Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update examples after mpes refactor #35

Merged
merged 10 commits into from
Apr 11, 2024
Merged

Update examples after mpes refactor #35

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
6a7140d
update examples after mpes refactor
lukaspie Apr 11, 2024
161200c
update default config files
lukaspie Apr 11, 2024
b33eb2b
replace entries and detectors in value strings
lukaspie Apr 11, 2024
27f909c
Map parameters to float in PHI reader
lukaspie Apr 11, 2024
c4c8e02
update example ELNs and nxs files
lukaspie Apr 11, 2024
ed23424
update test files
lukaspie Apr 11, 2024
92be28f
Replace _TYPE by TYPE in source and beam
lukaspie Apr 11, 2024
fa1292e
add @depends_on attributes for transformations
lukaspie Apr 11, 2024
b54817f
update examples after config changes
lukaspie Apr 11, 2024
0a52f04
update config template
lukaspie Apr 11, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file modified examples/phi/SnO2_10nm.spe.nxs
View file
Open in desktop
Binary file not shown.
Binary file modified examples/phi/SnO2_10nm_1.pro.nxs
View file
Open in desktop
Binary file not shown.
2 changes: 1 addition & 1 deletion examples/phi/eln_data_phi.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,7 @@ sample:
unit: g/mol
cas_number: 18282-10-5
molecular_formula_hill: SnO2
sample_history:
history:
sample_preparation:
start_time: 2022-01-22T12:48:00.200Z
end_time: 2022-01-22T13:18:00.200Z
Expand Down
9 changes: 6 additions & 3 deletions examples/regenerate_examples.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,12 +1,15 @@
#!/bin/bash
READER=xps
NXDL=NXmpes

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
dataconverter SnO2_10nm.spe eln_data_phi.yaml --reader $READER --nxdl $NXDL --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
dataconverter SnO2_10nm_1.pro eln_data_phi.yaml --reader $READER --nxdl $NXDL --output SnO2_10nm_1.pro.nxs
cd ..
echo
}
Expand All @@ -15,7 +18,7 @@ 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
dataconverter Cu-HHTP_*.txt eln_data.yaml --reader $READER --nxdl $NXDL --output Cu-HHTP.nxs
cd ..
echo
}
Expand Down
Binary file modified examples/scienta/Cu-HHTP.nxs
View file
Open in desktop
Binary file not shown.
2 changes: 1 addition & 1 deletion examples/scienta/eln_data.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -160,7 +160,7 @@ sample:
chemical_formula: Cu
description: Cu-HHTP/Glass on standard sample holder
situation: vacuum
sample_history:
history:
sample_preparation:
start_time: 2022-04-08T11:25:00.200Z
end_time: 2022-04-08T11:45:00.200Z
Expand Down
Binary file modified examples/sle/Au_25_mbar_O2_no_align.nxs
View file
Open in desktop
Binary file not shown.
6 changes: 3 additions & 3 deletions examples/sle/eln_data_sle.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,14 +25,14 @@ instrument:
resolution:
value: 0.2
unit: eV
source_probe:
source_xray:
type: Fixed Tube X-ray
probe: photon
device_information:
vendor: SPECS GmbH
model: µFOCUS 500
identifier: null
beam_probe:
beam_xray:
distance:
value: 0.0
unit: mm
Expand Down Expand Up @@ -152,7 +152,7 @@ sample:
unit: g/mol
cas_number: 7440-57-5
molecular_formula_hill: Au
sample_history:
history:
sample_preparation:
start_time: 2022-04-08T11:25:00.200Z
end_time: 2022-04-08T11:45:00.200Z
Expand Down
35 changes: 14 additions & 21 deletions pynxtools_xps/config/config_phi.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,9 @@
"resolution":"@eln",
"resolution/@units":"@eln"
},
"depends_on": "/entry/instrument/source_xray/transformations/source_analyser_angle",
"TRANSFORMATIONS[transformations]": {
"AXISNAME[source_analyser_angle]/@depends_on":".",
"AXISNAME[source_analyser_angle]":"@xps_token/source_analyser_angle",
"AXISNAME[source_analyser_angle]/@transformation_type": "rotation",
"AXISNAME[source_analyser_angle]/@units":"@xps_token/source_analyser_angle/@units",
Expand All @@ -47,7 +49,7 @@
1
]
},
"source_TYPE[source_xray]":{
"sourceTYPE[source_xray]":{
"type":"@eln",
"name":"@xps_token:xray_source/name",
"probe":"@eln",
Expand All @@ -73,9 +75,11 @@
"power/@units":"@xps_token:xray_source/xray_power/@units",
"offset":"@xps_token:xray_source/xray_offset",
"offset/@units":"@xps_token:xray_source/xray_offset/@units",
"rotation":"@xps_token:xray_source/xray_rotation",
"rotation/@units":"@xps_token:xray_source/xray_rotation/@units",
"voltage":"@xps_token:xray_source/xray_high_voltage",
"voltage/@units":"@xps_token:xray_source/xray_high_voltage/@units",
"associated_beam":"@link:/entry/instrument/beam_xray",
"associated_beam":"/entry/instrument/beam_xray",
"LENS_EM[blanking_lens]":{
"name":"blanking lens",
"voltage":"@xps_token:xray_source/xray_blanking_voltage",
Expand Down Expand Up @@ -108,20 +112,9 @@
"offset_x/@units":"@xps_token:xray_source/xray_stigmator_x/@units",
"offset_y":"@xps_token:xray_source/xray_stigmator_y",
"offset_y/@units":"@xps_token:xray_source/xray_stigmator_y/@units"
},
"depends_on": "/entry/instrument/source_xray/transformations/trans_z",
"TRANSFORMATIONS[transformations]": {
"AXISNAME[xray_rotation]":"@xps_token:xray_source/xray_rotation",
"AXISNAME[xray_rotation]/@transformation_type": "rotation",
"AXISNAME[xray_rotation]/@units":"@xps_token:xray_source/xray_rotation/@units",
"AXISNAME[xray_rotation]/@vector": [
0,
0,
1
]
}
},
"beam_TYPE[beam_xray]":{
"beamTYPE[beam_xray]":{
"distance":"@eln",
"distance/@units":"@eln",
"incident_energy":"@xps_token:beam/xray_energy",
Expand All @@ -132,9 +125,9 @@
"incident_polarization/@units":"None",
"extent":"@xps_token:beam/xray_beam_diameter",
"extent/@units":"@xps_token:beam/xray_beam_diameter/@units",
"associated_source":"@link:/entry/instrument/source_xray"
"associated_source":"/entry/instrument/source_xray"
},
"source_TYPE[source_flood_gun]":{
"sourceTYPE[source_flood_gun]":{
"current":"@xps_token:flood_gun/flood_gun_current",
"current/@units":"@xps_token:flood_gun/flood_gun_current/@units",
"energy":"@xps_token:flood_gun/flood_gun_energy",
Expand All @@ -161,7 +154,7 @@
"voltage/@units":"@xps_token:flood_gun/extractor_voltage/@units"
}
},
"source_TYPE[source_gas_cluster_ion_beam]":{
"sourceTYPE[source_gas_cluster_ion_beam]":{
"description":"@eln",
"cluster_size":"@xps_token:gcib/gcib_cluster_size",
"cluster_size/@units":"@xps_token:gcib/gcib_cluster_size/@units",
Expand Down Expand Up @@ -207,7 +200,7 @@
"voltage/@units":"@xps_token:gcib/gcib_objective/@units"
}
},
"source_TYPE[source_neutral_ion_gun]":{
"sourceTYPE[source_neutral_ion_gun]":{
"description":"@eln",
"current":"@xps_token:neutral_ion_gun/neutral_current",
"current/@units":"@xps_token:neutral_ion_gun/neutral_current/@units",
Expand Down Expand Up @@ -252,7 +245,7 @@
"voltage/@units":"@xps_token:neutral_ion_gun/neutral_objective_lens_voltage/@units"
}
},
"source_TYPE[source_sputter_gun]":{
"sourceTYPE[source_sputter_gun]":{
"description":"@eln",
"current":"@xps_token:sputter_gun/sputter_current",
"current/@units":"@xps_token:sputter_gun/sputter_current/@units",
Expand Down Expand Up @@ -520,7 +513,7 @@
"value":"@link:/entry/instrument/source_flood_gun/current"
}
},
"/ENTRY[entry]/PROCESS[process]":{
"/ENTRY[entry]/PROCESS_MPES[process]":{
"energy_calibration":"None",
"energy_referencing":{
"level":"None",
Expand All @@ -547,7 +540,7 @@
"cas_number":"@eln",
"molecular_formula_hill":"@eln"
},
"sample_history":{
"history":{
"sample_preparation":{
"start_time":"@eln",
"end_time":"@eln",
Expand Down
10 changes: 5 additions & 5 deletions pynxtools_xps/config/config_scienta_txt.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
"resolution":"@xps_token:region/step_size",
"resolution/@units":"@xps_token:region/step_size/@units"
},
"source_TYPE[source_xray]":{
"sourceTYPE[source_xray]":{
"type":"@eln",
"name":"@eln",
"probe":"photon",
Expand All @@ -45,9 +45,9 @@
"identifier":"@eln",
"model":"@eln"
},
"associated_beam":"@link:/entry/instrument/beam_xray"
"associated_beam":"/entry/instrument/beam_xray"
},
"beam_TYPE[beam_xray]":{
"beamTYPE[beam_xray]":{
"distance":"@eln",
"distance/@units":"@eln",
"incident_energy":"@xps_token:beam/excitation_energy",
Expand All @@ -57,7 +57,7 @@
"incident_polarization":"None",
"incident_polarization/@units":"None",
"extent":"None",
"associated_source":"@link:/entry/instrument/source_xray"
"associated_source":"/entry/instrument/source_xray"
},
"ELECTRONANALYSER[electronanalyser]":{
"@default":"detector0",
Expand Down Expand Up @@ -232,7 +232,7 @@
"cas_number":"@eln",
"molecular_formula_hill":"@eln"
},
"sample_history":{
"history":{
"sample_preparation":{
"start_time":"@eln",
"end_time":"@eln",
Expand Down
10 changes: 5 additions & 5 deletions pynxtools_xps/config/config_sle_specs.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
"resolution":"@eln",
"resolution/@units":"@eln"
},
"source_TYPE[source_probe]":{
"sourceTYPE[source_xray]":{
"type":"@eln",
"name":"@xps_token:source/name",
"probe":"@eln",
Expand All @@ -49,9 +49,9 @@
"identifier":"@eln",
"model":"@eln"
},
"associated_beam":"@link:/entry/instrument/beam_probe"
"associated_beam":"/entry/instrument/beam_xray"
},
"beam_TYPE[beam_probe]":{
"beamTYPE[beam_xray]":{
"distance":"@eln",
"distance/@units":"@eln",
"incident_energy":"@xps_token:beam/excitation_energy",
Expand All @@ -61,7 +61,7 @@
"incident_polarization":"None",
"incident_polarization/@units":"None",
"extent":"None",
"associated_source":"@link:/entry/instrument/source_probe"
"associated_source":"/entry/instrument/source_xray"
},
"ELECTRONANALYSER[electronanalyser]":{
"@default": "detector0",
Expand Down Expand Up @@ -272,7 +272,7 @@
"cas_number":"@eln",
"molecular_formula_hill":"@eln"
},
"sample_history":{
"history":{
"sample_preparation":{
"start_time":"@eln",
"end_time":"@eln",
Expand Down
10 changes: 5 additions & 5 deletions pynxtools_xps/config/config_specs_xy.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
"resolution":"@xps_token:data/step_size",
"resolution/@units":"eV"
},
"source_TYPE[source_probe]":{
"sourceTYPE[source_xray]":{
"type":"@eln",
"name": "@xps_token:source/source_label",
"probe":"photon",
Expand All @@ -44,9 +44,9 @@
"identifier":"@eln",
"model":"@eln"
},
"associated_beam":"@link:/entry/instrument/beam_probe"
"associated_beam":"/entry/instrument/beam_xray"
},
"beam_TYPE[beam_probe]":{
"beamTYPE[beam_xray]":{
"distance":"@eln",
"distance/@units":"@eln",
"incident_energy":"@xps_token:beam/excitation_energy",
Expand All @@ -56,7 +56,7 @@
"incident_polarization":"None",
"incident_polarization/@units":"None",
"extent":"None",
"associated_source":"@link:/entry/instrument/source_probe"
"associated_source":"/entry/instrument/source_xray"
},
"ELECTRONANALYSER[electronanalyser]":{
"@default": "detector0",
Expand Down Expand Up @@ -238,7 +238,7 @@
"cas_number":"@eln",
"molecular_formula_hill":"@eln"
},
"sample_history":{
"history":{
"sample_preparation":{
"start_time":"@eln",
"end_time":"@eln",
Expand Down
10 changes: 5 additions & 5 deletions pynxtools_xps/config/config_txt_vamas_export.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
"resolution":"@xps_token:data/step_size",
"resolution/@units":"@eln"
},
"source_TYPE[source_probe]":{
"sourceTYPE[source_xray]":{
"type":"@eln",
"name":"@eln",
"probe":"photon",
Expand All @@ -45,9 +45,9 @@
"identifier":"@eln",
"model":"@eln"
},
"associated_beam":"@link:/entry/instrument/beam_probe"
"associated_beam":"/entry/instrument/beam_xray"
},
"beam_TYPE[beam_probe]":{
"beamTYPE[beam_xray]":{
"distance":"@eln",
"distance/@units":"@eln",
"incident_energy":"@xps_token:beam/excitation_energy",
Expand All @@ -57,7 +57,7 @@
"incident_polarization":"None",
"incident_polarization/@units":"None",
"extent":"None",
"associated_source":"@link:/entry/instrument/source_probe"
"associated_source":"/entry/instrument/source_xray"
},
"ELECTRONANALYSER[electronanalyser]":{
"@default": "detector0",
Expand Down Expand Up @@ -209,7 +209,7 @@
"cas_number":"@eln",
"molecular_formula_hill":"@eln"
},
"sample_history":{
"history":{
"sample_preparation":{
"start_time":"@eln",
"end_time":"@eln",
Expand Down
24 changes: 17 additions & 7 deletions pynxtools_xps/config/config_vms.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
"resolution":"@xps_token:data/step_size",
"resolution/@units":"eV"
},
"source_TYPE[source_probe]":{
"sourceTYPE[source_xray]":{
"type":"@eln",
"name":"@xps_token:source/source_label",
"probe":"photon",
Expand All @@ -45,11 +45,21 @@
"identifier":"@eln",
"model":"@eln"
},
"associated_beam":"@link:/entry/instrument/beam_probe",
"source_analyzer_angle":"source_analyzer_angle",
"source_analyzer_angle/@units":"degree"
"associated_beam":"/entry/instrument/beam_xray",
"depends_on": "/entry/instrument/source_xray/transformations/source_analyzer_angle",
"TRANSFORMATIONS[transformations]": {
"AXISNAME[source_analyzer_angle]/@depends_on":".",
"AXISNAME[source_analyzer_angle]":"@xps_token:source/source_analyzer_angle",
"AXISNAME[source_analyzer_angle]/@transformation_type": "rotation",
"AXISNAME[source_analyzer_angle]/@units":"degree",
"AXISNAME[source_analyzer_angle]/@vector": [
0,
0,
1
lukaspie marked this conversation as resolved.
Show resolved Hide resolved
]
}
},
"beam_TYPE[beam_probe]":{
"beamTYPE[beam_xray]":{
"distance":"@eln",
"distance/@units":"@eln",
"incident_energy":"@xps_token:beam/excitation_energy",
Expand All @@ -59,7 +69,7 @@
"incident_polarization":"None",
"incident_polarization/@units":"None",
"extent":"None",
"associated_source":"@link:/entry/instrument/source_probe"
"associated_source":"/entry/instrument/source_xray"
},
"ELECTRONANALYSER[electronanalyser]":{
"@default":"detector0",
Expand Down Expand Up @@ -242,7 +252,7 @@
"cas_number":"@eln",
"molecular_formula_hill":"@eln"
},
"sample_history":{
"history":{
"sample_preparation":{
"start_time":"@eln",
"end_time":"@eln",
Expand Down
Loading
Loading