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-rw-r--r--libcrystfel/src/peaks.c94
1 files changed, 54 insertions, 40 deletions
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 99a12ae5..fe836c3f 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -147,17 +147,18 @@ static int cull_peaks(struct image *image)
}
-static unsigned char *make_BgMask(struct image *image, struct panel *p,
- double ir_out, int cfs, int css, double ir_in)
+/* cfs, css relative to panel origin */
+static int *make_BgMask(struct image *image, struct panel *p,
+ double ir_out, int cfs, int css, double ir_in)
{
Reflection *refl;
RefListIterator *iter;
- unsigned char *mask;
+ int *mask;
int w, h;
w = p->max_fs - p->min_fs + 1;
h = p->max_ss - p->min_ss + 1;
- mask = calloc(w*h, sizeof(unsigned char));
+ mask = calloc(w*h, sizeof(int));
if ( mask == NULL ) return NULL;
/* Loop over all reflections */
@@ -167,7 +168,8 @@ static unsigned char *make_BgMask(struct image *image, struct panel *p,
{
struct panel *p2;
double pk2_fs, pk2_ss;
- signed int fs, ss;
+ signed int dfs, dss;
+ double pk2_cfs, pk2_css;
get_detector_pos(refl, &pk2_fs, &pk2_ss);
@@ -175,22 +177,27 @@ static unsigned char *make_BgMask(struct image *image, struct panel *p,
p2 = find_panel(image->det, pk2_fs, pk2_ss);
if ( p2 != p ) continue;
- for ( fs=-ir_in; fs<=ir_in; fs++ ) {
- for ( ss=-ir_in; ss<=ir_in; ss++ ) {
+ pk2_cfs = pk2_fs - p->min_fs;
+ pk2_css = pk2_ss - p->min_ss;
- double d_fs, d_ss, distSq;
+ for ( dfs=-ir_in; dfs<=ir_in; dfs++ ) {
+ for ( dss=-ir_in; dss<=ir_in; dss++ ) {
- d_fs = cfs + fs;
- d_ss = css + ss;
- distSq = d_fs*d_fs + d_ss*d_ss;
+ signed int fs, ss;
- if ( distSq < ir_in*ir_in ) {
+ /* In peak region for this peak? */
+ if ( dfs*dfs + dss*dss > ir_in*ir_in ) continue;
- int idx;
- idx = fs+ir_out+2*ir_out*(ss+ir_out);
- mask[idx] = 1;
+ fs = pk2_cfs + dfs;
+ ss = pk2_css + dss;
- }
+ /* On panel? */
+ if ( fs >= w ) continue;
+ if ( ss >= h ) continue;
+ if ( fs < 0 ) continue;
+ if ( ss < 0 ) continue;
+
+ mask[fs + ss*w] = 1;
}
}
@@ -209,7 +216,7 @@ static int integrate_peak(struct image *image, int cfs, int css,
double ir_inn, double ir_mid, double ir_out,
int use_max_adu)
{
- signed int fs, ss;
+ signed int dfs, dss;
double lim_sq, out_lim_sq, mid_lim_sq;
double pk_total;
int pk_counts;
@@ -221,14 +228,19 @@ static int integrate_peak(struct image *image, int cfs, int css,
double bg_tot_sq = 0.0;
double var;
double aduph;
- unsigned char *bgPkMask;
+ int *bgPkMask;
+ int p_cfs, p_css, p_w, p_h;
p = find_panel(image->det, cfs, css);
if ( p == NULL ) return 1;
if ( p->no_index ) return 1;
/* Determine regions where there is expected to be a peak */
- bgPkMask = make_BgMask(image, p, ir_out, cfs, css, ir_inn);
+ p_cfs = cfs - p->min_fs;
+ 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, p_cfs, p_css, ir_inn);
if ( bgPkMask == NULL ) return 1;
aduph = p->adu_per_eV * ph_lambda_to_eV(image->lambda);
@@ -238,26 +250,27 @@ static int integrate_peak(struct image *image, int cfs, int css,
out_lim_sq = pow(ir_out, 2.0);
/* Estimate the background */
- for ( fs=-ir_out; fs<=+ir_out; fs++ ) {
- for ( ss=-ir_out; ss<=+ir_out; ss++ ) {
+ for ( dfs=-ir_out; dfs<=+ir_out; dfs++ ) {
+ for ( dss=-ir_out; dss<=+ir_out; dss++ ) {
double val;
uint16_t flags;
- struct panel *p2;
int idx;
/* Restrict to annulus */
- if ( fs*fs + ss*ss > out_lim_sq ) continue;
- if ( fs*fs + ss*ss < mid_lim_sq ) continue;
-
- /* Check if there is a peak in the background region */
- if (bgPkMask[(int)(fs+ir_out+2*ir_out*(ss+ir_out))]) continue;
+ if ( dfs*dfs + dss*dss > out_lim_sq ) continue;
+ if ( dfs*dfs + dss*dss < mid_lim_sq ) continue;
/* Strayed off one panel? */
- p2 = find_panel(image->det, fs+cfs, ss+css);
- if ( p2 != p ) return 1;
+ if ( p_cfs+dfs >= p_w ) continue;
+ if ( p_css+dss >= p_h ) continue;
+ if ( p_cfs+dfs < 0 ) continue;
+ if ( p_css+dss < 0 ) continue;
+
+ /* Check if there is a peak in the background region */
+ if ( bgPkMask[(p_cfs+dfs) + p_w*(p_css+dss)] ) continue;
- idx = fs+cfs+image->width*(ss+css);
+ idx = dfs+cfs+image->width*(dss+css);
/* Veto this peak if we tried to integrate in a bad region */
if ( image->flags != NULL ) {
@@ -293,22 +306,23 @@ static int integrate_peak(struct image *image, int cfs, int css,
pk_total = 0.0;
pk_counts = 0;
fsct = 0.0; ssct = 0.0;
- for ( fs=-ir_inn; fs<=+ir_inn; fs++ ) {
- for ( ss=-ir_inn; ss<=+ir_inn; ss++ ) {
+ for ( dfs=-ir_inn; dfs<=+ir_inn; dfs++ ) {
+ for ( dss=-ir_inn; dss<=+ir_inn; dss++ ) {
double val;
uint16_t flags;
- struct panel *p2;
int idx;
/* Inner mask radius */
- if ( fs*fs + ss*ss > lim_sq ) continue;
+ if ( dfs*dfs + dss*dss > lim_sq ) continue;
/* Strayed off one panel? */
- p2 = find_panel(image->det, fs+cfs, ss+css);
- if ( p2 != p ) return 1;
+ if ( p_cfs+dfs >= p_w ) continue;
+ if ( p_css+dss >= p_h ) continue;
+ if ( p_cfs+dfs < 0 ) continue;
+ if ( p_css+dss < 0 ) continue;
- idx = fs+cfs+image->width*(ss+css);
+ idx = dfs+cfs+image->width*(dss+css);
/* Veto this peak if we tried to integrate in a bad region */
if ( image->flags != NULL ) {
@@ -332,8 +346,8 @@ static int integrate_peak(struct image *image, int cfs, int css,
pk_counts++;
pk_total += val;
- fsct += val*(cfs+fs);
- ssct += val*(css+ss);
+ fsct += val*(cfs+dfs);
+ ssct += val*(css+dss);
}
}
@@ -726,7 +740,7 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
1);
/* I/sigma(I) cutoff */
- if ( !r && (intensity/sigma < min_snr) ) r = 1;
+ if ( intensity/sigma < min_snr ) r = 1;
/* Record intensity and set redundancy to 1 on success */
if ( r == 0 ) {
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 15:41:10 +0000