Crystal: Remove reference to image structure (part 1)

7 files changed, 28 insertions, 71 deletions

diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
index 71d707d6..cece3eb4 100644
--- a/libcrystfel/src/crystal.c
+++ b/libcrystfel/src/crystal.c
@@ -41,9 +41,6 @@
 
 struct _crystal
 {
-	/* The image containing the crystal */
-	struct image            *image;
-
 	/* Information about the crystal */
 	UnitCell                *cell;
 	double                  m;     /* Mosaicity in radians */
@@ -222,18 +219,6 @@ long long int crystal_get_num_implausible_reflections(Crystal *cryst)
 }
 
 
-struct image *crystal_get_image(Crystal *cryst)
-{
-	return cryst->image;
-}
-
-
-const struct image *crystal_get_image_const(const Crystal *cryst)
-{
-	return cryst->image;
-}
-
-
 double crystal_get_osf(Crystal *cryst)
 {
 	return cryst->osf;
@@ -311,12 +296,6 @@ void crystal_set_num_implausible_reflections(Crystal *cryst, long long int n)
 }
 
 
-void crystal_set_image(Crystal *cryst, struct image *image)
-{
-	cryst->image = image;
-}
-
-
 void crystal_set_osf(Crystal *cryst, double osf)
 {
 	cryst->osf = osf;
diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h
index 5a4ca3f6..33764bc0 100644
--- a/libcrystfel/src/crystal.h
+++ b/libcrystfel/src/crystal.h
@@ -64,8 +64,6 @@ extern long long int crystal_get_num_implausible_reflections(Crystal *cryst);
 extern int crystal_get_user_flag(Crystal *cryst);
 extern double crystal_get_osf(Crystal *cryst);
 extern double crystal_get_Bfac(Crystal *cryst);
-extern struct image *crystal_get_image(Crystal *cryst);
-extern const struct image *crystal_get_image_const(const Crystal *cryst);
 extern double crystal_get_mosaicity(Crystal *cryst);
 extern const char *crystal_get_notes(Crystal *cryst);
 extern void crystal_get_det_shift(Crystal *cryst,
@@ -82,7 +80,6 @@ extern void crystal_set_num_implausible_reflections(Crystal *cryst,
 extern void crystal_set_user_flag(Crystal *cryst, int flag);
 extern void crystal_set_osf(Crystal *cryst, double osf);
 extern void crystal_set_Bfac(Crystal *cryst, double B);
-extern void crystal_set_image(Crystal *cryst, struct image *image);
 extern void crystal_set_mosaicity(Crystal *cryst, double m);
 extern void crystal_set_notes(Crystal *cryst, const char *notes);
 extern void crystal_set_det_shift(Crystal *cryst,
diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index 674fe4d0..32da348a 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -425,14 +425,15 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
 
 /**
  * \param cryst: A \ref Crystal
+ * \param image: An image structure
  * \param max_res: Maximum resolution to predict to (m^-1)
  *
- * Calculates reflection positions for \p crys, up to maximum 1/d value
- * \p max_res
+ * Calculates reflection positions for \p crys, as seen in \p image,
+ * up to maximum 1/d value \p max_res
  *
  * \returns A list of predicted reflections
  */
-RefList *predict_to_res(Crystal *cryst, double max_res)
+RefList *predict_to_res(Crystal *cryst, struct image *image, double max_res)
 {
 	double ax, ay, az;
 	double bx, by, bz;
@@ -445,7 +446,6 @@ RefList *predict_to_res(Crystal *cryst, double max_res)
 	double mres;
 	signed int h, k, l;
 	UnitCell *cell;
-	struct image *image;
 
 	cell = crystal_get_cell(cryst);
 	if ( cell == NULL ) return NULL;
@@ -462,7 +462,6 @@ RefList *predict_to_res(Crystal *cryst, double max_res)
 
 	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
 
-	image = crystal_get_image(cryst);
 	mres = detgeom_max_resolution(image->detgeom, image->lambda);
 	if ( mres > max_res ) mres = max_res;
 
@@ -498,7 +497,7 @@ RefList *predict_to_res(Crystal *cryst, double max_res)
 		yl = h*asy + k*bsy + l*csy;
 		zl = h*asz + k*bsz + l*csz;
 
-		refl = check_reflection(crystal_get_image(cryst), cryst,
+		refl = check_reflection(image, cryst,
 		                        h, k, l, xl, yl, zl, NULL);
 
 		if ( refl != NULL ) {
@@ -534,12 +533,11 @@ static void set_unity_partialities(Crystal *cryst)
 }
 
 
-static void set_random_partialities(Crystal *cryst)
+static void set_random_partialities(Crystal *cryst, int image_serial)
 {
 	RefList *list;
 	Reflection *refl;
 	RefListIterator *iter;
-	struct image *image;
 
 	list = crystal_get_reflections(cryst);
 	if ( list == NULL ) {
@@ -547,19 +545,13 @@ static void set_random_partialities(Crystal *cryst)
 		return;
 	}
 
-	image = crystal_get_image(cryst);
-	if ( image == NULL ) {
-		ERROR("No image structure for partiality calculation!\n");
-		return;
-	}
-
 	for ( refl = first_refl(list, &iter);
 	      refl != NULL;
 	      refl = next_refl(refl, iter) )
 	{
 		signed int h, k, l;
 		get_symmetric_indices(refl, &h, &k, &l);
-		set_partiality(refl, random_partiality(h, k, l, image->serial));
+		set_partiality(refl, random_partiality(h, k, l, image_serial));
 		set_lorentz(refl, 1.0);
 	}
 }
@@ -682,13 +674,12 @@ static double do_integral(double q2, double zl, double R,
 }
 
 
-static void ginn_spectrum_partialities(Crystal *cryst)
+static void ginn_spectrum_partialities(Crystal *cryst, struct image *image)
 {
 	RefList *list;
 	Reflection *refl;
 	RefListIterator *iter;
 	double r0, m;
-	struct image *image;
 	UnitCell *cell;
 	double asx, asy, asz, bsx, bsy, bsz, csx, csy, csz;
 
@@ -698,12 +689,6 @@ static void ginn_spectrum_partialities(Crystal *cryst)
 		return;
 	}
 
-	image = crystal_get_image(cryst);
-	if ( image == NULL ) {
-		ERROR("No image for partiality calculation!\n");
-		return;
-	}
-
 	cell = crystal_get_cell(cryst);
 	if ( cell == NULL ) {
 		ERROR("No unit cell for partiality calculation!\n");
@@ -753,13 +738,12 @@ static void ginn_spectrum_partialities(Crystal *cryst)
 }
 
 
-static void ewald_offset_partialities(Crystal *cryst)
+static void ewald_offset_partialities(Crystal *cryst, struct image *image)
 {
 	RefList *list;
 	Reflection *refl;
 	RefListIterator *iter;
 	double r0, m;
-	struct image *image;
 	UnitCell *cell;
 	double asx, asy, asz, bsx, bsy, bsz, csx, csy, csz;
 
@@ -769,12 +753,6 @@ static void ewald_offset_partialities(Crystal *cryst)
 		return;
 	}
 
-	image = crystal_get_image(cryst);
-	if ( image == NULL ) {
-		ERROR("No image for partiality calculation!\n");
-		return;
-	}
-
 	cell = crystal_get_cell(cryst);
 	if ( cell == NULL ) {
 		ERROR("No unit cell for partiality calculation!\n");
@@ -826,7 +804,8 @@ static void ewald_offset_partialities(Crystal *cryst)
  * called \ref predict_to_res or \ref update_predictions, because this function
  * relies on the limiting wavelength values calculated by those functions.
  */
-void calculate_partialities(Crystal *cryst, PartialityModel pmodel)
+void calculate_partialities(Crystal *cryst, struct image *image,
+                            PartialityModel pmodel)
 {
 	switch ( pmodel ) {
 
@@ -835,15 +814,15 @@ void calculate_partialities(Crystal *cryst, PartialityModel pmodel)
 		break;
 
 		case PMODEL_XSPHERE :
-		ginn_spectrum_partialities(cryst);
+		ginn_spectrum_partialities(cryst, image);
 		break;
 
 		case PMODEL_OFFSET :
-		ewald_offset_partialities(cryst);
+		ewald_offset_partialities(cryst, image);
 		break;
 
 		case PMODEL_RANDOM :
-		set_random_partialities(cryst);
+		set_random_partialities(cryst, image->serial);
 		break;
 
 		case PMODEL_GGPM :
@@ -861,22 +840,23 @@ void calculate_partialities(Crystal *cryst, PartialityModel pmodel)
 
 /**
  * \param cryst A \ref Crystal
+ * \param image An image structure
  *
  * Updates the predicted reflections (positions and excitation errors, but not
- * the actual partialities) of \p cryst's reflections according to
- * the current state of the crystal (e.g. its unit cell parameters).
+ * the actual partialities) of \p cryst's reflections as seen in \p image,
+ * according to the current state of the crystal (e.g. its unit cell
+ * parameters).
  *
  * If you need to update the partialities as well, call
  * \ref calculate_partialities afterwards.
  */
-void update_predictions(Crystal *cryst)
+void update_predictions(Crystal *cryst, struct image *image)
 {
 	Reflection *refl;
 	RefListIterator *iter;
 	double asx, asy, asz;
 	double bsx, bsy, bsz;
 	double csx, csy, csz;
-	struct image *image = crystal_get_image(cryst);
 
 	cell_get_reciprocal(crystal_get_cell(cryst), &asx, &asy, &asz,
 	                    &bsx, &bsy, &bsz, &csx, &csy, &csz);
diff --git a/libcrystfel/src/geometry.h b/libcrystfel/src/geometry.h
index d05c8832..b9f98694 100644
--- a/libcrystfel/src/geometry.h
+++ b/libcrystfel/src/geometry.h
@@ -35,6 +35,7 @@
 #include "cell.h"
 #include "crystal.h"
 #include "detgeom.h"
+#include "image.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -77,11 +78,12 @@ struct polarisation
 };
 
 
-extern RefList *predict_to_res(Crystal *cryst, double max_res);
+extern RefList *predict_to_res(Crystal *cryst, struct image *image, double max_res);
 
-extern void calculate_partialities(Crystal *cryst, PartialityModel pmodel);
+extern void calculate_partialities(Crystal *cryst, struct image *image,
+                                   PartialityModel pmodel);
 
-extern void update_predictions(Crystal *cryst);
+extern void update_predictions(Crystal *cryst, struct image *image);
 extern struct polarisation parse_polarisation(const char *text);
 extern void polarisation_correction(RefList *list, UnitCell *cell,
                                     struct polarisation p);
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index d93664b1..db2058a5 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -701,7 +701,6 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 		/* ... starting at the end of the (complete) list ... */
 		Crystal *cr = image->crystals[this_crystal];
 
-		crystal_set_image(cr, image);
 		crystal_set_profile_radius(cr, 0.02e9);
 		crystal_set_mosaicity(cr, 0.0);
 
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 8b05efe7..3912114a 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1665,7 +1665,7 @@ void integrate_all_5(struct image *image, IntegrationMethod meth,
 		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);
+		list = predict_to_res(image->crystals[i], image, res+push_res);
 		crystal_set_reflections(image->crystals[i], list);
 
 		if ( overpredict ) {
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index d5a3b403..24045ddb 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -489,7 +489,7 @@ static int pair_peaks(struct image *image, Crystal *cr,
 	/* Get the excitation errors and detector positions for the candidate
 	 * reflections */
 	crystal_set_reflections(cr, all_reflist);
-	update_predictions(cr);
+	update_predictions(cr, image);
 
 	/* Pass over the peaks again, keeping only the ones which look like
 	 * good pairings */
@@ -570,7 +570,7 @@ int refine_radius(Crystal *cr, struct image *image)
 		return 1;
 	}
 	crystal_set_reflections(cr, reflist);
-	update_predictions(cr);
+	update_predictions(cr, image);
 	crystal_set_reflections(cr, NULL);
 
 	qsort(rps, n_acc, sizeof(struct reflpeak), cmpd2);
@@ -855,7 +855,7 @@ int refine_prediction(struct image *image, Crystal *cr,
 
 	/* Refine (max 5 cycles) */
 	for ( i=0; i<5; i++ ) {
-		update_predictions(cr);
+		update_predictions(cr, image);
 		if ( iterate(rps, n, crystal_get_cell(cr), image, Minvs, total_shifts) )
 		{
 			crystal_set_reflections(cr, NULL);