Banish find_projected_peaks()

6 files changed, 19 insertions, 121 deletions

diff --git a/Makefile.am b/Makefile.am
index db70f378..63d0e291 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -41,7 +41,8 @@ src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c src/utils.c \
                           src/image.c src/cell.c src/hdf5-file.c \
                           src/detector.c src/peaks.c \
                           src/reflist-utils.c src/beam-parameters.c \
-                          src/symmetry.c src/thread-pool.c src/reflist.c
+                          src/symmetry.c src/thread-pool.c src/reflist.c \
+                          src/geometry.c
 if HAVE_OPENCL
 src_pattern_sim_SOURCES += src/diffraction-gpu.c src/cl-utils.c
 
diff --git a/Makefile.in b/Makefile.in
index 584d4ace..82ea4793 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -193,14 +193,15 @@ am__src_pattern_sim_SOURCES_DIST = src/pattern_sim.c src/diffraction.c \
 	src/utils.c src/image.c src/cell.c src/hdf5-file.c \
 	src/detector.c src/peaks.c src/reflist-utils.c \
 	src/beam-parameters.c src/symmetry.c src/thread-pool.c \
-	src/reflist.c src/diffraction-gpu.c src/cl-utils.c
+	src/reflist.c src/geometry.c src/diffraction-gpu.c \
+	src/cl-utils.c
 am_src_pattern_sim_OBJECTS = src/pattern_sim.$(OBJEXT) \
 	src/diffraction.$(OBJEXT) src/utils.$(OBJEXT) \
 	src/image.$(OBJEXT) src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
 	src/detector.$(OBJEXT) src/peaks.$(OBJEXT) \
 	src/reflist-utils.$(OBJEXT) src/beam-parameters.$(OBJEXT) \
 	src/symmetry.$(OBJEXT) src/thread-pool.$(OBJEXT) \
-	src/reflist.$(OBJEXT) $(am__objects_1)
+	src/reflist.$(OBJEXT) src/geometry.$(OBJEXT) $(am__objects_1)
 src_pattern_sim_OBJECTS = $(am_src_pattern_sim_OBJECTS)
 src_pattern_sim_LDADD = $(LDADD)
 src_pattern_sim_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
@@ -634,7 +635,7 @@ src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
 	src/utils.c src/image.c src/cell.c src/hdf5-file.c \
 	src/detector.c src/peaks.c src/reflist-utils.c \
 	src/beam-parameters.c src/symmetry.c src/thread-pool.c \
-	src/reflist.c $(am__append_3)
+	src/reflist.c src/geometry.c $(am__append_3)
 @HAVE_OPENCL_TRUE@tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c src/utils.c \
 @HAVE_OPENCL_TRUE@                              src/diffraction.c src/diffraction-gpu.c \
 @HAVE_OPENCL_TRUE@                              src/thread-pool.c src/cell.c src/cl-utils.c \
diff --git a/src/indexamajig.c b/src/indexamajig.c
index eef9a381..49c7118e 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -146,10 +146,6 @@ static void show_help(const char *s)
 "\n\n"
 "You can control what information is included in the output stream using\n"
 "' --record=<flag1>,<flag2>,<flag3>' and so on.  Possible flags are:\n\n"
-" pixels            Include a list of sums of pixel values within the\n"
-"                    integration domain, correcting for individual pixel\n"
-"                    solid angles.\n"
-"\n"
 " integrated        Include a list of reflection intensities, produced by\n"
 "                    integrating around predicted peak locations.\n"
 "\n"
@@ -160,8 +156,7 @@ static void show_help(const char *s)
 "\n"
 " peaksifnotindexed As 'peaks', but only if the pattern could NOT be indexed.\n"
 "\n\n"
-"The default is '--record=integrated'.  The flags 'pixels' and 'integrated'\n"
-"are mutually exclusive, as are the flags 'peaks' and 'peaksifindexed'.\n"
+"The default is '--record=integrated'.\n"
 "\n\n"
 "For more control over the process, you might need:\n\n"
 "     --cell-reduction=<m> Use <m> as the cell reduction method. Choose from:\n"
@@ -324,26 +319,19 @@ static void process_image(void *pp, int cookie)
 
 	/* Do EITHER: */
 
-	//image.div = beam->divergence;
-	//image.bw = beam->bandwidth;
-	//image.profile_radius = 0.0001e9;
-	//image.reflections = find_intersections(&image,
-	//                                       image.indexed_cell, 0);
 
 	if ( image.indexed_cell != NULL ) {
-		image.reflections = find_projected_peaks(&image,
-			                                 image.indexed_cell,
-			                                 0, 0.1);
+
+		image.div = beam->divergence;
+		image.bw = beam->bandwidth;
+		image.profile_radius = 0.0001e9;
+		image.reflections = find_intersections(&image,
+			                               image.indexed_cell, 0);
 
 		integrate_reflections(&image, config_polar,
 			              pargs->static_args.config_closer,
 			              pargs->static_args.config_bgsub);
 
-		/* OR */
-
-		//image.reflections = integrate_pixels(&image, 0, 0.1,
-		//                                     config_polar);
-
 	} else {
 
 		image.reflections = NULL;
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index f1fbce7e..89fffbc5 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -33,6 +33,7 @@
 #include "symmetry.h"
 #include "reflist.h"
 #include "reflist-utils.h"
+#include "geometry.h"
 
 
 static void show_help(const char *s)
@@ -547,24 +548,14 @@ int main(int argc, char *argv[])
 
 		if ( config_nearbragg ) {
 
-			/* Do EITHER: */
-
-			//image.div = beam->divergence;
-			//image.bw = beam->bandwidth;
-			//image.profile_radius = 0.0001e9;
-			//image.reflections = find_intersections(&image,
-			//                               image.indexed_cell, 0);
-
-			image.reflections = find_projected_peaks(&image,
-			                            image.indexed_cell, 0, 0.1);
+			image.div = image.beam->divergence;
+			image.bw = image.beam->bandwidth;
+			image.profile_radius = 0.0001e9;
+			image.reflections = find_intersections(&image,
+			                               image.indexed_cell, 0);
 
 			integrate_reflections(&image, 0, 0, 0);
 
-			/* OR */
-
-			//image.reflections = integrate_pixels(&image, 0, 0.1,
-			//                                     config_polar);
-
 		}
 
 		if ( powder_fn != NULL ) {
diff --git a/src/peaks.c b/src/peaks.c
index 2e7e7804..e4a7cfb1 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -449,86 +449,6 @@ void search_peaks(struct image *image, float threshold, float min_gradient)
 }
 
 
-RefList *find_projected_peaks(struct image *image, UnitCell *cell,
-                              int circular_domain, double domain_r)
-{
-	int fs, ss;
-	double ax, ay, az;
-	double bx, by, bz;
-	double cx, cy, cz;
-	RefList *reflections;
-	double alen, blen, clen;
-	int n_reflections = 0;
-
-	reflections = reflist_new();
-
-	/* "Borrow" direction values to get reciprocal lengths */
-	cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-	alen = modulus(ax, ay, az);
-	blen = modulus(bx, by, bz);
-	clen = modulus(cx, cy, cz);
-
-	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-
-	fesetround(1);  /* Round towards nearest */
-	for ( fs=0; fs<image->width; fs++ ) {
-	for ( ss=0; ss<image->height; ss++ ) {
-
-		double hd, kd, ld;  /* Indices with decimal places */
-		double dh, dk, dl;  /* Distances in h,k,l directions */
-		signed int h, k, l;
-		struct rvec q;
-		double dist;
-		Reflection *refl;
-		double cur_dist;
-
-		q = get_q(image, fs, ss, NULL, 1.0/image->lambda);
-
-		hd = q.u * ax + q.v * ay + q.w * az;
-		kd = q.u * bx + q.v * by + q.w * bz;
-		ld = q.u * cx + q.v * cy + q.w * cz;
-
-		h = lrint(hd);
-		k = lrint(kd);
-		l = lrint(ld);
-
-		dh = hd - h;
-		dk = kd - k;
-		dl = ld - l;
-
-		if ( circular_domain ) {
-			/* Circular integration domain */
-			dist = sqrt(pow(dh*alen, 2.0) + pow(dk*blen, 2.0)
-			                              + pow(dl*clen, 2.0));
-			if ( dist > domain_r ) continue;
-		} else {
-			/* "Crystallographic" integration domain */
-			dist = sqrt(pow(dh, 2.0) + pow(dk, 2.0) + pow(dl, 2.0));
-			if ( dist > domain_r ) continue;
-		}
-
-		refl = find_refl(reflections, h, k, l);
-		if ( refl != NULL ) {
-			cur_dist = get_excitation_error(refl);
-			if ( dist < cur_dist ) {
-				set_detector_pos(refl, dist, fs, ss);
-			}
-		} else {
-			Reflection *new;
-			new = add_refl(reflections, h, k, l);
-			set_detector_pos(new, dist, fs, ss);
-			n_reflections++;
-		}
-
-	}
-	}
-
-	optimise_reflist(reflections);
-
-	return reflections;
-}
-
-
 int peak_sanity_check(struct image *image, UnitCell *cell,
                       int circular_domain, double domain_r)
 {
diff --git a/src/peaks.h b/src/peaks.h
index ec473fd1..3d21bbde 100644
--- a/src/peaks.h
+++ b/src/peaks.h
@@ -30,9 +30,6 @@ extern void integrate_reflections(struct image *image,
 extern int peak_sanity_check(struct image *image, UnitCell *cell,
                              int circular_domain, double domain_r);
 
-extern RefList *find_projected_peaks(struct image *image, UnitCell *cell,
-                                     int circular_domain, double domain_r);
-
 /* Exported so it can be poked by integration_check */
 extern int integrate_peak(struct image *image, int cfs, int css,
                           double *pfs, double *pss, double *intensity,