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[package.extras] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [extras] all = [] @@ -5060,4 +5050,4 @@ notebook = ["ipykernel", "jupyter", "jupyterlab", "jupyterlab-h5web"] [metadata] lock-version = "2.0" python-versions = ">=3.9, <3.12.3, !=3.11.9" -content-hash = "265a1dbea287706d3c38523717243712ed11ab3d8ffa0d8ac55cf3fa29e7a635" +content-hash = "8c1003f86a5981c9514947b1ba8ddb44933aacd6ec695a57ea2d94f610dc8858" diff --git a/pyproject.toml b/pyproject.toml index 2ad3f4f9..75e4892b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "sed-processor" packages = [ {include = "sed"} ] -version = "0.1.10a9" +version = "0.2.1a0" description = "Single Event Data Frame Processor: Backend to handle photoelectron resolved datastreams" authors = ["OpenCOMPES team "] readme = "README.md" @@ -27,8 +27,8 @@ numba = ">=0.55.1" numpy = ">=1.18, <2.0" pandas = ">=1.4.1" psutil = ">=5.9.0" -pynxtools-mpes = "^0.1.1" -pynxtools = "^0.5.1" +pynxtools-mpes = "^0.2.0" +pynxtools = "^0.7.0" pyyaml = ">=6.0.0" scipy = ">=1.8.0" symmetrize = ">=0.5.5" diff --git a/sed/calibrator/energy.py b/sed/calibrator/energy.py index 68cbb3f3..62e5a4ff 100644 --- a/sed/calibrator/energy.py +++ b/sed/calibrator/energy.py @@ -959,9 +959,11 @@ def gather_calibration_metadata(self, calibration: dict = None) -> dict: metadata["applied"] = True metadata["calibration"] = deepcopy(calibration) metadata["tof"] = deepcopy(self.tof) + if metadata["tof"] is None: + metadata["tof"] = 0.0 # create empty calibrated axis entry, if it is not present. if "axis" not in metadata["calibration"]: - metadata["calibration"]["axis"] = 0 + metadata["calibration"]["axis"] = 0.0 return metadata diff --git a/sed/config/NXmpes_config.json b/sed/config/NXmpes_config.json index af065f1d..62110337 100755 --- a/sed/config/NXmpes_config.json +++ b/sed/config/NXmpes_config.json @@ -1,30 +1,31 @@ { "/@default": "entry", - "/ENTRY[entry]/@default": "data", - "/ENTRY[entry]/definition": "NXmpes", - "/ENTRY[entry]/title": "@attrs:metadata/entry_title", - "/ENTRY[entry]/start_time": "@attrs:metadata/timing/acquisition_start", - "/ENTRY[entry]/experiment_institution": "Fritz Haber Institute - Max Planck Society", - "/ENTRY[entry]/experiment_facility": "Time Resolved ARPES", - "/ENTRY[entry]/experiment_laboratory": "Clean Room 4", - "/ENTRY[entry]/entry_identifier": "@attrs:metadata/entry_identifier", - "/ENTRY[entry]/end_time": "@attrs:metadata/timing/acquisition_stop", - "/ENTRY[entry]/duration": "@attrs:metadata/timing/acquisition_duration", - "/ENTRY[entry]/duration/@units": "s", - "/ENTRY[entry]/collection_time": "@attrs:metadata/timing/collection_time", - "/ENTRY[entry]/collection_time/@units": "s", - "/ENTRY[entry]/USER[user]": { - "name": "!@attrs:metadata/user0/name", - "role": "@attrs:metadata/user0/role", - "affiliation": "!@attrs:metadata/user0/affiliation", - "address": "@attrs:metadata/user0/address", - "email": "@attrs:metadata/user0/email" + "/ENTRY/@default": "data", + "/ENTRY/title": "['@eln:/ENTRY/title', '@attrs:metadata/entry_title']", + "/ENTRY/start_time": "@attrs:metadata/timing/acquisition_start", + "/ENTRY/experiment_institution": "Fritz Haber Institute - Max Planck Society", + "/ENTRY/experiment_facility": "Time Resolved ARPES", + "/ENTRY/experiment_laboratory": "Clean Room 4", + "/ENTRY/entry_identifier": { + "identifier":"@attrs:metadata/entry_identifier" }, - "/ENTRY[entry]/INSTRUMENT[instrument]": { + "/ENTRY/end_time": "@attrs:metadata/timing/acquisition_stop", + "/ENTRY/duration": "@attrs:metadata/timing/acquisition_duration", + "/ENTRY/duration/@units": "s", + "/ENTRY/collection_time": "@attrs:metadata/timing/collection_time", + "/ENTRY/collection_time/@units": "s", + "/ENTRY/USER[user]": { + "name": "!['@eln:/ENTRY/User/name', '@attrs:metadata/user0/name']", + "role": "['@eln:/ENTRY/User/role', '@attrs:metadata/user0/role']", + "affiliation": "!['@eln:/ENTRY/User/affiliation', '@attrs:metadata/user0/affiliation']", + "address": "['@eln:/ENTRY/User/address', '@attrs:metadata/user0/address']", + "email": "['@eln:/ENTRY/User/email', '@attrs:metadata/user0/email']" + }, + "/ENTRY/INSTRUMENT[instrument]": { "name": "Time-of-flight momentum microscope equipped delay line detector, at the endstation of the high rep-rate HHG source at FHI", "name/@short_name": "TR-ARPES @ FHI", "energy_resolution": { - "resolution": 140.0, + "resolution": "!['@eln:/ENTRY/Instrument/Analyzer/energy_resolution', '@attrs:metadata/instrument/energy_resolution']", "resolution/@units": "meV", "physical_quantity": "energy", "type": "estimated" @@ -44,229 +45,203 @@ "pressure_gauge": { "name": "sample_chamber_pressure", "measurement": "pressure", - "value": "!@attrs:metadata/file/trARPES:XGS600:PressureAC:P_RD", + "value": "!['@eln:/ENTRY/Sample/gas_pressure', '@attrs:metadata/file/trARPES:XGS600:PressureAC:P_RD']", "value/@units": "mbar" - } - }, - - "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]": { - "description": "SPECS Metis 1000 Momentum Microscope", - "device_information": { - "vendor": "SPECS GmbH", - "model": "Metis 1000 Momentum Microscope" }, - "fast_axes": [ - "kx", - "ky", - "E" - ], - "slow_axes": "@attrs:metadata/instrument/analyzer/slow_axes", - "energy_resolution": { - "resolution": "!@attrs:metadata/instrument/analyzer/energy_resolution", - "resolution/@units": "meV", - "physical_quantity": "energy", - "type": "estimated" + "ELECTRONANALYSER[electronanalyser]": { + "description": "SPECS Metis 1000 Momentum Microscope", + "device_information": { + "vendor": "SPECS GmbH", + "model": "Metis 1000 Momentum Microscope" + }, + "fast_axes": ["kx", "ky", "E"], + "slow_axes": "@attrs:metadata/instrument/analyzer/slow_axes", + "energy_resolution": { + "resolution": "!['@eln:/ENTRY/Instrument/Analyzer/energy_resolution', '@attrs:metadata/instrument/analyzer/energy_resolution']", + "resolution/@units": "meV", + "physical_quantity": "energy", + "type": "estimated" + }, + "momentum_resolution": { + "resolution": "!['@eln:/ENTRY/Instrument/Analyzer/momentum_resolution', '@attrs:metadata/instrument/analyzer/momentum_resolution']", + "resolution/@units": "1/angstrom", + "physical_quantity": "momentum", + "type": "estimated" + }, + "spatial_resolution": { + "resolution": "!['@eln:/ENTRY/Instrument/Analyzer/spatial_resolution', '@attrs:metadata/instrument/analyzer/spatial_resolution']", + "resolution/@units": "µm", + "physical_quantity": "length", + "type": "estimated" + }, + "depends_on": "/entry/instrument/electronanalyser/transformations/trans_z", + "TRANSFORMATIONS[transformations]": { + "AXISNAME[trans_z]": 4.0, + "AXISNAME[trans_z]/@depends_on": "rot_y", + "AXISNAME[trans_z]/@transformation_type": "translation", + "AXISNAME[trans_z]/@units": "mm", + "AXISNAME[trans_z]/@vector": [0, 0, 1], + "AXISNAME[rot_y]": -115.0, + "AXISNAME[rot_y]/@depends_on": ".", + "AXISNAME[rot_y]/@transformation_type": "rotation", + "AXISNAME[rot_y]/@units": "degrees", + "AXISNAME[rot_y]/@vector": [0, 1, 0] + }, + "COLLECTIONCOLUMN[collectioncolumn]": { + "projection": "@attrs:metadata/instrument/analyzer/projection", + "scheme": "@attrs:metadata/instrument/analyzer/scheme", + "lens_mode": "@attrs:metadata/instrument/analyzer/lens_mode", + "extractor_voltage": "@attrs:metadata/file/KTOF:Lens:Extr:V", + "extractor_voltage/@units": "V", + "extractor_current": "@attrs:metadata/file/KTOF:Lens:Extr:I", + "extractor_current/@units": "µA", + "working_distance": 4.0, + "working_distance/@units": "mm", + "LENS_EM[lens_*{A,B,C,D,E,F,G,H,I,UCA,UFA,Foc}]": { + "name": "*", + "voltage": "@attrs:metadata/file/KTOF:Lens:*:V", + "voltage/@units": "V" + }, + "field_aperture": { + "shape": "@attrs:metadata/instrument/analyzer/fa_shape", + "size": "@attrs:metadata/instrument/analyzer/fa_size", + "size/@units": "µm", + "POSITIONER[fa_m1]": { + "value": "@attrs:metadata/file/KTOF:Apertures:m1.RBV", + "value/@units": "mm" + }, + "POSITIONER[fa_m2]": { + "value": "@attrs:metadata/file/KTOF:Apertures:m2.RBV", + "value/@units": "mm" + } + }, + "contrast_aperture": { + "shape": "@attrs:metadata/instrument/analyzer/ca_shape", + "size": "@attrs:metadata/instrument/analyzer/ca_size", + "size/@units": "µm", + "POSITIONER[ca_m3]": { + "value": "@attrs:metadata/file/KTOF:Apertures:m3.RBV", + "value/@units": "mm" + } + } + }, + "ENERGYDISPERSION[energydispersion]": { + "pass_energy": "@attrs:metadata/file/KTOF:Lens:TOF:V", + "pass_energy/@units": "eV", + "scheme": "tof", + "tof_distance": 0.9, + "tof_distance/@units": "m" + }, + "DETECTOR[detector]": { + "amplifier_type": "MCP", + "detector_type": "DLD", + "sensor_pixels": [1800, 1800], + "sensor_pixels/@units": "", + "amplifier_bias": "@attrs:metadata/file/KTOF:Lens:MCPfront:V", + "amplifier_bias/@units": "V", + "amplifier_voltage": "@attrs:metadata/file/KTOF:Lens:MCPback:V", + "amplifier_voltage/@units": "V", + "detector_voltage": "@attrs:metadata/file/KTOF:Lens:UDLD:V", + "detector_voltage/@units": "V" + } }, - "momentum_resolution": { - "resolution": "!@attrs:metadata/instrument/analyzer/momentum_resolution", - "resolution/@units": "1/angstrom", - "physical_quantity": "momentum", - "type": "estimated" + "sourceTYPE[source_probe]": { + "name": "HHG @ TR-ARPES @ FHI", + "probe": "photon", + "type": "HHG laser", + "mode": "Single Bunch", + "frequency": "['@eln:/ENTRY/Instrument/Source/Probe/frequency', '@attrs:metadata/instrument/beam/probe/frequency']", + "frequency/@units": "kHz", + "associated_beam": "/entry/instrument/beam_probe" }, - "spatial_resolution": { - "resolution": "!@attrs:metadata/instrument/analyzer/spatial_resolution", - "resolution/@units": "µm", - "physical_quantity": "length", - "type": "estimated" + "beamTYPE[beam_probe]": { + "distance": 0.0, + "distance/@units": "mm", + "incident_energy": "!['@eln:/ENTRY/Instrument/Beam/Probe/incident_energy', '@attrs:metadata/instrument/beam/probe/incident_energy']", + "incident_energy/@units": "eV", + "incident_energy_spread": "['@eln:/ENTRY/Instrument/Beam/Probe/incident_energy_spread', '@attrs:metadata/instrument/beam/probe/incident_energy_spread']", + "incident_energy_spread/@units": "eV", + "pulse_duration": "['@eln:/ENTRY/Instrument/Beam/Probe/pulse_duration', '@attrs:metadata/instrument/beam/probe/pulse_duration']", + "pulse_duration/@units": "fs", + "incident_polarization": "['@eln:/ENTRY/Instrument/Beam/Probe/incident_polarization', '@attrs:metadata/instrument/beam/probe/incident_polarization']", + "incident_polarization/@units": "V^2/mm^2", + "extent": "['@eln:/ENTRY/Instrument/Beam/Probe/extent', '@attrs:metadata/instrument/beam/probe/extent']", + "extent/@units": "µm", + "associated_source": "/entry/instrument/source_probe" }, - "depends_on": "/entry/instrument/electronanalyser/transformations/trans_z", - "TRANSFORMATIONS[transformations]": { - "AXISNAME[trans_z]": 4.0, - "AXISNAME[trans_z]/@depends_on": "rot_y", - "AXISNAME[trans_z]/@transformation_type": "translation", - "AXISNAME[trans_z]/@units": "mm", - "AXISNAME[trans_z]/@vector": [ - 0, - 0, - 1 - ], - "AXISNAME[rot_y]": -115.0, - "AXISNAME[rot_y]/@depends_on": ".", - "AXISNAME[rot_y]/@transformation_type": "rotation", - "AXISNAME[rot_y]/@units": "degrees", - "AXISNAME[rot_y]/@vector": [ - 0, - 1, - 0 - ] - } - }, - "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]": { - "projection": "@attrs:metadata/instrument/analyzer/projection", - "scheme": "@attrs:metadata/instrument/analyzer/scheme", - "lens_mode": "@attrs:metadata/instrument/analyzer/lens_mode", - "extractor_voltage": "@attrs:metadata/file/KTOF:Lens:Extr:V", - "extractor_voltage/@units": "V", - "extractor_current": "@attrs:metadata/file/KTOF:Lens:Extr:I", - "extractor_current/@units": "µA", - "working_distance": 4.0, - "working_distance/@units": "mm", - "LENS_EM[lens_*{A,B,C,D,E,F,G,H,I,UCA,UFA,Foc}]": { - "name": "*", - "voltage": "@attrs:metadata/file/KTOF:Lens:*:V", - "voltage/@units": "V" + "sourceTYPE[source_pump]": { + "name": "OPCPA @ TR-ARPES @ FHI", + "probe": "visible light", + "type": "Optical Laser", + "mode": "Single Bunch", + "frequency": "['@eln:/ENTRY/Instrument/Source/Pump/frequency', '@attrs:metadata/instrument/beam/pump/frequency']", + "frequency/@units": "kHz", + "associated_beam": "/entry/instrument/beam_pump" }, - "field_aperture": { - "shape": "@attrs:metadata/instrument/analyzer/fa_shape", - "size": "@attrs:metadata/instrument/analyzer/fa_size", - "size/@units": "µm", - "POSITIONER[fa_m1]": { - "value": "@attrs:metadata/file/KTOF:Apertures:m1.RBV", - "value/@units": "mm" - }, - "POSITIONER[fa_m2]": { - "value": "@attrs:metadata/file/KTOF:Apertures:m2.RBV", - "value/@units": "mm" - } + "beamTYPE[beam_pump]": { + "distance": 0.0, + "distance/@units": "mm", + "incident_energy": "!['@eln:/ENTRY/Instrument/Beam/Pump/incident_energy', '@attrs:metadata/instrument/beam/pump/incident_energy']", + "incident_energy/@units": "eV", + "incident_energy_spread": "['@eln:/ENTRY/Instrument/Beam/Pump/incident_energy_spread', '@attrs:metadata/instrument/beam/pump/incident_energy_spread']", + "incident_energy_spread/@units": "eV", + "incident_wavelength": "['@eln:/ENTRY/Instrument/Beam/Pump/incident_wavelength', '@attrs:metadata/instrument/beam/pump/incident_wavelength']", + "incident_wavelength/@units": "nm", + "pulse_duration": "['@eln:/ENTRY/Instrument/Beam/Pump/pulse_duration', '@attrs:metadata/instrument/beam/pump/pulse_duration']", + "pulse_duration/@units": "fs", + "incident_polarization": "['@eln:/ENTRY/Instrument/Beam/Pump/incident_polarization', '@attrs:metadata/instrument/beam/pump/incident_polarization']", + "incident_polarization/@units": "V^2/mm^2", + "pulse_energy": "['@eln:/ENTRY/Instrument/Beam/Pump/pulse_energy', '@attrs:metadata/instrument/beam/pump/pulse_energy']", + "pulse_energy/@units": "µJ", + "average_power": "['@eln:/ENTRY/Instrument/Beam/Pump/average_power', '@attrs:metadata/instrument/beam/pump/average_power']", + "average_power/@units": "mW", + "extent": "['@eln:/ENTRY/Instrument/Beam/Pump/extent', '@attrs:metadata/instrument/beam/pump/extent']", + "extent/@units": "µm", + "fluence": "['@eln:/ENTRY/Instrument/Beam/Pump/fluence', '@attrs:metadata/instrument/beam/pump/fluence']", + "fluence/@units": "mJ/cm^2", + "associated_source": "/entry/instrument/source_pump" }, - "contrast_aperture": { - "shape": "@attrs:metadata/instrument/analyzer/ca_shape", - "size": "@attrs:metadata/instrument/analyzer/ca_size", - "size/@units": "µm", - "POSITIONER[ca_m3]": { - "value": "@attrs:metadata/file/KTOF:Apertures:m3.RBV", - "value/@units": "mm" + "MANIPULATOR[manipulator]": { + "temperature_sensor": { + "name": "sample_temperature", + "measurement": "temperature", + "value": "!['@eln:/ENTRY/Instrument/Manipulator/sample_temperature', '@attrs:metadata/file/trARPES:Carving:TEMP_RBV']", + "value/@units": "K" + }, + "sample_bias_voltmeter": { + "name": "sample_bias", + "measurement": "voltage", + "value": "!@attrs:metadata/file/KTOF:Lens:Sample:V", + "value/@units": "V" + }, + "depends_on": "/entry/instrument/manipulator/transformations/trans_z", + "TRANSFORMATIONS[transformations]": { + "AXISNAME[trans_z]": -0.32, + "AXISNAME[trans_z]/@depends_on": "rot_z", + "AXISNAME[trans_z]/@transformation_type": "translation", + "AXISNAME[trans_z]/@units": "m", + "AXISNAME[trans_z]/@vector": [0, 0, 1], + "AXISNAME[rot_z]/@depends_on": "rot_x", + "AXISNAME[rot_z]": -25.0, + "AXISNAME[rot_z]/@transformation_type": "rotation", + "AXISNAME[rot_z]/@units": "degrees", + "AXISNAME[rot_z]/@vector": [0, 0, 1], + "AXISNAME[rot_x]/@depends_on": ".", + "AXISNAME[rot_x]": -90.0, + "AXISNAME[rot_x]/@transformation_type": "rotation", + "AXISNAME[rot_x]/@units": "degrees", + "AXISNAME[rot_x]/@vector": [1, 0, 0] } } }, - "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]": { - "pass_energy": "@attrs:metadata/file/KTOF:Lens:TOF:V", - "pass_energy/@units": "eV", - "scheme": "tof", - "tof_distance": 0.9, - "tof_distance/@units": "m" - }, - "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]": { - "amplifier_type": "MCP", - "detector_type": "DLD", - "sensor_pixels": [ - 1800, - 1800 - ], - "amplifier_bias": "@attrs:metadata/file/KTOF:Lens:MCPfront:V", - "amplifier_bias/@units": "V", - "amplifier_voltage": "@attrs:metadata/file/KTOF:Lens:MCPback:V", - "amplifier_voltage/@units": "V", - "detector_voltage": "@attrs:metadata/file/KTOF:Lens:UDLD:V", - "detector_voltage/@units": "V" - }, - "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_probe]": { - "name": "HHG @ TR-ARPES @ FHI", - "probe": "photon", - "type": "HHG laser", - "mode": "Single Bunch", - "frequency": "@attrs:metadata/instrument/beam/probe/frequency", - "frequency/@units": "kHz", - "associated_beam": "/entry/instrument/beam_probe" - }, - "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_probe]": { - "distance": 0.0, - "distance/@units": "mm", - "incident_energy": "!@attrs:metadata/instrument/beam/probe/incident_energy", - "incident_energy/@units": "eV", - "incident_energy_spread": "@attrs:metadata/instrument/beam/probe/incident_energy_spread", - "incident_energy_spread/@units": "eV", - "pulse_duration": "@attrs:metadata/instrument/beam/probe/pulse_duration", - "pulse_duration/@units": "fs", - "incident_polarization": "@attrs:metadata/instrument/beam/probe/incident_polarization", - "incident_polarization/@units": "V^2/mm^2", - "extent": "@attrs:metadata/instrument/beam/probe/extent", - "extent/@units": "µm", - "associated_source": "/entry/instrument/source_probe" - }, - "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_pump]": { - "name": "OPCPA @ TR-ARPES @ FHI", - "probe": "visible light", - "type": "Optical Laser", - "mode": "Single Bunch", - "frequency": "@attrs:metadata/instrument/beam/pump/frequency", - "frequency/@units": "kHz", - "associated_beam": "/entry/instrument/beam_pump" - }, - "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]": { - "distance": 0.0, - "distance/@units": "mm", - "incident_energy": "!@attrs:metadata/instrument/beam/pump/incident_energy", - "incident_energy/@units": "eV", - "incident_energy_spread": "@attrs:metadata/instrument/beam/pump/incident_energy_spread", - "incident_energy_spread/@units": "eV", - "incident_wavelength": "@attrs:metadata/instrument/beam/pump/incident_wavelength", - "incident_wavelength/@units": "nm", - "pulse_duration": "@attrs:metadata/instrument/beam/pump/pulse_duration", - "pulse_duration/@units": "fs", - "incident_polarization": "@attrs:metadata/instrument/beam/pump/incident_polarization", - "incident_polarization/@units": "V^2/mm^2", - "pulse_energy": "@attrs:metadata/instrument/beam/pump/pulse_energy", - "pulse_energy/@units": "µJ", - "average_power": "@attrs:metadata/instrument/beam/pump/average_power", - "average_power/@units": "mW", - "extent": "@attrs:metadata/instrument/beam/pump/extent", - "extent/@units": "µm", - "fluence": "@attrs:metadata/instrument/beam/pump/fluence", - "fluence/@units": "mJ/cm^2", - "associated_source": "/entry/instrument/source_pump" - }, - "/ENTRY[entry]/INSTRUMENT[instrument]/MANIPULATOR[manipulator]": { - "temperature_sensor": { - "name": "sample_temperature", - "measurement": "temperature", - "value": "!@attrs:metadata/file/trARPES:Carving:TEMP_RBV", - "value/@units": "K" - }, - "sample_bias_voltmeter": { - "name": "sample_bias", - "measurement": "voltage", - "value": "!@attrs:metadata/file/KTOF:Lens:Sample:V", - "value/@units": "V" - }, - "depends_on": "/entry/instrument/manipulator/transformations/trans_z", - "TRANSFORMATIONS[transformations]": { - "AXISNAME[trans_z]": -0.32, - "AXISNAME[trans_z]/@depends_on": "rot_z", - "AXISNAME[trans_z]/@transformation_type": "translation", - "AXISNAME[trans_z]/@units": "m", - "AXISNAME[trans_z]/@vector": [ - 0, - 0, - 1 - ], - "AXISNAME[rot_z]/@depends_on": "rot_x", - "AXISNAME[rot_z]": -25.0, - "AXISNAME[rot_z]/@transformation_type": "rotation", - "AXISNAME[rot_z]/@units": "degrees", - "AXISNAME[rot_z]/@vector": [ - 0, - 0, - 1 - ], - "AXISNAME[rot_x]/@depends_on": ".", - "AXISNAME[rot_x]": -90.0, - "AXISNAME[rot_x]/@transformation_type": "rotation", - "AXISNAME[rot_x]/@units": "degrees", - "AXISNAME[rot_x]/@vector": [ - 1, - 0, - 0 - ] - } - }, - "/ENTRY[entry]/SAMPLE[sample]": { - "preparation_date": "@attrs:metadata/sample/preparation_date", - "history/notes/description": "@attrs:metadata/sample/sample_history", - "description": "@attrs:metadata/sample/chemical_formula", - "name": "@attrs:metadata/sample/name", + "/ENTRY/SAMPLE[sample]": { + "preparation_date": "['@eln:/ENTRY/Sample/preparation_date', '@attrs:metadata/sample/preparation_date']", + "history/notes/description": "['@eln:/ENTRY/Sample/sample_history', '@attrs:metadata/sample/sample_history']", + "history/notes/type": "text/plain", + "description": "['@eln:/ENTRY/Sample/description', '@attrs:metadata/sample/chemical_formula']", + "name": "['@eln:/ENTRY/Sample/name', '@attrs:metadata/sample/name']", "situation": "vacuum", - "SUBSTANCE[substance]/molecular_formula_hill": "@attrs:metadata/sample/chemical_formula", + "SUBSTANCE[substance]/molecular_formula_hill": "['@eln:/ENTRY/Sample/chemical_formula', '@attrs:metadata/sample/chemical_formula']", "temperature_env": { "temperature_sensor": "@link:/entry/instrument/manipulator/temperature_sensor" }, @@ -282,122 +257,105 @@ "AXISNAME[corrected_phi]": 90.0, "AXISNAME[corrected_phi]/@units": "degrees", "AXISNAME[corrected_phi]/@transformation_type": "rotation", - "AXISNAME[corrected_phi]/@vector": [ - 0, - 1, - 0 - ], + "AXISNAME[corrected_phi]/@vector": [0, 1, 0], "AXISNAME[rot_omg]/@depends_on": "rot_phi", "AXISNAME[rot_omg]": "@attrs:metadata/file/trARPES:Carving:OMG.RBV", "AXISNAME[rot_omg]/@units": "degrees", "AXISNAME[rot_omg]/@transformation_type": "rotation", - "AXISNAME[rot_omg]/@vector": [ - 1, - 0, - 0 - ], + "AXISNAME[rot_omg]/@vector": [1, 0, 0], "AXISNAME[rot_phi]/@depends_on": "rot_tht", "AXISNAME[rot_phi]": "@attrs:metadata/file/trARPES:Carving:PHI.RBV", "AXISNAME[rot_phi]/@units": "degrees", "AXISNAME[rot_phi]/@transformation_type": "rotation", - "AXISNAME[rot_phi]/@vector": [ - 0, - 1, - 0 - ], + "AXISNAME[rot_phi]/@vector": [0, 1, 0], "AXISNAME[rot_tht]/@depends_on": "trans_z", "AXISNAME[rot_tht]": "@attrs:metadata/file/trARPES:Carving:THT.RBV", "AXISNAME[rot_tht]/@units": "degrees", "AXISNAME[rot_tht]/@transformation_type": "rotation", - "AXISNAME[rot_tht]/@vector": [ - 0, - 0, - 1 - ], + "AXISNAME[rot_tht]/@vector": [0, 0, 1], "AXISNAME[trans_z]/@depends_on": "trans_y", "AXISNAME[trans_z]": "@attrs:metadata/file/trARPES:Carving:TRZ.RBV", "AXISNAME[trans_z]/@units": "mm", "AXISNAME[trans_z]/@transformation_type": "translation", - "AXISNAME[trans_z]/@vector": [ - 0, - 0, - 1 - ], + "AXISNAME[trans_z]/@vector": [0, 0, 1], "AXISNAME[trans_y]/@depends_on": "trans_x", "AXISNAME[trans_y]": "@attrs:metadata/file/trARPES:Carving:TRY.RBV", "AXISNAME[trans_y]/@units": "mm", "AXISNAME[trans_y]/@transformation_type": "translation", - "AXISNAME[trans_y]/@vector": [ - 0, - 1, - 0 - ], + "AXISNAME[trans_y]/@vector": [0, 1, 0], "AXISNAME[trans_x]/@depends_on": "/entry/instrument/manipulator/transformations/trans_z", "AXISNAME[trans_x]": "@attrs:metadata/file/trARPES:Carving:TRX.RBV", "AXISNAME[trans_x]/@units": "mm", "AXISNAME[trans_x]/@transformation_type": "translation", - "AXISNAME[trans_x]/@vector": [ - 1, - 0, - 0 - ] + "AXISNAME[trans_x]/@vector": [1, 0, 0] } }, - "/ENTRY[entry]/PROCESS[process]/DISTORTION[distortion]": { - "symmetry": "@attrs:metadata/momentum_correction/correction/rotation_symmetry", + "/ENTRY/PROCESS_MPES[process]/DISTORTION[distortion]": { + "symmetry": "!@attrs:metadata/momentum_correction/correction/rotation_symmetry", + "symmetry/@units": "", "original_centre": "@attrs:metadata/momentum_correction/correction/center_point", + "original_centre/@units": "", "original_points": "@attrs:metadata/momentum_correction/correction/outer_points", + "original_points/@units": "", "cdeform_field": "@attrs:metadata/momentum_correction/correction/cdeform_field", - "rdeform_field": "@attrs:metadata/momentum_correction/correction/rdeform_field" + "cdeform_field/@units": "", + "rdeform_field": "@attrs:metadata/momentum_correction/correction/rdeform_field", + "rdeform_field/@units": "" }, - "/ENTRY[entry]/PROCESS[process]/REGISTRATION[registration]": { - "depends_on": "@attrs:metadata/momentum_correction/registration/depends_on", + "/ENTRY/PROCESS_MPES[process]/REGISTRATION[registration]": { + "depends_on": "/entry/process/registration/transformations/rot_z", "TRANSFORMATIONS[transformations]": { "AXISNAME[trans_x]": "@attrs:metadata/momentum_correction/registration/trans_x/value", - "AXISNAME[trans_x]/@transformation_type": "@attrs:metadata/momentum_correction/registration/trans_x/type", - "AXISNAME[trans_x]/@units": "@attrs:metadata/momentum_correction/registration/trans_x/units", + "AXISNAME[trans_x]/@transformation_type": "translation", + "AXISNAME[trans_x]/@units": "pixels", "AXISNAME[trans_x]/@vector": "@attrs:metadata/momentum_correction/registration/trans_x/vector", "AXISNAME[trans_x]/@depends_on": "@attrs:metadata/momentum_correction/registration/trans_x/depends_on", "AXISNAME[trans_y]": "@attrs:metadata/momentum_correction/registration/trans_y/value", - "AXISNAME[trans_y]/@units": "@attrs:metadata/momentum_correction/registration/trans_y/units", - "AXISNAME[trans_y]/@transformation_type": "@attrs:metadata/momentum_correction/registration/trans_y/type", + "AXISNAME[trans_y]/@units": "pixels", + "AXISNAME[trans_y]/@transformation_type": "translation", "AXISNAME[trans_y]/@vector": "@attrs:metadata/momentum_correction/registration/trans_y/vector", "AXISNAME[trans_y]/@depends_on": "@attrs:metadata/momentum_correction/registration/trans_y/depends_on", "AXISNAME[rot_z]": "@attrs:metadata/momentum_correction/registration/rot_z/value", - "AXISNAME[rot_z]/@units": "@attrs:metadata/momentum_correction/registration/rot_z/units", - "AXISNAME[rot_z]/@transformation_type": "@attrs:metadata/momentum_correction/registration/rot_z/type", + "AXISNAME[rot_z]/@units": "degrees", + "AXISNAME[rot_z]/@transformation_type": "rotation", "AXISNAME[rot_z]/@offset": "@attrs:metadata/momentum_correction/registration/rot_z/offset", "AXISNAME[rot_z]/@vector": "@attrs:metadata/momentum_correction/registration/rot_z/vector", "AXISNAME[rot_z]/@depends_on": "@attrs:metadata/momentum_correction/registration/rot_z/depends_on" } }, - "/ENTRY[entry]/PROCESS_MPES[process]/energy_calibration":{ + "/ENTRY/PROCESS_MPES[process]/energy_calibration":{ "coefficients": "@attrs:metadata/energy_calibration/calibration/coefficients", + "coefficients/@units": "", "fit_function": "@attrs:metadata/energy_calibration/calibration/fit_function", "original_axis": "@attrs:metadata/energy_calibration/tof", + "original_axis/@units": "ns", "calibrated_axis": "@attrs:metadata/energy_calibration/calibration/axis", - "calibrated_axis/@units": "eV" + "calibrated_axis/@units": "eV", + "physical_quantity": "energy" }, - "/ENTRY[entry]/PROCESS_MPES[process]/kx_calibration": { + "/ENTRY/PROCESS_MPES[process]/kx_calibration": { "scaling": "@attrs:metadata/momentum_calibration/calibration/kx_scale", + "scaling/@units": "", "offset": "@attrs:metadata/momentum_calibration/calibration/x_center", + "offset/@units": "", "calibrated_axis": "@attrs:metadata/momentum_calibration/calibration/kx_axis", - "calibrated_axis/@units": "Angstrom^-1" + "calibrated_axis/@units": "1/angstrom", + "physical_quantity": "momentum" }, - "/ENTRY[entry]/PROCESS_MPES[process]/ky_calibration": { + "/ENTRY/PROCESS_MPES[process]/ky_calibration": { "scaling": "@attrs:metadata/momentum_calibration/calibration/ky_scale", "offset": "@attrs:metadata/momentum_calibration/calibration/y_center", "calibrated_axis": "@attrs:metadata/momentum_calibration/calibration/ky_axis", "calibrated_axis/@units": "Angstrom^-1" }, - "/ENTRY[entry]/data": { + "/ENTRY/data": { "@axes": "@data:dims", - "AXISNAME_indices[@*_indices]": "@data:*.index", + "@*_indices": "@data:*.index", "@signal": "data", "data": "@data:data", "data/@units": "counts", - "AXISNAME[*]": "@data:*.data", - "AXISNAME[*]/@units": "@data:*.unit", + "*": "@data:*.data", + "*/@units": "@data:*.unit", "energy/@type": "@attrs:metadata/energy_calibration/calibration/energy_scale" } } diff --git a/tests/test_processor.py b/tests/test_processor.py index 84ee76a2..21e4df86 100644 --- a/tests/test_processor.py +++ b/tests/test_processor.py @@ -5,6 +5,7 @@ import csv import glob import itertools +import json import logging import os import tempfile @@ -1045,6 +1046,7 @@ def test_get_normalization_histogram() -> None: metadata["user0"]["affiliation"] = "affiliation" # instrument metadata["instrument"] = {} +metadata["instrument"]["energy_resolution"] = 150.0 # analyzer metadata["instrument"]["analyzer"] = {} metadata["instrument"]["analyzer"]["energy_resolution"] = 110.0 @@ -1119,21 +1121,33 @@ def test_save(caplog) -> None: caplog.clear() with open("temp_eln.yaml", "w") as f: yaml.dump({"Instrument": {"undocumented_field": "undocumented entry"}}, f) + with open("temp_config.json", "w") as f: + with open( + df_folder + "../../../../sed/config/NXmpes_config.json", + encoding="utf-8", + ) as stream: + config_dict = json.load(stream) + config_dict[ + "/ENTRY[entry]/INSTRUMENT[instrument]/undocumented_field" + ] = "@eln:/ENTRY/Instrument/undocumented_field" + json.dump(config_dict, f, indent=2) with caplog.at_level(logging.WARNING): processor.save( "result.nxs", - input_files=[df_folder + "../../../../sed/config/NXmpes_config.json"], + input_files=["temp_config.json"], eln_data="temp_eln.yaml", + suppress_warning=True, ) assert ( caplog.messages[0] - == "The data entry corresponding to /ENTRY[entry]/SAMPLE[sample]/name is required and " - "hasn't been supplied by the reader." + == "WARNING: The data entry corresponding to /ENTRY[entry]/SAMPLE[sample]/name is " + "required and hasn't been supplied by the reader." ) assert ( caplog.messages[1] - == "Field /ENTRY[entry]/INSTRUMENT[instrument]/undocumented_field written without " - "documentation." + == "WARNING: Field /ENTRY[entry]/INSTRUMENT[instrument]/undocumented_field written " + "without documentation." ) os.remove("output.nxs") os.remove("temp_eln.yaml") + os.remove("temp_config.json") diff --git a/tutorial/3_metadata_collection_and_export_to_NeXus.ipynb b/tutorial/3_metadata_collection_and_export_to_NeXus.ipynb index 260e5e4d..98c1258c 100644 --- a/tutorial/3_metadata_collection_and_export_to_NeXus.ipynb +++ b/tutorial/3_metadata_collection_and_export_to_NeXus.ipynb @@ -75,6 +75,7 @@ "\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",