ImageFeatureList: Store panel number, not pointer

This makes the conversion to DataTemplate/detgeom MUCH easier.

12 files changed, 75 insertions, 55 deletions

diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index e2738a8b..ec0d77f2 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -400,6 +400,7 @@ int get_peaks_cxi_2(struct image *image, struct hdfile *f, const char *p,
 
 		float fs, ss, val;
 		struct panel *p;
+		int pn;
 
 		fs = buf_x[pk] + peak_offset;
 		ss = buf_y[pk] + peak_offset;
@@ -413,7 +414,10 @@ int get_peaks_cxi_2(struct image *image, struct hdfile *f, const char *p,
 		fs = fs - p->orig_min_fs;
 		ss = ss - p->orig_min_ss;
 
-		image_add_feature(image->features, fs, ss, p, image, val, NULL);
+		pn = panel_number(image->det, p);
+
+		image_add_feature(image->features, fs, ss, pn,
+		                  image, val, NULL);
 
 	}
 
@@ -543,6 +547,7 @@ int get_peaks_2(struct image *image, struct hdfile *f, const char *p,
 
 		float fs, ss, val;
 		struct panel *p;
+		int pn;
 
 		fs = buf[tw*i+0] + peak_offset;
 		ss = buf[tw*i+1] + peak_offset;
@@ -556,8 +561,10 @@ int get_peaks_2(struct image *image, struct hdfile *f, const char *p,
 		fs = fs - p->orig_min_fs;
 		ss = ss - p->orig_min_ss;
 
-		image_add_feature(image->features, fs, ss, p, image, val,
-		                  NULL);
+		pn = panel_number(image->det, p);
+
+		image_add_feature(image->features, fs, ss, pn,
+		                  image, val, NULL);
 
 	}
 
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index b0f23871..63050a40 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -65,7 +65,7 @@ struct _imagefeaturelist
 
 
 void image_add_feature(ImageFeatureList *flist, double fs, double ss,
-                       struct panel *p,
+                       int pn,
                        struct image *parent, double intensity, const char *name)
 {
 	if ( flist->n_features == flist->max_features ) {
@@ -79,7 +79,7 @@ void image_add_feature(ImageFeatureList *flist, double fs, double ss,
 
 	flist->features[flist->n_features].fs = fs;
 	flist->features[flist->n_features].ss = ss;
-	flist->features[flist->n_features].p = p;
+	flist->features[flist->n_features].pn = pn;
 	flist->features[flist->n_features].intensity = intensity;
 	flist->features[flist->n_features].parent = parent;
 	flist->features[flist->n_features].name = name;
@@ -155,7 +155,7 @@ void image_feature_list_free(ImageFeatureList *flist)
 
 struct imagefeature *image_feature_closest(ImageFeatureList *flist,
                                            double fs, double ss,
-                                           struct panel *p, double *d, int *idx)
+                                           int pn, double *d, int *idx)
 {
 	int i;
 	double dmin = +HUGE_VAL;
@@ -165,7 +165,7 @@ struct imagefeature *image_feature_closest(ImageFeatureList *flist,
 
 		double ds;
 
-		if ( p != flist->features[i].p ) continue;
+		if ( pn != flist->features[i].pn ) continue;
 
 		ds = distance(flist->features[i].fs, flist->features[i].ss,
 		              fs, ss);
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index f9257560..a7d7165f 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -78,7 +78,7 @@ struct imagefeature {
 	double                          ss;
 	/**@}*/
 
-	struct panel                    *p;         /**< Pointer to panel */
+	int                             pn;         /**< Panel number */
 	double                          intensity;  /**< Intensity */
 
 	/** \name Reciprocal space coordinates (m^-1) of this feature */
@@ -203,7 +203,7 @@ extern ImageFeatureList *image_feature_list_new(void);
 extern void image_feature_list_free(ImageFeatureList *flist);
 
 extern void image_add_feature(ImageFeatureList *flist, double x, double y,
-                              struct panel *p,
+                              int pn,
                               struct image *parent, double intensity,
                               const char *name);
 
@@ -211,7 +211,7 @@ extern void image_remove_feature(ImageFeatureList *flist, int idx);
 
 extern struct imagefeature *image_feature_closest(ImageFeatureList *flist,
                                                   double fs, double ss,
-                                                  struct panel *p,
+                                                  int pn,
                                                   double *d, int *idx);
 
 extern Reflection *image_reflection_closest(RefList *rlist,
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index dc689df2..7e0dd9a9 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -565,7 +565,8 @@ void map_all_peaks(struct image *image)
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
 
-		r = get_q_for_panel(f->p, f->fs, f->ss,
+		r = get_q_for_panel(&image->det->panels[f->pn],
+		                    f->fs, f->ss,
 		                    NULL, 1.0/image->lambda);
 		f->rx = r.u;  f->ry = r.v;  f->rz = r.w;
 
@@ -819,7 +820,8 @@ static int delete_explained_peaks(struct image *image, Crystal *cr)
 		nspots++;
 
 		/* Reciprocal space position of found peak */
-		q = get_q_for_panel(f->p, f->fs, f->ss,
+		q = get_q_for_panel(&image->det->panels[f->pn],
+		                    f->fs, f->ss,
 		                    NULL, 1.0/image->lambda);
 
 		/* Decimal and fractional Miller indices of nearest
diff --git a/libcrystfel/src/peakfinder8.c b/libcrystfel/src/peakfinder8.c
index c3f7c391..492f5741 100644
--- a/libcrystfel/src/peakfinder8.c
+++ b/libcrystfel/src/peakfinder8.c
@@ -1205,9 +1205,7 @@ int peakfinder8(struct image *img, int max_n_peaks,
 			image_add_feature(img->features,
 			                  pkdata->com_fs[pki]+0.5,
 			                  pkdata->com_ss[pki]+0.5,
-			                  p,
-			                  img,
-			                  pkdata->tot_i[pki],
+			                  pi, img, pkdata->tot_i[pki],
 			                  NULL);
 		}
 	}
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 7f2526bc..ed6c8995 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -219,7 +219,7 @@ int *make_BgMask(struct image *image, struct panel *p, double ir_inn)
 /* Returns non-zero if peak has been vetoed.
  * i.e. don't use result if return value is not zero. */
 static int integrate_peak(struct image *image,
-                          int p_cfs, int p_css, struct panel *p,
+                          int p_cfs, int p_css, int pn,
                           double *pfs, double *pss,
                           double *intensity, double *sigma,
                           double ir_inn, double ir_mid, double ir_out,
@@ -236,22 +236,18 @@ static int integrate_peak(struct image *image,
 	double bg_tot_sq = 0.0;
 	double var;
 	double aduph;
-	int pn;
+	struct detgeom_panel *p;
 
 	if ( saturated != NULL ) *saturated = 0;
 
+	p = &image->detgeom->panels[pn];
+
 	aduph = p->adu_per_photon;
 
 	lim_sq = pow(ir_inn, 2.0);
 	mid_lim_sq = pow(ir_mid, 2.0);
 	out_lim_sq = pow(ir_out, 2.0);
 
-	pn = panel_number(image->det, p);
-	if ( pn == image->det->n_panels ) {
-		ERROR("Couldn't find panel %p\n", p);
-		return 20;
-	}
-
 	/* Estimate the background */
 	for ( dss=-ir_out; dss<=+ir_out; dss++ ) {
 	for ( dfs=-ir_out; dfs<=+ir_out; dfs++ ) {
@@ -456,7 +452,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 		assert(mask_ss >= 0);
 
 		/* Centroid peak and get better coordinates. */
-		r = integrate_peak(image, mask_fs, mask_ss, p,
+		r = integrate_peak(image, mask_fs, mask_ss, pn,
 		                   &f_fs, &f_ss, &intensity, &sigma,
 		                   ir_inn, ir_mid, ir_out, &saturated);
 
@@ -479,7 +475,8 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 		}
 
 		/* Check for a nearby feature */
-		image_feature_closest(image->features, f_fs, f_ss, p, &d, &idx);
+		image_feature_closest(image->features, f_fs, f_ss, pn,
+		                      &d, &idx);
 		if ( d < 2.0*ir_inn ) {
 			nrej_pro++;
 			continue;
@@ -491,7 +488,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 		}
 
 		/* Add using "better" coordinates */
-		image_add_feature(image->features, f_fs, f_ss, p,
+		image_add_feature(image->features, f_fs, f_ss, pn,
 		                  image, intensity, NULL);
 		nacc++;
 
@@ -648,8 +645,7 @@ int search_peaks_peakfinder9(struct image *image, float min_snr_biggest_pix,
 			image_add_feature(image->features,
 			                  peakList.centerOfMass_rawX[peak_number],
 			                  peakList.centerOfMass_rawY[peak_number],
-			                  &image->det->panels[panel_number],
-			                  image,
+			                  panel_number, image,
 			                  peakList.totalIntensity[peak_number],
 			                  NULL);
 		}
@@ -709,7 +705,8 @@ int indexing_peak_check(struct image *image, Crystal **crystals, int n_cryst,
 		n_feat++;
 
 		/* Reciprocal space position of found peak */
-		q = get_q_for_panel(f->p, f->fs, f->ss,
+		q = get_q_for_panel(&image->det->panels[f->pn],
+		                    f->fs, f->ss,
 		                    NULL, 1.0/image->lambda);
 
 		for ( j=0; j<n_cryst; j++ ) {
@@ -797,7 +794,7 @@ void validate_peaks(struct image *image, double min_snr,
 			continue;
 		}
 
-		r = integrate_peak(image, f->fs, f->ss, f->p,
+		r = integrate_peak(image, f->fs, f->ss, f->pn,
 		                   &f_fs, &f_ss, &intensity, &sigma,
 		                   ir_inn, ir_mid, ir_out, &saturated);
 		if ( r ) {
@@ -818,8 +815,8 @@ void validate_peaks(struct image *image, double min_snr,
 		}
 
 		/* Add using "better" coordinates */
-		image_add_feature(flist, f->fs, f->ss, f->p, image, intensity,
-		                  NULL);
+		image_add_feature(flist, f->fs, f->ss, f->pn, image,
+		                  intensity, NULL);
 
 	}
 
@@ -841,7 +838,8 @@ static int compare_double(const void *av, const void *bv)
 }
 
 
-double estimate_peak_resolution(ImageFeatureList *peaks, double lambda)
+double estimate_peak_resolution(ImageFeatureList *peaks, double lambda,
+                                struct detector *det)
 {
 	int i, npk, ncut;
 	double *rns;
@@ -863,7 +861,8 @@ double estimate_peak_resolution(ImageFeatureList *peaks, double lambda)
 
 		f = image_get_feature(peaks, i);
 
-		r = get_q_for_panel(f->p, f->fs, f->ss, NULL, 1.0/lambda);
+		r = get_q_for_panel(&det->panels[f->pn],
+		                    f->fs, f->ss, NULL, 1.0/lambda);
 		rns[i] = modulus(r.u, r.v, r.w);
 
 	}
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index 89388652..5a143d2a 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -79,7 +79,9 @@ extern void validate_peaks(struct image *image, double min_snr,
                            int ir_inn, int ir_mid, int ir_out,
                            int use_saturated, int check_snr);
 
-extern double estimate_peak_resolution(ImageFeatureList *peaks, double lambda);
+extern double estimate_peak_resolution(ImageFeatureList *peaks,
+                                       double lambda,
+                                       struct detector *det);
 
 #ifdef __cplusplus
 }
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index aff5fc22..0b33c211 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -267,11 +267,11 @@ static int pair_peaks(struct image *image, Crystal *cr,
 		 * in how far away it is from the peak location.
 		 * The predicted position and excitation errors will be
 		 * filled in by update_predictions(). */
-		set_panel(refl, f->p);
+		set_panel(refl, &image->det->panels[f->pn]);
 
 		rps[n].refl = refl;
 		rps[n].peak = f;
-		rps[n].panel = f->p;
+		rps[n].panel = &image->det->panels[f->pn];
 		n++;
 
 	}
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index bfe4a50a..875285e5 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -99,7 +99,6 @@ static int read_peaks(Stream *st, struct image *image)
 		char line[1024];
 		float x, y, d, intensity;
 		int r;
-		struct panel *p = NULL;
 		float add_x, add_y;
 
 		rval = fgets(line, 1023, st->fh);
@@ -121,6 +120,8 @@ static int read_peaks(Stream *st, struct image *image)
 
 			if ( image->det != NULL ) {
 
+				int pn;
+				struct panel *p = NULL;
 				p = find_orig_panel(image->det, x, y);
 				if ( p == NULL ) {
 					ERROR("Panel not found\n");
@@ -129,14 +130,15 @@ static int read_peaks(Stream *st, struct image *image)
 
 				add_x = x-p->orig_min_fs;
 				add_y = y-p->orig_min_ss;
+				pn = panel_number(image->det, p);
 
 				image_add_feature(image->features, add_x, add_y,
-				                  p, image, intensity, NULL);
+				                  pn, image, intensity, NULL);
 
 			} else {
 
 				image_add_feature(image->features, x, y,
-				                  p, image, intensity, NULL);
+				                  0, image, intensity, NULL);
 			}
 		}
 
@@ -160,7 +162,6 @@ static int read_peaks_2_3(Stream *st, struct image *image)
 		char pn[32];
 		float x, y, d, intensity;
 		int r;
-		struct panel *p = NULL;
 		float add_x, add_y;
 
 		rval = fgets(line, 1023, st->fh);
@@ -181,6 +182,8 @@ static int read_peaks_2_3(Stream *st, struct image *image)
 
 		if ( r == 5 ) {
 
+			int pnum;
+			struct panel *p;
 			p = find_panel_by_name(image->det, pn);
 			if ( p == NULL ) {
 				ERROR("Panel not found: %s\n", pn);
@@ -190,7 +193,10 @@ static int read_peaks_2_3(Stream *st, struct image *image)
 			add_x = x-p->orig_min_fs;
 			add_y = y-p->orig_min_ss;
 
-			image_add_feature(image->features, add_x, add_y, p,
+			pnum = panel_number(image->det, p);
+
+			image_add_feature(image->features,
+			                  add_x, add_y, pnum,
 			                  image, intensity, NULL);
 
 		}
@@ -218,7 +224,8 @@ static int write_peaks(struct image *image, FILE *ofh)
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
 
-		r = get_q_for_panel(f->p, f->fs, f->ss,
+		r = get_q_for_panel(&image->det->panels[f->pn],
+		                    f->fs, f->ss,
 		                    NULL, 1.0/image->lambda);
 		q = modulus(r.u, r.v, r.w);
 
@@ -268,21 +275,24 @@ static int write_peaks_2_3(struct image *image, FILE *ofh)
 		struct rvec r;
 		double q;
 		double write_fs, write_ss;
+		struct panel *p;
 
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
 
-		r = get_q_for_panel(f->p, f->fs, f->ss,
+		p = &image->det->panels[f->pn];
+		r = get_q_for_panel(p, f->fs, f->ss,
 		                    NULL, 1.0/image->lambda);
 		q = modulus(r.u, r.v, r.w);
 
 		/* Convert coordinates to match arrangement of panels in HDF5
 		 * file */
-		write_fs = f->fs + f->p->orig_min_fs;
-		write_ss = f->ss + f->p->orig_min_ss;
+		write_fs = f->fs + p->orig_min_fs;
+		write_ss = f->ss + p->orig_min_ss;
 
 		fprintf(ofh, "%7.2f %7.2f %10.2f  %10.2f   %s\n",
-		        write_fs, write_ss, q/1.0e9, f->intensity, f->p->name);
+		        write_fs, write_ss, q/1.0e9, f->intensity,
+		        p->name);
 
 	}
 
diff --git a/src/geoptimiser.c b/src/geoptimiser.c
index 136cca39..73e37249 100644
--- a/src/geoptimiser.c
+++ b/src/geoptimiser.c
@@ -768,7 +768,8 @@ static int compute_pixel_displacements(struct image *images, int n_images,
 			imfe = image_get_feature(flist, fi);
 			if ( imfe == NULL ) continue;
 
-			compute_x_y(imfe->fs, imfe->ss, imfe->p, &fx, &fy);
+			compute_x_y(imfe->fs, imfe->ss,
+			            &det->panels[imfe->pn], &fx, &fy);
 
 			/* Find the closest reflection (from all crystals) */
 			refl = find_closest_reflection(&images[cp], fx, fy,
@@ -779,7 +780,7 @@ static int compute_pixel_displacements(struct image *images, int n_images,
 
 				struct gpanel *gp;
 				int r;
-				gp = &gpanels[panel_number(det, imfe->p)];
+				gp = &gpanels[imfe->pn];
 
 				r = add_distance_to_list(gp, imfe, refl, fx, fy,
 				                         det_shift);
diff --git a/src/process_image.c b/src/process_image.c
index 1e6bb814..930052c4 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -359,7 +359,8 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	}
 
 	image.peak_resolution = estimate_peak_resolution(image.features,
-	                                                 image.lambda);
+	                                                 image.lambda,
+	                                                 image.det);
 
 	restore_image_data(image.dp, image.det, prefilter);
 
diff --git a/tests/ring_check.c b/tests/ring_check.c
index e0667e37..f286d5e7 100644
--- a/tests/ring_check.c
+++ b/tests/ring_check.c
@@ -67,7 +67,7 @@ static void third_integration_check(struct image *image, int n_trials,
 		}
 		}
 
-		r = integrate_peak(image, 64, 64, &image->det->panels[0],
+		r = integrate_peak(image, 64, 64, 0,
 		                   &fsp, &ssp, &intensity, &sigma,
 		                   10.0, 15.0, 17.0, NULL);
 
@@ -129,7 +129,7 @@ static void fourth_integration_check(struct image *image, int n_trials,
 		}
 		}
 
-		r = integrate_peak(image, 64, 64, &image->det->panels[0],
+		r = integrate_peak(image, 64, 64, 0,
 		                   &fsp, &ssp, &intensity, &sigma,
 		                   10.0, 15.0, 17.0, NULL);
 
@@ -219,7 +219,7 @@ int main(int argc, char *argv[])
 	image.crystals = NULL;
 
 	/* First check: no intensity -> no peak, or very low intensity */
-	r = integrate_peak(&image, 64, 64, &image.det->panels[0],
+	r = integrate_peak(&image, 64, 64, 0,
 	                   &fsp, &ssp, &intensity, &sigma,
 	                   10.0, 15.0, 17.0, NULL);
 	STATUS("  First check: integrate_peak() returned %i", r);
@@ -246,7 +246,7 @@ int main(int argc, char *argv[])
 	}
 	}
 
-	r = integrate_peak(&image, 64, 64, &image.det->panels[0],
+	r = integrate_peak(&image, 64, 64, 0,
 	                   &fsp, &ssp, &intensity, &sigma,
 	                   10.0, 15.0, 17.0, NULL);
 	if ( r ) {
@@ -289,7 +289,7 @@ int main(int argc, char *argv[])
 	}
 	}
 
-	r = integrate_peak(&image, 64, 64, &image.det->panels[0],
+	r = integrate_peak(&image, 64, 64, 0,
 	                   &fsp, &ssp, &intensity, &sigma,
 	                   10.0, 15.0, 17.0, NULL);
 	if ( r ) {