Ellips reader attribute issues (#115)

* Update writer.py

trying to fix issues with writing attributes

* testing writing attributes to plot(NXdata)

* fix for adding units to existing elements

* Updated reader to be consisent with NXellipsometry

* fixing pycodestyle errors in reader

* fixing pycodestyle errors in reader

* fixing pycodestyle errors in reader

* fixing pylint errors

* removed redundant backslash

---------

Co-authored-by: Sandor Brockhauser <sandor.brockhauser@xfel.eu>

pynxtools/dataconverter/readers/ellips/reader.py

@@ -319,21 +319,29 @@ def read(self,
         template["/ENTRY[entry]/plot/wavelength"] = {"link":
                                                      "/entry/instrument/spectrometer/wavelength"
                                                      }
-        template["/ENTRY[entry]/plot/wavelength/@units"] = header["wavelength_unit"]
-        for data_indx in range(0, len(labels.keys())):
-            for index, key in enumerate(data_list[data_indx]):
-                template[f"/ENTRY[entry]/plot/{key}"] = {"link":
-                                                         "/entry/sample/measured_data",
-                                                         "shape":
-                                                         np.index_exp[0, 0, index, data_indx, :]
-                                                         }
-                template[f"/ENTRY[entry]/plot/{key}/@units"] = "degrees"
+        template["/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/wavelength/@units"] = \
+            "Angstroms"
+        template["/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/wavelength/@long_name"] = \
+            "wavelength (Angstroms)"
+
+        for dindx in range(0, len(labels.keys())):
+            for index, key in enumerate(data_list[dindx]):
+                template[f"/ENTRY[entry]/plot/DATA[{key}]"] = {"link":
+                                                               "/entry/sample/measured_data",
+                                                               "shape":
+                                                               np.index_exp[0, 0, index, dindx, :]
+                                                               }
+                template[f"/ENTRY[entry]/plot/DATA[{key}]/@units"] = "degrees"
+                if dindx == 0 and index == 0:
+                    template[f"/ENTRY[entry]/plot/DATA[{key}]/@long_name"] = \
+                        "Psi and Delta (degrees)"
 
         # Define default plot showing psi and delta at all angles:
         template["/@default"] = "entry"
         template["/ENTRY[entry]/@default"] = "plot"
         template["/ENTRY[entry]/plot/@signal"] = f"{data_list[0][0]}"
         template["/ENTRY[entry]/plot/@axes"] = "wavelength"
+        template["/ENTRY[entry]/plot/title"] = "Psi and Delta"
 
         # if len(data_list[0]) > 1:
         template["/ENTRY[entry]/plot/@auxiliary_signals"] = data_list[0][1:]

pynxtools/dataconverter/writer.py

@@ -104,7 +104,7 @@ def handle_shape_entries(data, file, path):
     return layout
 
 
-def handle_dicts_entries(data, grp, entry_name, output_path):
+def handle_dicts_entries(data, grp, entry_name, output_path, path):
     """Handle function for dictionaries found as value of the nexus file.
 
 Several cases can be encoutered:
@@ -253,12 +253,34 @@ def add_units_key(dataset, path):
                     grp = self.ensure_and_get_parent_node(path, self.data.undocumented.keys())
                     if isinstance(data, dict):
                         if "compress" in data.keys():
-                            dataset = handle_dicts_entries(data, grp, entry_name, self.output_path)
+                            dataset = handle_dicts_entries(data, grp, entry_name,
+                                                           self.output_path, path)
                         else:
-                            hdf5_links_for_later.append([data, grp, entry_name, self.output_path])
+                            hdf5_links_for_later.append([data, grp, entry_name,
+                                                         self.output_path, path])
                     else:
                         dataset = grp.create_dataset(entry_name, data=data)
-                    add_units_key(dataset, path)
+            except Exception as exc:
+                raise IOError(f"Unknown error occured writing the path: {path} "
+                              f"with the following message: {str(exc)}") from exc
+
+        for links in hdf5_links_for_later:
+            dataset = handle_dicts_entries(*links)
+
+        for path, value in self.data.items():
+            try:
+                if path[path.rindex('/') + 1:] == '@units':
+                    continue
+
+                entry_name = helpers.get_name_from_data_dict_entry(path[path.rindex('/') + 1:])
+                if is_not_data_empty(value):
+                    data = value
+                else:
+                    continue
+
+                if entry_name[0] != "@":
+                    path_hdf5 = helpers.convert_data_dict_path_to_hdf5_path(path)
+                    add_units_key(self.output_nexus[path_hdf5], path)
                 else:
                     # consider changing the name here the lvalue can also be group!
                     dataset = self.ensure_and_get_parent_node(path, self.data.undocumented.keys())
@@ -267,7 +289,4 @@ def add_units_key(dataset, path):
                 raise IOError(f"Unknown error occured writing the path: {path} "
                               f"with the following message: {str(exc)}") from exc
 
-        for links in hdf5_links_for_later:
-            dataset = handle_dicts_entries(*links)
-
         self.output_nexus.close()