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) 2005-2013 |
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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 | |
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13 | // ASAP |
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14 | // STLineFinder must be included first to avoid compiler warnings related with _XOPEN_SOURCE |
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15 | #include "STLineFinder.h" |
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16 | #include "MathUtils.h" |
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17 | #include "STAttr.h" |
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18 | #include "STBaselineTable.h" |
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19 | #include "STPolCircular.h" |
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20 | #include "STPolLinear.h" |
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21 | #include "STPolStokes.h" |
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22 | #include "STUpgrade.h" |
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23 | #include "STFitter.h" |
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24 | #include "Scantable.h" |
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25 | |
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26 | #include <map> |
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27 | #include <sys/time.h> |
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28 | #include <iostream> |
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29 | |
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30 | #include <atnf/PKSIO/SrcType.h> |
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31 | |
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32 | #include <casa/aips.h> |
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33 | #include <casa/iomanip.h> |
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34 | #include <casa/iostream.h> |
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35 | #include <casa/OS/File.h> |
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36 | #include <casa/OS/Path.h> |
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37 | #include <casa/Logging/LogIO.h> |
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38 | #include <casa/Arrays/Array.h> |
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39 | #include <casa/Arrays/ArrayAccessor.h> |
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40 | #include <casa/Arrays/ArrayLogical.h> |
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41 | #include <casa/Arrays/ArrayMath.h> |
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42 | #include <casa/Arrays/MaskArrMath.h> |
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43 | #include <casa/Arrays/Slice.h> |
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44 | #include <casa/Arrays/Vector.h> |
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45 | #include <casa/Arrays/VectorSTLIterator.h> |
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46 | #include <casa/BasicMath/Math.h> |
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47 | #include <casa/BasicSL/Constants.h> |
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48 | #include <casa/Containers/RecordField.h> |
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49 | #include <casa/Logging/LogIO.h> |
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50 | #include <casa/Quanta/MVAngle.h> |
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51 | #include <casa/Quanta/MVTime.h> |
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52 | #include <casa/Utilities/GenSort.h> |
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53 | #include <casa/Utilities/Assert.h> |
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54 | |
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55 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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56 | |
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57 | // needed to avoid error in .tcc |
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58 | #include <measures/Measures/MCDirection.h> |
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59 | // |
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60 | #include <measures/Measures/MDirection.h> |
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61 | #include <measures/Measures/MEpoch.h> |
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62 | #include <measures/Measures/MFrequency.h> |
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63 | #include <measures/Measures/MeasRef.h> |
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64 | #include <measures/Measures/MeasTable.h> |
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65 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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66 | #include <measures/TableMeasures/TableMeasDesc.h> |
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67 | #include <measures/TableMeasures/TableMeasRefDesc.h> |
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68 | #include <measures/TableMeasures/TableMeasValueDesc.h> |
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69 | |
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70 | #include <tables/Tables/ArrColDesc.h> |
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71 | #include <tables/TaQL/ExprNode.h> |
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72 | #include <tables/Tables/ScaColDesc.h> |
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73 | #include <tables/Tables/SetupNewTab.h> |
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74 | #include <tables/Tables/TableCopy.h> |
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75 | #include <tables/Tables/TableDesc.h> |
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76 | #include <tables/Tables/TableIter.h> |
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77 | #include <tables/TaQL/TableParse.h> |
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78 | #include <tables/Tables/TableRecord.h> |
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79 | #include <tables/Tables/TableRow.h> |
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80 | #include <tables/Tables/TableVector.h> |
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81 | |
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82 | #define debug 1 |
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83 | |
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84 | using namespace casa; |
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85 | |
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86 | namespace asap { |
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87 | |
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88 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_; |
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89 | |
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90 | void Scantable::initFactories() { |
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91 | if ( factories_.empty() ) { |
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92 | Scantable::factories_["linear"] = &STPolLinear::myFactory; |
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93 | Scantable::factories_["circular"] = &STPolCircular::myFactory; |
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94 | Scantable::factories_["stokes"] = &STPolStokes::myFactory; |
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95 | } |
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96 | } |
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97 | |
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98 | Scantable::Scantable(Table::TableType ttype) : |
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99 | type_(ttype), |
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100 | cubicSplineModelPool_() |
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101 | { |
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102 | initFactories(); |
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103 | setupMainTable(); |
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104 | freqTable_ = STFrequencies(*this); |
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105 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table()); |
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106 | weatherTable_ = STWeather(*this); |
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107 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table()); |
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108 | focusTable_ = STFocus(*this); |
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109 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table()); |
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110 | tcalTable_ = STTcal(*this); |
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111 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table()); |
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112 | moleculeTable_ = STMolecules(*this); |
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113 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table()); |
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114 | historyTable_ = STHistory(*this); |
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115 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table()); |
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116 | fitTable_ = STFit(*this); |
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117 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table()); |
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118 | table_.tableInfo().setType( "Scantable" ) ; |
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119 | originalTable_ = table_; |
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120 | attach(); |
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121 | } |
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122 | |
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123 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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124 | type_(ttype), |
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125 | cubicSplineModelPool_() |
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126 | { |
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127 | initFactories(); |
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128 | |
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129 | Table tab(name, Table::Update); |
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130 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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131 | if (version != version_) { |
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132 | STUpgrade upgrader(version_); |
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133 | LogIO os( LogOrigin( "Scantable" ) ) ; |
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134 | os << LogIO::WARN |
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135 | << name << " data format version " << version |
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136 | << " is deprecated" << endl |
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137 | << "Running upgrade."<< endl |
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138 | << LogIO::POST ; |
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139 | std::string outname = upgrader.upgrade(name); |
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140 | if ( outname != name ) { |
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141 | os << LogIO::WARN |
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142 | << "Data will be loaded from " << outname << " instead of " |
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143 | << name << LogIO::POST ; |
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144 | tab = Table(outname, Table::Update ) ; |
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145 | } |
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146 | } |
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147 | if ( type_ == Table::Memory ) { |
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148 | table_ = tab.copyToMemoryTable(generateName()); |
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149 | } else { |
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150 | table_ = tab; |
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151 | } |
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152 | table_.tableInfo().setType( "Scantable" ) ; |
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153 | |
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154 | attachSubtables(); |
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155 | originalTable_ = table_; |
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156 | attach(); |
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157 | } |
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158 | /* |
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159 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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160 | type_(ttype) |
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161 | { |
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162 | initFactories(); |
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163 | Table tab(name, Table::Update); |
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164 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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165 | if (version != version_) { |
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166 | throw(AipsError("Unsupported version of ASAP file.")); |
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167 | } |
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168 | if ( type_ == Table::Memory ) { |
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169 | table_ = tab.copyToMemoryTable(generateName()); |
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170 | } else { |
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171 | table_ = tab; |
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172 | } |
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173 | |
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174 | attachSubtables(); |
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175 | originalTable_ = table_; |
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176 | attach(); |
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177 | } |
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178 | */ |
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179 | |
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180 | Scantable::Scantable( const Scantable& other, bool clear ) |
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181 | { |
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182 | // with or without data |
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183 | String newname = String(generateName()); |
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184 | type_ = other.table_.tableType(); |
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185 | if ( other.table_.tableType() == Table::Memory ) { |
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186 | if ( clear ) { |
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187 | table_ = TableCopy::makeEmptyMemoryTable(newname, |
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188 | other.table_, True); |
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189 | } else { |
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190 | table_ = other.table_.copyToMemoryTable(newname); |
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191 | } |
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192 | } else { |
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193 | other.table_.deepCopy(newname, Table::New, False, |
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194 | other.table_.endianFormat(), |
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195 | Bool(clear)); |
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196 | table_ = Table(newname, Table::Update); |
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197 | table_.markForDelete(); |
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198 | } |
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199 | table_.tableInfo().setType( "Scantable" ) ; |
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200 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
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201 | if ( clear ) copySubtables(other); |
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202 | attachSubtables(); |
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203 | originalTable_ = table_; |
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204 | attach(); |
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205 | } |
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206 | |
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207 | void Scantable::copySubtables(const Scantable& other) { |
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208 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES"); |
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209 | TableCopy::copyRows(t, other.freqTable_.table()); |
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210 | t = table_.rwKeywordSet().asTable("FOCUS"); |
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211 | TableCopy::copyRows(t, other.focusTable_.table()); |
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212 | t = table_.rwKeywordSet().asTable("WEATHER"); |
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213 | TableCopy::copyRows(t, other.weatherTable_.table()); |
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214 | t = table_.rwKeywordSet().asTable("TCAL"); |
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215 | TableCopy::copyRows(t, other.tcalTable_.table()); |
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216 | t = table_.rwKeywordSet().asTable("MOLECULES"); |
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217 | TableCopy::copyRows(t, other.moleculeTable_.table()); |
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218 | t = table_.rwKeywordSet().asTable("HISTORY"); |
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219 | TableCopy::copyRows(t, other.historyTable_.table()); |
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220 | t = table_.rwKeywordSet().asTable("FIT"); |
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221 | TableCopy::copyRows(t, other.fitTable_.table()); |
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222 | } |
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223 | |
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224 | void Scantable::attachSubtables() |
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225 | { |
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226 | freqTable_ = STFrequencies(table_); |
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227 | focusTable_ = STFocus(table_); |
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228 | weatherTable_ = STWeather(table_); |
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229 | tcalTable_ = STTcal(table_); |
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230 | moleculeTable_ = STMolecules(table_); |
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231 | historyTable_ = STHistory(table_); |
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232 | fitTable_ = STFit(table_); |
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233 | } |
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234 | |
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235 | Scantable::~Scantable() |
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236 | { |
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237 | } |
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238 | |
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239 | void Scantable::setupMainTable() |
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240 | { |
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241 | TableDesc td("", "1", TableDesc::Scratch); |
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242 | td.comment() = "An ASAP Scantable"; |
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243 | td.rwKeywordSet().define("VERSION", uInt(version_)); |
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244 | |
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245 | // n Cycles |
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246 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO")); |
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247 | // new index every nBeam x nIF x nPol |
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248 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO")); |
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249 | |
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250 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO")); |
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251 | td.addColumn(ScalarColumnDesc<uInt>("IFNO")); |
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252 | // linear, circular, stokes |
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253 | td.rwKeywordSet().define("POLTYPE", String("linear")); |
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254 | td.addColumn(ScalarColumnDesc<uInt>("POLNO")); |
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255 | |
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256 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID")); |
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257 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID")); |
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258 | |
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259 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO"); |
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260 | refbeamnoColumn.setDefault(Int(-1)); |
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261 | td.addColumn(refbeamnoColumn); |
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262 | |
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263 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW"); |
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264 | flagrowColumn.setDefault(uInt(0)); |
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265 | td.addColumn(flagrowColumn); |
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266 | |
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267 | td.addColumn(ScalarColumnDesc<Double>("TIME")); |
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268 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default |
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269 | TableMeasValueDesc measVal(td, "TIME"); |
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270 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef); |
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271 | mepochCol.write(td); |
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272 | |
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273 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL")); |
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274 | |
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275 | td.addColumn(ScalarColumnDesc<String>("SRCNAME")); |
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276 | // Type of source (on=0, off=1, other=-1) |
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277 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE"); |
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278 | stypeColumn.setDefault(Int(-1)); |
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279 | td.addColumn(stypeColumn); |
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280 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME")); |
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281 | |
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282 | //The actual Data Vectors |
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283 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA")); |
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284 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA")); |
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285 | td.addColumn(ArrayColumnDesc<Float>("TSYS")); |
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286 | |
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287 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION", |
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288 | IPosition(1,2), |
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289 | ColumnDesc::Direct)); |
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290 | TableMeasRefDesc mdirRef(MDirection::J2000); // default |
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291 | TableMeasValueDesc tmvdMDir(td, "DIRECTION"); |
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292 | // the TableMeasDesc gives the column a type |
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293 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef); |
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294 | // a uder set table type e.g. GALCTIC, B1950 ... |
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295 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000")); |
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296 | // writing create the measure column |
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297 | mdirCol.write(td); |
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298 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH")); |
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299 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION")); |
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300 | td.addColumn(ScalarColumnDesc<Float>("OPACITY")); |
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301 | |
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302 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID")); |
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303 | ScalarColumnDesc<Int> fitColumn("FIT_ID"); |
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304 | fitColumn.setDefault(Int(-1)); |
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305 | td.addColumn(fitColumn); |
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306 | |
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307 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID")); |
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308 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID")); |
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309 | |
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310 | // columns which just get dragged along, as they aren't used in asap |
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311 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY")); |
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312 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION")); |
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313 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION")); |
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314 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE")); |
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315 | |
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316 | td.rwKeywordSet().define("OBSMODE", String("")); |
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317 | |
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318 | // Now create Table SetUp from the description. |
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319 | SetupNewTable aNewTab(generateName(), td, Table::Scratch); |
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320 | table_ = Table(aNewTab, type_, 0); |
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321 | originalTable_ = table_; |
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322 | } |
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323 | |
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324 | void Scantable::attach() |
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325 | { |
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326 | timeCol_.attach(table_, "TIME"); |
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327 | srcnCol_.attach(table_, "SRCNAME"); |
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328 | srctCol_.attach(table_, "SRCTYPE"); |
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329 | specCol_.attach(table_, "SPECTRA"); |
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330 | flagsCol_.attach(table_, "FLAGTRA"); |
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331 | tsysCol_.attach(table_, "TSYS"); |
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332 | cycleCol_.attach(table_,"CYCLENO"); |
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333 | scanCol_.attach(table_, "SCANNO"); |
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334 | beamCol_.attach(table_, "BEAMNO"); |
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335 | ifCol_.attach(table_, "IFNO"); |
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336 | polCol_.attach(table_, "POLNO"); |
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337 | integrCol_.attach(table_, "INTERVAL"); |
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338 | azCol_.attach(table_, "AZIMUTH"); |
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339 | elCol_.attach(table_, "ELEVATION"); |
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340 | dirCol_.attach(table_, "DIRECTION"); |
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341 | fldnCol_.attach(table_, "FIELDNAME"); |
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342 | rbeamCol_.attach(table_, "REFBEAMNO"); |
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343 | |
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344 | mweatheridCol_.attach(table_,"WEATHER_ID"); |
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345 | mfitidCol_.attach(table_,"FIT_ID"); |
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346 | mfreqidCol_.attach(table_, "FREQ_ID"); |
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347 | mtcalidCol_.attach(table_, "TCAL_ID"); |
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348 | mfocusidCol_.attach(table_, "FOCUS_ID"); |
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349 | mmolidCol_.attach(table_, "MOLECULE_ID"); |
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350 | |
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351 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki) |
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352 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0); |
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353 | |
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354 | } |
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355 | |
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356 | template<class T, class T2> |
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357 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col, |
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358 | const String& colName, |
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359 | const T2& defValue) |
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360 | { |
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361 | try { |
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362 | col.attach(table_, colName); |
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363 | } catch (TableError& err) { |
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364 | String errMesg = err.getMesg(); |
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365 | if (errMesg == "Table column " + colName + " is unknown") { |
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366 | table_.addColumn(ScalarColumnDesc<T>(colName)); |
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367 | col.attach(table_, colName); |
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368 | col.fillColumn(static_cast<T>(defValue)); |
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369 | } else { |
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370 | throw; |
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371 | } |
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372 | } catch (...) { |
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373 | throw; |
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374 | } |
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375 | } |
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376 | |
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377 | template<class T, class T2> |
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378 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col, |
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379 | const String& colName, |
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380 | const Array<T2>& defValue) |
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381 | { |
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382 | try { |
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383 | col.attach(table_, colName); |
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384 | } catch (TableError& err) { |
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385 | String errMesg = err.getMesg(); |
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386 | if (errMesg == "Table column " + colName + " is unknown") { |
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387 | table_.addColumn(ArrayColumnDesc<T>(colName)); |
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388 | col.attach(table_, colName); |
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389 | |
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390 | int size = 0; |
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391 | ArrayIterator<T2>& it = defValue.begin(); |
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392 | while (it != defValue.end()) { |
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393 | ++size; |
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394 | ++it; |
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395 | } |
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396 | IPosition ip(1, size); |
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397 | Array<T>& arr(ip); |
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398 | for (int i = 0; i < size; ++i) |
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399 | arr[i] = static_cast<T>(defValue[i]); |
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400 | |
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401 | col.fillColumn(arr); |
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402 | } else { |
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403 | throw; |
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404 | } |
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405 | } catch (...) { |
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406 | throw; |
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407 | } |
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408 | } |
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409 | |
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410 | void Scantable::setHeader(const STHeader& sdh) |
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411 | { |
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412 | table_.rwKeywordSet().define("nIF", sdh.nif); |
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413 | table_.rwKeywordSet().define("nBeam", sdh.nbeam); |
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414 | table_.rwKeywordSet().define("nPol", sdh.npol); |
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415 | table_.rwKeywordSet().define("nChan", sdh.nchan); |
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416 | table_.rwKeywordSet().define("Observer", sdh.observer); |
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417 | table_.rwKeywordSet().define("Project", sdh.project); |
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418 | table_.rwKeywordSet().define("Obstype", sdh.obstype); |
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419 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname); |
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420 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition); |
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421 | table_.rwKeywordSet().define("Equinox", sdh.equinox); |
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422 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref); |
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423 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq); |
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424 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth); |
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425 | table_.rwKeywordSet().define("UTC", sdh.utc); |
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426 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit); |
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427 | table_.rwKeywordSet().define("Epoch", sdh.epoch); |
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428 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype); |
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429 | } |
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430 | |
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431 | STHeader Scantable::getHeader() const |
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432 | { |
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433 | STHeader sdh; |
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434 | table_.keywordSet().get("nBeam",sdh.nbeam); |
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435 | table_.keywordSet().get("nIF",sdh.nif); |
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436 | table_.keywordSet().get("nPol",sdh.npol); |
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437 | table_.keywordSet().get("nChan",sdh.nchan); |
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438 | table_.keywordSet().get("Observer", sdh.observer); |
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439 | table_.keywordSet().get("Project", sdh.project); |
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440 | table_.keywordSet().get("Obstype", sdh.obstype); |
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441 | table_.keywordSet().get("AntennaName", sdh.antennaname); |
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442 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition); |
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443 | table_.keywordSet().get("Equinox", sdh.equinox); |
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444 | table_.keywordSet().get("FreqRefFrame", sdh.freqref); |
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445 | table_.keywordSet().get("FreqRefVal", sdh.reffreq); |
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446 | table_.keywordSet().get("Bandwidth", sdh.bandwidth); |
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447 | table_.keywordSet().get("UTC", sdh.utc); |
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448 | table_.keywordSet().get("FluxUnit", sdh.fluxunit); |
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449 | table_.keywordSet().get("Epoch", sdh.epoch); |
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450 | table_.keywordSet().get("POLTYPE", sdh.poltype); |
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451 | return sdh; |
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452 | } |
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453 | |
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454 | void Scantable::setSourceType( int stype ) |
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455 | { |
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456 | if ( stype < 0 || stype > 1 ) |
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457 | throw(AipsError("Illegal sourcetype.")); |
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458 | TableVector<Int> tabvec(table_, "SRCTYPE"); |
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459 | tabvec = Int(stype); |
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460 | } |
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461 | |
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462 | void Scantable::setSourceName( const std::string& name ) |
---|
463 | { |
---|
464 | TableVector<String> tabvec(table_, "SRCNAME"); |
---|
465 | tabvec = name; |
---|
466 | } |
---|
467 | |
---|
468 | bool Scantable::conformant( const Scantable& other ) |
---|
469 | { |
---|
470 | return this->getHeader().conformant(other.getHeader()); |
---|
471 | } |
---|
472 | |
---|
473 | |
---|
474 | |
---|
475 | std::string Scantable::formatSec(Double x) const |
---|
476 | { |
---|
477 | Double xcop = x; |
---|
478 | MVTime mvt(xcop/24./3600.); // make days |
---|
479 | |
---|
480 | if (x < 59.95) |
---|
481 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s"; |
---|
482 | else if (x < 3599.95) |
---|
483 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" "; |
---|
484 | else { |
---|
485 | ostringstream oss; |
---|
486 | oss << setw(2) << std::right << setprecision(1) << mvt.hour(); |
---|
487 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " "; |
---|
488 | return String(oss); |
---|
489 | } |
---|
490 | }; |
---|
491 | |
---|
492 | std::string Scantable::formatDirection(const MDirection& md, Int prec) const |
---|
493 | { |
---|
494 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue(); |
---|
495 | if (prec<0) |
---|
496 | prec = 7; |
---|
497 | |
---|
498 | String ref = md.getRefString(); |
---|
499 | MVAngle mvLon(t[0]); |
---|
500 | String sLon = mvLon.string(MVAngle::TIME,prec); |
---|
501 | uInt tp = md.getRef().getType(); |
---|
502 | if (tp == MDirection::GALACTIC || |
---|
503 | tp == MDirection::SUPERGAL ) { |
---|
504 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec); |
---|
505 | } |
---|
506 | MVAngle mvLat(t[1]); |
---|
507 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec); |
---|
508 | return ref + String(" ") + sLon + String(" ") + sLat; |
---|
509 | } |
---|
510 | |
---|
511 | |
---|
512 | std::string Scantable::getFluxUnit() const |
---|
513 | { |
---|
514 | return table_.keywordSet().asString("FluxUnit"); |
---|
515 | } |
---|
516 | |
---|
517 | void Scantable::setFluxUnit(const std::string& unit) |
---|
518 | { |
---|
519 | String tmp(unit); |
---|
520 | Unit tU(tmp); |
---|
521 | if (tU==Unit("K") || tU==Unit("Jy")) { |
---|
522 | table_.rwKeywordSet().define(String("FluxUnit"), tmp); |
---|
523 | } else { |
---|
524 | throw AipsError("Illegal unit - must be compatible with Jy or K"); |
---|
525 | } |
---|
526 | } |
---|
527 | |
---|
528 | void Scantable::setInstrument(const std::string& name) |
---|
529 | { |
---|
530 | bool throwIt = true; |
---|
531 | // create an Instrument to see if this is valid |
---|
532 | STAttr::convertInstrument(name, throwIt); |
---|
533 | String nameU(name); |
---|
534 | nameU.upcase(); |
---|
535 | table_.rwKeywordSet().define(String("AntennaName"), nameU); |
---|
536 | } |
---|
537 | |
---|
538 | void Scantable::setFeedType(const std::string& feedtype) |
---|
539 | { |
---|
540 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) { |
---|
541 | std::string msg = "Illegal feed type "+ feedtype; |
---|
542 | throw(casa::AipsError(msg)); |
---|
543 | } |
---|
544 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype); |
---|
545 | } |
---|
546 | |
---|
547 | MPosition Scantable::getAntennaPosition() const |
---|
548 | { |
---|
549 | Vector<Double> antpos; |
---|
550 | table_.keywordSet().get("AntennaPosition", antpos); |
---|
551 | MVPosition mvpos(antpos(0),antpos(1),antpos(2)); |
---|
552 | return MPosition(mvpos); |
---|
553 | } |
---|
554 | |
---|
555 | void Scantable::makePersistent(const std::string& filename) |
---|
556 | { |
---|
557 | String inname(filename); |
---|
558 | Path path(inname); |
---|
559 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
---|
560 | inname = path.expandedName(); |
---|
561 | // 2011/03/04 TN |
---|
562 | // We can comment out this workaround since the essential bug is |
---|
563 | // fixed in casacore (r20889 in google code). |
---|
564 | table_.deepCopy(inname, Table::New); |
---|
565 | // // WORKAROUND !!! for Table bug |
---|
566 | // // Remove when fixed in casacore |
---|
567 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) { |
---|
568 | // Table tab = table_.copyToMemoryTable(generateName()); |
---|
569 | // tab.deepCopy(inname, Table::New); |
---|
570 | // tab.markForDelete(); |
---|
571 | // |
---|
572 | // } else { |
---|
573 | // table_.deepCopy(inname, Table::New); |
---|
574 | // } |
---|
575 | } |
---|
576 | |
---|
577 | int Scantable::nbeam( int scanno ) const |
---|
578 | { |
---|
579 | if ( scanno < 0 ) { |
---|
580 | Int n; |
---|
581 | table_.keywordSet().get("nBeam",n); |
---|
582 | return int(n); |
---|
583 | } else { |
---|
584 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
585 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
586 | ROTableRow row(t); |
---|
587 | const TableRecord& rec = row.get(0); |
---|
588 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
589 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
590 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
591 | ROTableVector<uInt> v(subt, "BEAMNO"); |
---|
592 | return int(v.nelements()); |
---|
593 | } |
---|
594 | return 0; |
---|
595 | } |
---|
596 | |
---|
597 | int Scantable::nif( int scanno ) const |
---|
598 | { |
---|
599 | if ( scanno < 0 ) { |
---|
600 | Int n; |
---|
601 | table_.keywordSet().get("nIF",n); |
---|
602 | return int(n); |
---|
603 | } else { |
---|
604 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these |
---|
605 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
606 | ROTableRow row(t); |
---|
607 | const TableRecord& rec = row.get(0); |
---|
608 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
609 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
610 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
611 | if ( subt.nrow() == 0 ) return 0; |
---|
612 | ROTableVector<uInt> v(subt, "IFNO"); |
---|
613 | return int(v.nelements()); |
---|
614 | } |
---|
615 | return 0; |
---|
616 | } |
---|
617 | |
---|
618 | int Scantable::npol( int scanno ) const |
---|
619 | { |
---|
620 | if ( scanno < 0 ) { |
---|
621 | Int n; |
---|
622 | table_.keywordSet().get("nPol",n); |
---|
623 | return n; |
---|
624 | } else { |
---|
625 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
626 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
627 | ROTableRow row(t); |
---|
628 | const TableRecord& rec = row.get(0); |
---|
629 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
630 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
631 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
632 | if ( subt.nrow() == 0 ) return 0; |
---|
633 | ROTableVector<uInt> v(subt, "POLNO"); |
---|
634 | return int(v.nelements()); |
---|
635 | } |
---|
636 | return 0; |
---|
637 | } |
---|
638 | |
---|
639 | int Scantable::ncycle( int scanno ) const |
---|
640 | { |
---|
641 | if ( scanno < 0 ) { |
---|
642 | Block<String> cols(2); |
---|
643 | cols[0] = "SCANNO"; |
---|
644 | cols[1] = "CYCLENO"; |
---|
645 | TableIterator it(table_, cols); |
---|
646 | int n = 0; |
---|
647 | while ( !it.pastEnd() ) { |
---|
648 | ++n; |
---|
649 | ++it; |
---|
650 | } |
---|
651 | return n; |
---|
652 | } else { |
---|
653 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
654 | ROTableRow row(t); |
---|
655 | const TableRecord& rec = row.get(0); |
---|
656 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
657 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
658 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) ); |
---|
659 | if ( subt.nrow() == 0 ) return 0; |
---|
660 | return int(subt.nrow()); |
---|
661 | } |
---|
662 | return 0; |
---|
663 | } |
---|
664 | |
---|
665 | |
---|
666 | int Scantable::nrow( int /*scanno*/ ) const |
---|
667 | { |
---|
668 | return int(table_.nrow()); |
---|
669 | } |
---|
670 | |
---|
671 | int Scantable::nchan( int ifno ) const |
---|
672 | { |
---|
673 | if ( ifno < 0 ) { |
---|
674 | Int n; |
---|
675 | table_.keywordSet().get("nChan",n); |
---|
676 | return int(n); |
---|
677 | } else { |
---|
678 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't |
---|
679 | // vary with these |
---|
680 | Table t = table_(table_.col("IFNO") == ifno, 1); |
---|
681 | if ( t.nrow() == 0 ) return 0; |
---|
682 | ROArrayColumn<Float> v(t, "SPECTRA"); |
---|
683 | return v.shape(0)(0); |
---|
684 | } |
---|
685 | return 0; |
---|
686 | } |
---|
687 | |
---|
688 | int Scantable::nscan() const { |
---|
689 | Vector<uInt> scannos(scanCol_.getColumn()); |
---|
690 | uInt nout = genSort( scannos, Sort::Ascending, |
---|
691 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
692 | return int(nout); |
---|
693 | } |
---|
694 | |
---|
695 | int Scantable::getChannels(int whichrow) const |
---|
696 | { |
---|
697 | return specCol_.shape(whichrow)(0); |
---|
698 | } |
---|
699 | |
---|
700 | int Scantable::getBeam(int whichrow) const |
---|
701 | { |
---|
702 | return beamCol_(whichrow); |
---|
703 | } |
---|
704 | |
---|
705 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const |
---|
706 | { |
---|
707 | Vector<uInt> nos(col.getColumn()); |
---|
708 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates ); |
---|
709 | nos.resize(n, True); |
---|
710 | std::vector<uint> stlout; |
---|
711 | nos.tovector(stlout); |
---|
712 | return stlout; |
---|
713 | } |
---|
714 | |
---|
715 | int Scantable::getIF(int whichrow) const |
---|
716 | { |
---|
717 | return ifCol_(whichrow); |
---|
718 | } |
---|
719 | |
---|
720 | int Scantable::getPol(int whichrow) const |
---|
721 | { |
---|
722 | return polCol_(whichrow); |
---|
723 | } |
---|
724 | |
---|
725 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const |
---|
726 | { |
---|
727 | return formatTime(me, showdate, 0); |
---|
728 | } |
---|
729 | |
---|
730 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const |
---|
731 | { |
---|
732 | MVTime mvt(me.getValue()); |
---|
733 | if (showdate) |
---|
734 | //mvt.setFormat(MVTime::YMD); |
---|
735 | mvt.setFormat(MVTime::YMD, prec); |
---|
736 | else |
---|
737 | //mvt.setFormat(MVTime::TIME); |
---|
738 | mvt.setFormat(MVTime::TIME, prec); |
---|
739 | ostringstream oss; |
---|
740 | oss << mvt; |
---|
741 | return String(oss); |
---|
742 | } |
---|
743 | |
---|
744 | void Scantable::calculateAZEL() |
---|
745 | { |
---|
746 | LogIO os( LogOrigin( "Scantable", "calculateAZEL()", WHERE ) ) ; |
---|
747 | MPosition mp = getAntennaPosition(); |
---|
748 | MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
749 | ostringstream oss; |
---|
750 | oss << mp; |
---|
751 | os << "Computed azimuth/elevation using " << endl |
---|
752 | << String(oss) << endl; |
---|
753 | for (Int i=0; i<nrow(); ++i) { |
---|
754 | MEpoch me = timeCol(i); |
---|
755 | MDirection md = getDirection(i); |
---|
756 | os << " Time: " << formatTime(me,False) |
---|
757 | << " Direction: " << formatDirection(md) |
---|
758 | << endl << " => "; |
---|
759 | MeasFrame frame(mp, me); |
---|
760 | Vector<Double> azel = |
---|
761 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL, |
---|
762 | frame) |
---|
763 | )().getAngle("rad").getValue(); |
---|
764 | azCol_.put(i,Float(azel[0])); |
---|
765 | elCol_.put(i,Float(azel[1])); |
---|
766 | os << "azel: " << azel[0]/C::pi*180.0 << " " |
---|
767 | << azel[1]/C::pi*180.0 << " (deg)" << LogIO::POST; |
---|
768 | } |
---|
769 | } |
---|
770 | |
---|
771 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
772 | { |
---|
773 | Vector<uInt> flagrow = flagrowCol_.getColumn(); |
---|
774 | for (uInt i=0; i<table_.nrow(); ++i) { |
---|
775 | // apply flag only when specified row is vaild |
---|
776 | if (flagrow[i] == 0) { |
---|
777 | Vector<uChar> flgs = flagsCol_(i); |
---|
778 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs); |
---|
779 | flagsCol_.put(i, flgs); |
---|
780 | } |
---|
781 | } |
---|
782 | } |
---|
783 | |
---|
784 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
785 | { |
---|
786 | Vector<uChar> flags; |
---|
787 | flagsCol_.get(uInt(whichrow), flags); |
---|
788 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags); |
---|
789 | Vector<Bool> bflag(flags.shape()); |
---|
790 | convertArray(bflag, flags); |
---|
791 | //bflag = !bflag; |
---|
792 | |
---|
793 | std::vector<bool> mask; |
---|
794 | bflag.tovector(mask); |
---|
795 | return mask; |
---|
796 | } |
---|
797 | |
---|
798 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag, |
---|
799 | Vector<uChar> flgs) |
---|
800 | { |
---|
801 | Vector<Float> spcs = specCol_(whichrow); |
---|
802 | uInt nchannel = spcs.nelements(); |
---|
803 | if (spcs.nelements() != nchannel) { |
---|
804 | throw(AipsError("Data has incorrect number of channels")); |
---|
805 | } |
---|
806 | uChar userflag = 1 << 7; |
---|
807 | if (unflag) { |
---|
808 | userflag = 0 << 7; |
---|
809 | } |
---|
810 | if (clipoutside) { |
---|
811 | for (uInt j = 0; j < nchannel; ++j) { |
---|
812 | Float spc = spcs(j); |
---|
813 | if ((spc >= uthres) || (spc <= dthres)) { |
---|
814 | flgs(j) = userflag; |
---|
815 | } |
---|
816 | } |
---|
817 | } else { |
---|
818 | for (uInt j = 0; j < nchannel; ++j) { |
---|
819 | Float spc = spcs(j); |
---|
820 | if ((spc < uthres) && (spc > dthres)) { |
---|
821 | flgs(j) = userflag; |
---|
822 | } |
---|
823 | } |
---|
824 | } |
---|
825 | } |
---|
826 | |
---|
827 | |
---|
828 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) { |
---|
829 | std::vector<bool>::const_iterator it; |
---|
830 | uInt ntrue = 0; |
---|
831 | if (whichrow >= int(table_.nrow()) ) { |
---|
832 | throw(AipsError("Invalid row number")); |
---|
833 | } |
---|
834 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
835 | if ( *it ) { |
---|
836 | ntrue++; |
---|
837 | } |
---|
838 | } |
---|
839 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
840 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
841 | throw(AipsError("Trying to flag whole scantable.")); |
---|
842 | uChar userflag = 1 << 7; |
---|
843 | if ( unflag ) { |
---|
844 | userflag = 0 << 7; |
---|
845 | } |
---|
846 | if (whichrow > -1 ) { |
---|
847 | // apply flag only when specified row is vaild |
---|
848 | if (flagrowCol_(whichrow) == 0) { |
---|
849 | applyChanFlag(uInt(whichrow), msk, userflag); |
---|
850 | } |
---|
851 | } else { |
---|
852 | Vector<uInt> flagrow = flagrowCol_.getColumn(); |
---|
853 | for ( uInt i=0; i<table_.nrow(); ++i) { |
---|
854 | // apply flag only when specified row is vaild |
---|
855 | if (flagrow[i] == 0) { |
---|
856 | applyChanFlag(i, msk, userflag); |
---|
857 | } |
---|
858 | } |
---|
859 | } |
---|
860 | } |
---|
861 | |
---|
862 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval ) |
---|
863 | { |
---|
864 | if (whichrow >= table_.nrow() ) { |
---|
865 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) ); |
---|
866 | } |
---|
867 | Vector<uChar> flgs = flagsCol_(whichrow); |
---|
868 | if ( msk.size() == 0 ) { |
---|
869 | flgs = flagval; |
---|
870 | flagsCol_.put(whichrow, flgs); |
---|
871 | return; |
---|
872 | } |
---|
873 | if ( int(msk.size()) != nchan( getIF(whichrow) ) ) { |
---|
874 | throw(AipsError("Mask has incorrect number of channels.")); |
---|
875 | } |
---|
876 | if ( flgs.nelements() != msk.size() ) { |
---|
877 | throw(AipsError("Mask has incorrect number of channels." |
---|
878 | " Probably varying with IF. Please flag per IF")); |
---|
879 | } |
---|
880 | std::vector<bool>::const_iterator it; |
---|
881 | uInt j = 0; |
---|
882 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
883 | if ( *it ) { |
---|
884 | flgs(j) = flagval; |
---|
885 | } |
---|
886 | ++j; |
---|
887 | } |
---|
888 | flagsCol_.put(whichrow, flgs); |
---|
889 | } |
---|
890 | |
---|
891 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag) |
---|
892 | { |
---|
893 | if (selector_.empty() && (rows.size() == table_.nrow()) && !unflag) |
---|
894 | throw(AipsError("Trying to flag whole scantable.")); |
---|
895 | |
---|
896 | uInt rowflag = (unflag ? 0 : 1); |
---|
897 | std::vector<uInt>::const_iterator it; |
---|
898 | for (it = rows.begin(); it != rows.end(); ++it) |
---|
899 | flagrowCol_.put(*it, rowflag); |
---|
900 | } |
---|
901 | |
---|
902 | std::vector<bool> Scantable::getMask(int whichrow) const |
---|
903 | { |
---|
904 | Vector<uChar> flags; |
---|
905 | flagsCol_.get(uInt(whichrow), flags); |
---|
906 | Vector<Bool> bflag(flags.shape()); |
---|
907 | convertArray(bflag, flags); |
---|
908 | bflag = !bflag; |
---|
909 | std::vector<bool> mask; |
---|
910 | bflag.tovector(mask); |
---|
911 | return mask; |
---|
912 | } |
---|
913 | |
---|
914 | std::vector<float> Scantable::getSpectrum( int whichrow, |
---|
915 | const std::string& poltype ) const |
---|
916 | { |
---|
917 | LogIO os( LogOrigin( "Scantable", "getSpectrum()", WHERE ) ) ; |
---|
918 | |
---|
919 | String ptype = poltype; |
---|
920 | if (poltype == "" ) ptype = getPolType(); |
---|
921 | if ( whichrow < 0 || whichrow >= nrow() ) |
---|
922 | throw(AipsError("Illegal row number.")); |
---|
923 | std::vector<float> out; |
---|
924 | Vector<Float> arr; |
---|
925 | uInt requestedpol = polCol_(whichrow); |
---|
926 | String basetype = getPolType(); |
---|
927 | if ( ptype == basetype ) { |
---|
928 | specCol_.get(whichrow, arr); |
---|
929 | } else { |
---|
930 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_, |
---|
931 | basetype)); |
---|
932 | uInt row = uInt(whichrow); |
---|
933 | stpol->setSpectra(getPolMatrix(row)); |
---|
934 | Float fang,fhand; |
---|
935 | fang = focusTable_.getTotalAngle(mfocusidCol_(row)); |
---|
936 | fhand = focusTable_.getFeedHand(mfocusidCol_(row)); |
---|
937 | stpol->setPhaseCorrections(fang, fhand); |
---|
938 | arr = stpol->getSpectrum(requestedpol, ptype); |
---|
939 | } |
---|
940 | if ( arr.nelements() == 0 ) |
---|
941 | |
---|
942 | os << "Not enough polarisations present to do the conversion." |
---|
943 | << LogIO::POST; |
---|
944 | arr.tovector(out); |
---|
945 | return out; |
---|
946 | } |
---|
947 | |
---|
948 | void Scantable::setSpectrum( const std::vector<float>& spec, |
---|
949 | int whichrow ) |
---|
950 | { |
---|
951 | Vector<Float> spectrum(spec); |
---|
952 | Vector<Float> arr; |
---|
953 | specCol_.get(whichrow, arr); |
---|
954 | if ( spectrum.nelements() != arr.nelements() ) |
---|
955 | throw AipsError("The spectrum has incorrect number of channels."); |
---|
956 | specCol_.put(whichrow, spectrum); |
---|
957 | } |
---|
958 | |
---|
959 | |
---|
960 | String Scantable::generateName() |
---|
961 | { |
---|
962 | return (File::newUniqueName("./","temp")).baseName(); |
---|
963 | } |
---|
964 | |
---|
965 | const casa::Table& Scantable::table( ) const |
---|
966 | { |
---|
967 | return table_; |
---|
968 | } |
---|
969 | |
---|
970 | casa::Table& Scantable::table( ) |
---|
971 | { |
---|
972 | return table_; |
---|
973 | } |
---|
974 | |
---|
975 | std::string Scantable::getPolType() const |
---|
976 | { |
---|
977 | return table_.keywordSet().asString("POLTYPE"); |
---|
978 | } |
---|
979 | |
---|
980 | void Scantable::unsetSelection() |
---|
981 | { |
---|
982 | table_ = originalTable_; |
---|
983 | attach(); |
---|
984 | selector_.reset(); |
---|
985 | } |
---|
986 | |
---|
987 | void Scantable::setSelection( const STSelector& selection ) |
---|
988 | { |
---|
989 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_); |
---|
990 | if ( tab.nrow() == 0 ) { |
---|
991 | throw(AipsError("Selection contains no data. Not applying it.")); |
---|
992 | } |
---|
993 | table_ = tab; |
---|
994 | attach(); |
---|
995 | // tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ; |
---|
996 | // vector<uint> selectedIFs = getIFNos() ; |
---|
997 | // Int newnIF = selectedIFs.size() ; |
---|
998 | // tab.rwKeywordSet().define("nIF",newnIF) ; |
---|
999 | // if ( newnIF != 0 ) { |
---|
1000 | // Int newnChan = 0 ; |
---|
1001 | // for ( Int i = 0 ; i < newnIF ; i++ ) { |
---|
1002 | // Int nChan = nchan( selectedIFs[i] ) ; |
---|
1003 | // if ( newnChan > nChan ) |
---|
1004 | // newnChan = nChan ; |
---|
1005 | // } |
---|
1006 | // tab.rwKeywordSet().define("nChan",newnChan) ; |
---|
1007 | // } |
---|
1008 | // tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ; |
---|
1009 | selector_ = selection; |
---|
1010 | } |
---|
1011 | |
---|
1012 | |
---|
1013 | std::string Scantable::headerSummary() |
---|
1014 | { |
---|
1015 | // Format header info |
---|
1016 | // STHeader sdh; |
---|
1017 | // sdh = getHeader(); |
---|
1018 | // sdh.print(); |
---|
1019 | ostringstream oss; |
---|
1020 | oss.flags(std::ios_base::left); |
---|
1021 | String tmp; |
---|
1022 | // Project |
---|
1023 | table_.keywordSet().get("Project", tmp); |
---|
1024 | oss << setw(15) << "Project:" << tmp << endl; |
---|
1025 | // Observation date |
---|
1026 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
1027 | // Observer |
---|
1028 | oss << setw(15) << "Observer:" |
---|
1029 | << table_.keywordSet().asString("Observer") << endl; |
---|
1030 | // Antenna Name |
---|
1031 | table_.keywordSet().get("AntennaName", tmp); |
---|
1032 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
1033 | // Obs type |
---|
1034 | table_.keywordSet().get("Obstype", tmp); |
---|
1035 | // Records (nrow) |
---|
1036 | oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl; |
---|
1037 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
1038 | // Beams, IFs, Polarizations, and Channels |
---|
1039 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
1040 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
1041 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
1042 | << "(" << getPolType() << ")" << endl |
---|
1043 | << setw(15) << "Channels:" << nchan() << endl; |
---|
1044 | // Flux unit |
---|
1045 | table_.keywordSet().get("FluxUnit", tmp); |
---|
1046 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
1047 | // Abscissa Unit |
---|
1048 | oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl; |
---|
1049 | // Selection |
---|
1050 | oss << selector_.print() << endl; |
---|
1051 | |
---|
1052 | return String(oss); |
---|
1053 | } |
---|
1054 | |
---|
1055 | void Scantable::summary( const std::string& filename ) |
---|
1056 | { |
---|
1057 | ostringstream oss; |
---|
1058 | ofstream ofs; |
---|
1059 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
1060 | |
---|
1061 | if (filename != "") |
---|
1062 | ofs.open( filename.c_str(), ios::out ); |
---|
1063 | |
---|
1064 | oss << endl; |
---|
1065 | oss << asap::SEPERATOR << endl; |
---|
1066 | oss << " Scan Table Summary" << endl; |
---|
1067 | oss << asap::SEPERATOR << endl; |
---|
1068 | |
---|
1069 | // Format header info |
---|
1070 | oss << headerSummary(); |
---|
1071 | oss << endl; |
---|
1072 | |
---|
1073 | if (table_.nrow() <= 0){ |
---|
1074 | oss << asap::SEPERATOR << endl; |
---|
1075 | oss << "The MAIN table is empty: there are no data!!!" << endl; |
---|
1076 | oss << asap::SEPERATOR << endl; |
---|
1077 | |
---|
1078 | ols << String(oss) << LogIO::POST; |
---|
1079 | if (ofs) { |
---|
1080 | ofs << String(oss) << flush; |
---|
1081 | ofs.close(); |
---|
1082 | } |
---|
1083 | return; |
---|
1084 | } |
---|
1085 | |
---|
1086 | |
---|
1087 | |
---|
1088 | // main table |
---|
1089 | String dirtype = "Position (" |
---|
1090 | + getDirectionRefString() |
---|
1091 | + ")"; |
---|
1092 | oss.flags(std::ios_base::left); |
---|
1093 | oss << setw(5) << "Scan" |
---|
1094 | << setw(15) << "Source" |
---|
1095 | << setw(35) << "Time range" |
---|
1096 | << setw(2) << "" << setw(7) << "Int[s]" |
---|
1097 | << setw(7) << "Record" |
---|
1098 | << setw(8) << "SrcType" |
---|
1099 | << setw(8) << "FreqIDs" |
---|
1100 | << setw(7) << "MolIDs" << endl; |
---|
1101 | oss << setw(7)<< "" << setw(6) << "Beam" |
---|
1102 | << setw(23) << dirtype << endl; |
---|
1103 | |
---|
1104 | oss << asap::SEPERATOR << endl; |
---|
1105 | |
---|
1106 | // Flush summary and clear up the string |
---|
1107 | ols << String(oss) << LogIO::POST; |
---|
1108 | if (ofs) ofs << String(oss) << flush; |
---|
1109 | oss.str(""); |
---|
1110 | oss.clear(); |
---|
1111 | |
---|
1112 | |
---|
1113 | // Get Freq_ID map |
---|
1114 | ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID"); |
---|
1115 | Int nfid = ftabIds.nrow(); |
---|
1116 | if (nfid <= 0){ |
---|
1117 | oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl; |
---|
1118 | oss << asap::SEPERATOR << endl; |
---|
1119 | |
---|
1120 | ols << String(oss) << LogIO::POST; |
---|
1121 | if (ofs) { |
---|
1122 | ofs << String(oss) << flush; |
---|
1123 | ofs.close(); |
---|
1124 | } |
---|
1125 | return; |
---|
1126 | } |
---|
1127 | // Storages of overall IFNO, POLNO, and nchan per FREQ_ID |
---|
1128 | // the orders are identical to ID in FREQ subtable |
---|
1129 | Block< Vector<uInt> > ifNos(nfid), polNos(nfid); |
---|
1130 | Vector<Int> fIdchans(nfid,-1); |
---|
1131 | Vector<Double> fIdfreq0(nfid,-1); |
---|
1132 | Vector<Double> fIdfcent(nfid,-1); |
---|
1133 | map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair |
---|
1134 | for (Int i=0; i < nfid; i++){ |
---|
1135 | // fidMap[freqId] returns row number in FREQ subtable |
---|
1136 | fidMap.insert(pair<uInt, Int>(ftabIds(i),i)); |
---|
1137 | ifNos[i] = Vector<uInt>(); |
---|
1138 | polNos[i] = Vector<uInt>(); |
---|
1139 | } |
---|
1140 | |
---|
1141 | TableIterator iter(table_, "SCANNO"); |
---|
1142 | |
---|
1143 | // Vars for keeping track of time, freqids, molIds in a SCANNO |
---|
1144 | //Vector<uInt> freqids; |
---|
1145 | //Vector<uInt> molids; |
---|
1146 | Vector<uInt> beamids(1,0); |
---|
1147 | Vector<MDirection> beamDirs; |
---|
1148 | Vector<Int> stypeids(1,0); |
---|
1149 | Vector<String> stypestrs; |
---|
1150 | Int nfreq(1); |
---|
1151 | Int nmol(1); |
---|
1152 | uInt nbeam(1); |
---|
1153 | uInt nstype(1); |
---|
1154 | |
---|
1155 | Double btime(0.0), etime(0.0); |
---|
1156 | Double meanIntTim(0.0); |
---|
1157 | |
---|
1158 | uInt currFreqId(0), ftabRow(0); |
---|
1159 | Int iflen(0), pollen(0); |
---|
1160 | |
---|
1161 | while (!iter.pastEnd()) { |
---|
1162 | Table subt = iter.table(); |
---|
1163 | uInt snrow = subt.nrow(); |
---|
1164 | ROTableRow row(subt); |
---|
1165 | const TableRecord& rec = row.get(0); |
---|
1166 | |
---|
1167 | // relevant columns |
---|
1168 | ROScalarColumn<Double> mjdCol(subt,"TIME"); |
---|
1169 | ROScalarColumn<Double> intervalCol(subt,"INTERVAL"); |
---|
1170 | MDirection::ROScalarColumn dirCol(subt,"DIRECTION"); |
---|
1171 | |
---|
1172 | ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID"); |
---|
1173 | ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID"); |
---|
1174 | ROScalarColumn<uInt> beamCol(subt,"BEAMNO"); |
---|
1175 | ROScalarColumn<Int> stypeCol(subt,"SRCTYPE"); |
---|
1176 | |
---|
1177 | ROScalarColumn<uInt> ifNoCol(subt,"IFNO"); |
---|
1178 | ROScalarColumn<uInt> polNoCol(subt,"POLNO"); |
---|
1179 | |
---|
1180 | |
---|
1181 | // Times |
---|
1182 | meanIntTim = sum(intervalCol.getColumn()) / (double) snrow; |
---|
1183 | minMax(btime, etime, mjdCol.getColumn()); |
---|
1184 | double shiftInDay(0.5*meanIntTim/C::day); |
---|
1185 | btime -= shiftInDay; |
---|
1186 | etime += shiftInDay; |
---|
1187 | |
---|
1188 | // MOLECULE_ID and FREQ_ID |
---|
1189 | Vector<uInt> molids(getNumbers(molIdCol)); |
---|
1190 | molids.shape(nmol); |
---|
1191 | |
---|
1192 | Vector<uInt> freqids(getNumbers(freqIdCol)); |
---|
1193 | freqids.shape(nfreq); |
---|
1194 | |
---|
1195 | // Add first beamid, and srcNames |
---|
1196 | beamids.resize(1,False); |
---|
1197 | beamDirs.resize(1,False); |
---|
1198 | beamids(0)=beamCol(0); |
---|
1199 | beamDirs(0)=dirCol(0); |
---|
1200 | nbeam = 1; |
---|
1201 | |
---|
1202 | stypeids.resize(1,False); |
---|
1203 | stypeids(0)=stypeCol(0); |
---|
1204 | nstype = 1; |
---|
1205 | |
---|
1206 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
1207 | currFreqId=freqIdCol(0); |
---|
1208 | ftabRow = fidMap[currFreqId]; |
---|
1209 | // Assumes an identical number of channels per FREQ_ID |
---|
1210 | if (fIdchans(ftabRow) < 0 ) { |
---|
1211 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
1212 | fIdchans(ftabRow)=(*spec).shape()(0); |
---|
1213 | } |
---|
1214 | if (fIdfreq0(ftabRow) < 0 ) { |
---|
1215 | SpectralCoordinate spc = frequencies().getSpectralCoordinate(ftabRow); |
---|
1216 | Double fs, fe; |
---|
1217 | spc.toWorld(fs, 0); |
---|
1218 | spc.toWorld(fe, fIdchans(ftabRow)-1); |
---|
1219 | fIdfreq0(ftabRow) = fs; |
---|
1220 | fIdfcent(ftabRow) = 0.5 * ( fs + fe ); |
---|
1221 | } |
---|
1222 | // Should keep ifNos and polNos form the previous SCANNO |
---|
1223 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) { |
---|
1224 | ifNos[ftabRow].shape(iflen); |
---|
1225 | iflen++; |
---|
1226 | ifNos[ftabRow].resize(iflen,True); |
---|
1227 | ifNos[ftabRow](iflen-1) = ifNoCol(0); |
---|
1228 | } |
---|
1229 | if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) { |
---|
1230 | polNos[ftabRow].shape(pollen); |
---|
1231 | pollen++; |
---|
1232 | polNos[ftabRow].resize(pollen,True); |
---|
1233 | polNos[ftabRow](pollen-1) = polNoCol(0); |
---|
1234 | } |
---|
1235 | |
---|
1236 | for (uInt i=1; i < snrow; i++){ |
---|
1237 | // Need to list BEAMNO and DIRECTION in the same order |
---|
1238 | if ( !anyEQ(beamids,beamCol(i)) ) { |
---|
1239 | nbeam++; |
---|
1240 | beamids.resize(nbeam,True); |
---|
1241 | beamids(nbeam-1)=beamCol(i); |
---|
1242 | beamDirs.resize(nbeam,True); |
---|
1243 | beamDirs(nbeam-1)=dirCol(i); |
---|
1244 | } |
---|
1245 | |
---|
1246 | // SRCTYPE is Int (getNumber takes only uInt) |
---|
1247 | if ( !anyEQ(stypeids,stypeCol(i)) ) { |
---|
1248 | nstype++; |
---|
1249 | stypeids.resize(nstype,True); |
---|
1250 | stypeids(nstype-1)=stypeCol(i); |
---|
1251 | } |
---|
1252 | |
---|
1253 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
1254 | currFreqId=freqIdCol(i); |
---|
1255 | ftabRow = fidMap[currFreqId]; |
---|
1256 | if (fIdchans(ftabRow) < 0 ) { |
---|
1257 | const TableRecord& rec = row.get(i); |
---|
1258 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
1259 | fIdchans(ftabRow) = (*spec).shape()(0); |
---|
1260 | } |
---|
1261 | if (fIdfreq0(ftabRow) < 0 ) { |
---|
1262 | SpectralCoordinate spc = frequencies().getSpectralCoordinate(ftabRow); |
---|
1263 | Double fs, fe; |
---|
1264 | spc.toWorld(fs, 0); |
---|
1265 | spc.toWorld(fe, fIdchans(ftabRow)-1); |
---|
1266 | fIdfreq0(ftabRow) = fs; |
---|
1267 | fIdfcent(ftabRow) = 5.e-1 * ( fs + fe ); |
---|
1268 | } |
---|
1269 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) { |
---|
1270 | ifNos[ftabRow].shape(iflen); |
---|
1271 | iflen++; |
---|
1272 | ifNos[ftabRow].resize(iflen,True); |
---|
1273 | ifNos[ftabRow](iflen-1) = ifNoCol(i); |
---|
1274 | } |
---|
1275 | if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) { |
---|
1276 | polNos[ftabRow].shape(pollen); |
---|
1277 | pollen++; |
---|
1278 | polNos[ftabRow].resize(pollen,True); |
---|
1279 | polNos[ftabRow](pollen-1) = polNoCol(i); |
---|
1280 | } |
---|
1281 | } // end of row iteration |
---|
1282 | |
---|
1283 | stypestrs.resize(nstype,False); |
---|
1284 | for (uInt j=0; j < nstype; j++) |
---|
1285 | stypestrs(j) = SrcType::getName(stypeids(j)); |
---|
1286 | |
---|
1287 | // Format Scan summary |
---|
1288 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
1289 | << std::left << setw(1) << "" |
---|
1290 | << setw(15) << rec.asString("SRCNAME") |
---|
1291 | << setw(21) << MVTime(btime).string(MVTime::YMD,8) |
---|
1292 | << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,8) |
---|
1293 | << setw(3) << "" << setw(6) << meanIntTim << setw(1) << "" |
---|
1294 | << std::right << setw(5) << snrow << setw(2) << "" |
---|
1295 | << std::left << stypestrs << setw(1) << "" |
---|
1296 | << freqids << setw(1) << "" |
---|
1297 | << molids << endl; |
---|
1298 | // Format Beam summary |
---|
1299 | for (uInt j=0; j < nbeam; j++) { |
---|
1300 | oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << "" |
---|
1301 | << formatDirection(beamDirs(j),9) << endl; |
---|
1302 | } |
---|
1303 | // Flush summary every scan and clear up the string |
---|
1304 | ols << String(oss) << LogIO::POST; |
---|
1305 | if (ofs) ofs << String(oss) << flush; |
---|
1306 | oss.str(""); |
---|
1307 | oss.clear(); |
---|
1308 | |
---|
1309 | ++iter; |
---|
1310 | } // end of scan iteration |
---|
1311 | oss << asap::SEPERATOR << endl; |
---|
1312 | |
---|
1313 | // List FRECUENCIES Table (using STFrequencies.print may be slow) |
---|
1314 | oss << "FREQUENCIES: " << nfreq << endl; |
---|
1315 | // oss << std::right << setw(5) << "ID" << setw(2) << "" |
---|
1316 | // << std::left << setw(5) << "IFNO" << setw(2) << "" |
---|
1317 | // << setw(8) << "Frame" |
---|
1318 | // << setw(16) << "RefVal" |
---|
1319 | // << setw(7) << "RefPix" |
---|
1320 | // << setw(15) << "Increment" |
---|
1321 | // << setw(9) << "Channels" |
---|
1322 | // << setw(6) << "POLNOs" << endl; |
---|
1323 | // Int tmplen; |
---|
1324 | // for (Int i=0; i < nfid; i++){ |
---|
1325 | // // List row=i of FREQUENCIES subtable |
---|
1326 | // ifNos[i].shape(tmplen); |
---|
1327 | // if (tmplen >= 1) { |
---|
1328 | // oss << std::right << setw(5) << ftabIds(i) << setw(2) << "" |
---|
1329 | // << setw(3) << ifNos[i](0) << setw(1) << "" |
---|
1330 | // << std::left << setw(46) << frequencies().print(ftabIds(i)) |
---|
1331 | // << setw(2) << "" |
---|
1332 | // << std::right << setw(8) << fIdchans[i] << setw(2) << "" |
---|
1333 | // << std::left << polNos[i]; |
---|
1334 | // if (tmplen > 1) { |
---|
1335 | // oss << " (" << tmplen << " chains)"; |
---|
1336 | // } |
---|
1337 | // oss << endl; |
---|
1338 | // } |
---|
1339 | oss << std::right << setw(4) << "ID" << setw(2) << "" |
---|
1340 | << std::left << setw(9) << "IFNO(SPW)" << setw(2) << "" |
---|
1341 | << setw(8) << "#Chans" |
---|
1342 | << setw(8) << "Frame" |
---|
1343 | << setw(12) << "Ch0[MHz]" |
---|
1344 | << setw(14) << "ChanWid[kHz]" |
---|
1345 | << setw(14) << "Center[MHz]" |
---|
1346 | << setw(6) << "POLNOs" << endl; |
---|
1347 | Int tmplen; |
---|
1348 | for (Int i=0; i < nfid; i++){ |
---|
1349 | // List row=i of FREQUENCIES subtable |
---|
1350 | ifNos[i].shape(tmplen); |
---|
1351 | Double refpix, refval, increment ; |
---|
1352 | if (tmplen >= 1) { |
---|
1353 | freqTable_.getEntry( refpix, refval, increment, ftabIds(i) ) ; |
---|
1354 | oss << std::right << setw(4) << ftabIds(i) << setw(2) << "" |
---|
1355 | << std::left << setw(9) << ifNos[i](0) << setw(2) << "" |
---|
1356 | << std::right << setw(6) << fIdchans[i] << setw(2) << "" |
---|
1357 | << setw(6) << frequencies().getFrameString(true) |
---|
1358 | << setw(2) << "" |
---|
1359 | << setw(10) << std::setprecision(9) << (fIdfreq0[i]*1.e-6) << setw(2) << "" |
---|
1360 | << setw(12) << (increment*1.e-3) << setw(2) << "" |
---|
1361 | << setw(12) << (fIdfcent[i]*1.e-6) << setw(2) << "" |
---|
1362 | << std::left << polNos[i]; |
---|
1363 | if (tmplen > 1) { |
---|
1364 | oss << " (" << tmplen << " chains)"; |
---|
1365 | } |
---|
1366 | oss << endl; |
---|
1367 | } |
---|
1368 | |
---|
1369 | } |
---|
1370 | oss << asap::SEPERATOR << endl; |
---|
1371 | |
---|
1372 | // List MOLECULES Table (currently lists all rows) |
---|
1373 | oss << "MOLECULES: " << endl; |
---|
1374 | if (molecules().nrow() <= 0) { |
---|
1375 | oss << " MOLECULES subtable is empty: there are no data" << endl; |
---|
1376 | } else { |
---|
1377 | ROTableRow row(molecules().table()); |
---|
1378 | oss << std::right << setw(5) << "ID" |
---|
1379 | << std::left << setw(3) << "" |
---|
1380 | << setw(18) << "RestFreq" |
---|
1381 | << setw(15) << "Name" << endl; |
---|
1382 | for (Int i=0; i < molecules().nrow(); i++){ |
---|
1383 | const TableRecord& rec=row.get(i); |
---|
1384 | oss << std::right << setw(5) << rec.asuInt("ID") |
---|
1385 | << std::left << setw(3) << "" |
---|
1386 | << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << "" |
---|
1387 | << rec.asArrayString("NAME") << endl; |
---|
1388 | } |
---|
1389 | } |
---|
1390 | oss << asap::SEPERATOR << endl; |
---|
1391 | ols << String(oss) << LogIO::POST; |
---|
1392 | if (ofs) { |
---|
1393 | ofs << String(oss) << flush; |
---|
1394 | ofs.close(); |
---|
1395 | } |
---|
1396 | // return String(oss); |
---|
1397 | } |
---|
1398 | |
---|
1399 | |
---|
1400 | std::string Scantable::oldheaderSummary() |
---|
1401 | { |
---|
1402 | // Format header info |
---|
1403 | // STHeader sdh; |
---|
1404 | // sdh = getHeader(); |
---|
1405 | // sdh.print(); |
---|
1406 | ostringstream oss; |
---|
1407 | oss.flags(std::ios_base::left); |
---|
1408 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
1409 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
1410 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
1411 | << "(" << getPolType() << ")" << endl |
---|
1412 | << setw(15) << "Channels:" << nchan() << endl; |
---|
1413 | String tmp; |
---|
1414 | oss << setw(15) << "Observer:" |
---|
1415 | << table_.keywordSet().asString("Observer") << endl; |
---|
1416 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
1417 | table_.keywordSet().get("Project", tmp); |
---|
1418 | oss << setw(15) << "Project:" << tmp << endl; |
---|
1419 | table_.keywordSet().get("Obstype", tmp); |
---|
1420 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
1421 | table_.keywordSet().get("AntennaName", tmp); |
---|
1422 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
1423 | table_.keywordSet().get("FluxUnit", tmp); |
---|
1424 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
1425 | int nid = moleculeTable_.nrow(); |
---|
1426 | Bool firstline = True; |
---|
1427 | oss << setw(15) << "Rest Freqs:"; |
---|
1428 | for (int i=0; i<nid; i++) { |
---|
1429 | Table t = table_(table_.col("MOLECULE_ID") == i, 1); |
---|
1430 | if (t.nrow() > 0) { |
---|
1431 | Vector<Double> vec(moleculeTable_.getRestFrequency(i)); |
---|
1432 | if (vec.nelements() > 0) { |
---|
1433 | if (firstline) { |
---|
1434 | oss << setprecision(10) << vec << " [Hz]" << endl; |
---|
1435 | firstline=False; |
---|
1436 | } |
---|
1437 | else{ |
---|
1438 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl; |
---|
1439 | } |
---|
1440 | } else { |
---|
1441 | oss << "none" << endl; |
---|
1442 | } |
---|
1443 | } |
---|
1444 | } |
---|
1445 | |
---|
1446 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl; |
---|
1447 | oss << selector_.print() << endl; |
---|
1448 | return String(oss); |
---|
1449 | } |
---|
1450 | |
---|
1451 | //std::string Scantable::summary( const std::string& filename ) |
---|
1452 | void Scantable::oldsummary( const std::string& filename ) |
---|
1453 | { |
---|
1454 | ostringstream oss; |
---|
1455 | ofstream ofs; |
---|
1456 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
1457 | |
---|
1458 | if (filename != "") |
---|
1459 | ofs.open( filename.c_str(), ios::out ); |
---|
1460 | |
---|
1461 | oss << endl; |
---|
1462 | oss << asap::SEPERATOR << endl; |
---|
1463 | oss << " Scan Table Summary" << endl; |
---|
1464 | oss << asap::SEPERATOR << endl; |
---|
1465 | |
---|
1466 | // Format header info |
---|
1467 | oss << oldheaderSummary(); |
---|
1468 | oss << endl; |
---|
1469 | |
---|
1470 | // main table |
---|
1471 | String dirtype = "Position (" |
---|
1472 | + getDirectionRefString() |
---|
1473 | + ")"; |
---|
1474 | oss.flags(std::ios_base::left); |
---|
1475 | oss << setw(5) << "Scan" << setw(15) << "Source" |
---|
1476 | << setw(10) << "Time" << setw(18) << "Integration" |
---|
1477 | << setw(15) << "Source Type" << endl; |
---|
1478 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl; |
---|
1479 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << "" |
---|
1480 | << setw(8) << "Frame" << setw(16) |
---|
1481 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" |
---|
1482 | << setw(7) << "Channels" |
---|
1483 | << endl; |
---|
1484 | oss << asap::SEPERATOR << endl; |
---|
1485 | |
---|
1486 | // Flush summary and clear up the string |
---|
1487 | ols << String(oss) << LogIO::POST; |
---|
1488 | if (ofs) ofs << String(oss) << flush; |
---|
1489 | oss.str(""); |
---|
1490 | oss.clear(); |
---|
1491 | |
---|
1492 | TableIterator iter(table_, "SCANNO"); |
---|
1493 | while (!iter.pastEnd()) { |
---|
1494 | Table subt = iter.table(); |
---|
1495 | ROTableRow row(subt); |
---|
1496 | MEpoch::ROScalarColumn timeCol(subt,"TIME"); |
---|
1497 | const TableRecord& rec = row.get(0); |
---|
1498 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
1499 | << std::left << setw(1) << "" |
---|
1500 | << setw(15) << rec.asString("SRCNAME") |
---|
1501 | << setw(10) << formatTime(timeCol(0), false); |
---|
1502 | // count the cycles in the scan |
---|
1503 | TableIterator cyciter(subt, "CYCLENO"); |
---|
1504 | int nint = 0; |
---|
1505 | while (!cyciter.pastEnd()) { |
---|
1506 | ++nint; |
---|
1507 | ++cyciter; |
---|
1508 | } |
---|
1509 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left |
---|
1510 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << "" |
---|
1511 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl; |
---|
1512 | |
---|
1513 | TableIterator biter(subt, "BEAMNO"); |
---|
1514 | while (!biter.pastEnd()) { |
---|
1515 | Table bsubt = biter.table(); |
---|
1516 | ROTableRow brow(bsubt); |
---|
1517 | const TableRecord& brec = brow.get(0); |
---|
1518 | uInt row0 = bsubt.rowNumbers(table_)[0]; |
---|
1519 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left; |
---|
1520 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl; |
---|
1521 | TableIterator iiter(bsubt, "IFNO"); |
---|
1522 | while (!iiter.pastEnd()) { |
---|
1523 | Table isubt = iiter.table(); |
---|
1524 | ROTableRow irow(isubt); |
---|
1525 | const TableRecord& irec = irow.get(0); |
---|
1526 | oss << setw(9) << ""; |
---|
1527 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left |
---|
1528 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID")) |
---|
1529 | << setw(3) << "" << nchan(irec.asuInt("IFNO")) |
---|
1530 | << endl; |
---|
1531 | |
---|
1532 | ++iiter; |
---|
1533 | } |
---|
1534 | ++biter; |
---|
1535 | } |
---|
1536 | // Flush summary every scan and clear up the string |
---|
1537 | ols << String(oss) << LogIO::POST; |
---|
1538 | if (ofs) ofs << String(oss) << flush; |
---|
1539 | oss.str(""); |
---|
1540 | oss.clear(); |
---|
1541 | |
---|
1542 | ++iter; |
---|
1543 | } |
---|
1544 | oss << asap::SEPERATOR << endl; |
---|
1545 | ols << String(oss) << LogIO::POST; |
---|
1546 | if (ofs) { |
---|
1547 | ofs << String(oss) << flush; |
---|
1548 | ofs.close(); |
---|
1549 | } |
---|
1550 | // return String(oss); |
---|
1551 | } |
---|
1552 | |
---|
1553 | // std::string Scantable::getTime(int whichrow, bool showdate) const |
---|
1554 | // { |
---|
1555 | // MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
1556 | // MEpoch me; |
---|
1557 | // if (whichrow > -1) { |
---|
1558 | // me = timeCol(uInt(whichrow)); |
---|
1559 | // } else { |
---|
1560 | // Double tm; |
---|
1561 | // table_.keywordSet().get("UTC",tm); |
---|
1562 | // me = MEpoch(MVEpoch(tm)); |
---|
1563 | // } |
---|
1564 | // return formatTime(me, showdate); |
---|
1565 | // } |
---|
1566 | |
---|
1567 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const |
---|
1568 | { |
---|
1569 | MEpoch me; |
---|
1570 | me = getEpoch(whichrow); |
---|
1571 | return formatTime(me, showdate, prec); |
---|
1572 | } |
---|
1573 | |
---|
1574 | MEpoch Scantable::getEpoch(int whichrow) const |
---|
1575 | { |
---|
1576 | if (whichrow > -1) { |
---|
1577 | return timeCol_(uInt(whichrow)); |
---|
1578 | } else { |
---|
1579 | Double tm; |
---|
1580 | table_.keywordSet().get("UTC",tm); |
---|
1581 | return MEpoch(MVEpoch(tm)); |
---|
1582 | } |
---|
1583 | } |
---|
1584 | |
---|
1585 | std::string Scantable::getDirectionString(int whichrow) const |
---|
1586 | { |
---|
1587 | return formatDirection(getDirection(uInt(whichrow))); |
---|
1588 | } |
---|
1589 | |
---|
1590 | |
---|
1591 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const { |
---|
1592 | const MPosition& mp = getAntennaPosition(); |
---|
1593 | const MDirection& md = getDirection(whichrow); |
---|
1594 | const MEpoch& me = timeCol_(whichrow); |
---|
1595 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
1596 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
1597 | return freqTable_.getSpectralCoordinate(md, mp, me, rf, |
---|
1598 | mfreqidCol_(whichrow)); |
---|
1599 | } |
---|
1600 | |
---|
1601 | std::vector< double > Scantable::getAbcissa( int whichrow ) const |
---|
1602 | { |
---|
1603 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number")); |
---|
1604 | std::vector<double> stlout; |
---|
1605 | int nchan = specCol_(whichrow).nelements(); |
---|
1606 | String us = freqTable_.getUnitString(); |
---|
1607 | if ( us == "" || us == "pixel" || us == "channel" ) { |
---|
1608 | for (int i=0; i<nchan; ++i) { |
---|
1609 | stlout.push_back(double(i)); |
---|
1610 | } |
---|
1611 | return stlout; |
---|
1612 | } |
---|
1613 | SpectralCoordinate spc = getSpectralCoordinate(whichrow); |
---|
1614 | Vector<Double> pixel(nchan); |
---|
1615 | Vector<Double> world; |
---|
1616 | indgen(pixel); |
---|
1617 | if ( Unit(us) == Unit("Hz") ) { |
---|
1618 | for ( int i=0; i < nchan; ++i) { |
---|
1619 | Double world; |
---|
1620 | spc.toWorld(world, pixel[i]); |
---|
1621 | stlout.push_back(double(world)); |
---|
1622 | } |
---|
1623 | } else if ( Unit(us) == Unit("km/s") ) { |
---|
1624 | Vector<Double> world; |
---|
1625 | spc.pixelToVelocity(world, pixel); |
---|
1626 | world.tovector(stlout); |
---|
1627 | } |
---|
1628 | return stlout; |
---|
1629 | } |
---|
1630 | void Scantable::setDirectionRefString( const std::string & refstr ) |
---|
1631 | { |
---|
1632 | MDirection::Types mdt; |
---|
1633 | if (refstr != "" && !MDirection::getType(mdt, refstr)) { |
---|
1634 | throw(AipsError("Illegal Direction frame.")); |
---|
1635 | } |
---|
1636 | if ( refstr == "" ) { |
---|
1637 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
1638 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr); |
---|
1639 | } else { |
---|
1640 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr)); |
---|
1641 | } |
---|
1642 | } |
---|
1643 | |
---|
1644 | std::string Scantable::getDirectionRefString( ) const |
---|
1645 | { |
---|
1646 | return table_.keywordSet().asString("DIRECTIONREF"); |
---|
1647 | } |
---|
1648 | |
---|
1649 | MDirection Scantable::getDirection(int whichrow ) const |
---|
1650 | { |
---|
1651 | String usertype = table_.keywordSet().asString("DIRECTIONREF"); |
---|
1652 | String type = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
1653 | if ( usertype != type ) { |
---|
1654 | MDirection::Types mdt; |
---|
1655 | if (!MDirection::getType(mdt, usertype)) { |
---|
1656 | throw(AipsError("Illegal Direction frame.")); |
---|
1657 | } |
---|
1658 | return dirCol_.convert(uInt(whichrow), mdt); |
---|
1659 | } else { |
---|
1660 | return dirCol_(uInt(whichrow)); |
---|
1661 | } |
---|
1662 | } |
---|
1663 | |
---|
1664 | std::string Scantable::getAbcissaLabel( int whichrow ) const |
---|
1665 | { |
---|
1666 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number")); |
---|
1667 | const MPosition& mp = getAntennaPosition(); |
---|
1668 | const MDirection& md = getDirection(whichrow); |
---|
1669 | const MEpoch& me = timeCol_(whichrow); |
---|
1670 | //const Double& rf = mmolidCol_(whichrow); |
---|
1671 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
1672 | SpectralCoordinate spc = |
---|
1673 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow)); |
---|
1674 | |
---|
1675 | String s = "Channel"; |
---|
1676 | Unit u = Unit(freqTable_.getUnitString()); |
---|
1677 | if (u == Unit("km/s")) { |
---|
1678 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True); |
---|
1679 | } else if (u == Unit("Hz")) { |
---|
1680 | Vector<String> wau(1);wau = u.getName(); |
---|
1681 | spc.setWorldAxisUnits(wau); |
---|
1682 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False); |
---|
1683 | } |
---|
1684 | return s; |
---|
1685 | |
---|
1686 | } |
---|
1687 | |
---|
1688 | /** |
---|
1689 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name, |
---|
1690 | const std::string& unit ) |
---|
1691 | **/ |
---|
1692 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name, |
---|
1693 | const std::string& unit ) |
---|
1694 | |
---|
1695 | { |
---|
1696 | ///@todo lookup in line table to fill in name and formattedname |
---|
1697 | Unit u(unit); |
---|
1698 | //Quantum<Double> urf(rf, u); |
---|
1699 | Quantum<Vector<Double> >urf(rf, u); |
---|
1700 | Vector<String> formattedname(0); |
---|
1701 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl; |
---|
1702 | |
---|
1703 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, ""); |
---|
1704 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname); |
---|
1705 | TableVector<uInt> tabvec(table_, "MOLECULE_ID"); |
---|
1706 | tabvec = id; |
---|
1707 | } |
---|
1708 | |
---|
1709 | /** |
---|
1710 | void asap::Scantable::setRestFrequencies( const std::string& name ) |
---|
1711 | { |
---|
1712 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI")); |
---|
1713 | ///@todo implement |
---|
1714 | } |
---|
1715 | **/ |
---|
1716 | |
---|
1717 | void Scantable::setRestFrequencies( const vector<std::string>& name ) |
---|
1718 | { |
---|
1719 | (void) name; // suppress unused warning |
---|
1720 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI")); |
---|
1721 | ///@todo implement |
---|
1722 | } |
---|
1723 | |
---|
1724 | std::vector< unsigned int > Scantable::rownumbers( ) const |
---|
1725 | { |
---|
1726 | std::vector<unsigned int> stlout; |
---|
1727 | Vector<uInt> vec = table_.rowNumbers(); |
---|
1728 | vec.tovector(stlout); |
---|
1729 | return stlout; |
---|
1730 | } |
---|
1731 | |
---|
1732 | |
---|
1733 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const |
---|
1734 | { |
---|
1735 | ROTableRow row(table_); |
---|
1736 | const TableRecord& rec = row.get(whichrow); |
---|
1737 | Table t = |
---|
1738 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO")) |
---|
1739 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
1740 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
1741 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
1742 | ROArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
1743 | return speccol.getColumn(); |
---|
1744 | } |
---|
1745 | |
---|
1746 | std::vector< std::string > Scantable::columnNames( ) const |
---|
1747 | { |
---|
1748 | Vector<String> vec = table_.tableDesc().columnNames(); |
---|
1749 | return mathutil::tovectorstring(vec); |
---|
1750 | } |
---|
1751 | |
---|
1752 | MEpoch::Types Scantable::getTimeReference( ) const |
---|
1753 | { |
---|
1754 | return MEpoch::castType(timeCol_.getMeasRef().getType()); |
---|
1755 | } |
---|
1756 | |
---|
1757 | void Scantable::addFit( const STFitEntry& fit, int row ) |
---|
1758 | { |
---|
1759 | //cout << mfitidCol_(uInt(row)) << endl; |
---|
1760 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ; |
---|
1761 | os << mfitidCol_(uInt(row)) << LogIO::POST ; |
---|
1762 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row))); |
---|
1763 | mfitidCol_.put(uInt(row), id); |
---|
1764 | } |
---|
1765 | |
---|
1766 | void Scantable::shift(int npix) |
---|
1767 | { |
---|
1768 | Vector<uInt> fids(mfreqidCol_.getColumn()); |
---|
1769 | genSort( fids, Sort::Ascending, |
---|
1770 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
1771 | for (uInt i=0; i<fids.nelements(); ++i) { |
---|
1772 | frequencies().shiftRefPix(npix, fids[i]); |
---|
1773 | } |
---|
1774 | } |
---|
1775 | |
---|
1776 | String Scantable::getAntennaName() const |
---|
1777 | { |
---|
1778 | String out; |
---|
1779 | table_.keywordSet().get("AntennaName", out); |
---|
1780 | String::size_type pos1 = out.find("@") ; |
---|
1781 | String::size_type pos2 = out.find("//") ; |
---|
1782 | if ( pos2 != String::npos ) |
---|
1783 | out = out.substr(pos2+2,pos1-pos2-2) ; |
---|
1784 | else if ( pos1 != String::npos ) |
---|
1785 | out = out.substr(0,pos1) ; |
---|
1786 | return out; |
---|
1787 | } |
---|
1788 | |
---|
1789 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const |
---|
1790 | { |
---|
1791 | String tbpath; |
---|
1792 | int ret = 0; |
---|
1793 | if ( table_.keywordSet().isDefined("GBT_GO") ) { |
---|
1794 | table_.keywordSet().get("GBT_GO", tbpath); |
---|
1795 | Table t(tbpath,Table::Old); |
---|
1796 | // check each scan if other scan of the pair exist |
---|
1797 | int nscan = scanlist.size(); |
---|
1798 | for (int i = 0; i < nscan; i++) { |
---|
1799 | Table subt = t( t.col("SCAN") == scanlist[i] ); |
---|
1800 | if (subt.nrow()==0) { |
---|
1801 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl; |
---|
1802 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1803 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
1804 | ret = 1; |
---|
1805 | break; |
---|
1806 | } |
---|
1807 | ROTableRow row(subt); |
---|
1808 | const TableRecord& rec = row.get(0); |
---|
1809 | int scan1seqn = rec.asuInt("PROCSEQN"); |
---|
1810 | int laston1 = rec.asuInt("LASTON"); |
---|
1811 | if ( rec.asuInt("PROCSIZE")==2 ) { |
---|
1812 | if ( i < nscan-1 ) { |
---|
1813 | Table subt2 = t( t.col("SCAN") == scanlist[i+1] ); |
---|
1814 | if ( subt2.nrow() == 0) { |
---|
1815 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1816 | |
---|
1817 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl; |
---|
1818 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
1819 | ret = 1; |
---|
1820 | break; |
---|
1821 | } |
---|
1822 | ROTableRow row2(subt2); |
---|
1823 | const TableRecord& rec2 = row2.get(0); |
---|
1824 | int scan2seqn = rec2.asuInt("PROCSEQN"); |
---|
1825 | int laston2 = rec2.asuInt("LASTON"); |
---|
1826 | if (scan1seqn == 1 && scan2seqn == 2) { |
---|
1827 | if (laston1 == laston2) { |
---|
1828 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1829 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
1830 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
1831 | i +=1; |
---|
1832 | } |
---|
1833 | else { |
---|
1834 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1835 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
1836 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
1837 | } |
---|
1838 | } |
---|
1839 | else if (scan1seqn==2 && scan2seqn == 1) { |
---|
1840 | if (laston1 == laston2) { |
---|
1841 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1842 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl; |
---|
1843 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST; |
---|
1844 | ret = 1; |
---|
1845 | break; |
---|
1846 | } |
---|
1847 | } |
---|
1848 | else { |
---|
1849 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1850 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl; |
---|
1851 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST; |
---|
1852 | ret = 1; |
---|
1853 | break; |
---|
1854 | } |
---|
1855 | } |
---|
1856 | } |
---|
1857 | else { |
---|
1858 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1859 | //cerr<<"The scan does not appear to be standard obsevation."<<endl; |
---|
1860 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST; |
---|
1861 | } |
---|
1862 | //if ( i >= nscan ) break; |
---|
1863 | } |
---|
1864 | } |
---|
1865 | else { |
---|
1866 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
1867 | //cerr<<"No reference to GBT_GO table."<<endl; |
---|
1868 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST; |
---|
1869 | ret = 1; |
---|
1870 | } |
---|
1871 | return ret; |
---|
1872 | } |
---|
1873 | |
---|
1874 | std::vector<double> Scantable::getDirectionVector(int whichrow) const |
---|
1875 | { |
---|
1876 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue(); |
---|
1877 | std::vector<double> dir; |
---|
1878 | Dir.tovector(dir); |
---|
1879 | return dir; |
---|
1880 | } |
---|
1881 | |
---|
1882 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax ) |
---|
1883 | throw( casa::AipsError ) |
---|
1884 | { |
---|
1885 | // assumed that all rows have same nChan |
---|
1886 | Vector<Float> arr = specCol_( 0 ) ; |
---|
1887 | int nChan = arr.nelements() ; |
---|
1888 | |
---|
1889 | // if nmin < 0 or nmax < 0, nothing to do |
---|
1890 | if ( nmin < 0 ) { |
---|
1891 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
1892 | } |
---|
1893 | if ( nmax < 0 ) { |
---|
1894 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
1895 | } |
---|
1896 | |
---|
1897 | // if nmin > nmax, exchange values |
---|
1898 | if ( nmin > nmax ) { |
---|
1899 | int tmp = nmax ; |
---|
1900 | nmax = nmin ; |
---|
1901 | nmin = tmp ; |
---|
1902 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
1903 | os << "Swap values. Applied range is [" |
---|
1904 | << nmin << ", " << nmax << "]" << LogIO::POST ; |
---|
1905 | } |
---|
1906 | |
---|
1907 | // if nmin exceeds nChan, nothing to do |
---|
1908 | if ( nmin >= nChan ) { |
---|
1909 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ; |
---|
1910 | } |
---|
1911 | |
---|
1912 | // if nmax exceeds nChan, reset nmax to nChan |
---|
1913 | if ( nmax >= nChan-1 ) { |
---|
1914 | if ( nmin == 0 ) { |
---|
1915 | // nothing to do |
---|
1916 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
1917 | os << "Whole range is selected. Nothing to do." << LogIO::POST ; |
---|
1918 | return ; |
---|
1919 | } |
---|
1920 | else { |
---|
1921 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
1922 | os << "Specified maximum exceeds nChan. Applied range is [" |
---|
1923 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ; |
---|
1924 | nmax = nChan - 1 ; |
---|
1925 | } |
---|
1926 | } |
---|
1927 | |
---|
1928 | // reshape specCol_ and flagCol_ |
---|
1929 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
1930 | reshapeSpectrum( nmin, nmax, irow ) ; |
---|
1931 | } |
---|
1932 | |
---|
1933 | // update FREQUENCIES subtable |
---|
1934 | Vector<uInt> freqIdArray = mfreqidCol_.getColumn(); |
---|
1935 | uInt numFreqId = GenSort<uInt>::sort(freqIdArray, Sort::Ascending, |
---|
1936 | Sort::HeapSort | Sort::NoDuplicates); |
---|
1937 | Double refpix ; |
---|
1938 | Double refval ; |
---|
1939 | Double increment ; |
---|
1940 | for (uInt irow = 0; irow < numFreqId; irow++) { |
---|
1941 | freqTable_.getEntry( refpix, refval, increment, freqIdArray[irow] ) ; |
---|
1942 | /*** |
---|
1943 | * need to shift refpix to nmin |
---|
1944 | * note that channel nmin in old index will be channel 0 in new one |
---|
1945 | ***/ |
---|
1946 | refval = refval - ( refpix - nmin ) * increment ; |
---|
1947 | refpix = 0 ; |
---|
1948 | freqTable_.setEntry( refpix, refval, increment, freqIdArray[irow] ) ; |
---|
1949 | } |
---|
1950 | |
---|
1951 | // update nchan |
---|
1952 | int newsize = nmax - nmin + 1 ; |
---|
1953 | table_.rwKeywordSet().define( "nChan", newsize ) ; |
---|
1954 | |
---|
1955 | // update bandwidth |
---|
1956 | // assumed all spectra in the scantable have same bandwidth |
---|
1957 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ; |
---|
1958 | |
---|
1959 | return ; |
---|
1960 | } |
---|
1961 | |
---|
1962 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) |
---|
1963 | { |
---|
1964 | // reshape specCol_ and flagCol_ |
---|
1965 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
1966 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
1967 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
1968 | uInt newsize = nmax - nmin + 1 ; |
---|
1969 | Slice slice( nmin, newsize, 1 ) ; |
---|
1970 | specCol_.put( irow, oldspec( slice ) ) ; |
---|
1971 | flagsCol_.put( irow, oldflag( slice ) ) ; |
---|
1972 | if ( oldspec.size() == oldtsys.size() ) |
---|
1973 | tsysCol_.put( irow, oldtsys( slice ) ) ; |
---|
1974 | |
---|
1975 | return ; |
---|
1976 | } |
---|
1977 | |
---|
1978 | void asap::Scantable::regridSpecChannel( double dnu, int nChan ) |
---|
1979 | { |
---|
1980 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
1981 | os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ; |
---|
1982 | int freqnrow = freqTable_.table().nrow() ; |
---|
1983 | Vector<bool> firstTime( freqnrow, true ) ; |
---|
1984 | double oldincr, factor; |
---|
1985 | uInt currId; |
---|
1986 | Double refpix ; |
---|
1987 | Double refval ; |
---|
1988 | Double increment ; |
---|
1989 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
1990 | currId = mfreqidCol_(irow); |
---|
1991 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
1992 | if (nChan < 0) { |
---|
1993 | int oldsize = abcissa.size() ; |
---|
1994 | double bw = (abcissa[oldsize-1]-abcissa[0]) + \ |
---|
1995 | 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ; |
---|
1996 | nChan = int( ceil( abs(bw/dnu) ) ) ; |
---|
1997 | } |
---|
1998 | // actual regridding |
---|
1999 | regridChannel( nChan, dnu, irow ) ; |
---|
2000 | |
---|
2001 | // update FREQUENCIES subtable |
---|
2002 | if (firstTime[currId]) { |
---|
2003 | oldincr = abcissa[1]-abcissa[0] ; |
---|
2004 | factor = dnu/oldincr ; |
---|
2005 | firstTime[currId] = false ; |
---|
2006 | freqTable_.getEntry( refpix, refval, increment, currId ) ; |
---|
2007 | |
---|
2008 | //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ; |
---|
2009 | if (factor > 0 ) { |
---|
2010 | refpix = (refpix + 0.5)/factor - 0.5; |
---|
2011 | } else { |
---|
2012 | refpix = (abcissa.size() - 0.5 - refpix)/abs(factor) - 0.5; |
---|
2013 | } |
---|
2014 | freqTable_.setEntry( refpix, refval, increment*factor, currId ) ; |
---|
2015 | //os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ; |
---|
2016 | //os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ; |
---|
2017 | } |
---|
2018 | } |
---|
2019 | } |
---|
2020 | |
---|
2021 | void asap::Scantable::regridChannel( int nChan, double dnu ) |
---|
2022 | { |
---|
2023 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
2024 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ; |
---|
2025 | // assumed that all rows have same nChan |
---|
2026 | Vector<Float> arr = specCol_( 0 ) ; |
---|
2027 | int oldsize = arr.nelements() ; |
---|
2028 | |
---|
2029 | // if oldsize == nChan, nothing to do |
---|
2030 | if ( oldsize == nChan ) { |
---|
2031 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ; |
---|
2032 | return ; |
---|
2033 | } |
---|
2034 | |
---|
2035 | // if oldChan < nChan, unphysical operation |
---|
2036 | if ( oldsize < nChan ) { |
---|
2037 | os << "Unphysical operation. Nothing to do." << LogIO::POST ; |
---|
2038 | return ; |
---|
2039 | } |
---|
2040 | |
---|
2041 | // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary) |
---|
2042 | vector<string> coordinfo = getCoordInfo() ; |
---|
2043 | string oldinfo = coordinfo[0] ; |
---|
2044 | coordinfo[0] = "Hz" ; |
---|
2045 | setCoordInfo( coordinfo ) ; |
---|
2046 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
2047 | regridChannel( nChan, dnu, irow ) ; |
---|
2048 | } |
---|
2049 | coordinfo[0] = oldinfo ; |
---|
2050 | setCoordInfo( coordinfo ) ; |
---|
2051 | |
---|
2052 | |
---|
2053 | // NOTE: this method does not update metadata such as |
---|
2054 | // FREQUENCIES subtable, nChan, Bandwidth, etc. |
---|
2055 | |
---|
2056 | return ; |
---|
2057 | } |
---|
2058 | |
---|
2059 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) |
---|
2060 | { |
---|
2061 | // logging |
---|
2062 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ; |
---|
2063 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ; |
---|
2064 | |
---|
2065 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
2066 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
2067 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
2068 | Vector<Float> newspec( nChan, 0 ) ; |
---|
2069 | Vector<uChar> newflag( nChan, true ) ; |
---|
2070 | Vector<Float> newtsys ; |
---|
2071 | bool regridTsys = false ; |
---|
2072 | if (oldtsys.size() == oldspec.size()) { |
---|
2073 | regridTsys = true ; |
---|
2074 | newtsys.resize(nChan,false) ; |
---|
2075 | newtsys = 0 ; |
---|
2076 | } |
---|
2077 | |
---|
2078 | // regrid |
---|
2079 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
2080 | int oldsize = abcissa.size() ; |
---|
2081 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
2082 | //int ichan = 0 ; |
---|
2083 | double wsum = 0.0 ; |
---|
2084 | Vector<double> zi( nChan+1 ) ; |
---|
2085 | Vector<double> yi( oldsize + 1 ) ; |
---|
2086 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
2087 | for ( int ii = 1 ; ii < oldsize ; ii++ ) |
---|
2088 | yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ; |
---|
2089 | yi[oldsize] = abcissa[oldsize-1] \ |
---|
2090 | + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ; |
---|
2091 | //zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
2092 | zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ; |
---|
2093 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
---|
2094 | zi[ii] = zi[0] + dnu * ii ; |
---|
2095 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
2096 | // Access zi and yi in ascending order |
---|
2097 | int izs = ((dnu > 0) ? 0 : nChan ) ; |
---|
2098 | int ize = ((dnu > 0) ? nChan : 0 ) ; |
---|
2099 | int izincr = ((dnu > 0) ? 1 : -1 ) ; |
---|
2100 | int ichan = ((olddnu > 0) ? 0 : oldsize ) ; |
---|
2101 | int iye = ((olddnu > 0) ? oldsize : 0 ) ; |
---|
2102 | int iyincr = ((olddnu > 0) ? 1 : -1 ) ; |
---|
2103 | //for ( int ii = izs ; ii != ize ; ii+=izincr ){ |
---|
2104 | int ii = izs ; |
---|
2105 | while (ii != ize) { |
---|
2106 | // always zl < zr |
---|
2107 | double zl = zi[ii] ; |
---|
2108 | double zr = zi[ii+izincr] ; |
---|
2109 | // Need to access smaller index for the new spec, flag, and tsys. |
---|
2110 | // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc. |
---|
2111 | int i = min(ii, ii+izincr) ; |
---|
2112 | //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) { |
---|
2113 | int jj = ichan ; |
---|
2114 | while (jj != iye) { |
---|
2115 | // always yl < yr |
---|
2116 | double yl = yi[jj] ; |
---|
2117 | double yr = yi[jj+iyincr] ; |
---|
2118 | // Need to access smaller index for the original spec, flag, and tsys. |
---|
2119 | // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc. |
---|
2120 | int j = min(jj, jj+iyincr) ; |
---|
2121 | if ( yr <= zl ) { |
---|
2122 | jj += iyincr ; |
---|
2123 | continue ; |
---|
2124 | } |
---|
2125 | else if ( yl <= zl ) { |
---|
2126 | if ( yr < zr ) { |
---|
2127 | if (!oldflag[j]) { |
---|
2128 | newspec[i] += oldspec[j] * ( yr - zl ) ; |
---|
2129 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ; |
---|
2130 | wsum += ( yr - zl ) ; |
---|
2131 | } |
---|
2132 | newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ; |
---|
2133 | } |
---|
2134 | else { |
---|
2135 | if (!oldflag[j]) { |
---|
2136 | newspec[i] += oldspec[j] * abs(dnu) ; |
---|
2137 | if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ; |
---|
2138 | wsum += abs(dnu) ; |
---|
2139 | } |
---|
2140 | newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ; |
---|
2141 | ichan = jj ; |
---|
2142 | break ; |
---|
2143 | } |
---|
2144 | } |
---|
2145 | else if ( yl < zr ) { |
---|
2146 | if ( yr <= zr ) { |
---|
2147 | if (!oldflag[j]) { |
---|
2148 | newspec[i] += oldspec[j] * ( yr - yl ) ; |
---|
2149 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ; |
---|
2150 | wsum += ( yr - yl ) ; |
---|
2151 | } |
---|
2152 | newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ; |
---|
2153 | } |
---|
2154 | else { |
---|
2155 | if (!oldflag[j]) { |
---|
2156 | newspec[i] += oldspec[j] * ( zr - yl ) ; |
---|
2157 | if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ; |
---|
2158 | wsum += ( zr - yl ) ; |
---|
2159 | } |
---|
2160 | newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ; |
---|
2161 | ichan = jj ; |
---|
2162 | break ; |
---|
2163 | } |
---|
2164 | } |
---|
2165 | else { |
---|
2166 | ichan = jj - iyincr ; |
---|
2167 | break ; |
---|
2168 | } |
---|
2169 | jj += iyincr ; |
---|
2170 | } |
---|
2171 | if ( wsum != 0.0 ) { |
---|
2172 | newspec[i] /= wsum ; |
---|
2173 | if (regridTsys) newtsys[i] /= wsum ; |
---|
2174 | } |
---|
2175 | wsum = 0.0 ; |
---|
2176 | ii += izincr ; |
---|
2177 | } |
---|
2178 | // if ( dnu > 0.0 ) { |
---|
2179 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
2180 | // double zl = zi[ii] ; |
---|
2181 | // double zr = zi[ii+1] ; |
---|
2182 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
2183 | // double yl = yi[j] ; |
---|
2184 | // double yr = yi[j+1] ; |
---|
2185 | // if ( yl <= zl ) { |
---|
2186 | // if ( yr <= zl ) { |
---|
2187 | // continue ; |
---|
2188 | // } |
---|
2189 | // else if ( yr <= zr ) { |
---|
2190 | // if (!oldflag[j]) { |
---|
2191 | // newspec[ii] += oldspec[j] * ( yr - zl ) ; |
---|
2192 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ; |
---|
2193 | // wsum += ( yr - zl ) ; |
---|
2194 | // } |
---|
2195 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2196 | // } |
---|
2197 | // else { |
---|
2198 | // if (!oldflag[j]) { |
---|
2199 | // newspec[ii] += oldspec[j] * dnu ; |
---|
2200 | // if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ; |
---|
2201 | // wsum += dnu ; |
---|
2202 | // } |
---|
2203 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2204 | // ichan = j ; |
---|
2205 | // break ; |
---|
2206 | // } |
---|
2207 | // } |
---|
2208 | // else if ( yl < zr ) { |
---|
2209 | // if ( yr <= zr ) { |
---|
2210 | // if (!oldflag[j]) { |
---|
2211 | // newspec[ii] += oldspec[j] * ( yr - yl ) ; |
---|
2212 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ; |
---|
2213 | // wsum += ( yr - yl ) ; |
---|
2214 | // } |
---|
2215 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2216 | // } |
---|
2217 | // else { |
---|
2218 | // if (!oldflag[j]) { |
---|
2219 | // newspec[ii] += oldspec[j] * ( zr - yl ) ; |
---|
2220 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ; |
---|
2221 | // wsum += ( zr - yl ) ; |
---|
2222 | // } |
---|
2223 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2224 | // ichan = j ; |
---|
2225 | // break ; |
---|
2226 | // } |
---|
2227 | // } |
---|
2228 | // else { |
---|
2229 | // ichan = j - 1 ; |
---|
2230 | // break ; |
---|
2231 | // } |
---|
2232 | // } |
---|
2233 | // if ( wsum != 0.0 ) { |
---|
2234 | // newspec[ii] /= wsum ; |
---|
2235 | // if (regridTsys) newtsys[ii] /= wsum ; |
---|
2236 | // } |
---|
2237 | // wsum = 0.0 ; |
---|
2238 | // } |
---|
2239 | // } |
---|
2240 | // else if ( dnu < 0.0 ) { |
---|
2241 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
2242 | // double zl = zi[ii] ; |
---|
2243 | // double zr = zi[ii+1] ; |
---|
2244 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
2245 | // double yl = yi[j] ; |
---|
2246 | // double yr = yi[j+1] ; |
---|
2247 | // if ( yl >= zl ) { |
---|
2248 | // if ( yr >= zl ) { |
---|
2249 | // continue ; |
---|
2250 | // } |
---|
2251 | // else if ( yr >= zr ) { |
---|
2252 | // if (!oldflag[j]) { |
---|
2253 | // newspec[ii] += oldspec[j] * abs( yr - zl ) ; |
---|
2254 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ; |
---|
2255 | // wsum += abs( yr - zl ) ; |
---|
2256 | // } |
---|
2257 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2258 | // } |
---|
2259 | // else { |
---|
2260 | // if (!oldflag[j]) { |
---|
2261 | // newspec[ii] += oldspec[j] * abs( dnu ) ; |
---|
2262 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ; |
---|
2263 | // wsum += abs( dnu ) ; |
---|
2264 | // } |
---|
2265 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2266 | // ichan = j ; |
---|
2267 | // break ; |
---|
2268 | // } |
---|
2269 | // } |
---|
2270 | // else if ( yl > zr ) { |
---|
2271 | // if ( yr >= zr ) { |
---|
2272 | // if (!oldflag[j]) { |
---|
2273 | // newspec[ii] += oldspec[j] * abs( yr - yl ) ; |
---|
2274 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ; |
---|
2275 | // wsum += abs( yr - yl ) ; |
---|
2276 | // } |
---|
2277 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2278 | // } |
---|
2279 | // else { |
---|
2280 | // if (!oldflag[j]) { |
---|
2281 | // newspec[ii] += oldspec[j] * abs( zr - yl ) ; |
---|
2282 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ; |
---|
2283 | // wsum += abs( zr - yl ) ; |
---|
2284 | // } |
---|
2285 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
2286 | // ichan = j ; |
---|
2287 | // break ; |
---|
2288 | // } |
---|
2289 | // } |
---|
2290 | // else { |
---|
2291 | // ichan = j - 1 ; |
---|
2292 | // break ; |
---|
2293 | // } |
---|
2294 | // } |
---|
2295 | // if ( wsum != 0.0 ) { |
---|
2296 | // newspec[ii] /= wsum ; |
---|
2297 | // if (regridTsys) newtsys[ii] /= wsum ; |
---|
2298 | // } |
---|
2299 | // wsum = 0.0 ; |
---|
2300 | // } |
---|
2301 | // } |
---|
2302 | // // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ; |
---|
2303 | // // pile += dnu ; |
---|
2304 | // // wedge = olddnu * ( refChan + 1 ) ; |
---|
2305 | // // while ( wedge < pile ) { |
---|
2306 | // // newspec[0] += olddnu * oldspec[refChan] ; |
---|
2307 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
2308 | // // //ofs << "channel " << refChan << " is included in new channel 0" << endl ; |
---|
2309 | // // refChan++ ; |
---|
2310 | // // wedge += olddnu ; |
---|
2311 | // // wsum += olddnu ; |
---|
2312 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
2313 | // // } |
---|
2314 | // // frac = ( wedge - pile ) / olddnu ; |
---|
2315 | // // wsum += ( 1.0 - frac ) * olddnu ; |
---|
2316 | // // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
2317 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
2318 | // // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
2319 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
2320 | // // newspec[0] /= wsum ; |
---|
2321 | // // //ofs << "newspec[0] = " << newspec[0] << endl ; |
---|
2322 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
2323 | |
---|
2324 | // // /*** |
---|
2325 | // // * ichan = 1 - nChan-2 |
---|
2326 | // // ***/ |
---|
2327 | // // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) { |
---|
2328 | // // pile += dnu ; |
---|
2329 | // // newspec[ichan] += frac * olddnu * oldspec[refChan] ; |
---|
2330 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
2331 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ; |
---|
2332 | // // refChan++ ; |
---|
2333 | // // wedge += olddnu ; |
---|
2334 | // // wsum = frac * olddnu ; |
---|
2335 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
2336 | // // while ( wedge < pile ) { |
---|
2337 | // // newspec[ichan] += olddnu * oldspec[refChan] ; |
---|
2338 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
2339 | // // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ; |
---|
2340 | // // refChan++ ; |
---|
2341 | // // wedge += olddnu ; |
---|
2342 | // // wsum += olddnu ; |
---|
2343 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
2344 | // // } |
---|
2345 | // // frac = ( wedge - pile ) / olddnu ; |
---|
2346 | // // wsum += ( 1.0 - frac ) * olddnu ; |
---|
2347 | // // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
2348 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
2349 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
2350 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
2351 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
2352 | // // newspec[ichan] /= wsum ; |
---|
2353 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ; |
---|
2354 | // // } |
---|
2355 | |
---|
2356 | // // /*** |
---|
2357 | // // * ichan = nChan-1 |
---|
2358 | // // ***/ |
---|
2359 | // // // NOTE: Assumed that all spectra have the same bandwidth |
---|
2360 | // // pile += dnu ; |
---|
2361 | // // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ; |
---|
2362 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ; |
---|
2363 | // // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
2364 | // // refChan++ ; |
---|
2365 | // // wedge += olddnu ; |
---|
2366 | // // wsum = frac * olddnu ; |
---|
2367 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
2368 | // // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) { |
---|
2369 | // // newspec[nChan-1] += olddnu * oldspec[jchan] ; |
---|
2370 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ; |
---|
2371 | // // wsum += olddnu ; |
---|
2372 | // // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
2373 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
2374 | // // } |
---|
2375 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
2376 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
2377 | // // newspec[nChan-1] /= wsum ; |
---|
2378 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ; |
---|
2379 | |
---|
2380 | // // // ofs.close() ; |
---|
2381 | |
---|
2382 | specCol_.put( irow, newspec ) ; |
---|
2383 | flagsCol_.put( irow, newflag ) ; |
---|
2384 | if (regridTsys) tsysCol_.put( irow, newtsys ); |
---|
2385 | |
---|
2386 | return ; |
---|
2387 | } |
---|
2388 | |
---|
2389 | void Scantable::regridChannel( int nChan, double dnu, double fmin, int irow ) |
---|
2390 | { |
---|
2391 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
2392 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
2393 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
2394 | Vector<Float> newspec( nChan, 0 ) ; |
---|
2395 | Vector<uChar> newflag( nChan, true ) ; |
---|
2396 | Vector<Float> newtsys ; |
---|
2397 | bool regridTsys = false ; |
---|
2398 | if (oldtsys.size() == oldspec.size()) { |
---|
2399 | regridTsys = true ; |
---|
2400 | newtsys.resize(nChan,false) ; |
---|
2401 | newtsys = 0 ; |
---|
2402 | } |
---|
2403 | |
---|
2404 | // regrid |
---|
2405 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
2406 | int oldsize = abcissa.size() ; |
---|
2407 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
2408 | //int ichan = 0 ; |
---|
2409 | double wsum = 0.0 ; |
---|
2410 | Vector<double> zi( nChan+1 ) ; |
---|
2411 | Vector<double> yi( oldsize + 1 ) ; |
---|
2412 | Block<uInt> count( nChan, 0 ) ; |
---|
2413 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
2414 | for ( int ii = 1 ; ii < oldsize ; ii++ ) |
---|
2415 | yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ; |
---|
2416 | yi[oldsize] = abcissa[oldsize-1] \ |
---|
2417 | + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ; |
---|
2418 | // cout << "olddnu=" << olddnu << ", dnu=" << dnu << " (diff=" << olddnu-dnu << ")" << endl ; |
---|
2419 | // cout << "yi[0]=" << yi[0] << ", fmin=" << fmin << " (diff=" << yi[0]-fmin << ")" << endl ; |
---|
2420 | // cout << "oldsize=" << oldsize << ", nChan=" << nChan << endl ; |
---|
2421 | |
---|
2422 | // do not regrid if input parameters are almost same as current |
---|
2423 | // spectral setup |
---|
2424 | double dnuDiff = abs( ( dnu - olddnu ) / olddnu ) ; |
---|
2425 | double oldfmin = min( yi[0], yi[oldsize] ) ; |
---|
2426 | double fminDiff = abs( ( fmin - oldfmin ) / oldfmin ) ; |
---|
2427 | double nChanDiff = nChan - oldsize ; |
---|
2428 | double eps = 1.0e-8 ; |
---|
2429 | if ( nChanDiff == 0 && dnuDiff < eps && fminDiff < eps ) |
---|
2430 | return ; |
---|
2431 | |
---|
2432 | //zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
2433 | //zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ; |
---|
2434 | if ( dnu > 0 ) |
---|
2435 | zi[0] = fmin - 0.5 * dnu ; |
---|
2436 | else |
---|
2437 | zi[0] = fmin + nChan * abs(dnu) ; |
---|
2438 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
---|
2439 | zi[ii] = zi[0] + dnu * ii ; |
---|
2440 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
2441 | // Access zi and yi in ascending order |
---|
2442 | int izs = ((dnu > 0) ? 0 : nChan ) ; |
---|
2443 | int ize = ((dnu > 0) ? nChan : 0 ) ; |
---|
2444 | int izincr = ((dnu > 0) ? 1 : -1 ) ; |
---|
2445 | int ichan = ((olddnu > 0) ? 0 : oldsize ) ; |
---|
2446 | int iye = ((olddnu > 0) ? oldsize : 0 ) ; |
---|
2447 | int iyincr = ((olddnu > 0) ? 1 : -1 ) ; |
---|
2448 | //for ( int ii = izs ; ii != ize ; ii+=izincr ){ |
---|
2449 | int ii = izs ; |
---|
2450 | while (ii != ize) { |
---|
2451 | // always zl < zr |
---|
2452 | double zl = zi[ii] ; |
---|
2453 | double zr = zi[ii+izincr] ; |
---|
2454 | // Need to access smaller index for the new spec, flag, and tsys. |
---|
2455 | // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc. |
---|
2456 | int i = min(ii, ii+izincr) ; |
---|
2457 | //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) { |
---|
2458 | int jj = ichan ; |
---|
2459 | while (jj != iye) { |
---|
2460 | // always yl < yr |
---|
2461 | double yl = yi[jj] ; |
---|
2462 | double yr = yi[jj+iyincr] ; |
---|
2463 | // Need to access smaller index for the original spec, flag, and tsys. |
---|
2464 | // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc. |
---|
2465 | int j = min(jj, jj+iyincr) ; |
---|
2466 | if ( yr <= zl ) { |
---|
2467 | jj += iyincr ; |
---|
2468 | continue ; |
---|
2469 | } |
---|
2470 | else if ( yl <= zl ) { |
---|
2471 | if ( yr < zr ) { |
---|
2472 | if (!oldflag[j]) { |
---|
2473 | newspec[i] += oldspec[j] * ( yr - zl ) ; |
---|
2474 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ; |
---|
2475 | wsum += ( yr - zl ) ; |
---|
2476 | count[i]++ ; |
---|
2477 | } |
---|
2478 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2479 | } |
---|
2480 | else { |
---|
2481 | if (!oldflag[j]) { |
---|
2482 | newspec[i] += oldspec[j] * abs(dnu) ; |
---|
2483 | if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ; |
---|
2484 | wsum += abs(dnu) ; |
---|
2485 | count[i]++ ; |
---|
2486 | } |
---|
2487 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2488 | ichan = jj ; |
---|
2489 | break ; |
---|
2490 | } |
---|
2491 | } |
---|
2492 | else if ( yl < zr ) { |
---|
2493 | if ( yr <= zr ) { |
---|
2494 | if (!oldflag[j]) { |
---|
2495 | newspec[i] += oldspec[j] * ( yr - yl ) ; |
---|
2496 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ; |
---|
2497 | wsum += ( yr - yl ) ; |
---|
2498 | count[i]++ ; |
---|
2499 | } |
---|
2500 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2501 | } |
---|
2502 | else { |
---|
2503 | if (!oldflag[j]) { |
---|
2504 | newspec[i] += oldspec[j] * ( zr - yl ) ; |
---|
2505 | if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ; |
---|
2506 | wsum += ( zr - yl ) ; |
---|
2507 | count[i]++ ; |
---|
2508 | } |
---|
2509 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
2510 | ichan = jj ; |
---|
2511 | break ; |
---|
2512 | } |
---|
2513 | } |
---|
2514 | else { |
---|
2515 | //ichan = jj - iyincr ; |
---|
2516 | break ; |
---|
2517 | } |
---|
2518 | jj += iyincr ; |
---|
2519 | } |
---|
2520 | if ( wsum != 0.0 ) { |
---|
2521 | newspec[i] /= wsum ; |
---|
2522 | if (regridTsys) newtsys[i] /= wsum ; |
---|
2523 | } |
---|
2524 | wsum = 0.0 ; |
---|
2525 | ii += izincr ; |
---|
2526 | } |
---|
2527 | |
---|
2528 | // flag out channels without data |
---|
2529 | // this is tentative since there is no specific definition |
---|
2530 | // on bit flag... |
---|
2531 | uChar noData = 1 << 7 ; |
---|
2532 | for ( Int i = 0 ; i < nChan ; i++ ) { |
---|
2533 | if ( count[i] == 0 ) |
---|
2534 | newflag[i] = noData ; |
---|
2535 | } |
---|
2536 | |
---|
2537 | specCol_.put( irow, newspec ) ; |
---|
2538 | flagsCol_.put( irow, newflag ) ; |
---|
2539 | if (regridTsys) tsysCol_.put( irow, newtsys ); |
---|
2540 | |
---|
2541 | return ; |
---|
2542 | } |
---|
2543 | |
---|
2544 | std::vector<float> Scantable::getWeather(int whichrow) const |
---|
2545 | { |
---|
2546 | std::vector<float> out(5); |
---|
2547 | //Float temperature, pressure, humidity, windspeed, windaz; |
---|
2548 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4], |
---|
2549 | mweatheridCol_(uInt(whichrow))); |
---|
2550 | |
---|
2551 | |
---|
2552 | return out; |
---|
2553 | } |
---|
2554 | |
---|
2555 | bool Scantable::isAllChannelsFlagged(uInt whichrow) |
---|
2556 | { |
---|
2557 | uInt rflag; |
---|
2558 | flagrowCol_.get(whichrow, rflag); |
---|
2559 | if (rflag > 0) |
---|
2560 | return true; |
---|
2561 | bool flag; |
---|
2562 | Vector<uChar> flags; |
---|
2563 | flagsCol_.get(whichrow, flags); |
---|
2564 | flag = (flags[0]>0); |
---|
2565 | for (uInt i = 1; i < flags.size(); ++i) { |
---|
2566 | flag &= (flags[i]>0); |
---|
2567 | } |
---|
2568 | // return ((flag >> 7) == 1); |
---|
2569 | return (flag > 0); |
---|
2570 | } |
---|
2571 | |
---|
2572 | std::size_t Scantable::nValidMask(const std::vector<bool>& mask) |
---|
2573 | { |
---|
2574 | std::size_t nvalid=0; |
---|
2575 | // the assertion lines had better be replaced with static_assert when c++11 is supported |
---|
2576 | AlwaysAssert(static_cast<std::size_t>(true)==1, AipsError); |
---|
2577 | AlwaysAssert(static_cast<std::size_t>(false)==0, AipsError); |
---|
2578 | for (uInt i = 1; i < mask.size(); ++i) { |
---|
2579 | nvalid += static_cast<std::size_t>(mask[i]); |
---|
2580 | } |
---|
2581 | return nvalid; |
---|
2582 | } |
---|
2583 | |
---|
2584 | |
---|
2585 | std::vector<std::string> Scantable::applyBaselineTable(const std::string& bltable, const bool returnfitresult, const std::string& outbltable, const bool outbltableexists, const bool overwrite) |
---|
2586 | { |
---|
2587 | STBaselineTable btin = STBaselineTable(bltable); |
---|
2588 | |
---|
2589 | Vector<Bool> applyCol = btin.getApply(); |
---|
2590 | int nRowBl = applyCol.size(); |
---|
2591 | if (nRowBl != nrow()) { |
---|
2592 | throw(AipsError("Scantable and bltable have different number of rows.")); |
---|
2593 | } |
---|
2594 | |
---|
2595 | std::vector<std::string> res; |
---|
2596 | res.clear(); |
---|
2597 | |
---|
2598 | bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite)); |
---|
2599 | bool bltableidentical = (bltable == outbltable); |
---|
2600 | STBaselineTable btout = STBaselineTable(*this); |
---|
2601 | ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME"); |
---|
2602 | Vector<Double> timeSecCol = tcol.getColumn(); |
---|
2603 | |
---|
2604 | for (int whichrow = 0; whichrow < nRowBl; ++whichrow) { |
---|
2605 | if (applyCol[whichrow]) { |
---|
2606 | std::vector<float> spec = getSpectrum(whichrow); |
---|
2607 | |
---|
2608 | std::vector<bool> mask = btin.getMask(whichrow); //use mask_bltable only |
---|
2609 | |
---|
2610 | STBaselineFunc::FuncName ftype = btin.getFunctionName(whichrow); |
---|
2611 | std::vector<int> fpar = btin.getFuncParam(whichrow); |
---|
2612 | std::vector<float> params; |
---|
2613 | float rms; |
---|
2614 | std::vector<float> resfit = doApplyBaselineTable(spec, mask, ftype, fpar, params, rms, whichrow); |
---|
2615 | setSpectrum(resfit, whichrow); |
---|
2616 | |
---|
2617 | if (returnfitresult) { |
---|
2618 | res.push_back(packFittingResults(whichrow, params, rms)); |
---|
2619 | } |
---|
2620 | |
---|
2621 | if (outBaselineTable) { |
---|
2622 | if (outbltableexists) { |
---|
2623 | if (overwrite) { |
---|
2624 | if (bltableidentical) { |
---|
2625 | btin.setresult(uInt(whichrow), Vector<Float>(params), Float(rms)); |
---|
2626 | } else { |
---|
2627 | btout.setresult(uInt(whichrow), Vector<Float>(params), Float(rms)); |
---|
2628 | } |
---|
2629 | } |
---|
2630 | } else { |
---|
2631 | btout.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
2632 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
2633 | true, ftype, fpar, std::vector<float>(), |
---|
2634 | getMaskListFromMask(mask), params, rms, spec.size(), |
---|
2635 | 3.0, 0, 0.0, 0, std::vector<int>()); |
---|
2636 | } |
---|
2637 | } |
---|
2638 | } |
---|
2639 | } |
---|
2640 | |
---|
2641 | if (outBaselineTable) { |
---|
2642 | if (bltableidentical) { |
---|
2643 | btin.save(outbltable); |
---|
2644 | } else { |
---|
2645 | btout.save(outbltable); |
---|
2646 | } |
---|
2647 | } |
---|
2648 | |
---|
2649 | return res; |
---|
2650 | } |
---|
2651 | |
---|
2652 | std::vector<std::string> Scantable::subBaseline(const std::vector<std::string>& blInfoList, const bool returnfitresult, const std::string& outbltable, const bool outbltableexists, const bool overwrite) |
---|
2653 | { |
---|
2654 | int nRowBl = blInfoList.size(); |
---|
2655 | int nRowSt = nrow(); |
---|
2656 | |
---|
2657 | std::vector<std::string> res; |
---|
2658 | res.clear(); |
---|
2659 | |
---|
2660 | bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite)); |
---|
2661 | if ((outbltable != "") && outbltableexists && !overwrite) { |
---|
2662 | throw(AipsError("Cannot overwrite bltable. Set overwrite=True.")); |
---|
2663 | } |
---|
2664 | |
---|
2665 | STBaselineTable* btp = NULL; |
---|
2666 | ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME"); |
---|
2667 | Vector<Double> timeSecCol = tcol.getColumn(); |
---|
2668 | |
---|
2669 | if (outBaselineTable) { |
---|
2670 | if (outbltableexists) { |
---|
2671 | btp = new STBaselineTable((String)outbltable); |
---|
2672 | } else { |
---|
2673 | btp = new STBaselineTable(*this); |
---|
2674 | // for (int i = 0; i < nRowSt; ++i) { |
---|
2675 | // btp->appendbasedata(getScan(i), getCycle(i), getBeam(i), getIF(i), getPol(i), |
---|
2676 | // 0, timeSecCol[i]); |
---|
2677 | // btp->setApply(i, false); |
---|
2678 | // } |
---|
2679 | } |
---|
2680 | int nrow = btp->nrow(); |
---|
2681 | for (int i = nrow; i < nRowSt; ++i) { |
---|
2682 | btp->appendbasedata(getScan(i), getCycle(i), getBeam(i), getIF(i), getPol(i), |
---|
2683 | 0, timeSecCol[i]); |
---|
2684 | btp->setApply(i, false); |
---|
2685 | } |
---|
2686 | } |
---|
2687 | |
---|
2688 | for (int i = 0; i < nRowBl; ++i) { |
---|
2689 | int irow; |
---|
2690 | STBaselineFunc::FuncName ftype; |
---|
2691 | std::vector<bool> mask; |
---|
2692 | std::vector<int> fpar; |
---|
2693 | float clipth; |
---|
2694 | int clipn; |
---|
2695 | bool uself; |
---|
2696 | float lfth; |
---|
2697 | std::vector<int> lfedge; |
---|
2698 | int lfavg; |
---|
2699 | parseBlInfo(blInfoList[i], irow, ftype, fpar, mask, clipth, clipn, uself, lfth, lfedge, lfavg); |
---|
2700 | |
---|
2701 | if (irow < nRowSt) { |
---|
2702 | std::vector<float> spec = getSpectrum(irow); |
---|
2703 | std::vector<float> params; |
---|
2704 | float rms; |
---|
2705 | std::vector<bool> finalmask; |
---|
2706 | Bool doApply = True; |
---|
2707 | |
---|
2708 | if (!isAllChannelsFlagged(irow)) { |
---|
2709 | std::vector<float> resfit = doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, clipth, clipn, uself, irow, lfth, lfedge, lfavg); |
---|
2710 | setSpectrum(resfit, irow); |
---|
2711 | } |
---|
2712 | else { |
---|
2713 | doApply = False; |
---|
2714 | } |
---|
2715 | |
---|
2716 | if (returnfitresult) { |
---|
2717 | res.push_back(packFittingResults(irow, params, rms)); |
---|
2718 | } |
---|
2719 | |
---|
2720 | if (outBaselineTable) { |
---|
2721 | Vector<Int> fparam(fpar.size()); |
---|
2722 | for (uInt j = 0; j < fparam.size(); ++j) { |
---|
2723 | fparam[j] = (Int)fpar[j]; |
---|
2724 | } |
---|
2725 | |
---|
2726 | btp->setdata(uInt(irow), |
---|
2727 | uInt(getScan(irow)), uInt(getCycle(irow)), |
---|
2728 | uInt(getBeam(irow)), uInt(getIF(irow)), uInt(getPol(irow)), |
---|
2729 | uInt(0), timeSecCol[irow], doApply, ftype, fparam, |
---|
2730 | Vector<Float>(), getMaskListFromMask(finalmask), Vector<Float>(params), |
---|
2731 | Float(rms), uInt(spec.size()), Float(clipth), uInt(clipn), |
---|
2732 | Float(0.0), uInt(0), Vector<uInt>()); |
---|
2733 | } |
---|
2734 | |
---|
2735 | } |
---|
2736 | } |
---|
2737 | |
---|
2738 | if (outBaselineTable) { |
---|
2739 | btp->save(outbltable); |
---|
2740 | } |
---|
2741 | |
---|
2742 | if (btp != NULL) { |
---|
2743 | delete btp; |
---|
2744 | } |
---|
2745 | |
---|
2746 | return res; |
---|
2747 | } |
---|
2748 | |
---|
2749 | std::vector<float> Scantable::doApplyBaselineTable(std::vector<float>& spec, |
---|
2750 | std::vector<bool>& mask, |
---|
2751 | const STBaselineFunc::FuncName ftype, |
---|
2752 | std::vector<int>& fpar, |
---|
2753 | std::vector<float>& params, |
---|
2754 | float&rms, |
---|
2755 | int irow) |
---|
2756 | { |
---|
2757 | std::vector<bool> finalmask; |
---|
2758 | std::vector<int> lfedge; |
---|
2759 | return doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, 0.0, 0, false, irow, 0.0, lfedge, 0); |
---|
2760 | } |
---|
2761 | |
---|
2762 | std::vector<float> Scantable::doSubtractBaseline(std::vector<float>& spec, |
---|
2763 | std::vector<bool>& mask, |
---|
2764 | const STBaselineFunc::FuncName ftype, |
---|
2765 | std::vector<int>& fpar, |
---|
2766 | std::vector<float>& params, |
---|
2767 | float&rms, |
---|
2768 | std::vector<bool>& finalmask, |
---|
2769 | float clipth, |
---|
2770 | int clipn, |
---|
2771 | bool uself, |
---|
2772 | int irow, |
---|
2773 | float lfth, |
---|
2774 | std::vector<int>& lfedge, |
---|
2775 | int lfavg) |
---|
2776 | { |
---|
2777 | if (uself) { |
---|
2778 | STLineFinder lineFinder = STLineFinder(); |
---|
2779 | initLineFinder(lfedge, lfth, lfavg, lineFinder); |
---|
2780 | std::vector<int> currentEdge; |
---|
2781 | mask = getCompositeChanMask(irow, mask, lfedge, currentEdge, lineFinder); |
---|
2782 | } else { |
---|
2783 | mask = getCompositeChanMask(irow, mask); |
---|
2784 | } |
---|
2785 | |
---|
2786 | std::vector<float> res; |
---|
2787 | if (ftype == STBaselineFunc::Polynomial) { |
---|
2788 | res = doPolynomialFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn); |
---|
2789 | } else if (ftype == STBaselineFunc::Chebyshev) { |
---|
2790 | res = doChebyshevFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn); |
---|
2791 | } else if (ftype == STBaselineFunc::CSpline) { |
---|
2792 | int nclip = 0; |
---|
2793 | size_t numChan = spec.size(); |
---|
2794 | if (cubicSplineModelPool_.find(numChan) == cubicSplineModelPool_.end()) { |
---|
2795 | cubicSplineModelPool_[numChan] = getPolynomialModel(3, numChan, &Scantable::getNormalPolynomial); |
---|
2796 | } |
---|
2797 | if (fpar.size() > 1) { // reading from baseline table in which pieceEdges are already calculated and stored. |
---|
2798 | //res = doCubicSplineFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn); |
---|
2799 | res = doCubicSplineLeastSquareFitting(spec, mask, |
---|
2800 | cubicSplineModelPool_[numChan], |
---|
2801 | fpar.size()-1, true, fpar, params, |
---|
2802 | rms, finalmask, nclip, clipth, |
---|
2803 | clipn); |
---|
2804 | } else { // usual cspline fitting by giving nPiece only. fpar will be replaced with pieceEdges. |
---|
2805 | //res = doCubicSplineFitting(spec, mask, fpar[0], fpar, params, rms, finalmask, clipth, clipn); |
---|
2806 | res = doCubicSplineLeastSquareFitting(spec, mask, |
---|
2807 | cubicSplineModelPool_[numChan], |
---|
2808 | fpar[0], false, fpar, params, |
---|
2809 | rms, finalmask, nclip, clipth, |
---|
2810 | clipn); |
---|
2811 | } |
---|
2812 | } else if (ftype == STBaselineFunc::Sinusoid) { |
---|
2813 | res = doSinusoidFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn); |
---|
2814 | } |
---|
2815 | |
---|
2816 | return res; |
---|
2817 | } |
---|
2818 | |
---|
2819 | std::string Scantable::packFittingResults(const int irow, const std::vector<float>& params, const float rms) |
---|
2820 | { |
---|
2821 | // returned value: "irow:params[0],params[1],..,params[n-1]:rms" |
---|
2822 | ostringstream os; |
---|
2823 | os << irow << ':'; |
---|
2824 | for (uInt i = 0; i < params.size(); ++i) { |
---|
2825 | if (i > 0) { |
---|
2826 | os << ','; |
---|
2827 | } |
---|
2828 | os << params[i]; |
---|
2829 | } |
---|
2830 | os << ':' << rms; |
---|
2831 | |
---|
2832 | return os.str(); |
---|
2833 | } |
---|
2834 | |
---|
2835 | void Scantable::parseBlInfo(const std::string& blInfo, int& irow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF) |
---|
2836 | { |
---|
2837 | // The baseline info to be parsed must be column-delimited string like |
---|
2838 | // "0:chebyshev:5:3,5,169,174,485,487" where the elements are |
---|
2839 | // row number, funcType, funcOrder, maskList, clipThreshold, clipNIter, |
---|
2840 | // useLineFinder, lfThreshold, lfEdge and lfChanAvgLimit. |
---|
2841 | |
---|
2842 | std::vector<string> res = splitToStringList(blInfo, ':'); |
---|
2843 | if (res.size() < 4) { |
---|
2844 | throw(AipsError("baseline info has bad format")) ; |
---|
2845 | } |
---|
2846 | |
---|
2847 | string ftype0, fpar0, masklist0, uself0, edge0; |
---|
2848 | std::vector<int> masklist; |
---|
2849 | |
---|
2850 | stringstream ss; |
---|
2851 | ss << res[0]; |
---|
2852 | ss >> irow; |
---|
2853 | ss.clear(); ss.str(""); |
---|
2854 | |
---|
2855 | ss << res[1]; |
---|
2856 | ss >> ftype0; |
---|
2857 | if (ftype0 == "poly") { |
---|
2858 | ftype = STBaselineFunc::Polynomial; |
---|
2859 | } else if (ftype0 == "cspline") { |
---|
2860 | ftype = STBaselineFunc::CSpline; |
---|
2861 | } else if (ftype0 == "sinusoid") { |
---|
2862 | ftype = STBaselineFunc::Sinusoid; |
---|
2863 | } else if (ftype0 == "chebyshev") { |
---|
2864 | ftype = STBaselineFunc::Chebyshev; |
---|
2865 | } else { |
---|
2866 | throw(AipsError("invalid function type.")); |
---|
2867 | } |
---|
2868 | ss.clear(); ss.str(""); |
---|
2869 | |
---|
2870 | ss << res[2]; |
---|
2871 | ss >> fpar0; |
---|
2872 | fpar = splitToIntList(fpar0, ','); |
---|
2873 | ss.clear(); ss.str(""); |
---|
2874 | |
---|
2875 | ss << res[3]; |
---|
2876 | ss >> masklist0; |
---|
2877 | mask = getMaskFromMaskList(nchan(getIF(irow)), splitToIntList(masklist0, ',')); |
---|
2878 | ss.clear(); ss.str(""); |
---|
2879 | |
---|
2880 | ss << res[4]; |
---|
2881 | ss >> thresClip; |
---|
2882 | ss.clear(); ss.str(""); |
---|
2883 | |
---|
2884 | ss << res[5]; |
---|
2885 | ss >> nIterClip; |
---|
2886 | ss.clear(); ss.str(""); |
---|
2887 | |
---|
2888 | ss << res[6]; |
---|
2889 | ss >> uself0; |
---|
2890 | if (uself0 == "true") { |
---|
2891 | useLineFinder = true; |
---|
2892 | } else { |
---|
2893 | useLineFinder = false; |
---|
2894 | } |
---|
2895 | ss.clear(); ss.str(""); |
---|
2896 | |
---|
2897 | if (useLineFinder) { |
---|
2898 | ss << res[7]; |
---|
2899 | ss >> thresLF; |
---|
2900 | ss.clear(); ss.str(""); |
---|
2901 | |
---|
2902 | ss << res[8]; |
---|
2903 | ss >> edge0; |
---|
2904 | edgeLF = splitToIntList(edge0, ','); |
---|
2905 | ss.clear(); ss.str(""); |
---|
2906 | |
---|
2907 | ss << res[9]; |
---|
2908 | ss >> avgLF; |
---|
2909 | ss.clear(); ss.str(""); |
---|
2910 | } |
---|
2911 | |
---|
2912 | } |
---|
2913 | |
---|
2914 | std::vector<int> Scantable::splitToIntList(const std::string& s, const char delim) |
---|
2915 | { |
---|
2916 | istringstream iss(s); |
---|
2917 | string tmp; |
---|
2918 | int tmpi; |
---|
2919 | std::vector<int> res; |
---|
2920 | stringstream ss; |
---|
2921 | while (getline(iss, tmp, delim)) { |
---|
2922 | ss << tmp; |
---|
2923 | ss >> tmpi; |
---|
2924 | res.push_back(tmpi); |
---|
2925 | ss.clear(); ss.str(""); |
---|
2926 | } |
---|
2927 | |
---|
2928 | return res; |
---|
2929 | } |
---|
2930 | |
---|
2931 | std::vector<string> Scantable::splitToStringList(const std::string& s, const char delim) |
---|
2932 | { |
---|
2933 | istringstream iss(s); |
---|
2934 | std::string tmp; |
---|
2935 | std::vector<string> res; |
---|
2936 | while (getline(iss, tmp, delim)) { |
---|
2937 | res.push_back(tmp); |
---|
2938 | } |
---|
2939 | |
---|
2940 | return res; |
---|
2941 | } |
---|
2942 | |
---|
2943 | std::vector<bool> Scantable::getMaskFromMaskList(const int nchan, const std::vector<int>& masklist) |
---|
2944 | { |
---|
2945 | if (masklist.size() % 2 != 0) { |
---|
2946 | throw(AipsError("masklist must have even number of elements.")); |
---|
2947 | } |
---|
2948 | |
---|
2949 | std::vector<bool> res(nchan); |
---|
2950 | |
---|
2951 | for (int i = 0; i < nchan; ++i) { |
---|
2952 | res[i] = false; |
---|
2953 | } |
---|
2954 | for (uInt j = 0; j < masklist.size(); j += 2) { |
---|
2955 | for (int i = masklist[j]; i <= min(nchan-1, masklist[j+1]); ++i) { |
---|
2956 | res[i] = true; |
---|
2957 | } |
---|
2958 | } |
---|
2959 | |
---|
2960 | return res; |
---|
2961 | } |
---|
2962 | |
---|
2963 | Vector<uInt> Scantable::getMaskListFromMask(const std::vector<bool>& mask) |
---|
2964 | { |
---|
2965 | std::vector<int> masklist; |
---|
2966 | masklist.clear(); |
---|
2967 | |
---|
2968 | for (uInt i = 0; i < mask.size(); ++i) { |
---|
2969 | if (mask[i]) { |
---|
2970 | if ((i == 0)||(i == mask.size()-1)) { |
---|
2971 | masklist.push_back(i); |
---|
2972 | } else { |
---|
2973 | if ((mask[i])&&(!mask[i-1])) { |
---|
2974 | masklist.push_back(i); |
---|
2975 | } |
---|
2976 | if ((mask[i])&&(!mask[i+1])) { |
---|
2977 | masklist.push_back(i); |
---|
2978 | } |
---|
2979 | } |
---|
2980 | } |
---|
2981 | } |
---|
2982 | |
---|
2983 | Vector<uInt> res(masklist.size()); |
---|
2984 | for (uInt i = 0; i < masklist.size(); ++i) { |
---|
2985 | res[i] = (uInt)masklist[i]; |
---|
2986 | } |
---|
2987 | |
---|
2988 | return res; |
---|
2989 | } |
---|
2990 | |
---|
2991 | void Scantable::initialiseBaselining(const std::string& blfile, |
---|
2992 | ofstream& ofs, |
---|
2993 | const bool outLogger, |
---|
2994 | bool& outTextFile, |
---|
2995 | bool& csvFormat, |
---|
2996 | String& coordInfo, |
---|
2997 | bool& hasSameNchan, |
---|
2998 | const std::string& progressInfo, |
---|
2999 | bool& showProgress, |
---|
3000 | int& minNRow, |
---|
3001 | Vector<Double>& timeSecCol) |
---|
3002 | { |
---|
3003 | csvFormat = false; |
---|
3004 | outTextFile = false; |
---|
3005 | |
---|
3006 | if (blfile != "") { |
---|
3007 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
3008 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
3009 | if (ofs) outTextFile = true; |
---|
3010 | } |
---|
3011 | |
---|
3012 | coordInfo = ""; |
---|
3013 | hasSameNchan = true; |
---|
3014 | |
---|
3015 | if (outLogger || outTextFile) { |
---|
3016 | coordInfo = getCoordInfo()[0]; |
---|
3017 | if (coordInfo == "") coordInfo = "channel"; |
---|
3018 | hasSameNchan = hasSameNchanOverIFs(); |
---|
3019 | } |
---|
3020 | |
---|
3021 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
3022 | |
---|
3023 | ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME"); |
---|
3024 | timeSecCol = tcol.getColumn(); |
---|
3025 | } |
---|
3026 | |
---|
3027 | void Scantable::finaliseBaselining(const bool outBaselineTable, |
---|
3028 | STBaselineTable* pbt, |
---|
3029 | const string& bltable, |
---|
3030 | const bool outTextFile, |
---|
3031 | ofstream& ofs) |
---|
3032 | { |
---|
3033 | if (outBaselineTable) { |
---|
3034 | pbt->save(bltable); |
---|
3035 | } |
---|
3036 | |
---|
3037 | if (outTextFile) ofs.close(); |
---|
3038 | } |
---|
3039 | |
---|
3040 | void Scantable::initLineFinder(const std::vector<int>& edge, |
---|
3041 | const float threshold, |
---|
3042 | const int chanAvgLimit, |
---|
3043 | STLineFinder& lineFinder) |
---|
3044 | { |
---|
3045 | if ((edge.size() > 2) && (edge.size() < getIFNos().size()*2)) { |
---|
3046 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
3047 | } |
---|
3048 | |
---|
3049 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
3050 | } |
---|
3051 | |
---|
3052 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, |
---|
3053 | float thresClip, int nIterClip, |
---|
3054 | bool getResidual, |
---|
3055 | const std::string& progressInfo, |
---|
3056 | const bool outLogger, const std::string& blfile, |
---|
3057 | const std::string& bltable) |
---|
3058 | { |
---|
3059 | /**** |
---|
3060 | double TimeStart = mathutil::gettimeofday_sec(); |
---|
3061 | ****/ |
---|
3062 | |
---|
3063 | try { |
---|
3064 | ofstream ofs; |
---|
3065 | String coordInfo; |
---|
3066 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
3067 | int minNRow; |
---|
3068 | int nRow = nrow(); |
---|
3069 | std::vector<bool> chanMask, finalChanMask; |
---|
3070 | float rms; |
---|
3071 | bool outBaselineTable = (bltable != ""); |
---|
3072 | STBaselineTable bt = STBaselineTable(*this); |
---|
3073 | Vector<Double> timeSecCol; |
---|
3074 | size_t flagged=0; |
---|
3075 | |
---|
3076 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
3077 | coordInfo, hasSameNchan, |
---|
3078 | progressInfo, showProgress, minNRow, |
---|
3079 | timeSecCol); |
---|
3080 | |
---|
3081 | std::vector<int> nChanNos; |
---|
3082 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
3083 | modelReservoir = getPolynomialModelReservoir(order, |
---|
3084 | &Scantable::getNormalPolynomial, |
---|
3085 | nChanNos); |
---|
3086 | int nModel = modelReservoir.size(); |
---|
3087 | |
---|
3088 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
3089 | std::vector<float> sp = getSpectrum(whichrow); |
---|
3090 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
3091 | std::vector<float> params; |
---|
3092 | |
---|
3093 | //if (flagrowCol_(whichrow) == 0) { |
---|
3094 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
3095 | int nClipped = 0; |
---|
3096 | std::vector<float> res; |
---|
3097 | res = doLeastSquareFitting(sp, chanMask, |
---|
3098 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
3099 | params, rms, finalChanMask, |
---|
3100 | nClipped, thresClip, nIterClip, getResidual); |
---|
3101 | |
---|
3102 | if (outBaselineTable) { |
---|
3103 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
3104 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
3105 | true, STBaselineFunc::Polynomial, order, std::vector<float>(), |
---|
3106 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
3107 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
3108 | } else { |
---|
3109 | setSpectrum(res, whichrow); |
---|
3110 | } |
---|
3111 | |
---|
3112 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
3113 | coordInfo, hasSameNchan, ofs, "polyBaseline()", |
---|
3114 | params, nClipped); |
---|
3115 | } else { |
---|
3116 | // no valid channels to fit (flag the row) |
---|
3117 | flagrowCol_.put(whichrow, 1); |
---|
3118 | ++flagged; |
---|
3119 | if (outBaselineTable) { |
---|
3120 | params.resize(nModel); |
---|
3121 | for (uInt i = 0; i < params.size(); ++i) { |
---|
3122 | params[i] = 0.0; |
---|
3123 | } |
---|
3124 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
3125 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
3126 | true, STBaselineFunc::Polynomial, order, std::vector<float>(), |
---|
3127 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
3128 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
3129 | } |
---|
3130 | } |
---|
3131 | |
---|
3132 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
3133 | } |
---|
3134 | |
---|
3135 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
3136 | if (flagged > 0) { |
---|
3137 | LogIO os( LogOrigin( "Scantable", "polyBaseline()") ) ; |
---|
3138 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
3139 | } |
---|
3140 | } catch (...) { |
---|
3141 | throw; |
---|
3142 | } |
---|
3143 | |
---|
3144 | /**** |
---|
3145 | double TimeEnd = mathutil::gettimeofday_sec(); |
---|
3146 | double elapse1 = TimeEnd - TimeStart; |
---|
3147 | std::cout << "poly-new : " << elapse1 << " (sec.)" << endl; |
---|
3148 | ****/ |
---|
3149 | } |
---|
3150 | |
---|
3151 | void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, |
---|
3152 | float thresClip, int nIterClip, |
---|
3153 | const std::vector<int>& edge, |
---|
3154 | float threshold, int chanAvgLimit, |
---|
3155 | bool getResidual, |
---|
3156 | const std::string& progressInfo, |
---|
3157 | const bool outLogger, const std::string& blfile, |
---|
3158 | const std::string& bltable) |
---|
3159 | { |
---|
3160 | try { |
---|
3161 | ofstream ofs; |
---|
3162 | String coordInfo; |
---|
3163 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
3164 | int minNRow; |
---|
3165 | int nRow = nrow(); |
---|
3166 | std::vector<bool> chanMask, finalChanMask; |
---|
3167 | float rms; |
---|
3168 | bool outBaselineTable = (bltable != ""); |
---|
3169 | STBaselineTable bt = STBaselineTable(*this); |
---|
3170 | Vector<Double> timeSecCol; |
---|
3171 | STLineFinder lineFinder = STLineFinder(); |
---|
3172 | size_t flagged=0; |
---|
3173 | |
---|
3174 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
3175 | coordInfo, hasSameNchan, |
---|
3176 | progressInfo, showProgress, minNRow, |
---|
3177 | timeSecCol); |
---|
3178 | |
---|
3179 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
3180 | |
---|
3181 | std::vector<int> nChanNos; |
---|
3182 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
3183 | modelReservoir = getPolynomialModelReservoir(order, |
---|
3184 | &Scantable::getNormalPolynomial, |
---|
3185 | nChanNos); |
---|
3186 | int nModel = modelReservoir.size(); |
---|
3187 | |
---|
3188 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
3189 | std::vector<float> sp = getSpectrum(whichrow); |
---|
3190 | std::vector<int> currentEdge; |
---|
3191 | chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder); |
---|
3192 | std::vector<float> params; |
---|
3193 | |
---|
3194 | //if (flagrowCol_(whichrow) == 0) { |
---|
3195 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
3196 | int nClipped = 0; |
---|
3197 | std::vector<float> res; |
---|
3198 | res = doLeastSquareFitting(sp, chanMask, |
---|
3199 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
3200 | params, rms, finalChanMask, |
---|
3201 | nClipped, thresClip, nIterClip, getResidual); |
---|
3202 | |
---|
3203 | if (outBaselineTable) { |
---|
3204 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
3205 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
3206 | true, STBaselineFunc::Polynomial, order, std::vector<float>(), |
---|
3207 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
3208 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
3209 | } else { |
---|
3210 | setSpectrum(res, whichrow); |
---|
3211 | } |
---|
3212 | |
---|
3213 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
3214 | coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", |
---|
3215 | params, nClipped); |
---|
3216 | } else { |
---|
3217 | // no valid channels to fit (flag the row) |
---|
3218 | flagrowCol_.put(whichrow, 1); |
---|
3219 | ++flagged; |
---|
3220 | if (outBaselineTable) { |
---|
3221 | params.resize(nModel); |
---|
3222 | for (uInt i = 0; i < params.size(); ++i) { |
---|
3223 | params[i] = 0.0; |
---|
3224 | } |
---|
3225 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
3226 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
3227 | true, STBaselineFunc::Polynomial, order, std::vector<float>(), |
---|
3228 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
3229 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
3230 | } |
---|
3231 | } |
---|
3232 | |
---|
3233 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
3234 | } |
---|
3235 | |
---|
3236 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
3237 | if (flagged > 0) { |
---|
3238 | LogIO os( LogOrigin( "Scantable", "autoPolyBaseline()") ) ; |
---|
3239 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
3240 | } |
---|
3241 | } catch (...) { |
---|
3242 | throw; |
---|
3243 | } |
---|
3244 | } |
---|
3245 | |
---|
3246 | void Scantable::chebyshevBaseline(const std::vector<bool>& mask, int order, |
---|
3247 | float thresClip, int nIterClip, |
---|
3248 | bool getResidual, |
---|
3249 | const std::string& progressInfo, |
---|
3250 | const bool outLogger, const std::string& blfile, |
---|
3251 | const std::string& bltable) |
---|
3252 | { |
---|
3253 | /* |
---|
3254 | double TimeStart = mathutil::gettimeofday_sec(); |
---|
3255 | */ |
---|
3256 | |
---|
3257 | try { |
---|
3258 | ofstream ofs; |
---|
3259 | String coordInfo; |
---|
3260 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
3261 | int minNRow; |
---|
3262 | int nRow = nrow(); |
---|
3263 | std::vector<bool> chanMask, finalChanMask; |
---|
3264 | float rms; |
---|
3265 | bool outBaselineTable = (bltable != ""); |
---|
3266 | STBaselineTable bt = STBaselineTable(*this); |
---|
3267 | Vector<Double> timeSecCol; |
---|
3268 | size_t flagged=0; |
---|
3269 | |
---|
3270 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
3271 | coordInfo, hasSameNchan, |
---|
3272 | progressInfo, showProgress, minNRow, |
---|
3273 | timeSecCol); |
---|
3274 | |
---|
3275 | std::vector<int> nChanNos; |
---|
3276 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
3277 | modelReservoir = getPolynomialModelReservoir(order, |
---|
3278 | &Scantable::getChebyshevPolynomial, |
---|
3279 | nChanNos); |
---|
3280 | int nModel = modelReservoir.size(); |
---|
3281 | |
---|
3282 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
3283 | std::vector<float> sp = getSpectrum(whichrow); |
---|
3284 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
3285 | std::vector<float> params; |
---|
3286 | |
---|
3287 | // if (flagrowCol_(whichrow) == 0) { |
---|
3288 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
3289 | int nClipped = 0; |
---|
3290 | std::vector<float> res; |
---|
3291 | res = doLeastSquareFitting(sp, chanMask, |
---|
3292 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
3293 | params, rms, finalChanMask, |
---|
3294 | nClipped, thresClip, nIterClip, getResidual); |
---|
3295 | |
---|
3296 | if (outBaselineTable) { |
---|
3297 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
3298 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
3299 | true, STBaselineFunc::Chebyshev, order, std::vector<float>(), |
---|
3300 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
3301 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
3302 | } else { |
---|
3303 | setSpectrum(res, whichrow); |
---|
3304 | } |
---|
3305 | |
---|
3306 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
3307 | coordInfo, hasSameNchan, ofs, "chebyshevBaseline()", |
---|
3308 | params, nClipped); |
---|
3309 | } else { |
---|
3310 | // no valid channels to fit (flag the row) |
---|
3311 | flagrowCol_.put(whichrow, 1); |
---|
3312 | ++flagged; |
---|
3313 | if (outBaselineTable) { |
---|
3314 | params.resize(nModel); |
---|
3315 | for (uInt i = 0; i < params.size(); ++i) { |
---|
3316 | params[i] = 0.0; |
---|
3317 | } |
---|
3318 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
3319 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
3320 | true, STBaselineFunc::Chebyshev, order, std::vector<float>(), |
---|
3321 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
3322 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
3323 | } |
---|
3324 | } |
---|
3325 | |
---|
3326 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
3327 | } |
---|
3328 | |
---|
3329 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
3330 | |
---|
3331 | if (flagged > 0) { |
---|
3332 | LogIO os( LogOrigin( "Scantable", "chebyshevBaseline()") ) ; |
---|
3333 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
3334 | } |
---|
3335 | } catch (...) { |
---|
3336 | throw; |
---|
3337 | } |
---|
3338 | |
---|
3339 | /* |
---|
3340 | double TimeEnd = mathutil::gettimeofday_sec(); |
---|
3341 | double elapse1 = TimeEnd - TimeStart; |
---|
3342 | std::cout << "cheby : " << elapse1 << " (sec.)" << endl; |
---|
3343 | */ |
---|
3344 | } |
---|
3345 | |
---|
3346 | void Scantable::autoChebyshevBaseline(const std::vector<bool>& mask, int order, |
---|
3347 | float thresClip, int nIterClip, |
---|
3348 | const std::vector<int>& edge, |
---|
3349 | float threshold, int chanAvgLimit, |
---|
3350 | bool getResidual, |
---|
3351 | const std::string& progressInfo, |
---|
3352 | const bool outLogger, const std::string& blfile, |
---|
3353 | const std::string& bltable) |
---|
3354 | { |
---|
3355 | try { |
---|
3356 | ofstream ofs; |
---|
3357 | String coordInfo; |
---|
3358 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
3359 | int minNRow; |
---|
3360 | int nRow = nrow(); |
---|
3361 | std::vector<bool> chanMask, finalChanMask; |
---|
3362 | float rms; |
---|
3363 | bool outBaselineTable = (bltable != ""); |
---|
3364 | STBaselineTable bt = STBaselineTable(*this); |
---|
3365 | Vector<Double> timeSecCol; |
---|
3366 | STLineFinder lineFinder = STLineFinder(); |
---|
3367 | size_t flagged=0; |
---|
3368 | |
---|
3369 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
3370 | coordInfo, hasSameNchan, |
---|
3371 | progressInfo, showProgress, minNRow, |
---|
3372 | timeSecCol); |
---|
3373 | |
---|
3374 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
3375 | |
---|
3376 | std::vector<int> nChanNos; |
---|
3377 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
3378 | modelReservoir = getPolynomialModelReservoir(order, |
---|
3379 | &Scantable::getChebyshevPolynomial, |
---|
3380 | nChanNos); |
---|
3381 | int nModel = modelReservoir.size(); |
---|
3382 | |
---|
3383 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
3384 | std::vector<float> sp = getSpectrum(whichrow); |
---|
3385 | std::vector<int> currentEdge; |
---|
3386 | chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder); |
---|
3387 | std::vector<float> params; |
---|
3388 | |
---|
3389 | // if (flagrowCol_(whichrow) == 0) { |
---|
3390 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
3391 | int nClipped = 0; |
---|
3392 | std::vector<float> res; |
---|
3393 | res = doLeastSquareFitting(sp, chanMask, |
---|
3394 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
3395 | params, rms, finalChanMask, |
---|
3396 | nClipped, thresClip, nIterClip, getResidual); |
---|
3397 | |
---|
3398 | if (outBaselineTable) { |
---|
3399 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
3400 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
3401 | true, STBaselineFunc::Chebyshev, order, std::vector<float>(), |
---|
3402 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
3403 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
3404 | } else { |
---|
3405 | setSpectrum(res, whichrow); |
---|
3406 | } |
---|
3407 | |
---|
3408 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
3409 | coordInfo, hasSameNchan, ofs, "autoChebyshevBaseline()", |
---|
3410 | params, nClipped); |
---|
3411 | } else { |
---|
3412 | // no valid channels to fit (flag the row) |
---|
3413 | flagrowCol_.put(whichrow, 1); |
---|
3414 | ++flagged; |
---|
3415 | if (outBaselineTable) { |
---|
3416 | params.resize(nModel); |
---|
3417 | for (uInt i = 0; i < params.size(); ++i) { |
---|
3418 | params[i] = 0.0; |
---|
3419 | } |
---|
3420 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
3421 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
3422 | true, STBaselineFunc::Chebyshev, order, std::vector<float>(), |
---|
3423 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
3424 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
3425 | } |
---|
3426 | } |
---|
3427 | |
---|
3428 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
3429 | } |
---|
3430 | |
---|
3431 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
3432 | |
---|
3433 | if (flagged > 0) { |
---|
3434 | LogIO os( LogOrigin( "Scantable", "autoChebyshevBaseline()") ) ; |
---|
3435 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
3436 | } |
---|
3437 | } catch (...) { |
---|
3438 | throw; |
---|
3439 | } |
---|
3440 | } |
---|
3441 | |
---|
3442 | double Scantable::calculateModelSelectionCriteria(const std::string& valname, |
---|
3443 | const std::string& blfunc, |
---|
3444 | int order, |
---|
3445 | const std::vector<bool>& inMask, |
---|
3446 | int whichrow, |
---|
3447 | bool useLineFinder, |
---|
3448 | const std::vector<int>& edge, |
---|
3449 | float threshold, |
---|
3450 | int chanAvgLimit) |
---|
3451 | { |
---|
3452 | std::vector<float> sp = getSpectrum(whichrow); |
---|
3453 | std::vector<bool> chanMask; |
---|
3454 | chanMask.clear(); |
---|
3455 | |
---|
3456 | if (useLineFinder) { |
---|
3457 | STLineFinder lineFinder = STLineFinder(); |
---|
3458 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
3459 | std::vector<int> currentEdge; |
---|
3460 | chanMask = getCompositeChanMask(whichrow, inMask, edge, currentEdge, lineFinder); |
---|
3461 | } else { |
---|
3462 | chanMask = getCompositeChanMask(whichrow, inMask); |
---|
3463 | } |
---|
3464 | |
---|
3465 | return doCalculateModelSelectionCriteria(valname, sp, chanMask, blfunc, order); |
---|
3466 | } |
---|
3467 | |
---|
3468 | double Scantable::doCalculateModelSelectionCriteria(const std::string& valname, const std::vector<float>& spec, const std::vector<bool>& mask, const std::string& blfunc, int order) |
---|
3469 | { |
---|
3470 | int nparam; |
---|
3471 | std::vector<float> params; |
---|
3472 | std::vector<bool> finalChanMask; |
---|
3473 | float rms; |
---|
3474 | int nClipped = 0; |
---|
3475 | std::vector<float> res; |
---|
3476 | if (blfunc == "poly") { |
---|
3477 | nparam = order + 1; |
---|
3478 | res = doPolynomialFitting(spec, mask, order, params, rms, finalChanMask, nClipped); |
---|
3479 | } else if (blfunc == "chebyshev") { |
---|
3480 | nparam = order + 1; |
---|
3481 | res = doChebyshevFitting(spec, mask, order, params, rms, finalChanMask, nClipped); |
---|
3482 | } else if (blfunc == "cspline") { |
---|
3483 | std::vector<int> pieceEdges;//(order+1); //order = npiece |
---|
3484 | nparam = order + 3; |
---|
3485 | res = doCubicSplineFitting(spec, mask, order, false, pieceEdges, params, rms, finalChanMask, nClipped); |
---|
3486 | } else if (blfunc == "sinusoid") { |
---|
3487 | std::vector<int> nWaves; |
---|
3488 | nWaves.clear(); |
---|
3489 | for (int i = 0; i <= order; ++i) { |
---|
3490 | nWaves.push_back(i); |
---|
3491 | } |
---|
3492 | nparam = 2*order + 1; // order = nwave |
---|
3493 | res = doSinusoidFitting(spec, mask, nWaves, params, rms, finalChanMask, nClipped); |
---|
3494 | } else { |
---|
3495 | throw(AipsError("blfunc must be poly, chebyshev, cspline or sinusoid.")); |
---|
3496 | } |
---|
3497 | |
---|
3498 | double msq = 0.0; |
---|
3499 | int nusedchan = 0; |
---|
3500 | int nChan = res.size(); |
---|
3501 | for (int i = 0; i < nChan; ++i) { |
---|
3502 | if (mask[i]) { |
---|
3503 | msq += (double)res[i]*(double)res[i]; |
---|
3504 | nusedchan++; |
---|
3505 | } |
---|
3506 | } |
---|
3507 | if (nusedchan == 0) { |
---|
3508 | throw(AipsError("all channels masked.")); |
---|
3509 | } |
---|
3510 | msq /= (double)nusedchan; |
---|
3511 | |
---|
3512 | nparam++; //add 1 for sigma of Gaussian distribution |
---|
3513 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
3514 | |
---|
3515 | if (valname.find("aic") == 0) { |
---|
3516 | // Original Akaike Information Criterion (AIC) |
---|
3517 | double aic = nusedchan * (log(2.0 * PI * msq) + 1.0) + 2.0 * nparam; |
---|
3518 | |
---|
3519 | // Corrected AIC by Sugiura(1978) (AICc) |
---|
3520 | if (valname == "aicc") { |
---|
3521 | if (nusedchan - nparam - 1 <= 0) { |
---|
3522 | throw(AipsError("channel size is too small to calculate AICc.")); |
---|
3523 | } |
---|
3524 | aic += 2.0*nparam*(nparam + 1)/(double)(nusedchan - nparam - 1); |
---|
3525 | } |
---|
3526 | |
---|
3527 | return aic; |
---|
3528 | |
---|
3529 | } else if (valname == "bic") { |
---|
3530 | // Bayesian Information Criterion (BIC) |
---|
3531 | double bic = nusedchan * log(msq) + nparam * log((double)nusedchan); |
---|
3532 | return bic; |
---|
3533 | |
---|
3534 | } else if (valname == "gcv") { |
---|
3535 | // Generalised Cross Validation |
---|
3536 | double x = 1.0 - (double)nparam / (double)nusedchan; |
---|
3537 | double gcv = msq / (x * x); |
---|
3538 | return gcv; |
---|
3539 | |
---|
3540 | } else { |
---|
3541 | throw(AipsError("valname must be aic, aicc, bic or gcv.")); |
---|
3542 | } |
---|
3543 | } |
---|
3544 | |
---|
3545 | double Scantable::getNormalPolynomial(int n, double x) { |
---|
3546 | if (n == 0) { |
---|
3547 | return 1.0; |
---|
3548 | } else if (n > 0) { |
---|
3549 | double res = 1.0; |
---|
3550 | for (int i = 0; i < n; ++i) { |
---|
3551 | res *= x; |
---|
3552 | } |
---|
3553 | return res; |
---|
3554 | } else { |
---|
3555 | if (x == 0.0) { |
---|
3556 | throw(AipsError("infinity result: x=0 given for negative power.")); |
---|
3557 | } else { |
---|
3558 | return pow(x, (double)n); |
---|
3559 | } |
---|
3560 | } |
---|
3561 | } |
---|
3562 | |
---|
3563 | double Scantable::getChebyshevPolynomial(int n, double x) { |
---|
3564 | if ((x < -1.0)||(x > 1.0)) { |
---|
3565 | throw(AipsError("out of definition range (-1 <= x <= 1).")); |
---|
3566 | } else if (x == 1.0) { |
---|
3567 | return 1.0; |
---|
3568 | } else if (x == 0.0) { |
---|
3569 | double res; |
---|
3570 | if (n%2 == 0) { |
---|
3571 | if (n%4 == 0) { |
---|
3572 | res = 1.0; |
---|
3573 | } else { |
---|
3574 | res = -1.0; |
---|
3575 | } |
---|
3576 | } else { |
---|
3577 | res = 0.0; |
---|
3578 | } |
---|
3579 | return res; |
---|
3580 | } else if (x == -1.0) { |
---|
3581 | double res = (n%2 == 0 ? 1.0 : -1.0); |
---|
3582 | return res; |
---|
3583 | } else if (n < 0) { |
---|
3584 | throw(AipsError("the order must be zero or positive.")); |
---|
3585 | } else if (n == 0) { |
---|
3586 | return 1.0; |
---|
3587 | } else if (n == 1) { |
---|
3588 | return x; |
---|
3589 | } else { |
---|
3590 | double res[n+1]; |
---|
3591 | for (int i = 0; i < n+1; ++i) { |
---|
3592 | double res0 = 0.0; |
---|
3593 | if (i == 0) { |
---|
3594 | res0 = 1.0; |
---|
3595 | } else if (i == 1) { |
---|
3596 | res0 = x; |
---|
3597 | } else { |
---|
3598 | res0 = 2.0 * x * res[i-1] - res[i-2]; |
---|
3599 | } |
---|
3600 | res[i] = res0; |
---|
3601 | } |
---|
3602 | return res[n]; |
---|
3603 | } |
---|
3604 | } |
---|
3605 | |
---|
3606 | std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data, |
---|
3607 | const std::vector<bool>& mask, |
---|
3608 | int order, |
---|
3609 | std::vector<float>& params, |
---|
3610 | float& rms, |
---|
3611 | std::vector<bool>& finalmask, |
---|
3612 | float clipth, |
---|
3613 | int clipn) |
---|
3614 | { |
---|
3615 | int nClipped = 0; |
---|
3616 | return doPolynomialFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn); |
---|
3617 | } |
---|
3618 | |
---|
3619 | std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data, |
---|
3620 | const std::vector<bool>& mask, |
---|
3621 | int order, |
---|
3622 | std::vector<float>& params, |
---|
3623 | float& rms, |
---|
3624 | std::vector<bool>& finalMask, |
---|
3625 | int& nClipped, |
---|
3626 | float thresClip, |
---|
3627 | int nIterClip, |
---|
3628 | bool getResidual) |
---|
3629 | { |
---|
3630 | return doLeastSquareFitting(data, mask, |
---|
3631 | getPolynomialModel(order, data.size(), &Scantable::getNormalPolynomial), |
---|
3632 | params, rms, finalMask, |
---|
3633 | nClipped, thresClip, nIterClip, |
---|
3634 | getResidual); |
---|
3635 | } |
---|
3636 | |
---|
3637 | std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data, |
---|
3638 | const std::vector<bool>& mask, |
---|
3639 | int order, |
---|
3640 | std::vector<float>& params, |
---|
3641 | float& rms, |
---|
3642 | std::vector<bool>& finalmask, |
---|
3643 | float clipth, |
---|
3644 | int clipn) |
---|
3645 | { |
---|
3646 | int nClipped = 0; |
---|
3647 | return doChebyshevFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn); |
---|
3648 | } |
---|
3649 | |
---|
3650 | std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data, |
---|
3651 | const std::vector<bool>& mask, |
---|
3652 | int order, |
---|
3653 | std::vector<float>& params, |
---|
3654 | float& rms, |
---|
3655 | std::vector<bool>& finalMask, |
---|
3656 | int& nClipped, |
---|
3657 | float thresClip, |
---|
3658 | int nIterClip, |
---|
3659 | bool getResidual) |
---|
3660 | { |
---|
3661 | return doLeastSquareFitting(data, mask, |
---|
3662 | getPolynomialModel(order, data.size(), &Scantable::getChebyshevPolynomial), |
---|
3663 | params, rms, finalMask, |
---|
3664 | nClipped, thresClip, nIterClip, |
---|
3665 | getResidual); |
---|
3666 | } |
---|
3667 | |
---|
3668 | std::vector<std::vector<double> > Scantable::getPolynomialModel(int order, int nchan, double (Scantable::*pfunc)(int, double)) |
---|
3669 | { |
---|
3670 | // model : contains model values for computing the least-square matrix. |
---|
3671 | // model.size() is nmodel and model[*].size() is nchan. |
---|
3672 | // Each model element are as follows: |
---|
3673 | // |
---|
3674 | // (for normal polynomials) |
---|
3675 | // model[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
3676 | // model[1] = {0.0, 1.0, 2.0, ..., (nchan-1)} |
---|
3677 | // model[n-1] = ..., |
---|
3678 | // model[n] = {0.0^n, 1.0^n, 2.0^n, ..., (nchan-1)^n} |
---|
3679 | // where (0 <= n <= order) |
---|
3680 | // |
---|
3681 | // (for Chebyshev polynomials) |
---|
3682 | // model[0] = {T0(-1), T0(2/(nchan-1)-1), T0(4/(nchan-1)-1), ..., T0(1)}, |
---|
3683 | // model[n-1] = ..., |
---|
3684 | // model[n] = {Tn(-1), Tn(2/(nchan-1)-1), Tn(4/(nchan-1)-1), ..., Tn(1)} |
---|
3685 | // where (0 <= n <= order), |
---|
3686 | |
---|
3687 | int nmodel = order + 1; |
---|
3688 | std::vector<std::vector<double> > model(nmodel, std::vector<double>(nchan)); |
---|
3689 | |
---|
3690 | double stretch, shift; |
---|
3691 | if (pfunc == &Scantable::getChebyshevPolynomial) { |
---|
3692 | stretch = 2.0/(double)(nchan - 1); |
---|
3693 | shift = -1.0; |
---|
3694 | } else { |
---|
3695 | stretch = 1.0; |
---|
3696 | shift = 0.0; |
---|
3697 | } |
---|
3698 | |
---|
3699 | for (int i = 0; i < nmodel; ++i) { |
---|
3700 | for (int j = 0; j < nchan; ++j) { |
---|
3701 | model[i][j] = (this->*pfunc)(i, stretch*(double)j + shift); |
---|
3702 | } |
---|
3703 | } |
---|
3704 | |
---|
3705 | return model; |
---|
3706 | } |
---|
3707 | |
---|
3708 | std::vector<std::vector<std::vector<double> > > Scantable::getPolynomialModelReservoir(int order, |
---|
3709 | double (Scantable::*pfunc)(int, double), |
---|
3710 | std::vector<int>& nChanNos) |
---|
3711 | { |
---|
3712 | std::vector<std::vector<std::vector<double> > > res; |
---|
3713 | res.clear(); |
---|
3714 | nChanNos.clear(); |
---|
3715 | |
---|
3716 | std::vector<uint> ifNos = getIFNos(); |
---|
3717 | for (uint i = 0; i < ifNos.size(); ++i) { |
---|
3718 | int currNchan = nchan(ifNos[i]); |
---|
3719 | bool hasDifferentNchan = (i == 0); |
---|
3720 | for (uint j = 0; j < i; ++j) { |
---|
3721 | if (currNchan != nchan(ifNos[j])) { |
---|
3722 | hasDifferentNchan = true; |
---|
3723 | break; |
---|
3724 | } |
---|
3725 | } |
---|
3726 | if (hasDifferentNchan) { |
---|
3727 | res.push_back(getPolynomialModel(order, currNchan, pfunc)); |
---|
3728 | nChanNos.push_back(currNchan); |
---|
3729 | } |
---|
3730 | } |
---|
3731 | |
---|
3732 | return res; |
---|
3733 | } |
---|
3734 | |
---|
3735 | std::vector<float> Scantable::doLeastSquareFitting(const std::vector<float>& data, |
---|
3736 | const std::vector<bool>& mask, |
---|
3737 | const std::vector<std::vector<double> >& model, |
---|
3738 | std::vector<float>& params, |
---|
3739 | float& rms, |
---|
3740 | std::vector<bool>& finalMask, |
---|
3741 | int& nClipped, |
---|
3742 | float thresClip, |
---|
3743 | int nIterClip, |
---|
3744 | bool getResidual) |
---|
3745 | { |
---|
3746 | int nDOF = model.size(); |
---|
3747 | int nChan = data.size(); |
---|
3748 | |
---|
3749 | if (nDOF == 0) { |
---|
3750 | throw(AipsError("no model data given")); |
---|
3751 | } |
---|
3752 | if (nChan < 2) { |
---|
3753 | throw(AipsError("data size is too few")); |
---|
3754 | } |
---|
3755 | if (nChan != (int)mask.size()) { |
---|
3756 | throw(AipsError("data and mask sizes are not identical")); |
---|
3757 | } |
---|
3758 | for (int i = 0; i < nDOF; ++i) { |
---|
3759 | if (nChan != (int)model[i].size()) { |
---|
3760 | throw(AipsError("data and model sizes are not identical")); |
---|
3761 | } |
---|
3762 | } |
---|
3763 | |
---|
3764 | params.clear(); |
---|
3765 | params.resize(nDOF); |
---|
3766 | |
---|
3767 | finalMask.clear(); |
---|
3768 | finalMask.resize(nChan); |
---|
3769 | |
---|
3770 | std::vector<int> maskArray(nChan); |
---|
3771 | int j = 0; |
---|
3772 | for (int i = 0; i < nChan; ++i) { |
---|
3773 | maskArray[i] = mask[i] ? 1 : 0; |
---|
3774 | if (isnan(data[i])) maskArray[i] = 0; |
---|
3775 | if (isinf(data[i])) maskArray[i] = 0; |
---|
3776 | |
---|
3777 | finalMask[i] = (maskArray[i] == 1); |
---|
3778 | if (finalMask[i]) { |
---|
3779 | j++; |
---|
3780 | } |
---|
3781 | |
---|
3782 | /* |
---|
3783 | maskArray[i] = mask[i] ? 1 : 0; |
---|
3784 | if (mask[i]) { |
---|
3785 | j++; |
---|
3786 | } |
---|
3787 | finalMask[i] = mask[i]; |
---|
3788 | */ |
---|
3789 | } |
---|
3790 | |
---|
3791 | int initNData = j; |
---|
3792 | int nData = initNData; |
---|
3793 | |
---|
3794 | std::vector<double> z1(nChan), r1(nChan), residual(nChan); |
---|
3795 | for (int i = 0; i < nChan; ++i) { |
---|
3796 | z1[i] = (double)data[i]; |
---|
3797 | r1[i] = 0.0; |
---|
3798 | residual[i] = 0.0; |
---|
3799 | } |
---|
3800 | |
---|
3801 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
3802 | // xMatrix : horizontal concatenation of |
---|
3803 | // the least-sq. matrix (left) and an |
---|
3804 | // identity matrix (right). |
---|
3805 | // the right part is used to calculate the inverse matrix of the left part. |
---|
3806 | double xMatrix[nDOF][2*nDOF]; |
---|
3807 | double zMatrix[nDOF]; |
---|
3808 | for (int i = 0; i < nDOF; ++i) { |
---|
3809 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
3810 | xMatrix[i][j] = 0.0; |
---|
3811 | } |
---|
3812 | xMatrix[i][nDOF+i] = 1.0; |
---|
3813 | zMatrix[i] = 0.0; |
---|
3814 | } |
---|
3815 | |
---|
3816 | int nUseData = 0; |
---|
3817 | for (int k = 0; k < nChan; ++k) { |
---|
3818 | if (maskArray[k] == 0) continue; |
---|
3819 | |
---|
3820 | for (int i = 0; i < nDOF; ++i) { |
---|
3821 | for (int j = i; j < nDOF; ++j) { |
---|
3822 | xMatrix[i][j] += model[i][k] * model[j][k]; |
---|
3823 | } |
---|
3824 | zMatrix[i] += z1[k] * model[i][k]; |
---|
3825 | } |
---|
3826 | |
---|
3827 | nUseData++; |
---|
3828 | } |
---|
3829 | |
---|
3830 | if (nUseData < 1) { |
---|
3831 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
3832 | } |
---|
3833 | |
---|
3834 | for (int i = 0; i < nDOF; ++i) { |
---|
3835 | for (int j = 0; j < i; ++j) { |
---|
3836 | xMatrix[i][j] = xMatrix[j][i]; |
---|
3837 | } |
---|
3838 | } |
---|
3839 | |
---|
3840 | //compute inverse matrix of the left half of xMatrix |
---|
3841 | std::vector<double> invDiag(nDOF); |
---|
3842 | for (int i = 0; i < nDOF; ++i) { |
---|
3843 | invDiag[i] = 1.0 / xMatrix[i][i]; |
---|
3844 | for (int j = 0; j < nDOF; ++j) { |
---|
3845 | xMatrix[i][j] *= invDiag[i]; |
---|
3846 | } |
---|
3847 | } |
---|
3848 | |
---|
3849 | for (int k = 0; k < nDOF; ++k) { |
---|
3850 | for (int i = 0; i < nDOF; ++i) { |
---|
3851 | if (i != k) { |
---|
3852 | double factor1 = xMatrix[k][k]; |
---|
3853 | double invfactor1 = 1.0 / factor1; |
---|
3854 | double factor2 = xMatrix[i][k]; |
---|
3855 | for (int j = k; j < 2*nDOF; ++j) { |
---|
3856 | xMatrix[i][j] *= factor1; |
---|
3857 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
3858 | xMatrix[i][j] *= invfactor1; |
---|
3859 | } |
---|
3860 | } |
---|
3861 | } |
---|
3862 | double invXDiag = 1.0 / xMatrix[k][k]; |
---|
3863 | for (int j = k; j < 2*nDOF; ++j) { |
---|
3864 | xMatrix[k][j] *= invXDiag; |
---|
3865 | } |
---|
3866 | } |
---|
3867 | |
---|
3868 | for (int i = 0; i < nDOF; ++i) { |
---|
3869 | for (int j = 0; j < nDOF; ++j) { |
---|
3870 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
3871 | } |
---|
3872 | } |
---|
3873 | //compute a vector y in which coefficients of the best-fit |
---|
3874 | //model functions are stored. |
---|
3875 | //in case of polynomials, y consists of (a0,a1,a2,...) |
---|
3876 | //where ai is the coefficient of the term x^i. |
---|
3877 | //in case of sinusoids, y consists of (a0,s1,c1,s2,c2,...) |
---|
3878 | //where a0 is constant term and s* and c* are of sine |
---|
3879 | //and cosine functions, respectively. |
---|
3880 | std::vector<double> y(nDOF); |
---|
3881 | for (int i = 0; i < nDOF; ++i) { |
---|
3882 | y[i] = 0.0; |
---|
3883 | for (int j = 0; j < nDOF; ++j) { |
---|
3884 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
3885 | } |
---|
3886 | params[i] = (float)y[i]; |
---|
3887 | } |
---|
3888 | |
---|
3889 | for (int i = 0; i < nChan; ++i) { |
---|
3890 | r1[i] = y[0]; |
---|
3891 | for (int j = 1; j < nDOF; ++j) { |
---|
3892 | r1[i] += y[j]*model[j][i]; |
---|
3893 | } |
---|
3894 | residual[i] = z1[i] - r1[i]; |
---|
3895 | } |
---|
3896 | |
---|
3897 | double mean = 0.0; |
---|
3898 | double mean2 = 0.0; |
---|
3899 | for (int i = 0; i < nChan; ++i) { |
---|
3900 | if (maskArray[i] == 0) continue; |
---|
3901 | mean += residual[i]; |
---|
3902 | mean2 += residual[i]*residual[i]; |
---|
3903 | } |
---|
3904 | mean /= (double)nData; |
---|
3905 | mean2 /= (double)nData; |
---|
3906 | double rmsd = sqrt(mean2 - mean*mean); |
---|
3907 | rms = (float)rmsd; |
---|
3908 | |
---|
3909 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
3910 | break; |
---|
3911 | } else { |
---|
3912 | |
---|
3913 | double thres = rmsd * thresClip; |
---|
3914 | int newNData = 0; |
---|
3915 | for (int i = 0; i < nChan; ++i) { |
---|
3916 | if (abs(residual[i]) >= thres) { |
---|
3917 | maskArray[i] = 0; |
---|
3918 | finalMask[i] = false; |
---|
3919 | } |
---|
3920 | if (maskArray[i] > 0) { |
---|
3921 | newNData++; |
---|
3922 | } |
---|
3923 | } |
---|
3924 | if (newNData == nData) { |
---|
3925 | break; //no more flag to add. stop iteration. |
---|
3926 | } else { |
---|
3927 | nData = newNData; |
---|
3928 | } |
---|
3929 | |
---|
3930 | } |
---|
3931 | } |
---|
3932 | |
---|
3933 | nClipped = initNData - nData; |
---|
3934 | |
---|
3935 | std::vector<float> result(nChan); |
---|
3936 | if (getResidual) { |
---|
3937 | for (int i = 0; i < nChan; ++i) { |
---|
3938 | result[i] = (float)residual[i]; |
---|
3939 | } |
---|
3940 | } else { |
---|
3941 | for (int i = 0; i < nChan; ++i) { |
---|
3942 | result[i] = (float)r1[i]; |
---|
3943 | } |
---|
3944 | } |
---|
3945 | |
---|
3946 | return result; |
---|
3947 | } //xMatrix |
---|
3948 | |
---|
3949 | void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, |
---|
3950 | float thresClip, int nIterClip, |
---|
3951 | bool getResidual, |
---|
3952 | const std::string& progressInfo, |
---|
3953 | const bool outLogger, const std::string& blfile, |
---|
3954 | const std::string& bltable) |
---|
3955 | { |
---|
3956 | /**** |
---|
3957 | double TimeStart = mathutil::gettimeofday_sec(); |
---|
3958 | ****/ |
---|
3959 | |
---|
3960 | try { |
---|
3961 | ofstream ofs; |
---|
3962 | String coordInfo; |
---|
3963 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
3964 | int minNRow; |
---|
3965 | int nRow = nrow(); |
---|
3966 | std::vector<bool> chanMask, finalChanMask; |
---|
3967 | float rms; |
---|
3968 | bool outBaselineTable = (bltable != ""); |
---|
3969 | STBaselineTable bt = STBaselineTable(*this); |
---|
3970 | Vector<Double> timeSecCol; |
---|
3971 | size_t flagged=0; |
---|
3972 | |
---|
3973 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
3974 | coordInfo, hasSameNchan, |
---|
3975 | progressInfo, showProgress, minNRow, |
---|
3976 | timeSecCol); |
---|
3977 | |
---|
3978 | std::vector<int> nChanNos; |
---|
3979 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
3980 | modelReservoir = getPolynomialModelReservoir(3, |
---|
3981 | &Scantable::getNormalPolynomial, |
---|
3982 | nChanNos); |
---|
3983 | int nDOF = nPiece + 3; |
---|
3984 | |
---|
3985 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
3986 | std::vector<float> sp = getSpectrum(whichrow); |
---|
3987 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
3988 | std::vector<int> pieceEdges; |
---|
3989 | std::vector<float> params; |
---|
3990 | |
---|
3991 | //if (flagrowCol_(whichrow) == 0) { |
---|
3992 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
3993 | int nClipped = 0; |
---|
3994 | std::vector<float> res; |
---|
3995 | res = doCubicSplineLeastSquareFitting(sp, chanMask, |
---|
3996 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
3997 | nPiece, false, pieceEdges, params, rms, finalChanMask, |
---|
3998 | nClipped, thresClip, nIterClip, getResidual); |
---|
3999 | |
---|
4000 | if (outBaselineTable) { |
---|
4001 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
4002 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
4003 | true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(), |
---|
4004 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
4005 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
4006 | } else { |
---|
4007 | setSpectrum(res, whichrow); |
---|
4008 | } |
---|
4009 | |
---|
4010 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
4011 | coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", |
---|
4012 | pieceEdges, params, nClipped); |
---|
4013 | } else { |
---|
4014 | // no valid channels to fit (flag the row) |
---|
4015 | flagrowCol_.put(whichrow, 1); |
---|
4016 | ++flagged; |
---|
4017 | if (outBaselineTable) { |
---|
4018 | pieceEdges.resize(nPiece+1); |
---|
4019 | for (uInt i = 0; i < pieceEdges.size(); ++i) { |
---|
4020 | pieceEdges[i] = 0; |
---|
4021 | } |
---|
4022 | params.resize(nDOF); |
---|
4023 | for (uInt i = 0; i < params.size(); ++i) { |
---|
4024 | params[i] = 0.0; |
---|
4025 | } |
---|
4026 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
4027 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
4028 | true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(), |
---|
4029 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
4030 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
4031 | } |
---|
4032 | } |
---|
4033 | |
---|
4034 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
4035 | } |
---|
4036 | |
---|
4037 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
4038 | |
---|
4039 | if (flagged > 0) { |
---|
4040 | LogIO os( LogOrigin( "Scantable", "cubicSplineBaseline()") ) ; |
---|
4041 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
4042 | } |
---|
4043 | } catch (...) { |
---|
4044 | throw; |
---|
4045 | } |
---|
4046 | |
---|
4047 | /**** |
---|
4048 | double TimeEnd = mathutil::gettimeofday_sec(); |
---|
4049 | double elapse1 = TimeEnd - TimeStart; |
---|
4050 | std::cout << "cspline-new : " << elapse1 << " (sec.)" << endl; |
---|
4051 | ****/ |
---|
4052 | } |
---|
4053 | |
---|
4054 | void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, |
---|
4055 | float thresClip, int nIterClip, |
---|
4056 | const std::vector<int>& edge, |
---|
4057 | float threshold, int chanAvgLimit, |
---|
4058 | bool getResidual, |
---|
4059 | const std::string& progressInfo, |
---|
4060 | const bool outLogger, const std::string& blfile, |
---|
4061 | const std::string& bltable) |
---|
4062 | { |
---|
4063 | try { |
---|
4064 | ofstream ofs; |
---|
4065 | String coordInfo; |
---|
4066 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
4067 | int minNRow; |
---|
4068 | int nRow = nrow(); |
---|
4069 | std::vector<bool> chanMask, finalChanMask; |
---|
4070 | float rms; |
---|
4071 | bool outBaselineTable = (bltable != ""); |
---|
4072 | STBaselineTable bt = STBaselineTable(*this); |
---|
4073 | Vector<Double> timeSecCol; |
---|
4074 | STLineFinder lineFinder = STLineFinder(); |
---|
4075 | size_t flagged=0; |
---|
4076 | |
---|
4077 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
4078 | coordInfo, hasSameNchan, |
---|
4079 | progressInfo, showProgress, minNRow, |
---|
4080 | timeSecCol); |
---|
4081 | |
---|
4082 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
4083 | |
---|
4084 | std::vector<int> nChanNos; |
---|
4085 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
4086 | modelReservoir = getPolynomialModelReservoir(3, |
---|
4087 | &Scantable::getNormalPolynomial, |
---|
4088 | nChanNos); |
---|
4089 | int nDOF = nPiece + 3; |
---|
4090 | |
---|
4091 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
4092 | std::vector<float> sp = getSpectrum(whichrow); |
---|
4093 | std::vector<int> currentEdge; |
---|
4094 | chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder); |
---|
4095 | std::vector<int> pieceEdges; |
---|
4096 | std::vector<float> params; |
---|
4097 | |
---|
4098 | //if (flagrowCol_(whichrow) == 0) { |
---|
4099 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
4100 | int nClipped = 0; |
---|
4101 | std::vector<float> res; |
---|
4102 | res = doCubicSplineLeastSquareFitting(sp, chanMask, |
---|
4103 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
4104 | nPiece, false, pieceEdges, params, rms, finalChanMask, |
---|
4105 | nClipped, thresClip, nIterClip, getResidual); |
---|
4106 | |
---|
4107 | if (outBaselineTable) { |
---|
4108 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
4109 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
4110 | true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(), |
---|
4111 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
4112 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
4113 | } else { |
---|
4114 | setSpectrum(res, whichrow); |
---|
4115 | } |
---|
4116 | |
---|
4117 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
4118 | coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", |
---|
4119 | pieceEdges, params, nClipped); |
---|
4120 | } else { |
---|
4121 | // no valid channels to fit (flag the row) |
---|
4122 | flagrowCol_.put(whichrow, 1); |
---|
4123 | ++flagged; |
---|
4124 | if (outBaselineTable) { |
---|
4125 | pieceEdges.resize(nPiece+1); |
---|
4126 | for (uInt i = 0; i < pieceEdges.size(); ++i) { |
---|
4127 | pieceEdges[i] = 0; |
---|
4128 | } |
---|
4129 | params.resize(nDOF); |
---|
4130 | for (uInt i = 0; i < params.size(); ++i) { |
---|
4131 | params[i] = 0.0; |
---|
4132 | } |
---|
4133 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
4134 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
4135 | true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(), |
---|
4136 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
4137 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
4138 | } |
---|
4139 | } |
---|
4140 | |
---|
4141 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
4142 | } |
---|
4143 | |
---|
4144 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
4145 | |
---|
4146 | if (flagged > 0) { |
---|
4147 | LogIO os( LogOrigin( "Scantable", "autoCubicSplineBaseline()") ) ; |
---|
4148 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
4149 | } |
---|
4150 | } catch (...) { |
---|
4151 | throw; |
---|
4152 | } |
---|
4153 | } |
---|
4154 | |
---|
4155 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, |
---|
4156 | const std::vector<bool>& mask, |
---|
4157 | std::vector<int>& idxEdge, |
---|
4158 | std::vector<float>& params, |
---|
4159 | float& rms, |
---|
4160 | std::vector<bool>& finalmask, |
---|
4161 | float clipth, |
---|
4162 | int clipn) |
---|
4163 | { |
---|
4164 | int nClipped = 0; |
---|
4165 | return doCubicSplineFitting(data, mask, idxEdge.size()-1, true, idxEdge, params, rms, finalmask, nClipped, clipth, clipn); |
---|
4166 | } |
---|
4167 | |
---|
4168 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, |
---|
4169 | const std::vector<bool>& mask, |
---|
4170 | int nPiece, |
---|
4171 | std::vector<int>& idxEdge, |
---|
4172 | std::vector<float>& params, |
---|
4173 | float& rms, |
---|
4174 | std::vector<bool>& finalmask, |
---|
4175 | float clipth, |
---|
4176 | int clipn) |
---|
4177 | { |
---|
4178 | int nClipped = 0; |
---|
4179 | return doCubicSplineFitting(data, mask, nPiece, false, idxEdge, params, rms, finalmask, nClipped, clipth, clipn); |
---|
4180 | } |
---|
4181 | |
---|
4182 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, |
---|
4183 | const std::vector<bool>& mask, |
---|
4184 | int nPiece, |
---|
4185 | bool useGivenPieceBoundary, |
---|
4186 | std::vector<int>& idxEdge, |
---|
4187 | std::vector<float>& params, |
---|
4188 | float& rms, |
---|
4189 | std::vector<bool>& finalMask, |
---|
4190 | int& nClipped, |
---|
4191 | float thresClip, |
---|
4192 | int nIterClip, |
---|
4193 | bool getResidual) |
---|
4194 | { |
---|
4195 | return doCubicSplineLeastSquareFitting(data, mask, |
---|
4196 | getPolynomialModel(3, data.size(), &Scantable::getNormalPolynomial), |
---|
4197 | nPiece, useGivenPieceBoundary, idxEdge, |
---|
4198 | params, rms, finalMask, |
---|
4199 | nClipped, thresClip, nIterClip, |
---|
4200 | getResidual); |
---|
4201 | } |
---|
4202 | |
---|
4203 | std::vector<float> Scantable::doCubicSplineLeastSquareFitting(const std::vector<float>& data, |
---|
4204 | const std::vector<bool>& mask, |
---|
4205 | const std::vector<std::vector<double> >& model, |
---|
4206 | int nPiece, |
---|
4207 | bool useGivenPieceBoundary, |
---|
4208 | std::vector<int>& idxEdge, |
---|
4209 | std::vector<float>& params, |
---|
4210 | float& rms, |
---|
4211 | std::vector<bool>& finalMask, |
---|
4212 | int& nClipped, |
---|
4213 | float thresClip, |
---|
4214 | int nIterClip, |
---|
4215 | bool getResidual) |
---|
4216 | { |
---|
4217 | int nDOF = nPiece + 3; //number of independent parameters to solve, namely, 4+(nPiece-1). |
---|
4218 | int nModel = model.size(); |
---|
4219 | int nChan = data.size(); |
---|
4220 | |
---|
4221 | if (nModel != 4) { |
---|
4222 | throw(AipsError("model size must be 4.")); |
---|
4223 | } |
---|
4224 | if (nPiece < 1) { |
---|
4225 | throw(AipsError("number of the sections must be one or more")); |
---|
4226 | } |
---|
4227 | if (nChan < 2*nPiece) { |
---|
4228 | throw(AipsError("data size is too few")); |
---|
4229 | } |
---|
4230 | if (nChan != (int)mask.size()) { |
---|
4231 | throw(AipsError("data and mask sizes are not identical")); |
---|
4232 | } |
---|
4233 | for (int i = 0; i < nModel; ++i) { |
---|
4234 | if (nChan != (int)model[i].size()) { |
---|
4235 | throw(AipsError("data and model sizes are not identical")); |
---|
4236 | } |
---|
4237 | } |
---|
4238 | |
---|
4239 | params.clear(); |
---|
4240 | params.resize(nPiece*nModel); |
---|
4241 | |
---|
4242 | finalMask.clear(); |
---|
4243 | finalMask.resize(nChan); |
---|
4244 | |
---|
4245 | std::vector<int> maskArray(nChan); |
---|
4246 | std::vector<int> x(nChan); |
---|
4247 | int j = 0; |
---|
4248 | for (int i = 0; i < nChan; ++i) { |
---|
4249 | maskArray[i] = mask[i] ? 1 : 0; |
---|
4250 | if (isnan(data[i])) maskArray[i] = 0; |
---|
4251 | if (isinf(data[i])) maskArray[i] = 0; |
---|
4252 | |
---|
4253 | finalMask[i] = (maskArray[i] == 1); |
---|
4254 | if (finalMask[i]) { |
---|
4255 | x[j] = i; |
---|
4256 | j++; |
---|
4257 | } |
---|
4258 | |
---|
4259 | /* |
---|
4260 | maskArray[i] = mask[i] ? 1 : 0; |
---|
4261 | if (mask[i]) { |
---|
4262 | x[j] = i; |
---|
4263 | j++; |
---|
4264 | } |
---|
4265 | finalMask[i] = mask[i]; |
---|
4266 | */ |
---|
4267 | } |
---|
4268 | |
---|
4269 | int initNData = j; |
---|
4270 | int nData = initNData; |
---|
4271 | |
---|
4272 | if (initNData < nPiece) { |
---|
4273 | throw(AipsError("too few non-flagged channels")); |
---|
4274 | } |
---|
4275 | |
---|
4276 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5)); |
---|
4277 | std::vector<double> invEdge(nPiece-1); |
---|
4278 | |
---|
4279 | if (useGivenPieceBoundary) { |
---|
4280 | if ((int)idxEdge.size() != nPiece+1) { |
---|
4281 | throw(AipsError("pieceEdge.size() must be equal to nPiece+1.")); |
---|
4282 | } |
---|
4283 | } else { |
---|
4284 | idxEdge.clear(); |
---|
4285 | idxEdge.resize(nPiece+1); |
---|
4286 | idxEdge[0] = x[0]; |
---|
4287 | } |
---|
4288 | for (int i = 1; i < nPiece; ++i) { |
---|
4289 | int valX = x[nElement*i]; |
---|
4290 | if (!useGivenPieceBoundary) { |
---|
4291 | idxEdge[i] = valX; |
---|
4292 | } |
---|
4293 | invEdge[i-1] = 1.0/(double)valX; |
---|
4294 | } |
---|
4295 | if (!useGivenPieceBoundary) { |
---|
4296 | idxEdge[nPiece] = x[initNData-1]+1; |
---|
4297 | } |
---|
4298 | |
---|
4299 | std::vector<double> z1(nChan), r1(nChan), residual(nChan); |
---|
4300 | for (int i = 0; i < nChan; ++i) { |
---|
4301 | z1[i] = (double)data[i]; |
---|
4302 | r1[i] = 0.0; |
---|
4303 | residual[i] = 0.0; |
---|
4304 | } |
---|
4305 | |
---|
4306 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
4307 | // xMatrix : horizontal concatenation of |
---|
4308 | // the least-sq. matrix (left) and an |
---|
4309 | // identity matrix (right). |
---|
4310 | // the right part is used to calculate the inverse matrix of the left part. |
---|
4311 | |
---|
4312 | double xMatrix[nDOF][2*nDOF]; |
---|
4313 | double zMatrix[nDOF]; |
---|
4314 | for (int i = 0; i < nDOF; ++i) { |
---|
4315 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
4316 | xMatrix[i][j] = 0.0; |
---|
4317 | } |
---|
4318 | xMatrix[i][nDOF+i] = 1.0; |
---|
4319 | zMatrix[i] = 0.0; |
---|
4320 | } |
---|
4321 | |
---|
4322 | for (int n = 0; n < nPiece; ++n) { |
---|
4323 | int nUseDataInPiece = 0; |
---|
4324 | for (int k = idxEdge[n]; k < idxEdge[n+1]; ++k) { |
---|
4325 | |
---|
4326 | if (maskArray[k] == 0) continue; |
---|
4327 | |
---|
4328 | for (int i = 0; i < nModel; ++i) { |
---|
4329 | for (int j = i; j < nModel; ++j) { |
---|
4330 | xMatrix[i][j] += model[i][k] * model[j][k]; |
---|
4331 | } |
---|
4332 | zMatrix[i] += z1[k] * model[i][k]; |
---|
4333 | } |
---|
4334 | |
---|
4335 | for (int i = 0; i < n; ++i) { |
---|
4336 | double q = 1.0 - model[1][k]*invEdge[i]; |
---|
4337 | q = q*q*q; |
---|
4338 | for (int j = 0; j < nModel; ++j) { |
---|
4339 | xMatrix[j][i+nModel] += q * model[j][k]; |
---|
4340 | } |
---|
4341 | for (int j = 0; j < i; ++j) { |
---|
4342 | double r = 1.0 - model[1][k]*invEdge[j]; |
---|
4343 | r = r*r*r; |
---|
4344 | xMatrix[j+nModel][i+nModel] += r*q; |
---|
4345 | } |
---|
4346 | xMatrix[i+nModel][i+nModel] += q*q; |
---|
4347 | zMatrix[i+nModel] += q*z1[k]; |
---|
4348 | } |
---|
4349 | |
---|
4350 | nUseDataInPiece++; |
---|
4351 | } |
---|
4352 | |
---|
4353 | if (nUseDataInPiece < 1) { |
---|
4354 | std::vector<string> suffixOfPieceNumber(4); |
---|
4355 | suffixOfPieceNumber[0] = "th"; |
---|
4356 | suffixOfPieceNumber[1] = "st"; |
---|
4357 | suffixOfPieceNumber[2] = "nd"; |
---|
4358 | suffixOfPieceNumber[3] = "rd"; |
---|
4359 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0; |
---|
4360 | ostringstream oss; |
---|
4361 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece]; |
---|
4362 | oss << " piece of the spectrum. can't execute fitting anymore."; |
---|
4363 | throw(AipsError(String(oss))); |
---|
4364 | } |
---|
4365 | } |
---|
4366 | |
---|
4367 | for (int i = 0; i < nDOF; ++i) { |
---|
4368 | for (int j = 0; j < i; ++j) { |
---|
4369 | xMatrix[i][j] = xMatrix[j][i]; |
---|
4370 | } |
---|
4371 | } |
---|
4372 | |
---|
4373 | std::vector<double> invDiag(nDOF); |
---|
4374 | for (int i = 0; i < nDOF; ++i) { |
---|
4375 | invDiag[i] = 1.0 / xMatrix[i][i]; |
---|
4376 | for (int j = 0; j < nDOF; ++j) { |
---|
4377 | xMatrix[i][j] *= invDiag[i]; |
---|
4378 | } |
---|
4379 | } |
---|
4380 | |
---|
4381 | for (int k = 0; k < nDOF; ++k) { |
---|
4382 | for (int i = 0; i < nDOF; ++i) { |
---|
4383 | if (i != k) { |
---|
4384 | double factor1 = xMatrix[k][k]; |
---|
4385 | double invfactor1 = 1.0 / factor1; |
---|
4386 | double factor2 = xMatrix[i][k]; |
---|
4387 | for (int j = k; j < 2*nDOF; ++j) { |
---|
4388 | xMatrix[i][j] *= factor1; |
---|
4389 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
4390 | xMatrix[i][j] *= invfactor1; |
---|
4391 | } |
---|
4392 | } |
---|
4393 | } |
---|
4394 | double invXDiag = 1.0 / xMatrix[k][k]; |
---|
4395 | for (int j = k; j < 2*nDOF; ++j) { |
---|
4396 | xMatrix[k][j] *= invXDiag; |
---|
4397 | } |
---|
4398 | } |
---|
4399 | |
---|
4400 | for (int i = 0; i < nDOF; ++i) { |
---|
4401 | for (int j = 0; j < nDOF; ++j) { |
---|
4402 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
4403 | } |
---|
4404 | } |
---|
4405 | |
---|
4406 | //compute a vector y which consists of the coefficients of the best-fit spline curves |
---|
4407 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of |
---|
4408 | //cubic terms for the other pieces (in case nPiece>1). |
---|
4409 | std::vector<double> y(nDOF); |
---|
4410 | for (int i = 0; i < nDOF; ++i) { |
---|
4411 | y[i] = 0.0; |
---|
4412 | for (int j = 0; j < nDOF; ++j) { |
---|
4413 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
4414 | } |
---|
4415 | } |
---|
4416 | |
---|
4417 | std::vector<double> a(nModel); |
---|
4418 | for (int i = 0; i < nModel; ++i) { |
---|
4419 | a[i] = y[i]; |
---|
4420 | } |
---|
4421 | |
---|
4422 | int j = 0; |
---|
4423 | for (int n = 0; n < nPiece; ++n) { |
---|
4424 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
4425 | r1[i] = 0.0; |
---|
4426 | for (int j = 0; j < nModel; ++j) { |
---|
4427 | r1[i] += a[j] * model[j][i]; |
---|
4428 | } |
---|
4429 | } |
---|
4430 | for (int i = 0; i < nModel; ++i) { |
---|
4431 | params[j+i] = a[i]; |
---|
4432 | } |
---|
4433 | j += nModel; |
---|
4434 | |
---|
4435 | if (n == nPiece-1) break; |
---|
4436 | |
---|
4437 | double d = y[n+nModel]; |
---|
4438 | double iE = invEdge[n]; |
---|
4439 | a[0] += d; |
---|
4440 | a[1] -= 3.0 * d * iE; |
---|
4441 | a[2] += 3.0 * d * iE * iE; |
---|
4442 | a[3] -= d * iE * iE * iE; |
---|
4443 | } |
---|
4444 | |
---|
4445 | //subtract constant value for masked regions at the edge of spectrum |
---|
4446 | if (idxEdge[0] > 0) { |
---|
4447 | int n = idxEdge[0]; |
---|
4448 | for (int i = 0; i < idxEdge[0]; ++i) { |
---|
4449 | //--cubic extrapolate-- |
---|
4450 | //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i]; |
---|
4451 | //--linear extrapolate-- |
---|
4452 | //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
4453 | //--constant-- |
---|
4454 | r1[i] = r1[n]; |
---|
4455 | } |
---|
4456 | } |
---|
4457 | |
---|
4458 | if (idxEdge[nPiece] < nChan) { |
---|
4459 | int n = idxEdge[nPiece]-1; |
---|
4460 | for (int i = idxEdge[nPiece]; i < nChan; ++i) { |
---|
4461 | //--cubic extrapolate-- |
---|
4462 | //int m = 4*(nPiece-1); |
---|
4463 | //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i]; |
---|
4464 | //--linear extrapolate-- |
---|
4465 | //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
4466 | //--constant-- |
---|
4467 | r1[i] = r1[n]; |
---|
4468 | } |
---|
4469 | } |
---|
4470 | |
---|
4471 | for (int i = 0; i < nChan; ++i) { |
---|
4472 | residual[i] = z1[i] - r1[i]; |
---|
4473 | } |
---|
4474 | |
---|
4475 | double mean = 0.0; |
---|
4476 | double mean2 = 0.0; |
---|
4477 | for (int i = 0; i < nChan; ++i) { |
---|
4478 | if (maskArray[i] == 0) continue; |
---|
4479 | mean += residual[i]; |
---|
4480 | mean2 += residual[i]*residual[i]; |
---|
4481 | } |
---|
4482 | mean /= (double)nData; |
---|
4483 | mean2 /= (double)nData; |
---|
4484 | double rmsd = sqrt(mean2 - mean*mean); |
---|
4485 | rms = (float)rmsd; |
---|
4486 | |
---|
4487 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
4488 | break; |
---|
4489 | } else { |
---|
4490 | |
---|
4491 | double thres = rmsd * thresClip; |
---|
4492 | int newNData = 0; |
---|
4493 | for (int i = 0; i < nChan; ++i) { |
---|
4494 | if (abs(residual[i]) >= thres) { |
---|
4495 | maskArray[i] = 0; |
---|
4496 | finalMask[i] = false; |
---|
4497 | } |
---|
4498 | if (maskArray[i] > 0) { |
---|
4499 | newNData++; |
---|
4500 | } |
---|
4501 | } |
---|
4502 | if (newNData == nData) { |
---|
4503 | break; //no more flag to add. iteration stops. |
---|
4504 | } else { |
---|
4505 | nData = newNData; |
---|
4506 | } |
---|
4507 | |
---|
4508 | } |
---|
4509 | } |
---|
4510 | |
---|
4511 | nClipped = initNData - nData; |
---|
4512 | |
---|
4513 | std::vector<float> result(nChan); |
---|
4514 | if (getResidual) { |
---|
4515 | for (int i = 0; i < nChan; ++i) { |
---|
4516 | result[i] = (float)residual[i]; |
---|
4517 | } |
---|
4518 | } else { |
---|
4519 | for (int i = 0; i < nChan; ++i) { |
---|
4520 | result[i] = (float)r1[i]; |
---|
4521 | } |
---|
4522 | } |
---|
4523 | |
---|
4524 | return result; |
---|
4525 | } |
---|
4526 | |
---|
4527 | std::vector<int> Scantable::selectWaveNumbers(const std::vector<int>& addNWaves, |
---|
4528 | const std::vector<int>& rejectNWaves) |
---|
4529 | { |
---|
4530 | std::vector<bool> chanMask; |
---|
4531 | std::string fftMethod; |
---|
4532 | std::string fftThresh; |
---|
4533 | |
---|
4534 | return selectWaveNumbers(0, chanMask, false, fftMethod, fftThresh, addNWaves, rejectNWaves); |
---|
4535 | } |
---|
4536 | |
---|
4537 | std::vector<int> Scantable::selectWaveNumbers(const int whichrow, |
---|
4538 | const std::vector<bool>& chanMask, |
---|
4539 | const bool applyFFT, |
---|
4540 | const std::string& fftMethod, |
---|
4541 | const std::string& fftThresh, |
---|
4542 | const std::vector<int>& addNWaves, |
---|
4543 | const std::vector<int>& rejectNWaves) |
---|
4544 | { |
---|
4545 | std::vector<int> nWaves; |
---|
4546 | nWaves.clear(); |
---|
4547 | |
---|
4548 | if (applyFFT) { |
---|
4549 | string fftThAttr; |
---|
4550 | float fftThSigma; |
---|
4551 | int fftThTop; |
---|
4552 | parseFFTThresholdInfo(fftThresh, fftThAttr, fftThSigma, fftThTop); |
---|
4553 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves); |
---|
4554 | } |
---|
4555 | |
---|
4556 | addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves); |
---|
4557 | |
---|
4558 | return nWaves; |
---|
4559 | } |
---|
4560 | |
---|
4561 | int Scantable::getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos) |
---|
4562 | { |
---|
4563 | int idx = -1; |
---|
4564 | for (uint i = 0; i < nChanNos.size(); ++i) { |
---|
4565 | if (nChan == nChanNos[i]) { |
---|
4566 | idx = i; |
---|
4567 | break; |
---|
4568 | } |
---|
4569 | } |
---|
4570 | |
---|
4571 | if (idx < 0) { |
---|
4572 | throw(AipsError("nChan not found in nChhanNos.")); |
---|
4573 | } |
---|
4574 | |
---|
4575 | return idx; |
---|
4576 | } |
---|
4577 | |
---|
4578 | void Scantable::parseFFTInfo(const std::string& fftInfo, bool& applyFFT, std::string& fftMethod, std::string& fftThresh) |
---|
4579 | { |
---|
4580 | istringstream iss(fftInfo); |
---|
4581 | std::string tmp; |
---|
4582 | std::vector<string> res; |
---|
4583 | while (getline(iss, tmp, ',')) { |
---|
4584 | res.push_back(tmp); |
---|
4585 | } |
---|
4586 | if (res.size() < 3) { |
---|
4587 | throw(AipsError("wrong value in 'fftinfo' parameter")) ; |
---|
4588 | } |
---|
4589 | applyFFT = (res[0] == "true"); |
---|
4590 | fftMethod = res[1]; |
---|
4591 | fftThresh = res[2]; |
---|
4592 | } |
---|
4593 | |
---|
4594 | void Scantable::parseFFTThresholdInfo(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop) |
---|
4595 | { |
---|
4596 | uInt idxSigma = fftThresh.find("sigma"); |
---|
4597 | uInt idxTop = fftThresh.find("top"); |
---|
4598 | |
---|
4599 | if (idxSigma == fftThresh.size() - 5) { |
---|
4600 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5)); |
---|
4601 | is >> fftThSigma; |
---|
4602 | fftThAttr = "sigma"; |
---|
4603 | } else if (idxTop == 0) { |
---|
4604 | std::istringstream is(fftThresh.substr(3)); |
---|
4605 | is >> fftThTop; |
---|
4606 | fftThAttr = "top"; |
---|
4607 | } else { |
---|
4608 | bool isNumber = true; |
---|
4609 | for (uInt i = 0; i < fftThresh.size()-1; ++i) { |
---|
4610 | char ch = (fftThresh.substr(i, 1).c_str())[0]; |
---|
4611 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) { |
---|
4612 | isNumber = false; |
---|
4613 | break; |
---|
4614 | } |
---|
4615 | } |
---|
4616 | if (isNumber) { |
---|
4617 | std::istringstream is(fftThresh); |
---|
4618 | is >> fftThSigma; |
---|
4619 | fftThAttr = "sigma"; |
---|
4620 | } else { |
---|
4621 | throw(AipsError("fftthresh has a wrong value")); |
---|
4622 | } |
---|
4623 | } |
---|
4624 | } |
---|
4625 | |
---|
4626 | 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) |
---|
4627 | { |
---|
4628 | std::vector<float> fspec; |
---|
4629 | if (fftMethod == "fft") { |
---|
4630 | fspec = execFFT(whichrow, chanMask, false, true); |
---|
4631 | //} else if (fftMethod == "lsp") { |
---|
4632 | // fspec = lombScarglePeriodogram(whichrow); |
---|
4633 | } |
---|
4634 | |
---|
4635 | if (fftThAttr == "sigma") { |
---|
4636 | float mean = 0.0; |
---|
4637 | float mean2 = 0.0; |
---|
4638 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
4639 | mean += fspec[i]; |
---|
4640 | mean2 += fspec[i]*fspec[i]; |
---|
4641 | } |
---|
4642 | mean /= float(fspec.size()); |
---|
4643 | mean2 /= float(fspec.size()); |
---|
4644 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean)); |
---|
4645 | |
---|
4646 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
4647 | if (fspec[i] >= thres) { |
---|
4648 | nWaves.push_back(i); |
---|
4649 | } |
---|
4650 | } |
---|
4651 | |
---|
4652 | } else if (fftThAttr == "top") { |
---|
4653 | for (int i = 0; i < fftThTop; ++i) { |
---|
4654 | float max = 0.0; |
---|
4655 | int maxIdx = 0; |
---|
4656 | for (uInt j = 0; j < fspec.size(); ++j) { |
---|
4657 | if (fspec[j] > max) { |
---|
4658 | max = fspec[j]; |
---|
4659 | maxIdx = j; |
---|
4660 | } |
---|
4661 | } |
---|
4662 | nWaves.push_back(maxIdx); |
---|
4663 | fspec[maxIdx] = 0.0; |
---|
4664 | } |
---|
4665 | |
---|
4666 | } |
---|
4667 | |
---|
4668 | if (nWaves.size() > 1) { |
---|
4669 | sort(nWaves.begin(), nWaves.end()); |
---|
4670 | } |
---|
4671 | } |
---|
4672 | |
---|
4673 | void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
4674 | { |
---|
4675 | std::vector<int> tempAddNWaves, tempRejectNWaves; |
---|
4676 | tempAddNWaves.clear(); |
---|
4677 | tempRejectNWaves.clear(); |
---|
4678 | |
---|
4679 | for (uInt i = 0; i < addNWaves.size(); ++i) { |
---|
4680 | tempAddNWaves.push_back(addNWaves[i]); |
---|
4681 | } |
---|
4682 | if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) { |
---|
4683 | setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves); |
---|
4684 | } |
---|
4685 | |
---|
4686 | for (uInt i = 0; i < rejectNWaves.size(); ++i) { |
---|
4687 | tempRejectNWaves.push_back(rejectNWaves[i]); |
---|
4688 | } |
---|
4689 | if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) { |
---|
4690 | setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves); |
---|
4691 | } |
---|
4692 | |
---|
4693 | for (uInt i = 0; i < tempAddNWaves.size(); ++i) { |
---|
4694 | bool found = false; |
---|
4695 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
4696 | if (nWaves[j] == tempAddNWaves[i]) { |
---|
4697 | found = true; |
---|
4698 | break; |
---|
4699 | } |
---|
4700 | } |
---|
4701 | if (!found) nWaves.push_back(tempAddNWaves[i]); |
---|
4702 | } |
---|
4703 | |
---|
4704 | for (uInt i = 0; i < tempRejectNWaves.size(); ++i) { |
---|
4705 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) { |
---|
4706 | if (*j == tempRejectNWaves[i]) { |
---|
4707 | j = nWaves.erase(j); |
---|
4708 | } else { |
---|
4709 | ++j; |
---|
4710 | } |
---|
4711 | } |
---|
4712 | } |
---|
4713 | |
---|
4714 | if (nWaves.size() > 1) { |
---|
4715 | sort(nWaves.begin(), nWaves.end()); |
---|
4716 | unique(nWaves.begin(), nWaves.end()); |
---|
4717 | } |
---|
4718 | } |
---|
4719 | |
---|
4720 | void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves) |
---|
4721 | { |
---|
4722 | int val = nWaves[0]; |
---|
4723 | int nyquistFreq = nchan(getIF(whichrow))/2+1; |
---|
4724 | nWaves.clear(); |
---|
4725 | if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759 |
---|
4726 | nWaves.push_back(0); |
---|
4727 | } |
---|
4728 | while (val <= nyquistFreq) { |
---|
4729 | nWaves.push_back(val); |
---|
4730 | val++; |
---|
4731 | } |
---|
4732 | } |
---|
4733 | |
---|
4734 | void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo, |
---|
4735 | const std::vector<int>& addNWaves, |
---|
4736 | const std::vector<int>& rejectNWaves, |
---|
4737 | float thresClip, int nIterClip, |
---|
4738 | bool getResidual, |
---|
4739 | const std::string& progressInfo, |
---|
4740 | const bool outLogger, const std::string& blfile, |
---|
4741 | const std::string& bltable) |
---|
4742 | { |
---|
4743 | /**** |
---|
4744 | double TimeStart = mathutil::gettimeofday_sec(); |
---|
4745 | ****/ |
---|
4746 | |
---|
4747 | try { |
---|
4748 | ofstream ofs; |
---|
4749 | String coordInfo; |
---|
4750 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
4751 | int minNRow; |
---|
4752 | int nRow = nrow(); |
---|
4753 | std::vector<bool> chanMask, finalChanMask; |
---|
4754 | float rms; |
---|
4755 | bool outBaselineTable = (bltable != ""); |
---|
4756 | STBaselineTable bt = STBaselineTable(*this); |
---|
4757 | Vector<Double> timeSecCol; |
---|
4758 | size_t flagged=0; |
---|
4759 | |
---|
4760 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
4761 | coordInfo, hasSameNchan, |
---|
4762 | progressInfo, showProgress, minNRow, |
---|
4763 | timeSecCol); |
---|
4764 | |
---|
4765 | bool applyFFT; |
---|
4766 | std::string fftMethod, fftThresh; |
---|
4767 | parseFFTInfo(fftInfo, applyFFT, fftMethod, fftThresh); |
---|
4768 | |
---|
4769 | std::vector<int> nWaves; |
---|
4770 | std::vector<int> nChanNos; |
---|
4771 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
4772 | if (!applyFFT) { |
---|
4773 | nWaves = selectWaveNumbers(addNWaves, rejectNWaves); |
---|
4774 | if (nWaves.size()==0) //no wave numbers to fit |
---|
4775 | throw(AipsError("No valid wave numbers to fit")); |
---|
4776 | modelReservoir = getSinusoidModelReservoir(nWaves, nChanNos); |
---|
4777 | } |
---|
4778 | |
---|
4779 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
4780 | std::vector<float> sp = getSpectrum(whichrow); |
---|
4781 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
4782 | std::vector<std::vector<double> > model; |
---|
4783 | bool canfit = true; |
---|
4784 | if (applyFFT) { |
---|
4785 | nWaves = selectWaveNumbers(whichrow, chanMask, true, fftMethod, fftThresh, |
---|
4786 | addNWaves, rejectNWaves); |
---|
4787 | if (nWaves.size()==0) {// no wave numbers to fit. |
---|
4788 | canfit = false; |
---|
4789 | break; |
---|
4790 | } |
---|
4791 | model = getSinusoidModel(nWaves, sp.size()); |
---|
4792 | } else { |
---|
4793 | model = modelReservoir[getIdxOfNchan(sp.size(), nChanNos)]; |
---|
4794 | } |
---|
4795 | int nModel = modelReservoir.size(); |
---|
4796 | |
---|
4797 | std::vector<float> params; |
---|
4798 | |
---|
4799 | //if (flagrowCol_(whichrow) == 0) { |
---|
4800 | if (canfit && flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
4801 | int nClipped = 0; |
---|
4802 | std::vector<float> res; |
---|
4803 | res = doLeastSquareFitting(sp, chanMask, model, |
---|
4804 | params, rms, finalChanMask, |
---|
4805 | nClipped, thresClip, nIterClip, getResidual); |
---|
4806 | |
---|
4807 | if (outBaselineTable) { |
---|
4808 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
4809 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
4810 | true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(), |
---|
4811 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
4812 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
4813 | } else { |
---|
4814 | setSpectrum(res, whichrow); |
---|
4815 | } |
---|
4816 | |
---|
4817 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
4818 | coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", |
---|
4819 | params, nClipped); |
---|
4820 | } else { |
---|
4821 | // no valid channels to fit (flag the row) |
---|
4822 | flagrowCol_.put(whichrow, 1); |
---|
4823 | ++flagged; |
---|
4824 | if (outBaselineTable) { |
---|
4825 | params.resize(nModel); |
---|
4826 | for (uInt i = 0; i < params.size(); ++i) { |
---|
4827 | params[i] = 0.0; |
---|
4828 | } |
---|
4829 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
4830 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
4831 | true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(), |
---|
4832 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
4833 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
4834 | } |
---|
4835 | } |
---|
4836 | |
---|
4837 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
4838 | } |
---|
4839 | |
---|
4840 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
4841 | |
---|
4842 | if (flagged > 0) { |
---|
4843 | LogIO os( LogOrigin( "Scantable", "sinusoidBaseline()") ) ; |
---|
4844 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
4845 | } |
---|
4846 | } catch (...) { |
---|
4847 | throw; |
---|
4848 | } |
---|
4849 | |
---|
4850 | /**** |
---|
4851 | double TimeEnd = mathutil::gettimeofday_sec(); |
---|
4852 | double elapse1 = TimeEnd - TimeStart; |
---|
4853 | std::cout << "sinusoid-old : " << elapse1 << " (sec.)" << endl; |
---|
4854 | ****/ |
---|
4855 | } |
---|
4856 | |
---|
4857 | void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo, |
---|
4858 | const std::vector<int>& addNWaves, |
---|
4859 | const std::vector<int>& rejectNWaves, |
---|
4860 | float thresClip, int nIterClip, |
---|
4861 | const std::vector<int>& edge, |
---|
4862 | float threshold, int chanAvgLimit, |
---|
4863 | bool getResidual, |
---|
4864 | const std::string& progressInfo, |
---|
4865 | const bool outLogger, const std::string& blfile, |
---|
4866 | const std::string& bltable) |
---|
4867 | { |
---|
4868 | try { |
---|
4869 | ofstream ofs; |
---|
4870 | String coordInfo; |
---|
4871 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
4872 | int minNRow; |
---|
4873 | int nRow = nrow(); |
---|
4874 | std::vector<bool> chanMask, finalChanMask; |
---|
4875 | float rms; |
---|
4876 | bool outBaselineTable = (bltable != ""); |
---|
4877 | STBaselineTable bt = STBaselineTable(*this); |
---|
4878 | Vector<Double> timeSecCol; |
---|
4879 | STLineFinder lineFinder = STLineFinder(); |
---|
4880 | size_t flagged=0; |
---|
4881 | |
---|
4882 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
4883 | coordInfo, hasSameNchan, |
---|
4884 | progressInfo, showProgress, minNRow, |
---|
4885 | timeSecCol); |
---|
4886 | |
---|
4887 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
4888 | |
---|
4889 | bool applyFFT; |
---|
4890 | string fftMethod, fftThresh; |
---|
4891 | parseFFTInfo(fftInfo, applyFFT, fftMethod, fftThresh); |
---|
4892 | |
---|
4893 | std::vector<int> nWaves; |
---|
4894 | std::vector<int> nChanNos; |
---|
4895 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
4896 | if (!applyFFT) { |
---|
4897 | nWaves = selectWaveNumbers(addNWaves, rejectNWaves); |
---|
4898 | if (nWaves.size()==0) //no wave numbers to fit |
---|
4899 | throw(AipsError("No valid wave numbers to fit")); |
---|
4900 | modelReservoir = getSinusoidModelReservoir(nWaves, nChanNos); |
---|
4901 | } |
---|
4902 | |
---|
4903 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
4904 | std::vector<float> sp = getSpectrum(whichrow); |
---|
4905 | std::vector<int> currentEdge; |
---|
4906 | chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder); |
---|
4907 | std::vector<std::vector<double> > model; |
---|
4908 | bool canfit=true; |
---|
4909 | if (applyFFT) { |
---|
4910 | nWaves = selectWaveNumbers(whichrow, chanMask, true, fftMethod, fftThresh, |
---|
4911 | addNWaves, rejectNWaves); |
---|
4912 | if (nWaves.size()==0) { // no wave numbers to fit. |
---|
4913 | canfit = false; |
---|
4914 | break; |
---|
4915 | } |
---|
4916 | model = getSinusoidModel(nWaves, sp.size()); |
---|
4917 | } else { |
---|
4918 | model = modelReservoir[getIdxOfNchan(sp.size(), nChanNos)]; |
---|
4919 | } |
---|
4920 | int nModel = modelReservoir.size(); |
---|
4921 | |
---|
4922 | std::vector<float> params; |
---|
4923 | |
---|
4924 | //if (flagrowCol_(whichrow) == 0) { |
---|
4925 | if (canfit && flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
4926 | int nClipped = 0; |
---|
4927 | std::vector<float> res; |
---|
4928 | res = doLeastSquareFitting(sp, chanMask, model, |
---|
4929 | params, rms, finalChanMask, |
---|
4930 | nClipped, thresClip, nIterClip, getResidual); |
---|
4931 | |
---|
4932 | if (outBaselineTable) { |
---|
4933 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
4934 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
4935 | true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(), |
---|
4936 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
4937 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
4938 | } else { |
---|
4939 | setSpectrum(res, whichrow); |
---|
4940 | } |
---|
4941 | |
---|
4942 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
4943 | coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", |
---|
4944 | params, nClipped); |
---|
4945 | } else { |
---|
4946 | // no valid channels to fit (flag the row) |
---|
4947 | flagrowCol_.put(whichrow, 1); |
---|
4948 | ++flagged; |
---|
4949 | if (outBaselineTable) { |
---|
4950 | params.resize(nModel); |
---|
4951 | for (uInt i = 0; i < params.size(); ++i) { |
---|
4952 | params[i] = 0.0; |
---|
4953 | } |
---|
4954 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
4955 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
4956 | true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(), |
---|
4957 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
4958 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
4959 | } |
---|
4960 | } |
---|
4961 | |
---|
4962 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
4963 | } |
---|
4964 | |
---|
4965 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
4966 | |
---|
4967 | if (flagged > 0) { |
---|
4968 | LogIO os( LogOrigin( "Scantable", "autoSinusoidBaseline()") ) ; |
---|
4969 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
4970 | } |
---|
4971 | } catch (...) { |
---|
4972 | throw; |
---|
4973 | } |
---|
4974 | } |
---|
4975 | |
---|
4976 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, |
---|
4977 | const std::vector<bool>& mask, |
---|
4978 | const std::vector<int>& waveNumbers, |
---|
4979 | std::vector<float>& params, |
---|
4980 | float& rms, |
---|
4981 | std::vector<bool>& finalmask, |
---|
4982 | float clipth, |
---|
4983 | int clipn) |
---|
4984 | { |
---|
4985 | int nClipped = 0; |
---|
4986 | return doSinusoidFitting(data, mask, waveNumbers, params, rms, finalmask, nClipped, clipth, clipn); |
---|
4987 | } |
---|
4988 | |
---|
4989 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, |
---|
4990 | const std::vector<bool>& mask, |
---|
4991 | const std::vector<int>& waveNumbers, |
---|
4992 | std::vector<float>& params, |
---|
4993 | float& rms, |
---|
4994 | std::vector<bool>& finalMask, |
---|
4995 | int& nClipped, |
---|
4996 | float thresClip, |
---|
4997 | int nIterClip, |
---|
4998 | bool getResidual) |
---|
4999 | { |
---|
5000 | return doLeastSquareFitting(data, mask, |
---|
5001 | getSinusoidModel(waveNumbers, data.size()), |
---|
5002 | params, rms, finalMask, |
---|
5003 | nClipped, thresClip, nIterClip, |
---|
5004 | getResidual); |
---|
5005 | } |
---|
5006 | |
---|
5007 | std::vector<std::vector<std::vector<double> > > Scantable::getSinusoidModelReservoir(const std::vector<int>& waveNumbers, |
---|
5008 | std::vector<int>& nChanNos) |
---|
5009 | { |
---|
5010 | std::vector<std::vector<std::vector<double> > > res; |
---|
5011 | res.clear(); |
---|
5012 | nChanNos.clear(); |
---|
5013 | |
---|
5014 | std::vector<uint> ifNos = getIFNos(); |
---|
5015 | for (uint i = 0; i < ifNos.size(); ++i) { |
---|
5016 | int currNchan = nchan(ifNos[i]); |
---|
5017 | bool hasDifferentNchan = (i == 0); |
---|
5018 | for (uint j = 0; j < i; ++j) { |
---|
5019 | if (currNchan != nchan(ifNos[j])) { |
---|
5020 | hasDifferentNchan = true; |
---|
5021 | break; |
---|
5022 | } |
---|
5023 | } |
---|
5024 | if (hasDifferentNchan) { |
---|
5025 | res.push_back(getSinusoidModel(waveNumbers, currNchan)); |
---|
5026 | nChanNos.push_back(currNchan); |
---|
5027 | } |
---|
5028 | } |
---|
5029 | |
---|
5030 | return res; |
---|
5031 | } |
---|
5032 | |
---|
5033 | std::vector<std::vector<double> > Scantable::getSinusoidModel(const std::vector<int>& waveNumbers, int nchan) |
---|
5034 | { |
---|
5035 | // model : contains elemental values for computing the least-square matrix. |
---|
5036 | // model.size() is nmodel and model[*].size() is nchan. |
---|
5037 | // Each model element are as follows: |
---|
5038 | // model[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
5039 | // model[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nchan])}, |
---|
5040 | // model[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nchan])}, |
---|
5041 | // where (1 <= n <= nMaxWavesInSW), |
---|
5042 | // or, |
---|
5043 | // model[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nchan])}, |
---|
5044 | // model[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nchan])}, |
---|
5045 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()). |
---|
5046 | |
---|
5047 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers |
---|
5048 | nWaves.reserve(waveNumbers.size()); |
---|
5049 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves)); |
---|
5050 | sort(nWaves.begin(), nWaves.end()); |
---|
5051 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end()); |
---|
5052 | nWaves.erase(end_it, nWaves.end()); |
---|
5053 | |
---|
5054 | if (nWaves.size()==0) |
---|
5055 | throw(AipsError("No valid wavenumbers to fit.")); |
---|
5056 | |
---|
5057 | int minNWaves = nWaves[0]; |
---|
5058 | if (minNWaves < 0) { |
---|
5059 | throw(AipsError("wave number must be positive or zero (i.e. constant)")); |
---|
5060 | } |
---|
5061 | bool hasConstantTerm = (minNWaves == 0); |
---|
5062 | int nmodel = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve. |
---|
5063 | |
---|
5064 | std::vector<std::vector<double> > model(nmodel, std::vector<double>(nchan)); |
---|
5065 | |
---|
5066 | if (hasConstantTerm) { |
---|
5067 | for (int j = 0; j < nchan; ++j) { |
---|
5068 | model[0][j] = 1.0; |
---|
5069 | } |
---|
5070 | } |
---|
5071 | |
---|
5072 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
5073 | double stretch0 = 2.0*PI/(double)(nchan-1); |
---|
5074 | |
---|
5075 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) { |
---|
5076 | int sidx = hasConstantTerm ? 2*i-1 : 2*i; |
---|
5077 | int cidx = sidx + 1; |
---|
5078 | double stretch = stretch0*(double)nWaves[i]; |
---|
5079 | |
---|
5080 | for (int j = 0; j < nchan; ++j) { |
---|
5081 | model[sidx][j] = sin(stretch*(double)j); |
---|
5082 | model[cidx][j] = cos(stretch*(double)j); |
---|
5083 | } |
---|
5084 | } |
---|
5085 | |
---|
5086 | return model; |
---|
5087 | } |
---|
5088 | |
---|
5089 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, |
---|
5090 | const std::vector<bool>& inMask) |
---|
5091 | { |
---|
5092 | std::vector<bool> mask = getMask(whichrow); |
---|
5093 | uInt maskSize = mask.size(); |
---|
5094 | if (inMask.size() != 0) { |
---|
5095 | if (maskSize != inMask.size()) { |
---|
5096 | throw(AipsError("mask sizes are not the same.")); |
---|
5097 | } |
---|
5098 | for (uInt i = 0; i < maskSize; ++i) { |
---|
5099 | mask[i] = mask[i] && inMask[i]; |
---|
5100 | } |
---|
5101 | } |
---|
5102 | |
---|
5103 | return mask; |
---|
5104 | } |
---|
5105 | |
---|
5106 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, |
---|
5107 | const std::vector<bool>& inMask, |
---|
5108 | const std::vector<int>& edge, |
---|
5109 | std::vector<int>& currEdge, |
---|
5110 | STLineFinder& lineFinder) |
---|
5111 | { |
---|
5112 | if (isAllChannelsFlagged(whichrow)) {//all channels flagged |
---|
5113 | std::vector<bool> res_mask(nchan(getIF(whichrow)),false); |
---|
5114 | return res_mask; |
---|
5115 | } else if (inMask.size() != 0 && nValidMask(inMask)==0){ //no valid mask channels |
---|
5116 | std::vector<bool> res_mask(inMask); |
---|
5117 | return res_mask; |
---|
5118 | } |
---|
5119 | |
---|
5120 | std::vector<uint> ifNos = getIFNos(); |
---|
5121 | if ((edge.size() > 2) && (edge.size() < ifNos.size()*2)) { |
---|
5122 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
5123 | } |
---|
5124 | |
---|
5125 | uint idx = 0; |
---|
5126 | if (edge.size() > 2) { |
---|
5127 | int ifVal = getIF(whichrow); |
---|
5128 | bool foundIF = false; |
---|
5129 | for (uint i = 0; i < ifNos.size(); ++i) { |
---|
5130 | if (ifVal == (int)ifNos[i]) { |
---|
5131 | idx = 2*i; |
---|
5132 | foundIF = true; |
---|
5133 | break; |
---|
5134 | } |
---|
5135 | } |
---|
5136 | if (!foundIF) { |
---|
5137 | throw(AipsError("bad IF number")); |
---|
5138 | } |
---|
5139 | } |
---|
5140 | |
---|
5141 | currEdge.clear(); |
---|
5142 | currEdge.resize(2); |
---|
5143 | currEdge[0] = edge[idx]; |
---|
5144 | currEdge[1] = edge[idx+1]; |
---|
5145 | |
---|
5146 | lineFinder.setData(getSpectrum(whichrow)); |
---|
5147 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currEdge, whichrow); |
---|
5148 | return lineFinder.getMask(); |
---|
5149 | } |
---|
5150 | |
---|
5151 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */ |
---|
5152 | void Scantable::outputFittingResult(bool outLogger, |
---|
5153 | bool outTextFile, |
---|
5154 | bool csvFormat, |
---|
5155 | const std::vector<bool>& chanMask, |
---|
5156 | int whichrow, |
---|
5157 | const casa::String& coordInfo, |
---|
5158 | bool hasSameNchan, |
---|
5159 | ofstream& ofs, |
---|
5160 | const casa::String& funcName, |
---|
5161 | const std::vector<int>& edge, |
---|
5162 | const std::vector<float>& params, |
---|
5163 | const int nClipped) |
---|
5164 | { |
---|
5165 | if (outLogger || outTextFile) { |
---|
5166 | float rms = getRms(chanMask, whichrow); |
---|
5167 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
5168 | std::vector<bool> fixed; |
---|
5169 | fixed.clear(); |
---|
5170 | |
---|
5171 | if (outLogger) { |
---|
5172 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
5173 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, |
---|
5174 | masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
5175 | } |
---|
5176 | if (outTextFile) { |
---|
5177 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, |
---|
5178 | masklist, whichrow, true, csvFormat) << flush; |
---|
5179 | } |
---|
5180 | } |
---|
5181 | } |
---|
5182 | |
---|
5183 | /* for poly/chebyshev/sinusoid. */ |
---|
5184 | void Scantable::outputFittingResult(bool outLogger, |
---|
5185 | bool outTextFile, |
---|
5186 | bool csvFormat, |
---|
5187 | const std::vector<bool>& chanMask, |
---|
5188 | int whichrow, |
---|
5189 | const casa::String& coordInfo, |
---|
5190 | bool hasSameNchan, |
---|
5191 | ofstream& ofs, |
---|
5192 | const casa::String& funcName, |
---|
5193 | const std::vector<float>& params, |
---|
5194 | const int nClipped) |
---|
5195 | { |
---|
5196 | if (outLogger || outTextFile) { |
---|
5197 | float rms = getRms(chanMask, whichrow); |
---|
5198 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
5199 | std::vector<bool> fixed; |
---|
5200 | fixed.clear(); |
---|
5201 | |
---|
5202 | if (outLogger) { |
---|
5203 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
5204 | ols << formatBaselineParams(params, fixed, rms, nClipped, |
---|
5205 | masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
5206 | } |
---|
5207 | if (outTextFile) { |
---|
5208 | ofs << formatBaselineParams(params, fixed, rms, nClipped, |
---|
5209 | masklist, whichrow, true, csvFormat) << flush; |
---|
5210 | } |
---|
5211 | } |
---|
5212 | } |
---|
5213 | |
---|
5214 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow) |
---|
5215 | { |
---|
5216 | int idxDelimiter = progressInfo.find(","); |
---|
5217 | if (idxDelimiter < 0) { |
---|
5218 | throw(AipsError("wrong value in 'showprogress' parameter")) ; |
---|
5219 | } |
---|
5220 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true"); |
---|
5221 | std::istringstream is(progressInfo.substr(idxDelimiter+1)); |
---|
5222 | is >> minNRow; |
---|
5223 | } |
---|
5224 | |
---|
5225 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold) |
---|
5226 | { |
---|
5227 | if (showProgress && (nTotal >= nTotalThreshold)) { |
---|
5228 | int nInterval = int(floor(double(nTotal)/100.0)); |
---|
5229 | if (nInterval == 0) nInterval++; |
---|
5230 | |
---|
5231 | if (nProcessed % nInterval == 0) { |
---|
5232 | printf("\r"); //go to the head of line |
---|
5233 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted |
---|
5234 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) ); |
---|
5235 | printf("\x1b[39m\x1b[0m"); //set default attributes |
---|
5236 | fflush(NULL); |
---|
5237 | } |
---|
5238 | |
---|
5239 | if (nProcessed == nTotal - 1) { |
---|
5240 | printf("\r\x1b[K"); //clear |
---|
5241 | fflush(NULL); |
---|
5242 | } |
---|
5243 | |
---|
5244 | } |
---|
5245 | } |
---|
5246 | |
---|
5247 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly) |
---|
5248 | { |
---|
5249 | std::vector<bool> mask = getMask(whichrow); |
---|
5250 | |
---|
5251 | if (inMask.size() > 0) { |
---|
5252 | uInt maskSize = mask.size(); |
---|
5253 | if (maskSize != inMask.size()) { |
---|
5254 | throw(AipsError("mask sizes are not the same.")); |
---|
5255 | } |
---|
5256 | for (uInt i = 0; i < maskSize; ++i) { |
---|
5257 | mask[i] = mask[i] && inMask[i]; |
---|
5258 | } |
---|
5259 | } |
---|
5260 | |
---|
5261 | Vector<Float> spec = getSpectrum(whichrow); |
---|
5262 | mathutil::doZeroOrderInterpolation(spec, mask); |
---|
5263 | |
---|
5264 | FFTServer<Float,Complex> ffts; |
---|
5265 | Vector<Complex> fftres; |
---|
5266 | ffts.fft0(fftres, spec); |
---|
5267 | |
---|
5268 | std::vector<float> res; |
---|
5269 | float norm = float(2.0/double(spec.size())); |
---|
5270 | |
---|
5271 | if (getRealImag) { |
---|
5272 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
5273 | res.push_back(real(fftres[i])*norm); |
---|
5274 | res.push_back(imag(fftres[i])*norm); |
---|
5275 | } |
---|
5276 | } else { |
---|
5277 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
5278 | res.push_back(abs(fftres[i])*norm); |
---|
5279 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i])); |
---|
5280 | } |
---|
5281 | } |
---|
5282 | |
---|
5283 | return res; |
---|
5284 | } |
---|
5285 | |
---|
5286 | |
---|
5287 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow) |
---|
5288 | { |
---|
5289 | /**** |
---|
5290 | double ms1TimeStart, ms1TimeEnd; |
---|
5291 | double elapse1 = 0.0; |
---|
5292 | ms1TimeStart = mathutil::gettimeofday_sec(); |
---|
5293 | ****/ |
---|
5294 | |
---|
5295 | Vector<Float> spec; |
---|
5296 | specCol_.get(whichrow, spec); |
---|
5297 | |
---|
5298 | /**** |
---|
5299 | ms1TimeEnd = mathutil::gettimeofday_sec(); |
---|
5300 | elapse1 = ms1TimeEnd - ms1TimeStart; |
---|
5301 | std::cout << "rm1 : " << elapse1 << " (sec.)" << endl; |
---|
5302 | ****/ |
---|
5303 | |
---|
5304 | return (float)doGetRms(mask, spec); |
---|
5305 | } |
---|
5306 | |
---|
5307 | double Scantable::doGetRms(const std::vector<bool>& mask, const Vector<Float>& spec) |
---|
5308 | { |
---|
5309 | double mean = 0.0; |
---|
5310 | double smean = 0.0; |
---|
5311 | int n = 0; |
---|
5312 | for (uInt i = 0; i < spec.nelements(); ++i) { |
---|
5313 | if (mask[i]) { |
---|
5314 | double val = (double)spec[i]; |
---|
5315 | mean += val; |
---|
5316 | smean += val*val; |
---|
5317 | n++; |
---|
5318 | } |
---|
5319 | } |
---|
5320 | |
---|
5321 | mean /= (double)n; |
---|
5322 | smean /= (double)n; |
---|
5323 | |
---|
5324 | return sqrt(smean - mean*mean); |
---|
5325 | } |
---|
5326 | |
---|
5327 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const |
---|
5328 | { |
---|
5329 | if (verbose) { |
---|
5330 | ostringstream oss; |
---|
5331 | |
---|
5332 | if (csvformat) { |
---|
5333 | oss << getScan(whichrow) << ","; |
---|
5334 | oss << getBeam(whichrow) << ","; |
---|
5335 | oss << getIF(whichrow) << ","; |
---|
5336 | oss << getPol(whichrow) << ","; |
---|
5337 | oss << getCycle(whichrow) << ","; |
---|
5338 | String commaReplacedMasklist = masklist; |
---|
5339 | string::size_type pos = 0; |
---|
5340 | while (pos = commaReplacedMasklist.find(","), pos != string::npos) { |
---|
5341 | commaReplacedMasklist.replace(pos, 1, ";"); |
---|
5342 | pos++; |
---|
5343 | } |
---|
5344 | oss << commaReplacedMasklist << ","; |
---|
5345 | } else { |
---|
5346 | oss << " Scan[" << getScan(whichrow) << "]"; |
---|
5347 | oss << " Beam[" << getBeam(whichrow) << "]"; |
---|
5348 | oss << " IF[" << getIF(whichrow) << "]"; |
---|
5349 | oss << " Pol[" << getPol(whichrow) << "]"; |
---|
5350 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl; |
---|
5351 | oss << "Fitter range = " << masklist << endl; |
---|
5352 | oss << "Baseline parameters" << endl; |
---|
5353 | } |
---|
5354 | oss << flush; |
---|
5355 | |
---|
5356 | return String(oss); |
---|
5357 | } |
---|
5358 | |
---|
5359 | return ""; |
---|
5360 | } |
---|
5361 | |
---|
5362 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const |
---|
5363 | { |
---|
5364 | if (verbose) { |
---|
5365 | ostringstream oss; |
---|
5366 | |
---|
5367 | if (csvformat) { |
---|
5368 | oss << rms << ","; |
---|
5369 | if (nClipped >= 0) { |
---|
5370 | oss << nClipped; |
---|
5371 | } |
---|
5372 | } else { |
---|
5373 | oss << "Results of baseline fit" << endl; |
---|
5374 | oss << " rms = " << setprecision(6) << rms << endl; |
---|
5375 | if (nClipped >= 0) { |
---|
5376 | oss << " Number of clipped channels = " << nClipped << endl; |
---|
5377 | } |
---|
5378 | for (int i = 0; i < 60; ++i) { |
---|
5379 | oss << "-"; |
---|
5380 | } |
---|
5381 | } |
---|
5382 | oss << endl; |
---|
5383 | oss << flush; |
---|
5384 | |
---|
5385 | return String(oss); |
---|
5386 | } |
---|
5387 | |
---|
5388 | return ""; |
---|
5389 | } |
---|
5390 | |
---|
5391 | std::string Scantable::formatBaselineParams(const std::vector<float>& params, |
---|
5392 | const std::vector<bool>& fixed, |
---|
5393 | float rms, |
---|
5394 | int nClipped, |
---|
5395 | const std::string& masklist, |
---|
5396 | int whichrow, |
---|
5397 | bool verbose, |
---|
5398 | bool csvformat, |
---|
5399 | int start, int count, |
---|
5400 | bool resetparamid) const |
---|
5401 | { |
---|
5402 | int nParam = (int)(params.size()); |
---|
5403 | |
---|
5404 | if (nParam < 1) { |
---|
5405 | return(" Not fitted"); |
---|
5406 | } else { |
---|
5407 | |
---|
5408 | ostringstream oss; |
---|
5409 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
5410 | |
---|
5411 | if (start < 0) start = 0; |
---|
5412 | if (count < 0) count = nParam; |
---|
5413 | int end = start + count; |
---|
5414 | if (end > nParam) end = nParam; |
---|
5415 | int paramidoffset = (resetparamid) ? (-start) : 0; |
---|
5416 | |
---|
5417 | for (int i = start; i < end; ++i) { |
---|
5418 | if (i > start) { |
---|
5419 | oss << ","; |
---|
5420 | } |
---|
5421 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : ""; |
---|
5422 | if (csvformat) { |
---|
5423 | oss << params[i] << sFix; |
---|
5424 | } else { |
---|
5425 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i]; |
---|
5426 | } |
---|
5427 | } |
---|
5428 | |
---|
5429 | if (csvformat) { |
---|
5430 | oss << ","; |
---|
5431 | } else { |
---|
5432 | oss << endl; |
---|
5433 | } |
---|
5434 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
5435 | |
---|
5436 | return String(oss); |
---|
5437 | } |
---|
5438 | |
---|
5439 | } |
---|
5440 | |
---|
5441 | 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 |
---|
5442 | { |
---|
5443 | int nOutParam = (int)(params.size()); |
---|
5444 | int nPiece = (int)(ranges.size()) - 1; |
---|
5445 | |
---|
5446 | if (nOutParam < 1) { |
---|
5447 | return(" Not fitted"); |
---|
5448 | } else if (nPiece < 0) { |
---|
5449 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose, csvformat); |
---|
5450 | } else if (nPiece < 1) { |
---|
5451 | return(" Bad count of the piece edge info"); |
---|
5452 | } else if (nOutParam % nPiece != 0) { |
---|
5453 | return(" Bad count of the output baseline parameters"); |
---|
5454 | } else { |
---|
5455 | |
---|
5456 | int nParam = nOutParam / nPiece; |
---|
5457 | |
---|
5458 | ostringstream oss; |
---|
5459 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
5460 | |
---|
5461 | if (csvformat) { |
---|
5462 | for (int i = 0; i < nPiece; ++i) { |
---|
5463 | oss << ranges[i] << "," << (ranges[i+1]-1) << ","; |
---|
5464 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
5465 | } |
---|
5466 | } else { |
---|
5467 | stringstream ss; |
---|
5468 | ss << ranges[nPiece] << flush; |
---|
5469 | int wRange = ss.str().size() * 2 + 5; |
---|
5470 | |
---|
5471 | for (int i = 0; i < nPiece; ++i) { |
---|
5472 | ss.str(""); |
---|
5473 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]"; |
---|
5474 | oss << left << setw(wRange) << ss.str(); |
---|
5475 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
5476 | //oss << endl; |
---|
5477 | } |
---|
5478 | } |
---|
5479 | |
---|
5480 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
5481 | |
---|
5482 | return String(oss); |
---|
5483 | } |
---|
5484 | |
---|
5485 | } |
---|
5486 | |
---|
5487 | bool Scantable::hasSameNchanOverIFs() |
---|
5488 | { |
---|
5489 | int nIF = nif(-1); |
---|
5490 | int nCh; |
---|
5491 | int totalPositiveNChan = 0; |
---|
5492 | int nPositiveNChan = 0; |
---|
5493 | |
---|
5494 | for (int i = 0; i < nIF; ++i) { |
---|
5495 | nCh = nchan(i); |
---|
5496 | if (nCh > 0) { |
---|
5497 | totalPositiveNChan += nCh; |
---|
5498 | nPositiveNChan++; |
---|
5499 | } |
---|
5500 | } |
---|
5501 | |
---|
5502 | return (totalPositiveNChan == (nPositiveNChan * nchan(0))); |
---|
5503 | } |
---|
5504 | |
---|
5505 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose) |
---|
5506 | { |
---|
5507 | if (mask.size() <= 0) { |
---|
5508 | throw(AipsError("The mask elements should be > 0")); |
---|
5509 | } |
---|
5510 | int IF = getIF(whichrow); |
---|
5511 | if (mask.size() != (uInt)nchan(IF)) { |
---|
5512 | throw(AipsError("Number of channels in scantable != number of mask elements")); |
---|
5513 | } |
---|
5514 | |
---|
5515 | if (verbose) { |
---|
5516 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE)); |
---|
5517 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo; |
---|
5518 | if (!hasSameNchan) { |
---|
5519 | logOs << endl << "This mask is only valid for IF=" << IF; |
---|
5520 | } |
---|
5521 | logOs << LogIO::POST; |
---|
5522 | } |
---|
5523 | |
---|
5524 | std::vector<double> abcissa = getAbcissa(whichrow); |
---|
5525 | std::vector<int> edge = getMaskEdgeIndices(mask); |
---|
5526 | |
---|
5527 | ostringstream oss; |
---|
5528 | oss.setf(ios::fixed); |
---|
5529 | oss << setprecision(1) << "["; |
---|
5530 | for (uInt i = 0; i < edge.size(); i+=2) { |
---|
5531 | if (i > 0) oss << ","; |
---|
5532 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]"; |
---|
5533 | } |
---|
5534 | oss << "]" << flush; |
---|
5535 | |
---|
5536 | return String(oss); |
---|
5537 | } |
---|
5538 | |
---|
5539 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask) |
---|
5540 | { |
---|
5541 | if (mask.size() <= 0) { |
---|
5542 | throw(AipsError("The mask elements should be > 0")); |
---|
5543 | } |
---|
5544 | |
---|
5545 | std::vector<int> out, startIndices, endIndices; |
---|
5546 | int maskSize = mask.size(); |
---|
5547 | |
---|
5548 | startIndices.clear(); |
---|
5549 | endIndices.clear(); |
---|
5550 | |
---|
5551 | if (mask[0]) { |
---|
5552 | startIndices.push_back(0); |
---|
5553 | } |
---|
5554 | for (int i = 1; i < maskSize; ++i) { |
---|
5555 | if ((!mask[i-1]) && mask[i]) { |
---|
5556 | startIndices.push_back(i); |
---|
5557 | } else if (mask[i-1] && (!mask[i])) { |
---|
5558 | endIndices.push_back(i-1); |
---|
5559 | } |
---|
5560 | } |
---|
5561 | if (mask[maskSize-1]) { |
---|
5562 | endIndices.push_back(maskSize-1); |
---|
5563 | } |
---|
5564 | |
---|
5565 | if (startIndices.size() != endIndices.size()) { |
---|
5566 | throw(AipsError("Inconsistent Mask Size: bad data?")); |
---|
5567 | } |
---|
5568 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
5569 | if (startIndices[i] > endIndices[i]) { |
---|
5570 | throw(AipsError("Mask start index > mask end index")); |
---|
5571 | } |
---|
5572 | } |
---|
5573 | |
---|
5574 | out.clear(); |
---|
5575 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
5576 | out.push_back(startIndices[i]); |
---|
5577 | out.push_back(endIndices[i]); |
---|
5578 | } |
---|
5579 | |
---|
5580 | return out; |
---|
5581 | } |
---|
5582 | |
---|
5583 | void Scantable::setTsys(const std::vector<float>& newvals, int whichrow) { |
---|
5584 | Vector<Float> tsys(newvals); |
---|
5585 | if (whichrow > -1) { |
---|
5586 | if (tsysCol_.shape(whichrow) != tsys.shape()) |
---|
5587 | throw(AipsError("Given Tsys values are not of the same shape")); |
---|
5588 | tsysCol_.put(whichrow, tsys); |
---|
5589 | } else { |
---|
5590 | tsysCol_.fillColumn(tsys); |
---|
5591 | } |
---|
5592 | } |
---|
5593 | |
---|
5594 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const |
---|
5595 | { |
---|
5596 | Vector<Float> tsys( tsysCol_(whichrow) ) ; |
---|
5597 | vector<float> stlTsys ; |
---|
5598 | tsys.tovector( stlTsys ) ; |
---|
5599 | return stlTsys ; |
---|
5600 | } |
---|
5601 | |
---|
5602 | vector<uint> Scantable::getMoleculeIdColumnData() const |
---|
5603 | { |
---|
5604 | Vector<uInt> molIds(mmolidCol_.getColumn()); |
---|
5605 | vector<uint> res; |
---|
5606 | molIds.tovector(res); |
---|
5607 | return res; |
---|
5608 | } |
---|
5609 | |
---|
5610 | void Scantable::setMoleculeIdColumnData(const std::vector<uint>& molids) |
---|
5611 | { |
---|
5612 | Vector<uInt> molIds(molids); |
---|
5613 | Vector<uInt> arr(mmolidCol_.getColumn()); |
---|
5614 | if ( molIds.nelements() != arr.nelements() ) |
---|
5615 | throw AipsError("The input data size must be the number of rows."); |
---|
5616 | mmolidCol_.putColumn(molIds); |
---|
5617 | } |
---|
5618 | |
---|
5619 | |
---|
5620 | std::vector<uint> Scantable::getRootTableRowNumbers() const |
---|
5621 | { |
---|
5622 | Vector<uInt> rowIds(table_.rowNumbers()); |
---|
5623 | vector<uint> res; |
---|
5624 | rowIds.tovector(res); |
---|
5625 | return res; |
---|
5626 | } |
---|
5627 | |
---|
5628 | |
---|
5629 | void Scantable::dropXPol() |
---|
5630 | { |
---|
5631 | if (npol() <= 2) { |
---|
5632 | return; |
---|
5633 | } |
---|
5634 | if (!selector_.empty()) { |
---|
5635 | throw AipsError("Can only operate with empty selection"); |
---|
5636 | } |
---|
5637 | std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]"; |
---|
5638 | Table tab = tableCommand(taql, table_); |
---|
5639 | table_ = tab; |
---|
5640 | table_.rwKeywordSet().define("nPol", Int(2)); |
---|
5641 | originalTable_ = table_; |
---|
5642 | attach(); |
---|
5643 | } |
---|
5644 | |
---|
5645 | } |
---|
5646 | //namespace asap |
---|