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-rw-r--r--libcrystfel/src/geometry.c6
-rw-r--r--libcrystfel/src/geometry.h5
-rw-r--r--libcrystfel/src/integration.c31
-rw-r--r--libcrystfel/src/integration.h7
-rw-r--r--src/partial_sim.c2
-rw-r--r--tests/pr_l_gradient_check.c11
-rw-r--r--tests/pr_p_gradient_check.c15
-rw-r--r--tests/pr_pl_gradient_check.c15
-rw-r--r--tests/prof2d_check.c6
9 files changed, 62 insertions, 36 deletions
diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index c1d433c8..5cc46b2e 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -257,7 +257,8 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
}
-RefList *find_intersections(struct image *image, Crystal *cryst)
+RefList *find_intersections(struct image *image, Crystal *cryst,
+ PartialityModel pmodel)
{
double ax, ay, az;
double bx, by, bz;
@@ -319,7 +320,7 @@ RefList *find_intersections(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_SPHERE,
+ refl = check_reflection(image, cryst, pmodel,
h, k, l, xl, yl, zl);
if ( refl != NULL ) {
@@ -334,6 +335,7 @@ RefList *find_intersections(struct image *image, Crystal *cryst)
}
+/* Deprecated: select reflections using Kirian-style pixel proximity */
RefList *select_intersections(struct image *image, Crystal *cryst)
{
double ax, ay, az;
diff --git a/libcrystfel/src/geometry.h b/libcrystfel/src/geometry.h
index 7188f6ed..1f465167 100644
--- a/libcrystfel/src/geometry.h
+++ b/libcrystfel/src/geometry.h
@@ -62,7 +62,10 @@ typedef enum {
} PartialityModel;
-extern RefList *find_intersections(struct image *image, Crystal *cryst);
+extern RefList *find_intersections(struct image *image, Crystal *cryst,
+ PartialityModel pmodel);
+
+/* Deprecated: select reflections using Kirian-style pixel proximity */
extern RefList *select_intersections(struct image *image, Crystal *cryst);
extern void update_partialities(Crystal *cryst, PartialityModel pmodel);
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 46e1451d..a0d23d2d 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1464,8 +1464,8 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list)
}
-static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
- struct image *image, IntDiag int_diag,
+static void integrate_prof2d(IntegrationMethod meth, PartialityModel pmodel,
+ Crystal *cr, struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
double ir_inn, double ir_mid, double ir_out)
{
@@ -1478,7 +1478,7 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
cell = crystal_get_cell(cr);
/* Create initial list of reflections with nominal parameters */
- list = find_intersections(image, cr);
+ list = find_intersections(image, cr, pmodel);
ic.halfw = ir_out;
ic.image = image;
@@ -1719,8 +1719,8 @@ static double estimate_resolution(UnitCell *cell, ImageFeatureList *flist)
}
-static void integrate_rings(IntegrationMethod meth, Crystal *cr,
- struct image *image, IntDiag int_diag,
+static void integrate_rings(IntegrationMethod meth, PartialityModel pmodel,
+ Crystal *cr, struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
double ir_inn, double ir_mid, double ir_out)
{
@@ -1730,7 +1730,7 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
UnitCell *cell;
struct intcontext ic;
- list = find_intersections(image, cr);
+ list = find_intersections(image, cr, pmodel);
if ( list == NULL ) return;
if ( num_reflections(list) == 0 ) return;
@@ -1799,8 +1799,8 @@ static void apply_resolution_cutoff(Crystal *cr, double res)
}
-void integrate_all_2(struct image *image, IntegrationMethod meth,
- double push_res,
+void integrate_all_3(struct image *image, IntegrationMethod meth,
+ PartialityModel pmodel, double push_res,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
signed int idh, signed int idk, signed int idl)
@@ -1818,7 +1818,7 @@ void integrate_all_2(struct image *image, IntegrationMethod meth,
break;
case INTEGRATION_RINGS :
- integrate_rings(meth, cr, image,
+ integrate_rings(meth, pmodel, cr, image,
int_diag, idh, idk, idl,
ir_inn, ir_mid, ir_out);
res = estimate_resolution(crystal_get_cell(cr),
@@ -1826,7 +1826,7 @@ void integrate_all_2(struct image *image, IntegrationMethod meth,
break;
case INTEGRATION_PROF2D :
- integrate_prof2d(meth, cr, image,
+ integrate_prof2d(meth, pmodel, cr, image,
int_diag, idh, idk, idl,
ir_inn, ir_mid, ir_out);
res = estimate_resolution(crystal_get_cell(cr),
@@ -1848,6 +1848,17 @@ void integrate_all_2(struct image *image, IntegrationMethod meth,
}
+void integrate_all_2(struct image *image, IntegrationMethod meth,
+ double push_res,
+ double ir_inn, double ir_mid, double ir_out,
+ IntDiag int_diag,
+ signed int idh, signed int idk, signed int idl)
+{
+ integrate_all_3(image, meth, PMODEL_SPHERE, 0.0, ir_inn, ir_mid, ir_out,
+ int_diag, idh, idk, idl);
+}
+
+
void integrate_all(struct image *image, IntegrationMethod meth,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index 84c1b900..f077be32 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -34,6 +34,8 @@
#endif
+#include "geometry.h"
+
typedef enum {
INTDIAG_NONE,
@@ -97,6 +99,11 @@ extern void integrate_all_2(struct image *image, IntegrationMethod meth,
IntDiag int_diag,
signed int idh, signed int idk, signed int idl);
+extern void integrate_all_3(struct image *image, IntegrationMethod meth,
+ PartialityModel pmodel, double push_res,
+ double ir_inn, double ir_mid, double ir_out,
+ IntDiag int_diag,
+ signed int idh, signed int idk, signed int idl);
#ifdef __cplusplus
}
diff --git a/src/partial_sim.c b/src/partial_sim.c
index fa68638f..862eadef 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -352,7 +352,7 @@ static void run_job(void *vwargs, int cookie)
snprintf(wargs->image.filename, 255, "dummy.h5");
}
- reflections = find_intersections(&wargs->image, cr);
+ reflections = find_intersections(&wargs->image, cr, PMODEL_SPHERE);
crystal_set_reflections(cr, reflections);
for ( i=0; i<NBINS; i++ ) {
diff --git a/tests/pr_l_gradient_check.c b/tests/pr_l_gradient_check.c
index 72d353f9..b707629f 100644
--- a/tests/pr_l_gradient_check.c
+++ b/tests/pr_l_gradient_check.c
@@ -89,7 +89,8 @@ static void shift_parameter(struct image *image, int k, double shift)
static void calc_either_side(Crystal *cr, double incr_val,
- int *valid, long double *vals[3], int refine)
+ int *valid, long double *vals[3], int refine,
+ PartialityModel pmodel)
{
RefList *compare;
struct image *image = crystal_get_image(cr);
@@ -97,14 +98,14 @@ static void calc_either_side(Crystal *cr, double incr_val,
im_moved = *image;
shift_parameter(&im_moved, refine, -incr_val);
- compare = find_intersections(&im_moved, cr);
+ compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 0);
reflist_free(compare);
im_moved = *image;
shift_parameter(&im_moved, refine, +incr_val);
- compare = find_intersections(&im_moved, cr);
+ compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 2);
reflist_free(compare);
@@ -133,7 +134,7 @@ static double test_gradients(Crystal *cr, double incr_val, int refine,
int n_line;
double cc;
- reflections = find_intersections(crystal_get_image(cr), cr);
+ reflections = find_intersections(crystal_get_image(cr), cr, pmodel);
crystal_set_reflections(cr, reflections);
nref = num_reflections(reflections);
@@ -159,7 +160,7 @@ static double test_gradients(Crystal *cr, double incr_val, int refine,
scan_partialities(reflections, reflections, valid, vals, 1);
- calc_either_side(cr, incr_val, valid, vals, refine);
+ calc_either_side(cr, incr_val, valid, vals, refine, pmodel);
if ( plot ) {
snprintf(tmp, 32, "gradient-test-%s.dat", file);
diff --git a/tests/pr_p_gradient_check.c b/tests/pr_p_gradient_check.c
index c3b55cfa..8f7a66e4 100644
--- a/tests/pr_p_gradient_check.c
+++ b/tests/pr_p_gradient_check.c
@@ -175,7 +175,8 @@ static Crystal *new_shifted_crystal(Crystal *cr, int refine, double incr_val)
}
static void calc_either_side(Crystal *cr, double incr_val,
- int *valid, long double *vals[3], int refine)
+ int *valid, long double *vals[3], int refine,
+ PartialityModel pmodel)
{
RefList *compare;
struct image *image = crystal_get_image(cr);
@@ -186,7 +187,7 @@ static void calc_either_side(Crystal *cr, double incr_val,
/* Crystal properties */
cr_new = new_shifted_crystal(cr, refine, -incr_val);
- compare = find_intersections(image, cr_new);
+ compare = find_intersections(image, cr_new, pmodel);
scan_partialities(crystal_get_reflections(cr), compare, valid,
vals, 0);
cell_free(crystal_get_cell(cr_new));
@@ -194,7 +195,7 @@ static void calc_either_side(Crystal *cr, double incr_val,
reflist_free(compare);
cr_new = new_shifted_crystal(cr, refine, +incr_val);
- compare = find_intersections(image, cr_new);
+ compare = find_intersections(image, cr_new, pmodel);
scan_partialities(crystal_get_reflections(cr), compare, valid,
vals, 2);
cell_free(crystal_get_cell(cr_new));
@@ -208,14 +209,14 @@ static void calc_either_side(Crystal *cr, double incr_val,
/* "Image" properties */
im_moved = *image;
shift_parameter(&im_moved, refine, -incr_val);
- compare = find_intersections(&im_moved, cr);
+ compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 0);
reflist_free(compare);
im_moved = *image;
shift_parameter(&im_moved, refine, +incr_val);
- compare = find_intersections(&im_moved, cr);
+ compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 2);
reflist_free(compare);
@@ -246,7 +247,7 @@ static double test_gradients(Crystal *cr, double incr_val, int refine,
int n_line;
double cc;
- reflections = find_intersections(crystal_get_image(cr), cr);
+ reflections = find_intersections(crystal_get_image(cr), cr, pmodel);
crystal_set_reflections(cr, reflections);
nref = num_reflections(reflections);
@@ -272,7 +273,7 @@ static double test_gradients(Crystal *cr, double incr_val, int refine,
scan_partialities(reflections, reflections, valid, vals, 1);
- calc_either_side(cr, incr_val, valid, vals, refine);
+ calc_either_side(cr, incr_val, valid, vals, refine, pmodel);
if ( plot ) {
snprintf(tmp, 32, "gradient-test-%s.dat", file);
diff --git a/tests/pr_pl_gradient_check.c b/tests/pr_pl_gradient_check.c
index ddbc1840..f83af335 100644
--- a/tests/pr_pl_gradient_check.c
+++ b/tests/pr_pl_gradient_check.c
@@ -175,7 +175,8 @@ static Crystal *new_shifted_crystal(Crystal *cr, int refine, double incr_val)
}
static void calc_either_side(Crystal *cr, double incr_val,
- int *valid, long double *vals[3], int refine)
+ int *valid, long double *vals[3], int refine,
+ PartialityModel pmodel)
{
RefList *compare;
struct image *image = crystal_get_image(cr);
@@ -186,7 +187,7 @@ static void calc_either_side(Crystal *cr, double incr_val,
/* Crystal properties */
cr_new = new_shifted_crystal(cr, refine, -incr_val);
- compare = find_intersections(image, cr_new);
+ compare = find_intersections(image, cr_new, pmodel);
scan_partialities(crystal_get_reflections(cr), compare, valid,
vals, 0);
cell_free(crystal_get_cell(cr_new));
@@ -194,7 +195,7 @@ static void calc_either_side(Crystal *cr, double incr_val,
reflist_free(compare);
cr_new = new_shifted_crystal(cr, refine, +incr_val);
- compare = find_intersections(image, cr_new);
+ compare = find_intersections(image, cr_new, pmodel);
scan_partialities(crystal_get_reflections(cr), compare, valid,
vals, 2);
cell_free(crystal_get_cell(cr_new));
@@ -208,14 +209,14 @@ static void calc_either_side(Crystal *cr, double incr_val,
/* "Image" properties */
im_moved = *image;
shift_parameter(&im_moved, refine, -incr_val);
- compare = find_intersections(&im_moved, cr);
+ compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 0);
reflist_free(compare);
im_moved = *image;
shift_parameter(&im_moved, refine, +incr_val);
- compare = find_intersections(&im_moved, cr);
+ compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 2);
reflist_free(compare);
@@ -246,7 +247,7 @@ static double test_gradients(Crystal *cr, double incr_val, int refine,
int n_line;
double cc;
- reflections = find_intersections(crystal_get_image(cr), cr);
+ reflections = find_intersections(crystal_get_image(cr), cr, pmodel);
crystal_set_reflections(cr, reflections);
nref = num_reflections(reflections);
@@ -272,7 +273,7 @@ static double test_gradients(Crystal *cr, double incr_val, int refine,
scan_partialities(reflections, reflections, valid, vals, 1);
- calc_either_side(cr, incr_val, valid, vals, refine);
+ calc_either_side(cr, incr_val, valid, vals, refine, pmodel);
if ( plot ) {
snprintf(tmp, 32, "gradient-test-%s.dat", file);
diff --git a/tests/prof2d_check.c b/tests/prof2d_check.c
index f1665a6c..75b9748e 100644
--- a/tests/prof2d_check.c
+++ b/tests/prof2d_check.c
@@ -139,7 +139,7 @@ int main(int argc, char *argv[])
image.n_crystals = 1;
image.crystals = &cr;
- list = find_intersections(&image, cr);
+ list = find_intersections(&image, cr, PMODEL_SPHERE);
for ( fs=0; fs<w; fs++ ) {
for ( ss=0; ss<h; ss++ ) {
@@ -176,8 +176,8 @@ int main(int argc, char *argv[])
STATUS("%i strong, %i weak\n", n_strong, n_weak);
reflist_free(list); /* integrate_prof2d() will predict again */
- integrate_prof2d(INTEGRATION_PROF2D, cr, &image, INTDIAG_NONE, 0, 0, 0,
- ir_inn, ir_mid, ir_out);
+ integrate_prof2d(INTEGRATION_PROF2D, PMODEL_SPHERE, cr, &image,
+ INTDIAG_NONE, 0, 0, 0, ir_inn, ir_mid, ir_out);
list = crystal_get_reflections(cr);
printf("Weak reflections:\n");
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-14 22:02:06 +0000