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);
}
}
