Initial CBF stuff

5 files changed, 46 insertions, 22 deletions

diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 09f4958d..2cc0d792 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -3,12 +3,12 @@
  *
  * Handle images and image features
  *
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
  *   2014      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
- *   2011-2016 Thomas White <taw@physics.org>
+ *   2011-2017 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 9fd9b495..2ed7140f 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -3,11 +3,11 @@
  *
  * Handle images and image features
  *
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2009-2016 Thomas White <taw@physics.org>
+ *   2009-2017 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
  *
  *
@@ -44,6 +44,8 @@ struct detector;
 struct imagefeature;
 struct sample;
 struct image;
+struct imagefile;
+struct imagefile_field_list;
 
 #include "utils.h"
 #include "cell.h"
@@ -51,6 +53,7 @@ struct image;
 #include "reflist.h"
 #include "crystal.h"
 #include "index.h"
+#include "events.h"
 
 /**
  * SpectrumType:
@@ -233,6 +236,16 @@ extern void image_add_crystal(struct image *image, Crystal *cryst);
 extern void remove_flagged_crystals(struct image *image);
 extern void free_all_crystals(struct image *image);
 
+/* Image files */
+extern struct imagefile *imagefile_open(const char *filename);
+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);
+extern void imagefile_close(struct imagefile *imfile);
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 17da74b2..fb4b0c70 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -806,8 +806,8 @@ static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
 }
 
 
-int write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
-                int include_peaks, int include_reflections, struct event* ev)
+int write_chunk(Stream *st, struct image *i, struct imagefile *imfile,
+                int include_peaks, int include_reflections, struct event *ev)
 {
 	int j;
 	char *indexer;
@@ -832,7 +832,7 @@ int write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
 	fprintf(st->fh, "beam_divergence = %.2e rad\n", i->div);
 	fprintf(st->fh, "beam_bandwidth = %.2e (fraction)\n", i->bw);
 
-	copy_hdf5_fields(hdfile, i->copyme, st->fh, ev);
+	imagefile_copy_fields(imfile, i->copyme, st->fh, ev);
 
 	if ( i->det != NULL ) {
 
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index ff8628c0..a95c7df0 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -3,11 +3,11 @@
  *
  * Stream tools
  *
- * Copyright © 2013-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2013-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2014 Thomas White <taw@physics.org>
+ *   2010-2017 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
  *   2011      Andrew Aquila
  *
@@ -110,6 +110,11 @@ extern int write_chunk(Stream *st, struct image *image, struct hdfile *hdfile,
                        int include_peaks, int include_reflections,
                        struct event *ev);
 
+extern int write_chunk_2(Stream *st, struct image *image,
+                         struct imagefile *imfile,
+                         int include_peaks, int include_reflections,
+                         struct event *ev);
+
 extern void write_command(Stream *st, int argc, char *argv[]);
 extern void write_geometry_file(Stream *st, const char *geom_filename);
 extern int rewind_stream(Stream *st);
diff --git a/src/process_image.c b/src/process_image.c
index cd5c0866..d3177d82 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -102,7 +102,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
                    int serial, struct sb_shm *sb_shared, TimeAccounts *taccs)
 {
 	int check;
-	struct hdfile *hdfile;
+	struct imagefile *imfile;
 	struct image image;
 	int i;
 	int r;
@@ -125,15 +125,15 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 	time_accounts_set(taccs, TACC_HDF5OPEN);
 	sb_shared->pings[cookie]++;
-	hdfile = hdfile_open(image.filename);
-	if ( hdfile == NULL ) {
+	imfile = imagefile_open(image.filename);
+	if ( imfile == NULL ) {
 		ERROR("Couldn't open file: %s\n", image.filename);
 		return;
 	}
 
 	time_accounts_set(taccs, TACC_HDF5READ);
 	sb_shared->pings[cookie]++;
-	check = hdf5_read2(hdfile, &image, image.event, 0);
+	check = imagefile_read(imfile, &image, image.event);
 	if ( check ) {
 		return;
 	}
@@ -159,9 +159,13 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	sb_shared->pings[cookie]++;
 	switch ( iargs->peaks ) {
 
+		struct hdfile *hdfile;
+
 		case PEAK_HDF5:
-		if ( get_peaks_2(&image, hdfile, iargs->hdf5_peak_path,
-		                 iargs->half_pixel_shift) )
+		hdfile = imagefile_get_hdfile(imfile);
+		if ( (hdfile == NULL)
+		  || (get_peaks_2(&image, hdfile, iargs->hdf5_peak_path,
+		                  iargs->half_pixel_shift)) )
 		{
 			ERROR("Failed to get peaks from HDF5 file.\n");
 		}
@@ -174,9 +178,11 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		break;
 
 		case PEAK_CXI:
-		if ( get_peaks_cxi_2(&image, hdfile, iargs->hdf5_peak_path,
-		                     pargs->filename_p_e,
-		                     iargs->half_pixel_shift) )
+		hdfile = imagefile_get_hdfile(imfile);
+		if ( (hdfile == NULL)
+		 ||  (get_peaks_cxi_2(&image, hdfile, iargs->hdf5_peak_path,
+		                      pargs->filename_p_e,
+		                      iargs->half_pixel_shift)) )
 		{
 			ERROR("Failed to get peaks from CXI file.\n");
 		}
@@ -227,7 +233,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	if ( r ) {
 		ERROR("Failed to chdir to temporary folder: %s\n",
 		      strerror(errno));
-		hdfile_close(hdfile);
+		imagefile_close(imfile);
 		return;
 	}
 
@@ -250,7 +256,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	r = chdir(rn);
 	if ( r ) {
 		ERROR("Failed to chdir: %s\n", strerror(errno));
-		hdfile_close(hdfile);
+		imagefile_close(imfile);
 		return;
 	}
 	free(rn);
@@ -288,7 +294,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 	time_accounts_set(taccs, TACC_WRITESTREAM);
 	sb_shared->pings[cookie]++;
-	ret = write_chunk(st, &image, hdfile,
+	ret = write_chunk(st, &image, imfile,
 	                  iargs->stream_peaks, iargs->stream_refls,
 	                  pargs->filename_p_e->ev);
 	if ( ret != 0 ) {
@@ -338,5 +344,5 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 	image_feature_list_free(image.features);
 	free_detector_geometry(image.det);
-	hdfile_close(hdfile);
+	imagefile_close(imfile);
 }