Skeleton image file API

6 files changed, 155 insertions, 18 deletions

diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 2cc0d792..f322cbdd 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -299,3 +299,132 @@ void free_all_crystals(struct image *image)
 	free(image->crystals);
 	image->n_crystals = 0;
 }
+
+
+/**************************** Image field lists *******************************/
+
+struct imagefile_field_list
+{
+	char **fields;
+	int n_fields;
+	int max_fields;
+};
+
+
+struct imagefile_field_list *new_imagefile_field_list()
+{
+	struct imagefile_field_list *n;
+
+	n = calloc(1, sizeof(struct imagefile_field_list));
+	if ( n == NULL ) return NULL;
+
+	n->max_fields = 32;
+	n->fields = malloc(n->max_fields*sizeof(char *));
+	if ( n->fields == NULL ) {
+		free(n);
+		return NULL;
+	}
+
+	return n;
+}
+
+
+void free_imagefile_field_list(struct imagefile_field_list *n)
+{
+	int i;
+	for ( i=0; i<n->n_fields; i++ ) {
+		free(n->fields[i]);
+	}
+	free(n->fields);
+	free(n);
+}
+
+
+void add_imagefile_field(struct imagefile_field_list *copyme, const char *name)
+{
+	int i;
+
+	/* Already on the list?   Don't re-add if so. */
+	for ( i=0; i<copyme->n_fields; i++ ) {
+		if ( strcmp(copyme->fields[i], name) == 0 ) return;
+	}
+
+	/* Need more space? */
+	if ( copyme->n_fields == copyme->max_fields ) {
+
+		char **nfields;
+		int nmax = copyme->max_fields + 32;
+
+		nfields = realloc(copyme->fields, nmax*sizeof(char *));
+		if ( nfields == NULL ) {
+			ERROR("Failed to allocate space for new HDF5 field.\n");
+			return;
+		}
+
+		copyme->max_fields = nmax;
+		copyme->fields = nfields;
+
+	}
+
+	copyme->fields[copyme->n_fields] = strdup(name);
+	if ( copyme->fields[copyme->n_fields] == NULL ) {
+		ERROR("Failed to add field for copying '%s'\n", name);
+		return;
+	}
+
+	copyme->n_fields++;
+}
+
+
+/****************************** Image files ***********************************/
+
+struct imagefile *imagefile_open(const char *filename)
+{
+}
+
+
+int imagefile_read(struct imagefile *imfile, struct image *image,
+                          struct event *event)
+{
+}
+
+
+struct hdfile *imagefile_get_hdfile(struct imagefile *imfile)
+{
+}
+
+
+void imagefile_copy_fields(struct imagefile *f,
+                           const struct imagefile_field_list *copyme,
+                           FILE *fh, struct event *ev)
+{
+	int i;
+
+	if ( copyme == NULL ) return;
+
+	for ( i=0; i<copyme->n_fields; i++ ) {
+
+#warning FIXME Implement imagefile field copying
+#if 0
+		char *val;
+		char *field;
+
+		field = copyme->fields[i];
+		val = hdfile_get_string_value(f, field, ev);
+
+		if ( field[0] == '/' ) {
+			fprintf(fh, "hdf5%s = %s\n", field, val);
+		} else {
+			fprintf(fh, "hdf5/%s = %s\n", field, val);
+		}
+
+		free(val);
+#endif
+
+	}
+}
+
+
+void imagefile_close(struct imagefile *imfile)
+{
+}
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 2ed7140f..f310a09b 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -123,7 +123,7 @@ struct beam_params
  *    struct detector         *det;
  *    struct beam_params      *beam;
  *    char                    *filename;
- *    const struct copy_hdf5_field *copyme;
+ *    const struct imagefile_field_list *copyme;
  *
  *    int                     id;
  *
@@ -155,8 +155,8 @@ struct beam_params
  * returned by the low-level indexing system. <structfield>n_crystals</structfield>
  * is the number of crystals which were found in the image.
  *
- * <structfield>copyme</structfield> represents a list of HDF5 fields to copy
- * to the output stream.
+ * <structfield>copyme</structfield> represents a list of fields in the image
+ * file (e.g. HDF5 fields or CBF headers) to copy to the output stream.
  **/
 struct image;
 
@@ -174,7 +174,7 @@ struct image {
 	struct beam_params      *beam;  /* The nominal beam parameters */
 	char                    *filename;
 	struct event            *event;
-	const struct copy_hdf5_field *copyme;
+	const struct imagefile_field_list *copyme;
 	struct stuff_from_stream *stuff_from_stream;
 
 	double                  avg_clen;  /* Average camera length extracted
@@ -242,10 +242,17 @@ extern int imagefile_read(struct imagefile *imfile, struct image *image,
                           struct event *event);
 extern struct hdfile *imagefile_get_hdfile(struct imagefile *imfile);
 extern void imagefile_copy_fields(struct imagefile *imfile,
-                                  struct copy_hdf5_file *copyme, FILE *fh,
-                                  struct event *ev);
+                                  const struct imagefile_field_list *copyme,
+                                  FILE *fh, struct event *ev);
 extern void imagefile_close(struct imagefile *imfile);
 
+/* 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.h b/libcrystfel/src/stream.h
index a95c7df0..764e3e36 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -39,6 +39,7 @@
 struct image;
 struct hdfile;
 struct event;
+struct imagefile;
 #include "cell.h"
 
 #define GEOM_START_MARKER "----- Begin geometry file -----"
@@ -106,7 +107,7 @@ extern int read_chunk(Stream *st, struct image *image);
 extern int read_chunk_2(Stream *st, struct image *image,
                            StreamReadFlags srf);
 
-extern int write_chunk(Stream *st, struct image *image, struct hdfile *hdfile,
+extern int write_chunk(Stream *st, struct image *image, struct imagefile *imfile,
                        int include_peaks, int include_reflections,
                        struct event *ev);
 
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 2dabf3e9..60400ad8 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -375,7 +375,7 @@ static void run_work(const struct index_args *iargs, Stream *st,
 	cleanup_indexing(iargs->ipriv);
 	free_detector_geometry(iargs->det);
 	free(iargs->hdf5_peak_path);
-	free_copy_hdf5_field_list(iargs->copyme);
+	free_imagefile_field_list(iargs->copyme);
 	cell_free(iargs->cell);
 	if ( iargs->profile ) time_accounts_print(taccs);
 	time_accounts_free(taccs);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index f48fac17..439f9be3 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -172,9 +172,9 @@ static void show_help(const char *s)
 }
 
 
-static void add_geom_beam_stuff_to_copy_hdf5(struct copy_hdf5_field *copyme,
-                                             struct detector *det,
-                                             struct beam_params *beam)
+static void add_geom_beam_stuff_to_field_list(struct imagefile_field_list *copyme,
+                                              struct detector *det,
+                                              struct beam_params *beam)
 {
 	int i;
 
@@ -183,12 +183,12 @@ static void add_geom_beam_stuff_to_copy_hdf5(struct copy_hdf5_field *copyme,
 		struct panel *p = &det->panels[i];
 
 		if ( p->clen_from != NULL ) {
-			add_copy_hdf5_field(copyme, p->clen_from);
+			add_imagefile_field(copyme, p->clen_from);
 		}
 	}
 
 	if ( beam->photon_energy_from != NULL ) {
-		add_copy_hdf5_field(copyme, beam->photon_energy_from);
+		add_imagefile_field(copyme, beam->photon_energy_from);
 	}
 }
 
@@ -257,7 +257,7 @@ int main(int argc, char *argv[])
 	iargs.stream_peaks = 1;
 	iargs.stream_refls = 1;
 	iargs.int_diag = INTDIAG_NONE;
-	iargs.copyme = new_copy_hdf5_field_list();
+	iargs.copyme = new_imagefile_field_list();
 	if ( iargs.copyme == NULL ) {
 		ERROR("Couldn't allocate HDF5 field list.\n");
 		return 1;
@@ -431,7 +431,7 @@ int main(int argc, char *argv[])
 			break;
 
 			case 10 :
-			add_copy_hdf5_field(iargs.copyme, optarg);
+			add_imagefile_field(iargs.copyme, optarg);
 			break;
 
 			case 11 :
@@ -627,7 +627,7 @@ int main(int argc, char *argv[])
 		      geom_filename);
 		return 1;
 	}
-	add_geom_beam_stuff_to_copy_hdf5(iargs.copyme, iargs.det, iargs.beam);
+	add_geom_beam_stuff_to_field_list(iargs.copyme, iargs.det, iargs.beam);
 
 	/* If no peak path from geometry file, use these (but see later) */
 	if ( iargs.hdf5_peak_path == NULL ) {
@@ -806,7 +806,7 @@ int main(int argc, char *argv[])
 	create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
 	               st, tempdir);
 
-	free_copy_hdf5_field_list(iargs.copyme);
+	free_imagefile_field_list(iargs.copyme);
 	cell_free(iargs.cell);
 	free(iargs.beam->photon_energy_from);
 	free(prefix);
diff --git a/src/process_image.h b/src/process_image.h
index d63679cf..14f90c78 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -80,7 +80,7 @@ struct index_args
 	int min_pix_count;
 	int max_pix_count;
 	int local_bg_radius;
-	struct copy_hdf5_field *copyme;
+	struct imagefile_field_list *copyme;
 	int integrate_saturated;
 	int use_saturated;
 	int no_revalidate;