libopenms-dev 1.11.1-5 / usr / include / OpenMS / COMPARISON / CLUSTERING / HashGrid.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: Lars Nilse $
// $Authors: Bastian Blank $
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#include <cmath>
#include <iterator>
#include <limits>

#include <boost/array.hpp>
#include <boost/functional/hash.hpp>
#include <boost/unordered/unordered_map.hpp>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/DPosition.h>

#ifndef OPENMS_COMPARISON_CLUSTERING_HASHGRID_H
#define OPENMS_COMPARISON_CLUSTERING_HASHGRID_H

namespace OpenMS
{
  /**
   * @brief Container for (2-dimensional coordinate, value) pairs.
   *
   * A hash-grid consists of hash-grid cells. The key of each cell is a pair of integers.
   * Each pair is assigned to a cell using a hash function.
   *
   * This container implements most parts of the C++ standard map interface.
   *
   * @tparam Cluster Type to be stored in the hash grid. (e.g. HierarchicalClustering::Cluster)
   */
  template <typename Cluster>
  class HashGrid
  {
public:
    /**
     * @brief Coordinate for stored pairs.
     */
    // XXX: Check is there is another type handy in OpenMS already
    typedef DPosition<2, DoubleReal> ClusterCenter;

    /**
     * @brief Index for cells.
     */
    typedef DPosition<2, Int64> CellIndex;

    /**
     * @brief Contents of a cell.
     */
    typedef typename boost::unordered_multimap<ClusterCenter, Cluster> CellContent;

    /**
     * @brief Map of (cell-index, cell-content).
     */
    typedef boost::unordered_map<CellIndex, CellContent> Grid;

    typedef typename CellContent::key_type key_type;
    typedef typename CellContent::mapped_type mapped_type;
    typedef typename CellContent::value_type value_type;

private:
    /**
     * @brief Element iterator for the hash grid.
     */
    class Iterator :
      public std::iterator<std::input_iterator_tag, value_type>
    {
private:
      friend class HashGrid;

      typedef typename Grid::iterator grid_iterator;
      typedef typename CellContent::iterator cell_iterator;

      Grid & grid_;
      grid_iterator grid_it_;
      cell_iterator cell_it_;

      // Search for next non-empty cell
      void searchNextCell_()
      {
        while (cell_it_ == grid_it_->second.end())
        {
          grid_it_++;

          // If we are at the last cell, set cell iterator to something well-known
          if (grid_it_ == grid_.end())
          {
            cell_it_ = cell_iterator();
            return;
          }

          cell_it_ = grid_it_->second.begin();
        }
      }

public:
      Iterator(Grid & grid) :
        grid_(grid), grid_it_(grid.end())
      {}

      Iterator(Grid & grid, grid_iterator grid_it, cell_iterator cell_it) :
        grid_(grid), grid_it_(grid_it), cell_it_(cell_it)
      {
        searchNextCell_();
      }

      Iterator & operator++()
      {
        ++cell_it_;
        searchNextCell_();
        return *this;
      }

      Iterator operator++(int)
      {
        Iterator ret(*this);
        operator++();
        return ret;
      }

      bool operator==(const Iterator & rhs) const
      { return grid_it_ == rhs.grid_it_ && cell_it_ == rhs.cell_it_; }

      bool operator!=(const Iterator & rhs) const
      { return !(*this == rhs); }

      value_type & operator*() const
      { return *cell_it_; }

      value_type * operator->() const
      { return &*cell_it_; }

      const CellIndex index() const
      {
        return grid_it_->first;
      }

    };

    /**
     * @brief Constant element iterator for the hash grid.
     */
    class ConstIterator :
      public std::iterator<std::input_iterator_tag, const value_type>
    {
private:
      friend class HashGrid;

      typedef typename Grid::const_iterator grid_iterator;
      typedef typename CellContent::const_iterator cell_iterator;

      const Grid & grid_;
      grid_iterator grid_it_;
      cell_iterator cell_it_;

      // Search for next non-empty cell
      void searchNextCell_()
      {
        while (cell_it_ == grid_it_->second.end())
        {
          grid_it_++;

          // If we are at the last cell, set cell iterator to something well-known
          if (grid_it_ == grid_.end())
          {
            cell_it_ = cell_iterator();
            return;
          }

          cell_it_ = grid_it_->second.begin();
        }
      }

public:
      ConstIterator(const Grid & grid) :
        grid_(grid), grid_it_(grid.end())
      {}

      ConstIterator(const Grid & grid, grid_iterator grid_it, cell_iterator cell_it) :
        grid_(grid), grid_it_(grid_it), cell_it_(cell_it)
      {
        searchNextCell_();
      }

      ConstIterator(const Iterator & it) :
        grid_(it.grid_), grid_it_(it.grid_it_), cell_it_(it.cell_it_)
      {}

      ConstIterator & operator++()
      {
        ++cell_it_;
        searchNextCell_();
        return *this;
      }

      ConstIterator operator++(int)
      {
        ConstIterator ret(*this);
        operator++();
        return ret;
      }

      bool operator==(const ConstIterator & rhs) const
      { return grid_it_ == rhs.grid_it_ && cell_it_ == rhs.cell_it_; }

      bool operator!=(const ConstIterator & rhs) const
      { return !(*this == rhs); }

      const value_type & operator*() const
      { return *cell_it_; }

      const value_type * operator->() const
      { return &*cell_it_; }

      const CellIndex index() const
      {
        return grid_it_->first;
      }

    };

public:
    typedef ConstIterator const_iterator;
    typedef Iterator iterator;
    typedef typename Grid::const_iterator const_grid_iterator;
    typedef typename Grid::iterator grid_iterator;
    typedef typename CellContent::const_iterator const_cell_iterator;
    typedef typename CellContent::iterator cell_iterator;
    typedef typename CellContent::size_type size_type;

private:
    Grid cells_;
    CellIndex grid_dimension_;

public:
    /**
     * @brief Dimension of cells.
     */
    const ClusterCenter cell_dimension;
    /**
     * @brief Upper-right corner of key space for cells.
     */
    const CellIndex & grid_dimension;

public:
    HashGrid(const ClusterCenter & cell_dimension) :
      cell_dimension(cell_dimension), grid_dimension(grid_dimension_)
    {}

    /**
     * @brief Inserts a (2-dimensional coordinate, value) pair.
     * @param v Pair to be inserted.
     * @return Iterator that points to the inserted pair.
     */
    cell_iterator insert(const value_type & v)
    {
      const CellIndex cellkey = cellindexAtClustercenter_(v.first);
      CellContent & cell = cells_[cellkey];
      updateGridDimension_(cellkey);
      return cell.insert(v);
    }

    /**
     * @brief Erases element on given iterator.
     */
    void erase(iterator pos)
    {
      CellContent & cell = pos.grid_it_->second;
      cell.erase(pos.cell_it_);
    }

    /**
     * @brief Erases elements matching the 2-dimensional coordinate.
     * @param key Key of element to be erased.
     * @return Number of elements erased.
     */
    size_type erase(const key_type & key)
    {
      const CellIndex cellkey = cellindexAtClustercenter_(key);
      try
      {
        CellContent & cell = cells_.at(cellkey);
        return cell.erase(key);
      }
      catch (std::out_of_range &) {}
      return 0;
    }

    /**
     * @brief Clears the map.
     */
    void clear() { cells_.clear(); }

    /**
     * @brief Returns iterator to first element.
     */
    iterator begin()
    {
      grid_iterator grid_it = cells_.begin();
      if (grid_it == cells_.end()) return end();

      cell_iterator cell_it = grid_it->second.begin();
      return iterator(cells_, grid_it, cell_it);
    }

    /**
     * @brief Returns iterator to first element.
     */
    const_iterator begin() const
    {
      const_grid_iterator grid_it = cells_.begin();
      if (grid_it == cells_.end()) return end();

      const_cell_iterator cell_it = grid_it->second.begin();
      return const_iterator(cells_, grid_it, cell_it);
    }

    /**
     * @brief Returns iterator to first element.
     */
    iterator end()
    {
      return iterator(cells_);
    }

    /**
     * @brief Returns iterator to first element.
     */
    const_iterator end() const
    {
      return const_iterator(cells_);
    }

    /**
     * @brief Return true if HashGrid is empty.
     */
    bool empty() const
    {
      return size() == 0;
    }

    /**
     * @brief Return number of elements.
     */
    size_type size() const
    {
      size_type ret = 0;

      for (const_grid_iterator it = grid_begin(); it != grid_end(); ++it)
      {
        ret += it->second.size();
      }

      return ret;
    }

    /**
     * @brief Returns iterator to first grid cell.
     */
    const_grid_iterator grid_begin() const { return cells_.begin(); }

    /**
     * @brief Returns iterator to on after last grid cell.
     */
    const_grid_iterator grid_end() const { return cells_.end(); }

    /**
     * @brief Returns the grid cell at given index.
     */
    const typename Grid::mapped_type & grid_at(const CellIndex & x) const { return cells_.at(x); }

    /**
     * @warning Currently needed non-const by HierarchicalClustering.
     */
    grid_iterator grid_begin() { return cells_.begin(); }
    /**
     * @warning Currently needed non-const by HierarchicalClustering.
     */
    grid_iterator grid_end() { return cells_.end(); }
    /**
     * @warning Currently needed non-const by HierarchicalClustering.
     */
    typename Grid::mapped_type & grid_at(const CellIndex & x) { return cells_.at(x); }

private:
    // XXX: Replace with proper operator
    CellIndex cellindexAtClustercenter_(const ClusterCenter & key)
    {
      CellIndex ret;
      typename CellIndex::iterator it = ret.begin();
      typename ClusterCenter::const_iterator lit = key.begin(), rit = cell_dimension.begin();
      for (; it != ret.end(); ++it, ++lit, ++rit)
      {
        DoubleReal t = std::floor(*lit / *rit);
        if (t < std::numeric_limits<Int64>::min() || t > std::numeric_limits<Int64>::max()) throw Exception::OutOfRange(__FILE__, __LINE__, __PRETTY_FUNCTION__);
        *it = static_cast<Int64>(t);
      }
      return ret;
    }

    void updateGridDimension_(const CellIndex & d)
    {
      typename CellIndex::const_iterator it_new = d.begin();
      typename CellIndex::iterator it_cur = grid_dimension_.begin();
      for (; it_new != d.end(); ++it_new, ++it_cur)
      {
        if (*it_cur < *it_new)
          *it_cur = *it_new;
      }
    }

  };

  /** Hash value for OpenMS::DPosition. */
  template <UInt N, typename T>
  std::size_t hash_value(const DPosition<N, T> & b)
  {
    boost::hash<T> hasher;
    std::size_t hash = 0;
    for (typename DPosition<N, T>::const_iterator it = b.begin(); it != b.end(); ++it)
      hash ^= hasher(*it);
    return hash;
  }

}

#endif /* OPENMS_COMPARISON_CLUSTERING_HASHGRID_H */