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Commit 1a206036 authored by Thomas White's avatar Thomas White Committed by Thomas White
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Start work on binary tree

parent 155ca006
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Makefile.am
View file @ 1a206036
......@@ -23,7 +23,7 @@ src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c src/utils.c \
src/image.c src/cell.c src/hdf5-file.c \
src/detector.c src/sfac.c src/peaks.c \
src/reflections.c src/beam-parameters.c \
src/symmetry.c src/thread-pool.c
src/symmetry.c src/thread-pool.c src/reflist.c
if HAVE_OPENCL
src_pattern_sim_SOURCES += src/diffraction-gpu.c src/cl-utils.c
endif
......@@ -38,7 +38,8 @@ src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c src/utils.c \
src/filters.c src/diffraction.c src/detector.c \
src/sfac.c src/dirax.c src/mosflm.c \
src/reflections.c src/templates.c src/symmetry.c \
src/geometry.c src/thread-pool.c src/beam-parameters.c
src/geometry.c src/thread-pool.c \
src/beam-parameters.c src/reflist.c
if HAVE_OPENCL
src_indexamajig_SOURCES += src/diffraction-gpu.c src/cl-utils.c
endif
......@@ -73,14 +74,14 @@ src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflections.c \
src_calibrate_detector_SOURCES = src/calibrate_detector.c src/utils.c \
src/hdf5-file.c src/image.c src/filters.c \
src/peaks.c src/detector.c src/cell.c \
src/thread-pool.c
src/thread-pool.c src/reflist.c
src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
src/utils.c src/detector.c src/peaks.c src/image.c \
src/geometry.c src/reflections.c src/stream.c \
src/thread-pool.c src/beam-parameters.c \
src/symmetry.c src/post-refinement.c \
src/hrs-scaling.c
src/hrs-scaling.c src/reflist.c
if HAVE_CAIRO
src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
......
Makefile.in
View file @ 1a206036
......@@ -83,7 +83,7 @@ am_src_calibrate_detector_OBJECTS = src/calibrate_detector.$(OBJEXT) \
src/utils.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
src/image.$(OBJEXT) src/filters.$(OBJEXT) src/peaks.$(OBJEXT) \
src/detector.$(OBJEXT) src/cell.$(OBJEXT) \
src/thread-pool.$(OBJEXT)
src/thread-pool.$(OBJEXT) src/reflist.$(OBJEXT)
src_calibrate_detector_OBJECTS = $(am_src_calibrate_detector_OBJECTS)
src_calibrate_detector_LDADD = $(LDADD)
src_calibrate_detector_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
......@@ -145,7 +145,8 @@ am__src_indexamajig_SOURCES_DIST = src/indexamajig.c src/hdf5-file.c \
src/filters.c src/diffraction.c src/detector.c src/sfac.c \
src/dirax.c src/mosflm.c src/reflections.c src/templates.c \
src/symmetry.c src/geometry.c src/thread-pool.c \
src/beam-parameters.c src/diffraction-gpu.c src/cl-utils.c
src/beam-parameters.c src/reflist.c src/diffraction-gpu.c \
src/cl-utils.c
@HAVE_OPENCL_TRUE@am__objects_1 = src/diffraction-gpu.$(OBJEXT) \
@HAVE_OPENCL_TRUE@ src/cl-utils.$(OBJEXT)
am_src_indexamajig_OBJECTS = src/indexamajig.$(OBJEXT) \
......@@ -156,7 +157,8 @@ am_src_indexamajig_OBJECTS = src/indexamajig.$(OBJEXT) \
src/mosflm.$(OBJEXT) src/reflections.$(OBJEXT) \
src/templates.$(OBJEXT) src/symmetry.$(OBJEXT) \
src/geometry.$(OBJEXT) src/thread-pool.$(OBJEXT) \
src/beam-parameters.$(OBJEXT) $(am__objects_1)
src/beam-parameters.$(OBJEXT) src/reflist.$(OBJEXT) \
$(am__objects_1)
src_indexamajig_OBJECTS = $(am_src_indexamajig_OBJECTS)
src_indexamajig_LDADD = $(LDADD)
src_indexamajig_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
......@@ -166,7 +168,8 @@ am_src_partialator_OBJECTS = src/partialator.$(OBJEXT) \
src/geometry.$(OBJEXT) src/reflections.$(OBJEXT) \
src/stream.$(OBJEXT) src/thread-pool.$(OBJEXT) \
src/beam-parameters.$(OBJEXT) src/symmetry.$(OBJEXT) \
src/post-refinement.$(OBJEXT) src/hrs-scaling.$(OBJEXT)
src/post-refinement.$(OBJEXT) src/hrs-scaling.$(OBJEXT) \
src/reflist.$(OBJEXT)
src_partialator_OBJECTS = $(am_src_partialator_OBJECTS)
src_partialator_LDADD = $(LDADD)
src_partialator_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
......@@ -174,14 +177,14 @@ am__src_pattern_sim_SOURCES_DIST = src/pattern_sim.c src/diffraction.c \
src/utils.c src/image.c src/cell.c src/hdf5-file.c \
src/detector.c src/sfac.c src/peaks.c src/reflections.c \
src/beam-parameters.c src/symmetry.c src/thread-pool.c \
src/diffraction-gpu.c src/cl-utils.c
src/reflist.c src/diffraction-gpu.c src/cl-utils.c
am_src_pattern_sim_OBJECTS = src/pattern_sim.$(OBJEXT) \
src/diffraction.$(OBJEXT) src/utils.$(OBJEXT) \
src/image.$(OBJEXT) src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
src/detector.$(OBJEXT) src/sfac.$(OBJEXT) src/peaks.$(OBJEXT) \
src/reflections.$(OBJEXT) src/beam-parameters.$(OBJEXT) \
src/symmetry.$(OBJEXT) src/thread-pool.$(OBJEXT) \
$(am__objects_1)
src/reflist.$(OBJEXT) $(am__objects_1)
src_pattern_sim_OBJECTS = $(am_src_pattern_sim_OBJECTS)
src_pattern_sim_LDADD = $(LDADD)
src_pattern_sim_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
......@@ -564,7 +567,7 @@ src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
src/utils.c src/image.c src/cell.c src/hdf5-file.c \
src/detector.c src/sfac.c src/peaks.c src/reflections.c \
src/beam-parameters.c src/symmetry.c src/thread-pool.c \
$(am__append_3)
src/reflist.c $(am__append_3)
src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c \
src/cell.c src/utils.c src/reflections.c \
src/symmetry.c src/stream.c src/beam-parameters.c \
......@@ -575,7 +578,7 @@ src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c \
src/filters.c src/diffraction.c src/detector.c src/sfac.c \
src/dirax.c src/mosflm.c src/reflections.c src/templates.c \
src/symmetry.c src/geometry.c src/thread-pool.c \
src/beam-parameters.c $(am__append_4)
src/beam-parameters.c src/reflist.c $(am__append_4)
@HAVE_GTK_TRUE@src_hdfsee_SOURCES = src/hdfsee.c src/displaywindow.c src/render.c \
@HAVE_GTK_TRUE@ src/hdf5-file.c src/utils.c src/image.c src/filters.c \
@HAVE_GTK_TRUE@ src/thread-pool.c
......@@ -603,14 +606,14 @@ src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflections.c \
src_calibrate_detector_SOURCES = src/calibrate_detector.c src/utils.c \
src/hdf5-file.c src/image.c src/filters.c \
src/peaks.c src/detector.c src/cell.c \
src/thread-pool.c
src/thread-pool.c src/reflist.c
src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
src/utils.c src/detector.c src/peaks.c src/image.c \
src/geometry.c src/reflections.c src/stream.c \
src/thread-pool.c src/beam-parameters.c \
src/symmetry.c src/post-refinement.c \
src/hrs-scaling.c
src/hrs-scaling.c src/reflist.c
@HAVE_CAIRO_TRUE@src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
@HAVE_CAIRO_TRUE@ src/detector.c src/render.c src/filters.c src/image.c \
......@@ -770,6 +773,8 @@ src/detector.$(OBJEXT): src/$(am__dirstamp) \
src/cell.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/thread-pool.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/reflist.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/calibrate_detector$(EXEEXT): $(src_calibrate_detector_OBJECTS) $(src_calibrate_detector_DEPENDENCIES) src/$(am__dirstamp)
@rm -f src/calibrate_detector$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(src_calibrate_detector_OBJECTS) $(src_calibrate_detector_LDADD) $(LIBS)
......@@ -907,6 +912,7 @@ mostlyclean-compile:
-rm -f src/powder_plot.$(OBJEXT)
-rm -f src/process_hkl.$(OBJEXT)
-rm -f src/reflections.$(OBJEXT)
-rm -f src/reflist.$(OBJEXT)
-rm -f src/reintegrate.$(OBJEXT)
-rm -f src/render.$(OBJEXT)
-rm -f src/render_hkl.$(OBJEXT)
......@@ -952,6 +958,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/powder_plot.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/process_hkl.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reflections.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reflist.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reintegrate.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render_hkl.Po@am__quote@
......
src/calibrate_detector.c
View file @ 1a206036
......@@ -168,8 +168,7 @@ static void add_image(void *args, int cookie)
image.flags = NULL;
image.indexed_cell = NULL;
image.filename = pargs->filename;
image.cpeaks = NULL;
image.n_cpeaks = 0;
image.reflections = NULL;
image.det = NULL;
STATUS("%3i: Processing '%s'\n", cookie, pargs->filename);
......
src/cubeit.c
View file @ 1a206036
......@@ -218,8 +218,7 @@ static void sum_image(void *pg, int cookie)
image.flags = NULL;
image.indexed_cell = NULL;
image.filename = apargs->filename;
image.cpeaks = NULL;
image.n_cpeaks = 0;
image.reflections = NULL;
image.det = pargs->det;
STATUS("Processing '%s'\n", apargs->filename);
......
src/geometry.c
View file @ 1a206036
......@@ -22,6 +22,7 @@
#include "image.h"
#include "peaks.h"
#include "beam-parameters.h"
#include "reflist.h"
#define MAX_CPEAKS (256 * 256)
......@@ -117,7 +118,7 @@ static double partiality(double r1, double r2, double r)
static int check_reflection(struct image *image, double mres, int output,
struct cpeak *cpeaks, int np,
RefList *reflections,
signed int h, signed int k, signed int l,
double asx, double asy, double asz,
double bsx, double bsy, double bsz,
......@@ -136,6 +137,7 @@ static int check_reflection(struct image *image, double mres, int output,
double divergence = image->div;
double lambda = image->lambda;
double klow, kcen, khigh; /* Wavenumber */
Reflection *refl;
/* "low" gives the largest Ewald sphere,
* "high" gives the smallest Ewald sphere. */
......@@ -207,17 +209,9 @@ static int check_reflection(struct image *image, double mres, int output,
if ( p == -1 ) return 0;
/* Add peak to list */
cpeaks[np].h = h;
cpeaks[np].k = k;
cpeaks[np].l = l;
cpeaks[np].x = xda;
cpeaks[np].y = yda;
cpeaks[np].r1 = rlow;
cpeaks[np].r2 = rhigh;
cpeaks[np].p = part;
cpeaks[np].clamp1 = clamp_low;
cpeaks[np].clamp2 = clamp_high;
np++;
refl = add_refl(reflections, h, k, l);
set_detector_pos(refl, 0.0, xda, yda);
set_partial(refl, rlow, rhigh, part, clamp_low, clamp_high);
if ( output ) {
printf("%3i %3i %3i %6f (at %5.2f,%5.2f) %5.2f\n",
......@@ -228,23 +222,18 @@ static int check_reflection(struct image *image, double mres, int output,
}
struct cpeak *find_intersections(struct image *image, UnitCell *cell,
int *n, int output)
RefList *find_intersections(struct image *image, UnitCell *cell,
int output)
{
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
struct cpeak *cpeaks;
int np = 0;
RefList *reflections;
int hmax, kmax, lmax;
double mres;
signed int h, k, l;
cpeaks = malloc(sizeof(struct cpeak)*MAX_CPEAKS);
if ( cpeaks == NULL ) {
*n = 0;
return NULL;
}
reflections = reflist_new();
cell_get_reciprocal(cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
......@@ -260,29 +249,30 @@ struct cpeak *find_intersections(struct image *image, UnitCell *cell,
for ( l=-lmax; l<lmax; l++ ) {
/* Ignore central beam */
if ( (h==0) && (k==0) && (l==0) ) continue;
np += check_reflection(image, mres, output, cpeaks, np, h, k, l,
asx,asy,asz,bsx,bsy,bsz,csx,csy,csz);
if ( np == MAX_CPEAKS ) goto out;
check_reflection(image, mres, output, reflections, h, k, l,
asx,asy,asz,bsx,bsy,bsz,csx,csy,csz);
}
}
}
out:
*n = np;
return cpeaks;
return reflections;
}
double integrate_all(struct image *image, struct cpeak *cpeaks, int n)
double integrate_all(struct image *image, RefList *reflections)
{
double itot = 0.0;
int i;
Reflection *refl;
for ( i=0; i<n; i++ ) {
for ( refl = first_refl(reflections);
refl != NULL;
refl = next_refl(refl) ) {
float x, y, intensity;
double xp, yp;
get_detector_pos(refl, &xp, &yp);
if ( integrate_peak(image, cpeaks[i].x, cpeaks[i].y, &x, &y,
if ( integrate_peak(image, xp, yp, &x, &y,
&intensity, NULL, NULL, 0, 0) ) continue;
itot += intensity;
......
src/geometry.h
View file @ 1a206036
......@@ -17,10 +17,12 @@
#include <config.h>
#endif
extern struct cpeak *find_intersections(struct image *image, UnitCell *cell,
int *n, int output);
#include "reflist.h"
extern double integrate_all(struct image *image, struct cpeak *cpeaks, int n);
extern RefList *find_intersections(struct image *image, UnitCell *cell,
int output);
extern double integrate_all(struct image *image, RefList *reflections);
#endif /* GEOMETRY_H */
src/image.h
View file @ 1a206036
......@@ -24,6 +24,7 @@
#include "utils.h"
#include "cell.h"
#include "detector.h"
#include "reflist.h"
#define MAX_CELL_CANDIDATES (32)
......@@ -52,35 +53,6 @@ struct imagefeature {
typedef struct _imagefeaturelist ImageFeatureList;
/* This structure represents a predicted peak in an image */
struct cpeak
{
/* Indices */
signed int h;
signed int k;
signed int l;
double min_distance;
int valid;
/* Partiality */
double r1; /* First excitation error */
double r2; /* Second excitation error */
double p; /* Partiality */
int clamp1; /* Clamp status for r1 */
int clamp2; /* Clamp status for r2 */
/* Location in image */
int x;
int y;
int scalable;
/* Intensity */
double intensity;
};
/* Structure describing an image */
struct image {
......@@ -93,8 +65,7 @@ struct image {
struct detector *det;
struct beam_params *beam; /* The nominal beam parameters */
char *filename;
struct cpeak *cpeaks;
int n_cpeaks;
RefList *reflections;
int id; /* ID number of the thread
* handling this image */
......
src/indexamajig.c
View file @ 1a206036
......@@ -263,8 +263,7 @@ static struct image *get_simage(struct image *template, int alternate)
image->f0 = template->f0;
/* Prevent muppetry */
image->cpeaks = NULL;
image->n_cpeaks = 0;
image->reflections = NULL;
return image;
}
......@@ -326,8 +325,7 @@ static void process_image(void *pp, int cookie)
image.indexed_cell = NULL;
image.id = cookie;
image.filename = filename;
image.cpeaks = NULL;
image.n_cpeaks = 0;
image.reflections = NULL;
image.det = pargs->static_args.det;
STATUS("Processing '%s'\n", image.filename);
......@@ -434,7 +432,7 @@ done:
free(image.data);
free(image.flags);
image_feature_list_free(image.features);
free(image.cpeaks);
reflist_free(image.reflections);
hdfile_close(hdfile);
}
......
src/partialator.c
View file @ 1a206036
......@@ -34,6 +34,7 @@
#include "beam-parameters.h"
#include "post-refinement.h"
#include "hrs-scaling.h"
#include "reflist.h"
/* Maximum number of iterations of NLSq to do for each image per macrocycle. */
......@@ -84,9 +85,9 @@ static void refine_image(int mytask, void *tasks)
struct image *image = pargs->image;
double nominal_photon_energy = pargs->image->beam->photon_energy;
struct hdfile *hdfile;
struct cpeak *spots;
int n, i;
int i;
double dev, last_dev;
RefList *reflections;
hdfile = hdfile_open(image->filename);
if ( hdfile == NULL ) {
......@@ -110,16 +111,17 @@ static void refine_image(int mytask, void *tasks)
a/1.0e-9, b/1.0e-9, c/1.0e-9,
rad2deg(al), rad2deg(be), rad2deg(ga));
spots = find_intersections(image, image->indexed_cell, &n, 0);
/* FIXME: Don't do this each time */
reflections = find_intersections(image, image->indexed_cell, 0);
dev = +INFINITY;
i = 0;
do {
last_dev = dev;
dev = pr_iterate(image, pargs->i_full, pargs->sym, &spots, &n);
dev = pr_iterate(image, pargs->i_full, pargs->sym, reflections);
STATUS("Iteration %2i: mean dev = %5.2f\n", i, dev);
i++;
} while ( (fabs(last_dev - dev) > 1.0) && (i < MAX_CYCLES) );
mean_partial_dev(image, spots, n, pargs->sym,
mean_partial_dev(image, reflections, pargs->sym,
pargs->i_full, pargs->graph);
if ( pargs->pgraph ) {
fprintf(pargs->pgraph, "%5i %5.2f\n", mytask, dev);
......@@ -128,7 +130,7 @@ static void refine_image(int mytask, void *tasks)
free(image->data);
if ( image->flags != NULL ) free(image->flags);
hdfile_close(hdfile);
free(spots);
reflist_free(reflections);
/* Muppet proofing */
image->data = NULL;
......@@ -163,22 +165,23 @@ static void refine_all(struct image *images, int n_total_patterns,
}
static void uniquify(struct cpeak *spot, const char *sym)
static void uniquify(Reflection *refl, const char *sym)
{
signed int h, k, l;
signed int ha, ka, la;
get_asymm(spot->h, spot->k, spot->l, &ha, &ka, &la, sym);
spot->h = ha;
spot->k = ka;
spot->l = la;
get_indices(refl, &h, &k, &l);
get_asymm(h, k, l, &ha, &ka, &la, sym);
set_indices(refl, h, k, l);
}
/* FIXME: Get rid of this */
static void integrate_image(struct image *image, ReflItemList *obs,
const char *sym)
{
struct cpeak *spots;
int j, n;
RefList *reflections;
Reflection *refl;
struct hdfile *hdfile;
double nominal_photon_energy = image->beam->photon_energy;
......@@ -199,42 +202,39 @@ static void integrate_image(struct image *image, ReflItemList *obs,
}
/* Figure out which spots should appear in this pattern */
spots = find_intersections(image, image->indexed_cell, &n, 0);
reflections = find_intersections(image, image->indexed_cell, 0);
/* For each reflection, estimate the partiality */
for ( j=0; j<n; j++ ) {
for ( refl = first_refl(reflections);
refl != NULL;
refl = next_refl(refl) ) {
signed int h, k, l;
float i_partial;
float xc, yc;
double x, y;
uniquify(&spots[j], sym);
h = spots[j].h;
k = spots[j].k;
l = spots[j].l;
uniquify(refl, sym);
get_indices(refl, &h, &k, &l);
/* Don't attempt to use spots with very small
* partialities, since it won't be accurate. */
if ( spots[j].p < 0.1 ) continue;
if ( get_partiality(refl) < 0.1 ) continue;
/* Actual measurement of this reflection from this
* pattern? */
/* FIXME: Coordinates aren't whole numbers */
if ( integrate_peak(image, spots[j].x, spots[j].y,
/* Actual measurement of this reflection from this pattern? */
get_detector_pos(refl, &x, &y);
if ( integrate_peak(image, x, y,
&xc, &yc, &i_partial, NULL, NULL, 1, 0) ) {
spots[j].valid = 0;
delete_refl(refl);
continue;
}
spots[j].intensity = i_partial;
spots[j].valid = 1;
set_int(refl, i_partial);
if ( !find_item(obs, h, k, l) ) add_item(obs, h, k, l);
}
image->cpeaks = spots;
image->n_cpeaks = n;
image->reflections = reflections;
free(image->data);
if ( image->flags != NULL ) free(image->flags);
......@@ -253,21 +253,20 @@ static void select_scalable_reflections(struct image *images, int n)
for ( m=0; m<n; m++ ) {
int j;
Reflection *refl;
for ( j=0; j<images[m].n_cpeaks; j++ ) {
for ( refl = first_refl(images[m].reflections);
refl != NULL;
refl = next_refl(refl) ) {
int scalable = 1;
double v;
if ( images[m].cpeaks[j].p < 0.1 ) scalable = 0;
if ( !images[m].cpeaks[j].valid ) {
scalable = 0;
} else {
double v = fabs(images[m].cpeaks[j].intensity);
if ( v < 0.1 ) scalable = 0;
}
if ( get_partiality(refl) < 0.1 ) scalable = 0;
v = fabs(get_intensity(refl));
if ( v < 0.1 ) scalable = 0;
images[m].cpeaks[j].scalable = scalable;
set_scalable(refl, scalable);
}
......@@ -525,7 +524,7 @@ int main(int argc, char *argv[])
/* Clean up */
for ( i=0; i<n_total_patterns; i++ ) {
free(images[i].cpeaks);
reflist_free(images[i].reflections);
}
free(I_full);
delete_items(obs);
......
src/pattern_sim.c
View file @ 1a206036
......@@ -567,7 +567,7 @@ int main(int argc, char *argv[])
find_projected_peaks(&image, cell, 0, 0.1);
output_intensities(&image, cell, NULL, 0, 0, stdout,
0, 0.1);
free(image.cpeaks);
reflist_free(image.reflections);
}
if ( powder_fn != NULL ) {
......
src/peaks.c
View file @ 1a206036
......@@ -32,9 +32,6 @@
#include "diffraction.h"
/* Maximum number of peaks which may be predicted by find_projected_peaks() */
#define MAX_CPEAKS (8192)
/* 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)
......@@ -483,12 +480,11 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
struct cpeak *cpeaks;
int n_cpeaks = 0;
RefList *reflections;
double alen, blen, clen;
int n_reflections = 0;
cpeaks = malloc(sizeof(struct cpeak)*MAX_CPEAKS);
if ( cpeaks == NULL ) return 0;
reflections = reflist_new();
/* "Borrow" direction values to get reciprocal lengths */
cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
......@@ -507,8 +503,8 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
signed int h, k, l;
struct rvec q;
double dist;
int found = 0;
int j;
Reflection *refl;
double cur_dist;
q = get_q(image, x, y, 1, NULL, 1.0/image->lambda);
......@@ -535,44 +531,26 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
if ( dist > domain_r ) continue;
}
for ( j=0; j<n_cpeaks; j++ ) {
if ( (cpeaks[j].h == h) && (cpeaks[j].k == k)
&& (cpeaks[j].l == l) ) {
if ( dist < cpeaks[j].min_distance ) {
cpeaks[j].min_distance = dist;
cpeaks[j].x = x;
cpeaks[j].y = y;
}
found = 1;
}
}
if ( !found ) {
cpeaks[n_cpeaks].min_distance = dist;
cpeaks[n_cpeaks].x = x;
cpeaks[n_cpeaks].y = y;
cpeaks[n_cpeaks].h = h;