tools.hxx

/*
Copyright (c) 2015, Florian Sittel (www.lettis.net)
All rights reserved.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

#include "tools.hpp"

#include <iostream>
#include <fstream>
#include <sstream>
#include <iterator>
#include <map>

namespace Clustering {
namespace Tools {

template <typename NUM>
std::tuple<NUM*, std::size_t, std::size_t>
read_coords(std::string filename, std::vector<std::size_t> usecols) {
  std::size_t n_rows=0;
  std::size_t n_cols=0;
  std::size_t n_cols_used=0;

  std::ifstream ifs(filename);
  {
    // determine n_cols
    std::string linebuf;
    while (linebuf.empty() && ifs.good()) {
      std::getline(ifs, linebuf);
    }
    std::stringstream ss(linebuf);
    n_cols = std::distance(std::istream_iterator<std::string>(ss),
                           std::istream_iterator<std::string>());
    // go back to beginning to read complete file
    ifs.seekg(0);
    // determine n_rows
    while (ifs.good()) {
      std::getline(ifs, linebuf);
      if ( ! linebuf.empty()) {
        ++n_rows;
      }
    }
    // go back again
    ifs.clear();
    ifs.seekg(0, std::ios::beg);
  }
  std::map<std::size_t, bool> col_used;
  if (usecols.size() == 0) {
    // use all columns
    n_cols_used = n_cols;
    for (std::size_t i=0; i < n_cols; ++i) {
      col_used[i] = true;
    }
  } else {
    // use only defined columns
    n_cols_used = usecols.size();
    for (std::size_t i=0; i < n_cols; ++i) {
      col_used[i] = false;
    }
    for (std::size_t i: usecols) {
      col_used[i] = true;
    }
  }
  // allocate memory
  // DC_MEM_ALIGNMENT is defined during cmake and
  // set depending on usage of SSE2, SSE4_1, AVX or Xeon Phi
  NUM* coords = (NUM*) _mm_malloc(sizeof(NUM)*n_rows*n_cols_used, DC_MEM_ALIGNMENT);
  ASSUME_ALIGNED(coords);
  // read data
  for (std::size_t cur_row = 0; cur_row < n_rows; ++cur_row) {
    std::size_t cur_col = 0;
    for (std::size_t i=0; i < n_cols; ++i) {
      NUM buf;
      ifs >> buf;
      if (col_used[i]) {
        coords[cur_row*n_cols_used + cur_col] = buf;
        ++cur_col;
      }
    }
  }
  return std::make_tuple(coords, n_rows, n_cols_used);
}


template <typename NUM>
void
free_coords(NUM* coords) {
  _mm_free(coords);
}

template <typename KEY, typename VAL>
void
write_map(std::string filename, std::map<KEY, VAL> mapping) {
  std::ofstream ofs(filename);
  if (ofs.fail()) {
    std::cerr << "error: cannot open file '" << filename << "' for writing." << std::endl;
    exit(EXIT_FAILURE);
  }
  for (auto key_val: mapping) {
    ofs << key_val.first << " " << key_val.second << "\n";
  }
}

template <typename NUM>
std::vector<NUM>
read_single_column(std::string filename) {
  std::vector<NUM> dat;
  std::ifstream ifs(filename);
  if (ifs.fail()) {
    std::cerr << "error: cannot open file '" << filename << "'" << std::endl;
    exit(EXIT_FAILURE);
  } else {
    while (ifs.good()) {
      NUM buf;
      ifs >> buf;
      if ( ! ifs.fail()) {
        dat.push_back(buf);
      }
    }
  }
  return dat;
}


template <typename NUM>
void
write_single_column(std::string filename, std::vector<NUM> dat, bool with_scientific_format) {
  std::ofstream ofs(filename);
  if (ofs.fail()) {
    std::cerr << "error: cannot open file '" << filename << "' for writing." << std::endl;
    exit(EXIT_FAILURE);
  }
  if (with_scientific_format) {
    ofs << std::scientific;
  }
  for (NUM i: dat) {
    ofs << i << "\n";
  }
}

template <typename NUM>
NUM
string_to_num(const std::string &s) {
  std::stringstream ss(s);
  NUM buf;
  ss >> buf;
  return buf;
}

} // end namespace Tools
} // end namespace Clustering