/// <summary>
/// Mutates a gene by applying boundary mutation.
/// </summary>
/// <param name="gene">An IntegerGene or DoubleGene to be mutated.</param>
/// <returns></returns>
public static Gene Mutate(Gene gene)
{
if (gene is IntegerGene)
{
IntegerGene ig = (IntegerGene)gene;
if (genX.Utils.Rand.NextDouble() < 0.5)
{
ig.Value = ig.Descriptor.MaxValue;
}
else
{
ig.Value = ig.Descriptor.MinValue;
}
}
else if (gene is DoubleGene)
{
DoubleGene dg = (DoubleGene)gene;
if (genX.Utils.Rand.NextDouble() < 0.5)
{
dg.Value = dg.Descriptor.MaxValue;
}
else
{
dg.Value = dg.Descriptor.MinValue;
}
}
else
{
throw new ArgumentException(
"Boundary mutation may only apply to IntegerGene or DoubleGene genes.",
"gene"
);
}
return(gene);
}
void Initialize(bool symmetricalBorders)
{
DoubleGene gene;
if (symmetricalBorders)
{
gene = new DoubleGene("OutputBorder", 0, 1);
gene.Value = 1;
geneList.Add(gene);
}
else
{
gene = new DoubleGene("OutputBorder1", -1, 1);
gene.Value = -1;
geneList.Add(gene);
gene = new DoubleGene("OutputBorder2", -1, 1);
gene.Value = 1;
geneList.Add(gene);
}
gene = new DoubleGene("P", 0, 1);
gene.Value = 1;
gene.IsMutable = false;
geneList.Add(gene);
GenesHasChanged();
}
/// <summary>
/// Mutates a gene by bitwise mutation.
/// </summary>
/// <param name="gene"></param>
/// <returns></returns>
public static Gene Mutate(Gene gene)
{
if (gene is BinaryGene)
{
BinaryGene g = (BinaryGene)gene.Clone();
g.Value = !(BinaryGene)gene;
return(g);
}
else if (gene is DoubleGene)
{
DoubleGene g = (DoubleGene)gene.Clone();
byte[] bytes = BitConverter.GetBytes(g.Value);
BitArray ba = new BitArray(bytes);
int p = Utils.Rand.Next(ba.Length);
ba.Set(p, !ba[p]);
ba.CopyTo(bytes, 0);
g.Value = BitConverter.ToDouble(bytes, 0);
return(g);
}
else if (gene is IntegerGene)
{
IntegerGene g = (IntegerGene)gene.Clone();
byte[] bytes = BitConverter.GetBytes(g.Value);
BitArray ba = new BitArray(bytes);
int p = Utils.Rand.Next(ba.Length);
ba.Set(p, !ba[p]);
ba.CopyTo(bytes, 0);
g.Value = BitConverter.ToInt32(bytes, 0);
return(g);
}
return((Gene)gene.Clone()); // default
}
public UniformCrossover()
{
var gene = new DoubleGene("CrossoverRate", 0, 1);
gene.Value = 0.1;
geneList.Add(gene);
}
public static EditDoubleGeneForm ShowDialogue(Window window, DoubleGene _gene, CloseEvent closeFunction = null, string category = null, ISkinFile file = null)
{
var form = new EditDoubleGeneForm();
form.Initialize(_gene, closeFunction, "Edit Gene", true, true, category, file);
form.Show(window);
return(form);
}
/// <summary>
/// Decode the genome to a network.
/// </summary>
public override void Decode()
{
double[] net = new double[networkChromosome.Genes.Count];
for (int i = 0; i < net.Length; i++)
{
DoubleGene gene = (DoubleGene)networkChromosome.Genes[i];
net[i] = gene.Value;
}
NetworkCODEC.ArrayToNetwork(net, (BasicNetwork)Organism);
}
/// <summary>
/// Perform a perturb mutation on the specified chromosome.
/// </summary>
/// <param name="chromosome">The chromosome to mutate.</param>
public void PerformMutation(Chromosome chromosome)
{
foreach (IGene gene in chromosome.Genes)
{
if (gene is DoubleGene)
{
DoubleGene doubleGene = (DoubleGene)gene;
double value = doubleGene.Value;
value += (perturbAmount - (ThreadSafeRandom.NextDouble()) * perturbAmount * 2);
doubleGene.Value = value;
}
}
}
/// <summary>
/// Perform a perturb mutation on the specified chromosome.
/// </summary>
/// <param name="chromosome">The chromosome to mutate.</param>
public void PerformMutation(Chromosome chromosome, GATracker.MatedElement mutatedElement, int childIndex)
{
bool usePertubAmount1 = ThreadSafeRandom.NextDouble() <= percentageUsePerturbAmount1;
foreach (IGene gene in chromosome.Genes)
{
if (gene is DoubleGene)
{
if (usePertubAmount1)
{
if (ThreadSafeRandom.NextDouble() < percentageGenesToPerturb1)
{
DoubleGene doubleGene = (DoubleGene)gene;
double value = doubleGene.Value;
double peturbAmount = (perturbAmount1 - (ThreadSafeRandom.NextDouble()) * perturbAmount1 * 2);
mutatedElement.AddChildMutation(new GATracker.MutationRecord(perturbAmount1, peturbAmount), childIndex);
value += peturbAmount;
doubleGene.Value = value;
}
}
else
{
//if (ThreadSafeRandom.NextDouble() < percentageGenesToPerturb1)
//{
// DoubleGene doubleGene = (DoubleGene)gene;
// double value = doubleGene.Value;
// double peturbAmount = (perturbAmount1 - (ThreadSafeRandom.NextDouble()) * perturbAmount1 * 2);
// mutatedElement.AddChildMutation(new GATracker.MutationRecord(perturbAmount1, peturbAmount), childIndex);
// value += peturbAmount;
// doubleGene.Value = value;
//}
if (ThreadSafeRandom.NextDouble() < percentageGenesToPerturb2)
{
DoubleGene doubleGene = (DoubleGene)gene;
double value = doubleGene.Value;
double peturbAmount = (perturbAmount2 - (ThreadSafeRandom.NextDouble()) * perturbAmount2 * 2);
mutatedElement.AddChildMutation(new GATracker.MutationRecord(perturbAmount2, peturbAmount), childIndex);
value += peturbAmount;
doubleGene.Value = value;
}
}
}
}
}
/// <summary>
/// Construct a neural network genome.
/// </summary>
/// <param name="nga">The neural genetic algorithm.</param>
/// <param name="network">The network.</param>
public NeuralGenome(NeuralGeneticAlgorithm nga, BasicNetwork network)
: base(nga.Helper)
{
this.Organism = network;
this.networkChromosome = new Chromosome();
// create an array of "double genes"
int size = network.Structure.CalculateSize();
for (int i = 0; i < size; i++)
{
IGene gene = new DoubleGene();
this.networkChromosome.Genes.Add(gene);
}
this.Chromosomes.Add(this.networkChromosome);
Encode();
}
/// <summary>
/// Construct a neural genome.
/// </summary>
///
/// <param name="network">The network to use.</param>
public NeuralGenome(BasicNetwork network)
{
Organism = network;
_networkChromosome = new Chromosome();
// create an array of "double genes"
int size = network.Structure.CalculateSize();
for (int i = 0; i < size; i++)
{
IGene gene = new DoubleGene();
_networkChromosome.Genes.Add(gene);
}
Chromosomes.Add(_networkChromosome);
Encode();
}
protected static int GetIntFromGene(DoubleGene gene, int min, int max)
{
return(min + (int)Math.Round((max - min) * gene.Value, 0));
}
protected static int GetIntFromGene(DoubleGene gene, int max)
{
return(GetIntFromGene(gene, 0, max));
}
public void Initialize(DoubleGene _gene, CloseEvent closeFunction = null, string title = null, bool resizable = false, bool isDialog = true, string category = null, ISkinFile file = null)
{
Result = _gene;
base.Initialize(closeFunction, title, resizable, isDialog, category, file);
}
public override void AddedToContainer()
{
base.AddedToContainer();
CloseButtonOn = false;
columnListBox = new ColumnListBox();
columnListBox.Initialize(7);
AddDrawBox(columnListBox);
columnListBox.SetIntOrStringSort(true, false, true, true, true, true, false);
columnListBox.SetColumnName(0, "Order");
columnListBox.SetColumnName(1, "Name");
columnListBox.SetColumnName(2, "ID");
columnListBox.SetColumnName(3, "Value");
columnListBox.SetColumnName(4, "Min");
columnListBox.SetColumnName(5, "Max");
columnListBox.SetColumnName(6, "IsMutable");
columnListBox.Width = 200;
columnListBox.Height = 200;
columnListBox.ItemDoubleClicked += delegate(object sender, ColumnListBox.ListBoxRow item, int index)
{
int n = 0;
foreach (var g in geneList)
{
if (g.ID == (uint)item.Values[2])
{
break;
}
n++;
}
EditDoubleGeneForm.ShowDialogue(Parent, geneList[n], delegate(object _sender)
{
geneList[n] = ((EditDoubleGeneForm)_sender).Result;
ReloadListBox();
});
};
ReloadListBox();
var moveUpButton = new ResizableButton();
moveUpButton.Initialize();
AddDrawBox(moveUpButton);
moveUpButton.Title = "Move Up";
moveUpButton.FitToText();
Push.ToTheBottomSideOf(moveUpButton, columnListBox, 3, Push.VerticalAlign.Left);
moveUpButton.Width = 200;
moveUpButton.Click += delegate(object sender)
{
if (columnListBox.SelectedRowIndex < 1)
{
return;
}
int index = columnListBox.SelectedRowIndex;
var selected = geneList[index];
var upper = geneList[index - 1];
geneList[index - 1] = selected;
geneList[index] = upper;
ReloadListBox();
columnListBox.SelectedRowIndex = index - 1;
};
var moveDownButton = new ResizableButton();
moveDownButton.Initialize();
AddDrawBox(moveDownButton);
moveDownButton.Title = "Move Down";
moveDownButton.FitToText();
Push.ToTheBottomSideOf(moveDownButton, moveUpButton, 3, Push.VerticalAlign.Left);
moveDownButton.Width = 200;
moveDownButton.Click += delegate(object sender)
{
if (columnListBox.SelectedRowIndex == -1 ||
columnListBox.SelectedRowIndex == columnListBox.Values.Count - 1)
{
return;
}
int index = columnListBox.SelectedRowIndex;
var selected = geneList[index];
var lower = geneList[index + 1];
geneList[index + 1] = selected;
geneList[index] = lower;
ReloadListBox();
columnListBox.SelectedRowIndex = index + 1;
};
var createGeneButton = new ResizableButton();
createGeneButton.Initialize();
AddDrawBox(createGeneButton);
createGeneButton.Title = "Create New Gene";
createGeneButton.FitToText();
Push.ToTheBottomSideOf(createGeneButton, moveDownButton, 3, Push.VerticalAlign.Left);
createGeneButton.Width = 200;
createGeneButton.Click += delegate(object sender)
{
var dGene = new DoubleGene();
dGene.SetMinMaxValue(0, 1, 0);
dGene.IsMutable = true;
EditDoubleGeneForm.ShowDialogue(Parent, dGene, delegate(object _sender)
{
geneList.Add(((EditDoubleGeneForm)_sender).Result);
ReloadListBox();
});
};
var deleteGeneButton = new ResizableButton();
deleteGeneButton.Initialize();
AddDrawBox(deleteGeneButton);
deleteGeneButton.Title = "Delete Gene";
deleteGeneButton.FitToText();
Push.ToTheBottomSideOf(deleteGeneButton, createGeneButton, 3, Push.VerticalAlign.Left);
deleteGeneButton.Width = 200;
deleteGeneButton.Click += delegate(object sender)
{
if (columnListBox.SelectedRow != null)
{
var findID = (uint)columnListBox.SelectedRow.Values[2];
int n = 0;
foreach (var g in geneList)
{
if (g.ID == findID)
{
geneList.RemoveAt(n);
ReloadListBox();
break;
}
n++;
}
}
};
var okButton = new ResizableButton();
okButton.Initialize();
AddDrawBox(okButton);
okButton.Title = "OK";
okButton.FitToText();
Push.ToTheBottomSideOf(okButton, deleteGeneButton, 3, Push.VerticalAlign.Left);
okButton.Width = 200;
okButton.Click += delegate(object sender)
{
Close();
};
Wrap();
columnListBox.Alignment = DrawBoxAlignment.GetFull();
moveUpButton.Alignment = DrawBoxAlignment.GetLeftRightBottom();
moveDownButton.Alignment = DrawBoxAlignment.GetLeftRightBottom();
createGeneButton.Alignment = DrawBoxAlignment.GetLeftRightBottom();
deleteGeneButton.Alignment = DrawBoxAlignment.GetLeftRightBottom();
okButton.Alignment = DrawBoxAlignment.GetLeftRightBottom();
X = (Parent.Width / 2) - (Width / 2);
Y = (Parent.Height / 2) - (Height / 2);
}
public IGene GetNewGene()
{
IGene instance = new DoubleGene();
return instance;
}
/// <summary>
/// Calculates the objective based on Ackley's function.
/// </summary>
/// <param name="c"></param>
/// <returns></returns>
/// <remarks>
/// Ackley's function is given by:
///
/// F(x) = 20 + e
/// - 20*exp(-0.2*sqrt((1/n)*Sum(i=1,n) {x_i^2}))
/// - exp((1/n)*Sum(i=1,n){cos(2*pi*x_i)})
/// </remarks>
public static double AckleyMinimizationObjective(Chromosome c)
{
int n = c.Genes.Length;
DoubleGene[] x = new DoubleGene[c.Genes.Length];
Array.Copy(c.Genes, x, c.Genes.Length); // performs type casting for each element
double f;
double objective;
// Split the equation into three parts:
// F(x) =
// (a) 20 + e
// (b) - 20*exp(-0.2*sqrt((1/n)*Sum(i=1,n) {x_i^2}))
// (c) - exp((1/n)*Sum(i=1,n){cos(2*pi*x_i)})
//
// Calculate the (c) part.
//
double f_c = 0;
for (int i = 0; i < n; i++)
{
f_c += Math.Cos(2 * Math.PI * x[i].Value);
}
f_c *= (1.0 / n);
f_c = -Math.Exp(f_c);
//
// Calculate the (b) part
//
double f_b = 0;
for (int i = 0; i < n; i++)
{
double sum;
sum = (x[i].Value * x[i].Value) / n;
f_b += sum;
}
f_b = Math.Sqrt(f_b);
f_b *= -0.2;
f_b = Math.Exp(f_b);
f_b *= -20.0;
//
// Calculate the (a) part
//
double f_a = 0;
f_a = 20.0 + Math.E;
//
// Calculate the total as (a) + (b) + (c)
//
f = f_a + f_b + f_c;
objective = Math.Abs(f);
return(objective);
}
protected static double GetDoubleFromGene(DoubleGene gene, double max)
{
return(GetDoubleFromGene(gene, 0, max));
}
protected static double GetDoubleFromGene(DoubleGene gene, double min, double max)
{
return(min + (max - min) * gene.Value);
}
public override void AddedToContainer()
{
base.AddedToContainer();
CloseButtonOn = false;
var builder = new FieldBuilder();
builder.BuildSessionStart(this);
var symmetricalBordersCheckBox = builder.AddCheckBoxField("Symmetrical Borders: ");
symmetricalBordersCheckBox.Checked = sigmoid.SymmetricalBorders;
builder.AddLabelField("P: ");
var pMin = builder.AddDoubleField("Min: ");
var pMax = builder.AddDoubleField("Max: ");
var pVal = builder.AddDoubleField("Value: ");
var pMutable = builder.AddCheckBoxField("IsMutable: ");
builder.AddVerticalMargin(4);
builder.AddLabelField("Output-Border: ");
var o1Min = builder.AddDoubleField("Min: ");
var o1Max = builder.AddDoubleField("Max: ");
var o1Val = builder.AddDoubleField("Value: ");
var o1Mutable = builder.AddCheckBoxField("IsMutable: ");
var switchBox = new SwitchBox();
switchBox.Initialize();
builder.AddDrawBoxAsField(switchBox, DrawBoxAlignment.GetLeftRight());
var emptyPanel = new Panel();
emptyPanel.Initialize();
switchBox.AddDrawBox(emptyPanel, "symmetrical");
var panel = new Panel();
panel.Initialize();
var builder2 = new FieldBuilder();
builder2.BuildSessionStart(panel);
builder2.AddLabelField("Output-Border 2: ");
var o2Min = builder2.AddDoubleField("Min: ");
var o2Max = builder2.AddDoubleField("Max: ");
var o2Val = builder2.AddDoubleField("Value: ");
var o2Mutable = builder2.AddCheckBoxField("IsMutable: ");
builder2.BuildSessionEnd();
switchBox.AddDrawBox(panel, "non-symmetrical");
int largestHeight = 0;
foreach (var p in switchBox.DrawBoxList)
{
if (p.Height > largestHeight)
{
largestHeight = panel.Height;
}
}
switchBox.Width = builder.FieldWidth;
switchBox.Height = largestHeight;
if (sigmoid.GeneList.Count != 0)
{
var o1Gene = (DoubleGene)sigmoid.GeneList[0];
o1Min.Value = o1Gene.Min;
o1Max.Value = o1Gene.Max;
o1Val.Value = o1Gene.Value;
o1Mutable.Checked = o1Gene.IsMutable;
int n = 1;
if (!sigmoid.SymmetricalBorders)
{
var o2Gene = (DoubleGene)sigmoid.GeneList[n++];
o2Min.Value = o2Gene.Min;
o2Max.Value = o2Gene.Max;
o2Val.Value = o2Gene.Value;
o2Mutable.Checked = o2Gene.IsMutable;
}
var pGene = (DoubleGene)sigmoid.GeneList[n++];
pMin.Value = pGene.Min;
pMax.Value = pGene.Max;
pVal.Value = pGene.Value;
pMutable.Checked = pGene.IsMutable;
}
if (sigmoid.SymmetricalBorders)
{
switchBox.SelectDrawBoxWithKey("symmetrical");
}
else
{
switchBox.SelectDrawBoxWithKey("non-symmetrical");
}
symmetricalBordersCheckBox.CheckedChanged += delegate(object sender, bool newValue)
{
if (newValue)
{
switchBox.SelectDrawBoxWithKey("symmetrical");
}
else
{
switchBox.SelectDrawBoxWithKey("non-symmetrical");
}
};
builder.AddResizableButtonField("OK", delegate(object sender)
{
Close();
}, FieldBuilder.ResizableButtonOrientation.Left);
builder.BuildSessionEnd();
IsClosing += delegate(object sender)
{
geneList.Clear();
var _o1Gene = new DoubleGene();
_o1Gene.SetMinMaxValue(o1Min.Value, o1Max.Value, o1Val.Value);
_o1Gene.IsMutable = o1Mutable.Checked;
geneList.Add(_o1Gene);
if (!symmetricalBordersCheckBox.Checked)
{
var _o2Gene = new DoubleGene();
_o2Gene.SetMinMaxValue(o2Min.Value, o2Max.Value, o2Val.Value);
_o2Gene.IsMutable = pMutable.Checked;
geneList.Add(_o2Gene);
}
var _pGene = new DoubleGene();
_pGene.SetMinMaxValue(pMin.Value, pMax.Value, pVal.Value);
_pGene.IsMutable = pMutable.Checked;
geneList.Add(_pGene);
};
CanResizeFormVertically = false;
X = (Parent.Width / 2) - (Width / 2);
Y = (Parent.Height / 2) - (Height / 2);
}
