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-rw-r--r--src/geometry.c2
-rw-r--r--src/indexamajig.c8
-rw-r--r--src/partialator.c3
-rw-r--r--src/pattern_sim.c2
-rw-r--r--src/peaks.c70
-rw-r--r--src/peaks.h6
-rw-r--r--src/post-refinement.c4
-rw-r--r--src/reintegrate.c3
8 files changed, 33 insertions, 65 deletions
diff --git a/src/geometry.c b/src/geometry.c
index 821aff2f..9bb41d12 100644
--- a/src/geometry.c
+++ b/src/geometry.c
@@ -283,7 +283,7 @@ double integrate_all(struct image *image, struct cpeak *cpeaks, int n)
float x, y, intensity;
if ( integrate_peak(image, cpeaks[i].x, cpeaks[i].y, &x, &y,
- &intensity, NULL, NULL, 0, 0, 0) ) continue;
+ &intensity, NULL, NULL, 0, 0) ) continue;
itot += intensity;
}
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 83eee4d1..774cfde4 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -62,7 +62,6 @@ struct static_index_args
int config_polar;
int config_sanity;
int config_satcorr;
- int config_sa;
int config_closer;
float threshold;
float min_gradient;
@@ -182,8 +181,6 @@ static void show_help(const char *s)
" --unpolarized Don't correct for the polarisation of the X-rays.\n"
" --no-sat-corr Don't correct values of saturated peaks using a\n"
" table included in the HDF5 file.\n"
-" --no-sa Don't correct for the differing solid angles of\n"
-" the pixels.\n"
" --threshold=<n> Only accept peaks above <n> ADU. Default: 800.\n"
" --min-gradient=<n> Minimum gradient for Zaefferer peak search.\n"
" Default: 100,000.\n"
@@ -415,7 +412,7 @@ static void process_image(void *pp, int cookie)
if ( config_nearbragg ) {
output_intensities(&image, image.indexed_cell,
pargs->static_args.output_mutex,
- config_polar, pargs->static_args.config_sa,
+ config_polar,
pargs->static_args.config_closer,
pargs->static_args.ofh, 0, 0.1);
}
@@ -525,7 +522,6 @@ int main(int argc, char *argv[])
int config_polar = 1;
int config_sanity = 0;
int config_satcorr = 1;
- int config_sa = 1;
int config_checkprefix = 1;
int config_closer = 1;
float threshold = 800.0;
@@ -586,7 +582,6 @@ int main(int argc, char *argv[])
{"check-sanity", 0, &config_sanity, 1},
{"no-sat-corr", 0, &config_satcorr, 0},
{"sat-corr", 0, &config_satcorr, 1}, /* Compat */
- {"no-sa", 0, &config_sa, 0},
{"threshold", 1, NULL, 't'},
{"min-gradient", 1, NULL, 4},
{"no-check-prefix", 0, &config_checkprefix, 0},
@@ -882,7 +877,6 @@ int main(int argc, char *argv[])
qargs.static_args.config_polar = config_polar;
qargs.static_args.config_sanity = config_sanity;
qargs.static_args.config_satcorr = config_satcorr;
- qargs.static_args.config_sa = config_sa;
qargs.static_args.config_closer = config_closer;
qargs.static_args.cellr = cellr;
qargs.static_args.threshold = threshold;
diff --git a/src/partialator.c b/src/partialator.c
index 7829f933..beef9b6f 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -208,8 +208,7 @@ static void integrate_image(struct image *image, ReflItemList *obs)
* pattern? */
/* FIXME: Coordinates aren't whole numbers */
if ( integrate_peak(image, spots[j].x, spots[j].y,
- &xc, &yc, &i_partial, NULL, NULL,
- 1, 1, 0) ) {
+ &xc, &yc, &i_partial, NULL, NULL, 1, 0) ) {
spots[j].valid = 0;
continue;
}
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 6c48c6ec..4584bb3c 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -565,7 +565,7 @@ int main(int argc, char *argv[])
if ( config_nearbragg ) {
find_projected_peaks(&image, cell, 0, 0.1);
- output_intensities(&image, cell, NULL, 0, 1, 0, stdout,
+ output_intensities(&image, cell, NULL, 0, 0, stdout,
0, 0.1);
free(image.cpeaks);
}
diff --git a/src/peaks.c b/src/peaks.c
index 1ad29a03..88ac50bf 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -182,7 +182,7 @@ static int cull_peaks(struct image *image)
int integrate_peak(struct image *image, int xp, int yp,
float *xc, float *yc, float *intensity,
double *pbg, double *pmax,
- int do_polar, int do_sa, int centroid)
+ int do_polar, int centroid)
{
signed int x, y;
int lim, out_lim;
@@ -204,7 +204,7 @@ int integrate_peak(struct image *image, int xp, int yp,
for ( x=-out_lim; x<+out_lim; x++ ) {
for ( y=-out_lim; y<+out_lim; y++ ) {
- double val, sa, pix_area, Lsq, dsq, proj_area;
+ double val;
float tt = 0.0;
double phi, pa, pb, pol;
uint16_t flags;
@@ -238,30 +238,9 @@ int integrate_peak(struct image *image, int xp, int yp,
if ( val > max ) max = val;
- if ( do_sa ) {
-
- /* 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 (approximate) */
- tt = get_tt(image, x+xp, y+yp);
- proj_area = pix_area * cos(tt);
-
- /* Calculate distance from crystal to pixel */
- dsq = pow(((double)(x+xp) - p->cx) / p->res, 2.0);
- dsq += pow(((double)(y+yp) - p->cy) / p->res, 2.0);
-
- /* Projected area of pixel divided by distance squared */
- sa = 1.0e7 * proj_area / (dsq + Lsq);
-
- val /= sa;
-
- }
-
if ( do_polar ) {
- if ( !do_sa ) tt = get_tt(image, x+xp, y+yp);
+ tt = get_tt(image, x+xp, y+yp);
phi = atan2(y+yp, x+xp);
pa = pow(sin(phi)*sin(tt), 2.0);
@@ -420,7 +399,7 @@ void search_peaks(struct image *image, float threshold, float min_gradient)
* 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_x, mask_y,
- &fx, &fy, &intensity, NULL, NULL, 0, 0, 1);
+ &fx, &fy, &intensity, NULL, NULL, 0, 1);
if ( r ) {
/* Bad region - don't detect peak */
nrej_bad++;
@@ -702,7 +681,7 @@ static void output_header(FILE *ofh, UnitCell *cell, struct image *image)
void output_intensities(struct image *image, UnitCell *cell,
- pthread_mutex_t *mutex, int polar, int sa,
+ pthread_mutex_t *mutex, int polar,
int use_closer, FILE *ofh,
int circular_domain, double domain_r)
{
@@ -766,7 +745,7 @@ void output_intensities(struct image *image, UnitCell *cell,
* revised coordinates. */
r = integrate_peak(image, f->x, f->y, &x, &y,
&intensity, &bg, &max,
- polar, sa, 1);
+ polar, 1);
if ( r ) {
/* The original peak (which also went
* through integrate_peak(), but with
@@ -788,7 +767,7 @@ void output_intensities(struct image *image, UnitCell *cell,
image->cpeaks[i].x,
image->cpeaks[i].y,
&x, &y, &intensity, &bg, &max,
- polar, sa, 1);
+ polar, 1);
if ( r ) {
/* Plain old ordinary peak veto */
n_veto++;
@@ -809,7 +788,7 @@ void output_intensities(struct image *image, UnitCell *cell,
image->cpeaks[i].x,
image->cpeaks[i].y,
&x, &y, &intensity, &bg, &max, polar,
- sa, 0);
+ 0);
if ( r ) {
/* Plain old ordinary peak veto */
n_veto++;
@@ -867,7 +846,7 @@ void output_intensities(struct image *image, UnitCell *cell,
void output_pixels(struct image *image, UnitCell *cell,
- pthread_mutex_t *mutex, int do_polar, int do_sa,
+ pthread_mutex_t *mutex, int do_polar,
FILE *ofh, int circular_domain, double domain_r)
{
int i;
@@ -962,30 +941,27 @@ void output_pixels(struct image *image, UnitCell *cell,
if ( p->no_index ) continue;
- if ( do_sa ) {
-
- /* 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 */
- tt = get_tt(image, x, y);
- proj_area = pix_area * cos(tt);
+ /* Area of one pixel */
+ pix_area = pow(1.0/p->res, 2.0);
+ Lsq = pow(p->clen, 2.0);
- /* Calculate distance from crystal to pixel */
- dsq = pow(((double)x - p->cx) / p->res, 2.0);
- dsq += pow(((double)y - p->cy) / p->res, 2.0);
+ /* Area of pixel as seen from crystal */
+ tt = get_tt(image, x, y);
+ proj_area = pix_area * cos(tt);
- /* Projected area of pixel / distance squared */
- sa = 1.0e7 * proj_area / (dsq + Lsq);
+ /* Calculate distance from crystal to pixel */
+ dsq = pow(((double)x - p->cx) / p->res, 2.0);
+ dsq += pow(((double)y - p->cy) / p->res, 2.0);
- val /= sa;
+ /* 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 ) {
- if ( !do_sa ) tt = get_tt(image, x, y);
+ tt = get_tt(image, x, y);
phi = atan2(y, x);
pa = pow(sin(phi)*sin(tt), 2.0);
diff --git a/src/peaks.h b/src/peaks.h
index ba1eea30..8b506e42 100644
--- a/src/peaks.h
+++ b/src/peaks.h
@@ -24,12 +24,12 @@ extern void search_peaks(struct image *image, float threshold,
extern void dump_peaks(struct image *image, FILE *ofh, pthread_mutex_t *mutex);
extern void output_intensities(struct image *image, UnitCell *cell,
- pthread_mutex_t *mutex, int polar, int sa,
+ pthread_mutex_t *mutex, int polar,
int use_closer, FILE *ofh, int circular_domain,
double domain_r);
extern void output_pixels(struct image *image, UnitCell *cell,
- pthread_mutex_t *mutex, int do_polar, int do_sa,
+ pthread_mutex_t *mutex, int do_polar,
FILE *ofh, int circular_domain, double domain_r);
extern int peak_sanity_check(struct image *image, UnitCell *cell,
@@ -39,6 +39,6 @@ extern int find_projected_peaks(struct image *image, UnitCell *cell,
extern int integrate_peak(struct image *image, int xp, int yp,
float *xc, float *yc, float *intensity,
double *pbg, double *pmax,
- int do_polar, int do_sa, int centroid);
+ int do_polar, int centroid);
#endif /* PEAKS_H */
diff --git a/src/post-refinement.c b/src/post-refinement.c
index d835a2ff..26bef459 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -246,7 +246,7 @@ double mean_partial_dev(struct image *image, struct cpeak *spots, int n,
/* FIXME: Coordinates aren't whole numbers */
if ( integrate_peak(image, spots[h].x, spots[h].y,
&xc, &yc, &I_partial, NULL, NULL,
- 1, 1, 0) ) {
+ 1, 0) ) {
continue;
}
@@ -318,7 +318,7 @@ double pr_iterate(struct image *image, double *i_full, const char *sym,
/* FIXME: Coordinates aren't whole numbers */
if ( integrate_peak(image, spots[h].x, spots[h].y,
&xc, &yc, &I_partial, NULL, NULL,
- 1, 1, 0) ) {
+ 1, 0) ) {
continue;
}
diff --git a/src/reintegrate.c b/src/reintegrate.c
index b5a388a6..9d882d4b 100644
--- a/src/reintegrate.c
+++ b/src/reintegrate.c
@@ -140,8 +140,7 @@ static void process_image(void *pg, int cookie)
output_intensities(&image, apargs->cell,
pargs->output_mutex, pargs->config_polar,
- pargs->config_sa, pargs->config_closer,
- pargs->ofh, 0, 0.1);
+ pargs->config_closer, pargs->ofh, 0, 0.1);
}
free(image.data);
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-29 09:53:11 +0000