From 212fc9a0a409eec74ebf567fefb100a1a68dd105 Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Wed, 13 Mar 2024 11:23:55 +0100 Subject: [PATCH 1/2] remove default attributes from fields --- pynxtools_xps/config/config_sle_specs.json | 6 +- pynxtools_xps/config/config_specs_xy.json | 5 +- pynxtools_xps/config/config_txt_scienta.json | 561 +++++++++-------- .../config/config_txt_vamas_export.json | 515 ++++++++-------- pynxtools_xps/config/config_vms.json | 574 +++++++++--------- pynxtools_xps/config/config_xml_specs.json | 7 +- pynxtools_xps/config/template.json | 5 +- 7 files changed, 832 insertions(+), 841 deletions(-) diff --git a/pynxtools_xps/config/config_sle_specs.json b/pynxtools_xps/config/config_sle_specs.json index 06d406c1..48ad4fc2 100644 --- a/pynxtools_xps/config/config_sle_specs.json +++ b/pynxtools_xps/config/config_sle_specs.json @@ -1,5 +1,5 @@ { - "/@default":"entry", + "/@default":"None", "/ENTRY[entry]":{ "@default":"data", "definition":"@eln", @@ -24,6 +24,7 @@ "email":"@eln" }, "/ENTRY[entry]/INSTRUMENT[instrument]":{ + "@default": "electronanalyser", "device_information":{ "vendor":"@eln", "identifier":"@eln", @@ -84,7 +85,6 @@ "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", @@ -171,7 +171,6 @@ }, "raw_data":{ "@signal":"raw", - "@default":"raw", "raw":"@detector_data:cycles/Cycle_", "raw/@units":"@xps_token:detector/raw_data/raw/@units" } @@ -308,7 +307,6 @@ }, "/ENTRY[entry]/data":{ "@signal":"data", - "@default":"data", "@axes":["energy"], "data":"@data:cycle", "data/@units":"@xps_token:data/intensity/@units", diff --git a/pynxtools_xps/config/config_specs_xy.json b/pynxtools_xps/config/config_specs_xy.json index 814ed84d..07a270f3 100644 --- a/pynxtools_xps/config/config_specs_xy.json +++ b/pynxtools_xps/config/config_specs_xy.json @@ -23,6 +23,7 @@ "email":"@eln" }, "/ENTRY[entry]/INSTRUMENT[instrument]":{ + "@default": "electronanalyser", "device_information":{ "vendor":"None", "identifier":"None", @@ -58,7 +59,7 @@ "associated_source":"@link:/entry/instrument/source_probe" }, "ELECTRONANALYSER[electronanalyser]":{ - "@default": "None", + "@default": "detector0", "description":"@eln", "name": "@eln", "work_function":"@eln", @@ -122,7 +123,6 @@ }, "raw_data":{ "@signal":"None", - "@default":"raw", "raw":"@detector_data:cycles/Cycle_", "raw/@units":"counts" } @@ -273,7 +273,6 @@ }, "/ENTRY[entry]/data":{ "@signal":"data", - "@default":"data", "@axes":["energy"], "data":"@data:cycle", "data/@units":"@xps_token:data/y_units", diff --git a/pynxtools_xps/config/config_txt_scienta.json b/pynxtools_xps/config/config_txt_scienta.json index 7d7a63b4..a66cd96c 100644 --- a/pynxtools_xps/config/config_txt_scienta.json +++ b/pynxtools_xps/config/config_txt_scienta.json @@ -1,282 +1,281 @@ -{ - "/@default":"None", - "/ENTRY[entry]":{ - "@default":"data", - "definition":"@eln", - "definition/@version":"@eln", - "title":"@eln", - "start_time":"@xps_token:time_stamp", - "end_time":"@eln", - "method":"@xps_token:region/analysis_method", - "experiment_institution":"@eln", - "experiment_facility":"@eln", - "experiment_laboratory":"@eln", - "entry_identifier":"@eln", - "data_file": "@xps_token:file_info/data_file", - "sequence_file": "@xps_token:file_info/sequence_file" - }, - "/ENTRY[entry]/USER[user]":{ - "name":"@eln", - "affiliation":"@eln", - "address":"@eln", - "orcid":"@eln", - "email":"@eln", - "initials": "xps_token:user/user_initials" - }, - "/ENTRY[entry]/INSTRUMENT[instrument]":{ - "name": "@xps_token:instrument/instrument_name", - "device_information":{ - "vendor":"None", - "identifier":"None", - "model":"None" - }, - "energy_resolution":{ - "physical_quantity":"energy", - "type":"derived", - "resolution":"@xps_token:data/step_size", - "resolution/@units":"eV" - }, - "source_TYPE[source_probe]":{ - "type":"@", - "name": "@eln", - "probe":"photon", - "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/excitation_energy", - "incident_energy/@units":"eV", - "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": "None", - "description":"@eln", - "name": "@eln", - "work_function":"@eln", - "work_function/@units":"@eln", - "fast_axes":"None", - "slow_axes":"energy", - "device_information":{ - "vendor":"None", - "model":"None", - "identifier":"None" - }, - "energy_resolution":{ - "physical_quantity":"energy", - "type":"@xps_token:data/step_size", - "resolution":"eV" - }, - "transmission_function":"None", - "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":"None", - "device_information":{ - "vendor":"@eln", - "model":"@eln", - "identifier":"@eln" - } - }, - "ENERGYDISPERSION[energydispersion]":{ - "scheme":"@eln", - "pass_energy":"@xps_token:energydispersion/pass_energy", - "pass_energy/@units":"eV", - "energy_scan_mode":"@xps_token:energydispersion/acquisition_mode", - "entrance_slit":{ - "description":"@eln", - "shape":"@eln", - "size":"@eln", - "size/@units": "@eln" - }, - "exit_slit":"None", - "device_information":{ - "vendor":"@eln", - "model":"@eln", - "identifier":"@eln" - } - }, - "DETECTOR[detector]":{ - "@default":"raw_data", - "amplifier_type":"@eln", - "count_time": "@xps_token:region/dwell_time", - "count_time/@units": "@xps_token:region/dwell_time/time", - "detector_type":"@eln", - "device_information":{ - "vendor":"@eln", - "model":"@eln", - "identifier":"@eln" - }, - "raw_data":{ - "@signal":"None", - "@default":"raw", - "raw":"@detector_data:cycles/Cycle_", - "raw/@units":"counts" - } - } - }, - "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" - }, - "POSITIONER[positioner_x]":{ - "value": "@eln", - "value/@units": "@eln" - }, - "POSITIONER[positioner_y]":{ - "value": "@eln", - "value/@units": "@eln" - }, - "POSITIONER[positioner_z]":{ - "value": "@eln", - "value/@units": "@eln" - }, - "POSITIONER[positioner_phi]":{ - "value": "@eln", - "value/@units": "@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":"@data:energy", - "calibrated_axis/@units": "eV" - }, - "energy_referencing":{ - "level":"None", - "reference_peak":"None", - "binding_energy":"None", - "offset":"None", - "calibrated_axis":"None" - }, - "transmission_correction":{ - "transmission_function":{ - "@axes":"None", - "@signal":"None", - "kinetic_energy":"None", - "kinetic_energy/@units":"None", - "relative_intensity":"None" - } - } - }, - "/ENTRY[entry]/SAMPLE[sample]":{ - "name":"@xps_token:sample/sample_name", - "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" - } - }, - "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":"counts_per_second", - "energy":"@data:energy", - "energy/@units":"eV", - "energy/@type":"@xps_token:data/energy_type", - "@energy_indices":"None", - "@energy_depends":"None" - } +{ + "/@default":"None", + "/ENTRY[entry]":{ + "@default":"data", + "definition":"@eln", + "definition/@version":"@eln", + "title":"@eln", + "start_time":"@xps_token:time_stamp", + "end_time":"@eln", + "method":"@xps_token:region/analysis_method", + "experiment_institution":"@eln", + "experiment_facility":"@eln", + "experiment_laboratory":"@eln", + "entry_identifier":"@eln", + "data_file": "@xps_token:file_info/data_file", + "sequence_file": "@xps_token:file_info/sequence_file" + }, + "/ENTRY[entry]/USER[user]":{ + "name":"@eln", + "affiliation":"@eln", + "address":"@eln", + "orcid":"@eln", + "email":"@eln", + "initials": "xps_token:user/user_initials" + }, + "/ENTRY[entry]/INSTRUMENT[instrument]":{ + "@default": "electronanalyser", + "name": "@xps_token:instrument/instrument_name", + "device_information":{ + "vendor":"None", + "identifier":"None", + "model":"None" + }, + "energy_resolution":{ + "physical_quantity":"energy", + "type":"derived", + "resolution":"@xps_token:data/step_size", + "resolution/@units":"eV" + }, + "source_TYPE[source_probe]":{ + "type":"@", + "name": "@eln", + "probe":"photon", + "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/excitation_energy", + "incident_energy/@units":"eV", + "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", + "description":"@eln", + "name": "@eln", + "work_function":"@eln", + "work_function/@units":"@eln", + "fast_axes":"None", + "slow_axes":"energy", + "device_information":{ + "vendor":"None", + "model":"None", + "identifier":"None" + }, + "energy_resolution":{ + "physical_quantity":"energy", + "type":"@xps_token:data/step_size", + "resolution":"eV" + }, + "transmission_function":"None", + "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":"None", + "device_information":{ + "vendor":"@eln", + "model":"@eln", + "identifier":"@eln" + } + }, + "ENERGYDISPERSION[energydispersion]":{ + "scheme":"@eln", + "pass_energy":"@xps_token:energydispersion/pass_energy", + "pass_energy/@units":"eV", + "energy_scan_mode":"@xps_token:energydispersion/acquisition_mode", + "entrance_slit":{ + "description":"@eln", + "shape":"@eln", + "size":"@eln", + "size/@units": "@eln" + }, + "exit_slit":"None", + "device_information":{ + "vendor":"@eln", + "model":"@eln", + "identifier":"@eln" + } + }, + "DETECTOR[detector]":{ + "@default":"raw_data", + "amplifier_type":"@eln", + "count_time": "@xps_token:region/dwell_time", + "count_time/@units": "@xps_token:region/dwell_time/time", + "detector_type":"@eln", + "device_information":{ + "vendor":"@eln", + "model":"@eln", + "identifier":"@eln" + }, + "raw_data":{ + "@signal":"None", + "raw":"@detector_data:cycles/Cycle_", + "raw/@units":"counts" + } + } + }, + "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" + }, + "POSITIONER[positioner_x]":{ + "value": "@eln", + "value/@units": "@eln" + }, + "POSITIONER[positioner_y]":{ + "value": "@eln", + "value/@units": "@eln" + }, + "POSITIONER[positioner_z]":{ + "value": "@eln", + "value/@units": "@eln" + }, + "POSITIONER[positioner_phi]":{ + "value": "@eln", + "value/@units": "@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":"@data:energy", + "calibrated_axis/@units": "eV" + }, + "energy_referencing":{ + "level":"None", + "reference_peak":"None", + "binding_energy":"None", + "offset":"None", + "calibrated_axis":"None" + }, + "transmission_correction":{ + "transmission_function":{ + "@axes":"None", + "@signal":"None", + "kinetic_energy":"None", + "kinetic_energy/@units":"None", + "relative_intensity":"None" + } + } + }, + "/ENTRY[entry]/SAMPLE[sample]":{ + "name":"@xps_token:sample/sample_name", + "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" + } + }, + "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", + "@axes":["energy"], + "data":"@data:cycle", + "data/@units":"counts_per_second", + "energy":"@data:energy", + "energy/@units":"eV", + "energy/@type":"@xps_token:data/energy_type", + "@energy_indices":"None", + "@energy_depends":"None" + } } \ No newline at end of file diff --git a/pynxtools_xps/config/config_txt_vamas_export.json b/pynxtools_xps/config/config_txt_vamas_export.json index 6de354d5..cfe328e0 100644 --- a/pynxtools_xps/config/config_txt_vamas_export.json +++ b/pynxtools_xps/config/config_txt_vamas_export.json @@ -1,259 +1,258 @@ -{ - "/@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":"@eln", - "duration/@units":"@eln", - "method":"@eln", - "program_name":"@eln" - }, - "/ENTRY[entry]/USER[user]":{ - "name":"@eln", - "affiliation":"@eln", - "address":"@eln", - "orcid":"@eln", - "email":"@eln" - }, - "/ENTRY[entry]/INSTRUMENT[instrument]":{ - "device_information":{ - "vendor":"@eln", - "identifier":"@eln", - "model":"@eln" - }, - "energy_resolution":{ - "physical_quantity":"energy", - "type":"@eln", - "resolution":"@xps_token:data/step_size", - "resolution/@units":"@eln" - }, - "source_TYPE[source_probe]":{ - "type":"@eln", - "name":"@eln", - "probe":"photon", - "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/excitation_energy", - "incident_energy/@units":"@xps_token:beam/excitation_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": "None", - "name":"@eln", - "description":"@eln", - "work_function":"@eln", - "work_function/@units":"@eln", - "fast_axes":"None", - "slow_axes":"energy", - "device_information":{ - "vendor":"@eln", - "model":"@eln", - "identifier":"@eln" - }, - "energy_resolution":{ - "physical_quantity":"energy", - "type":"@eln", - "resolution":"@xps_token:data/step_size", - "resolution/@units":"@eln" - }, - "transmission_function":"None", - "COLLECTIONCOLUMN[collectioncolumn]":{ - "scheme":"@eln", - "lens_mode":"@eln", - "projection":"None", - "angular_acceptance":"None", - "spatial_acceptance":"None", - "field_aperture":"None", - "contrast_aperture":"None", - "device_information":{ - "vendor":"@eln", - "model":"@eln", - "identifier":"@eln" - } - }, - "ENERGYDISPERSION[energydispersion]":{ - "scheme":"@eln", - "pass_energy":"@eln", - "pass_energy/@units":"@eln", - "energy_scan_mode":"@eln", - "entrance_slit":"@eln", - "exit_slit":"@eln", - "device_information":{ - "vendor":"@eln", - "model":"@eln", - "identifier":"@eln" - } - }, - "DETECTOR[detector]":{ - "@default":"raw_data", - "amplifier_type":"@eln", - "detector_type":"@eln", - "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/Scan_", - "raw/@units":"counts" - } - } - }, - "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":"@data:energy", - "calibrated_axis/@units":"eV" - }, - "energy_referencing":{ - "level":"None", - "reference_peak":"None", - "binding_energy":"None", - "offset":"None", - "calibrated_axis":"None" - } - }, - "/ENTRY[entry]/SAMPLE[sample]":{ - "name":"@xps_token:parameters/Group", - "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/y_units", - "energy":"@link:/entry/process/energy_calibration/calibrated_axis", - "energy/@type":"@xps_token:data/x_units", - "energy/@units":"eV", - "@energy_indices":"None", - "@energy_depends":"None" - } - } - +{ + "/@default":"None", + "/ENTRY[entry]":{ + "@default":"data", + "definition":"@eln", + 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"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":"@data:energy", + "calibrated_axis/@units":"eV", + }, + "energy_referencing":{ + "level":"None", + "reference_peak":"None", + "binding_energy":"None", + "offset":"None", + "calibrated_axis":"None" + }, + "transmission_correction":{ + "transmission_function":{ + "@axes":"None", + "@signal":"None", + "kinetic_energy":"None", + "kinetic_energy/@units":"None", + "relative_intensity":"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", + "@axes":["energy"], + "data":"@data:cycle", + "data/@units":"@xps_token:data/y_units_1", + "energy": "@data:energy", + "energy/@type":"@xps_token:data/x_units_1", + "energy/@units":"eV", + "@energy_indices":"None", + "@energy_depends":"None" + } } \ No newline at end of file diff --git a/pynxtools_xps/config/config_xml_specs.json b/pynxtools_xps/config/config_xml_specs.json index 1bc5df06..a592125e 100644 --- a/pynxtools_xps/config/config_xml_specs.json +++ b/pynxtools_xps/config/config_xml_specs.json @@ -1,5 +1,5 @@ { - "/@default":"entry", + "/@default":"None", "/ENTRY[entry]":{ "@default":"data", "definition":"@eln", @@ -22,6 +22,7 @@ "email":"@eln" }, "/ENTRY[entry]/INSTRUMENT[instrument]":{ + "@default": "electronanalyser", "device_information":{ "vendor":"@eln", "identifier":"@eln", @@ -57,7 +58,7 @@ "associated_source":"@link:/entry/instrument/source_probe" }, "ELECTRONANALYSER[electronanalyser]":{ - "@default": "None", + "@default": "detector0", "name":"@xps_token:analyzer_info/name", "description":"@eln", "work_function":"@eln", @@ -116,7 +117,6 @@ }, "raw_data":{ "@signal":"raw", - "@default":"raw", "raw":"@detector_data:cycles/Cycle_", "raw/@units":"counts" } @@ -236,7 +236,6 @@ }, "/ENTRY[entry]/data":{ "@signal":"data", - "@default":"data", "@axes":["energy"], "data":"@data:cycle", "data/@units":"counts", diff --git a/pynxtools_xps/config/template.json b/pynxtools_xps/config/template.json index 478b4a99..d303c31b 100644 --- a/pynxtools_xps/config/template.json +++ b/pynxtools_xps/config/template.json @@ -14,6 +14,7 @@ "affiliation":"None" }, "/ENTRY[entry]/INSTRUMENT[instrument]":{ + "@default": "electronanalyser", "device_information":{ "vendor":"None", "identifier":"None", @@ -50,7 +51,7 @@ "associated_source":"None" }, "ELECTRONANALYSER[electronanalyser]":{ - "@default": "None", + "@default": "detector0", "description":"None", "work_function":"None", "work_function/@units":"None", @@ -106,7 +107,6 @@ }, "raw_data":{ "@signal":"None", - "@default":"raw", "raw":"None" } } @@ -238,7 +238,6 @@ }, "/ENTRY[entry]/data":{ "@signal":"data", - "@default":"data", "@axes":["energy"], "data":"None", "data/@units":"None", From 97cf12e924e574aa27db7109cb6f7f3de7125977 Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Fri, 15 Mar 2024 09:20:38 +0100 Subject: [PATCH 2/2] fix vms config file --- pynxtools_xps/config/config_vms.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pynxtools_xps/config/config_vms.json b/pynxtools_xps/config/config_vms.json index 626b111e..ecbefdfa 100644 --- a/pynxtools_xps/config/config_vms.json +++ b/pynxtools_xps/config/config_vms.json @@ -71,7 +71,7 @@ "slow_axes":"energy", "analyzer_take_off_azimuth": "@xps_token:analyser/analyzer_take_off_azimuth", "analyzer_take_off_azimuth/@units": "degree", - "analyzer_take_off_polar/": "@xps_token:analyser/analyzer_take_off_polar", + "analyzer_take_off_polar": "@xps_token:analyser/analyzer_take_off_polar", "analyzer_take_off_polar/@units": "degree", "analysis_width_x": "@xps_token:analyser/analysis_width_x", "analysis_width_x/@units": "mm",