Get rid of imagefile_field_list and stuff_from_stream

The only place this is used is in geoptimiser, to get the
average_camera_length, itself a very bad solution.

12 files changed, 62 insertions, 112 deletions

diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index f0e23ded..60c36358 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -1270,3 +1270,11 @@ void data_template_file_to_panel_coords(const DataTemplate *dt,
 	*pfs = *pfs - dt->panels[pn].orig_min_fs;
 	*pss = *pss - dt->panels[pn].orig_min_ss;
 }
+
+
+void data_template_add_copy_header(DataTemplate *dt,
+                                   const char *header)
+{
+	/* FIXME: Add "header" to list of things to copy */
+	STATUS("Adding %s\n", header);
+}
diff --git a/libcrystfel/src/datatemplate.h b/libcrystfel/src/datatemplate.h
index 0adcdb0b..ac76c578 100644
--- a/libcrystfel/src/datatemplate.h
+++ b/libcrystfel/src/datatemplate.h
@@ -59,6 +59,9 @@ extern signed int data_template_find_panel(const DataTemplate *dt,
 extern void data_template_file_to_panel_coords(const DataTemplate *dt,
                                                float *pfs, float *pss);
 
+extern void data_template_add_copy_header(DataTemplate *dt,
+                                          const char *header);
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index c7d46978..8b73e414 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -838,8 +838,7 @@ struct image *image_new()
 	image->detgeom = NULL;
 	image->filename = NULL;
 	image->ev = NULL;
-	image->copyme = NULL;
-	image->stuff_from_stream = NULL;
+	image->copied_headers = NULL;
 	image->avg_clen = -1.0;
 	image->id = 0;
 	image->serial = 0;
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 90cb823d..1ea0bc35 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -44,8 +44,6 @@ struct detector;
 struct imagefeature;
 struct sample;
 struct image;
-struct imagefile;
-struct imagefile_field_list;
 
 #include "utils.h"
 #include "cell.h"
@@ -155,11 +153,8 @@ struct image
 	char                    *ev;
 	/** @} */
 
-	/** A list of image file headers to copy to the stream */
-	const struct imagefile_field_list *copyme;
-
 	/** A list of metadata read from the stream */
-	struct stuff_from_stream *stuff_from_stream;
+	char                    *copied_headers;
 
 	/** Mean of the camera length values for all panels */
 	double                  avg_clen;
@@ -235,9 +230,6 @@ extern int imagefile_read(struct imagefile *f, struct image *image,
 extern int imagefile_read_simple(struct imagefile *f, struct image *image);
 extern struct hdfile *imagefile_get_hdfile(struct imagefile *f);
 extern enum imagefile_type imagefile_get_type(struct imagefile *f);
-extern void imagefile_copy_fields(struct imagefile *f,
-                                  const struct imagefile_field_list *copyme,
-                                  FILE *fh, struct event *ev);
 extern void imagefile_close(struct imagefile *f);
 extern signed int is_cbf_file(const char *filename);
 
@@ -256,13 +248,6 @@ extern ImageFeatureList *image_read_peaks(const DataTemplate *dtempl,
 extern struct event_list *image_expand_frames(const DataTemplate *dtempl,
                                               const char *filename);
 
-/* Field lists */
-extern struct imagefile_field_list *new_imagefile_field_list(void);
-extern void free_imagefile_field_list(struct imagefile_field_list *f);
-
-extern void add_imagefile_field(struct imagefile_field_list *copyme,
-                                const char *name);
-
 #ifdef __cplusplus
 }
 #endif
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 8255a711..419acd36 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -1144,55 +1144,6 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 }
 
 
-void free_stuff_from_stream(struct stuff_from_stream *sfs)
-{
-	int i;
-	if ( sfs == NULL ) return;
-	for ( i=0; i<sfs->n_fields; i++ ) {
-		free(sfs->fields[i]);
-	}
-	free(sfs->fields);
-	free(sfs);
-}
-
-
-static int read_and_store_field(struct image *image, const char *line)
-{
-	char **new_fields;
-	char *nf;
-
-	if ( image->stuff_from_stream == NULL ) {
-		image->stuff_from_stream =
-		       malloc(sizeof(struct stuff_from_stream));
-		if ( image->stuff_from_stream == NULL) {
-			ERROR("Failed reading entries from stream\n");
-			return 1;
-		}
-		image->stuff_from_stream->fields = NULL;
-		image->stuff_from_stream->n_fields = 0;
-	}
-
-	new_fields = realloc(image->stuff_from_stream->fields,
-			     (1+image->stuff_from_stream->n_fields)*
-			     sizeof(char *));
-	if ( new_fields == NULL ) {
-		ERROR("Failed reading entries from stream\n");
-		return 1;
-	}
-	image->stuff_from_stream->fields = new_fields;
-
-	nf = strdup(line);
-	if ( nf == NULL ) {
-		ERROR("Failed to allocate field from stream\n");
-		return 1;
-	}
-	image->stuff_from_stream->fields[image->stuff_from_stream->n_fields] = nf;
-	image->stuff_from_stream->n_fields++;
-
-	return 0;
-}
-
-
 /**
  * Read the next chunk from a stream and fill in 'image'
  */
@@ -1210,7 +1161,7 @@ int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf)
 	image->crystals = NULL;
 	image->n_crystals = 0;
 	image->ev = NULL;
-	image->stuff_from_stream = NULL;
+	image->copied_headers = NULL;
 
 	if ( (srf & STREAM_READ_REFLECTIONS) || (srf & STREAM_READ_UNITCELL) ) {
 		srf |= STREAM_READ_CRYSTALS;
@@ -1291,17 +1242,6 @@ int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf)
 			}
 		}
 
-		if ( strstr(line, " = ") != NULL ) {
-
-			int fail;
-
-			fail = read_and_store_field(image, line);
-			if ( fail ) {
-				ERROR("Failed to read fields from stream.\n");
-				return 1;
-			}
-		}
-
 		if ( (srf & STREAM_READ_PEAKS)
 		    && strcmp(line, PEAK_LIST_START_MARKER) == 0 ) {
 
diff --git a/src/geoptimiser.c b/src/geoptimiser.c
index cae2ae4e..ec4fbcd4 100644
--- a/src/geoptimiser.c
+++ b/src/geoptimiser.c
@@ -219,21 +219,22 @@ static Reflection *find_closest_reflection(struct image *image,
 static double get_average_clen(struct image *image)
 {
 	int i;
-	struct stuff_from_stream *stuff = image->stuff_from_stream;
-
-	if ( stuff == NULL ) {
-		ERROR("No 'stuff' from stream!\n");
-		return -1.0;
-	}
-
-	for ( i=0; i<stuff->n_fields; i++ ) {
-
-		if ( strncmp(stuff->fields[i], "average_camera_length = ",
-		             24) == 0 )
-		{
-			return atof(stuff->fields[i]+24);
-		}
-	}
+	// FIXME!
+	//	struct stuff_from_stream *stuff = image->stuff_from_stream;
+	//
+	//	if ( stuff == NULL ) {
+	//		ERROR("No 'stuff' from stream!\n");
+	//		return -1.0;
+	//	}
+	//
+	//	for ( i=0; i<stuff->n_fields; i++ ) {
+	//
+	//		if ( strncmp(stuff->fields[i], "average_camera_length = ",
+	//		             24) == 0 )
+	//		{
+	//			return atof(stuff->fields[i]+24);
+	//		}
+	//	}
 
 	ERROR("Failed to recover average camera length from stream file\n");
 	return -1.0;
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index c7840f94..660c2ae1 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -415,7 +415,6 @@ static int run_work(const struct index_args *iargs, Stream *st,
 
 	time_accounts_set(taccs, TACC_FINALCLEANUP);
 	cleanup_indexing(iargs->ipriv);
-	free_imagefile_field_list(iargs->copyme);
 	cell_free(iargs->cell);
 	if ( sb->profile ) time_accounts_print(taccs);
 	time_accounts_free(taccs);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index f4c3af50..bff9e90f 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -92,6 +92,8 @@ struct indexamajig_arguments
 	int if_multi;
 	int if_retry;
 	int profile;  /* Whether to do wall-clock time profiling */
+	char **copy_headers;
+	int n_copy_headers;
 
 	TakeTwoOptions **taketwo_opts_ptr;
 	FelixOptions **felix_opts_ptr;
@@ -107,6 +109,21 @@ static void show_version(FILE *fh, struct argp_state *state)
 }
 
 
+static void add_copy_header(struct indexamajig_arguments *args,
+                            const char *header)
+{
+	char **new_copy_headers = realloc(args->copy_headers,
+	                                  (args->n_copy_headers+1)*sizeof(char *));
+	if ( new_copy_headers == NULL ) {
+		ERROR("Failed to add copy header '%s'\n", header);
+		return;
+	}
+
+	args->copy_headers = new_copy_headers;
+	args->copy_headers[args->n_copy_headers++] = strdup(header);
+}
+
+
 static error_t parse_arg(int key, char *arg, struct argp_state *state)
 {
 	float tmp;
@@ -525,7 +542,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		break;
 
 		case 602 :
-		add_imagefile_field(args->iargs.copyme, arg);
+		add_copy_header(args, arg);
 		break;
 
 		case 603 :
@@ -587,6 +604,8 @@ int main(int argc, char *argv[])
 	args.if_refine = 1;
 	args.if_checkcell = 1;
 	args.profile = 0;
+	args.copy_headers = NULL;
+	args.n_copy_headers = 0;
 	args.taketwo_opts_ptr = &taketwo_opts;
 	args.felix_opts_ptr = &felix_opts;
 	args.xgandalf_opts_ptr = &xgandalf_opts;
@@ -618,7 +637,6 @@ int main(int argc, char *argv[])
 	args.iargs.dtempl = NULL;
 	args.iargs.peaks = PEAK_ZAEF;
 	args.iargs.half_pixel_shift = 1;
-	args.iargs.copyme = NULL;
 	args.iargs.pk_inn = -1.0;
 	args.iargs.pk_mid = -1.0;
 	args.iargs.pk_out = -1.0;
@@ -634,11 +652,6 @@ int main(int argc, char *argv[])
 	args.iargs.min_peaks = 0;
 	args.iargs.overpredict = 0;
 	args.iargs.wait_for_file = 0;
-	args.iargs.copyme = new_imagefile_field_list();
-	if ( args.iargs.copyme == NULL ) {
-		ERROR("Couldn't allocate HDF5 field list.\n");
-		return 1;
-	}
 	args.iargs.ipriv = NULL;  /* No default */
 	args.iargs.int_meth = integration_method("rings-nocen-nosat-nograd", NULL);
 	args.iargs.push_res = +INFINITY;
@@ -759,8 +772,9 @@ int main(int argc, char *argv[])
 		{NULL, 0, 0, OPTION_DOC, "Output options:", 6},
 		{"no-non-hits-in-stream", 601, NULL, OPTION_NO_USAGE, "Don't include non-hits in "
 		        "stream (see --min-peaks)"},
-		{"copy-hdf5-field", 602, "f", OPTION_NO_USAGE, "Put the value of this HDF5 field "
-		        "into the stream"},
+		{"copy-hdf5-field", 602, "f", OPTION_HIDDEN, NULL},
+		{"copy-header", 602, "f", OPTION_NO_USAGE, "Put the value of this image header "
+		        "field into the stream"},
 		{"no-peaks-in-stream", 603, NULL, OPTION_NO_USAGE, "Don't put peak search results "
 		        "in stream"},
 		{"no-refls-in-stream", 604, NULL, OPTION_NO_USAGE, "Don't put integration results "
@@ -831,6 +845,12 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
+	/* Add any headers we need to copy */
+	for ( r=0; r<args.n_copy_headers; r++ ) {
+		data_template_add_copy_header(args.iargs.dtempl,
+		                              args.copy_headers[r]);
+	}
+
 	/* If no integration radii were given, apply the defaults */
 	if ( args.iargs.ir_inn < 0 ) {
 		STATUS("WARNING: You did not specify --int-radius.\n");
@@ -1008,7 +1028,6 @@ int main(int argc, char *argv[])
 	                   fh, st, tmpdir, args.serial_start, zmq_address,
 	                   timeout, args.profile);
 
-	free_imagefile_field_list(args.iargs.copyme);
 	cell_free(args.iargs.cell);
 	free(args.prefix);
 	free(args.temp_location);
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 32263cad..9e774431 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -899,7 +899,7 @@ int main(int argc, char *argv[])
 	image.spectrum = spectrum_generate_gaussian(image.lambda, image.bw);
 	image.filename = "dummy.h5";
 	image.ev = "(none)";
-	image.copyme = NULL;
+	image.copied_headers = NULL;
 	image.crystals = NULL;
 	image.n_crystals = 0;
 	image.indexed_by = INDEXING_SIMULATION;
diff --git a/src/partialator.c b/src/partialator.c
index 47a752b0..032eb0d9 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -1389,9 +1389,6 @@ int main(int argc, char *argv[])
 			return 1;
 		}
 
-		free_stuff_from_stream(cur.stuff_from_stream);
-		cur.stuff_from_stream = NULL;
-
 		for ( i=0; i<cur.n_crystals; i++ ) {
 
 			Crystal *cr;
diff --git a/src/process_image.c b/src/process_image.c
index bca2a7f2..60e3edbc 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -201,7 +201,8 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		image = file_wait_open_read(pargs->filename, pargs->event,
 		                            iargs->dtempl,
 		                            sb_shared, taccs, last_task,
-		                            iargs->wait_for_file, cookie);
+		                            iargs->wait_for_file,
+		                            cookie);
 		if ( image == NULL ) {
 			if ( iargs->wait_for_file != 0 ) {
 				pthread_mutex_lock(&sb_shared->totals_lock);
@@ -213,7 +214,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	}
 
 	image->serial = serial;
-	image->copyme = iargs->copyme;
 
 	/* Take snapshot of image before applying horrible noise filters */
 	time_accounts_set(taccs, TACC_FILTER);
diff --git a/src/process_image.h b/src/process_image.h
index 908a2e06..354641c3 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -80,7 +80,6 @@ struct index_args
 	float min_snr_peak_pix;
 	float min_sig;
 	float min_peak_over_neighbour;
-	struct imagefile_field_list *copyme;
 	int integrate_saturated;
 	int use_saturated;
 	int no_revalidate;