From a946d35212c41da107b27809fb54b02c0dcfd49d Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Wed, 31 Jan 2024 16:24:38 +0100 Subject: [PATCH] initial commit for phi config file --- .../readers/xps/config/config_phi.json | 278 ++++++++++++++++++ .../readers/xps/phi/spe_pro_phi.py | 4 +- 2 files changed, 280 insertions(+), 2 deletions(-) create mode 100644 pynxtools/dataconverter/readers/xps/config/config_phi.json diff --git a/pynxtools/dataconverter/readers/xps/config/config_phi.json b/pynxtools/dataconverter/readers/xps/config/config_phi.json new file mode 100644 index 000000000..0bb6813ac --- /dev/null +++ b/pynxtools/dataconverter/readers/xps/config/config_phi.json @@ -0,0 +1,278 @@ +{ + "/@default":"entry", + "/ENTRY[entry]":{ + "@default":"data", + "definition":"@eln", + "definition/@version":"@eln", + "title":"@eln", + "start_time":"@eln", + "end_time":"@eln", + "experiment_institution":"@eln", + "experiment_facility":"@eln", + "experiment_laboratory":"@eln", + "entry_identifier":"@eln", + "duration":"None", + "duration/@units":"s", + "method":"@xps_token:region/analysis_method", + "program_name":"@eln" + }, + "/ENTRY[entry]/USER[user]":{ + "name":"@xps_token:user/user_name", + "affiliation":"@eln", + "address":"@eln", + "orcid":"@eln", + "email":"@eln" + }, + "/ENTRY[entry]/INSTRUMENT[instrument]":{ + "device_information":{ + "vendor":"@xps_token:user/vendor", + "identifier":"@eln", + "model":"@xps_token:user/instrument_model" + }, + "energy_resolution":{ + "physical_quantity":"energy", + "type":"@eln", + "resolution":"@eln", + "resolution/@units":"@eln" + }, + "source_TYPE[source_probe]":{ + "type":"@eln", + "name":"@xps_token:source/name", + "probe":"@eln", + "device_information":{ + "vendor":"@eln", + "identifier":"@eln", + "model":"@eln" + }, + "associated_beam":"@link:/entry/instrument/beam_probe" + }, + "beam_TYPE[beam_probe]":{ + "distance":"@eln", + "distance/@units":"@eln", + "incident_energy":"@xps_token:beam/xray_energy", + "incident_energy/@units":"@xps_token:beam/xray_energy/@units", + "incident_energy_spread":"None", + "incident_energy_spread/@units":"None", + "incident_polarization":"None", + "incident_polarization/@units":"None", + "extent":"None", + "associated_source":"@link:/entry/instrument/source_probe" + }, + "ELECTRONANALYSER[electronanalyser]":{ + "@default": "detector0", + "name":"@xps_token:analyser/name", + "description":"@eln", + "voltage_energy_range":"@xps_token:analyser/voltage_energy_range", + "voltage_energy_range/@units":"@xps_token:analyser/voltage_energy_range/@units", + "work_function":"@xps_token:analyser/work_function", + "work_function/@units":"@xps_token:analyser/work_function/@units", + "fast_axes":"None", + "slow_axes":"energy", + "device_information":{ + "vendor":"@eln", + "model":"@eln", + "identifier":"@eln" + }, + "energy_resolution":{ + "physical_quantity":"energy", + "type":"estimated", + "resolution":"@xps_token:data/step_size", + "resolution/@units":"@xps_token:data/step_size/@units" + }, + "transmission_function":{ + "@default":"relative_intensity", + "@signal":"relative_intensity", + "@axes":["kinetic_energy"], + "kinetic_energy":"@xps_token:transmission_function/kinetic_energy", + "kinetic_energy/@units":"@xps_token:transmission_function/kinetic_energy/@units", + "relative_intensity":"@xps_token:collectioncolumn/transmission_function/relative_intensity" + }, + "COLLECTIONCOLUMN[collectioncolumn]":{ + "scheme":"@eln", + "lens_mode":"@xps_token:collectioncolumn/lens_mode", + "projection":"None", + "angular_acceptance":"None", + "spatial_acceptance":"None", + "field_aperture":"None", + "contrast_aperture":"None", + "iris":{ + "size":"@xps_token:collectioncolumn/iris_diameter", + "size/@units":"@xps_token:collectioncolumn/iris_diameter/@units" + }, + "device_information":{ + "vendor":"@eln", + "model":"@eln", + "identifier":"@eln" + }, + }, + "ENERGYDISPERSION[energydispersion]":{ + "scheme":"@eln", + "pass_energy":"@xps_token:energydispersion/pass_energy", + "pass_energy/@units":"@xps_token:energydispersion/pass_energy/@units", + "energy_scan_mode":"@xps_token:energydispersion/scan_mode", + "entrance_slit/description":"@xps_token:energydispersion/entrance_slit", + "exit_slit/description":"@xps_token:energydispersion/exit_slit", + "device_information":{ + "vendor":"@eln", + "model":"@eln", + "identifier":"@eln" + }, + "diameter":"@eln", + "diameter/@units":"@eln" + }, + "DETECTOR[detector]":{ + "@default":"raw_data", + "amplifier_type":"@eln", + "detector_type":"@eln", + "detector_voltage":"@xps_token:detector/detector_voltage", + "detector_voltage/@units":"@xps_token:detector/detector_voltage/@units", + "amplifier_bias":"@xps_token:detector/bias_voltage_electrons", + "amplifier_bias/@units":"@xps_token:detector/bias_voltage_electrons/@units", + "count_time":"@xps_token:detector/dwell_time", + "count_time/@units":"@xps_token:detector/dwell_time/@units", + "device_information":{ + "vendor":"@eln", + "model":"@eln", + "identifier":"@eln" + }, + "raw_data":{ + "@signal":"raw", + "@default":"raw", + "raw":"@detector_data:cycles/Cycle_", + "raw/@units":"@xps_token:detector/raw_data/raw/@units" + } + } + }, + "MANIPULATOR[manipulator]":{ + "device_information":{ + "vendor":"@eln", + "model":"@eln", + "identifier":"@eln" + }, + "temperature_sensor":{ + "name":"@eln", + "measurement":"@eln", + "type":"@eln", + "attached_to":"@eln", + "value":"@eln" + }, + "sample_heater":{ + "name":"@eln", + "physical_quantity":"@eln", + "type":"@eln", + "heater_power":"@eln", + "PID[pid]/setpoint":"@eln" + }, + "cryostat":{ + "name":"None", + "physical_quantity":"None", + "type":"None", + "PID[pid]/setpoint":"None" + }, + "drain_current_amperemeter":{ + "name":"@eln", + "measurement":"@eln", + "type":"@eln", + "value":"@eln" + }, + "sample_bias_voltmeter":{ + "name":"@eln", + "measurement":"@eln", + "type":"@eln", + "value":"@eln" + }, + "sample_bias_potentiostat":{ + "name":"@eln", + "physical_quantity":"@eln", + "type":"@eln", + "PID[pid]/setpoint":"@eln" + } + }, + "pressure_gauge":{ + "name":"@eln", + "measurement":"@eln", + "type":"@eln", + "value":"@eln", + "value_log/value":"@eln" + }, + "flood_gun":{ + "name":"@eln", + "physical_quantity":"@eln", + "type":"@eln", + "current":"@eln", + "current_log/value":"@eln" + } + }, + "/ENTRY[entry]/PROCESS[process]":{ + "energy_calibration":{ + "calibrated_axis":"@xps_token:process/energy_calibration/energy", + "calibrated_axis/@units":"@xps_token:process/energy_calibration/energy/@units", + }, + "energy_referencing":{ + "level":"None", + "reference_peak":"None", + "binding_energy":"None", + "offset":"None", + "calibrated_axis":"None" + }, + "transmission_correction":"None" + } + }, + "/ENTRY[entry]/SAMPLE[sample]":{ + "name":"@eln", + "sample_id":"@eln", + "atom_types":"@eln", + "physical_form":"@eln", + "situation":"@eln", + "SUBSTANCE[substance]":{ + "name":"@eln", + "molecular_mass":"@eln", + "cas_number":"@eln", + "molecular_formula_hill":"@eln" + }, + "sample_history":{ + "sample_preparation":{ + "start_time":"@eln", + "end_time":"@eln", + "description":"@eln", + "method":"@eln" + }, + "PHYSICAL_PROCESS[sample_loading]":{ + "start_time":"@eln", + "end_time":"@eln", + "description":"@eln", + "method":"@eln" + } + }, + "temperature":{ + "temperature_sensor": "@link:/entry/instrument/manipulator/temperature_sensor", + "sample_heater":"@link:/entry/instrument/manipulator/sample_heater", + "cryostat":"None" + }, + "gas_pressure":{ + "pressure_gauge":"@link:/entry/instrument/pressure_gauge" + }, + "bias":{ + "potentiostat":"@link:/entry/instrument/manipulator/sample_bias_potentiostat", + "voltmeter":"@link:/entry/instrument/manipulator/sample_bias_voltmeter" + }, + "drain_current":{ + "amperemeter":"@link:/entry/instrument/manipulator/drain_current_amperemeter" + }, + "flood_gun_current":{ + "flood_gun":"@link:/entry/instrument/flood_gun" + } + }, + "/ENTRY[entry]/data":{ + "@signal":"data", + "@default":"data", + "@axes":["energy"], + "data":"@data:cycle", + "data/@units":"@xps_token:data/intensity/@units", + "energy":"@link:/entry/process/energy_calibration/calibrated_axis", + "energy/@type":"@xps_token:data/energy/@type", + "energy/@units":"@xps_token:data/energy/@units", + "@energy_indices":"None", + "@energy_depends":"None" + } +} \ No newline at end of file diff --git a/pynxtools/dataconverter/readers/xps/phi/spe_pro_phi.py b/pynxtools/dataconverter/readers/xps/phi/spe_pro_phi.py index d59a830d1..46dfa55b3 100644 --- a/pynxtools/dataconverter/readers/xps/phi/spe_pro_phi.py +++ b/pynxtools/dataconverter/readers/xps/phi/spe_pro_phi.py @@ -119,8 +119,6 @@ def construct_data(self): "xray_emission_control", "xray_emission_current", "xray_emission_current/@units", - "xray_energy", - "xray_energy/@units", "xray_filament_current", "xray_filament_current/@units", "xray_high_power", @@ -150,6 +148,8 @@ def construct_data(self): "beam": [ "xray_beam_diameter", "xray_beam_diameter/@units", + "xray_energy", + "xray_energy/@units", ], "analyser": [ "analyser_retardation_gain",