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-rw-r--r--libcrystfel/src/peaks.c106
1 files changed, 55 insertions, 51 deletions
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 973dd523..b87eb56e 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -215,7 +215,7 @@ static int integrate_peak(struct image *image, int cfs, int css,
double *pfs, double *pss,
double *intensity, double *sigma,
double ir_inn, double ir_mid, double ir_out,
- int use_max_adu)
+ int use_max_adu, int *bgPkMask)
{
signed int dfs, dss;
double lim_sq, out_lim_sq, mid_lim_sq;
@@ -229,7 +229,6 @@ static int integrate_peak(struct image *image, int cfs, int css,
double bg_tot_sq = 0.0;
double var;
double aduph;
- int *bgPkMask;
int p_cfs, p_css, p_w, p_h;
p = find_panel(image->det, cfs, css);
@@ -241,8 +240,6 @@ static int integrate_peak(struct image *image, int cfs, int css,
p_css = css - p->min_ss; /* Panel-relative coordinates */
p_w = p->max_fs - p->min_fs + 1;
p_h = p->max_ss - p->min_ss + 1;
- bgPkMask = make_BgMask(image, p, ir_out, ir_inn);
- if ( bgPkMask == NULL ) return 1;
aduph = p->adu_per_eV * ph_lambda_to_eV(image->lambda);
@@ -264,14 +261,11 @@ static int integrate_peak(struct image *image, int cfs, int css,
/* Strayed off one panel? */
if ( (p_cfs+dfs >= p_w) || (p_css+dss >= p_h)
- || (p_cfs+dfs < 0 ) || (p_css+dss < 0) )
- {
- free(bgPkMask);
- return 1;
- };
+ || (p_cfs+dfs < 0 ) || (p_css+dss < 0) ) return 1;
/* Check if there is a peak in the background region */
- if ( bgPkMask[(p_cfs+dfs) + p_w*(p_css+dss)] ) continue;
+ if ( (bgPkMask != NULL)
+ && bgPkMask[(p_cfs+dfs) + p_w*(p_css+dss)] ) continue;
idx = dfs+cfs+image->width*(dss+css);
@@ -282,26 +276,17 @@ static int integrate_peak(struct image *image, int cfs, int css,
/* It must have all the "good" bits to be valid */
if ( !((flags & image->det->mask_good)
- == image->det->mask_good) ) {
- free(bgPkMask);
- return 1;
- }
+ == image->det->mask_good) ) return 1;
/* If it has any of the "bad" bits, reject */
- if ( flags & image->det->mask_bad ) {
- free(bgPkMask);
- return 1;
- }
+ if ( flags & image->det->mask_bad ) return 1;
}
val = image->data[idx];
/* Veto peak if it contains saturation in bg region */
- if ( use_max_adu && (val > p->max_adu) ) {
- free(bgPkMask);
- return 1;
- }
+ if ( use_max_adu && (val > p->max_adu) ) return 1;
bg_tot += val;
bg_tot_sq += pow(val, 2.0);
@@ -310,10 +295,7 @@ static int integrate_peak(struct image *image, int cfs, int css,
}
}
- if ( bg_counts == 0 ) {
- free(bgPkMask);
- return 1;
- }
+ if ( bg_counts == 0 ) return 1;
bg_mean = bg_tot / bg_counts;
bg_var = (bg_tot_sq/bg_counts) - pow(bg_mean, 2.0);
@@ -333,11 +315,7 @@ static int integrate_peak(struct image *image, int cfs, int css,
/* Strayed off one panel? */
if ( (p_cfs+dfs >= p_w) || (p_css+dss >= p_h)
- || (p_cfs+dfs < 0 ) || (p_css+dss < 0) )
- {
- free(bgPkMask);
- return 1;
- };
+ || (p_cfs+dfs < 0 ) || (p_css+dss < 0) ) return 1;
idx = dfs+cfs+image->width*(dss+css);
@@ -348,26 +326,17 @@ static int integrate_peak(struct image *image, int cfs, int css,
/* It must have all the "good" bits to be valid */
if ( !((flags & image->det->mask_good)
- == image->det->mask_good) ) {
- free(bgPkMask);
- return 1;
- }
+ == image->det->mask_good) ) return 1;
/* If it has any of the "bad" bits, reject */
- if ( flags & image->det->mask_bad ) {
- free(bgPkMask);
- return 1;
- }
+ if ( flags & image->det->mask_bad ) return 1;
}
val = image->data[idx] - bg_mean;
/* Veto peak if it contains saturation */
- if ( use_max_adu && (image->data[idx] > p->max_adu) ) {
- free(bgPkMask);
- return 1;
- }
+ if ( use_max_adu && (image->data[idx] > p->max_adu) ) return 1;
pk_counts++;
pk_total += val;
@@ -385,16 +354,11 @@ static int integrate_peak(struct image *image, int cfs, int css,
var = pk_counts * bg_var;
var += aduph * pk_total;
- if ( var < 0.0 ) {
- free(bgPkMask);
- return 1;
- }
+ if ( var < 0.0 ) return 1;
if ( intensity != NULL ) *intensity = pk_total;
if ( sigma != NULL ) *sigma = sqrt(var);
- free(bgPkMask);
-
return 0;
}
@@ -506,7 +470,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
/* Centroid peak and get better coordinates. */
r = integrate_peak(image, mask_fs, mask_ss,
&f_fs, &f_ss, &intensity, &sigma,
- ir_inn, ir_mid, ir_out, 0);
+ ir_inn, ir_mid, ir_out, 0, NULL);
if ( r ) {
/* Bad region - don't detect peak */
@@ -718,6 +682,7 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
int n, i;
double av = 0.0;
int first = 1;
+ int **bgMasks;
il = sort_reflections(image->reflections, image->indexed_cell, &n);
if ( il == NULL ) {
@@ -725,6 +690,23 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
return;
}
+ /* Make background masks for all panels */
+ bgMasks = calloc(image->det->n_panels, sizeof(int *));
+ if ( bgMasks == NULL ) {
+ ERROR("Couldn't create list of background masks.\n");
+ return;
+ }
+ for ( i=0; i<image->det->n_panels; i++ ) {
+ int *mask;
+ mask = make_BgMask(image, &image->det->panels[i],
+ ir_out, ir_inn);
+ if ( mask == NULL ) {
+ ERROR("Couldn't create background mask.\n");
+ return;
+ }
+ bgMasks[i] = mask;
+ }
+
for ( i=0; i<n; i++ ) {
double fs, ss, intensity;
@@ -735,6 +717,8 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
int r;
Reflection *refl;
signed int h, k, l;
+ struct panel *p;
+ int pnum, j, found;
refl = il[i].refl;
@@ -769,9 +753,24 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
}
+ p = find_panel(image->det, pfs, pss);
+ if ( p == NULL ) continue; /* Next peak */
+ found = 0;
+ for ( j=0; j<image->det->n_panels; j++ ) {
+ if ( &image->det->panels[j] == p ) {
+ pnum = j;
+ found = 1;
+ break;
+ }
+ }
+ if ( !found ) {
+ ERROR("Couldn't find panel %p in list.\n", p);
+ return;
+ }
+
r = integrate_peak(image, pfs, pss, &fs, &ss,
&intensity, &sigma, ir_inn, ir_mid, ir_out,
- 1);
+ 1, bgMasks[j]);
/* I/sigma(I) cutoff */
if ( intensity/sigma < min_snr ) r = 1;
@@ -799,6 +798,11 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
}
}
+ for ( i=0; i<image->det->n_panels; i++ ) {
+ free(bgMasks[i]);
+ }
+ free(bgMasks);
+
image->diffracting_resolution = 0.0;
free(il);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 20:38:13 +0000