Debugging

Debug API functions available to LabVIEW. More...

Functions
CDLL_EXPORT void DLL_CALLCONV	qtrk_set_logfile_path (const char *path)
CDLL_EXPORT void DLL_CALLCONV	qtrk_get_computed_config (QueuedTracker *qtrk, QTrkComputedConfig *cc, ErrorCluster *err)
CDLL_EXPORT void DLL_CALLCONV	qtrk_set_pixel_calib_factors (QueuedTracker *qtrk, float offsetFactor, float gainFactor, ErrorCluster *e)
	Set pixel calibration factors. More...
CDLL_EXPORT void DLL_CALLCONV	qtrk_set_pixel_calib (QueuedTracker *qtrk, LVArray3D< float > **offset, LVArray3D< float > **gain, ErrorCluster *e)
	Set pixel calibration images. More...
CDLL_EXPORT void DLL_CALLCONV	qtrk_dump_memleaks ()
CDLL_EXPORT void	qtrk_get_profile_report (QueuedTracker *qtrk, LStrHandle str)
CDLL_EXPORT void	qtrk_enable_zlut_cmpprof (QueuedTracker *qtrk, bool enable, ErrorCluster *e)
CDLL_EXPORT void	qtrk_get_zlut_cmpprof (QueuedTracker *qtrk, LVArray2D< float > **output, ErrorCluster *e)
CDLL_EXPORT int	qtrk_get_debug_image (QueuedTracker *qtrk, int id, LVArray2D< float > **data, ErrorCluster *e)
CDLL_EXPORT void	qtrk_compute_fisher (LVArray2D< float > **lut, QTrkSettings *cfg, vector3f *pos, LVArray2D< float > **fisherMatrix, LVArray2D< float > **inverseMatrix, vector3f *xyzVariance, int Nsamples, float maxPixelValue)
CDLL_EXPORT void	qtrk_test_array_passing (int n, LVArray< float > **flt1D, LVArray2D< float > **flt2D, LVArray< int > **int1D, LVArray2D< int > **int2D)
CDLL_EXPORT void	qtrk_simulate_tracking (QueuedTracker *qtrk, int nsmp, int beadIndex, vector3f *centerPos, vector3f *range, vector3f *outBias, vector3f *outScatter, float photonsPerWell, ErrorCluster *e)
CDLL_EXPORT void DLL_CALLCONV	qtrk_generate_gaussian_spot (LVArray2D< float > **image, vector2f *pos, float sigma, float I0, float Ibg, int applyNoise)
CDLL_EXPORT void DLL_CALLCONV	qtrk_generate_image_from_lut (LVArray2D< float > **image, LVArray2D< float > **lut, float *LUTradii, vector2f *position, float z, float M, float sigma_noise)

Detailed Description

Debug API functions available to LabVIEW.

Function Documentation

qtrk_compute_fisher()

CDLL_EXPORT void qtrk_compute_fisher	(	LVArray2D< float > **	lut,
		QTrkSettings *	cfg,
		vector3f *	pos,
		LVArray2D< float > **	fisherMatrix,
		LVArray2D< float > **	inverseMatrix,
		vector3f *	xyzVariance,
		int	Nsamples,
		float	maxPixelValue
	)

Definition at line 514 of file lv_queuetrk_api.cpp.

{
    QTrkComputedConfig cc (*cfg);
    ImageData lutImg( (*lut)->elem, (*lut)->dimSizes[1], (*lut)->dimSizes[0] );
    SampleFisherMatrix fm(maxPixelValue);
    Matrix3X3 mat = fm.ComputeAverageFisher(*pos, Nsamples, vector3f(1,1,1), vector3f(1,1,1)*0.001f, cfg->width, cfg->height, [&](ImageData&out, vector3f pos) {
        GenerateImageFromLUT(&out, &lutImg, cc.zlut_minradius,cc.zlut_maxradius, pos);
    });
    
    if (fisherMatrix) {
        ResizeLVArray2D( fisherMatrix, 3, 3);
        for (int i=0;i<9;i++)
            (*fisherMatrix)->elem[i] = mat[i];
    }

    if (inverseMatrix) {
        Matrix3X3 inv = mat.Inverse();
        ResizeLVArray2D( inverseMatrix, 3, 3);
        for (int i=0;i<9;i++)
            (*inverseMatrix)->elem[i] = inv[i];
    }

    if (xyzVariance)
        *xyzVariance = mat.Inverse().diag();
}

qtrk_dump_memleaks()

CDLL_EXPORT void DLL_CALLCONV qtrk_dump_memleaks

(

)

Definition at line 501 of file lv_queuetrk_api.cpp.

{
#ifdef USE_MEMDBG
    _CrtDumpMemoryLeaks();
#endif
}

qtrk_enable_zlut_cmpprof()

CDLL_EXPORT void qtrk_enable_zlut_cmpprof	(	QueuedTracker *	qtrk,
		bool	enable,
		ErrorCluster *	e
	)

Definition at line 430 of file lv_queuetrk_api.cpp.

{
    if (ValidateTracker(qtrk, e, "enable zlut cmpprof"))
        qtrk->EnableRadialZLUTCompareProfile(enable);
}

qtrk_generate_gaussian_spot()

CDLL_EXPORT void DLL_CALLCONV qtrk_generate_gaussian_spot	(	LVArray2D< float > **	image,
		vector2f *	pos,
		float	sigma,
		float	I0,
		float	Ibg,
		int	applyNoise
	)

Definition at line 477 of file lv_queuetrk_api.cpp.

{
    ImageData img((*image)->elem, (*image)->dimSizes[1], (*image)->dimSizes[0]);

    GenerateGaussianSpotImage(&img, *pos, sigma, I0, Ibg);

    if (applyNoise)
        ApplyPoissonNoise(img,1);
}

qtrk_generate_image_from_lut()

CDLL_EXPORT void DLL_CALLCONV qtrk_generate_image_from_lut	(	LVArray2D< float > **	image,
		LVArray2D< float > **	lut,
		float *	LUTradii,
		vector2f *	position,
		float	z,
		float	M,
		float	sigma_noise
	)

Definition at line 487 of file lv_queuetrk_api.cpp.

{
    ImageData img((*image)->elem, (*image)->dimSizes[1], (*image)->dimSizes[0]);
    ImageData zlut((*lut)->elem, (*lut)->dimSizes[1], (*lut)->dimSizes[0]);

    vector3f pos (position->x, position->y, z);
    GenerateImageFromLUT(&img, &zlut, LUTradii[0], LUTradii[1], pos);
    //img.normalize();
    if(sigma_noise>0)
        ApplyGaussianNoise(img, sigma_noise);
}

qtrk_get_computed_config()

CDLL_EXPORT void DLL_CALLCONV qtrk_get_computed_config	(	QueuedTracker *	qtrk,
		QTrkComputedConfig *	cc,
		ErrorCluster *	err
	)

Definition at line 95 of file lv_queuetrk_api.cpp.

{
    if (ValidateTracker(qtrk, err, "get computed config"))
        *cc = qtrk->cfg;
}

qtrk_get_debug_image()

CDLL_EXPORT int qtrk_get_debug_image	(	QueuedTracker *	qtrk,
		int	id,
		LVArray2D< float > **	data,
		ErrorCluster *	e
	)

Definition at line 75 of file lv_queuetrk_api.cpp.

{
    int w,h;
    if (ValidateTracker(qtrk, e, "qtrk_get_debug_image")) {
        float* img;
        if (qtrk->GetDebugImage(id, &w,&h, &img)) {
            ResizeLVArray2D(data, h, w);
            for (int i=0;i<w*h;i++) (*data)->elem[i]=img[i];
            delete[] img;
            return 1;
        }
    }
    return 0;
}

qtrk_get_profile_report()

CDLL_EXPORT void qtrk_get_profile_report	(	QueuedTracker *	qtrk,
		LStrHandle	str
	)

Definition at line 508 of file lv_queuetrk_api.cpp.

{
    SetLVString(str, qtrk->GetProfileReport().c_str());
}

qtrk_get_zlut_cmpprof()

CDLL_EXPORT void qtrk_get_zlut_cmpprof	(	QueuedTracker *	qtrk,
		LVArray2D< float > **	output,
		ErrorCluster *	e
	)

Definition at line 418 of file lv_queuetrk_api.cpp.

{
    if (ValidateTracker(qtrk, e, "get zlut compare profiles"))
    {
        int cnt,planes,rsteps;
        qtrk->GetRadialZLUTSize(cnt,planes,rsteps);
        ResizeLVArray2D(output, cnt, planes);

        qtrk->GetRadialZLUTCompareProfile((*output)->elem);
    }
}

qtrk_set_logfile_path()

CDLL_EXPORT void DLL_CALLCONV qtrk_set_logfile_path

(

const char *

path

)

Definition at line 90 of file lv_queuetrk_api.cpp.

{
    dbgsetlogfile(path);
}

qtrk_set_pixel_calib()

CDLL_EXPORT void DLL_CALLCONV qtrk_set_pixel_calib	(	QueuedTracker *	qtrk,
		LVArray3D< float > **	offset,
		LVArray3D< float > **	gain,
		ErrorCluster *	e
	)

Set pixel calibration images.

The offset and gain provided will be used to scale incoming images to reduce background influence.

Definition at line 185 of file lv_queuetrk_api.cpp.

{
    if (ValidateTracker(qtrk, e, "set pixel calibration images")) {
        int count, planes, radialSteps;
        qtrk->GetRadialZLUTSize(count, planes, radialSteps);

        float *offset_data = 0, *gain_data = 0;

        if((*offset)->dimSizes[0] != 0) {
            if (qtrk->cfg.width != (*offset)->dimSizes[2] || qtrk->cfg.height != (*offset)->dimSizes[1]) {
                ArgumentErrorMsg(e, SPrintf("set_pixel_calib: Offset images passed with invalid dimension (%d,%d)", (*offset)->dimSizes[2], (*offset)->dimSizes[1]));
                return;
            }
            if (count != (*offset)->dimSizes[0]) {
                ArgumentErrorMsg(e, SPrintf("set_pixel_calib: Expecting offset to have %d images (same as ZLUT). %d given", count, (*offset)->dimSizes[0]));
                return;
            }
            offset_data = (*offset)->elem;
        }

        if((*gain)->dimSizes[0] != 0) {
            if (qtrk->cfg.width != (*gain)->dimSizes[2] || qtrk->cfg.height != (*gain)->dimSizes[1]) {
                ArgumentErrorMsg(e, SPrintf("set_pixel_calib: Gain images passed with invalid dimension (%d,%d)", (*gain)->dimSizes[2], (*gain)->dimSizes[1]));
                return;
            }
            if (count != (*gain)->dimSizes[0]) {
                ArgumentErrorMsg(e, SPrintf("set_pixel_calib: Expecting gain to have %d images (same as ZLUT). %d given", count, (*gain)->dimSizes[0]));
                return;
            }
            gain_data = (*gain)->elem;
        }

        qtrk->SetPixelCalibrationImages(offset_data, gain_data);
    }
}

qtrk_set_pixel_calib_factors()

CDLL_EXPORT void DLL_CALLCONV qtrk_set_pixel_calib_factors	(	QueuedTracker *	qtrk,
		float	offsetFactor,
		float	gainFactor,
		ErrorCluster *	e
	)

Set pixel calibration factors.

The offset and gain factors provided will be used to scale incoming images to reduce background influence.

Use together with qtrk_set_pixel_calib. If manual factors are not given, 1.0 (no change) is used as default.

Definition at line 178 of file lv_queuetrk_api.cpp.

{
    if (ValidateTracker(qtrk, e, "set pixel calib factors")) {
        qtrk->SetPixelCalibrationFactors(offsetFactor, gainFactor);
    }
}

qtrk_simulate_tracking()

CDLL_EXPORT void qtrk_simulate_tracking	(	QueuedTracker *	qtrk,
		int	nsmp,
		int	beadIndex,
		vector3f *	centerPos,
		vector3f *	range,
		vector3f *	outBias,
		vector3f *	outScatter,
		float	photonsPerWell,
		ErrorCluster *	e
	)

Definition at line 584 of file lv_queuetrk_api.cpp.

{
    if (ValidateTracker(qtrk, e, "qtrk_simulate_tracking")) {

        int nZLUT, nPlanes, nRadialSteps;
        qtrk->GetRadialZLUTSize(nZLUT, nPlanes, nRadialSteps);

        float* lut = new float[nZLUT*nPlanes*nRadialSteps];
        qtrk->GetRadialZLUT(lut);

        ImageData img = ImageData::alloc(qtrk->cfg.width,qtrk->cfg.height);
        ImageData zlut;
        zlut.data = & lut [nRadialSteps*nPlanes*beadIndex];
        zlut.w = nRadialSteps;
        zlut.h = nPlanes;

        // Generate images
        std::vector<vector3f> positions(nsmp);
        for (int i=0;i<nsmp;i++) {
            vector3f pos = *centerPos + *range * vector3f(rand_uniform<float>(), rand_uniform<float>(), rand_uniform<float>());
            positions[i]=pos;
            GenerateImageFromLUT( &img, &zlut, qtrk->cfg.zlut_minradius, qtrk->cfg.zlut_maxradius, pos);
            ApplyPoissonNoise(img, photonsPerWell);
            qtrk->ScheduleLocalization((uchar*)img.data, sizeof(float)*img.w, QTrkFloat,i,i,0,beadIndex);
        }

        img.free();

        qtrk->Flush();
        while (!qtrk->IsIdle());

        LocalizationResult* results=new LocalizationResult[nsmp];
        qtrk->FetchResults(results, nsmp);
        vector3f sumBias, sumScatter;
        for (int i=0;i<nsmp;i++) {
            vector3f truepos = positions [ results[i].job.frame ];
            vector3f diff = results[i].pos - truepos;
            sumBias += diff;
        }
        vector3f meanBias = sumBias / nsmp;
        for (int i=0;i<nsmp;i++) {
            vector3f truepos = positions [ results[i].job.frame ];
            vector3f diff = results[i].pos - truepos;
            diff -= meanBias;
            sumScatter += diff*diff;
        }
        *outScatter = sqrt (sumScatter / nsmp);
        *outBias = sumBias;
    }
}

qtrk_test_array_passing()

CDLL_EXPORT void qtrk_test_array_passing	(	int	n,
		LVArray< float > **	flt1D,
		LVArray2D< float > **	flt2D,
		LVArray< int > **	int1D,
		LVArray2D< int > **	int2D
	)

Definition at line 559 of file lv_queuetrk_api.cpp.

{
    for (int i=0;i<(*int2D)->dimSizes[0];i++)
    {
        for (int j=0;j<(*int2D)->dimSizes[1];j++)
        {
            dbgprintf("%d\t", (*int2D)->get(i, j));
        }
        dbgprintf("\n");
    }

    ResizeLVArray(flt1D, n);
    ResizeLVArray(int1D, n);
    ResizeLVArray2D(flt2D, n/2,n);
    ResizeLVArray2D(int2D, n/2,n);
    for (int i=0;i<n;i++) {
        (*int1D)->elem[i]=(i+1)*i;
        (*flt1D)->elem[i]=sqrtf(i);
        for (int j=0;j<n/2;j++) {
            (*int2D)->get(j, i) = j*2+i;
            (*flt2D)->get(j, i) = j*2+i;
        }
    }
}