Pass the partiality model down from the API level

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");