Merge branch 'master' into taketwo

17 files changed, 379 insertions, 170 deletions

diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index c8bbb069..f6c2c590 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -658,7 +658,9 @@ static void scan_cells(CellWindow *w)
 
 		if ( ignore ) continue;
 
-		cell_get_parameters(cells[i], &a, &b, &c, &al, &be, &ga);
+		if ( cell_get_parameters(cells[i], &a, &b, &c, &al, &be, &ga) ) {
+			continue;
+		}
 		a *= 1e10;  b *= 1e10;  c *= 1e10;
 		al = rad2deg(al);  be = rad2deg(be);  ga = rad2deg(ga);
 
@@ -719,7 +721,10 @@ static void scan_minmax(CellWindow *w)
 		int j;
 		int found = 0;
 
-		cell_get_parameters(w->cells[i], &a, &b, &c, &al, &be, &ga);
+		if ( cell_get_parameters(w->cells[i], &a, &b, &c, &al, &be, &ga) ) {
+			ERROR("Cell %i is bad\n", i);
+			continue;
+		}
 		a *= 1e10;  b *= 1e10;  c *= 1e10;
 		al = rad2deg(al);  be = rad2deg(be);  ga = rad2deg(ga);
 
@@ -1555,6 +1560,8 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
+	gsl_set_error_handler_off();
+
 	w.cells = NULL;
 	w.indms = NULL;
 	w.n_cells = 0;
diff --git a/src/check_hkl.c b/src/check_hkl.c
index def986c9..c7afb6cc 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -501,7 +501,8 @@ static void plot_shells(RefList *list, UnitCell *cell, const SymOpList *sym,
 		signed int hs, ks, ls;
 		int bin;
 
-		d = 2.0 * resolution(cell, h, k, l);
+		get_asymm(sym, h, k, l, &hs, &ks, &ls);
+		d = 2.0 * resolution(cell, hs, ks, ls);
 
 		if ( forbidden_reflection(cell, h, k, l) ) continue;
 
@@ -514,7 +515,6 @@ static void plot_shells(RefList *list, UnitCell *cell, const SymOpList *sym,
 		}
 		if ( bin == -1 ) continue;
 
-		get_asymm(sym, h, k, l, &hs, &ks, &ls);
 		if ( find_refl(counted, hs, ks, ls) != NULL ) continue;
 		add_refl(counted, hs, ks, ls);
 
@@ -530,7 +530,7 @@ static void plot_shells(RefList *list, UnitCell *cell, const SymOpList *sym,
 	      refl != NULL;
 	      refl = next_refl(refl, iter) )
 	{
-		signed int h, k, l;
+		signed int h, k, l, hs, ks, ls;
 		double d, val, esd;
 		int bin;
 		int j;
@@ -538,7 +538,8 @@ static void plot_shells(RefList *list, UnitCell *cell, const SymOpList *sym,
 		get_indices(refl, &h, &k, &l);
 		if ( forbidden_reflection(cell, h, k, l) ) continue;
 
-		d = resolution(cell, h, k, l) * 2.0;
+		get_asymm(sym, h, k, l, &hs, &ks, &ls);
+		d = resolution(cell, hs, ks, ls) * 2.0;
 		val = get_intensity(refl);
 		esd = get_esd_intensity(refl);
 
diff --git a/src/cl-utils.c b/src/cl-utils.c
index dc0a2713..a7e500cd 100644
--- a/src/cl-utils.c
+++ b/src/cl-utils.c
@@ -50,6 +50,15 @@ const char *clError(cl_int err)
 		case CL_SUCCESS :
 		return "no error";
 
+		case CL_DEVICE_NOT_AVAILABLE :
+		return "device not available";
+
+		case CL_DEVICE_NOT_FOUND :
+		return "device not found";
+
+		case CL_INVALID_DEVICE_TYPE :
+		return "invalid device type";
+
 		case CL_INVALID_PLATFORM :
 		return "invalid platform";
 
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 51e51dc9..81f12c94 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -286,13 +286,13 @@ static void add_to_fom(struct fom_context *fctx, double i1, double i2,
 		break;
 
 		case FOM_D1SIG :
-		if ( fabs(i1-i2) < (sig1+sig2)/2.0 ) {
+		if ( fabs(i1-i2) < sqrt(sig1*sig1 + sig2*sig2) ) {
 			fctx->n_within[bin]++;
 		}
 		break;
 
 		case FOM_D2SIG :
-		if ( fabs(i1-i2) < sig1+sig2 ) {  /* = 2 * (sig1+sig2)/2 */
+		if ( fabs(i1-i2) < 2.0*sqrt(sig1*sig1 + sig2*sig2) ) {
 			fctx->n_within[bin]++;
 		}
 		break;
@@ -1125,7 +1125,7 @@ int main(int argc, char *argv[])
 	char *bfile = NULL;
 	char *sym_str = NULL;
 	SymOpList *sym;
-	int ncom, nrej, nneg, nres, nbij, ncen;
+	int ncom, nrej, nmul, nneg, nres, nbij, ncen;
 	RefList *list1_acc;
 	RefList *list2_acc;
 	RefList *list1;
@@ -1149,6 +1149,7 @@ int main(int argc, char *argv[])
 	double min_I = +INFINITY;
 	double max_I = -INFINITY;
 	float highres, lowres;
+	int mul_cutoff = 0;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -1164,6 +1165,7 @@ int main(int argc, char *argv[])
 		{"shell-file",         1, NULL,                7},
 		{"highres",            1, NULL,                8},
 		{"lowres",             1, NULL,                9},
+		{"min-measurements",   1, NULL,               11},
 		{"ignore-negs",        0, &config_ignorenegs,  1},
 		{"zero-negs",          0, &config_zeronegs,    1},
 		{"intensity-shells",   0, &config_intshells,   1},
@@ -1260,6 +1262,13 @@ int main(int argc, char *argv[])
 			rmin_fix = 1.0 / (lowres/1e10);
 			break;
 
+			case 11 :
+			if ( sscanf(optarg, "%i", &mul_cutoff) != 1 ) {
+				ERROR("Invalid value for --min-measurements\n");
+				return 1;
+			}
+			break;
+
 			case '?' :
 			break;
 
@@ -1413,6 +1422,7 @@ int main(int argc, char *argv[])
 	/* Select reflections to be used */
 	ncom = 0;
 	nrej = 0;
+	nmul = 0;
 	nneg = 0;
 	nres = 0;
 	nbij = 0;
@@ -1426,6 +1436,7 @@ int main(int argc, char *argv[])
 		signed int h, k, l;
 		double val1, val2;
 		double esd1, esd2;
+		int mul1, mul2;
 		Reflection *refl2;
 		Reflection *refl1_acc;
 		Reflection *refl2_acc;
@@ -1441,6 +1452,9 @@ int main(int argc, char *argv[])
 		esd1 = get_esd_intensity(refl1);
 		esd2 = get_esd_intensity(refl2);
 
+		mul1 = get_redundancy(refl1);
+		mul2 = get_redundancy(refl2);
+
 		if ( (val1 < sigma_cutoff * esd1)
 		  || (val2 < sigma_cutoff * esd2) )
 		{
@@ -1453,6 +1467,11 @@ int main(int argc, char *argv[])
 			continue;
 		}
 
+		if ( (mul1 < mul_cutoff) || (mul2 < mul_cutoff) ) {
+			nmul++;
+			continue;
+		}
+
 		if ( config_zeronegs ) {
 			int d = 0;
 			if ( val1 < 0.0 ) {
@@ -1544,6 +1563,11 @@ int main(int argc, char *argv[])
 		       " negative intensities which were set to zero.\n", nneg);
 	}
 
+	if ( nmul > 0 ) {
+		STATUS("%i reflection pairs rejected because either or both"
+		       " versions had too few measurements.\n", nmul);
+	}
+
 	if ( nres > 0 ) {
 		STATUS("%i reflection pairs rejected because either or both"
 		       " versions were outside the resolution range.\n", nres);
diff --git a/src/diffraction-gpu.c b/src/diffraction-gpu.c
index 331170ae..22abcfd2 100644
--- a/src/diffraction-gpu.c
+++ b/src/diffraction-gpu.c
@@ -379,6 +379,7 @@ struct gpu_context *setup_gpu(int no_sfac,
 	float *flags_ptr;
 	size_t maxwgsize;
 	int i;
+	int have_ctx = 0;
 	char cflags[512] = "";
 	char *insert_stuff = NULL;
 
@@ -393,16 +394,37 @@ struct gpu_context *setup_gpu(int no_sfac,
 		ERROR("Couldn't find at least one platform!\n");
 		return NULL;
 	}
-	prop[0] = CL_CONTEXT_PLATFORM;
-	prop[1] = (cl_context_properties)platforms[0];
-	prop[2] = 0;
 
-	gctx = malloc(sizeof(*gctx));
-	gctx->ctx = clCreateContextFromType(prop, CL_DEVICE_TYPE_GPU,
-	                                    NULL, NULL, &err);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't create OpenCL context: %i\n", err);
-		free(gctx);
+	/* Find a GPU platform in the list */
+	for ( i=0; i<nplat; i++ ) {
+
+		prop[0] = CL_CONTEXT_PLATFORM;
+		prop[1] = (cl_context_properties)platforms[i];
+		prop[2] = 0;
+
+		gctx = malloc(sizeof(*gctx));
+		gctx->ctx = clCreateContextFromType(prop, CL_DEVICE_TYPE_GPU,
+		                                    NULL, NULL, &err);
+
+		if ( err != CL_SUCCESS ) {
+			if ( err == CL_DEVICE_NOT_FOUND ) {
+				/* No GPU device in this platform */
+				continue; /* Try next platform */
+			} else {
+				ERROR("Couldn't create OpenCL context: %s (%i)\n",
+				clError(err), err);
+				free(gctx);
+				return NULL;
+			}
+		} else {
+			STATUS("Using OpenCL platform %i (%i total)\n", i, nplat);
+			have_ctx = 1;
+			break;
+		}
+	}
+
+	if ( !have_ctx ) {
+		ERROR("Couldn't find a GPU device in any platform.\n");
 		return NULL;
 	}
 
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/geoptimiser.c b/src/geoptimiser.c
index e0337358..da9b16c4 100644
--- a/src/geoptimiser.c
+++ b/src/geoptimiser.c
@@ -631,10 +631,18 @@ static int add_distance_to_list(struct gpanel *gp,
                                 double *det_shift)
 {
 	int pix_index;
+	int ifs, iss;
 	double rfs, rss;
 	double crx, cry;
 
-	pix_index = ((int)rint(imfe->fs) + gp->p->w*(int)rint(imfe->ss));
+	ifs = imfe->fs;
+	iss = imfe->ss;  /* Explicit rounding towards zero (truncation) */
+	pix_index = ifs + gp->p->w*iss;
+
+	if ( (ifs >= gp->p->w) || (iss >= gp->p->h) ) {
+		ERROR("Peak is outside panel!\n");
+		return 1;
+	}
 
 	if ( gp->num_pix_displ[pix_index] > 0 ) {
 
@@ -782,7 +790,14 @@ static int compute_pixel_displacements(struct image *images, int n_images,
 
 				r = add_distance_to_list(gp, imfe, refl, fx, fy,
 				                         det_shift);
-				if ( r ) return r;
+				if ( r ) {
+					ERROR("Error processing peak %f,%f "
+					      "(panel %s), image %s %s\n",
+					      imfe->fs, imfe->ss, gp->p->name,
+					      images[cp].filename,
+					      get_event_string(images[cp].event));
+					return r;
+				}
 
 			}
 		}
@@ -1070,12 +1085,7 @@ static void correct_rotation_and_stretch(struct rg_collection *connected,
 
 			/* Calculate corner adjustment
 			 * NB All panels follow the first one */
-			if ( ip == 0 ) {
-
-				new_cnx = p->cnx * cs;
-				new_cny = p->cny * cs;
-
-			} else {
+			if ( ip > 0 && connected->rigid_groups[di]->n_panels == 2 && !gparams->no_cspad ) {
 
 				struct panel *p0;
 				double delta_x, delta_y, delta;
@@ -1090,6 +1100,10 @@ static void correct_rotation_and_stretch(struct rg_collection *connected,
 				new_cnx = p0->cnx + delta*p0->fsx;
 				new_cny = p0->cny + delta*p0->fsy;
 
+			} else {
+
+				new_cnx = p->cnx * cs;
+				new_cny = p->cny * cs;
 			}
 
 			/* The average displacements now need to be updated */
@@ -2488,8 +2502,10 @@ int main(int argc, char *argv[])
 	}
 
 #ifdef HAVE_SAVE_TO_PNG
+#if !GLIB_CHECK_VERSION(2,36,0)
 	g_type_init();
 #endif
+#endif
 
 	ret_val = optimize_geometry(gparams, det, quadrants, connected);
 
diff --git a/src/get_hkl.c b/src/get_hkl.c
index d6efe747..77f34da2 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -98,7 +98,9 @@ static void show_help(const char *s)
 
 static void copy_notes(RefList *out, RefList *in)
 {
-	reflist_add_notes(out, reflist_get_notes(in));
+	if ( reflist_get_notes(in) != NULL ) {
+		reflist_add_notes(out, reflist_get_notes(in));
+	}
 }
 
 
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index f5493453..60400ad8 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -372,10 +372,10 @@ static void run_work(const struct index_args *iargs, Stream *st,
 	}
 
 	time_accounts_set(taccs, TACC_FINALCLEANUP);
-	cleanup_indexing(iargs->indm, iargs->ipriv);
+	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 a1997b9e..ce87fde6 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -3,16 +3,17 @@
  *
  * Index patterns, output hkl+intensity etc.
  *
- * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  * Copyright © 2012 Richard Kirian
  * Copyright © 2012 Lorenzo Galli
  *
  * Authors:
- *   2010-2015 Thomas White <taw@physics.org>
+ *   2010-2017 Thomas White <taw@physics.org>
  *   2011      Richard Kirian
  *   2012      Lorenzo Galli
  *   2012      Chunhong Yoon
+ *   2017      Valerio Mariani <valerio.mariani@desy.de>
  *
  * This file is part of CrystFEL.
  *
@@ -88,6 +89,7 @@ static void show_help(const char *s)
 "     --peaks=<method>     Use 'method' for finding peaks.  Choose from:\n"
 "                           zaef  : Use Zaefferer (2000) gradient detection.\n"
 "                                    This is the default method.\n"
+"                           peakfinder8: Use Peakfinder8 algorithm.\n"
 "                           hdf5  : Get from a table in HDF5 file.\n"
 "                           cxi   : Get from CXI format HDF5 file.\n"
 "     --hdf5-peaks=<p>     Find peaks table in HDF5 file here.\n"
@@ -95,32 +97,52 @@ static void show_help(const char *s)
 "     --integration=<meth> Perform final pattern integration using <meth>.\n"
 "\n\n"
 "For more control over the process, you might need:\n\n"
-"    --tolerance=<tol>   Set the tolerances for cell comparison.\n"
-"                          Default: 5,5,5,1.5.\n"
-"    --filter-noise      Apply an aggressive noise filter which sets all\n"
-"                         pixels in each 3x3 region to zero if any of them\n"
-"                         have negative values.  Intensity measurement will\n"
-"                         be performed on the image as it was before this.\n"
-"    --median-filter=<n> Apply a median filter to the image data.  Intensity\n"
-"                         measurement will be performed on the image as it\n"
-"                         was before this.  The side length of the median\n"
-"                         filter box will be 2<n>+1.  Default: 0 (no filter).\n"
-"    --no-sat-corr       Don't correct values of saturated peaks using a\n"
-"                         table included in the HDF5 file.\n"
-"    --threshold=<n>     Only accept peaks above <n> ADU.  Default: 800.\n"
-"    --min-gradient=<n>  Minimum squared gradient for Zaefferer peak search.\n"
-"                         Default: 100,000.\n"
-"    --min-snr=<n>       Minimum signal-to-noise ratio for peaks.\n"
-"                         Default: 5.\n"
-"    --check-hdf5-snr    Check SNR for peaks from --peaks=hdf5.\n"
-"    --peak-radius=<r>   Integration radii for peak search.\n"
-"    --int-radius=<r>    Set the integration radii.  Default: 4,5,7.\n"
-"    --push-res=<n>      Integrate higher than apparent resolution cutoff.\n"
-"    --highres=<n>       Absolute resolution cutoff in Angstroms.\n"
-"    --fix-profile-radius Fix the reciprocal space profile radius for spot\n"
-"                         prediction (default: automatically determine.\n"
-"    --fix-bandwidth     Set the bandwidth for spot prediction.\n"
-"    --fix-divergence    Set the divergence (full angle) for spot prediction.\n"
+"    --tolerance=<tol>     Set the tolerances for cell comparison.\n"
+"                            Default: 5,5,5,1.5.\n"
+"    --filter-noise        Apply an aggressive noise filter which sets all\n"
+"                           pixels in each 3x3 region to zero if any of them\n"
+"                           have negative values.  Intensity measurement will\n"
+"                           be performed on the image as it was before this.\n"
+"    --median-filter=<n>   Apply a median filter to the image data. Intensity\n"
+"                           measurement will be performed on the image as it\n"
+"                           was before this.  The side length of the median\n"
+"                           filter box will be 2<n>+1.\n"
+"                           Default: 0 (no filter).\n"
+"    --no-sat-corr         Don't correct values of saturated peaks using a\n"
+"                           table included in the HDF5 file.\n"
+"    --threshold=<n>       Only accept peaks above <n> ADU in both the\n"
+"	                    Zaefferer and Peakfinder8 algorithms.\n"
+"                           Default: 800.\n"
+"    --min-gradient=<n>    Minimum squared gradient for Zaefferer peak\n"
+"                           search. Default: 100,000.\n"
+"    --min-snr=<n>         Minimum signal-to-noise ratio for peaks, with both\n"
+"                           Zaefferer and Peakfinder8 algorithms.\n"
+"                           Default: 5.\n"
+"    --min-pix-count=<n>   Only accept peaks if they include more than <n>\n"
+"                           pixels, in the Peakfinder8 algorithm.\n"
+"                           Default: 2.\n"
+"    --max-pix-count=<n>   Only accept peaks if they include less than <n>\n"
+"                           pixels, in the Peakfinder8 algorithm.\n"
+"                           Default: 200.\n"
+"    --min-peaks=<n>       Minimum number of peaks for indexing.\n"
+"    --local-bg-radius=<n> Radius (in pixels) to use for the estimation of\n"
+"	                    local background in the Peakfinder8 algorithm.\n"
+"                           Default: 3.\n"
+"    --min-res=<n>         Only accept peaks if they lay at more than <n>\n"
+"	                    pixels from the center of the detector, in the\n"
+"                           peakfinder8 algorithm. Default: 0.\n"
+"    --max-res=<n>         Only accept peaks if they lay at less than <n>\n"
+"	                    pixels from the center of the detector, in the\n"
+"                           peakfinder8 algorithm. Default: 1200.\n"
+"    --check-hdf5-snr      Check SNR for peaks from --peaks=hdf5.\n"
+"    --peak-radius=<r>     Integration radii for peak search.\n"
+"    --int-radius=<r>      Set the integration radii.  Default: 4,5,7.\n"
+"    --push-res=<n>        Integrate higher than apparent resolution cutoff.\n"
+"    --highres=<n>         Absolute resolution cutoff in Angstroms.\n"
+"    --fix-profile-radius  Fix the reciprocal space profile radius for spot\n"
+"                           prediction (default: automatically determine.\n"
+"    --fix-bandwidth       Set the bandwidth for spot prediction.\n"
+"    --fix-divergence      Set the divergence (full angle) for spot prediction.\n"
 "\n"
 "\nFor time-resolved stuff, you might want to use:\n\n"
 "     --copy-hdf5-field <f>  Copy the value of field <f> into the stream. You\n"
@@ -131,16 +153,19 @@ static void show_help(const char *s)
 " --temp-dir=<path>        Put the temporary folder under <path>.\n"
 "\n"
 "\nOptions you probably won't need:\n\n"
-"     --no-check-prefix    Don't attempt to correct the --prefix.\n"
-"     --no-use-saturated   During the initial peak search, reject\n"
-"                           peaks which contain pixels above max_adu.\n"
-"     --no-revalidate      Don't re-integrate and check HDF5 peaks for\n"
-"                           validity.\n"
-"     --no-peaks-in-stream Do not record peak search results in the stream.\n"
-"     --no-refls-in-stream Do not record integrated reflections in the stream.\n"
-"     --int-diag=<cond>    Show debugging information about reflections.\n"
-"     --no-refine          Skip the prediction refinement step.\n"
-"     --profile            Show timing data for performance monitoring.\n"
+"     --no-check-prefix     Don't attempt to correct the --prefix.\n"
+"     --no-use-saturated    During the initial peak search, reject\n"
+"                            peaks which contain pixels above max_adu.\n"
+"     --no-revalidate       Don't re-integrate and check HDF5 peaks for\n"
+"                            validity.\n"
+"     --no-peaks-in-stream  Do not record peak search results in the stream.\n"
+"     --no-refls-in-stream  Do not record integrated reflections in the stream.\n"
+"     --no-non-hits-in-stream  Do not include non-hit frames in the stream.\n"
+"                               (see --min-peaks)\n"
+"     --int-diag=<cond>     Show debugging information about reflections.\n"
+"     --no-refine           Skip the prediction refinement step.\n"
+"     --profile             Show timing data for performance monitoring.\n"
+"     --no-half-pixel-shift Don't offset the HDF5 peak locations by 0.5 px.\n"
 "\nLow-level options for the felix indexer:\n\n"
 "     --felix-options      Change the default arguments passed to the indexer.\n"
 "                          Given as a list of comma separated list of \n"
@@ -150,9 +175,9 @@ 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;
 
@@ -161,12 +186,12 @@ 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);
 	}
 }
 
@@ -181,8 +206,6 @@ int main(int argc, char *argv[])
 	int config_checkprefix = 1;
 	int config_basename = 0;
 	int integrate_saturated = 0;
-	IndexingMethod *indm;
-	IndexingPrivate **ipriv;
 	char *indm_str = NULL;
 	char *cellfile = NULL;
 	char *prefix = NULL;
@@ -214,11 +237,17 @@ int main(int argc, char *argv[])
 	iargs.threshold = 800.0;
 	iargs.min_gradient = 100000.0;
 	iargs.min_snr = 5.0;
+	iargs.min_pix_count = 2;
+	iargs.max_pix_count = 200;
+	iargs.min_res = 0;
+	iargs.max_res = 1200;
+	iargs.local_bg_radius = 3;
 	iargs.check_hdf5_snr = 0;
 	iargs.det = NULL;
 	iargs.peaks = PEAK_ZAEF;
 	iargs.beam = &beam;
 	iargs.hdf5_peak_path = NULL;
+	iargs.half_pixel_shift = 1;
 	iargs.copyme = NULL;
 	iargs.pk_inn = -1.0;
 	iargs.pk_mid = -1.0;
@@ -230,13 +259,14 @@ int main(int argc, char *argv[])
 	iargs.no_revalidate = 0;
 	iargs.stream_peaks = 1;
 	iargs.stream_refls = 1;
+	iargs.stream_nonhits = 1;
 	iargs.int_diag = INTDIAG_NONE;
-	iargs.copyme = new_copy_hdf5_field_list();
+	iargs.copyme = new_imagefile_field_list();
+	iargs.min_peaks = 0;
 	if ( iargs.copyme == NULL ) {
 		ERROR("Couldn't allocate HDF5 field list.\n");
 		return 1;
 	}
-	iargs.indm = NULL;  /* No default */
 	iargs.ipriv = NULL;  /* No default */
 	iargs.int_meth = integration_method("rings-nocen-nosat-nograd", NULL);
 	iargs.push_res = 0.0;
@@ -268,12 +298,14 @@ int main(int argc, char *argv[])
 		{"basename",           0, &config_basename,          1},
 		{"no-peaks-in-stream", 0, &iargs.stream_peaks,       0},
 		{"no-refls-in-stream", 0, &iargs.stream_refls,       0},
+		{"no-non-hits-in-stream", 0, &iargs.stream_nonhits,  0},
 		{"integrate-saturated",0, &integrate_saturated,      1},
 		{"no-use-saturated",   0, &iargs.use_saturated,      0},
 		{"no-revalidate",      0, &iargs.no_revalidate,      1},
 		{"check-hdf5-snr",     0, &iargs.check_hdf5_snr,     1},
 		{"no-refine",          0, &no_refine,                1},
 		{"profile",            0, &iargs.profile,            1},
+		{"no-half-pixel-shift",0, &iargs.half_pixel_shift,   0},
 
 		/* Long-only options which don't actually do anything */
 		{"no-sat-corr",        0, &iargs.satcorr,            0},
@@ -306,6 +338,12 @@ int main(int argc, char *argv[])
 		{"fix-bandwidth",      1, NULL,               23},
 		{"fix-divergence",     1, NULL,               24},
 		{"felix-options",      1, NULL,               25},
+	        {"min-pix-count",      1, NULL,               26},
+	        {"max-pix-count",      1, NULL,               27},
+	        {"local-bg-radius",    1, NULL,               28},
+	        {"min-res",            1, NULL,               29},
+	        {"max-res",            1, NULL,               30},
+	        {"min-peaks",          1, NULL,               31},
 
 		{0, 0, NULL, 0}
 	};
@@ -400,7 +438,7 @@ 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 :
@@ -489,6 +527,30 @@ int main(int argc, char *argv[])
 			}
 			break;
 
+		        case 26:
+			iargs.min_pix_count = atoi(optarg);
+			break;
+
+		        case 27:
+			iargs.max_pix_count = atoi(optarg);
+			break;
+
+		        case 28:
+			iargs.local_bg_radius = atoi(optarg);
+			break;
+
+		        case 29:
+			iargs.min_res = atoi(optarg);
+			break;
+
+		        case 30:
+			iargs.max_res = atoi(optarg);
+			break;
+
+			case 31:
+			iargs.min_peaks = atoi(optarg);
+			break;
+
 			case 0 :
 			break;
 
@@ -541,6 +603,8 @@ int main(int argc, char *argv[])
 	}
 	if ( strcmp(speaks, "zaef") == 0 ) {
 		iargs.peaks = PEAK_ZAEF;
+	} else if ( strcmp(speaks, "peakfinder8") == 0 ) {
+		iargs.peaks = PEAK_PEAKFINDER8;
 	} else if ( strcmp(speaks, "hdf5") == 0 ) {
 		iargs.peaks = PEAK_HDF5;
 	} else if ( strcmp(speaks, "cxi") == 0 ) {
@@ -574,7 +638,7 @@ 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 ) {
@@ -591,35 +655,6 @@ int main(int argc, char *argv[])
 		iargs.hdf5_peak_path = command_line_peak_path;
 	}
 
-	/* Parse indexing methods */
-	if ( indm_str == NULL ) {
-
-		STATUS("You didn't specify an indexing method, so I  won't try "
-		       " to index anything.\n"
-		       "If that isn't what you wanted, re-run with"
-		       " --indexing=<methods>.\n");
-		indm = NULL;
-
-	} else {
-
-		int i = 0;
-
-		indm = build_indexer_list(indm_str);
-		if ( indm == NULL ) {
-			ERROR("Invalid indexer list '%s'\n", indm_str);
-			return 1;
-		}
-		free(indm_str);
-
-		/* If --no-refine, unset the refinement flag on all methods */
-		if ( no_refine ) {
-			while ( indm[i] != INDEXING_NONE ) {
-				indm[i] &= ~INDEXING_REFINE;
-				i++;
-			}
-		}
-	}
-
 	/* Parse integration method */
 	if ( int_str != NULL ) {
 
@@ -755,27 +790,34 @@ int main(int argc, char *argv[])
 	}
 	free(outfile);
 
-	/* Prepare the indexer */
-	if ( indm != NULL ) {
-		ipriv = prepare_indexing(indm, iargs.cell, iargs.det,
-		                         iargs.tols, iargs.felix_options);
-		if ( ipriv == NULL ) {
-			ERROR("Failed to prepare indexing.\n");
+	/* Prepare the indexing system */
+	if ( indm_str == NULL ) {
+
+		STATUS("You didn't specify an indexing method, so I  won't try "
+		       " to index anything.\n"
+		       "If that isn't what you wanted, re-run with"
+		       " --indexing=<methods>.\n");
+		iargs.ipriv = NULL;
+
+	} else {
+
+		iargs.ipriv = setup_indexing(indm_str, iargs.cell, iargs.det,
+		                             iargs.tols, no_refine,
+		                             iargs.felix_options);
+		if ( iargs.ipriv == NULL ) {
+			ERROR("Failed to set up indexing system\n");
 			return 1;
 		}
-	} else {
-		ipriv = NULL;
+		free(indm_str);
+
 	}
 
 	gsl_set_error_handler_off();
 
-	iargs.indm = indm;
-	iargs.ipriv = ipriv;
-
 	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);
@@ -783,7 +825,7 @@ int main(int argc, char *argv[])
 	free_detector_geometry(iargs.det);
 	free(iargs.hdf5_peak_path);
 	close_stream(st);
-	cleanup_indexing(indm, ipriv);
+	cleanup_indexing(iargs.ipriv);
 
 	return 0;
 }
diff --git a/src/merge.c b/src/merge.c
index 8d1fae0f..9734c469 100644
--- a/src/merge.c
+++ b/src/merge.c
@@ -237,10 +237,7 @@ RefList *merge_intensities(Crystal **crystals, int n, int n_threads,
 	Reflection *refl;
 	RefListIterator *iter;
 
-	if ( n == 0 ) {
-		ERROR("No crystals!\n");
-		return NULL;
-	}
+	if ( n == 0 ) return NULL;
 
 	full = reflist_new();
 
diff --git a/src/partialator.c b/src/partialator.c
index 09feebb4..569145e8 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -191,6 +191,12 @@ static void write_split(Crystal **crystals, int n_crystals, const char *outfile,
 	snprintf(tmp, 1024, "%s1", outfile);
 	split = merge_intensities(crystals1, n_crystals1, nthreads,
 		                  pmodel, min_measurements, push_res, 1);
+
+	if ( split == NULL ) {
+		ERROR("Not enough crystals for two way split!\n");
+		return;
+	}
+
 	STATUS("Writing two-way split to %s ", tmp);
 	write_reflist_2(tmp, split, sym);
 	reflist_free(split);
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index e1e04789..e9fc9916 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -745,7 +745,7 @@ int main(int argc, char *argv[])
 		       "each of a, b and c\n");
 	}
 	if ( intfile == NULL ) {
-		STATUS("               Full intensities: all equal");
+		STATUS("               Full intensities: all equal\n");
 	} else {
 		STATUS("               Full intensities: from %s\n", intfile);
 	}
diff --git a/src/process_hkl.c b/src/process_hkl.c
index d2cf640b..301bc6e4 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -287,7 +287,8 @@ static int merge_crystal(RefList *model, struct image *image, Crystal *cr,
 		if ( isnan(scale) ) return 1;
 		if ( scale <= 0.0 ) return 1;
 		if ( stat != NULL ) {
-			fprintf(stat, "%s %f %f\n", image->filename, scale, cc);
+			fprintf(stat, "%s %s %f %f\n", image->filename,
+			        get_event_string(image->event), scale, cc);
 		}
 
 	} else {
diff --git a/src/process_image.c b/src/process_image.c
index bcaee543..498b3398 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -8,7 +8,7 @@
  *
  * Authors:
  *   2010-2017 Thomas White <taw@physics.org>
- *   2014      Valerio Mariani
+ *   2014-2017 Valerio Mariani <valerio.mariani@desy.de>
  *
  * This file is part of CrystFEL.
  *
@@ -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;
 	}
@@ -159,8 +159,14 @@ 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(&image, hdfile, iargs->hdf5_peak_path) ) {
+		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");
 		}
 		if ( !iargs->no_revalidate ) {
@@ -172,8 +178,12 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		break;
 
 		case PEAK_CXI:
-		if ( get_peaks_cxi(&image, hdfile, iargs->hdf5_peak_path,
-		                   pargs->filename_p_e) ) {
+		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");
 		}
 		if ( !iargs->no_revalidate ) {
@@ -191,6 +201,28 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		             iargs->use_saturated);
 		break;
 
+	        case PEAK_PEAKFINDER8:
+		if ( search_peaks_peakfinder8(&image, 2048,
+		                               iargs->threshold,
+		                               iargs->min_snr,
+		                               iargs->min_pix_count,
+		                               iargs->max_pix_count,
+		                               iargs->local_bg_radius,
+		                               iargs->min_res,
+		                               iargs->max_res,
+		                               iargs->use_saturated) ) {
+			if ( image.event != NULL ) {
+				ERROR("Failed to find peaks in image %s"
+				      "(event %s).\n", image.filename,
+				      get_event_string(image.event));
+			} else {
+				ERROR("Failed to find peaks in image %s.",
+				      image.filename);
+			}
+
+		}
+		break;
+
 	}
 
 	restore_image_data(image.dp, image.det, prefilter);
@@ -201,7 +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;
 	}
 
@@ -217,15 +249,30 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		image.bw = 0.00000001;
 	}
 
+	if ( image_feature_count(image.features) < iargs->min_peaks ) {
+		r = chdir(rn);
+		if ( r ) {
+			ERROR("Failed to chdir: %s\n", strerror(errno));
+			imagefile_close(imfile);
+			return;
+		}
+		free(rn);
+
+		if ( iargs->stream_nonhits ) {
+			goto streamwrite;
+		} else {
+			goto out;
+		}
+	}
+
 	/* Index the pattern */
 	time_accounts_set(taccs, TACC_INDEXING);
-	index_pattern_2(&image, iargs->indm, iargs->ipriv,
-	                &sb_shared->pings[cookie]);
+	index_pattern_2(&image, iargs->ipriv, &sb_shared->pings[cookie]);
 
 	r = chdir(rn);
 	if ( r ) {
 		ERROR("Failed to chdir: %s\n", strerror(errno));
-		hdfile_close(hdfile);
+		imagefile_close(imfile);
 		return;
 	}
 	free(rn);
@@ -261,9 +308,10 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	                iargs->int_diag_k, iargs->int_diag_l,
 	                &sb_shared->term_lock);
 
+streamwrite:
 	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 ) {
@@ -280,6 +328,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		       get_event_string(image.event));
 	}
 
+out:
 	/* Count crystals which are still good */
 	time_accounts_set(taccs, TACC_TOTALS);
 	sb_shared->pings[cookie]++;
@@ -313,5 +362,5 @@ 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 d41c23f5..ec51c188 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -3,12 +3,12 @@
  *
  * The processing pipeline for one image
  *
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
  *   2010-2016 Thomas White <taw@physics.org>
- *   2014      Valerio Mariani
+ *   2014-2017 Valerio Mariani <valerio.mariani@desy.de>
  *
  * This file is part of CrystFEL.
  *
@@ -42,6 +42,7 @@ struct index_args;
 
 
 enum {
+        PEAK_PEAKFINDER8,
 	PEAK_ZAEF,
 	PEAK_HDF5,
 	PEAK_CXI,
@@ -61,24 +62,32 @@ struct index_args
 	float min_snr;
 	int check_hdf5_snr;
 	struct detector *det;
-	IndexingMethod *indm;
-	IndexingPrivate **ipriv;
+	IndexingPrivate *ipriv;
 	int peaks;                /* Peak detection method */
 	float tols[4];
 	struct beam_params *beam;
 	char *hdf5_peak_path;
+	int half_pixel_shift;
 	float pk_inn;
 	float pk_mid;
 	float pk_out;
 	float ir_inn;
 	float ir_mid;
 	float ir_out;
-	struct copy_hdf5_field *copyme;
+	int min_res;
+	int max_res;
+	int max_n_peaks;
+	int min_pix_count;
+	int max_pix_count;
+	int local_bg_radius;
+	int min_peaks;
+	struct imagefile_field_list *copyme;
 	int integrate_saturated;
 	int use_saturated;
 	int no_revalidate;
 	int stream_peaks;
 	int stream_refls;
+	int stream_nonhits;
 	IntegrationMethod int_meth;
 	IntDiag int_diag;
 	signed int int_diag_h;