Merge pull request #5 from FAIRmat-NFDI/1-add-xps-sub-reader-for-phi-…

…versaprobe-data

Add sub-reader for PHI Versaprobe data

README.md

@@ -31,6 +31,7 @@ within the field of X-ray photoelectron spectroscopy into a standardized represe
 
 ## Supported file formats
 The reader decides which parser to use based on the file extension of the files provided. For the main XPS files, the following file extensions are supported:
+- .spe, .pro: [Phi MultiPak](https://www.phi.com/surface-analysis-equipment/genesis.html#software:multi-pak-data-reduction-software/) files, propietary format of PHI Electronics
 - .sle: [SpecsLabProdigy](https://www.specs-group.com/nc/specs/products/detail/prodigy/) files, propietary format of SPECS GmbH (1 and v4)
 - .xml: SpecsLab 2files, XML format from SPECS GmbH (v1.6)
 - .vms: VAMAS files, ISO standard data transfer format ([ISO 14976](https://www.iso.org/standard/24269.html)), both in regular and irregular format

examples/phi/README.md

@@ -0,0 +1,18 @@
+# Example for data from Phi VersaProbe 4 instruments
+
+This is an example for [Phi MultiPak](https://www.phi.com/surface-analysis-equipment/genesis.html#software:multi-pak-data-reduction-software/) .spe (single spectra) and .pro (sputter profile / external parameter scan / ....) files, which is the propietary format of PHI Electronics used for their VersaProbe 4 instrumens. The Phi MultiPak software version that was used to measure this data is SS 3.3.3.2.1. 
+We thank Sebastian Benz and Dr. Joachim Sann from [Justus-Liebig-Universität Gießen](https://www.uni-giessen.de/de) for providing these example data sets.
+
+The example conversion can be run with the following commands.
+
+### For the .spe data (single spectrum):
+```console_
+user@box:~$ dataconverter SnO2_10nm.spe eln_data_phi.yaml --reader xps --nxdl NXmpes --output SnO2_10nm.spe.nxs
+```
+### For the .pro data (profiling):
+```console_
+user@box:~$ dataconverter SnO2_10nm_1.pro eln_data_phi.yaml --reader xps --nxdl NXmpes --output SnO2_10nm_1.pro.nxs
+```
+
+## Contact person in FAIRmat for this example
+Lukas Pielsticker

examples/phi/eln_data_phi.yaml

@@ -0,0 +1,162 @@
+definition:
+  value: NXmpes
+  version: 1.0
+title: SnO2_10nnm
+experiment_institution: Justus-Liebig-Universität Gießen
+experiment_facility: AG Spektroskopie und Optik
+experiment_laboratory: XPS Lab
+user:
+  name: Sebastian Benz
+  affiliation: Justus-Liebig-Universität Gießen, AG Spektroskopie und Optik
+  orcid: null
+  email: null
+instrument:
+  energy_resolution:
+    type: calibrated
+    resolution:
+      value: 0.1
+      unit: eV
+  source_xray:
+    type: Fixed Tube X-ray
+    probe: photon
+    device_information:
+      vendor: PHI Electronics
+      model: VersaProbe 4 X-ray Source
+      identifier: null
+  beam_xray:
+    distance:
+      value: 0.0
+      unit: mm
+  source_gas_cluster_ion_beam:
+    description: argon cluster GCIB
+  source_neutral_ion_gun:
+    description: monoatomic ion source
+  source_sputter_gun:
+    description: sputter gun
+  analyser:
+    description: hemispherical
+    device_information:
+      vendor: PHI Electronics
+      model: VersaProbe 4 Hemispherical Analyser
+      identifier: null
+    collectioncolumn:
+      scheme: angular dispersive
+      device_information:
+        vendor: PHI Electronics
+        model: VersaProbe 4
+        identifier: null
+    energydispersion:
+      scheme: hemispherical
+      diameter:
+        unit: mm
+        value: 150
+      device_information:
+        vendor: PHI Electronics
+        model: VersaProbe 4 Hemispherical Analyser
+        identifier: null
+    detector:
+      amplifier_type: channeltron
+      detector_type: Multi-anode
+      device_information:
+        vendor: PHI Electronics
+        model: 1D-DLD detector
+        identifier: null
+  manipulator:
+    device_information:
+      vendor: PHI Electronics
+      model: 5-axis manipulator
+      identifier: null
+    temperature_sensor:
+      name: type K thermocouple
+      measurement: temperature
+      attached_to: sample
+      type: type K thermocouple
+      value:
+        value: 298.0
+        unit: K
+    sample_heater:
+      name: Sample heater
+      physical_quantity: temperature
+      type: IR diode laser
+      heater_power:
+        value: 0.0
+        unit: W
+      pid:
+        setpoint:
+          value: 298.0
+          unit: K
+    cryostat:
+      name: null
+      physical_quantity: null
+      type: null
+      pid:
+        setpoint: null
+    drain_current_amperemeter:
+      name: Amperemeter 1.0
+      measurement: current
+      type: wire
+      value:
+        value: 0.1
+        unit: nA
+    sample_bias_voltmeter:
+      name: XPS sample voltmeter
+      measurement: voltage
+      attached_to: sample
+      type: oscilloscope
+      value:
+        value: 0.0
+        unit: V
+    sample_bias_potentiostat:
+      name: XPS sample potentiostat
+      physical_quantity: voltage
+      type: potentiostat
+      pid:
+        setpoint:
+          value: 0.0
+          unit: V
+  pressure_gauge:
+    name: Pirani
+    measurement: pressure
+    type: pirani gauge
+    value:
+      value: 0.000000001
+      unit: mbar
+    value_log:
+      value:
+        value: null
+        unit: null
+  flood_gun:
+    name: VersaProbe 4 flood gun
+    physical_quantity: current
+    type: low energy electron source
+    current:
+      value: 0.0
+      unit: A
+    current_log:
+      value:
+        value: null
+        unit: null
+sample:
+  name: SnO2 10nnm
+  sample_id: 1
+  atom_types: Sn, O
+  physical_form: pellet
+  situation: vacuum
+  substance:
+    name: SnO2
+    molecular_mass:
+      value: 150.71
+      unit: g/mol
+    cas_number: 18282-10-5
+    molecular_formula_hill: SnO2
+  sample_history:
+    sample_preparation:
+      start_time: 2022-01-22T12:48:00.200Z
+      end_time: 2022-01-22T13:18:00.200Z
+      description: sputter cleaned with Ar ions for 20 min
+      method: Ar sputtering
+    PHYSICAL_PROCESS[sample_loading]:
+      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