void
fill_host(thrust::host_vector<TType> &v)
{
int s = size();
v.resize(s);
thrust::copy(mBuffer.begin(), mBuffer.begin() + s, v.begin());
}
// 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;
}
}
}
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() );
}