1 | #ifndef MARS_ofits
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2 | #define MARS_ofits
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3 |
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4 | #include <string>
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5 | #include <string.h>
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6 | #include <algorithm>
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7 | #include <sstream>
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8 | #include <iostream>
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9 | #include <fstream>
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10 | #include <iomanip>
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11 | #include <vector>
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12 | #include <algorithm>
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13 | #include <stdexcept>
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14 |
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15 | #define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
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16 |
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17 | #ifdef __CINT__
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18 | #define off_t size_t
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19 | #endif
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20 |
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21 | #ifndef __MARS__
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22 | #ifndef gLog
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23 | #define gLog std::cerr
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24 | #define ___err___ ""
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25 | #define ___warn___ ""
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26 | #define ___all___ ""
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27 | #endif
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28 | #else
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29 | #include "MLog.h"
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30 | #include "MLogManip.h"
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31 | #define ___err___ err
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32 | #define ___warn___ warn
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33 | #define ___all___ all
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34 | #endif
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35 |
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36 | #include "FITS.h"
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37 | #include "checksum.h"
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38 |
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39 | // Sloppy: allow / <--- left
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40 | // allow all characters (see specs for what is possible)
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41 |
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42 | // units: m kg s rad sr K A mol cd Hz J W V N Pa C Ohm S F Wb T Hlm lx
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43 |
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44 | class ofits : public std::ofstream
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45 | {
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46 | public:
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47 | struct Key
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48 | {
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49 | std::string key;
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50 | bool delim;
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51 | std::string value;
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52 | std::string comment;
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53 | std::string fitsString;
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54 |
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55 | off_t offset; // offset in file
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56 |
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57 | bool changed; // For closing the file
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58 |
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59 | Key(const std::string &k="") : key(k), delim(false), fitsString(""), offset(0), changed(true) { }
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60 |
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61 | std::string Trim(const std::string &str)
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62 | {
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63 | // Trim Both leading and trailing spaces
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64 | const size_t first = str.find_first_not_of(' '); // Find the first character position after excluding leading blank spaces
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65 | const size_t last = str.find_last_not_of(' '); // Find the first character position from reverse af
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66 |
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67 | // if all spaces or empty return an empty string
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68 | if (std::string::npos==first || std::string::npos==last)
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69 | return std::string();
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70 |
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71 | return str.substr(first, last-first+1);
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72 | }
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73 |
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74 | bool FormatKey()
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75 | {
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76 | key = Trim(key);
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77 | if (key.empty())
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78 | {
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79 | #ifdef __EXCEPTIONS
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80 | throw std::runtime_error("Key name empty.");
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81 | #else
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82 | gLog << ___err___ << "ERROR - Key name empty." << std::endl;
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83 | return false;
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84 | #endif
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85 | }
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86 | if (key.size()>8)
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87 | {
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88 | std::ostringstream sout;
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89 | sout << "Key '" << key << "' exceeds 8 bytes.";
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90 | #ifdef __EXCEPTIONS
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91 | throw std::runtime_error(sout.str());
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92 | #else
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93 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
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94 | return false;
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95 | #endif
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96 | }
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97 |
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98 | //transform(key.begin(), key.end(), key.begin(), toupper);
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99 | #if GCC_VERSION < 40603
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100 | for (std::string::const_iterator c=key.begin(); c<key.end(); c++)
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101 | #else
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102 | for (std::string::const_iterator c=key.cbegin(); c<key.cend(); c++)
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103 | #endif
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104 | if ((*c<'A' || *c>'Z') && (*c<'0' || *c>'9') && *c!='-' && *c!='_')
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105 | {
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106 | std::ostringstream sout;
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107 | sout << "Invalid character '" << *c << "' found in key '" << key << "'";
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108 | #ifdef __EXCEPTIONS
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109 | throw std::runtime_error(sout.str());
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110 | #else
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111 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
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112 | return false;
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113 | #endif
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114 | }
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115 |
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116 | return true;
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117 | }
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118 |
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119 | bool FormatComment()
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120 | {
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121 | comment = Trim(comment);
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122 |
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123 | #if GCC_VERSION < 40603
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124 | for (std::string::const_iterator c=key.begin(); c<key.end(); c++)
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125 | #else
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126 | for (std::string::const_iterator c=key.cbegin(); c<key.cend(); c++)
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127 | #endif
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128 | if (*c<32 || *c>126)
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129 | {
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130 | std::ostringstream sout;
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131 | sout << "Invalid character '" << *c << "' [" << int(*c) << "] found in comment '" << comment << "'";
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132 | #ifdef __EXCEPTIONS
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133 | throw std::runtime_error(sout.str());
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134 | #else
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135 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
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136 | return false;
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137 | #endif
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138 | }
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139 |
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140 | return true;
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141 | }
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142 |
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143 | bool check(bool trim=false)
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144 | {
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145 | if (!FormatKey())
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146 | return false;
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147 |
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148 | if (!FormatComment())
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149 | return false;
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150 |
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151 | size_t sz = CalcSize();
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152 | if (sz<=80)
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153 | return true;
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154 |
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155 | if (!trim)
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156 | {
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157 | std::ostringstream sout;
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158 | sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters.";
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159 | #ifdef __EXCEPTIONS
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160 | throw std::runtime_error(sout.str());
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161 | #else
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162 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
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163 | #endif
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164 | return false;
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165 | }
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166 |
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167 | //looks like something went wrong. Maybe entry is too long ?
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168 | //try to remove the comment
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169 | comment = "";
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170 |
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171 | sz = CalcSize();
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172 | if (sz<=80)
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173 | {
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174 | #ifndef __EXCEPTIONS
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175 | std::ostringstream sout;
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176 | sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters... removed comment.";
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177 | gLog << ___warn___ << "WARNING - " << sout.str() << std::endl;
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178 | #endif
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179 | return true;
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180 | }
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181 |
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182 | std::ostringstream sout;
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183 | sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters even without comment.";
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184 | #ifdef __EXCEPTIONS
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185 | throw std::runtime_error(sout.str());
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186 | #else
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187 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
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188 | return false;
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189 | #endif
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190 | }
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191 |
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192 | size_t CalcSize() const
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193 | {
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194 | if (!delim)
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195 | return 10+comment.size();
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196 |
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197 | return 10 + (value.size()<20?20:value.size()) + 3 + comment.size();
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198 | }
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199 |
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200 | std::string Compile()
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201 | {
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202 |
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203 | if (fitsString != "")
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204 | return fitsString;
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205 |
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206 | std::ostringstream sout;
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207 | sout << std::left << std::setw(8) << key;
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208 |
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209 | if (!delim)
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210 | {
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211 | sout << " " << comment;
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212 | return sout.str();
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213 | }
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214 |
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215 | sout << "= ";
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216 | sout << (!value.empty() && value[0]=='\''?std::left:std::right);
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217 | sout << std::setw(20) << value << std::left;
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218 |
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219 | if (!comment.empty())
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220 | sout << " / " << comment;
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221 |
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222 | return sout.str();
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223 | }
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224 |
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225 | Checksum checksum;
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226 |
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227 | void Out(std::ofstream &fout)
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228 | {
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229 | if (!changed)
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230 | return;
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231 |
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232 | std::string str = Compile();
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233 | str.insert(str.end(), 80-str.size(), ' ');
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234 |
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235 | if (offset==0)
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236 | offset = fout.tellp();
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237 |
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238 | //cout << "Write[" << offset << "]: " << key << "/" << value << endl;
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239 |
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240 | fout.seekp(offset);
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241 | fout << str;
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242 |
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243 | checksum.reset();
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244 | checksum.add(str.c_str(), 80);
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245 |
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246 | changed = false;
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247 | }
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248 | /*
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249 | void Out(ostream &out)
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250 | {
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251 | std::string str = Compile();
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252 |
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253 | str.insert(str.end(), 80-str.size(), ' ');
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254 |
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255 | out << str;
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256 | changed = false;
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257 | }*/
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258 | };
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259 |
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260 | private:
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261 | std::vector<Key> fKeys;
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262 |
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263 | std::vector<Key>::iterator findkey(const std::string &key)
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264 | {
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265 | for (auto it=fKeys.begin(); it!=fKeys.end(); it++)
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266 | if (key==it->key)
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267 | return it;
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268 |
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269 | return fKeys.end();
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270 | }
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271 |
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272 | bool Set(const std::string &key="", bool delim=false, const std::string &value="", const std::string &comment="")
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273 | {
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274 | // If no delimit add the row no matter if it alread exists
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275 | if (delim)
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276 | {
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277 | // if the row already exists: update it
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278 | auto it = findkey(key);
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279 | if (it!=fKeys.end())
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280 | {
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281 | it->value = value;
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282 | it->changed = true;
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283 | return true;
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284 | }
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285 | }
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286 |
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287 | if (fTable.num_rows>0)
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288 | {
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289 | std::ostringstream sout;
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290 | sout << "No new header key can be defined, rows were already written to the file... ignoring new key '" << key << "'";
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291 | #ifdef __EXCEPTIONS
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292 | throw std::runtime_error(sout.str());
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293 | #else
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294 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
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295 | return false;
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296 | #endif
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297 | }
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298 |
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299 | Key entry;
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300 |
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301 | entry.key = key;
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302 | entry.delim = delim;
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303 | entry.value = value;
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304 | entry.comment = comment;
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305 | entry.offset = 0;
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306 | entry.changed = true;
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307 |
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308 | if (!entry.check(fCommentTrimming))
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309 | return false;
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310 |
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311 | fKeys.push_back(entry);
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312 | return true;
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313 | }
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314 |
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315 | protected:
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316 | struct Table
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317 | {
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318 | off_t offset;
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319 |
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320 | size_t bytes_per_row;
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321 | size_t num_rows;
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322 | size_t num_cols;
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323 |
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324 | struct Column
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325 | {
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326 | std::string name;
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327 | size_t offset;
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328 | size_t num;
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329 | size_t size;
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330 | char type;
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331 | };
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332 |
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333 | std::vector<Column> cols;
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334 |
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335 | Table() : offset(0), bytes_per_row(0), num_rows(0), num_cols(0)
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336 | {
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337 | }
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338 | };
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339 |
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340 |
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341 | Table fTable;
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342 |
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343 | std::vector<char> fOutputBuffer;
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344 |
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345 | std::vector<Table::Column>::const_iterator findcol(const std::string &name)
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346 | {
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347 | for (auto it=fTable.cols.cbegin(); it!=fTable.cols.cend(); it++)
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348 | if (name==it->name)
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349 | return it;
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350 |
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351 | return fTable.cols.cend();
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352 | }
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353 |
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354 | Checksum fDataSum;
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355 | Checksum fHeaderSum;
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356 |
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357 | bool fCommentTrimming;
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358 | bool fManualExtName;
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359 |
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360 | public:
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361 | ofits() : fCommentTrimming(false),
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362 | fManualExtName(false)
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363 | {
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364 | }
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365 | ofits(const char *fname) : std::ofstream(),
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366 | fCommentTrimming(false),
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367 | fManualExtName(false)
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368 | {
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369 | this->open(fname);
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370 | }
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371 | virtual ~ofits() { if (is_open()) close(); }
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372 |
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373 | virtual void open(const char * filename, bool addEXTNAMEKey=true)
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374 | {
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375 | fDataSum = 0;
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376 | fHeaderSum = 0;
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377 |
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378 | fTable = Table();
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379 | fKeys.clear();
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380 |
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381 | SetStr("XTENSION", "BINTABLE", "binary table extension");
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382 | SetInt("BITPIX", 8, "8-bit bytes");
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383 | SetInt("NAXIS", 2, "2-dimensional binary table");
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384 | SetInt("NAXIS1", 0, "width of table in bytes");
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385 | SetInt("NAXIS2", 0, "number of rows in table");
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386 | SetInt("PCOUNT", 0, "size of special data area");
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387 | SetInt("GCOUNT", 1, "one data group (required keyword)");
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388 | SetInt("TFIELDS", 0, "number of fields in each row");
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389 | if (addEXTNAMEKey)
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390 | SetStr("EXTNAME", "", "name of extension table");
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391 | else
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392 | fManualExtName = true;
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393 | SetStr("CHECKSUM", "0000000000000000", "Checksum for the whole HDU");
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394 | SetStr("DATASUM", " 0", "Checksum for the data block");
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395 |
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396 | std::ofstream::open(filename);
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397 | }
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398 |
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399 | void AllowCommentsTrimming(bool allow)
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400 | {
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401 | fCommentTrimming = allow;
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402 | }
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403 | //Etienne: required to enable 1 to 1 reconstruction of files
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404 | bool SetKeyComment(const std::string& key, const std::string& comment)
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405 | {
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406 | auto it = findkey(key);
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407 | if (it==fKeys.end())
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408 | return false;
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409 | it->comment = comment;
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410 | it->changed = true;
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411 | return true;
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412 | }
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413 | bool SetKeyFromFitsString(const std::string& fitsString)
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414 | {
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415 | if (fTable.num_rows>0)
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416 | {
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417 | std::ostringstream sout;
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418 | sout << "No new header key can be defined, rows were already written to the file... ignoring new key '" << fitsString << "'";
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419 | #ifdef __EXCEPTIONS
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420 | throw std::runtime_error(sout.str());
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421 | #else
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422 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
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423 | return false;
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424 | #endif
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425 | }
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426 |
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427 | Key entry;
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428 | entry.fitsString = fitsString;
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429 | entry.changed = true;
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430 | fKeys.push_back(entry);
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431 | return true;
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432 | }
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433 | bool SetRaw(const std::string &key, const std::string &val, const std::string &comment)
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434 | {
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435 | return Set(key, true, val, comment);
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436 | }
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437 |
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438 | bool SetBool(const std::string &key, bool b, const std::string &comment="")
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439 | {
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440 | return Set(key, true, b?"T":"F", comment);
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441 | }
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442 |
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443 | bool AddEmpty(const std::string &key, const std::string &comment="")
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444 | {
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445 | return Set(key, true, "", comment);
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446 | }
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447 |
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448 | bool SetStr(const std::string &key, std::string s, const std::string &comment="")
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449 | {
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450 | for (uint i=0; i<s.length(); i++)
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451 | if (s[i]=='\'')
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452 | s.insert(i++, "\'");
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453 |
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454 | return Set(key, true, "'"+s+"'", comment);
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455 | }
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456 |
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457 | bool SetInt(const std::string &key, int64_t i, const std::string &comment="")
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458 | {
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459 | std::ostringstream sout;
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460 | sout << i;
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461 |
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462 | return Set(key, true, sout.str(), comment);
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463 | }
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464 |
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465 | bool SetFloat(const std::string &key, double f, int p, const std::string &comment="")
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466 | {
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467 | std::ostringstream sout;
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468 |
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469 | if (p<0)
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470 | sout << std::setprecision(-p) << fixed;
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471 | if (p>0)
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472 | sout << std::setprecision(p);
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473 | if (p==0)
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474 | sout << std::setprecision(f>1e-100 && f<1e100 ? 15 : 14);
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475 |
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476 | sout << f;
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477 |
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478 | std::string str = sout.str();
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479 |
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480 | replace(str.begin(), str.end(), 'e', 'E');
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481 |
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482 | if (str.find_first_of('E')==std::string::npos && str.find_first_of('.')==std::string::npos)
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483 | str += ".";
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484 |
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485 | return Set(key, true, str, comment);
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486 | }
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487 |
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488 | bool SetFloat(const std::string &key, double f, const std::string &comment="")
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489 | {
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490 | return SetFloat(key, f, 0, comment);
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491 | }
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492 |
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493 | bool SetHex(const std::string &key, uint64_t i, const std::string &comment="")
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494 | {
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495 | std::ostringstream sout;
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496 | sout << std::hex << "0x" << i;
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497 | return SetStr(key, sout.str(), comment);
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498 | }
|
---|
499 |
|
---|
500 | bool AddComment(const std::string &comment)
|
---|
501 | {
|
---|
502 | return Set("COMMENT", false, "", comment);
|
---|
503 | }
|
---|
504 |
|
---|
505 | bool AddHistory(const std::string &comment)
|
---|
506 | {
|
---|
507 | return Set("HISTORY", false, "", comment);
|
---|
508 | }
|
---|
509 |
|
---|
510 | void End()
|
---|
511 | {
|
---|
512 | Set("END");
|
---|
513 | while (fKeys.size()%36!=0)
|
---|
514 | fKeys.emplace_back();
|
---|
515 | }
|
---|
516 |
|
---|
517 | std::string CommentFromType(char type)
|
---|
518 | {
|
---|
519 | std::string comment;
|
---|
520 |
|
---|
521 | switch (type)
|
---|
522 | {
|
---|
523 | case 'L': comment = "[1-byte BOOL]"; break;
|
---|
524 | case 'A': comment = "[1-byte CHAR]"; break;
|
---|
525 | case 'B': comment = "[1-byte BOOL]"; break;
|
---|
526 | case 'I': comment = "[2-byte INT]"; break;
|
---|
527 | case 'J': comment = "[4-byte INT]"; break;
|
---|
528 | case 'K': comment = "[8-byte INT]"; break;
|
---|
529 | case 'E': comment = "[4-byte FLOAT]"; break;
|
---|
530 | case 'D': comment = "[8-byte FLOAT]"; break;
|
---|
531 | case 'Q': comment = "[var. Length]"; break;
|
---|
532 | }
|
---|
533 |
|
---|
534 | return comment;
|
---|
535 | }
|
---|
536 |
|
---|
537 | uint32_t SizeFromType(char type)
|
---|
538 | {
|
---|
539 | size_t size = 0;
|
---|
540 |
|
---|
541 | switch (type)
|
---|
542 | {
|
---|
543 | case 'L': size = 1; break;
|
---|
544 | case 'A': size = 1; break;
|
---|
545 | case 'B': size = 1; break;
|
---|
546 | case 'I': size = 2; break;
|
---|
547 | case 'J': size = 4; break;
|
---|
548 | case 'K': size = 8; break;
|
---|
549 | case 'E': size = 4; break;
|
---|
550 | case 'D': size = 8; break;
|
---|
551 | case 'Q': size = 16; break;
|
---|
552 | }
|
---|
553 |
|
---|
554 | return size;
|
---|
555 | }
|
---|
556 | //ETIENNE to be able to restore the file 1 to 1, I must restore the header keys myself
|
---|
557 | virtual bool AddColumn(uint32_t cnt, char typechar, const std::string &name, const std::string &unit, const std::string &comment="", bool addHeaderKeys=true)
|
---|
558 | {
|
---|
559 | if (tellp()<0)
|
---|
560 | {
|
---|
561 | std::ostringstream sout;
|
---|
562 | sout << "File not open... ignoring column '" << name << "'";
|
---|
563 | #ifdef __EXCEPTIONS
|
---|
564 | throw std::runtime_error(sout.str());
|
---|
565 | #else
|
---|
566 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
|
---|
567 | return false;
|
---|
568 | #endif
|
---|
569 | }
|
---|
570 |
|
---|
571 | if (tellp()>0)
|
---|
572 | {
|
---|
573 | std::ostringstream sout;
|
---|
574 | sout << "Header already written, no new column can be defined... ignoring column '" << name << "'";
|
---|
575 | #ifdef __EXCEPTIONS
|
---|
576 | throw std::runtime_error(sout.str());
|
---|
577 | #else
|
---|
578 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
|
---|
579 | return false;
|
---|
580 | #endif
|
---|
581 | }
|
---|
582 |
|
---|
583 | if (findcol(name)!=fTable.cols.cend())
|
---|
584 | {
|
---|
585 | std::ostringstream sout;
|
---|
586 | sout << "A column with the name '" << name << "' already exists.";
|
---|
587 | #ifdef __EXCEPTIONS
|
---|
588 | throw std::runtime_error(sout.str());
|
---|
589 | #else
|
---|
590 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
|
---|
591 | return false;
|
---|
592 | #endif
|
---|
593 | }
|
---|
594 |
|
---|
595 | typechar = toupper(typechar);
|
---|
596 |
|
---|
597 | static const std::string allow("LABIJKEDQ");
|
---|
598 | #if GCC_VERSION < 40603
|
---|
599 | if (std::find(allow.begin(), allow.end(), typechar)==allow.end())
|
---|
600 | #else
|
---|
601 | if (std::find(allow.cbegin(), allow.cend(), typechar)==allow.end())
|
---|
602 | #endif
|
---|
603 | {
|
---|
604 | std::ostringstream sout;
|
---|
605 | sout << "Column type '" << typechar << "' not supported.";
|
---|
606 | #ifdef __EXCEPTIONS
|
---|
607 | throw std::runtime_error(sout.str());
|
---|
608 | #else
|
---|
609 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
|
---|
610 | return false;
|
---|
611 | #endif
|
---|
612 | }
|
---|
613 |
|
---|
614 | std::ostringstream type;
|
---|
615 | type << cnt;
|
---|
616 | if (typechar=='Q')
|
---|
617 | type << "QB";
|
---|
618 | else
|
---|
619 | type << typechar;
|
---|
620 |
|
---|
621 | fTable.num_cols++;
|
---|
622 |
|
---|
623 | if (addHeaderKeys)
|
---|
624 | {
|
---|
625 | #if GCC_VERSION < 40603
|
---|
626 | const std::string nc = std::to_string((long long int)(fTable.num_cols));
|
---|
627 | #else
|
---|
628 | const std::string nc = std::to_string(fTable.num_cols);
|
---|
629 | #endif
|
---|
630 | SetStr("TFORM"+nc, type.str(), "format of "+name+" "+CommentFromType(typechar));
|
---|
631 | SetStr("TTYPE"+nc, name, comment);
|
---|
632 | if (!unit.empty())
|
---|
633 | SetStr("TUNIT"+nc, unit, "unit of "+name);
|
---|
634 | }
|
---|
635 | size_t size = SizeFromType(typechar);
|
---|
636 |
|
---|
637 | Table::Column col;
|
---|
638 |
|
---|
639 | col.name = name;
|
---|
640 | col.type = typechar;
|
---|
641 | col.num = cnt;
|
---|
642 | col.size = size;
|
---|
643 | col.offset = fTable.bytes_per_row;
|
---|
644 |
|
---|
645 | fTable.cols.push_back(col);
|
---|
646 |
|
---|
647 | fTable.bytes_per_row += size*cnt;
|
---|
648 |
|
---|
649 | // Align to four bytes
|
---|
650 | fOutputBuffer.resize(fTable.bytes_per_row + 4-fTable.bytes_per_row%4);
|
---|
651 |
|
---|
652 | return true;
|
---|
653 | }
|
---|
654 |
|
---|
655 | virtual bool AddColumn(const FITS::Compression&, uint32_t cnt, char typechar, const std::string& name, const std::string& unit, const std::string& comment="", bool addHeaderKeys=true)
|
---|
656 | {
|
---|
657 | return AddColumn(cnt, typechar, name, unit, comment, addHeaderKeys);
|
---|
658 | }
|
---|
659 |
|
---|
660 | bool AddColumnShort(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
661 | { return AddColumn(cnt, 'I', name, unit, comment); }
|
---|
662 | bool AddColumnInt(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
663 | { return AddColumn(cnt, 'J', name, unit, comment); }
|
---|
664 | bool AddColumnLong(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
665 | { return AddColumn(cnt, 'K', name, unit, comment); }
|
---|
666 | bool AddColumnFloat(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
667 | { return AddColumn(cnt, 'E', name, unit, comment); }
|
---|
668 | bool AddColumnDouble(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
669 | { return AddColumn(cnt, 'D', name, unit, comment); }
|
---|
670 | bool AddColumnChar(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
671 | { return AddColumn(cnt, 'A', name, unit, comment); }
|
---|
672 | bool AddColumnByte(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
673 | { return AddColumn(cnt, 'B', name, unit, comment); }
|
---|
674 | bool AddColumnBool(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
675 | { return AddColumn(cnt, 'L', name, unit, comment); }
|
---|
676 |
|
---|
677 | bool AddColumnShort(const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
678 | { return AddColumn(1, 'I', name, unit, comment); }
|
---|
679 | bool AddColumnInt(const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
680 | { return AddColumn(1, 'J', name, unit, comment); }
|
---|
681 | bool AddColumnLong(const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
682 | { return AddColumn(1, 'K', name, unit, comment); }
|
---|
683 | bool AddColumnFloat(const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
684 | { return AddColumn(1, 'E', name, unit, comment); }
|
---|
685 | bool AddColumnDouble(const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
686 | { return AddColumn(1, 'D', name, unit, comment); }
|
---|
687 | bool AddColumnChar(const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
688 | { return AddColumn(1, 'A', name, unit, comment); }
|
---|
689 | bool AddColumnByte(const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
690 | { return AddColumn(1, 'B', name, unit, comment); }
|
---|
691 | bool AddColumnBool(const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
692 | { return AddColumn(1, 'L', name, unit, comment); }
|
---|
693 |
|
---|
694 | bool AddColumnShort(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
695 | { return AddColumn(comp, cnt, 'I', name, unit, comment); }
|
---|
696 | bool AddColumnInt(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
697 | { return AddColumn(comp, cnt, 'J', name, unit, comment); }
|
---|
698 | bool AddColumnLong(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
699 | { return AddColumn(comp, cnt, 'K', name, unit, comment); }
|
---|
700 | bool AddColumnFloat(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
701 | { return AddColumn(comp, cnt, 'E', name, unit, comment); }
|
---|
702 | bool AddColumnDouble(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
703 | { return AddColumn(comp, cnt, 'D', name, unit, comment); }
|
---|
704 | bool AddColumnChar(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
705 | { return AddColumn(comp, cnt, 'A', name, unit, comment); }
|
---|
706 | bool AddColumnByte(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
707 | { return AddColumn(comp, cnt, 'B', name, unit, comment); }
|
---|
708 | bool AddColumnBool(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
709 | { return AddColumn(comp, cnt, 'L', name, unit, comment); }
|
---|
710 |
|
---|
711 | bool AddColumnShort(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
712 | { return AddColumn(comp, 1, 'I', name, unit, comment); }
|
---|
713 | bool AddColumnInt(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
714 | { return AddColumn(comp, 1, 'J', name, unit, comment); }
|
---|
715 | bool AddColumnLong(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
716 | { return AddColumn(comp, 1, 'K', name, unit, comment); }
|
---|
717 | bool AddColumnFloat(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
718 | { return AddColumn(comp, 1, 'E', name, unit, comment); }
|
---|
719 | bool AddColumnDouble(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
720 | { return AddColumn(comp, 1, 'D', name, unit, comment); }
|
---|
721 | bool AddColumnChar(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
722 | { return AddColumn(comp, 1, 'A', name, unit, comment); }
|
---|
723 | bool AddColumnByte(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
724 | { return AddColumn(comp, 1, 'B', name, unit, comment); }
|
---|
725 | bool AddColumnBool(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
|
---|
726 | { return AddColumn(comp, 1, 'L', name, unit, comment); }
|
---|
727 |
|
---|
728 | /*
|
---|
729 | bool AddKey(string key, double d, const std::string &comment)
|
---|
730 | {
|
---|
731 | ostringstream out;
|
---|
732 | out << d;
|
---|
733 |
|
---|
734 | std::string s = out.str();
|
---|
735 |
|
---|
736 | replace(s.begin(), s.end(), "e", "E");
|
---|
737 |
|
---|
738 | return AddKey(key, s, comment);
|
---|
739 | }*/
|
---|
740 |
|
---|
741 |
|
---|
742 | Checksum WriteHeader(std::ofstream &fout)
|
---|
743 | {
|
---|
744 | Checksum sum;
|
---|
745 | uint32_t count=0;
|
---|
746 | for (auto it=fKeys.begin(); it!=fKeys.end(); it++)
|
---|
747 | {
|
---|
748 | it->Out(fout);
|
---|
749 | sum += it->checksum;
|
---|
750 | count++;
|
---|
751 | }
|
---|
752 | fout.flush();
|
---|
753 |
|
---|
754 | return sum;
|
---|
755 | }
|
---|
756 |
|
---|
757 | Checksum WriteHeader()
|
---|
758 | {
|
---|
759 | return WriteHeader(*this);
|
---|
760 | }
|
---|
761 |
|
---|
762 | void FlushHeader()
|
---|
763 | {
|
---|
764 | const off_t pos = tellp();
|
---|
765 | WriteHeader();
|
---|
766 | seekp(pos);
|
---|
767 | }
|
---|
768 |
|
---|
769 | Checksum WriteFitsHeader()
|
---|
770 | {
|
---|
771 | ofits h;
|
---|
772 |
|
---|
773 | h.SetBool("SIMPLE", true, "file does conform to FITS standard");
|
---|
774 | h.SetInt ("BITPIX", 8, "number of bits per data pixel");
|
---|
775 | h.SetInt ("NAXIS", 0, "number of data axes");
|
---|
776 | h.SetBool("EXTEND", true, "FITS dataset may contain extensions");
|
---|
777 | h.SetStr ("CHECKSUM","0000000000000000", "Checksum for the whole HDU");
|
---|
778 | h.SetStr ("DATASUM", " 0", "Checksum for the data block");
|
---|
779 | h.AddComment("FITS (Flexible Image Transport System) format is defined in 'Astronomy");
|
---|
780 | h.AddComment("and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H");
|
---|
781 | h.End();
|
---|
782 |
|
---|
783 | const Checksum sum = h.WriteHeader(*this);
|
---|
784 |
|
---|
785 | h.SetStr("CHECKSUM", sum.str());
|
---|
786 |
|
---|
787 | const size_t offset = tellp();
|
---|
788 | h.WriteHeader(*this);
|
---|
789 | seekp(offset);
|
---|
790 |
|
---|
791 | return sum;
|
---|
792 | }
|
---|
793 |
|
---|
794 | virtual bool WriteDrsOffsetsTable ()
|
---|
795 | {
|
---|
796 | return true;
|
---|
797 | }
|
---|
798 |
|
---|
799 | virtual bool WriteCatalog()
|
---|
800 | {
|
---|
801 | return true;
|
---|
802 | }
|
---|
803 |
|
---|
804 | virtual bool WriteTableHeader(const char *name="DATA")
|
---|
805 | {
|
---|
806 | if (tellp()>0)
|
---|
807 | {
|
---|
808 | #ifdef __EXCEPTIONS
|
---|
809 | throw std::runtime_error("File not empty anymore.");
|
---|
810 | #else
|
---|
811 | gLog << ___err___ << "ERROR - File not empty anymore." << std::endl;
|
---|
812 | return false;
|
---|
813 | #endif
|
---|
814 | }
|
---|
815 |
|
---|
816 | fHeaderSum = WriteFitsHeader();
|
---|
817 |
|
---|
818 | WriteDrsOffsetsTable();
|
---|
819 |
|
---|
820 | if (!fManualExtName)
|
---|
821 | SetStr("EXTNAME", name);
|
---|
822 | SetInt("NAXIS1", fTable.bytes_per_row);
|
---|
823 | SetInt("TFIELDS", fTable.cols.size());
|
---|
824 |
|
---|
825 | End();
|
---|
826 |
|
---|
827 | WriteHeader();
|
---|
828 |
|
---|
829 | WriteCatalog();
|
---|
830 |
|
---|
831 | return good();
|
---|
832 | }
|
---|
833 |
|
---|
834 | template<size_t N>
|
---|
835 | void revcpy(char *dest, const char *src, int num)
|
---|
836 | {
|
---|
837 | const char *pend = src + num*N;
|
---|
838 | for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
|
---|
839 | std::reverse_copy(ptr, ptr+N, dest);
|
---|
840 | }
|
---|
841 |
|
---|
842 | virtual uint32_t GetBytesPerRow() const { return fTable.bytes_per_row; }
|
---|
843 |
|
---|
844 | virtual bool WriteRow(const void *ptr, size_t cnt, bool byte_swap=true)
|
---|
845 | {
|
---|
846 | // FIXME: Make sure that header was already written
|
---|
847 | // or write header now!
|
---|
848 | if (cnt!=fTable.bytes_per_row)
|
---|
849 | {
|
---|
850 | std::ostringstream sout;
|
---|
851 | sout << "WriteRow - Size " << cnt << " does not match expected size " << fTable.bytes_per_row;
|
---|
852 | #ifdef __EXCEPTIONS
|
---|
853 | throw std::runtime_error(sout.str());
|
---|
854 | #else
|
---|
855 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
|
---|
856 | return false;
|
---|
857 | #endif
|
---|
858 | }
|
---|
859 |
|
---|
860 | // For the checksum we need everything to be correctly aligned
|
---|
861 | const uint8_t offset = fTable.offset%4;
|
---|
862 |
|
---|
863 | char *buffer = fOutputBuffer.data() + offset;
|
---|
864 |
|
---|
865 | auto ib = fOutputBuffer.begin();
|
---|
866 | auto ie = fOutputBuffer.rbegin();
|
---|
867 | *ib++ = 0;
|
---|
868 | *ib++ = 0;
|
---|
869 | *ib++ = 0;
|
---|
870 | *ib = 0;
|
---|
871 |
|
---|
872 | *ie++ = 0;
|
---|
873 | *ie++ = 0;
|
---|
874 | *ie++ = 0;
|
---|
875 | *ie = 0;
|
---|
876 |
|
---|
877 | if (!byte_swap)
|
---|
878 | memcpy(buffer, ptr, cnt);
|
---|
879 | else
|
---|
880 | {
|
---|
881 | for (auto it=fTable.cols.cbegin(); it!=fTable.cols.cend(); it++)
|
---|
882 | {
|
---|
883 | const char *src = reinterpret_cast<const char*>(ptr) + it->offset;
|
---|
884 | char *dest = buffer + it->offset;
|
---|
885 |
|
---|
886 | // Let the compiler do some optimization by
|
---|
887 | // knowing the we only have 1, 2, 4 and 8
|
---|
888 | switch (it->size)
|
---|
889 | {
|
---|
890 | case 1: memcpy (dest, src, it->num*it->size); break;
|
---|
891 | case 2: revcpy<2>(dest, src, it->num); break;
|
---|
892 | case 4: revcpy<4>(dest, src, it->num); break;
|
---|
893 | case 8: revcpy<8>(dest, src, it->num); break;
|
---|
894 | }
|
---|
895 | }
|
---|
896 | }
|
---|
897 |
|
---|
898 | write(buffer, cnt);
|
---|
899 | fDataSum.add(fOutputBuffer);
|
---|
900 |
|
---|
901 | fTable.num_rows++;
|
---|
902 | fTable.offset += cnt;
|
---|
903 | return good();
|
---|
904 | }
|
---|
905 |
|
---|
906 | template<typename N>
|
---|
907 | bool WriteRow(const std::vector<N> &vec)
|
---|
908 | {
|
---|
909 | return WriteRow(vec.data(), vec.size()*sizeof(N));
|
---|
910 | }
|
---|
911 |
|
---|
912 | // Flushes the number of rows to the header on disk
|
---|
913 | virtual void FlushNumRows()
|
---|
914 | {
|
---|
915 | SetInt("NAXIS2", fTable.num_rows);
|
---|
916 | FlushHeader();
|
---|
917 | }
|
---|
918 |
|
---|
919 | size_t GetNumRows() const { return fTable.num_rows; }
|
---|
920 |
|
---|
921 | void AlignTo2880Bytes()
|
---|
922 | {
|
---|
923 | if (tellp()%(80*36)>0)
|
---|
924 | {
|
---|
925 | std::vector<char> filler(80*36-tellp()%(80*36));
|
---|
926 | write(filler.data(), filler.size());
|
---|
927 | }
|
---|
928 | }
|
---|
929 |
|
---|
930 | Checksum UpdateHeaderChecksum()
|
---|
931 | {
|
---|
932 |
|
---|
933 | std::ostringstream dataSumStr;
|
---|
934 | dataSumStr << fDataSum.val();
|
---|
935 | SetStr("DATASUM", dataSumStr.str());
|
---|
936 |
|
---|
937 | const Checksum sum = WriteHeader();
|
---|
938 |
|
---|
939 | //sum += headersum;
|
---|
940 |
|
---|
941 | SetStr("CHECKSUM", (sum+fDataSum).str());
|
---|
942 |
|
---|
943 | return WriteHeader();
|
---|
944 | }
|
---|
945 | virtual bool close()
|
---|
946 | {
|
---|
947 | if (tellp()<0)
|
---|
948 | return false;
|
---|
949 |
|
---|
950 | AlignTo2880Bytes();
|
---|
951 |
|
---|
952 | // We don't have to jump back to the end of the file
|
---|
953 | SetInt("NAXIS2", fTable.num_rows);
|
---|
954 |
|
---|
955 |
|
---|
956 | const Checksum chk = UpdateHeaderChecksum();
|
---|
957 |
|
---|
958 | std::ofstream::close();
|
---|
959 |
|
---|
960 | if ((chk+fDataSum).valid())
|
---|
961 | return true;
|
---|
962 |
|
---|
963 | std::ostringstream sout;
|
---|
964 | sout << "Checksum (" << std::hex << chk.val() << ") invalid.";
|
---|
965 | #ifdef __EXCEPTIONS
|
---|
966 | throw std::runtime_error(sout.str());
|
---|
967 | #else
|
---|
968 | gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
|
---|
969 | return false;
|
---|
970 | #endif
|
---|
971 | }
|
---|
972 |
|
---|
973 | std::pair<std::string, int> GetChecksumData()
|
---|
974 | {
|
---|
975 | std::string datasum;
|
---|
976 | std::string checksum;
|
---|
977 | //cannot directly use the Get methods, because they are only in fits.h
|
---|
978 | for (std::vector<Key>::const_iterator it=fKeys.cbegin(); it!= fKeys.cend(); it++)
|
---|
979 | {
|
---|
980 | if (it->key == "CHECKSUM") checksum = it->value;
|
---|
981 | if (it->key == "DATASUM") datasum = it->value;
|
---|
982 | }
|
---|
983 | if (checksum[0] == '\'')
|
---|
984 | checksum = checksum.substr(1,checksum.size()-2);
|
---|
985 | if (datasum[0] == '\'')
|
---|
986 | datasum = datasum.substr(1, datasum.size()-2);
|
---|
987 | return std::make_pair(checksum, atoi(datasum.c_str()));
|
---|
988 | }
|
---|
989 |
|
---|
990 | void SetDefaultKeys()
|
---|
991 | {
|
---|
992 | SetStr("TELESCOP", "FACT", "Telescope that acquired this data");
|
---|
993 | SetStr("CREATOR", typeid(*this).name(), "Class that wrote this file");
|
---|
994 | SetFloat("EXTREL", 1.0, "Release Number");
|
---|
995 | SetStr("COMPILED", __DATE__" "__TIME__, "Compile time");
|
---|
996 | SetStr("ORIGIN", "FACT", "Institution that wrote the file");
|
---|
997 | SetStr("TIMESYS", "UTC", "Time system");
|
---|
998 | SetStr("TIMEUNIT", "d", "Time given in days w.r.t. to MJDREF");
|
---|
999 | SetInt("MJDREF", 40587, "MJD to UNIX time (seconds since 1970/1/1)");
|
---|
1000 | SetStr("PACKAGE", PACKAGE_NAME, "Package name");
|
---|
1001 | SetStr("VERSION", PACKAGE_VERSION, "Package description");
|
---|
1002 | SetStr("REVISION", REVISION, "SVN revision");
|
---|
1003 |
|
---|
1004 | const time_t t0 = time(NULL);
|
---|
1005 | const struct tm *tmp1 = gmtime(&t0);
|
---|
1006 |
|
---|
1007 | std::string str(19, '\0');
|
---|
1008 | if (tmp1 && strftime(const_cast<char*>(str.data()), 20, "%Y-%m-%dT%H:%M:%S", tmp1))
|
---|
1009 | SetStr("DATE", str, "File creation date");
|
---|
1010 | }
|
---|
1011 | };
|
---|
1012 |
|
---|
1013 | #if 0
|
---|
1014 | #include "fits.h"
|
---|
1015 |
|
---|
1016 | int main()
|
---|
1017 | {
|
---|
1018 | using namespace std;
|
---|
1019 |
|
---|
1020 | ofits h2("delme.fits");
|
---|
1021 |
|
---|
1022 | h2.SetInt("KEY1", 1, "comment 1");
|
---|
1023 | h2.AddColumnInt(2, "testcol1", "counts", "My comment");
|
---|
1024 | h2.AddColumnInt("testcol2", "counts", "My comment");
|
---|
1025 | //h2.AddColumnInt("testcol2", "counts", "My comment");
|
---|
1026 | h2.SetInt("KEY2", 2, "comment 2");
|
---|
1027 |
|
---|
1028 | /*
|
---|
1029 | AddFloat("X0", 0.000123456, "number of fields in each row");
|
---|
1030 | AddFloat("X1", 0, "number of fields in each row");
|
---|
1031 | AddFloat("X2", 12345, "number of fields in each row");
|
---|
1032 | AddFloat("X3", 123456.67890, "number of fields in each row");
|
---|
1033 | AddFloat("X4", 1234567890123456789.12345678901234567890, "number of fields in each row");
|
---|
1034 | AddFloat("X5", 1234567890.1234567890e20, "number of fields in each row");
|
---|
1035 | AddFloat("X6", 1234567890.1234567890e-20, "number of fields in each row");
|
---|
1036 | AddFloat("XB", 1234567890.1234567890e-111, "number of fields in each row");
|
---|
1037 | AddFloat("X7", 1e-5, "number of fields in each row");
|
---|
1038 | AddFloat("X8", 1e-6, "number of fields in each row");
|
---|
1039 | //AddStr("12345678", "123456789012345678", "12345678901234567890123456789012345678901234567");
|
---|
1040 | */
|
---|
1041 | // -
|
---|
1042 |
|
---|
1043 | h2.WriteTableHeader("TABLE_NAME");
|
---|
1044 |
|
---|
1045 | for (int i=0; i<10; i++)
|
---|
1046 | {
|
---|
1047 | int j[3] = { i+10, i*10, i*100 };
|
---|
1048 | h2.WriteRow(j, 3*sizeof(i));
|
---|
1049 | }
|
---|
1050 |
|
---|
1051 | //h2.AddColumnInt("testcol2", "counts", "My comment");
|
---|
1052 | //h2.SetInt("KEY3", 2, "comment 2");
|
---|
1053 | h2.SetInt("KEY2", 2, "comment 2xxx");
|
---|
1054 | h2.SetInt("KEY1", 11);
|
---|
1055 |
|
---|
1056 | h2.close();
|
---|
1057 |
|
---|
1058 | cout << "---" << endl;
|
---|
1059 |
|
---|
1060 | fits f("delme.fits");
|
---|
1061 | if (!f)
|
---|
1062 | throw std::runtime_error("xxx");
|
---|
1063 |
|
---|
1064 | cout << "Header is valid: " << f.IsHeaderOk() << endl;
|
---|
1065 |
|
---|
1066 | while (f.GetNextRow());
|
---|
1067 |
|
---|
1068 | cout << "File is valid: " << f.IsFileOk() << endl;
|
---|
1069 |
|
---|
1070 | cout << "---" << endl;
|
---|
1071 |
|
---|
1072 | return 0;
|
---|
1073 | }
|
---|
1074 | #endif
|
---|
1075 |
|
---|
1076 | #endif
|
---|