From 21c67699d352cb95549a225694575db2808d8a91 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Fri, 18 Dec 2020 12:17:21 +0100
Subject: Add peak_list_type in geometry file

---
 libcrystfel/src/datatemplate.c      | 25 +++++++++++++++++++++++++
 libcrystfel/src/datatemplate_priv.h |  8 ++++++++
 libcrystfel/src/image.c             | 34 ++++++++++++++++++++++++++++++----
 3 files changed, 63 insertions(+), 4 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index 18b09c12..0da913d4 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -756,6 +756,28 @@ static int parse_photon_energy(const char *val,
 }
 
 
+static int parse_peak_layout(const char *val,
+                             enum peak_layout *layout)
+{
+	if ( strcmp(val, "auto") == 0 ) {
+		*layout = PEAK_LIST_AUTO;
+		return 0;
+	}
+
+	if ( strcmp(val, "cxi") == 0 ) {
+		*layout = PEAK_LIST_CXI;
+		return 0;
+	}
+
+	if ( (strcmp(val, "list3") == 0) ) {
+		*layout = PEAK_LIST_LIST3;
+		return 0;
+	}
+
+	return 1;
+}
+
+
 static int parse_toplevel(DataTemplate *dt,
                           const char *key,
                           const char *val,
@@ -812,6 +834,9 @@ static int parse_toplevel(DataTemplate *dt,
 	} else if ( strcmp(key, "peak_list") == 0 ) {
 		dt->peak_list = strdup(val);
 
+	} else if ( strcmp(key, "peak_list_type") == 0 ) {
+		return parse_peak_layout(val, &dt->peak_list_type);
+
 	} else if ( strcmp(key, "bandwidth") == 0 ) {
 		double v;
 		char *end;
diff --git a/libcrystfel/src/datatemplate_priv.h b/libcrystfel/src/datatemplate_priv.h
index 593ebaa8..5f598184 100644
--- a/libcrystfel/src/datatemplate_priv.h
+++ b/libcrystfel/src/datatemplate_priv.h
@@ -65,6 +65,13 @@ enum flag_value_type
 	FLAG_LESSTHAN
 };
 
+enum peak_layout
+{
+	PEAK_LIST_AUTO,
+	PEAK_LIST_CXI,
+	PEAK_LIST_LIST3
+};
+
 /* Special values for dimension IDs */
 #define DIM_FS (-1)
 #define DIM_SS (-2)
@@ -203,6 +210,7 @@ struct _datatemplate
 	int                        n_rg_collections;
 
 	char                      *peak_list;
+	enum peak_layout           peak_list_type;
 
 	/* Shift of whole detector, in m */
 	char *                     shift_x_from;
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index d50bcf43..54171321 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -938,19 +938,45 @@ ImageFeatureList *image_read_peaks(const DataTemplate *dtempl,
 {
 	if ( is_hdf5_file(filename) ) {
 
-		const char *ext;
-		ext = filename_extension(filename, NULL);
-		if ( strcmp(ext, ".cxi") == 0 ) {
+		enum peak_layout layout;
+
+		if ( dtempl->peak_list_type == PEAK_LIST_AUTO ) {
+
+			const char *ext;
+			ext = filename_extension(filename, NULL);
+
+			if ( strcmp(ext, ".cxi") == 0 ) {
+				layout = PEAK_LIST_CXI;
+			} else if ( strcmp(ext, ".h5") == 0 ) {
+				layout = PEAK_LIST_LIST3;
+			} else {
+				ERROR("Couldn't determine peak list layout.\n");
+				ERROR("Specify peak_layout = cxi or list3n in geometry file.\n");
+				return NULL;
+			}
+
+		} else {
+			layout = dtempl->peak_list_type;
+		}
+
+		switch ( layout ) {
+
+			case PEAK_LIST_CXI :
 			return image_hdf5_read_peaks_cxi(dtempl,
 			                                 filename,
 			                                 event,
 			                                 half_pixel_shift);
 
-		} else {
+			case PEAK_LIST_LIST3 :
 			return image_hdf5_read_peaks_hdf5(dtempl,
 			                                  filename,
 			                                  event,
 			                                  half_pixel_shift);
+
+			default :
+			ERROR("Invalid peak list type %i\n", layout);
+			return NULL;
+
 		}
 
 	} else  {
-- 
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