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authorThomas White <taw@physics.org>2013-05-23 12:01:59 +0200
committerThomas White <taw@physics.org>2013-05-27 17:33:15 +0200
commit4fd346391387f740c29561257a5af3fdfdd56700 (patch)
tree0eee358d475d4ca3bef2d45596fb4de33f71bf1b
parent2977589d2201ade9aa02289a54359288af2ff16e (diff)
Initial integration stuff
-rw-r--r--doc/man/indexamajig.15
-rw-r--r--libcrystfel/Makefile.am4
-rw-r--r--libcrystfel/src/geometry.c12
-rw-r--r--libcrystfel/src/integration.c672
-rw-r--r--libcrystfel/src/integration.h75
-rw-r--r--libcrystfel/src/peaks.c240
-rw-r--r--libcrystfel/src/peaks.h13
-rw-r--r--src/indexamajig.c33
-rw-r--r--src/process_image.c28
-rw-r--r--src/process_image.h7
10 files changed, 804 insertions, 285 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 738614ef..550d04e8 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -300,11 +300,6 @@ with old scripts because this option selects the behaviour which is now the
default.
.PD 0
-.IP \fB--no-bg-sub\fR
-.PD
-Don't subtract local background estimates from integrated intensities. This is almost never useful, but might help to detect problems from troublesome background noise.
-
-.PD 0
.IP \fB--use-saturated\fR
.PD
Normally, peaks which contain one or more pixels above max_adu (defined in the detector geometry file) will not be used for indexing. Using this option skips this check, possibly improving the indexing rate if there is a large proportion of saturated peaks.
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index a9bda55b..2812fa52 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -9,7 +9,7 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
src/reflist-utils.c src/filters.c \
src/render.c src/index.c src/dirax.c src/mosflm.c \
src/cell-utils.c src/integer_matrix.c src/crystal.c \
- src/grainspotter.c src/xds.c
+ src/grainspotter.c src/xds.c src/integration.c
if HAVE_FFTW
libcrystfel_la_SOURCES += src/reax.c
@@ -26,7 +26,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
src/filters.h src/dirax.h src/mosflm.h \
src/reax.h src/cell-utils.h \
src/integer_matrix.h src/crystal.h \
- src/grainspotter.h src/xds.h
+ src/grainspotter.h src/xds.h src/integration.h
AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -Wall
AM_CPPFLAGS += -I$(top_srcdir)/lib @LIBCRYSTFEL_CFLAGS@
diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index efb3f2ce..273ac7f0 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -135,11 +135,13 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
double cet, cez;
double pr;
double L;
+ double del;
/* Don't predict 000 */
if ( abs(h)+abs(k)+abs(l) == 0 ) return NULL;
pr = crystal_get_profile_radius(cryst);
+ del = image->div + crystal_get_mosaicity(cryst);
/* "low" gives the largest Ewald sphere (wavelength short => k large)
* "high" gives the smallest Ewald sphere (wavelength long => k small)
@@ -152,12 +154,12 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
tl = sqrt(xl*xl + yl*yl);
- cet = -sin(image->div/2.0) * khigh;
- cez = -cos(image->div/2.0) * khigh;
+ cet = -sin(del/2.0) * khigh;
+ cez = -cos(del/2.0) * khigh;
rhigh = khigh - distance(cet, cez, tl, zl); /* Loss of precision */
- cet = sin(image->div/2.0) * klow;
- cez = -cos(image->div/2.0) * klow;
+ cet = sin(del/2.0) * klow;
+ cez = -cos(del/2.0) * klow;
rlow = klow - distance(cet, cez, tl, zl); /* Loss of precision */
if ( (signbit(rlow) == signbit(rhigh))
@@ -168,7 +170,7 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
ERROR("Reflection with rlow < rhigh!\n");
ERROR("%3i %3i %3i rlow = %e, rhigh = %e\n",
h, k, l, rlow, rhigh);
- ERROR("div = %e\n", image->div);
+ ERROR("div + m = %e\n", del);
return NULL;
}
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
new file mode 100644
index 00000000..d6860fec
--- /dev/null
+++ b/libcrystfel/src/integration.c
@@ -0,0 +1,672 @@
+/*
+ * integration.c
+ *
+ * Integration of intensities
+ *
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2010-2013 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <assert.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_linalg.h>
+#include <gsl/gsl_eigen.h>
+
+#include "reflist.h"
+#include "cell.h"
+#include "crystal.h"
+#include "cell-utils.h"
+#include "geometry.h"
+#include "image.h"
+#include "peaks.h"
+#include "integration.h"
+
+
+struct integr_ind
+{
+ double res;
+ Reflection *refl;
+};
+
+
+static int compare_resolution(const void *av, const void *bv)
+{
+ const struct integr_ind *a = av;
+ const struct integr_ind *b = bv;
+
+ return a->res > b->res;
+}
+
+
+static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell,
+ int *np)
+{
+ struct integr_ind *il;
+ Reflection *refl;
+ RefListIterator *iter;
+ int i, n;
+
+ n = num_reflections(list);
+ *np = 0; /* For now */
+
+ if ( n == 0 ) return NULL;
+
+ il = calloc(n, sizeof(struct integr_ind));
+ if ( il == NULL ) return NULL;
+
+ i = 0;
+ for ( refl = first_refl(list, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ signed int h, k, l;
+ double res;
+
+ if ( get_redundancy(refl) == 0 ) continue;
+
+ get_indices(refl, &h, &k, &l);
+ res = resolution(cell, h, k, l);
+
+ il[i].res = res;
+ il[i].refl = refl;
+
+ i++;
+ assert(i <= n);
+ }
+
+ qsort(il, n, sizeof(struct integr_ind), compare_resolution);
+
+ *np = n;
+ return il;
+}
+
+
+static void check_eigen(gsl_vector *e_val)
+{
+ int i;
+ double vmax, vmin;
+ const int n = e_val->size;
+ const double max_condition = 1e6;
+ const int verbose = 0;
+
+ if ( verbose ) STATUS("Eigenvalues:\n");
+ vmin = +INFINITY;
+ vmax = 0.0;
+ for ( i=0; i<n; i++ ) {
+ double val = gsl_vector_get(e_val, i);
+ if ( verbose ) STATUS("%i: %e\n", i, val);
+ if ( val > vmax ) vmax = val;
+ if ( val < vmin ) vmin = val;
+ }
+
+ for ( i=0; i<n; i++ ) {
+ double val = gsl_vector_get(e_val, i);
+ if ( val < vmax/max_condition ) {
+ gsl_vector_set(e_val, i, 0.0);
+ }
+ }
+
+ vmin = +INFINITY;
+ vmax = 0.0;
+ for ( i=0; i<n; i++ ) {
+ double val = gsl_vector_get(e_val, i);
+ if ( val == 0.0 ) continue;
+ if ( val > vmax ) vmax = val;
+ if ( val < vmin ) vmin = val;
+ }
+ if ( verbose ) {
+ STATUS("Condition number: %e / %e = %5.2f\n",
+ vmax, vmin, vmax/vmin);
+ }
+}
+
+
+static gsl_vector *solve_svd(gsl_vector *v, gsl_matrix *M)
+{
+ gsl_matrix *s_vec;
+ gsl_vector *s_val;
+ int err, n;
+ gsl_vector *shifts;
+
+ n = v->size;
+ if ( v->size != M->size1 ) return NULL;
+ if ( v->size != M->size2 ) return NULL;
+
+ s_val = gsl_vector_calloc(n);
+ s_vec = gsl_matrix_calloc(n, n);
+
+ err = gsl_linalg_SV_decomp_jacobi(M, s_vec, s_val);
+ if ( err ) {
+ ERROR("SVD failed: %s\n", gsl_strerror(err));
+ gsl_matrix_free(s_vec);
+ gsl_vector_free(s_val);
+ return NULL;
+ }
+ /* "M" is now "U" */
+
+ check_eigen(s_val);
+
+ shifts = gsl_vector_calloc(n);
+ err = gsl_linalg_SV_solve(M, s_vec, s_val, v, shifts);
+ if ( err ) {
+ ERROR("Matrix solution failed: %s\n", gsl_strerror(err));
+ gsl_matrix_free(s_vec);
+ gsl_vector_free(s_val);
+ gsl_vector_free(shifts);
+ return NULL;
+ }
+
+ gsl_matrix_free(s_vec);
+ gsl_vector_free(s_val);
+
+ return shifts;
+}
+
+
+struct intcontext
+{
+ int halfw;
+ int w;
+ struct image *image;
+ gsl_matrix *bgm;
+};
+
+
+static void addm(gsl_matrix *m, int i, int j, double val)
+{
+ double v = gsl_matrix_get(m, i, j);
+ gsl_matrix_set(m, i, j, v+val);
+}
+
+
+static void addv(gsl_vector *v, int i, double val)
+{
+ double k = gsl_vector_get(v, i);
+ gsl_vector_set(v, i, k+val);
+}
+
+
+static double boxi(struct intcontext *ic,
+ int fid_fs, int fid_ss, int p, int q)
+{
+ int fs, ss;
+
+ fs = fid_fs + p;
+ ss = fid_ss + q;
+
+ /* FIXME: Wrong panel? */
+ return ic->image->data[fs + ic->image->width*ss];
+}
+
+
+static void fit_bg(struct intcontext *ic,
+ int fid_fs, int fid_ss,
+ double *pa, double *pb, double *pc)
+{
+ int p, q;
+ gsl_vector *v;
+ gsl_vector *ans;
+
+ v = gsl_vector_calloc(3);
+
+ for ( p=0; p<ic->w; p++ ) {
+ for ( q=0; q<ic->w; q++ ) {
+ double bi;
+ bi = boxi(ic, fid_fs, fid_ss, p, q);
+
+ addv(v, 0, bi*p);
+ addv(v, 1, bi*q);
+ addv(v, 2, bi);
+ }
+ }
+
+ ans = solve_svd(v, ic->bgm);
+ gsl_vector_free(v);
+
+ *pa = gsl_vector_get(ans, 0);
+ *pb = gsl_vector_get(ans, 1);
+ *pc = gsl_vector_get(ans, 2);
+
+ gsl_vector_free(ans);
+}
+
+
+static void init_intcontext(struct intcontext *ic)
+{
+ int p, q;
+
+ ic->w = 2*ic->halfw + 1;
+
+ ic->bgm = gsl_matrix_calloc(3, 3);
+ if ( ic->bgm == NULL ) {
+ ERROR("Failed to initialise matrix.\n");
+ return;
+ }
+
+ for ( p=0; p<ic->w; p++ ) {
+ for ( q=0; q<ic->w; q++ ) {
+ addm(ic->bgm, 0, 0, p*p);
+ addm(ic->bgm, 0, 1, p*q);
+ addm(ic->bgm, 0, 2, p);
+ addm(ic->bgm, 1, 0, p*q);
+ addm(ic->bgm, 1, 1, q*q);
+ addm(ic->bgm, 1, 2, q);
+ addm(ic->bgm, 2, 0, p);
+ addm(ic->bgm, 2, 1, q);
+ addm(ic->bgm, 2, 2, 1);
+ }
+ }
+}
+
+
+static void measure_all_intensities(RefList *list, struct image *image)
+{
+ Reflection *refl;
+ RefListIterator *iter;
+ struct intcontext ic;
+
+ ic.halfw = 4;
+ ic.image = image;
+ init_intcontext(&ic);
+
+ for ( refl = first_refl(list, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ double pfs, pss;
+ int fid_fs, fid_ss;
+ double a, b, c;
+
+ get_detector_pos(refl, &pfs, &pss);
+ fid_fs = lrint(pfs);
+ fid_ss = lrint(pss);
+ fit_bg(&ic, fid_fs, fid_ss, &a, &b, &c);
+
+ //set_intensity(refl, intensity);
+ }
+}
+
+
+static void estimate_mosaicity(Crystal *cr, struct image *image)
+{
+ int msteps = 50;
+ int i;
+ const double mest = crystal_get_mosaicity(cr);
+ const double mmax = 2.0 * mest;
+ RefList *list;
+
+ STATUS("Initial estimate: m = %f\n", mest);
+
+ crystal_set_mosaicity(cr, mmax);
+ list = find_intersections(image, cr);
+ crystal_set_reflections(cr, list);
+ measure_all_intensities(list, image);
+
+ for ( i=1; i<=msteps; i++ ) {
+
+ /* "m" varies from just over zero up to 2x the given estimate */
+ Reflection *refl;
+ RefListIterator *iter;
+ const double m = mmax*((double)i/msteps);
+ int n_gained = 0;
+ int n_lost = 0;
+ double i_gained = 0.0;
+ double i_lost = 0.0;
+
+ crystal_set_mosaicity(cr, m);
+ update_partialities(cr, PMODEL_SPHERE);
+
+ for ( refl = first_refl(list, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ if ( get_redundancy(refl) == 0 ) {
+ if ( get_temp1(refl) > 0.0 ) {
+ i_lost += get_intensity(refl);
+ n_lost++;
+ }
+ set_temp1(refl, -1.0);
+ } else if ( get_temp1(refl) < 0.0 ) {
+ i_gained += get_intensity(refl);
+ n_gained++;
+ set_temp1(refl, 1.0);
+ }
+ }
+
+ if ( i > 1 ) {
+ STATUS("%.2e %10.2f %4i %10.2f %4i %10.2f\n", m,
+ i_gained, n_gained, i_lost, n_lost,
+ i_gained - i_lost);
+ }
+
+ }
+}
+
+
+static void estimate_resolution(RefList *reflections, Crystal *cr,
+ struct image *image)
+{
+ struct integr_ind *il;
+ int n, i;
+ int score = 1000; /* FIXME */
+ int cutoff = 0;
+ double limit = 0.0;
+
+ if ( num_reflections(reflections) == 0 ) return;
+
+ il = sort_reflections(reflections, crystal_get_cell(cr), &n);
+ if ( il == NULL ) {
+ ERROR("Couldn't sort reflections\n");
+ return;
+ }
+
+ for ( i=0; i<n; i++ ) {
+
+ double intensity, sigma, snr;
+ Reflection *refl;
+
+ refl = il[i].refl;
+ intensity = get_intensity(refl);
+ sigma = get_esd_intensity(refl);
+
+ /* I/sigma(I) cutoff
+ * Rejects reflections below --min-integration-snr, or if the
+ * SNR is clearly silly. Silly indicates that the intensity
+ * was zero. */
+ snr = fabs(intensity)/sigma;
+
+ /* Record intensity and set redundancy to 1 on success */
+ if ( !cutoff ) {
+ set_redundancy(refl, 1);
+ } else {
+ set_redundancy(refl, 0);
+ }
+
+ if ( snr > 3.0 ) {
+ score++;
+ } else {
+ score--;
+ }
+
+ //STATUS("%5.2f A, %5.2f, %i\n", 1e10/il[i].res, snr, score);
+ if ( score == 0 ) {
+ limit = il[i].res;
+ cutoff = 1;
+ }
+
+ }
+
+ crystal_set_resolution_limit(cr, limit);
+
+ free(il);
+}
+
+
+static void integrate_refine(Crystal *cr, struct image *image, int use_closer,
+ double min_snr,
+ double ir_inn, double ir_mid, double ir_out,
+ int integrate_saturated, int **bgMasks)
+{
+ RefList *reflections;
+
+ /* Create initial list of reflections with nominal parameters */
+ reflections = find_intersections(image, cr);
+ measure_all_intensities(reflections, image);
+
+ /* Find resolution limit of pattern using this list */
+ estimate_resolution(reflections, cr, image);
+
+ reflist_free(reflections);
+
+ STATUS("Initial resolution estimate = %.2f nm^-1 or %.2f A\n",
+ crystal_get_resolution_limit(cr)/1e9,
+ 1e9 / crystal_get_resolution_limit(cr));
+
+ /* Estimate the mosaicity of the crystal using this resolution limit */
+ estimate_mosaicity(cr, image);
+
+ /* Create new list of reflections with refined mosaicity */
+ reflections = find_intersections(image, cr);
+ measure_all_intensities(reflections, image);
+
+ estimate_resolution(reflections, cr, image);
+}
+
+
+static void integrate_rings(Crystal *cr, struct image *image, int use_closer,
+ double min_snr,
+ double ir_inn, double ir_mid, double ir_out,
+ int integrate_saturated, int **bgMasks)
+{
+ RefList *list;
+ Reflection *refl;
+ RefListIterator *iter;
+ UnitCell *cell;
+ int n_saturated = 0;
+ double limit = 0.0;
+
+ list = find_intersections(image, cr);
+ if ( list == NULL ) return;
+
+ if ( num_reflections(list) == 0 ) return;
+
+ cell = crystal_get_cell(cr);
+
+ for ( refl = first_refl(list, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ double fs, ss, intensity;
+ double d;
+ int idx;
+ double sigma, snr;
+ double pfs, pss;
+ int r;
+ signed int h, k, l;
+ struct panel *p;
+ int pnum, j, found;
+ int saturated;
+ double one_over_d;
+
+ get_detector_pos(refl, &pfs, &pss);
+ get_indices(refl, &h, &k, &l);
+
+ /* 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;
+ }
+
+ /* FIXME: Horrible hardcoded value */
+ if ( (f != NULL) && (d < 10.0) ) {
+
+ double exe;
+
+ exe = get_excitation_error(refl);
+
+ pfs = f->fs;
+ pss = f->ss;
+
+ set_detector_pos(refl, exe, pfs, pss);
+
+ }
+
+ }
+
+ p = find_panel(image->det, pfs, pss);
+ if ( p == NULL ) continue; /* Next peak */
+ found = 0;
+ for ( j=0; j<image->det->n_panels; j++ ) {
+ if ( &image->det->panels[j] == p ) {
+ pnum = j;
+ found = 1;
+ break;
+ }
+ }
+ if ( !found ) {
+ ERROR("Couldn't find panel %p in list.\n", p);
+ return;
+ }
+
+ r = integrate_peak(image, pfs, pss, &fs, &ss,
+ &intensity, &sigma, ir_inn, ir_mid, ir_out,
+ bgMasks[pnum], &saturated);
+
+ if ( !r && saturated ) {
+ n_saturated++;
+ if ( !integrate_saturated ) r = 1;
+ }
+
+ /* I/sigma(I) cutoff
+ * Rejects reflections below --min-integration-snr, or if the
+ * SNR is clearly silly. Silly indicates that the intensity
+ * was zero. */
+ snr = fabs(intensity)/sigma;
+ if ( !r && (isnan(snr) || (snr < min_snr)) ) {
+ r = 1;
+ }
+
+ /* Record intensity and set redundancy to 1 on success */
+ if ( !r ) {
+ set_intensity(refl, intensity);
+ set_esd_intensity(refl, sigma);
+ set_redundancy(refl, 1);
+ } else {
+ set_redundancy(refl, 0);
+ }
+
+ one_over_d = resolution(cell, h, k, l);
+ if ( one_over_d > limit ) limit = one_over_d;
+
+ }
+
+ crystal_set_num_saturated_reflections(cr, n_saturated);
+ crystal_set_resolution_limit(cr, limit);
+ crystal_set_reflections(cr, list);
+}
+
+
+void integrate_all(struct image *image, IntegrationMethod meth,
+ int use_closer, double min_snr,
+ double ir_inn, double ir_mid, double ir_out,
+ int integrate_saturated)
+{
+ int i;
+ int **bgMasks;
+
+ /* Make background masks for all panels */
+ bgMasks = calloc(image->det->n_panels, sizeof(int *));
+ if ( bgMasks == NULL ) {
+ ERROR("Couldn't create list of background masks.\n");
+ return;
+ }
+ for ( i=0; i<image->det->n_panels; i++ ) {
+ int *mask;
+ mask = make_BgMask(image, &image->det->panels[i], ir_inn);
+ if ( mask == NULL ) {
+ ERROR("Couldn't create background mask.\n");
+ return;
+ }
+ bgMasks[i] = mask;
+ }
+
+ for ( i=0; i<image->n_crystals; i++ ) {
+
+ switch ( meth & INTEGRATION_METHOD_MASK ) {
+
+ case INTEGRATION_NONE :
+ return;
+
+ case INTEGRATION_RINGS :
+ integrate_rings(image->crystals[i], image, use_closer,
+ min_snr, ir_inn, ir_mid, ir_out,
+ integrate_saturated, bgMasks);
+ return;
+
+ case INTEGRATION_REFINE :
+ integrate_refine(image->crystals[i], image, use_closer,
+ min_snr, ir_inn, ir_mid, ir_out,
+ integrate_saturated, bgMasks);
+ return;
+
+ default :
+ ERROR("Unrecognised integration method %i\n", meth);
+ return;
+
+ }
+
+ }
+
+ for ( i=0; i<image->det->n_panels; i++ ) {
+ free(bgMasks[i]);
+ }
+ free(bgMasks);
+}
+
+
+IntegrationMethod integration_method(const char *str, int *err)
+{
+ int n, i;
+ char **methods;
+ IntegrationMethod meth = INTEGRATION_NONE;
+
+ if ( err != NULL ) *err = 0;
+ n = assplode(str, ",-", &methods, ASSPLODE_NONE);
+
+ for ( i=0; i<n; i++ ) {
+
+ if ( strcmp(methods[i], "rings") == 0) {
+ meth = INTEGRATION_DEFAULTS_RINGS;
+
+ } else if ( strcmp(methods[i], "refine") == 0) {
+ meth = INTEGRATION_DEFAULTS_REFINE;
+
+ } else if ( strcmp(methods[i], "none") == 0) {
+ return INTEGRATION_NONE;
+
+ } else {
+ ERROR("Bad integration method: '%s'\n", str);
+ if ( err != NULL ) *err = 1;
+ return INTEGRATION_NONE;
+ }
+
+ free(methods[i]);
+
+ }
+ free(methods);
+
+ return meth;
+
+}
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
new file mode 100644
index 00000000..12e47ff5
--- /dev/null
+++ b/libcrystfel/src/integration.h
@@ -0,0 +1,75 @@
+/*
+ * integration.h
+ *
+ * Integration of intensities
+ *
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2010-2013 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef INTEGRATION_H
+#define INTEGRATION_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#define INTEGRATION_DEFAULTS_RINGS (INTEGRATION_RINGS | INTEGRATION_SATURATED)
+#define INTEGRATION_DEFAULTS_REFINE (INTEGRATION_REFINE | INTEGRATION_SATURATED)
+
+/**
+ * IntegrationMethod:
+ * @INTEGRATION_NONE: No integration at all
+ * @INTEGRATION_RINGS: Predict reflections and integrate them all
+ * @INTEGRATION_REFINE: As @INTEGRATION_RINGS, but
+ *
+ * @INTEGRATION_SATURATED: Integrate saturated reflections
+ *
+ * An enumeration of all the available integration methods.
+ **/
+typedef enum {
+
+ INTEGRATION_NONE = 0,
+
+ /* The core integration methods themselves */
+ INTEGRATION_RINGS = 1,
+ INTEGRATION_REFINE = 2,
+
+ /* Bits at the top of the IntegrationMethod are flags which modify the
+ * behaviour of the integration. */
+ INTEGRATION_SATURATED = 256,
+ INTEGRATION_CLOSER = 512,
+
+} IntegrationMethod;
+
+/* This defines the bits in "IntegrationMethod" which are used to represent the
+ * core of the integration method */
+#define INTEGRATION_METHOD_MASK (0xff)
+
+extern IntegrationMethod integration_method(const char *t, int *err);
+
+extern void integrate_all(struct image *image, IntegrationMethod meth,
+ int use_closer, double min_snr,
+ double ir_inn, double ir_mid, double ir_out,
+ int integrate_saturated);
+
+#endif /* INTEGRATION_H */
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 4b8a8ee8..05c564ba 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -52,6 +52,7 @@
#include "reflist-utils.h"
#include "beam-parameters.h"
#include "cell-utils.h"
+#include "geometry.h"
/* Degree of polarisation of X-ray beam */
@@ -200,7 +201,7 @@ static void add_crystal_to_mask(struct image *image, struct panel *p,
/* cfs, css relative to panel origin */
-static int *make_BgMask(struct image *image, struct panel *p, double ir_inn)
+int *make_BgMask(struct image *image, struct panel *p, double ir_inn)
{
int *mask;
int w, h;
@@ -224,11 +225,11 @@ static int *make_BgMask(struct image *image, struct panel *p, double ir_inn)
/* Returns non-zero if peak has been vetoed.
* i.e. don't use result if return value is not zero. */
-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 *bgPkMask, int *saturated)
+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 *bgPkMask, int *saturated)
{
signed int dfs, dss;
double lim_sq, out_lim_sq, mid_lim_sq;
@@ -653,233 +654,6 @@ int peak_sanity_check(struct image *image, Crystal **crystals, int n_cryst)
}
-struct integr_ind
-{
- double res;
- Reflection *refl;
-};
-
-
-static int compare_resolution(const void *av, const void *bv)
-{
- const struct integr_ind *a = av;
- const struct integr_ind *b = bv;
-
- return a->res > b->res;
-}
-
-
-static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell,
- int *np)
-{
- struct integr_ind *il;
- Reflection *refl;
- RefListIterator *iter;
- int i, n;
-
- n = num_reflections(list);
- *np = 0; /* For now */
-
- if ( n == 0 ) return NULL;
-
- il = calloc(n, sizeof(struct integr_ind));
- if ( il == NULL ) return NULL;
-
- i = 0;
- for ( refl = first_refl(list, &iter);
- refl != NULL;
- refl = next_refl(refl, iter) )
- {
- signed int h, k, l;
- double res;
-
- get_indices(refl, &h, &k, &l);
- res = resolution(cell, h, k, l);
-
- il[i].res = res;
- il[i].refl = refl;
-
- i++;
- assert(i <= n);
- }
-
- qsort(il, n, sizeof(struct integr_ind), compare_resolution);
-
- *np = n;
- return il;
-}
-
-
-static void integrate_crystal(Crystal *cr, struct image *image, int use_closer,
- int bgsub, double min_snr,
- double ir_inn, double ir_mid, double ir_out,
- int integrate_saturated, int **bgMasks,
- int res_cutoff)
-{
- RefList *reflections;
- struct integr_ind *il;
- int n, i;
- double av = 0.0;
- int first = 1;
- int n_saturated = 0;
-
- reflections = crystal_get_reflections(cr);
-
- if ( num_reflections(reflections) == 0 ) return;
-
- il = sort_reflections(reflections, crystal_get_cell(cr), &n);
- if ( il == NULL ) {
- ERROR("Couldn't sort reflections\n");
- return;
- }
-
- for ( i=0; i<n; i++ ) {
-
- double fs, ss, intensity;
- double d;
- int idx;
- double sigma, snr;
- double pfs, pss;
- int r;
- Reflection *refl;
- signed int h, k, l;
- struct panel *p;
- int pnum, j, found;
- int saturated;
-
- refl = il[i].refl;
-
- get_detector_pos(refl, &pfs, &pss);
- get_indices(refl, &h, &k, &l);
-
- /* 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;
- }
-
- /* FIXME: Horrible hardcoded value */
- if ( (f != NULL) && (d < 10.0) ) {
-
- double exe;
-
- exe = get_excitation_error(refl);
-
- pfs = f->fs;
- pss = f->ss;
-
- set_detector_pos(refl, exe, pfs, pss);
-
- }
-
- }
-
- p = find_panel(image->det, pfs, pss);
- if ( p == NULL ) continue; /* Next peak */
- found = 0;
- for ( j=0; j<image->det->n_panels; j++ ) {
- if ( &image->det->panels[j] == p ) {
- pnum = j;
- found = 1;
- break;
- }
- }
- if ( !found ) {
- ERROR("Couldn't find panel %p in list.\n", p);
- return;
- }
-
- r = integrate_peak(image, pfs, pss, &fs, &ss,
- &intensity, &sigma, ir_inn, ir_mid, ir_out,
- bgMasks[pnum], &saturated);
-
- if ( !r && saturated ) {
- n_saturated++;
- if ( !integrate_saturated ) r = 1;
- }
-
- /* I/sigma(I) cutoff
- * Rejects reflections below --min-integration-snr, or if the
- * SNR is clearly silly. Silly indicates that the intensity
- * was zero. */
- snr = fabs(intensity)/sigma;
- if ( isnan(snr) || (snr < min_snr) ) {
- r = 1;
- }
-
- /* Record intensity and set redundancy to 1 on success */
- if ( r == 0 ) {
- set_intensity(refl, intensity);
- set_esd_intensity(refl, sigma);
- set_redundancy(refl, 1);
- } else {
- set_redundancy(refl, 0);
- }
-
- if ( snr > 1.0 ) {
- if ( first ) {
- av = snr;
- first = 0;
- } else {
- av = av + 0.1*(snr - av);
- }
- //STATUS("%5.2f A, %5.2f, av %5.2f\n",
- // 1e10/il[i].res, snr, av);
- if ( res_cutoff && (av < 1.0) ) break;
- }
- }
-
- crystal_set_num_saturated_reflections(cr, n_saturated);
- crystal_set_resolution_limit(cr, 0.0);
-
- free(il);
-}
-
-
-/* Integrate the list of predicted reflections in "image" */
-void integrate_reflections(struct image *image, int use_closer, int bgsub,
- double min_snr,
- double ir_inn, double ir_mid, double ir_out,
- int integrate_saturated, int res_cutoff)
-{
- int i;
- int **bgMasks;
-
- /* Make background masks for all panels */
- bgMasks = calloc(image->det->n_panels, sizeof(int *));
- if ( bgMasks == NULL ) {
- ERROR("Couldn't create list of background masks.\n");
- return;
- }
- for ( i=0; i<image->det->n_panels; i++ ) {
- int *mask;
- mask = make_BgMask(image, &image->det->panels[i], ir_inn);
- if ( mask == NULL ) {
- ERROR("Couldn't create background mask.\n");
- return;
- }
- bgMasks[i] = mask;
- }
-
- for ( i=0; i<image->n_crystals; i++ ) {
- integrate_crystal(image->crystals[i], image, use_closer,
- bgsub, min_snr, ir_inn, ir_mid, ir_out,
- integrate_saturated, bgMasks, res_cutoff);
- }
-
- for ( i=0; i<image->det->n_panels; i++ ) {
- free(bgMasks[i]);
- }
- free(bgMasks);
-}
-
-
void validate_peaks(struct image *image, double min_snr,
int ir_inn, int ir_mid, int ir_out, int use_saturated)
{
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index f788bae5..b94ebee5 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -37,16 +37,13 @@
#include "reflist.h"
+extern int *make_BgMask(struct image *image, struct panel *p, double ir_inn);
+
extern void search_peaks(struct image *image, float threshold,
float min_gradient, float min_snr,
double ir_inn, double ir_mid, double ir_out,
int use_saturated);
-extern void integrate_reflections(struct image *image,
- int use_closer, int bgsub, double min_snr,
- double ir_inn, double ir_mid, double ir_out,
- int integrate_saturated, int res_cutoff);
-
extern int peak_sanity_check(struct image *image, Crystal **crystals,
int n_cryst);
@@ -54,4 +51,10 @@ extern void validate_peaks(struct image *image, double min_snr,
int ir_inn, int ir_mid, int ir_out,
int use_saturated);
+extern 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 *bgPkMask, int *saturated);
+
#endif /* PEAKS_H */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 208c0ed0..7d26c15d 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -66,6 +66,7 @@
#include "stream.h"
#include "reflist-utils.h"
#include "cell-utils.h"
+#include "integration.h"
#include "im-sandbox.h"
@@ -100,6 +101,7 @@ static void show_help(const char *s)
" hdf5 : Get from a table in HDF5 file.\n"
" --hdf5-peaks=<p> Find peaks table in HDF5 file here.\n"
" Default: /processing/hitfinder/peakinfo\n"
+" --integration=<meth> Perform final pattern integration using <meth>.\n"
"\n\n"
"For more control over the process, you might need:\n\n"
" --tolerance=<tol> Set the tolerances for cell comparison.\n"
@@ -139,17 +141,12 @@ static void show_help(const char *s)
" --no-check-prefix Don't attempt to correct the --prefix.\n"
" --closer-peak Don't integrate from the location of a nearby peak\n"
" instead of the predicted spot. Don't use.\n"
-" --no-bg-sub Don't subtract local background estimates from\n"
-" integrated intensities.\n"
" --use-saturated During the initial peak search, don't reject\n"
" peaks which contain pixels above max_adu.\n"
" --integrate-saturated During the final integration stage, don't reject\n"
" peaks which contain pixels above max_adu.\n"
" --no-revalidate Don't re-integrate and check HDF5 peaks for\n"
" validity.\n"
-" --integrate-found Skip the spot prediction step, and just integrate\n"
-" the intensities of the spots found by the initial\n"
-" peak search.\n"
" --no-peaks-in-stream Do not record peak search results in the stream.\n"
" --no-refls-in-stream Do not record integrated reflections in the stream.\n"
);
@@ -179,6 +176,7 @@ int main(int argc, char *argv[])
char *use_this_one_instead;
struct index_args iargs;
char *intrad = NULL;
+ char *int_str = NULL;
/* Defaults */
iargs.cell = NULL;
@@ -186,7 +184,6 @@ int main(int argc, char *argv[])
iargs.median_filter = 0;
iargs.satcorr = 1;
iargs.closer = 0;
- iargs.bgsub = 1;
iargs.tols[0] = 5.0;
iargs.tols[1] = 5.0;
iargs.tols[2] = 5.0;
@@ -207,10 +204,8 @@ int main(int argc, char *argv[])
iargs.use_saturated = 0;
iargs.integrate_saturated = 0;
iargs.no_revalidate = 0;
- iargs.integrate_found = 0;
iargs.stream_peaks = 1;
iargs.stream_refls = 1;
- iargs.res_cutoff = 0;
iargs.copyme = new_copy_hdf5_field_list();
if ( iargs.copyme == NULL ) {
ERROR("Couldn't allocate HDF5 field list.\n");
@@ -218,6 +213,7 @@ int main(int argc, char *argv[])
}
iargs.indm = NULL; /* No default */
iargs.ipriv = NULL; /* No default */
+ iargs.int_meth = integration_method("rings", NULL);
/* Long options */
const struct option longopts[] = {
@@ -242,15 +238,11 @@ int main(int argc, char *argv[])
{"no-closer-peak", 0, &iargs.closer, 0},
{"closer-peak", 0, &iargs.closer, 1},
{"basename", 0, &config_basename, 1},
- {"bg-sub", 0, &iargs.bgsub, 1},
- {"no-bg-sub", 0, &iargs.bgsub, 0},
{"no-peaks-in-stream", 0, &iargs.stream_peaks, 0},
{"no-refls-in-stream", 0, &iargs.stream_refls, 0},
- {"res-cutoff", 0, &iargs.res_cutoff, 1},
{"integrate-saturated",0, &iargs.integrate_saturated,1},
{"use-saturated", 0, &iargs.use_saturated, 1},
{"no-revalidate", 0, &iargs.no_revalidate, 1},
- {"integrate-found", 0, &iargs.integrate_found, 1},
/* Long-only options with arguments */
{"peaks", 1, NULL, 2},
@@ -267,6 +259,7 @@ int main(int argc, char *argv[])
{"tolerance", 1, NULL, 13},
{"int-radius", 1, NULL, 14},
{"median-filter", 1, NULL, 15},
+ {"integration", 1, NULL, 16},
{0, 0, NULL, 0}
};
@@ -391,6 +384,10 @@ int main(int argc, char *argv[])
iargs.median_filter = atoi(optarg);
break;
+ case 16 :
+ int_str = strdup(optarg);
+ break;
+
case 0 :
break;
@@ -465,6 +462,18 @@ int main(int argc, char *argv[])
free(indm_str);
}
+ if ( int_str != NULL ) {
+
+ int err;
+
+ iargs.int_meth = integration_method(int_str, &err);
+ if ( err ) {
+ ERROR("Invalid integration method '%s'\n", int_str);
+ return 1;
+ }
+ free(int_str);
+ }
+
if ( toler != NULL ) {
int ttt;
ttt = sscanf(toler, "%f,%f,%f,%f",
diff --git a/src/process_image.c b/src/process_image.c
index ef673c84..bf694623 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -46,6 +46,7 @@
#include "stream.h"
#include "reflist-utils.h"
#include "process_image.h"
+#include "integration.h"
void process_image(const struct index_args *iargs, struct pattern_args *pargs,
@@ -188,34 +189,21 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Integrate each crystal's diffraction spots */
for ( i=0; i<image.n_crystals; i++ ) {
- RefList *reflections;
-
/* Set default crystal parameter(s) */
crystal_set_profile_radius(image.crystals[i],
image.beam->profile_radius);
-
- if ( iargs->integrate_found ) {
- reflections = select_intersections(&image,
- image.crystals[i]);
- } else {
- reflections = find_intersections(&image,
- image.crystals[i]);
- }
-
- crystal_set_reflections(image.crystals[i], reflections);
+ crystal_set_mosaicity(image.crystals[i], 2e-3); /* radians */
+ crystal_set_image(image.crystals[i], &image);
}
/* Integrate all the crystals at once - need all the crystals so that
* overlaps can be detected. */
- integrate_reflections(&image, iargs->closer,
- iargs->bgsub,
- iargs->min_int_snr,
- iargs->ir_inn,
- iargs->ir_mid,
- iargs->ir_out,
- iargs->integrate_saturated,
- iargs->res_cutoff);
+ integrate_all(&image, iargs->int_meth,
+ iargs->closer,
+ iargs->min_int_snr,
+ iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
+ iargs->integrate_saturated);
write_chunk(st, &image, hdfile,
iargs->stream_peaks, iargs->stream_refls);
diff --git a/src/process_image.h b/src/process_image.h
index 5fe11e33..03041562 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -34,6 +34,9 @@
#endif
+#include "integration.h"
+
+
enum {
PEAK_ZAEF,
PEAK_HDF5,
@@ -49,7 +52,6 @@ struct index_args
int median_filter;
int satcorr;
int closer;
- int bgsub;
float threshold;
float min_gradient;
float min_snr;
@@ -69,10 +71,9 @@ struct index_args
int integrate_saturated;
int use_saturated;
int no_revalidate;
- int integrate_found;
int stream_peaks;
int stream_refls;
- int res_cutoff;
+ IntegrationMethod int_meth;
};