NEURON interface to GAUL (Neymotin and Lytton)

Accession:102464
This interface allows the use of genetic algorithms for optimization and search in high-dimensional spaces from within the NEURON environment. It includes converted .c,.h files from GAUL wrapped in proper MOD file syntax as well as MOD code interfacing to the library. It also comes with hoc utilitiy functions to make it easier to use the GA.
Tool Information (Click on a link to find other Tools with that property)
Tool Type: Control Simulations;
Simulation Environment: NEURON;
\
neuron_gaul_2
gaul
readme.txt
compatibility.mod
ga_bitstring.mod
ga_chromo.mod
ga_climbing.mod
ga_compare.mod
ga_core.mod
ga_crossover.mod
ga_de.mod
ga_deterministiccrowding.mod
ga_gradient.mod
ga_hoc.mod
ga_intrinsics.mod
ga_io.mod
ga_mutate.mod
ga_optim.mod
ga_qsort.mod
ga_randomsearch.mod
ga_rank.mod
ga_replace.mod
ga_sa.mod
ga_seed.mod
ga_select.mod
ga_similarity.mod
ga_simplex.mod
ga_stats.mod
ga_systematicsearch.mod
ga_tabu.mod
ga_utility.mod
linkedlist.mod
log_util.mod
memory_chunks.mod
memory_util.mod
nn_util.mod
random_util.mod
avltree.mod
table_util.mod
timer_util.mod
vecst.mod
mosinit.hoc
ga_utils.hoc
init.hoc
declist.hoc
setup.hoc
decvec.hoc
ga_test.hoc
gaul.h
xtmp
                            
:$Id: ga_compare.mod,v 1.1 2006/12/22 16:49:51 samn Exp $
NEURON {
  SUFFIX nothing
}

VERBATIM

/**********************************************************************
  ga_compare.c
 **********************************************************************

  ga_compare - Entity comparison routines.
  Copyright   2003-2004, Stewart Adcock <stewart@linux-domain.com>
  All rights reserved.

  The latest version of this program should be available at:
  http://gaul.sourceforge.net/

  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version.  Alternatively, if your project
  is incompatible with the GPL, I will probably agree to requests
  for permission to use the terms of any other license.

  This program is distributed in the hope that it will be useful, but
  WITHOUT ANY WARRANTY WHATSOEVER.

  A full copy of the GNU General Public License should be in the file
  "COPYING" provided with this distribution; if not, see:
  http://www.gnu.org/

 **********************************************************************

  Synopsis:     Routines for comparing entities.

		These routines return a distance between two entities.

 **********************************************************************/

#include "gaul/ga_core.h"

/**********************************************************************
  ga_compare_char_hamming()
  synopsis:	Compares two char-array genomes and returns their
		hamming distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Hamming distance between two entities' genomes.
  last updated:	21 May 2003
 **********************************************************************/

double ga_compare_char_hamming(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;		/* Loop variable over all chromosomes, alleles. */
  int		dist=0;		/* Genomic distance. */
  char		*a, *b;		/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (char *)(alpha->chromosome[i]);
    b = (char *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      dist += abs((int)a[j]-b[j]);
      }
    }

  return (double) dist;
  }


/**********************************************************************
  ga_compare_char_euclidean()
  synopsis:	Compares two char-array genomes and returns their
		euclidean distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Euclidean distance between two entities' genomes.
  last updated:	25 Aug 2004
 **********************************************************************/

double ga_compare_char_euclidean(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;			/* Loop variable over all chromosomes, alleles. */
  double	sqdistsum=0.0;		/* Genomic distance. */
  char		*a, *b;			/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (char *)(alpha->chromosome[i]);
    b = (char *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      sqdistsum += SQU((int)a[j]-b[j]);
      }
    }

  return sqrt(sqdistsum);
  }


/**********************************************************************
  ga_compare_integer_hamming()
  synopsis:	Compares two integer-array genomes and returns their
		hamming distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Hamming distance between two entities' genomes.
  last updated:	25 Aug 2004
 **********************************************************************/

double ga_compare_integer_hamming(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;		/* Loop variable over all chromosomes, alleles. */
  int		dist=0;		/* Genomic distance. */
  int		*a, *b;		/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (int *)(alpha->chromosome[i]);
    b = (int *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      dist += abs(a[j]-b[j]);
      }
    }

  return (double) dist;
  }


/**********************************************************************
  ga_compare_integer_euclidean()
  synopsis:	Compares two integer-array genomes and returns their
		euclidean distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Euclidean distance between two entities' genomes.
  last updated:	25 Aug 2004
 **********************************************************************/

double ga_compare_integer_euclidean(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;			/* Loop variable over all chromosomes, alleles. */
  double	sqdistsum=0.0;		/* Genomic distance. */
  int		*a, *b;			/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (int *)(alpha->chromosome[i]);
    b = (int *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      sqdistsum += SQU(a[j]-b[j]);
      }
    }

  return sqrt(sqdistsum);
  }


/**********************************************************************
  ga_compare_double_hamming()
  synopsis:	Compares two double-array genomes and returns their
		hamming distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Hamming distance between two entities' genomes.
  last updated:	25 Aug 2004
 **********************************************************************/

double ga_compare_double_hamming(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;		/* Loop variable over all chromosomes, alleles. */
  double	dist=0.0;	/* Genomic distance. */
  double	*a, *b;		/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (double *)(alpha->chromosome[i]);
    b = (double *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      dist += ABS(a[j]-b[j]);
      }
    }

  return dist;
  }


/**********************************************************************
  ga_compare_double_euclidean()
  synopsis:	Compares two double-array genomes and returns their
		euclidean distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Euclidean distance between two entities' genomes.
  last updated:	25 Aug 2004
 **********************************************************************/

double ga_compare_double_euclidean(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;			/* Loop variable over all chromosomes, alleles. */
  double	sqdistsum=0.0;		/* Genomic distance. */
  double	*a, *b;			/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (double *)(alpha->chromosome[i]);
    b = (double *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      sqdistsum += SQU(a[j]-b[j]);
      }
    }

  return sqrt(sqdistsum);
  }


/**********************************************************************
  ga_compare_boolean_hamming()
  synopsis:	Compares two boolean-array genomes and returns their
		hamming distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Hamming distance between two entities' genomes.
  last updated:	25 Aug 2004
 **********************************************************************/

double ga_compare_boolean_hamming(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;		/* Loop variable over all chromosomes, alleles. */
  int		dist=0;		/* Genomic distance. */
  boolean	*a, *b;		/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (boolean *)(alpha->chromosome[i]);
    b = (boolean *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      dist += (a[j]!=b[j]);
      }
    }

  return (double) dist;
  }


/**********************************************************************
  ga_compare_boolean_euclidean()
  synopsis:	Compares two boolean-array genomes and returns their
		euclidean distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Euclidean distance between two entities' genomes.
  last updated:	25 Aug 2004
 **********************************************************************/

double ga_compare_boolean_euclidean(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;			/* Loop variable over all chromosomes, alleles. */
  double	sqdistsum=0.0;		/* Genomic distance. */
  boolean	*a, *b;			/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (boolean *)(alpha->chromosome[i]);
    b = (boolean *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      sqdistsum += (a[j]!=b[j]);
      }
    }

  return sqrt(sqdistsum);
  }


/**********************************************************************
  ga_compare_bitstring_hamming()
  synopsis:	Compares two bitstring-array genomes and returns their
		hamming distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Hamming distance between two entities' genomes.
  last updated:	25 Aug 2004
 **********************************************************************/

double ga_compare_bitstring_hamming(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;		/* Loop variable over all chromosomes, alleles. */
  int		dist=0;		/* Genomic distance. */
  byte		*a, *b;		/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (byte *)(alpha->chromosome[i]);
    b = (byte *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      dist += (ga_bit_get(a,j)!=ga_bit_get(b,j));
      }
    }

  return (double) dist;
  }


/**********************************************************************
  ga_compare_bitstring_euclidean()
  synopsis:	Compares two bitstring-array genomes and returns their
		euclidean distance.
  parameters:	population *pop	Population of entities (you may use
			differing populations if they are "compatible")
		entity *alpha	Test entity.
		entity *beta	Test entity.
  return:	Returns Euclidean distance between two entities' genomes.
  last updated:	25 Aug 2004
 **********************************************************************/

double ga_compare_bitstring_euclidean(population *pop, entity *alpha, entity *beta)
  {
  int		i,j;			/* Loop variable over all chromosomes, alleles. */
  double	sqdistsum=0.0;		/* Genomic distance. */
  byte		*a, *b;			/* Pointers to chromosomes. */

  /* Checks */
  if (!alpha || !beta) die("Null pointer to entity structure passed");

  for (i=0; i<pop->num_chromosomes; i++)
    {
    a = (byte *)(alpha->chromosome[i]);
    b = (byte *)(beta->chromosome[i]);

    for (j=0; j<pop->len_chromosomes; j++)
      {
      sqdistsum += (ga_bit_get(a,j)!=ga_bit_get(b,j));
      }
    }

  return sqrt(sqdistsum);
  }


ENDVERBATIM