1 | //#---------------------------------------------------------------------------
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2 | //# SDMemTable.cc: A MemoryTable container for single dish integrations
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3 | //#---------------------------------------------------------------------------
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4 | //# Copyright (C) 2004
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5 | //# Malte Marquarding, ATNF
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6 | //#
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7 | //# This program is free software; you can redistribute it and/or modify it
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8 | //# under the terms of the GNU General Public License as published by the Free
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9 | //# Software Foundation; either version 2 of the License, or (at your option)
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10 | //# any later version.
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11 | //#
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12 | //# This program is distributed in the hope that it will be useful, but
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13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of
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14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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15 | //# Public License for more details.
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16 | //#
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17 | //# You should have received a copy of the GNU General Public License along
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18 | //# with this program; if not, write to the Free Software Foundation, Inc.,
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19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
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20 | //#
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21 | //# Correspondence concerning this software should be addressed as follows:
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22 | //# Internet email: Malte.Marquarding@csiro.au
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23 | //# Postal address: Malte Marquarding,
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24 | //# Australia Telescope National Facility,
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25 | //# P.O. Box 76,
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26 | //# Epping, NSW, 2121,
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27 | //# AUSTRALIA
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28 | //#
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29 | //# $Id:
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30 | //#---------------------------------------------------------------------------
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31 |
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32 |
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33 | #include <aips/iostream.h>
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34 | #include <aips/Arrays/Array.h>
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35 | #include <aips/Arrays/ArrayMath.h>
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36 | #include <aips/Arrays/MaskArrMath.h>
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37 | #include <aips/Arrays/ArrayLogical.h>
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38 | #include <aips/Arrays/ArrayAccessor.h>
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39 |
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40 | #include <aips/Tables/TableParse.h>
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41 | #include <aips/Tables/TableDesc.h>
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42 | #include <aips/Tables/SetupNewTab.h>
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43 | #include <aips/Tables/ScaColDesc.h>
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44 | #include <aips/Tables/ArrColDesc.h>
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45 |
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46 | #include <aips/Tables/ExprNode.h>
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47 | #include <aips/Tables/ScalarColumn.h>
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48 | #include <aips/Tables/ArrayColumn.h>
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49 | #include <aips/Tables/TableRecord.h>
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50 |
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51 |
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52 | #include "SDMemTable.h"
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53 | #include "SDContainer.h"
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54 |
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55 | using namespace atnf_sd;
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56 |
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57 | SDMemTable::SDMemTable() :
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58 | IFSel_(0),
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59 | beamSel_(0),
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60 | polSel_(0) {
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61 | setup();
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62 | }
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63 | SDMemTable::SDMemTable(const std::string& name) :
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64 | IFSel_(0),
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65 | beamSel_(0),
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66 | polSel_(0) {
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67 | Table tab("dummy");
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68 | table_ = tab.copyToMemoryTable("dummy");
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69 | }
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70 |
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71 | SDMemTable::SDMemTable(const SDMemTable& other, Bool clear) {
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72 | this->IFSel_= other.IFSel_;
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73 | this->beamSel_= other.beamSel_;
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74 | this->polSel_= other.polSel_;
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75 | this->chanMask_ = other.chanMask_;
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76 | this->table_ = other.table_.copyToMemoryTable(String("dummy"));
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77 | // clear all rows()
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78 | if (clear) {
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79 | this->table_.removeRow(this->table_.rowNumbers());
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80 | } else {
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81 | this->IFSel_ = other.IFSel_;
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82 | this->beamSel_ = other.beamSel_;
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83 | this->polSel_ = other.polSel_;
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84 | }
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85 | }
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86 |
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87 | SDMemTable::SDMemTable(const Table& tab, Int scanID) :
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88 | IFSel_(0),
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89 | beamSel_(0),
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90 | polSel_(0) {
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91 | String exprs = String("select * from $1 where SCANID == ")
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92 | +String::toString(scanID);
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93 | cerr << exprs << endl;
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94 | Table t = tableCommand(exprs,tab);
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95 | table_ = t.copyToMemoryTable("dummy");
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96 | }
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97 |
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98 | SDMemTable::~SDMemTable(){
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99 | cerr << "goodbye from SDMemTable @ " << this << endl;
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100 | }
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101 |
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102 | SDMemTable SDMemTable::getScan(Int scanID) {
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103 | return SDMemTable(table_, scanID);
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104 | }
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105 |
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106 | void SDMemTable::setup() {
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107 | TableDesc td("", "1", TableDesc::Scratch);
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108 | td.comment() = "A SDMemTable";
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109 | td.addColumn(ScalarColumnDesc<Double>("TIME"));
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110 | td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
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111 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
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112 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
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113 | td.addColumn(ArrayColumnDesc<Float>("TSYS"));
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114 | td.addColumn(ScalarColumnDesc<Int>("SCANID"));
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115 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
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116 | // Now create a new table from the description.
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117 |
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118 | SetupNewTable aNewTab("dummy", td, Table::New);
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119 | table_ = Table(aNewTab, Table::Memory, 0);
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120 | }
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121 |
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122 | std::string SDMemTable::getSourceName(Int whichRow) const {
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123 | ROScalarColumn<String> src(table_, "SRCNAME");
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124 | String name;
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125 | src.get(whichRow, name);
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126 | return name;
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127 | }
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128 |
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129 | Double SDMemTable::getTime(Int whichRow) const {
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130 | ROScalarColumn<Double> src(table_, "TIME");
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131 | Double tm;
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132 | src.get(whichRow, tm);
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133 | return tm;
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134 | }
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135 |
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136 | bool SDMemTable::setIF(Int whichIF) {
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137 | //if ( whichIF >= 0 && whichIF < nIF_) {
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138 | IFSel_ = whichIF;
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139 | return true;
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140 | //}
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141 | //return false;
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142 | }
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143 | bool SDMemTable::setBeam(Int whichBeam) {
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144 | //if ( whichBeam >= 0 && whichBeam < nBeam_) {
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145 | beamSel_ = whichBeam;
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146 | return true;
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147 | //}
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148 | //return false;
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149 |
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150 | }
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151 | bool SDMemTable::setPol(Int whichPol) {
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152 | //if ( whichPol >= 0 && whichPol < nPol_) {
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153 | polSel_ = whichPol;
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154 | return true;
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155 | //}
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156 | //return false;
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157 | }
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158 |
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159 | bool SDMemTable::setMask(const std::vector<int>& whichChans) {
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160 | ROArrayColumn<uChar> spec(table_, "FLAGTRA");
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161 |
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162 | std::vector<int>::iterator it;
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163 | uInt n = spec.shape(0)(3);
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164 | chanMask_.resize(n,true);
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165 | for (it = whichChans.begin(); it != whichChans.end(); it++) {
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166 | if (*it < n)
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167 | chanMask_[*it] = false;
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168 | }
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169 | return true;
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170 | }
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171 |
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172 | std::vector<bool> SDMemTable::getMask(Int whichRow) const {
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173 | std::vector<bool> mask;
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174 | ROArrayColumn<uChar> spec(table_, "FLAGTRA");
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175 | Array<uChar> arr;
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176 | spec.get(whichRow, arr);
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177 | ArrayAccessor<uChar, Axis<0> > aa0(arr);
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178 | aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
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179 | ArrayAccessor<uChar, Axis<1> > aa1(aa0);
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180 | aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
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181 | ArrayAccessor<uChar, Axis<2> > aa2(aa1);
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182 | aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
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183 |
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184 | Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
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185 |
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186 | std::vector<bool> tmp;
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187 | tmp = chanMask_; // WHY the fxxx do I have to make a copy here
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188 | std::vector<bool>::iterator miter;
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189 | miter = tmp.begin();
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190 |
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191 | for (ArrayAccessor<uChar, Axis<3> > i(aa2); i != i.end(); ++i) {
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192 | bool out =!static_cast<bool>(*i);
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193 | if (useUserMask) {
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194 | out = out && (*miter);
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195 | miter++;
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196 | }
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197 | mask.push_back(out);
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198 | }
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199 | return mask;
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200 | }
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201 | std::vector<float> SDMemTable::getSpectrum(Int whichRow) {
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202 |
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203 | std::vector<float> spectrum;
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204 | ROArrayColumn<Float> spec(table_, "SPECTRA");
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205 | Array<Float> arr;
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206 | spec.get(whichRow, arr);
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207 | ArrayAccessor<Float, Axis<0> > aa0(arr);
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208 | aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
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209 | ArrayAccessor<Float, Axis<1> > aa1(aa0);
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210 | aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
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211 | ArrayAccessor<Float, Axis<2> > aa2(aa1);
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212 | aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
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213 | for (ArrayAccessor<Float, Axis<3> > i(aa2); i != i.end(); ++i) {
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214 | spectrum.push_back(*i);
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215 | }
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216 | return spectrum;
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217 | }
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218 | void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow=0) {
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219 | ROArrayColumn<Float> spec(table_, "SPECTRA");
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220 | Array<Float> arr;
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221 | spec.get(whichRow, arr);
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222 | spectrum.resize(arr.shape()(3));
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223 | ArrayAccessor<Float, Axis<0> > aa0(arr);
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224 | aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
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225 | ArrayAccessor<Float, Axis<1> > aa1(aa0);
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226 | aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
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227 | ArrayAccessor<Float, Axis<2> > aa2(aa1);
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228 | aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
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229 |
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230 | ArrayAccessor<Float, Axis<0> > va(spectrum);
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231 | for (ArrayAccessor<Float, Axis<3> > i(aa2); i != i.end(); ++i) {
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232 | (*va) = (*i);
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233 | va++;
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234 | }
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235 | }
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236 |
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237 | void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow=0) const {
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238 | ROArrayColumn<uChar> spec(table_, "FLAGTRA");
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239 | Array<uChar> arr;
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240 | spec.get(whichRow, arr);
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241 | mask.resize(arr.shape()(3));
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242 |
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243 | ArrayAccessor<uChar, Axis<0> > aa0(arr);
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244 | aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
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245 | ArrayAccessor<uChar, Axis<1> > aa1(aa0);
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246 | aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
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247 | ArrayAccessor<uChar, Axis<2> > aa2(aa1);
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248 | aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
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249 |
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250 | Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
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251 |
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252 | ArrayAccessor<Bool, Axis<0> > va(mask);
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253 | std::vector<bool> tmp;
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254 | tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
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255 | // iterator should work on chanMask_??
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256 | std::vector<bool>::iterator miter;
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257 | miter = tmp.begin();
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258 |
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259 | for (ArrayAccessor<uChar, Axis<3> > i(aa2); i != i.end(); ++i) {
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260 | bool out =!static_cast<bool>(*i);
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261 | if (useUserMask) {
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262 | out = out && (*miter);
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263 | miter++;
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264 | }
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265 | (*va) = out;
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266 | va++;
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267 | }
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268 | }
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269 |
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270 | MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
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271 | Bool useSelection) {
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272 | ROArrayColumn<Float> spec(table_, "SPECTRA");
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273 | Array<Float> arr;
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274 | ROArrayColumn<uChar> flag(table_, "FLAGTRA");
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275 | Array<uChar> farr;
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276 | spec.get(whichRow, arr);
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277 | flag.get(whichRow, farr);
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278 | Array<Bool> barr(farr.shape());convertArray(barr, farr);
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279 | MaskedArray<Float> marr;
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280 | if (useSelection) {
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281 | ArrayAccessor<Float, Axis<0> > aa0(arr);
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282 | aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
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283 | ArrayAccessor<Float, Axis<1> > aa1(aa0);
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284 | aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
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285 | ArrayAccessor<Float, Axis<2> > aa2(aa1);
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286 | aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
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287 |
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288 | ArrayAccessor<Bool, Axis<0> > baa0(barr);
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289 | baa0.reset(baa0.begin(uInt(beamSel_)));//go to beam
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290 | ArrayAccessor<Bool, Axis<1> > baa1(baa0);
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291 | baa1.reset(baa1.begin(uInt(IFSel_)));// go to IF
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292 | ArrayAccessor<Bool, Axis<2> > baa2(baa1);
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293 | baa2.reset(baa2.begin(uInt(polSel_)));// go to pol
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294 |
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295 | Vector<Float> a(arr.shape()(3));
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296 | Vector<Bool> b(barr.shape()(3));
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297 | ArrayAccessor<Float, Axis<0> > a0(a);
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298 | ArrayAccessor<Bool, Axis<0> > b0(b);
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299 |
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300 | ArrayAccessor<Bool, Axis<3> > j(baa2);
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301 | for (ArrayAccessor<Float, Axis<3> > i(aa2); i != i.end(); ++i) {
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302 | (*a0) = (*i);
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303 | (*b0) = !(*j);
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304 | j++;
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305 | a0++;
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306 | b0++;
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307 | }
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308 | marr.setData(a,b);
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309 | } else {
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310 | marr.setData(arr,!barr);
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311 | }
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312 | return marr;
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313 | }
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314 |
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315 | Float SDMemTable::getTsys(Int whichRow) const {
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316 | ROArrayColumn<Float> ts(table_, "TSYS");
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317 | Array<Float> arr;
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318 | ts.get(whichRow, arr);
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319 | Float out;
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320 | IPosition ip(arr.shape());
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321 | ip(0) = beamSel_;ip(1) = IFSel_;ip(2) = polSel_;ip(3)=0;
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322 | out = arr(ip);
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323 | return out;
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324 | }
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325 |
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326 | bool SDMemTable::putSDContainer(const SDContainer& sdc) {
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327 | ScalarColumn<Double> mjd(table_, "TIME");
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328 | ScalarColumn<String> srcn(table_, "SRCNAME");
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329 | ArrayColumn<Float> spec(table_, "SPECTRA");
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330 | ArrayColumn<uChar> flags(table_, "FLAGTRA");
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331 | ArrayColumn<Float> ts(table_, "TSYS");
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332 | ScalarColumn<Int> scan(table_, "SCANID");
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333 | ScalarColumn<Double> integr(table_, "INTERVAL");
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334 |
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335 | uInt rno = table_.nrow();
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336 | table_.addRow();
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337 |
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338 | mjd.put(rno, sdc.timestamp);
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339 | srcn.put(rno, sdc.sourcename);
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340 | spec.put(rno, sdc.getSpectrum());
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341 | flags.put(rno, sdc.getFlags());
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342 | ts.put(rno, sdc.getTsys());
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343 | scan.put(rno, sdc.scanid);
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344 | integr.put(rno, sdc.interval);
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345 |
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346 | return true;
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347 | }
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348 |
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349 | SDContainer SDMemTable::getSDContainer(uInt whichRow) const {
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350 | ROScalarColumn<Double> mjd(table_, "TIME");
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351 | ROScalarColumn<String> srcn(table_, "SRCNAME");
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352 | ROArrayColumn<Float> spec(table_, "SPECTRA");
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353 | ROArrayColumn<uChar> flags(table_, "FLAGTRA");
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354 | ROArrayColumn<Float> ts(table_, "TSYS");
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355 | ROScalarColumn<Int> scan(table_, "SCANID");
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356 | ROScalarColumn<Double> integr(table_, "INTERVAL");
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357 |
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358 | SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
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359 | mjd.get(whichRow, sdc.timestamp);
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360 | srcn.get(whichRow, sdc.sourcename);
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361 | integr.get(whichRow, sdc.interval);
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362 | scan.get(whichRow, sdc.scanid);
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363 | Array<Float> spectrum;
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364 | Array<Float> tsys;
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365 | Array<uChar> flagtrum;
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366 | spec.get(whichRow, spectrum);
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367 | sdc.putSpectrum(spectrum);
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368 | flags.get(whichRow, flagtrum);
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369 | sdc.putFlags(flagtrum);
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370 | ts.get(whichRow, tsys);
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371 | sdc.putTsys(tsys);
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372 | return sdc;
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373 | }
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374 | bool SDMemTable::putSDHeader(const SDHeader& sdh) {
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375 | table_.lock();
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376 | table_.rwKeywordSet().define("nIF", sdh.nif);
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377 | table_.rwKeywordSet().define("nBeam", sdh.nbeam);
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378 | table_.rwKeywordSet().define("nPol", sdh.npol);
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379 | table_.rwKeywordSet().define("nChan", sdh.nchan);
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380 | table_.rwKeywordSet().define("Observer", sdh.observer);
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381 | table_.rwKeywordSet().define("Project", sdh.project);
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382 | table_.rwKeywordSet().define("Obstype", sdh.obstype);
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383 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
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384 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
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385 | table_.rwKeywordSet().define("Equinox", sdh.equinox);
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386 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
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387 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
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388 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
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389 | table_.rwKeywordSet().define("UTC", sdh.utc);
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390 | table_.unlock();
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391 | cerr << "Table Header set" << endl;
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392 | return true;
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393 | }\
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394 |
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395 | SDHeader SDMemTable::getSDHeader() const {
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396 | SDHeader sdh;
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397 | table_.keywordSet().get("nBeam",sdh.nbeam);
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398 | table_.keywordSet().get("nIF",sdh.nif);
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399 | table_.keywordSet().get("nPol",sdh.npol);
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400 | table_.keywordSet().get("nChan",sdh.nchan);
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401 | table_.keywordSet().get("Observer", sdh.observer);
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402 | table_.keywordSet().get("Project", sdh.project);
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403 | table_.keywordSet().get("Obstype", sdh.obstype);
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404 | table_.keywordSet().get("AntennaName", sdh.antennaname);
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405 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
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406 | table_.keywordSet().get("Equinox", sdh.equinox);
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407 | table_.keywordSet().get("FreqRefFrame", sdh.freqref);
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408 | table_.keywordSet().get("FreqRefVal", sdh.reffreq);
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409 | table_.keywordSet().get("Bandwidth", sdh.bandwidth);
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410 | table_.keywordSet().get("UTC", sdh.utc);
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411 | return sdh;
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412 | }
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413 | void SDMemTable::makePersistent(const std::string& filename) {
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414 | table_.deepCopy(filename,Table::New);
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415 | }
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416 |
|
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417 | void SDMemTable::summary() const {
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418 | ROScalarColumn<Int> scans(table_, "SCANID");
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419 | ROScalarColumn<String> srcs(table_, "SRCNAME");
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420 | cout << "*************** Header ***************" << endl;
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421 | cout << "nBeam = " << nBeam() << "\t"
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422 | << "nIF = " << nIF() << endl
|
---|
423 | << "nPol = " << nPol() << "\t"
|
---|
424 | << "nChan = " << nChan() << "\t" << endl;
|
---|
425 | cout << "*************** Header ***************" << endl;
|
---|
426 | uInt count = 0;
|
---|
427 | String name;
|
---|
428 | Int previous = -1;Int current=0;
|
---|
429 | cout << "Scan\tSource" << endl;
|
---|
430 | for (uInt i=0; i< scans.nrow();i++) {
|
---|
431 | scans.getScalar(i,current);
|
---|
432 | if (previous != current) {
|
---|
433 | srcs.getScalar(i,name);
|
---|
434 | previous = current;
|
---|
435 | count++;
|
---|
436 | cout << count << "\t"
|
---|
437 | << name
|
---|
438 | << endl;
|
---|
439 | }
|
---|
440 | }
|
---|
441 | cout << "Table contains " << table_.nrow() << " integration(s)." << endl;
|
---|
442 | cout << "in " << count << " scan(s)." << endl;
|
---|
443 | }
|
---|
444 |
|
---|
445 | Int SDMemTable::nBeam() const {
|
---|
446 | Int n;
|
---|
447 | table_.keywordSet().get("nBeam",n);
|
---|
448 | return n;
|
---|
449 | }
|
---|
450 | Int SDMemTable::nIF() const {
|
---|
451 | Int n;
|
---|
452 | table_.keywordSet().get("nIF",n);
|
---|
453 | return n;
|
---|
454 | }
|
---|
455 | Int SDMemTable::nPol() const {
|
---|
456 | Int n;
|
---|
457 | table_.keywordSet().get("nPol",n);
|
---|
458 | return n;
|
---|
459 | }
|
---|
460 | Int SDMemTable::nChan() const {
|
---|
461 | Int n;
|
---|
462 | table_.keywordSet().get("nChan",n);
|
---|
463 | return n;
|
---|
464 | }
|
---|
465 | /*
|
---|
466 | void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
|
---|
467 |
|
---|
468 | std::vector<int>::iterator it;
|
---|
469 | ArrayAccessor<uChar, Axis<2> > j(flags_);
|
---|
470 | for (it = whichChans.begin(); it != whichChans.end(); it++) {
|
---|
471 | j.reset(j.begin(uInt(*it)));
|
---|
472 | for (ArrayAccessor<uChar, Axis<0> > i(j); i != i.end(); ++i) {
|
---|
473 | for (ArrayAccessor<uChar, Axis<1> > ii(i); ii != ii.end(); ++ii) {
|
---|
474 | for (ArrayAccessor<uChar, Axis<3> > iii(ii);
|
---|
475 | iii != iii.end(); ++iii) {
|
---|
476 | (*iii) =
|
---|
477 | }
|
---|
478 | }
|
---|
479 | }
|
---|
480 | }
|
---|
481 |
|
---|
482 | }
|
---|
483 | */
|
---|