diff options
| -rw-r--r-- | libcrystfel/src/integration.c | 67 |
1 files changed, 26 insertions, 41 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c index 83cf8d0e..2c358ccd 100644 --- a/libcrystfel/src/integration.c +++ b/libcrystfel/src/integration.c @@ -1319,6 +1319,31 @@ static int get_int_diag(struct intcontext *ic, Reflection *refl) } + +static void integrate_prof2d_once(struct intcontext *ic, struct peak_box *bx) +{ + bx->intensity = fit_intensity(ic, bx); + bx->sigma = calc_sigma(ic, bx); + + if ( bg_ok(bx) ) { + + double pfs, pss; + + set_intensity(bx->refl, bx->intensity); + set_esd_intensity(bx->refl, bx->sigma); + set_redundancy(bx->refl, 1); + + /* Update position */ + get_detector_pos(bx->refl, &pfs, &pss); + pfs += bx->offs_fs; + pss += bx->offs_ss; + set_detector_pos(bx->refl, 0.0, pfs, pss); + + if ( get_int_diag(ic, bx->refl) ) show_peak_box(ic, bx); + + } +} + static void integrate_prof2d(IntegrationMethod meth, Crystal *cr, struct image *image, IntDiag int_diag, signed int idh, signed int idk, signed int idl, @@ -1430,49 +1455,9 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr, calculate_reference_profiles(&ic); for ( i=0; i<ic.n_boxes; i++ ) { - struct peak_box *bx; - bx = &ic.boxes[i]; - bx->intensity = fit_intensity(&ic, bx); - bx->sigma = calc_sigma(&ic, bx); - -#if 0 - if ( isnan(bx->intensity) ) { - signed int h, k, l; - get_indices(bx->refl, &h, &k, &l); - STATUS("NaN intensity for %i %i %i !\n", h, k, l); - STATUS("panel %s\n", image->det->panels[bx->pn].name); - show_reference_profile(&ic, bx->rp); - } - if ( bx->intensity < 0.0 ) { - signed int h, k, l; - get_indices(bx->refl, &h, &k, &l); - STATUS("Negative intensity (%f) for %i %i %i !\n", - bx->intensity, h, k, l); - STATUS("panel %s\n", image->det->panels[bx->pn].name); - show_reference_profile(&ic, bx->rp); - } -#endif - - if ( bg_ok(bx) ) { - - double pfs, pss; - - set_intensity(bx->refl, bx->intensity); - set_esd_intensity(bx->refl, bx->sigma); - set_redundancy(bx->refl, 1); - - /* Update position */ - get_detector_pos(bx->refl, &pfs, &pss); - pfs += bx->offs_fs; - pss += bx->offs_ss; - set_detector_pos(bx->refl, 0.0, pfs, pss); - - if ( get_int_diag(&ic, refl) ) show_peak_box(&ic, bx); - - } - + integrate_prof2d_once(&ic, bx); } refine_rigid_groups(&ic); |