Added support for adding references to proprietary/Cameca/non-Cameca …

…workflow-related files in the NeXus file so that NOMAD is available could use them further, also added feedback of best practice metadata to report from T. Blum et al. from the geoscience community, next steps: i) fix eln parsing, ii) add 176case study specific citation code, iii) customize nomad schema, iv) runthrough

debug/eln_data_apm.yaml

@@ -1,23 +1,8 @@
 atom_probe:
-  analysis_chamber_pressure:
-    unit: torr
-    value: 2.0e-10
-  control_software_program: IVAS
-  control_software_program__attr_version: 3.6.8
   fabrication_identifier: '12'
   fabrication_model: LEAP3000
   fabrication_vendor: Cameca
-  field_of_view:
-    unit: nm
-    value: 20.
-  flight_path_length:
-    unit: m
-    value: 1.2
   instrument_name: LEAP
-  ion_detector_model: n/a
-  ion_detector_name: n/a
-  ion_detector_serial_number: n/a
-  ion_detector_type: mcp_dld
   local_electrode_name: L1
   location: Denton
   pulser:
@@ -47,72 +32,91 @@ atom_probe:
       unit: kHz
       value: 250.0
     pulse_mode: laser_and_voltage
-  reflectron_applied: true
-  specimen_monitoring_detection_rate: 0.8
-  specimen_monitoring_initial_radius:
-    unit: nm
-    value: 12.0
-  specimen_monitoring_shank_angle:
-    unit: °
-    value: 5.0
-  stage_lab_base_temperature:
+  reflectron_status: used
+  evaporation_control: detection_rate
+  target_detection_rate: 0.01
+  chamber_pressure:
+    unit: torr
+    value: 2.0e-10
+  base_temperature:
     unit: K
     value: 20.0
+  nominal_flight_path:
+    unit: m
+    value: 1.2
   status: success
 entry:
   experiment_description: '<p>Normal</p>
 
     <p><strong>Bold</strong></p>
 
     <p><em>Italics</em></p>'
-  experiment_identifier: Si test
   start_time: '2023-06-11T11:20:00+00:00'
   end_time: '2023-06-11T11:20:00+00:00'
   run_number: '2121'
   operation_mode: apt
+workflow:
+  raw_dat_file: str.str
+  hit_dat_file: hits.hits
+  recon_cfg_file: hits.root
+  recon_res_file: recon.apt
+  range_dat_file: recon.rrng
 ranging:
   program: IVAS
-  program__attr_version: 3.6.8
+  program_version: 3.6.8
 reconstruction:
+  program: IVAS
+  program_version: 3.6.8
   crystallographic_calibration: n/a
   parameter: kf = 1.8, icf = 3.3
-  program: IVAS
-  program__attr_version: 3.6.8
   protocol_name: bas
+  field_of_view:
+    unit: nm
+    value: 20.
 sample:
   composition:
   - Mo
   - Al 12 +- 3
   - B 50 ppm +- 12
   - C 3.6
+  method: measurement
+  alias: Si
   grain_diameter:
     unit: µm
     value: 200.0
   grain_diameter_error:
     unit: µm
     value: 50.0
-  heat_treatment_quenching_rate:
-    unit: K / s
-    value: 150.0
-  heat_treatment_quenching_rate_error:
-    unit: K / s
-    value: 10.0
   heat_treatment_temperature:
     unit: K
     value: 600.0
   heat_treatment_temperature_error:
     unit: K
     value: 20.0
+  heat_treatment_quenching_rate:
+    unit: K / s
+    value: 150.0
+  heat_treatment_quenching_rate_error:
+    unit: K / s
+    value: 10.0
+  description: '<p>nothing</p>'
 specimen:
-  alias: Si
+  method: measurement
+  alias: usa_denton_smith_si
   description: '<p>normal</p>
 
     <p><em>bold</em></p>
 
     <p><em>italics</em></p>'
   is_polycrystalline: true
-  name: usa_denton_smith_si
+  is_amorphous: false
   preparation_date: '2023-06-11T12:51:00+00:00'
+  initial_radius:
+    unit: nm
+    value: 12.0
+  shank_angle:
+    unit: °
+    value: 5.0
 user:
 - {}
 - {}