detgeom_transform_coords: Take an additional detector shift

This allows the refined detector position to be used in a lot of places.

17 files changed, 52 insertions, 28 deletions

diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
index ebd1e6a5..c9f59bb7 100644
--- a/libcrystfel/src/crystal.c
+++ b/libcrystfel/src/crystal.c
@@ -67,7 +67,7 @@ struct _crystal
 	/* Text notes, which go in the stream */
 	char                    *notes;
 
-	/* Detector shift */
+	/* Detector shift in metres */
 	double			det_shift_x;
 	double			det_shift_y;
 };
diff --git a/libcrystfel/src/detgeom.c b/libcrystfel/src/detgeom.c
index 0ddbcbf4..5612a225 100644
--- a/libcrystfel/src/detgeom.c
+++ b/libcrystfel/src/detgeom.c
@@ -45,14 +45,15 @@
 void detgeom_transform_coords(struct detgeom_panel *p,
                               double fs, double ss,
                               double wavelength,
+                              double dx, double dy,
                               double *r)
 {
 	double xs, ys, zs;
 	double fac;
 
 	/* Calculate 3D position of given position, in pixels */
-	xs = p->cnx + fs*p->fsx + ss*p->ssx;
-	ys = p->cny + fs*p->fsy + ss*p->ssy;
+	xs = p->cnx + fs*p->fsx + ss*p->ssx + dx*p->pixel_pitch;
+	ys = p->cny + fs*p->fsy + ss*p->ssy + dy*p->pixel_pitch;
 	zs = p->cnz + fs*p->fsz + ss*p->ssz;
 
 	fac = wavelength * sqrt(xs*xs + ys*ys + zs*zs);
@@ -82,16 +83,16 @@ static double panel_max_res(struct detgeom_panel *p,
 	double r[3];
 	double max_res = 0.0;
 
-	detgeom_transform_coords(p, 0, 0, wavelength, r);
+	detgeom_transform_coords(p, 0, 0, wavelength, 0.0, 0.0, r);
 	max_res = biggest(max_res, modulus(r[0], r[1], r[2]));
 
-	detgeom_transform_coords(p, 0, p->h, wavelength, r);
+	detgeom_transform_coords(p, 0, p->h, wavelength, 0.0, 0.0, r);
 	max_res = biggest(max_res, modulus(r[0], r[1], r[2]));
 
-	detgeom_transform_coords(p, p->w, 0, wavelength, r);
+	detgeom_transform_coords(p, p->w, 0, wavelength, 0.0, 0.0, r);
 	max_res = biggest(max_res, modulus(r[0], r[1], r[2]));
 
-	detgeom_transform_coords(p, p->w, p->h, wavelength, r);
+	detgeom_transform_coords(p, p->w, p->h, wavelength, 0.0, 0.0, r);
 	max_res = biggest(max_res, modulus(r[0], r[1], r[2]));
 
 	return max_res;
diff --git a/libcrystfel/src/detgeom.h b/libcrystfel/src/detgeom.h
index 255c6cfb..5e3815ac 100644
--- a/libcrystfel/src/detgeom.h
+++ b/libcrystfel/src/detgeom.h
@@ -95,6 +95,7 @@ struct detgeom
 extern void detgeom_transform_coords(struct detgeom_panel *p,
                                      double fs, double ss,
                                      double wavelength,
+                                     double dx, double dy,
                                      double *r);
 
 extern void detgeom_free(struct detgeom *detgeom);
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 7e4a7549..f6971b1e 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -1175,7 +1175,7 @@ void mark_resolution_range_as_bad(struct image *image,
 				double r;
 				detgeom_transform_coords(p, fs, ss,
 				                         image->lambda,
-				                         q);
+				                         0.0, 0.0, q);
 				r = modulus(q[0], q[1], q[2]);
 				if ( (r >= min) && (r <= max) ) {
 					image->bad[i][fs+p->w*ss] = 1;
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 62df3cd6..e0959657 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -831,6 +831,7 @@ static int delete_explained_peaks(struct image *image, Crystal *cr)
 	double ax, ay, az;
 	double bx, by, bz;
 	double cx, cy, cz;
+	double dx, dy;
 	const double min_dist = 0.25;
 	int i, nspots = 0, nindexed = 0;
 
@@ -841,6 +842,8 @@ static int delete_explained_peaks(struct image *image, Crystal *cr)
 	cell_get_cartesian(crystal_get_cell(cr), &ax, &ay, &az,
 	                   &bx, &by, &bz, &cx, &cy, &cz);
 
+	crystal_get_det_shift(cr, &dx, &dy);
+
 	/* Loop over peaks, checking proximity to nearest reflection */
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
 
@@ -855,7 +858,8 @@ static int delete_explained_peaks(struct image *image, Crystal *cr)
 
 		/* Reciprocal space position of found peak */
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
-		                         f->fs, f->ss, image->lambda, q);
+		                         f->fs, f->ss, image->lambda, dx, dy,
+		                         q);
 
 		/* Decimal and fractional Miller indices of nearest
 		 * reciprocal lattice point */
diff --git a/libcrystfel/src/indexers/asdf.c b/libcrystfel/src/indexers/asdf.c
index af8acd78..0c57f9f0 100644
--- a/libcrystfel/src/indexers/asdf.c
+++ b/libcrystfel/src/indexers/asdf.c
@@ -1123,7 +1123,7 @@ int run_asdf(struct image *image, void *ipriv)
 
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
 		                         f->fs, f->ss, image->lambda,
-		                         r);
+		                         0.0, 0.0, r);
 
 		reflections[N_reflections] = gsl_vector_alloc(3);
 		gsl_vector_set(reflections[N_reflections], 0, r[0]/1e10);
diff --git a/libcrystfel/src/indexers/dirax.c b/libcrystfel/src/indexers/dirax.c
index d19cc8b0..4b59f6cb 100644
--- a/libcrystfel/src/indexers/dirax.c
+++ b/libcrystfel/src/indexers/dirax.c
@@ -497,7 +497,7 @@ static void write_drx(struct image *image)
 
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
 		                         f->fs, f->ss, image->lambda,
-		                         r);
+		                         0.0, 0.0, r);
 
 		fprintf(fh, "%10f %10f %10f %8f\n",
 		        r[0]/1e10, r[1]/1e10, r[2]/1e10, 1.0);
diff --git a/libcrystfel/src/indexers/felix.c b/libcrystfel/src/indexers/felix.c
index de49ac0b..89de5f70 100644
--- a/libcrystfel/src/indexers/felix.c
+++ b/libcrystfel/src/indexers/felix.c
@@ -371,7 +371,7 @@ static void write_gve(struct image *image, struct felix_private *gp)
 
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
 		                         f->fs, f->ss, image->lambda,
-		                         r);
+		                         0.0, 0.0, r);
 
 		fprintf(fh, "%.6f %.6f %.6f 0 0 %.6f %.6f %.6f 0\n",
 		        r[2]/1e10, r[0]/1e10, r[1]/1e10,
diff --git a/libcrystfel/src/indexers/mosflm.c b/libcrystfel/src/indexers/mosflm.c
index 9f674d9c..b0e0b121 100644
--- a/libcrystfel/src/indexers/mosflm.c
+++ b/libcrystfel/src/indexers/mosflm.c
@@ -364,7 +364,7 @@ static void write_spt(struct image *image, const char *filename)
 
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
 		                         f->fs, f->ss, image->lambda,
-		                         r);
+		                         0.0, 0.0, r);
 
 		ttx = angle_between_2d(0.0, 1.0,
 		                       r[0], 1.0/image->lambda + r[2]);
diff --git a/libcrystfel/src/indexers/pinkindexer.c b/libcrystfel/src/indexers/pinkindexer.c
index 03442764..6d98d3c0 100644
--- a/libcrystfel/src/indexers/pinkindexer.c
+++ b/libcrystfel/src/indexers/pinkindexer.c
@@ -112,7 +112,8 @@ int run_pinkIndexer(struct image *image, void *ipriv)
 		if ( f == NULL ) continue;
 
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
-		                         f->fs, f->ss, image->lambda, r);
+		                         f->fs, f->ss, image->lambda,
+		                         0.0, 0.0, r);
 		reciprocalPeaks_1_per_A->coordinates_x[reciprocalPeaks_1_per_A->peakCount] = r[2] * 1e-10;
 		reciprocalPeaks_1_per_A->coordinates_y[reciprocalPeaks_1_per_A->peakCount] = r[0] * 1e-10;
 		reciprocalPeaks_1_per_A->coordinates_z[reciprocalPeaks_1_per_A->peakCount] = r[1] * 1e-10;
diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c
index 66c0d1cc..1bccf1e0 100644
--- a/libcrystfel/src/indexers/taketwo.c
+++ b/libcrystfel/src/indexers/taketwo.c
@@ -2164,7 +2164,7 @@ int taketwo_index(struct image *image, void *priv)
 
 		detgeom_transform_coords(&image->detgeom->panels[pk->pn],
 		                         pk->fs, pk->ss, image->lambda,
-		                         r);
+		                         0.0, 0.0, r);
 
 		rlps[n_rlps].u = r[0];
 		rlps[n_rlps].v = r[1];
diff --git a/libcrystfel/src/indexers/xds.c b/libcrystfel/src/indexers/xds.c
index c66f734a..3b2f2b87 100644
--- a/libcrystfel/src/indexers/xds.c
+++ b/libcrystfel/src/indexers/xds.c
@@ -221,7 +221,7 @@ static void write_spot(struct image *image)
 
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
 		                         f->fs, f->ss, image->lambda,
-		                         r);
+		                         0.0, 0.0, r);
 
 		ttx = angle_between_2d(0.0, 1.0,
 		                       r[0], 1.0/image->lambda + r[2]);
diff --git a/libcrystfel/src/indexers/xgandalf.c b/libcrystfel/src/indexers/xgandalf.c
index 04cd6a87..6b09f65c 100644
--- a/libcrystfel/src/indexers/xgandalf.c
+++ b/libcrystfel/src/indexers/xgandalf.c
@@ -101,7 +101,7 @@ int run_xgandalf(struct image *image, void *ipriv)
 
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
 		                         f->fs, f->ss, image->lambda,
-		                         r);
+		                         0.0, 0.0, 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;
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index d88e769c..4c813a11 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1518,7 +1518,7 @@ int integrate_rings_once(Reflection *refl,
 }
 
 
-static double estimate_resolution(UnitCell *cell, struct image *image)
+static double estimate_resolution(Crystal *cr, struct image *image)
 {
 	int i;
 	const double min_dist = 0.25;
@@ -1527,6 +1527,9 @@ static double estimate_resolution(UnitCell *cell, struct image *image)
 	int n_acc = 0;
 	int max_acc = 1024;
 	int n;
+	double dx, dy;
+	UnitCell *cell;
+
 
 	acc = malloc(max_acc*sizeof(double));
 	if ( acc == NULL ) {
@@ -1534,6 +1537,9 @@ static double estimate_resolution(UnitCell *cell, struct image *image)
 		return INFINITY;
 	}
 
+	cell = crystal_get_cell(cr);
+	crystal_get_det_shift(cr, &dx, &dy);
+
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
 
 		struct imagefeature *f;
@@ -1554,7 +1560,7 @@ static double estimate_resolution(UnitCell *cell, struct image *image)
 
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
 		                         f->fs, f->ss, image->lambda,
-		                         r);
+		                         dx, dy, r);
 
 		/* Decimal and fractional Miller indices of nearest
 		 * reciprocal lattice point */
@@ -1670,8 +1676,7 @@ void integrate_all_5(struct image *image, IntegrationMethod meth,
 			                           saved_R * 5);
 		}
 
-		res = estimate_resolution(crystal_get_cell(image->crystals[i]),
-		                          image);
+		res = estimate_resolution(image->crystals[i], image);
 		crystal_set_resolution_limit(image->crystals[i], res);
 
 		list = predict_to_res(image->crystals[i], res+push_res);
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 685e8492..d55ddd03 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -600,15 +600,22 @@ int indexing_peak_check(struct image *image, Crystal **crystals, int n_cryst,
 		if ( f == NULL ) continue;
 		n_feat++;
 
-		/* Reciprocal space position of found peak */
-		detgeom_transform_coords(&image->detgeom->panels[f->pn],
-		                         f->fs, f->ss, image->lambda, q);
-
 		for ( j=0; j<n_cryst; j++ ) {
 
 			double ax, ay, az;
 			double bx, by, bz;
 			double cx, cy, cz;
+			double dx, dy;
+
+			crystal_get_det_shift(crystals[j], &dx, &dy);
+
+			/* Reciprocal space position of found peak,
+			 * based on a calculation including any updates to the
+			 * detector position from the refinement of the
+			 * current crystal. */
+			detgeom_transform_coords(&image->detgeom->panels[f->pn],
+			                         f->fs, f->ss, image->lambda,
+			                         dx, dy, q);
 
 			cell_get_cartesian(crystal_get_cell(crystals[j]),
 			                   &ax, &ay, &az,
@@ -748,7 +755,7 @@ double estimate_peak_resolution(ImageFeatureList *peaks, double lambda,
 
 		detgeom_transform_coords(&det->panels[f->pn],
 		                         f->fs, f->ss,
-		                         lambda, r);
+		                         lambda, 0.0, 0.0, r);
 		rns[i] = modulus(r[0], r[1], r[2]);
 
 	}
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index 7166b3d9..2432055f 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -178,12 +178,15 @@ static int pair_peaks(struct image *image, Crystal *cr,
 	double ax, ay, az;
 	double bx, by, bz;
 	double cx, cy, cz;
+	double dx, dy;
 	RefList *all_reflist;
 
 	all_reflist = reflist_new();
 	cell_get_cartesian(crystal_get_cell(cr),
 	                   &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
 
+	crystal_get_det_shift(cr, &dx, &dy);
+
 	/* First, create a RefList containing the most likely indices for each
 	 * peak, with no exclusion criteria */
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
@@ -199,7 +202,7 @@ static int pair_peaks(struct image *image, Crystal *cr,
 
 		detgeom_transform_coords(&image->detgeom->panels[f->pn],
 		                         f->fs, f->ss, image->lambda,
-		                         r);
+		                         dx, dy, r);
 
 		/* Decimal and fractional Miller indices of nearest reciprocal
 		 * lattice point */
@@ -584,6 +587,8 @@ int refine_prediction(struct image *image, Crystal *cr)
 	}
 	crystal_set_reflections(cr, reflist);
 
+	crystal_get_det_shift(cr, &total_x, &total_y);
+
 	/* Normalise the intensities to max 1 */
 	max_I = -INFINITY;
 	for ( i=0; i<n; i++ ) {
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 3b4f033b..83756c7a 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -207,7 +207,7 @@ static int write_peaks(const struct image *image,
 
 		p = &image->detgeom->panels[f->pn];
 		detgeom_transform_coords(p, f->fs, f->ss,
-		                         image->lambda, r);
+		                         image->lambda, 0.0, 0.0, r);
 		q = modulus(r[0], r[1], r[2]);
 
 		write_fs = f->fs;