void executeAlgorithmOnHost(Image::pointer input, Image::pointer output) { ImageAccess inputAccess = input->getImageAccess(ACCESS_READ); ImageAccess outputAccess = output->getImageAccess(ACCESS_READ_WRITE); T * inputData = (T*)inputAccess.get(); T * outputData = (T*)outputAccess.get(); unsigned int nrOfElements = input->getWidth()*input->getHeight()*input->getDepth()*input->getNrOfComponents(); for(unsigned int i = 0; i < nrOfElements; i++) { outputData[i] = 2.0*inputData[i]; } }
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); } }}} } }
static igtl::ImageMessage::Pointer createIGTLImageMessage(Image::pointer image) { // size parameters int size[3] = {(int)image->getWidth(), (int)image->getHeight(), (int)image->getDepth()}; // image dimension float spacing[3] = {image->getSpacing().x(), image->getSpacing().y(), image->getSpacing().z()}; // spacing (mm/pixel) int svoffset[3] = {0, 0, 0}; // sub-volume offset int scalarType; size_t totalSize = image->getWidth()*image->getHeight()*image->getDepth()*image->getNrOfChannels(); switch(image->getDataType()) { case TYPE_UINT8: scalarType = igtl::ImageMessage::TYPE_UINT8; totalSize *= sizeof(unsigned char); break; case TYPE_INT8: scalarType = igtl::ImageMessage::TYPE_INT8; totalSize *= sizeof(char); break; case TYPE_UINT16: scalarType = igtl::ImageMessage::TYPE_UINT16; totalSize *= sizeof(unsigned short); break; case TYPE_INT16: scalarType = igtl::ImageMessage::TYPE_INT16; totalSize *= sizeof(short); break; case TYPE_FLOAT: scalarType = igtl::ImageMessage::TYPE_FLOAT32; totalSize *= sizeof(float); break; } //------------------------------------------------------------ // Create a new IMAGE type message igtl::ImageMessage::Pointer imgMsg = igtl::ImageMessage::New(); imgMsg->SetDimensions(size); imgMsg->SetSpacing(spacing); imgMsg->SetNumComponents(image->getNrOfChannels()); imgMsg->SetScalarType(scalarType); imgMsg->SetDeviceName("DummyImage"); imgMsg->SetSubVolume(size, svoffset); imgMsg->AllocateScalars(); ImageAccess::pointer access = image->getImageAccess(ACCESS_READ); memcpy(imgMsg->GetScalarPointer(), access->get(), totalSize); return imgMsg; }
void executeAlgorithmOnHost(Image::pointer input, Image::pointer output, unsigned char group, unsigned char window, float strength, unsigned char sigma) { throw Exception("This is on host, does not work atm"); ImageAccess::pointer inputAccess = input->getImageAccess(ACCESS_READ); ImageAccess::pointer outputAccess = output->getImageAccess(ACCESS_READ_WRITE); T * inputData = (T*)inputAccess->get(); T * outputData = (T*)outputAccess->get(); unsigned int width = input->getWidth(); unsigned int height = input->getHeight(); //Window is window-1/2 //group is group-1/2 //strength is strength*strength //sigma is sigma*sigma //Not working atm with the T //Does not work with outofbounds atm //So this code is for all pixels inbound, meaning x + group + window < width / x - group - window > 0 //same for y for (int x = 0; x < width; x++){ for (int y = 0; y < height; y++){ double normSum = 0.0; double totSum = 0.0; double indi = 0.0; double groupTot = 0.0; double value = 0.0; for (int i = x - window; i <= x + window; i++){ for (int j = y - window; j <= y + window; j++){ if (i != x && j != y){ int mX = x - group; int mY = y - group; for (int k = i - group; k <= i + group; k++, mX++){ for (int l = j - group; l <= j + group; l++, mY++){ //This is wrong, need to fix T //indi = inputData[mX][mY] - inputData[k][l]; indi = abs(indi*indi); indi = exp( - (indi/strength)); groupTot += indi; } } //This is wrong, need to fix T //value = inputData[i][j]; double pA[] = {i,j}; double pB[] = {x,y}; //double dist = i, j - x, y; double dist = std::inner_product(std::begin(pA), std::end(pA), std::begin(pB), 0.0); double gaussWeight = exp(-(dist / (2.0 * sigma))); gaussWeight = gaussWeight / (2.0 * sigma); groupTot *= gaussWeight; normSum += groupTot; totSum += groupTot * value; groupTot = 0.0; } } } value = totSum / normSum; /* Not sure it needed if (value < 0){ value = 0; } if (value > 1.0){ value = 1.0f; } */ //This is wrong, need to fix T //outputData[x][y] = (T)value; } } }
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); } }