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"source": [
"## Example 3: Export to NeXus\n",
"This is an example showcasing the loading of a tilt map Fermi surface mapping\n",
"\n",
"The band dispersion is loaded as a xarray dataframe following a conversion to the [NXmpes_arpes NeXus format](https://manual.nexusformat.org/classes/contributed_definitions/NXmpes.html#nxmpes) using the [FAIRmat pynxtools](https://github.com/FAIRMAT-nfdi/pynxtools)."
]
},
{
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"metadata": {},
"source": [
"First, the SpecsScan class is imported which has the scan loader as its class method."
]
},
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"execution_count": null,
"metadata": {
"tags": []
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"source": [
"%load_ext autoreload\n",
"%autoreload 2\n",
"from specsscan import SpecsScan\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"%matplotlib widget"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Definition of manual scan metadata. These should ideally come from an Electronic Lab Notebook."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
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"metadata = {}\n",
"#General\n",
"metadata['experiment_summary'] = 'TbTe3 tilt map around EF with 800nm pump at 20fs after pump-probe overlap'\n",
"metadata['entry_title'] = 'TbTe3 XUV Fermi surface map at 20 fs'\n",
"metadata['experiment_title'] = 'TbTe3 XUV Fermi surface map at 20 fs'\n",
"\n",
"#User\n",
"# Fill general parameters of NXuser\n",
"metadata['user0'] = {}\n",
"metadata['user0']['name'] = 'Laurenz Rettig'\n",
"metadata['user0']['role'] = 'Principal Investigator'\n",
"metadata['user0']['affiliation'] = 'Fritz Haber Institute of the Max Planck Society'\n",
"metadata['user0']['address'] = 'Faradayweg 4-6, 14195 Berlin'\n",
"metadata['user0']['email'] = 'rettig@fhi-berlin.mpg.de'\n",
"\n",
"metadata['instrument'] = {}\n",
"# energy resolution\n",
"metadata['instrument']['energy_resolution'] = 150.\n",
"metadata['instrument']['electronanalyzer'] = {}\n",
"metadata['instrument']['electronanalyzer']['energy_resolution'] = 120.\n",
"metadata['instrument']['electronanalyzer']['angular_resolution'] = 0.2\n",
"metadata['instrument']['electronanalyzer']['spatial_resolution'] = 0.5\n",
"metadata['instrument']['electronanalyzer']['slit_shape'] = \"curved slit\"\n",
"metadata['instrument']['electronanalyzer']['slit_size'] = 1.0\n",
"#probe beam\n",
"metadata['instrument']['beam']={}\n",
"metadata['instrument']['beam']['probe']={}\n",
"metadata['instrument']['beam']['probe']['incident_energy'] = 21.7\n",
"metadata['instrument']['beam']['probe']['incident_energy_spread'] = 0.11\n",
"metadata['instrument']['beam']['probe']['pulse_duration'] = 20.\n",
"metadata['instrument']['beam']['probe']['frequency'] = 500.\n",
"metadata['instrument']['beam']['probe']['incident_polarization'] = [1, 1, 0, 0] # p pol Stokes vector\n",
"metadata['instrument']['beam']['probe']['extent'] = [80., 80.]\n",
"#pump beam\n",
"metadata['instrument']['beam']['pump']={}\n",
"metadata['instrument']['beam']['pump']['incident_energy'] = 1.55\n",
"metadata['instrument']['beam']['pump']['incident_energy_spread'] = 0.08\n",
"metadata['instrument']['beam']['pump']['pulse_duration'] = 35.\n",
"metadata['instrument']['beam']['pump']['frequency'] = 500.\n",
"metadata['instrument']['beam']['pump']['incident_polarization'] = [1, -1, 0, 0] # s pol Stokes vector\n",
"metadata['instrument']['beam']['pump']['incident_wavelength'] = 800.\n",
"metadata['instrument']['beam']['pump']['average_power'] = 224.\n",
"metadata['instrument']['beam']['pump']['pulse_energy'] = metadata['instrument']['beam']['pump']['average_power']/metadata['instrument']['beam']['pump']['frequency']#µJ\n",
"metadata['instrument']['beam']['pump']['extent'] = [300/4*2.34, 270/4*2.35] #Gaussian 4sigma -> FWHM\n",
"metadata['instrument']['beam']['pump']['fluence'] = 1.00\n",
"metadata['instrument']['beam']['pump']['delay'] = 0.02\n",
"\n",
"#sample\n",
"metadata['sample']={}\n",
"metadata['sample']['preparation_date'] = '2017-03-19T10:00:00+00:00'\n",
"metadata['sample']['preparation_description'] = 'Cleaved'\n",
"metadata['sample']['sample_history'] = 'Cleaved in UHV'\n",
"metadata['sample']['chemical_formula'] = 'TbTe3'\n",
"metadata['sample']['description'] = 'cleaved single crystal of TbTe3'\n",
"metadata['sample']['name'] = 'TbTe3 Single Crystal'\n",
"\n",
"metadata[\"scan_info\"] = {}\n",
"metadata[\"scan_info\"][\"trARPES:XGS600:PressureAC:P_RD\"] = 2.5E-11\n",
"metadata[\"scan_info\"][\"trARPES:Carving:TEMP_RBV\"] = 70.\n",
"metadata[\"scan_info\"][\"trARPES:Sample:Measure\"] = 0.\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The SpecsScan instance is created from a config, that contains a rewrite entry to change names of axes"
]
},
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"cell_type": "code",
"execution_count": null,
"metadata": {
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"config = {\"nexus\":{\"definition\": \"NXmpes_arpes\"}, \"spa_params\":{\"crop\":True, \"ek_range_min\":0.07597844332538181, \"ek_range_max\":0.9117413199045858, \"ang_range_min\":0.16453159041394336, \"ang_range_max\":0.8840087145969499,}}\n",
"sps = SpecsScan(config=config, user_config=\"../src/specsscan/config/example_config_FHI.yaml\", system_config={})\n",
"path = \"../tests/data/\" # Path to the test data set"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The load_scan method loads the scan as an xarray along with the metadata needed for nexus conversion."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
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"source": [
"res_xarray = sps.load_scan(\n",
" scan=1496, # Tilt scan\n",
" path=path,\n",
" metadata=metadata,\n",
" collect_metadata=True,\n",
")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The resulting 3-dimensional data cube"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"res_xarray.dims"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"A Gamma-point cut"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"plt.figure()\n",
"res_xarray[:,30,:].T.plot()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The Fermi surface"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"plt.figure()\n",
"res_xarray.loc[{\"energy\":slice(21.6, 21.8)}].sum(axis=2).plot()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Save as nexus file"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"sps.save(\"FSmapping.nxs\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
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