Merge pull request #27 from FAIRmat-NFDI/20-read-in-scienta-igor-data…

…-fix-scienta-txt-reader

Fix scienta txt reader

.gitignore

@@ -201,6 +201,7 @@ cython_debug/
 *.txt
 !requirements.txt
 !dev-requirements.txt
-!mkdocs-requirements.txt
+!Cu-*.txt
+!Ag_*.txt
 build/
 .python-version

examples/regenerate_examples.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+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
+  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
+  cd ..
+  echo
+}
+
+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
+  cd ..
+  echo
+}
+
+function update_sle_examples {
+  echo "Update SPECS examples"
+  cd sle/
+  echo "Update .sle example"
+  dataconverter --params-file params.yaml
+  cd ..
+  echo
+}
+
+update_phi_examples
+update_scienta_examples
+update_sle_examples

examples/scienta/README.md

@@ -0,0 +1,14 @@
+# Example for .txt data exported from Scienta spectrometer
+
+This is an example for parsing the .txt data export of Scienta Omicron
+[Scienta Omicron](https://www.scientaomicron.com/en/). We thank Dr. Alexei Nefedov from [KIT](https://www.ifg.kit.edu/21_1296.php) for providing this example data set.
+
+The example conversion can be run with the following command.
+
+```console
+user@box:~$ dataconverter Cu-HHTP_*.txt eln_data.yaml --reader xps --nxdl NXmpes --output Cu-HHTP.nxs
+```
+
+## Contact person in FAIRmat for this example
+Lukas Pielsticker
+

examples/scienta/eln_data.yaml

@@ -0,0 +1,173 @@
+title: Cu-HTTP
+definition:
+  value: NXmpes
+  version: "1.0"
+method: XPS
+start_time: 2022-04-08T11:47:02.0200Z
+experiment_institution: Helmholtz-Zentrum Berlin
+experiment_facility: BESSY II
+experiment_laboratory: XPS beamline
+user:
+  name: Alexei Nefedov
+  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
+    resolution:
+      value: 0.1
+      unit: eV
+  source_xray:
+    type: Synchrotron X-ray Source
+    name: BESSY II
+    probe: x-ray
+    device_information:
+      vendor: Helmholtz-Zentrum Berlin
+      model: BESSY II
+      identifier: null
+    current:
+      value: 298
+      unit: mA
+  beam_xray:
+    distance:
+      unit: mm
+      value: 0.0
+    current:
+      value: 30
+      unit: "pA"
+  analyser:
+    name: Hemispherical Analyser dummy
+    description: hemispherical
+    device_information:
+      vendor: Scienta Omicron
+      model: null
+      identifier: null
+    collectioncolumn:
+      device_information:
+        vendor: Scienta Omicron
+        model: null
+        identifier: null
+      scheme: angular dispersive
+    energydispersion:
+      device_information:
+        vendor: Scienta Omicron
+        model: null
+        identifier: null
+      scheme: hemispherical
+      pass_energy:
+        unit: eV
+      APERTURE[entrance_slit]:
+        description: Analyser slit Nr. 3
+        shape: curved slit
+        size:
+          value: 0.4
+          unit: mm
+    detector:
+      amplifier_type: channeltron
+      detector_type: Multi-anode
+  manipulator:
+    device_information:
+      vendor: Scienta Omicron
+    temperature_sensor:
+      name: type K thermocouple
+      measurement: temperature
+      attached_to: sample
+      type: type K thermocouple
+      value:
+        value: 298.0
+        unit: K
+    sample_heater:
+      name: Coherent Compact Evolution IR Diode LASER (DILAS)
+      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
+    POSITIONER[positioner_x]:
+      value:
+        value: 15.5
+        unit: cm
+    POSITIONER[positioner_y]:
+      value:
+        value: 11
+        unit: cm
+    POSITIONER[positioner_z]:
+      value:
+        value: 36
+        unit: cm
+    POSITIONER[positioner_phi]:
+      value:
+        value: 45
+        unit: degree
+  pressure_gauge:
+    name: Atmion
+    measurement: pressure
+    type: hot-filament ionization gauge
+    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
+  description: Cu-HHTP/Glass on standard sample holder
+  situation: vacuum
+  sample_history:
+    sample_preparation:
+      start_time: 2022-04-08T11:25:00.200Z
+      end_time: 2022-04-08T11:45:00.200Z
+      description: sputter cleaned with Ar ions for 20 min
+      method: Ar sputtering
+    PHYSICAL_PROCESS[sample_loading]:
+      start_time: 2023-03-08T10:49:12+01:00
+      end_time: 2023-03-08T10:52:47+01:00
+      description: loaded in the endstation and transferred to analysis chamber
+      method: vacuum transfer

pynxtools_xps/config/config_phi.json

@@ -408,7 +408,7 @@
         "raw_data":{
           "@signal":"raw",
           "raw":"@detector_data:cycles/Cycle_",
-          "raw/@units":"@xps_token:detector/raw_data/raw/@units"
+          "raw/@units":"counts"
         }
       }
     },
@@ -528,7 +528,8 @@
       "binding_energy":"@xps_token:process/energy_reference_energy",
       "binding_energy/@units":"@xps_token:process/energy_reference_energy/@units",
       "offset":"None",
-      "calibrated_axis":"@data:energy"
+      "calibrated_axis":"@data:energy",
+      "calibrated_axis/@units":"@xps_token:data/energy/@units"
     },
     "transmission_correction":{
       "intensity_calibration_coefficients":"@xps_token:data/intensity_calibration_coefficients"