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Fix the 2D width clamp and the shared-background Jacobian #71

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Merged
HazenBabcock merged 2 commits into from
Oct 18, 2026
Merged

Fix the 2D width clamp and the shared-background Jacobian #71

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4fe31c1
Tie YWIDTH to the clamped XWIDTH in the 2D Gaussian model
HazenBabcock Oct 18, 2026
9b3e948
Divide the background Jacobian column by bg_counts
HazenBabcock Oct 18, 2026
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3 changes: 2 additions & 1 deletion storm_analysis/psf_fft/fft_fit.c
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,8 @@ void ftFitCalcJH3D(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = rqei*height*(dx[l]);
jt[2] = rqei*height*(dy[l]);
jt[3] = rqei*height*(dz[l]);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate jacobian. */
t1 = 2.0*(1.0 - xi/fi);
Expand Down
3 changes: 2 additions & 1 deletion storm_analysis/pupilfn/pupil_fit.c
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Expand Up @@ -104,7 +104,8 @@ void pfitCalcJH3D(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = rqei*2.0*height*(psf_r[l]*dx_r[l]+psf_c[l]*dx_c[l]);
jt[2] = rqei*2.0*height*(psf_r[l]*dy_r[l]+psf_c[l]*dy_c[l]);
jt[3] = rqei*2.0*height*(psf_r[l]*dz_r[l]+psf_c[l]*dz_c[l]);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate jacobian. */
t1 = 2.0*(1.0 - xi/fi);
Expand Down
62 changes: 47 additions & 15 deletions storm_analysis/sa_library/dao_fit.c
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Expand Up @@ -86,7 +86,8 @@ void daoCalcJH2DFixed(fitData *fit_data, double *jacobian, double *hessian)
jt[0] = rqei*e_t;
jt[1] = rqei*2.0*a1*width*xt*e_t;
jt[2] = rqei*2.0*a1*width*yt*e_t;
jt[3] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[3] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t1 = 2.0*(1.0 - xi/fi);
Expand Down Expand Up @@ -163,7 +164,8 @@ void daoCalcJH2DFixedALS(fitData *fit_data, double *jacobian, double *hessian)
jt[0] = t1*e_t;
jt[1] = t1*2.0*a1*width*xt*e_t;
jt[2] = t1*2.0*a1*width*yt*e_t;
jt[3] = t1;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[3] = t1/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t2 = (fi - fit_data->as_xi[k]);
Expand Down Expand Up @@ -238,7 +240,8 @@ void daoCalcJH2DFixedLS(fitData *fit_data, double *jacobian, double *hessian)
jt[0] = rqei*e_t;
jt[1] = rqei*2.0*a1*width*xt*e_t;
jt[2] = rqei*2.0*a1*width*yt*e_t;
jt[3] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[3] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t1 = (fi - fit_data->x_data[k]);
Expand Down Expand Up @@ -310,7 +313,8 @@ void daoCalcJH2DFixedDWLS(fitData *fit_data, double *jacobian, double *hessian)
jt[0] = rqei*e_t;
jt[1] = rqei*2.0*a1*width*xt*e_t;
jt[2] = rqei*2.0*a1*width*yt*e_t;
jt[3] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[3] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t1 = (fi - xi)/xi;
Expand Down Expand Up @@ -378,7 +382,8 @@ void daoCalcJH2DFixedFWLS(fitData *fit_data, double *jacobian, double *hessian)
jt[0] = rqei*e_t;
jt[1] = rqei*2.0*a1*width*xt*e_t;
jt[2] = rqei*2.0*a1*width*yt*e_t;
jt[3] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[3] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t1 = (fi - xi)/fi;
Expand Down Expand Up @@ -448,7 +453,8 @@ void daoCalcJH2D(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = rqei*2.0*a1*width*xt*e_t;
jt[2] = rqei*2.0*a1*width*yt*e_t;
jt[3] = rqei*(-a1*xt*xt*e_t-a1*yt*yt*e_t);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector */
t1 = 2.0*(1.0 - xi/fi);
Expand Down Expand Up @@ -527,7 +533,8 @@ void daoCalcJH2DALS(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = t1*2.0*a1*width*xt*e_t;
jt[2] = t1*2.0*a1*width*yt*e_t;
jt[3] = t1*(-a1*xt*xt*e_t-a1*yt*yt*e_t);
jt[4] = t1;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = t1/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t2 = (fi - fit_data->as_xi[k]);
Expand Down Expand Up @@ -632,7 +639,8 @@ void daoCalcJH2DLS(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = rqei*2.0*a1*width*xt*e_t;
jt[2] = rqei*2.0*a1*width*yt*e_t;
jt[3] = rqei*(-a1*xt*xt*e_t-a1*yt*yt*e_t);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t1 = (fi - fit_data->x_data[k]);
Expand Down Expand Up @@ -706,7 +714,8 @@ void daoCalcJH2DDWLS(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = rqei*2.0*a1*width*xt*e_t;
jt[2] = rqei*2.0*a1*width*yt*e_t;
jt[3] = rqei*(-a1*xt*xt*e_t-a1*yt*yt*e_t);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t1 = (fi - xi)/xi;
Expand Down Expand Up @@ -780,7 +789,8 @@ void daoCalcJH2DFWLS(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = rqei*2.0*a1*width*xt*e_t;
jt[2] = rqei*2.0*a1*width*yt*e_t;
jt[3] = rqei*(-a1*xt*xt*e_t-a1*yt*yt*e_t);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t1 = (fi - fit_data->x_data[k])/fi;
Expand Down Expand Up @@ -852,7 +862,8 @@ void daoCalcJH3D(fitData *fit_data, double *jacobian, double *hessian)
jt[2] = rqei*(-a1*xt*xt*e_t);
jt[3] = rqei*2.0*a1*a5*yt*e_t;
jt[4] = rqei*(-a1*yt*yt*e_t);
jt[5] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[5] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t1 = 2.0*(1.0 - xi/fi);
Expand Down Expand Up @@ -946,7 +957,8 @@ void daoCalcJHZ(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = rqei*2.0*a1*a3*xt*e_t;
jt[2] = rqei*2.0*a1*a5*yt*e_t;
jt[3] = rqei*(-a1*xt*xt*gx*e_t-a1*yt*yt*gy*e_t);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate b vector. */
t1 = 2.0*(1.0 - xi/fi);
Expand Down Expand Up @@ -1090,7 +1102,16 @@ int daoCheck2D(fitData *fit_data){
else if(peak->params[XWIDTH] > dao_fit->width_max){
peak->params[XWIDTH] = dao_fit->width_max;
}


/*
* The 2D model has a single width, but the peak shape is drawn from
* XWIDTH in x and YWIDTH in y. Copy it after the clamp, otherwise a
* clamped peak is drawn with an unclamped YWIDTH. This is also the
* only place that multi-plane DAO fitting, mpDaoUpdate(), gets its
* YWIDTH from.
*/
peak->params[YWIDTH] = peak->params[XWIDTH];

return 0;
}

Expand All @@ -1110,11 +1131,22 @@ int daoCheck3D(fitData *fit_data){

peak = fit_data->working_peak;
dao_fit = (daoFit *)fit_data->fit_model;
if(daoCheck2D(fit_data)){

if(mFitCheck(fit_data)){
return 1;
}

/*
* Width range clamp, XWIDTH and YWIDTH independently. Not done by
* calling daoCheck2D() as that ties YWIDTH to XWIDTH.
*/
if(peak->params[XWIDTH] < dao_fit->width_min){
peak->params[XWIDTH] = dao_fit->width_min;
}
else if(peak->params[XWIDTH] > dao_fit->width_max){
peak->params[XWIDTH] = dao_fit->width_max;
}

if(peak->params[YWIDTH] < dao_fit->width_min){
peak->params[YWIDTH] = dao_fit->width_min;
}
Expand Down
15 changes: 10 additions & 5 deletions storm_analysis/spliner/cubic_fit.c
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Expand Up @@ -89,7 +89,8 @@ void cfCalcJH2D(fitData *fit_data, double *jacobian, double *hessian)
jt[0] = rqei*peak->psf[j];
jt[1] = -rqei*height*dxfAt2D(spline_fit->spline_data,l+y_start,m+x_start);
jt[2] = -rqei*height*dyfAt2D(spline_fit->spline_data,l+y_start,m+x_start);
jt[3] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[3] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate jacobian. */
t1 = 2.0*(1.0 - xi/fi);
Expand Down Expand Up @@ -163,7 +164,8 @@ void cfCalcJH3D(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = -rqei*height*dxfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[2] = -rqei*height*dyfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[3] = rqei*height*dzfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate jacobian. */
t1 = 2.0*(1.0 - xi/fi);
Expand Down Expand Up @@ -245,7 +247,8 @@ void cfCalcJH3DALS(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = -t1*height*dxfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[2] = -t1*height*dyfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[3] = t1*height*dzfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[4] = t1;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = t1/((double)fit_data->bg_counts[k]);

/* Calculate jacobian. */
t2 = (fi - fit_data->as_xi[k]);
Expand Down Expand Up @@ -325,7 +328,8 @@ void cfCalcJH3DLS(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = -rqei*height*dxfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[2] = -rqei*height*dyfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[3] = rqei*height*dzfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate jacobian. */
t1 = (fi - fit_data->x_data[k]);
Expand Down Expand Up @@ -406,7 +410,8 @@ void cfCalcJH3DFWLS(fitData *fit_data, double *jacobian, double *hessian)
jt[1] = -rqei*height*dxfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[2] = -rqei*height*dyfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[3] = rqei*height*dzfAt3D(spline_fit->spline_data,zi,l+y_start,m+x_start);
jt[4] = rqei;
/* The background is shared with any overlapping peaks, see mFitCalcErr(). */
jt[4] = rqei/((double)fit_data->bg_counts[k]);

/* Calculate jacobian. */
t1 = (fi - xi)/fi;
Expand Down
10 changes: 6 additions & 4 deletions storm_analysis/test/test_multifit.py
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Expand Up @@ -337,9 +337,10 @@ def test_mfit_8():
"z" : numpy.array([16.0, 26.0])}
mfit.newPeaks(peaks, "text")

# Round trip verification.
# Round trip verification. The 2D model has a single width, so ysigma
# comes back as the (clamped) xsigma, not as the ysigma asked for.
for pname in peaks:
pvals = peaks[pname]
pvals = peaks["xsigma"] if (pname == "ysigma") else peaks[pname]
mvals = mfit.getPeakProperty(pname)
for i in range(pvals.size):
assert(abs(pvals[i] - mvals[i]) < 1.0e-6)
Expand Down Expand Up @@ -402,9 +403,10 @@ def test_mfit_10():
"z" : numpy.array([16.0, 26.0])}
mfit.newPeaks(peaks, "hdf5")

# Round trip verification.
# Round trip verification. The 2D model has a single width, so ysigma
# comes back as the (clamped) xsigma, not as the ysigma asked for.
for pname in peaks:
pvals = peaks[pname]
pvals = peaks["xsigma"] if (pname == "ysigma") else peaks[pname]
mvals = mfit.getPeakProperty(pname)
for i in range(pvals.size):
assert(abs(pvals[i] - mvals[i]) < 1.0e-6)
Expand Down
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