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/*
* peaks.c
*
* Peak search and other image analysis
*
* (c) 2006-2011 Thomas White <taw@physics.org>
* 2011 Andrew Martin
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <assert.h>
#include <gsl/gsl_statistics_int.h>
#include <pthread.h>
#include <fenv.h>
#include "image.h"
#include "utils.h"
#include "index.h"
#include "peaks.h"
#include "detector.h"
#include "filters.h"
#include "diffraction.h"
/* How close a peak must be to an indexed position to be considered "close"
* for the purposes of double hit detection and sanity checking. */
#define PEAK_CLOSE (30.0)
/* How close a peak must be to an indexed position to be considered "close"
* for the purposes of integration. */
#define PEAK_REALLY_CLOSE (10.0)
/* Degree of polarisation of X-ray beam */
#define POL (1.0)
/* Window size for Zaefferer peak detection */
#define PEAK_WINDOW_SIZE (10)
static int cull_peaks_in_panel(struct image *image, struct panel *p)
{
int i, n;
int nelim = 0;
n = image_feature_count(image->features);
for ( i=0; i<n; i++ ) {
struct imagefeature *f;
int j, ncol;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
if ( f->fs < p->min_fs ) continue;
if ( f->fs > p->max_fs ) continue;
if ( f->ss < p->min_ss ) continue;
if ( f->ss > p->max_ss ) continue;
/* How many peaks are in the same column? */
ncol = 0;
for ( j=0; j<n; j++ ) {
struct imagefeature *g;
if ( i==j ) continue;
g = image_get_feature(image->features, j);
if ( g == NULL ) continue;
if ( p->badrow == 'f' ) {
if ( fabs(f->ss - g->ss) < 2.0 ) ncol++;
} else if ( p->badrow == 's' ) {
if ( fabs(f->fs - g->fs) < 2.0 ) ncol++;
} /* else do nothing */
}
/* More than three? */
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);
if ( g == NULL ) continue;
if ( p->badrow == 'f' ) {
if ( fabs(f->ss - g->ss) < 2.0 ) {
image_remove_feature(image->features,
j);
nelim++;
}
} else if ( p->badrow == 's' ) {
if ( fabs(f->fs - g->ss) < 2.0 ) {
image_remove_feature(image->features,
j);
nelim++;
}
} else {
ERROR("Invalid badrow direction.\n");
abort();
}
}
}
return nelim;
}
/* Post-processing of the peak list to remove noise */
static int cull_peaks(struct image *image)
{
int nelim = 0;
struct panel *p;
int i;
for ( i=0; i<image->det->n_panels; i++ ) {
p = &image->det->panels[i];
if ( p->badrow != '-' ) {
nelim += cull_peaks_in_panel(image, p);
}
}
return nelim;
}
/* 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 *pbg, double *pmax, double *sigma,
int do_polar, int centroid, int bgsub)
{
signed int fs, ss;
double lim, out_lim;
double lim_sq, out_lim_sq;
double total = 0.0;
double fsct = 0.0;
double ssct = 0.0;
double noise = 0.0;
int noise_counts = 0;
double max = 0.0;
struct panel *p = NULL;
int pixel_counts = 0;
double noise_mean = 0.0;
double noise_meansq = 0.0;
p = find_panel(image->det, cfs, css);
if ( p == NULL ) return 1;
if ( p->no_index ) return 1;
lim = p->integr_radius;
out_lim = 2.0 + lim;
lim_sq = pow(lim, 2.0);
out_lim_sq = pow(out_lim, 2.0);
for ( fs=-out_lim; fs<+out_lim; fs++ ) {
for ( ss=-out_lim; ss<+out_lim; ss++ ) {
double val;
double tt = 0.0;
double phi, pa, pb, pol;
uint16_t flags;
struct panel *p2;
int idx;
/* Outer mask radius */
if ( fs*fs + ss*ss > out_lim_sq ) continue;
if ( ((fs+cfs)>=image->width) || ((fs+cfs)<0) ) continue;
if ( ((ss+css)>=image->height) || ((ss+css)<0) ) continue;
/* Strayed off one panel? */
p2 = find_panel(image->det, fs+cfs, ss+css);
if ( p2 != p ) return 1;
idx = fs+cfs+image->width*(ss+css);
/* Veto this peak if we tried to integrate in a bad region */
if ( image->flags != NULL ) {
flags = image->flags[idx];
/* It must have all the "good" bits to be valid */
if ( !((flags & image->det->mask_good)
== image->det->mask_good) ) return 1;
/* If it has any of the "bad" bits, reject */
if ( flags & image->det->mask_bad ) return 1;
}
val = image->data[idx];
if ( do_polar ) {
tt = get_tt(image, fs+cfs, ss+css);
phi = atan2(ss+css, fs+cfs);
pa = pow(sin(phi)*sin(tt), 2.0);
pb = pow(cos(tt), 2.0);
pol = 1.0 - 2.0*POL*(1-pa) + POL*(1.0+pb);
val /= pol;
}
if ( val > max ) max = val;
/* Inner mask */
if ( fs*fs + ss*ss > lim_sq ) {
/* Estimate noise from this region */
noise += val; //fabs(val);
noise_counts++;
/* Estimate the standard deviation of the noise */
noise_meansq += fabs(val)*fabs(val) ;
continue;
}
pixel_counts ++;
total += val;
fsct += val*(cfs+fs);
ssct += val*(css+ss);
}
}
noise_mean = noise / noise_counts;
/* The centroid is excitingly undefined if there is no intensity */
if ( centroid && (total != 0) ) {
*pfs = (double)fsct / total;
*pss = (double)ssct / total;
} else {
*pfs = (double)cfs;
*pss = (double)css;
}
if ( bgsub ) {
*intensity = total - pixel_counts*noise_mean;
} else {
*intensity = total;
}
if ( in_bad_region(image->det, *pfs, *pss) ) return 1;
if ( sigma != NULL ) {
/* First term is standard deviation of background per pixel
* sqrt(pixel_counts) - increase of error for integrated value
* sqrt(2) - increase of error for background subtraction
*/
*sigma = sqrt(noise_meansq/noise_counts-(noise_mean*noise_mean))
* sqrt(2.0*pixel_counts);
}
if ( pbg != NULL ) {
*pbg = (noise / noise_counts);
}
if ( pmax != NULL ) {
*pmax = max;
}
return 0;
}
static void search_peaks_in_panel(struct image *image, float threshold,
float min_gradient, struct panel *p)
{
int fs, ss, stride;
float *data;
double d;
int idx;
double f_fs = 0.0;
double f_ss = 0.0;
double intensity = 0.0;
int nrej_dis = 0;
int nrej_pro = 0;
int nrej_fra = 0;
int nrej_bad = 0;
int nacc = 0;
int ncull;
data = image->data;
stride = image->width;
for ( fs = p->min_fs+1; fs <= p->max_fs-1; fs++ ) {
for ( ss = p->min_ss+1; ss <= p->max_ss-1; ss++ ) {
double dx1, dx2, dy1, dy2;
double dxs, dys;
double grad;
int mask_fs, mask_ss;
int s_fs, s_ss;
double max;
unsigned int did_something;
int r;
/* Overall threshold */
if ( data[fs+stride*ss] < threshold ) continue;
/* Get gradients */
dx1 = data[fs+stride*ss] - data[(fs+1)+stride*ss];
dx2 = data[(fs-1)+stride*ss] - data[fs+stride*ss];
dy1 = data[fs+stride*ss] - data[(fs+1)+stride*(ss+1)];
dy2 = data[fs+stride*(ss-1)] - data[fs+stride*ss];
/* Average gradient measurements from both sides */
dxs = ((dx1*dx1) + (dx2*dx2)) / 2;
dys = ((dy1*dy1) + (dy2*dy2)) / 2;
/* Calculate overall gradient */
grad = dxs + dys;
if ( grad < min_gradient ) continue;
mask_fs = fs;
mask_ss = ss;
do {
max = data[mask_fs+stride*mask_ss];
did_something = 0;
for ( s_ss=biggest(mask_ss-PEAK_WINDOW_SIZE/2,
p->min_ss);
s_ss<=smallest(mask_ss+PEAK_WINDOW_SIZE/2,
p->max_ss);
s_ss++ ) {
for ( s_fs=biggest(mask_fs-PEAK_WINDOW_SIZE/2,
p->min_fs);
s_fs<=smallest(mask_fs+PEAK_WINDOW_SIZE/2,
p->max_fs);
s_fs++ ) {
if ( data[s_fs+stride*s_ss] > max ) {
max = data[s_fs+stride*s_ss];
mask_fs = s_fs;
mask_ss = s_ss;
did_something = 1;
}
}
}
/* Abort if drifted too far from the foot point */
if ( distance(mask_fs, mask_ss, fs, ss) >
p->peak_sep/2.0 )
{
break;
}
} while ( did_something );
/* Too far from foot point? */
if ( distance(mask_fs, mask_ss, fs, ss) > p->peak_sep/2.0 ) {
nrej_dis++;
continue;
}
/* Should be enforced by bounds used above. Muppet check. */
assert(mask_fs <= p->max_fs);
assert(mask_ss <= p->max_ss);
assert(mask_fs >= p->min_fs);
assert(mask_ss >= p->min_ss);
/* Centroid peak and get better coordinates.
* Don't bother doing polarisation/SA correction, because the
* intensity of this peak is only an estimate at this stage. */
r = integrate_peak(image, mask_fs, mask_ss,
&f_fs, &f_ss, &intensity,
NULL, NULL, NULL, 0, 1, 0);
if ( r ) {
/* Bad region - don't detect peak */
nrej_bad++;
continue;
}
/* It is possible for the centroid to fall outside the image */
if ( (f_fs < p->min_fs) || (f_fs > p->max_fs)
|| (f_ss < p->min_ss) || (f_ss > p->max_ss) ) {
nrej_fra++;
continue;
}
/* Check for a nearby feature */
image_feature_closest(image->features, f_fs, f_ss, &d, &idx);
if ( d < p->peak_sep/2.0 ) {
nrej_pro++;
continue;
}
/* Add using "better" coordinates */
image_add_feature(image->features, f_fs, f_ss, image, intensity,
NULL);
nacc++;
}
}
if ( image->det != NULL ) {
ncull = cull_peaks(image);
nacc -= ncull;
} else {
STATUS("Not culling peaks because I don't have a "
"detector geometry file.\n");
ncull = 0;
}
// STATUS("%i accepted, %i box, %i proximity, %i outside panel, "
// "%i in bad regions, %i badrow culled.\n",
// nacc, nrej_dis, nrej_pro, nrej_fra, nrej_bad, ncull);
}
void search_peaks(struct image *image, float threshold, float min_gradient)
{
int i;
if ( image->features != NULL ) {
image_feature_list_free(image->features);
}
image->features = image_feature_list_new();
for ( i=0; i<image->det->n_panels; i++ ) {
struct panel *p = &image->det->panels[i];
if ( p->no_index ) continue;
search_peaks_in_panel(image, threshold, min_gradient, p);
}
}
RefList *find_projected_peaks(struct image *image, UnitCell *cell,
int circular_domain, double domain_r)
{
int fs, ss;
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
RefList *reflections;
double alen, blen, clen;
int n_reflections = 0;
reflections = reflist_new();
/* "Borrow" direction values to get reciprocal lengths */
cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
alen = modulus(ax, ay, az);
blen = modulus(bx, by, bz);
clen = modulus(cx, cy, cz);
cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
fesetround(1); /* Round towards nearest */
for ( fs=0; fs<image->width; fs++ ) {
for ( ss=0; ss<image->height; ss++ ) {
double hd, kd, ld; /* Indices with decimal places */
double dh, dk, dl; /* Distances in h,k,l directions */
signed int h, k, l;
struct rvec q;
double dist;
Reflection *refl;
double cur_dist;
q = get_q(image, fs, ss, NULL, 1.0/image->lambda);
hd = q.u * ax + q.v * ay + q.w * az;
kd = q.u * bx + q.v * by + q.w * bz;
ld = q.u * cx + q.v * cy + q.w * cz;
h = lrint(hd);
k = lrint(kd);
l = lrint(ld);
dh = hd - h;
dk = kd - k;
dl = ld - l;
if ( circular_domain ) {
/* Circular integration domain */
dist = sqrt(pow(dh*alen, 2.0) + pow(dk*blen, 2.0)
+ pow(dl*clen, 2.0));
if ( dist > domain_r ) continue;
} else {
/* "Crystallographic" integration domain */
dist = sqrt(pow(dh, 2.0) + pow(dk, 2.0) + pow(dl, 2.0));
if ( dist > domain_r ) continue;
}
refl = find_refl(reflections, h, k, l);
if ( refl != NULL ) {
cur_dist = get_excitation_error(refl);
if ( dist < cur_dist ) {
set_detector_pos(refl, dist, fs, ss);
}
} else {
Reflection *new;
new = add_refl(reflections, h, k, l);
set_detector_pos(new, dist, fs, ss);
n_reflections++;
}
}
}
optimise_reflist(reflections);
return reflections;
}
int peak_sanity_check(struct image *image, UnitCell *cell,
int circular_domain, double domain_r)
{
int i;
int n_feat = 0;
int n_sane = 0;
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
double aslen, bslen, cslen;
/* "Borrow" direction values to get reciprocal lengths */
cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
aslen = modulus(ax, ay, az);
bslen = modulus(bx, by, bz);
cslen = modulus(cx, cy, cz);
cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
fesetround(1); /* Round towards nearest */
for ( i=0; i<image_feature_count(image->features); i++ ) {
double dist;
struct rvec q;
struct imagefeature *f;
double hd, kd, ld;
signed int h, k, l;
double dh, dk, dl;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
n_feat++;
/* Get closest hkl */
q = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda);
hd = q.u * ax + q.v * ay + q.w * az;
kd = q.u * bx + q.v * by + q.w * bz;
ld = q.u * cx + q.v * cy + q.w * cz;
h = lrint(hd); k = lrint(kd); l = lrint(ld);
dh = hd - h; dk = kd - k; dl = ld - l;
if ( circular_domain ) {
/* Circular integration domain */
dist = sqrt(pow(dh*aslen, 2.0) + pow(dk*bslen, 2.0)
+ pow(dl*cslen, 2.0));
if ( dist <= domain_r ) n_sane++;
} else {
/* "Crystallographic" integration domain */
dist = sqrt(pow(dh, 2.0) + pow(dk, 2.0) + pow(dl, 2.0));
if ( dist <= domain_r ) n_sane++;
}
}
if ( (float)n_sane / (float)n_feat < 0.1 ) return 0;
return 1;
}
/* Integrate the list of predicted reflections in "image" */
void integrate_reflections(struct image *image, int polar, int use_closer,
int bgsub)
{
Reflection *refl;
RefListIterator *iter;
for ( refl = first_refl(image->reflections, &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
double fs, ss, intensity;
double d;
int idx;
double bg, max;
double sigma;
struct panel *p;
double pfs, pss;
int r;
get_detector_pos(refl, &pfs, &pss);
p = find_panel(image->det, pfs, pss);
if ( p == NULL ) continue;
if ( p->no_index ) continue;
/* Is there a really close feature which was detected? */
if ( use_closer ) {
struct imagefeature *f;
if ( image->features != NULL ) {
f = image_feature_closest(image->features,
pfs, pss, &d, &idx);
} else {
f = NULL;
}
if ( (f != NULL) && (d < PEAK_REALLY_CLOSE) ) {
pfs = f->fs;
pss = f->ss;
}
}
r = integrate_peak(image, pfs, pss, &fs, &ss,
&intensity, &bg, &max, &sigma, polar, 0,
bgsub);
/* Record intensity and set redundancy to 1 on success */
if ( r == 0 ) {
set_int(refl, intensity);
set_esd_intensity(refl, sigma);
set_redundancy(refl, 1);
}
}
}
RefList *integrate_pixels(struct image *image, int circular_domain,
double domain_r, int do_polar)
{
int i;
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
int fs, ss;
double aslen, bslen, cslen;
double *intensities;
double *xmom;
double *ymom;
ReflItemList *obs;
RefList *reflections;
obs = new_items();
intensities = new_list_intensity();
xmom = new_list_intensity();
ymom = new_list_intensity();
reflections = reflist_new();
/* "Borrow" direction values to get reciprocal lengths */
cell_get_reciprocal(image->indexed_cell, &ax, &ay, &az,
&bx, &by, &bz,
&cx, &cy, &cz);
aslen = modulus(ax, ay, az);
bslen = modulus(bx, by, bz);
cslen = modulus(cx, cy, cz);
cell_get_cartesian(image->indexed_cell, &ax, &ay, &az,
&bx, &by, &bz,
&cx, &cy, &cz);
/* For each pixel */
fesetround(1); /* Round towards nearest */
for ( fs=0; fs<image->width; fs++ ) {
for ( ss=0; ss<image->height; ss++ ) {
double hd, kd, ld; /* Indices with decimal places */
double dh, dk, dl; /* Distances in h,k,l directions */
signed int h, k, l;
struct rvec q;
double dist;
struct panel *p;
double twotheta;
p = find_panel(image->det, fs, ss);
if ( p == NULL ) continue;
if ( p->no_index ) continue;
q = get_q(image, fs, ss, &twotheta, 1.0/image->lambda);
hd = q.u * ax + q.v * ay + q.w * az;
kd = q.u * bx + q.v * by + q.w * bz;
ld = q.u * cx + q.v * cy + q.w * cz;
h = lrint(hd);
k = lrint(kd);
l = lrint(ld);
dh = hd - h; dk = kd - k; dl = ld - l;
if ( circular_domain ) {
/* Circular integration domain */
dist = sqrt(pow(dh*aslen, 2.0) + pow(dk*bslen, 2.0)
+ pow(dl*cslen, 2.0));
} else {
/* "Crystallographic" integration domain */
dist = sqrt(pow(dh, 2.0) + pow(dk, 2.0) + pow(dl, 2.0));
}
if ( dist < domain_r ) {
double val;
double pix_area, Lsq, proj_area, dsq, sa;
double phi, pa, pb, pol;
double xs, ys, rx, ry;
/* Veto if we want to integrate a bad region */
if ( image->flags != NULL ) {
int flags;
flags = image->flags[fs+image->width*ss];
if ( !(flags & 0x01) ) continue;
}
val = image->data[fs+image->width*ss];
/* Area of one pixel */
pix_area = pow(1.0/p->res, 2.0);
Lsq = pow(p->clen, 2.0);
/* Area of pixel as seen from crystal */
proj_area = pix_area * cos(twotheta);
/* Calculate distance from crystal to pixel */
xs = (fs-p->min_fs)*p->fsx + (ss-p->min_ss)*p->ssx;
ys = (fs-p->min_fs)*p->fsy + (ss-p->min_ss)*p->ssy;
rx = (xs + p->cnx) / p->res;
ry = (ys + p->cny) / p->res;
dsq = sqrt(pow(rx, 2.0) + pow(ry, 2.0));
/* Projected area of pixel / distance squared */
sa = 1.0e7 * proj_area / (dsq + Lsq);
/* Solid angle correction is needed in this case */
val /= sa;
if ( do_polar ) {
phi = atan2(ry, rx);
pa = pow(sin(phi)*sin(twotheta), 2.0);
pb = pow(cos(twotheta), 2.0);
pol = 1.0 - 2.0*POL*(1-pa) + POL*(1.0+pb);
val /= pol;
}
/* Add value to sum */
integrate_intensity(intensities, h, k, l, val);
integrate_intensity(xmom, h, k, l, val*fs);
integrate_intensity(ymom, h, k, l, val*ss);
if ( !find_item(obs, h, k, l) ) {
add_item(obs, h, k, l);
}
}
}
}
for ( i=0; i<num_items(obs); i++ ) {
struct refl_item *it;
double intensity, xmomv, ymomv;
double xp, yp;
Reflection *refl;
it = get_item(obs, i);
intensity = lookup_intensity(intensities, it->h, it->k, it->l);
xmomv = lookup_intensity(xmom, it->h, it->k, it->l);
ymomv = lookup_intensity(ymom, it->h, it->k, it->l);
xp = xmomv / (double)intensity;
yp = ymomv / (double)intensity;
refl = add_refl(reflections, it->h, it->k, it->l);
set_int(refl, intensity);
set_detector_pos(refl, 0.0, xp, yp);
}
free(xmom);
free(ymom);
free(intensities);
delete_items(obs);
return reflections;
}
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