3f56f1f9
 dmayerich
initial commit
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#include "dataTypes.h"
#include "colormap.h"
#include <QImage>
__global__ void bandpass(bsComplex* U, int uR, int vR, ptype du, ptype dv, ptype NAin, ptype NAout, ptype lambda)
{
//get the current coordinate in the plane slice
int iu = blockIdx.x * blockDim.x + threadIdx.x;
int iv = blockIdx.y * blockDim.y + threadIdx.y;
//make sure that the thread indices are in-bounds
if(iu >= uR || iv >= vR) return;
//compute the index (easier access to the scalar field array)
int i = iv*uR + iu;
ptype u, v;
if(iu <= uR / 2)
u = (ptype)iu * du;
else
u = -(ptype)(uR - 1 - iu) * du;
if(iv <= vR / 2)
v = (ptype)iv * dv;
else
v = -(ptype)(vR - 1 - iv) * dv;
ptype fmag = sqrt(u*u + v*v);
if(fmag < NAin / lambda || fmag > NAout / lambda)
U[i] = 0;
//U[i] = U[i];
}
microscopeStruct::microscopeStruct()
{
scalarSim = true;
D = NULL;
Di = NULL;
}
void microscopeStruct::init()
{
//Ud.scalarField = scalarSim;
//Ufd.scalarField = scalarSim;
//Ud.init_gpu();
//Ufd.init_gpu();
//initialize the near field
nf.init();
//allocate space for the detector
D = new scalarslice(Ud.R[0] / ss, Ud.R[1] / ss);
Di = new scalarslice(Ud.R[0] / ss, Ud.R[1] / ss);
//clear the detector
clearDetector();
}
void microscopeStruct::destroy()
{
delete D;
D = NULL;
delete Di;
Di = NULL;
Ud.kill_gpu();
Ufd.kill_gpu();
//destroy the near field
nf.destroy();
}
void microscopeStruct::applyBandpass()
{
//This function applies the objective bandpass to the near field
//The near field structure stores the results, in order to save memory
//first convert the near field to an angular spectrum (FFT)
nf.U.toAngularSpectrum();
//create one thread for each pixel of the field slice
dim3 dimBlock(SQRT_BLOCK, SQRT_BLOCK);
dim3 dimGrid((nf.U.R[0] + SQRT_BLOCK -1)/SQRT_BLOCK, (nf.U.R[1] + SQRT_BLOCK - 1)/SQRT_BLOCK);
//compute the step size in the frequency domain
ptype du = 1.0 / (nf.pos.X.len());
ptype dv = 1.0 / (nf.pos.Y.len());
//apply the objective band-pass filter
bandpass<<<dimGrid, dimBlock>>>(nf.U.x_hat, nf.U.R[0], nf.U.R[1], du, dv, objective[0], objective[1], nf.lambda);
//convert the near field image back to the spatial domain
// (this is the field at the detector)
nf.U.fromAngularSpectrum();
}
void microscopeStruct::getFarField()
{
//Compute the Far Field image of the focal plane
//clear the memory from previous detector fields
Ud.kill_gpu();
Ufd.kill_gpu();
//first crop the filtered near-field image of the source and scattered fields
Ud = nf.U.crop(padding * Ud.R[0], padding * Ud.R[1], Ud.R[0], Ud.R[1]);
Ufd = nf.Uf.crop(padding * Ufd.R[0], padding * Ufd.R[1], Ufd.R[0], Ufd.R[1]);
}
void microscopeStruct::integrateDetector()
{
Ud.IntegrateAndResample(D, ss);
Ufd.IntegrateAndResample(Di, ss);
}
void microscopeStruct::clearDetector()
{
//zero-out the detector
D->clear();
Di->clear();
}
//flag for a vector simulation
void microscopeStruct::setPos(bsPoint pMin, bsPoint pMax, bsVector normal)
{
pos = rts::rtsQuad<ptype, 3>(pMin, pMax, normal);
}
void microscopeStruct::setRes(int x_res, int y_res, int pad, int supersampling)
{
padding = pad;
ss = supersampling;
Ufd.R[0] = Ud.R[0] = x_res * ss;
Ufd.R[1] = Ud.R[1] = y_res * ss;
}
void microscopeStruct::setNearfield()
{
//sets the values for the near field in order to create the specified detector image
//compute the size of the near-field slice necessary to create the detector image
nf.pos = pos * (padding * 2 + 1);
//compute the resolution of the near-field slice necessary to create the detector image
nf.setRes(Ud.R[0] * (padding * 2 + 1), Ud.R[1] * (padding * 2 + 1));
}
__global__ void calc_absorbance(ptype* A, ptype* D, ptype* Di, int N)
{
//compute the index for this thread
int i = blockIdx.x * blockDim.x + threadIdx.x;
if(i >= N) return;
A[i] = -log10(D[i] / Di[i]);
}
scalarslice microscopeStruct::getAbsorbance()
{
//compute the magnitude of the field at each rtsPoint in the slice
//create a scalar slice at the same resolution as the field
scalarslice* A = new scalarslice(D->R[0], D->R[1]);
//compute the total number of values in the slice
unsigned int N = D->R[0] * D->R[1];
int gridDim = (N+BLOCK-1)/BLOCK;
calc_absorbance<<<gridDim, BLOCK>>>(A->S, D->S, Di->S, N);
return *A;
}
__global__ void calc_transmittance(ptype* A, ptype* D, ptype* Di, int N)
{
//compute the index for this thread
int i = blockIdx.x * blockDim.x + threadIdx.x;
if(i >= N) return;
A[i] = D[i] / Di[i];
}
scalarslice microscopeStruct::getTransmittance()
{
//compute the magnitude of the field at each rtsPoint in the slice
//create a scalar slice at the same resolution as the field
scalarslice* T = new scalarslice(D->R[0], D->R[1]);
//compute the total number of values in the slice
unsigned int N = D->R[0] * D->R[1];
int gridDim = (N+BLOCK-1)/BLOCK;
calc_transmittance<<<gridDim, BLOCK>>>(T->S, D->S, Di->S, N);
return *T;
}
scalarslice microscopeStruct::getIntensity()
{
//create a scalar slice at the same resolution as the field
scalarslice* I = new scalarslice(D->R[0], D->R[1]);
HANDLE_ERROR(cudaMemcpy(I->S, D->S, sizeof(ptype) * D->R[0] * D->R[1], cudaMemcpyDeviceToDevice));
return *I;
}
void microscopeStruct::SimulateScattering()
{
nf.Simulate();
}
void microscopeStruct::SimulateImaging()
{
applyBandpass();
getFarField();
integrateDetector();
}
void microscopeStruct::Simulate()
{
SimulateScattering();
SimulateImaging();
}
void microscopeStruct::SimulateExtendedSource()
{
clearDetector();
//for each source in the source list
int npts = focalPoints.size();
float t=0;
for(int i = 0; i<npts; i++)
{
nf.focus = focalPoints[i].f;
nf.A = focalPoints[i].A;
gpuStartTimer();
Simulate();
t += gpuStopTimer();
rtsProgressBar((double)(i+1)/(double)npts * 100);
}
cout<<endl;
cout<<"Time per source: "<<t/npts<<"ms"<<endl;
}
void microscopeStruct::LoadExtendedSource(std::string filename)
{
//this function loads an image of an extended source and creates a list of corresponding point sources
QImage sourceImage(filename.c_str());
//get the resolution of the image (the boundary is scaled to match the detector)
int Rx = sourceImage.width();
int Ry = sourceImage.height();
//for each pixel
int x, y;
float u, v;
for(x=0; x<Rx; x++)
for(y=0; y<Ry; y++)
{
//create a new point source
sourcePoint p;
//compute the coordinate of the focal point
u = (ptype)x / (ptype)Rx;
v = (ptype)y / (ptype)Ry;
p.f = pos(u, v);
//get the amplitude of the focal point
QRgb rgb = sourceImage.pixel(x, y);
//float A = qGray(rgb);
p.A = (ptype) qGray(rgb) / 255;
//insert the point source into the list
focalPoints.push_back(p);
}
}
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