Merge pull request #74 from FAIRmat-NFDI/use-multiformat-reader

Use multiformat reader

.github/workflows/pylint.yml

@@ -25,10 +25,10 @@ jobs:
       - name: Install dev requirements
         run: |
           uv pip install -r dev-requirements.txt
-      - name: ruff
+      - name: ruff check
         run: |
-          ruff src/pynxtools_xps tests
-      - name: ruff formatting
+          ruff check src/pynxtools_xps tests
+      - name: ruff format
         run: |
           ruff format --check src/pynxtools_xps tests
       - name: mypy

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.8
+    rev: v0.5.5
     hooks:
       # Run the linter.
       - id: ruff

dev-requirements.txt

@@ -156,7 +156,7 @@ pymdown-extensions==10.8.1
     # via
     #   pynxtools-xps (pyproject.toml)
     #   mkdocs-material
-pynxtools==0.3.2
+pynxtools==0.6.0
     # via pynxtools-xps (pyproject.toml)
 pyparsing==3.1.1
     # via matplotlib
@@ -192,14 +192,12 @@ regex==2024.4.28
     # via mkdocs-material
 requests==2.31.0
     # via mkdocs-material
-ruff==0.4.8
+ruff==0.5.5
     # via pynxtools-xps (pyproject.toml)
 scipy==1.9.1
     # via ase
 setuptools==70.0.0
-    # via
-    #   pynxtools-xps (pyproject.toml)
-    #   nodeenv
+    # via nodeenv
 six==1.16.0
     # via
     #   anytree

examples/coordinate_system/config_vms_cs_fixed.json

@@ -1,38 +1,38 @@
 {
-  "/ENTRY[entry]/geometries":{
+  "/ENTRY/geometries":{
     "COORDINATE_SYSTEM[xps_coordinate_system]":{
       "origin":"sample stage",
       "handedness":"left_handed",
       "z_direction":"sample stage normal",
-      "depends_on": "/entry/geometries/xps_coordinate_system/coordinate_transformations/z_rotation",
-      "x": [-1, 0 , 0],
-      "y": [0, 1, 0],
-      "z": [0, 0 , 1],
-      "TRANSFORMATIONS[coordinate_transformations]": {
+      "depends_on":"/entry/geometries/xps_coordinate_system/coordinate_transformations/z_rotation",
+      "x":[-1, 0 , 0],
+      "y":[0, 1, 0],
+      "z":[0, 0 , 1],
+      "TRANSFORMATIONS[coordinate_transformations]":{
         "AXISNAME[z_rotation]":150.0,
         "AXISNAME[z_rotation]/@units":"degree",
-        "AXISNAME[z_rotation]/@transformation_type": "rotation",
-        "AXISNAME[z_rotation]/@vector": [0, 0, 1],
+        "AXISNAME[z_rotation]/@transformation_type":"rotation",
+        "AXISNAME[z_rotation]/@vector":[0, 0, 1],
         "AXISNAME[z_rotation]/@depends_on":"y_flip",
 
         "AXISNAME[y_flip]":180.0,
         "AXISNAME[y_flip]/@units":"degree",
-        "AXISNAME[y_flip]/@transformation_type": "rotation",
-        "AXISNAME[y_flip]/@vector": [0, 1, 0],
+        "AXISNAME[y_flip]/@transformation_type":"rotation",
+        "AXISNAME[y_flip]/@vector":[0, 1, 0],
         "AXISNAME[y_flip]/@depends_on":"y_rotation",
 
         "AXISNAME[y_rotation]":54.5,
         "AXISNAME[y_rotation]/@units":"degree",
-        "AXISNAME[y_rotation]/@transformation_type": "rotation",
-        "AXISNAME[y_rotation]/@vector": [0, -1, 0],
+        "AXISNAME[y_rotation]/@transformation_type":"rotation",
+        "AXISNAME[y_rotation]/@vector":[0, -1, 0],
         "AXISNAME[y_rotation]/@depends_on":"."
       }
     }
   },
-  "/ENTRY[entry]/INSTRUMENT[instrument]":{
+  "/ENTRY/INSTRUMENT[instrument]":{
     "beamTYPE[beam_xray]":{
-      "depends_on": "/entry/instrument/beam_xray/transformations/beam_polar_angle_of_incidence",
-      "TRANSFORMATIONS[transformations]": {
+      "depends_on":"/entry/instrument/beam_xray/transformations/beam_polar_angle_of_incidence",
+      "TRANSFORMATIONS[transformations]":{
         "AXISNAME[beam_polar_angle_of_incidence]":54.5,
         "AXISNAME[beam_polar_angle_of_incidence]/@units":"degree",
         "AXISNAME[beam_polar_angle_of_incidence]/@transformation_type":"rotation",
@@ -42,13 +42,13 @@
         "AXISNAME[beam_azimuth_angle]":150.0,
         "AXISNAME[beam_azimuth_angle]/@units":"degree",
         "AXISNAME[beam_azimuth_angle]/@transformation_type":"rotation",
-        "AXISNAME[beam_azimuth_angle]/@vector": [0, 0, -1],
+        "AXISNAME[beam_azimuth_angle]/@vector":[0, 0, -1],
         "AXISNAME[beam_azimuth_angle]/@depends_on":"/entry/geometries/xps_coordinate_system/coordinate_transformations/z_rotation"
       }
-    },         
+    },
     "ELECTRONANALYSER[electronanalyser]":{
       "depends_on":"/entry/instrument/electronanalyser/transformations/analyser_take_off_polar_angle",
-      "TRANSFORMATIONS[transformations]": {
+      "TRANSFORMATIONS[transformations]":{
         "AXISNAME[analyser_take_off_polar_angle]":0.0,
         "AXISNAME[analyser_take_off_polar_angle]/@units":"degree",
         "AXISNAME[analyser_take_off_polar_angle]/@transformation_type":"rotation",
@@ -62,13 +62,13 @@
         "AXISNAME[analyser_take_off_azimuth_angle]/@depends_on":"/entry/geometries/xps_coordinate_system/coordinate_transformations/z_rotation"
       }
     }
-  }, 
-  "/ENTRY[entry]/SAMPLE[sample]":{
+  },
+  "/ENTRY/SAMPLE[sample]":{
     "depends_on":"/entry/sample/transformations/sample_rotation_angle",
-    "TRANSFORMATIONS[transformations]": {
+    "TRANSFORMATIONS[transformations]":{
       "AXISNAME[sample_rotation_angle]":50.0,
       "AXISNAME[sample_rotation_angle]/@units":"degree",
-      "AXISNAME[sample_rotation_angle]/@transformation_type": "rotation",
+      "AXISNAME[sample_rotation_angle]/@transformation_type":"rotation",
       "AXISNAME[sample_rotation_angle]/@vector":[0, 0, -1],
       "AXISNAME[sample_rotation_angle]/@depends_on":"sample_normal_tilt_azimuth_angle",
 

examples/phi/eln_data_phi.yaml

@@ -5,8 +5,8 @@ experiment_laboratory: XPS Lab
 user:
   name: Sebastian Benz
   affiliation: Justus-Liebig-Universität Gießen, AG Spektroskopie und Optik
-  orcid: null
   email: null
+  IDENTIFIER[orcid]: null
 instrument:
   energy_resolution:
     type: calibrated
@@ -15,6 +15,7 @@ instrument:
       unit: eV
   source_xray:
     type: Fixed Tube X-ray
+    name: VersaProbe 4 X-ray Source
     probe: photon
     device_information:
       vendor: PHI Electronics
@@ -52,7 +53,7 @@ instrument:
         identifier: null
     energydispersion:
       scheme: hemispherical
-      diameter:
+      radius:
         unit: mm
         value: 150
       device_information:
@@ -144,7 +145,6 @@ instrument:
 sample:
   name: SnO2 10nnm
   sample_id: 1
-  atom_types: Sn, O
   physical_form: pellet
   situation: vacuum
   substance:
@@ -164,4 +164,4 @@ sample:
       start_time: 2022-01-22T12:30:00.200Z
       end_time: 2022-01-22T12:31:00.200Z
       description: loaded into the VersaProbe 4
-      method: vacuum transfer
+      method: vacuum transfer

examples/scienta/ibw/eln_data_scienta_ibw.yaml

@@ -9,7 +9,6 @@ user:
   email: [email protected]
   affiliation: Karlsruhe Institute of Technology (KIT), Institut für Funktionelle Grenzflächen
   address: KIT
-  orcid: 0000-0001-9361-8333
 instrument:
   energy_resolution:
     type: calibrated
@@ -140,25 +139,21 @@ instrument:
     value:
       value: 0.000000001
       unit: mbar
-    value_log:
-      value:
-        value: null
-        unit: null
   flood_gun:
     name: FG 22/35
     physical_quantity: current
     type: low energy electron source
     current:
       value: 0.0
       unit: A
-    current_log:
-      value:
-        value: null
-        unit: null
 sample:
-  chemical_formula: Cu
+  sample_id: 1
   description: Cu-HHTP/Glass on standard sample holder
+  physical_form: pellet
   situation: vacuum
+  substance:
+    name: Cu
+    molecular_formula_hill: Cu
   history:
     sample_preparation:
       start_time: 2022-04-08T11:25:00.200Z

examples/scienta/txt/eln_data_scienta_txt.yaml

@@ -9,7 +9,6 @@ user:
   email: [email protected]
   affiliation: Karlsruhe Institute of Technology (KIT), Institut für Funktionelle Grenzflächen
   address: KIT
-  orcid: 0000-0001-9361-8333
 instrument:
   energy_resolution:
     type: calibrated
@@ -140,25 +139,21 @@ instrument:
     value:
       value: 0.000000001
       unit: mbar
-    value_log:
-      value:
-        value: null
-        unit: null
   flood_gun:
     name: FG 22/35
     physical_quantity: current
     type: low energy electron source
     current:
       value: 0.0
       unit: A
-    current_log:
-      value:
-        value: null
-        unit: null
 sample:
-  chemical_formula: Cu
+  sample_id: 1
   description: Cu-HHTP/Glass on standard sample holder
+  physical_form: pellet
   situation: vacuum
+  substance:
+    name: Cu
+    molecular_formula_hill: Cu
   history:
     sample_preparation:
       start_time: 2022-04-08T11:25:00.200Z

examples/specs/sle/eln_data_sle.yaml

@@ -9,7 +9,7 @@ program_name: SpecsLabProdigy
 user:
   name: Lukas Pielsticker
   affiliation: Max Planck Institute for Chemical Energy Conversion
-  address: Lukas Pielsticker
+  address: Muelheim an der Ruhr
   email: [email protected]
   orcid:
     service: orcid
@@ -49,7 +49,7 @@ instrument:
         identifier: null
     energydispersion:
       scheme: hemispherical
-      diameter:
+      radius:
         unit: mm
         value: 150
       device_information:
@@ -141,7 +141,6 @@ instrument:
 sample:
   name: Polycristalline Au foil
   sample_id: S718
-  atom_types: Au
   physical_form: foil
   situation: vacuum
   substance:

examples/specs/xml/eln_data_xml.yaml

@@ -45,7 +45,7 @@ instrument:
       scheme: hemispherical
       entrance_slit: unknown
       energy_scan_mode: fixed_analyser_transmission
-      diameter:
+      radius:
         unit: mm
         value: 150
       device_information:
@@ -135,7 +135,7 @@ sample:
   substance:
     molecular_formula_hill: (C42H62S4)n
   situation: vacuum
-  sample_history:
+  history:
     sample_preparation:
       start_time: 2022-04-08T11:02:38.0200Z
       end_time: 2022-04-08T11:06:42.200Z

examples/specs/xy/eln_data_xy.yaml

@@ -1,6 +1,4 @@
 title: EX439_S718_Au in 25 mbar O2
-start_time: 2022-04-08T11:47:02.0200Z
-end_time: 2022-04-08T14:52:26.0400Z
 entry_identifier: EX439
 experiment_institution: Max Planck Institute for Chemical Energy Conversion
 experiment_facility: Surface and Interface Analysis Group
@@ -37,6 +35,7 @@ instrument:
       unit: mm
   analyser:
     description: hemispherical
+    name: PHOIBOS 150 NAP-XPS analyser
     device_information:
       vendor: SPECS GmbH
       model: PHOIBOS 150 NAP
@@ -49,7 +48,7 @@ instrument:
         identifier: null
     energydispersion:
       scheme: hemispherical
-      diameter:
+      radius:
         unit: mm
         value: 150
       device_information:
@@ -141,7 +140,6 @@ instrument:
 sample:
   name: Polycristalline Au foil
   sample_id: S718
-  atom_types: Au
   physical_form: foil
   situation: vacuum
   substance:

examples/vms/eln_data_vms.yaml

@@ -1,10 +1,9 @@
 title: XPS Experiment
-start_time: 2022-04-08T11:47:02.0200Z
-end_time: 2022-04-08T12:32:06.0200Z
 program_name: SpecsLab 2
 user:
   name: Lukas Pielsticker
   affiliation: Max Planck Institute for Chemical Energy Conversion
+  address: Muelheim an der Ruhr
   email: [email protected]
 instrument:
   device_information:
@@ -36,14 +35,15 @@ instrument:
       identifier: null
     collectioncolumn:
       scheme: angular dispersive
+      lens_mode: ARM22
       device_information:
         vendor: null
         model: null
         identifier: null
     energydispersion:
       scheme: hemispherical
       energy_scan_mode: fixed_analyser_transmission
-      diameter:
+      radius:
         unit: mm
         value: 150
       device_information:
@@ -130,7 +130,9 @@ instrument:
         unit: null
 sample:
   description: CoO powder
+  physical_form: powder
   substance:
+    name: CoO
     molecular_formula_hill: CoO
   situation: vacuum
   history: