Merge 0a52f04 into 00bdee3

FAIRmat-NFDI · Apr 11, 2024 · b77b51d · b77b51d
2 parents 00bdee3 + 0a52f04
commit b77b51d
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Showing 24 changed files with 91 additions and 78 deletions.
diff --git a/examples/phi/SnO2_10nm.spe.nxs b/examples/phi/SnO2_10nm.spe.nxs
diff --git a/examples/phi/SnO2_10nm_1.pro.nxs b/examples/phi/SnO2_10nm_1.pro.nxs
diff --git a/examples/phi/eln_data_phi.yaml b/examples/phi/eln_data_phi.yaml
@@ -149,7 +149,7 @@ sample:
       unit: g/mol
     cas_number: 18282-10-5
     molecular_formula_hill: SnO2
-  sample_history:
+  history:
     sample_preparation:
       start_time: 2022-01-22T12:48:00.200Z
       end_time: 2022-01-22T13:18:00.200Z

diff --git a/examples/regenerate_examples.sh b/examples/regenerate_examples.sh
@@ -1,12 +1,15 @@
 #!/bin/bash
+READER=xps
+NXDL=NXmpes
+
 function update_phi_examples {
   echo "Update Phi examples"
   cd phi/
   echo "Update .spe (single spectrum) examples"
-  dataconverter SnO2_10nm.spe eln_data_phi.yaml --reader xps --nxdl NXmpes --output SnO2_10nm.spe.nxs
+  dataconverter SnO2_10nm.spe eln_data_phi.yaml --reader $READER --nxdl $NXDL --output SnO2_10nm.spe.nxs
   echo
   echo "Update .pro (depth_profiling) examples"
-  dataconverter SnO2_10nm_1.pro eln_data_phi.yaml --reader xps --nxdl NXmpes --output SnO2_10nm_1.pro.nxs
+  dataconverter SnO2_10nm_1.pro eln_data_phi.yaml --reader $READER --nxdl $NXDL --output SnO2_10nm_1.pro.nxs
   cd ..
   echo
 }
@@ -15,7 +18,7 @@ function update_scienta_examples {
   echo "Update scienta examples"
   cd scienta/
   echo "Update .txt example"
-  dataconverter Cu-HHTP_*.txt eln_data.yaml --reader xps --nxdl NXmpes --output Cu-HHTP.nxs
+  dataconverter Cu-HHTP_*.txt eln_data.yaml --reader $READER --nxdl $NXDL --output Cu-HHTP.nxs
   cd ..
   echo
 }

diff --git a/examples/scienta/Cu-HHTP.nxs b/examples/scienta/Cu-HHTP.nxs
diff --git a/examples/scienta/eln_data.yaml b/examples/scienta/eln_data.yaml
@@ -160,7 +160,7 @@ sample:
   chemical_formula: Cu
   description: Cu-HHTP/Glass on standard sample holder
   situation: vacuum
-  sample_history:
+  history:
     sample_preparation:
       start_time: 2022-04-08T11:25:00.200Z
       end_time: 2022-04-08T11:45:00.200Z

diff --git a/examples/sle/Au_25_mbar_O2_no_align.nxs b/examples/sle/Au_25_mbar_O2_no_align.nxs
diff --git a/examples/sle/eln_data_sle.yaml b/examples/sle/eln_data_sle.yaml
@@ -25,14 +25,14 @@ 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
@@ -152,7 +152,7 @@ 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

diff --git a/pynxtools_xps/config/config_phi.json b/pynxtools_xps/config/config_phi.json
@@ -37,7 +37,9 @@
       "resolution":"@eln",
       "resolution/@units":"@eln"
     },
+    "depends_on": "/entry/instrument/source_xray/transformations/source_analyser_angle",
     "TRANSFORMATIONS[transformations]": {
+      "AXISNAME[source_analyser_angle]/@depends_on":".",
       "AXISNAME[source_analyser_angle]":"@xps_token/source_analyser_angle",
       "AXISNAME[source_analyser_angle]/@transformation_type": "rotation",
       "AXISNAME[source_analyser_angle]/@units":"@xps_token/source_analyser_angle/@units",
@@ -47,7 +49,7 @@
         1
       ]
     },
-    "source_TYPE[source_xray]":{
+    "sourceTYPE[source_xray]":{
       "type":"@eln",
       "name":"@xps_token:xray_source/name",
       "probe":"@eln",
@@ -73,9 +75,11 @@
       "power/@units":"@xps_token:xray_source/xray_power/@units",
       "offset":"@xps_token:xray_source/xray_offset",
       "offset/@units":"@xps_token:xray_source/xray_offset/@units",
+      "rotation":"@xps_token:xray_source/xray_rotation",
+      "rotation/@units":"@xps_token:xray_source/xray_rotation/@units",
       "voltage":"@xps_token:xray_source/xray_high_voltage",
       "voltage/@units":"@xps_token:xray_source/xray_high_voltage/@units",
-      "associated_beam":"@link:/entry/instrument/beam_xray",
+      "associated_beam":"/entry/instrument/beam_xray",
       "LENS_EM[blanking_lens]":{
         "name":"blanking lens",
         "voltage":"@xps_token:xray_source/xray_blanking_voltage",
@@ -108,20 +112,9 @@
         "offset_x/@units":"@xps_token:xray_source/xray_stigmator_x/@units",
         "offset_y":"@xps_token:xray_source/xray_stigmator_y",
         "offset_y/@units":"@xps_token:xray_source/xray_stigmator_y/@units"
-      },
-      "depends_on": "/entry/instrument/source_xray/transformations/trans_z",
-      "TRANSFORMATIONS[transformations]": {
-        "AXISNAME[xray_rotation]":"@xps_token:xray_source/xray_rotation",
-        "AXISNAME[xray_rotation]/@transformation_type": "rotation",
-        "AXISNAME[xray_rotation]/@units":"@xps_token:xray_source/xray_rotation/@units",
-        "AXISNAME[xray_rotation]/@vector": [
-          0,
-          0,
-          1
-        ]
       }
     },
-    "beam_TYPE[beam_xray]":{
+    "beamTYPE[beam_xray]":{
       "distance":"@eln",
       "distance/@units":"@eln",
       "incident_energy":"@xps_token:beam/xray_energy",
@@ -132,9 +125,9 @@
       "incident_polarization/@units":"None",
       "extent":"@xps_token:beam/xray_beam_diameter",
       "extent/@units":"@xps_token:beam/xray_beam_diameter/@units",
-      "associated_source":"@link:/entry/instrument/source_xray"
+      "associated_source":"/entry/instrument/source_xray"
     },
-    "source_TYPE[source_flood_gun]":{
+    "sourceTYPE[source_flood_gun]":{
       "current":"@xps_token:flood_gun/flood_gun_current",
       "current/@units":"@xps_token:flood_gun/flood_gun_current/@units",
       "energy":"@xps_token:flood_gun/flood_gun_energy",
@@ -161,7 +154,7 @@
         "voltage/@units":"@xps_token:flood_gun/extractor_voltage/@units"
       }
     },
-    "source_TYPE[source_gas_cluster_ion_beam]":{
+    "sourceTYPE[source_gas_cluster_ion_beam]":{
       "description":"@eln",
       "cluster_size":"@xps_token:gcib/gcib_cluster_size",
       "cluster_size/@units":"@xps_token:gcib/gcib_cluster_size/@units",
@@ -207,7 +200,7 @@
         "voltage/@units":"@xps_token:gcib/gcib_objective/@units"
       }
     },
-    "source_TYPE[source_neutral_ion_gun]":{
+    "sourceTYPE[source_neutral_ion_gun]":{
       "description":"@eln",
       "current":"@xps_token:neutral_ion_gun/neutral_current",
       "current/@units":"@xps_token:neutral_ion_gun/neutral_current/@units",
@@ -252,7 +245,7 @@
         "voltage/@units":"@xps_token:neutral_ion_gun/neutral_objective_lens_voltage/@units"
       }
     },
-    "source_TYPE[source_sputter_gun]":{
+    "sourceTYPE[source_sputter_gun]":{
       "description":"@eln",
       "current":"@xps_token:sputter_gun/sputter_current",
       "current/@units":"@xps_token:sputter_gun/sputter_current/@units",
@@ -520,7 +513,7 @@
       "value":"@link:/entry/instrument/source_flood_gun/current"   
     }
   },
-  "/ENTRY[entry]/PROCESS[process]":{
+  "/ENTRY[entry]/PROCESS_MPES[process]":{
     "energy_calibration":"None",
     "energy_referencing":{
       "level":"None",
@@ -547,7 +540,7 @@
       "cas_number":"@eln",
       "molecular_formula_hill":"@eln"
     },
-    "sample_history":{
+    "history":{
       "sample_preparation":{
         "start_time":"@eln",
         "end_time":"@eln",

diff --git a/pynxtools_xps/config/config_scienta_txt.json b/pynxtools_xps/config/config_scienta_txt.json
@@ -36,7 +36,7 @@
       "resolution":"@xps_token:region/step_size",
       "resolution/@units":"@xps_token:region/step_size/@units"
     },
-    "source_TYPE[source_xray]":{
+    "sourceTYPE[source_xray]":{
       "type":"@eln",
       "name":"@eln",
       "probe":"photon",
@@ -45,9 +45,9 @@
         "identifier":"@eln",
         "model":"@eln"
       },
-      "associated_beam":"@link:/entry/instrument/beam_xray"
+      "associated_beam":"/entry/instrument/beam_xray"
     },
-    "beam_TYPE[beam_xray]":{
+    "beamTYPE[beam_xray]":{
       "distance":"@eln",
       "distance/@units":"@eln",
       "incident_energy":"@xps_token:beam/excitation_energy",
@@ -57,7 +57,7 @@
       "incident_polarization":"None",
       "incident_polarization/@units":"None",
       "extent":"None",
-      "associated_source":"@link:/entry/instrument/source_xray"
+      "associated_source":"/entry/instrument/source_xray"
     },
     "ELECTRONANALYSER[electronanalyser]":{
       "@default":"detector0",
@@ -232,7 +232,7 @@
       "cas_number":"@eln",
       "molecular_formula_hill":"@eln"
     },
-    "sample_history":{
+    "history":{
       "sample_preparation":{
         "start_time":"@eln",
         "end_time":"@eln",

diff --git a/pynxtools_xps/config/config_sle_specs.json b/pynxtools_xps/config/config_sle_specs.json
@@ -36,7 +36,7 @@
       "resolution":"@eln",
       "resolution/@units":"@eln"
     },
-    "source_TYPE[source_probe]":{
+    "sourceTYPE[source_xray]":{
       "type":"@eln",
       "name":"@xps_token:source/name",
       "probe":"@eln",
@@ -49,9 +49,9 @@
         "identifier":"@eln",
         "model":"@eln"
       },
-      "associated_beam":"@link:/entry/instrument/beam_probe"
+      "associated_beam":"/entry/instrument/beam_xray"
     },
-    "beam_TYPE[beam_probe]":{
+    "beamTYPE[beam_xray]":{
       "distance":"@eln",
       "distance/@units":"@eln",
       "incident_energy":"@xps_token:beam/excitation_energy",
@@ -61,7 +61,7 @@
       "incident_polarization":"None",
       "incident_polarization/@units":"None",
       "extent":"None",
-      "associated_source":"@link:/entry/instrument/source_probe"
+      "associated_source":"/entry/instrument/source_xray"
     },
     "ELECTRONANALYSER[electronanalyser]":{
       "@default": "detector0",
@@ -272,7 +272,7 @@
       "cas_number":"@eln",
       "molecular_formula_hill":"@eln"
     },
-    "sample_history":{
+    "history":{
       "sample_preparation":{
         "start_time":"@eln",
         "end_time":"@eln",

diff --git a/pynxtools_xps/config/config_specs_xy.json b/pynxtools_xps/config/config_specs_xy.json
@@ -35,7 +35,7 @@
         "resolution":"@xps_token:data/step_size",
         "resolution/@units":"eV"
       },
-      "source_TYPE[source_probe]":{
+      "sourceTYPE[source_xray]":{
         "type":"@eln",
         "name": "@xps_token:source/source_label",
         "probe":"photon",
@@ -44,9 +44,9 @@
           "identifier":"@eln",
           "model":"@eln"
         },
-        "associated_beam":"@link:/entry/instrument/beam_probe"
+        "associated_beam":"/entry/instrument/beam_xray"
       },
-      "beam_TYPE[beam_probe]":{
+      "beamTYPE[beam_xray]":{
         "distance":"@eln",
         "distance/@units":"@eln",
         "incident_energy":"@xps_token:beam/excitation_energy",
@@ -56,7 +56,7 @@
         "incident_polarization":"None",
         "incident_polarization/@units":"None",
         "extent":"None",
-        "associated_source":"@link:/entry/instrument/source_probe"
+        "associated_source":"/entry/instrument/source_xray"
       },
       "ELECTRONANALYSER[electronanalyser]":{
         "@default": "detector0",
@@ -238,7 +238,7 @@
         "cas_number":"@eln",
         "molecular_formula_hill":"@eln"
       },
-      "sample_history":{
+      "history":{
         "sample_preparation":{
           "start_time":"@eln",
           "end_time":"@eln",

diff --git a/pynxtools_xps/config/config_txt_vamas_export.json b/pynxtools_xps/config/config_txt_vamas_export.json
@@ -36,7 +36,7 @@
         "resolution":"@xps_token:data/step_size",
         "resolution/@units":"@eln"
       },
-      "source_TYPE[source_probe]":{
+      "sourceTYPE[source_xray]":{
         "type":"@eln",
         "name":"@eln",
         "probe":"photon",
@@ -45,9 +45,9 @@
           "identifier":"@eln",
           "model":"@eln"
         },
-        "associated_beam":"@link:/entry/instrument/beam_probe"
+        "associated_beam":"/entry/instrument/beam_xray"
       },
-      "beam_TYPE[beam_probe]":{
+      "beamTYPE[beam_xray]":{
         "distance":"@eln",
         "distance/@units":"@eln",
         "incident_energy":"@xps_token:beam/excitation_energy",
@@ -57,7 +57,7 @@
         "incident_polarization":"None",
         "incident_polarization/@units":"None",
         "extent":"None",
-        "associated_source":"@link:/entry/instrument/source_probe"
+        "associated_source":"/entry/instrument/source_xray"
       },
       "ELECTRONANALYSER[electronanalyser]":{
         "@default": "detector0",
@@ -209,7 +209,7 @@
         "cas_number":"@eln",
         "molecular_formula_hill":"@eln"
       },
-      "sample_history":{
+      "history":{
         "sample_preparation":{
           "start_time":"@eln",
           "end_time":"@eln",

diff --git a/pynxtools_xps/config/config_vms.json b/pynxtools_xps/config/config_vms.json
@@ -36,7 +36,7 @@
        "resolution":"@xps_token:data/step_size",
        "resolution/@units":"eV"
      },
-     "source_TYPE[source_probe]":{
+     "sourceTYPE[source_xray]":{
        "type":"@eln",
        "name":"@xps_token:source/source_label",
        "probe":"photon",
@@ -45,11 +45,21 @@
          "identifier":"@eln",
          "model":"@eln"
        },
-       "associated_beam":"@link:/entry/instrument/beam_probe",
-       "source_analyzer_angle":"source_analyzer_angle",
-       "source_analyzer_angle/@units":"degree"
+       "associated_beam":"/entry/instrument/beam_xray",
+       "depends_on": "/entry/instrument/source_xray/transformations/source_analyzer_angle",
+       "TRANSFORMATIONS[transformations]": {
+         "AXISNAME[source_analyzer_angle]/@depends_on":".",
+         "AXISNAME[source_analyzer_angle]":"@xps_token:source/source_analyzer_angle",
+         "AXISNAME[source_analyzer_angle]/@transformation_type": "rotation",
+         "AXISNAME[source_analyzer_angle]/@units":"degree",
+         "AXISNAME[source_analyzer_angle]/@vector": [
+           0,
+           0,
+           1
+         ]
+       }
      },
-     "beam_TYPE[beam_probe]":{
+     "beamTYPE[beam_xray]":{
        "distance":"@eln",
        "distance/@units":"@eln",
        "incident_energy":"@xps_token:beam/excitation_energy",
@@ -59,7 +69,7 @@
        "incident_polarization":"None",
        "incident_polarization/@units":"None",
        "extent":"None",
-       "associated_source":"@link:/entry/instrument/source_probe"
+       "associated_source":"/entry/instrument/source_xray"
      },
      "ELECTRONANALYSER[electronanalyser]":{
        "@default":"detector0",
@@ -242,7 +252,7 @@
        "cas_number":"@eln",
        "molecular_formula_hill":"@eln"
      },
-     "sample_history":{
+     "history":{
        "sample_preparation":{
          "start_time":"@eln",
          "end_time":"@eln",