bool
OsdCLKernelBundle::Compile(cl_context clContext,
int numVertexElements, int numVaryingElements) {
cl_int ciErrNum;
_numVertexElements = numVertexElements;
_numVaryingElements = numVaryingElements;
char constantDefine[256];
snprintf(constantDefine, sizeof(constantDefine),
"#define NUM_VERTEX_ELEMENTS %d\n"
"#define NUM_VARYING_ELEMENTS %d\n",
numVertexElements, numVaryingElements);
const char *sources[] = { constantDefine, clSource };
_clProgram = clCreateProgramWithSource(clContext, 2, sources, 0, &ciErrNum);
CL_CHECK_ERROR(ciErrNum, "clCreateProgramWithSource\n");
ciErrNum = clBuildProgram(_clProgram, 0, NULL, NULL, NULL, NULL);
if (ciErrNum != CL_SUCCESS) {
OsdError(OSD_CL_PROGRAM_BUILD_ERROR, "CLerr=%d", ciErrNum);
cl_int numDevices = 0;
clGetContextInfo(clContext, CL_CONTEXT_NUM_DEVICES,
sizeof(cl_uint), &numDevices, NULL);
cl_device_id *devices = new cl_device_id[numDevices];
clGetContextInfo(clContext, CL_CONTEXT_DEVICES,
sizeof(cl_device_id)*numDevices, devices, NULL);
for (int i = 0; i < numDevices; ++i) {
char cBuildLog[10240];
clGetProgramBuildInfo(_clProgram, devices[i], CL_PROGRAM_BUILD_LOG,
sizeof(cBuildLog), cBuildLog, NULL);
OsdError(OSD_CL_PROGRAM_BUILD_ERROR, cBuildLog);
}
delete[] devices;
return false;
}
_clBilinearEdge = buildKernel(_clProgram, "computeBilinearEdge");
_clBilinearVertex = buildKernel(_clProgram, "computeBilinearVertex");
_clCatmarkFace = buildKernel(_clProgram, "computeFace");
_clCatmarkEdge = buildKernel(_clProgram, "computeEdge");
_clCatmarkVertexA = buildKernel(_clProgram, "computeVertexA");
_clCatmarkVertexB = buildKernel(_clProgram, "computeVertexB");
_clLoopEdge = buildKernel(_clProgram, "computeEdge");
_clLoopVertexA = buildKernel(_clProgram, "computeVertexA");
_clLoopVertexB = buildKernel(_clProgram, "computeLoopVertexB");
_clVertexEditAdd = buildKernel(_clProgram, "editVertexAdd");
return true;
}
kernel device::buildKernelFromString(const std::string &content,
const std::string &kernelName,
const occa::properties &props) const {
occa::properties allProps = props + kernelProperties();
allProps["mode"] = mode();
hash_t kernelHash = (hash()
^ occa::hash(allProps)
^ occa::hash(content));
io::lock_t lock(kernelHash, "occa-device");
std::string stringSourceFile = io::hashDir(kernelHash);
stringSourceFile += "stringSource.okl";
if (lock.isMine()) {
if (!sys::fileExists(stringSourceFile)) {
io::write(stringSourceFile, content);
}
lock.release();
}
return buildKernel(stringSourceFile,
kernelName,
props);
}
bool DeconvolutionTool::doDeconvolution(QImage *inputImage, QImage *outputImage, Blur* blur) {
isProcessingCancelled = false;
// Create kernel
buildKernel(kernelMatrix, width, height, blur);
fftw_execute(realForwardKernelPlan);
// Fill processingContext
ProcessingContext* processingContext = new ProcessingContext();
processingContext->inputImage = inputImage;
processingContext->outputImage = outputImage;
processingContext->inputImageMatrix = inputImageMatrix;
processingContext->outputImageMatrix = outputImageMatrix;
processingContext->kernelFFT = kernelFFT;
processingContext->width = width;
processingContext->height = height;
processingContext->blur = blur;
if (blur->mode == PREVIEW_GRAY) {
doDeconvolutionForChannel(processingContext, GRAY);
} else {
QString progressText= "High-Quality";
if (blur->mode == PREVIEW_COLOR) {
progressText = "Color Preview";
}
setProgressInterval(10,40, progressText);
doDeconvolutionForChannel(processingContext, RED);
setProgressInterval(40,70, progressText);
doDeconvolutionForChannel(processingContext, GREEN);
setProgressInterval(70,100, progressText);
doDeconvolutionForChannel(processingContext, BLUE);
}
delete(processingContext);
return !isProcessingCancelled;
}
void OpenCL::init(int isGPU)
{
if (isGPU)
getDevices(CL_DEVICE_TYPE_GPU);
else
getDevices(CL_DEVICE_TYPE_CPU);
buildKernel();
}
PTEX_NAMESPACE_BEGIN
void PtexTriangleFilter::eval(float* result, int firstChan, int nChannels,
int faceid, float u, float v,
float uw1, float vw1, float uw2, float vw2,
float width, float blur)
{
// init
if (!_tx || nChannels <= 0) return;
if (faceid < 0 || faceid >= _tx->numFaces()) return;
_ntxchan = _tx->numChannels();
_dt = _tx->dataType();
_firstChanOffset = firstChan*DataSize(_dt);
_nchan = PtexUtils::min(nChannels, _ntxchan-firstChan);
// get face info
const FaceInfo& f = _tx->getFaceInfo(faceid);
// if neighborhood is constant, just return constant value of face
if (f.isNeighborhoodConstant()) {
PtexPtr<PtexFaceData> data ( _tx->getData(faceid, 0) );
if (data) {
char* d = (char*) data->getData() + _firstChanOffset;
Ptex::ConvertToFloat(result, d, _dt, _nchan);
}
return;
}
// clamp u and v
u = PtexUtils::clamp(u, 0.0f, 1.0f);
v = PtexUtils::clamp(v, 0.0f, 1.0f);
// build kernel
PtexTriangleKernel k;
buildKernel(k, u, v, uw1, vw1, uw2, vw2, width, blur, f.res);
// accumulate the weight as we apply
_weight = 0;
// allocate temporary result
_result = (float*) alloca(sizeof(float)*_nchan);
memset(_result, 0, sizeof(float)*_nchan);
// apply to faces
splitAndApply(k, faceid, f);
// normalize (both for data type and cumulative kernel weight applied)
// and output result
float scale = 1.0f / (_weight * OneValue(_dt));
for (int i = 0; i < _nchan; i++) result[i] = float(_result[i] * scale);
// clear temp result
_result = 0;
}
void device::loadKernels(const std::string &library) {
// TODO 1.1: Load kernels
#if 0
std::string devHash = hash().toFullString();
strVector dirs = io::directories("occa://" + library);
const int dirCount = (int) dirs.size();
int kernelsLoaded = 0;
for (int d = 0; d < dirCount; ++d) {
const std::string buildFile = dirs[d] + kc::buildFile;
if (!sys::fileExists(buildFile)) {
continue;
}
json info = json::read(buildFile)["info"];
if ((std::string) info["device/hash"] != devHash) {
continue;
}
++kernelsLoaded;
const std::string sourceFilename = dirs[d] + kc::parsedSourceFile;
json &kInfo = info["kernel"];
hash_t hash = hash_t::fromString(kInfo["hash"]);
jsonArray metadataArray = kInfo["metadata"].array();
occa::properties kernelProps = kInfo["props"];
// Ignore how the kernel was setup, turn off verbose
kernelProps["verbose"] = false;
const int kernels = metadataArray.size();
for (int k = 0; k < kernels; ++k) {
buildKernel(sourceFilename,
hash,
kernelProps,
lang::kernelMetadata::fromJson(metadataArray[k]));
}
}
// Print loaded info
if (properties().get("verbose", false) && kernelsLoaded) {
std::cout << "Loaded " << kernelsLoaded;
if (library.size()) {
std::cout << " ["<< library << "]";
} else {
std::cout << " cached";
}
std::cout << ((kernelsLoaded == 1)
? " kernel\n"
: " kernels\n");
}
#endif
}
bool Engine::start() {
bool retval {false};
m_media = std::make_unique<Media>();
if (m_media->init()) {
buildKernel();
if (buildModules()) {
m_kernel->start();
retval = true;
}
}
return retval;
}
bool
OsdClKernelDispatcher::ClKernel::Compile(cl_context clContext, int numVertexElements, int numVaryingElements) {
cl_int ciErrNum;
_numVertexElements = numVertexElements;
_numVaryingElements = numVaryingElements;
char constantDefine[256];
snprintf(constantDefine, 256, "#define NUM_VERTEX_ELEMENTS %d\n"
"#define NUM_VARYING_ELEMENTS %d\n", numVertexElements, numVaryingElements);
const char *sources[] = { constantDefine, clSource };
_clProgram = clCreateProgramWithSource(clContext, 2, sources, 0, &ciErrNum);
CL_CHECK_ERROR(ciErrNum, "clCreateProgramWithSource\n");
ciErrNum = clBuildProgram(_clProgram, 0, NULL, NULL, NULL, NULL);
if (ciErrNum != CL_SUCCESS) {
OSD_ERROR("ERROR in clBuildProgram %d\n", ciErrNum);
char cBuildLog[10240];
clGetProgramBuildInfo(_clProgram, _clDevice, CL_PROGRAM_BUILD_LOG,
sizeof(cBuildLog), cBuildLog, NULL);
OSD_ERROR(cBuildLog);
return false;
}
// -------
_clBilinearEdge = buildKernel(_clProgram, "computeBilinearEdge");
_clBilinearVertex = buildKernel(_clProgram, "computeBilinearVertex");
_clCatmarkFace = buildKernel(_clProgram, "computeFace");
_clCatmarkEdge = buildKernel(_clProgram, "computeEdge");
_clCatmarkVertexA = buildKernel(_clProgram, "computeVertexA");
_clCatmarkVertexB = buildKernel(_clProgram, "computeVertexB");
_clLoopEdge = buildKernel(_clProgram, "computeEdge");
_clLoopVertexA = buildKernel(_clProgram, "computeVertexA");
_clLoopVertexB = buildKernel(_clProgram, "computeLoopVertexB");
return true;
}
VolumeMaxCLProcessor::VolumeMaxCLProcessor()
: Processor()
, ProcessorKernelOwner(this)
, inport_("inVolume")
, outport_("outVolume")
, volumeRegionSize_("region", "Region size", 8, 1, 100)
, workGroupSize_("wgsize", "Work group size", ivec3(8), ivec3(0), ivec3(256))
, useGLSharing_("glsharing", "Use OpenGL sharing", true)
, supportsVolumeWrite_(false)
, tmpVolume_(nullptr)
, kernel_(nullptr) {
addPort(inport_);
addPort(outport_);
addProperty(volumeRegionSize_);
addProperty(workGroupSize_);
addProperty(useGLSharing_);
buildKernel();
}
///apply filter effect to the PixelBuffer* buffer passed into this function
void FBlur::applyFilter(PixelBuffer* imageBuffer){
// if kernel is already initialized, do not need initialize it again.
kernel = buildKernel(std::round(getFloatParameter()));
// printKernel();
if(getName() == "FEdgeDetection"){
imageBuffer -> convertToLuminance();
}
int width = imageBuffer -> getWidth();
int height = imageBuffer -> getHeight();
//create a new pixel buffer for storing the convolution result.
PixelBuffer* newImageBuffer
= new PixelBuffer(width, height, imageBuffer -> getBackgroundColor());
for(int i = 0; i < width; i++){
for(int j = 0; j < height; j++){
float newRed = 0;
float newGreen = 0;
float newBlue = 0;
for(size_t filterI = 0; filterI < kernel.size(); filterI++){
for(size_t filterJ = 0; filterJ < kernel[filterI].size(); filterJ++){
//The location imageI and imageJ is calculated so that
//for the center element of the filter it'll be i, j
int imageI = (i - kernel.size()/2 + filterI + width) % width;
int imageJ = (j - kernel[filterI].size()/2 + filterJ + height) % height;
ColorData currPixel = imageBuffer -> getPixel(imageI, imageJ);
newRed += currPixel.getRed() * kernel[filterI][filterJ];
newGreen += currPixel.getGreen()*kernel[filterI][filterJ];
newBlue += currPixel.getBlue()*kernel[filterI][filterJ];
}
}
ColorData newPixel = ColorData(newRed, newGreen, newBlue);
newPixel = newPixel.clampedColor();
newImageBuffer -> setPixel(i, j, newPixel);
}
}
newImageBuffer -> copyPixelBuffer(newImageBuffer, imageBuffer);
delete newImageBuffer;
}
JNIEXPORT jint JNICALL Java_pt_floraon_ecospace_nativeFunctions_computeKernelDensities(JNIEnv *env, jclass obj, jstring filename, jstring outfilename, jintArray variables,jint freqthresh,jfloat sigmapercent,jboolean downweight) {
// NOTE: "variables" must be in increasing order! 0 is latitude, 1 is longitude, 2... are the other climatic variables
const char *pfilename=(*env)->GetStringUTFChars(env, filename , NULL );
const char *poutfilename=(*env)->GetStringUTFChars(env, outfilename , NULL );
FILE *varsfile,*densfile,*freqfile;
int nvars,i,j,k,*freqs,ntaxafiltered=0,*mapIDs,*outIDs,d1,d2,d1from,d1to,d2from,d2to,d3from,d3to,d1kern,d2kern,sidesq;
int lastID=-1,d2p,kernelhalfside,kernelside,kernelsidesq;
register int d3p,d3;
register float *d3kern;
jsize nrecs;
jint ntaxa,*pIDs;
VARIABLE *vararray;
VARIABLEHEADER *varheader;
int nvarstouse=(int)(*env)->GetArrayLength(env,variables); // how many vars will be used for kernel density
jint *pvariables=(*env)->GetIntArrayElements(env, variables, 0);
float sigma;
float *kernel,*tmpdens;
unsigned long *weight;
DENSITY *densities;
bool anythingtosave=false,skiprec;
size_t dummy;
varsfile=fopen(STANDARDVARIABLEFILE(pfilename),"r");
dummy=fread(&nrecs,sizeof(jsize),1,varsfile);
dummy=fread(&ntaxa,sizeof(jint),1,varsfile);
dummy=fread(&nvars,sizeof(int),1,varsfile);
// fseek(varsfile,nvars*sizeof(tmp.filename)+sizeof(long)*ntaxa,SEEK_CUR);
fseek(varsfile,sizeof(long)*ntaxa,SEEK_CUR); // skip index
{ // redirect stdout to file
int fd;
fpos_t pos;
fflush(stdout);
fgetpos(stdout, &pos);
fd = dup(fileno(stdout));
FILE *dummy=freopen("logfile.txt", "a", stdout);
}
vararray=malloc(nvarstouse*nrecs*sizeof(VARIABLE));
varheader=malloc(nvarstouse*sizeof(VARIABLEHEADER));
pIDs=malloc(nrecs*sizeof(jint));
dummy=fread(pIDs,sizeof(jint),nrecs,varsfile);
fseek(varsfile,2*sizeof(jfloat)*nrecs,SEEK_CUR); // skip original coordinates
weight=malloc(sizeof(long)*nrecs);
dummy=fread(weight,sizeof(long),nrecs,varsfile);
for(i=0;i<nvarstouse;i++) {
fseek(varsfile,(sizeof(VARIABLEHEADER) + sizeof(VARIABLE)*nrecs)*(pvariables[i]-(i==0 ? 0 : (pvariables[i-1]+1))),SEEK_CUR);
dummy=fread(&varheader[i],sizeof(VARIABLEHEADER),1,varsfile);
printf("Variable %d: min %f max %f\n",pvariables[i],varheader[i].min,varheader[i].max);
dummy=fread(&vararray[i*nrecs],sizeof(VARIABLE),nrecs,varsfile);
}
// count the # of records of each taxon
freqs=calloc(ntaxa,sizeof(int));
for(i=0;i<nrecs;i++) freqs[pIDs[i]]++;
// write out frequencies in a text file (for java)
freqfile=fopen(FREQANALYSISFILE(pfilename),"w");
for(i=0;i<ntaxa;i++) fprintf(freqfile,"%d\n",freqs[i]);
fclose(freqfile);
// count the # of taxa after filtering out rarest
for(i=0;i<ntaxa;i++) if(freqs[i] >= freqthresh) ntaxafiltered++;
// create a mapping of IDs: because some IDs were removed, make them sequential without holes (remember that memory is the limiting factor here!)
mapIDs=malloc(ntaxa*sizeof(int));
for(i=0;i<ntaxa;i++) mapIDs[i]=-1;
for(i=0,j=0;i<nrecs;i++) {
if(freqs[pIDs[i]] >= freqthresh) {
if(mapIDs[pIDs[i]]==-1) {
mapIDs[pIDs[i]]=j;
j++;
}
}
}
//for(i=0;i<ntaxa;i++) printf("%d ",mapIDs[i]);
// compute the resolution of the multidimensional space so that not too much memory is occupied
side=(int)pow((float)(MAXMEMORYPERBATCH)/(float)ntaxafiltered,(float)1/nvarstouse);
if(side>MAXSIDE) side=MAXSIDE;
//side=40;
sidesq=side*side;
sigma=side*sigmapercent;
arraysize=(int)pow(side,nvarstouse);
printf("Using a grid with a side of %d cells, in %d variables (dimensions).\n",side,nvarstouse);
printf("Reading %d variables of %d records of %d taxa (after filtering out those with less than %d occurrences)...\n",nvars,nrecs,ntaxafiltered,freqthresh);
// build the kernel for this case
kernel=buildKernel(side,sigma,nvarstouse,&kernelhalfside,&kernelside,&kernelsidesq);
// compute densities
// allocate N multidimensional arrays (multidimensional grids to compute kernel densities in each cell)
densities=malloc(ntaxafiltered*sizeof(DENSITY));
outIDs=calloc(ntaxafiltered,sizeof(int));
for(i=0;i<ntaxafiltered;i++) {
densities[i].density=malloc(arraysize);
memset(densities[i].density,0,arraysize);
}
printf("Computing kernel densities");fflush(stdout);
// scale the variables to the size of the grid
for(i=0;i<nrecs;i++) {
for(k=0;k<nvarstouse;k++) {
if(vararray[i+nrecs*k]!=RASTERNODATA) vararray[i+nrecs*k]=(vararray[i+nrecs*k]*side)/10000;
}
}
#pragma omp parallel private(i,k,skiprec,tmpdens,anythingtosave,d1from,d1to,d1,d1kern,d2,d2from,d2to,d2p,d2kern,d3,d3from,d3to,d3p,d3kern)
{
tmpdens=malloc(arraysize*sizeof(float));
memset(tmpdens,0,arraysize*sizeof(float));
#pragma omp for
for(j=0;j<ntaxa;j++) { // NOTE: this loop doesn't need the records to be sorted, that's why it takes much longer
// TODO: we might have an index here, i.e. for each taxon, a list of tthe respective records, but it's so fast that maybe it's not a big issue, we're talking about a few thousands of taxa only.
if(freqs[j]<freqthresh) continue;
anythingtosave=false;
for(i=0;i<nrecs;i++) { // iterate through all records in search for this taxon ACK!! give me an index
if(pIDs[i]!=j) continue;
for(k=0,skiprec=false;k<nvarstouse;k++) { // check if any one of the variables is NA. if it is, skip this record
if(vararray[i+nrecs*k] == RASTERNODATA) {
skiprec=true;
break;
}
}
if(skiprec) continue; // skip NAs
// now yeah, create density surface by summing the kernels record by record
// since it is not computationally feasible more than 3 dimensions, just make the optimized code for each case...
switch(nvarstouse) {
case 1:
d1from=(vararray[i]-kernelhalfside)<0 ? 0 : (vararray[i]-kernelhalfside);
d1to=(vararray[i]+kernelhalfside+1>side ? side : vararray[i]+kernelhalfside+1);
for(d1=d1from,d1kern=vararray[i]-kernelhalfside<0 ? kernelhalfside-vararray[i] : 0;d1<d1to;d1++,d1kern++) {
tmpdens[d1]+=kernel[d1kern] * (downweight ? ((float)weight[i]/MULTIPLIER) : 1);
}
anythingtosave=true;
break;
case 2:
d1from=(vararray[i]-kernelhalfside)<0 ? 0 : (vararray[i]-kernelhalfside);
d1to=(vararray[i]+kernelhalfside+1>side ? side : vararray[i]+kernelhalfside+1);
d2from=(vararray[i+nrecs]-kernelhalfside)<0 ? 0 : (vararray[i+nrecs]-kernelhalfside);
d2to=(vararray[i+nrecs]+kernelhalfside+1>side ? side : vararray[i+nrecs]+kernelhalfside+1);
for(d1=d1from,d1kern=vararray[i]-kernelhalfside<0 ? kernelhalfside-vararray[i] : 0;d1<d1to;d1++,d1kern++) {
for(d2=d2from,d2p=d1+d2from*side,d2kern=d1kern+((vararray[i+nrecs]-kernelhalfside)<0 ? (kernelhalfside-vararray[i+nrecs])*kernelside : 0);d2<d2to;d2++,d2p+=side,d2kern+=kernelside) {
tmpdens[d2p]+=kernel[d2kern] * (downweight ? ((float)weight[i]/MULTIPLIER) : 1);
}
}
anythingtosave=true;
break;
case 3:
d1from=(vararray[i]-kernelhalfside)<0 ? 0 : (vararray[i]-kernelhalfside);
d1to=(vararray[i]+kernelhalfside+1>side ? side : vararray[i]+kernelhalfside+1);
d2from=(vararray[i+nrecs]-kernelhalfside)<0 ? 0 : (vararray[i+nrecs]-kernelhalfside);
d2to=(vararray[i+nrecs]+kernelhalfside+1>side ? side : vararray[i+nrecs]+kernelhalfside+1);
d3from=(vararray[i+nrecs*2]-kernelhalfside)<0 ? 0 : (vararray[i+nrecs*2]-kernelhalfside);
d3to=(vararray[i+nrecs*2]+kernelhalfside+1>side ? side : vararray[i+nrecs*2]+kernelhalfside+1);
for(d1=d1from,d1kern=vararray[i]-kernelhalfside<0 ? kernelhalfside-vararray[i] : 0;
d1<d1to;
d1++,d1kern++) {
for(d2=d2from,d2p=d1+d2from*side,d2kern=d1kern+((vararray[i+nrecs]-kernelhalfside)<0 ? (kernelhalfside-vararray[i+nrecs])*kernelside : 0)
;d2<d2to
;d2++,d2p+=side,d2kern+=kernelside) {
for(d3=d3from,d3p=d2p+d3from*sidesq
,d3kern=&kernel[d2kern+((vararray[i+nrecs*2]-kernelhalfside)<0 ? (kernelhalfside-vararray[i+nrecs*2])*kernelsidesq : 0)]
;d3<d3to
;d3++,d3p+=sidesq,d3kern+=kernelsidesq) {
tmpdens[d3p]+=*d3kern * (downweight ? ((float)weight[i]/MULTIPLIER) : 1);
//kernel[d3kern];
}
}
}
anythingtosave=true;
break;
}
} // end record loop
if(anythingtosave) {
saveKernelDensity(tmpdens,freqs[j],&densities[mapIDs[j]]); // save kernel density of previous taxon
outIDs[mapIDs[j]]=j;
} else {
saveKernelDensity(NULL, freqs[j], &densities[mapIDs[j]]); // save kernel density of previous taxon
outIDs[mapIDs[j]]=j;
// outIDs[mapIDs[j]]=-1;
}
anythingtosave = false;
memset(tmpdens,0,arraysize*sizeof(float));
printf(".");
fflush(stdout);
} // end taxon loop
}
/* THIS is the working code. Above still developing.
for(i=0;i<nrecs;i++) { // iterate through all records IMPORTANT: records must be sorted by taxon ID
if(freqs[pIDs[i]]>=freqthresh) {
if(pIDs[i]!=lastID) { // this record is already a different species
if(anythingtosave) {
saveKernelDensity(tmpdens,freqs[lastID],&densities[mapIDs[lastID]]); // save kernel density of previous taxon
outIDs[mapIDs[lastID]]=lastID;
} else outIDs[mapIDs[lastID]]=-1;
anythingtosave=false;
memset(tmpdens,0,arraysize*sizeof(float));
lastID=pIDs[i];
printf(".");
fflush(stdout);
}
// scale the variables to the size of the grid
for(j=0,skiprec=false;j<nvarstouse;j++) {
if(vararray[i+nrecs*j]==RASTERNODATA) {
skiprec=true;
continue;
} else vararray[i+nrecs*j]=(vararray[i+nrecs*j]*side)/10000;
}
if(skiprec) continue; // skip NAs
// now yeah, create density surface by summing the kernels record by record
// since it is not computationally feasible more than 3 dimensions, just make the optimized code for each case...
switch(nvarstouse) {
case 1:
d1from=(vararray[i]-kernelhalfside)<0 ? 0 : (vararray[i]-kernelhalfside);
d1to=(vararray[i]+kernelhalfside+1>side ? side : vararray[i]+kernelhalfside+1);
for(d1=d1from,d1kern=vararray[i]-kernelhalfside<0 ? kernelhalfside-vararray[i] : 0;d1<d1to;d1++,d1kern++) {
tmpdens[d1]+=kernel[d1kern] * (downweight ? ((float)weight[i]/MULTIPLIER) : 1);
}
anythingtosave=true;
break;
case 2:
d1from=(vararray[i]-kernelhalfside)<0 ? 0 : (vararray[i]-kernelhalfside);
d1to=(vararray[i]+kernelhalfside+1>side ? side : vararray[i]+kernelhalfside+1);
d2from=(vararray[i+nrecs]-kernelhalfside)<0 ? 0 : (vararray[i+nrecs]-kernelhalfside);
d2to=(vararray[i+nrecs]+kernelhalfside+1>side ? side : vararray[i+nrecs]+kernelhalfside+1);
for(d1=d1from,d1kern=vararray[i]-kernelhalfside<0 ? kernelhalfside-vararray[i] : 0;d1<d1to;d1++,d1kern++) {
for(d2=d2from,d2p=d1+d2from*side,d2kern=d1kern+((vararray[i+nrecs]-kernelhalfside)<0 ? (kernelhalfside-vararray[i+nrecs])*kernelside : 0);d2<d2to;d2++,d2p+=side,d2kern+=kernelside) {
tmpdens[d2p]+=kernel[d2kern] * (downweight ? ((float)weight[i]/MULTIPLIER) : 1);
}
}
anythingtosave=true;
break;
case 3:
d1from=(vararray[i]-kernelhalfside)<0 ? 0 : (vararray[i]-kernelhalfside);
d1to=(vararray[i]+kernelhalfside+1>side ? side : vararray[i]+kernelhalfside+1);
d2from=(vararray[i+nrecs]-kernelhalfside)<0 ? 0 : (vararray[i+nrecs]-kernelhalfside);
d2to=(vararray[i+nrecs]+kernelhalfside+1>side ? side : vararray[i+nrecs]+kernelhalfside+1);
d3from=(vararray[i+nrecs*2]-kernelhalfside)<0 ? 0 : (vararray[i+nrecs*2]-kernelhalfside);
d3to=(vararray[i+nrecs*2]+kernelhalfside+1>side ? side : vararray[i+nrecs*2]+kernelhalfside+1);
for(d1=d1from,d1kern=vararray[i]-kernelhalfside<0 ? kernelhalfside-vararray[i] : 0;
d1<d1to;
d1++,d1kern++) {
for(d2=d2from,d2p=d1+d2from*side,d2kern=d1kern+((vararray[i+nrecs]-kernelhalfside)<0 ? (kernelhalfside-vararray[i+nrecs])*kernelside : 0)
;d2<d2to
;d2++,d2p+=side,d2kern+=kernelside) {
for(d3=d3from,d3p=d2p+d3from*sidesq
,d3kern=&kernel[d2kern+((vararray[i+nrecs*2]-kernelhalfside)<0 ? (kernelhalfside-vararray[i+nrecs*2])*kernelsidesq : 0)]
;d3<d3to
;d3++,d3p+=sidesq,d3kern+=kernelsidesq) {
tmpdens[d3p]+=*d3kern * (downweight ? ((float)weight[i]/MULTIPLIER) : 1);
//kernel[d3kern];
}
}
}
anythingtosave=true;
break;
}
}
}
saveKernelDensity(tmpdens,freqs[lastID],&densities[mapIDs[lastID]]); // save kernel density of the last taxon
outIDs[mapIDs[lastID]]=lastID;
*/
// scale all densities to the absolute maximum
/* unsigned long maxmax=0;
float factor;
for(i=0;i<ntaxafiltered;i++) if(maxmax<densities[i].max) maxmax=densities[i].max;
for(i=0;i<ntaxafiltered;i++) {
factor=(float)densities[i].max/maxmax;
for(j=0;j<arraysize;j++) densities[i].density[j]=(unsigned char)((float)densities[i].density[j]*factor);
}
*/
// now write to output file
printf("\nWriting file...\n");
densfile=fopen(DENSITYFILE(pfilename,poutfilename),"w");
fwrite(&ntaxafiltered,sizeof(int),1,densfile); // how many densities in file
fwrite(outIDs,sizeof(int),ntaxafiltered,densfile); // the real taxon IDs of each density
fwrite(&side,sizeof(int),1,densfile); // the size of the grid
fwrite(&nvarstouse,sizeof(int),1,densfile); // the number of variables
for(k=0;k<ntaxafiltered;k++) { // now the densities!
fwrite(&densities[k],sizeof(DENSITY),1,densfile); // of course, the pointer will be meaningless
fwrite(densities[k].density,arraysize,1,densfile);
}
fclose(densfile);
#ifdef VERBOSE
for(k=3;k<4;k++) { //ntaxafiltered
printf("************* Taxon Nrecs: %d ************\n",densities[k].nrecords);
switch(nvarstouse) {
case 2:
for(d1=0;d1<side;d1++) {
for(d2=0;d2<side;d2++) {
printf("%3d",densities[k].density[d1+d2*side]);
}
printf("\n");
}
break;
case 3:
for(d1=0;d1<5;d1++) {
for(d2=0;d2<side;d2++) {
for(d3=0;d3<side;d3++) {
printf("%3d",densities[k].density[d1+d2*side+d3*sidesq]);
}
printf("\n");
}
printf("*****************\n");
}
break;
}
printf("********SUM: %f NRECS: %d*********\n",sum,densities[k].nrecords);
}
for(k=0;k<ntaxafiltered;k++) {
for(d1=0,sum=0;d1<arraysize;d1++) sum+=(float)densities[k].density[d1]*densities[k].max/255.0;
printf("SUM: %f NRECS: %d\n",sum,densities[k].nrecords);
}
#endif
fclose(varsfile);
free(pIDs);
free(freqs);
free(vararray);
free(varheader);
free(kernel);
free(mapIDs);
free(tmpdens);
for(i=0;i<ntaxafiltered;i++) free(densities[i].density);
free(densities);
free(outIDs);
(*env)->ReleaseStringUTFChars(env,filename,pfilename);
(*env)->ReleaseStringUTFChars(env,outfilename,poutfilename);
return 1;
}
void PtexSeparableFilter::eval(float* result, int firstChan, int nChannels,
int faceid, float u, float v,
float uw1, float vw1, float uw2, float vw2,
float width, float blur)
{
// init
if (!_tx || nChannels <= 0) return;
if (faceid < 0 || faceid >= _tx->numFaces()) return;
_ntxchan = _tx->numChannels();
_dt = _tx->dataType();
_firstChanOffset = firstChan*DataSize(_dt);
_nchan = PtexUtils::min(nChannels, _ntxchan-firstChan);
// get face info
const FaceInfo& f = _tx->getFaceInfo(faceid);
// if neighborhood is constant, just return constant value of face
if (f.isNeighborhoodConstant()) {
PtexPtr<PtexFaceData> data ( _tx->getData(faceid, 0) );
if (data) {
char* d = (char*) data->getData() + _firstChanOffset;
Ptex::ConvertToFloat(result, d, _dt, _nchan);
}
return;
}
// find filter width as bounding box of vectors w1 and w2
float uw = fabs(uw1) + fabs(uw2), vw = fabs(vw1) + fabs(vw2);
// handle border modes
switch (_uMode) {
case m_clamp: u = PtexUtils::clamp(u, 0.0f, 1.0f); break;
case m_periodic: u = u-floor(u); break;
case m_black: break; // do nothing
}
switch (_vMode) {
case m_clamp: v = PtexUtils::clamp(v, 0.0f, 1.0f); break;
case m_periodic: v = v-floor(v);
case m_black: break; // do nothing
}
// build kernel
PtexSeparableKernel k;
if (f.isSubface()) {
// for a subface, build the kernel as if it were on a main face and then downres
uw = uw * width + blur * 2;
vw = vw * width + blur * 2;
buildKernel(k, u*.5, v*.5, uw*.5, vw*.5, f.res);
if (k.res.ulog2 == 0) k.upresU();
if (k.res.vlog2 == 0) k.upresV();
k.res.ulog2--; k.res.vlog2--;
}
else {
uw = uw * width + blur;
vw = vw * width + blur;
buildKernel(k, u, v, uw, vw, f.res);
}
k.stripZeros();
// check kernel (debug only)
assert(k.uw > 0 && k.vw > 0);
assert(k.uw <= PtexSeparableKernel::kmax && k.vw <= PtexSeparableKernel::kmax);
_weight = k.weight();
// allocate temporary double-precision result
_result = (double*) alloca(sizeof(double)*_nchan);
memset(_result, 0, sizeof(double)*_nchan);
// apply to faces
splitAndApply(k, faceid, f);
// normalize (both for data type and cumulative kernel weight applied)
// and output result
double scale = 1.0 / (_weight * OneValue(_dt));
for (int i = 0; i < _nchan; i++) result[i] = float(_result[i] * scale);
// clear temp result
_result = 0;
}
CLKernel *EasyCL::buildKernel(string kernelfilepath, string kernelname) {
return buildKernel(kernelfilepath, kernelname, "");
}
void VolumeMaxCLProcessor::initialize() {
Processor::initialize();
buildKernel();
}
// Serial ray casting
unsigned char* raycast_serial(unsigned char* data, unsigned char* region){
unsigned char* image = (unsigned char*)malloc(sizeof(unsigned char)*IMAGE_DIM*IMAGE_DIM);
// Camera/eye position, and direction of viewing. These can be changed to look
// at the volume from different angles.
float3 camera = {.x=1000,.y=1000,.z=1000};
float3 forward = {.x=-1, .y=-1, .z=-1};
float3 z_axis = {.x=0, .y=0, .z = 1};
// Finding vectors aligned with the axis of the image
float3 right = cross(forward, z_axis);
float3 up = cross(right, forward);
// Creating unity lenght vectors
forward = normalize(forward);
right = normalize(right);
up = normalize(up);
float fov = 3.14/4;
float pixel_width = tan(fov/2.0)/(IMAGE_DIM/2);
float step_size = 0.5;
// For each pixel
for(int y = -(IMAGE_DIM/2); y < (IMAGE_DIM/2); y++){
for(int x = -(IMAGE_DIM/2); x < (IMAGE_DIM/2); x++){
// Find the ray for this pixel
float3 screen_center = add(camera, forward);
float3 ray = add(add(screen_center, scale(right, x*pixel_width)), scale(up, y*pixel_width));
ray = add(ray, scale(camera, -1));
ray = normalize(ray);
float3 pos = camera;
// Move along the ray, we stop if the color becomes completely white,
// or we've done 5000 iterations (5000 is a bit arbitrary, it needs
// to be big enough to let rays pass through the entire volume)
int i = 0;
float color = 0;
while(color < 255 && i < 5000){
i++;
pos = add(pos, scale(ray, step_size)); // Update position
int r = value_at(pos, region); // Check if we're in the region
color += value_at(pos, data)*(0.01 + r) ; // Update the color based on data value, and if we're in the region
}
// Write final color to image
image[(y+(IMAGE_DIM/2)) * IMAGE_DIM + (x+(IMAGE_DIM/2))] = color > 255 ? 255 : color;
}
}
return image;
}
// Check if two values are similar, threshold can be changed.
int similar(unsigned char* data, int3 a, int3 b){
unsigned char va = data[a.z * DATA_DIM*DATA_DIM + a.y*DATA_DIM + a.x];
unsigned char vb = data[b.z * DATA_DIM*DATA_DIM + b.y*DATA_DIM + b.x];
int i = abs(va-vb) < 1;
return i;
}
// Serial region growing, same algorithm as in assignment 2
unsigned char* grow_region_serial(unsigned char* data){
unsigned char* region = (unsigned char*)calloc(sizeof(unsigned char), DATA_DIM*DATA_DIM*DATA_DIM);
stack_t* stack = new_stack();
int3 seed = {.x=50, .y=300, .z=300};
push(stack, seed);
region[seed.z *DATA_DIM*DATA_DIM + seed.y*DATA_DIM + seed.x] = 1;
int dx[6] = {-1,1,0,0,0,0};
int dy[6] = {0,0,-1,1,0,0};
int dz[6] = {0,0,0,0,-1,1};
while(stack->size > 0){
int3 pixel = pop(stack);
for(int n = 0; n < 6; n++){
int3 candidate = pixel;
candidate.x += dx[n];
candidate.y += dy[n];
candidate.z += dz[n];
if(!inside_int(candidate)){
continue;
}
if(region[candidate.z * DATA_DIM*DATA_DIM + candidate.y*DATA_DIM + candidate.x]){
continue;
}
if(similar(data, pixel, candidate)){
push(stack, candidate);
region[candidate.z * DATA_DIM*DATA_DIM + candidate.y*DATA_DIM + candidate.x] = 1;
}
}
}
return region;
}
unsigned char* grow_region_gpu(unsigned char* data){
cl_platform_id platform;
cl_device_id device;
cl_context context;
cl_command_queue queue;
cl_kernel kernel;
cl_int err;
char *source;
int i;
clGetPlatformIDs(1, &platform, NULL);
clGetDeviceIDs(platform, CL_DEVICE_TYPE_GPU, 1, &device, NULL);
context = clCreateContext(NULL, 1, &device, NULL, NULL, &err);
printPlatformInfo(platform);
queue = clCreateCommandQueue(context, device, 0, &err);
kernel = buildKernel("region.cl", "region", NULL, context, device);
//Host variables
unsigned char* host_region = (unsigned char*)calloc(sizeof(unsigned char), DATA_SIZE);
int host_unfinished;
cl_mem device_region = clCreateBuffer(context, CL_MEM_READ_WRITE, DATA_SIZE * sizeof(cl_uchar) ,NULL,&err);
cl_mem device_data = clCreateBuffer(context, CL_MEM_READ_ONLY, DATA_SIZE * sizeof(cl_uchar), NULL,&err);
cl_mem device_unfinished = clCreateBuffer(context, CL_MEM_READ_WRITE, sizeof(cl_int), NULL,&err);
clError("Error allocating memory", err);
//plant seed
int3 seed = {.x=50, .y=300, .z=300};
host_region[index(seed.z, seed.y, seed.x)] = 2;
//Copy data to the device
clEnqueueWriteBuffer(queue, device_data , CL_FALSE, 0, DATA_SIZE * sizeof(cl_uchar), data , 0, NULL, NULL);
clEnqueueWriteBuffer(queue, device_region, CL_FALSE, 0, DATA_SIZE * sizeof(cl_uchar), host_region, 0, NULL, NULL);
//Calculate block and grid sizes
size_t global[] = { 512, 512, 512 };
size_t local[] = { 8, 8, 8 };
//Run kernel untill completion
do{
host_unfinished = 0;
clEnqueueWriteBuffer(queue, device_unfinished, CL_FALSE, 0, sizeof(cl_int), &host_unfinished , 0, NULL, NULL);
clFinish(queue);
err = clSetKernelArg(kernel, 0, sizeof(device_data), (void*)&device_data);
err = clSetKernelArg(kernel, 1, sizeof(device_region), (void*)&device_region);
err = clSetKernelArg(kernel, 2, sizeof(device_unfinished), (void*)&device_unfinished);
clError("Error setting arguments", err);
//Run the kernel
clEnqueueNDRangeKernel(queue, kernel, 3, NULL, &global, &local, 0, NULL, NULL);
clFinish(queue);
clError("Error running kernel", err);
err = clEnqueueReadBuffer(queue, device_unfinished, CL_TRUE, 0, sizeof(cl_int), &host_unfinished, 0, NULL, NULL);
clFinish(queue);
clError("Error reading buffer 1", err);
}while(host_unfinished);
//Copy result to host
err = clEnqueueReadBuffer(queue, device_region, CL_TRUE, 0, DATA_SIZE * sizeof(cl_uchar), host_region, 0, NULL, NULL);
clFinish(queue);
clError("Error reading buffer 2", err);
return host_region;
}
unsigned char* raycast_gpu(unsigned char* data, unsigned char* region){
cl_platform_id platform;
cl_device_id device;
cl_context context;
cl_command_queue queue;
cl_kernel kernel;
cl_int err;
char *source;
int i;
clGetPlatformIDs(1, &platform, NULL);
clGetDeviceIDs(platform, CL_DEVICE_TYPE_GPU, 1, &device, NULL);
context = clCreateContext(NULL, 1, &device, NULL, NULL, &err);
printPlatformInfo(platform);
printDeviceInfo(device);
queue = clCreateCommandQueue(context, device, 0, &err);
kernel = buildKernel("raycast.cl", "raycast", NULL, context, device);
cl_mem device_region = clCreateBuffer(context, CL_MEM_READ_ONLY, DATA_SIZE * sizeof(cl_uchar) ,NULL,&err);
cl_mem device_data = clCreateBuffer(context, CL_MEM_READ_ONLY, DATA_SIZE * sizeof(cl_uchar), NULL,&err);
cl_mem device_image = clCreateBuffer(context, CL_MEM_READ_WRITE, IMAGE_SIZE * sizeof(cl_uchar),NULL,&err);
clError("Error allocating memory", err);
//Copy data to the device
clEnqueueWriteBuffer(queue, device_data , CL_FALSE, 0, DATA_SIZE * sizeof(cl_uchar), data , 0, NULL, NULL);
clEnqueueWriteBuffer(queue, device_region, CL_FALSE, 0, DATA_SIZE * sizeof(cl_uchar), region, 0, NULL, NULL);
int grid_size = IMAGE_DIM;
int block_size = IMAGE_DIM;
//Set up kernel arguments
err = clSetKernelArg(kernel, 0, sizeof(device_data), (void*)&device_data);
err = clSetKernelArg(kernel, 1, sizeof(device_region), (void*)&device_region);
err = clSetKernelArg(kernel, 2, sizeof(device_image), (void*)&device_image);
clError("Error setting arguments", err);
//Run the kernel
const size_t globalws[2] = {IMAGE_DIM, IMAGE_DIM};
const size_t localws[2] = {8, 8};
clEnqueueNDRangeKernel(queue, kernel, 2, NULL, &globalws, &localws, 0, NULL, NULL);
clFinish(queue);
//Allocate memory for the result
unsigned char* host_image = (unsigned char*)malloc(IMAGE_SIZE_BYTES);
//Copy result from device
err = clEnqueueReadBuffer(queue, device_image, CL_TRUE, 0, IMAGE_SIZE * sizeof(cl_uchar), host_image, 0, NULL, NULL);
clFinish(queue);
//Free device memory
return host_image;
}
int main(int argc, char** argv){
unsigned char* data = create_data();
unsigned char* region = grow_region_gpu(data);
unsigned char* image = raycast_gpu(data, region);
write_bmp(image, IMAGE_DIM, IMAGE_DIM);
}