public override IImage <double> CloneSize(int newWidth, int newHeight)
{
IRegularGrid2D gridClone = grid.CloneSize(newWidth, newHeight);
GridImage clone = new GridImage(gridClone);
return(clone);
}
/// <summary>
/// Compute the Root Mean Square difference betweeen two grids of the same dimensions.
/// Nodes which are null in either grid will be ignored.
/// </summary>
/// <param name="otherGrid">The grid against which this grid will be compared.</param>
/// <param name="beginI">The minimumI</param>
/// <param name="endI">One beyond the maximumI (half-open range)</param>
/// <param name="beginJ">The minimumJ</param>
/// <param name="endJ">One beyond the maximumJ (half-open range)</param>
/// <returns>The Root Mean Square difference of the z values.</returns>
public double?RmsDifference(IRegularGrid2D otherGrid, int beginI, int endI, int beginJ, int endJ)
{
Debug.Assert(this.SizeI == otherGrid.SizeI);
Debug.Assert(this.SizeJ == otherGrid.SizeJ);
Debug.Assert(beginI >= 0 && beginI < SizeI);
Debug.Assert(beginJ >= 0 && beginJ < SizeJ);
Debug.Assert(endI > 0 && endI <= SizeI);
Debug.Assert(endJ > 0 && endJ <= SizeJ);
double total = 0.0;
int count = 0;
for (int i = beginI; i < endI; ++i)
{
for (int j = beginJ; j < endJ; ++j)
{
if (this[i, j].HasValue && otherGrid[i, j].HasValue)
{
double diff = this[i, j].Value - otherGrid[i, j].Value;
Debug.Assert(!double.IsNaN(diff));
Debug.Assert(!double.IsInfinity(diff));
total += diff * diff;
++count;
}
}
}
if (count == 0)
{
return(null);
}
double mean = total / count;
return(Math.Sqrt(mean));
}
public Histogram CreateDipAzimuthHistogram(int numberOfClasses)
{
Histogram histogram = new Histogram(numberOfClasses, -Math.PI, +Math.PI);
IRegularGrid2D dZdX = CreatePartialDerivativeIGrid();
IRegularGrid2D dZdY = CreatePartialDerivativeJGrid();
for (int i = 0; i < SizeI; ++i)
{
for (int j = 0; j < SizeJ; ++j)
{
double?x = dZdX[i, j];
double?y = dZdY[i, j];
if (x.HasValue && y.HasValue)
{
if (x != 0.0 && y != 0.0)
{
double dipAzimuth = Math.Atan2(-y.Value, -x.Value); // Negate x and y to give down-dip rather than up-dip
histogram.Accumulate(dipAzimuth);
}
}
}
}
return(histogram);
}
public override IImage <double> CloneSize()
{
IRegularGrid2D gridClone = grid.CloneSize();
GridImage clone = new GridImage(gridClone);
return(clone);
}
public override object Clone()
{
IRegularGrid2D gridClone = (IRegularGrid2D)this.grid.Clone();
GridImage clone = new GridImage(gridClone);
return(clone);
}
public Grid2DPhenotype(Grid2DDomain domain) :
base(domain)
{
Point2D origin = domain.Min;
Vector2D diagonal = domain.Max - domain.Min;
Vector2D spacing = new Vector2D(diagonal.DeltaX / domain.SizeI, diagonal.DeltaY / domain.SizeJ);
this.grid = new RegularGrid2D(origin, spacing, domain.SizeI, domain.SizeJ, 0.0);
}
public Grid2DDomain(IRegularGrid2D grid) :
base(new Grid2DPhenotype(grid))
{
Target.Domain = this;
Min = new Point2D(grid.MinX, grid.MinY);
Max = new Point2D(grid.MaxX, grid.MaxY);
this.sizeI = grid.SizeI;
this.sizeJ = grid.SizeJ;
}
private static void WriteBinaryImageSurfer6Grid(IRegularGrid2D prototypeGrid, IImage <bool> image, string uri)
{
IRegularGrid2D thresholdGrid = prototypeGrid.CloneSize(image.Width, image.Height);
for (int i = 0; i < image.Width; ++i)
{
for (int j = 0; j < image.Height; ++j)
{
thresholdGrid[i, j] = image[i, j] ? 1.0 : 0.0;
}
}
thresholdGrid.WriteSurfer6BinaryFile(uri);
}
// usage : Training: C:\Users\rjs\Documents\dev\p4workspace\sandbox\geodyssey\proto\Athena\testdata\training.irap
// Expected: C:\Users\rjs\Documents\dev\p4workspace\sandbox\geodyssey\proto\Athena\testdata\expected.grd
// Grid for analysis: F:\sapere_aude\data\IrapClassic\grid_surface\ASCII\RMS\analysis.irap
static int Main(string[] args)
{
// Get a URI from the command line argument
Uri trainingInputUri = UriFromArg(args, 0);
Uri trainingExpectedUri = UriFromArg(args, 1);
Uri analysisUri = UriFromArg(args, 2);
GeodysseyModel model = new GeodysseyModel();
LoaderController.Instance.Open(trainingInputUri, model);
IRegularGrid2D trainingInputGrid = model[0]; // The first grid
LoaderController.Instance.Open(trainingExpectedUri, model);
IRegularGrid2D trainingExpectedGrid = model[1]; // The second grid
LoaderController.Instance.Open(analysisUri, model);
IRegularGrid2D analysisGrid = model[2]; // The third grid
// Replaces blanks with 0.0
for (int j = 0; j < trainingExpectedGrid.SizeJ; ++j)
{
for (int i = 0; i < trainingExpectedGrid.SizeI; ++i)
{
if (!trainingExpectedGrid[i, j].HasValue)
{
trainingExpectedGrid[i, j] = 0.0;
}
else
{
if (trainingExpectedGrid[i, j] < 0.0)
{
trainingExpectedGrid[i, j] = 0.0;
}
else if (trainingExpectedGrid[i, j] > 1.0)
{
trainingExpectedGrid[i, j] = 1.0;
}
}
}
}
int matrixWidth = 5;
FaultInHorizonClassifer classifier = new FaultInHorizonClassifer(matrixWidth);
classifier.Learn(trainingInputGrid, trainingExpectedGrid);
IRegularGrid2D predictedGrid = classifier.CreateFaultProbability(analysisGrid);
predictedGrid.WriteSurfer6BinaryFile("predicted.grd");
return(0);
}
public double RandomHistogramDipAzimuth()
{
if (dipAzimuthHistogramGenerator == null)
{
Grid2DPhenotype p = (Grid2DPhenotype)Target;
IRegularGrid2D g = p.Grid;
Histogram dipAzimuthHistogram = g.CreateDipAzimuthHistogram(24);
dipAzimuthHistogramGenerator = new ContinuousHistogramGenerator(dipAzimuthHistogram);
}
double value = dipAzimuthHistogramGenerator.NextDouble();
//Console.WriteLine("randomAzimuth = {0}", Angle.RadiansToDegrees(value));
return(value);
}
public void MaskFrom(IRegularGrid2D maskGrid)
{
Debug.Assert(this.SizeI == maskGrid.SizeI);
Debug.Assert(this.SizeJ == maskGrid.SizeJ);
for (int i = 0; i < SizeI; ++i)
{
for (int j = 0; j < SizeJ; ++j)
{
if (!maskGrid[i, j].HasValue)
{
this[i, j] = null;
}
}
}
}
public IRegularGrid2D CreateFaultProbability(IRegularGrid2D horizon)
{
// TODO: This is a little hacky and wasteful - replace this
// with a Transform method on the Grid class
IRegularGrid2D probabilityGrid = (IRegularGrid2D)horizon.Clone();
for (int j = 0; j < horizon.SizeJ; ++j)
{
for (int i = 0; i < horizon.SizeI; ++i)
{
double[] matrix = MatrixInput(horizon, i, j, false);
double prediction = network.Run(matrix)[0]; // TODO : Assumes only one result
probabilityGrid[i, j] = prediction;
}
}
return(probabilityGrid);
}
/// <summary>
/// Compute a normalized correspondence value between two grids of the same dimensions.
/// </summary>
/// <param name="otherGrid">The grid against which this grid will be compared.</param>
/// <returns>
/// A number between 0.0 and 1.0 indicating the proportion of corresponding
/// grid nodes which either both contain a value, or both contain a null.
/// </returns>
public double Correspondence(IRegularGrid2D otherGrid)
{
Debug.Assert(this.SizeI == otherGrid.SizeI);
Debug.Assert(this.SizeJ == otherGrid.SizeJ);
int correspondence = 0;
for (int i = 0; i < SizeI; ++i)
{
for (int j = 0; j < SizeJ; ++j)
{
if (this[i, j].HasValue == otherGrid[i, j].HasValue)
{
correspondence += 1;
}
}
}
return((double)correspondence / (double)zs.Length);
}
private static void RecordBest(IRegularGrid2D targetGrid, Population population, int generation, RectangularDomain domain)
{
List <Individual> best = population.Best;
for (int j = 0; j < best.Count; ++j)
{
Console.Write("best[{0}] = [", j);
foreach (double f in best[j].Fitness)
{
Console.Write(f);
Console.Write(" ");
}
Console.WriteLine("] with {0} genes", best[j].Genome.Count);
// Express the genome to create a grid
Individual bestIndividual = (Individual)best[j].Clone();
Grid2DPhenotype bestPhenotype = (Grid2DPhenotype)bestIndividual.Phenome;
bestPhenotype.Grid.MaskFrom(targetGrid);
StringBuilder gridFileName = new StringBuilder();
gridFileName.AppendFormat("evolved_{0}_{1}.grd", generation + 1, j);
bestPhenotype.Grid.WriteSurfer6BinaryFile(gridFileName.ToString());
ReportLogger.Instance.Writer.WriteStartElement("Grid");
ReportLogger.Instance.Writer.WriteStartAttribute("file");
ReportLogger.Instance.Writer.WriteValue(gridFileName.ToString());
ReportLogger.Instance.Writer.WriteEndAttribute();
ReportLogger.Instance.Writer.WriteEndElement();
// Express the genome to create a fault polygon map
OutlineMapDomain mapDomain = new OutlineMapDomain(domain);
OutlineMapPhenotype mapPhenotype = (OutlineMapPhenotype)bestIndividual.Genome.Express(mapDomain);
StringBuilder polygonFileName = new StringBuilder();
polygonFileName.AppendFormat("evolved_{0}_{1}.poly", generation + 1, j);
using (StreamWriter writer = File.CreateText(polygonFileName.ToString()))
{
writer.Write(mapPhenotype.ToString());
}
ReportLogger.Instance.Writer.WriteStartElement("Polygons");
ReportLogger.Instance.Writer.WriteStartAttribute("file");
ReportLogger.Instance.Writer.WriteValue(polygonFileName.ToString());
ReportLogger.Instance.Writer.WriteEndAttribute();
ReportLogger.Instance.Writer.WriteEndElement();
}
}
public void Learn(IRegularGrid2D input, IRegularGrid2D expected)
{
// Build the training samples
for (int j = 0; j < input.SizeJ; ++j)
{
for (int i = 0; i < input.SizeI; ++i)
{
double[] inValues = MatrixInput(input, i, j, true);
double[] expectedValues = TrainingExpected(expected, i, j);
network.TrainingSamples.Add(new TrainingSample(inValues, expectedValues));
}
}
network.Learn();
network.Save("athena.net");
//double[] validate1 = network.Run(new double[] { 0.013, -0.026, -0.060, 0.043, 0.0, -0.037, 0.013, -0.026, -0.060 }); // 0.0
//double[] validate2 = network.Run(new double[] { 0.134, 0.050, -0.004, 0.078, 0.0, -0.034, 0.031, -0.044, -0.062 }); // 0.49
//double[] validate3 = network.Run(new double[] { -0.060, 0.071, 0.246, -0.170, 0.0, 0.296, -0.277, 0.327, 0.943 }); // 0.94
}
/// <summary>
/// Returns the array of normalised training values for the
/// specified grid node, or null if the specified grid node
/// has no value.
/// </summary>
/// <param name="i"></param>
/// <param name="j"></param>
/// <returns>Either an array of numInputNodes doubles, or null.</returns>
private double[] MatrixInput(IRegularGrid2D grid, int i, int j, bool deBias)
{
Debug.Assert(grid != null);
if (!grid[i, j].HasValue)
{
return(null);
}
double zCentre = grid[i, j].Value;
int centre = (matrixWidth - 1) / 2;
// Must return a 1D array, since that's what training sample requires
double[] matrix = new double[matrixWidth * matrixWidth];
for (int q = 0; q < matrixWidth; ++q)
{
for (int p = 0; p < matrixWidth; ++p)
{
int relativeI = p - centre;
int relativeJ = q - centre;
int absoluteI = i + relativeI;
int absoluteJ = j + relativeJ;
int index = q * matrixWidth + p;
double?z = PaddedGridValue(grid, absoluteI, absoluteJ);
Debug.Assert(z.HasValue);
// TODO: Assumes square cells
double zDiff = z.Value - zCentre;
double zNorm = zDiff / grid.Spacing.DeltaX;
matrix[index] = zNorm;
}
}
if (deBias)
{
DeBiasMatrix(matrix, centre, matrixWidth);
}
return(matrix);
}
/// <summary>
/// Returns the value for the specified grid cell, padding data off the image
/// boundaries to allow matrix sampling to work right up to the image edges.
/// This version reflects the data at the image boundaries.
/// </summary>
/// <param name="grid">The grid</param>
/// <param name="absoluteI">The column coordinate</param>
/// <param name="absoluteJ">The row coodinate</param>
/// <returns>Either a real grid value, for in-range i and j, or an interpolated value</returns>
private double?PaddedGridValue(IRegularGrid2D grid, int absoluteI, int absoluteJ)
{
// Modify i co-ordinate if necessary
if (absoluteI < 0)
{
absoluteI = 0 - absoluteI;
}
else if (absoluteI > grid.SizeI - 1)
{
absoluteI = 2 * (grid.SizeI - 1) - absoluteI;
}
// Modify j co-ordinate if necessary
if (absoluteJ < 0)
{
absoluteJ = 0 - absoluteJ;
}
else if (absoluteJ > grid.SizeJ - 1)
{
absoluteJ = 2 * (grid.SizeJ - 1) - absoluteJ;
}
return(grid[absoluteI, absoluteJ]);
}
private double[] TrainingExpected(IRegularGrid2D grid, int i, int j)
{
Debug.Assert(grid[i, j].HasValue);
return(new double[] { grid[i, j].Value });
}
static void Main(string[] args)
{
Uri faultProbabilityUri = UriFromArg(args, 0);
Uri horizonUri = UriFromArg(args, 1);
GeodysseyModel model = new GeodysseyModel();
LoaderController.Instance.Open(faultProbabilityUri, model);
IRegularGrid2D pFaultGrid = model[0]; // The first grid
LoaderController.Instance.Open(horizonUri, model);
IRegularGrid2D horizon = model[1]; // Horizon grid
GridImage pFaultImage = new GridImage(pFaultGrid);
GridImage pFaultImageX = (GridImage)pFaultImage.Clone();
pFaultImageX.Clear();
GridImage pFaultImageY = (GridImage)pFaultImage.Clone();
pFaultImageY.Clear();
Convolver.GaussianGradient(pFaultImage, pFaultImageX, pFaultImageY, 1.0);
GridImage pFaultImageXX = (GridImage)pFaultImage.Clone();
pFaultImageXX.Clear();
GridImage pFaultImageYY = (GridImage)pFaultImage.Clone();
pFaultImageYY.Clear();
GridImage pFaultImageXY = (GridImage)pFaultImage.Clone();
pFaultImageXY.Clear();
Convolver.HessianMatrixOfGaussian(pFaultImage, pFaultImageXX, pFaultImageYY, pFaultImageXY, 1.0);
//GridImage pFaultImageBeta = (GridImage) RidgeDetector.PrincipleCurvatureDirection(pFaultImageXX, pFaultImageYY, pFaultImageXY);
//GridImage pFaultImagePQ = (GridImage) RidgeDetector.LocalLpq(pFaultImageXX, pFaultImageYY, pFaultImageXY, pFaultImageBeta);
//GridImage pFaultImageP = (GridImage) RidgeDetector.LocalLp(pFaultImageX, pFaultImageY, pFaultImageBeta);
//GridImage pFaultImageQ = (GridImage) RidgeDetector.LocalLq(pFaultImageX, pFaultImageY, pFaultImageBeta);
//GridImage pFaultImagePP = (GridImage) RidgeDetector.LocalLpp(pFaultImageXX, pFaultImageYY, pFaultImageXY, pFaultImageBeta);
//GridImage pFaultImageQQ = (GridImage) RidgeDetector.LocalLqq(pFaultImageXX, pFaultImageYY, pFaultImageXY, pFaultImageBeta);
Trace.WriteLine("Ridge detector");
GridImage pFaultImageRidge = (GridImage)RidgeDetector.Detect(pFaultImageX, pFaultImageY, pFaultImageXX, pFaultImageYY, pFaultImageXY);
IImage <bool> ridge = pFaultImageRidge.CreateBinaryImage(0.0);
Trace.WriteLine("Pepper filter");
IImage <bool> filtered = Morphology.PepperFiltering(5, ridge);
Trace.WriteLine("Closing gaps");
IImage <bool> closed = Morphology.Closing(filtered);
Trace.WriteLine("Thinning until convergence");
IImage <bool> thinned = Morphology.ThinUntilConvergence(closed);
Trace.WriteLine("Thinning blocks until convergence");
IImage <bool> blockthinned = Morphology.ThinBlockUntilConvergence(thinned);
Trace.WriteLine("Filling");
IImage <bool> filled = Morphology.Fill(blockthinned);
Trace.WriteLine("Connectivity");
IImage <int> connectivity = BitImage.Analysis.Connectivity(filled);
Trace.WriteLine("Connected components");
IImage <int> components = BitImage.Analysis.ConnectedComponents(filled);
Trace.WriteLine("Mapping faults");
FaultNetwork network = FaultNetworkMapper.MapFaultNetwork(filled, horizon);
Trace.WriteLine("Mapping displacements");
FaultDisplacementMapper displacementMapper = new FaultDisplacementMapper(network);
var mesh = displacementMapper.GetResult();
// Output files of mesh
Trace.WriteLine("Writing faults");
string faultSegmentsPath = faultProbabilityUri.LocalPath.Replace(".grd", "_faults.poly");
string monoSegmentsPath = faultProbabilityUri.LocalPath.Replace(".grd", "_mono.poly");
using (StreamWriter faultFile = new StreamWriter(faultSegmentsPath))
using (StreamWriter monoFile = new StreamWriter(monoSegmentsPath))
{
foreach (EdgeBase edge in mesh.Edges)
{
StreamWriter file = edge is FaultEdge ? faultFile : monoFile;
Point2D source = ((PositionedVertexBase)edge.Source).Position;
Point2D target = ((PositionedVertexBase)edge.Target).Position;
file.WriteLine("{0}\t{1}", source.X, source.Y);
file.WriteLine("{0}\t{1}", target.X, target.Y);
file.WriteLine("%");
}
}
// Establish order in the mesh
Trace.WriteLine("Build planar subdivision - Ordering mesh and inserting faces");
var orderer = new Orderer2D <PositionedVertexBase, EdgeBase, FaceBase>(mesh);
var orderedMesh = orderer.GetResult();
Debug.Assert(orderedMesh.Euler == 2);
// Triangulate the mesh
// Copy the list of monotone faces, so we can iterate over it it
// whilst modifying the faces in the mesh during triangulation.
Trace.WriteLine("Triangulating");
List <FaceBase> faces = new List <FaceBase>(orderedMesh.Faces);
foreach (FaceBase face in faces)
{
var triangulator = new MonotonePolygonTriangulator <PositionedVertexBase, EdgeBase, FaceBase>(orderedMesh, face);
triangulator.GetResult();
}
// Improve triangulation quality
var improver = new TriangulationQualityImprover <PositionedVertexBase, EdgeBase, FaceBase>(mesh); // TODO: Add a flippable critera
improver.Improve();
Trace.WriteLine("Writing mesh");
// Output the mesh
Random rng = new Random();
string facesPath = faultProbabilityUri.LocalPath.Replace(".grd", "_faces.poly");
using (StreamWriter facesFile = new StreamWriter(facesPath))
{
// All faces except the last one...
foreach (FaceBase face in orderedMesh.Faces.Take(orderedMesh.FaceCount - 1))
{
foreach (VertexBase vertex in face.Vertices)
{
PositionedVertexBase pos = (PositionedVertexBase)vertex;
Point2D point = pos.Position;
facesFile.WriteLine("{0}\t{1}", point.X, point.Y);
}
int red = rng.Next(255);
int green = rng.Next(255);
int blue = rng.Next(255);
facesFile.WriteLine("% -W0/{0}/{1}/{2} -G{0}/{1}/{2}", red, green, blue);
}
}
// Convert images to grids for convenient output
//GridImage filteredGrid = (GridImage) pFaultImageRidge.Clone();
//for (int i = 0; i < filteredGrid.Width; ++i)
//{
// for (int j = 0; j < filteredGrid.Height; ++j)
// {
// filteredGrid[i, j] = filtered[i, j] ? 1.0 : 0.0;
// }
//}
//GridImage closedGrid = (GridImage) pFaultImageRidge.Clone();
//for (int i = 0; i < closedGrid.Width; ++i)
//{
// for (int j = 0; j < closedGrid.Height; ++j)
// {
// closedGrid[i, j] = closed[i, j] ? 1.0 : 0.0;
// }
//}
//GridImage thinnedGrid = (GridImage) pFaultImageRidge.Clone();
//for (int i = 0; i < thinnedGrid.Width; ++i)
//{
// for (int j = 0; j < thinnedGrid.Height; ++j)
// {
// thinnedGrid[i, j] = thinned[i, j] ? 1.0 : 0.0;
// }
//}
//GridImage blockThinnedGrid = (GridImage) pFaultImageRidge.Clone();
//for (int i = 0; i < blockThinnedGrid.Width; ++i)
//{
// for (int j = 0; j < blockThinnedGrid.Height; ++j)
// {
// blockThinnedGrid[i, j] = blockthinned[i, j] ? 1.0 : 0.0;
// }
//}
GridImage filledGrid = (GridImage)pFaultImageRidge.Clone();
for (int i = 0; i < filledGrid.Width; ++i)
{
for (int j = 0; j < filledGrid.Height; ++j)
{
filledGrid[i, j] = filled[i, j] ? 1.0 : 0.0;
}
}
//GridImage connectivityGrid = (GridImage) pFaultImageRidge.Clone();
//for (int i = 0; i < filledGrid.Width; ++i)
//{
// for (int j = 0; j < filledGrid.Height; ++j)
// {
// connectivityGrid[i, j] = connectivity[i, j];
// }
//}
//GridImage componentsGrid = (GridImage) pFaultImageRidge.Clone();
//for (int i = 0; i < componentsGrid.Width; ++i)
//{
// for (int j = 0; j < componentsGrid.Height; ++j)
// {
// componentsGrid[i, j] = components[i, j];
// }
//}
//string pathX = faultProbabilityUri.LocalPath.Replace(".", "_x.");
//string pathY = faultProbabilityUri.LocalPath.Replace(".", "_y.");
//string pathXX = faultProbabilityUri.LocalPath.Replace(".", "_xx.");
//string pathYX = faultProbabilityUri.LocalPath.Replace(".", "_yy.");
//string pathXY = faultProbabilityUri.LocalPath.Replace(".", "_xy.");
//string pathBeta = faultProbabilityUri.LocalPath.Replace(".", "_beta.");
//string pathPQ = faultProbabilityUri.LocalPath.Replace(".", "_pq.");
//string pathP = faultProbabilityUri.LocalPath.Replace(".", "_p.");
//string pathQ = faultProbabilityUri.LocalPath.Replace(".", "_q.");
//string pathPP = faultProbabilityUri.LocalPath.Replace(".", "_pp.");
//string pathQQ = faultProbabilityUri.LocalPath.Replace(".", "_qq.");
//string pathRidge = faultProbabilityUri.LocalPath.Replace(".", "_ridge.");
//string pathFiltered = faultProbabilityUri.LocalPath.Replace(".", "_filtered.");
//string pathClosed = faultProbabilityUri.LocalPath.Replace(".", "_closed.");
//string pathThinned = faultProbabilityUri.LocalPath.Replace(".", "_thinned.");
//string pathBlockThinned = faultProbabilityUri.LocalPath.Replace(".", "_blockthinned.");
string pathFilled = faultProbabilityUri.LocalPath.Replace(".", "_filled.");
//string pathConnectivity = faultProbabilityUri.LocalPath.Replace(".", "_connectivity.");
//string pathComponents = faultProbabilityUri.LocalPath.Replace(".", "_components.");
//string pathFaultLines = faultProbabilityUri.LocalPath.Replace(".grd", "_faults.poly");
string pathBisectors = faultProbabilityUri.LocalPath.Replace(".grd", "_bisectors.poly");
string pathLabels = faultProbabilityUri.LocalPath.Replace(".grd", "_labels.xy");
string pathStrands = faultProbabilityUri.LocalPath.Replace(".grd", "_strands.poly");
//pFaultImageX.Grid.WriteSurfer6BinaryFile(pathX);
//pFaultImageY.Grid.WriteSurfer6BinaryFile(pathY);
//pFaultImageXX.Grid.WriteSurfer6BinaryFile(pathXX);
//pFaultImageYY.Grid.WriteSurfer6BinaryFile(pathXY);
//pFaultImageXY.Grid.WriteSurfer6BinaryFile(pathXY);
//pFaultImageBeta.Grid.WriteSurfer6BinaryFile(pathBeta);
//pFaultImagePQ.Grid.WriteSurfer6BinaryFile(pathPQ);
//pFaultImageP.Grid.WriteSurfer6BinaryFile(pathP);
//pFaultImageQ.Grid.WriteSurfer6BinaryFile(pathQ);
//pFaultImagePP.Grid.WriteSurfer6BinaryFile(pathPP);
//pFaultImageQQ.Grid.WriteSurfer6BinaryFile(pathQQ);
//pFaultImageRidge.Grid.WriteSurfer6BinaryFile(pathRidge);
//filteredGrid.Grid.WriteSurfer6BinaryFile(pathFiltered);
//closedGrid.Grid.WriteSurfer6BinaryFile(pathClosed);
//thinnedGrid.Grid.WriteSurfer6BinaryFile(pathThinned);
//blockThinnedGrid.Grid.WriteSurfer6BinaryFile(pathBlockThinned);
filledGrid.Grid.WriteSurfer6BinaryFile(pathFilled);
//connectivityGrid.Grid.WriteSurfer6BinaryFile(pathConnectivity);
//componentsGrid.Grid.WriteSurfer6BinaryFile(pathComponents);
//mapper.OutputPolygons(pathFaultLines);
//displacementMapper.OutputBisectors(pathBisectors);
//displacementMapper.OutputLabels(pathLabels);
//displacementMapper.OutputStrands(pathStrands);
}
public void Add(IRegularGrid2D grid)
{
grids.Add(grid);
//Console.WriteLine(grid.ToString());
}
public Grid2DPhenotype(IRegularGrid2D grid) :
base(null)
{
this.grid = grid;
}
/// <summary>
/// Construct from a grid. The grid is not copied. The image serves as
/// an adaptor for the grid.
/// </summary>
/// <param name="grid"></param>
public GridImage(IRegularGrid2D grid)
{
this.grid = grid;
}
/// <summary>
/// Compute the Root Mean Square difference betweeen two grids of the same dimensions.
/// Nodes which are null in either grid will be ignored.
/// </summary>
/// <param name="otherGrid">The grid against which this grid will be compared.</param>
/// <returns>The Root Mean Square difference of the z values.</returns>
public double?RmsDifference(IRegularGrid2D otherGrid)
{
return(RmsDifference(otherGrid, 0, SizeI, 0, SizeJ));
}
static void Main(string[] args)
{
Uri horizonUri = UriFromArg(args, 0);
GeodysseyModel model = new GeodysseyModel();
LoaderController.Instance.Open(horizonUri, model);
IRegularGrid2D horizon = model[0];
//string pathOriginal = horizonUri.LocalPath.Replace(".dat", ".grd");
//horizon.WriteSurfer6BinaryFile(pathOriginal);
// TODO: Make IRegularGrid IEnumerable
var extentMap = new FastImage <bool>(horizon.SizeI, horizon.SizeJ, horizon.Select(item => item.HasValue));
IImage <bool> faultMap = Morphology.Invert(extentMap);
IImage <double> distanceMap = DistanceMap.EuclideanTransform(extentMap);
// Remove anything above a threshold distance from data
const double threshold = 50;
var clippedFaultMap = extentMap.CloneTransform((i, j) => distanceMap[i, j] < threshold &&
faultMap[i, j]);
Trace.WriteLine("Pepper filter");
IImage <bool> filtered = Morphology.PepperFiltering(5, clippedFaultMap);
Trace.WriteLine("Closing gaps");
IImage <bool> closed = Morphology.Closing(filtered);
Trace.WriteLine("Thinning until convergence");
IImage <bool> thinned = Morphology.ThinUntilConvergence(closed);
Trace.WriteLine("Thinning blocks until convergence");
IImage <bool> blockthinned = Morphology.ThinBlockUntilConvergence(thinned);
Trace.WriteLine("Filling");
IImage <bool> filled = Morphology.Fill(blockthinned);
WriteBinaryImageSurfer6Grid(horizon, filled, horizonUri.LocalPath.Replace(".grd", "_filled.grd"));
//// Create a double valued 'binary' image showing the extent of the horizon data
//FastImage<double> extentMap = new FastImage<double>(horizon.SizeI, horizon.SizeJ);
//for (int i = 0; i < horizon.SizeI; ++i)
//{
// for (int j = 0; j < horizon.SizeJ; ++j)
// {
// bool hasValue = horizon[i, j].HasValue;
// extentMap[i, j] = hasValue ? 1.0 : 0.0;
// }
//}
//int extent = extentMap.Where(v => v == 1.0).Count();
//double extentProportion = (double) extent / (extentMap.Width * extentMap.Height);
//IImage<double> scaledExtentMap = Scaler.Downscale(extentMap, 5);
//IImage<double> smoothedExtentMap = scaledExtentMap.CloneSize();
//Convolver.GaussianSmooth(scaledExtentMap, smoothedExtentMap, 3.0);
//IRegularGrid2D smoothedGrid = horizon.CloneSize(smoothedExtentMap.Width, smoothedExtentMap.Height);
//for (int i = 0 ; i < smoothedGrid.SizeI; ++i)
//{
// for (int j = 0 ; j < smoothedGrid.SizeJ; ++j)
// {
// smoothedGrid[i, j] = smoothedExtentMap[i, j];
// }
//}
//PriorityQueue<double> orderedIntensities = PriorityQueue<double>.CreateHighFirstOut(smoothedExtentMap);
//int k = (int) (extentProportion * orderedIntensities.Count);
//Debug.Assert(k >= 0);
//for (int i = 0 ; i < k - 1; ++i)
//{
// orderedIntensities.Dequeue();
//}
//double threshold = orderedIntensities.Dequeue();
//string pathSmoothed = horizonUri.LocalPath.Replace(".grd", "_smoothed.grd");
//smoothedGrid.WriteSurfer6BinaryFile(pathSmoothed);
//IImage<bool> thresholdMap = BitImage.Analysis.Threshold(smoothedExtentMap, threshold * 2.0);
//int actual = thresholdMap.Where(v => v).Count();
//double actualProportion = (double) actual / (thresholdMap.Width * thresholdMap.Height);
//IRegularGrid2D thresholdGrid = horizon.CloneSize(thresholdMap.Width, thresholdMap.Height);
//for (int i = 0; i < smoothedGrid.SizeI; ++i)
//{
// for (int j = 0; j < smoothedGrid.SizeJ; ++j)
// {
// thresholdGrid[i, j] = thresholdMap[i, j] ? 1.0 : 0.0;
// }
//}
//string pathThresholded = horizonUri.LocalPath.Replace(".grd", "_thresholded.grd");
//thresholdGrid.WriteSurfer6BinaryFile(pathThresholded);
//IImage<double> distanceMap = DistanceMap.EuclideanTransform(scaledExtentMap);
// Convert the image back to a grid for convenient output
IRegularGrid2D distanceGrid = horizon.CloneSize(distanceMap.Width, distanceMap.Height);
for (int i = 0; i < distanceMap.Width; ++i)
{
for (int j = 0; j < distanceMap.Height; ++j)
{
distanceGrid[i, j] = distanceMap[i, j];
}
}
string pathDistance = horizonUri.LocalPath.Replace(".grd", "_distance.grd");
distanceGrid.WriteSurfer6BinaryFile(pathDistance);
}
static int Main(string[] args)
{
// Get a URI from the command line argument
Uri uri;
try
{
uri = new Uri(args[0]);
}
catch (UriFormatException)
{
string absPath = Directory.GetCurrentDirectory() + Path.DirectorySeparatorChar + args[0];
try
{
uri = new Uri(absPath);
}
catch (UriFormatException)
{
return(1);
}
}
ReportLogger.Instance.Create("report.xml");
ReportLogger.Instance.Writer.WriteStartDocument();
ReportLogger.Instance.Writer.WriteStartElement("GeodysseyRun");
Stopwatch overallWatch = new Stopwatch();
overallWatch.Start();
//Console.WriteLine("Start!");
int initialMinimumGenomeLength = 50;
int initialMaximumGenomeLength = 100;
int initialPopulationSize = 1000;
int finalPopulationSize = 100;
int numberOfGenerations = 100;
double populationPowerBase = Math.Pow((double)finalPopulationSize / (double)initialPopulationSize, 1.0 / numberOfGenerations);
int totalNumberOfIndividuals = 0;
// Determine how many individuals will be produced in this run
for (int i = 0; i < numberOfGenerations; ++i)
{
int inc = (int)Math.Round(initialPopulationSize * Math.Pow(populationPowerBase, i + 1));
//Console.WriteLine(inc);
totalNumberOfIndividuals += inc;
}
Console.WriteLine("Total Number of Individuals = {0}", totalNumberOfIndividuals);
Console.WriteLine("Mean Invididuals per Generation = {0}", totalNumberOfIndividuals / numberOfGenerations);
// Load a target grid
//RegularGrid2D targetGrid;
//using (StreamReader reader = File.OpenText("target.grd"))
//{
// targetGrid = RegularGrid2D.Create(reader);
//}
GeodysseyModel model = new GeodysseyModel();
LoaderController.Instance.Open(uri, model);
IRegularGrid2D targetGrid = model[0]; // The first grid
Debug.Assert(targetGrid != null);
Grid2DDomain domain = new Grid2DDomain(targetGrid);
Stopwatch stopWatch = new Stopwatch();
Population population = new Population(domain, initialPopulationSize, initialMinimumGenomeLength, initialMaximumGenomeLength);
for (int i = 0; i < numberOfGenerations; ++i)
{
stopWatch.Reset();
stopWatch.Start();
population.ComputeFitnesses();
stopWatch.Stop();
TimeSpan ts = stopWatch.Elapsed;
ReportLogger.Instance.Writer.WriteStartElement("Generation");
ReportLogger.Instance.Writer.WriteStartAttribute("number");
ReportLogger.Instance.Writer.WriteValue(i + 1);
ReportLogger.Instance.Writer.WriteEndAttribute();
ReportLogger.Instance.Writer.WriteStartAttribute("elapsedTime");
ReportLogger.Instance.Writer.WriteValue(ts);
ReportLogger.Instance.Writer.WriteEndAttribute();
RecordBest(targetGrid, population, i, domain);
population.LogSummaryStatistics();
ReportLogger.Instance.Writer.WriteEndElement();
Console.WriteLine("Generation {0} of {1} with size {2} in {3}) ", i + 1, numberOfGenerations, population.Count, ts);
int nextGenerationSize = (int)Math.Round(initialPopulationSize * Math.Pow(populationPowerBase, i + 1));
population.Evolve(nextGenerationSize);
}
population.ComputeFitnesses();
RecordBest(targetGrid, population, numberOfGenerations, domain);
Console.WriteLine("Generation {0} of {1} with size {2}) ", numberOfGenerations, numberOfGenerations, population.Count);
overallWatch.Stop();
Console.WriteLine("Running time : {0}", overallWatch.Elapsed);
ReportLogger.Instance.Writer.WriteEndElement();
ReportLogger.Instance.Writer.WriteEndDocument();
ReportLogger.Instance.Close();
Console.ReadKey();
return(0);
}
