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Merged
rettigl merged 6 commits into from
Mar 20, 2025
Merged

Update definitions #5

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a0821e2
update config file to new validation
rettigl Mar 14, 2025
2ceb1d4
update reference files
rettigl Mar 19, 2025
f7c4a09
update examples
rettigl Mar 20, 2025
b27e10e
update reference files again
rettigl Mar 20, 2025
f9b90f2
do not run NOMAD tests for python 3.9
lukaspie Mar 20, 2025
769b0a2
update CITATION for new release
lukaspie Mar 20, 2025
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2 changes: 2 additions & 0 deletions .cspell/custom-dictionary.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,15 @@ Bessy
binarywave
bnote
caplog
codemirror
configfile
dataconverter
Dobener
dsml
Dyna
Ecut
FEMTOSPEX
FIELDNAME
fluence
fluences
fontawesome
Expand Down
45 changes: 23 additions & 22 deletions src/pynxtools_igor/nomad/examples/Conversion of time-resolved x-ray diffraction data.ipynb
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Expand Up @@ -40,7 +40,7 @@
" \"user0/name\": \"Laurenz Rettig\",\n",
" \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
" \"instrument/beam/incident_energy\": 1187.5,\n",
" \"instrument/beam/probe/pulse_duration\": 70,\n",
" \"instrument/beam/probe/pulse_duration\": 70.0,\n",
" \"sample/chemical_formula\": \"GdIr2Si2\",\n",
" \"sample/name\": \"GdIr2Si2 single crystal\",\n",
"}\n",
Expand All @@ -57,14 +57,14 @@
" \"metadata\": {\n",
" **metadata,\n",
" **{\n",
" \"sample/temperature\": temperature,\n",
" \"sample/temperature\": float(temperature),\n",
" \"entry_title\": f\"Resolved resonant x-ray diffraction data of GdIr2Si2 at {temperature} K\",\n",
" },\n",
" },\n",
" }\n",
"\n",
"entry_dict\n",
"convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
"convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
]
},
{
Expand All @@ -81,7 +81,7 @@
" \"user0/name\": \"Laurenz Rettig\",\n",
" \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
" \"instrument/beam/incident_energy\": 1187.5,\n",
" \"instrument/beam/probe/pulse_duration\": 70,\n",
" \"instrument/beam/probe/pulse_duration\": 70.0,\n",
" \"sample/chemical_formula\": \"GdCo2Si2\",\n",
" \"sample/name\": \"GdCo2Si2 single crystal\",\n",
"}\n",
Expand All @@ -98,14 +98,14 @@
" \"metadata\": {\n",
" **metadata,\n",
" **{\n",
" \"sample/temperature\": temperature,\n",
" \"sample/temperature\": float(temperature),\n",
" \"entry_title\": f\"Resolved resonant x-ray diffraction data of GdIr2Si2 at {temperature} K\",\n",
" },\n",
" },\n",
" }\n",
"\n",
"entry_dict\n",
"convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
"convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
]
},
{
Expand All @@ -129,7 +129,7 @@
" \"user0/name\": \"Laurenz Rettig\",\n",
" \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
" \"instrument/beam/incident_energy\": 1187.5,\n",
" \"instrument/beam/probe/pulse_duration\": 70,\n",
" \"instrument/beam/probe/pulse_duration\": 70.0,\n",
"}\n",
"entry_dict = {}\n",
"scans = [\n",
Expand Down Expand Up @@ -160,7 +160,7 @@
" },\n",
" }\n",
"\n",
"convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
"convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
]
},
{
Expand All @@ -184,7 +184,8 @@
" \"user0/name\": \"Laurenz Rettig\",\n",
" \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
" \"instrument/beam/incident_energy\": 1187.5,\n",
" \"instrument/beam/probe/pulse_duration\": 70,\n",
" \"instrument/beam/probe/pulse_duration\": 70.0,\n",
" \"sample/temperature\": 20.0,\n",
"}\n",
"entry_dict = {}\n",
"scans = [\"GdRh/voigt_area\", \"GdIr/voigt_area\", \"GdCo/voigt1_area_left\"]\n",
Expand All @@ -207,7 +208,7 @@
" },\n",
" }\n",
"\n",
"convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
"convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
]
},
{
Expand All @@ -231,10 +232,10 @@
" \"user0/name\": \"Laurenz Rettig\",\n",
" \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
" \"instrument/beam/incident_energy\": 1187.5,\n",
" \"instrument/beam/probe/pulse_duration\": 100,\n",
" \"instrument/beam/probe/pulse_duration\": 100.0,\n",
" \"sample/chemical_formula\": \"GdIr2Si2\",\n",
" \"sample/name\": \"GdIr2Si2 single crystal\",\n",
" \"sample/temperature\": 20,\n",
" \"sample/temperature\": 20.0,\n",
"}\n",
"entry_dict = {}\n",
"scans = [\"correction_2022Jan/GdCo_amp_08\", \"GdRh_ds_030_amp\", \"GdIr_ds_0200_amp\"]\n",
Expand All @@ -260,7 +261,7 @@
" },\n",
" }\n",
"\n",
"convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
"convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
]
},
{
Expand All @@ -277,10 +278,10 @@
" \"user0/name\": \"Laurenz Rettig\",\n",
" \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
" \"instrument/beam/incident_energy\": 1187.5,\n",
" \"instrument/beam/probe/pulse_duration\": 100,\n",
" \"instrument/beam/probe/pulse_duration\": 100.0,\n",
" \"sample/chemical_formula\": \"GdCo2Si2\",\n",
" \"sample/name\": \"GdCo2Si2 single crystal\",\n",
" \"sample/temperature\": 20,\n",
" \"sample/temperature\": 20.0,\n",
"}\n",
"entry_dict = {}\n",
"scans = [\"02\", \"04\", \"06\", \"08\", \"12\", \"20\"]\n",
Expand All @@ -302,7 +303,7 @@
" },\n",
" }\n",
"\n",
"convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
"convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
]
},
{
Expand All @@ -319,10 +320,10 @@
" \"user0/name\": \"Laurenz Rettig\",\n",
" \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
" \"instrument/beam/incident_energy\": 1187.5,\n",
" \"instrument/beam/probe/pulse_duration\": 100,\n",
" \"instrument/beam/probe/pulse_duration\": 100.0,\n",
" \"sample/chemical_formula\": \"GdRh2Si2\",\n",
" \"sample/name\": \"GdRh2Si2 single crystal\",\n",
" \"sample/temperature\": 20,\n",
" \"sample/temperature\": 20.0,\n",
"}\n",
"entry_dict = {}\n",
"scans = [\"005\", \"010\", \"015\", \"020\", \"030\", \"050\"]\n",
Expand All @@ -344,7 +345,7 @@
" },\n",
" }\n",
"\n",
"convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
"convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
]
},
{
Expand All @@ -361,10 +362,10 @@
" \"user0/name\": \"Laurenz Rettig\",\n",
" \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
" \"instrument/beam/incident_energy\": 1187.5,\n",
" \"instrument/beam/probe/pulse_duration\": 100,\n",
" \"instrument/beam/probe/pulse_duration\": 100.0,\n",
" \"sample/chemical_formula\": \"GdIr2Si2\",\n",
" \"sample/name\": \"GdIr2Si2 single crystal\",\n",
" \"sample/temperature\": 20,\n",
" \"sample/temperature\": 20.0,\n",
"}\n",
"entry_dict = {}\n",
"scans = [\"0025\", \"0050\", \"0100\", \"0150\", \"0200\", \"0300\"]\n",
Expand All @@ -386,7 +387,7 @@
" },\n",
" }\n",
"\n",
"convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
"convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
]
},
{
Expand Down
4 changes: 2 additions & 2 deletions src/pynxtools_igor/nomad/examples/config_file.json
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Expand Up @@ -3,8 +3,8 @@
"/ENTRY/DATA[data]/@axes": "@data:dims",
"/ENTRY/DATA[data]/AXISNAME_indices[@*_indices]": "@data:*.index",
"/ENTRY/DATA[data]/@signal": "data",
"/ENTRY/DATA[data]/data": "@data:data",
"/ENTRY/DATA[data]/data/@units": "@data:data.units",
"/ENTRY/DATA[data]/DATA[data]": "@data:data",
"/ENTRY/DATA[data]/DATA[data]/@units": "@data:data.units",
"/ENTRY/DATA[data]/AXISNAME[*]": "@data:*.data",
"/ENTRY/DATA[data]/AXISNAME[*]/@units": "@data:*.units"
}
24 changes: 13 additions & 11 deletions src/pynxtools_igor/nomad/examples/config_file_delay_scans.json
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Expand Up @@ -12,7 +12,7 @@
"name": "Bessy II",
"probe": "x-ray",
"type": "Synchrotron X-ray Source",
"mode": "Slicing"
"mode": "Single Bunch"
},
"BEAM[beam_probe]": {
"distance": 0.0,
Expand All @@ -32,36 +32,38 @@
"BEAM[beam_pump]": {
"distance": 0.0,
"distance/@units": "mm",
"incident_energy": "1.55",
"incident_energy": 1.55,
"incident_energy/@units": "eV",
"pulse_duration": "['@eln:/ENTRY/Instrument/Beam/Probe/pulse_duration', '50']",
"pulse_duration": "['@eln:/ENTRY/Instrument/Beam/Pump/pulse_duration', '50.']",
"pulse_duration/@units": "fs",
"incident_polarization": [1, 1, 0, 0],
"incident_polarization/@units": "V^2/mm^2",
"fluence": "@attrs:instrument/beam/pump/fluence",
"fluence/@units": "mJ/cm^2"
},
"DETECTOR[detector]": {
"amplifier_type": "APD",
"detector_type": "APD",
"amplifier_voltage": 150,
"amplifier_voltage/@units": "V"
"type": "APD",
"acquisition_mode": "event",
"COLLECTION[detector_parameters]": {
"amplifier_voltage": 150,
"amplifier_voltage/@units": "V"
}
}
},
"/ENTRY/SAMPLE[sample]": {
"description": "['@eln:/ENTRY/Sample/description', '@attrs:sample/chemical_formula']",
"name": "['@eln:/ENTRY/Sample/name', '@attrs:sample/name']",
"situation": "vacuum",
"SUBSTANCE[substance]/molecular_formula_hill": "['@eln:/ENTRY/Sample/chemical_formula', '@attrs:sample/chemical_formula']",
"chemical_formula": "['@eln:/ENTRY/Sample/chemical_formula', '@attrs:sample/chemical_formula']",
"temperature": "@attrs:sample/temperature",
"temperature/@units": "K"
},
"/ENTRY/DATA[data]/@axes": "@data:dims",
"/ENTRY/DATA[data]/@signal": "data",
"/ENTRY/DATA[data]/AXISNAME_indices[@*_indices]": "@data:*.index",
"/ENTRY/DATA[data]/data": "@data:data",
"/ENTRY/DATA[data]/data_errors": "@data:data.errors",
"/ENTRY/DATA[data]/data/@units": "@data:data.units",
"/ENTRY/DATA[data]/DATA[data]": "@data:data",
"/ENTRY/DATA[data]/FIELDNAME_errors[data_errors]": "@data:data.errors",
"/ENTRY/DATA[data]/DATA[data]/@units": "@data:data.units",
"/ENTRY/DATA[data]/AXISNAME[*]": "@data:*.data",
"/ENTRY/DATA[data]/AXISNAME[*]/@units": "@data:*.units"
}
17 changes: 9 additions & 8 deletions src/pynxtools_igor/nomad/examples/config_file_energies.json
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Expand Up @@ -25,26 +25,27 @@
"incident_polarization/@units": "V^2/mm^2"
},
"DETECTOR[detector]": {
"amplifier_type": "APD",
"detector_type": "APD",
"amplifier_voltage": 150,
"amplifier_voltage/@units": "V"
"type": "APD",
"acquisition_mode": "event",
"COLLECTION[detector_parameters]": {
"amplifier_voltage": 150,
"amplifier_voltage/@units": "V"
}
}
},
"/ENTRY/SAMPLE[sample]": {
"description": "['@eln:/ENTRY/Sample/description', '@attrs:sample/chemical_formula']",
"name": "['@eln:/ENTRY/Sample/name', '@attrs:sample/name']",
"situation": "vacuum",
"chemical_formula": "['@eln:/ENTRY/Sample/chemical_formula', '@attrs:sample/chemical_formula']",
"temperature": "20",
"temperature": "@attrs:sample/temperature",
"temperature/@units": "K"
},
"/ENTRY/DATA[data]/@axes": "@data:dims",
"/ENTRY/DATA[data]/@signal": "data",
"/ENTRY/DATA[data]/AXISNAME_indices[@*_indices]": "@data:*.index",
"/ENTRY/DATA[data]/data": "@data:data",
"/ENTRY/DATA[data]/data_errors": "@data:data.errors",
"/ENTRY/DATA[data]/data/@units": "@data:data.units",
"/ENTRY/DATA[data]/DATA[data]": "@data:data",
"/ENTRY/DATA[data]/DATA[data]/@units": "@data:data.units",
"/ENTRY/DATA[data]/AXISNAME[*]": "@data:*.data",
"/ENTRY/DATA[data]/AXISNAME[*]/@units": "@data:*.units"
}
14 changes: 8 additions & 6 deletions src/pynxtools_igor/nomad/examples/config_file_peaks.json
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Expand Up @@ -25,10 +25,12 @@
"incident_polarization/@units": "V^2/mm^2"
},
"DETECTOR[detector]": {
"amplifier_type": "APD",
"detector_type": "APD",
"amplifier_voltage": 150,
"amplifier_voltage/@units": "V"
"type": "APD",
"acquisition_mode": "event",
"COLLECTION[detector_parameters]": {
"detector_bias": 150,
"detector_bias/@units": "V"
}
}
},
"/ENTRY/SAMPLE[sample]": {
Expand All @@ -42,8 +44,8 @@
"/ENTRY/DATA[data]/@axes": "@data:dims",
"/ENTRY/DATA[data]/@signal": "data",
"/ENTRY/DATA[data]/AXISNAME_indices[@*_indices]": "@data:*.index",
"/ENTRY/DATA[data]/data": "@data:data",
"/ENTRY/DATA[data]/data/@units": "@data:data.units",
"/ENTRY/DATA[data]/DATA[data]": "@data:data",
"/ENTRY/DATA[data]/DATA[data]/@units": "@data:data.units",
"/ENTRY/DATA[data]/AXISNAME[*]": "@data:*.data",
"/ENTRY/DATA[data]/AXISNAME[*]/@units": "@data:*.units"
}
15 changes: 8 additions & 7 deletions src/pynxtools_igor/nomad/examples/config_file_temperatures.json
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Expand Up @@ -25,11 +25,13 @@
"incident_polarization/@units": "V^2/mm^2"
},
"DETECTOR[detector]": {
"amplifier_type": "APD",
"detector_type": "APD",
"amplifier_voltage": 150,
"amplifier_voltage/@units": "V"
"type": "APD",
"acquisition_mode": "event",
"COLLECTION[detector_parameters]": {
"amplifier_voltage": 150,
"amplifier_voltage/@units": "V"
}
}
},
"/ENTRY/SAMPLE[sample]": {
"description": "['@eln:/ENTRY/Sample/description', '@attrs:sample/chemical_formula']",
Expand All @@ -42,9 +44,8 @@
"/ENTRY/DATA[data]/@axes": "@data:dims",
"/ENTRY/DATA[data]/@signal": "data",
"/ENTRY/DATA[data]/AXISNAME_indices[@*_indices]": "@data:*.index",
"/ENTRY/DATA[data]/data": "@data:data",
"/ENTRY/DATA[data]/data_errors": "@data:data.errors",
"/ENTRY/DATA[data]/data/@units": "@data:data.units",
"/ENTRY/DATA[data]/DATA[data]": "@data:data",
"/ENTRY/DATA[data]/DATA[data]/@units": "@data:data.units",
"/ENTRY/DATA[data]/AXISNAME[*]": "@data:*.data",
"/ENTRY/DATA[data]/AXISNAME[*]/@units": "@data:*.units"
}
4 changes: 2 additions & 2 deletions tests/data/config_file.json
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Expand Up @@ -3,8 +3,8 @@
"/ENTRY/DATA[data]/@axes": "@data:dims",
"/ENTRY/DATA[data]/AXISNAME_indices[@*_indices]": "@data:*.index",
"/ENTRY/DATA[data]/@signal": "data",
"/ENTRY/DATA[data]/data": "@data:data",
"/ENTRY/DATA[data]/data/@units": "@data:data.units",
"/ENTRY/DATA[data]/DATA[data]": "@data:data",
"/ENTRY/DATA[data]/DATA[data]/@units": "@data:data.units",
"/ENTRY/DATA[data]/AXISNAME[*]": "@data:*.data",
"/ENTRY/DATA[data]/AXISNAME[*]/@units": "@data:*.units"
}
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