1 | //****************************************************************
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2 | /** @class FitsDumper
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3 |
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4 | @brief Dumps contents of fits tables to stdout or a file
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5 |
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6 | */
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7 | //****************************************************************
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8 | #include "Configuration.h"
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9 |
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10 | #include <map>
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11 | #include <fstream>
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12 |
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13 | #include <CCfits/CCfits>
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14 |
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15 | //#define PLOTTING_PLEASE
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16 |
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17 | #ifdef PLOTTING_PLEASE
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18 | #include <QPen>
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19 | #include <QtGui>
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20 | #include <QApplication>
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21 |
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22 | #include <qwt_plot.h>
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23 | #include <qwt_plot_grid.h>
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24 | #include <qwt_plot_curve.h>
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25 | #include <qwt_plot_zoomer.h>
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26 | #include <qwt_legend.h>
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27 | #include <qwt_scale_draw.h>
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28 |
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29 | #include "Time.h"
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30 | #endif
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31 |
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32 | using namespace std;
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33 |
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34 | class MyColumn : public CCfits::Column
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35 | {
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36 | public:
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37 | const string &comment() const { return CCfits::Column::comment(); }
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38 | long width() const
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39 | {//the width() method seems to be buggy (or empty ?) as it always return 1... redo it ourselves.
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40 | string inter = format();
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41 | inter = inter.substr(0, inter.size()-1);
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42 | return atoi(inter.c_str());
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43 | }
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44 | };
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45 |
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46 | #ifdef PLOTTING_PLEASE
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47 | class TimeScaleDraw: public QwtScaleDraw
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48 | {
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49 | public:
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50 | virtual QwtText label(double v) const
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51 | {
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52 | Time t(v);
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53 | string time = t.GetAsStr("%H:%M:%S%F");
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54 | while (time[time.size()-1] == '0' && time.size() > 2)
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55 | {
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56 | time = time.substr(0, time.size()-1);
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57 | }
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58 | return QwtText(time.c_str());
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59 | }
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60 | };
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61 | #endif
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62 |
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63 | class FitsDumper
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64 | {
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65 | public:
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66 | FitsDumper();
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67 | ~FitsDumper();
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68 |
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69 | private:
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70 |
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71 | CCfits::FITS *fFile; /// FITS pointer
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72 | CCfits::Table *fTable; /// Table pointer
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73 | map<string, MyColumn*> fColMap; /// map between the column names and their CCfits objects
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74 |
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75 | // Convert CCfits::ValueType into a human readable string
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76 | string ValueTypeToStr(CCfits::ValueType type) const;
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77 |
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78 | // Convert CCfits::ValueType into a number of associated bytes
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79 | int ValueTypeToSize(CCfits::ValueType type) const;
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80 |
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81 | /// Calculate the buffer size required to read a row of the fits table, as well as the offsets to each column
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82 | vector<int> CalculateOffsets() const;
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83 |
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84 | template<class T>
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85 | T PtrToValue(const unsigned char* &ptr) const;
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86 | // template<class T>
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87 | // double PtrToDouble(const unsigned char *ptr) const;
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88 | // double PtrToDouble(const unsigned char *ptr, CCfits::ValueType type) const;
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89 |
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90 | /// Write a single row of the selected data
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91 | int WriteRow(ostream &, const vector<MyColumn*> &, const vector<int> &, unsigned char *, const vector<pair<int, int> >&) const;
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92 |
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93 | bool OpenFile(const string &); /// Open a file
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94 | bool OpenTable(const string &); /// Open a table
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95 |
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96 | /// Lists all columns of an open file
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97 | void List();
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98 | void ListHeader();
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99 | void ListKeywords(ostream &);
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100 |
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101 | bool separateColumnsFromRanges(const vector<string>& list,
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102 | vector<pair<int, int> >& ranges,
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103 | vector<string>& listNamesOnly);
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104 | /// Perform the dumping, based on the current dump list
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105 | bool Dump(const string &, const vector<string> &list, int);
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106 | ///Display the selected columns values VS time
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107 | int doCurvesDisplay( const vector<string> &list, const string& tableName);
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108 | // bool Plot(const vector<string> &list);
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109 |
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110 | public:
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111 | ///Configures the fitsLoader from the config file and/or command arguments.
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112 | int ExecConfig(Configuration& conf);
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113 | };
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114 |
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115 | // --------------------------------------------------------------------------
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116 | //
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117 | //! Constructor
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118 | //! @param out
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119 | //! the ostream where to redirect the outputs
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120 | //
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121 | FitsDumper::FitsDumper() : fFile(0), fTable(0)
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122 | {
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123 | }
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124 |
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125 | // --------------------------------------------------------------------------
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126 | //
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127 | //! Destructor
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128 | //
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129 | FitsDumper::~FitsDumper()
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130 | {
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131 | if (fFile)
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132 | delete fFile;
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133 | }
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134 |
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135 |
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136 | string FitsDumper::ValueTypeToStr(CCfits::ValueType type) const
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137 | {
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138 | switch (type)
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139 | {
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140 | case CCfits::Tbyte: return "uint8_t";
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141 | case CCfits::Tushort: return "uint16_t";
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142 | case CCfits::Tshort: return "int16_t";
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143 | case CCfits::Tuint: return "uint32_t";
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144 | case CCfits::Tint: return "int32_t";
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145 | case CCfits::Tulong: return "uint32_t";
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146 | case CCfits::Tlong: return "int32_t";
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147 | case CCfits::Tlonglong: return "int64_t";
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148 | case CCfits::Tfloat: return "float";
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149 | case CCfits::Tdouble: return "double";
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150 |
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151 | default:
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152 | return "unknwown";
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153 | }
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154 | }
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155 |
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156 | int FitsDumper::ValueTypeToSize(CCfits::ValueType type) const
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157 | {
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158 | switch (type)
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159 | {
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160 | case CCfits::Tbyte: return sizeof(uint8_t);
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161 | case CCfits::Tushort:
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162 | case CCfits::Tshort: return sizeof(uint16_t);
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163 | case CCfits::Tuint:
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164 | case CCfits::Tint:
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165 | case CCfits::Tulong:
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166 | case CCfits::Tlong: return sizeof(uint32_t);
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167 | case CCfits::Tlonglong: return sizeof(uint64_t);
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168 | case CCfits::Tfloat: return sizeof(float);
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169 | case CCfits::Tdouble: return sizeof(double);
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170 |
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171 | default:
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172 | return 0;
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173 | }
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174 | }
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175 |
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176 | template<class T>
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177 | T FitsDumper::PtrToValue(const unsigned char* &ptr) const
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178 | {
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179 | T t;
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180 | reverse_copy(ptr, ptr+sizeof(T), reinterpret_cast<unsigned char*>(&t));
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181 | ptr += sizeof(T);
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182 |
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183 | return t;
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184 | }
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185 | /*
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186 | template<class T>
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187 | double FitsDumper::PtrToDouble(const unsigned char *ptr) const
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188 | {
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189 | T t;
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190 | reverse_copy(ptr, ptr+sizeof(T), reinterpret_cast<unsigned char*>(&t));
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191 | return t;
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192 | }
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193 |
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194 | double FitsDumper::PtrToDouble(const unsigned char *ptr, CCfits::ValueType type) const
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195 | {
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196 | switch (type)
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197 | {
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198 | case CCfits::Tbyte: return PtrToDouble<uint8_t> (ptr);
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199 | case CCfits::Tushort: return PtrToDouble<uint16_t>(ptr);
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200 | case CCfits::Tuint:
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201 | case CCfits::Tulong: return PtrToDouble<uint32_t>(ptr);
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202 | case CCfits::Tshort: return PtrToDouble<int16_t> (ptr);
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203 | case CCfits::Tint:
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204 | case CCfits::Tlong: return PtrToDouble<int32_t> (ptr);
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205 | case CCfits::Tlonglong: return PtrToDouble<int64_t> (ptr);
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206 | case CCfits::Tfloat: return PtrToDouble<float> (ptr);
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207 | case CCfits::Tdouble: return PtrToDouble<double> (ptr);
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208 |
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209 | default:
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210 | throw runtime_error("Data type not implemented yet.");
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211 | }
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212 | }
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213 | */
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214 |
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215 | // --------------------------------------------------------------------------
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216 | //
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217 | //! Writes a single row of the selected FITS data to the output file.
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218 | //!
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219 | //! Data type \b not yet implemented:
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220 | //! CCfits::Tnull, CCfits::Tbit, CCfits::Tlogical, CCfits::Tstring,
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221 | //! CCfits::Tcomplex, CCfits::Tdblcomplex, CCfits::VTbit,
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222 | //! CCfits::VTbyte, CCfits::VTlogical, CCfits::VTushort,
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223 | //! CCfits::VTshort, CCfits::VTuint, CCfits::VTint, CCfits::VTulong,
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224 | //! CCfits::VTlong, CCfits::VTlonglong, CCfits::VTfloat,
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225 | //! CCfits::VTdouble, CCfits::VTcomplex, CCfits::VTdblcomplex
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226 | //!
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227 | //! @param offsets
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228 | //! a vector containing the offsets to the columns (in bytes)
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229 | //! @param targetFile
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230 | //! the ofstream where to write to
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231 | //! @param fitsBuffer
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232 | //! the memory were the row has been loaded by cfitsio
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233 | //
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234 | int FitsDumper::WriteRow(ostream &out, const vector<MyColumn*> &list, const vector<int> &offsets, unsigned char* fitsBuffer, const vector<pair<int, int> >& ranges) const
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235 | {
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236 | int cnt = 0;
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237 | vector<pair<int, int> >::const_iterator jt = ranges.begin();
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238 | for (vector<MyColumn*>::const_iterator it=list.begin(); it!=list.end(); it++, jt++)
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239 | {
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240 | if (jt == ranges.end())
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241 | {
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242 | cout << "ERROR: END OF RANGE POINTER REACHED" << endl;
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243 | return false;
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244 | }
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245 | const MyColumn *col = *it;
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246 |
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247 | // CCfits starts counting at 1 not 0
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248 | const int offset = offsets[col->index()-1];
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249 |
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250 | // Get the pointer to the array which we are supposed to print
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251 | const unsigned char *ptr = fitsBuffer + offset;
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252 |
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253 | // Loop over all array entries
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254 | int sizeToSkip = 0;
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255 | switch (col->type())
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256 | {
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257 | case CCfits::Tbyte: sizeToSkip = sizeof(uint8_t); break;
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258 | case CCfits::Tushort: sizeToSkip = sizeof(uint16_t); break;
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259 | case CCfits::Tuint:
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260 | case CCfits::Tulong: sizeToSkip = sizeof(uint32_t); break;
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261 | case CCfits::Tshort: sizeToSkip = sizeof(int16_t); break;
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262 | case CCfits::Tint:
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263 | case CCfits::Tlong: sizeToSkip = sizeof(int32_t); break;
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264 | case CCfits::Tlonglong: sizeToSkip = sizeof(int64_t); break;
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265 | case CCfits::Tfloat: sizeToSkip = sizeof(float); break;
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266 | case CCfits::Tdouble: sizeToSkip = sizeof(double); break;
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267 | default:
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268 | cerr << "Data type not implemented yet." << endl;
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269 | return 0;
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270 | }
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271 | ptr += sizeToSkip*jt->first;
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272 | for (int width=jt->first; width<jt->second; width++)
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273 | {
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274 | switch (col->type())
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275 | {
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276 | case CCfits::Tbyte: out << PtrToValue<uint8_t> (ptr); break;
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277 | case CCfits::Tushort: out << PtrToValue<uint16_t>(ptr); break;
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278 | case CCfits::Tuint:
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279 | case CCfits::Tulong: out << PtrToValue<uint32_t>(ptr); break;
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280 | case CCfits::Tshort: out << PtrToValue<int16_t> (ptr); break;
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281 | case CCfits::Tint:
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282 | case CCfits::Tlong: out << PtrToValue<int32_t> (ptr); break;
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283 | case CCfits::Tlonglong: out << PtrToValue<int64_t> (ptr); break;
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284 | case CCfits::Tfloat: out << PtrToValue<float> (ptr); break;
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285 | case CCfits::Tdouble: out << PtrToValue<double> (ptr); break;
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286 |
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287 | default:
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288 | cerr << "Data type not implemented yet." << endl;
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289 | return 0;
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290 | }
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291 |
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292 | out << " ";
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293 | cnt++;
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294 | }
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295 | }
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296 |
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297 | if (cnt>0)
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298 | out << endl;
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299 |
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300 | if (out.fail())
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301 | {
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302 | cerr << "ERROR - writing output: " << strerror(errno) << endl;
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303 | return -1;
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304 | }
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305 |
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306 | return cnt;
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307 | }
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308 |
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309 | // --------------------------------------------------------------------------
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310 | //
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311 | //! Calculates the required buffer size for reading one row of the current
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312 | //! table. Also calculates the offsets to all the columns
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313 | //
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314 | vector<int> FitsDumper::CalculateOffsets() const
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315 | {
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316 | map<int,int> sizes;
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317 |
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318 | for (map<string, MyColumn*>::const_iterator it=fColMap.begin();
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319 | it!=fColMap.end(); it++)
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320 | {
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321 | const int &width = it->second->width();
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322 | const int &idx = it->second->index();
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323 |
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324 | const int size = ValueTypeToSize(it->second->type());
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325 | if (size==0)
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326 | {
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327 | cerr << "Data type " << (int)it->second->type() << " not implemented yet." << endl;
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328 | return vector<int>();
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329 | }
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330 |
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331 | sizes[idx] = size*width;
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332 | }
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333 |
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334 | //calculate the offsets in the vector.
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335 | vector<int> result(1, 0);
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336 |
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337 | int size = 0;
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338 | int idx = 0;
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339 |
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340 | for (map<int,int>::const_iterator it=sizes.begin(); it!=sizes.end(); it++)
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341 | {
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342 | size += it->second;
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343 | result.push_back(size);
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344 |
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345 | if (it->first == ++idx)
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346 | continue;
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347 |
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348 | cerr << "Expected index " << idx << ", but found " << it->first << endl;
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349 | return vector<int>();
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350 | }
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351 |
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352 | return result;
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353 | }
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354 |
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355 | // --------------------------------------------------------------------------
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356 | //
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357 | //! Loads the fits file based on the current parameters
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358 | //
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359 | bool FitsDumper::OpenFile(const string &filename)
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360 | {
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361 | if (fFile)
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362 | delete fFile;
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363 |
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364 | ostringstream str;
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365 | try
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366 | {
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367 | fFile = new CCfits::FITS(filename);
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368 | }
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369 | catch (CCfits::FitsException e)
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370 | {
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371 | cerr << "Could not open FITS file " << filename << " reason: " << e.message() << endl;
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372 | return false;
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373 | }
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374 |
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375 | return true;
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376 | }
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377 |
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378 | bool FitsDumper::OpenTable(const string &tablename)
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379 | {
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380 | if (!fFile)
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381 | {
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382 | cerr << "No file open." << endl;
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383 | return false;
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384 | }
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385 |
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386 | const multimap< string, CCfits::ExtHDU * > extMap = fFile->extension();
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387 | if (extMap.find(tablename) == extMap.end())
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388 | {
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389 | cerr << "Table '" << tablename << "' not found." << endl;
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390 | return false;
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391 | }
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392 |
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393 | fTable = dynamic_cast<CCfits::Table*>(extMap.find(tablename)->second);
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394 | if (!fTable)
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395 | {
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396 | cerr << "Object '" << tablename << "' returned not a CCfits::Table." << endl;
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397 | return false;
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398 | }
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399 |
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400 | map<string, CCfits::Column*>& tCols = fTable->column();
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401 | for (map<string, CCfits::Column*>::const_iterator it = tCols.begin(); it != tCols.end(); it++)
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402 | {
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403 | fColMap.insert(make_pair(it->first, static_cast<MyColumn*>(it->second)));
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404 | }
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405 | // fColMap = fTable->column();
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406 |
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407 | fTable->makeThisCurrent();
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408 |
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409 | fTable->getComments();
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410 | fTable->getHistory();
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411 | fTable->readAllKeys();
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412 |
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413 | return true;
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414 | }
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415 |
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416 |
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417 | void FitsDumper::List()
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418 | {
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419 | if (!fFile)
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420 | {
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421 | cerr << "No file open." << endl;
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422 | return;
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423 | }
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424 |
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425 | cout << "\nFile: " << fFile->name() << "\n";
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426 |
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427 | const multimap< string, CCfits::ExtHDU * > extMap = fFile->extension();
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428 | for (std::multimap<string, CCfits::ExtHDU*>::const_iterator it=extMap.begin(); it != extMap.end(); it++)
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429 | {
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430 |
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431 | CCfits::Table *table = dynamic_cast<CCfits::Table*>(extMap.find(it->first)->second);
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432 |
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433 | table->makeThisCurrent();
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434 | table->readData();
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435 |
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436 | cout << " " << it->first << " [" << table->rows() << "]\n";
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437 |
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438 | const map<string, CCfits::Column*> &cols = table->column();
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439 |
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440 | // for (map<string, CCfits::Column*>::const_iterator id = cols.begin(); ib != cols.end(); ib++)
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441 | // {
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442 | // TFORM
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443 | // }
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444 |
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445 | for (map<string, CCfits::Column*>::const_iterator ic=cols.begin();
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446 | ic != cols.end(); ic++)
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447 | {
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448 | const MyColumn *col = static_cast<MyColumn*>(ic->second);
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449 |
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450 | cout << " " << col->name() << "[" << col->width() << "] * " << col->scale() << " (" << col->unit() << ":" << ValueTypeToStr(col->type())<< ") " << col->comment() << "\n";
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451 | /*
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452 | inline size_t Column::repeat () const
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453 | inline bool Column::varLength () const
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454 | inline double Column::zero () const
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455 | inline const String& Column::display () const
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456 | inline const String& Column::dimen () const
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457 | inline const String& Column::TBCOL ()
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458 | inline const String& Column::TTYPE ()
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459 | inline const String& Column::TFORM ()
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460 | inline const String& Column::TDISP ()
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461 | inline const String& Column::TZERO ()
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462 | inline const String& Column::TDIM ()
|
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463 | inline const String& Column::TNULL ()
|
---|
464 | inline const String& Column::TLMIN ()
|
---|
465 | inline const String& Column::TLMAX ()
|
---|
466 | inline const String& Column::TDMAX ()
|
---|
467 | inline const String& Column::TDMIN ()
|
---|
468 | */
|
---|
469 | }
|
---|
470 | cout << '\n';
|
---|
471 | }
|
---|
472 | cout << flush;
|
---|
473 | }
|
---|
474 |
|
---|
475 | class MyKeyword : public CCfits::Keyword
|
---|
476 | {
|
---|
477 | public:
|
---|
478 | CCfits::ValueType keytype() const { return CCfits::Keyword::keytype(); }
|
---|
479 | };
|
---|
480 |
|
---|
481 | void FitsDumper::ListKeywords(ostream &out)
|
---|
482 | {
|
---|
483 | map<string,CCfits::Keyword*> keys = fTable->keyWord();
|
---|
484 | for (map<string,CCfits::Keyword*>::const_iterator it=keys.begin();
|
---|
485 | it!=keys.end(); it++)
|
---|
486 | {
|
---|
487 | string str;
|
---|
488 | double d;
|
---|
489 | int l;
|
---|
490 |
|
---|
491 | const MyKeyword *kw = static_cast<MyKeyword*>(it->second);
|
---|
492 | kw->keytype();
|
---|
493 | out << "## " << setw(8) << kw->name() << " = " << setw(10);
|
---|
494 | if (kw->keytype()==16)
|
---|
495 | out << ("'"+kw->value(str)+"'");
|
---|
496 | if (kw->keytype()==31)
|
---|
497 | out << kw->value(l);
|
---|
498 | if (kw->keytype()==82)
|
---|
499 | out << kw->value(d);
|
---|
500 | out << " / " << kw->comment() << endl;
|
---|
501 | }
|
---|
502 | }
|
---|
503 |
|
---|
504 | void FitsDumper::ListHeader()
|
---|
505 | {
|
---|
506 | if (!fTable)
|
---|
507 | {
|
---|
508 | cerr << "No table open." << endl;
|
---|
509 | return;
|
---|
510 | }
|
---|
511 |
|
---|
512 | cout << "\nTable: " << fTable->name() << " (rows=" << fTable->rows() << ")\n";
|
---|
513 | if (!fTable->comment().empty())
|
---|
514 | cout << "Comment: \t" << fTable->comment() << '\n';
|
---|
515 | if (!fTable->history().empty())
|
---|
516 | cout << "History: \t" << fTable->history() << '\n';
|
---|
517 |
|
---|
518 | ListKeywords(cout);
|
---|
519 | cout << endl;
|
---|
520 | }
|
---|
521 |
|
---|
522 | bool FitsDumper::separateColumnsFromRanges(const vector<string>& list,
|
---|
523 | vector<pair<int, int> >& ranges,
|
---|
524 | vector<string>& listNamesOnly)
|
---|
525 | {
|
---|
526 | for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
|
---|
527 | {
|
---|
528 | string columnNameOnly = *it;
|
---|
529 | unsigned long bracketIndex0 = columnNameOnly.find_first_of('[');
|
---|
530 | unsigned long bracketIndex1 = columnNameOnly.find_first_of(']');
|
---|
531 | unsigned long colonIndex = columnNameOnly.find_first_of(':');
|
---|
532 | // cout << bracketIndex0 << " " << bracketIndex1 << " " << colonIndex << endl;
|
---|
533 | int columnStart = -1;
|
---|
534 | int columnEnd = -1;
|
---|
535 | if (bracketIndex0 != string::npos)
|
---|
536 | {//there is a range given. Extract the range
|
---|
537 | if (colonIndex != string::npos)
|
---|
538 | {//we have a range here
|
---|
539 | columnStart = atoi(columnNameOnly.substr(bracketIndex0+1, colonIndex-(bracketIndex0+1)).c_str());
|
---|
540 | columnEnd = atoi(columnNameOnly.substr(colonIndex+1, bracketIndex1-(colonIndex+1)).c_str());
|
---|
541 | columnEnd++;
|
---|
542 | }
|
---|
543 | else
|
---|
544 | {//only a single index there
|
---|
545 | columnStart = atoi(columnNameOnly.substr(bracketIndex0+1, bracketIndex1 - (bracketIndex0+1)).c_str());
|
---|
546 | columnEnd = columnStart+1;
|
---|
547 | // cout << "Cstart " << columnStart << " end: " << columnEnd << endl;
|
---|
548 | }
|
---|
549 | columnNameOnly = columnNameOnly.substr(0, bracketIndex0);
|
---|
550 | }
|
---|
551 |
|
---|
552 | if (fColMap.find(columnNameOnly) == fColMap.end())
|
---|
553 | {
|
---|
554 | cerr << "ERROR - Column '" << columnNameOnly << "' not found in table." << endl;
|
---|
555 | return false;
|
---|
556 | }
|
---|
557 | // cout << "The column name is: " << columnNameOnly << endl;
|
---|
558 | MyColumn *cCol = static_cast<MyColumn*>(fColMap.find(columnNameOnly)->second);
|
---|
559 | if (bracketIndex0 == string::npos)
|
---|
560 | {//no range given: use the full range
|
---|
561 | ranges.push_back(make_pair(0, cCol->width()));
|
---|
562 | columnStart = 0;
|
---|
563 | columnEnd = 1;
|
---|
564 | }
|
---|
565 | else
|
---|
566 | {//use the range extracted earlier
|
---|
567 | if (columnStart < 0)
|
---|
568 | {
|
---|
569 | cerr << "ERROR - Start range for column " << columnNameOnly << " is less than zero (" << columnStart << "). Aborting" << endl;
|
---|
570 | return false;
|
---|
571 | }
|
---|
572 | if (columnEnd > cCol->width())
|
---|
573 | {
|
---|
574 | cerr << "ERROR - End range for column " << columnNameOnly << " is greater than the last element (" << cCol->width() << " vs " << columnEnd << "). Aborting" << endl;
|
---|
575 | return false;
|
---|
576 | }
|
---|
577 | ranges.push_back(make_pair(columnStart, columnEnd));
|
---|
578 | }
|
---|
579 | // cout << "Will be exporting from " << columnStart << " to " << columnEnd-1 << " for column " << columnNameOnly << endl;
|
---|
580 | listNamesOnly.push_back(columnNameOnly);
|
---|
581 | }
|
---|
582 | return true;
|
---|
583 | }
|
---|
584 | // --------------------------------------------------------------------------
|
---|
585 | //
|
---|
586 | //! Perform the actual dump, based on the current parameters
|
---|
587 | //
|
---|
588 | bool FitsDumper::Dump(const string &filename, const vector<string> &list, int precision)
|
---|
589 | {
|
---|
590 |
|
---|
591 | //first of all, let's separate the columns from their ranges and check that the requested columns are indeed part of the file
|
---|
592 | vector<pair<int, int> > ranges;
|
---|
593 | vector<string> listNamesOnly;
|
---|
594 |
|
---|
595 | if (!separateColumnsFromRanges(list, ranges, listNamesOnly))
|
---|
596 | {
|
---|
597 | cerr << "Something went wrong while extracting the columns names from parameters. Aborting" << endl;
|
---|
598 | return false;
|
---|
599 | }
|
---|
600 |
|
---|
601 | // FIXME: Maybe do this when opening a table?
|
---|
602 | const vector<int> offsets = CalculateOffsets();
|
---|
603 | if (offsets.size()==0)
|
---|
604 | return false;
|
---|
605 |
|
---|
606 | ofstream out(filename=="-"?"/dev/stdout":filename);
|
---|
607 | if (!out)
|
---|
608 | {
|
---|
609 | cerr << "Cannot open file " << filename << ": " << strerror(errno) << endl;
|
---|
610 | return false;
|
---|
611 | }
|
---|
612 |
|
---|
613 | out.precision(precision);
|
---|
614 |
|
---|
615 | out << "## --------------------------------------------------------------------------\n";
|
---|
616 | if (filename!="-")
|
---|
617 | out << "## File: \t" << filename << '\n';
|
---|
618 | out << "## Table: \t" << fTable->name() << '\n';
|
---|
619 | if (!fTable->comment().empty())
|
---|
620 | out << "## Comment: \t" << fTable->comment() << '\n';
|
---|
621 | if (!fTable->history().empty())
|
---|
622 | out << "## History: \t" << fTable->history() << '\n';
|
---|
623 | out << "## NumRows: \t" << fTable->rows() << '\n';
|
---|
624 | out << "## --------------------------------------------------------------------------\n";
|
---|
625 | ListKeywords(out);
|
---|
626 | out << "## --------------------------------------------------------------------------\n";
|
---|
627 | out << "#\n";
|
---|
628 | //vector<pair<int, int> >::const_iterator rangesIt = ranges.begin();
|
---|
629 | //the above is soooo yesterday ;) let's try the new auto feature of c++0x
|
---|
630 | auto rangesIt = ranges.begin();
|
---|
631 | for (vector<string>::const_iterator it=listNamesOnly.begin(); it!=listNamesOnly.end(); it++, rangesIt++)
|
---|
632 | {
|
---|
633 | const MyColumn *col = static_cast<MyColumn*>(fTable->column()[*it]);
|
---|
634 | if (rangesIt->first != 0 || rangesIt->second != col->width())
|
---|
635 | {
|
---|
636 | out << "#";
|
---|
637 | for (int i=rangesIt->first; i<rangesIt->second; i++)
|
---|
638 | out << " " << col->name() << "[" << i << "]";
|
---|
639 | out << ": " << col->unit();
|
---|
640 | }
|
---|
641 | else
|
---|
642 | out << "# " << col->name() << "[" << col->width() << "]: " << col->unit();
|
---|
643 |
|
---|
644 | if (!col->comment().empty())
|
---|
645 | out << " (" <<col->comment() << ")";
|
---|
646 | out << '\n';
|
---|
647 | }
|
---|
648 | out << "#" << endl;
|
---|
649 |
|
---|
650 |
|
---|
651 | // Loop over all columns in our list of requested columns
|
---|
652 | vector<MyColumn*> columns;
|
---|
653 | for (vector<string>::const_iterator it=listNamesOnly.begin(); it!=listNamesOnly.end(); it++)
|
---|
654 | {
|
---|
655 | MyColumn *cCol = static_cast<MyColumn*>(fColMap.find(*it)->second);
|
---|
656 | columns.push_back(cCol);
|
---|
657 | }
|
---|
658 | const int size = offsets[offsets.size()-1];
|
---|
659 | unsigned char* fitsBuffer = new unsigned char[size];
|
---|
660 |
|
---|
661 | int status = 0;
|
---|
662 | for (int i=1; i<=fTable->rows(); i++)
|
---|
663 | {
|
---|
664 | fits_read_tblbytes(fFile->fitsPointer(), i, 1, size, fitsBuffer, &status);
|
---|
665 | if (status)
|
---|
666 | {
|
---|
667 | cerr << "An error occurred while reading fits row #" << i << " error code: " << status << endl;
|
---|
668 | break;
|
---|
669 | }
|
---|
670 | if (WriteRow(out, columns, offsets, fitsBuffer, ranges)<0)
|
---|
671 | {
|
---|
672 | status=1;
|
---|
673 | break;
|
---|
674 | }
|
---|
675 | }
|
---|
676 | delete[] fitsBuffer;
|
---|
677 |
|
---|
678 | return status==0;
|
---|
679 | }
|
---|
680 |
|
---|
681 | // --------------------------------------------------------------------------
|
---|
682 | //
|
---|
683 | //! Perform the actual dump, based on the current parameters
|
---|
684 | //
|
---|
685 | /*
|
---|
686 | bool FitsDumper::Plot(const vector<string> &list)
|
---|
687 | {
|
---|
688 | for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
|
---|
689 | if (fColMap.find(*it) == fColMap.end())
|
---|
690 | {
|
---|
691 | cerr << "WARNING - Column '" << *it << "' not found in table." << endl;
|
---|
692 | return false;
|
---|
693 | }
|
---|
694 |
|
---|
695 | // FIXME: Maybe do this when opening a table?
|
---|
696 | const vector<int> offsets = CalculateOffsets();
|
---|
697 | if (offsets.size()==0)
|
---|
698 | return false;
|
---|
699 |
|
---|
700 | // Loop over all columns in our list of requested columns
|
---|
701 | const CCfits::Column *col[3] =
|
---|
702 | {
|
---|
703 | list.size()>0 ? fColMap.find(list[0])->second : 0,
|
---|
704 | list.size()>1 ? fColMap.find(list[1])->second : 0,
|
---|
705 | list.size()>2 ? fColMap.find(list[2])->second : 0
|
---|
706 | };
|
---|
707 |
|
---|
708 | const int size = offsets[offsets.size()-1];
|
---|
709 | unsigned char* fitsBuffer = new unsigned char[size];
|
---|
710 |
|
---|
711 | const int idx = 0;
|
---|
712 |
|
---|
713 | // CCfits starts counting at 1 not 0
|
---|
714 | const size_t pos[3] =
|
---|
715 | {
|
---|
716 | col[0] ? offsets[col[0]->index()-1] + idx*col[0]->width()*ValueTypeToSize(col[0]->type()) : 0,
|
---|
717 | col[1] ? offsets[col[1]->index()-1] + idx*col[1]->width()*ValueTypeToSize(col[1]->type()) : 0,
|
---|
718 | col[2] ? offsets[col[2]->index()-1] + idx*col[2]->width()*ValueTypeToSize(col[2]->type()) : 0
|
---|
719 | };
|
---|
720 |
|
---|
721 | int status = 0;
|
---|
722 | for (int i=1; i<=fTable->rows(); i++)
|
---|
723 | {
|
---|
724 | fits_read_tblbytes(fFile->fitsPointer(), i, 1, size, fitsBuffer, &status);
|
---|
725 | if (status)
|
---|
726 | {
|
---|
727 | cerr << "An error occurred while reading fits row #" << i << " error code: " << status << endl;
|
---|
728 | break;
|
---|
729 | }
|
---|
730 |
|
---|
731 | try
|
---|
732 | {
|
---|
733 | const double x[3] =
|
---|
734 | {
|
---|
735 | col[0] ? PtrToDouble(fitsBuffer+pos[0], col[0]->type()) : 0,
|
---|
736 | col[1] ? PtrToDouble(fitsBuffer+pos[1], col[1]->type()) : 0,
|
---|
737 | col[2] ? PtrToDouble(fitsBuffer+pos[2], col[2]->type()) : 0
|
---|
738 | };
|
---|
739 | }
|
---|
740 | catch (const runtime_error &e)
|
---|
741 | {
|
---|
742 | cerr << e.what() << endl;
|
---|
743 | status=1;
|
---|
744 | break;
|
---|
745 | }
|
---|
746 | }
|
---|
747 | delete[] fitsBuffer;
|
---|
748 |
|
---|
749 | return status==0;
|
---|
750 | }
|
---|
751 | */
|
---|
752 |
|
---|
753 | // --------------------------------------------------------------------------
|
---|
754 | //
|
---|
755 | //! Retrieves the configuration parameters
|
---|
756 | //! @param conf
|
---|
757 | //! the configuration object
|
---|
758 | //
|
---|
759 | int FitsDumper::ExecConfig(Configuration& conf)
|
---|
760 | {
|
---|
761 | if (conf.Has("fitsfile"))
|
---|
762 | {
|
---|
763 | if (!OpenFile(conf.Get<string>("fitsfile")))
|
---|
764 | return -1;
|
---|
765 | }
|
---|
766 |
|
---|
767 | if (conf.Get<bool>("list"))
|
---|
768 | List();
|
---|
769 |
|
---|
770 | if (conf.Has("tablename"))
|
---|
771 | {
|
---|
772 | if (!OpenTable(conf.Get<string>("tablename")))
|
---|
773 | return -1;
|
---|
774 | }
|
---|
775 |
|
---|
776 | if (conf.Get<bool>("graph"))
|
---|
777 | {
|
---|
778 | if (!conf.Has("col"))
|
---|
779 | {
|
---|
780 | cout << "Please specify the columns that should be dumped as arguments. Aborting" << endl;
|
---|
781 | return 0;
|
---|
782 | }
|
---|
783 | doCurvesDisplay(conf.Get<vector<string>>("col"),
|
---|
784 | conf.Get<string>("tablename"));
|
---|
785 | return 1;
|
---|
786 | }
|
---|
787 |
|
---|
788 |
|
---|
789 | if (conf.Get<bool>("header"))
|
---|
790 | ListHeader();
|
---|
791 |
|
---|
792 | if (conf.Get<bool>("header") || conf.Get<bool>("list"))
|
---|
793 | return 1;
|
---|
794 |
|
---|
795 | if (conf.Has("outfile"))
|
---|
796 | {
|
---|
797 | if (!conf.Has("col"))
|
---|
798 | {
|
---|
799 | cout << "Please specify the columns that should be dumped as arguments. Aborting" << endl;
|
---|
800 | return 0;
|
---|
801 | }
|
---|
802 | if (!Dump(conf.Get<string>("outfile"),
|
---|
803 | conf.Get<vector<string>>("col"),
|
---|
804 | conf.Get<int>("precision")))
|
---|
805 | return -1;
|
---|
806 | }
|
---|
807 |
|
---|
808 |
|
---|
809 | return 0;
|
---|
810 | }
|
---|
811 |
|
---|
812 | void PrintUsage()
|
---|
813 | {
|
---|
814 | cout <<
|
---|
815 | "fitsdump is a tool to dump data from a FITS table as ascii.\n"
|
---|
816 | "\n"
|
---|
817 | "Usage: fitsdump [OPTIONS] fitsfile col col ... \n"
|
---|
818 | " or: fitsdump [OPTIONS]\n";
|
---|
819 | cout << endl;
|
---|
820 | }
|
---|
821 |
|
---|
822 | void PrintHelp()
|
---|
823 | {
|
---|
824 | //
|
---|
825 | }
|
---|
826 | #ifdef PLOTTING_PLEASE
|
---|
827 | int FitsDumper::doCurvesDisplay( const vector<string> &list, const string& tableName)
|
---|
828 | {
|
---|
829 | //first of all, let's separate the columns from their ranges and check that the requested columns are indeed part of the file
|
---|
830 | vector<pair<int, int> > ranges;
|
---|
831 | vector<string> listNamesOnly;
|
---|
832 | if (!separateColumnsFromRanges(list, ranges, listNamesOnly))
|
---|
833 | {
|
---|
834 | cerr << "Something went wrong while extracting the columns names from parameters. Aborting" << endl;
|
---|
835 | return false;
|
---|
836 | }
|
---|
837 | vector<string> curvesNames;
|
---|
838 | stringstream str;
|
---|
839 | for (auto it=ranges.begin(), jt=listNamesOnly.begin(); it != ranges.end(); it++, jt++)
|
---|
840 | {
|
---|
841 | for (int i=it->first; i<it->second;i++)
|
---|
842 | {
|
---|
843 | str.str("");
|
---|
844 | str << *jt << "[" << i << "]";
|
---|
845 | curvesNames.push_back(str.str());
|
---|
846 | }
|
---|
847 | }
|
---|
848 | char* handle = new char[17];
|
---|
849 | sprintf(handle,"FitsDump Display");
|
---|
850 | // Qt::HANDLE h = *handle;//NULL
|
---|
851 | int argc = 1;
|
---|
852 | char ** argv = &handle;
|
---|
853 | QApplication a(argc, argv);
|
---|
854 |
|
---|
855 |
|
---|
856 |
|
---|
857 | QwtPlot* plot = new QwtPlot();
|
---|
858 | QwtPlotGrid* grid = new QwtPlotGrid;
|
---|
859 | grid->enableX(false);
|
---|
860 | grid->enableY(true);
|
---|
861 | grid->enableXMin(false);
|
---|
862 | grid->enableYMin(false);
|
---|
863 | grid->setMajPen(QPen(Qt::black, 0, Qt::DotLine));
|
---|
864 | grid->attach(plot);
|
---|
865 | plot->setAutoReplot(true);
|
---|
866 | string title = tableName;
|
---|
867 | plot->setAxisScaleDraw( QwtPlot::xBottom, new TimeScaleDraw());
|
---|
868 |
|
---|
869 | QWidget window;
|
---|
870 | QHBoxLayout* layout = new QHBoxLayout(&window);
|
---|
871 | layout->setContentsMargins(0,0,0,0);
|
---|
872 | layout->addWidget(plot);
|
---|
873 |
|
---|
874 | QwtPlotZoomer zoom(plot->canvas());
|
---|
875 | zoom.setRubberBandPen(QPen(Qt::gray, 2, Qt::DotLine));
|
---|
876 | zoom.setTrackerPen(QPen(Qt::gray));
|
---|
877 | int totalSize = 0;
|
---|
878 | for (unsigned int i=0;i<list.size();i++)
|
---|
879 | totalSize += ranges[i].second - ranges[i].first;
|
---|
880 | cout << "Total size: " << totalSize << endl;
|
---|
881 | vector<QwtPlotCurve*> curves(totalSize);
|
---|
882 | int ii=0;
|
---|
883 | for (auto it = curves.begin(), jt=curvesNames.begin(); it != curves.end(); it++, jt++)
|
---|
884 | {
|
---|
885 | *it = new QwtPlotCurve(jt->c_str());
|
---|
886 | switch (ii%6)
|
---|
887 | {
|
---|
888 | case 0:
|
---|
889 | (*it)->setPen(QColor(255,0,0));
|
---|
890 | break;
|
---|
891 | case 1:
|
---|
892 | (*it)->setPen(QColor(0,255,0));
|
---|
893 | break;
|
---|
894 | case 2:
|
---|
895 | (*it)->setPen(QColor(0,0,255));
|
---|
896 | break;
|
---|
897 | case 3:
|
---|
898 | (*it)->setPen(QColor(255,255,0));
|
---|
899 | break;
|
---|
900 | case 4:
|
---|
901 | (*it)->setPen(QColor(0,255,255));
|
---|
902 | break;
|
---|
903 | case 5:
|
---|
904 | (*it)->setPen(QColor(255,0,255));
|
---|
905 | break;
|
---|
906 | default:
|
---|
907 | (*it)->setPen(QColor(0,0,0));
|
---|
908 | };
|
---|
909 | ii++;
|
---|
910 | (*it)->setStyle(QwtPlotCurve::Lines);
|
---|
911 | (*it)->attach(plot);
|
---|
912 | }
|
---|
913 | plot->insertLegend(new QwtLegend(), QwtPlot::RightLegend);
|
---|
914 |
|
---|
915 | const vector<int> offsets = CalculateOffsets();
|
---|
916 | if (offsets.size()==0)
|
---|
917 | return false;
|
---|
918 |
|
---|
919 |
|
---|
920 | // Loop over all columns in our list of requested columns
|
---|
921 | vector<MyColumn*> columns;
|
---|
922 | for (vector<string>::const_iterator it=listNamesOnly.begin(); it!=listNamesOnly.end(); it++)
|
---|
923 | {
|
---|
924 | MyColumn *cCol = static_cast<MyColumn*>(fColMap.find(*it)->second);
|
---|
925 | columns.push_back(cCol);
|
---|
926 | }
|
---|
927 | //add the time column to the given columns
|
---|
928 | MyColumn* timeCol = static_cast<MyColumn*>(fColMap.find("Time")->second);
|
---|
929 | if (!timeCol)
|
---|
930 | {
|
---|
931 | cerr << "Error: time column could not be found in given table. Aborting" << endl;
|
---|
932 | return false;
|
---|
933 | }
|
---|
934 | columns.push_back(timeCol);
|
---|
935 | ranges.push_back(make_pair(0,1));
|
---|
936 | /////
|
---|
937 | const int size = offsets[offsets.size()-1];
|
---|
938 | unsigned char* fitsBuffer = new unsigned char[size];
|
---|
939 |
|
---|
940 | // stringstream str;
|
---|
941 | str.str("");
|
---|
942 | int status = 0;
|
---|
943 |
|
---|
944 | vector<double*> xValues(totalSize);
|
---|
945 | double* yValues;
|
---|
946 | cout.precision(10);
|
---|
947 | str.precision(20);
|
---|
948 | for (auto it=xValues.begin(); it!=xValues.end(); it++)
|
---|
949 | *it = new double[fTable->rows()];
|
---|
950 |
|
---|
951 | yValues = new double[fTable->rows()];
|
---|
952 |
|
---|
953 | for (int i=1; i<=fTable->rows(); i++)
|
---|
954 | {
|
---|
955 | fits_read_tblbytes(fFile->fitsPointer(), i, 1, size, fitsBuffer, &status);
|
---|
956 | if (status)
|
---|
957 | {
|
---|
958 | cerr << "An error occurred while reading fits row #" << i << " error code: " << status << endl;
|
---|
959 | break;
|
---|
960 | }
|
---|
961 | if (WriteRow(str, columns, offsets, fitsBuffer, ranges)<0)
|
---|
962 | {
|
---|
963 | status=1;
|
---|
964 | cerr << "An Error occured while reading the fits row " << i << endl;
|
---|
965 | return -1;
|
---|
966 | }
|
---|
967 | // yValues[i-1] = i;
|
---|
968 | for (auto it=xValues.begin(); it!= xValues.end(); it++)
|
---|
969 | {
|
---|
970 | str >> (*it)[i-1];
|
---|
971 | // cout << (*it)[i-1] << " ";
|
---|
972 | }
|
---|
973 | str >> yValues[i-1];
|
---|
974 | if (i==1)
|
---|
975 | {
|
---|
976 | Time t(yValues[0]);
|
---|
977 | title += " - " + t.GetAsStr("%Y-%m-%d");
|
---|
978 | plot->setTitle(title.c_str());
|
---|
979 | }
|
---|
980 | // cout << yValues[i-1] << " ";
|
---|
981 | // cout << endl;
|
---|
982 | }
|
---|
983 | //set the actual data.
|
---|
984 | auto jt = xValues.begin();
|
---|
985 | for (auto it=curves.begin(); it != curves.end(); it++, jt++)
|
---|
986 | (*it)->setRawData(yValues, *jt, fTable->rows());
|
---|
987 |
|
---|
988 | QStack<QRectF> stack;
|
---|
989 | double minX, minY, maxX, maxY;
|
---|
990 | minX = minY = 1e10;
|
---|
991 | maxX = maxY = -1e10;
|
---|
992 | QRectF rect;
|
---|
993 | QPointF point;
|
---|
994 | for (auto it=curves.begin(); it!= curves.end(); it++)
|
---|
995 | {
|
---|
996 | rect = (*it)->boundingRect();
|
---|
997 | point = rect.bottomRight();
|
---|
998 | if (point.x() < minX) minX = point.x();
|
---|
999 | if (point.y() < minY) minY = point.y();
|
---|
1000 | if (point.x() > maxX) maxX = point.x();
|
---|
1001 | if (point.y() > maxY) maxY = point.y();
|
---|
1002 | point = rect.topLeft();
|
---|
1003 | if (point.x() < minX) minX = point.x();
|
---|
1004 | if (point.y() < minY) minY = point.y();
|
---|
1005 | if (point.x() > maxX) maxX = point.x();
|
---|
1006 | if (point.y() > maxY) maxY = point.y();
|
---|
1007 | }
|
---|
1008 | QPointF bottomRight(maxX, minY);
|
---|
1009 | QPointF topLeft(minX, maxY);
|
---|
1010 | QPointF center((bottomRight+topLeft)/2.f);
|
---|
1011 | stack.push(QRectF(topLeft + (topLeft-center)*(.5f),bottomRight + (bottomRight-center)*(.5f)));
|
---|
1012 | zoom.setZoomStack(stack);
|
---|
1013 |
|
---|
1014 | delete[] fitsBuffer;
|
---|
1015 | window.resize(600, 400);
|
---|
1016 | window.show();
|
---|
1017 |
|
---|
1018 | a.exec();
|
---|
1019 |
|
---|
1020 | for (auto it = curves.begin(); it != curves.end(); it++)
|
---|
1021 | delete *it;
|
---|
1022 | for (auto it = xValues.begin(); it != xValues.end(); it++)
|
---|
1023 | delete[] *it;
|
---|
1024 | delete[] yValues;
|
---|
1025 | delete[] handle;
|
---|
1026 | return 0;
|
---|
1027 | }
|
---|
1028 | #else
|
---|
1029 | int FitsDumper::doCurvesDisplay( const vector<string> &list, const string& tableName)
|
---|
1030 | {
|
---|
1031 | cerr << "Sorry, but plotting features seem to have been disabled at compilation time." << endl;
|
---|
1032 | cerr << "Please recompile with PLOTTING_PLEASE defined and try again." << endl;
|
---|
1033 | return 0;
|
---|
1034 | }
|
---|
1035 | #endif
|
---|
1036 | void SetupConfiguration(Configuration& conf)
|
---|
1037 | {
|
---|
1038 | po::options_description configs("Fitsdump options");
|
---|
1039 | configs.add_options()
|
---|
1040 | ("fitsfile,f", var<string>()
|
---|
1041 | #if BOOST_VERSION >= 104200
|
---|
1042 | ->required()
|
---|
1043 | #endif
|
---|
1044 | , "Name of FITS file")
|
---|
1045 | ("tablename,t", var<string>("DATA")
|
---|
1046 | #if BOOST_VERSION >= 104200
|
---|
1047 | ->required()
|
---|
1048 | #endif
|
---|
1049 | , "Name of input table")
|
---|
1050 | ("col,c", vars<string>(), "List of columns to dump\narg is a list of columns, separated by a space.\nAdditionnally, a list of sub-columns can be added\ne.g. Data[3] will dump sub-column 3 of column Data\nData[3:4] will dump sub-columns 3 and 4\nOmitting this argument dump the entire column\nnota: all indices start at zero")
|
---|
1051 | ("outfile,o", var<string>("/dev/stdout"), "Name of output file (-:/dev/stdout)")
|
---|
1052 | ("precision,p", var<int>(20), "Precision of ofstream")
|
---|
1053 | ("list,l", po_switch(), "List all tables and columns in file")
|
---|
1054 | ("header,h", po_switch(), "Dump header of given table")
|
---|
1055 | ("graph,g", po_switch(), "Plot the columns instead of dumping them")
|
---|
1056 | ;
|
---|
1057 |
|
---|
1058 | po::positional_options_description p;
|
---|
1059 | p.add("fitsfile", 1); // The first positional options
|
---|
1060 | p.add("col", -1); // All others
|
---|
1061 |
|
---|
1062 | conf.AddOptions(configs);
|
---|
1063 | conf.SetArgumentPositions(p);
|
---|
1064 | }
|
---|
1065 |
|
---|
1066 | int main(int argc, const char** argv)
|
---|
1067 | {
|
---|
1068 | Configuration conf(argv[0]);
|
---|
1069 | conf.SetPrintUsage(PrintUsage);
|
---|
1070 | SetupConfiguration(conf);
|
---|
1071 |
|
---|
1072 | if (!conf.DoParse(argc, argv, PrintHelp))
|
---|
1073 | return -1;
|
---|
1074 |
|
---|
1075 | FitsDumper loader;
|
---|
1076 | return loader.ExecConfig(conf);
|
---|
1077 | }
|
---|