ZLUT Bias Correction

Functions related to correcting the bias in the z lookup table scheme. More...

Functions
void	QueuedTracker::ComputeZBiasCorrection (int bias_planes, CImageData *result, int smpPerPixel, bool useSplineInterp)
float	QueuedTracker::ZLUTBiasCorrection (float z, int zlut_planes, int bead)
void	QueuedTracker::SetZLUTBiasCorrection (const CImageData &data)
CImageData *	QueuedTracker::GetZLUTBiasCorrection ()

Variables
CImageData *	QueuedTracker::zlut_bias_correction

Detailed Description

Functions related to correcting the bias in the z lookup table scheme.

For more information, see Jelmer's paper on this software environment [1]. This is not used on setups as far as I (Jordi) am aware, since it was still in a development stage when Jelmer left.

Function Documentation

ComputeZBiasCorrection()

void QueuedTracker::ComputeZBiasCorrection	(	int	bias_planes,
		CImageData *	result,
		int	smpPerPixel,
		bool	useSplineInterp
	)

Definition at line 173 of file QueuedTracker.cpp.

{
    int count,zlut_planes,radialsteps;
    GetRadialZLUTSize(count, zlut_planes, radialsteps);
    float* zlut_data = new float[count*zlut_planes*radialsteps];
    GetRadialZLUT(zlut_data);

    std::vector<float> qi_rweights = ComputeRadialBinWindow(cfg.qi_radialsteps);
    std::vector<float> zlut_rweights = ComputeRadialBinWindow(cfg.zlut_radialsteps);

    if (zlut_bias_correction)
        delete zlut_bias_correction;

    zlut_bias_correction = new CImageData(bias_planes, count);

    parallel_for(count*bias_planes, [&](int job) {
    //for (int job=0;job<count*bias_planes;job++) {
        int bead = job/bias_planes;
        int plane = job%bias_planes;
        
        float *zlut_ptr = &zlut_data[ bead * (zlut_planes*radialsteps) ];
        CPUTracker trk (cfg.width,cfg.height);
        ImageData zlut(zlut_ptr, radialsteps, zlut_planes);
        trk.SetRadialZLUT(zlut.data, zlut.h, zlut.w, 1, cfg.zlut_minradius,cfg.zlut_maxradius, false, false);
        trk.SetRadialWeights(&zlut_rweights[0]);

        vector3f pos(cfg.width/2,cfg.height/2, plane /(float) bias_planes * zlut_planes );
        ImageData img = ImageData::alloc(cfg.width,cfg.height);
        GenerateImageFromLUT(&img, &zlut, cfg.zlut_minradius, cfg.zlut_maxradius, pos, useSplineInterp,smpPerPixel);

        bool bhit;
        trk.SetImageFloat(img.data);
        vector2f com = trk.ComputeMeanAndCOM();
        vector2f qi = trk.ComputeQI(com, 2, cfg.qi_radialsteps, cfg.qi_angstepspq, cfg.qi_angstep_factor, cfg.qi_minradius, cfg.qi_maxradius, bhit, &qi_rweights[0]);
        float z = trk.ComputeZ(qi, cfg.zlut_angularsteps, 0);
        zlut_bias_correction->at(plane, bead) = z - pos.z;

        //trk.ComputeRadialProfile(
        img.free();
        if ((job%(count*bias_planes/10)) == 0) 
            dbgprintf("job=%d\n", job);
//  }
    });

    if (result)
        *result = *zlut_bias_correction;
}

GetZLUTBiasCorrection()

CImageData * QueuedTracker::GetZLUTBiasCorrection

(

)

Definition at line 227 of file QueuedTracker.cpp.

{
    if (zlut_bias_correction) return new CImageData(*zlut_bias_correction);
    return 0;
}

SetZLUTBiasCorrection()

void QueuedTracker::SetZLUTBiasCorrection

(

const CImageData &

data

)

Definition at line 221 of file QueuedTracker.cpp.

{
    if (zlut_bias_correction) delete zlut_bias_correction;
    zlut_bias_correction = new CImageData(bc);
}

ZLUTBiasCorrection()

float QueuedTracker::ZLUTBiasCorrection	(	float	z,
		int	zlut_planes,
		int	bead
	)

Definition at line 147 of file QueuedTracker.cpp.

{
    if (!zlut_bias_correction)
        return z;

    /*
        bias = d(r,4);
        measured_pos = d(r,1) + bias;
        pos = measured_pos;
        for k=1:2
            guess_bias = interp1(d(r,1), bias, pos);
            pos = measured_pos - guess_bias;
        end
        */

    // we have to reverse the bias table: we know that true_z + bias(true_z) = measured_z, but we can only get bias(measured_z)
    // It seems that one can iterate towards the right position:
    
    float pos = z;
    for (int k=0;k<4;k++) {
        float tblpos = pos / (float)zlut_planes * zlut_bias_correction->w;
        float bias = zlut_bias_correction->interpolate1D(bead, tblpos);
        pos = z - bias;
    }
    return pos;
}

Variable Documentation

zlut_bias_correction

CImageData* QueuedTracker::zlut_bias_correction

protected

Definition at line 388 of file QueuedTracker.h.