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authorThomas White <taw@physics.org>2016-11-08 16:20:58 +0100
committerThomas White <taw@physics.org>2018-02-27 11:02:02 +0100
commitd813960912ddc76d5cff0501b4f7783c3eeca95d (patch)
tree4dc11e2ecd789d34a451abc81d799508118a6b86 /libcrystfel/src
parentcc64a9ae6c4ca7518ba904d6cdf38b3d8dccbbf7 (diff)
Separate partiality calculation from prediction
Diffstat (limited to 'libcrystfel/src')
-rw-r--r--libcrystfel/src/geometry.c130
-rw-r--r--libcrystfel/src/geometry.h14
-rw-r--r--libcrystfel/src/integration.c3
-rw-r--r--libcrystfel/src/predict-refine.c8
4 files changed, 95 insertions, 60 deletions
diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index b968dc06..576655de 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -266,15 +266,12 @@ static double partiality(PartialityModel pmodel,
static Reflection *check_reflection(struct image *image, Crystal *cryst,
- PartialityModel pmodel,
signed int h, signed int k, signed int l,
double xl, double yl, double zl,
Reflection *updateme)
{
- const int output = 0;
double tl;
- double rlow, rhigh; /* "Excitation error" */
- double part; /* Partiality */
+ double rlow, rhigh; /* "Excitation error" */
double klow, khigh; /* Wavenumber */
Reflection *refl;
double cet, cez; /* Centre of Ewald sphere */
@@ -312,20 +309,6 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
&& (fabs(rlow) > pr)
&& (fabs(rhigh) > pr) ) return NULL;
- /* Calculate partiality */
- part = partiality(pmodel, h, k, l, image->serial, rlow, rhigh, pr);
-
- if ( isnan(part) && ((h!=0) || (k!=0) || (l!=0)) ) {
- ERROR("Assigning NAN partiality!\n");
- ERROR("%3i %3i %3i rlow = %e, rhigh = %e\n",
- h, k, l, rlow, rhigh);
- ERROR("div + m = %e, R = %e, bw = %e\n", del, pr, image->bw);
- ERROR("D = %e\n", rlow - rhigh);
- ERROR("klow = %e khigh = %e\n", klow, khigh);
- ERROR("distance(..) = %e\n", distance(cet, cez, tl, zl));
- abort();
- }
-
if ( updateme == NULL ) {
refl = reflection_new(h, k, l);
} else {
@@ -373,15 +356,12 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
}
}
- set_partial(refl, rlow, rhigh, part);
+ set_partial(refl, rlow, rhigh, 1.0); /* Actual partiality set by
+ * calculate_partialities() */
set_lorentz(refl, 1.0);
set_symmetric_indices(refl, h, k, l);
set_redundancy(refl, 1);
- if ( output ) {
- printf("%3i %3i %3i %6f %5.2f\n", h, k, l, 0.0, part);
- }
-
return refl;
}
@@ -472,15 +452,7 @@ double r_gradient(UnitCell *cell, int k, Reflection *refl, struct image *image)
}
-RefList *find_intersections(struct image *image, Crystal *cryst,
- PartialityModel pmodel)
-{
- return find_intersections_to_res(image, cryst, pmodel, INFINITY);
-}
-
-
-RefList *find_intersections_to_res(struct image *image, Crystal *cryst,
- PartialityModel pmodel, double max_res)
+RefList *predict_to_res(Crystal *cryst, double max_res)
{
double ax, ay, az;
double bx, by, bz;
@@ -509,7 +481,7 @@ RefList *find_intersections_to_res(struct image *image, Crystal *cryst,
cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
- mres = largest_q(image);
+ mres = largest_q(crystal_get_image(cryst));
if ( mres > max_res ) mres = max_res;
hmax = mres * modulus(ax, ay, az);
@@ -544,7 +516,7 @@ RefList *find_intersections_to_res(struct image *image, Crystal *cryst,
yl = h*asy + k*bsy + l*csy;
zl = h*asz + k*bsz + l*csz;
- refl = check_reflection(image, cryst, pmodel,
+ refl = check_reflection(crystal_get_image(cryst), cryst,
h, k, l, xl, yl, zl, NULL);
if ( refl != NULL ) {
@@ -559,12 +531,12 @@ RefList *find_intersections_to_res(struct image *image, Crystal *cryst,
}
-static void set_unity_partialities(Crystal *cryst)
+static void set_unity_partialities(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
- for ( refl = first_refl(crystal_get_reflections(cryst), &iter);
+ for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
@@ -575,14 +547,85 @@ static void set_unity_partialities(Crystal *cryst)
/**
- * update_partialities:
+ * calculate_partialities:
* @cryst: A %Crystal
* @pmodel: A %PartialityModel
*
- * Updates the partialities of @cryst's reflections according to @pmodel and
+ * Calculates the partialities for the reflections in @cryst, given the current
+ * crystal and image parameters. The crystal's image and reflection lists
+ * must be set. The specified %PartialityModel will be used.
+ *
+ * You must not have changed the crystal or image parameters since you last
+ * called predict_to_res() or update_predictions(), because this function
+ * relies on the limiting wavelength values calculated by those functions.
+ */
+void calculate_partialities(Crystal *cryst, PartialityModel pmodel)
+{
+ RefList *list;
+ Reflection *refl;
+ RefListIterator *iter;
+ double pr;
+ struct image *image;
+
+ list = crystal_get_reflections(cryst);
+ if ( list == NULL ) {
+ ERROR("No reflections for partiality calculation!\n");
+ return;
+ }
+
+ if ( pmodel == PMODEL_UNITY ) {
+ set_unity_partialities(list);
+ return;
+ }
+
+ image = crystal_get_image(cryst);
+ if ( image == NULL ) {
+ ERROR("No image for partiality calculation!\n");
+ return;
+ }
+
+ pr = crystal_get_profile_radius(cryst);
+
+ for ( refl = first_refl(crystal_get_reflections(cryst), &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ double rlow, rhigh, part;
+ signed int h, k, l;
+
+ get_symmetric_indices(refl, &h, &k, &l);
+ get_partial(refl, &rlow, &rhigh, &part);
+
+ part = partiality(pmodel, h, k, l, image->serial,
+ rlow, rhigh, pr);
+
+ if ( isnan(part) && ((h!=0) || (k!=0) || (l!=0)) ) {
+ ERROR("Assigning NAN partiality!\n");
+ ERROR("%3i %3i %3i rlow = %e, rhigh = %e\n",
+ h, k, l, rlow, rhigh);
+ ERROR("R = %e, bw = %e\n", pr, image->bw);
+ ERROR("D = %e\n", rlow - rhigh);
+ abort();
+ }
+
+ set_partiality(refl, part);
+
+ }
+}
+
+
+/**
+ * update_predictions:
+ * @cryst: A %Crystal
+ *
+ * Updates the predicted reflections (positions and excitation errors, but not
+ * the actual partialities) of @cryst's reflections according to
* the current state of the crystal (e.g. its unit cell parameters).
+ *
+ * If you need to update the partialities as well, call calculate_partialities()
+ * afterwards.
*/
-void update_partialities(Crystal *cryst, PartialityModel pmodel)
+void update_predictions(Crystal *cryst)
{
Reflection *refl;
RefListIterator *iter;
@@ -591,11 +634,6 @@ void update_partialities(Crystal *cryst, PartialityModel pmodel)
double csx, csy, csz;
struct image *image = crystal_get_image(cryst);
- if ( pmodel == PMODEL_UNITY ) {
- set_unity_partialities(cryst);
- return;
- }
-
cell_get_reciprocal(crystal_get_cell(cryst), &asx, &asy, &asz,
&bsx, &bsy, &bsz, &csx, &csy, &csz);
@@ -613,8 +651,8 @@ void update_partialities(Crystal *cryst, PartialityModel pmodel)
yl = h*asy + k*bsy + l*csy;
zl = h*asz + k*bsz + l*csz;
- check_reflection(image, cryst, pmodel,
- h, k, l, xl, yl, zl, refl);
+ check_reflection(image, cryst, h, k, l,
+ xl, yl, zl, refl);
}
}
diff --git a/libcrystfel/src/geometry.h b/libcrystfel/src/geometry.h
index 6b035175..4fbd0bca 100644
--- a/libcrystfel/src/geometry.h
+++ b/libcrystfel/src/geometry.h
@@ -3,12 +3,12 @@
*
* Geometry of diffraction
*
- * Copyright © 2013-2015 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2013-2016 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
*
* Authors:
- * 2010-2015 Thomas White <taw@physics.org>
+ * 2010-2016 Thomas White <taw@physics.org>
* 2012 Richard Kirian
*
* This file is part of CrystFEL.
@@ -85,15 +85,13 @@ enum gparam {
};
-extern RefList *find_intersections(struct image *image, Crystal *cryst,
- PartialityModel pmodel);
-extern RefList *find_intersections_to_res(struct image *image, Crystal *cryst,
- PartialityModel pmodel,
- double max_res);
+extern RefList *predict_to_res(Crystal *cryst, double max_res);
+
+extern void calculate_partialities(Crystal *cryst, PartialityModel pmodel);
extern double r_gradient(UnitCell *cell, int k, Reflection *refl,
struct image *image);
-extern void update_partialities(Crystal *cryst, PartialityModel pmodel);
+extern void update_predictions(Crystal *cryst);
extern void polarisation_correction(RefList *list, UnitCell *cell,
struct image *image);
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index d50f8d6b..96eec92a 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1673,8 +1673,7 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
image->features);
crystal_set_resolution_limit(image->crystals[i], res);
- list = find_intersections_to_res(image, image->crystals[i],
- pmodel, res+push_res);
+ list = predict_to_res(image->crystals[i], res+push_res);
crystal_set_reflections(image->crystals[i], list);
}
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index e702cf33..3246dbec 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -262,7 +262,7 @@ static int pair_peaks(struct image *image, Crystal *cr,
* doesn't fall on this panel. We're only interested
* in how far away it is from the peak location.
* The predicted position and excitation errors will be
- * filled in by update_partialities(). */
+ * filled in by update_predictions(). */
set_panel(refl, f->p);
rps[n].refl = refl;
@@ -275,7 +275,7 @@ static int pair_peaks(struct image *image, Crystal *cr,
/* Get the excitation errors and detector positions for the candidate
* reflections */
crystal_set_reflections(cr, all_reflist);
- update_partialities(cr, PMODEL_SCSPHERE);
+ update_predictions(cr);
/* Pass over the peaks again, keeping only the ones which look like
* good pairings */
@@ -339,7 +339,7 @@ void refine_radius(Crystal *cr, struct image *image)
return;
}
crystal_set_reflections(cr, reflist);
- update_partialities(cr, PMODEL_SCSPHERE);
+ update_predictions(cr);
crystal_set_reflections(cr, NULL);
qsort(rps, n_acc, sizeof(struct reflpeak), cmpd2);
@@ -635,7 +635,7 @@ int refine_prediction(struct image *image, Crystal *cr)
/* Refine */
for ( i=0; i<MAX_CYCLES; i++ ) {
- update_partialities(cr, PMODEL_SCSPHERE);
+ update_predictions(cr);
if ( iterate(rps, n, crystal_get_cell(cr), image,
&total_x, &total_y, &total_z) ) return 1;
//STATUS("Residual after %i = %e\n", i,