[io][utils] Fix save of maps to nexus file

darfix/io/utils.py

@@ -26,7 +26,7 @@
 
 __authors__ = ["J. Garriga"]
 __license__ = "MIT"
-__date__ = "06/02/2020"
+__date__ = "03/07/2021"
 
 import logging
 import h5py
@@ -71,7 +71,9 @@ def advancement_display(iteration, total, prefix='', suffix='', decimals=1, leng
     if iteration == total:
         print()
 
-def write_maps(h5_file, list_of_maps, data_path='/', overwrite=True):
+
+def write_maps(h5_file, list_of_maps, default_map, entry, processing_order, data_path='/',
+               overwrite=True):
     """
     Write a stack of components and its parameters into .h5
 
@@ -118,7 +120,7 @@ def write_maps(h5_file, list_of_maps, data_path='/', overwrite=True):
                         nx[key_path].attrs['interpretation'] = interpretation
 
     with h5py.File(h5_file, 'a') as h5f:
-        h5f.attrs["default"] = "entry"
+        h5f.attrs["default"] = entry
         nx_entry = h5f.require_group('/'.join((data_path, entry)))
         nx_entry.attrs["NX_class"] = "NXentry"
         nx_entry.attrs["default"] = "data"
@@ -136,15 +138,24 @@ def write_maps(h5_file, list_of_maps, data_path='/', overwrite=True):
 
         results = nx_process.require_group("results")
         results.attrs["NX_class"] = "NXcollection"
+        nx_data = nx_entry.require_group("data")
+        nx_data.attrs["NX_class"] = "NXdata"
+        default = list_of_maps[default_map]
+        source_addr = entry + "/" + process_name + "/results/" + default_map
+        results.attrs["target"] = default_map
+        save_key(results.name, default_map, default)
+        save_key(nx_data.name, default_map, h5f[source_addr])
 
         for _map in list_of_maps:
-            nx_data = nx_entry.require_group(_map)
-            nx_data.attrs["NX_class"] = "NXdata"
-            nx_data.attrs["signal"] = _map
-            source_addr = "entry/" + process_name + "/results/" + _map
-            results.attrs["target"] = write_maps
-            save_key(results.name, _map, W)
-            save_key(nx_data.name, _map, h5f[source_addr])
+            if _map == default_map:
+                continue
+            if isinstance(list_of_maps[_map], dict):
+                maps = results.require_group(_map)
+                maps.attrs["NX_class"] = "NXcollection"
+                for method in list_of_maps[_map]:
+                    save_key(maps.name, method, list_of_maps[_map][method])
+            else:
+                save_key(results.name, _map, list_of_maps[_map])
 
 
 def read_components(h5_file):
@@ -217,7 +228,7 @@ def write_components(h5_file, entry, dimensions, W, data, processing_order,
                         nx[key_path].attrs['interpretation'] = interpretation
 
     with h5py.File(h5_file, 'a') as h5f:
-        h5f.attrs["default"] = "entry"
+        h5f.attrs["default"] = entry
         nx_entry = h5f.require_group('/'.join((data_path, entry)))
         nx_entry.attrs["NX_class"] = "NXentry"
         nx_entry.attrs["default"] = "data"
@@ -244,7 +255,7 @@ def write_components(h5_file, entry, dimensions, W, data, processing_order,
         nx_data = nx_entry.require_group("data")
         nx_data.attrs["NX_class"] = "NXdata"
         nx_data.attrs["signal"] = "components"
-        source_addr = "entry/" + process_name + "/results/components"
+        source_addr = entry + "/" + process_name + "/results/components"
         results.attrs["target"] = "components"
 
         save_key(results.name, "W", W)