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.

11 files changed, 85 insertions, 70 deletions

diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 91a0afc4..fb33f2d9 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -68,13 +68,6 @@ struct imagefeature {
 	int                             pn;         /**< Panel number */
 	double                          intensity;  /**< Intensity */
 
-	/** \name Reciprocal space coordinates (m^-1) of this feature */
-	/** @{ */
-	double                          rx;
-	double                          ry;
-	double                          rz;
-	/** @} */
-
 	const char                      *name;  /**< Text name, e.g. "5,3,-1" */
 };
 
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 457fd7fe..130b4262 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -563,32 +563,6 @@ void cleanup_indexing(IndexingPrivate *ipriv)
 }
 
 
-void map_all_peaks(struct image *image)
-{
-	int i, n;
-
-	n = image_feature_count(image->features);
-
-	/* Map positions to 3D */
-	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);
-		f->rx = r[0];
-		f->ry = r[1];
-		f->rz = r[2];
-
-	}
-}
-
-
 /* Return 0 for cell OK, 1 for cell incorrect */
 static int check_cell(IndexingFlags flags, Crystal *cr, UnitCell *target,
                       double *tolerance)
@@ -953,7 +927,6 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 
 	if ( ipriv == NULL ) return;
 
-	map_all_peaks(image);
 	image->crystals = NULL;
 	image->n_crystals = 0;
 
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++;
 	}
 
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 4a66363b..c15d66ba 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1533,7 +1533,7 @@ int integrate_rings_once(Reflection *refl,
 }
 
 
-static double estimate_resolution(UnitCell *cell, ImageFeatureList *flist)
+static double estimate_resolution(UnitCell *cell, struct image *image)
 {
 	int i;
 	const double min_dist = 0.25;
@@ -1549,27 +1549,33 @@ static double estimate_resolution(UnitCell *cell, ImageFeatureList *flist)
 		return INFINITY;
 	}
 
-	for ( i=0; i<image_feature_count(flist); i++ ) {
+	for ( i=0; i<image_feature_count(image->features); i++ ) {
 
 		struct imagefeature *f;
 		double h, k, l, hd, kd, ld;
-
-		/* Assume all image "features" are genuine peaks */
-		f = image_get_feature(flist, i);
-		if ( f == NULL ) continue;
-
 		double ax, ay, az;
 		double bx, by, bz;
 		double cx, cy, cz;
+		double r[3];
+
+		/* Assume all image "features" are genuine peaks */
+		f = image_get_feature(image->features, i);
+		if ( f == NULL ) continue;
 
 		cell_get_cartesian(cell,
-		                   &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+		                   &ax, &ay, &az,
+		                   &bx, &by, &bz,
+		                   &cx, &cy, &cz);
+
+		detgeom_transform_coords(&image->detgeom->panels[f->pn],
+		                         f->fs, f->ss, image->lambda,
+		                         r);
 
 		/* Decimal and fractional Miller indices of nearest
 		 * reciprocal lattice point */
-		hd = f->rx * ax + f->ry * ay + f->rz * az;
-		kd = f->rx * bx + f->ry * by + f->rz * bz;
-		ld = f->rx * cx + f->ry * cy + f->rz * cz;
+		hd = r[0] * ax + r[1] * ay + r[2] * az;
+		kd = r[0] * bx + r[1] * by + r[2] * bz;
+		ld = r[0] * cx + r[1] * cy + r[2] * cz;
 		h = lrint(hd);
 		k = lrint(kd);
 		l = lrint(ld);
@@ -1680,7 +1686,7 @@ void integrate_all_5(struct image *image, IntegrationMethod meth,
 		}
 
 		res = estimate_resolution(crystal_get_cell(image->crystals[i]),
-		                          image->features);
+		                          image);
 		crystal_set_resolution_limit(image->crystals[i], res);
 
 		list = predict_to_res(image->crystals[i], res+push_res);
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index 43a52cae..1c9e8504 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -191,16 +191,21 @@ static int pair_peaks(struct image *image, Crystal *cr,
 		struct imagefeature *f;
 		double h, k, l, hd, kd, ld;
 		Reflection *refl;
+		double r[3];
 
 		/* Assume all image "features" are genuine peaks */
 		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);
+
 		/* Decimal and fractional Miller indices of nearest reciprocal
 		 * lattice point */
-		hd = f->rx * ax + f->ry * ay + f->rz * az;
-		kd = f->rx * bx + f->ry * by + f->rz * bz;
-		ld = f->rx * cx + f->ry * cy + f->rz * cz;
+		hd = r[0] * ax + r[1] * ay + r[2] * az;
+		kd = r[0] * bx + r[1] * by + r[2] * bz;
+		ld = r[0] * cx + r[1] * cy + r[2] * cz;
 		h = lrint(hd);
 		k = lrint(kd);
 		l = lrint(ld);