void VTKMeshFileExporter::execute() {
if(mFilename == "")
throw Exception("No filename given to the VTKMeshFileExporter");
Mesh::pointer surface = getStaticInputData<Mesh>();
// Get transformation
AffineTransformation::pointer transform = SceneGraph::getAffineTransformationFromData(surface);
std::ofstream file(mFilename.c_str());
if(!file.is_open())
throw Exception("Unable to open the file " + mFilename);
// Write header
file << "# vtk DataFile Version 3.0\n"
"vtk output\n"
"ASCII\n"
"DATASET POLYDATA\n";
// Write vertices
MeshAccess::pointer access = surface->getMeshAccess(ACCESS_READ);
std::vector<MeshVertex> vertices = access->getVertices();
file << "POINTS " << vertices.size() << " float\n";
for(int i = 0; i < vertices.size(); i++) {
MeshVertex vertex = vertices[i];
vertex.position = (transform->matrix()*vertex.position.homogeneous()).head(3);
file << vertex.position.x() << " " << vertex.position.y() << " " << vertex.position.z() << "\n";
}
// Write triangles
std::vector<Vector3ui> triangles = access->getTriangles();
file << "POLYGONS " << surface->getNrOfTriangles() << " " << surface->getNrOfTriangles()*4 << "\n";
for(int i = 0; i < triangles.size(); i++) {
Vector3ui triangle = triangles[i];
file << "3 " << triangle.x() << " " << triangle.y() << " " << triangle.z() << "\n";
}
// Write normals
file << "POINT_DATA " << vertices.size() << "\n";
file << "NORMALS Normals float\n";
for(int i = 0; i < vertices.size(); i++) {
MeshVertex vertex = vertices[i];
// Transform it
vertex.normal = transform->linear()*vertex.normal;
// Normalize it
float length = vertex.normal.norm();
if(length == 0) { // prevent NaN situations
file << "0 1 0\n";
} else {
file << (vertex.normal.x()/length) << " " << (vertex.normal.y()/length) << " " << (vertex.normal.z()/length) << "\n";
}
}
file.close();
}
void setScalarAsFloat(T* data, uint position, Image::pointer image, float value, uchar channel) {
Vector3ui size = image->getSize();
if(position >= size.x()*size.y()*size.z())
throw OutOfBoundsException();
uint address = position*image->getNrOfComponents() + channel;
if(image->getDataType() == TYPE_SNORM_INT16) {
data[address] = value * 32767.0f;;
} else if(image->getDataType() == TYPE_UNORM_INT16) {
data[address] = value * 65535.0f;;
} else {
data[address] = value;
}
}
float getScalarAsFloat(T* data, uint position, Image::pointer image, uchar channel) {
Vector3ui size = image->getSize();
if(position >= size.x()*size.y()*size.z())
throw OutOfBoundsException();
T value = data[position*image->getNrOfComponents() + channel];
float floatValue;
if(image->getDataType() == TYPE_SNORM_INT16) {
floatValue = std::max(-1.0f, (float)value / 32767.0f);
} else if(image->getDataType() == TYPE_UNORM_INT16) {
floatValue = (float)value / 65535.0f;
} else {
floatValue = value;
}
return floatValue;
}
void LODNode::computeWorldBox_( const Vector3ui &levelTotalBlockDimensions )
{
Vector3f lBoxCoordMin( getAbsolutePosition( ));
Vector3f lBoxCoordMax( lBoxCoordMin + Vector3i( 1 ));
const size_t index = levelTotalBlockDimensions.find_max_index();
lBoxCoordMin = lBoxCoordMin / levelTotalBlockDimensions[index];
lBoxCoordMax = lBoxCoordMax / levelTotalBlockDimensions[index];
worldBox_ = Boxf( lBoxCoordMin, lBoxCoordMax );
}
void Dilation::execute() {
Image::pointer input = getInputData<Image>();
if(input->getDataType() != TYPE_UINT8) {
throw Exception("Data type of image given to Dilation must be UINT8");
}
Image::pointer output = getOutputData<Image>();
output->createFromImage(input);
SceneGraph::setParentNode(output, input);
output->fill(0);
OpenCLDevice::pointer device = std::dynamic_pointer_cast<OpenCLDevice>(getMainDevice());
cl::CommandQueue queue = device->getCommandQueue();
cl::Program program = getOpenCLProgram(device);
cl::Kernel dilateKernel(program, "dilate");
Vector3ui size = input->getSize();
OpenCLImageAccess::pointer access = input->getOpenCLImageAccess(ACCESS_READ, device);
dilateKernel.setArg(0, *access->get3DImage());
dilateKernel.setArg(2, mSize/2);
if(!device->isWritingTo3DTexturesSupported()) {
OpenCLBufferAccess::pointer access2 = output->getOpenCLBufferAccess(ACCESS_READ_WRITE, device);
dilateKernel.setArg(1, *access2->get());
queue.enqueueNDRangeKernel(
dilateKernel,
cl::NullRange,
cl::NDRange(size.x(), size.y(), size.z()),
cl::NullRange
);
} else {
OpenCLImageAccess::pointer access2 = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
dilateKernel.setArg(1, *access2->get3DImage());
queue.enqueueNDRangeKernel(
dilateKernel,
cl::NullRange,
cl::NDRange(size.x(), size.y(), size.z()),
cl::NullRange
);
}
}
/*===========================================================================*/
void ExtractEdges::calculate_connections( const kvs::StructuredVolumeObject* volume )
{
const size_t line_size = volume->numberOfNodesPerLine();
const size_t slice_size = volume->numberOfNodesPerSlice();
const Vector3ui resolution( volume->resolution() );
const size_t nedges =
3 * ( resolution.x() - 1 ) * ( resolution.y() - 1 ) * ( resolution.z() - 1 ) +
2 * ( resolution.x() - 1 ) * ( resolution.y() - 1 ) +
2 * ( resolution.y() - 1 ) * ( resolution.z() - 1 ) +
2 * ( resolution.z() - 1 ) * ( resolution.x() - 1 ) +
resolution.x() - 1 + resolution.y() - 1 + resolution.z() - 1;
kvs::ValueArray<kvs::UInt32> connections( 2 * nedges );
kvs::UInt32* connection = connections.data();
kvs::UInt32 volume_vertex = 0;
kvs::UInt32 connection_index = 0;
for ( size_t z = 0; z < resolution.z(); ++z )
{
for ( size_t y = 0; y < resolution.y(); ++y )
{
for ( size_t x = 0; x < resolution.x(); ++x )
{
if ( x != resolution.x() - 1 )
{
connection[ connection_index++ ] = volume_vertex;
connection[ connection_index++ ] = volume_vertex + 1;
}
if ( y != resolution.y() - 1 )
{
connection[ connection_index++ ] = volume_vertex;
connection[ connection_index++ ] = volume_vertex + line_size;
}
if ( z != resolution.z() - 1 )
{
connection[ connection_index++ ] = volume_vertex;
connection[ connection_index++ ] = volume_vertex + slice_size;
}
++volume_vertex;
}
}
}
SuperClass::setConnections( connections );
}
bool fillRegularVolumeInfo(VolumeInformation& info)
{
info.worldSpacePerVoxel = 1.0f / float(info.voxels.find_max());
info.worldSize = Vector3f(info.voxels[0], info.voxels[1], info.voxels[2]) *
info.worldSpacePerVoxel;
// Create the rootNode of the LOD hierarchy
const Vector3ui blockSize = info.maximumBlockSize - info.overlap * 2;
const Vector3ui numBlocks(std::ceil(float(info.voxels.x()) / blockSize.x()),
std::ceil(float(info.voxels.y()) / blockSize.y()),
std::ceil(float(info.voxels.z()) /
blockSize.z()));
const Vector3ui lodLevels(std::ceil(std::log2(numBlocks.x())),
std::ceil(std::log2(numBlocks.y())),
std::ceil(std::log2(numBlocks.z())));
const uint32_t depth = lodLevels.find_min();
const Vector3ui rootNodeBlocksCount(
std::ceil(float(info.voxels.x() >> depth) / blockSize.x()),
std::ceil(float(info.voxels.y() >> depth) / blockSize.y()),
std::ceil(float(info.voxels.z() >> depth) / blockSize.z()));
info.rootNode = RootNode(depth + 1, rootNodeBlocksCount);
return true;
}
bool checkCompatibility( const Vector3ui& volumeDim,
const Vector3ui& blockSize )
{
if( volumeDim.x() % blockSize.x() )
return false;
if( volumeDim.y() % blockSize.y() )
return false;
if( volumeDim.z() % blockSize.z() )
return false;
if( !isPowerOfTwo( volumeDim.x() / blockSize.x() ) )
return false;
if( !isPowerOfTwo( volumeDim.y() / blockSize.y() ) )
return false;
if( !isPowerOfTwo( volumeDim.z() / blockSize.z() ) )
return false;
return true;
}
cl::size_t<3> createRegion(Vector3ui size) {
return createRegion(size.x(), size.y(), size.z());
}
void SeededRegionGrowing::executeOnHost(T* input, Image::pointer output) {
ImageAccess::pointer outputAccess = output->getImageAccess(ACCESS_READ_WRITE);
uchar* outputData = (uchar*)outputAccess->get();
// initialize output to all zero
memset(outputData, 0, output->getWidth()*output->getHeight()*output->getDepth());
std::stack<Vector3ui> queue;
// Add seeds to queue
for(int i = 0; i < mSeedPoints.size(); i++) {
Vector3ui pos = mSeedPoints[i];
// Check if seed point is in bounds
if(pos.x() < 0 || pos.y() < 0 || pos.z() < 0 ||
pos.x() >= output->getWidth() || pos.y() >= output->getHeight() || pos.z() >= output->getDepth())
throw Exception("One of the seed points given to SeededRegionGrowing was out of bounds.");
queue.push(pos);
}
// Process queue
while(!queue.empty()) {
Vector3ui pos = queue.top();
queue.pop();
// Add neighbors to queue
for(int a = -1; a < 2; a++) {
for(int b = -1; b < 2; b++) {
for(int c = -1; c < 2; c++) {
if(abs(a)+abs(b)+abs(c) != 1) // connectivity
continue;
Vector3ui neighbor(pos.x()+a,pos.y()+b,pos.z()+c);
// Check for out of bounds
if(neighbor.x() < 0 || neighbor.y() < 0 || neighbor.z() < 0 ||
neighbor.x() >= output->getWidth() || neighbor.y() >= output->getHeight() || neighbor.z() >= output->getDepth())
continue;
// Check that voxel is not already segmented
if(outputData[neighbor.x()+neighbor.y()*output->getWidth()+neighbor.z()*output->getWidth()*output->getHeight()] == 1)
continue;
// Check condition
T value = input[neighbor.x()+neighbor.y()*output->getWidth()+neighbor.z()*output->getWidth()*output->getHeight()];
if(value >= mMinimumIntensity && value <= mMaximumIntensity) {
// add it to segmentation
outputData[neighbor.x()+neighbor.y()*output->getWidth()+neighbor.z()*output->getWidth()*output->getHeight()] = 1;
// Add to queue
queue.push(neighbor);
}
}}}
}
}
void SeededRegionGrowing::execute() {
if(mSeedPoints.size() == 0)
throw Exception("No seed points supplied to SeededRegionGrowing");
Image::pointer input = getStaticInputData<Image>();
if(input->getNrOfComponents() != 1)
throw Exception("Seeded region growing currently doesn't support images with several components.");
Segmentation::pointer output = getStaticOutputData<Segmentation>();
// Initialize output image
output->createFromImage(input, getMainDevice());
if(getMainDevice()->isHost()) {
ImageAccess::pointer inputAccess = input->getImageAccess(ACCESS_READ);
void* inputData = inputAccess->get();
switch(input->getDataType()) {
fastSwitchTypeMacro(executeOnHost<FAST_TYPE>((FAST_TYPE*)inputData, output));
}
} else {
OpenCLDevice::pointer device = getMainDevice();
recompileOpenCLCode(input);
ImageAccess::pointer access = output->getImageAccess(ACCESS_READ_WRITE);
uchar* outputData = (uchar*)access->get();
// Initialize to all 0s
memset(outputData,0,sizeof(uchar)*output->getWidth()*output->getHeight()*output->getDepth());
// Add sedd points
for(int i = 0; i < mSeedPoints.size(); i++) {
Vector3ui pos = mSeedPoints[i];
// Check if seed point is in bounds
if(pos.x() < 0 || pos.y() < 0 || pos.z() < 0 ||
pos.x() >= output->getWidth() || pos.y() >= output->getHeight() || pos.z() >= output->getDepth())
throw Exception("One of the seed points given to SeededRegionGrowing was out of bounds.");
outputData[pos.x() + pos.y()*output->getWidth() + pos.z()*output->getWidth()*output->getHeight()] = 2;
}
access->release();
cl::NDRange globalSize;
if(output->getDimensions() == 2) {
globalSize = cl::NDRange(input->getWidth(),input->getHeight());
OpenCLImageAccess2D::pointer inputAccess = input->getOpenCLImageAccess2D(ACCESS_READ, device);
mKernel.setArg(0, *inputAccess->get());
} else {
globalSize = cl::NDRange(input->getWidth(),input->getHeight(), input->getDepth());
OpenCLImageAccess3D::pointer inputAccess = input->getOpenCLImageAccess3D(ACCESS_READ, device);
mKernel.setArg(0, *inputAccess->get());
}
OpenCLBufferAccess::pointer outputAccess = output->getOpenCLBufferAccess(ACCESS_READ_WRITE, device);
cl::Buffer stopGrowingBuffer = cl::Buffer(
device->getContext(),
CL_MEM_READ_WRITE,
sizeof(char));
cl::CommandQueue queue = device->getCommandQueue();
mKernel.setArg(1, *outputAccess->get());
mKernel.setArg(2, stopGrowingBuffer);
mKernel.setArg(3, mMinimumIntensity);
mKernel.setArg(4, mMaximumIntensity);
bool stopGrowing = false;
char stopGrowingInit = 1;
char * stopGrowingResult = new char;
int iterations = 0;
do {
iterations++;
queue.enqueueWriteBuffer(stopGrowingBuffer, CL_TRUE, 0, sizeof(char), &stopGrowingInit);
queue.enqueueNDRangeKernel(
mKernel,
cl::NullRange,
globalSize,
cl::NullRange
);
queue.enqueueReadBuffer(stopGrowingBuffer, CL_TRUE, 0, sizeof(char), stopGrowingResult);
if(*stopGrowingResult == 1)
stopGrowing = true;
} while(!stopGrowing);
}
}