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authorThomas White <taw@physics.org>2013-06-02 13:53:28 -0700
committerThomas White <taw@physics.org>2013-06-02 13:53:28 -0700
commit8a44164cfd5013687a0eb5cb10dc39c44db399c0 (patch)
tree5a6c35a3d3e93d5d7d19c83e29e34ff61c31c95f /libcrystfel/src
parentbf06abfb01d009d604c9f734e4d77ad0bf9b2eba (diff)
Refine rigid group positions and orientations
Diffstat (limited to 'libcrystfel/src')
-rw-r--r--libcrystfel/src/detector.c13
-rw-r--r--libcrystfel/src/detector.h11
-rw-r--r--libcrystfel/src/integration.c139
-rw-r--r--libcrystfel/src/stream.c20
4 files changed, 175 insertions, 8 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index a30d3ccf..2fdd63f1 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -1168,6 +1168,19 @@ struct detector *simple_geometry(const struct image *image)
}
+void twod_mapping(double fs, double ss, double *px, double *py,
+ struct panel *p)
+{
+ double xs, ys;
+
+ xs = fs*p->fsx + ss*p->ssx;
+ ys = fs*p->fsy + ss*p->ssy;
+
+ *px = xs + p->cnx;
+ *py = ys + p->cny;
+}
+
+
int reverse_2d_mapping(double x, double y, double *pfs, double *pss,
struct detector *det)
{
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index b6a90fbf..8ff8db2f 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -52,6 +52,14 @@ struct rigid_group
char *name;
struct panel **panels;
int n_panels;
+
+ /* Updates to panel position calculated during integration */
+ double d_fsx;
+ double d_ssx;
+ double d_cnx;
+ double d_fsy;
+ double d_ssy;
+ double d_cny;
};
@@ -164,6 +172,9 @@ extern void fill_in_values(struct detector *det, struct hdfile *f);
extern struct detector *copy_geom(const struct detector *in);
+extern void twod_mapping(double fs, double ss, double *px, double *py,
+ struct panel *p);
+
extern int reverse_2d_mapping(double x, double y, double *pfs, double *pss,
struct detector *det);
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 1a2c0585..c264f671 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -93,16 +93,21 @@ static void check_eigen(gsl_vector *e_val)
}
-static gsl_vector *solve_svd(gsl_vector *v, gsl_matrix *M)
+static gsl_vector *solve_svd(gsl_vector *v, gsl_matrix *Mp)
{
gsl_matrix *s_vec;
gsl_vector *s_val;
int err, n;
gsl_vector *shifts;
+ gsl_matrix *M;
n = v->size;
- if ( v->size != M->size1 ) return NULL;
- if ( v->size != M->size2 ) return NULL;
+ if ( v->size != Mp->size1 ) return NULL;
+ if ( v->size != Mp->size2 ) return NULL;
+
+ M = gsl_matrix_alloc(n, n);
+ if ( M == NULL ) return NULL;
+ gsl_matrix_memcpy(M, Mp);
s_val = gsl_vector_calloc(n);
s_vec = gsl_matrix_calloc(n, n);
@@ -130,6 +135,7 @@ static gsl_vector *solve_svd(gsl_vector *v, gsl_matrix *M)
gsl_matrix_free(s_vec);
gsl_vector_free(s_val);
+ gsl_matrix_free(M);
return shifts;
}
@@ -382,7 +388,6 @@ static void fit_bg(struct intcontext *ic, struct peak_box *bx)
int p, q;
gsl_vector *v;
gsl_vector *ans;
- gsl_matrix *M;
v = gsl_vector_calloc(3);
@@ -408,11 +413,8 @@ static void fit_bg(struct intcontext *ic, struct peak_box *bx)
show_matrix_eqn(ic->bgm, v, 3);
}
- M = gsl_matrix_alloc(3, 3);
- gsl_matrix_memcpy(M, ic->bgm);
- ans = solve_svd(v, M);
+ ans = solve_svd(v, ic->bgm);
gsl_vector_free(v);
- gsl_matrix_free(M);
bx->a = gsl_vector_get(ans, 0);
bx->b = gsl_vector_get(ans, 1);
@@ -1095,8 +1097,128 @@ static int suitable_reference(struct intcontext *ic, struct peak_box *bx)
}
+static void add_to_rg_matrix(struct intcontext *ic, struct panel *p,
+ gsl_matrix *M, gsl_vector *vx, gsl_vector *vy,
+ int *pn)
+{
+ int i;
+
+ for ( i=0; i<ic->n_boxes; i++ ) {
+
+ double x, y, w;
+ double fs, ss;
+ double offs_x, offs_y;
+
+ if ( ic->boxes[i].p != p ) continue;
+
+ fs = ic->boxes[i].cfs + ic->halfw;
+ ss = ic->boxes[i].css + ic->halfw;
+
+ twod_mapping(fs, ss, &x, &y, ic->boxes[i].p);
+
+ w = ic->boxes[i].intensity;
+
+ addm(M, 0, 0, w*fs*fs);
+ addm(M, 0, 1, w*fs*ss);
+ addm(M, 0, 2, w*fs);
+ addm(M, 1, 0, w*fs*ss);
+ addm(M, 1, 1, w*ss*ss);
+ addm(M, 1, 2, w*ss);
+ addm(M, 2, 0, w*fs);
+ addm(M, 2, 1, w*ss);
+ addm(M, 2, 2, w);
+
+ /* Offsets in lab coordinate system */
+ offs_x = p->fsx * ic->boxes[i].offs_fs
+ + p->ssx * ic->boxes[i].offs_ss;
+
+ offs_y = p->fsy * ic->boxes[i].offs_fs
+ + p->ssy * ic->boxes[i].offs_ss;
+
+ addv(vx, 0, w*offs_x*fs);
+ addv(vx, 1, w*offs_x*ss);
+ addv(vx, 2, w*offs_x);
+
+ addv(vy, 0, w*offs_y*fs);
+ addv(vy, 1, w*offs_y*ss);
+ addv(vy, 2, w*offs_y);
+
+ (*pn)++;
+ }
+}
+
+
static void refine_rigid_groups(struct intcontext *ic)
{
+ int i;
+
+ for ( i=0; i<ic->image->det->n_rigid_groups; i++ ) {
+
+ struct rigid_group *rg;
+ gsl_matrix *M;
+ gsl_vector *vx;
+ gsl_vector *vy;
+ gsl_vector *dq1;
+ gsl_vector *dq2;
+ int j;
+ int n;
+
+ M = gsl_matrix_calloc(3, 3);
+ if ( M == NULL ) {
+ ERROR("Failed to allocate matrix\n");
+ return;
+ }
+
+ vx = gsl_vector_calloc(3);
+ if ( vx == NULL ) {
+ ERROR("Failed to allocate vector\n");
+ return;
+ }
+
+ vy = gsl_vector_calloc(3);
+ if ( vy == NULL ) {
+ ERROR("Failed to allocate vector\n");
+ return;
+ }
+
+ rg = ic->image->det->rigid_groups[i];
+
+ n = 0;
+ for ( j=0; j<rg->n_panels; j++ ) {
+ add_to_rg_matrix(ic, rg->panels[j], M, vx, vy, &n);
+ }
+
+ if ( n > 10 ) {
+
+ dq1 = solve_svd(vx, M);
+ dq2 = solve_svd(vy, M);
+
+ rg->d_fsx = gsl_vector_get(dq1, 0);
+ rg->d_ssx = gsl_vector_get(dq1, 1);
+ rg->d_cnx = gsl_vector_get(dq1, 2);
+ rg->d_fsy = gsl_vector_get(dq2, 0);
+ rg->d_ssy = gsl_vector_get(dq2, 1);
+ rg->d_cny = gsl_vector_get(dq2, 2);
+
+ gsl_vector_free(dq1);
+ gsl_vector_free(dq2);
+
+ } else {
+
+ rg->d_fsx = 0.0;
+ rg->d_ssx = 0.0;
+ rg->d_cnx = 0.0;
+ rg->d_fsy = 0.0;
+ rg->d_ssy = 0.0;
+ rg->d_cny = 0.0;
+
+ }
+
+ gsl_vector_free(vx);
+ gsl_vector_free(vy);
+ gsl_matrix_free(M);
+
+ }
}
@@ -1639,6 +1761,7 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
integrate_box(&ic, bx, &intensity, &sigma);
/* Record intensity and set redundancy to 1 */
+ bx->intensity = intensity;
set_intensity(refl, intensity);
set_esd_intensity(refl, sigma);
set_redundancy(refl, 1);
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 91f644fa..8c12aa3b 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -222,6 +222,26 @@ void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
i->det->panels[j].name, i->det->panels[j].clen);
}
+ for ( j=0; j<i->det->n_rigid_groups; j++ ) {
+
+ struct rigid_group *rg = i->det->rigid_groups[j];
+
+ fprintf(st->fh, "rg_delta_%s_fsx = %f\n",
+ rg->name, rg->d_fsx);
+ fprintf(st->fh, "rg_delta_%s_ssx = %f\n",
+ rg->name, rg->d_ssx);
+ fprintf(st->fh, "rg_delta_%s_cnx = %f\n",
+ rg->name, rg->d_cnx);
+
+ fprintf(st->fh, "rg_delta_%s_fsy = %f\n",
+ rg->name, rg->d_fsx);
+ fprintf(st->fh, "rg_delta_%s_ssy = %f\n",
+ rg->name, rg->d_ssx);
+ fprintf(st->fh, "rg_delta_%s_cny = %f\n",
+ rg->name, rg->d_cnx);
+
+ }
+
}
copy_hdf5_fields(hdfile, i->copyme, st->fh);