bring in additional changes from SprintNomadBaseSectionEmApmFixes branch

src/pynxtools_apm/nomad/examples/apm.archive.json

@@ -0,0 +1 @@
+{"data":{"m_def":"../upload/raw/nxapm.schema.archive.yaml#/definitions/section_definitions/0","reader":"apm","nxdl":"NXapm","input_files":["eln_data.yaml","Si.apt","Si.RRNG","apm.oasis.specific.yaml"],"output":"apm.nxs","entry":{"experiment_description":"<p>Normal</p>\n<p><strong>Bold</strong></p>\n<p><em>Italics</em></p>","start_time":"2023-06-12T13:57:00+00:00","end_time":"2023-06-12T13:57:00+00:00","run_number":"2121","operation_mode":"apt"},"workflow":{"raw_dat_file":"","hit_dat_file":"","recon_cfg_file":""},"sample":{"alias":"Si","method":"experiment","composition":["Si","Cr 2 +- 0.5","C 50 ppm +- 12"],"grain_diameter":200,"grain_diameter_error":50,"heat_treatment_temperature":600,"heat_treatment_temperature_error":20,"heat_treatment_quenching_rate":150,"heat_treatment_quenching_rate_error":10},"specimen":{"alias":"Si","method":"experiment","preparation_date":"2023-06-12T13:59:00+00:00","is_polycrystalline":false,"is_amorphous":false,"description":"this is a NOMAD example","initial_radius":20,"shank_angle":5},"user":[{"name":"MarkusK"},{"name":"Jesse Smith"}],"instrument":{"status":"success","instrument_name":"LEAP","location":"Denton","nominal_flight_path":1.2,"fabrication_vendor":"Cameca","fabrication_model":"LEAP3000","fabrication_identifier":"12","reflectron_status":"used","base_temperature":20,"chamber_pressure":2e-10,"target_detection_rate":0.8,"pulser":{"pulse_mode":"laser","pulse_frequency":250,"pulse_fraction":0.8,"laser_source":[{"name":"laser1","wavelength":254,"power":12,"pulse_energy":20},{"name":"laser2","wavelength":355,"power":24,"pulse_energy":40}]},"local_electrode_name":"L1"},"reconstruction":{"program":"IVAS","program_version":"3.6.8","protocol_name":"bas","parameter":"kf = 1.8, icf = 3.3","crystallographic_calibration":"n/a","field_of_view":20},"ranging":{"program":"IVAS","program_version":"3.6.8"}}}

src/pynxtools_apm/examples/nomad/eln_data.yaml → src/pynxtools_apm/nomad/examples/eln_data.yaml

@@ -81,6 +81,10 @@ sample:
   - C 3.6
   method: experiment
   alias: Si
+  identifier:
+    service: undefined
+    identifier: 'Si in sample'
+    is_persistent: false
   grain_diameter:
     unit: µm
     value: 200.
@@ -103,6 +107,10 @@ sample:
 specimen:
   method: experiment
   alias: usa_denton_smith_si
+  identifier:
+    service: undefined
+    identifier: 'Si in specimen'
+    is_persistent: false
   description: '<p>normal</p>
 
     <p><em>bold</em></p>