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rettiglrettigl
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update pynxtools version and adjust nexus config
1 parent 5869eca commit 0a8a866

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Lines changed: 32 additions & 35 deletions

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‎pyproject.toml‎

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@@ -45,7 +45,7 @@ dependencies = [
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"photutils<2.0",
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"psutil>=5.9.0",
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"pynxtools-mpes>=0.2.2",
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"pynxtools>=0.10.1",
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"pynxtools>=0.10.6",
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"pyyaml>=6.0.0",
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"scipy>=1.8.0",
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"symmetrize>=0.5.5",

‎src/sed/config/NXmpes_config-HEXTOF.json‎

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@@ -6,7 +6,7 @@
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"/ENTRY[entry]/experiment_institution": "Deutsches Elektronen-Synchrotron DESY",
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"/ENTRY[entry]/experiment_facility": "Free-Electron Laser FLASH",
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"/ENTRY[entry]/experiment_laboratory": "@attrs:metadata/creationLocation",
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"/ENTRY/identifierNAME[entry_identifier]": "@attrs:metadata/pid",
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"/ENTRY/identifierNAME[identifier_entry]": "@attrs:metadata/pid",
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"/ENTRY[entry]/USER[user0]": {
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"name": "!@attrs:metadata/principalInvestigator",
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"role": "Principal investigator",
@@ -139,7 +139,7 @@
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"incident_polarization_stokes/@units": "V^2/mm^2",
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"associated_source": "/entry/instrument/source_probe"
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},
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"/ENTRY[entry]/INSTRUMENT[instrument]/monochromator[MONOCHROMATOR]": {
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"/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]": {
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"energy_dispersion": "@attrs:metadata/scientificMetadata/Source/dispersion/value",
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"energy_dispersion/@units": "@attrs:metadata/scientificMetadata/Source/dispersion/unit"
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},
@@ -196,12 +196,12 @@
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"voltmeter": "@link:/entry/instrument/manipulator/sample_bias_voltmeter"
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}
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},
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"/ENTRY[entry]/data": {
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"/ENTRY[entry]/DATA[data]": {
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"@axes": "@data:dims",
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"AXISNAME_indices[@*_indices]": "@data:*.index",
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"@signal": "data",
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"data": "@data:data",
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"data/@units": "counts",
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"DATA[data]": "@data:data",
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"DATA[data]/@units": "counts",
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"AXISNAME[*]": "@data:*.data",
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"AXISNAME[*]/@units": "@data:*.unit",
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"AXISNAME[energy]/@type": "@attrs:metadata/energy_calibration/calibration/energy_scale"

‎src/sed/config/NXmpes_config.json‎

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Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
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"/ENTRY/experiment_institution": "Fritz Haber Institute - Max Planck Society",
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"/ENTRY/experiment_facility": "Time Resolved ARPES",
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"/ENTRY/experiment_laboratory": "Clean Room 4",
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"/ENTRY/identifierNAME[entry_identifier]": "@attrs:metadata/entry_identifier",
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"/ENTRY/identifierNAME[identifier_entry]": "@attrs:metadata/entry_identifier",
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"/ENTRY/end_time": "@attrs:metadata/timing/acquisition_stop",
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"/ENTRY/duration": "@attrs:metadata/timing/acquisition_duration",
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"/ENTRY/duration/@units": "s",
@@ -24,22 +24,17 @@
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"name/@short_name": "TR-ARPES @ FHI",
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"energy_resolution": {
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"resolution": "!['@eln:/ENTRY/Instrument/Analyzer/energy_resolution', '@attrs:metadata/instrument/energy_resolution', '@attrs:metadata/elabFTW/trarpes_metis/energy_resolution']",
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"resolution/@units": "meV",
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"resolution/@units": "['@eln:/ENTRY/Instrument/energy_resolution/@units', 'meV']",
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"physical_quantity": "energy",
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"type": "estimated"
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},
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"RESOLUTION[temporal_resolution]": {
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"resolution": "!['@attrs:metadata/elabFTW/laser_status/temporal_resolution', '35.0']",
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"resolution/@units": "fs",
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"resolution": "!['@eln:/ENTRY/Instrument/temporal_resolution', '@attrs:metadata/instrument/temporal_resolution', '@attrs:metadata/elabFTW/laser_status/temporal_resolution']",
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"resolution/@units": "['@eln:/ENTRY/Instrument/temporal_resolution/@units', 'fs']",
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"physical_quantity": "time",
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"type": "estimated"
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},
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"RESOLUTION[momentum_resolution]": {
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"resolution": "@link:/entry/instrument/electronanalyzer/momentum_resolution",
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"resolution/@units": "1/angstrom",
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"physical_quantity": "momentum",
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"type": "estimated"
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},
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"RESOLUTION[momentum_resolution]": "@link:/entry/instrument/electronanalyzer/momentum_resolution",
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"pressure_gauge": {
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"name": "sample_chamber_pressure",
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"measurement": "pressure",
@@ -323,41 +318,41 @@
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},
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"/ENTRY/CALIBRATION[energy_calibration]":{
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"applied": "!@attrs:metadata/energy_calibration/applied",
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"fit_formula_inputs/TERM[coefficients]": "@attrs:metadata/energy_calibration/calibration/coefficients",
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"fit_formula_inputs/TERM[coefficients]/@units": "",
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"fit_formula_description": "@attrs:metadata/energy_calibration/calibration/fit_function",
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"original_axis": "@attrs:metadata/energy_calibration/tof",
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"fit_formula_inputs/PARAMETER[coefficients]": "['@attrs:metadata/energy_calibration/calibration/coefficients', '@attrs:metadata/energy_correction/calibration/coefficients']",
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"fit_formula_inputs/PARAMETER[coefficients]/@units": "",
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"fit_formula_description": "['@attrs:metadata/energy_calibration/calibration/fit_function', '@attrs:metadata/energy_correction/calibration/fit_function']",
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"original_axis": "['@attrs:metadata/energy_calibration/tof', '@attrs:metadata/energy_correction/tof']",
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"original_axis/@units": "",
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"calibrated_axis": "@attrs:metadata/energy_calibration/calibration/axis",
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"calibrated_axis": "['@attrs:metadata/energy_calibration/calibration/axis', '@attrs:metadata/energy_correction/calibration/axis']",
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"calibrated_axis/@units": "eV",
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"physical_quantity": "energy"
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},
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"/ENTRY/CALIBRATION[kx_calibration]": {
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"applied": "!@attrs:metadata/momentum_calibration/applied",
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"scaling_factor": "@attrs:metadata/momentum_calibration/calibration/kx_scale",
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"scaling_factor/@units": "",
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"offset": "@attrs:metadata/momentum_calibration/calibration/x_center",
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"offset/@units": "",
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"calibrated_axis": "@attrs:metadata/momentum_calibration/calibration/kx_axis",
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"calibration_parameters/scaling_factor": "['@attrs:metadata/momentum_calibration/calibration/kx_scale', '@attrs:metadata/momentum_correction/calibration/scale_kx']",
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"calibration_parameters/scaling_factor/@units": "",
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"calibration_parameters/offset": "['@attrs:metadata/momentum_calibration/calibration/x_center', '@attrs:metadata/momentum_correction/offset_kx']",
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"calibration_parameters/offset/@units": "",
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"calibrated_axis": "['@attrs:metadata/momentum_calibration/calibration/kx_axis', '@attrs:metadata/momentum_correction/calibration/axis_kx']",
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"calibrated_axis/@units": "1/angstrom",
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"physical_quantity": "momentum"
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},
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"/ENTRY/CALIBRATION[ky_calibration]": {
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"applied": "!@attrs:metadata/momentum_calibration/applied",
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"scaling_factor": "@attrs:metadata/momentum_calibration/calibration/ky_scale",
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"scaling_factor/@units": "",
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"offset": "@attrs:metadata/momentum_calibration/calibration/y_center",
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"offset/@units": "",
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"calibrated_axis": "@attrs:metadata/momentum_calibration/calibration/ky_axis",
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"calibration_parameters/scaling_factor": "['@attrs:metadata/momentum_calibration/calibration/ky_scale', '@attrs:metadata/momentum_correction/calibration/scale_ky']",
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"calibration_parameters/scaling_factor/@units": "",
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"calibration_parameters/offset": "['@attrs:metadata/momentum_calibration/calibration/y_center', '@attrs:metadata/momentum_correction/offset_ky']",
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"calibration_parameters/offset/@units": "",
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"calibrated_axis": "['@attrs:metadata/momentum_calibration/calibration/ky_axis', '@attrs:metadata/momentum_correction/calibration/axis_ky']",
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"calibrated_axis/@units": "1/angstrom",
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"physical_quantity": "momentum"
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},
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"/ENTRY/data": {
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"/ENTRY/DATA[data]": {
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"@axes": "@data:dims",
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"AXISNAME_indices[@*_indices]": "@data:*.index",
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"@AXISNAME_indices[@*_indices]": "@data:*.index",
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"@signal": "data",
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"data": "@data:data",
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"data/@units": "counts",
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"DATA[data]": "@data:data",
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"DATA[data]/@units": "counts",
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"AXISNAME[*]": "@data:*.data",
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"AXISNAME[*]/@units": "@data:*.unit",
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"AXISNAME[energy]/@type": "['@attrs:metadata/energy_calibration/calibration/energy_scale', 'kinetic']"

‎tutorial/3_metadata_collection_and_export_to_NeXus.ipynb‎

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@@ -76,6 +76,7 @@
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"#NXinstrument\n",
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"metadata['instrument'] = {}\n",
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"metadata['instrument']['energy_resolution'] = 140.\n",
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"metadata['instrument']['temporal_resolution'] = 35.\n",
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"#analyzer\n",
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"metadata['instrument']['analyzer']={}\n",
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"metadata['instrument']['analyzer']['slow_axes'] = \"delay\" # the scanned axes\n",

‎tutorial/4_hextof_workflow.ipynb‎

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@@ -896,6 +896,7 @@
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"# Fix metadata\n",
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"metadata[\"scientificMetadata\"][\"Source\"][\"photon_energy\"][\"value\"] = float(metadata[\"scientificMetadata\"][\"Source\"][\"photon_energy\"][\"value\"])\n",
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"metadata[\"scientificMetadata\"][\"Source\"][\"repetition_rate\"][\"value\"] = float(metadata[\"scientificMetadata\"][\"Source\"][\"repetition_rate\"][\"value\"])\n",
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"metadata[\"scientificMetadata\"][\"Source\"][\"dispersion\"][\"value\"] = float(metadata[\"scientificMetadata\"][\"Source\"][\"dispersion\"][\"value\"])\n",
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"metadata[\"scientificMetadata\"][\"Laser\"][\"wavelength\"][\"value\"] = float(metadata[\"scientificMetadata\"][\"Laser\"][\"wavelength\"][\"value\"][:-2])\n",
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"metadata[\"scientificMetadata\"][\"Laser\"][\"pulse duration\"][\"value\"] = float(metadata[\"scientificMetadata\"][\"Laser\"][\"pulse duration\"][\"value\"])\n",
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"metadata[\"scientificMetadata\"][\"Laser\"][\"pulse_energy\"][\"value\"] = float(metadata[\"scientificMetadata\"][\"Laser\"][\"pulse_energy\"][\"value\"])\n",

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