Convert stream to DataTemplate

13 files changed, 151 insertions, 339 deletions

diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index 60c36358..6cc57d2d 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -3,11 +3,11 @@
  *
  * Data template structure
  *
- * Copyright © 2019 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
+ * Copyright © 2019-2020 Deutsches Elektronen-Synchrotron DESY,
+ *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2019 Thomas White <taw@physics.org>
+ *   2019-2020 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -1242,8 +1242,8 @@ void data_template_free(DataTemplate *dt)
 }
 
 
-signed int data_template_find_panel(const DataTemplate *dt,
-                                    int fs, int ss)
+static int data_template_find_panel(const DataTemplate *dt,
+                                    int fs, int ss, int *ppn)
 {
 	int p;
 
@@ -1251,24 +1251,47 @@ signed int data_template_find_panel(const DataTemplate *dt,
 		if ( (fs >= dt->panels[p].orig_min_fs)
 		  && (fs < dt->panels[p].orig_max_fs+1)
 		  && (ss >= dt->panels[p].orig_min_ss)
-		  && (ss < dt->panels[p].orig_max_ss+1) ) return p;
+		  && (ss < dt->panels[p].orig_max_ss+1) ) {
+			*ppn = p;
+			return 0;
+		}
 	}
 
-	return -1;
+	return 1;
 }
 
 
-void data_template_file_to_panel_coords(const DataTemplate *dt,
-                                        float *pfs, float *pss)
+int data_template_file_to_panel_coords(const DataTemplate *dt,
+                                       float *pfs, float *pss,
+                                       int *ppn)
 {
-	signed int pn = data_template_find_panel(dt, *pfs, *pss);
-	if ( pn == -1 ) {
-		ERROR("Can't convert coordinates - no panel found\n");
-		return;
+	int pn;
+
+	if ( data_template_find_panel(dt, *pfs, *pss, &pn) ) {
+		return 1;
 	}
 
+	*ppn = pn;
 	*pfs = *pfs - dt->panels[pn].orig_min_fs;
 	*pss = *pss - dt->panels[pn].orig_min_ss;
+	return 0;
+}
+
+
+int data_template_panel_to_file_coords(const DataTemplate *dt,
+                                       int pn, float *pfs, float *pss)
+{
+	if ( pn >= dt->n_panels ) return 1;
+	*pfs = *pfs + dt->panels[pn].orig_min_fs;
+	*pss = *pss + dt->panels[pn].orig_min_ss;
+	return 0;
+}
+
+
+const char *data_template_panel_name(const DataTemplate *dt, int pn)
+{
+	if ( pn >= dt->n_panels ) return NULL;
+	return dt->panels[pn].name;
 }
 
 
diff --git a/libcrystfel/src/datatemplate.h b/libcrystfel/src/datatemplate.h
index ac76c578..fd99d5f0 100644
--- a/libcrystfel/src/datatemplate.h
+++ b/libcrystfel/src/datatemplate.h
@@ -3,11 +3,11 @@
  *
  * Template for loading data
  *
- * Copyright © 2019 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
+ * Copyright © 2019-2020 Deutsches Elektronen-Synchrotron DESY,
+ *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2019 Thomas White <taw@physics.org>
+ *   2019-2020 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -53,11 +53,16 @@ extern "C" {
 extern DataTemplate *data_template_new_from_file(const char *filename);
 extern void data_template_free(DataTemplate *dt);
 
-extern signed int data_template_find_panel(const DataTemplate *dt,
-                                           int fs, int ss);
+extern const char *data_template_panel_name(const DataTemplate *dt,
+                                            int pn);
 
-extern void data_template_file_to_panel_coords(const DataTemplate *dt,
-                                               float *pfs, float *pss);
+extern int data_template_file_to_panel_coords(const DataTemplate *dt,
+                                              float *pfs, float *pss,
+                                              int *pn);
+
+extern int data_template_panel_to_file_coords(const DataTemplate *dt,
+                                              int pn,
+                                              float *pfs, float *pss);
 
 extern void data_template_add_copy_header(DataTemplate *dt,
                                           const char *header);
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 8cfe3473..9474d266 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -1882,18 +1882,17 @@ ImageFeatureList *get_peaks_cxi_dtempl(const DataTemplate *dtempl,
 		ss = buf_y[pk] + peak_offset;
 		val = buf_i[pk];
 
-		pn = data_template_find_panel(dtempl, fs, ss);
-		if ( pn < -1 ) {
-			ERROR("Peak not in panel!\n");
-			continue;
+		if ( data_template_file_to_panel_coords(dtempl,
+		                                        &fs, &ss,
+		                                        &pn) )
+		{
+			ERROR("Failed to convert %i,%i to "
+			      "panel-relative coordinates\n", fs, ss);
+		} else {
+			image_add_feature(features, fs, ss, pn,
+			                  NULL, val, NULL);
 		}
 
-		/* Convert coordinates to panel-relative */
-		data_template_file_to_panel_coords(dtempl, &fs, &ss);
-
-		image_add_feature(features, fs, ss, pn,
-		                  NULL, val, NULL);
-
 	}
 
 	return features;
@@ -2022,18 +2021,17 @@ ImageFeatureList *get_peaks_hdf5_dtempl(const DataTemplate *dtempl,
 		ss = buf[tw*i+1] + peak_offset;
 		val = buf[tw*i+2];
 
-		pn = data_template_find_panel(dtempl, fs, ss);
-		if ( pn < -1 ) {
-			ERROR("Peak not in panel!\n");
-			continue;
+		if ( data_template_file_to_panel_coords(dtempl,
+		                                        &fs, &ss,
+		                                        &pn) )
+		{
+			ERROR("Failed to convert %i,%i to "
+			      "panel-relative coordinates\n", fs, ss);
+		} else {
+			image_add_feature(features, fs, ss, pn,
+			                  NULL, val, NULL);
 		}
 
-		/* Convert coordinates to panel-relative */
-		data_template_file_to_panel_coords(dtempl, &fs, &ss);
-
-		image_add_feature(features, fs, ss, pn,
-		                  NULL, val, NULL);
-
 	}
 
 	free(buf);
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index bb8c5c35..a3841e8c 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -73,8 +73,8 @@ struct reflpeak {
 	Reflection *refl;
 	struct imagefeature *peak;
 	double Ih;   /* normalised */
-	struct panel *panel;  /* panel the reflection appears on
-                               * (we assume this never changes) */
+	struct detgeom_panel *panel;  /* panel the reflection appears on
+                                       * (we assume this never changes) */
 };
 
 
@@ -122,50 +122,6 @@ static double y_dev(struct reflpeak *rp, struct detector *det)
 }
 
 
-static void UNUSED write_pairs(const char *filename, struct reflpeak *rps,
-                               int n, struct detector *det)
-{
-	int i;
-	FILE *fh;
-
-	fh = fopen(filename, "w");
-	if ( fh == NULL ) {
-		ERROR("Failed to open '%s'\n", filename);
-		return;
-	}
-
-	for ( i=0; i<n; i++ ) {
-
-		double write_fs, write_ss;
-		double fs, ss;
-		struct panel *p;
-		signed int h, k, l;
-
-		fs = rps[i].peak->fs;
-		ss = rps[i].peak->ss;
-		p = rps[i].panel;
-		get_indices(rps[i].refl, &h, &k, &l);
-
-		write_fs = fs + p->orig_min_fs;
-		write_ss = ss + p->orig_min_ss;
-
-		fprintf(fh, "%7.2f %7.2f dev r,x,y: %9f %9f %9f %9f\n",
-		        write_fs, write_ss,
-		        r_dev(&rps[i])/1e9, fabs(r_dev(&rps[i])/1e9),
-		        x_dev(&rps[i], det),
-		        y_dev(&rps[i], det));
-
-		//fprintf(fh, "%4i %4i %4i 0.0 - 0.0 1 %7.2f %7.2f %s\n",
-		//        h, k, l, write_fs, write_ss, p->name);
-
-	}
-
-	fclose(fh);
-
-	STATUS("Wrote %i pairs to %s\n", n, filename);
-}
-
-
 static int cmpd2(const void *av, const void *bv)
 {
 	struct reflpeak *a, *b;
@@ -186,7 +142,6 @@ static int check_outlier_transition(struct reflpeak *rps, int n,
 	if ( n < 3 ) return n;
 
 	qsort(rps, n, sizeof(struct reflpeak), cmpd2);
-	//write_pairs("pairs-before-outlier.lst", rps, n, det);
 
 	for ( i=1; i<n-1; i++ ) {
 
@@ -267,11 +222,11 @@ 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, &image->det->panels[f->pn]);
+		set_panel_number(refl, f->pn);
 
 		rps[n].refl = refl;
 		rps[n].peak = f;
-		rps[n].panel = &image->det->panels[f->pn];
+		rps[n].panel = &image->detgeom->panels[f->pn];
 		n++;
 
 	}
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 419acd36..3343750c 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -51,6 +51,7 @@
 #include "stream.h"
 #include "reflist.h"
 #include "reflist-utils.h"
+#include "datatemplate.h"
 
 /** \file stream.h */
 
@@ -301,7 +302,8 @@ static int write_peaks_2_3(struct image *image, FILE *ofh)
 }
 
 
-static RefList *read_stream_reflections_2_3(Stream *st, struct detector *det)
+static RefList *read_stream_reflections_2_3(Stream *st,
+                                            const DataTemplate *dtempl)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -342,24 +344,19 @@ static RefList *read_stream_reflections_2_3(Stream *st, struct detector *det)
 
 		if ( r == 10 ) {
 
-			struct panel *p;
-
 			refl = add_refl(out, h, k, l);
 			if ( refl == NULL ) {
 				ERROR("Failed to add reflection\n");
 				return NULL;
 			}
 			set_intensity(refl, intensity);
-			if ( det != NULL ) {
-				double write_fs, write_ss;
-				p = find_panel_by_name(det,pn);
-				if ( p == NULL ) {
-					ERROR("Couldn't find panel '%s'\n", pn);
+			if ( dtempl != NULL ) {
+				int pn;
+				if ( data_template_file_to_panel_coords(dtempl, &fs, &ss, &pn) ) {
+					ERROR("Failed to convert\n");
 				} else {
-					write_fs = fs - p->orig_min_fs;
-					write_ss = ss - p->orig_min_ss;
-					set_detector_pos(refl, write_fs, write_ss);
-					set_panel(refl, p);
+					set_detector_pos(refl, fs, ss);
+					set_panel_number(refl, pn);
 				}
 			}
 			set_esd_intensity(refl, sigma);
@@ -376,7 +373,8 @@ static RefList *read_stream_reflections_2_3(Stream *st, struct detector *det)
 }
 
 
-static RefList *read_stream_reflections_2_1(Stream *st, struct detector *det)
+static RefList *read_stream_reflections_2_1(Stream *st,
+                                            const DataTemplate *dtempl)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -426,19 +424,14 @@ static RefList *read_stream_reflections_2_1(Stream *st, struct detector *det)
 			}
 			set_intensity(refl, intensity);
 
-			if ( det != NULL ) {
+			if ( dtempl != NULL ) {
 
-				double write_fs, write_ss;
-				struct panel *p;
-
-				p = find_orig_panel(det, fs, ss);
-				if ( p == NULL ) {
-					ERROR("No panel at %.2f,%.2f\n",
-					      fs, ss);
+				int pn;
+				if ( data_template_file_to_panel_coords(dtempl, &fs, &ss, &pn) ) {
+					ERROR("Failed to convert\n");
 				} else {
-					write_fs = fs - p->orig_min_fs;
-					write_ss = ss - p->orig_min_ss;
-					set_detector_pos(refl, write_fs, write_ss);
+					set_detector_pos(refl, fs, ss);
+					set_panel_number(refl, pn);
 				}
 
 			} else {
@@ -462,7 +455,8 @@ static RefList *read_stream_reflections_2_1(Stream *st, struct detector *det)
 }
 
 
-static RefList *read_stream_reflections_2_2(Stream *st, struct detector *det)
+static RefList *read_stream_reflections_2_2(Stream *st,
+                                            const DataTemplate *dtempl)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -502,19 +496,17 @@ static RefList *read_stream_reflections_2_2(Stream *st, struct detector *det)
 			}
 			set_intensity(refl, intensity);
 
-			if ( det != NULL ) {
+			if ( dtempl != NULL ) {
 
-				double write_fs, write_ss;
-				struct panel *p;
+				int pn;
 
-				p = find_orig_panel(det, fs, ss);
-				if ( p == NULL ) {
-					ERROR("No panel at %.2f,%.2f\n",
-					      fs, ss);
+				if ( data_template_file_to_panel_coords(dtempl, &fs, &ss, &pn) ) {
+					ERROR("Failed to convert to "
+					      "panel-relative coordinates: "
+					      "%i,%i\n", fs, ss);
 				} else {
-					write_fs = fs - p->orig_min_fs;
-					write_ss = ss - p->orig_min_ss;
-					set_detector_pos(refl, write_fs, write_ss);
+					set_detector_pos(refl, fs, ss);
+					set_panel_number(refl, pn);
 				}
 
 			} else {
@@ -538,139 +530,8 @@ static RefList *read_stream_reflections_2_2(Stream *st, struct detector *det)
 }
 
 
-static int 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");
-
-	for ( refl = first_refl(list, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) )
-	{
-
-		signed int h, k, l;
-		double intensity, esd_i, ph;
-		int red;
-		double fs, ss;
-		char phs[16];
-		int have_phase;
-
-		get_indices(refl, &h, &k, &l);
-		get_detector_pos(refl, &fs, &ss);
-		intensity = get_intensity(refl);
-		esd_i = get_esd_intensity(refl);
-		red = get_redundancy(refl);
-		ph = get_phase(refl, &have_phase);
-
-		/* Reflections with redundancy = 0 are not written */
-		if ( red == 0 ) continue;
-
-		if ( have_phase ) {
-			snprintf(phs, 16, "%8.2f", rad2deg(ph));
-		} else {
-			strncpy(phs, "       -", 15);
-		}
-
-		if ( image->det != NULL ) {
-
-			struct panel *p;
-			double write_fs, write_ss;
-
-			p = find_orig_panel(image->det, fs, ss);
-			if ( p == NULL ) {
-				ERROR("Panel not found\n");
-				return 1;
-			}
-
-			/* Convert coordinates to match arrangement of panels
-			 * in HDF5 file */
-			write_fs = fs + p->orig_min_fs;
-			write_ss = 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,
-				     write_fs, write_ss);
-
-		} else {
-
-			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);
-
-		}
-	}
-	return 0;
-}
-
-
-static int write_stream_reflections_2_2(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");
-
-	for ( refl = first_refl(list, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) )
-	{
-
-		signed int h, k, l;
-		double intensity, esd_i, bg, pk;
-		double fs, ss;
-
-		get_indices(refl, &h, &k, &l);
-		get_detector_pos(refl, &fs, &ss);
-		intensity = get_intensity(refl);
-		esd_i = get_esd_intensity(refl);
-		pk = get_peak(refl);
-		bg = get_mean_bg(refl);
-
-		/* Reflections with redundancy = 0 are not written */
-		if ( get_redundancy(refl) == 0 ) continue;
-
-		if ( image->det != NULL ) {
-
-			struct panel *p;
-			double write_fs, write_ss;
-
-			p = find_orig_panel(image->det, fs, ss);
-			if ( p == NULL ) {
-				ERROR("Panel not found\n");
-				return 1;
-			}
-
-			/* Convert coordinates to match arrangement of panels in HDF5
-			 * file */
-			write_fs = fs + p->orig_min_fs;
-			write_ss = 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, write_fs,
-			        write_ss);
-
-		} else {
-
-			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);
-		}
-	}
-	return 0;
-}
-
-
-static int write_stream_reflections_2_3(FILE *fh, RefList *list,
-                                        struct image *image)
+static int write_stream_reflections(FILE *fh, RefList *list,
+                                    const DataTemplate *dtempl)
 {
 	Reflection *refl;
 	RefListIterator *iter;
@@ -685,13 +546,14 @@ static int write_stream_reflections_2_3(FILE *fh, RefList *list,
 
 		signed int h, k, l;
 		double intensity, esd_i, pk, bg;
-		double fs, ss;
-		double write_fs, write_ss;
-		struct panel *p;
+		double dfs, dss;
+		float fs, ss;
+		int pn;
 
 		get_indices(refl, &h, &k, &l);
-		get_detector_pos(refl, &fs, &ss);
-		p = get_panel(refl);
+		get_detector_pos(refl, &dfs, &dss);
+		fs = dfs;  ss = dss;
+		pn = get_panel_number(refl);
 		intensity = get_intensity(refl);
 		esd_i = get_esd_intensity(refl);
 		pk = get_peak(refl);
@@ -700,14 +562,13 @@ static int write_stream_reflections_2_3(FILE *fh, RefList *list,
 		/* Reflections with redundancy = 0 are not written */
 		if ( get_redundancy(refl) == 0 ) continue;
 
-		write_fs = fs+p->orig_min_fs;
-		write_ss = ss+p->orig_min_ss;
+		data_template_panel_to_file_coords(dtempl, pn,
+		                                   &fs, &ss);
 
-		fprintf(fh,
-                          "%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);
+		fprintf(fh, "%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,
+		        fs, ss, data_template_panel_name(dtempl, pn));
 
 	}
 	return 0;
@@ -731,7 +592,9 @@ static int num_integrated_reflections(RefList *list)
 }
 
 
-static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
+static int write_crystal(Stream *st, Crystal *cr,
+                         const DataTemplate *dtempl,
+                         int include_reflections)
 {
 	UnitCell *cell;
 	RefList *reflist;
@@ -802,26 +665,9 @@ static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
 
 		if ( reflist != NULL ) {
 
-			struct image *image;
-
-			image = crystal_get_image(cr);
-
 			fprintf(st->fh, REFLECTION_START_MARKER"\n");
-			if ( AT_LEAST_VERSION(st, 2, 3) ) {
-				ret = write_stream_reflections_2_3(st->fh,
-				                                   reflist,
-				                                   image);
-			} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
-				ret = write_stream_reflections_2_2(st->fh,
-			                                           reflist,
-			                                           image);
-			} else {
-				/* This function writes like a normal reflection
-				 * list was written in stream 2.1 */
-				ret = write_stream_reflections_2_1(st->fh,
-				                                   reflist,
-				                                   image);
-			}
+			ret = write_stream_reflections(st->fh, reflist,
+			                               dtempl);
 			fprintf(st->fh, REFLECTION_END_MARKER"\n");
 
 		} else {
@@ -848,6 +694,7 @@ static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
  * \returns non-zero on error.
  */
 int write_chunk(Stream *st, struct image *i,
+                const DataTemplate *dtempl,
                 int include_peaks, int include_reflections)
 {
 	int j;
@@ -903,7 +750,7 @@ int write_chunk(Stream *st, struct image *i,
 
 	for ( j=0; j<i->n_crystals; j++ ) {
 		if ( crystal_get_user_flag(i->crystals[j]) == 0 ) {
-			ret = write_crystal(st, i->crystals[j],
+			ret = write_crystal(st, i->crystals[j], dtempl,
 			                    include_reflections);
 		}
 	}
@@ -945,7 +792,8 @@ static int find_start_of_chunk(Stream *st)
 }
 
 
-static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
+static void read_crystal(Stream *st, struct image *image,
+                         const DataTemplate *dtempl, StreamReadFlags srf)
 {
 	char line[1024];
 	char *rval = NULL;
@@ -1073,13 +921,13 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 			 * after 2.2 */
 			if ( AT_LEAST_VERSION(st, 2, 3) ) {
 				reflist = read_stream_reflections_2_3(st,
-                                                      image->det);
+                                                      dtempl);
 			} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
 				reflist = read_stream_reflections_2_2(st,
-				          image->det);
+				                                      dtempl);
 			} else {
 				reflist = read_stream_reflections_2_1(st,
-				          image->det);
+				                                      dtempl);
 			}
 			if ( reflist == NULL ) {
 				ERROR("Failed while reading reflections\n");
@@ -1147,7 +995,8 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 /**
  * Read the next chunk from a stream and fill in 'image'
  */
-int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf)
+int read_chunk(Stream *st, struct image *image,
+               const DataTemplate *dtempl, StreamReadFlags srf)
 {
 	char line[1024];
 	char *rval = NULL;
@@ -1260,7 +1109,7 @@ int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf)
 
 		if ( (srf & STREAM_READ_CRYSTALS)
 		  && (strcmp(line, CRYSTAL_START_MARKER) == 0) ) {
-			read_crystal(st, image, srf);
+			read_crystal(st, image, dtempl, srf);
 		}
 
 		/* A chunk must have at least a filename and a wavelength,
@@ -1282,23 +1131,6 @@ int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf)
 }
 
 
-
-/**
- * \param st A \ref Stream
- * \param image An \ref image structure to be filled
- *
- * Reads a chunk from \p st, placing the information in \p image.
- *
- * \returns non-zero on error.
- */
-int read_chunk(Stream *st, struct image *image)
-{
-	return read_chunk_2(st, image, STREAM_READ_UNITCELL
-	                               | STREAM_READ_REFLECTIONS
-	                               | STREAM_READ_PEAKS);
-}
-
-
 void write_stream_header(FILE *ofh, int argc, char *argv[])
 {
 	int i;
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index 18a983c9..0a726bfb 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -41,9 +41,8 @@
  */
 
 struct image;
-struct hdfile;
-struct event;
-struct imagefile;
+
+#include "datatemplate.h"
 #include "cell.h"
 
 #define GEOM_START_MARKER "----- Begin geometry file -----"
@@ -116,12 +115,13 @@ extern void close_stream(Stream *st);
 
 extern void free_stuff_from_stream(struct stuff_from_stream *sfs);
 
-extern int read_chunk(Stream *st, struct image *image);
-extern int read_chunk_2(Stream *st, struct image *image,
-                           StreamReadFlags srf);
+extern int read_chunk(Stream *st, struct image *image,
+                      const DataTemplate *dtempl,
+                      StreamReadFlags srf);
 extern int stream_has_old_indexers(Stream *st);
 
 extern int write_chunk(Stream *st, struct image *image,
+                       const DataTemplate *dtempl,
                        int include_peaks, int include_reflections);
 
 extern void write_command(Stream *st, int argc, char *argv[]);
diff --git a/src/ambigator.c b/src/ambigator.c
index 800c05de..b4e4b8f8 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -1256,8 +1256,9 @@ int main(int argc, char *argv[])
 
 		cur.det = NULL;
 
-		if ( read_chunk_2(st, &cur, STREAM_READ_UNITCELL
-		                          | STREAM_READ_REFLECTIONS) != 0 ) {
+		if ( read_chunk(st, &cur, NULL,
+		                STREAM_READ_UNITCELL | STREAM_READ_REFLECTIONS) != 0 )
+		{
 			break;
 		}
 
diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index 4ae406ce..5648ac3c 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -2001,7 +2001,7 @@ int main(int argc, char *argv[])
 
 		cur.det = NULL;
 
-		if ( read_chunk_2(st, &cur, STREAM_READ_UNITCELL) != 0 ) {
+		if ( read_chunk(st, &cur, NULL, STREAM_READ_UNITCELL) != 0 ) {
 			break;
 		}
 
diff --git a/src/im-zmq.c b/src/im-zmq.c
index 39f1d207..09230938 100644
--- a/src/im-zmq.c
+++ b/src/im-zmq.c
@@ -228,17 +228,13 @@ ImageFeatureList *get_peaks_msgpack(msgpack_object *obj,
 		ss = peak_y->via.array.ptr[pk].via.f64 + peak_offset;
 		val = peak_i->via.array.ptr[pk].via.f64;
 
-		pn = data_template_find_panel(dtempl, fs, ss);
-		if ( pn < -1 ) {
+		/* Convert coordinates to panel-relative */
+		if ( data_template_file_to_panel_coords(dtempl, &fs, &ss, &pn) ) {
 			ERROR("Peak not in panel!\n");
-			continue;
+		} else {
+			image_add_feature(features, fs, ss, pn,
+			                  NULL, val, NULL);
 		}
-
-		/* Convert coordinates to panel-relative */
-		data_template_file_to_panel_coords(dtempl, &fs, &ss);
-
-		image_add_feature(features, fs, ss, pn,
-		                  NULL, val, NULL);
 	}
 
 	return features;
diff --git a/src/partialator.c b/src/partialator.c
index 032eb0d9..b7641d08 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -1379,8 +1379,9 @@ int main(int argc, char *argv[])
 		cur.div = NAN;
 		cur.bw = NAN;
 		cur.det = NULL;
-		if ( read_chunk_2(st, &cur, STREAM_READ_REFLECTIONS
-		                            | STREAM_READ_UNITCELL) != 0 ) {
+		if ( read_chunk(st, &cur, NULL,
+		                STREAM_READ_REFLECTIONS | STREAM_READ_UNITCELL) != 0 )
+		{
 			break;
 		}
 
diff --git a/src/process_hkl.c b/src/process_hkl.c
index 5aadda47..ec980db1 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -429,8 +429,8 @@ static int merge_all(Stream *st, RefList *model, RefList *reference,
 		image.det = NULL;
 
 		/* Get data from next chunk */
-		rval = read_chunk_2(st, &image, STREAM_READ_REFLECTIONS |
-		                    STREAM_READ_UNITCELL);
+		rval = read_chunk(st, &image, NULL,
+		                  STREAM_READ_REFLECTIONS | STREAM_READ_UNITCELL);
 		if ( rval ) break;
 
 		n_images++;
diff --git a/src/process_image.c b/src/process_image.c
index 5fdafdbe..34483f46 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -407,8 +407,8 @@ streamwrite:
 	time_accounts_set(taccs, TACC_WRITESTREAM);
 	set_last_task(last_task, "stream write");
 	sb_shared->pings[cookie]++;
-	ret = write_chunk(st, image, iargs->stream_peaks,
-	                  iargs->stream_refls);
+	ret = write_chunk(st, image, iargs->dtempl,
+	                  iargs->stream_peaks, iargs->stream_refls);
 	if ( ret != 0 ) {
 		ERROR("Error writing stream file.\n");
 	}
diff --git a/src/whirligig.c b/src/whirligig.c
index ee74a25e..843403ec 100644
--- a/src/whirligig.c
+++ b/src/whirligig.c
@@ -719,8 +719,9 @@ int main(int argc, char *argv[])
 		cur.div = NAN;
 		cur.bw = NAN;
 		cur.det = NULL;
-		if ( read_chunk_2(st, &cur, STREAM_READ_REFLECTIONS
-		                            | STREAM_READ_UNITCELL) != 0 ) {
+		if ( read_chunk(st, &cur, NULL,
+		                STREAM_READ_REFLECTIONS | STREAM_READ_UNITCELL) != 0 )
+		{
 			break;
 		}