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-rw-r--r--libcrystfel/src/geometry.c25
-rw-r--r--libcrystfel/src/integration.c37
-rw-r--r--libcrystfel/src/reflist.c18
-rw-r--r--libcrystfel/src/reflist.h6
-rw-r--r--tests/integration_check.c2
5 files changed, 39 insertions, 49 deletions
diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index 8f8a9672..a1b76a87 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -52,7 +52,7 @@
/** \file geometry.h */
static int locate_peak_on_panel(double x, double y, double z, double k,
- struct panel *p,
+ struct detgeom_panel *p,
double *pfs, double *pss)
{
double ctt, tta, phi;
@@ -85,7 +85,7 @@ static int locate_peak_on_panel(double x, double y, double z, double k,
gsl_matrix_set(M, 1, 0, p->cny);
gsl_matrix_set(M, 1, 1, p->fsy);
gsl_matrix_set(M, 1, 2, p->ssy);
- gsl_matrix_set(M, 2, 0, p->clen*p->res);
+ gsl_matrix_set(M, 2, 0, p->cnz);
gsl_matrix_set(M, 2, 1, p->fsz);
gsl_matrix_set(M, 2, 2, p->ssz);
@@ -113,7 +113,8 @@ static int locate_peak_on_panel(double x, double y, double z, double k,
}
static signed int locate_peak(double x, double y, double z, double k,
- struct detector *det, double *pfs, double *pss)
+ struct detgeom *det,
+ double *pfs, double *pss)
{
int i;
@@ -121,7 +122,7 @@ static signed int locate_peak(double x, double y, double z, double k,
for ( i=0; i<det->n_panels; i++ ) {
- struct panel *p;
+ struct detgeom_panel *p;
p = &det->panels[i];
@@ -379,29 +380,31 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
/* If we are updating a previous reflection, assume it stays
* on the same panel and calculate the new position even if it's
* fallen off the edge of the panel. */
- if ( (image->det != NULL) && (updateme != NULL) ) {
+ if ( (image->detgeom != NULL) && (updateme != NULL) ) {
double fs, ss;
+ assert(get_panel_number(updateme) <= image->detgeom->n_panels);
locate_peak_on_panel(xl, yl, zl, mean_kpred,
- get_panel(updateme), &fs, &ss);
+ &image->detgeom->panels[get_panel_number(updateme)],
+ &fs, &ss);
set_detector_pos(refl, fs, ss);
}
- /* Otherwise, calculate position if we have a detector structure, and
+ /* otherwise, calculate position if we have a detector structure, and
* if we don't then just make do with partiality calculation */
if ( (image->det != NULL) && (updateme == NULL) ) {
- double fs, ss; /* Position on detector */
- signed int p; /* Panel number */
+ double fs, ss; /* position on detector */
+ signed int p; /* panel number */
p = locate_peak(xl, yl, zl, mean_kpred,
- image->det, &fs, &ss);
+ image->detgeom, &fs, &ss);
if ( p == -1 ) {
reflection_free(refl);
return NULL;
}
set_detector_pos(refl, fs, ss);
- set_panel(refl, &image->det->panels[p]);
+ set_panel_number(refl, p);
}
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 3d8258c1..681aef02 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -52,6 +52,7 @@
#include "image.h"
#include "peaks.h"
#include "integration.h"
+#include "detgeom.h"
/** \file integration.h */
@@ -110,7 +111,7 @@ struct peak_box
enum boxmask_val *bm; /* Box mask */
int pn; /* Panel number */
- struct panel *p; /* The panel itself */
+ struct detgeom_panel *p; /* The panel itself */
/* Fitted background parameters */
double a;
@@ -273,9 +274,6 @@ static void show_peak_box(struct intcontext *ic, struct peak_box *bx,
get_indices(bx->refl, &h, &k, &l);
get_detector_pos(bx->refl, &fs, &ss);
- /* Convert coordinates to match arrangement of panels in HDF5 file */
- fs = fs + bx->p->orig_min_fs;
- ss = ss + bx->p->orig_min_ss;
printw("Indices %i %i %i\nPanel %s\nPosition fs = %.1f, ss = %.1f\n\n",
h, k, l, bx->p->name, fs, ss);
@@ -806,7 +804,7 @@ static int check_box(struct intcontext *ic, struct peak_box *bx, int *sat)
int fs, ss;
double hd, kd, ld;
signed int h, k, l;
- struct rvec dv;
+ double dv[3];
float lsat;
fs = bx->cfs + p;
@@ -864,10 +862,11 @@ static int check_box(struct intcontext *ic, struct peak_box *bx, int *sat)
/* Ignore if this pixel is closer to the next reciprocal lattice
* point */
- dv = get_q_for_panel(bx->p, fs, ss, NULL, ic->k);
- hd = dv.u * adx + dv.v * ady + dv.w * adz;
- kd = dv.u * bdx + dv.v * bdy + dv.w * bdz;
- ld = dv.u * cdx + dv.v * cdy + dv.w * cdz;
+ detgeom_transform_coords(bx->p, fs, ss,
+ 1.0/ic->k, dv);
+ hd = dv[0] * adx + dv[1] * ady + dv[2] * adz;
+ kd = dv[0] * bdx + dv[1] * bdy + dv[2] * bdz;
+ ld = dv[0] * cdx + dv[1] * cdy + dv[2] * cdz;
h = lrint(hd);
k = lrint(kd);
l = lrint(ld);
@@ -1273,7 +1272,6 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list)
double pfs, pss;
struct peak_box *bx;
int pn;
- struct panel *p;
int fid_fs, fid_ss; /* Center coordinates, rounded,
* in overall data block */
int cfs, css; /* Corner coordinates */
@@ -1283,12 +1281,7 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list)
set_redundancy(refl, 0);
get_detector_pos(refl, &pfs, &pss);
- p = get_panel(refl);
- pn = panel_number(ic->image->det, p);
- if ( pn == ic->image->det->n_panels ) {
- ERROR("Couldn't find panel %p\n", p);
- continue;
- }
+ pn = get_panel_number(refl);
/* Explicit truncation of digits after the decimal point.
* This is actually the correct thing to do here, not
@@ -1307,7 +1300,7 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list)
bx->refl = refl;
bx->cfs = cfs;
bx->css = css;
- bx->p = p;
+ bx->p = &ic->image->detgeom->panels[pn];
bx->pn = pn;
/* Which reference profile? */
@@ -1406,7 +1399,6 @@ static int integrate_rings_once(Reflection *refl, struct image *image,
double pfs, pss;
struct peak_box *bx;
int pn;
- struct panel *p;
int fid_fs, fid_ss; /* Center coordinates, rounded,
* in overall data block */
int cfs, css; /* Corner coordinates */
@@ -1419,12 +1411,7 @@ static int integrate_rings_once(Reflection *refl, struct image *image,
set_redundancy(refl, 0);
get_detector_pos(refl, &pfs, &pss);
- p = get_panel(refl);
- pn = panel_number(image->det, p);
- if ( pn == image->det->n_panels ) {
- ERROR("Couldn't find panel %p\n", p);
- return 1;
- }
+ pn = get_panel_number(refl);
/* Explicit truncation of digits after the decimal point.
* This is actually the correct thing to do here, not
@@ -1442,7 +1429,7 @@ static int integrate_rings_once(Reflection *refl, struct image *image,
bx->refl = refl;
bx->cfs = cfs;
bx->css = css;
- bx->p = p;
+ bx->p = &image->detgeom->panels[pn];
bx->pn = pn;
if ( ic->meth & INTEGRATION_CENTER ) {
diff --git a/libcrystfel/src/reflist.c b/libcrystfel/src/reflist.c
index 9cedfc86..df8f24fc 100644
--- a/libcrystfel/src/reflist.c
+++ b/libcrystfel/src/reflist.c
@@ -53,7 +53,7 @@ struct _refldata {
/* Location in image */
double fs;
double ss;
- struct panel *panel;
+ int panel_number;
/* Non-zero if this reflection can be used for scaling */
int scalable;
@@ -308,12 +308,13 @@ void get_detector_pos(const Reflection *refl, double *fs, double *ss)
/**
* \param refl: Reflection
*
- * \returns the panel which the reflection appears on
+ * \returns panel number (index in detgeom/DataTemplate structure)
+ * which the reflection appears on
*
**/
-struct panel *get_panel(const Reflection *refl)
+int get_panel_number(const Reflection *refl)
{
- return refl->data.panel;
+ return refl->data.panel_number;
}
@@ -589,14 +590,13 @@ void set_detector_pos(Reflection *refl, double fs, double ss)
/**
* \param refl: Reflection
- * \param p: Pointer to the panel structure on which the reflection appears
- *
- * Note that the pointer will be stored, not the contents of the structure.
+ * \param pn: Panel number (index in detgeom/DataTemplate structure) of
+ * the panel on which the reflection appears.
*
**/
-void set_panel(Reflection *refl, struct panel *p)
+void set_panel_number(Reflection *refl, int pn)
{
- refl->data.panel = p;
+ refl->data.panel_number = pn;
}
diff --git a/libcrystfel/src/reflist.h b/libcrystfel/src/reflist.h
index 3085a2aa..91f740a5 100644
--- a/libcrystfel/src/reflist.h
+++ b/libcrystfel/src/reflist.h
@@ -7,7 +7,7 @@
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2011-2018 Thomas White <taw@physics.org>
+ * 2011-2020 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -109,7 +109,7 @@ extern Reflection *next_found_refl(Reflection *refl);
/* Get */
extern void get_detector_pos(const Reflection *refl, double *fs, double *ss);
-extern struct panel *get_panel(const Reflection *refl);
+extern int get_panel_number(const Reflection *refl);
extern double get_partiality(const Reflection *refl);
extern double get_khalf(const Reflection *refl);
extern double get_kpred(const Reflection *refl);
@@ -134,7 +134,7 @@ extern struct reflection_contributions *get_contributions(const Reflection *refl
/* Set */
extern void copy_data(Reflection *to, const Reflection *from);
extern void set_detector_pos(Reflection *refl, double fs, double ss);
-extern void set_panel(Reflection *refl, struct panel *p);
+extern void set_panel_number(Reflection *refl, int pn);
extern void set_kpred(Reflection *refl, double kpred);
extern void set_khalf(Reflection *refl, double khalf);
extern void set_exerr(Reflection *refl, double exerr);
diff --git a/tests/integration_check.c b/tests/integration_check.c
index da808cce..50e99d65 100644
--- a/tests/integration_check.c
+++ b/tests/integration_check.c
@@ -124,7 +124,7 @@ int main(int argc, char *argv[])
list = reflist_new();
refl = add_refl(list, 0, 0, 0);
set_detector_pos(refl, 64, 64);
- set_panel(refl, &image.det->panels[0]);
+ set_panel_number(refl, 0);
cell = cell_new();
cell_set_lattice_type(cell, L_CUBIC);
cell_set_centering(cell, 'P');
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-28 15:28:36 +0000