1 | #include <random>
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2 |
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3 | #include <boost/regex.hpp>
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4 | #include <boost/filesystem.hpp>
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5 | #include <boost/algorithm/string/join.hpp>
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6 |
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7 | #include "tools.h"
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8 | #include "Time.h"
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9 | #include "Configuration.h"
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10 |
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11 | #include <TROOT.h>
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12 | #include <TSystem.h>
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13 | #include <TFile.h>
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14 | #include <TTree.h>
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15 | #include <TError.h>
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16 | #include <TObjArray.h>
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17 |
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18 | using namespace std;
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19 | namespace fs = boost::filesystem;
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20 |
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21 | // ------------------------------------------------------------------------
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22 |
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23 | void SetupConfiguration(Configuration &conf)
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24 | {
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25 | po::options_description control("Root to SQL");
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26 | control.add_options()
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27 | ("file", var<string>()->required(), "The csv input file")
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28 | ("out,o", var<string>(""), "Output root file name")
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29 | ("force,f", po_switch(), "Force overwrite if output file already exists.")
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30 | ("update,u", po_switch(), "Update an existing file")
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31 | ("tree,t", var<string>("Events"), "Name of the root tree to convert")
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32 | ("compression,c", var<uint16_t>(1), "zlib compression level for the root file")
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33 | ("no-header,n", po_switch(), "Use if the first line contains no header")
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34 | ("dry-run", po_switch(), "Do not create or manipulate any output file")
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35 | ;
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36 |
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37 | po::options_description split("Splitting options");
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38 | split.add_options()
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39 | ("split-sequence,S", vars<uint16_t>(), "Split data sequentially into several trees/files (e.g. 1, 1, 2)")
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40 | ("split-quantile,Q", vars<double>(), "Split data randomly into several trees/files (e.g. 0.5, 1)")
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41 | ("seed", var<uint64_t>(mt19937_64::default_seed), "Seed value in case of random split")
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42 | ;
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43 |
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44 | po::options_description debug("Debug options");
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45 | debug.add_options()
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46 | ("verbose,v", var<uint16_t>(1), "Verbosity (0: quiet, 1: default, 2: more, 3, ...)")
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47 | ;
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48 |
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49 | po::positional_options_description p;
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50 | p.add("file", 1); // All positional options
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51 | p.add("out", 1); // All positional options
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52 | p.add("tree", 1); // All positional options
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53 |
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54 | conf.AddOptions(control);
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55 | conf.AddOptions(split);
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56 | conf.AddOptions(debug);
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57 | conf.SetArgumentPositions(p);
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58 | }
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59 |
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60 | void PrintUsage()
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61 | {
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62 | cout <<
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63 | "csv2root - Converts a data table from a csv file to a root tree\n"
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64 | "\n"
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65 | "For convenience, this documentation uses the extended version of the options, "
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66 | "refer to the output below to get the abbreviations.\n"
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67 | "\n"
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68 | "As a default, the first row in the file is considered to contain the column "
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69 | "names separated by a whitespace. Column names must not contain whitespaces "
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70 | "themselves and special characters (':') are replaces by an underscore. "
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71 | "If the first line contains the first data row, the --no-header directive "
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72 | "can be used to instruct the program to consider the first line as the first "
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73 | "data row and use it only for column count. The branch names in the tree "
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74 | "are then 'colN' where N is the column index starting from 0.\n"
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75 | "\n"
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76 | "Each consecutive row in the file is supposed to contain an identical number "
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77 | "of floating point values. Leading and trailing whitespaces are ignored. "
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78 | "Empty lines or lines starting with a '#' are discarded.\n"
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79 | "\n"
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80 | "Input and output file are given either as first and second positional argument "
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81 | "or with the --file and --out command line option. If no output file name is "
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82 | "provided then the input file is used instead and the extension replaced by .root. "
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83 | "The target tree name of the root file is given with the --tree command line "
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84 | "option or the third positional argument. The default tree name is 'Events'.\n"
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85 | "\n"
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86 | "As a default, existing files are not overwritten. If overwriting is intended, "
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87 | "it can be turned on with --force. To update an existing root file, the "
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88 | "--update option can be used. If a tree with the same name already exists, "
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89 | "the tree is updated. The compression level for a new root file can be set "
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90 | "with --compression.\n"
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91 | "\n"
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92 | "For several purposes, it might be convenient to split the output to several "
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93 | "different root-treess. This can be done using the --split-sequence (-S) "
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94 | "and the --split-quantile (-Q) options. If a split sequence is defined as "
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95 | "-S 1 -S 2 -S 1 the events are split by 1:2:1 in this sequence order. If "
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96 | "quantiles are given as -Q 0.5 -Q 0.6, the first tree will contain 50% of "
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97 | "the second one 10% and the third one 40%. The corresponding seed value can "
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98 | "be set with --seed.\n"
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99 | "\n"
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100 | "In case of success, 0 is returned, a value>0 otherwise.\n"
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101 | "\n"
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102 | "Usage: csv2root input.csv [output.root] [-t tree] [-u] [-f] [-n] [-vN] [-cN]\n"
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103 | "\n"
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104 | ;
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105 | cout << endl;
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106 | }
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107 |
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108 | /*
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109 | void ErrorHandlerAll(Int_t level, Bool_t abort, const char *location, const char *msg)
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110 | {
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111 | if (string(msg).substr(0,24)=="no dictionary for class ")
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112 | return;
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113 | if (string(msg).substr(0,15)=="unknown branch ")
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114 | return;
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115 |
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116 | DefaultErrorHandler(level, abort, location, msg);
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117 | }*/
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118 |
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119 |
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120 | bool AddTree(vector<TTree*> &ttree, TFile &file, const string &tree, bool update, int verbose)
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121 | {
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122 | bool found = false;
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123 |
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124 | TTree *T = 0;
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125 | if (update)
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126 | {
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127 | file.GetObject(tree.c_str(), T);
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128 | if (T)
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129 | {
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130 | ttree.emplace_back(T);
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131 | found = true;
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132 | if (verbose>0)
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133 | cout << "Updating tree: " << tree << endl;
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134 | }
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135 | }
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136 | if (!T)
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137 | ttree.emplace_back(new TTree(tree.c_str(), "csv2root"));
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138 |
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139 | return found;
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140 | }
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141 |
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142 | int main(int argc, const char* argv[])
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143 | {
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144 | Time start;
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145 |
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146 | gROOT->SetBatch();
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147 | //SetErrorHandler(ErrorHandlerAll);
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148 |
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149 | Configuration conf(argv[0]);
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150 | conf.SetPrintUsage(PrintUsage);
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151 | SetupConfiguration(conf);
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152 |
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153 | if (!conf.DoParse(argc, argv))
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154 | return 127;
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155 |
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156 | // ----------------------------- Evaluate options --------------------------
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157 | const string file = conf.Get<string>("file");
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158 | const string tree = conf.Get<string>("tree");
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159 |
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160 | const bool force = conf.Get<bool>("force");
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161 | const bool update = conf.Get<bool>("update");
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162 | // const bool dryrun = conf.Get<bool>("dry-run");
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163 | const bool noheader = conf.Get<bool>("no-header");
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164 |
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165 | const uint16_t verbose = conf.Get<uint16_t>("verbose");
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166 | // const int64_t first = conf.Get<int64_t>("first");
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167 | // const int64_t max = conf.Get<int64_t>("max");
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168 |
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169 | const uint16_t compression = conf.Get<uint16_t>("compression");
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170 |
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171 | string out = conf.Get<string>("out");
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172 | if (out.empty())
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173 | {
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174 | out = file;
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175 | const auto p = out.find_last_of('.');
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176 | if (p!=string::npos)
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177 | out = string(out.substr(0, p))+".root";
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178 | }
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179 |
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180 | // ----------------------------- Setup splitting ---------------------------
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181 |
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182 | vector<uint16_t> split_seq = conf.Vec<uint16_t>("split-sequence");
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183 | vector<double> split_quant = conf.Vec<double>("split-quantile");
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184 |
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185 | if (!split_seq.empty() && !split_quant.empty())
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186 | throw runtime_error("Only splitting by --split-sequence or --split-quantile is allowed.");
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187 |
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188 | const size_t num_split = split_seq.size()+split_quant.size()==0 ? 0 :
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189 | ::max(split_seq.size(), split_quant.size()+1);
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190 |
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191 | map<size_t, size_t> split_lut;
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192 | for (size_t i=0; i<split_seq.size(); i++)
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193 | {
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194 | const size_t sz = split_lut.size();
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195 | for (size_t j=0; j<split_seq[i]; j++)
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196 | split_lut.emplace(j+sz, i);
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197 | }
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198 |
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199 | for (size_t i=0; i<split_quant.size(); i++)
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200 | if (split_quant[i]<0 || split_quant[i]>=1)
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201 | throw runtime_error("Splitting quantiles must be in the range [0;1)");
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202 |
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203 | for (size_t i=1; i<split_quant.size(); i++)
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204 | {
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205 | if (split_quant[i]<=split_quant[i-1])
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206 | throw runtime_error("Splitting quantiles must be in increasing order.");
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207 | }
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208 |
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209 | // -------------------------------------------------------------------------
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210 |
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211 | const uniform_real_distribution<double> distribution(0,1);
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212 | mt19937_64 generator;
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213 | generator.seed(conf.Get<uint64_t>("seed"));
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214 | auto rndm = bind(distribution, generator);
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215 |
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216 | // -------------------------------------------------------------------------
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217 |
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218 | if (verbose>0)
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219 | {
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220 | cout << "\n-------------------------- Evaluating input ------------------------\n";
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221 | cout << "Start Time: " << Time::sql << Time(Time::local) << endl;
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222 | }
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223 |
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224 |
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225 | // -------------------------------------------------------------------------
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226 |
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227 | cout << "Reading from '" << file << "'.\n";
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228 |
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229 | ifstream fin(file.c_str());
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230 | if (!fin.good())
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231 | {
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232 | cerr << file << ": " << strerror(errno) << endl;
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233 | return 1;
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234 | }
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235 |
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236 | TString buf;
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237 | buf.ReadLine(fin);
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238 | if (!fin)
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239 | {
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240 | cerr << file << ": " << strerror(errno) << endl;
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241 | return 2;
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242 | }
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243 |
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244 | buf = buf.Strip(TString::kBoth);
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245 | TObjArray *title = buf.Tokenize(" ");
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246 | if (title->GetEntries()==0)
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247 | {
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248 | cerr << "First line empty." << endl;
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249 | return 3;
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250 | }
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251 |
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252 | if (title->At(0)->GetName()[0]=='#')
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253 | title->RemoveAt(0);
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254 |
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255 | const auto numcol = title->GetEntries();
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256 |
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257 | if (verbose>0)
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258 | cout << "Found " << numcol << " columns." << endl;
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259 |
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260 | if (noheader)
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261 | {
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262 | fin.seekg(0);
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263 | if (verbose>0)
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264 | cout << "No header line interpreted." << endl;
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265 | }
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266 |
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267 | // -------------------------------------------------------------------------
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268 |
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269 | TString path(out.c_str());
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270 | gSystem->ExpandPathName(path);
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271 |
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272 | // if (!dryrun)
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273 | {
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274 | FileStat_t stat;
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275 | const Int_t exist = !gSystem->GetPathInfo(path, stat);
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276 | const Bool_t _write = !gSystem->AccessPathName(path, kWritePermission) && R_ISREG(stat.fMode);
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277 |
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278 | if ((update && !exist) || (update && exist && !_write) || (force && exist && !_write))
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279 | {
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280 | cerr << "File '" << path << "' is not writable." << endl;
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281 | return 4;
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282 | }
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283 |
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284 | if (!update && !force && exist)
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285 | {
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286 | cerr << "File '" << path << "' already exists." << endl;
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287 | return 5;
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288 | }
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289 | }
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290 |
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291 | TFile tfile(path, update?"UPDATE":(force?"RECREATE":"CREATE"), file.c_str(), compression);
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292 | if (tfile.IsZombie())
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293 | {
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294 | cerr << "Opening file '" << path << "' failed." << endl;
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295 | return 6;
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296 | }
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297 |
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298 | if (verbose>0)
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299 | {
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300 | cout << "Opened root file '" << path << "'.\n";
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301 | cout << "Writing to tree: " << tree << ".\n";
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302 | }
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303 |
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304 | // -------------------- Configure branches of TTree ------------------------
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305 | vector<TTree*> ttree;
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306 |
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307 | size_t entries = 0;
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308 | if (num_split==0)
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309 | {
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310 | if (AddTree(ttree, tfile, tree, update, verbose))
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311 | {
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312 | entries = ttree[0]->GetEntries();
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313 | if (verbose>0)
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314 | cout << "Tree has " << entries << " entries." << endl;
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315 | }
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316 | }
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317 | else
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318 | {
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319 | bool found = false;
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320 | for (size_t i=0; i<num_split; i++)
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321 | found |= AddTree(ttree, tfile, tree+"["+to_string(i)+"]", update, verbose);
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322 |
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323 | if (found && update)
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324 | {
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325 | cerr << "Trees can not be updated in split mode, only files!" << endl;
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326 | return 7;
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327 | }
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328 | }
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329 |
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330 | vector<float> vec(numcol);
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331 | for (int i=0; i<numcol; i++)
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332 | {
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333 | string col = noheader ? Tools::Form("col%d", i) : title->At(i)->GetName();
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334 |
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335 | boost::regex rexpr(":");
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336 | col = boost::regex_replace(col, rexpr, "");
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337 |
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338 | if (verbose>1)
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339 | cout << "Column: " << col << '\n';
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340 |
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341 | for (auto it=ttree.begin(); it!=ttree.end(); it++)
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342 | it[0]->Branch(col.c_str(), vec.data()+i);
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343 | }
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344 |
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345 | delete title;
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346 |
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347 | // -------------------------------------------------------------------------
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348 |
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349 | size_t line = 0;
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350 | size_t valid = 0;
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351 |
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352 | while (1)
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353 | {
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354 | buf.ReadLine(fin);
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355 | if (!fin)
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356 | break;
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357 |
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358 | line++;
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359 |
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360 | buf = buf.Strip(TString::kBoth);
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361 | if (buf.IsNull() || buf[0]=='#')
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362 | continue;
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363 |
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364 | valid++;
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365 |
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366 | TObjArray *arr = buf.Tokenize(" ");
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367 | if (arr->GetEntries()!=numcol)
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368 | {
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369 | cerr << "Column count mismatch in line " << line+1 << "!" << endl;
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370 | return 7;
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371 | }
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372 |
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373 | for (int i=0; i<numcol; i++)
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374 | {
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375 | try
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376 | {
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377 | vec[i] = stof(arr->At(i)->GetName());
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378 | }
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379 | catch (const exception &e)
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380 | {
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381 | cerr << "Conversion of '" << arr->At(i)->GetName() << "' failed!" << endl;
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382 | return 8;
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383 | }
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384 | }
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385 |
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386 | delete arr;
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387 |
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388 |
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389 | size_t index = 0;
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390 | if (!split_lut.empty())
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391 | index = split_lut[line % split_lut.size()];
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392 | if (!split_quant.empty())
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393 | {
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394 | const float r = rndm();
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395 | for (; r>=split_quant[index]; index++)
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396 | if (index==split_quant.size())
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397 | break;
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398 | }
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399 |
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400 | ttree[index]->Fill();
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401 | }
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402 |
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403 | if (verbose>0)
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404 | {
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405 | cout << valid << " data rows found in " << line << " lines (excl. title)." << endl;
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406 | if (!update || !entries)
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407 | {
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408 | for (size_t i=0; i<ttree.size(); i++)
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409 | cout << ttree[i]->GetEntries() << " rows filled into tree #" << i << "." << endl;
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410 | }
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411 | }
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412 |
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413 | if (entries && entries!=line)
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414 | cerr << "\nWARNING - Number of updated entries does not match number of entries in tree!\n" << endl;
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415 |
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416 | for (auto it=ttree.begin(); it!=ttree.end(); it++)
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417 | (*it)->Write("", TObject::kOverwrite);
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418 | tfile.Close();
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419 |
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420 | if (verbose>0)
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421 | {
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422 | const auto sec = Time().UnixTime()-start.UnixTime();
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423 |
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424 | cout << Tools::Scientific(tfile.GetSize()) << "B written to disk.\n";
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425 | cout << "File closed.\n";
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426 | cout << "Execution time: " << sec << "s ";
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427 | cout << "(" << Tools::Fractional(sec/line) << "s/row)\n";
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428 | cout << "--------------------------------------------------------------" << endl;
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429 | }
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430 |
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431 | return 0;
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432 | }
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