{
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"# Binning with metadata generation, and storing into a NeXus file\n",
"In this example, we show how to bin the same data used for example 3, but using the values for correction/calibration parameters generated in the example notebook 3, which are locally saved in the file sed_config.yaml. These data and the corresponding (machine and processing) metadata are then stored to a NeXus file following the NXmpes NeXus standard (https://fairmat-experimental.github.io/nexus-fairmat-proposal/9636feecb79bb32b828b1a9804269573256d7696/classes/contributed_definitions/NXmpes.html#nxmpes) using the 'dataconverter' of the pynxtools package (https://github.com/FAIRmat-NFDI/pynxtools)."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "fb045e17-fa89-4c11-9d51-7f06e80d96d5",
"metadata": {},
"outputs": [],
"source": [
"%load_ext autoreload\n",
"%autoreload 2\n",
"\n",
"import sed\n",
"from sed.dataset import dataset\n",
"\n",
"%matplotlib widget"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "42a6afaa-17dd-4637-ba75-a28c4ead1adf",
"metadata": {},
"source": [
"## Load Data"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "34f46d54",
"metadata": {},
"outputs": [],
"source": [
"dataset.get(\"WSe2\") # Put in Path to a storage of at least 20 GByte free space.\n",
"data_path = dataset.dir # This is the path to the data\n",
"scandir, _ = dataset.subdirs # scandir contains the data, _ contains the calibration files"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "23effa13",
"metadata": {},
"outputs": [],
"source": [
"metadata = {}\n",
"# manual Meta data. These should ideally come from an Electronic Lab Notebook.\n",
"#General\n",
"metadata['experiment_summary'] = 'WSe2 XUV NIR pump probe data.'\n",
"metadata['entry_title'] = 'Valence Band Dynamics - 800 nm linear s-polarized pump, 0.6 mJ/cm2 absorbed fluence'\n",
"metadata['experiment_title'] = 'Valence band dynamics of 2H-WSe2'\n",
"\n",
"#User\n",
"# Fill general parameters of NXuser\n",
"# TODO: discuss how to deal with multiple users?\n",
"metadata['user0'] = {}\n",
"metadata['user0']['name'] = 'Julian Maklar'\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'] = 'maklar@fhi-berlin.mpg.de'\n",
"\n",
"#NXinstrument\n",
"metadata['instrument'] = {}\n",
"metadata['instrument']['energy_resolution'] = 140.\n",
"#analyzer\n",
"metadata['instrument']['analyzer']={}\n",
"metadata['instrument']['analyzer']['slow_axes'] = \"delay\" # the scanned axes\n",
"metadata['instrument']['analyzer']['spatial_resolution'] = 10.\n",
"metadata['instrument']['analyzer']['energy_resolution'] = 110.\n",
"metadata['instrument']['analyzer']['momentum_resolution'] = 0.08\n",
"metadata['instrument']['analyzer']['working_distance'] = 4.\n",
"metadata['instrument']['analyzer']['lens_mode'] = \"6kV_kmodem4.0_30VTOF.sav\"\n",
"\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'] = 300.\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'] = [230., 265.]\n",
"metadata['instrument']['beam']['pump']['fluence'] = 0.15\n",
"\n",
"#sample\n",
"metadata['sample']={}\n",
"metadata['sample']['preparation_date'] = '2019-01-13T10:00:00+00:00'\n",
"metadata['sample']['preparation_description'] = 'Cleaved'\n",
"metadata['sample']['sample_history'] = 'Cleaved'\n",
"metadata['sample']['chemical_formula'] = 'WSe2'\n",
"metadata['sample']['description'] = 'Sample'\n",
"metadata['sample']['name'] = 'WSe2 Single Crystal'\n",
"\n",
"metadata['file'] = {}\n",
"metadata['file'][\"trARPES:Carving:TEMP_RBV\"] = 300.\n",
"metadata['file'][\"trARPES:XGS600:PressureAC:P_RD\"] = 5.e-11\n",
"metadata['file'][\"KTOF:Lens:Extr:I\"] = -0.12877\n",
"metadata['file'][\"KTOF:Lens:UDLD:V\"] = 399.99905\n",
"metadata['file'][\"KTOF:Lens:Sample:V\"] = 17.19976\n",
"metadata['file'][\"KTOF:Apertures:m1.RBV\"] = 3.729931\n",
"metadata['file'][\"KTOF:Apertures:m2.RBV\"] = -5.200078\n",
"metadata['file'][\"KTOF:Apertures:m3.RBV\"] = -11.000425\n",
"\n",
"# Sample motor positions\n",
"metadata['file']['trARPES:Carving:TRX.RBV'] = 7.1900000000000004\n",
"metadata['file']['trARPES:Carving:TRY.RBV'] = -6.1700200225439552\n",
"metadata['file']['trARPES:Carving:TRZ.RBV'] = 33.4501953125\n",
"metadata['file']['trARPES:Carving:THT.RBV'] = 423.30500940561586\n",
"metadata['file']['trARPES:Carving:PHI.RBV'] = 0.99931647456264949\n",
"metadata['file']['trARPES:Carving:OMG.RBV'] = 11.002500171914066"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f1f82054",
"metadata": {},
"outputs": [],
"source": [
"# create sed processor using the config file, and collect the meta data from the files:\n",
"sp = sed.SedProcessor(folder=scandir, config=\"../sed/config/mpes_example_config.yaml\", metadata=metadata, collect_metadata=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "85ac3c83",
"metadata": {},
"outputs": [],
"source": [
"# Apply jittering to X, Y, t, ADC columns.\n",
"sp.add_jitter()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "17586169",
"metadata": {},
"outputs": [],
"source": [
"# Calculate machine-coordinate data for pose adjustment\n",
"sp.bin_and_load_momentum_calibration(df_partitions=10, plane=33, width=10, apply=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b99629a5",
"metadata": {},
"outputs": [],
"source": [
"# Adjust pose alignment, using stored distortion correction\n",
"sp.pose_adjustment(xtrans=8, ytrans=7, angle=-4, apply=True, use_correction=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "845f002d",
"metadata": {},
"outputs": [],
"source": [
"# Apply stored momentum correction\n",
"sp.apply_momentum_correction()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f9ae5066",
"metadata": {},
"outputs": [],
"source": [
"# Apply stored config momentum calibration\n",
"sp.apply_momentum_calibration()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "eb1e2bee",
"metadata": {},
"outputs": [],
"source": [
"# Apply stored config energy correction\n",
"sp.apply_energy_correction()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c470ffd9",
"metadata": {},
"outputs": [],
"source": [
"# Apply stored config energy calibration\n",
"sp.append_energy_axis()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0943d349",
"metadata": {},
"outputs": [],
"source": [
"# Apply delay calibration\n",
"delay_range = (-500, 1500)\n",
"sp.calibrate_delay_axis(delay_range=delay_range, preview=True)"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "6902fd56-1456-4da6-83a4-0f3f6b831eb6",
"metadata": {},
"source": [
"## Compute final data volume"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a7601cd7-cd51-40a9-8fc7-8b7d32ff15d0",
"metadata": {},
"outputs": [],
"source": [
"axes = ['kx', 'ky', 'energy', 'delay']\n",
"bins = [100, 100, 200, 50]\n",
"ranges = [[-2, 2], [-2, 2], [-4, 2], [-600, 1600]]\n",
"res = sp.compute(bins=bins, axes=axes, ranges=ranges)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "44fece87",
"metadata": {},
"outputs": [],
"source": [
"# save to NXmpes NeXus (including standardized metadata)\n",
"sp.save(data_path + \"/binned.nxs\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "3073b9ba",
"metadata": {},
"outputs": [],
"source": [
"# Visualization (requires JupyterLab)\n",
"from jupyterlab_h5web import H5Web\n",
"H5Web(data_path + \"/binned.nxs\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ee543128",
"metadata": {},
"outputs": [],
"source": []
}
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