); |
---|
828 | } else { |
---|
829 | for ( uInt i=0; i<table_.nrow(); ++i) { |
---|
830 | applyChanFlag(i, msk, userflag); |
---|
831 | } |
---|
832 | } |
---|
833 | } |
---|
834 | |
---|
835 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval ) |
---|
836 | { |
---|
837 | if (whichrow >= table_.nrow() ) { |
---|
838 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) ); |
---|
839 | } |
---|
840 | Vector<uChar> flgs = flagsCol_(whichrow); |
---|
841 | if ( msk.size() == 0 ) { |
---|
842 | flgs = flagval; |
---|
843 | flagsCol_.put(whichrow, flgs); |
---|
844 | return; |
---|
845 | } |
---|
846 | if ( int(msk.size()) != nchan( getIF(whichrow) ) ) { |
---|
847 | throw(AipsError("Mask has incorrect number of channels.")); |
---|
848 | } |
---|
849 | if ( flgs.nelements() != msk.size() ) { |
---|
850 | throw(AipsError("Mask has incorrect number of channels." |
---|
851 | " Probably varying with IF. Please flag per IF")); |
---|
852 | } |
---|
853 | std::vector<bool>::const_iterator it; |
---|
854 | uInt j = 0; |
---|
855 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
856 | if ( *it ) { |
---|
857 | flgs(j) = flagval; |
---|
858 | } |
---|
859 | ++j; |
---|
860 | } |
---|
861 | flagsCol_.put(whichrow, flgs); |
---|
862 | } |
---|
863 | |
---|
864 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag) |
---|
865 | { |
---|
866 | if (selector_.empty() && (rows.size() == table_.nrow()) && !unflag) |
---|
867 | throw(AipsError("Trying to flag whole scantable.")); |
---|
868 | |
---|
869 | uInt rowflag = (unflag ? 0 : 1); |
---|
870 | std::vector<uInt>::const_iterator it; |
---|
871 | for (it = rows.begin(); it != rows.end(); ++it) |
---|
872 | flagrowCol_.put(*it, rowflag); |
---|
873 | } |
---|
874 | |
---|
875 | std::vector<bool> Scantable::getMask(int whichrow) const |
---|
876 | { |
---|
877 | Vector<uChar> flags; |
---|
878 | flagsCol_.get(uInt(whichrow), flags); |
---|
879 | Vector<Bool> bflag(flags.shape()); |
---|
880 | convertArray(bflag, flags); |
---|
881 | bflag = !bflag; |
---|
882 | std::vector<bool> mask; |
---|
883 | bflag.tovector(mask); |
---|
884 | return mask; |
---|
885 | } |
---|
886 | |
---|
887 | std::vector<float> Scantable::getSpectrum( int whichrow, |
---|
888 | const std::string& poltype ) const |
---|
889 | { |
---|
890 | LogIO os( LogOrigin( "Scantable", "getSpectrum()", WHERE ) ) ; |
---|
891 | |
---|
892 | String ptype = poltype; |
---|
893 | if (poltype == "" ) ptype = getPolType(); |
---|
894 | if ( whichrow < 0 || whichrow >= nrow() ) |
---|
895 | throw(AipsError("Illegal row number.")); |
---|
896 | std::vector<float> out; |
---|
897 | Vector<Float> arr; |
---|
898 | uInt requestedpol = polCol_(whichrow); |
---|
899 | String basetype = getPolType(); |
---|
900 | if ( ptype == basetype ) { |
---|
901 | specCol_.get(whichrow, arr); |
---|
902 | } else { |
---|
903 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_, |
---|
904 | basetype)); |
---|
905 | uInt row = uInt(whichrow); |
---|
906 | stpol->setSpectra(getPolMatrix(row)); |
---|
907 | Float fang,fhand; |
---|
908 | fang = focusTable_.getTotalAngle(mfocusidCol_(row)); |
---|
909 | fhand = focusTable_.getFeedHand(mfocusidCol_(row)); |
---|
910 | stpol->setPhaseCorrections(fang, fhand); |
---|
911 | arr = stpol->getSpectrum(requestedpol, ptype); |
---|
912 | } |
---|
913 | if ( arr.nelements() == 0 ) |
---|
914 | |
---|
915 | os << "Not enough polarisations present to do the conversion." |
---|
916 | << LogIO::POST; |
---|
917 | arr.tovector(out); |
---|
918 | return out; |
---|
919 | } |
---|
920 | |
---|
921 | void Scantable::setSpectrum( const std::vector<float>& spec, |
---|
922 | int whichrow ) |
---|
923 | { |
---|
924 | Vector<Float> spectrum(spec); |
---|
925 | Vector<Float> arr; |
---|
926 | specCol_.get(whichrow, arr); |
---|
927 | if ( spectrum.nelements() != arr.nelements() ) |
---|
928 | throw AipsError("The spectrum has incorrect number of channels."); |
---|
929 | specCol_.put(whichrow, spectrum); |
---|
930 | } |
---|
931 | |
---|
932 | |
---|
933 | String Scantable::generateName() |
---|
934 | { |
---|
935 | return (File::newUniqueName("./","temp")).baseName(); |
---|
936 | } |
---|
937 | |
---|
938 | const casa::Table& Scantable::table( ) const |
---|
939 | { |
---|
940 | return table_; |
---|
941 | } |
---|
942 | |
---|
943 | casa::Table& Scantable::table( ) |
---|
944 | { |
---|
945 | return table_; |
---|
946 | } |
---|
947 | |
---|
948 | std::string Scantable::getPolType() const |
---|
949 | { |
---|
950 | return table_.keywordSet().asString("POLTYPE"); |
---|
951 | } |
---|
952 | |
---|
953 | void Scantable::unsetSelection() |
---|
954 | { |
---|
955 | table_ = originalTable_; |
---|
956 | attach(); |
---|
957 | selector_.reset(); |
---|
958 | } |
---|
959 | |
---|
960 | void Scantable::setSelection( const STSelector& selection ) |
---|
961 | { |
---|
962 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_); |
---|
963 | if ( tab.nrow() == 0 ) { |
---|
964 | throw(AipsError("Selection contains no data. Not applying it.")); |
---|
965 | } |
---|
966 | table_ = tab; |
---|
967 | attach(); |
---|
968 | // tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ; |
---|
969 | // vector<uint> selectedIFs = getIFNos() ; |
---|
970 | // Int newnIF = selectedIFs.size() ; |
---|
971 | // tab.rwKeywordSet().define("nIF",newnIF) ; |
---|
972 | // if ( newnIF != 0 ) { |
---|
973 | // Int newnChan = 0 ; |
---|
974 | // for ( Int i = 0 ; i < newnIF ; i++ ) { |
---|
975 | // Int nChan = nchan( selectedIFs[i] ) ; |
---|
976 | // if ( newnChan > nChan ) |
---|
977 | // newnChan = nChan ; |
---|
978 | // } |
---|
979 | // tab.rwKeywordSet().define("nChan",newnChan) ; |
---|
980 | // } |
---|
981 | // tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ; |
---|
982 | selector_ = selection; |
---|
983 | } |
---|
984 | |
---|
985 | |
---|
986 | std::string Scantable::headerSummary() |
---|
987 | { |
---|
988 | // Format header info |
---|
989 | // STHeader sdh; |
---|
990 | // sdh = getHeader(); |
---|
991 | // sdh.print(); |
---|
992 | ostringstream oss; |
---|
993 | oss.flags(std::ios_base::left); |
---|
994 | String tmp; |
---|
995 | // Project |
---|
996 | table_.keywordSet().get("Project", tmp); |
---|
997 | oss << setw(15) << "Project:" << tmp << endl; |
---|
998 | // Observation date |
---|
999 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
1000 | // Observer |
---|
1001 | oss << setw(15) << "Observer:" |
---|
1002 | << table_.keywordSet().asString("Observer") << endl; |
---|
1003 | // Antenna Name |
---|
1004 | table_.keywordSet().get("AntennaName", tmp); |
---|
1005 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
1006 | // Obs type |
---|
1007 | table_.keywordSet().get("Obstype", tmp); |
---|
1008 | // Records (nrow) |
---|
1009 | oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl; |
---|
1010 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
1011 | // Beams, IFs, Polarizations, and Channels |
---|
1012 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
1013 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
1014 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
1015 | << "(" << getPolType() << ")" << endl |
---|
1016 | << setw(15) << "Channels:" << nchan() << endl; |
---|
1017 | // Flux unit |
---|
1018 | table_.keywordSet().get("FluxUnit", tmp); |
---|
1019 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
1020 | // Abscissa Unit |
---|
1021 | oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl; |
---|
1022 | // Selection |
---|
1023 | oss << selector_.print() << endl; |
---|
1024 | |
---|
1025 | return String(oss); |
---|
1026 | } |
---|
1027 | |
---|
1028 | void Scantable::summary( const std::string& filename ) |
---|
1029 | { |
---|
1030 | ostringstream oss; |
---|
1031 | ofstream ofs; |
---|
1032 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
1033 | |
---|
1034 | if (filename != "") |
---|
1035 | ofs.open( filename.c_str(), ios::out ); |
---|
1036 | |
---|
1037 | oss << endl; |
---|
1038 | oss << asap::SEPERATOR << endl; |
---|
1039 | oss << " Scan Table Summary" << endl; |
---|
1040 | oss << asap::SEPERATOR << endl; |
---|
1041 | |
---|
1042 | // Format header info |
---|
1043 | oss << headerSummary(); |
---|
1044 | oss << endl; |
---|
1045 | |
---|
1046 | if (table_.nrow() <= 0){ |
---|
1047 | oss << asap::SEPERATOR << endl; |
---|
1048 | oss << "The MAIN table is empty: there are no data!!!" << endl; |
---|
1049 | oss << asap::SEPERATOR << endl; |
---|
1050 | |
---|
1051 | ols << String(oss) << LogIO::POST; |
---|
1052 | if (ofs) { |
---|
1053 | ofs << String(oss) << flush; |
---|
1054 | ofs.close(); |
---|
1055 | } |
---|
1056 | return; |
---|
1057 | } |
---|
1058 | |
---|
1059 | |
---|
1060 | |
---|
1061 | // main table |
---|
1062 | String dirtype = "Position (" |
---|
1063 | + getDirectionRefString() |
---|
1064 | + ")"; |
---|
1065 | oss.flags(std::ios_base::left); |
---|
1066 | oss << setw(5) << "Scan" |
---|
1067 | << setw(15) << "Source" |
---|
1068 | << setw(35) << "Time range" |
---|
1069 | << setw(2) << "" << setw(7) << "Int[s]" |
---|
1070 | << setw(7) << "Record" |
---|
1071 | << setw(8) << "SrcType" |
---|
1072 | << setw(8) << "FreqIDs" |
---|
1073 | << setw(7) << "MolIDs" << endl; |
---|
1074 | oss << setw(7)<< "" << setw(6) << "Beam" |
---|
1075 | << setw(23) << dirtype << endl; |
---|
1076 | |
---|
1077 | oss << asap::SEPERATOR << endl; |
---|
1078 | |
---|
1079 | // Flush summary and clear up the string |
---|
1080 | ols << String(oss) << LogIO::POST; |
---|
1081 | if (ofs) ofs << String(oss) << flush; |
---|
1082 | oss.str(""); |
---|
1083 | oss.clear(); |
---|
1084 | |
---|
1085 | |
---|
1086 | // Get Freq_ID map |
---|
1087 | ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID"); |
---|
1088 | Int nfid = ftabIds.nrow(); |
---|
1089 | if (nfid <= 0){ |
---|
1090 | oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl; |
---|
1091 | oss << asap::SEPERATOR << endl; |
---|
1092 | |
---|
1093 | ols << String(oss) << LogIO::POST; |
---|
1094 | if (ofs) { |
---|
1095 | ofs << String(oss) << flush; |
---|
1096 | ofs.close(); |
---|
1097 | } |
---|
1098 | return; |
---|
1099 | } |
---|
1100 | // Storages of overall IFNO, POLNO, and nchan per FREQ_ID |
---|
1101 | // the orders are identical to ID in FREQ subtable |
---|
1102 | Block< Vector<uInt> > ifNos(nfid), polNos(nfid); |
---|
1103 | Vector<Int> fIdchans(nfid,-1); |
---|
1104 | map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair |
---|
1105 | for (Int i=0; i < nfid; i++){ |
---|
1106 | // fidMap[freqId] returns row number in FREQ subtable |
---|
1107 | fidMap.insert(pair<uInt, Int>(ftabIds(i),i)); |
---|
1108 | ifNos[i] = Vector<uInt>(); |
---|
1109 | polNos[i] = Vector<uInt>(); |
---|
1110 | } |
---|
1111 | |
---|
1112 | TableIterator iter(table_, "SCANNO"); |
---|
1113 | |
---|
1114 | // Vars for keeping track of time, freqids, molIds in a SCANNO |
---|
1115 | Vector<uInt> freqids; |
---|
1116 | Vector<uInt> molids; |
---|
1117 | Vector<uInt> beamids(1,0); |
---|
1118 | Vector<MDirection> beamDirs; |
---|
1119 | Vector<Int> stypeids(1,0); |
---|
1120 | Vector<String> stypestrs; |
---|
1121 | Int nfreq(1); |
---|
1122 | Int nmol(1); |
---|
1123 | uInt nbeam(1); |
---|
1124 | uInt nstype(1); |
---|
1125 | |
---|
1126 | Double btime(0.0), etime(0.0); |
---|
1127 | Double meanIntTim(0.0); |
---|
1128 | |
---|
1129 | uInt currFreqId(0), ftabRow(0); |
---|
1130 | Int iflen(0), pollen(0); |
---|
1131 | |
---|
1132 | while (!iter.pastEnd()) { |
---|
1133 | Table subt = iter.table(); |
---|
1134 | uInt snrow = subt.nrow(); |
---|
1135 | ROTableRow row(subt); |
---|
1136 | const TableRecord& rec = row.get(0); |
---|
1137 | |
---|
1138 | // relevant columns |
---|
1139 | ROScalarColumn<Double> mjdCol(subt,"TIME"); |
---|
1140 | ROScalarColumn<Double> intervalCol(subt,"INTERVAL"); |
---|
1141 | MDirection::ROScalarColumn dirCol(subt,"DIRECTION"); |
---|
1142 | |
---|
1143 | ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID"); |
---|
1144 | ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID"); |
---|
1145 | ROScalarColumn<uInt> beamCol(subt,"BEAMNO"); |
---|
1146 | ROScalarColumn<Int> stypeCol(subt,"SRCTYPE"); |
---|
1147 | |
---|
1148 | ROScalarColumn<uInt> ifNoCol(subt,"IFNO"); |
---|
1149 | ROScalarColumn<uInt> polNoCol(subt,"POLNO"); |
---|
1150 | |
---|
1151 | |
---|
1152 | // Times |
---|
1153 | meanIntTim = sum(intervalCol.getColumn()) / (double) snrow; |
---|
1154 | minMax(btime, etime, mjdCol.getColumn()); |
---|
1155 | etime += meanIntTim/C::day; |
---|
1156 | |
---|
1157 | // MOLECULE_ID and FREQ_ID |
---|
1158 | molids = getNumbers(molIdCol); |
---|
1159 | molids.shape(nmol); |
---|
1160 | |
---|
1161 | freqids = getNumbers(freqIdCol); |
---|
1162 | freqids.shape(nfreq); |
---|
1163 | |
---|
1164 | // Add first beamid, and srcNames |
---|
1165 | beamids.resize(1,False); |
---|
1166 | beamDirs.resize(1,False); |
---|
1167 | beamids(0)=beamCol(0); |
---|
1168 | beamDirs(0)=dirCol(0); |
---|
1169 | nbeam = 1; |
---|
1170 | |
---|
1171 | stypeids.resize(1,False); |
---|
1172 | stypeids(0)=stypeCol(0); |
---|
1173 | nstype = 1; |
---|
1174 | |
---|
1175 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
1176 | currFreqId=freqIdCol(0); |
---|
1177 | ftabRow = fidMap[currFreqId]; |
---|
1178 | // Assumes an identical number of channels per FREQ_ID |
---|
1179 | if (fIdchans(ftabRow) < 0 ) { |
---|
1180 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
1181 | fIdchans(ftabRow)=(*spec).shape()(0); |
---|
1182 | } |
---|
1183 | // Should keep ifNos and polNos form the previous SCANNO |
---|
1184 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) { |
---|
1185 | ifNos[ftabRow].shape(iflen); |
---|
1186 | iflen++; |
---|
1187 | ifNos[ftabRow].resize(iflen,True); |
---|
1188 | ifNos[ftabRow](iflen-1) = ifNoCol(0); |
---|
1189 | } |
---|
1190 | if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) { |
---|
1191 | polNos[ftabRow].shape(pollen); |
---|
1192 | pollen++; |
---|
1193 | polNos[ftabRow].resize(pollen,True); |
---|
1194 | polNos[ftabRow](pollen-1) = polNoCol(0); |
---|
1195 | } |
---|
1196 | |
---|
1197 | for (uInt i=1; i < snrow; i++){ |
---|
1198 | // Need to list BEAMNO and DIRECTION in the same order |
---|
1199 | if ( !anyEQ(beamids,beamCol(i)) ) { |
---|
1200 | nbeam++; |
---|
1201 | beamids.resize(nbeam,True); |
---|
1202 | beamids(nbeam-1)=beamCol(i); |
---|
1203 | beamDirs.resize(nbeam,True); |
---|
1204 | beamDirs(nbeam-1)=dirCol(i); |
---|
1205 | } |
---|
1206 | |
---|
1207 | // SRCTYPE is Int (getNumber takes only uInt) |
---|
1208 | if ( !anyEQ(stypeids,stypeCol(i)) ) { |
---|
1209 | nstype++; |
---|
1210 | stypeids.resize(nstype,True); |
---|
1211 | stypeids(nstype-1)=stypeCol(i); |
---|
1212 | } |
---|
1213 | |
---|
1214 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
1215 | currFreqId=freqIdCol(i); |
---|
1216 | ftabRow = fidMap[currFreqId]; |
---|
1217 | if (fIdchans(ftabRow) < 0 ) { |
---|
1218 | const TableRecord& rec = row.get(i); |
---|
1219 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
1220 | fIdchans(ftabRow) = (*spec).shape()(0); |
---|
1221 | } |
---|
1222 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) { |
---|
1223 | ifNos[ftabRow].shape(iflen); |
---|
1224 | iflen++; |
---|
1225 | ifNos[ftabRow].resize(iflen,True); |
---|
1226 | ifNos[ftabRow](iflen-1) = ifNoCol(i); |
---|
1227 | } |
---|
1228 | if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) { |
---|
1229 | polNos[ftabRow].shape(pollen); |
---|
1230 | pollen++; |
---|
1231 | polNos[ftabRow].resize(pollen,True); |
---|
1232 | polNos[ftabRow](pollen-1) = polNoCol(i); |
---|
1233 | } |
---|
1234 | } // end of row iteration |
---|
1235 | |
---|
1236 | stypestrs.resize(nstype,False); |
---|
1237 | for (uInt j=0; j < nstype; j++) |
---|
1238 | stypestrs(j) = SrcType::getName(stypeids(j)); |
---|
1239 | |
---|
1240 | // Format Scan summary |
---|
1241 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
1242 | << std::left << setw(1) << "" |
---|
1243 | << setw(15) << rec.asString("SRCNAME") |
---|
1244 | << setw(21) << MVTime(btime).string(MVTime::YMD,7) |
---|
1245 | << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7) |
---|
1246 | << setw(3) << "" << setw(6) << meanIntTim << setw(1) << "" |
---|
1247 | << std::right << setw(5) << snrow << setw(2) << "" |
---|
1248 | << std::left << stypestrs << setw(1) << "" |
---|
1249 | << freqids << setw(1) << "" |
---|
1250 | << molids << endl; |
---|
1251 | // Format Beam summary |
---|
1252 | for (uInt j=0; j < nbeam; j++) { |
---|
1253 | oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << "" |
---|
1254 | << formatDirection(beamDirs(j)) << endl; |
---|
1255 | } |
---|
1256 | // Flush summary every scan and clear up the string |
---|
1257 | ols << String(oss) << LogIO::POST; |
---|
1258 | if (ofs) ofs << String(oss) << flush; |
---|
1259 | oss.str(""); |
---|
1260 | oss.clear(); |
---|
1261 | |
---|
1262 | ++iter; |
---|
1263 | } // end of scan iteration |
---|
1264 | oss << asap::SEPERATOR << endl; |
---|
1265 | |
---|
1266 | // List FRECUENCIES Table (using STFrequencies.print may be slow) |
---|
1267 | oss << "FREQUENCIES: " << nfreq << endl; |
---|
1268 | oss << std::right << setw(5) << "ID" << setw(2) << "" |
---|
1269 | << std::left << setw(5) << "IFNO" << setw(2) << "" |
---|
1270 | << setw(8) << "Frame" |
---|
1271 | << setw(16) << "RefVal" |
---|
1272 | << setw(7) << "RefPix" |
---|
1273 | << setw(15) << "Increment" |
---|
1274 | << setw(9) << "Channels" |
---|
1275 | << setw(6) << "POLNOs" << endl; |
---|
1276 | Int tmplen; |
---|
1277 | for (Int i=0; i < nfid; i++){ |
---|
1278 | // List row=i of FREQUENCIES subtable |
---|
1279 | ifNos[i].shape(tmplen); |
---|
1280 | if (tmplen >= 1) { |
---|
1281 | oss << std::right << setw(5) << ftabIds(i) << setw(2) << "" |
---|
1282 | << setw(3) << ifNos[i](0) << setw(1) << "" |
---|
1283 | << std::left << setw(46) << frequencies().print(ftabIds(i)) |
---|
1284 | << setw(2) << "" |
---|
1285 | << std::right << setw(8) << fIdchans[i] << setw(2) << "" |
---|
1286 | << std::left << polNos[i]; |
---|
1287 | if (tmplen > 1) { |
---|
1288 | oss << " (" << tmplen << " chains)"; |
---|
1289 | } |
---|
1290 | oss << endl; |
---|
1291 | } |
---|
1292 | |
---|
1293 | } |
---|
1294 | oss << asap::SEPERATOR << endl; |
---|
1295 | |
---|
1296 | // List MOLECULES Table (currently lists all rows) |
---|
1297 | oss << "MOLECULES: " << endl; |
---|
1298 | if (molecules().nrow() <= 0) { |
---|
1299 | oss << " MOLECULES subtable is empty: there are no data" << endl; |
---|
1300 | } else { |
---|
1301 | ROTableRow row(molecules().table()); |
---|
1302 | oss << std::right << setw(5) << "ID" |
---|
1303 | << std::left << setw(3) << "" |
---|
1304 | << setw(18) << "RestFreq" |
---|
1305 | << setw(15) << "Name" << endl; |
---|
1306 | for (Int i=0; i < molecules().nrow(); i++){ |
---|
1307 | const TableRecord& rec=row.get(i); |
---|
1308 | oss << std::right << setw(5) << rec.asuInt("ID") |
---|
1309 | << std::left << setw(3) << "" |
---|
1310 | << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << "" |
---|
1311 | << rec.asArrayString("NAME") << endl; |
---|
1312 | } |
---|
1313 | } |
---|
1314 | oss << asap::SEPERATOR << endl; |
---|
1315 | ols << String(oss) << LogIO::POST; |
---|
1316 | if (ofs) { |
---|
1317 | ofs << String(oss) << flush; |
---|
1318 | ofs.close(); |
---|
1319 | } |
---|
1320 | // return String(oss); |
---|
1321 | } |
---|
1322 | |
---|
1323 | |
---|
1324 | std::string Scantable::oldheaderSummary() |
---|
1325 | { |
---|
1326 | // Format header info |
---|
1327 | // STHeader sdh; |
---|
1328 | // sdh = getHeader(); |
---|
1329 | // sdh.print(); |
---|
1330 | ostringstream oss; |
---|
1331 | oss.flags(std::ios_base::left); |
---|
1332 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
1333 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
1334 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
1335 | << "(" << getPolType() << ")" << endl |
---|
1336 | << setw(15) << "Channels:" << nchan() << endl; |
---|
1337 | String tmp; |
---|
1338 | oss << setw(15) << "Observer:" |
---|
1339 | << table_.keywordSet().asString("Observer") << endl; |
---|
1340 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
1341 | table_.keywordSet().get("Project", tmp); |
---|
1342 | oss << setw(15) << "Project:" << tmp << endl; |
---|
1343 | table_.keywordSet().get("Obstype", tmp); |
---|
1344 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
1345 | table_.keywordSet().get("AntennaName", tmp); |
---|
1346 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
1347 | table_.keywordSet().get("FluxUnit", tmp); |
---|
1348 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
1349 | int nid = moleculeTable_.nrow(); |
---|
1350 | Bool firstline = True; |
---|
1351 | oss << setw(15) << "Rest Freqs:"; |
---|
1352 | for (int i=0; i<nid; i++) { |
---|
1353 | Table t = table_(table_.col("MOLECULE_ID") == i, 1); |
---|
1354 | if (t.nrow() > 0) { |
---|
1355 | Vector<Double> vec(moleculeTable_.getRestFrequency(i)); |
---|
1356 | if (vec.nelements() > 0) { |
---|
1357 | if (firstline) { |
---|
1358 | oss << setprecision(10) << vec << " [Hz]" << endl; |
---|
1359 | firstline=False; |
---|
1360 | } |
---|
1361 | else{ |
---|
1362 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl; |
---|
1363 | } |
---|
1364 | } else { |
---|
1365 | oss << "none" << endl; |
---|
1366 | } |
---|
1367 | } |
---|
1368 | } |
---|
1369 | |
---|
1370 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl; |
---|
1371 | oss << selector_.print() << endl; |
---|
1372 | return String(oss); |
---|
1373 | } |
---|
1374 | |
---|
1375 | //std::string Scantable::summary( const std::string& filename ) |
---|
1376 | void Scantable::oldsummary( const std::string& filename ) |
---|
1377 | { |
---|
1378 | ostringstream oss; |
---|
1379 | ofstream ofs; |
---|
1380 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
1381 | |
---|
1382 | if (filename != "") |
---|
1383 | ofs.open( filename.c_str(), ios::out ); |
---|
1384 | |
---|
1385 | oss << endl; |
---|
1386 | oss << asap::SEPERATOR << endl; |
---|
1387 | oss << " Scan Table Summary" << endl; |
---|
1388 | oss << asap::SEPERATOR << endl; |
---|
1389 | |
---|
1390 | // Format header info |
---|
1391 | oss << oldheaderSummary(); |
---|
1392 | oss << endl; |
---|
1393 | |
---|
1394 | // main table |
---|
1395 | String dirtype = "Position (" |
---|
1396 | + getDirectionRefString() |
---|
1397 | + ")"; |
---|
1398 | oss.flags(std::ios_base::left); |
---|
1399 | oss << setw(5) << "Scan" << setw(15) << "Source" |
---|
1400 | << setw(10) << "Time" << setw(18) << "Integration" |
---|
1401 | << setw(15) << "Source Type" << endl; |
---|
1402 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl; |
---|
1403 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << "" |
---|
1404 | << setw(8) << "Frame" << setw(16) |
---|
1405 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" |
---|
1406 | << setw(7) << "Channels" |
---|
1407 | << endl; |
---|
1408 | oss << asap::SEPERATOR << endl; |
---|
1409 | |
---|
1410 | // Flush summary and clear up the string |
---|
1411 | ols << String(oss) << LogIO::POST; |
---|
1412 | if (ofs) ofs << String(oss) << flush; |
---|
1413 | oss.str(""); |
---|
1414 | oss.clear(); |
---|
1415 | |
---|
1416 | TableIterator iter(table_, "SCANNO"); |
---|
1417 | while (!iter.pastEnd()) { |
---|
1418 | Table subt = iter.table(); |
---|
1419 | ROTableRow row(subt); |
---|
1420 | MEpoch::ROScalarColumn timeCol(subt,"TIME"); |
---|
1421 | const TableRecord& rec = row.get(0); |
---|
1422 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
1423 | << std::left << setw(1) << "" |
---|
1424 | << setw(15) << rec.asString("SRCNAME") |
---|
1425 | << setw(10) << formatTime(timeCol(0), false); |
---|
1426 | // count the cycles in the scan |
---|
1427 | TableIterator cyciter(subt, "CYCLENO"); |
---|
1428 | int nint = 0; |
---|
1429 | while (!cyciter.pastEnd()) { |
---|
1430 | ++nint; |
---|
1431 | ++cyciter; |
---|
1432 | } |
---|
1433 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left |
---|
1434 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << "" |
---|
1435 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl; |
---|
1436 | |
---|
1437 | TableIterator biter(subt, "BEAMNO"); |
---|
1438 | while (!biter.pastEnd()) { |
---|
1439 | Table bsubt = biter.table(); |
---|
1440 | ROTableRow brow(bsubt); |
---|
1441 | const TableRecord& brec = brow.get(0); |
---|
1442 | uInt row0 = bsubt.rowNumbers(table_)[0]; |
---|
1443 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left; |
---|
1444 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl; |
---|
1445 | TableIterator iiter(bsubt, "IFNO"); |
---|
1446 | while (!iiter.pastEnd()) { |
---|
1447 | Table isubt = iiter.table(); |
---|
1448 | ROTableRow irow(isubt); |
---|
1449 | const TableRecord& irec = irow.get(0); |
---|
1450 | oss << setw(9) << ""; |
---|
1451 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left |
---|
1452 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID")) |
---|
1453 | << setw(3) << "" << nchan(irec.asuInt("IFNO")) |
---|
1454 | << endl; |
---|
1455 | |
---|
1456 | ++iiter; |
---|
1457 | } |
---|
1458 | ++biter; |
---|
1459 | } |
---|
1460 | // Flush summary every scan and clear up the string |
---|
1461 | ols << String(oss) << LogIO::POST; |
---|
1462 | if (ofs) ofs << String(oss) << flush; |
---|
1463 | oss.str(""); |
---|
1464 | oss.clear(); |
---|
1465 | |
---|
1466 | ++iter; |
---|
1467 | } |
---|
1468 | oss << asap::SEPERATOR << endl; |
---|
1469 | ols << String(oss) << LogIO::POST; |
---|
1470 | if (ofs) { |
---|
1471 | ofs << String(oss) << flush; |
---|
1472 | ofs.close(); |
---|
1473 | } |
---|
1474 | // return String(oss); |
---|
1475 | } |
---|
1476 | |
---|
1477 | // std::string Scantable::getTime(int whichrow, bool showdate) const |
---|
1478 | // { |
---|
1479 | // MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
1480 | // MEpoch me; |
---|
1481 | // if (whichrow > -1) { |
---|
1482 | // me = timeCol(uInt(whichrow)); |
---|
1483 | // } else { |
---|
1484 | // Double tm; |
---|
1485 | // table_.keywordSet().get("UTC",tm); |
---|
1486 | // me = MEpoch(MVEpoch(tm)); |
---|
1487 | // } |
---|
1488 | // return formatTime(me, showdate); |
---|
1489 | // } |
---|
1490 | |
---|
1491 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const |
---|
1492 | { |
---|
1493 | MEpoch me; |
---|
1494 | me = getEpoch(whichrow); |
---|
1495 | return formatTime(me, showdate, prec); |
---|
1496 | } |
---|
1497 | |
---|
1498 | MEpoch Scantable::getEpoch(int whichrow) const |
---|
1499 | { |
---|
1500 | if (whichrow > -1) { |
---|
1501 | return timeCol_(uInt(whichrow)); |
---|
1502 | } else { |
---|
1503 | Double tm; |
---|
1504 | table_.keywordSet().get("UTC",tm); |
---|
1505 | return MEpoch(MVEpoch(tm)); |
---|
1506 | } |
---|
1507 | } |
---|
1508 | |
---|
1509 | std::string Scantable::getDirectionString(int whichrow) const |
---|
1510 | { |
---|
1511 | return formatDirection(getDirection(uInt(whichrow))); |
---|
1512 | } |
---|
1513 | |
---|
1514 | |
---|
1515 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const { |
---|
1516 | const MPosition& mp = getAntennaPosition(); |
---|
1517 | const MDirection& md = getDirection(whichrow); |
---|
1518 | const MEpoch& me = timeCol_(whichrow); |
---|
1519 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
1520 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
1521 | return freqTable_.getSpectralCoordinate(md, mp, me, rf, |
---|
1522 | mfreqidCol_(whichrow)); |
---|
1523 | } |
---|
1524 | |
---|
1525 | std::vector< double > Scantable::getAbcissa( int whichrow ) const |
---|
1526 | { |
---|
1527 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number")); |
---|
1528 | std::vector<double> stlout; |
---|
1529 | int nchan = specCol_(whichrow).nelements(); |
---|
1530 | String us = freqTable_.getUnitString(); |
---|
1531 | if ( us == "" || us == "pixel" || us == "channel" ) { |
---|
1532 | for (int i=0; i<nchan; ++i) { |
---|
1533 | stlout.push_back(double(i)); |
---|
1534 | } |
---|
1535 | return stlout; |
---|
1536 | } |
---|
1537 | SpectralCoordinate spc = getSpectralCoordinate(whichrow); |
---|
1538 | Vector<Double> pixel(nchan); |
---|
1539 | Vector<Double> world; |
---|
1540 | indgen(pixel); |
---|
1541 | if ( Unit(us) == Unit("Hz") ) { |
---|
1542 | for ( int i=0; i < nchan; ++i) { |
---|
1543 | Double world; |
---|
1544 | spc.toWorld(world, pixel[i]); |
---|
1545 | stlout.push_back(double(world)); |
---|
1546 | } |
---|
1547 | } else if ( Unit(us) == Unit("km/s") ) { |
---|
1548 | Vector<Double> world; |
---|
1549 | spc.pixelToVelocity(world, pixel); |
---|
1550 | world.tovector(stlout); |
---|
1551 | } |
---|
1552 | return stlout; |
---|
1553 | } |
---|
1554 | void Scantable::setDirectionRefString( const std::string & refstr ) |
---|
1555 | { |
---|
1556 | MDirection::Types mdt; |
---|
1557 | if (refstr != "" && !MDirection::getType(mdt, refstr)) { |
---|
1558 | throw(AipsError("Illegal Direction frame.")); |
---|
1559 | } |
---|
1560 | if ( refstr == "" ) { |
---|
1561 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
1562 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr); |
---|
1563 | } else { |
---|
1564 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr)); |
---|
1565 | } |
---|
1566 | } |
---|
1567 | |
---|
1568 | std::string Scantable::getDirectionRefString( ) const |
---|
1569 | { |
---|
1570 | return table_.keywordSet().asString("DIRECTIONREF"); |
---|
1571 | } |
---|
1572 | |
---|
1573 | MDirection Scantable::getDirection(int whichrow ) const |
---|
1574 | { |
---|
1575 | String usertype = table_.keywordSet().asString("DIRECTIONREF"); |
---|
1576 | String type = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
1577 | if ( usertype != type ) { |
---|
1578 | MDirection::Types mdt; |
---|
1579 | if (!MDirection::getType(mdt, usertype)) { |
---|
1580 | throw(AipsError("Illegal Direction frame.")); |
---|
1581 | } |
---|
1582 | return dirCol_.convert(uInt(whichrow), mdt); |
---|
1583 | } else { |
---|
1584 | return dirCol_(uInt(whichrow)); |
---|
1585 | } |
---|
1586 | } |
---|
1587 | |
---|
1588 | std::string Scantable::getAbcissaLabel( int whichrow ) const |
---|
1589 | { |
---|
1590 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number")); |
---|
1591 | const MPosition& mp = getAntennaPosition(); |
---|
1592 | const MDirection& md = getDirection(whichrow); |
---|
1593 | const MEpoch& me = timeCol_(whichrow); |
---|
1594 | //const Double& rf = mmolidCol_(whichrow); |
---|
1595 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
1596 | SpectralCoordinate spc = |
---|
1597 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow)); |
---|
1598 | |
---|
1599 | String s = "Channel"; |
---|
1600 | Unit u = Unit(freqTable_.getUnitString()); |
---|
1601 | if (u == Unit("km/s")) { |
---|
1602 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True); |
---|
1603 | } else if (u == Unit("Hz")) { |
---|
1604 | Vector<String> wau(1);wau = u.getName(); |
---|
1605 | spc.setWorldAxisUnits(wau); |
---|
1606 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False); |
---|
1607 | } |
---|
1608 | return s; |
---|
1609 | |
---|
1610 | } |
---|
1611 | |
---|
1612 | /** |
---|
1613 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name, |
---|
1614 | const std::string& unit ) |
---|
1615 | **/ |
---|
1616 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name, |
---|
1617 | const std::string& unit ) |
---|
1618 | |
---|
1619 | { |
---|
1620 | ///@todo lookup in line table to fill in name and formattedname |
---|
1621 | Unit u(unit); |
---|
1622 | //Quantum<Double> urf(rf, u); |
---|
1623 | Quantum<Vector<Double> >urf(rf, u); |
---|
1624 | Vector<String> formattedname(0); |
---|
1625 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl; |
---|
1626 | |
---|
1627 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, ""); |
---|
1628 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname); |
---|
1629 | TableVector<uInt> tabvec(table_, "MOLECULE_ID"); |
---|
1630 | tabvec = id; |
---|
1631 | } |
---|
1632 | |
---|
1633 | /** |
---|
1634 | void asap::Scantable::setRestFrequencies( const std::string& name ) |
---|
1635 | { |
---|
1636 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI")); |
---|
1637 | ///@todo implement |
---|
1638 | } |
---|
1639 | **/ |
---|
1640 | |
---|
1641 | void Scantable::setRestFrequencies( const vector<std::string>& name ) |
---|
1642 | { |
---|
1643 | (void) name; // suppress unused warning |
---|
1644 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI")); |
---|
1645 | ///@todo implement |
---|
1646 | } |
---|
1647 | |
---|
1648 | std::vector< unsigned int > Scantable::rownumbers( ) const |
---|
1649 | { |
---|
1650 | std::vector<unsigned int> stlout; |
---|
1651 | Vector<uInt> vec = table_.rowNumbers(); |
---|
1652 | vec.tovector(stlout); |
---|
1653 | return stlout; |
---|
1654 | } |
---|
1655 | |
---|
1656 | |
---|
1657 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const |
---|
1658 | { |
---|
1659 | ROTableRow row(table_); |
---|
1660 | const TableRecord& rec = row.get(whichrow); |
---|
1661 | Table t = |
---|
1662 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO")) |
---|
1663 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
1664 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
1665 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
1666 | ROArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
1667 | return speccol.getColumn(); |
---|
1668 | } |
---|
1669 | |
---|
1670 | std::vector< std::string > Scantable::columnNames( ) const |
---|
1671 | { |
---|
1672 | Vector<String> vec = table_.tableDesc().columnNames(); |
---|
1673 | return mathutil::tovectorstring(vec); |
---|
1674 | } |
---|
1675 | |
---|
1676 | MEpoch::Types Scantable::getTimeReference( ) const |
---|
1677 | { |
---|
1678 | return MEpoch::castType(timeCol_.getMeasRef().getType()); |
---|
1679 | } |
---|
1680 | |
---|
1681 | void Scantable::addFit( const STFitEntry& fit, int row ) |
---|
1682 | { |
---|
1683 | //cout << mfitidCol_(uInt(row)) << endl; |
---|
1684 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ; |
---|
1685 | os << mfitidCol_(uInt(row)) << LogIO::POST ; |
---|
1686 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row))); |
---|
1687 | mfitidCol_.put(uInt(row), id); |
---|
1688 | } |
---|
1689 | |
---|
1690 | void Scantable::shift(int npix) |
---|
1691 | { |
---|
1692 | Vector<uInt> fids(mfreqidCol_.getColumn()); |
---|
1693 | genSort( fids, Sort::Ascending, |
---|
1694 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
1695 | for (uInt i=0; i<fids.nelements(); ++i) { |
---|
1696 | frequencies().shiftRefPix(npix, fids[i]); |
---|
1697 | } |
---|
1698 | } |
---|
1699 | |
---|
1700 | String Scantable::getAntennaName() const |
---|
1701 | { |
---|
1702 | String out; |
---|
1703 | table_.keywordSet().get("AntennaName", out); |
---|
1704 | String::size_type pos1 = out.find("@") ; |
---|
1705 | String::size_type pos2 = out.find("//") ; |
---|
1706 | if ( pos2 != String::npos ) |
---|
1707 | out = out.substr(pos2+2,pos1-pos2-2) ; |
---|
1708 | else if ( pos1 != String::npos ) |
---|
1709 | out = out.substr(0,pos1) ; |
---|
1710 | return out; |
---|
1711 | } |
---|
1712 | |
---|
1713 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const |
---|
1714 | { |
---|
1715 | String tbpath; |
---|
1716 | int ret = 0; |
---|
1717 | if ( table_.keywordSet().isDefined("GBT_GO") ) { |
---|
1718 | table_.keywordSet().get("GBT_GO", tbpath); |
---|
1719 | Table t(tbpath,Table::Old); |
---|
1720 | // check each scan if other scan of the pair exist |
---|
1721 | int nscan = scanlist.size(); |
---|
1722 | for (int i = 0; i < nscan; i++) { |
---|
1723 | Table subt = t( t.col("SCAN") == scanlist[i]+1 ); |
---|
1724 | if (subt.nrow()==0) { |
---|
1725 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl; |
---|
1726 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1727 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
1728 | ret = 1; |
---|
1729 | break; |
---|
1730 | } |
---|
1731 | ROTableRow row(subt); |
---|
1732 | const TableRecord& rec = row.get(0); |
---|
1733 | int scan1seqn = rec.asuInt("PROCSEQN"); |
---|
1734 | int laston1 = rec.asuInt("LASTON"); |
---|
1735 | if ( rec.asuInt("PROCSIZE")==2 ) { |
---|
1736 | if ( i < nscan-1 ) { |
---|
1737 | Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 ); |
---|
1738 | if ( subt2.nrow() == 0) { |
---|
1739 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1740 | |
---|
1741 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl; |
---|
1742 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
1743 | ret = 1; |
---|
1744 | break; |
---|
1745 | } |
---|
1746 | ROTableRow row2(subt2); |
---|
1747 | const TableRecord& rec2 = row2.get(0); |
---|
1748 | int scan2seqn = rec2.asuInt("PROCSEQN"); |
---|
1749 | int laston2 = rec2.asuInt("LASTON"); |
---|
1750 | if (scan1seqn == 1 && scan2seqn == 2) { |
---|
1751 | if (laston1 == laston2) { |
---|
1752 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1753 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
1754 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
1755 | i +=1; |
---|
1756 | } |
---|
1757 | else { |
---|
1758 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1759 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
1760 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
1761 | } |
---|
1762 | } |
---|
1763 | else if (scan1seqn==2 && scan2seqn == 1) { |
---|
1764 | if (laston1 == laston2) { |
---|
1765 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1766 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl; |
---|
1767 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST; |
---|
1768 | ret = 1; |
---|
1769 | break; |
---|
1770 | } |
---|
1771 | } |
---|
1772 | else { |
---|
1773 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1774 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl; |
---|
1775 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST; |
---|
1776 | ret = 1; |
---|
1777 | break; |
---|
1778 | } |
---|
1779 | } |
---|
1780 | } |
---|
1781 | else { |
---|
1782 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1783 | //cerr<<"The scan does not appear to be standard obsevation."<<endl; |
---|
1784 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST; |
---|
1785 | } |
---|
1786 | //if ( i >= nscan ) break; |
---|
1787 | } |
---|
1788 | } |
---|
1789 | else { |
---|
1790 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1791 | //cerr<<"No reference to GBT_GO table."<<endl; |
---|
1792 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST; |
---|
1793 | ret = 1; |
---|
1794 | } |
---|
1795 | return ret; |
---|
1796 | } |
---|
1797 | |
---|
1798 | std::vector<double> Scantable::getDirectionVector(int whichrow) const |
---|
1799 | { |
---|
1800 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue(); |
---|
1801 | std::vector<double> dir; |
---|
1802 | Dir.tovector(dir); |
---|
1803 | return dir; |
---|
1804 | } |
---|
1805 | |
---|
1806 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax ) |
---|
1807 | throw( casa::AipsError ) |
---|
1808 | { |
---|
1809 | // assumed that all rows have same nChan |
---|
1810 | Vector<Float> arr = specCol_( 0 ) ; |
---|
1811 | int nChan = arr.nelements() ; |
---|
1812 | |
---|
1813 | // if nmin < 0 or nmax < 0, nothing to do |
---|
1814 | if ( nmin < 0 ) { |
---|
1815 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
1816 | } |
---|
1817 | if ( nmax < 0 ) { |
---|
1818 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
1819 | } |
---|
1820 | |
---|
1821 | // if nmin > nmax, exchange values |
---|
1822 | if ( nmin > nmax ) { |
---|
1823 | int tmp = nmax ; |
---|
1824 | nmax = nmin ; |
---|
1825 | nmin = tmp ; |
---|
1826 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
1827 | os << "Swap values. Applied range is [" |
---|
1828 | << nmin << ", " << nmax << "]" << LogIO::POST ; |
---|
1829 | } |
---|
1830 | |
---|
1831 | // if nmin exceeds nChan, nothing to do |
---|
1832 | if ( nmin >= nChan ) { |
---|
1833 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ; |
---|
1834 | } |
---|
1835 | |
---|
1836 | // if nmax exceeds nChan, reset nmax to nChan |
---|
1837 | if ( nmax >= nChan-1 ) { |
---|
1838 | if ( nmin == 0 ) { |
---|
1839 | // nothing to do |
---|
1840 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
1841 | os << "Whole range is selected. Nothing to do." << LogIO::POST ; |
---|
1842 | return ; |
---|
1843 | } |
---|
1844 | else { |
---|
1845 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
1846 | os << "Specified maximum exceeds nChan. Applied range is [" |
---|
1847 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ; |
---|
1848 | nmax = nChan - 1 ; |
---|
1849 | } |
---|
1850 | } |
---|
1851 | |
---|
1852 | // reshape specCol_ and flagCol_ |
---|
1853 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
1854 | reshapeSpectrum( nmin, nmax, irow ) ; |
---|
1855 | } |
---|
1856 | |
---|
1857 | // update FREQUENCIES subtable |
---|
1858 | Double refpix ; |
---|
1859 | Double refval ; |
---|
1860 | Double increment ; |
---|
1861 | int freqnrow = freqTable_.table().nrow() ; |
---|
1862 | Vector<uInt> oldId( freqnrow ) ; |
---|
1863 | Vector<uInt> newId( freqnrow ) ; |
---|
1864 | for ( int irow = 0 ; irow < freqnrow ; irow++ ) { |
---|
1865 | freqTable_.getEntry( refpix, refval, increment, irow ) ; |
---|
1866 | /*** |
---|
1867 | * need to shift refpix to nmin |
---|
1868 | * note that channel nmin in old index will be channel 0 in new one |
---|
1869 | ***/ |
---|
1870 | refval = refval - ( refpix - nmin ) * increment ; |
---|
1871 | refpix = 0 ; |
---|
1872 | freqTable_.setEntry( refpix, refval, increment, irow ) ; |
---|
1873 | } |
---|
1874 | |
---|
1875 | // update nchan |
---|
1876 | int newsize = nmax - nmin + 1 ; |
---|
1877 | table_.rwKeywordSet().define( "nChan", newsize ) ; |
---|
1878 | |
---|
1879 | // update bandwidth |
---|
1880 | // assumed all spectra in the scantable have same bandwidth |
---|
1881 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ; |
---|
1882 | |
---|
1883 | return ; |
---|
1884 | } |
---|
1885 | |
---|
1886 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) |
---|
1887 | { |
---|
1888 | // reshape specCol_ and flagCol_ |
---|
1889 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
1890 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
1891 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
1892 | uInt newsize = nmax - nmin + 1 ; |
---|
1893 | Slice slice( nmin, newsize, 1 ) ; |
---|
1894 | specCol_.put( irow, oldspec( slice ) ) ; |
---|
1895 | flagsCol_.put( irow, oldflag( slice ) ) ; |
---|
1896 | if ( oldspec.size() == oldtsys.size() ) |
---|
1897 | tsysCol_.put( irow, oldtsys( slice ) ) ; |
---|
1898 | |
---|
1899 | return ; |
---|
1900 | } |
---|
1901 | |
---|
1902 | void asap::Scantable::regridSpecChannel( double dnu, int nChan ) |
---|
1903 | { |
---|
1904 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
1905 | os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ; |
---|
1906 | int freqnrow = freqTable_.table().nrow() ; |
---|
1907 | Vector<bool> firstTime( freqnrow, true ) ; |
---|
1908 | double oldincr, factor; |
---|
1909 | uInt currId; |
---|
1910 | Double refpix ; |
---|
1911 | Double refval ; |
---|
1912 | Double increment ; |
---|
1913 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
1914 | currId = mfreqidCol_(irow); |
---|
1915 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
1916 | if (nChan < 0) { |
---|
1917 | int oldsize = abcissa.size() ; |
---|
1918 | double bw = (abcissa[oldsize-1]-abcissa[0]) + \ |
---|
1919 | 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ; |
---|
1920 | nChan = int( ceil( abs(bw/dnu) ) ) ; |
---|
1921 | } |
---|
1922 | // actual regridding |
---|
1923 | regridChannel( nChan, dnu, irow ) ; |
---|
1924 | |
---|
1925 | // update FREQUENCIES subtable |
---|
1926 | if (firstTime[currId]) { |
---|
1927 | oldincr = abcissa[1]-abcissa[0] ; |
---|
1928 | factor = dnu/oldincr ; |
---|
1929 | firstTime[currId] = false ; |
---|
1930 | freqTable_.getEntry( refpix, refval, increment, currId ) ; |
---|
1931 | |
---|
1932 | //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ; |
---|
1933 | if (factor > 0 ) { |
---|
1934 | refpix = (refpix + 0.5)/factor - 0.5; |
---|
1935 | } else { |
---|
1936 | refpix = (abcissa.size() - 0.5 - refpix)/abs(factor) - 0.5; |
---|
1937 | } |
---|
1938 | freqTable_.setEntry( refpix, refval, increment*factor, currId ) ; |
---|
1939 | //os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ; |
---|
1940 | //os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ; |
---|
1941 | } |
---|
1942 | } |
---|
1943 | } |
---|
1944 | |
---|
1945 | void asap::Scantable::regridChannel( int nChan, double dnu ) |
---|
1946 | { |
---|
1947 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
1948 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ; |
---|
1949 | // assumed that all rows have same nChan |
---|
1950 | Vector<Float> arr = specCol_( 0 ) ; |
---|
1951 | int oldsize = arr.nelements() ; |
---|
1952 | |
---|
1953 | // if oldsize == nChan, nothing to do |
---|
1954 | if ( oldsize == nChan ) { |
---|
1955 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ; |
---|
1956 | return ; |
---|
1957 | } |
---|
1958 | |
---|
1959 | // if oldChan < nChan, unphysical operation |
---|
1960 | if ( oldsize < nChan ) { |
---|
1961 | os << "Unphysical operation. Nothing to do." << LogIO::POST ; |
---|
1962 | return ; |
---|
1963 | } |
---|
1964 | |
---|
1965 | // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary) |
---|
1966 | vector<string> coordinfo = getCoordInfo() ; |
---|
1967 | string oldinfo = coordinfo[0] ; |
---|
1968 | coordinfo[0] = "Hz" ; |
---|
1969 | setCoordInfo( coordinfo ) ; |
---|
1970 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
1971 | regridChannel( nChan, dnu, irow ) ; |
---|
1972 | } |
---|
1973 | coordinfo[0] = oldinfo ; |
---|
1974 | setCoordInfo( coordinfo ) ; |
---|
1975 | |
---|
1976 | |
---|
1977 | // NOTE: this method does not update metadata such as |
---|
1978 | // FREQUENCIES subtable, nChan, Bandwidth, etc. |
---|
1979 | |
---|
1980 | return ; |
---|
1981 | } |
---|
1982 | |
---|
1983 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) |
---|
1984 | { |
---|
1985 | // logging |
---|
1986 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ; |
---|
1987 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ; |
---|
1988 | |
---|
1989 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
1990 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
1991 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
1992 | Vector<Float> newspec( nChan, 0 ) ; |
---|
1993 | Vector<uChar> newflag( nChan, true ) ; |
---|
1994 | Vector<Float> newtsys ; |
---|
1995 | bool regridTsys = false ; |
---|
1996 | if (oldtsys.size() == oldspec.size()) { |
---|
1997 | regridTsys = true ; |
---|
1998 | newtsys.resize(nChan,false) ; |
---|
1999 | newtsys = 0 ; |
---|
2000 | } |
---|
2001 | |
---|
2002 | // regrid |
---|
2003 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
2004 | int oldsize = abcissa.size() ; |
---|
2005 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
2006 | //int ichan = 0 ; |
---|
2007 | double wsum = 0.0 ; |
---|
2008 | Vector<double> zi( nChan+1 ) ; |
---|
2009 | Vector<double> yi( oldsize + 1 ) ; |
---|
2010 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
2011 | for ( int ii = 1 ; ii < oldsize ; ii++ ) |
---|
2012 | yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ; |
---|
2013 | yi[oldsize] = abcissa[oldsize-1] \ |
---|
2014 | + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ; |
---|
2015 | //zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
2016 | zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ; |
---|
2017 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
---|
2018 | zi[ii] = zi[0] + dnu * ii ; |
---|
2019 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
2020 | // Access zi and yi in ascending order |
---|
2021 | int izs = ((dnu > 0) ? 0 : nChan ) ; |
---|
2022 | int ize = ((dnu > 0) ? nChan : 0 ) ; |
---|
2023 | int izincr = ((dnu > 0) ? 1 : -1 ) ; |
---|
2024 | int ichan = ((olddnu > 0) ? 0 : oldsize ) ; |
---|
2025 | int iye = ((olddnu > 0) ? oldsize : 0 ) ; |
---|
2026 | int iyincr = ((olddnu > 0) ? 1 : -1 ) ; |
---|
2027 | //for ( int ii = izs ; ii != ize ; ii+=izincr ){ |
---|
2028 | int ii = izs ; |
---|
2029 | while (ii != ize) { |
---|
2030 | // always zl < zr |
---|
2031 | double zl = zi[ii] ; |
---|
2032 | double zr = zi[ii+izincr] ; |
---|
2033 | // Need to access smaller index for the new spec, flag, and tsys. |
---|
2034 | // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc. |
---|
2035 | int i = min(ii, ii+izincr) ; |
---|
2036 | //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) { |
---|
2037 | int jj = ichan ; |
---|
2038 | while (jj != iye) { |
---|
2039 | // always yl < yr |
---|
2040 | double yl = yi[jj] ; |
---|
2041 | double yr = yi[jj+iyincr] ; |
---|
2042 | // Need to access smaller index for the original spec, flag, and tsys. |
---|
2043 | // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc. |
---|
2044 | int j = min(jj, jj+iyincr) ; |
---|
2045 | if ( yr <= zl ) { |
---|
2046 | jj += iyincr ; |
---|
2047 | continue ; |
---|
2048 | } |
---|
2049 | else if ( yl <= zl ) { |
---|
2050 | if ( yr < zr ) { |
---|
2051 | if (!oldflag[j]) { |
---|
2052 | newspec[i] += oldspec[j] * ( yr - zl ) ; |
---|
2053 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ; |
---|
2054 | wsum += ( yr - zl ) ; |
---|
2055 | } |
---|
2056 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2057 | } |
---|
2058 | else { |
---|
2059 | if (!oldflag[j]) { |
---|
2060 | newspec[i] += oldspec[j] * abs(dnu) ; |
---|
2061 | if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ; |
---|
2062 | wsum += abs(dnu) ; |
---|
2063 | } |
---|
2064 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2065 | ichan = jj ; |
---|
2066 | break ; |
---|
2067 | } |
---|
2068 | } |
---|
2069 | else if ( yl < zr ) { |
---|
2070 | if ( yr <= zr ) { |
---|
2071 | if (!oldflag[j]) { |
---|
2072 | newspec[i] += oldspec[j] * ( yr - yl ) ; |
---|
2073 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ; |
---|
2074 | wsum += ( yr - yl ) ; |
---|
2075 | } |
---|
2076 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2077 | } |
---|
2078 | else { |
---|
2079 | if (!oldflag[j]) { |
---|
2080 | newspec[i] += oldspec[j] * ( zr - yl ) ; |
---|
2081 | if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ; |
---|
2082 | wsum += ( zr - yl ) ; |
---|
2083 | } |
---|
2084 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2085 | ichan = jj ; |
---|
2086 | break ; |
---|
2087 | } |
---|
2088 | } |
---|
2089 | else { |
---|
2090 | ichan = jj - iyincr ; |
---|
2091 | break ; |
---|
2092 | } |
---|
2093 | jj += iyincr ; |
---|
2094 | } |
---|
2095 | if ( wsum != 0.0 ) { |
---|
2096 | newspec[i] /= wsum ; |
---|
2097 | if (regridTsys) newtsys[i] /= wsum ; |
---|
2098 | } |
---|
2099 | wsum = 0.0 ; |
---|
2100 | ii += izincr ; |
---|
2101 | } |
---|
2102 | // if ( dnu > 0.0 ) { |
---|
2103 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
2104 | // double zl = zi[ii] ; |
---|
2105 | // double zr = zi[ii+1] ; |
---|
2106 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
2107 | // double yl = yi[j] ; |
---|
2108 | // double yr = yi[j+1] ; |
---|
2109 | // if ( yl <= zl ) { |
---|
2110 | // if ( yr <= zl ) { |
---|
2111 | // continue ; |
---|
2112 | // } |
---|
2113 | // else if ( yr <= zr ) { |
---|
2114 | // if (!oldflag[j]) { |
---|
2115 | // newspec[ii] += oldspec[j] * ( yr - zl ) ; |
---|
2116 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ; |
---|
2117 | // wsum += ( yr - zl ) ; |
---|
2118 | // } |
---|
2119 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2120 | // } |
---|
2121 | // else { |
---|
2122 | // if (!oldflag[j]) { |
---|
2123 | // newspec[ii] += oldspec[j] * dnu ; |
---|
2124 | // if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ; |
---|
2125 | // wsum += dnu ; |
---|
2126 | // } |
---|
2127 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2128 | // ichan = j ; |
---|
2129 | // break ; |
---|
2130 | // } |
---|
2131 | // } |
---|
2132 | // else if ( yl < zr ) { |
---|
2133 | // if ( yr <= zr ) { |
---|
2134 | // if (!oldflag[j]) { |
---|
2135 | // newspec[ii] += oldspec[j] * ( yr - yl ) ; |
---|
2136 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ; |
---|
2137 | // wsum += ( yr - yl ) ; |
---|
2138 | // } |
---|
2139 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2140 | // } |
---|
2141 | // else { |
---|
2142 | // if (!oldflag[j]) { |
---|
2143 | // newspec[ii] += oldspec[j] * ( zr - yl ) ; |
---|
2144 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ; |
---|
2145 | // wsum += ( zr - yl ) ; |
---|
2146 | // } |
---|
2147 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2148 | // ichan = j ; |
---|
2149 | // break ; |
---|
2150 | // } |
---|
2151 | // } |
---|
2152 | // else { |
---|
2153 | // ichan = j - 1 ; |
---|
2154 | // break ; |
---|
2155 | // } |
---|
2156 | // } |
---|
2157 | // if ( wsum != 0.0 ) { |
---|
2158 | // newspec[ii] /= wsum ; |
---|
2159 | // if (regridTsys) newtsys[ii] /= wsum ; |
---|
2160 | // } |
---|
2161 | // wsum = 0.0 ; |
---|
2162 | // } |
---|
2163 | // } |
---|
2164 | // else if ( dnu < 0.0 ) { |
---|
2165 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
2166 | // double zl = zi[ii] ; |
---|
2167 | // double zr = zi[ii+1] ; |
---|
2168 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
2169 | // double yl = yi[j] ; |
---|
2170 | // double yr = yi[j+1] ; |
---|
2171 | // if ( yl >= zl ) { |
---|
2172 | // if ( yr >= zl ) { |
---|
2173 | // continue ; |
---|
2174 | // } |
---|
2175 | // else if ( yr >= zr ) { |
---|
2176 | // if (!oldflag[j]) { |
---|
2177 | // newspec[ii] += oldspec[j] * abs( yr - zl ) ; |
---|
2178 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ; |
---|
2179 | // wsum += abs( yr - zl ) ; |
---|
2180 | // } |
---|
2181 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2182 | // } |
---|
2183 | // else { |
---|
2184 | // if (!oldflag[j]) { |
---|
2185 | // newspec[ii] += oldspec[j] * abs( dnu ) ; |
---|
2186 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ; |
---|
2187 | // wsum += abs( dnu ) ; |
---|
2188 | // } |
---|
2189 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2190 | // ichan = j ; |
---|
2191 | // break ; |
---|
2192 | // } |
---|
2193 | // } |
---|
2194 | // else if ( yl > zr ) { |
---|
2195 | // if ( yr >= zr ) { |
---|
2196 | // if (!oldflag[j]) { |
---|
2197 | // newspec[ii] += oldspec[j] * abs( yr - yl ) ; |
---|
2198 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ; |
---|
2199 | // wsum += abs( yr - yl ) ; |
---|
2200 | // } |
---|
2201 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2202 | // } |
---|
2203 | // else { |
---|
2204 | // if (!oldflag[j]) { |
---|
2205 | // newspec[ii] += oldspec[j] * abs( zr - yl ) ; |
---|
2206 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ; |
---|
2207 | // wsum += abs( zr - yl ) ; |
---|
2208 | // } |
---|
2209 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2210 | // ichan = j ; |
---|
2211 | // break ; |
---|
2212 | // } |
---|
2213 | // } |
---|
2214 | // else { |
---|
2215 | // ichan = j - 1 ; |
---|
2216 | // break ; |
---|
2217 | // } |
---|
2218 | // } |
---|
2219 | // if ( wsum != 0.0 ) { |
---|
2220 | // newspec[ii] /= wsum ; |
---|
2221 | // if (regridTsys) newtsys[ii] /= wsum ; |
---|
2222 | // } |
---|
2223 | // wsum = 0.0 ; |
---|
2224 | // } |
---|
2225 | // } |
---|
2226 | // // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ; |
---|
2227 | // // pile += dnu ; |
---|
2228 | // // wedge = olddnu * ( refChan + 1 ) ; |
---|
2229 | // // while ( wedge < pile ) { |
---|
2230 | // // newspec[0] += olddnu * oldspec[refChan] ; |
---|
2231 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
2232 | // // //ofs << "channel " << refChan << " is included in new channel 0" << endl ; |
---|
2233 | // // refChan++ ; |
---|
2234 | // // wedge += olddnu ; |
---|
2235 | // // wsum += olddnu ; |
---|
2236 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
2237 | // // } |
---|
2238 | // // frac = ( wedge - pile ) / olddnu ; |
---|
2239 | // // wsum += ( 1.0 - frac ) * olddnu ; |
---|
2240 | // // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
2241 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
2242 | // // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
2243 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
2244 | // // newspec[0] /= wsum ; |
---|
2245 | // // //ofs << "newspec[0] = " << newspec[0] << endl ; |
---|
2246 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
2247 | |
---|
2248 | // // /*** |
---|
2249 | // // * ichan = 1 - nChan-2 |
---|
2250 | // // ***/ |
---|
2251 | // // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) { |
---|
2252 | // // pile += dnu ; |
---|
2253 | // // newspec[ichan] += frac * olddnu * oldspec[refChan] ; |
---|
2254 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
2255 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ; |
---|
2256 | // // refChan++ ; |
---|
2257 | // // wedge += olddnu ; |
---|
2258 | // // wsum = frac * olddnu ; |
---|
2259 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
2260 | // // while ( wedge < pile ) { |
---|
2261 | // // newspec[ichan] += olddnu * oldspec[refChan] ; |
---|
2262 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
2263 | // // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ; |
---|
2264 | // // refChan++ ; |
---|
2265 | // // wedge += olddnu ; |
---|
2266 | // // wsum += olddnu ; |
---|
2267 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
2268 | // // } |
---|
2269 | // // frac = ( wedge - pile ) / olddnu ; |
---|
2270 | // // wsum += ( 1.0 - frac ) * olddnu ; |
---|
2271 | // // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
2272 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
2273 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
2274 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
2275 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
2276 | // // newspec[ichan] /= wsum ; |
---|
2277 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ; |
---|
2278 | // // } |
---|
2279 | |
---|
2280 | // // /*** |
---|
2281 | // // * ichan = nChan-1 |
---|
2282 | // // ***/ |
---|
2283 | // // // NOTE: Assumed that all spectra have the same bandwidth |
---|
2284 | // // pile += dnu ; |
---|
2285 | // // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ; |
---|
2286 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ; |
---|
2287 | // // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
2288 | // // refChan++ ; |
---|
2289 | // // wedge += olddnu ; |
---|
2290 | // // wsum = frac * olddnu ; |
---|
2291 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
2292 | // // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) { |
---|
2293 | // // newspec[nChan-1] += olddnu * oldspec[jchan] ; |
---|
2294 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ; |
---|
2295 | // // wsum += olddnu ; |
---|
2296 | // // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
2297 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
2298 | // // } |
---|
2299 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
2300 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
2301 | // // newspec[nChan-1] /= wsum ; |
---|
2302 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ; |
---|
2303 | |
---|
2304 | // // // ofs.close() ; |
---|
2305 | |
---|
2306 | specCol_.put( irow, newspec ) ; |
---|
2307 | flagsCol_.put( irow, newflag ) ; |
---|
2308 | if (regridTsys) tsysCol_.put( irow, newtsys ); |
---|
2309 | |
---|
2310 | return ; |
---|
2311 | } |
---|
2312 | |
---|
2313 | void Scantable::regridChannel( int nChan, double dnu, double fmin, int irow ) |
---|
2314 | { |
---|
2315 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
2316 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
2317 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
2318 | Vector<Float> newspec( nChan, 0 ) ; |
---|
2319 | Vector<uChar> newflag( nChan, true ) ; |
---|
2320 | Vector<Float> newtsys ; |
---|
2321 | bool regridTsys = false ; |
---|
2322 | if (oldtsys.size() == oldspec.size()) { |
---|
2323 | regridTsys = true ; |
---|
2324 | newtsys.resize(nChan,false) ; |
---|
2325 | newtsys = 0 ; |
---|
2326 | } |
---|
2327 | |
---|
2328 | // regrid |
---|
2329 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
2330 | int oldsize = abcissa.size() ; |
---|
2331 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
2332 | //int ichan = 0 ; |
---|
2333 | double wsum = 0.0 ; |
---|
2334 | Vector<double> zi( nChan+1 ) ; |
---|
2335 | Vector<double> yi( oldsize + 1 ) ; |
---|
2336 | Block<uInt> count( nChan, 0 ) ; |
---|
2337 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
2338 | for ( int ii = 1 ; ii < oldsize ; ii++ ) |
---|
2339 | yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ; |
---|
2340 | yi[oldsize] = abcissa[oldsize-1] \ |
---|
2341 | + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ; |
---|
2342 | // cout << "olddnu=" << olddnu << ", dnu=" << dnu << " (diff=" << olddnu-dnu << ")" << endl ; |
---|
2343 | // cout << "yi[0]=" << yi[0] << ", fmin=" << fmin << " (diff=" << yi[0]-fmin << ")" << endl ; |
---|
2344 | // cout << "oldsize=" << oldsize << ", nChan=" << nChan << endl ; |
---|
2345 | |
---|
2346 | // do not regrid if input parameters are almost same as current |
---|
2347 | // spectral setup |
---|
2348 | double dnuDiff = abs( ( dnu - olddnu ) / olddnu ) ; |
---|
2349 | double oldfmin = min( yi[0], yi[oldsize] ) ; |
---|
2350 | double fminDiff = abs( ( fmin - oldfmin ) / oldfmin ) ; |
---|
2351 | double nChanDiff = nChan - oldsize ; |
---|
2352 | double eps = 1.0e-8 ; |
---|
2353 | if ( nChanDiff == 0 && dnuDiff < eps && fminDiff < eps ) |
---|
2354 | return ; |
---|
2355 | |
---|
2356 | //zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
2357 | //zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ; |
---|
2358 | if ( dnu > 0 ) |
---|
2359 | zi[0] = fmin - 0.5 * dnu ; |
---|
2360 | else |
---|
2361 | zi[0] = fmin + nChan * abs(dnu) ; |
---|
2362 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
---|
2363 | zi[ii] = zi[0] + dnu * ii ; |
---|
2364 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
2365 | // Access zi and yi in ascending order |
---|
2366 | int izs = ((dnu > 0) ? 0 : nChan ) ; |
---|
2367 | int ize = ((dnu > 0) ? nChan : 0 ) ; |
---|
2368 | int izincr = ((dnu > 0) ? 1 : -1 ) ; |
---|
2369 | int ichan = ((olddnu > 0) ? 0 : oldsize ) ; |
---|
2370 | int iye = ((olddnu > 0) ? oldsize : 0 ) ; |
---|
2371 | int iyincr = ((olddnu > 0) ? 1 : -1 ) ; |
---|
2372 | //for ( int ii = izs ; ii != ize ; ii+=izincr ){ |
---|
2373 | int ii = izs ; |
---|
2374 | while (ii != ize) { |
---|
2375 | // always zl < zr |
---|
2376 | double zl = zi[ii] ; |
---|
2377 | double zr = zi[ii+izincr] ; |
---|
2378 | // Need to access smaller index for the new spec, flag, and tsys. |
---|
2379 | // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc. |
---|
2380 | int i = min(ii, ii+izincr) ; |
---|
2381 | //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) { |
---|
2382 | int jj = ichan ; |
---|
2383 | while (jj != iye) { |
---|
2384 | // always yl < yr |
---|
2385 | double yl = yi[jj] ; |
---|
2386 | double yr = yi[jj+iyincr] ; |
---|
2387 | // Need to access smaller index for the original spec, flag, and tsys. |
---|
2388 | // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc. |
---|
2389 | int j = min(jj, jj+iyincr) ; |
---|
2390 | if ( yr <= zl ) { |
---|
2391 | jj += iyincr ; |
---|
2392 | continue ; |
---|
2393 | } |
---|
2394 | else if ( yl <= zl ) { |
---|
2395 | if ( yr < zr ) { |
---|
2396 | if (!oldflag[j]) { |
---|
2397 | newspec[i] += oldspec[j] * ( yr - zl ) ; |
---|
2398 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ; |
---|
2399 | wsum += ( yr - zl ) ; |
---|
2400 | count[i]++ ; |
---|
2401 | } |
---|
2402 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2403 | } |
---|
2404 | else { |
---|
2405 | if (!oldflag[j]) { |
---|
2406 | newspec[i] += oldspec[j] * abs(dnu) ; |
---|
2407 | if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ; |
---|
2408 | wsum += abs(dnu) ; |
---|
2409 | count[i]++ ; |
---|
2410 | } |
---|
2411 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2412 | ichan = jj ; |
---|
2413 | break ; |
---|
2414 | } |
---|
2415 | } |
---|
2416 | else if ( yl < zr ) { |
---|
2417 | if ( yr <= zr ) { |
---|
2418 | if (!oldflag[j]) { |
---|
2419 | newspec[i] += oldspec[j] * ( yr - yl ) ; |
---|
2420 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ; |
---|
2421 | wsum += ( yr - yl ) ; |
---|
2422 | count[i]++ ; |
---|
2423 | } |
---|
2424 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2425 | } |
---|
2426 | else { |
---|
2427 | if (!oldflag[j]) { |
---|
2428 | newspec[i] += oldspec[j] * ( zr - yl ) ; |
---|
2429 | if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ; |
---|
2430 | wsum += ( zr - yl ) ; |
---|
2431 | count[i]++ ; |
---|
2432 | } |
---|
2433 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2434 | ichan = jj ; |
---|
2435 | break ; |
---|
2436 | } |
---|
2437 | } |
---|
2438 | else { |
---|
2439 | //ichan = jj - iyincr ; |
---|
2440 | break ; |
---|
2441 | } |
---|
2442 | jj += iyincr ; |
---|
2443 | } |
---|
2444 | if ( wsum != 0.0 ) { |
---|
2445 | newspec[i] /= wsum ; |
---|
2446 | if (regridTsys) newtsys[i] /= wsum ; |
---|
2447 | } |
---|
2448 | wsum = 0.0 ; |
---|
2449 | ii += izincr ; |
---|
2450 | } |
---|
2451 | |
---|
2452 | // flag out channels without data |
---|
2453 | // this is tentative since there is no specific definition |
---|
2454 | // on bit flag... |
---|
2455 | uChar noData = 1 << 7 ; |
---|
2456 | for ( Int i = 0 ; i < nChan ; i++ ) { |
---|
2457 | if ( count[i] == 0 ) |
---|
2458 | newflag[i] = noData ; |
---|
2459 | } |
---|
2460 | |
---|
2461 | specCol_.put( irow, newspec ) ; |
---|
2462 | flagsCol_.put( irow, newflag ) ; |
---|
2463 | if (regridTsys) tsysCol_.put( irow, newtsys ); |
---|
2464 | |
---|
2465 | return ; |
---|
2466 | } |
---|
2467 | |
---|
2468 | std::vector<float> Scantable::getWeather(int whichrow) const |
---|
2469 | { |
---|
2470 | std::vector<float> out(5); |
---|
2471 | //Float temperature, pressure, humidity, windspeed, windaz; |
---|
2472 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4], |
---|
2473 | mweatheridCol_(uInt(whichrow))); |
---|
2474 | |
---|
2475 | |
---|
2476 | return out; |
---|
2477 | } |
---|
2478 | |
---|
2479 | bool Scantable::getFlagtraFast(uInt whichrow) |
---|
2480 | { |
---|
2481 | uChar flag; |
---|
2482 | Vector<uChar> flags; |
---|
2483 | flagsCol_.get(whichrow, flags); |
---|
2484 | flag = flags[0]; |
---|
2485 | for (uInt i = 1; i < flags.size(); ++i) { |
---|
2486 | flag &= flags[i]; |
---|
2487 | } |
---|
2488 | return ((flag >> 7) == 1); |
---|
2489 | } |
---|
2490 | |
---|
2491 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
2492 | { |
---|
2493 | try { |
---|
2494 | ofstream ofs; |
---|
2495 | String coordInfo = ""; |
---|
2496 | bool hasSameNchan = true; |
---|
2497 | bool outTextFile = false; |
---|
2498 | bool csvFormat = false; |
---|
2499 | |
---|
2500 | if (blfile != "") { |
---|
2501 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
2502 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
2503 | if (ofs) outTextFile = true; |
---|
2504 | } |
---|
2505 | |
---|
2506 | if (outLogger || outTextFile) { |
---|
2507 | coordInfo = getCoordInfo()[0]; |
---|
2508 | if (coordInfo == "") coordInfo = "channel"; |
---|
2509 | hasSameNchan = hasSameNchanOverIFs(); |
---|
2510 | } |
---|
2511 | |
---|
2512 | Fitter fitter = Fitter(); |
---|
2513 | fitter.setExpression("poly", order); |
---|
2514 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
2515 | |
---|
2516 | int nRow = nrow(); |
---|
2517 | std::vector<bool> chanMask; |
---|
2518 | bool showProgress; |
---|
2519 | int minNRow; |
---|
2520 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
2521 | |
---|
2522 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
2523 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
2524 | fitBaseline(chanMask, whichrow, fitter); |
---|
2525 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
2526 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter); |
---|
2527 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
2528 | } |
---|
2529 | |
---|
2530 | if (outTextFile) ofs.close(); |
---|
2531 | |
---|
2532 | } catch (...) { |
---|
2533 | throw; |
---|
2534 | } |
---|
2535 | } |
---|
2536 | |
---|
2537 | 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) |
---|
2538 | { |
---|
2539 | try { |
---|
2540 | ofstream ofs; |
---|
2541 | String coordInfo = ""; |
---|
2542 | bool hasSameNchan = true; |
---|
2543 | bool outTextFile = false; |
---|
2544 | bool csvFormat = false; |
---|
2545 | |
---|
2546 | if (blfile != "") { |
---|
2547 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
2548 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
2549 | if (ofs) outTextFile = true; |
---|
2550 | } |
---|
2551 | |
---|
2552 | if (outLogger || outTextFile) { |
---|
2553 | coordInfo = getCoordInfo()[0]; |
---|
2554 | if (coordInfo == "") coordInfo = "channel"; |
---|
2555 | hasSameNchan = hasSameNchanOverIFs(); |
---|
2556 | } |
---|
2557 | |
---|
2558 | Fitter fitter = Fitter(); |
---|
2559 | fitter.setExpression("poly", order); |
---|
2560 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
2561 | |
---|
2562 | int nRow = nrow(); |
---|
2563 | std::vector<bool> chanMask; |
---|
2564 | int minEdgeSize = getIFNos().size()*2; |
---|
2565 | STLineFinder lineFinder = STLineFinder(); |
---|
2566 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
2567 | |
---|
2568 | bool showProgress; |
---|
2569 | int minNRow; |
---|
2570 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
2571 | |
---|
2572 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
2573 | |
---|
2574 | //------------------------------------------------------- |
---|
2575 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
2576 | //------------------------------------------------------- |
---|
2577 | int edgeSize = edge.size(); |
---|
2578 | std::vector<int> currentEdge; |
---|
2579 | if (edgeSize >= 2) { |
---|
2580 | int idx = 0; |
---|
2581 | if (edgeSize > 2) { |
---|
2582 | if (edgeSize < minEdgeSize) { |
---|
2583 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
2584 | } |
---|
2585 | idx = 2 * getIF(whichrow); |
---|
2586 | } |
---|
2587 | currentEdge.push_back(edge[idx]); |
---|
2588 | currentEdge.push_back(edge[idx+1]); |
---|
2589 | } else { |
---|
2590 | throw(AipsError("Wrong length of edge element")); |
---|
2591 | } |
---|
2592 | lineFinder.setData(getSpectrum(whichrow)); |
---|
2593 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
2594 | chanMask = lineFinder.getMask(); |
---|
2595 | //------------------------------------------------------- |
---|
2596 | |
---|
2597 | fitBaseline(chanMask, whichrow, fitter); |
---|
2598 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
2599 | |
---|
2600 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter); |
---|
2601 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
2602 | } |
---|
2603 | |
---|
2604 | if (outTextFile) ofs.close(); |
---|
2605 | |
---|
2606 | } catch (...) { |
---|
2607 | throw; |
---|
2608 | } |
---|
2609 | } |
---|
2610 | |
---|
2611 | void Scantable::chebyshevBaseline(const std::vector<bool>& mask, int order, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
2612 | { |
---|
2613 | try { |
---|
2614 | ofstream ofs; |
---|
2615 | String coordInfo = ""; |
---|
2616 | bool hasSameNchan = true; |
---|
2617 | bool outTextFile = false; |
---|
2618 | bool csvFormat = false; |
---|
2619 | |
---|
2620 | if (blfile != "") { |
---|
2621 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
2622 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
2623 | if (ofs) outTextFile = true; |
---|
2624 | } |
---|
2625 | |
---|
2626 | if (outLogger || outTextFile) { |
---|
2627 | coordInfo = getCoordInfo()[0]; |
---|
2628 | if (coordInfo == "") coordInfo = "channel"; |
---|
2629 | hasSameNchan = hasSameNchanOverIFs(); |
---|
2630 | } |
---|
2631 | |
---|
2632 | bool showProgress; |
---|
2633 | int minNRow; |
---|
2634 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
2635 | |
---|
2636 | int nRow = nrow(); |
---|
2637 | std::vector<bool> chanMask; |
---|
2638 | |
---|
2639 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
2640 | std::vector<float> sp = getSpectrum(whichrow); |
---|
2641 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
2642 | std::vector<float> params(order+1); |
---|
2643 | int nClipped = 0; |
---|
2644 | std::vector<float> res = doChebyshevFitting(sp, chanMask, order, params, nClipped, thresClip, nIterClip, getResidual); |
---|
2645 | |
---|
2646 | setSpectrum(res, whichrow); |
---|
2647 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "chebyshevBaseline()", params, nClipped); |
---|
2648 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
2649 | } |
---|
2650 | |
---|
2651 | if (outTextFile) ofs.close(); |
---|
2652 | |
---|
2653 | } catch (...) { |
---|
2654 | throw; |
---|
2655 | } |
---|
2656 | } |
---|
2657 | |
---|
2658 | void Scantable::autoChebyshevBaseline(const std::vector<bool>& mask, int order, 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) |
---|
2659 | { |
---|
2660 | try { |
---|
2661 | ofstream ofs; |
---|
2662 | String coordInfo = ""; |
---|
2663 | bool hasSameNchan = true; |
---|
2664 | bool outTextFile = false; |
---|
2665 | bool csvFormat = false; |
---|
2666 | |
---|
2667 | if (blfile != "") { |
---|
2668 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
2669 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
2670 | if (ofs) outTextFile = true; |
---|
2671 | } |
---|
2672 | |
---|
2673 | if (outLogger || outTextFile) { |
---|
2674 | coordInfo = getCoordInfo()[0]; |
---|
2675 | if (coordInfo == "") coordInfo = "channel"; |
---|
2676 | hasSameNchan = hasSameNchanOverIFs(); |
---|
2677 | } |
---|
2678 | |
---|
2679 | int nRow = nrow(); |
---|
2680 | std::vector<bool> chanMask; |
---|
2681 | int minEdgeSize = getIFNos().size()*2; |
---|
2682 | STLineFinder lineFinder = STLineFinder(); |
---|
2683 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
2684 | |
---|
2685 | bool showProgress; |
---|
2686 | int minNRow; |
---|
2687 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
2688 | |
---|
2689 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
2690 | std::vector<float> sp = getSpectrum(whichrow); |
---|
2691 | |
---|
2692 | //------------------------------------------------------- |
---|
2693 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
2694 | //------------------------------------------------------- |
---|
2695 | int edgeSize = edge.size(); |
---|
2696 | std::vector<int> currentEdge; |
---|
2697 | if (edgeSize >= 2) { |
---|
2698 | int idx = 0; |
---|
2699 | if (edgeSize > 2) { |
---|
2700 | if (edgeSize < minEdgeSize) { |
---|
2701 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
2702 | } |
---|
2703 | idx = 2 * getIF(whichrow); |
---|
2704 | } |
---|
2705 | currentEdge.push_back(edge[idx]); |
---|
2706 | currentEdge.push_back(edge[idx+1]); |
---|
2707 | } else { |
---|
2708 | throw(AipsError("Wrong length of edge element")); |
---|
2709 | } |
---|
2710 | //lineFinder.setData(getSpectrum(whichrow)); |
---|
2711 | lineFinder.setData(sp); |
---|
2712 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
2713 | chanMask = lineFinder.getMask(); |
---|
2714 | //------------------------------------------------------- |
---|
2715 | |
---|
2716 | |
---|
2717 | //fitBaseline(chanMask, whichrow, fitter); |
---|
2718 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
2719 | std::vector<float> params(order+1); |
---|
2720 | int nClipped = 0; |
---|
2721 | std::vector<float> res = doChebyshevFitting(sp, chanMask, order, params, nClipped, thresClip, nIterClip, getResidual); |
---|
2722 | setSpectrum(res, whichrow); |
---|
2723 | |
---|
2724 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoChebyshevBaseline()", params, nClipped); |
---|
2725 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
2726 | } |
---|
2727 | |
---|
2728 | if (outTextFile) ofs.close(); |
---|
2729 | |
---|
2730 | } catch (...) { |
---|
2731 | throw; |
---|
2732 | } |
---|
2733 | } |
---|
2734 | |
---|
2735 | /* |
---|
2736 | double Scantable::getChebyshevPolynomial(int n, double x) { |
---|
2737 | if ((x < -1.0)||(x > 1.0)) { |
---|
2738 | throw(AipsError("out of definition range (-1 <= x <= 1).")); |
---|
2739 | } else if (n < 0) { |
---|
2740 | throw(AipsError("the order must be zero or positive.")); |
---|
2741 | } else if (n == 0) { |
---|
2742 | return 1.0; |
---|
2743 | } else if (n == 1) { |
---|
2744 | return x; |
---|
2745 | } else { |
---|
2746 | return 2.0*x*getChebyshevPolynomial(n-1, x) - getChebyshevPolynomial(n-2, x); |
---|
2747 | } |
---|
2748 | } |
---|
2749 | */ |
---|
2750 | double Scantable::getChebyshevPolynomial(int n, double x) { |
---|
2751 | if ((x < -1.0)||(x > 1.0)) { |
---|
2752 | throw(AipsError("out of definition range (-1 <= x <= 1).")); |
---|
2753 | } else if (n < 0) { |
---|
2754 | throw(AipsError("the order must be zero or positive.")); |
---|
2755 | } else if (n == 0) { |
---|
2756 | return 1.0; |
---|
2757 | } else if (n == 1) { |
---|
2758 | return x; |
---|
2759 | } else { |
---|
2760 | double res = 0.0; |
---|
2761 | for (int m = 0; m <= n/2; ++m) { |
---|
2762 | double c = 1.0; |
---|
2763 | if (m > 0) { |
---|
2764 | for (int i = 1; i <= m; ++i) { |
---|
2765 | c *= (double)(n-2*m+i)/(double)i; |
---|
2766 | } |
---|
2767 | } |
---|
2768 | res += (m%2 == 0 ? 1.0 : -1.0)*(double)n/(double)(n-m)*pow(2.0*x, (double)(n-2*m-1))/2.0*c; |
---|
2769 | } |
---|
2770 | return res; |
---|
2771 | } |
---|
2772 | } |
---|
2773 | |
---|
2774 | std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data, const std::vector<bool>& mask, int order, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
2775 | { |
---|
2776 | if (data.size() != mask.size()) { |
---|
2777 | throw(AipsError("data and mask sizes are not identical")); |
---|
2778 | } |
---|
2779 | if (order < 0) { |
---|
2780 | throw(AipsError("maximum order of Chebyshev polynomial must not be negative.")); |
---|
2781 | } |
---|
2782 | |
---|
2783 | int nChan = data.size(); |
---|
2784 | std::vector<int> maskArray; |
---|
2785 | std::vector<int> x; |
---|
2786 | for (int i = 0; i < nChan; ++i) { |
---|
2787 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
2788 | if (mask[i]) { |
---|
2789 | x.push_back(i); |
---|
2790 | } |
---|
2791 | } |
---|
2792 | |
---|
2793 | int initNData = x.size(); |
---|
2794 | |
---|
2795 | int nData = initNData; |
---|
2796 | int nDOF = order + 1; //number of parameters to solve. |
---|
2797 | |
---|
2798 | // xArray : contains elemental values for computing the least-square matrix. |
---|
2799 | // xArray.size() is nDOF and xArray[*].size() is nChan. |
---|
2800 | // Each xArray element are as follows: |
---|
2801 | // xArray[0] = {T0(-1), T0(2/(nChan-1)-1), T0(4/(nChan-1)-1), ..., T0(1)}, |
---|
2802 | // xArray[n-1] = ..., |
---|
2803 | // xArray[n] = {Tn(-1), Tn(2/(nChan-1)-1), Tn(4/(nChan-1)-1), ..., Tn(1)} |
---|
2804 | // where (0 <= n <= order), |
---|
2805 | std::vector<std::vector<double> > xArray; |
---|
2806 | for (int i = 0; i < nDOF; ++i) { |
---|
2807 | double xFactor = 2.0/(double)(nChan - 1); |
---|
2808 | std::vector<double> xs; |
---|
2809 | xs.clear(); |
---|
2810 | for (int j = 0; j < nChan; ++j) { |
---|
2811 | xs.push_back(getChebyshevPolynomial(i, xFactor*(double)j-1.0)); |
---|
2812 | } |
---|
2813 | xArray.push_back(xs); |
---|
2814 | } |
---|
2815 | |
---|
2816 | std::vector<double> z1, r1, residual; |
---|
2817 | for (int i = 0; i < nChan; ++i) { |
---|
2818 | z1.push_back((double)data[i]); |
---|
2819 | r1.push_back(0.0); |
---|
2820 | residual.push_back(0.0); |
---|
2821 | } |
---|
2822 | |
---|
2823 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
2824 | // xMatrix : horizontal concatenation of |
---|
2825 | // the least-sq. matrix (left) and an |
---|
2826 | // identity matrix (right). |
---|
2827 | // the right part is used to calculate the inverse matrix of the left part. |
---|
2828 | double xMatrix[nDOF][2*nDOF]; |
---|
2829 | double zMatrix[nDOF]; |
---|
2830 | for (int i = 0; i < nDOF; ++i) { |
---|
2831 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
2832 | xMatrix[i][j] = 0.0; |
---|
2833 | } |
---|
2834 | xMatrix[i][nDOF+i] = 1.0; |
---|
2835 | zMatrix[i] = 0.0; |
---|
2836 | } |
---|
2837 | |
---|
2838 | int nUseData = 0; |
---|
2839 | for (int k = 0; k < nChan; ++k) { |
---|
2840 | if (maskArray[k] == 0) continue; |
---|
2841 | |
---|
2842 | for (int i = 0; i < nDOF; ++i) { |
---|
2843 | for (int j = i; j < nDOF; ++j) { |
---|
2844 | xMatrix[i][j] += xArray[i][k] * xArray[j][k]; |
---|
2845 | } |
---|
2846 | zMatrix[i] += z1[k] * xArray[i][k]; |
---|
2847 | } |
---|
2848 | |
---|
2849 | nUseData++; |
---|
2850 | } |
---|
2851 | |
---|
2852 | if (nUseData < 1) { |
---|
2853 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
2854 | } |
---|
2855 | |
---|
2856 | for (int i = 0; i < nDOF; ++i) { |
---|
2857 | for (int j = 0; j < i; ++j) { |
---|
2858 | xMatrix[i][j] = xMatrix[j][i]; |
---|
2859 | } |
---|
2860 | } |
---|
2861 | |
---|
2862 | std::vector<double> invDiag; |
---|
2863 | for (int i = 0; i < nDOF; ++i) { |
---|
2864 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
2865 | for (int j = 0; j < nDOF; ++j) { |
---|
2866 | xMatrix[i][j] *= invDiag[i]; |
---|
2867 | } |
---|
2868 | } |
---|
2869 | |
---|
2870 | for (int k = 0; k < nDOF; ++k) { |
---|
2871 | for (int i = 0; i < nDOF; ++i) { |
---|
2872 | if (i != k) { |
---|
2873 | double factor1 = xMatrix[k][k]; |
---|
2874 | double factor2 = xMatrix[i][k]; |
---|
2875 | for (int j = k; j < 2*nDOF; ++j) { |
---|
2876 | xMatrix[i][j] *= factor1; |
---|
2877 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
2878 | xMatrix[i][j] /= factor1; |
---|
2879 | } |
---|
2880 | } |
---|
2881 | } |
---|
2882 | double xDiag = xMatrix[k][k]; |
---|
2883 | for (int j = k; j < 2*nDOF; ++j) { |
---|
2884 | xMatrix[k][j] /= xDiag; |
---|
2885 | } |
---|
2886 | } |
---|
2887 | |
---|
2888 | for (int i = 0; i < nDOF; ++i) { |
---|
2889 | for (int j = 0; j < nDOF; ++j) { |
---|
2890 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
2891 | } |
---|
2892 | } |
---|
2893 | //compute a vector y which consists of the coefficients of the sinusoids forming the |
---|
2894 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine |
---|
2895 | //and cosine functions, respectively. |
---|
2896 | std::vector<double> y; |
---|
2897 | params.clear(); |
---|
2898 | for (int i = 0; i < nDOF; ++i) { |
---|
2899 | y.push_back(0.0); |
---|
2900 | for (int j = 0; j < nDOF; ++j) { |
---|
2901 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
2902 | } |
---|
2903 | params.push_back(y[i]); |
---|
2904 | } |
---|
2905 | |
---|
2906 | for (int i = 0; i < nChan; ++i) { |
---|
2907 | r1[i] = y[0]; |
---|
2908 | for (int j = 1; j < nDOF; ++j) { |
---|
2909 | r1[i] += y[j]*xArray[j][i]; |
---|
2910 | } |
---|
2911 | residual[i] = z1[i] - r1[i]; |
---|
2912 | } |
---|
2913 | |
---|
2914 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
2915 | break; |
---|
2916 | } else { |
---|
2917 | double stdDev = 0.0; |
---|
2918 | for (int i = 0; i < nChan; ++i) { |
---|
2919 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
2920 | } |
---|
2921 | stdDev = sqrt(stdDev/(double)nData); |
---|
2922 | |
---|
2923 | double thres = stdDev * thresClip; |
---|
2924 | int newNData = 0; |
---|
2925 | for (int i = 0; i < nChan; ++i) { |
---|
2926 | if (abs(residual[i]) >= thres) { |
---|
2927 | maskArray[i] = 0; |
---|
2928 | } |
---|
2929 | if (maskArray[i] > 0) { |
---|
2930 | newNData++; |
---|
2931 | } |
---|
2932 | } |
---|
2933 | if (newNData == nData) { |
---|
2934 | break; //no more flag to add. iteration stops. |
---|
2935 | } else { |
---|
2936 | nData = newNData; |
---|
2937 | } |
---|
2938 | } |
---|
2939 | } |
---|
2940 | |
---|
2941 | nClipped = initNData - nData; |
---|
2942 | |
---|
2943 | std::vector<float> result; |
---|
2944 | if (getResidual) { |
---|
2945 | for (int i = 0; i < nChan; ++i) { |
---|
2946 | result.push_back((float)residual[i]); |
---|
2947 | } |
---|
2948 | } else { |
---|
2949 | for (int i = 0; i < nChan; ++i) { |
---|
2950 | result.push_back((float)r1[i]); |
---|
2951 | } |
---|
2952 | } |
---|
2953 | |
---|
2954 | return result; |
---|
2955 | } |
---|
2956 | |
---|
2957 | 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) |
---|
2958 | { |
---|
2959 | /************* |
---|
2960 | double totTimeStart, totTimeEnd, blTimeStart, blTimeEnd, ioTimeStart, ioTimeEnd, msTimeStart, msTimeEnd, seTimeStart, seTimeEnd, otTimeStart, otTimeEnd, prTimeStart, prTimeEnd; |
---|
2961 | double elapseMs = 0.0; |
---|
2962 | double elapseSe = 0.0; |
---|
2963 | double elapseOt = 0.0; |
---|
2964 | double elapsePr = 0.0; |
---|
2965 | double elapseBl = 0.0; |
---|
2966 | double elapseIo = 0.0; |
---|
2967 | totTimeStart = mathutil::gettimeofday_sec(); |
---|
2968 | *************/ |
---|
2969 | |
---|
2970 | try { |
---|
2971 | ofstream ofs; |
---|
2972 | String coordInfo = ""; |
---|
2973 | bool hasSameNchan = true; |
---|
2974 | bool outTextFile = false; |
---|
2975 | bool csvFormat = false; |
---|
2976 | |
---|
2977 | if (blfile != "") { |
---|
2978 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
2979 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
2980 | if (ofs) outTextFile = true; |
---|
2981 | } |
---|
2982 | |
---|
2983 | if (outLogger || outTextFile) { |
---|
2984 | coordInfo = getCoordInfo()[0]; |
---|
2985 | if (coordInfo == "") coordInfo = "channel"; |
---|
2986 | hasSameNchan = hasSameNchanOverIFs(); |
---|
2987 | } |
---|
2988 | |
---|
2989 | //Fitter fitter = Fitter(); |
---|
2990 | //fitter.setExpression("cspline", nPiece); |
---|
2991 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
2992 | |
---|
2993 | bool showProgress; |
---|
2994 | int minNRow; |
---|
2995 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
2996 | |
---|
2997 | int nRow = nrow(); |
---|
2998 | std::vector<bool> chanMask; |
---|
2999 | |
---|
3000 | //-------------------------------- |
---|
3001 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
3002 | /****************** |
---|
3003 | ioTimeStart = mathutil::gettimeofday_sec(); |
---|
3004 | **/ |
---|
3005 | std::vector<float> sp = getSpectrum(whichrow); |
---|
3006 | /** |
---|
3007 | ioTimeEnd = mathutil::gettimeofday_sec(); |
---|
3008 | elapseIo += (double)(ioTimeEnd - ioTimeStart); |
---|
3009 | msTimeStart = mathutil::gettimeofday_sec(); |
---|
3010 | ******************/ |
---|
3011 | |
---|
3012 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
3013 | |
---|
3014 | /** |
---|
3015 | msTimeEnd = mathutil::gettimeofday_sec(); |
---|
3016 | elapseMs += (double)(msTimeEnd - msTimeStart); |
---|
3017 | blTimeStart = mathutil::gettimeofday_sec(); |
---|
3018 | **/ |
---|
3019 | |
---|
3020 | //fitBaseline(chanMask, whichrow, fitter); |
---|
3021 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
3022 | std::vector<int> pieceEdges(nPiece+1); |
---|
3023 | std::vector<float> params(nPiece*4); |
---|
3024 | int nClipped = 0; |
---|
3025 | std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
3026 | |
---|
3027 | /** |
---|
3028 | blTimeEnd = mathutil::gettimeofday_sec(); |
---|
3029 | elapseBl += (double)(blTimeEnd - blTimeStart); |
---|
3030 | seTimeStart = mathutil::gettimeofday_sec(); |
---|
3031 | **/ |
---|
3032 | |
---|
3033 | |
---|
3034 | setSpectrum(res, whichrow); |
---|
3035 | // |
---|
3036 | |
---|
3037 | /** |
---|
3038 | seTimeEnd = mathutil::gettimeofday_sec(); |
---|
3039 | elapseSe += (double)(seTimeEnd - seTimeStart); |
---|
3040 | otTimeStart = mathutil::gettimeofday_sec(); |
---|
3041 | **/ |
---|
3042 | |
---|
3043 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
3044 | |
---|
3045 | /** |
---|
3046 | otTimeEnd = mathutil::gettimeofday_sec(); |
---|
3047 | elapseOt += (double)(otTimeEnd - otTimeStart); |
---|
3048 | prTimeStart = mathutil::gettimeofday_sec(); |
---|
3049 | **/ |
---|
3050 | |
---|
3051 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
3052 | |
---|
3053 | /****************** |
---|
3054 | prTimeEnd = mathutil::gettimeofday_sec(); |
---|
3055 | elapsePr += (double)(prTimeEnd - prTimeStart); |
---|
3056 | ******************/ |
---|
3057 | } |
---|
3058 | //-------------------------------- |
---|
3059 | |
---|
3060 | if (outTextFile) ofs.close(); |
---|
3061 | |
---|
3062 | } catch (...) { |
---|
3063 | throw; |
---|
3064 | } |
---|
3065 | /*************** |
---|
3066 | totTimeEnd = mathutil::gettimeofday_sec(); |
---|
3067 | std::cout << "io : " << elapseIo << " (sec.)" << endl; |
---|
3068 | std::cout << "ms : " << elapseMs << " (sec.)" << endl; |
---|
3069 | std::cout << "bl : " << elapseBl << " (sec.)" << endl; |
---|
3070 | std::cout << "se : " << elapseSe << " (sec.)" << endl; |
---|
3071 | std::cout << "ot : " << elapseOt << " (sec.)" << endl; |
---|
3072 | std::cout << "pr : " << elapsePr << " (sec.)" << endl; |
---|
3073 | std::cout << "total : " << (double)(totTimeEnd - totTimeStart) << " (sec.)" << endl; |
---|
3074 | ***************/ |
---|
3075 | } |
---|
3076 | |
---|
3077 | 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) |
---|
3078 | { |
---|
3079 | try { |
---|
3080 | ofstream ofs; |
---|
3081 | String coordInfo = ""; |
---|
3082 | bool hasSameNchan = true; |
---|
3083 | bool outTextFile = false; |
---|
3084 | bool csvFormat = false; |
---|
3085 | |
---|
3086 | if (blfile != "") { |
---|
3087 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
3088 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
3089 | if (ofs) outTextFile = true; |
---|
3090 | } |
---|
3091 | |
---|
3092 | if (outLogger || outTextFile) { |
---|
3093 | coordInfo = getCoordInfo()[0]; |
---|
3094 | if (coordInfo == "") coordInfo = "channel"; |
---|
3095 | hasSameNchan = hasSameNchanOverIFs(); |
---|
3096 | } |
---|
3097 | |
---|
3098 | //Fitter fitter = Fitter(); |
---|
3099 | //fitter.setExpression("cspline", nPiece); |
---|
3100 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
3101 | |
---|
3102 | int nRow = nrow(); |
---|
3103 | std::vector<bool> chanMask; |
---|
3104 | int minEdgeSize = getIFNos().size()*2; |
---|
3105 | STLineFinder lineFinder = STLineFinder(); |
---|
3106 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
3107 | |
---|
3108 | bool showProgress; |
---|
3109 | int minNRow; |
---|
3110 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
3111 | |
---|
3112 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
3113 | std::vector<float> sp = getSpectrum(whichrow); |
---|
3114 | |
---|
3115 | //------------------------------------------------------- |
---|
3116 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
3117 | //------------------------------------------------------- |
---|
3118 | int edgeSize = edge.size(); |
---|
3119 | std::vector<int> currentEdge; |
---|
3120 | if (edgeSize >= 2) { |
---|
3121 | int idx = 0; |
---|
3122 | if (edgeSize > 2) { |
---|
3123 | if (edgeSize < minEdgeSize) { |
---|
3124 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
3125 | } |
---|
3126 | idx = 2 * getIF(whichrow); |
---|
3127 | } |
---|
3128 | currentEdge.push_back(edge[idx]); |
---|
3129 | currentEdge.push_back(edge[idx+1]); |
---|
3130 | } else { |
---|
3131 | throw(AipsError("Wrong length of edge element")); |
---|
3132 | } |
---|
3133 | //lineFinder.setData(getSpectrum(whichrow)); |
---|
3134 | lineFinder.setData(sp); |
---|
3135 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
3136 | chanMask = lineFinder.getMask(); |
---|
3137 | //------------------------------------------------------- |
---|
3138 | |
---|
3139 | |
---|
3140 | //fitBaseline(chanMask, whichrow, fitter); |
---|
3141 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
3142 | std::vector<int> pieceEdges(nPiece+1); |
---|
3143 | std::vector<float> params(nPiece*4); |
---|
3144 | int nClipped = 0; |
---|
3145 | std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
3146 | setSpectrum(res, whichrow); |
---|
3147 | // |
---|
3148 | |
---|
3149 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
3150 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
3151 | } |
---|
3152 | |
---|
3153 | if (outTextFile) ofs.close(); |
---|
3154 | |
---|
3155 | } catch (...) { |
---|
3156 | throw; |
---|
3157 | } |
---|
3158 | } |
---|
3159 | |
---|
3160 | 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) |
---|
3161 | { |
---|
3162 | if (data.size() != mask.size()) { |
---|
3163 | throw(AipsError("data and mask sizes are not identical")); |
---|
3164 | } |
---|
3165 | if (nPiece < 1) { |
---|
3166 | throw(AipsError("number of the sections must be one or more")); |
---|
3167 | } |
---|
3168 | |
---|
3169 | int nChan = data.size(); |
---|
3170 | std::vector<int> maskArray(nChan); |
---|
3171 | std::vector<int> x(nChan); |
---|
3172 | int j = 0; |
---|
3173 | for (int i = 0; i < nChan; ++i) { |
---|
3174 | maskArray[i] = mask[i] ? 1 : 0; |
---|
3175 | if (mask[i]) { |
---|
3176 | x[j] = i; |
---|
3177 | j++; |
---|
3178 | } |
---|
3179 | } |
---|
3180 | int initNData = j; |
---|
3181 | |
---|
3182 | if (initNData < nPiece) { |
---|
3183 | throw(AipsError("too few non-flagged channels")); |
---|
3184 | } |
---|
3185 | |
---|
3186 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5)); |
---|
3187 | std::vector<double> invEdge(nPiece-1); |
---|
3188 | idxEdge[0] = x[0]; |
---|
3189 | for (int i = 1; i < nPiece; ++i) { |
---|
3190 | int valX = x[nElement*i]; |
---|
3191 | idxEdge[i] = valX; |
---|
3192 | invEdge[i-1] = 1.0/(double)valX; |
---|
3193 | } |
---|
3194 | idxEdge[nPiece] = x[initNData-1]+1; |
---|
3195 | |
---|
3196 | int nData = initNData; |
---|
3197 | int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1). |
---|
3198 | |
---|
3199 | std::vector<double> x1(nChan), x2(nChan), x3(nChan); |
---|
3200 | std::vector<double> z1(nChan), x1z1(nChan), x2z1(nChan), x3z1(nChan); |
---|
3201 | std::vector<double> r1(nChan), residual(nChan); |
---|
3202 | for (int i = 0; i < nChan; ++i) { |
---|
3203 | double di = (double)i; |
---|
3204 | double dD = (double)data[i]; |
---|
3205 | x1[i] = di; |
---|
3206 | x2[i] = di*di; |
---|
3207 | x3[i] = di*di*di; |
---|
3208 | z1[i] = dD; |
---|
3209 | x1z1[i] = dD*di; |
---|
3210 | x2z1[i] = dD*di*di; |
---|
3211 | x3z1[i] = dD*di*di*di; |
---|
3212 | r1[i] = 0.0; |
---|
3213 | residual[i] = 0.0; |
---|
3214 | } |
---|
3215 | |
---|
3216 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
3217 | // xMatrix : horizontal concatenation of |
---|
3218 | // the least-sq. matrix (left) and an |
---|
3219 | // identity matrix (right). |
---|
3220 | // the right part is used to calculate the inverse matrix of the left part. |
---|
3221 | double xMatrix[nDOF][2*nDOF]; |
---|
3222 | double zMatrix[nDOF]; |
---|
3223 | for (int i = 0; i < nDOF; ++i) { |
---|
3224 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
3225 | xMatrix[i][j] = 0.0; |
---|
3226 | } |
---|
3227 | xMatrix[i][nDOF+i] = 1.0; |
---|
3228 | zMatrix[i] = 0.0; |
---|
3229 | } |
---|
3230 | |
---|
3231 | for (int n = 0; n < nPiece; ++n) { |
---|
3232 | int nUseDataInPiece = 0; |
---|
3233 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
3234 | |
---|
3235 | if (maskArray[i] == 0) continue; |
---|
3236 | |
---|
3237 | xMatrix[0][0] += 1.0; |
---|
3238 | xMatrix[0][1] += x1[i]; |
---|
3239 | xMatrix[0][2] += x2[i]; |
---|
3240 | xMatrix[0][3] += x3[i]; |
---|
3241 | xMatrix[1][1] += x2[i]; |
---|
3242 | xMatrix[1][2] += x3[i]; |
---|
3243 | xMatrix[1][3] += x2[i]*x2[i]; |
---|
3244 | xMatrix[2][2] += x2[i]*x2[i]; |
---|
3245 | xMatrix[2][3] += x3[i]*x2[i]; |
---|
3246 | xMatrix[3][3] += x3[i]*x3[i]; |
---|
3247 | zMatrix[0] += z1[i]; |
---|
3248 | zMatrix[1] += x1z1[i]; |
---|
3249 | zMatrix[2] += x2z1[i]; |
---|
3250 | zMatrix[3] += x3z1[i]; |
---|
3251 | |
---|
3252 | for (int j = 0; j < n; ++j) { |
---|
3253 | double q = 1.0 - x1[i]*invEdge[j]; |
---|
3254 | q = q*q*q; |
---|
3255 | xMatrix[0][j+4] += q; |
---|
3256 | xMatrix[1][j+4] += q*x1[i]; |
---|
3257 | xMatrix[2][j+4] += q*x2[i]; |
---|
3258 | xMatrix[3][j+4] += q*x3[i]; |
---|
3259 | for (int k = 0; k < j; ++k) { |
---|
3260 | double r = 1.0 - x1[i]*invEdge[k]; |
---|
3261 | r = r*r*r; |
---|
3262 | xMatrix[k+4][j+4] += r*q; |
---|
3263 | } |
---|
3264 | xMatrix[j+4][j+4] += q*q; |
---|
3265 | zMatrix[j+4] += q*z1[i]; |
---|
3266 | } |
---|
3267 | |
---|
3268 | nUseDataInPiece++; |
---|
3269 | } |
---|
3270 | |
---|
3271 | if (nUseDataInPiece < 1) { |
---|
3272 | std::vector<string> suffixOfPieceNumber(4); |
---|
3273 | suffixOfPieceNumber[0] = "th"; |
---|
3274 | suffixOfPieceNumber[1] = "st"; |
---|
3275 | suffixOfPieceNumber[2] = "nd"; |
---|
3276 | suffixOfPieceNumber[3] = "rd"; |
---|
3277 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0; |
---|
3278 | ostringstream oss; |
---|
3279 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece]; |
---|
3280 | oss << " piece of the spectrum. can't execute fitting anymore."; |
---|
3281 | throw(AipsError(String(oss))); |
---|
3282 | } |
---|
3283 | } |
---|
3284 | |
---|
3285 | for (int i = 0; i < nDOF; ++i) { |
---|
3286 | for (int j = 0; j < i; ++j) { |
---|
3287 | xMatrix[i][j] = xMatrix[j][i]; |
---|
3288 | } |
---|
3289 | } |
---|
3290 | |
---|
3291 | std::vector<double> invDiag(nDOF); |
---|
3292 | for (int i = 0; i < nDOF; ++i) { |
---|
3293 | invDiag[i] = 1.0/xMatrix[i][i]; |
---|
3294 | for (int j = 0; j < nDOF; ++j) { |
---|
3295 | xMatrix[i][j] *= invDiag[i]; |
---|
3296 | } |
---|
3297 | } |
---|
3298 | |
---|
3299 | for (int k = 0; k < nDOF; ++k) { |
---|
3300 | for (int i = 0; i < nDOF; ++i) { |
---|
3301 | if (i != k) { |
---|
3302 | double factor1 = xMatrix[k][k]; |
---|
3303 | double factor2 = xMatrix[i][k]; |
---|
3304 | for (int j = k; j < 2*nDOF; ++j) { |
---|
3305 | xMatrix[i][j] *= factor1; |
---|
3306 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
3307 | xMatrix[i][j] /= factor1; |
---|
3308 | } |
---|
3309 | } |
---|
3310 | } |
---|
3311 | double xDiag = xMatrix[k][k]; |
---|
3312 | for (int j = k; j < 2*nDOF; ++j) { |
---|
3313 | xMatrix[k][j] /= xDiag; |
---|
3314 | } |
---|
3315 | } |
---|
3316 | |
---|
3317 | for (int i = 0; i < nDOF; ++i) { |
---|
3318 | for (int j = 0; j < nDOF; ++j) { |
---|
3319 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
3320 | } |
---|
3321 | } |
---|
3322 | //compute a vector y which consists of the coefficients of the best-fit spline curves |
---|
3323 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of |
---|
3324 | //cubic terms for the other pieces (in case nPiece>1). |
---|
3325 | std::vector<double> y(nDOF); |
---|
3326 | for (int i = 0; i < nDOF; ++i) { |
---|
3327 | y[i] = 0.0; |
---|
3328 | for (int j = 0; j < nDOF; ++j) { |
---|
3329 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
3330 | } |
---|
3331 | } |
---|
3332 | |
---|
3333 | double a0 = y[0]; |
---|
3334 | double a1 = y[1]; |
---|
3335 | double a2 = y[2]; |
---|
3336 | double a3 = y[3]; |
---|
3337 | |
---|
3338 | int j = 0; |
---|
3339 | for (int n = 0; n < nPiece; ++n) { |
---|
3340 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
3341 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i]; |
---|
3342 | } |
---|
3343 | params[j] = a0; |
---|
3344 | params[j+1] = a1; |
---|
3345 | params[j+2] = a2; |
---|
3346 | params[j+3] = a3; |
---|
3347 | j += 4; |
---|
3348 | |
---|
3349 | if (n == nPiece-1) break; |
---|
3350 | |
---|
3351 | double d = y[4+n]; |
---|
3352 | double iE = invEdge[n]; |
---|
3353 | a0 += d; |
---|
3354 | a1 -= 3.0*d*iE; |
---|
3355 | a2 += 3.0*d*iE*iE; |
---|
3356 | a3 -= d*iE*iE*iE; |
---|
3357 | } |
---|
3358 | |
---|
3359 | //subtract constant value for masked regions at the edge of spectrum |
---|
3360 | if (idxEdge[0] > 0) { |
---|
3361 | int n = idxEdge[0]; |
---|
3362 | for (int i = 0; i < idxEdge[0]; ++i) { |
---|
3363 | //--cubic extrapolate-- |
---|
3364 | //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i]; |
---|
3365 | //--linear extrapolate-- |
---|
3366 | //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
3367 | //--constant-- |
---|
3368 | r1[i] = r1[n]; |
---|
3369 | } |
---|
3370 | } |
---|
3371 | if (idxEdge[nPiece] < nChan) { |
---|
3372 | int n = idxEdge[nPiece]-1; |
---|
3373 | for (int i = idxEdge[nPiece]; i < nChan; ++i) { |
---|
3374 | //--cubic extrapolate-- |
---|
3375 | //int m = 4*(nPiece-1); |
---|
3376 | //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i]; |
---|
3377 | //--linear extrapolate-- |
---|
3378 | //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
3379 | //--constant-- |
---|
3380 | r1[i] = r1[n]; |
---|
3381 | } |
---|
3382 | } |
---|
3383 | |
---|
3384 | for (int i = 0; i < nChan; ++i) { |
---|
3385 | residual[i] = z1[i] - r1[i]; |
---|
3386 | } |
---|
3387 | |
---|
3388 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
3389 | break; |
---|
3390 | } else { |
---|
3391 | double stdDev = 0.0; |
---|
3392 | for (int i = 0; i < nChan; ++i) { |
---|
3393 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
3394 | } |
---|
3395 | stdDev = sqrt(stdDev/(double)nData); |
---|
3396 | |
---|
3397 | double thres = stdDev * thresClip; |
---|
3398 | int newNData = 0; |
---|
3399 | for (int i = 0; i < nChan; ++i) { |
---|
3400 | if (abs(residual[i]) >= thres) { |
---|
3401 | maskArray[i] = 0; |
---|
3402 | } |
---|
3403 | if (maskArray[i] > 0) { |
---|
3404 | newNData++; |
---|
3405 | } |
---|
3406 | } |
---|
3407 | if (newNData == nData) { |
---|
3408 | break; //no more flag to add. iteration stops. |
---|
3409 | } else { |
---|
3410 | nData = newNData; |
---|
3411 | } |
---|
3412 | } |
---|
3413 | } |
---|
3414 | |
---|
3415 | nClipped = initNData - nData; |
---|
3416 | |
---|
3417 | std::vector<float> result(nChan); |
---|
3418 | if (getResidual) { |
---|
3419 | for (int i = 0; i < nChan; ++i) { |
---|
3420 | result[i] = (float)residual[i]; |
---|
3421 | } |
---|
3422 | } else { |
---|
3423 | for (int i = 0; i < nChan; ++i) { |
---|
3424 | result[i] = (float)r1[i]; |
---|
3425 | } |
---|
3426 | } |
---|
3427 | |
---|
3428 | return result; |
---|
3429 | } |
---|
3430 | |
---|
3431 | 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) |
---|
3432 | { |
---|
3433 | nWaves.clear(); |
---|
3434 | |
---|
3435 | if (applyFFT) { |
---|
3436 | string fftThAttr; |
---|
3437 | float fftThSigma; |
---|
3438 | int fftThTop; |
---|
3439 | parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop); |
---|
3440 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves); |
---|
3441 | } |
---|
3442 | |
---|
3443 | addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves); |
---|
3444 | } |
---|
3445 | |
---|
3446 | void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop) |
---|
3447 | { |
---|
3448 | uInt idxSigma = fftThresh.find("sigma"); |
---|
3449 | uInt idxTop = fftThresh.find("top"); |
---|
3450 | |
---|
3451 | if (idxSigma == fftThresh.size() - 5) { |
---|
3452 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5)); |
---|
3453 | is >> fftThSigma; |
---|
3454 | fftThAttr = "sigma"; |
---|
3455 | } else if (idxTop == 0) { |
---|
3456 | std::istringstream is(fftThresh.substr(3)); |
---|
3457 | is >> fftThTop; |
---|
3458 | fftThAttr = "top"; |
---|
3459 | } else { |
---|
3460 | bool isNumber = true; |
---|
3461 | for (uInt i = 0; i < fftThresh.size()-1; ++i) { |
---|
3462 | char ch = (fftThresh.substr(i, 1).c_str())[0]; |
---|
3463 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) { |
---|
3464 | isNumber = false; |
---|
3465 | break; |
---|
3466 | } |
---|
3467 | } |
---|
3468 | if (isNumber) { |
---|
3469 | std::istringstream is(fftThresh); |
---|
3470 | is >> fftThSigma; |
---|
3471 | fftThAttr = "sigma"; |
---|
3472 | } else { |
---|
3473 | throw(AipsError("fftthresh has a wrong value")); |
---|
3474 | } |
---|
3475 | } |
---|
3476 | } |
---|
3477 | |
---|
3478 | 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) |
---|
3479 | { |
---|
3480 | std::vector<float> fspec; |
---|
3481 | if (fftMethod == "fft") { |
---|
3482 | fspec = execFFT(whichrow, chanMask, false, true); |
---|
3483 | //} else if (fftMethod == "lsp") { |
---|
3484 | // fspec = lombScarglePeriodogram(whichrow); |
---|
3485 | } |
---|
3486 | |
---|
3487 | if (fftThAttr == "sigma") { |
---|
3488 | float mean = 0.0; |
---|
3489 | float mean2 = 0.0; |
---|
3490 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
3491 | mean += fspec[i]; |
---|
3492 | mean2 += fspec[i]*fspec[i]; |
---|
3493 | } |
---|
3494 | mean /= float(fspec.size()); |
---|
3495 | mean2 /= float(fspec.size()); |
---|
3496 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean)); |
---|
3497 | |
---|
3498 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
3499 | if (fspec[i] >= thres) { |
---|
3500 | nWaves.push_back(i); |
---|
3501 | } |
---|
3502 | } |
---|
3503 | |
---|
3504 | } else if (fftThAttr == "top") { |
---|
3505 | for (int i = 0; i < fftThTop; ++i) { |
---|
3506 | float max = 0.0; |
---|
3507 | int maxIdx = 0; |
---|
3508 | for (uInt j = 0; j < fspec.size(); ++j) { |
---|
3509 | if (fspec[j] > max) { |
---|
3510 | max = fspec[j]; |
---|
3511 | maxIdx = j; |
---|
3512 | } |
---|
3513 | } |
---|
3514 | nWaves.push_back(maxIdx); |
---|
3515 | fspec[maxIdx] = 0.0; |
---|
3516 | } |
---|
3517 | |
---|
3518 | } |
---|
3519 | |
---|
3520 | if (nWaves.size() > 1) { |
---|
3521 | sort(nWaves.begin(), nWaves.end()); |
---|
3522 | } |
---|
3523 | } |
---|
3524 | |
---|
3525 | void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
3526 | { |
---|
3527 | std::vector<int> tempAddNWaves, tempRejectNWaves; |
---|
3528 | for (uInt i = 0; i < addNWaves.size(); ++i) { |
---|
3529 | tempAddNWaves.push_back(addNWaves[i]); |
---|
3530 | } |
---|
3531 | if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) { |
---|
3532 | setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves); |
---|
3533 | } |
---|
3534 | |
---|
3535 | for (uInt i = 0; i < rejectNWaves.size(); ++i) { |
---|
3536 | tempRejectNWaves.push_back(rejectNWaves[i]); |
---|
3537 | } |
---|
3538 | if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) { |
---|
3539 | setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves); |
---|
3540 | } |
---|
3541 | |
---|
3542 | for (uInt i = 0; i < tempAddNWaves.size(); ++i) { |
---|
3543 | bool found = false; |
---|
3544 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
3545 | if (nWaves[j] == tempAddNWaves[i]) { |
---|
3546 | found = true; |
---|
3547 | break; |
---|
3548 | } |
---|
3549 | } |
---|
3550 | if (!found) nWaves.push_back(tempAddNWaves[i]); |
---|
3551 | } |
---|
3552 | |
---|
3553 | for (uInt i = 0; i < tempRejectNWaves.size(); ++i) { |
---|
3554 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) { |
---|
3555 | if (*j == tempRejectNWaves[i]) { |
---|
3556 | j = nWaves.erase(j); |
---|
3557 | } else { |
---|
3558 | ++j; |
---|
3559 | } |
---|
3560 | } |
---|
3561 | } |
---|
3562 | |
---|
3563 | if (nWaves.size() > 1) { |
---|
3564 | sort(nWaves.begin(), nWaves.end()); |
---|
3565 | unique(nWaves.begin(), nWaves.end()); |
---|
3566 | } |
---|
3567 | } |
---|
3568 | |
---|
3569 | void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves) |
---|
3570 | { |
---|
3571 | if ((nWaves.size() == 2)&&(nWaves[1] == -999)) { |
---|
3572 | int val = nWaves[0]; |
---|
3573 | int nyquistFreq = nchan(getIF(whichrow))/2+1; |
---|
3574 | nWaves.clear(); |
---|
3575 | if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759 |
---|
3576 | nWaves.push_back(0); |
---|
3577 | } |
---|
3578 | while (val <= nyquistFreq) { |
---|
3579 | nWaves.push_back(val); |
---|
3580 | val++; |
---|
3581 | } |
---|
3582 | } |
---|
3583 | } |
---|
3584 | |
---|
3585 | 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) |
---|
3586 | { |
---|
3587 | try { |
---|
3588 | ofstream ofs; |
---|
3589 | String coordInfo = ""; |
---|
3590 | bool hasSameNchan = true; |
---|
3591 | bool outTextFile = false; |
---|
3592 | bool csvFormat = false; |
---|
3593 | |
---|
3594 | if (blfile != "") { |
---|
3595 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
3596 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
3597 | if (ofs) outTextFile = true; |
---|
3598 | } |
---|
3599 | |
---|
3600 | if (outLogger || outTextFile) { |
---|
3601 | coordInfo = getCoordInfo()[0]; |
---|
3602 | if (coordInfo == "") coordInfo = "channel"; |
---|
3603 | hasSameNchan = hasSameNchanOverIFs(); |
---|
3604 | } |
---|
3605 | |
---|
3606 | //Fitter fitter = Fitter(); |
---|
3607 | //fitter.setExpression("sinusoid", nWaves); |
---|
3608 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
3609 | |
---|
3610 | int nRow = nrow(); |
---|
3611 | std::vector<bool> chanMask; |
---|
3612 | std::vector<int> nWaves; |
---|
3613 | |
---|
3614 | bool showProgress; |
---|
3615 | int minNRow; |
---|
3616 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
3617 | |
---|
3618 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
3619 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
3620 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
3621 | |
---|
3622 | //FOR DEBUGGING------------ |
---|
3623 | /* |
---|
3624 | if (whichrow < 0) {// == nRow -1) { |
---|
3625 | cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow); |
---|
3626 | if (applyFFT) { |
---|
3627 | cout << "[ "; |
---|
3628 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
3629 | cout << nWaves[j] << ", "; |
---|
3630 | } |
---|
3631 | cout << " ] " << endl; |
---|
3632 | } |
---|
3633 | cout << flush; |
---|
3634 | } |
---|
3635 | */ |
---|
3636 | //------------------------- |
---|
3637 | |
---|
3638 | //fitBaseline(chanMask, whichrow, fitter); |
---|
3639 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
3640 | std::vector<float> params; |
---|
3641 | int nClipped = 0; |
---|
3642 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
3643 | setSpectrum(res, whichrow); |
---|
3644 | // |
---|
3645 | |
---|
3646 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped); |
---|
3647 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
3648 | } |
---|
3649 | |
---|
3650 | if (outTextFile) ofs.close(); |
---|
3651 | |
---|
3652 | } catch (...) { |
---|
3653 | throw; |
---|
3654 | } |
---|
3655 | } |
---|
3656 | |
---|
3657 | 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) |
---|
3658 | { |
---|
3659 | try { |
---|
3660 | ofstream ofs; |
---|
3661 | String coordInfo = ""; |
---|
3662 | bool hasSameNchan = true; |
---|
3663 | bool outTextFile = false; |
---|
3664 | bool csvFormat = false; |
---|
3665 | |
---|
3666 | if (blfile != "") { |
---|
3667 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
3668 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
3669 | if (ofs) outTextFile = true; |
---|
3670 | } |
---|
3671 | |
---|
3672 | if (outLogger || outTextFile) { |
---|
3673 | coordInfo = getCoordInfo()[0]; |
---|
3674 | if (coordInfo == "") coordInfo = "channel"; |
---|
3675 | hasSameNchan = hasSameNchanOverIFs(); |
---|
3676 | } |
---|
3677 | |
---|
3678 | //Fitter fitter = Fitter(); |
---|
3679 | //fitter.setExpression("sinusoid", nWaves); |
---|
3680 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
3681 | |
---|
3682 | int nRow = nrow(); |
---|
3683 | std::vector<bool> chanMask; |
---|
3684 | std::vector<int> nWaves; |
---|
3685 | |
---|
3686 | int minEdgeSize = getIFNos().size()*2; |
---|
3687 | STLineFinder lineFinder = STLineFinder(); |
---|
3688 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
3689 | |
---|
3690 | bool showProgress; |
---|
3691 | int minNRow; |
---|
3692 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
3693 | |
---|
3694 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
3695 | |
---|
3696 | //------------------------------------------------------- |
---|
3697 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
3698 | //------------------------------------------------------- |
---|
3699 | int edgeSize = edge.size(); |
---|
3700 | std::vector<int> currentEdge; |
---|
3701 | if (edgeSize >= 2) { |
---|
3702 | int idx = 0; |
---|
3703 | if (edgeSize > 2) { |
---|
3704 | if (edgeSize < minEdgeSize) { |
---|
3705 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
3706 | } |
---|
3707 | idx = 2 * getIF(whichrow); |
---|
3708 | } |
---|
3709 | currentEdge.push_back(edge[idx]); |
---|
3710 | currentEdge.push_back(edge[idx+1]); |
---|
3711 | } else { |
---|
3712 | throw(AipsError("Wrong length of edge element")); |
---|
3713 | } |
---|
3714 | lineFinder.setData(getSpectrum(whichrow)); |
---|
3715 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
3716 | chanMask = lineFinder.getMask(); |
---|
3717 | //------------------------------------------------------- |
---|
3718 | |
---|
3719 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
3720 | |
---|
3721 | //fitBaseline(chanMask, whichrow, fitter); |
---|
3722 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
3723 | std::vector<float> params; |
---|
3724 | int nClipped = 0; |
---|
3725 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
3726 | setSpectrum(res, whichrow); |
---|
3727 | // |
---|
3728 | |
---|
3729 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped); |
---|
3730 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
3731 | } |
---|
3732 | |
---|
3733 | if (outTextFile) ofs.close(); |
---|
3734 | |
---|
3735 | } catch (...) { |
---|
3736 | throw; |
---|
3737 | } |
---|
3738 | } |
---|
3739 | |
---|
3740 | 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) |
---|
3741 | { |
---|
3742 | if (data.size() != mask.size()) { |
---|
3743 | throw(AipsError("data and mask sizes are not identical")); |
---|
3744 | } |
---|
3745 | if (data.size() < 2) { |
---|
3746 | throw(AipsError("data size is too short")); |
---|
3747 | } |
---|
3748 | if (waveNumbers.size() == 0) { |
---|
3749 | throw(AipsError("no wave numbers given")); |
---|
3750 | } |
---|
3751 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers |
---|
3752 | nWaves.reserve(waveNumbers.size()); |
---|
3753 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves)); |
---|
3754 | sort(nWaves.begin(), nWaves.end()); |
---|
3755 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end()); |
---|
3756 | nWaves.erase(end_it, nWaves.end()); |
---|
3757 | |
---|
3758 | int minNWaves = nWaves[0]; |
---|
3759 | if (minNWaves < 0) { |
---|
3760 | throw(AipsError("wave number must be positive or zero (i.e. constant)")); |
---|
3761 | } |
---|
3762 | bool hasConstantTerm = (minNWaves == 0); |
---|
3763 | |
---|
3764 | int nChan = data.size(); |
---|
3765 | std::vector<int> maskArray; |
---|
3766 | std::vector<int> x; |
---|
3767 | for (int i = 0; i < nChan; ++i) { |
---|
3768 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
3769 | if (mask[i]) { |
---|
3770 | x.push_back(i); |
---|
3771 | } |
---|
3772 | } |
---|
3773 | |
---|
3774 | int initNData = x.size(); |
---|
3775 | |
---|
3776 | int nData = initNData; |
---|
3777 | int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve. |
---|
3778 | |
---|
3779 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
3780 | 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) |
---|
3781 | |
---|
3782 | // xArray : contains elemental values for computing the least-square matrix. |
---|
3783 | // xArray.size() is nDOF and xArray[*].size() is nChan. |
---|
3784 | // Each xArray element are as follows: |
---|
3785 | // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
3786 | // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])}, |
---|
3787 | // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])}, |
---|
3788 | // where (1 <= n <= nMaxWavesInSW), |
---|
3789 | // or, |
---|
3790 | // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])}, |
---|
3791 | // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])}, |
---|
3792 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()). |
---|
3793 | std::vector<std::vector<double> > xArray; |
---|
3794 | if (hasConstantTerm) { |
---|
3795 | std::vector<double> xu; |
---|
3796 | for (int j = 0; j < nChan; ++j) { |
---|
3797 | xu.push_back(1.0); |
---|
3798 | } |
---|
3799 | xArray.push_back(xu); |
---|
3800 | } |
---|
3801 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) { |
---|
3802 | double xFactor = baseXFactor*(double)nWaves[i]; |
---|
3803 | std::vector<double> xs, xc; |
---|
3804 | xs.clear(); |
---|
3805 | xc.clear(); |
---|
3806 | for (int j = 0; j < nChan; ++j) { |
---|
3807 | xs.push_back(sin(xFactor*(double)j)); |
---|
3808 | xc.push_back(cos(xFactor*(double)j)); |
---|
3809 | } |
---|
3810 | xArray.push_back(xs); |
---|
3811 | xArray.push_back(xc); |
---|
3812 | } |
---|
3813 | |
---|
3814 | std::vector<double> z1, r1, residual; |
---|
3815 | for (int i = 0; i < nChan; ++i) { |
---|
3816 | z1.push_back((double)data[i]); |
---|
3817 | r1.push_back(0.0); |
---|
3818 | residual.push_back(0.0); |
---|
3819 | } |
---|
3820 | |
---|
3821 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
3822 | // xMatrix : horizontal concatenation of |
---|
3823 | // the least-sq. matrix (left) and an |
---|
3824 | // identity matrix (right). |
---|
3825 | // the right part is used to calculate the inverse matrix of the left part. |
---|
3826 | double xMatrix[nDOF][2*nDOF]; |
---|
3827 | double zMatrix[nDOF]; |
---|
3828 | for (int i = 0; i < nDOF; ++i) { |
---|
3829 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
3830 | xMatrix[i][j] = 0.0; |
---|
3831 | } |
---|
3832 | xMatrix[i][nDOF+i] = 1.0; |
---|
3833 | zMatrix[i] = 0.0; |
---|
3834 | } |
---|
3835 | |
---|
3836 | int nUseData = 0; |
---|
3837 | for (int k = 0; k < nChan; ++k) { |
---|
3838 | if (maskArray[k] == 0) continue; |
---|
3839 | |
---|
3840 | for (int i = 0; i < nDOF; ++i) { |
---|
3841 | for (int j = i; j < nDOF; ++j) { |
---|
3842 | xMatrix[i][j] += xArray[i][k] * xArray[j][k]; |
---|
3843 | } |
---|
3844 | zMatrix[i] += z1[k] * xArray[i][k]; |
---|
3845 | } |
---|
3846 | |
---|
3847 | nUseData++; |
---|
3848 | } |
---|
3849 | |
---|
3850 | if (nUseData < 1) { |
---|
3851 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
3852 | } |
---|
3853 | |
---|
3854 | for (int i = 0; i < nDOF; ++i) { |
---|
3855 | for (int j = 0; j < i; ++j) { |
---|
3856 | xMatrix[i][j] = xMatrix[j][i]; |
---|
3857 | } |
---|
3858 | } |
---|
3859 | |
---|
3860 | std::vector<double> invDiag; |
---|
3861 | for (int i = 0; i < nDOF; ++i) { |
---|
3862 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
3863 | for (int j = 0; j < nDOF; ++j) { |
---|
3864 | xMatrix[i][j] *= invDiag[i]; |
---|
3865 | } |
---|
3866 | } |
---|
3867 | |
---|
3868 | for (int k = 0; k < nDOF; ++k) { |
---|
3869 | for (int i = 0; i < nDOF; ++i) { |
---|
3870 | if (i != k) { |
---|
3871 | double factor1 = xMatrix[k][k]; |
---|
3872 | double factor2 = xMatrix[i][k]; |
---|
3873 | for (int j = k; j < 2*nDOF; ++j) { |
---|
3874 | xMatrix[i][j] *= factor1; |
---|
3875 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
3876 | xMatrix[i][j] /= factor1; |
---|
3877 | } |
---|
3878 | } |
---|
3879 | } |
---|
3880 | double xDiag = xMatrix[k][k]; |
---|
3881 | for (int j = k; j < 2*nDOF; ++j) { |
---|
3882 | xMatrix[k][j] /= xDiag; |
---|
3883 | } |
---|
3884 | } |
---|
3885 | |
---|
3886 | for (int i = 0; i < nDOF; ++i) { |
---|
3887 | for (int j = 0; j < nDOF; ++j) { |
---|
3888 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
3889 | } |
---|
3890 | } |
---|
3891 | //compute a vector y which consists of the coefficients of the sinusoids forming the |
---|
3892 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine |
---|
3893 | //and cosine functions, respectively. |
---|
3894 | std::vector<double> y; |
---|
3895 | params.clear(); |
---|
3896 | for (int i = 0; i < nDOF; ++i) { |
---|
3897 | y.push_back(0.0); |
---|
3898 | for (int j = 0; j < nDOF; ++j) { |
---|
3899 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
3900 | } |
---|
3901 | params.push_back(y[i]); |
---|
3902 | } |
---|
3903 | |
---|
3904 | for (int i = 0; i < nChan; ++i) { |
---|
3905 | r1[i] = y[0]; |
---|
3906 | for (int j = 1; j < nDOF; ++j) { |
---|
3907 | r1[i] += y[j]*xArray[j][i]; |
---|
3908 | } |
---|
3909 | residual[i] = z1[i] - r1[i]; |
---|
3910 | } |
---|
3911 | |
---|
3912 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
3913 | break; |
---|
3914 | } else { |
---|
3915 | double stdDev = 0.0; |
---|
3916 | for (int i = 0; i < nChan; ++i) { |
---|
3917 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
3918 | } |
---|
3919 | stdDev = sqrt(stdDev/(double)nData); |
---|
3920 | |
---|
3921 | double thres = stdDev * thresClip; |
---|
3922 | int newNData = 0; |
---|
3923 | for (int i = 0; i < nChan; ++i) { |
---|
3924 | if (abs(residual[i]) >= thres) { |
---|
3925 | maskArray[i] = 0; |
---|
3926 | } |
---|
3927 | if (maskArray[i] > 0) { |
---|
3928 | newNData++; |
---|
3929 | } |
---|
3930 | } |
---|
3931 | if (newNData == nData) { |
---|
3932 | break; //no more flag to add. iteration stops. |
---|
3933 | } else { |
---|
3934 | nData = newNData; |
---|
3935 | } |
---|
3936 | } |
---|
3937 | } |
---|
3938 | |
---|
3939 | nClipped = initNData - nData; |
---|
3940 | |
---|
3941 | std::vector<float> result; |
---|
3942 | if (getResidual) { |
---|
3943 | for (int i = 0; i < nChan; ++i) { |
---|
3944 | result.push_back((float)residual[i]); |
---|
3945 | } |
---|
3946 | } else { |
---|
3947 | for (int i = 0; i < nChan; ++i) { |
---|
3948 | result.push_back((float)r1[i]); |
---|
3949 | } |
---|
3950 | } |
---|
3951 | |
---|
3952 | return result; |
---|
3953 | } |
---|
3954 | |
---|
3955 | void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter) |
---|
3956 | { |
---|
3957 | std::vector<double> dAbcissa = getAbcissa(whichrow); |
---|
3958 | std::vector<float> abcissa; |
---|
3959 | for (uInt i = 0; i < dAbcissa.size(); ++i) { |
---|
3960 | abcissa.push_back((float)dAbcissa[i]); |
---|
3961 | } |
---|
3962 | std::vector<float> spec = getSpectrum(whichrow); |
---|
3963 | |
---|
3964 | fitter.setData(abcissa, spec, mask); |
---|
3965 | fitter.lfit(); |
---|
3966 | } |
---|
3967 | |
---|
3968 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask) |
---|
3969 | { |
---|
3970 | /**** |
---|
3971 | double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd; |
---|
3972 | double elapse1 = 0.0; |
---|
3973 | double elapse2 = 0.0; |
---|
3974 | |
---|
3975 | ms1TimeStart = mathutil::gettimeofday_sec(); |
---|
3976 | ****/ |
---|
3977 | |
---|
3978 | std::vector<bool> mask = getMask(whichrow); |
---|
3979 | |
---|
3980 | /**** |
---|
3981 | ms1TimeEnd = mathutil::gettimeofday_sec(); |
---|
3982 | elapse1 = ms1TimeEnd - ms1TimeStart; |
---|
3983 | std::cout << "ms1 : " << elapse1 << " (sec.)" << endl; |
---|
3984 | ms2TimeStart = mathutil::gettimeofday_sec(); |
---|
3985 | ****/ |
---|
3986 | |
---|
3987 | uInt maskSize = mask.size(); |
---|
3988 | if (inMask.size() != 0) { |
---|
3989 | if (maskSize != inMask.size()) { |
---|
3990 | throw(AipsError("mask sizes are not the same.")); |
---|
3991 | } |
---|
3992 | for (uInt i = 0; i < maskSize; ++i) { |
---|
3993 | mask[i] = mask[i] && inMask[i]; |
---|
3994 | } |
---|
3995 | } |
---|
3996 | |
---|
3997 | /**** |
---|
3998 | ms2TimeEnd = mathutil::gettimeofday_sec(); |
---|
3999 | elapse2 = ms2TimeEnd - ms2TimeStart; |
---|
4000 | std::cout << "ms2 : " << elapse2 << " (sec.)" << endl; |
---|
4001 | ****/ |
---|
4002 | |
---|
4003 | return mask; |
---|
4004 | } |
---|
4005 | |
---|
4006 | /* |
---|
4007 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder) |
---|
4008 | { |
---|
4009 | int edgeSize = edge.size(); |
---|
4010 | std::vector<int> currentEdge; |
---|
4011 | if (edgeSize >= 2) { |
---|
4012 | int idx = 0; |
---|
4013 | if (edgeSize > 2) { |
---|
4014 | if (edgeSize < minEdgeSize) { |
---|
4015 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
4016 | } |
---|
4017 | idx = 2 * getIF(whichrow); |
---|
4018 | } |
---|
4019 | currentEdge.push_back(edge[idx]); |
---|
4020 | currentEdge.push_back(edge[idx+1]); |
---|
4021 | } else { |
---|
4022 | throw(AipsError("Wrong length of edge element")); |
---|
4023 | } |
---|
4024 | |
---|
4025 | lineFinder.setData(getSpectrum(whichrow)); |
---|
4026 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow); |
---|
4027 | |
---|
4028 | return lineFinder.getMask(); |
---|
4029 | } |
---|
4030 | */ |
---|
4031 | |
---|
4032 | /* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */ |
---|
4033 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter) |
---|
4034 | { |
---|
4035 | if (outLogger || outTextFile) { |
---|
4036 | std::vector<float> params = fitter.getParameters(); |
---|
4037 | std::vector<bool> fixed = fitter.getFixedParameters(); |
---|
4038 | float rms = getRms(chanMask, whichrow); |
---|
4039 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
4040 | |
---|
4041 | if (outLogger) { |
---|
4042 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
4043 | ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
4044 | } |
---|
4045 | if (outTextFile) { |
---|
4046 | ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true, csvFormat) << flush; |
---|
4047 | } |
---|
4048 | } |
---|
4049 | } |
---|
4050 | |
---|
4051 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */ |
---|
4052 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, 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) |
---|
4053 | { |
---|
4054 | if (outLogger || outTextFile) { |
---|
4055 | /**** |
---|
4056 | double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd; |
---|
4057 | double elapse1 = 0.0; |
---|
4058 | double elapse2 = 0.0; |
---|
4059 | |
---|
4060 | ms1TimeStart = mathutil::gettimeofday_sec(); |
---|
4061 | ****/ |
---|
4062 | |
---|
4063 | float rms = getRms(chanMask, whichrow); |
---|
4064 | |
---|
4065 | /**** |
---|
4066 | ms1TimeEnd = mathutil::gettimeofday_sec(); |
---|
4067 | elapse1 = ms1TimeEnd - ms1TimeStart; |
---|
4068 | std::cout << "ot1 : " << elapse1 << " (sec.)" << endl; |
---|
4069 | ms2TimeStart = mathutil::gettimeofday_sec(); |
---|
4070 | ****/ |
---|
4071 | |
---|
4072 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
4073 | std::vector<bool> fixed; |
---|
4074 | fixed.clear(); |
---|
4075 | |
---|
4076 | if (outLogger) { |
---|
4077 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
4078 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
4079 | } |
---|
4080 | if (outTextFile) { |
---|
4081 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush; |
---|
4082 | } |
---|
4083 | |
---|
4084 | /**** |
---|
4085 | ms2TimeEnd = mathutil::gettimeofday_sec(); |
---|
4086 | elapse2 = ms2TimeEnd - ms2TimeStart; |
---|
4087 | std::cout << "ot2 : " << elapse2 << " (sec.)" << endl; |
---|
4088 | ****/ |
---|
4089 | |
---|
4090 | } |
---|
4091 | } |
---|
4092 | |
---|
4093 | /* for chebyshev/sinusoid. will be merged once chebyshev/sinusoid is available in fitter (2011/3/10 WK) */ |
---|
4094 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, 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) |
---|
4095 | { |
---|
4096 | if (outLogger || outTextFile) { |
---|
4097 | float rms = getRms(chanMask, whichrow); |
---|
4098 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
4099 | std::vector<bool> fixed; |
---|
4100 | fixed.clear(); |
---|
4101 | |
---|
4102 | if (outLogger) { |
---|
4103 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
4104 | ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
4105 | } |
---|
4106 | if (outTextFile) { |
---|
4107 | ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush; |
---|
4108 | } |
---|
4109 | } |
---|
4110 | } |
---|
4111 | |
---|
4112 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow) |
---|
4113 | { |
---|
4114 | int idxDelimiter = progressInfo.find(","); |
---|
4115 | if (idxDelimiter < 0) { |
---|
4116 | throw(AipsError("wrong value in 'showprogress' parameter")) ; |
---|
4117 | } |
---|
4118 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true"); |
---|
4119 | std::istringstream is(progressInfo.substr(idxDelimiter+1)); |
---|
4120 | is >> minNRow; |
---|
4121 | } |
---|
4122 | |
---|
4123 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold) |
---|
4124 | { |
---|
4125 | if (showProgress && (nTotal >= nTotalThreshold)) { |
---|
4126 | int nInterval = int(floor(double(nTotal)/100.0)); |
---|
4127 | if (nInterval == 0) nInterval++; |
---|
4128 | |
---|
4129 | if (nProcessed % nInterval == 0) { |
---|
4130 | printf("\r"); //go to the head of line |
---|
4131 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted |
---|
4132 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) ); |
---|
4133 | printf("\x1b[39m\x1b[0m"); //set default attributes |
---|
4134 | fflush(NULL); |
---|
4135 | } |
---|
4136 | |
---|
4137 | if (nProcessed == nTotal - 1) { |
---|
4138 | printf("\r\x1b[K"); //clear |
---|
4139 | fflush(NULL); |
---|
4140 | } |
---|
4141 | |
---|
4142 | } |
---|
4143 | } |
---|
4144 | |
---|
4145 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly) |
---|
4146 | { |
---|
4147 | std::vector<bool> mask = getMask(whichrow); |
---|
4148 | |
---|
4149 | if (inMask.size() > 0) { |
---|
4150 | uInt maskSize = mask.size(); |
---|
4151 | if (maskSize != inMask.size()) { |
---|
4152 | throw(AipsError("mask sizes are not the same.")); |
---|
4153 | } |
---|
4154 | for (uInt i = 0; i < maskSize; ++i) { |
---|
4155 | mask[i] = mask[i] && inMask[i]; |
---|
4156 | } |
---|
4157 | } |
---|
4158 | |
---|
4159 | Vector<Float> spec = getSpectrum(whichrow); |
---|
4160 | mathutil::doZeroOrderInterpolation(spec, mask); |
---|
4161 | |
---|
4162 | FFTServer<Float,Complex> ffts; |
---|
4163 | Vector<Complex> fftres; |
---|
4164 | ffts.fft0(fftres, spec); |
---|
4165 | |
---|
4166 | std::vector<float> res; |
---|
4167 | float norm = float(2.0/double(spec.size())); |
---|
4168 | |
---|
4169 | if (getRealImag) { |
---|
4170 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
4171 | res.push_back(real(fftres[i])*norm); |
---|
4172 | res.push_back(imag(fftres[i])*norm); |
---|
4173 | } |
---|
4174 | } else { |
---|
4175 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
4176 | res.push_back(abs(fftres[i])*norm); |
---|
4177 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i])); |
---|
4178 | } |
---|
4179 | } |
---|
4180 | |
---|
4181 | return res; |
---|
4182 | } |
---|
4183 | |
---|
4184 | |
---|
4185 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow) |
---|
4186 | { |
---|
4187 | /**** |
---|
4188 | double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd; |
---|
4189 | double elapse1 = 0.0; |
---|
4190 | double elapse2 = 0.0; |
---|
4191 | |
---|
4192 | ms1TimeStart = mathutil::gettimeofday_sec(); |
---|
4193 | ****/ |
---|
4194 | |
---|
4195 | Vector<Float> spec; |
---|
4196 | |
---|
4197 | specCol_.get(whichrow, spec); |
---|
4198 | |
---|
4199 | /**** |
---|
4200 | ms1TimeEnd = mathutil::gettimeofday_sec(); |
---|
4201 | elapse1 = ms1TimeEnd - ms1TimeStart; |
---|
4202 | std::cout << "rm1 : " << elapse1 << " (sec.)" << endl; |
---|
4203 | ms2TimeStart = mathutil::gettimeofday_sec(); |
---|
4204 | ****/ |
---|
4205 | |
---|
4206 | float mean = 0.0; |
---|
4207 | float smean = 0.0; |
---|
4208 | int n = 0; |
---|
4209 | for (uInt i = 0; i < spec.nelements(); ++i) { |
---|
4210 | if (mask[i]) { |
---|
4211 | mean += spec[i]; |
---|
4212 | smean += spec[i]*spec[i]; |
---|
4213 | n++; |
---|
4214 | } |
---|
4215 | } |
---|
4216 | |
---|
4217 | mean /= (float)n; |
---|
4218 | smean /= (float)n; |
---|
4219 | |
---|
4220 | /**** |
---|
4221 | ms2TimeEnd = mathutil::gettimeofday_sec(); |
---|
4222 | elapse2 = ms2TimeEnd - ms2TimeStart; |
---|
4223 | std::cout << "rm2 : " << elapse2 << " (sec.)" << endl; |
---|
4224 | ****/ |
---|
4225 | |
---|
4226 | return sqrt(smean - mean*mean); |
---|
4227 | } |
---|
4228 | |
---|
4229 | |
---|
4230 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const |
---|
4231 | { |
---|
4232 | if (verbose) { |
---|
4233 | ostringstream oss; |
---|
4234 | |
---|
4235 | if (csvformat) { |
---|
4236 | oss << getScan(whichrow) << ","; |
---|
4237 | oss << getBeam(whichrow) << ","; |
---|
4238 | oss << getIF(whichrow) << ","; |
---|
4239 | oss << getPol(whichrow) << ","; |
---|
4240 | oss << getCycle(whichrow) << ","; |
---|
4241 | String commaReplacedMasklist = masklist; |
---|
4242 | string::size_type pos = 0; |
---|
4243 | while (pos = commaReplacedMasklist.find(","), pos != string::npos) { |
---|
4244 | commaReplacedMasklist.replace(pos, 1, ";"); |
---|
4245 | pos++; |
---|
4246 | } |
---|
4247 | oss << commaReplacedMasklist << ","; |
---|
4248 | } else { |
---|
4249 | oss << " Scan[" << getScan(whichrow) << "]"; |
---|
4250 | oss << " Beam[" << getBeam(whichrow) << "]"; |
---|
4251 | oss << " IF[" << getIF(whichrow) << "]"; |
---|
4252 | oss << " Pol[" << getPol(whichrow) << "]"; |
---|
4253 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl; |
---|
4254 | oss << "Fitter range = " << masklist << endl; |
---|
4255 | oss << "Baseline parameters" << endl; |
---|
4256 | } |
---|
4257 | oss << flush; |
---|
4258 | |
---|
4259 | return String(oss); |
---|
4260 | } |
---|
4261 | |
---|
4262 | return ""; |
---|
4263 | } |
---|
4264 | |
---|
4265 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const |
---|
4266 | { |
---|
4267 | if (verbose) { |
---|
4268 | ostringstream oss; |
---|
4269 | |
---|
4270 | if (csvformat) { |
---|
4271 | oss << rms << ","; |
---|
4272 | if (nClipped >= 0) { |
---|
4273 | oss << nClipped; |
---|
4274 | } |
---|
4275 | } else { |
---|
4276 | oss << "Results of baseline fit" << endl; |
---|
4277 | oss << " rms = " << setprecision(6) << rms << endl; |
---|
4278 | if (nClipped >= 0) { |
---|
4279 | oss << " Number of clipped channels = " << nClipped << endl; |
---|
4280 | } |
---|
4281 | for (int i = 0; i < 60; ++i) { |
---|
4282 | oss << "-"; |
---|
4283 | } |
---|
4284 | } |
---|
4285 | oss << endl; |
---|
4286 | oss << flush; |
---|
4287 | |
---|
4288 | return String(oss); |
---|
4289 | } |
---|
4290 | |
---|
4291 | return ""; |
---|
4292 | } |
---|
4293 | |
---|
4294 | std::string Scantable::formatBaselineParams(const std::vector<float>& params, |
---|
4295 | const std::vector<bool>& fixed, |
---|
4296 | float rms, |
---|
4297 | int nClipped, |
---|
4298 | const std::string& masklist, |
---|
4299 | int whichrow, |
---|
4300 | bool verbose, |
---|
4301 | bool csvformat, |
---|
4302 | int start, int count, |
---|
4303 | bool resetparamid) const |
---|
4304 | { |
---|
4305 | int nParam = (int)(params.size()); |
---|
4306 | |
---|
4307 | if (nParam < 1) { |
---|
4308 | return(" Not fitted"); |
---|
4309 | } else { |
---|
4310 | |
---|
4311 | ostringstream oss; |
---|
4312 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
4313 | |
---|
4314 | if (start < 0) start = 0; |
---|
4315 | if (count < 0) count = nParam; |
---|
4316 | int end = start + count; |
---|
4317 | if (end > nParam) end = nParam; |
---|
4318 | int paramidoffset = (resetparamid) ? (-start) : 0; |
---|
4319 | |
---|
4320 | for (int i = start; i < end; ++i) { |
---|
4321 | if (i > start) { |
---|
4322 | oss << ","; |
---|
4323 | } |
---|
4324 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : ""; |
---|
4325 | if (csvformat) { |
---|
4326 | oss << params[i] << sFix; |
---|
4327 | } else { |
---|
4328 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i]; |
---|
4329 | } |
---|
4330 | } |
---|
4331 | |
---|
4332 | if (csvformat) { |
---|
4333 | oss << ","; |
---|
4334 | } else { |
---|
4335 | oss << endl; |
---|
4336 | } |
---|
4337 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
4338 | |
---|
4339 | return String(oss); |
---|
4340 | } |
---|
4341 | |
---|
4342 | } |
---|
4343 | |
---|
4344 | 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, bool csvformat) const |
---|
4345 | { |
---|
4346 | int nOutParam = (int)(params.size()); |
---|
4347 | int nPiece = (int)(ranges.size()) - 1; |
---|
4348 | |
---|
4349 | if (nOutParam < 1) { |
---|
4350 | return(" Not fitted"); |
---|
4351 | } else if (nPiece < 0) { |
---|
4352 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose, csvformat); |
---|
4353 | } else if (nPiece < 1) { |
---|
4354 | return(" Bad count of the piece edge info"); |
---|
4355 | } else if (nOutParam % nPiece != 0) { |
---|
4356 | return(" Bad count of the output baseline parameters"); |
---|
4357 | } else { |
---|
4358 | |
---|
4359 | int nParam = nOutParam / nPiece; |
---|
4360 | |
---|
4361 | ostringstream oss; |
---|
4362 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
4363 | |
---|
4364 | if (csvformat) { |
---|
4365 | for (int i = 0; i < nPiece; ++i) { |
---|
4366 | oss << ranges[i] << "," << (ranges[i+1]-1) << ","; |
---|
4367 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
4368 | } |
---|
4369 | } else { |
---|
4370 | stringstream ss; |
---|
4371 | ss << ranges[nPiece] << flush; |
---|
4372 | int wRange = ss.str().size() * 2 + 5; |
---|
4373 | |
---|
4374 | for (int i = 0; i < nPiece; ++i) { |
---|
4375 | ss.str(""); |
---|
4376 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]"; |
---|
4377 | oss << left << setw(wRange) << ss.str(); |
---|
4378 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
4379 | //oss << endl; |
---|
4380 | } |
---|
4381 | } |
---|
4382 | |
---|
4383 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
4384 | |
---|
4385 | return String(oss); |
---|
4386 | } |
---|
4387 | |
---|
4388 | } |
---|
4389 | |
---|
4390 | bool Scantable::hasSameNchanOverIFs() |
---|
4391 | { |
---|
4392 | int nIF = nif(-1); |
---|
4393 | int nCh; |
---|
4394 | int totalPositiveNChan = 0; |
---|
4395 | int nPositiveNChan = 0; |
---|
4396 | |
---|
4397 | for (int i = 0; i < nIF; ++i) { |
---|
4398 | nCh = nchan(i); |
---|
4399 | if (nCh > 0) { |
---|
4400 | totalPositiveNChan += nCh; |
---|
4401 | nPositiveNChan++; |
---|
4402 | } |
---|
4403 | } |
---|
4404 | |
---|
4405 | return (totalPositiveNChan == (nPositiveNChan * nchan(0))); |
---|
4406 | } |
---|
4407 | |
---|
4408 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose) |
---|
4409 | { |
---|
4410 | if (mask.size() <= 0) { |
---|
4411 | throw(AipsError("The mask elements should be > 0")); |
---|
4412 | } |
---|
4413 | int IF = getIF(whichrow); |
---|
4414 | if (mask.size() != (uInt)nchan(IF)) { |
---|
4415 | throw(AipsError("Number of channels in scantable != number of mask elements")); |
---|
4416 | } |
---|
4417 | |
---|
4418 | if (verbose) { |
---|
4419 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE)); |
---|
4420 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo; |
---|
4421 | if (!hasSameNchan) { |
---|
4422 | logOs << endl << "This mask is only valid for IF=" << IF; |
---|
4423 | } |
---|
4424 | logOs << LogIO::POST; |
---|
4425 | } |
---|
4426 | |
---|
4427 | std::vector<double> abcissa = getAbcissa(whichrow); |
---|
4428 | std::vector<int> edge = getMaskEdgeIndices(mask); |
---|
4429 | |
---|
4430 | ostringstream oss; |
---|
4431 | oss.setf(ios::fixed); |
---|
4432 | oss << setprecision(1) << "["; |
---|
4433 | for (uInt i = 0; i < edge.size(); i+=2) { |
---|
4434 | if (i > 0) oss << ","; |
---|
4435 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]"; |
---|
4436 | } |
---|
4437 | oss << "]" << flush; |
---|
4438 | |
---|
4439 | return String(oss); |
---|
4440 | } |
---|
4441 | |
---|
4442 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask) |
---|
4443 | { |
---|
4444 | if (mask.size() <= 0) { |
---|
4445 | throw(AipsError("The mask elements should be > 0")); |
---|
4446 | } |
---|
4447 | |
---|
4448 | std::vector<int> out, startIndices, endIndices; |
---|
4449 | int maskSize = mask.size(); |
---|
4450 | |
---|
4451 | startIndices.clear(); |
---|
4452 | endIndices.clear(); |
---|
4453 | |
---|
4454 | if (mask[0]) { |
---|
4455 | startIndices.push_back(0); |
---|
4456 | } |
---|
4457 | for (int i = 1; i < maskSize; ++i) { |
---|
4458 | if ((!mask[i-1]) && mask[i]) { |
---|
4459 | startIndices.push_back(i); |
---|
4460 | } else if (mask[i-1] && (!mask[i])) { |
---|
4461 | endIndices.push_back(i-1); |
---|
4462 | } |
---|
4463 | } |
---|
4464 | if (mask[maskSize-1]) { |
---|
4465 | endIndices.push_back(maskSize-1); |
---|
4466 | } |
---|
4467 | |
---|
4468 | if (startIndices.size() != endIndices.size()) { |
---|
4469 | throw(AipsError("Inconsistent Mask Size: bad data?")); |
---|
4470 | } |
---|
4471 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
4472 | if (startIndices[i] > endIndices[i]) { |
---|
4473 | throw(AipsError("Mask start index > mask end index")); |
---|
4474 | } |
---|
4475 | } |
---|
4476 | |
---|
4477 | out.clear(); |
---|
4478 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
4479 | out.push_back(startIndices[i]); |
---|
4480 | out.push_back(endIndices[i]); |
---|
4481 | } |
---|
4482 | |
---|
4483 | return out; |
---|
4484 | } |
---|
4485 | |
---|
4486 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const |
---|
4487 | { |
---|
4488 | Vector<Float> tsys( tsysCol_(whichrow) ) ; |
---|
4489 | vector<float> stlTsys ; |
---|
4490 | tsys.tovector( stlTsys ) ; |
---|
4491 | return stlTsys ; |
---|
4492 | } |
---|
4493 | |
---|
4494 | vector<uint> Scantable::getMoleculeIdColumnData() const |
---|
4495 | { |
---|
4496 | Vector<uInt> molIds(mmolidCol_.getColumn()); |
---|
4497 | vector<uint> res; |
---|
4498 | molIds.tovector(res); |
---|
4499 | return res; |
---|
4500 | } |
---|
4501 | |
---|
4502 | void Scantable::setMoleculeIdColumnData(const std::vector<uint>& molids) |
---|
4503 | { |
---|
4504 | Vector<uInt> molIds(molids); |
---|
4505 | Vector<uInt> arr(mmolidCol_.getColumn()); |
---|
4506 | if ( molIds.nelements() != arr.nelements() ) |
---|
4507 | throw AipsError("The input data size must be the number of rows."); |
---|
4508 | mmolidCol_.putColumn(molIds); |
---|
4509 | } |
---|
4510 | |
---|
4511 | |
---|
4512 | } |
---|
4513 | //namespace asap |
---|