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Merge pull request #35 from FAIRmat-NFDI/update-examples-after-mpes-refactor
Update examples after mpes refactor
2 parents 00bdee3 + 0a52f04 commit 35baae6

24 files changed

+91
-78
lines changed

‎examples/phi/SnO2_10nm.spe.nxs

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‎examples/phi/SnO2_10nm_1.pro.nxs

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‎examples/phi/eln_data_phi.yaml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -149,7 +149,7 @@ sample:
149149
unit: g/mol
150150
cas_number: 18282-10-5
151151
molecular_formula_hill: SnO2
152-
sample_history:
152+
history:
153153
sample_preparation:
154154
start_time: 2022-01-22T12:48:00.200Z
155155
end_time: 2022-01-22T13:18:00.200Z

‎examples/regenerate_examples.sh

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,15 @@
11
#!/bin/bash
2+
READER=xps
3+
NXDL=NXmpes
4+
25
function update_phi_examples {
36
echo "Update Phi examples"
47
cd phi/
58
echo "Update .spe (single spectrum) examples"
6-
dataconverter SnO2_10nm.spe eln_data_phi.yaml --reader xps --nxdl NXmpes --output SnO2_10nm.spe.nxs
9+
dataconverter SnO2_10nm.spe eln_data_phi.yaml --reader $READER --nxdl $NXDL --output SnO2_10nm.spe.nxs
710
echo
811
echo "Update .pro (depth_profiling) examples"
9-
dataconverter SnO2_10nm_1.pro eln_data_phi.yaml --reader xps --nxdl NXmpes --output SnO2_10nm_1.pro.nxs
12+
dataconverter SnO2_10nm_1.pro eln_data_phi.yaml --reader $READER --nxdl $NXDL --output SnO2_10nm_1.pro.nxs
1013
cd ..
1114
echo
1215
}
@@ -15,7 +18,7 @@ function update_scienta_examples {
1518
echo "Update scienta examples"
1619
cd scienta/
1720
echo "Update .txt example"
18-
dataconverter Cu-HHTP_*.txt eln_data.yaml --reader xps --nxdl NXmpes --output Cu-HHTP.nxs
21+
dataconverter Cu-HHTP_*.txt eln_data.yaml --reader $READER --nxdl $NXDL --output Cu-HHTP.nxs
1922
cd ..
2023
echo
2124
}

‎examples/scienta/Cu-HHTP.nxs

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‎examples/scienta/eln_data.yaml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -160,7 +160,7 @@ sample:
160160
chemical_formula: Cu
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description: Cu-HHTP/Glass on standard sample holder
162162
situation: vacuum
163-
sample_history:
163+
history:
164164
sample_preparation:
165165
start_time: 2022-04-08T11:25:00.200Z
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end_time: 2022-04-08T11:45:00.200Z

‎examples/sle/Au_25_mbar_O2_no_align.nxs

-5.91 KB
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‎examples/sle/eln_data_sle.yaml

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -25,14 +25,14 @@ instrument:
2525
resolution:
2626
value: 0.2
2727
unit: eV
28-
source_probe:
28+
source_xray:
2929
type: Fixed Tube X-ray
3030
probe: photon
3131
device_information:
3232
vendor: SPECS GmbH
3333
model: µFOCUS 500
3434
identifier: null
35-
beam_probe:
35+
beam_xray:
3636
distance:
3737
value: 0.0
3838
unit: mm
@@ -152,7 +152,7 @@ sample:
152152
unit: g/mol
153153
cas_number: 7440-57-5
154154
molecular_formula_hill: Au
155-
sample_history:
155+
history:
156156
sample_preparation:
157157
start_time: 2022-04-08T11:25:00.200Z
158158
end_time: 2022-04-08T11:45:00.200Z

‎pynxtools_xps/config/config_phi.json

Lines changed: 14 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,9 @@
3737
"resolution":"@eln",
3838
"resolution/@units":"@eln"
3939
},
40+
"depends_on": "/entry/instrument/source_xray/transformations/source_analyser_angle",
4041
"TRANSFORMATIONS[transformations]": {
42+
"AXISNAME[source_analyser_angle]/@depends_on":".",
4143
"AXISNAME[source_analyser_angle]":"@xps_token/source_analyser_angle",
4244
"AXISNAME[source_analyser_angle]/@transformation_type": "rotation",
4345
"AXISNAME[source_analyser_angle]/@units":"@xps_token/source_analyser_angle/@units",
@@ -47,7 +49,7 @@
4749
1
4850
]
4951
},
50-
"source_TYPE[source_xray]":{
52+
"sourceTYPE[source_xray]":{
5153
"type":"@eln",
5254
"name":"@xps_token:xray_source/name",
5355
"probe":"@eln",
@@ -73,9 +75,11 @@
7375
"power/@units":"@xps_token:xray_source/xray_power/@units",
7476
"offset":"@xps_token:xray_source/xray_offset",
7577
"offset/@units":"@xps_token:xray_source/xray_offset/@units",
78+
"rotation":"@xps_token:xray_source/xray_rotation",
79+
"rotation/@units":"@xps_token:xray_source/xray_rotation/@units",
7680
"voltage":"@xps_token:xray_source/xray_high_voltage",
7781
"voltage/@units":"@xps_token:xray_source/xray_high_voltage/@units",
78-
"associated_beam":"@link:/entry/instrument/beam_xray",
82+
"associated_beam":"/entry/instrument/beam_xray",
7983
"LENS_EM[blanking_lens]":{
8084
"name":"blanking lens",
8185
"voltage":"@xps_token:xray_source/xray_blanking_voltage",
@@ -108,20 +112,9 @@
108112
"offset_x/@units":"@xps_token:xray_source/xray_stigmator_x/@units",
109113
"offset_y":"@xps_token:xray_source/xray_stigmator_y",
110114
"offset_y/@units":"@xps_token:xray_source/xray_stigmator_y/@units"
111-
},
112-
"depends_on": "/entry/instrument/source_xray/transformations/trans_z",
113-
"TRANSFORMATIONS[transformations]": {
114-
"AXISNAME[xray_rotation]":"@xps_token:xray_source/xray_rotation",
115-
"AXISNAME[xray_rotation]/@transformation_type": "rotation",
116-
"AXISNAME[xray_rotation]/@units":"@xps_token:xray_source/xray_rotation/@units",
117-
"AXISNAME[xray_rotation]/@vector": [
118-
0,
119-
0,
120-
1
121-
]
122115
}
123116
},
124-
"beam_TYPE[beam_xray]":{
117+
"beamTYPE[beam_xray]":{
125118
"distance":"@eln",
126119
"distance/@units":"@eln",
127120
"incident_energy":"@xps_token:beam/xray_energy",
@@ -132,9 +125,9 @@
132125
"incident_polarization/@units":"None",
133126
"extent":"@xps_token:beam/xray_beam_diameter",
134127
"extent/@units":"@xps_token:beam/xray_beam_diameter/@units",
135-
"associated_source":"@link:/entry/instrument/source_xray"
128+
"associated_source":"/entry/instrument/source_xray"
136129
},
137-
"source_TYPE[source_flood_gun]":{
130+
"sourceTYPE[source_flood_gun]":{
138131
"current":"@xps_token:flood_gun/flood_gun_current",
139132
"current/@units":"@xps_token:flood_gun/flood_gun_current/@units",
140133
"energy":"@xps_token:flood_gun/flood_gun_energy",
@@ -161,7 +154,7 @@
161154
"voltage/@units":"@xps_token:flood_gun/extractor_voltage/@units"
162155
}
163156
},
164-
"source_TYPE[source_gas_cluster_ion_beam]":{
157+
"sourceTYPE[source_gas_cluster_ion_beam]":{
165158
"description":"@eln",
166159
"cluster_size":"@xps_token:gcib/gcib_cluster_size",
167160
"cluster_size/@units":"@xps_token:gcib/gcib_cluster_size/@units",
@@ -207,7 +200,7 @@
207200
"voltage/@units":"@xps_token:gcib/gcib_objective/@units"
208201
}
209202
},
210-
"source_TYPE[source_neutral_ion_gun]":{
203+
"sourceTYPE[source_neutral_ion_gun]":{
211204
"description":"@eln",
212205
"current":"@xps_token:neutral_ion_gun/neutral_current",
213206
"current/@units":"@xps_token:neutral_ion_gun/neutral_current/@units",
@@ -252,7 +245,7 @@
252245
"voltage/@units":"@xps_token:neutral_ion_gun/neutral_objective_lens_voltage/@units"
253246
}
254247
},
255-
"source_TYPE[source_sputter_gun]":{
248+
"sourceTYPE[source_sputter_gun]":{
256249
"description":"@eln",
257250
"current":"@xps_token:sputter_gun/sputter_current",
258251
"current/@units":"@xps_token:sputter_gun/sputter_current/@units",
@@ -520,7 +513,7 @@
520513
"value":"@link:/entry/instrument/source_flood_gun/current"
521514
}
522515
},
523-
"/ENTRY[entry]/PROCESS[process]":{
516+
"/ENTRY[entry]/PROCESS_MPES[process]":{
524517
"energy_calibration":"None",
525518
"energy_referencing":{
526519
"level":"None",
@@ -547,7 +540,7 @@
547540
"cas_number":"@eln",
548541
"molecular_formula_hill":"@eln"
549542
},
550-
"sample_history":{
543+
"history":{
551544
"sample_preparation":{
552545
"start_time":"@eln",
553546
"end_time":"@eln",

‎pynxtools_xps/config/config_scienta_txt.json

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636
"resolution":"@xps_token:region/step_size",
3737
"resolution/@units":"@xps_token:region/step_size/@units"
3838
},
39-
"source_TYPE[source_xray]":{
39+
"sourceTYPE[source_xray]":{
4040
"type":"@eln",
4141
"name":"@eln",
4242
"probe":"photon",
@@ -45,9 +45,9 @@
4545
"identifier":"@eln",
4646
"model":"@eln"
4747
},
48-
"associated_beam":"@link:/entry/instrument/beam_xray"
48+
"associated_beam":"/entry/instrument/beam_xray"
4949
},
50-
"beam_TYPE[beam_xray]":{
50+
"beamTYPE[beam_xray]":{
5151
"distance":"@eln",
5252
"distance/@units":"@eln",
5353
"incident_energy":"@xps_token:beam/excitation_energy",
@@ -57,7 +57,7 @@
5757
"incident_polarization":"None",
5858
"incident_polarization/@units":"None",
5959
"extent":"None",
60-
"associated_source":"@link:/entry/instrument/source_xray"
60+
"associated_source":"/entry/instrument/source_xray"
6161
},
6262
"ELECTRONANALYSER[electronanalyser]":{
6363
"@default":"detector0",
@@ -232,7 +232,7 @@
232232
"cas_number":"@eln",
233233
"molecular_formula_hill":"@eln"
234234
},
235-
"sample_history":{
235+
"history":{
236236
"sample_preparation":{
237237
"start_time":"@eln",
238238
"end_time":"@eln",

‎pynxtools_xps/config/config_sle_specs.json

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636
"resolution":"@eln",
3737
"resolution/@units":"@eln"
3838
},
39-
"source_TYPE[source_probe]":{
39+
"sourceTYPE[source_xray]":{
4040
"type":"@eln",
4141
"name":"@xps_token:source/name",
4242
"probe":"@eln",
@@ -49,9 +49,9 @@
4949
"identifier":"@eln",
5050
"model":"@eln"
5151
},
52-
"associated_beam":"@link:/entry/instrument/beam_probe"
52+
"associated_beam":"/entry/instrument/beam_xray"
5353
},
54-
"beam_TYPE[beam_probe]":{
54+
"beamTYPE[beam_xray]":{
5555
"distance":"@eln",
5656
"distance/@units":"@eln",
5757
"incident_energy":"@xps_token:beam/excitation_energy",
@@ -61,7 +61,7 @@
6161
"incident_polarization":"None",
6262
"incident_polarization/@units":"None",
6363
"extent":"None",
64-
"associated_source":"@link:/entry/instrument/source_probe"
64+
"associated_source":"/entry/instrument/source_xray"
6565
},
6666
"ELECTRONANALYSER[electronanalyser]":{
6767
"@default": "detector0",
@@ -272,7 +272,7 @@
272272
"cas_number":"@eln",
273273
"molecular_formula_hill":"@eln"
274274
},
275-
"sample_history":{
275+
"history":{
276276
"sample_preparation":{
277277
"start_time":"@eln",
278278
"end_time":"@eln",

‎pynxtools_xps/config/config_specs_xy.json

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@
3535
"resolution":"@xps_token:data/step_size",
3636
"resolution/@units":"eV"
3737
},
38-
"source_TYPE[source_probe]":{
38+
"sourceTYPE[source_xray]":{
3939
"type":"@eln",
4040
"name": "@xps_token:source/source_label",
4141
"probe":"photon",
@@ -44,9 +44,9 @@
4444
"identifier":"@eln",
4545
"model":"@eln"
4646
},
47-
"associated_beam":"@link:/entry/instrument/beam_probe"
47+
"associated_beam":"/entry/instrument/beam_xray"
4848
},
49-
"beam_TYPE[beam_probe]":{
49+
"beamTYPE[beam_xray]":{
5050
"distance":"@eln",
5151
"distance/@units":"@eln",
5252
"incident_energy":"@xps_token:beam/excitation_energy",
@@ -56,7 +56,7 @@
5656
"incident_polarization":"None",
5757
"incident_polarization/@units":"None",
5858
"extent":"None",
59-
"associated_source":"@link:/entry/instrument/source_probe"
59+
"associated_source":"/entry/instrument/source_xray"
6060
},
6161
"ELECTRONANALYSER[electronanalyser]":{
6262
"@default": "detector0",
@@ -238,7 +238,7 @@
238238
"cas_number":"@eln",
239239
"molecular_formula_hill":"@eln"
240240
},
241-
"sample_history":{
241+
"history":{
242242
"sample_preparation":{
243243
"start_time":"@eln",
244244
"end_time":"@eln",

‎pynxtools_xps/config/config_txt_vamas_export.json

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636
"resolution":"@xps_token:data/step_size",
3737
"resolution/@units":"@eln"
3838
},
39-
"source_TYPE[source_probe]":{
39+
"sourceTYPE[source_xray]":{
4040
"type":"@eln",
4141
"name":"@eln",
4242
"probe":"photon",
@@ -45,9 +45,9 @@
4545
"identifier":"@eln",
4646
"model":"@eln"
4747
},
48-
"associated_beam":"@link:/entry/instrument/beam_probe"
48+
"associated_beam":"/entry/instrument/beam_xray"
4949
},
50-
"beam_TYPE[beam_probe]":{
50+
"beamTYPE[beam_xray]":{
5151
"distance":"@eln",
5252
"distance/@units":"@eln",
5353
"incident_energy":"@xps_token:beam/excitation_energy",
@@ -57,7 +57,7 @@
5757
"incident_polarization":"None",
5858
"incident_polarization/@units":"None",
5959
"extent":"None",
60-
"associated_source":"@link:/entry/instrument/source_probe"
60+
"associated_source":"/entry/instrument/source_xray"
6161
},
6262
"ELECTRONANALYSER[electronanalyser]":{
6363
"@default": "detector0",
@@ -209,7 +209,7 @@
209209
"cas_number":"@eln",
210210
"molecular_formula_hill":"@eln"
211211
},
212-
"sample_history":{
212+
"history":{
213213
"sample_preparation":{
214214
"start_time":"@eln",
215215
"end_time":"@eln",

‎pynxtools_xps/config/config_vms.json

Lines changed: 17 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636
"resolution":"@xps_token:data/step_size",
3737
"resolution/@units":"eV"
3838
},
39-
"source_TYPE[source_probe]":{
39+
"sourceTYPE[source_xray]":{
4040
"type":"@eln",
4141
"name":"@xps_token:source/source_label",
4242
"probe":"photon",
@@ -45,11 +45,21 @@
4545
"identifier":"@eln",
4646
"model":"@eln"
4747
},
48-
"associated_beam":"@link:/entry/instrument/beam_probe",
49-
"source_analyzer_angle":"source_analyzer_angle",
50-
"source_analyzer_angle/@units":"degree"
48+
"associated_beam":"/entry/instrument/beam_xray",
49+
"depends_on": "/entry/instrument/source_xray/transformations/source_analyzer_angle",
50+
"TRANSFORMATIONS[transformations]": {
51+
"AXISNAME[source_analyzer_angle]/@depends_on":".",
52+
"AXISNAME[source_analyzer_angle]":"@xps_token:source/source_analyzer_angle",
53+
"AXISNAME[source_analyzer_angle]/@transformation_type": "rotation",
54+
"AXISNAME[source_analyzer_angle]/@units":"degree",
55+
"AXISNAME[source_analyzer_angle]/@vector": [
56+
0,
57+
0,
58+
1
59+
]
60+
}
5161
},
52-
"beam_TYPE[beam_probe]":{
62+
"beamTYPE[beam_xray]":{
5363
"distance":"@eln",
5464
"distance/@units":"@eln",
5565
"incident_energy":"@xps_token:beam/excitation_energy",
@@ -59,7 +69,7 @@
5969
"incident_polarization":"None",
6070
"incident_polarization/@units":"None",
6171
"extent":"None",
62-
"associated_source":"@link:/entry/instrument/source_probe"
72+
"associated_source":"/entry/instrument/source_xray"
6373
},
6474
"ELECTRONANALYSER[electronanalyser]":{
6575
"@default":"detector0",
@@ -242,7 +252,7 @@
242252
"cas_number":"@eln",
243253
"molecular_formula_hill":"@eln"
244254
},
245-
"sample_history":{
255+
"history":{
246256
"sample_preparation":{
247257
"start_time":"@eln",
248258
"end_time":"@eln",

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