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-rw-r--r--libcrystfel/src/detector.c7
-rw-r--r--libcrystfel/src/detector.h1
-rw-r--r--libcrystfel/src/peaks.c168
-rw-r--r--libcrystfel/src/reflist.c5
-rw-r--r--libcrystfel/src/stream.c1
5 files changed, 132 insertions, 50 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index b7d809df..f212821d 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -608,8 +608,6 @@ static int parse_field_for_panel(struct panel *panel, const char *key,
panel->res = atof(val);
} else if ( strcmp(key, "max_adu") == 0 ) {
panel->max_adu = atof(val);
- } else if ( strcmp(key, "peak_sep") == 0 ) {
- panel->peak_sep = atof(val);
} else if ( strcmp(key, "badrow_direction") == 0 ) {
panel->badrow = val[0]; /* First character only */
if ( (panel->badrow != 'x') && (panel->badrow != 'y')
@@ -687,8 +685,6 @@ static void parse_toplevel(struct detector *det, const char *key,
det->mask_good = v;
}
- } else if ( strcmp(key, "peak_sep") == 0 ) {
- det->defaults.peak_sep = atof(val);
} else if ( strcmp(key, "coffset") == 0 ) {
det->defaults.coffset = atof(val);
} else if ( parse_field_for_panel(&det->defaults, key, val, det) ) {
@@ -738,7 +734,6 @@ struct detector *get_detector_geometry(const char *filename)
det->defaults.res = -1.0;
det->defaults.badrow = '-';
det->defaults.no_index = 0;
- det->defaults.peak_sep = 50.0;
det->defaults.fsx = 1.0;
det->defaults.fsy = 0.0;
det->defaults.ssx = 0.0;
@@ -887,7 +882,6 @@ struct detector *get_detector_geometry(const char *filename)
}
/* It's OK if the badrow direction is '0' */
/* It's not a problem if "no_index" is still zero */
- /* The default peak_sep is OK (maybe) */
/* The default transformation matrix is at least valid */
if ( det->panels[i].max_fs > max_fs ) {
@@ -1250,7 +1244,6 @@ int write_detector_geometry(const char *filename, struct detector *det)
fprintf(fh, "%s/max_ss = %d\n", p->name, p->max_ss);
fprintf(fh, "%s/badrow_direction = %C\n", p->name, p->badrow);
fprintf(fh, "%s/res = %g\n", p->name, p->res);
- fprintf(fh, "%s/peak_sep = %g\n", p->name, p->peak_sep);
fprintf(fh, "%s/clen = %s\n", p->name, p->clen_from);
fprintf(fh, "%s/fs = %+fx %+fy\n", p->name, p->fsx, p->fsy);
fprintf(fh, "%s/ss = %+fx %+fy\n", p->name, p->ssx, p->ssy);
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 2b4ac5c6..b740965c 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -62,7 +62,6 @@ struct panel
double res; /* Resolution in pixels per metre */
char badrow; /* 'x' or 'y' */
int no_index; /* Don't index peaks in this panel if non-zero */
- double peak_sep; /* Characteristic peak separation */
char *rigid_group; /* Rigid group, or -1 for none */
double adu_per_eV; /* Number of ADU per eV */
double max_adu; /* Treat pixel as unreliable if higher than this */
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 583dff4c..ffe77290 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -9,6 +9,7 @@
*
* Authors:
* 2010-2012 Thomas White <taw@physics.org>
+ * 2012 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
* 2011 Andrew Martin <andrew.martin@desy.de>
* 2011 Richard Kirian
*
@@ -98,7 +99,6 @@ static int cull_peaks_in_panel(struct image *image, struct panel *p)
if ( ncol <= 3 ) continue;
/* Yes? Delete them all... */
- nelim = 0;
for ( j=0; j<n; j++ ) {
struct imagefeature *g;
g = image_get_feature(image->features, j);
@@ -146,13 +146,76 @@ static int cull_peaks(struct image *image)
}
+/* 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;
+ 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(int));
+ if ( mask == NULL ) return NULL;
+
+ /* Loop over all reflections */
+ for ( refl = first_refl(image->reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ struct panel *p2;
+ double pk2_fs, pk2_ss;
+ signed int dfs, dss;
+ double pk2_cfs, pk2_css;
+
+ get_detector_pos(refl, &pk2_fs, &pk2_ss);
+
+ /* Determine if reflection is in the same panel */
+ p2 = find_panel(image->det, pk2_fs, pk2_ss);
+ if ( p2 != p ) continue;
+
+ pk2_cfs = pk2_fs - p->min_fs;
+ pk2_css = pk2_ss - p->min_ss;
+
+ for ( dfs=-ir_in; dfs<=ir_in; dfs++ ) {
+ for ( dss=-ir_in; dss<=ir_in; dss++ ) {
+
+ signed int fs, ss;
+
+ /* In peak region for this peak? */
+ if ( dfs*dfs + dss*dss > ir_in*ir_in ) continue;
+
+ 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;
+
+ }
+ }
+
+ }
+
+ return mask;
+}
+
+
/* Returns non-zero if peak has been vetoed.
* i.e. don't use result if return value is not zero. */
-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)
+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)
{
- signed int fs, ss;
+ signed int dfs, dss;
double lim_sq, out_lim_sq, mid_lim_sq;
double pk_total;
int pk_counts;
@@ -164,11 +227,21 @@ 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);
if ( p == NULL ) return 1;
if ( p->no_index ) return 1;
+ /* Determine regions where there is expected to be a peak */
+ 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);
lim_sq = pow(ir_inn, 2.0);
@@ -176,23 +249,27 @@ 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;
+ 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 ) {
@@ -211,7 +288,7 @@ int integrate_peak(struct image *image, int cfs, int css,
val = image->data[idx];
/* Veto peak if it contains saturation in bg region */
- if ( val > p->max_adu ) return 1;
+ if ( use_max_adu && (val > p->max_adu) ) return 1;
bg_tot += val;
bg_tot_sq += pow(val, 2.0);
@@ -228,22 +305,23 @@ 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 ) {
@@ -262,13 +340,13 @@ int integrate_peak(struct image *image, int cfs, int css,
val = image->data[idx] - bg_mean;
/* Veto peak if it contains saturation */
- if ( image->data[idx] > p->max_adu ) return 1;
+ if ( use_max_adu && (image->data[idx] > p->max_adu) ) return 1;
pk_counts++;
pk_total += val;
- fsct += val*(cfs+fs);
- ssct += val*(css+ss);
+ fsct += val*(cfs+dfs);
+ ssct += val*(css+dss);
}
}
@@ -285,6 +363,8 @@ int integrate_peak(struct image *image, int cfs, int css,
if ( intensity != NULL ) *intensity = pk_total;
if ( sigma != NULL ) *sigma = sqrt(var);
+ free(bgPkMask);
+
return 0;
}
@@ -309,7 +389,6 @@ static void search_peaks_in_panel(struct image *image, float threshold,
int nrej_snr = 0;
int nacc = 0;
int ncull;
- const int pws = p->peak_sep/2;
data = image->data;
stride = image->width;
@@ -352,16 +431,14 @@ static void search_peaks_in_panel(struct image *image, float threshold,
max = data[mask_fs+stride*mask_ss];
did_something = 0;
- for ( s_ss=biggest(mask_ss-pws/2,
- p->min_ss);
- s_ss<=smallest(mask_ss+pws/2,
- p->max_ss);
- s_ss++ ) {
- for ( s_fs=biggest(mask_fs-pws/2,
- p->min_fs);
- s_fs<=smallest(mask_fs+pws/2,
- p->max_fs);
- s_fs++ ) {
+ for ( s_ss=biggest(mask_ss-ir_inn, p->min_ss);
+ s_ss<=smallest(mask_ss+ir_inn, p->max_ss);
+ s_ss++ )
+ {
+ for ( s_fs=biggest(mask_fs-ir_inn, p->min_fs);
+ s_fs<=smallest(mask_fs+ir_inn, p->max_fs);
+ s_fs++ )
+ {
if ( data[s_fs+stride*s_ss] > max ) {
max = data[s_fs+stride*s_ss];
@@ -374,8 +451,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
}
/* Abort if drifted too far from the foot point */
- if ( distance(mask_fs, mask_ss, fs, ss) >
- p->peak_sep/2.0 )
+ if ( distance(mask_fs, mask_ss, fs, ss) > ir_inn )
{
break;
}
@@ -383,7 +459,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
} while ( did_something );
/* Too far from foot point? */
- if ( distance(mask_fs, mask_ss, fs, ss) > p->peak_sep/2.0 ) {
+ if ( distance(mask_fs, mask_ss, fs, ss) > ir_inn ) {
nrej_dis++;
continue;
}
@@ -397,7 +473,7 @@ 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);
+ ir_inn, ir_mid, ir_out, 0);
if ( r ) {
/* Bad region - don't detect peak */
@@ -419,7 +495,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
/* Check for a nearby feature */
image_feature_closest(image->features, f_fs, f_ss, &d, &idx);
- if ( d < p->peak_sep/2.0 ) {
+ if ( d < 2.0*ir_inn ) {
nrej_pro++;
continue;
}
@@ -445,6 +521,12 @@ static void search_peaks_in_panel(struct image *image, float threshold,
// "%i in bad regions, %i with SNR < %g, %i badrow culled.\n",
// nacc, nrej_dis, nrej_pro, nrej_fra, nrej_bad,
// nrej_snr, min_snr, ncull);
+
+ if ( ncull != 0 ) {
+ STATUS("WARNING: %i peaks were badrow culled. This feature"
+ " should not usually be used.\nConsider setting"
+ " badrow=- in the geometry file.\n", ncull);
+ }
}
@@ -655,7 +737,11 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
}
r = integrate_peak(image, pfs, pss, &fs, &ss,
- &intensity, &sigma, ir_inn, ir_mid, ir_out);
+ &intensity, &sigma, ir_inn, ir_mid, ir_out,
+ 1);
+
+ /* I/sigma(I) cutoff */
+ if ( intensity/sigma < min_snr ) r = 1;
/* Record intensity and set redundancy to 1 on success */
if ( r == 0 ) {
diff --git a/libcrystfel/src/reflist.c b/libcrystfel/src/reflist.c
index cea25bf3..64154774 100644
--- a/libcrystfel/src/reflist.c
+++ b/libcrystfel/src/reflist.c
@@ -900,6 +900,7 @@ struct _reflistiterator {
**/
Reflection *first_refl(RefList *list, RefListIterator **piter)
{
+ Reflection *refl;
RefListIterator *iter;
iter = malloc(sizeof(struct _reflistiterator));
@@ -908,7 +909,9 @@ Reflection *first_refl(RefList *list, RefListIterator **piter)
iter->stack_ptr = 0;
*piter = iter;
- Reflection *refl = list->head;
+ if ( list == NULL ) return NULL;
+
+ refl = list->head;
do {
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 81f4d722..ce0ee33e 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -474,6 +474,7 @@ int skip_some_files(FILE *fh, int n)
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
+ chomp(line);
if ( strcmp(line, CHUNK_END_MARKER) == 0 ) n_patterns++;
} while ( rval != NULL );
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-14 10:03:22 +0000