[io][utils] Add overwrite option to write_process function

darfix/io/utils.py

@@ -117,7 +117,7 @@ def write_process(h5_file, entry, dimensions, W, data, processing_order,
                 return 'image'
         return None
 
-    def save_key(path_name, key_path, value):
+    def save_key(path_name, key_path, value, overwrite=True):
         """Save the given value to the associated path. Manage numpy arrays
         and dictionaries"""
         key_path = key_path.replace('.', '/')
@@ -129,6 +129,8 @@ def write_process(h5_file, entry, dimensions, W, data, processing_order,
         else:
             with h5py.File(h5_file, 'a') as h5f:
                 nx = h5f.require_group(path_name)
+                if overwrite and key_path in nx:
+                    del nx[key_path]
                 try:
                     nx[key_path] = value
                 except TypeError as e:
@@ -147,8 +149,7 @@ def write_process(h5_file, entry, dimensions, W, data, processing_order,
         nx_process = nx_entry.require_group(process_name)
         nx_process.attrs['NX_class'] = "NXprocess"
         if overwrite:
-            for key in ('program', 'version', 'date', 'processing_order',
-                        'class_instance', 'ft'):
+            for key in ('program', 'version', 'date', 'processing_order'):
                 if key in nx_process:
                     del nx_process[key]
         nx_process['program'] = 'darfix'
@@ -158,19 +159,18 @@ def write_process(h5_file, entry, dimensions, W, data, processing_order,
 
         nx_parameters = nx_process.require_group("inputs")
         nx_parameters.attrs['NX_class'] = "NXparameters"
-        nx_parameters_path = nx_parameters.name
+        for key, value in dimensions.items():
+            save_key(nx_parameters.name, key_path=key, value=value)
+
         results = nx_process.require_group("results")
         results.attrs["NX_class"] = "NXcollection"
-        results_path = results.name
 
         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"
         results.attrs["target"] = "components"
-        save_key(results_path, "W", W)
-        save_key(results_path, "components", data)
-        nx_data["components"] = h5f[source_addr]
 
-    for key, value in dimensions.items():
-        save_key(nx_parameters_path, key_path=key, value=value)
+        save_key(results.name, "W", W)
+        save_key(results.name, "components", data)
+        save_key(nx_data.name, "components", h5f[source_addr])