Make Stream responsible for its own DataTemplate

It makes no sense for a different DataTemplate to be used for every
frame in a stream.  And this way makes everything much easier for users
ot the API.

13 files changed, 55 insertions, 92 deletions

diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 6242071b..a79e006d 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -73,6 +73,8 @@ struct _stream
 	char *audit_info;
 	char *geometry_file;
 
+	const DataTemplate *dtempl;
+
 	long long int ln;
 
 	int old_indexers;  /* True if the stream reader encountered a deprecated
@@ -95,7 +97,6 @@ int stream_has_old_indexers(Stream *st)
 
 
 static ImageFeatureList *read_peaks(Stream *st,
-                                    const DataTemplate *dtempl,
                                     struct image *image)
 {
 	char *rval = NULL;
@@ -145,11 +146,11 @@ static ImageFeatureList *read_peaks(Stream *st,
 			return NULL;
 		}
 
-		if ( (panel_name[0] != '\0') && (dtempl != NULL) ) {
+		if ( (panel_name[0] != '\0') && (st->dtempl != NULL) ) {
 
 			int pn;
 
-			if ( data_template_panel_name_to_number(dtempl,
+			if ( data_template_panel_name_to_number(st->dtempl,
 			                                        panel_name,
 			                                        &pn) )
 			{
@@ -157,7 +158,7 @@ static ImageFeatureList *read_peaks(Stream *st,
 				      panel_name);
 			} else {
 
-				data_template_file_to_panel_coords(dtempl,
+				data_template_file_to_panel_coords(st->dtempl,
 				                                   &x, &y, &pn);
 
 				image_add_feature(features, x, y,
@@ -224,8 +225,7 @@ static int write_peaks(struct image *image,
 }
 
 
-static RefList *read_stream_reflections_2_3(Stream *st,
-                                            const DataTemplate *dtempl)
+static RefList *read_stream_reflections_2_3(Stream *st)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -272,9 +272,9 @@ static RefList *read_stream_reflections_2_3(Stream *st,
 				return NULL;
 			}
 			set_intensity(refl, intensity);
-			if ( dtempl != NULL ) {
+			if ( st->dtempl != NULL ) {
 				int pn;
-				if ( data_template_file_to_panel_coords(dtempl, &fs, &ss, &pn) ) {
+				if ( data_template_file_to_panel_coords(st->dtempl, &fs, &ss, &pn) ) {
 					ERROR("Failed to convert\n");
 				} else {
 					set_detector_pos(refl, fs, ss);
@@ -295,8 +295,7 @@ static RefList *read_stream_reflections_2_3(Stream *st,
 }
 
 
-static RefList *read_stream_reflections_2_1(Stream *st,
-                                            const DataTemplate *dtempl)
+static RefList *read_stream_reflections_2_1(Stream *st)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -346,10 +345,10 @@ static RefList *read_stream_reflections_2_1(Stream *st,
 			}
 			set_intensity(refl, intensity);
 
-			if ( dtempl != NULL ) {
+			if ( st->dtempl != NULL ) {
 
 				int pn;
-				if ( data_template_file_to_panel_coords(dtempl, &fs, &ss, &pn) ) {
+				if ( data_template_file_to_panel_coords(st->dtempl, &fs, &ss, &pn) ) {
 					ERROR("Failed to convert\n");
 				} else {
 					set_detector_pos(refl, fs, ss);
@@ -377,8 +376,7 @@ static RefList *read_stream_reflections_2_1(Stream *st,
 }
 
 
-static RefList *read_stream_reflections_2_2(Stream *st,
-                                            const DataTemplate *dtempl)
+static RefList *read_stream_reflections_2_2(Stream *st)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -418,11 +416,11 @@ static RefList *read_stream_reflections_2_2(Stream *st,
 			}
 			set_intensity(refl, intensity);
 
-			if ( dtempl != NULL ) {
+			if ( st->dtempl != NULL ) {
 
 				int pn;
 
-				if ( data_template_file_to_panel_coords(dtempl, &fs, &ss, &pn) ) {
+				if ( data_template_file_to_panel_coords(st->dtempl, &fs, &ss, &pn) ) {
 					ERROR("Failed to convert to "
 					      "panel-relative coordinates: "
 					      "%i,%i\n", fs, ss);
@@ -515,7 +513,6 @@ static int num_integrated_reflections(RefList *list)
 
 
 static int write_crystal(Stream *st, Crystal *cr,
-                         const DataTemplate *dtempl,
                          int include_reflections)
 {
 	UnitCell *cell;
@@ -589,7 +586,7 @@ static int write_crystal(Stream *st, Crystal *cr,
 
 			fprintf(st->fh, STREAM_REFLECTION_START_MARKER"\n");
 			ret = write_stream_reflections(st->fh, reflist,
-			                               dtempl);
+			                               st->dtempl);
 			fprintf(st->fh, STREAM_REFLECTION_END_MARKER"\n");
 
 		} else {
@@ -616,7 +613,7 @@ static int write_crystal(Stream *st, Crystal *cr,
  * \returns non-zero on error.
  */
 int stream_write_chunk(Stream *st, struct image *i,
-                       const DataTemplate *dtempl, StreamFlags srf)
+                       StreamFlags srf)
 {
 	int j;
 	char *indexer;
@@ -666,7 +663,7 @@ int stream_write_chunk(Stream *st, struct image *i,
 	fprintf(st->fh, "peak_resolution = %f nm^-1 or %f A\n",
 	        i->peak_resolution/1e9, 1e10/i->peak_resolution);
 	if ( srf & STREAM_PEAKS ) {
-		ret = write_peaks(i, dtempl, st->fh);
+		ret = write_peaks(i, st->dtempl, st->fh);
 	}
 
 	if ( srf & STREAM_CRYSTALS ) {
@@ -674,7 +671,7 @@ int stream_write_chunk(Stream *st, struct image *i,
 			if ( crystal_get_user_flag(i->crystals[j]) ) {
 				continue;
 			}
-			ret = write_crystal(st, i->crystals[j], dtempl,
+			ret = write_crystal(st, i->crystals[j],
 			                    srf & STREAM_REFLECTIONS);
 		}
 	}
@@ -717,7 +714,7 @@ static int find_start_of_chunk(Stream *st)
 
 
 static void read_crystal(Stream *st, struct image *image,
-                         const DataTemplate *dtempl, StreamFlags srf)
+                         StreamFlags srf)
 {
 	char line[1024];
 	char *rval = NULL;
@@ -844,14 +841,11 @@ static void read_crystal(Stream *st, struct image *image,
 			/* The reflection list format in the stream diverges
 			 * after 2.2 */
 			if ( AT_LEAST_VERSION(st, 2, 3) ) {
-				reflist = read_stream_reflections_2_3(st,
-                                                      dtempl);
+				reflist = read_stream_reflections_2_3(st);
 			} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
-				reflist = read_stream_reflections_2_2(st,
-				                                      dtempl);
+				reflist = read_stream_reflections_2_2(st);
 			} else {
-				reflist = read_stream_reflections_2_1(st,
-				                                      dtempl);
+				reflist = read_stream_reflections_2_1(st);
 			}
 			if ( reflist == NULL ) {
 				ERROR("Failed while reading reflections\n");
@@ -919,8 +913,7 @@ static void read_crystal(Stream *st, struct image *image,
 /**
  * Read the next chunk from a stream and return an image structure
  */
-struct image *stream_read_chunk(Stream *st, const DataTemplate *dtempl,
-                                StreamFlags srf)
+struct image *stream_read_chunk(Stream *st, StreamFlags srf)
 {
 	char line[1024];
 	char *rval = NULL;
@@ -991,7 +984,7 @@ struct image *stream_read_chunk(Stream *st, const DataTemplate *dtempl,
 		    && strcmp(line, STREAM_PEAK_LIST_START_MARKER) == 0 ) {
 
 			ImageFeatureList *peaks;
-			peaks = read_peaks(st, dtempl, image);
+			peaks = read_peaks(st, image);
 
 			if ( peaks == NULL ) {
 				ERROR("Failed while reading peaks\n");
@@ -1006,7 +999,7 @@ struct image *stream_read_chunk(Stream *st, const DataTemplate *dtempl,
 
 		if ( (srf & STREAM_CRYSTALS)
 		  && (strcmp(line, STREAM_CRYSTAL_START_MARKER) == 0) ) {
-			read_crystal(st, image, dtempl, srf);
+			read_crystal(st, image, srf);
 		}
 
 		/* A chunk must have at least a filename and a wavelength,
@@ -1014,16 +1007,16 @@ struct image *stream_read_chunk(Stream *st, const DataTemplate *dtempl,
 		if ( strcmp(line, STREAM_CHUNK_END_MARKER) == 0 ) {
 			if ( have_filename && have_ev ) {
 				/* Success */
-				create_detgeom(image, dtempl);
+				create_detgeom(image, st->dtempl);
 				if ( srf & STREAM_IMAGE_DATA ) {
 					image_read_image_data(image,
-					                      dtempl,
+					                      st->dtempl,
 					                      image->filename,
 					                      image->ev);
 				} else {
-					image_set_zero_data(image, dtempl);
+					image_set_zero_data(image, st->dtempl);
 				}
-				image_set_zero_mask(image, dtempl);
+				image_set_zero_mask(image, st->dtempl);
 				return image;
 			}
 			ERROR("Incomplete chunk found in input file.\n");
@@ -1170,6 +1163,7 @@ static void read_geometry_file(Stream *st)
 
 	if ( success ) {
 		st->geometry_file = geom;
+		st->dtempl = data_template_new_from_string(geom);
 	}
 }
 
@@ -1248,7 +1242,7 @@ Stream *stream_open_for_read(const char *filename)
  *
  * \returns A \ref Stream, or NULL on failure.
  */
-Stream *stream_open_fd_for_write(int fd)
+Stream *stream_open_fd_for_write(int fd, const DataTemplate *dtempl)
 {
 	Stream *st;
 
@@ -1267,6 +1261,7 @@ Stream *stream_open_fd_for_write(int fd)
 		return NULL;
 	}
 
+	st->dtempl = dtempl;
 	st->major_version = LATEST_MAJOR_VERSION;
 	st->minor_version = LATEST_MINOR_VERSION;
 
@@ -1289,13 +1284,15 @@ void stream_write_target_cell(Stream *st, const UnitCell *cell)
 
 /**
  * \param filename Filename of new stream
+ * \param dtempl A DataTemplate
  *
  * Creates a new stream with name \p filename.  If \p filename already
  * exists, it will be overwritten.
  *
  * \returns A \ref Stream, or NULL on failure.
  */
-Stream *stream_open_for_write(const char *filename)
+Stream *stream_open_for_write(const char *filename,
+                              const DataTemplate *dtempl)
 
 {
 	Stream *st;
@@ -1308,6 +1305,7 @@ Stream *stream_open_for_write(const char *filename)
 	st->in_chunk = 0;
 	st->n_chunks = 0;
 	st->chunk_offsets = NULL;
+	st->dtempl = dtempl;
 
 	st->fh = fopen(filename, "w");
 	if ( st->fh == NULL ) {
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index ab98f3f9..0f28a4f8 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -92,8 +92,10 @@ extern "C" {
 
 /* Opening/closing streams */
 extern Stream *stream_open_for_read(const char *filename);
-extern Stream *stream_open_for_write(const char *filename);
-extern Stream *stream_open_fd_for_write(int fd);
+extern Stream *stream_open_for_write(const char *filename,
+                                     const DataTemplate *dtempl);
+extern Stream *stream_open_fd_for_write(int fd,
+                                        const DataTemplate *dtempl);
 extern void stream_close(Stream *st);
 
 /* Writing things to stream header */
@@ -120,12 +122,8 @@ extern int stream_scan_chunks(Stream *st);
 extern int stream_select_chunk(Stream *st, int chunk_number);
 
 /* Read/write chunks */
-extern struct image *stream_read_chunk(Stream *st,
-                                       const DataTemplate *dtempl,
-                                       StreamFlags srf);
-
+extern struct image *stream_read_chunk(Stream *st, StreamFlags srf);
 extern int stream_write_chunk(Stream *st, struct image *image,
-                              const DataTemplate *dtempl,
                               StreamFlags srf);
 
 #ifdef __cplusplus
diff --git a/src/ambigator.c b/src/ambigator.c
index fa405b4f..c3afd6c1 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -1259,7 +1259,7 @@ int main(int argc, char *argv[])
 		struct image *image;
 		int i;
 
-		image = stream_read_chunk(st, NULL, STREAM_UNITCELL
+		image = stream_read_chunk(st, STREAM_UNITCELL
 		                          | STREAM_REFLECTIONS);
 		if ( image == NULL ) break;
 
diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index 2eec4a19..84a8aa16 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -2002,7 +2002,7 @@ int main(int argc, char *argv[])
 		struct image *image;
 		int i;
 
-		image = stream_read_chunk(st, NULL, STREAM_UNITCELL);
+		image = stream_read_chunk(st, STREAM_UNITCELL);
 		if ( image == NULL ) break;
 
 		for ( i=0; i<image->n_crystals; i++ ) {
diff --git a/src/crystfel_gui.c b/src/crystfel_gui.c
index a941dca6..7f4f29f0 100644
--- a/src/crystfel_gui.c
+++ b/src/crystfel_gui.c
@@ -145,7 +145,6 @@ static void update_imageview(struct crystfelproject *proj)
 		}
 
 		image = stream_read_chunk(proj->stream,
-		                          proj->dtempl,
 		                          STREAM_UNITCELL
 		                        | STREAM_REFLECTIONS
 		                        | STREAM_PEAKS
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 32c4fc13..1024b738 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -661,7 +661,7 @@ static void start_worker_process(struct sandbox *sb, int slot)
 		 *               prefix
 		 */
 
-		st = stream_open_fd_for_write(stream_pipe[1]);
+		st = stream_open_fd_for_write(stream_pipe[1], sb->iargs->dtempl);
 		r = run_work(sb->iargs, st, slot, tmp, sb);
 		stream_close(st);
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 2d0e53c8..15315952 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -993,7 +993,7 @@ int main(int argc, char *argv[])
 	free(rn);
 
 	/* Open output stream */
-	st = stream_open_for_write(args.outfile);
+	st = stream_open_for_write(args.outfile, args.iargs.dtempl);
 	if ( st == NULL ) {
 		ERROR("Failed to open stream '%s'\n", args.outfile);
 		return 1;
diff --git a/src/partial_sim.c b/src/partial_sim.c
index dfadb94f..a0f60e1e 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -346,7 +346,6 @@ static void *create_job(void *vqargs)
 		struct image *image;
 
 		image = stream_read_chunk(qargs->template_stream,
-		                          qargs->dtempl,
 		                          STREAM_UNITCELL | STREAM_REFLECTIONS);
 		if ( image == NULL ) {
 			ERROR("Failed to read template chunk!\n");
@@ -474,7 +473,7 @@ static void finalise_job(void *vqargs, void *vwargs)
 	int ret;
 
 	ret = stream_write_chunk(qargs->stream, wargs->image,
-	                         qargs->dtempl, STREAM_UNITCELL
+	                         STREAM_UNITCELL
 	                                      | STREAM_REFLECTIONS
 	                                      | STREAM_CRYSTALS);
 	if ( ret != 0 ) {
@@ -852,7 +851,7 @@ int main(int argc, char *argv[])
 		ERROR("You must give a filename for the output.\n");
 		return 1;
 	}
-	stream = stream_open_for_write(output_file);
+	stream = stream_open_for_write(output_file, dtempl);
 	if ( stream == NULL ) {
 		ERROR("Couldn't open output file '%s'\n", output_file);
 		return 1;
diff --git a/src/partialator.c b/src/partialator.c
index 959338ca..1a28e3f3 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -973,8 +973,6 @@ int main(int argc, char *argv[])
 	PartialityModel pmodel = PMODEL_XSPHERE;
 	int min_measurements = 2;
 	char *rval;
-	const char *geom_str;
-	DataTemplate *dtempl;
 	struct polarisation polarisation = {.fraction = 1.0,
 	                                    .angle = 0.0,
 	                                    .disable = 0};
@@ -1249,19 +1247,6 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
-	geom_str = stream_geometry_file(st);
-	if ( geom_str == NULL ) {
-		ERROR("No geometry file\n");
-		stream_close(st);
-		return 1;
-	}
-
-	dtempl = data_template_new_from_string(geom_str);
-	if ( dtempl == NULL ) {
-		stream_close(st);
-		return 1;
-	}
-
 	if ( outfile == NULL ) {
 		outfile = strdup("partialator.hkl");
 	}
@@ -1420,7 +1405,7 @@ int main(int argc, char *argv[])
 		RefList *as;
 		int i;
 
-		image = stream_read_chunk(st, dtempl, STREAM_REFLECTIONS
+		image = stream_read_chunk(st, STREAM_REFLECTIONS
 		                                    | STREAM_UNITCELL);
 		if ( image == NULL ) break;
 
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 4d74589b..b83677b7 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -1049,7 +1049,7 @@ int main(int argc, char *argv[])
 			Crystal *cr;
 
 			/* Get data from next chunk */
-			templ_image = stream_read_chunk(st, dtempl,
+			templ_image = stream_read_chunk(st,
 			                                STREAM_CRYSTALS);
 			if ( templ_image == NULL ) break;
 			if ( templ_image->n_crystals == 0 ) continue;
diff --git a/src/process_hkl.c b/src/process_hkl.c
index 352bea4a..812903a2 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -397,7 +397,7 @@ static void display_progress(int n_images, int n_crystals, int n_crystals_used)
 }
 
 
-static int merge_all(Stream *st, DataTemplate *dtempl,
+static int merge_all(Stream *st,
                      RefList *model, RefList *reference,
                      const SymOpList *sym,
                      double **hist_vals, signed int hist_h,
@@ -431,7 +431,7 @@ static int merge_all(Stream *st, DataTemplate *dtempl,
 		int i;
 
 		/* Get data from next chunk */
-		image = stream_read_chunk(st, dtempl,
+		image = stream_read_chunk(st,
 		                          STREAM_REFLECTIONS
 		                        | STREAM_UNITCELL);
 		if ( image == NULL ) break;
@@ -517,8 +517,6 @@ int main(int argc, char *argv[])
 	int hist_i;
 	int space_for_hist = 0;
 	char *histo_params = NULL;
-	const char *geom_str;
-	DataTemplate *dtempl;
 	struct polarisation polarisation = {.fraction = 1.0,
 	                                    .angle = 0.0,
 	                                    .disable = 0};
@@ -730,19 +728,6 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
-	geom_str = stream_geometry_file(st);
-	if ( geom_str == NULL ) {
-		ERROR("No geometry file found in stream\n");
-		stream_close(st);
-		return 1;
-	}
-
-	dtempl = data_template_new_from_string(geom_str);
-	if ( dtempl == NULL ) {
-		stream_close(st);
-		return 1;
-	}
-
 	model = reflist_new();
 
 	if ( histo != NULL ) {
@@ -799,7 +784,7 @@ int main(int argc, char *argv[])
 	if ( config_scale ) twopass = 1;
 
 	hist_i = 0;
-	r = merge_all(st, dtempl, model, NULL, sym,
+	r = merge_all(st, model, NULL, sym,
 	              &hist_vals, hist_h, hist_k, hist_l,
 	              &hist_i, polarisation, min_measurements, min_snr,
 	              max_adu, start_after, stop_after, min_res, push_res,
@@ -834,7 +819,7 @@ int main(int argc, char *argv[])
 				hist_i = 0;
 			}
 
-			r = merge_all(st, dtempl, model, reference, sym, &hist_vals,
+			r = merge_all(st, model, reference, sym, &hist_vals,
 			              hist_h, hist_k, hist_l, &hist_i,
 				      polarisation, min_measurements, min_snr,
 				      max_adu, start_after, stop_after, min_res,
diff --git a/src/process_image.c b/src/process_image.c
index a04e9468..60568ede 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -404,8 +404,7 @@ streamwrite:
 	time_accounts_set(taccs, TACC_WRITESTREAM);
 	set_last_task(last_task, "stream write");
 	sb_shared->pings[cookie]++;
-	ret = stream_write_chunk(st, image, iargs->dtempl,
-	                         iargs->stream_flags);
+	ret = stream_write_chunk(st, image, iargs->stream_flags);
 	if ( ret != 0 ) {
 		ERROR("Error writing stream file.\n");
 	}
diff --git a/src/whirligig.c b/src/whirligig.c
index 16688559..0d5a2f0d 100644
--- a/src/whirligig.c
+++ b/src/whirligig.c
@@ -720,7 +720,7 @@ int main(int argc, char *argv[])
 
 		struct image *image;
 
-		image = stream_read_chunk(st, NULL, STREAM_REFLECTIONS
+		image = stream_read_chunk(st, STREAM_REFLECTIONS
 		                                  | STREAM_UNITCELL);
 
 		if ( image == NULL ) break;