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authorThomas White <taw@physics.org>2013-10-09 15:08:50 +0200
committerThomas White <taw@physics.org>2013-10-09 15:08:50 +0200
commitaeff068d752b902cd121610e0409ecbfb7840f8f (patch)
tree8500affd146d77060594a0c9a73efcf710e41253
parentca0bd5924ce038d42b731fbf45324bd05a35f636 (diff)
Integration verbosity fixes
-rw-r--r--libcrystfel/src/integration.c78
1 files changed, 57 insertions, 21 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 0643dc23..1e02d9c9 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -824,7 +824,10 @@ static int check_box(struct intcontext *ic, struct peak_box *bx, int *sat)
if ( sat != NULL ) *sat = 0;
bx->bm = malloc(ic->w*ic->w*sizeof(int));
- if ( bx->bm == NULL ) return 1;
+ if ( bx->bm == NULL ) {
+ ERROR("Failed to allocate box mask\n");
+ return 1;
+ }
cell_get_cartesian(ic->cell,
&adx, &ady, &adz,
@@ -844,9 +847,15 @@ static int check_box(struct intcontext *ic, struct peak_box *bx, int *sat)
ss = bx->css + q;
if ( (fs < 0) || (fs >= bx->p->w)
- || (ss < 0) || (ss >= bx->p->h) ) return 1;
+ || (ss < 0) || (ss >= bx->p->h) ) {
+ if ( bx->verbose ) {
+ ERROR("Box fell off edge of panel\n");
+ }
+ return 1;
+ }
if ( (p < 0) || (p >= ic->w) || (q < 0) || (q >= ic->w) ) {
+ ERROR("WTF?\n");
return 1;
}
@@ -881,8 +890,20 @@ static int check_box(struct intcontext *ic, struct peak_box *bx, int *sat)
}
}
- if ( n_pk < 4 ) return 1;
- if ( n_bg < 4 ) return 1;
+ if ( n_pk < 4 ) {
+ if ( bx->verbose ) {
+ ERROR("Not enough peak pixels (%i)\n", n_pk);
+ show_peak_box(ic, bx);
+ }
+ return 1;
+ }
+ if ( n_bg < 4 ) {
+ if ( bx->verbose ) {
+ ERROR("Not enough bg pixels (%i)\n", n_bg);
+ show_peak_box(ic, bx);
+ }
+ return 1;
+ }
setup_peak_integrals(ic, bx);
@@ -926,6 +947,9 @@ static int center_and_check_box(struct intcontext *ic, struct peak_box *bx,
bx->offs_ss = 0.0;
if ( check_box(ic, bx, sat) ) return 1;
+ fit_bg(ic, bx);
+
+ if ( bx->verbose ) show_peak_box(ic, bx);
for ( i=0; i<10; i++ ) {
@@ -961,16 +985,32 @@ static int center_and_check_box(struct intcontext *ic, struct peak_box *bx,
bx->offs_ss += iss;
bx->cfs += ifs;
bx->css += iss;
-
- t_offs_fs += rint(offs_fs);
- t_offs_ss += rint(offs_fs);
+ t_offs_fs += ifs;
+ t_offs_ss += iss;
+ if ( bx->verbose ) {
+ STATUS("Centering step %i,%i\n", ifs, iss);
+ }
free(bx->bm);
- if ( check_box(ic, bx, sat) ) return 1;
+ if ( check_box(ic, bx, sat) ) {
+ if ( bx->verbose ) {
+ ERROR("Box invalid after centering step.\n");
+ }
+ return 1;
+ }
if ( t_offs_fs*t_offs_fs + t_offs_ss*t_offs_ss > ic->w*ic->w ) {
+ if ( bx->verbose ) {
+ ERROR("Box drifted too far during centering.\n");
+ }
return 1;
}
+
+ fit_bg(ic, bx);
+ if ( bx->verbose ) show_peak_box(ic, bx);
+
+ if ( (ifs==0) && (iss==0) ) break;
+
}
return 0;
@@ -1337,6 +1377,11 @@ static void measure_all_intensities(IntegrationMethod meth, RefList *list,
bx->p = p;
bx->pn = pn;
+ get_indices(refl, &h, &k, &l);
+ if ( VERBOSITY ) {
+ bx->verbose = 1;
+ }
+
/* Which reference profile? */
bx->rp = 0;//bx->pn;
@@ -1360,11 +1405,6 @@ static void measure_all_intensities(IntegrationMethod meth, RefList *list,
}
}
- get_indices(refl, &h, &k, &l);
- if ( VERBOSITY ) {
- bx->verbose = 1;
- }
-
fit_bg(&ic, bx);
bx->intensity = tentative_intensity(&ic, bx);
@@ -1718,11 +1758,15 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
bx->css = css;
bx->p = p;
bx->pn = pn;
+ get_indices(refl, &h, &k, &l);
+ bx->verbose = VERBOSITY;
if ( meth & INTEGRATION_CENTER ) {
r = center_and_check_box(&ic, bx, &saturated);
} else {
r = check_box(&ic, bx, &saturated);
+ fit_bg(&ic, bx);
+ if ( bx->verbose ) show_peak_box(&ic, bx);
bx->offs_fs = 0.0;
bx->offs_ss = 0.0;
}
@@ -1739,20 +1783,12 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
}
}
- get_indices(refl, &h, &k, &l);
- if ( VERBOSITY ) {
- bx->verbose = 1;
- }
-
- fit_bg(&ic, bx);
intensity = tentative_intensity(&ic, bx);
mean_var_background(&ic, bx, &bgmean, &sig2_bg);
aduph = bx->p->adu_per_eV * ph_lambda_to_eV(ic.image->lambda);
sig2_poisson = aduph * intensity;
sigma = sqrt(sig2_poisson + bx->m*sig2_bg);
- if ( bx->verbose ) show_peak_box(&ic, bx);
-
/* Record intensity and set redundancy to 1 */
bx->intensity = intensity;
set_intensity(refl, intensity);