Get rid of ImageFeature->rx,ry,rz

These needed to be kept up to date with a call to map_all_peaks every
time anything changed - wavelength, detector position etc.  Not doing so
has already led to bugs in another branch, and probably already causes
problems on this branch.

This patch eliminates the rx,ry,rz completely.  Anyone who needs
reciprocal space coordinates for a peak is now responsible for calling
detgeom_transform_coords themselves.

7 files changed, 59 insertions, 21 deletions

diff --git a/libcrystfel/src/indexers/asdf.c b/libcrystfel/src/indexers/asdf.c
index 806501cc..68b714a9 100644
--- a/libcrystfel/src/indexers/asdf.c
+++ b/libcrystfel/src/indexers/asdf.c
@@ -1116,14 +1116,19 @@ int run_asdf(struct image *image, void *ipriv)
 
 	for ( i=0; i<n; i++ ) {
 		struct imagefeature *f;
+		double r[3];
 
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
 
+		detgeom_transform_coords(&image->detgeom->panels[f->pn],
+		                         f->fs, f->ss, image->lambda,
+		                         r);
+
 		reflections[N_reflections] = gsl_vector_alloc(3);
-		gsl_vector_set(reflections[N_reflections], 0, f->rx/1e10);
-		gsl_vector_set(reflections[N_reflections], 1, f->ry/1e10);
-		gsl_vector_set(reflections[N_reflections], 2, f->rz/1e10);
+		gsl_vector_set(reflections[N_reflections], 0, r[0]/1e10);
+		gsl_vector_set(reflections[N_reflections], 1, r[1]/1e10);
+		gsl_vector_set(reflections[N_reflections], 2, r[2]/1e10);
 		N_reflections++;
 	}
 
diff --git a/libcrystfel/src/indexers/dirax.c b/libcrystfel/src/indexers/dirax.c
index 24be87ba..a21dd7e2 100644
--- a/libcrystfel/src/indexers/dirax.c
+++ b/libcrystfel/src/indexers/dirax.c
@@ -490,12 +490,17 @@ static void write_drx(struct image *image)
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
 
 		struct imagefeature *f;
+		double r[3];
 
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
 
+		detgeom_transform_coords(&image->detgeom->panels[f->pn],
+		                         f->fs, f->ss, image->lambda,
+		                         r);
+
 		fprintf(fh, "%10f %10f %10f %8f\n",
-		        f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0);
+		        r[0]/1e10, r[1]/1e10, r[2]/1e10, 1.0);
 
 	}
 	fclose(fh);
diff --git a/libcrystfel/src/indexers/felix.c b/libcrystfel/src/indexers/felix.c
index b94227d0..0db5ecbb 100644
--- a/libcrystfel/src/indexers/felix.c
+++ b/libcrystfel/src/indexers/felix.c
@@ -364,14 +364,19 @@ static void write_gve(struct image *image, struct felix_private *gp)
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
 
 		struct imagefeature *f;
+		double r[3];
 
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
 
+		detgeom_transform_coords(&image->detgeom->panels[f->pn],
+		                         f->fs, f->ss, image->lambda,
+		                         r);
+
 		fprintf(fh, "%.6f %.6f %.6f 0 0 %.6f %.6f %.6f 0\n",
-		        f->rz/1e10, f->rx/1e10, f->ry/1e10,
-		        modulus(f->rx, f->ry, f->rz)/1e10, /* dstar */
-		        rad2deg(atan2(f->ry, f->rx)), 0.0);   /* eta, omega */
+		        r[2]/1e10, r[0]/1e10, r[1]/1e10,
+		        modulus(r[0], r[1], r[2])/1e10, /* dstar */
+		        rad2deg(atan2(r[1], r[0])), 0.0);   /* eta, omega */
 
 	}
 	fclose(fh);
diff --git a/libcrystfel/src/indexers/mosflm.c b/libcrystfel/src/indexers/mosflm.c
index bacd345f..4c1d2906 100644
--- a/libcrystfel/src/indexers/mosflm.c
+++ b/libcrystfel/src/indexers/mosflm.c
@@ -357,16 +357,21 @@ static void write_spt(struct image *image, const char *filename)
 
 		struct imagefeature *f;
 		double ttx, tty, x, y;
+		double r[3];
 
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
 
+		detgeom_transform_coords(&image->detgeom->panels[f->pn],
+		                         f->fs, f->ss, image->lambda,
+		                         r);
+
 		ttx = angle_between_2d(0.0, 1.0,
-		                       f->rx, 1.0/image->lambda + f->rz);
+		                       r[0], 1.0/image->lambda + r[2]);
 		tty = angle_between_2d(0.0, 1.0,
-		                       f->ry, 1.0/image->lambda + f->rz);
-		if ( f->rx < 0.0 ) ttx *= -1.0;
-		if ( f->ry < 0.0 ) tty *= -1.0;
+		                       r[1], 1.0/image->lambda + r[2]);
+		if ( r[0] < 0.0 ) ttx *= -1.0;
+		if ( r[1] < 0.0 ) tty *= -1.0;
 		x = -tan(ttx)*FAKE_CLEN;
 		y = tan(tty)*FAKE_CLEN;
 
diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c
index 4243adcb..18845ce5 100644
--- a/libcrystfel/src/indexers/taketwo.c
+++ b/libcrystfel/src/indexers/taketwo.c
@@ -2157,11 +2157,18 @@ int taketwo_index(struct image *image, void *priv)
 
 	rlps = malloc((image_feature_count(image->features)+1)*sizeof(struct rvec));
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
+
+		double r[3];
 		struct imagefeature *pk = image_get_feature(image->features, i);
 		if ( pk == NULL ) continue;
-		rlps[n_rlps].u = pk->rx;
-		rlps[n_rlps].v = pk->ry;
-		rlps[n_rlps].w = pk->rz;
+
+		detgeom_transform_coords(&image->detgeom->panels[pk->pn],
+		                         pk->fs, pk->ss, image->lambda,
+		                         r);
+
+		rlps[n_rlps].u = r[0];
+		rlps[n_rlps].v = r[1];
+		rlps[n_rlps].w = r[2];
 		n_rlps++;
 	}
 	rlps[n_rlps].u = 0.0;
diff --git a/libcrystfel/src/indexers/xds.c b/libcrystfel/src/indexers/xds.c
index 02610d5e..76c657c6 100644
--- a/libcrystfel/src/indexers/xds.c
+++ b/libcrystfel/src/indexers/xds.c
@@ -213,17 +213,22 @@ static void write_spot(struct image *image)
         {
 		struct imagefeature *f;
 		double ttx, tty, x, y;
+		double r[3];
 
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
 		if ( f->intensity <= 0 ) continue;
 
+		detgeom_transform_coords(&image->detgeom->panels[f->pn],
+		                         f->fs, f->ss, image->lambda,
+		                         r);
+
 		ttx = angle_between_2d(0.0, 1.0,
-		                       f->rx, 1.0/image->lambda + f->rz);
+		                       r[0], 1.0/image->lambda + r[2]);
 		tty = angle_between_2d(0.0, 1.0,
-		                       f->ry, 1.0/image->lambda + f->rz);
-		if ( f->rx < 0.0 ) ttx *= -1.0;
-		if ( f->ry < 0.0 ) tty *= -1.0;
+		                       r[1], 1.0/image->lambda + r[2]);
+		if ( r[0] < 0.0 ) ttx *= -1.0;
+		if ( r[1] < 0.0 ) tty *= -1.0;
 		x = tan(ttx)*FAKE_CLEN;
 		y = tan(tty)*FAKE_CLEN;
 
diff --git a/libcrystfel/src/indexers/xgandalf.c b/libcrystfel/src/indexers/xgandalf.c
index a0ce768d..a4773e18 100644
--- a/libcrystfel/src/indexers/xgandalf.c
+++ b/libcrystfel/src/indexers/xgandalf.c
@@ -92,14 +92,20 @@ int run_xgandalf(struct image *image, void *ipriv)
 	reciprocalPeaks_1_per_A->peakCount = 0;
 	for ( i = 0; i < peakCountMax && i < MAX_PEAK_COUNT_FOR_INDEXER; i++) {
 		struct imagefeature *f;
+		double r[3];
+
 		f = image_get_feature(image->features, i);
 		if (f == NULL) {
 			continue;
 		}
 
-		reciprocalPeaks_1_per_A->coordinates_x[reciprocalPeaks_1_per_A->peakCount] = f->rx * 1e-10;
-		reciprocalPeaks_1_per_A->coordinates_y[reciprocalPeaks_1_per_A->peakCount] = f->ry * 1e-10;
-		reciprocalPeaks_1_per_A->coordinates_z[reciprocalPeaks_1_per_A->peakCount] = f->rz * 1e-10;
+		detgeom_transform_coords(&image->detgeom->panels[f->pn],
+		                         f->fs, f->ss, image->lambda,
+		                         r);
+
+		reciprocalPeaks_1_per_A->coordinates_x[reciprocalPeaks_1_per_A->peakCount] = r[0] * 1e-10;
+		reciprocalPeaks_1_per_A->coordinates_y[reciprocalPeaks_1_per_A->peakCount] = r[1] * 1e-10;
+		reciprocalPeaks_1_per_A->coordinates_z[reciprocalPeaks_1_per_A->peakCount] = r[2] * 1e-10;
 		reciprocalPeaks_1_per_A->peakCount++;
 	}