Zap quats

The "orientation" quaternion should not rotate the Ewald sphere, but the crystal.
This cleans things up a little, removing "orientation" from "struct image".

12 files changed, 45 insertions, 54 deletions

diff --git a/src/calibrate_detector.c b/src/calibrate_detector.c
index b20b1619..7feeb16c 100644
--- a/src/calibrate_detector.c
+++ b/src/calibrate_detector.c
@@ -172,12 +172,6 @@ static void add_image(void *args, int cookie)
 	image.n_cpeaks = 0;
 	image.det = NULL;
 
-	/* View head-on (unit cell is tilted) */
-	image.orientation.w = 1.0;
-	image.orientation.x = 0.0;
-	image.orientation.y = 0.0;
-	image.orientation.z = 0.0;
-
 	STATUS("%3i: Processing '%s'\n", cookie, pargs->filename);
 
 	hdfile = hdfile_open(pargs->filename);
diff --git a/src/cell.c b/src/cell.c
index 7b5379a5..e95a0573 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -486,6 +486,28 @@ static const char *cell_rep(UnitCell *cell)
 }
 
 
+UnitCell *cell_rotate(UnitCell *in, struct quaternion quat)
+{
+	struct rvec a, b, c;
+	struct rvec an, bn, cn;
+	UnitCell *out = cell_new();
+
+	cell_get_cartesian(in, &a.u, &a.v, &a.w,
+	                       &b.u, &b.v, &b.w,
+	                       &c.u, &c.v, &c.w);
+
+	an = quat_rot(a, quat);
+	bn = quat_rot(b, quat);
+	cn = quat_rot(c, quat);
+
+	cell_set_cartesian(out, an.u, an.v, an.w,
+	                        bn.u, bn.v, bn.w,
+	                        cn.u, cn.v, cn.w);
+
+	return out;
+}
+
+
 void cell_print(UnitCell *cell)
 {
 	double asx, asy, asz;
diff --git a/src/cell.h b/src/cell.h
index c5b5d888..5a6bfda9 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -16,6 +16,8 @@
 #include <config.h>
 #endif
 
+#include "utils.h"
+
 /* A 3D vector in reciprocal space */
 struct rvec
 {
@@ -73,6 +75,8 @@ extern const char *cell_get_pointgroup(UnitCell *cell);
 extern double resolution(UnitCell *cell,
                          signed int h, signed int k, signed int l);
 
+extern UnitCell *cell_rotate(UnitCell *in, struct quaternion quat);
+
 extern void cell_print(UnitCell *cell);
 
 extern UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose,
diff --git a/src/cubeit.c b/src/cubeit.c
index b613a3fa..a47a8893 100644
--- a/src/cubeit.c
+++ b/src/cubeit.c
@@ -220,12 +220,6 @@ static void sum_image(void *pg, int cookie)
 	image.n_cpeaks = 0;
 	image.det = pargs->det;
 
-	/* View head-on (unit cell is tilted) */
-	image.orientation.w = 1.0;
-	image.orientation.x = 0.0;
-	image.orientation.y = 0.0;
-	image.orientation.z = 0.0;
-
 	STATUS("Processing '%s'\n", apargs->filename);
 
 	hdfile = hdfile_open(apargs->filename);
diff --git a/src/detector.c b/src/detector.c
index fa3208a6..da423235 100644
--- a/src/detector.c
+++ b/src/detector.c
@@ -59,7 +59,7 @@ struct rvec get_q(struct image *image, double xs, double ys,
 	q.v = k * sin(twotheta)*sin(az);
 	q.w = k * (cos(twotheta) - 1.0);
 
-	return quat_rot(q, image->orientation);
+	return q;
 }
 
 
diff --git a/src/diffraction-gpu.c b/src/diffraction-gpu.c
index bbed9a9b..6e73a52c 100644
--- a/src/diffraction-gpu.c
+++ b/src/diffraction-gpu.c
@@ -140,12 +140,6 @@ void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
 	khigh = 1.0/(image->lambda*(1.0 - image->beam->bandwidth/2.0));
 	bwstep = (khigh-klow) / BWSAMPLING;
 
-	/* Orientation */
-	orientation.s[0] = image->orientation.w;
-	orientation.s[1] = image->orientation.x;
-	orientation.s[2] = image->orientation.y;
-	orientation.s[3] = image->orientation.z;
-
 	ncells.s[0] = na;
 	ncells.s[1] = nb;
 	ncells.s[2] = nc;
diff --git a/src/facetron.c b/src/facetron.c
index 02de26f5..53fb00f2 100644
--- a/src/facetron.c
+++ b/src/facetron.c
@@ -412,10 +412,6 @@ int main(int argc, char *argv[])
 		images[i].filename = fnamereal;
 		images[i].div = beam->divergence;
 		images[i].bw = beam->bandwidth;
-		images[i].orientation.w = 1.0;
-		images[i].orientation.x = 0.0;
-		images[i].orientation.y = 0.0;
-		images[i].orientation.z = 0.0;
 		images[i].det = det;
 		images[i].beam = beam;
 
diff --git a/src/image.h b/src/image.h
index 76e986ea..6b09dfc4 100644
--- a/src/image.h
+++ b/src/image.h
@@ -92,7 +92,6 @@ struct image {
 	                               * handling this image */
 
 	/* Information about the crystal */
-	struct quaternion       orientation;
 	double                  m;  /* Mosaicity in radians */
 
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 05a91683..984c1e45 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -217,12 +217,6 @@ static struct image *get_simage(struct image *template, int alternate)
 	image->f0_available = 0;
 	image->f0 = 1.0;
 
-	/* View head-on (unit cell is tilted) */
-	image->orientation.w = 1.0;
-	image->orientation.x = 0.0;
-	image->orientation.y = 0.0;
-	image->orientation.z = 0.0;
-
 	/* Detector geometry for the simulation
 	 * - not necessarily the same as the original. */
 	image->width = 1024;
@@ -329,12 +323,6 @@ static void process_image(void *pp, int cookie)
 	image.n_cpeaks = 0;
 	image.det = pargs->static_args.det;
 
-	/* View head-on (unit cell is tilted) */
-	image.orientation.w = 1.0;
-	image.orientation.x = 0.0;
-	image.orientation.y = 0.0;
-	image.orientation.z = 0.0;
-
 	STATUS("Processing '%s'\n", image.filename);
 
 	pargs->sane = 0;
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 4531c85b..3c1afe07 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -201,7 +201,8 @@ int main(int argc, char *argv[])
 	int number = 1;   /* Number used for filename of image */
 	int n_images = 1; /* Generate one image by default */
 	int done = 0;
-	UnitCell *cell;
+	UnitCell *input_cell;
+	struct quaternion orientation;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -384,10 +385,14 @@ int main(int argc, char *argv[])
 	image.width = image.det->max_x + 1;
 	image.height = image.det->max_y + 1;
 	image.lambda = ph_en_to_lambda(eV_to_J(image.beam->photon_energy));
-	cell = load_cell_from_pdb(filename);
-	if ( cell == NULL ) {
+
+	/* Load unit cell */
+	input_cell = load_cell_from_pdb(filename);
+	if ( input_cell == NULL ) {
 		exit(1);
 	}
+
+	/* Initialise stuff */
 	image.filename = NULL;
 	image.features = NULL;
 	image.flags = NULL;
@@ -403,6 +408,7 @@ int main(int argc, char *argv[])
 
 		int na, nb, nc;
 		double a, b, c, d;
+		UnitCell *cell;
 
 		//na = 8*random()/RAND_MAX + 4;
 		//nb = 8*random()/RAND_MAX + 4;
@@ -413,20 +419,22 @@ int main(int argc, char *argv[])
 
 		/* Read quaternion from stdin */
 		if ( config_randomquat ) {
-			image.orientation = random_quaternion();
+			orientation = random_quaternion();
 		} else {
-			image.orientation = read_quaternion();
+			orientation = read_quaternion();
 		}
 
 		STATUS("Orientation is %5.3f %5.3f %5.3f %5.3f\n",
-		       image.orientation.w, image.orientation.x,
-		       image.orientation.y, image.orientation.z);
+		       orientation.w, orientation.x,
+		       orientation.y, orientation.z);
 
-		if ( !quaternion_valid(image.orientation) ) {
+		if ( !quaternion_valid(orientation) ) {
 			ERROR("Orientation modulus is not zero!\n");
 			return 1;
 		}
 
+		cell = cell_rotate(input_cell, orientation);
+
 		/* Ensure no residual information */
 		image.data = NULL;
 		image.twotheta = NULL;
@@ -500,6 +508,7 @@ int main(int argc, char *argv[])
 		/* Clean up */
 		free(image.data);
 		free(image.twotheta);
+		cell_free(cell);
 
 skip:
 		ndone++;
@@ -516,7 +525,7 @@ skip:
 	free(image.det);
 	free(image.beam);
 	free(powder);
-	cell_free(cell);
+	cell_free(input_cell);
 	free(intensities);
 	free(outfile);
 	free(filename);
diff --git a/src/peaks.c b/src/peaks.c
index e7ec9c9e..7c91f817 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -668,9 +668,6 @@ static void output_header(FILE *ofh, UnitCell *cell, struct image *image)
 	double a, b, c, al, be, ga;
 
 	fprintf(ofh, "Reflections from indexing in %s\n", image->filename);
-	fprintf(ofh, "Orientation (wxyz): %7.5f %7.5f %7.5f %7.5f\n",
-	       image->orientation.w, image->orientation.x,
-	       image->orientation.y, image->orientation.z);
 
 	cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
 	fprintf(ofh, "Cell parameters %7.5f %7.5f %7.5f nm, %7.5f %7.5f %7.5f deg\n",
diff --git a/src/reintegrate.c b/src/reintegrate.c
index 220cad26..906d1859 100644
--- a/src/reintegrate.c
+++ b/src/reintegrate.c
@@ -112,12 +112,6 @@ static void process_image(void *pg, int cookie)
 	image.n_cpeaks = 0;
 	image.det = pargs->det;
 
-	/* View head-on (unit cell is tilted) */
-	image.orientation.w = 1.0;
-	image.orientation.x = 0.0;
-	image.orientation.y = 0.0;
-	image.orientation.z = 0.0;
-
 	STATUS("Processing '%s'\n", apargs->filename);
 
 	hdfile = hdfile_open(apargs->filename);