EnvCellSet.cpp

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/* **************************************
 *  GARP Modeling Package
 *
 * **************************************
 *
 * Copyright (c), The Center for Research, University of Kansas, 2385 Irving Hill Road, Lawrence, KS 66044-4755, USA.
 * Copyright (C), David R.B. Stockwell of Symbiotik Pty. Ltd.
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the license that is distributed with the software.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * license.txt file included with this software for more details.
 */

// EnvCellSet.cpp: implementation of the EnvCellSet class.

#include "EnvCell.h"
#include "EnvCellSet.h"
#include "Utilities.h"

// ============================================================================
EnvCellSet::EnvCellSet()
{
  intCount = 0;
  intSize = 0;
  objCells = NULL;

  histogram = NULL;

  resampled = false;
}

// ============================================================================
EnvCellSet::EnvCellSet(int size)
{ 
  intCount = 0;
  intSize = 0;
  objCells = NULL;

  histogram = NULL;

  resampled = false;

  initialize(size); 
}

// ============================================================================
EnvCellSet::~EnvCellSet()
{ 
  if (histogram)
    delete histogram;

  if (objCells != NULL)
  {
    if (!resampled)
    {
      // not resampled:
      // it is not a copy of another CellSet
      // can delete all the EnvCells
      for (int i = 0; i < intCount; i++)
      {
        // EnvCellSet takes care of EnvCell property alocation and dealocation
        // possible bug!!!
        if (objCells[i])
        {
          delete[] objCells[i]->values;
          delete objCells[i];
        }
      }
    }

    delete[] objCells;
  }
}

// ============================================================================
void EnvCellSet::resampleInPlace()
{
  int p, q;
  EnvCell * oAuxCell;

  // shuffle pointers to cells
  for (int i = 0; i < intSize; i++)
  {
    // pick two random numbers
    p = GarpUtil::randint(0, intSize - 1);
    q = GarpUtil::randint(0, intSize - 1);

    // change places between cells <p> and <q>
    oAuxCell = objCells[p];
    objCells[p] = objCells[q];
    objCells[q] = oAuxCell;
  }
}

// ============================================================================
EnvCellSet * EnvCellSet::resample()
{
  // create an EnvCellSet to hold shuffled pointers to the original set
  // it is a resampled set so the cells won't be dealocate upon destruction
  // of the resampled object
  EnvCellSet * objResampled = new EnvCellSet(intSize);
  objResampled->resampled = true;

  // point to random data
  for (int i = 0; i < intSize; i++)
    objResampled->add(objCells[GarpUtil::randint(0, intSize - 1)]);

  return objResampled;
}

// ============================================================================
void EnvCellSet::initialize(int size)
{
  intCount = 0;
  intSize = size;
  objCells = new EnvCell*[intSize];
}

// ============================================================================
int EnvCellSet::genes()
{
  if (intCount)
    return objCells[0]->size();
  else
    return 0;
}

// ============================================================================
int EnvCellSet::size()
{ 
  return intSize; 
}

// ============================================================================
int EnvCellSet::count()
{ 
  return intCount; 
}

// ============================================================================
EnvCell * EnvCellSet::get(int index)
{ 
  if (index < intCount)
    return objCells[index]; 
  else
    throw GarpException(1, "EnvCellSet::get(): index out of bounds");
}

// ============================================================================
void EnvCellSet::add(EnvCell * cell)
{ 
  if (intCount < intSize)
    objCells[intCount++] = cell; 
  else
    throw GarpException(1, "EnvCellSet::add(): cell set already full");
}

// ==========================================================================
BioclimHistogram * EnvCellSet::getBioclimHistogram()
{ return histogram; }

// ==========================================================================
void EnvCellSet::createBioclimHistogram()
{
  //EnvCell * cell;
  int i, j, nc, ng;
  BYTE pred, val;

  if (!histogram)
    histogram = new BioclimHistogram;

  histogram->reset();

  // number of genes
  ng = genes();

  // number of cells
  nc = intCount;

  // calculate occurrence of value for each gene
  for (i = 0; i < ng; i++)
  {
    // take into account the occurrence of each value for each cell in train set
    for (j = 0; j < nc; j++)
    {
      // cell = objCells[j];
      
      // get presence or absence
      pred = objCells[j]->values[0];
      val  = objCells[j]->values[i];
      histogram->matrix[pred][i][val]++;
    }
  }
}

// ============================================================================
// ============================================================================
// ============================================================================