Refactoring of peaks and reflections I/O

6 files changed, 143 insertions, 36 deletions

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 4681ab28..a7829474 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -1488,3 +1488,43 @@ void mark_resolution_range_as_bad(struct image *image,
 
 	}
 }
+
+
+extern int single_source (struct detector *det, char *element)
+{
+	int pi;
+	char *first_datafrom = NULL;
+	char *curr_datafrom = NULL;
+
+	if ( det->panels[0].data_from == NULL ) {
+		if ( element != NULL ) {
+			first_datafrom = strdup(element);
+		} else {
+			first_datafrom = strdup("/data/data");
+		}
+	} else {
+		first_datafrom = strdup(det->panels[0].data_from);
+	}
+
+	for ( pi=1;pi<det->n_panels;pi++ ) {
+
+		if ( det->panels[pi].data_from == NULL ) {
+			if ( element != NULL ) {
+				curr_datafrom = strdup(element);
+			} else {
+				curr_datafrom = strdup("/data/data");
+			}
+		} else {
+			curr_datafrom = strdup(det->panels[pi].data_from);
+		}
+
+		if ( strcmp(curr_datafrom, first_datafrom) != 0 ) {
+			return 0;
+		}
+	}
+
+	free(first_datafrom);
+	free(curr_datafrom);
+
+	return 1;
+}
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index fcd44ed2..6dc398d7 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -209,6 +209,9 @@ extern int write_detector_geometry(const char *filename, struct detector *det);
 extern void mark_resolution_range_as_bad(struct image *image,
                                          double min, double max);
 
+extern int single_source (struct detector *det, char *element);
+
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 69edb768..c3fe4505 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -69,6 +69,7 @@ struct imagefeature {
 	struct image                    *parent;
 	double                          fs;
 	double                          ss;
+	char                            *pn;
 	double                          intensity;
 
 	/* Reciprocal space coordinates (m^-1 of course) of this feature */
diff --git a/libcrystfel/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c
index 5d52ec93..e033791b 100644
--- a/libcrystfel/src/reflist-utils.c
+++ b/libcrystfel/src/reflist-utils.c
@@ -286,6 +286,12 @@ int write_reflist(const char *filename, RefList *list)
 
 RefList *read_reflections_from_file(FILE *fh)
 {
+	return read_reflections_from_file2(fh, NULL);
+}
+
+
+RefList *read_reflections_from_file2(FILE *fh, struct detector *det)
+{
 	char *rval = NULL;
 	RefList *out;
 	int major_version;  /* Minor version as well, but not used yet */
@@ -364,12 +370,15 @@ RefList *read_reflections_from_file(FILE *fh)
 			signed int h, k, l;
 			float intensity, sigma, fs, ss;
 			char phs[1024];
+			char pn[32];
 			int cts;
 			int r;
+			struct panel *p;
+			float read_fs, read_ss;
 
-			r = sscanf(line, "%i %i %i %f %s %f %i %f %f",
+			r = sscanf(line, "%i %i %i %f %s %f %i %f %f %s",
 				   &h, &k, &l, &intensity, phs, &sigma,
-				   &cts, &fs, &ss);
+				   &cts, &fs, &ss, pn);
 
 			if ( r != 9 ) {
 				reflist_free(out);
@@ -378,7 +387,14 @@ RefList *read_reflections_from_file(FILE *fh)
 
 			refl = add_refl(out, h, k, l);
 			set_intensity(refl, intensity);
-			set_detector_pos(refl, 0.0, fs, ss);
+
+			if ( det != NULL) {
+				p = find_panel_by_name(det, pn);
+				read_ss = ss-p->orig_min_ss+p->min_ss;
+				read_fs = fs-p->orig_min_fs+p->min_fs;
+				set_detector_pos(refl, 0.0, read_fs, read_ss);
+			}
+
 			set_esd_intensity(refl, sigma);
 			set_redundancy(refl, cts);
 
@@ -396,6 +412,12 @@ RefList *read_reflections_from_file(FILE *fh)
 
 RefList *read_reflections(const char *filename)
 {
+	return read_reflections2(filename, NULL);
+}
+
+
+RefList *read_reflections2(const char *filename, struct detector *det)
+{
 	FILE *fh;
 	RefList *out;
 
@@ -410,7 +432,7 @@ RefList *read_reflections(const char *filename)
 		return NULL;
 	}
 
-	out = read_reflections_from_file(fh);
+	out = read_reflections_from_file2(fh, det);
 
 	fclose(fh);
 
diff --git a/libcrystfel/src/reflist-utils.h b/libcrystfel/src/reflist-utils.h
index 86f61bbf..6bd2af47 100644
--- a/libcrystfel/src/reflist-utils.h
+++ b/libcrystfel/src/reflist-utils.h
@@ -33,7 +33,7 @@
 #ifndef REFLIST_UTILS_H
 #define REFLIST_UTILS_H
 
-
+#include "image.h"
 #include "reflist.h"
 #include "cell.h"
 #include "symmetry.h"
@@ -50,8 +50,10 @@ extern void write_reflections_to_file(FILE *fh, RefList *list);
 extern int write_reflist(const char *filename, RefList *list);
 extern int write_reflist_2(const char *filename, RefList *list, SymOpList *sym);
 
+extern RefList *read_reflections_from_file2(FILE *fh, struct detector* det);
 extern RefList *read_reflections_from_file(FILE *fh);
 
+extern RefList *read_reflections2(const char *filename, struct detector* det);
 extern RefList *read_reflections(const char *filename);
 
 extern int check_list_symmetry(RefList *list, const SymOpList *sym);
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 9aaa53df..e1a67714 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -78,8 +78,11 @@ static int read_peaks(FILE *fh, struct image *image)
 	do {
 
 		char line[1024];
+		char pn[32];
 		float x, y, d, intensity;
 		int r;
+		struct panel *p = NULL;
+		int add_x, add_y;
 
 		rval = fgets(line, 1023, fh);
 		if ( rval == NULL ) continue;
@@ -87,16 +90,22 @@ static int read_peaks(FILE *fh, struct image *image)
 
 		if ( strcmp(line, PEAK_LIST_END_MARKER) == 0 ) return 0;
 
-		r = sscanf(line, "%f %f %f %f", &x, &y, &d, &intensity);
-		if ( (r != 4) && (!first) ) {
+		r = sscanf(line, "%f %f %s %f %f", &x, &y, pn, &d, &intensity);
+		if ( (r != 5) && (!first) ) {
 			ERROR("Failed to parse peak list line.\n");
 			ERROR("The failed line was: '%s'\n", line);
 			return 1;
 		}
 
 		first = 0;
-		if ( r == 4 ) {
-			image_add_feature(image->features, x, y,
+
+		p = find_panel_by_name(image->det, pn);
+
+		add_x = x-p->orig_min_fs+p->min_fs;
+		add_y = x-p->orig_min_ss+p->min_ss;
+
+		if ( r == 5 ) {
+			image_add_feature(image->features, add_x, add_y,
 			                  image, intensity, NULL);
 		}
 
@@ -112,13 +121,16 @@ static void write_peaks(struct image *image, FILE *ofh)
 	int i;
 
 	fprintf(ofh, PEAK_LIST_START_MARKER"\n");
-	fprintf(ofh, "  fs/px   ss/px  (1/d)/nm^-1   Intensity\n");
+	fprintf(ofh, "  fs/px   ss/px panel  (1/d)/nm^-1   Intensity\n");
 
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
 
 		struct imagefeature *f;
 		struct rvec r;
 		double q;
+		struct panel *p;
+		double write_fs, write_ss;
+
 
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
@@ -126,8 +138,12 @@ static void write_peaks(struct image *image, FILE *ofh)
 		r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda);
 		q = modulus(r.u, r.v, r.w);
 
-		fprintf(ofh, "%7.2f %7.2f   %10.2f  %10.2f\n",
-		       f->fs, f->ss, q/1.0e9, f->intensity);
+		p = find_panel(image->det,f->fs,f->ss);
+		write_fs = f->fs-p->min_fs+p->orig_min_fs;
+		write_ss = f->ss-p->min_ss+p->orig_min_ss;
+
+		fprintf(ofh, "%7.2f %7.2f %s %10.2f  %10.2f\n",
+			   write_fs, write_ss, p->name, q/1.0e9, f->intensity);
 
 	}
 
@@ -135,7 +151,7 @@ static void write_peaks(struct image *image, FILE *ofh)
 }
 
 
-static RefList *read_stream_reflections_2_1(FILE *fh)
+static RefList *read_stream_reflections_2_1(FILE *fh, struct detector *det)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -149,6 +165,7 @@ static RefList *read_stream_reflections_2_1(FILE *fh)
 		signed int h, k, l;
 		float intensity, sigma, fs, ss;
 		char phs[1024];
+		char pn[32];
 		int cts;
 		int r;
 		Reflection *refl;
@@ -159,25 +176,29 @@ static RefList *read_stream_reflections_2_1(FILE *fh)
 
 		if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
 
-		r = sscanf(line, "%i %i %i %f %s %f %i %f %f",
-		           &h, &k, &l, &intensity, phs, &sigma, &cts, &fs, &ss);
-		if ( (r != 9) && (!first) ) {
+		r = sscanf(line, "%i %i %i %f %s %f %i %f %f %s",
+				   &h, &k, &l, &intensity, phs, &sigma, &cts, &fs, &ss, pn);
+		if ( (r != 10) && (!first) ) {
 			reflist_free(out);
 			return NULL;
 		}
 
 		first = 0;
-		if ( r == 9 ) {
+		if ( r == 10 ) {
 
 			double ph;
 			char *v;
+			struct panel *p;
+			float write_fs, write_ss;
 
+			p = find_panel_by_name(det,pn);
 			refl = add_refl(out, h, k, l);
 			set_intensity(refl, intensity);
-			set_detector_pos(refl, 0.0, fs, ss);
+			write_ss = ss-p->orig_min_ss+p->min_ss;
+			write_fs = fs-p->orig_min_fs+p->min_fs;
+			set_detector_pos(refl, 0.0, write_fs, write_ss);
 			set_esd_intensity(refl, sigma);
 			set_redundancy(refl, cts);
-
 			ph = strtod(phs, &v);
 			if ( v != phs ) set_phase(refl, deg2rad(ph));
 
@@ -190,7 +211,7 @@ static RefList *read_stream_reflections_2_1(FILE *fh)
 }
 
 
-static RefList *read_stream_reflections(FILE *fh)
+static RefList *read_stream_reflections(FILE *fh, struct detector *det)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -204,7 +225,10 @@ static RefList *read_stream_reflections(FILE *fh)
 		signed int h, k, l;
 		float intensity, sigma, fs, ss, pk, bg;
 		int r;
+		char pn[32];
 		Reflection *refl;
+		struct panel *p;
+		float write_fs, write_ss;
 
 		rval = fgets(line, 1023, fh);
 		if ( rval == NULL ) continue;
@@ -212,19 +236,22 @@ static RefList *read_stream_reflections(FILE *fh)
 
 		if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
 
-		r = sscanf(line, "%i %i %i %f %f %f %f %f %f",
-		           &h, &k, &l, &intensity, &sigma, &pk, &bg, &fs, &ss);
-		if ( (r != 9) && (!first) ) {
+		r = sscanf(line, "%i %i %i %f %f %f %f %f %f %s",
+				   &h, &k, &l, &intensity, &sigma, &pk, &bg, &fs, &ss, pn);
+		if ( (r != 10) && (!first) ) {
 			reflist_free(out);
 			return NULL;
 		}
 
 		first = 0;
-		if ( r == 9 ) {
+		if ( r == 10 ) {
 
+			p = find_panel_by_name(det,pn);
 			refl = add_refl(out, h, k, l);
 			set_intensity(refl, intensity);
-			set_detector_pos(refl, 0.0, fs, ss);
+			write_ss = ss-p->orig_min_ss+p->min_ss;
+			write_fs = fs-p->orig_min_fs+p->min_fs;
+			set_detector_pos(refl, 0.0, write_fs, write_ss);
 			set_esd_intensity(refl, sigma);
 			set_redundancy(refl, 1);
 			set_peak(refl, pk);
@@ -239,13 +266,13 @@ static RefList *read_stream_reflections(FILE *fh)
 }
 
 
-static void write_stream_reflections(FILE *fh, RefList *list)
+static void write_stream_reflections(FILE *fh, RefList *list, struct image *image)
 {
 	Reflection *refl;
 	RefListIterator *iter;
 
 	fprintf(fh, "   h    k    l          I   sigma(I)       peak background"
-	            "  fs/px  ss/px\n");
+				"  fs/px  ss/px  panel\n");
 
 	for ( refl = first_refl(list, &iter);
 	      refl != NULL;
@@ -255,6 +282,8 @@ static void write_stream_reflections(FILE *fh, RefList *list)
 		signed int h, k, l;
 		double intensity, esd_i, bg, pk;
 		double fs, ss;
+		double write_fs, write_ss;
+		struct panel *p = NULL;
 
 		get_indices(refl, &h, &k, &l);
 		get_detector_pos(refl, &fs, &ss);
@@ -266,21 +295,25 @@ static void write_stream_reflections(FILE *fh, RefList *list)
 		/* Reflections with redundancy = 0 are not written */
 		if ( get_redundancy(refl) == 0 ) continue;
 
+		p = find_panel(image->det,fs,ss);
+		write_fs = fs-p->min_fs+p->orig_min_fs;
+		write_ss = ss-p->min_ss+p->orig_min_ss;
+
 		fprintf(fh,
-		       "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f %6.1f %6.1f\n",
-		       h, k, l, intensity, esd_i, pk, bg, fs, ss);
+			   "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f %6.1f %6.1f %s\n",
+			   h, k, l, intensity, esd_i, pk, bg, write_fs, write_ss, p->name);
 
 	}
 }
 
 
-static void write_stream_reflections_2_1(FILE *fh, RefList *list)
+static void write_stream_reflections_2_1(FILE *fh, RefList *list, struct image *image)
 {
 	Reflection *refl;
 	RefListIterator *iter;
 
 	fprintf(fh, "  h   k   l          I    phase   sigma(I) "
-		     " counts  fs/px  ss/px\n");
+			 " counts  fs/px  ss/px  panel\n");
 
 	for ( refl = first_refl(list, &iter);
 	      refl != NULL;
@@ -291,8 +324,10 @@ static void write_stream_reflections_2_1(FILE *fh, RefList *list)
 		double intensity, esd_i, ph;
 		int red;
 		double fs, ss;
+		double write_fs, write_ss;
 		char phs[16];
 		int have_phase;
+		struct panel *p = NULL;
 
 		get_indices(refl, &h, &k, &l);
 		get_detector_pos(refl, &fs, &ss);
@@ -310,9 +345,13 @@ static void write_stream_reflections_2_1(FILE *fh, RefList *list)
 			strncpy(phs, "       -", 15);
 		}
 
+		p = find_panel(image->det,fs,ss);
+		write_fs = fs-p->min_fs+p->orig_min_fs;
+		write_ss = ss-p->min_ss+p->orig_min_ss;
+
 		fprintf(fh,
 		       "%3i %3i %3i %10.2f %s %10.2f %7i %6.1f %6.1f\n",
-		       h, k, l, intensity, phs, esd_i, red,  fs, ss);
+			   h, k, l, intensity, phs, esd_i, red,  write_fs, write_ss);
 
 	}
 }
@@ -395,11 +434,11 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
 
 			fprintf(st->fh, REFLECTION_START_MARKER"\n");
 			if ( AT_LEAST_VERSION(st, 2, 2) ) {
-				write_stream_reflections(st->fh, reflist);
+				write_stream_reflections(st->fh, reflist, crystal_get_image(cr));
 			} else {
 				/* This function writes like a normal reflection
 				 * list was written in stream 2.1 */
-				write_stream_reflections_2_1(st->fh, reflist);
+				write_stream_reflections_2_1(st->fh, reflist, crystal_get_image(cr));
 			}
 			fprintf(st->fh, REFLECTION_END_MARKER"\n");
 
@@ -619,9 +658,9 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 			/* The reflection list format in the stream diverges
 			 * after 2.2 */
 			if ( AT_LEAST_VERSION(st, 2, 2) ) {
-				reflist = read_stream_reflections(st->fh);
+				reflist = read_stream_reflections(st->fh, image->det);
 			} else {
-				reflist = read_stream_reflections_2_1(st->fh);
+				reflist = read_stream_reflections_2_1(st->fh, image->det);
 			}
 			if ( reflist == NULL ) {
 				ERROR("Failed while reading reflections\n");