Added detector shift to crystal structure, wrote get and get functions

4 files changed, 42 insertions, 6 deletions

diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
index dc2b28fb..116b6bce 100644
--- a/libcrystfel/src/crystal.c
+++ b/libcrystfel/src/crystal.c
@@ -72,6 +72,10 @@ struct _crystal
 
 	/* Text notes, which go in the stream */
 	char                    *notes;
+
+	/* Detector shift */
+	double			det_shift_x;
+	double			det_shift_y;
 };
 
 
@@ -100,6 +104,8 @@ Crystal *crystal_new()
 	cryst->n_implausible = 0;
 	cryst->notes = NULL;
 	cryst->user_flag = 0;
+	cryst->det_shift_x = 0;
+	cryst->det_shift_y = 0;
 
 	return cryst;
 }
@@ -219,6 +225,15 @@ const char *crystal_get_notes(Crystal *cryst)
 }
 
 
+void crystal_get_det_shift(Crystal *cryst, double* shift_x,
+                                       double *shift_y)
+{
+	*shift_x = cryst->det_shift_x;
+	*shift_y = cryst->det_shift_y;
+}
+
+
+
 /********************************** Setters ***********************************/
 
 
@@ -318,3 +333,10 @@ void crystal_add_notes(Crystal *cryst, const char *notes_add)
 	free(cryst->notes);
 	cryst->notes = nnotes;
 }
+
+
+void crystal_set_det_shift(Crystal *cryst, double shift_x, double shift_y)
+{
+	cryst->det_shift_x = shift_x;
+	cryst->det_shift_y = shift_y;
+}
diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h
index f0d732ff..cf9582d7 100644
--- a/libcrystfel/src/crystal.h
+++ b/libcrystfel/src/crystal.h
@@ -66,6 +66,8 @@ extern double crystal_get_Bfac(Crystal *cryst);
 extern struct image *crystal_get_image(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, double *shift_x,
+                                  double* shift_y);
 
 extern void crystal_set_cell(Crystal *cryst, UnitCell *cell);
 extern void crystal_set_profile_radius(Crystal *cryst, double r);
@@ -81,7 +83,8 @@ 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, double shift_x,
+                                  double shift_y);
 extern void crystal_add_notes(Crystal *cryst, const char *notes_add);
 
 #ifdef __cplusplus
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index 743b4d04..dfc7242f 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -584,7 +584,6 @@ int refine_prediction(struct image *image, Crystal *cr)
 	double total_x = 0.0;
 	double total_y = 0.0;
 	double total_z = 0.0;
-	char tmp[1024];
 
 	rps = malloc(image_feature_count(image->features)
 	                       * sizeof(struct reflpeak));
@@ -626,9 +625,7 @@ int refine_prediction(struct image *image, Crystal *cr)
 	}
 	//STATUS("Final residual = %e\n", residual(rps, n, image->det));
 
-	snprintf(tmp, 1024, "predict_refine/det_shift x = %.3f y = %.3f mm",
-	                    total_x*1e3, total_y*1e3);
-	crystal_add_notes(cr, tmp);
+	crystal_set_det_shift(cr, total_x, total_y);
 
 	crystal_set_reflections(cr, NULL);
 	reflist_free(reflist);
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index d374a3d3..c8218790 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -702,6 +702,7 @@ static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
 	double csx, csy, csz;
 	double a, b, c, al, be, ga;
 	double rad;
+	double det_shift_x, det_shift_y;
 	int ret = 0;
 
 	fprintf(st->fh, CRYSTAL_START_MARKER"\n");
@@ -737,6 +738,11 @@ static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
 		fprintf(st->fh, "%s\n", crystal_get_notes(cr));
 	}
 
+	crystal_get_det_shift(cr, &det_shift_x, &det_shift_y);
+
+	fprintf(st->fh, "predict_refine/det_shift x = %.3f y = %.3f mm",
+	        det_shift_x*1e3, det_shift_y*1e3);
+
 	reflist = crystal_get_reflections(cr);
 	if ( reflist != NULL ) {
 
@@ -918,6 +924,7 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 	Crystal *cr;
 	int n;
 	Crystal **crystals_new;
+	double shift_x, shift_y;
 
 	as.u = 0.0;  as.v = 0.0;  as.w = 0.0;
 	bs.u = 0.0;  bs.v = 0.0;  bs.w = 0.0;
@@ -1008,6 +1015,12 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 			crystal_set_profile_radius(cr, rad*1e9);
 		}
 
+		if ( sscanf(line, "predict_refine/det_shift x = %lf "
+		                  "y = %lf mm\n", &shift_x, &shift_y ) == 2 ) {
+			crystal_set_det_shift(cr, shift_x*1e-3, shift_y*1e-3);
+		}
+
+
 		if ( (strcmp(line, REFLECTION_START_MARKER) == 0)
 		  && (srf & STREAM_READ_REFLECTIONS) )
 		{
@@ -1029,7 +1042,8 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 			if ( reflist == NULL ) {
 				ERROR("Failed while reading reflections\n");
 				ERROR("Filename = %s\n", image->filename);
-				ERROR("Event = %s\n", get_event_string(image->event));
+				ERROR("Event = %s\n",
+				      get_event_string(image->event));
 				break;
 			}