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-rw-r--r--src/calibrate_detector.c4
-rw-r--r--src/cubeit.c4
-rw-r--r--src/facetron.c2
-rw-r--r--src/geometry.c30
-rw-r--r--src/geometry.h8
-rw-r--r--src/image.h7
-rw-r--r--src/indexamajig.c12
-rw-r--r--src/peaks.c80
-rw-r--r--src/reintegrate.c4
-rw-r--r--src/render_hkl.c4
-rw-r--r--src/templates.c22
11 files changed, 89 insertions, 88 deletions
diff --git a/src/calibrate_detector.c b/src/calibrate_detector.c
index 0d613849..5ca468c6 100644
--- a/src/calibrate_detector.c
+++ b/src/calibrate_detector.c
@@ -168,8 +168,8 @@ static void add_image(void *args, int cookie)
image.flags = NULL;
image.indexed_cell = NULL;
image.filename = pargs->filename;
- image.hits = NULL;
- image.n_hits = 0;
+ image.cpeaks = NULL;
+ image.n_cpeaks = 0;
image.det = NULL;
/* View head-on (unit cell is tilted) */
diff --git a/src/cubeit.c b/src/cubeit.c
index ebb21151..ad78704e 100644
--- a/src/cubeit.c
+++ b/src/cubeit.c
@@ -216,8 +216,8 @@ static void sum_image(void *pg, int cookie)
image.flags = NULL;
image.indexed_cell = NULL;
image.filename = apargs->filename;
- image.hits = NULL;
- image.n_hits = 0;
+ image.cpeaks = NULL;
+ image.n_cpeaks = 0;
image.det = pargs->det;
/* View head-on (unit cell is tilted) */
diff --git a/src/facetron.c b/src/facetron.c
index fa9754e4..9bef1682 100644
--- a/src/facetron.c
+++ b/src/facetron.c
@@ -87,7 +87,7 @@ static void integrate_image(int mytask, void *tasks)
{
struct integrate_args *all_args = tasks;
struct integrate_args *pargs = &all_args[mytask];
- struct reflhit *spots;
+ struct cpeak *spots;
int j, n;
struct hdfile *hdfile;
struct image *image = pargs->image;
diff --git a/src/geometry.c b/src/geometry.c
index 09865822..cca2d050 100644
--- a/src/geometry.c
+++ b/src/geometry.c
@@ -22,24 +22,24 @@
#include "peaks.h"
-#define MAX_HITS (1024)
+#define MAX_CPEAKS (1024)
-struct reflhit *find_intersections(struct image *image, UnitCell *cell,
- double divergence, double bandwidth,
- int *n, int output)
+struct cpeak *find_intersections(struct image *image, UnitCell *cell,
+ double divergence, double bandwidth,
+ int *n, int output)
{
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
- struct reflhit *hits;
+ struct cpeak *cpeaks;
int np = 0;
int hmax, kmax, lmax;
double mres;
signed int h, k, l;
- hits = malloc(sizeof(struct reflhit)*MAX_HITS);
- if ( hits == NULL ) {
+ cpeaks = malloc(sizeof(struct cpeak)*MAX_CPEAKS);
+ if ( cpeaks == NULL ) {
*n = 0;
return NULL;
}
@@ -118,11 +118,11 @@ struct reflhit *find_intersections(struct image *image, UnitCell *cell,
if ( !found ) continue;
- hits[np].h = h;
- hits[np].k = k;
- hits[np].l = l;
- hits[np].x = xda;
- hits[np].y = yda;
+ cpeaks[np].h = h;
+ cpeaks[np].k = k;
+ cpeaks[np].l = l;
+ cpeaks[np].x = xda;
+ cpeaks[np].y = yda;
np++;
if ( output ) {
@@ -134,7 +134,7 @@ struct reflhit *find_intersections(struct image *image, UnitCell *cell,
}
*n = np;
- return hits;
+ return cpeaks;
}
@@ -145,7 +145,7 @@ double partiality(struct image *image, signed int h, signed int k, signed int l)
}
-double integrate_all(struct image *image, struct reflhit *hits, int n)
+double integrate_all(struct image *image, struct cpeak *cpeaks, int n)
{
double itot = 0.0;
int i;
@@ -154,7 +154,7 @@ double integrate_all(struct image *image, struct reflhit *hits, int n)
float x, y, intensity;
- if ( integrate_peak(image, hits[i].x, hits[i].y, &x, &y,
+ if ( integrate_peak(image, cpeaks[i].x, cpeaks[i].y, &x, &y,
&intensity, NULL, NULL, 0, 0) ) continue;
itot += intensity;
diff --git a/src/geometry.h b/src/geometry.h
index 3e25a8a3..8ebfc1b2 100644
--- a/src/geometry.h
+++ b/src/geometry.h
@@ -17,13 +17,13 @@
#include <config.h>
#endif
-extern struct reflhit *find_intersections(struct image *image, UnitCell *cell,
- double divergence, double bandwidth,
- int *n, int output);
+extern struct cpeak *find_intersections(struct image *image, UnitCell *cell,
+ double divergence, double bandwidth,
+ int *n, int output);
extern double partiality(struct image *image, signed int h,
signed int k, signed int l);
-extern double integrate_all(struct image *image, struct reflhit *hits, int n);
+extern double integrate_all(struct image *image, struct cpeak *cpeaks, int n);
#endif /* GEOMETRY_H */
diff --git a/src/image.h b/src/image.h
index 71bf0d3a..4f5052bb 100644
--- a/src/image.h
+++ b/src/image.h
@@ -58,7 +58,8 @@ struct imagefeature {
typedef struct _imagefeaturelist ImageFeatureList;
-struct reflhit {
+/* This structure represents a predicted peak in an image */
+struct cpeak {
signed int h;
signed int k;
signed int l;
@@ -79,8 +80,8 @@ struct image {
int ncells;
struct detector *det;
char *filename;
- struct reflhit *hits;
- int n_hits;
+ struct cpeak *cpeaks;
+ int n_cpeaks;
int id; /* ID number of the thread
* handling this image */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index d0260a8e..54d5e630 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -1,7 +1,7 @@
/*
* indexamajig.c
*
- * Find hits, index patterns, output hkl+intensity etc.
+ * Index patterns, output hkl+intensity etc.
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
@@ -258,8 +258,8 @@ static struct image *get_simage(struct image *template, int alternate)
image->f0 = template->f0;
/* Prevent muppetry */
- image->hits = NULL;
- image->n_hits = 0;
+ image->cpeaks = NULL;
+ image->n_cpeaks = 0;
return image;
}
@@ -317,8 +317,8 @@ static void process_image(void *pp, int cookie)
image.indexed_cell = NULL;
image.id = cookie;
image.filename = filename;
- image.hits = NULL;
- image.n_hits = 0;
+ image.cpeaks = NULL;
+ image.n_cpeaks = 0;
image.det = pargs->static_args.det;
/* View head-on (unit cell is tilted) */
@@ -442,7 +442,7 @@ done:
free(image.data);
free(image.flags);
image_feature_list_free(image.features);
- free(image.hits);
+ free(image.cpeaks);
hdfile_close(hdfile);
}
diff --git a/src/peaks.c b/src/peaks.c
index 0cf7c232..e70ebfe2 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -33,7 +33,7 @@
/* Maximum number of peaks which may be predicted by find_projected_peaks() */
-#define MAX_HITS (1024)
+#define MAX_CPEAKS (1024)
/* How close a peak must be to an indexed position to be considered "close"
* for the purposes of double hit detection and sanity checking. */
@@ -495,12 +495,12 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
- struct reflhit *hits;
- int n_hits = 0;
+ struct cpeak *cpeaks;
+ int n_cpeaks = 0;
double alen, blen, clen;
- hits = malloc(sizeof(struct reflhit)*MAX_HITS);
- if ( hits == NULL ) return 0;
+ cpeaks = malloc(sizeof(struct cpeak)*MAX_CPEAKS);
+ if ( cpeaks == NULL ) return 0;
/* "Borrow" direction values to get reciprocal lengths */
cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
@@ -547,14 +547,14 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
if ( dist > domain_r ) continue;
}
- for ( j=0; j<n_hits; j++ ) {
- if ( (hits[j].h == h) && (hits[j].k == k)
- && (hits[j].l == l) ) {
+ for ( j=0; j<n_cpeaks; j++ ) {
+ if ( (cpeaks[j].h == h) && (cpeaks[j].k == k)
+ && (cpeaks[j].l == l) ) {
- if ( dist < hits[j].min_distance ) {
- hits[j].min_distance = dist;
- hits[j].x = x;
- hits[j].y = y;
+ if ( dist < cpeaks[j].min_distance ) {
+ cpeaks[j].min_distance = dist;
+ cpeaks[j].x = x;
+ cpeaks[j].y = y;
}
found = 1;
@@ -563,14 +563,14 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
}
if ( !found ) {
- hits[n_hits].min_distance = dist;
- hits[n_hits].x = x;
- hits[n_hits].y = y;
- hits[n_hits].h = h;
- hits[n_hits].k = k;
- hits[n_hits].l = l;
- n_hits++;
- if ( n_hits == MAX_HITS ) {
+ cpeaks[n_cpeaks].min_distance = dist;
+ cpeaks[n_cpeaks].x = x;
+ cpeaks[n_cpeaks].y = y;
+ cpeaks[n_cpeaks].h = h;
+ cpeaks[n_cpeaks].k = k;
+ cpeaks[n_cpeaks].l = l;
+ n_cpeaks++;
+ if ( n_cpeaks == MAX_CPEAKS ) {
ERROR("Unit cell is insanely large!\n");
goto out;
}
@@ -580,11 +580,11 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
}
out:
- STATUS("Found %i reflections\n", n_hits);
- image->hits = hits;
- image->n_hits = n_hits;
+ STATUS("Found %i reflections\n", n_cpeaks);
+ image->cpeaks = cpeaks;
+ image->n_cpeaks = n_cpeaks;
- return n_hits;
+ return n_cpeaks;
}
@@ -710,10 +710,10 @@ void output_intensities(struct image *image, UnitCell *cell,
double bsx, bsy, bsz;
double csx, csy, csz;
- if ( image->n_hits == 0 ) {
+ if ( image->n_cpeaks == 0 ) {
find_projected_peaks(image, cell, circular_domain, domain_r);
}
- if ( image->n_hits == 0 ) return;
+ if ( image->n_cpeaks == 0 ) return;
/* Get exclusive access to the output stream if necessary */
if ( mutex != NULL ) pthread_mutex_lock(mutex);
@@ -724,7 +724,7 @@ void output_intensities(struct image *image, UnitCell *cell,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
- for ( i=0; i<image->n_hits; i++ ) {
+ for ( i=0; i<image->n_cpeaks; i++ ) {
float x, y, intensity;
double d;
@@ -738,8 +738,8 @@ void output_intensities(struct image *image, UnitCell *cell,
if ( image->features != NULL ) {
f = image_feature_closest(image->features,
- image->hits[i].x,
- image->hits[i].y,
+ image->cpeaks[i].x,
+ image->cpeaks[i].y,
&d, &idx);
} else {
f = NULL;
@@ -773,8 +773,8 @@ void output_intensities(struct image *image, UnitCell *cell,
int r;
r = integrate_peak(image,
- image->hits[i].x,
- image->hits[i].y,
+ image->cpeaks[i].x,
+ image->cpeaks[i].y,
&x, &y, &intensity, &bg, &max,
polar, sa);
if ( r ) {
@@ -794,8 +794,8 @@ void output_intensities(struct image *image, UnitCell *cell,
int r;
r = integrate_peak(image,
- image->hits[i].x,
- image->hits[i].y,
+ image->cpeaks[i].x,
+ image->cpeaks[i].y,
&x, &y, &intensity, &bg, &max, polar,
sa);
if ( r ) {
@@ -808,11 +808,11 @@ void output_intensities(struct image *image, UnitCell *cell,
/* Write h,k,l, integrated intensity and centroid coordinates */
fprintf(ofh, "%3i %3i %3i %6f (at %5.2f,%5.2f) max=%6f bg=%6f\n",
- image->hits[i].h, image->hits[i].k, image->hits[i].l,
+ image->cpeaks[i].h, image->cpeaks[i].k, image->cpeaks[i].l,
intensity, x, y, max, bg);
- image->hits[i].x = x;
- image->hits[i].y = y;
+ image->cpeaks[i].x = x;
+ image->cpeaks[i].y = y;
}
@@ -826,12 +826,12 @@ void output_intensities(struct image *image, UnitCell *cell,
if ( f == NULL ) continue;
- for ( j=0; j<image->n_hits; j++ ) {
+ for ( j=0; j<image->n_cpeaks; j++ ) {
double d;
- d = pow(image->hits[j].x-f->x, 2.0)
- + pow(image->hits[j].y-f->y, 2.0);
+ d = pow(image->cpeaks[j].x-f->x, 2.0)
+ + pow(image->cpeaks[j].y-f->y, 2.0);
if ( d < PEAK_CLOSE ) n_foundclose++;
@@ -842,7 +842,7 @@ void output_intensities(struct image *image, UnitCell *cell,
fprintf(ofh, "Peak statistics: %i peaks found by the peak search out of "
"%i were close to indexed positions. "
"%i indexed positions out of %i were close to detected peaks.\n",
- n_foundclose, n_found, n_indclose, image->n_hits);
+ n_foundclose, n_found, n_indclose, image->n_cpeaks);
fprintf(ofh, "%i integrations using indexed locations were aborted because "
"they hit one or more bad pixels.\n", n_veto);
fprintf(ofh, "%i integrations using peak search locations were aborted "
diff --git a/src/reintegrate.c b/src/reintegrate.c
index 43db6092..c9de3338 100644
--- a/src/reintegrate.c
+++ b/src/reintegrate.c
@@ -108,8 +108,8 @@ static void process_image(void *pg, int cookie)
image.flags = NULL;
image.indexed_cell = NULL;
image.filename = apargs->filename;
- image.hits = NULL;
- image.n_hits = 0;
+ image.cpeaks = NULL;
+ image.n_cpeaks = 0;
image.det = pargs->det;
/* View head-on (unit cell is tilted) */
diff --git a/src/render_hkl.c b/src/render_hkl.c
index e333da7f..4b077ba7 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -63,9 +63,9 @@ static void show_help(const char *s)
" according to:\n"
" I : the intensity of the reflection.\n"
" sqrtI : the square root of the intensity.\n"
-" count : the number of hits for the reflection.\n"
+" count : the number of measurements for the reflection.\n"
" (after correcting for 'epsilon')\n"
-" rawcts : the raw number of hits for the\n"
+" rawcts : the raw number of measurements for the\n"
" reflection (no 'epsilon' correction).\n"
"\n"
" --colour-key Draw (only) the key for the current colour scale.\n"
diff --git a/src/templates.c b/src/templates.c
index 468612f2..105fa755 100644
--- a/src/templates.c
+++ b/src/templates.c
@@ -43,7 +43,7 @@ struct template {
double omega;
double phi;
int n;
- struct reflhit *spots;
+ struct cpeak *spots;
};
@@ -165,16 +165,16 @@ IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
for ( phi = 0.0; phi < phi_max-phi_step; phi += phi_step ) {
int n;
- struct reflhit *hits;
+ struct cpeak *cpeaks;
UnitCell *cell_rot;
assert(i < n_templates);
cell_rot = rotate_cell(cell, omega, phi, 0.0);
- hits = find_intersections(&image, cell_rot, 5.0e-3,
+ cpeaks = find_intersections(&image, cell_rot, 5.0e-3,
3.0/100.0, &n, 0);
- if ( hits == NULL ) {
+ if ( cpeaks == NULL ) {
ERROR("Template calculation failed.\n");
return NULL;
}
@@ -182,7 +182,7 @@ IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
priv->templates[i].omega = omega;
priv->templates[i].phi = phi;
priv->templates[i].n = n;
- priv->templates[i].spots = hits;
+ priv->templates[i].spots = cpeaks;
i++;
free(cell_rot);
@@ -228,7 +228,7 @@ static int fast_integrate_peak(struct image *image, int xp, int yp)
}
-static double integrate_all_rot(struct image *image, struct reflhit *hits,
+static double integrate_all_rot(struct image *image, struct cpeak *cpeaks,
int n, double rot)
{
double itot = 0.0;
@@ -243,8 +243,8 @@ static double integrate_all_rot(struct image *image, struct reflhit *hits,
float xp, yp;
- xp = cosr*hits[i].x + sinr*hits[i].y;
- yp = -sinr*hits[i].x + cosr*hits[i].y;
+ xp = cosr*cpeaks[i].x + sinr*cpeaks[i].y;
+ yp = -sinr*cpeaks[i].x + cosr*cpeaks[i].y;
itot += fast_integrate_peak(image, rint(xp), rint(yp));
num_int++;
@@ -257,7 +257,7 @@ static double integrate_all_rot(struct image *image, struct reflhit *hits,
/* Return the mean of the distances between peaks in the image and peaks from
* the given template. */
-static double mean_distance(struct image *image, struct reflhit *hits,
+static double mean_distance(struct image *image, struct cpeak *cpeaks,
int n, double rot)
{
double dtot = 0.0;
@@ -275,8 +275,8 @@ static double mean_distance(struct image *image, struct reflhit *hits,
int j;
double min_dsq;
- xp = cosr*hits[i].x + sinr*hits[i].y;
- yp = -sinr*hits[i].x + cosr*hits[i].y;
+ xp = cosr*cpeaks[i].x + sinr*cpeaks[i].y;
+ yp = -sinr*cpeaks[i].x + cosr*cpeaks[i].y;
/* Compare to every real peak */
min_dsq = +INFINITY;
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-08 01:53:46 +0000