void
fill_host(thrust::host_vector<TType> &v)
{
int s = size();
v.resize(s);
thrust::copy(mBuffer.begin(), mBuffer.begin() + s, v.begin());
}
void writeVectorToFile_CPU(thrust::host_vector< thrust::pair<unsigned int, unsigned int> > h_pairVector, thrust::host_vector< float > h_distVector, string pairFileName, string distFileName, unsigned long long count, int fileId) {
FILE * pairFile, * distFile;
string tempStr;
char buf[1000];
sprintf(buf, "_%d", fileId);
tempStr = pairFileName;
tempStr.append(buf);
pairFile = fopen(tempStr.c_str(), "wb");
if (pairFile == NULL){
printf("cannot open pairFile: %s\n", tempStr.c_str());
exit(-1);
}
tempStr = distFileName;
tempStr.append(buf);
distFile = fopen(tempStr.c_str(), "wb");
if (distFile == NULL){
printf("cannot open distFile: %s\n", tempStr.c_str());
exit(-1);
}
thrust::sort_by_key(h_distVector.begin(), h_distVector.end(), h_pairVector.begin());
int pairArray[BUF_SIZE*2];
float distArray[BUF_SIZE];
int h = 0;
thrust::pair<unsigned int, unsigned int> aPair;
cout << "write to : " << tempStr << " " << count << " pairs" << endl;
for (unsigned int i = 0; i < count; ++i)
{
aPair = h_pairVector[i];
distArray[h] = h_distVector[i];
pairArray[h*2] = aPair.first;
pairArray[h*2+1] = aPair.second;
++h;
/*
if (i <= 100)
cout << aPair.first << "\t" << aPair.second << "\t" << distArray[i] << endl;
*/
if (h == BUF_SIZE) {
fwrite(pairArray, sizeof(unsigned int), BUF_SIZE * 2, pairFile);
fwrite(distArray, sizeof(float), BUF_SIZE, distFile);
h = 0;
}
}
if (h > 0) {
fwrite(pairArray, sizeof(unsigned int), h * 2, pairFile);
fwrite(distArray, sizeof(float), h, distFile);
h = 0;
}
fclose(pairFile);
fclose(distFile);
}
void LoadBCE_fromFile(thrust::host_vector<Real3> &posRadBCE, // do not set the
// size here since
// you are using
// push back later
std::string fileName) {
std::string ddSt;
char buff[256];
int numBce = 0;
const int cols = 3;
std::cout << " reading BCE data from: " << fileName << " ...\n";
std::ifstream inMarker;
inMarker.open(fileName);
if (!inMarker) {
std::cout << " Error! Unable to open file: " << fileName << std::endl;
}
getline(inMarker, ddSt);
Real q[cols];
while (getline(inMarker, ddSt)) {
std::stringstream linestream(ddSt);
for (int i = 0; i < cols; i++) {
linestream.getline(buff, 50, ',');
q[i] = atof(buff);
}
posRadBCE.push_back(mR3(q[0], q[1], q[2]));
numBce++;
}
std::cout << " Loaded BCE data from: " << fileName << std::endl;
}
void interactRays(thrust::host_vector<Ray> &h_rays) {
int n = h_rays.size();
for (int i = 0; i < n; i++) {
Ray &r = h_rays[i];
interact(r);
}
}
void traceRays(thrust::host_vector<Ray> &h_rays, Scene &scene) {
int n = h_rays.size();
for (int i = 0; i < n; i++) {
Ray &r = h_rays[i];
trace(r, scene);
}
}
// copy scoring data to host, converting to io::AlignmentResult
void GPUOutputBatch::readback_scores(thrust::host_vector<io::AlignmentResult>& output,
const AlignmentMate mate,
const AlignmentScore score) const
{
// copy alignment data into a staging buffer
thrust::host_vector<io::BestAlignments> best_data_staging;
nvbio::cuda::thrust_copy_vector(best_data_staging, best_data_dvec, count);
// convert the contents of the staging buffer into io::AlignmentResult
output.resize(count);
for(uint32 c = 0; c < count; c++)
{
io::BestAlignments& old_best_aln = best_data_staging[c];
io::Alignment& old_aln = (score == BEST_SCORE ? old_best_aln.m_a1 : old_best_aln.m_a2);
io::AlignmentResult& new_aln = output[c];
if (score == BEST_SCORE)
{
new_aln.best[mate] = old_aln;
} else {
new_aln.second_best[mate] = old_aln;
}
if (mate == MATE_2)
{
new_aln.is_paired_end = true;
}
}
}
// =============================================================================
// note, the function in the current implementation creates boundary BCE (zero
// velocity)
// x=1, y=2, z =3; therefore 12 means creating markers on the top surface
// parallel to xy plane,
// similarly -12 means bottom face paralel to xy. similarly 13, -13, 23, -23
void CreateBCE_On_Box(thrust::host_vector<Real3> &posRadBCE, const Real3 &hsize,
int face, SimParams *paramsH) {
Real initSpace0 = paramsH->MULT_INITSPACE * paramsH->HSML;
int nFX = ceil(hsize.x / (initSpace0));
int nFY = ceil(hsize.y / (initSpace0));
int nFZ = ceil(hsize.z / (initSpace0));
Real initSpaceX = hsize.x / nFX;
Real initSpaceY = hsize.y / nFY;
Real initSpaceZ = hsize.z / nFZ;
int2 iBound = mI2(-nFX, nFX);
int2 jBound = mI2(-nFY, nFY);
int2 kBound = mI2(-nFZ, nFZ);
switch (face) {
case 12:
kBound = mI2(nFZ - paramsH->NUM_BOUNDARY_LAYERS + 1, nFZ);
break;
case -12:
kBound = mI2(-nFZ, -nFZ + paramsH->NUM_BOUNDARY_LAYERS - 1);
break;
case 13:
jBound = mI2(nFY - paramsH->NUM_BOUNDARY_LAYERS + 1, nFY);
break;
case -13:
jBound = mI2(-nFY, -nFY + paramsH->NUM_BOUNDARY_LAYERS - 1);
break;
case 23:
iBound = mI2(nFX - paramsH->NUM_BOUNDARY_LAYERS + 1, nFX);
break;
case -23:
iBound = mI2(-nFX, -nFX + paramsH->NUM_BOUNDARY_LAYERS - 1);
break;
default:
printf("wrong argument box bce initialization\n");
break;
}
for (int i = iBound.x; i <= iBound.y; i++) {
for (int j = jBound.x; j <= jBound.y; j++) {
for (int k = kBound.x; k <= kBound.y; k++) {
Real3 relMarkerPos =
mR3(i * initSpaceX, j * initSpaceY, k * initSpaceZ);
if ((relMarkerPos.x < paramsH->cMin.x ||
relMarkerPos.x > paramsH->cMax.x) ||
(relMarkerPos.y < paramsH->cMin.y ||
relMarkerPos.y > paramsH->cMax.y) ||
(relMarkerPos.z < paramsH->cMin.z ||
relMarkerPos.z > paramsH->cMax.z)) {
continue;
}
posRadBCE.push_back(relMarkerPos);
}
}
}
}
void CreateBCE_On_Cylinder(thrust::host_vector<Real3> &posRadBCE, Real cyl_rad,
Real cyl_h, SimParams *paramsH) {
// Arman : take care of velocity and w stuff for BCE
Real spacing = paramsH->MULT_INITSPACE * paramsH->HSML;
for (Real s = -0.5 * cyl_h; s <= 0.5 * cyl_h; s += spacing) {
Real3 centerPointLF = mR3(0, s, 0);
posRadBCE.push_back(centerPointLF);
for (Real r = spacing; r < cyl_rad - paramsH->solidSurfaceAdjust;
r += spacing) {
Real deltaTeta = spacing / r;
for (Real teta = .1 * deltaTeta;
teta < 2 * chrono::CH_C_PI - .1 * deltaTeta; teta += deltaTeta) {
Real3 BCE_Pos_local =
mR3(r * cos(teta), 0, r * sin(teta)) + centerPointLF;
posRadBCE.push_back(BCE_Pos_local);
}
}
}
}
// =============================================================================
void CreateBCE_On_Sphere(thrust::host_vector<Real3> &posRadBCE, Real rad,
SimParams *paramsH) {
Real spacing = paramsH->MULT_INITSPACE * paramsH->HSML;
for (Real r = spacing; r < rad - paramsH->solidSurfaceAdjust; r += spacing) {
Real deltaTeta = spacing / r;
Real deltaPhi = deltaTeta;
for (Real phi = .1 * deltaPhi; phi < chrono::CH_C_PI - .1 * deltaPhi;
phi += deltaPhi) {
for (Real teta = .1 * deltaTeta;
teta < 2 * chrono::CH_C_PI - .1 * deltaTeta; teta += deltaTeta) {
Real3 BCE_Pos_local = mR3(r * sin(phi) * cos(teta),
r * sin(phi) * sin(teta), r * cos(phi));
posRadBCE.push_back(BCE_Pos_local);
}
}
}
}
void initRays() {
int n = h_rays.size();
int w = width, h = height;
for (int i = 0; i < n; i++) {
Ray &r = h_rays[i];
r.done = false;
r.color = Vector3(0, 0, 0);
int ix = i%w;
int iy = i/w;
Number px = ((Number)ix + (Number)0.5)/w;
Number py = ((Number)iy + (Number)0.5)/h;
r.pos = frustum.pointOnNearPlane(px, py);
r.dir = r.pos - eye;
r.dir.normalize();
addVector(eye, r.pos);
addVectorDir(r.pos, r.dir);
}
}
void GLWindow::paintGL()
{
timer->stop();
if (frame_count == 0) gettimeofday(&begin, 0);
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
if (wireframe) glPolygonMode(GL_FRONT_AND_BACK, GL_LINE);
else glPolygonMode(GL_FRONT_AND_BACK, GL_FILL);
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
gluPerspective( cameraFOV, 1.0, 1.0, grid_size*4.0);
// set view matrix for 3D scene
glMatrixMode(GL_MODELVIEW);
glPushMatrix();
qrot.getRotMat(rotationMatrix);
glMultMatrixf(rotationMatrix);
// glTranslatef(-(grid_size-1)/2, -(grid_size-1)/2, -(grid_size-1)/2);
size_t num_bytes; GLenum drawType = GL_TRIANGLES;
#ifdef TANGLE
#ifdef USE_INTEROP
isosurface->vboResources[0] = quads_pos_res; isosurface->vboResources[1] = quads_color_res; isosurface->vboResources[2] = quads_normal_res;
isosurface->minIso = 31.0f; isosurface->maxIso = 500.0f; isosurface->useInterop = true;
isosurface->vboSize = buffer_size;
#endif
(*isosurface)();
#ifndef USE_INTEROP
vertices.assign(isosurface->vertices_begin(), isosurface->vertices_end());
normals.assign(isosurface->normals_begin(), isosurface->normals_end());
colors.assign(thrust::make_transform_iterator(isosurface->scalars_begin(), color_map<float>(31.0f, 500.0f)),
thrust::make_transform_iterator(isosurface->scalars_end(), color_map<float>(31.0f, 500.0f)));
#endif
#endif
#ifdef CUTPLANE
#ifdef USE_INTEROP
cutplane->vboResources[0] = quads_pos_res; cutplane->vboResources[1] = quads_color_res; cutplane->vboResources[2] = quads_normal_res;
cutplane->minIso = 0.0f; cutplane->maxIso = 1.0f; cutplane->useInterop = true;
cutplane->vboSize = buffer_size;
#endif
(*cutplane)();
#ifndef USE_INTEROP
vertices.assign(cutplane->vertices_begin(), cutplane->vertices_end());
normals.assign(cutplane->normals_begin(), cutplane->normals_end());
colors.assign(thrust::make_transform_iterator(cutplane->scalars_begin(), color_map<float>(0.0f, 1.0f)),
thrust::make_transform_iterator(cutplane->scalars_end(), color_map<float>(0.0f, 1.0f)));
#endif
#endif
#ifdef THRESHOLD
#ifdef USE_INTEROP
threshold->vboResources[0] = quads_pos_res; threshold->vboResources[1] = quads_color_res; threshold->vboResources[2] = quads_normal_res;
threshold->minThresholdRange = 4.0f; threshold->maxThresholdRange = 1600.0f; threshold->useInterop = true;
threshold->vboSize = buffer_size;
#endif
(*threshold)();
#ifndef USE_INTEROP
vertices.resize(threshold->vertices_end() - threshold->vertices_begin());
normals.resize(threshold->normals_end() - threshold->normals_begin());
thrust::device_vector<float4> device_colors(vertices.size());
// thrust::copy(thrust::make_transform_iterator(threshold->vertices_begin(), tuple2float4()),
// thrust::make_transform_iterator(threshold->vertices_end(), tuple2float4()), vertices.begin());
thrust::copy(threshold->vertices_begin(),
threshold->vertices_end(),
vertices.begin());
thrust::copy(threshold->normals_begin(), threshold->normals_end(), normals.begin());
thrust::transform(threshold->scalars_begin(), threshold->scalars_end(), device_colors.begin(), color_map<float>(4.0f, 1600.0f));
colors = device_colors;
#endif
drawType = GL_QUADS;
#endif
#ifdef USE_INTEROP
glBindBuffer(GL_ARRAY_BUFFER, quads_vbo[0]);
glVertexPointer(4, GL_FLOAT, 0, 0);
glBindBuffer(GL_ARRAY_BUFFER, quads_vbo[1]);
glNormalPointer(GL_FLOAT, 0, 0);
glBindBuffer(GL_ARRAY_BUFFER, quads_vbo[2]);
glColorPointer(4, GL_FLOAT, 0, 0);
glDrawArrays(drawType, 0, buffer_size/sizeof(float4));
#else
glColorPointer(4, GL_FLOAT, 0, &colors[0]);
glNormalPointer(GL_FLOAT, 0, &normals[0]);
glVertexPointer(4, GL_FLOAT, 0, &vertices[0]);
glDrawArrays(drawType, 0, vertices.size());
#endif
glPopMatrix();
gettimeofday(&end, 0);
timersub(&end, &begin, &diff);
frame_count++;
float seconds = diff.tv_sec + 1.0E-6*diff.tv_usec;
if (seconds > 0.5f)
{
char title[256];
sprintf(title, "Marching Cube, fps: %2.2f", float(frame_count)/seconds);
std::cout << title << std::endl;
seconds = 0.0f;
frame_count = 0;
}
timer->start(1);
}
static void resize( thrust::host_vector< T > &x , const thrust::host_vector< T > &y )
{
x.resize( y.size() );
}
static bool same_size( const thrust::host_vector< T > &x , const thrust::host_vector< T > &y )
{
return x.size() == y.size();
}
