Merge branch 'update-xps-example' into 'develop'

Update XPS example to match the new NXmpes NeXus application definition

See merge request !1867

docs/examples/experiment_data/xps.md

+# Domain-specific examples for X-ray photoelectron spectroscopy
+
+!!! warning "Attention"
+    We are currently working to update this content.
+
+## Contextualization for the technique and the scientific domain
+A variety of file formats are used in the research field of X-ray photoelectron spectroscopy and related techniques. The pynxtools-xps plugin of the pynxtools parsing library solves the challenge of how these formats can be parsed and normalized into a common representation that increases interoperability and adds semantic expressiveness.
+- [pynxtools-xps](https://fairmat-nfdi.github.io/pynxtools-xps/)
+
+
+pynxtools-xps, which is a plugin for [pynxtools](https://github.com/FAIRmat-NFDI/pynxtools), provides a tool for reading data from various propietary and open data formats from technology partners and the wider XPS community and standardizing it such that it is compliant with the [NeXus](https://www.nexusformat.org/) application definition [`NXmpes`](https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXmpes.html) 
+
+## Supported file formats
+A list of the supported file formats can be found in the [pynxtools-xps](https://fairmat-nfdi.github.io/pynxtools-xps/) documentation.
\ No newline at end of file

examples/data/xps/Specs_conversion.archive.json

@@ -8,9 +8,7 @@
             "eln_data.yaml"
         ],
         "output": "Au_25_mbar_O2_no_align.nxs",
-        "definition":"NXmpes",
-        "definition/@version":"1.0",
-        "title":"XPS Experiment",
+        "title":"EX439_S718_Au in 25 mbar O2",
         "start_time":"2022-04-08T09:47:00.000Z",
         "end_time":"2022-04-08T10:32:00.000Z",
         "entry_identifier":"EX439",
@@ -19,12 +17,19 @@
         "experiment_laboratory":"Near-Ambient Pressure XPS Lab",
         "user":{
             "name":"Lukas Pielsticker",
-            "affiliation":"MPI CEC"
+            "affiliation":"MPI CEC",
+            "address":"Lukas Pielsticker",
+            "email":"lukas.pielsticker@cec.mpg.de",
+            "orcid":{
+                "service":"orcid",
+                "identifier":"0000-0001-9361-8333"
+            }
         },
         "instrument":{
             "device_information":{
                 "vendor":"SPECS GmbH",
-                "model":"XPS setup"
+                "model":"Custom NAP-XPS instrument",
+                "identifier":"null"
             },
             "energy_resolution":{
                 "type":"calibrated",
@@ -47,20 +52,22 @@
                     "description":"hemispherical",
                     "device_information":{
                         "vendor":"SPECS GmbH",
-                        "model":"PHOIBOS 150 NAP"
+                        "model":"PHOIBOS 150 NAP",
+                        "identifier":"null"
                     },
                     "collectioncolumn":{
                         "scheme":"angular dispersive",
                         "device_information":{
                             "vendor":"SPECS GmbH",
-                            "model":"PHOIBOS 150 NAP"
+                            "model":"PHOIBOS 150 NAP",
+                            "identifier":"null"
                         }
                     },
                     "energydispersion":{
                         "scheme":"hemispherical",
                         "diameter":{
                             "unit":"mm",
-                            "value":"150"
+                            "value":150
                         },
                         "device_information":{
                             "vendor":"SPECS GmbH",
@@ -73,15 +80,16 @@
                         "detector_type":"Multi-anode",
                         "device_information":{
                             "vendor":"Surface Concept GmbH",
-                            "model":"1D-DLD detector"
+                            "model":"1D-DLD detector",
+                            "identifier":"null"
                         }
                     }
                 },
                 "manipulator":{
-                    "description":"hemispherical",
                     "device_information":{
                         "vendor":"SPECS GmbH",
-                        "model":"5-axis manipulator"
+                        "model":"5-axis manipulator",
+                        "identifier":"null"
                     },
                     "temperature_sensor":{
                         "name":"type K thermocouple",
@@ -173,7 +181,7 @@
                     "cas_number":"7440-57-5",
                     "molecular_formula_hill":"Au"
                 },
-                "sample_history":{
+                "history":{
                     "sample_preparation":{
                         "start_time":"2022-04-08T11:25:00.200Z",
                         "end_time":"2022-04-08T11:45:00.200Z",

examples/data/xps/eln_data.yaml

-definition:
-  value: NXmpes
-  version: 1.0
 title: EX439_S718_Au in 25 mbar O2
 start_time: 2022-04-08T11:47:02.0200Z
 end_time: 2022-04-08T14:52:26.0400Z
@@ -13,8 +10,10 @@ user:
   name: Lukas Pielsticker
   affiliation: Max Planck Institute for Chemical Energy Conversion
   address: Lukas Pielsticker
-  orcid: 0000-0001-9361-8333
   email: lukas.pielsticker@cec.mpg.de
+  orcid:
+    service: orcid
+    identifier: 0000-0001-9361-8333
 instrument:
   device_information:
     vendor: SPECS GmbH
@@ -25,14 +24,14 @@ instrument:
     resolution:
       value: 0.2
       unit: eV
-  source_probe:
+  source_xray:
     type: Fixed Tube X-ray
     probe: photon
     device_information:
       vendor: SPECS GmbH
       model: µFOCUS 500
       identifier: null
-  beam_probe:
+  beam_xray:
     distance:
       value: 0.0
       unit: mm
@@ -68,7 +67,7 @@ instrument:
     device_information:
       vendor: SPECS GmbH
       model: 5-axis manipulator
-      identifier: null
+      identifier: v1.0
     temperature_sensor:
       name: type K thermocouple
       measurement: temperature
@@ -152,14 +151,9 @@ sample:
       unit: g/mol
     cas_number: 7440-57-5
     molecular_formula_hill: Au
-  sample_history:
+  history:
     sample_preparation:
       start_time: 2022-04-08T11:25:00.200Z
       end_time: 2022-04-08T11:45:00.200Z
       description: sputter cleaned with Ar ions for 20 min
       method: Ar sputtering
-    PHYSICAL_PROCESS[sample_loading]:
-      start_time: 2022-04-08T11:02:00.0200Z
-      end_time: 2022-04-08T11:03:00.0200Z
-      description: loaded in the endstation and transferred to analysis chamber
-      method: vacuum transfer