public static Bitmap ConvertToBitmapUInt16(IImageRaster <IRaster3DInteger, uint> image, int index_z)
{
Bitmap bitmap = new Bitmap(image.Raster.Size0, image.Raster.Size1, System.Drawing.Imaging.PixelFormat.Format16bppGrayScale);
//Get a reference to the images pixel data
Rectangle dimension = new Rectangle(0, 0, image.Raster.Size0, image.Raster.Size1);
BitmapData bitmap_data = bitmap.LockBits(dimension, ImageLockMode.ReadWrite, System.Drawing.Imaging.PixelFormat.Format16bppGrayScale);
IntPtr pixel_start_address = bitmap_data.Scan0;
byte[] pixel_values = new byte[image.Raster.Size0 * image.Raster.Size1 * 2];
//Copy the pixel data into the bitmap structure
int byte_index = 0;
for (int index_y = 0; index_y < image.Raster.Size1; index_y++)
{
for (int index_x = 0; index_x < image.Raster.Size0; index_x++)
{
byte[] bytes = BitConverter.GetBytes(image.GetElementValue(image.Raster.GetElementIndex(index_x, index_y, index_z)));
pixel_values[byte_index] = bytes[0];
byte_index++;
pixel_values[byte_index] = bytes[1];
byte_index++;
}
}
System.Runtime.InteropServices.Marshal.Copy(pixel_values, 0, pixel_start_address, pixel_values.Length);
bitmap.UnlockBits(bitmap_data);
return(bitmap);
}
public static void SaveImageRaster3DAsTIFF3D2(string save_path, IImageRaster <IRaster3DInteger, uint> image)
{
Stream destination_stream = new FileStream(save_path, FileMode.OpenOrCreate, FileAccess.Write, FileShare.None);
TiffBitmapEncoder encoder = new TiffBitmapEncoder();
encoder.Compression = TiffCompressOption.None;
for (int index_z = 0; index_z < image.Raster.Size2; index_z++)
{
Bitmap bitmap = ConvertToBitmapUInt16(image, index_z);
BitmapSource bitmap_source = ToolsRendering.CreateBitmapSourceFromBitmap16Bit(bitmap);
encoder.Frames.Add(BitmapFrame.Create(bitmap_source));
}
encoder.Save(destination_stream);
//TiffBitmapEncoder encoder = new TiffBitmapEncoder(destination_stream_, BitmapCreateOptions.PreservePixelFormat, BitmapCacheOption.Default);
//Stream imageStreamSource = new FileStream(load_path, FileMode.Open, FileAccess.Read, FileShare.Read);
//TiffBitmapDecoder decoder = new TiffBitmapDecoder(imageStreamSource, BitmapCreateOptions.PreservePixelFormat, BitmapCacheOption.Default);
//BitmapSource test_frame = decoder.Frames[0];
//int size_x = test_frame.PixelWidth;
//int size_y = test_frame.PixelHeight;
//int size_z = decoder.Frames.Count;
//int bits_per_pixel = test_frame.Format.BitsPerPixel;
//for (int index_z = 0; index_z < size_z; index_z++)
//{
// // save each frame to a bytestream
// BitmapSource frame = decoder.Frames[index_z];
// // img.CopyPixels(pixels, stride, 0)
// MemoryStream byte_stream = new MemoryStream();
// // bitmap.Save(byte_stream, ImageFormat.Tiff);
// // and then create a new Image from it
// System.Drawing.Image image = System.Drawing.Image.FromStream(byte_stream);
// // d
//}
}
public ImageRaster2DWrapperSlice3D(IImageRaster <IRaster3DInteger, RangeType> image, int index_2)
{
Debug.Assert(index_2 < image.Raster.Size2);
Raster = new Raster2DInteger(image.Raster.Size0, image.Raster.Size1);
this.wrapped_image = image;
this.index_2 = index_2;
}
public static void CreateMultipageTiff1(string save_path, IImageRaster <IRaster3DInteger, ushort> image)
{
int size_x = image.Raster.Size0;
int size_y = image.Raster.Size1;
int size_z = image.Raster.Size2;
const int samplesPerPixel = 1;
const int bitsPerSample = 16;
byte[][] firstPageBuffer = new byte[size_y][];
for (int j = 0; j < size_y; j++)
{
firstPageBuffer[j] = new byte[size_x];
for (int i = 0; i < size_x; i++)
{
firstPageBuffer[j][i] = (byte)(j * i);
}
}
using (Tiff output = Tiff.Open(save_path, "w"))
{
for (int page = 0; page < size_z; ++page)
{
output.SetField(TiffTag.IMAGEWIDTH, size_x / samplesPerPixel);
output.SetField(TiffTag.IMAGELENGTH, size_y);
output.SetField(TiffTag.SAMPLESPERPIXEL, samplesPerPixel);
output.SetField(TiffTag.BITSPERSAMPLE, bitsPerSample);
output.SetField(TiffTag.ORIENTATION, Orientation.TOPLEFT);
output.SetField(TiffTag.PLANARCONFIG, PlanarConfig.CONTIG);
if (page % 2 == 0)
{
output.SetField(TiffTag.PHOTOMETRIC, Photometric.MINISBLACK);
}
else
{
output.SetField(TiffTag.PHOTOMETRIC, Photometric.MINISWHITE);
}
output.SetField(TiffTag.ROWSPERSTRIP, 1);
output.SetField(TiffTag.XRESOLUTION, 100.0);
output.SetField(TiffTag.YRESOLUTION, 100.0);
output.SetField(TiffTag.RESOLUTIONUNIT, ResUnit.INCH);
// specify that it's a page within the multipage file
output.SetField(TiffTag.SUBFILETYPE, FileType.PAGE);
// specify the page number
output.SetField(TiffTag.PAGENUMBER, page, size_z);
for (int j = 0; j < size_y; ++j)
{
output.WriteEncodedStrip(j, firstPageBuffer[j], firstPageBuffer.Length);
}
output.WriteDirectory();
}
}
}
public ImageSpace3DFloatLinear(IImageRaster <IRaster3DInteger, float> image)
{
this.image = image;
this.algebra = new AlgebraRealFloat32();
this.space_size_0 = 1;
this.space_size_1 = 1;
this.space_size_2 = 1;
this.background_value = 0;
}
public AlphaPartitionTree3D(
IAlphaPartitionTreeBuilder <ElementValueType, EdgeValueType> builder,
ITopologyElementEdgeRaster <IRaster3DInteger> topology,
IFunctionDissimilarity <ElementValueType, EdgeValueType> edge_function,
IImageRaster <IRaster3DInteger, ElementValueType> image)
{
//TODO make sure topology matches image
ElementValueType[] element_values = image.GetElementValues(false);
tree = builder.BuildAlphaPartitionTree(topology, edge_function, element_values);
}
public Bitmap Render(IImageRaster <IRaster3DInteger, bool> source_image)
{
IRaster3DInteger source_raster = source_image.Raster;
List <int> elements_true = source_image.GetElementIndexesWithValue(true);
float[,] coordinates_image = new float[elements_true.Count, 3];
float[,] elements_projection = new float[elements_true.Count, 3];
int [] coordinates = new int [3];
for (int element_index_index = 0; element_index_index < elements_true.Count; element_index_index++)
{
source_raster.GetElementCoordinatesRBA(elements_true[element_index_index], coordinates);
coordinates_image[element_index_index, 0] = coordinates[0];
coordinates_image[element_index_index, 1] = coordinates[1];
coordinates_image[element_index_index, 2] = coordinates[2];
}
for (int element_index = 0; element_index < elements_true.Count; element_index++)
{
elements_projection[element_index, 0] = ((coordinates_image[element_index, 0] - image_focus[0]) * projection_vector_x[0]) +
((coordinates_image[element_index, 1] - image_focus[1]) * projection_vector_x[1]) +
((coordinates_image[element_index, 2] - image_focus[2]) * projection_vector_x[2]);
elements_projection[element_index, 1] = ((coordinates_image[element_index, 0] - image_focus[0]) * projection_vector_y[0]) +
((coordinates_image[element_index, 1] - image_focus[1]) * projection_vector_y[1]) +
((coordinates_image[element_index, 2] - image_focus[2]) * projection_vector_y[2]);
elements_projection[element_index, 2] = ((coordinates_image[element_index, 0] - image_focus[0]) * projection_vector_z[0]) +
((coordinates_image[element_index, 1] - image_focus[1]) * projection_vector_z[1]) +
((coordinates_image[element_index, 2] - image_focus[2]) * projection_vector_z[2]);
}
Raster2DInteger bitmap_raster = new Raster2DInteger(bitmap_size_x, bitmap_size_y);
Bitmap destination_image = new Bitmap(bitmap_size_x, bitmap_size_y);
for (int index_y = 0; index_y < bitmap_raster.Size1; index_y++)
{
for (int index_x = 0; index_x < bitmap_raster.Size0; index_x++)
{
destination_image.SetPixel(index_x, index_y, Color.Black);
}
}
for (int element_index = 0; element_index < elements_true.Count; element_index++)
{
int x_target = (int)elements_projection[element_index, 0] + (bitmap_raster.Size0 / 2);
int y_target = (int)elements_projection[element_index, 1] + (bitmap_raster.Size1 / 2);
if (bitmap_raster.ContainsCoordinates(x_target, y_target))
{
destination_image.SetPixel(x_target, y_target, Color.White);
}
}
return(destination_image);
}
public void ComputeCentroids(
IImageRaster <IRasterType, int> image_labeling,
IImageRaster <IRasterType, DomainType> image_data,
IList <int[]> cluster_spatial_centroids,
IList <DomainType> cluster_feature_centroids)
{
//Use the cluster raster for spacing the clusters in the image
IList <IList <DomainType> > clusters = new List <IList <DomainType> >();
int dimension_count = image_labeling.Raster.DimensionCount;
int element_count = image_labeling.Raster.ElementCount;
int [] element_coordinates = new int[dimension_count];
//clear clusters
// TODO make paralel
for (int cluster_index = 0; cluster_index < cluster_spatial_centroids.Count; cluster_index++)
{
clusters.Add(new List <DomainType>());
for (int dimension_index = 0; dimension_index < image_labeling.Raster.DimensionCount; dimension_index++)
{
cluster_spatial_centroids[cluster_index][dimension_index] = 0;
}
}
// Aggregate cluster.
// TODO make paralel
for (int element_index = 0; element_index < element_count; element_index++)
{
int cluster_index = image_labeling.GetElementValue(element_index);
image_data.Raster.GetElementCoordinatesRBA(element_index, element_coordinates);
clusters[cluster_index].Add(image_data.GetElementValue(element_index));
ToolsMathCollectionInteger.AddFill(cluster_spatial_centroids[cluster_index], element_coordinates, cluster_spatial_centroids[cluster_index]);
}
// Compute new cluster centers.
// TODO make paralel
for (int cluster_index = 0; cluster_index < clusters.Count; cluster_index++)
{
if (clusters[cluster_index].Count != 0)
{
for (int dimension_index = 0; dimension_index < image_labeling.Raster.DimensionCount; dimension_index++)
{
cluster_spatial_centroids[cluster_index][dimension_index] /= clusters[cluster_index].Count;
}
cluster_feature_centroids[cluster_index] = d_centroid_feature_calculator.Compute(clusters[cluster_index]);
}
else
{
// reduce cluster count
cluster_feature_centroids.RemoveAt(cluster_index);
cluster_spatial_centroids.RemoveAt(cluster_index);
clusters.RemoveAt(cluster_index);
cluster_index--;
}
}
}
public Bitmap Render(IImageRaster <IRaster2DInteger, ElementType> source_image)
{
IRaster2DInteger raster = source_image.Raster;
Bitmap destination_image = new Bitmap(raster.Size0, raster.Size1);
for (int index_y = 0; index_y < raster.Size1; index_y++)
{
for (int index_x = 0; index_x < raster.Size0; index_x++)
{
destination_image.SetPixel(index_x, index_y, converter.Compute(source_image.GetElementValue(raster.GetElementIndex(index_x, index_y))));
}
}
return(destination_image);
}
public void AssignElements(
IImageRaster <IRasterType, int> image_labeling,
IImageRaster <IRasterType, float> image_distance,
IImageRaster <IRasterType, DomainType> image_data,
IList <int[]> cluster_spatial_centroids,
IList <DomainType> cluster_feature_centroids,
int[] neigbourhood_element_indexes)
{
int dimension_count = image_labeling.Raster.DimensionCount;
int[] element_coordinates = new int[dimension_count];
for (int element_index = 0; element_index < image_distance.Raster.ElementCount; element_index++)
{
image_distance.SetElementValue(element_index, Single.MaxValue);
}
//for each cluster
// TODO make paralel (Beware race conditoin in setting labeling and distance RB ordering might help or make it image driven)
for (int index_cluster = 0; index_cluster < cluster_spatial_centroids.Count; index_cluster++)
{
DomainType centroid = cluster_feature_centroids[index_cluster];
int[] coordinates_cluster = cluster_spatial_centroids[index_cluster];
//for each pixel in a region around the cluster neigbourhood
image_data.Raster.GetNeigbourhoodElementIndexesRBA(coordinates_cluster, this.d_cluster_dimensions, neigbourhood_element_indexes);
for (int element_index_index = 0; element_index_index < neigbourhood_element_indexes.Length; element_index_index++)
{
int index_element = neigbourhood_element_indexes[element_index_index];
if (index_element != -1)
{
image_data.Raster.GetElementCoordinatesRBA(index_element, element_coordinates);
//Compute the distance D between the element and the cluster.
float distance = 0;
for (int dimension_index = 0; dimension_index < dimension_count; dimension_index++)
{
float dimension_distance = ((float)Math.Abs(coordinates_cluster[dimension_index] - element_coordinates[dimension_index])) / this.d_cluster_dimensions[dimension_index];
distance += dimension_distance * dimension_distance;
}
distance += d_distance_features.Compute(centroid, image_data.GetElementValue(index_element)) * this.feature_weight;
//Compute if it is less than the current distance update cluster membership
if (distance < image_distance.GetElementValue(index_element))
{
image_labeling.SetElementValue(index_element, index_cluster);
image_distance.SetElementValue(index_element, distance);
}
}
}
}
}
public MaxTreeFloat3DFeaturesDouble(IImageRaster <IRaster3DInteger, float> image, FeatureGeneratorElementNode3DDouble generator, IProgressReporter reporter)
{
this.raster = image.Raster;
this.inner_max_tree = new MaxTreeBuilderSingleQueue <float>().BuildMaxTree(image.GetElementValues(false), new ComparerNatural <float>(), new TopologyElementRaster3D6Connectivity(image.Raster), image.Raster.ElementCount);
if (generator != null)
{
this.features = new double[inner_max_tree.NodeCount, generator.FeatureCount];
generator.GenerateFeaturesTree(raster, inner_max_tree.BottomLevelNode, features);
}
else
{
this.features = null;
}
}
public void TestInitialize()
{
int iteration_count = 1;
int [] desired_cluster_dimensions = new int [] { 3, 3, 3 };
SLIC3D slick = new SLIC3D(iteration_count, desired_cluster_dimensions, 1);
Tuple <IImageRaster <IRaster3DInteger, int>, IImageRaster <IRaster3DInteger, float>, IList <int[]>, IList <float[]> > initialization = slick.Initialize(new Raster3DInteger(9, 9, 9));
IImageRaster <IRaster3DInteger, int> image_labeling = initialization.Item1;
IImageRaster <IRaster3DInteger, float> image_distance = initialization.Item2;
IList <int[]> cluster_spatial_centroids = initialization.Item3;
IList <float[]> cluster_feature_centroids = initialization.Item4;
Assert.AreEqual(27, cluster_spatial_centroids.Count);
}
public static ImageRaster <CommonRasterType, ToElementType> Convert <CommonRasterType, FromElementType, ToElementType>(
IImageRaster <CommonRasterType, FromElementType> source,
IFunction <FromElementType, ToElementType> converter)
where CommonRasterType : IRasterInteger
{
CommonRasterType raster = source.Raster;
int element_count = raster.ElementCount;
ToElementType [] image = new ToElementType[element_count];
Parallel.For(0, element_count, element_index =>
{
image[element_index] = converter.Compute(source.GetElementValue(element_index));
});
return(new ImageRaster <CommonRasterType, ToElementType>(raster, image, false));
}
public BitmapSource Render(RenderSourceType render_source)
{
IImageRaster <IRaster2DInteger, ElementValueType> rendered_image = inner_renderer.Render(render_source);
BitmapFast bitmap_fast = new BitmapFast(rendered_image.Raster.Size0, rendered_image.Raster.Size1);
bitmap_fast.Lock();
for (int y_index = 0; y_index < rendered_image.Raster.Size1; y_index++)
{
for (int x_index = 0; x_index < rendered_image.Raster.Size0; x_index++)
{
bitmap_fast.SetPixel(x_index, y_index, converter.Compute(rendered_image.GetElementValue(rendered_image.Raster.GetElementIndex(x_index, y_index))));
}
}
bitmap_fast.Unlock();
return(ToolsRendering.CreateBitmapSourceFromBitmap(bitmap_fast.Bitmap));
}
public ImageRaster2DWrapperSlice4D(IImageRaster <IRaster4DInteger, RangeType> image, int index_2, int index_3)
{
if (image.Raster.Size2 <= index_2)
{
throw new Exception("index_2 with value " + index_2 + " out of bounds size_2 = " + image.Raster.Size2);
}
if (image.Raster.Size3 <= index_3)
{
throw new Exception("index_3 with value " + index_3 + " out of bounds size_3 = " + image.Raster.Size3);
}
Raster = new Raster2DInteger(image.Raster.Size0, image.Raster.Size1);
this.wrapped_image = image;
this.index_2 = index_2;
this.index_3 = index_3;
}
public BitmapFast Render(RenderSourceType render_source)
{
IImageRaster <IRaster2DInteger, ElementValueType> rendered_image = inner_renderer.Render(render_source);
BitmapFast bitmap_fast = new BitmapFast(rendered_image.Raster.Size0, rendered_image.Raster.Size1);
bitmap_fast.Lock();
//for (int y_index = 0; y_index < rendered_image.Raster.SizeY; y_index++)
//{
Parallel.For(0, rendered_image.Raster.Size1, y_index =>
{
for (int x_index = 0; x_index < rendered_image.Raster.Size0; x_index++)
{
bitmap_fast.SetPixel(x_index, y_index, converter.Compute(rendered_image.GetElementValue(rendered_image.Raster.GetElementIndex(x_index, y_index))));
}
});
bitmap_fast.Unlock();
return(bitmap_fast);
}
public IImageRaster <IRaster3DInteger, float> Predict(IImageRaster <IRaster3DInteger, float []> feature_image)
{
AlphaPartitionTree3D <float[], float> tree = new AlphaPartitionTree3D <float[], float>(
builder,
topology,
edge_model,
feature_image);
IList <IElementTreeNode <float> > nodes = tree.GetSmallestSatisfiers(node_detector);
IImageRaster <IRaster3DInteger, float> image = new ImageRaster3D <float>(feature_image.Raster, Single.MaxValue);
for (int element_index = 0; element_index < nodes.Count; element_index++)
{
}
return(image);
}
public static void SetOverlay <RasterType, DomainType> (
IImageRaster <RasterType, DomainType> destination,
IImageRaster <RasterType, bool> overlay_mask,
DomainType overlay_value)
where RasterType : IRasterInteger
{
if (!destination.Raster.Equals(overlay_mask.Raster))
{
throw new Exception("Raster mismatch");
}
Parallel.For(0, overlay_mask.Raster.ElementCount, element_index =>
{
if (overlay_mask.GetElementValue(element_index))
{
destination.SetElementValue(element_index, overlay_value);
}
});
}
public Bitmap Render(IImageRaster <IRaster3DInteger, ElementType> source_image)
{
IRaster3DInteger raster = source_image.Raster;
Bitmap destination_image = new Bitmap(raster.Size0, raster.Size1);
for (int index_y = 0; index_y < raster.Size1; index_y++)
{
for (int index_x = 0; index_x < raster.Size0; index_x++)
{
ElementType mean_value = source_image.GetElementValue(raster.GetElementIndex(index_x, index_y, 0));
for (int index_z = 1; index_z < raster.Size2; index_z++)
{
mean_value = this.algebra.Add(mean_value, source_image.GetElementValue(raster.GetElementIndex(index_x, index_y, index_z)));
}
mean_value = algebra.Divide(mean_value, this.algebra.ToDomain(raster.Size2));
destination_image.SetPixel(index_x, index_y, this.converter.Compute(mean_value));
}
}
return(destination_image);
}
public void TestComputeCentroids()
{
int iteration_count = 1;
int[] desired_cluster_dimensions = new int[] { 5, 5, 1 };
SLIC3D slick = new SLIC3D(iteration_count, desired_cluster_dimensions, 1);
IRaster3DInteger raster = new Raster3DInteger(100, 100, 1);
IList <IImageRaster <IRaster3DInteger, float> > stack = new List <IImageRaster <IRaster3DInteger, float> >();
stack.Add(new ImageRaster3D <float>(raster, 0));
stack.Add(new ImageRaster3D <float>(raster, 0));
stack.Add(new ImageRaster3D <float>(raster, 0));
IImageRaster <IRaster3DInteger, float[]> image_features = new ImageRasterWrapperStack <IRaster3DInteger, float>(stack);
Tuple <IImageRaster <IRaster3DInteger, int>, IImageRaster <IRaster3DInteger, float>, IList <int[]>, IList <float[]> > initialization = slick.Initialize(raster);
IImageRaster <IRaster3DInteger, int> image_labeling = initialization.Item1;
IImageRaster <IRaster3DInteger, float> image_distance = initialization.Item2;
IList <int[]> cluster_spatial_centroids = initialization.Item3;
IList <float[]> cluster_feature_centroids = initialization.Item4;
slick.ComputeCentroids(image_labeling, image_features, cluster_spatial_centroids, cluster_feature_centroids);
}
public static void GetShellRBA <RasterType>(IImageRaster <RasterType, bool> source, ITopologyElement topology, IImageRaster <RasterType, bool> target, bool border_is_shell)
where RasterType : IRasterInteger
{
int[] element_neigbour_array = new int[topology.MaximumConnectivity];
for (int element_index = 0; element_index < source.Raster.ElementCount; element_index++)
{
if (source.GetElementValue(element_index))
{
bool is_shell = false;
topology.ElementNeighboursRBA(element_index, element_neigbour_array);
foreach (int other_element_index in element_neigbour_array)
{
if (other_element_index != -1)
{
if (!source.GetElementValue(other_element_index))
{
is_shell = true;
}
}
else
{
if (border_is_shell)
{
is_shell = true;
}
}
}
if (is_shell)
{
target.SetElementValue(element_index, true);
}
}
}
}
public void ImproveLabeling(
IImageRaster <RasterType, int> initial_labeling,
IImageRaster <RasterType, int> new_labeling,
IList <IImageRaster <RasterType, FeatureType> > feature_images)
{
int element_count = initial_labeling.Raster.ElementCount;
int neighborhood_size = 0;
int [] element_coordinates = new int [initial_labeling.Raster.DimensionCount];
int [] element_neighborhood_indexes = new int [this.neighborhood_element_count];
int [] state_vector = new int [this.neighborhood_element_count];
FeatureType [] feature_neighborhood_values = new FeatureType [neighborhood_size];
FeatureType [] feature_vector = new FeatureType [neighborhood_size];
for (int element_index = 0; element_index < element_count; element_index++)
{
initial_labeling.Raster.GetNeigbourhoodElementIndexesRBA(element_coordinates, this.neighborhood_size, element_neighborhood_indexes);
// initial_labeling.GetElementValuesFill(element_neighborhood_indexes, this.background_label, state_vector);
for (int feature_image_index = 0; feature_image_index < feature_image_count; feature_image_index++)
{
//feature_images[feature_image_index].GetElementValuesFill(element_neighborhood_indexes, this.background_feature, feature_neighborhood_values);
Array.Copy(feature_neighborhood_values, 0, feature_vector, this.neighborhood_element_count * feature_image_index, this.neighborhood_element_count);
}
float best_likelyhood = Single.MinValue;
for (int label_index = 0; label_index < this.label_count; label_index++)
{
float likelyhood = label_likelyhood_models[label_index].Compute(state_vector) * feature_likelyhood_models[label_index].Compute(feature_vector);
if (best_likelyhood < likelyhood)
{
best_likelyhood = likelyhood;
new_labeling.SetElementValue(label_index, label_index);
}
}
}
}
public void TestSlick3Cluster()
{
int iteration_count = 5;
int[] desired_cluster_dimensions = new int[] { 5, 1, 1 };
SLIC3D slick = new SLIC3D(iteration_count, desired_cluster_dimensions, 1);
IRaster3DInteger raster = new Raster3DInteger(15, 1, 1);
IList <IImageRaster <IRaster3DInteger, float> > stack = new List <IImageRaster <IRaster3DInteger, float> >();
IImageRaster <IRaster3DInteger, float> feature_image = new ImageRaster3D <float>(raster, 0);
for (int element_index = 3; element_index < 12; element_index++)
{
feature_image.SetElementValue(element_index, 1);
}
stack.Add(feature_image);
IImageRaster <IRaster3DInteger, float[]> image_features = new ImageRasterWrapperStack <IRaster3DInteger, float>(stack);
Tuple <IImageRaster <IRaster3DInteger, int>, IImageRaster <IRaster3DInteger, float>, IList <int[]>, IList <float[]> > initialization = slick.Initialize(raster);
IImageRaster <IRaster3DInteger, int> image_labeling = initialization.Item1;
IImageRaster <IRaster3DInteger, float> image_distance = initialization.Item2;
IList <int[]> cluster_spatial_centroids = initialization.Item3;
IList <float[]> cluster_feature_centroids = initialization.Item4;
Assert.AreEqual(3, cluster_spatial_centroids.Count);
slick.ComputeCentroids(image_labeling, image_features, cluster_spatial_centroids, cluster_feature_centroids);
int [] neigbourhood_element_indexes = new int [99];
for (int iteration_index = 0; iteration_index < iteration_count; iteration_index++)
{
slick.AssignElements(image_labeling, image_distance, image_features, cluster_spatial_centroids, cluster_feature_centroids, neigbourhood_element_indexes);
slick.ComputeCentroids(image_labeling, image_features, cluster_spatial_centroids, cluster_feature_centroids);
}
Assert.AreEqual(3, cluster_spatial_centroids.Count);
for (int element_index = 3; element_index < 12; element_index++)
{
Assert.AreEqual(1, feature_image.GetElementValue(element_index));
}
}
public Bitmap Render(IImageRaster <IRaster3DInteger, ElementType> source_image)
{
IRaster3DInteger raster = source_image.Raster;
Bitmap destination_image = new Bitmap(raster.Size0, raster.Size1);
for (int index_y = 0; index_y < raster.Size1; index_y++)
{
for (int index_x = 0; index_x < raster.Size0; index_x++)
{
ElementType max_value = source_image.GetElementValue(raster.GetElementIndex(index_x, index_y, 0));
for (int index_z = 1; index_z < raster.Size2; index_z++)
{
ElementType value = source_image.GetElementValue(raster.GetElementIndex(index_x, index_y, index_z));
if (this.comparer.Compare(max_value, value) == -1)
{
max_value = value;
}
}
destination_image.SetPixel(index_x, index_y, this.converter.Compute(max_value));
}
}
return(destination_image);
}
public Tuple <IImageRaster <IRasterType, int>, IList <int[]>, IList <DomainType> > Cluster(IImageRaster <IRasterType, DomainType> image_features)
{
Debug.Assert(image_features.Raster.DimensionCount == d_cluster_dimensions.Length);
//Initialize cluster spatial centress at regular grid steps S.
Tuple <IImageRaster <IRasterType, int>, IImageRaster <IRasterType, float>, IList <int[]>, IList <DomainType> > initialization = Initialize(image_features.Raster);
IImageRaster <IRasterType, int> image_labeling = initialization.Item1;
IImageRaster <IRasterType, float> image_distance = initialization.Item2;
IList <int[]> cluster_spatial_centroids = initialization.Item3;
IList <DomainType> cluster_feature_centroids = initialization.Item4;
int dimensions_count = image_features.Raster.DimensionCount;
int cluster_count = cluster_spatial_centroids.Count;
// Find out how big the neighborhood should be
int count_neigbourhood_elements = 1;
for (int index_dimension = 0; index_dimension < dimensions_count; index_dimension++)
{
count_neigbourhood_elements *= (d_cluster_dimensions[index_dimension] * 2) + 1;
}
int[] neigbourhood_element_indexes = new int[count_neigbourhood_elements];
//Initialize cluster feature centroids at their suposed positions
ComputeCentroids(image_labeling, image_features, cluster_spatial_centroids, cluster_feature_centroids);
for (int iteration_index = 0; iteration_index < d_iteration_count; iteration_index++)
{
AssignElements(image_labeling, image_distance, image_features, cluster_spatial_centroids, cluster_feature_centroids, neigbourhood_element_indexes);
ComputeCentroids(image_labeling, image_features, cluster_spatial_centroids, cluster_feature_centroids);
}
//TODO postprocessing Remove small isolated components
return(new Tuple <IImageRaster <IRasterType, int>, IList <int[]>, IList <DomainType> >(image_labeling, cluster_spatial_centroids, cluster_feature_centroids));
}
public ImageSpace3DCast(IImageRaster <IRaster3DInteger, RangeType> image, float[] space_size, RangeType background_value)
{
this.image = image;
this.space_size = space_size;
this.background_value = background_value;
}
public MaxTreeFloat3DFeaturesDouble(IImageRaster <IRaster3DInteger, float> image, FeatureGeneratorElementNode3DDouble generator)
: this(image, generator, null)
{
}
public MaxTreeFloat3DFeaturesDouble(IImageRaster <IRaster3DInteger, float> image, IProgressReporter reporter)
: this(image, null, reporter)
{
}
public ImageRaster3D(IImageRaster <IRaster2DInteger, RangeType> other, bool copy_values)
: this(other.Raster.Size0, other.Raster.Size1, 1, other.GetElementValues(copy_values), false)
{
}
public ImageRaster3D(IImageRaster <IRaster3DInteger, RangeType> other)
: this(other.Raster, other.GetElementValues(true), false)
{
}