Merge branch 'tom/cbf'

6 files changed, 79 insertions, 49 deletions

diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c
index 87c23f4e..0336f25e 100644
--- a/src/dw-hdfsee.c
+++ b/src/dw-hdfsee.c
@@ -74,8 +74,8 @@ static void displaywindow_error(DisplayWindow *dw, const char *message)
 static gint displaywindow_closed(GtkWidget *window, DisplayWindow *dw)
 {
 
-	if ( dw->hdfile != NULL ) {
-		hdfile_close(dw->hdfile);
+	if ( dw->imagefile != NULL ) {
+		imagefile_close(dw->imagefile);
 	}
 
 	if ( dw->surf != NULL ) cairo_surface_destroy(dw->surf);
@@ -725,7 +725,7 @@ static gint displaywindow_set_binning(GtkWidget *widget, DisplayWindow *dw)
 		return 0;
 	}
 
-	if ( dw->hdfile == NULL ) {
+	if ( dw->imagefile == NULL ) {
 		return 0;
 	}
 
@@ -852,8 +852,8 @@ static gint displaywindow_set_boostint(GtkWidget *widget, DisplayWindow *dw)
 		return 0;
 	}
 
-	if ( dw->hdfile == NULL ) {
-	    return 0;
+	if ( dw->imagefile == NULL ) {
+		return 0;
 	}
 
 	bd = malloc(sizeof(BoostIntDialog));
@@ -927,8 +927,8 @@ static gint displaywindow_newevent(DisplayWindow *dw, int new_event)
 	float **old_dp = dw->image->dp;
 	int **old_bad = dw->image->bad;
 
-	fail = hdf5_read2(dw->hdfile, dw->image,
-                          dw->ev_list->events[new_event], 0);
+	fail = imagefile_read(dw->imagefile, dw->image,
+	                      dw->ev_list->events[new_event]);
 	if ( fail ) {
 		ERROR("Couldn't load image");
 		dw->image->dp = old_dp;
@@ -1046,8 +1046,8 @@ static gint displaywindow_set_newevent(GtkWidget *widget, DisplayWindow *dw)
 		return 0;
 	}
 
-	if ( dw->hdfile == NULL ) {
-	    return 0;
+	if ( dw->imagefile == NULL ) {
+		return 0;
 	}
 
 	ed = malloc(sizeof(EventDialog));
@@ -1162,7 +1162,7 @@ static gint displaywindow_set_ringradius(GtkWidget *widget, DisplayWindow *dw)
 		return 0;
 	}
 
-	if ( dw->hdfile == NULL ) {
+	if ( dw->imagefile == NULL ) {
 		return 0;
 	}
 
@@ -1796,7 +1796,7 @@ static gint displaywindow_show_numbers(GtkWidget *widget, DisplayWindow *dw)
 		return 0;
 	}
 
-	if ( dw->hdfile == NULL ) {
+	if ( dw->imagefile == NULL ) {
 		return 0;
 	}
 
@@ -2306,12 +2306,14 @@ struct newhdf {
 	char name[1024];
 };
 
+/* New HDF5 element selected from menu */
 static gint displaywindow_newhdf(GtkMenuItem *item, struct newhdf *nh)
 {
 	gboolean a;
 	int fail;
 
 	if ( nh->dw->not_ready_yet ) return 0;
+	assert(imagefile_get_type(nh->dw->imagefile) == IMAGEFILE_HDF5);
 
 	a = gtk_check_menu_item_get_active(GTK_CHECK_MENU_ITEM(nh->widget));
 	if ( !a ) return 0;
@@ -2320,7 +2322,8 @@ static gint displaywindow_newhdf(GtkMenuItem *item, struct newhdf *nh)
 	 * one */
 	free_detector_geometry(nh->dw->image->det);
 	nh->dw->image->det = NULL;
-	fail = hdf5_read(nh->dw->hdfile, nh->dw->image, nh->name, 0);
+	fail = hdf5_read(imagefile_get_hdfile(nh->dw->imagefile),
+	                 nh->dw->image, nh->name, 0);
 	if ( fail ) {
 		ERROR("Couldn't load image");
 		return 1;
@@ -2456,7 +2459,12 @@ static int displaywindow_update_menus(DisplayWindow *dw, const char *selectme)
 	GtkWidget *ms;
 	GtkWidget *w;
 
-	ms = displaywindow_createhdfmenus(dw->hdfile, dw, selectme);
+	if ( imagefile_get_type(dw->imagefile) != IMAGEFILE_HDF5 ) {
+		return 0;
+	}
+
+	ms = displaywindow_createhdfmenus(imagefile_get_hdfile(dw->imagefile),
+	                                  dw, selectme);
 
 	if ( ms == NULL ) return 1;
 
@@ -2828,8 +2836,8 @@ DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
 	dw->image->lambda = 0.0;
 	dw->image->filename = filename;
 
-	dw->hdfile = hdfile_open(filename);
-	if ( dw->hdfile == NULL ) {
+	dw->imagefile = imagefile_open(filename);
+	if ( dw->imagefile == NULL ) {
 		ERROR("Couldn't open file: %s\n", filename);
 		free(dw->geom_filename);
 		free(dw);
@@ -2842,11 +2850,19 @@ DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
 	}
 
 	if ( dw->image->det != NULL && ( dw->image->det->path_dim != 0 ||
-	                                 dw->image->det->dim_dim != 0  )) {
+	                                 dw->image->det->dim_dim != 0  ))
+	{
+		struct hdfile *hdfile;
+
+		if ( imagefile_get_type(dw->imagefile) != IMAGEFILE_HDF5 ) {
+			ERROR("Multi-event geometry, but not HDF5 file!\n");
+			return NULL;
+		}
+		hdfile = imagefile_get_hdfile(dw->imagefile);
 
 		dw->multi_event = 1;
 
-		dw->ev_list = fill_event_list(dw->hdfile, dw->image->det);
+		dw->ev_list = fill_event_list(hdfile, dw->image->det);
 
 		if ( dw->ev_list == NULL ) {
 			ERROR("Error while parsing file structure\n");
@@ -2883,18 +2899,26 @@ DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
 				dw->curr_event = 0;
 				ev = dw->ev_list->events[dw->curr_event];
 			}
-			check = hdf5_read2(dw->hdfile, dw->image, ev, 0);
+			check = imagefile_read(dw->imagefile, dw->image, ev);
 		} else {
-			check = hdf5_read2(dw->hdfile, dw->image, NULL, 0);
+			check = imagefile_read(dw->imagefile, dw->image, NULL);
 		}
 
 	} else {
-		check =	hdf5_read(dw->hdfile, dw->image, element, 0);
+		if ( element != NULL ) {
+			if ( imagefile_get_type(dw->imagefile) != IMAGEFILE_HDF5 ) {
+				ERROR("-e/--image requiest an HDF5 file\n");
+				return NULL;
+			}
+			hdfile_set_image(imagefile_get_hdfile(dw->imagefile),
+			                 element);
+		}
+		check =	imagefile_read_simple(dw->imagefile, dw->image);
 		dw->simple = 1;
 	}
 	if ( check ) {
 		ERROR("Couldn't load file\n");
-		hdfile_close(dw->hdfile);
+		imagefile_close(dw->imagefile);
 		free(dw->geom_filename);
 		return NULL;
 	}
diff --git a/src/dw-hdfsee.h b/src/dw-hdfsee.h
index 85c82ac7..fdbea231 100644
--- a/src/dw-hdfsee.h
+++ b/src/dw-hdfsee.h
@@ -3,12 +3,12 @@
  *
  * Quick yet non-crappy HDF viewer
  *
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  * Copyright © 2012 Richard Kirian
  *
  * Authors:
- *   2009-2014 Thomas White <taw@physics.org>
+ *   2009-2017 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
  *   2014      Takanori Nakane <nakane.t@gmail.com>
  *   2012      Richard Kirian
@@ -101,8 +101,8 @@ typedef struct {
 
 	int             simple;
 
-	struct hdfile	*hdfile;
-	struct image	*image;
+	struct imagefile *imagefile;
+	struct image	 *image;
 
 	char            *geom_filename;
 	char            *rg_coll_name;
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.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);
 }
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;