void Grid::paint(void)
{
int i;
int j;
int k;
if (mpBox == NULL)
return;
printf("Grid::paint entry\n");
Vec3f minp = mpBox->getMin();
Vec3f maxp = mpBox->getMax();
float xBox = maxp.x() - minp.x();
float yBox = maxp.y() - minp.y();
float zBox = maxp.z() - minp.z();
int xSize = getXSize();
int ySize = getYSize();
int zSize = getZSize();
float xDelta = xBox / xSize;
float yDelta = yBox / ySize;
float zDelta = zBox / zSize;
for (k = 0; k < zSize; k++)
for (j = 0; j < ySize; j++)
for (i = 0; i < xSize; i++)
{
printf("Obj:%d %d %d, num=%d\n", i, j, k, mObjects[offset(i, j, k)].getNumObjects());
if (mObjects[offset(i, j, k)].getNumObjects() > 0) {
printf("Paint:%d, %d, %d\n", i, j, k);
Vec3f curMinPoint(minp.x() + i*xDelta,
minp.y() + j*yDelta,
minp.z() + k*zDelta );
Vec3f curMaxPoint(curMinPoint.x() + xDelta,
curMinPoint.y() + yDelta,
curMinPoint.z() + zDelta );
glBegin(GL_QUADS);
//The up plane
Vec3f normalUp;
Vec3f::Cross3( normalUp,
Vec3f(0.0, curMaxPoint.y() - curMinPoint.y() , 0.0),
Vec3f(curMaxPoint.x() - curMinPoint.x(), 0.0, 0.0) );
glNormal3f(normalUp.x(), normalUp.y(), normalUp.z());
glVertex3f(curMinPoint.x(), curMinPoint.y(), curMaxPoint.z());
glVertex3f(curMaxPoint.x(), curMinPoint.y(), curMaxPoint.z());
glVertex3f(curMaxPoint.x(), curMaxPoint.y(), curMaxPoint.z());
glVertex3f(curMinPoint.x(), curMaxPoint.y(), curMaxPoint.z());
//the down plane
Vec3f normalDown;
Vec3f::Cross3( normalDown,
Vec3f(curMaxPoint.x() - curMinPoint.x(), 0.0, 0.0),
Vec3f(0.0, curMaxPoint.y() - curMinPoint.y(), 0.0) );
glNormal3f(normalDown.x(), normalDown.y(), normalDown.z());
glVertex3f(curMinPoint.x(), curMinPoint.y(), curMinPoint.z());
glVertex3f(curMaxPoint.x(), curMinPoint.y(), curMinPoint.z());
glVertex3f(curMaxPoint.x(), curMaxPoint.y(), curMinPoint.z());
glVertex3f(curMinPoint.x(), curMaxPoint.y(), curMinPoint.z());
//the front plane
Vec3f normalFront;
Vec3f::Cross3( normalFront,
Vec3f(0.0, curMaxPoint.y() - curMinPoint.y(), 0.0),
Vec3f(0.0, 0.0, curMaxPoint.z() - curMinPoint.z()) );
glNormal3f(normalFront.x(), normalFront.y(), normalFront.z());
glVertex3f(curMinPoint.x(), curMinPoint.y(), curMinPoint.z());
glVertex3f(curMinPoint.x(), curMinPoint.y(), curMaxPoint.z());
glVertex3f(curMinPoint.x(), curMaxPoint.y(), curMaxPoint.z());
glVertex3f(curMinPoint.x(), curMaxPoint.y(), curMinPoint.z());
//the back plane
Vec3f normalBack;
Vec3f::Cross3( normalBack,
Vec3f(0.0, 0.0, curMaxPoint.z() - curMinPoint.z()),
Vec3f(0.0, curMaxPoint.y() - curMinPoint.y(), 0.0) );
glNormal3f(normalBack.x(), normalBack.y(), normalBack.z());
glVertex3f(curMaxPoint.x(), curMinPoint.y(), curMinPoint.z());
glVertex3f(curMaxPoint.x(), curMinPoint.y(), curMaxPoint.z());
glVertex3f(curMaxPoint.x(), curMaxPoint.y(), curMaxPoint.z());
glVertex3f(curMaxPoint.x(), curMaxPoint.y(), curMinPoint.z());
//the left plane
Vec3f normalLeft;
Vec3f::Cross3( normalLeft,
Vec3f(curMinPoint.x() - curMaxPoint.x(), 0.0, 0.0),
Vec3f(0.0, 0.0, curMaxPoint.z() - curMinPoint.z()) );
glNormal3f(normalLeft.x(), normalLeft.y(), normalLeft.z());
glVertex3f(curMaxPoint.x(), curMinPoint.y(), curMinPoint.z());
glVertex3f(curMaxPoint.x(), curMinPoint.y(), curMaxPoint.z());
glVertex3f(curMinPoint.x(), curMinPoint.y(), curMaxPoint.z());
glVertex3f(curMinPoint.x(), curMinPoint.y(), curMinPoint.z());
//the right plane
Vec3f normalRight;
Vec3f::Cross3( normalRight,
Vec3f(0.0, 0.0, curMaxPoint.z() - curMinPoint.z()),
Vec3f(curMinPoint.x() - curMaxPoint.x(), 0.0, 0.0) );
glNormal3f(normalRight.x(), normalRight.y(), normalRight.z());
glVertex3f(curMaxPoint.x(), curMaxPoint.y(), curMinPoint.z());
glVertex3f(curMaxPoint.x(), curMaxPoint.y(), curMaxPoint.z());
glVertex3f(curMinPoint.x(), curMaxPoint.y(), curMaxPoint.z());
glVertex3f(curMinPoint.x(), curMaxPoint.y(), curMinPoint.z());
glEnd();
}
}
printf("Grid::paint Exit\n");
}
/*
* newPeaks()
*
* Create initial fit data structures for spline fitting from the peak array. The
* format of the initial values is the same as what was used for 3D-DAOSTORM.
*
* peaks - pointer to the initial values for the parameters for each peak.
* 1. height
* 2. x-center
* 3. x-sigma
* 4. y-center
* 5. y-sigma
* 6. background
* 7. z-center
* 8. status
* 9. error
* .. repeat ..
* n_peaks - The number of parameters (peaks).
*/
void newPeaks(double *peaks, int n_peaks, int fit_type)
{
int i,j,n_fit_params,sx,sy,sz;
double temp;
if(fit_type == F2D){
n_fit_params = 4;
}
else{
n_fit_params = 5;
}
/* Delete old fit data structures, if they exist. */
freePeaks();
/* Reset the fit array. */
resetFit();
/* Allocate storage for fit data structure. */
n_fit_data = n_peaks;
new_fit_data = (fitData *)malloc(sizeof(fitData)*n_peaks);
old_fit_data = (fitData *)malloc(sizeof(fitData)*n_peaks);
sx = getXSize()/2 - 1;
sy = getYSize()/2 - 1;
sz = getZSize();
/* Note the assumption here that the splines are square. */
if((sx%2)==1){
xoff = (double)(sx/2) - 1.0;
yoff = (double)(sy/2) - 1.0;
}
else{
xoff = (double)(sx/2) - 1.5;
yoff = (double)(sy/2) - 1.5;
}
//zoff = -(double)(sz/2);
zoff = 0.0;
/* Initialize fit data structure. */
for(i=0;i<n_fit_data;i++){
new_fit_data[i].index = i;
new_fit_data[i].n_params = n_fit_params;
new_fit_data[i].size_x = sx;
new_fit_data[i].size_y = sy;
new_fit_data[i].size_z = sz;
new_fit_data[i].status = (int)(peaks[i*NRESULTSPAR+STATUS]);
new_fit_data[i].type = fit_type;
new_fit_data[i].lambda = 1.0;
mallocFitData(&(new_fit_data[i]), n_fit_params, sx*sy*(n_fit_params+1));
for(j=0;j<n_fit_params;j++){
new_fit_data[i].sign[j] = 0;
}
new_fit_data[i].clamp[CF_HEIGHT] = 100.0;
new_fit_data[i].clamp[CF_XCENTER] = 1.0;
new_fit_data[i].clamp[CF_YCENTER] = 1.0;
new_fit_data[i].clamp[CF_BACKGROUND] = 20.0;
if (fit_type == F3D){
new_fit_data[i].clamp[CF_ZCENTER] = 2.0;
}
if (DEBUG){
printf(" peaks: %.2f %.2f %.2f\n", peaks[i*NRESULTSPAR+XCENTER], peaks[i*NRESULTSPAR+YCENTER], peaks[i*NRESULTSPAR+ZCENTER]);
}
new_fit_data[i].params[CF_HEIGHT] = peaks[i*NRESULTSPAR+HEIGHT];
new_fit_data[i].params[CF_XCENTER] = peaks[i*NRESULTSPAR+XCENTER] - xoff;
new_fit_data[i].params[CF_YCENTER] = peaks[i*NRESULTSPAR+YCENTER] - yoff;
new_fit_data[i].params[CF_BACKGROUND] = peaks[i*NRESULTSPAR+BACKGROUND];
if (fit_type == F3D){
new_fit_data[i].params[CF_ZCENTER] = peaks[i*NRESULTSPAR+ZCENTER] - zoff;
}
new_fit_data[i].xi = (int)(new_fit_data[i].params[CF_XCENTER]);
new_fit_data[i].yi = (int)(new_fit_data[i].params[CF_YCENTER]);
if (fit_type == F3D){
new_fit_data[i].zi = (int)(new_fit_data[i].params[CF_ZCENTER]);
}
if (fit_type == F2D){
updateFitValues2D(&(new_fit_data[i]));
}
else{
updateFitValues3D(&(new_fit_data[i]));
}
/*
* The derivative with respect to background term is always 1.0
*/
for(j=0;j<(sx*sy);j++){
new_fit_data[i].values[(CF_BACKGROUND+1)*sx*sy+j] = 1.0;
}
addPeak(&(new_fit_data[i]));
mallocFitData(&(old_fit_data[i]), n_fit_params, sx*sy*(n_fit_params+1));
copyFitData(&(new_fit_data[i]), &(old_fit_data[i]));
if(new_fit_data[i].status == RUNNING){
if (TESTING){
temp = calcError(&(new_fit_data[i]), new_fit_data[i].params[CF_BACKGROUND]);
new_fit_data[i].error = temp;
}
else{
new_fit_data[i].error = 1.0e+12;
}
old_fit_data[i].error = 1.0e+13;
}
else{
new_fit_data[i].error = peaks[i*NRESULTSPAR+IERROR];
old_fit_data[i].error = new_fit_data[i].error;
}
}
}
