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-rw-r--r--libcrystfel/src/integration.c68
-rw-r--r--libcrystfel/src/integration.h2
-rw-r--r--src/process_image.c2
-rw-r--r--tests/integration_check.c1
-rw-r--r--tests/prof2d_check.c3
5 files changed, 33 insertions, 43 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 4d9a1219..07a3e393 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -159,6 +159,7 @@ struct intcontext
int w;
enum boxmask_val *bm; /* Box mask */
struct image *image;
+ int **masks; /* Peak location mask from make_BgMask() */
struct peak_box *boxes;
int n_boxes;
@@ -872,6 +873,20 @@ static int check_box(struct intcontext *ic, struct peak_box *bx, int *sat)
bx->bm[p+ic->w*q] = BM_BH;
}
+ /* If this is a background pixel, it shouldn't contain any
+ * pixels which are in the peak region of ANY reflection */
+ if ( (ic->masks != NULL) && (bx->bm[p+ic->w*q] == BM_BG)
+ && (ic->masks[bx->pn][fs + bx->p->w*ss] > 0) ) {
+ bx->bm[p+ic->w*q] = BM_BH;
+ }
+
+ /* If this is a peak pixel, it shouldn't contain any pixels
+ * which are in the peak region of more than one reflection */
+ if ( (ic->masks != NULL) && (bx->bm[p+ic->w*q] == BM_PK)
+ && (ic->masks[bx->pn][fs + bx->p->w*ss] > 1) ) {
+ bx->bm[p+ic->w*q] = BM_BH;
+ }
+
if ( (bx->bm[p+ic->w*q] != BM_IG)
&& (bx->bm[p+ic->w*q] != BM_BH)
&& (boxi(ic, bx, p, q) > bx->p->max_adu) ) {
@@ -1476,7 +1491,7 @@ static void integrate_prof2d(IntegrationMethod meth, PartialityModel pmodel,
Crystal *cr, struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
double ir_inn, double ir_mid, double ir_out,
- int results_pipe)
+ int results_pipe, int **masks)
{
RefList *list;
UnitCell *cell;
@@ -1500,6 +1515,7 @@ static void integrate_prof2d(IntegrationMethod meth, PartialityModel pmodel,
ic.int_diag_h = idh;
ic.int_diag_k = idk;
ic.int_diag_l = idl;
+ ic.masks = masks;
if ( init_intcontext(&ic) ) {
ERROR("Failed to initialise integration.\n");
return;
@@ -1733,7 +1749,7 @@ static void integrate_rings(IntegrationMethod meth, PartialityModel pmodel,
Crystal *cr, struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
double ir_inn, double ir_mid, double ir_out,
- int results_pipe)
+ int results_pipe, int **masks)
{
RefList *list;
Reflection *refl;
@@ -1762,6 +1778,7 @@ static void integrate_rings(IntegrationMethod meth, PartialityModel pmodel,
ic.int_diag_k = idk;
ic.int_diag_l = idl;
ic.meth = meth;
+ ic.masks = masks;
if ( init_intcontext(&ic) ) {
ERROR("Failed to initialise integration.\n");
return;
@@ -1818,6 +1835,11 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
int results_pipe)
{
int i;
+ int *masks[image->det->n_panels];
+
+ for ( i=0; i<image->det->n_panels; i++ ) {
+ masks[i] = make_BgMask(image, &image->det->panels[i], ir_inn);
+ }
for ( i=0; i<image->n_crystals; i++ ) {
@@ -1833,7 +1855,7 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
integrate_rings(meth, pmodel, cr, image,
int_diag, idh, idk, idl,
ir_inn, ir_mid, ir_out,
- results_pipe);
+ results_pipe, masks);
res = estimate_resolution(crystal_get_cell(cr),
image->features);
break;
@@ -1842,7 +1864,7 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
integrate_prof2d(meth, pmodel, cr, image,
int_diag, idh, idk, idl,
ir_inn, ir_mid, ir_out,
- results_pipe);
+ results_pipe, masks);
res = estimate_resolution(crystal_get_cell(cr),
image->features);
break;
@@ -1859,6 +1881,10 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
}
}
+
+ for ( i=0; i<image->det->n_panels; i++ ) {
+ free(masks[i]);
+ }
}
@@ -1947,37 +1973,3 @@ IntegrationMethod integration_method(const char *str, int *err)
}
-
-/**
- * flag_overlaps:
- * @image: An image structure
- * @ir_inn: The radius of the peak region to use
- *
- * Flags, in the bad pixel mask for @image, every pixel for which more than one
- * reflection is predicted to have its peak region.
- *
- */
-void flag_overlaps(struct image *image, double ir_inn)
-{
- int i;
-
- for ( i=0; i<image->det->n_panels; i++ ) {
-
- int *mask;
- int fs, ss;
- struct panel *p = &image->det->panels[i];
-
- mask = make_BgMask(image, p, ir_inn);
-
- for ( ss=0; ss<p->h; ss++ ) {
- for ( fs=0; fs<p->w; fs++ ) {
- if ( mask[fs+p->w*ss] > 1 ) {
- image->bad[i][fs+p->w*ss] = 1;
- }
- }
- }
-
- free(mask);
-
- }
-}
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index 6e80405c..9e1c8ee1 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -112,8 +112,6 @@ extern void integrate_all_4(struct image *image, IntegrationMethod meth,
signed int idh, signed int idk, signed int idl,
int results_pipe);
-extern void flag_overlaps(struct image *image, double ir_inn);
-
#ifdef __cplusplus
}
diff --git a/src/process_image.c b/src/process_image.c
index 77c5ece7..96752832 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -181,8 +181,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
crystal_set_mosaicity(image.crystals[i], 0.0); /* radians */
}
- flag_overlaps(&image, iargs->ir_inn);
-
/* Integrate all the crystals at once - need all the crystals so that
* overlaps can be detected. */
integrate_all_4(&image, iargs->int_meth, PMODEL_SPHERE, iargs->push_res,
diff --git a/tests/integration_check.c b/tests/integration_check.c
index b5dbea67..06bdd7d8 100644
--- a/tests/integration_check.c
+++ b/tests/integration_check.c
@@ -140,6 +140,7 @@ int main(int argc, char *argv[])
ic.ir_out = ir_out;
ic.meth = INTEGRATION_RINGS;
ic.int_diag = INTDIAG_NONE;
+ ic.masks = NULL;
if ( init_intcontext(&ic) ) {
ERROR("Failed to initialise integration.\n");
return 1;
diff --git a/tests/prof2d_check.c b/tests/prof2d_check.c
index a1c89d36..3352db49 100644
--- a/tests/prof2d_check.c
+++ b/tests/prof2d_check.c
@@ -177,7 +177,8 @@ int main(int argc, char *argv[])
reflist_free(list); /* integrate_prof2d() will predict again */
integrate_prof2d(INTEGRATION_PROF2D, PMODEL_SPHERE, cr, &image,
- INTDIAG_NONE, 0, 0, 0, ir_inn, ir_mid, ir_out, 0);
+ INTDIAG_NONE, 0, 0, 0, ir_inn, ir_mid, ir_out, 0,
+ NULL);
list = crystal_get_reflections(cr);
printf("Weak reflections:\n");
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 02:12:59 +0000