2.3.3.3.169. NXoptical_spectroscopy

Status:

application definition, extends NXobject

Description:

A general application definition of optical spectroscopy elements, which may ...

A general application definition of optical spectroscopy elements, which may be used as a template to derive specialized optical spectroscopy experiments.

Possible specializations are ellipsometry, Raman spectroscopy, photoluminescence, reflectivity/transmission spectroscopy.

A general optical experiment consists of (i) a light/photon source, (ii) a sample, (iii) a detector.

For any free text descriptions, it is recommended to enter data in english language, as this is the most FAIR representation.

Symbols:

Variables used throughout the document, e.g. dimensions or parameters.

N_spectrum: Length of the spectrum array (e.g. wavelength or energy) of the measured data.

N_measurements: Number of measurements (1st dimension of measured_data array). This is equal to the number of parameters scanned. For example, if the experiment was performed at three different temperatures and two different pressures N_measurements = 2*3 = 6.

Groups cited:

NXactuator, NXbeam_device, NXbeam_transfer_matrix_table, NXbeam, NXcalibration, NXcoordinate_system_set, NXcoordinate_system, NXdata, NXdetector, NXentry, NXenvironment, NXfabrication, NXhistory, NXidentifier, NXinstrument, NXlens_opt, NXmanipulator, NXmonochromator, NXopt_window, NXpid, NXprocess, NXprogram, NXresolution, NXsample, NXsensor, NXsource, NXtransformations, NXuser, NXwaveplate

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

An application definition describing a general optical experiment. ...

An application definition describing a general optical experiment.

Obligatory value: NXoptical_spectroscopy

@version: (required) NX_CHAR ⤆

Version number to identify which definition of this application ...

Version number to identify which definition of this application definition was used for this entry/data.

@URL: (required) NX_CHAR ⤆

URL where to find further material (documentation, examples) relevant ...

URL where to find further material (documentation, examples) relevant to the application definition.

title: (recommended) NX_CHAR ⤆

start_time: (recommended) NX_DATE_TIME ⤆

Datetime of the start of the measurement. ...

Datetime of the start of the measurement. Should be a ISO8601 date/time stamp. It is recommended to add an explicit time zone, otherwise, the local time zone is assumed per ISO8601.

It is required to enter at least one of both measurement times, either “start_time” or “end_time”.

end_time: (recommended) NX_DATE_TIME ⤆

Datetime of the end of the measurement. ...

Datetime of the end of the measurement. Should be a ISO8601 date/time stamp. It is recommended to add an explicit time zone, otherwise the local time zone is assumed per ISO8601.

It is required to enter at least one of both measurement times, either “start_time” or “end_time”.

experiment_description: (optional) NX_CHAR ⤆

An optional free-text description of the experiment. ...

An optional free-text description of the experiment.

Users are strongly advised to parameterize the description of their experiment by using respective groups and fields and base classes instead of writing prose into this field.

The reason is that such a free-text field is difficult to machine-interpret. The motivation behind keeping this field for now is to learn how far the current base classes need extension based on user feedback.

experiment_type: (required) NX_CHAR

Specify the type of the optical experiment. ...

Specify the type of the optical experiment.

Chose other if none of these methods are suitable. You may specify fundamental characteristics or properties in the experimental sub-type.

For Raman spectroscopy or ellipsometry use the respective specializations of NXoptical_spectroscopy.

Any of these values:

  • photoluminescence

  • transmission spectroscopy

  • reflection spectroscopy

  • other

experiment_sub_type: (optional) NX_CHAR

Specify a special property or characteristic of the experiment, which specif ...

Specify a special property or characteristic of the experiment, which specifies the generic experiment type.

Any of these values: time resolved | imaging | pump-probe | other

experiment_type_other: (optional) NX_CHAR

If "other" was selected in "experiment_type" and/or in "experiment_sub_type" ...

If “other” was selected in “experiment_type” and/or in “experiment_sub_type”, specify the experiment here with a free text name, which is knwon in the respective community of interest.

experiment_identifier: (recommended) NXidentifier ⤆

A (globally persistent) unique identifier of the experiment. ...

A (globally persistent) unique identifier of the experiment. (i) The identifier is usually defined by the facility, laboratory or principal investigator. (ii) The identifier enables to link experiments to e.g. proposals.

service: (optional) NX_CHAR ⤆

identifier: (recommended) NX_CHAR ⤆

identifier_type: (recommended) NX_CHAR

Select the range of validity of this identier. ...

Select the range of validity of this identier. Local: Setup#1 at Institute building #2 in Room #3 Global: Unique identification of with by unique location and unique globally persistent time stamp.

Any of these values: local | global

is_persistent: (optional) NX_BOOLEAN ⤆

reference_frames: (optional) NXcoordinate_system_set

Description of one or more coordinate systems that are specific to the ...

Description of one or more coordinate systems that are specific to the experiment. Examples are beam centered, sample-normal centered, laboratory-system centered, sample-stage centered, crystal-symmetry centered.

beam_ref_frame: (optional) NXcoordinate_system ⤆

depends_on: (required) NX_CHAR ⤆

This refers to the coordinate system along the beam path. The origin and ...

This refers to the coordinate system along the beam path. The origin and base is defined at z=0, where the incident beam hits the sample at the surface.

TRANSFORMATIONS: (required) NXtransformations ⤆

This is the default NeXus coordinate system (McStas), if the transformat ...

This is the default NeXus coordinate system (McStas), if the transformation does not change the coordinate system at all - i.e. it is unity. Otherwise, by this a respective transformation of the beam reference frame to the default reference frame could be made. i.e. exchange of x and z coordinate, rotation of respective coordinates towards each other.

sample_normal_ref_frame: (optional) NXcoordinate_system ⤆

depends_on: (required) NX_CHAR ⤆

Link to transformations defining the sample-normal base coordinate syste ...

Link to transformations defining the sample-normal base coordinate system, which is defined such that the positive z-axis is parallel to the sample normal, and the x-y-plane lies inside the sample surface.

TRANSFORMATIONS: (required) NXtransformations ⤆

Set of transformations, describing the orientation of the sample-normal ...

Set of transformations, describing the orientation of the sample-normal coordinate system with respect to the beam coordinate system (.).

USER: (optional) NXuser ⤆

Contact information and eventually details of at persons who ...

Contact information and eventually details of at persons who performed the measurements. This can be for example the principal investigator or student. Examples are: name, affiliation, address, telephone number, email, role as well as identifiers such as orcid or similar. It is recommended to add multiple users if relevant.

Due to data privacy concerns, there is no minimum requirement. If no user with specific name is allowed to be given, it is required to assign at least an affiliation

INSTRUMENT: (required) NXinstrument ⤆

Devices or elements of the optical spectroscopy setup described with its ...

Devices or elements of the optical spectroscopy setup described with its properties and general information.

This includes for example: - The beam device’s or instrument’s model, company, serial number, construction year, etc. - Used software or code - Experiment descriptive parameters as reference frames, resolution, calibration - Photon beams with their respective properties such as angles and polarization - Various optical beam path devices, which interact, manipulate or measure optical beams - Characteristics of the medium surrounding the sample - “Beam devices” for a beam path description - Stages(NXmanipulator) - Sensors and actuators to control or measure sample or beam properties

angle_reference_frame: (recommended) NX_CHAR

Defines the reference frame which is used to describe the sample orientati ...

Defines the reference frame which is used to describe the sample orientation with respect to the beam directions.

A beam centered description is the default and uses 4 angles(similar to XRD):

  • Omega (angle between sample surface and incident beam)

  • 2Theta (angle between the transmitted beam and the detection beam)

  • Chi (sample tilt angle, angle between plane#1 and the surface normal,

    plane#1 = spanned by incidence beam and detection and detection. If Chi=0°, then plane#1 is the plane of incidence in reflection setups)

  • Phi (inplane rotation of sample, rotation axis is the samples

    surface normal)

A sample normal centered description is as well possible:

  • angle of incidence (angle between incident beam and sample surface)

  • angle of detection (angle between detection beam and sample surface)

  • angle of incident and detection beam

  • angle of in-plane sample rotation (direction along the sample’s surface normal)

An arbitrary reference frame can be defined by “reference_frames” and used via “instrument/angle_sample_and_beam_TYPE”

Any of these values: beam centered | sample-normal centered

omega: (optional) NX_NUMBER {units=NX_ANGLE}

Angle between sample incident beam and sample surface.

twotheta: (optional) NX_NUMBER {units=NX_ANGLE}

Angle between incident and detection beam

chi: (optional) NX_NUMBER {units=NX_ANGLE}

Sample tilt between sample normal, and the plane spanned by detection and ...

Sample tilt between sample normal, and the plane spanned by detection and incident beam.

phi: (optional) NX_NUMBER {units=NX_ANGLE}

Inplane rotation of the sample, with rotation axis along sample normal.

angle_of_incidence: (optional) NX_NUMBER {units=NX_ANGLE}

Angle(s) of the incident beam vs. the normal of the bottom reflective ...

Angle(s) of the incident beam vs. the normal of the bottom reflective (substrate) surface in the sample. These two directions span the plane of incidence.

angle_of_detection: (optional) NX_NUMBER {units=NX_ANGLE}

Detection angle(s) of the beam reflected or scattered off the sample ...

Detection angle(s) of the beam reflected or scattered off the sample vs. the normal of the bottom reflective (substrate) surface in the sample if not equal to the angle(s) of incidence. These two directions span the plane of detection.

angle_of_incident_and_detection_beam: (optional) NX_NUMBER {units=NX_ANGLE}

Angle between the incident and detection beam. ...

Angle between the incident and detection beam. If angle_of_detection + angle_of_incidence = angle_of_incident_and_detection_beam, then the setup is a reflection setup. If angle_of_detection + angle_of_incidence != angle_of_incident_and_detection_beam then the setup may be a light scattering setup. (i.e. 90° + 90° != 90°, i.e. incident and detection beam in the sample surface, but the angle source-sample-detector is 90°)

angle_of_in_plane_sample_rotation: (optional) NX_NUMBER {units=NX_ANGLE}

Angle of the inplane orientation of the sample. This might be an arbitrary ...

Angle of the inplane orientation of the sample. This might be an arbitrary, angle without specific relation to the sample symmetry, of the angle to a specific sample property (i.e. crystallographic axis or sample shape such as wafer flat)

lateral_focal_point_offset: (optional) NX_NUMBER {units=NX_LENGTH}

Specify if there is a lateral offset on the sample surface, between the fo ...

Specify if there is a lateral offset on the sample surface, between the focal points of the incident beam and the detection beam.

sample_medium_refractive_indices: (optional) NX_FLOAT (Rank: 2, Dimensions: [2, N_spectrum]) {units=NX_UNITLESS}

Array of pairs of complex refractive indices n + ik of the medium ...

Array of pairs of complex refractive indices n + ik of the medium for every measured spectral point/wavelength/energy. Only necessary if the measurement was performed not in air, or something very well known, e.g. high purity water.

beam_TYPE: (required) NXbeam ⤆

This can be used to describe properties of a photon beam. ...

This can be used to describe properties of a photon beam. A beam is always defined between two beam_devices, via “previous_device” and “next_device”.

It is required to define at least one incident beam which is incident to the sample. You may specify if this beam parameters are acutally measured or just nominal. If this beam is the output of a source, chose the same name appendix as for the NXsource instance (e.g. TYPE=532nm)

parameter_reliability: (required) NX_CHAR

Select the reliability of the respective beam characteristics. Either, ...

Select the reliability of the respective beam characteristics. Either, the parameters are measured via another device or method or just given nominally via the properties of a light source properties (532nm, 100mW).

Any of these values: measured | nominal

incident_wavelength: (recommended) NX_NUMBER

incident_wavelength_spread: (recommended) NX_NUMBER

incident_polarization: (recommended) NX_NUMBER ⤆

extent: (recommended) NX_FLOAT ⤆

associated_source: (optional) NX_CHAR

The path to the device which emitted this beam (light source or frequenc ...

The path to the device which emitted this beam (light source or frequency doubler).

This parameter is recommended, if the previous optical element is a photon source. In this way, the properties of the laser or light souce can be described and associated. The beam should be named with the same appendix as the source, e.g., for TYPE=532nmlaser, there should be both a NXsource named “source_532nmlaser” and a NXbeam named “beam_532nmlaser”.

Example: /entry/instrument/source_532nmlaser

beam_polarization_type: (optional) NX_CHAR

Any of these values:

  • linear

  • circular

  • ellipically

  • unpolarized

linear_beam_sample_polarization: (optional) NX_NUMBER {units=NX_ANGLE}

Angle of the linear polarized light, with respect to a fixed arbitrary ...

Angle of the linear polarized light, with respect to a fixed arbitrary defined 0° position. This can be used if no definition of respective cooridnate systems for beam and sample normal is done. If coordinate systems are defined, refer to beam “incident_polarization”.

detector_TYPE: (required) NXdetector ⤆

detector_channel_type: (required) NX_CHAR

Any of these values: single-channel | multichannel

detector_type: (recommended) NX_CHAR ⤆

Description of the detector type. ...

Description of the detector type.

Any of these values:

  • CCD

  • photomultiplier

  • photodiode

  • avalanche-photodiode

  • streak camera

  • bolometer

  • golay detectors

  • pyroelectric detector

  • deuterated triglycine sulphate

  • other

detector_type_other: (optional) NX_CHAR

Type of detector, if “other” was selected in “detector_type”.

additional_detector_hardware: (optional) NX_CHAR

Specify respective hardware which was used for the detector. For ...

Specify respective hardware which was used for the detector. For example special electronics required for time-correlated single photon counting (TCSPC).

raw_data: (recommended) NXdata ⤆

Contains the raw data collected by the detector before calibration. ...

Contains the raw data collected by the detector before calibration. The data which is considered raw might change from experiment to experiment due to hardware pre-processing of the data. This field ideally collects the data with the lowest level of processing possible.

@signal: (required) NX_CHAR ⤆

Obligatory value: raw

raw: (required) NX_NUMBER ⤆

Raw data before calibration.

device_information: (recommended) NXfabrication ⤆

source_TYPE: (recommended) NXsource ⤆

type: (recommended) NX_CHAR ⤆

Any of these values:

  • Synchrotron X-ray Source

  • Rotating Anode X-ray

  • Fixed Tube X-ray

  • UV Laser

  • Optical Laser

  • Laser

  • Dye-Laser

  • Broadband Tunable Light Source

  • Halogen lamp

  • LED

  • Mercury Cadmium Telluride

  • Deuterium Lamp

  • Xenon Lamp

  • Globar

  • other

type_other: (optional) NX_CHAR ⤆

Specification of type, may also go to name.

name: (recommended) NX_CHAR ⤆

standard: (optional) NX_CHAR

If available, name/ID/norm of the light source standard.

associated_beam: (recommended) NX_CHAR

The path to a beam emitted by this source. ...

The path to a beam emitted by this source. Should be named with the same appendix, e.g., for TYPE=532nmlaser, there should as well be a NXbeam named “beam_532nmlaser” together with this source instance named “source_532nmlaser”

Example: /entry/instrument/beam_532nmlaser

device_information: (recommended) NXfabrication ⤆

Details about the device information.

MONOCHROMATOR: (recommended) NXmonochromator ⤆

device_information: (recommended) NXfabrication

generic_beam_sample_angle_TYPE: (recommended) NXtransformations ⤆

Set of transformations, describing the relative orientation of different ...

Set of transformations, describing the relative orientation of different parts of the experiment (beams or sample). You may select one of the specified angles for incident and detection beam or sample, and then use polar and azimuthal angles to define the direction via sperical coordinates. This allows consistent defintion between different coordinate system. You may refer to self defined coordinate system as well.

If “angle_reference_frame = beam centered”, then this coordinate system is used: McStas system (NeXus default) (https://manual.nexusformat.org/design.html#mcstas-and-nxgeometry-system)

i.e. the z-coordinate math:[0,0,1] is along the incident beam direction and the x-coordinate math:[1,0,0] is in the horizontal plane. Hence, usually math:[0,1,0] is vertically oriented.

If “angle_reference_frame = sample-normal centered”, then this coordinate system is used z - math:[0,0,1] along sample surface normal x - math:[1,0,0] defined by sample surface projected incident beam. y - math:[0,1,0] in the sample surface, orthogonal to z and x. For this case, x may be ill defined, if the incident beam is perpendicular to the sample surface. In this case, use the beam centered description.

type: (required) NX_CHAR

Any of these values: incident beam | detection beam | sample

polar: (required) NX_NUMBER {units=NX_ANGLE} ⤆

Rotation about the y axis (polar rotation within the sample plane).

@transformation_type: (required) NX_CHAR ⤆

Obligatory value: rotation

@vector: (required) NX_CHAR

Obligatory value: [0, 1, 0]

@depends_on: (required) NX_CHAR ⤆

Path to a transformation that places the sample surface ...

Path to a transformation that places the sample surface into the origin of the arpes_geometry coordinate system.

azimuth: (required) NX_NUMBER {units=NX_ANGLE} ⤆

Rotation about the z axis (azimuthal rotation within the sample plane).

@transformation_type: (required) NX_CHAR ⤆

Obligatory value: rotation

@vector: (required) NX_CHAR

Obligatory value: [0, 0, 1]

@depends_on: (required) NX_CHAR ⤆

Obligatory value: offset_tilt

BEAM_DEVICE: (optional) NXbeam_device

Describes the order of respective beam devices in the optical beam ...

Describes the order of respective beam devices in the optical beam path.

Everything object which interacts or modifies optical beam properties, may be an beam device, e.g. Filter, Window, Beamsplitter, Photon Source, Detector, etc,

It is intended, to include this functionality later to “older” beam components, such as NXsource, NXdetector, NXlens, etc. Until this is possbible, auxillary beam devices have to be created, for each “older” beam component instead, to allow a beam path description. To link the auxillary beam device to the real device properties, the attribute @device should be used.

@device: (recommended) NX_CHAR

Reference to beam device, which is described by a NeXus concept ...

Reference to beam device, which is described by a NeXus concept (e.g. for NXsource, entry/instrument/source_TYPE).

previous_device: (recommended) NX_CHAR

Reference to the previous beam device, from which the photon beam came ...

Reference to the previous beam device, from which the photon beam came to reach this beam device. A photon source is related as origin by “.”. This enables a logical order description of the optical setup.

LENS_OPT: (optional) NXlens_opt

This is the optical element used to focus or collect light. This may ...

This is the optical element used to focus or collect light. This may be a genereic lens or microcope objectives which are used for the Raman scattering process.

type: (required) NX_CHAR ⤆

Any of these values:

  • objective

  • lens

  • glass fiber

  • none

  • other

device_information: (optional) NXfabrication

WAVEPLATE: (optional) NXwaveplate

OPT_WINDOW: (optional) NXopt_window

polfilter_TYPE: (optional) NXbeam_device

polarization filter to prepare light to be measured or to be incident ...

polarization filter to prepare light to be measured or to be incident on the sample. Genereric polarization filter porperties may be implemented via NXfilter_pol at a later stage.

filter_mechanism: (optional) NX_CHAR

Physical principle of the polarization filter used to create a ...

Physical principle of the polarization filter used to create a defined incident or scattered light state.

Any of these values:

  • polarization by Fresnel reflection

  • birefringent polarizers

  • thin film polarizers

  • wire-grid polarizers

  • other

specific_polarization_filter_type: (optional) NX_CHAR

Specific name or type of the polarizer used. ...

Specific name or type of the polarizer used.

Free text, for example: Glan-Thompson, Glan-Taylor, Rochon Prism, Wollaston Polarizer…

device_information: (optional) NXfabrication

spectralfilter_TYPE: (optional) NXbeam_device

Spectral filter used to modify properties of the scattered or incident lig ...

Spectral filter used to modify properties of the scattered or incident light. Genereric spectral filter porperties may be implemented via NXfilter_spec at a later stage.

filter_type: (optional) NX_CHAR

Type of laserline filter used to supress the laser, if measurements ...

Type of laserline filter used to supress the laser, if measurements close to the laserline are performed.

Any of these values:

  • long-pass filter

  • short-pass filter

  • notch filter

  • reflection filter

  • neutral density filter

  • other

intended_use: (optional) NX_CHAR

Type of laserline filter used to supress the laser, if measurements ...

Type of laserline filter used to supress the laser, if measurements close to the laserline are performed.

Any of these values:

  • laser line cleanup

  • raylight line removal

  • spectral filtering

  • intensity manipulation

  • other

filter_characteristics: (optional) NXdata

Properties of the spectral filter such as wavelength dependent Transmiss ...

Properties of the spectral filter such as wavelength dependent Transmission or reflectivity.

@characteristics_type: (optional) NX_CHAR

Which property is used to form the spectral properties of light, ...

Which property is used to form the spectral properties of light, i.e. transmission or reflection properties.

Any of these values: transmission | reflection

device_information: (optional) NXfabrication

BEAM_TRANSFER_MATRIX_TABLE: (optional) NXbeam_transfer_matrix_table

Allows description of beam properties via matrices, which relate ingoing w ...

Allows description of beam properties via matrices, which relate ingoing with outgoing beam properties.

sample_stage: (optional) NXmanipulator

Sample stage (or manipulator) for positioning of the sample. This should ...

Sample stage (or manipulator) for positioning of the sample. This should only contain the spatial orientation of movement.

stage_type: (optional) NX_CHAR

Specify the type of the sample stage. ...

Specify the type of the sample stage.

Any of these values:

  • manual stage

  • scanning stage

  • liquid stage

  • gas cell

  • cryostat

  • heater

  • other

stage_type_other: (optional) NX_CHAR

If "other" was chosen in stage_type, enter here a free text description ...

If “other” was chosen in stage_type, enter here a free text description of the stage type.

beam_sample_relation: (optional) NX_CHAR

Description of relation of the beam with the sample. How dit the ...

Description of relation of the beam with the sample. How dit the sample hit the beam, e.g. ‘center of sample, long edge parallel to the plane of incidence’. Is redundent, if a full orientation description is done via the stages “transformations” entry.

transformations: (optional) NXtransformations ⤆

This allows a description of the stages relation or orientation and ...

This allows a description of the stages relation or orientation and position with respect to the sample or beam, if an laboratory or an stage coordinate system is defined.

device_information: (optional) NXfabrication ⤆

temperature_sensor: (recommended) NXsensor ⤆

name: (recommended) NX_CHAR ⤆

measurement: (required) NX_CHAR ⤆

Obligatory value: temperature

type: (optional) NX_CHAR ⤆

value: (required) NX_FLOAT ⤆

device_information: (optional) NXfabrication ⤆

temp_control_TYPE: (optional) NXactuator ⤆

Type of control for the sample temperature. Replace TYPE by "cryostat" or ...

Type of control for the sample temperature. Replace TYPE by “cryostat” or “heater” to specify it.

name: (recommended) NX_CHAR ⤆

physical_quantity: (required) NX_CHAR ⤆

Obligatory value: temperature

cooler_or_heater: (recommended) NX_CHAR

Any of these values: cooler | heater

type: (optional) NX_CHAR ⤆

Hardware used for actuation, i.e. laser, gas lamp, filament, resistive

PID: (recommended) NXpid ⤆

setpoint: (recommended) NX_FLOAT ⤆

device_information: (optional) NXfabrication ⤆

device_information: (recommended) NXfabrication ⤆

General device information of the optical spectroscopy setup, if ...

General device information of the optical spectroscopy setup, if suitable (e.g. for a tabletop spectrometer or other non-custom build setups). For custom build setups, this may be limited to the construction year.

vendor: (recommended) NX_CHAR ⤆

model: (recommended) NX_CHAR ⤆

construction_year: (optional) NX_DATE_TIME

identifier: (recommended) NXidentifier ⤆

software_TYPE: (recommended) NXprogram

program: (required) NX_CHAR ⤆

Commercial or otherwise defined given name of the program that was ...

Commercial or otherwise defined given name of the program that was used to control any parts of the optical spectroscopy setup. The uppercase TYPE should be replaced by a specification name, i.e. “software_detector” or “software_stage” to specify the respective program or software components.

@version: (recommended) NX_CHAR ⤆

Either version with build number, commit hash, or description of a ...

Either version with build number, commit hash, or description of a (online) repository where the source code of the program and build instructions can be found so that the program can be configured in such a way that result files can be created ideally in a deterministic manner.

@URL: (optional) NX_CHAR

Description of the software by persistent resource, where the program, ...

Description of the software by persistent resource, where the program, code, script etc. can be found.

instrument_calibration_DEVICE: (recommended) NXcalibration

Pre-calibration of an arbitrary device of the instrumental setup, which ...

Pre-calibration of an arbitrary device of the instrumental setup, which has the name DEVICE. You can specify here how, at which time by which method the calibration was done. As well the accuracy and a link to the calibration dataset.

device_path: (recommended) NX_CHAR

Path to the device, which was calibrated. ...

Path to the device, which was calibrated. Example: entry/instrument/DEVICE

calibration_status: (recommended) NX_CHAR

Was a calibration performed? If yes, when was it done? If the ...

Was a calibration performed? If yes, when was it done? If the calibration time is provided, it should be specified in ENTRY/INSTRUMENT/calibration/calibration_time.

Any of these values:

  • calibration time provided

  • no calibration

  • within 1 hour

  • within 1 day

  • within 1 week

calibration_time: (optional) NX_DATE_TIME

If calibtration status is 'calibration time provided', specify the ...

If calibtration status is ‘calibration time provided’, specify the ISO8601 date when calibration was last performed before this measurement. UTC offset should be specified.

calibration_accuracy: (optional) NXdata ⤆

Provide data about the determined accuracy of the device, this may ...

Provide data about the determined accuracy of the device, this may may be a single value or a dataset like wavelength error vs. wavelength etc.

DATA: (optional) NXdata ⤆

Generic data which does not fit to the 'NX_FLOAT' fields in NXproces. ...

Generic data which does not fit to the ‘NX_FLOAT’ fields in NXproces. This can be for example the instrument response function.

wavelength_resolution: (optional) NXresolution ⤆

The overall resolution of the optical instrument.

physical_quantity: (required) NX_CHAR ⤆

Obligatory value: wavelength

type: (recommended) NX_CHAR ⤆

resolution: (required) NX_FLOAT {units=NX_WAVELENGTH} ⤆

Minimum distinguishable wavelength separation of peaks in spectra.

SAMPLE: (required) NXsample ⤆

Properties of the sample, such as sample type, layer structure, ...

Properties of the sample, such as sample type, layer structure, chemical formula, atom types, its history etc. Information about the sample stage and sample environment should be described in ENTRY/INSTRUMENT/sample_stage.

name: (required) NX_CHAR ⤆

sample_id: (recommended) NX_CHAR ⤆

Locally unique ID of the sample, used in the reasearch institute or group.

physical_form: (recommended) NX_CHAR ⤆

State the form of the sample, examples are: ...

State the form of the sample, examples are: thin film, single crystal, poly crystal, amorphous, single layer, multi layer, liquid, gas, pellet, powder. Generic properties of liquids or gases see NXsample properties.

description: (optional) NX_CHAR ⤆

Free text description of the sample.

chemical_formula: (recommended) NX_CHAR ⤆

Chemical formula of the sample. Use the Hill system (explained here: ...

Chemical formula of the sample. Use the Hill system (explained here: https://en.wikipedia.org/wiki/Chemical_formula#Hill_system) to write the chemical formula. In case the sample consists of several layers, this should be a list of the chemical formulas of the individual layers, where the first entry is the chemical formula of the top layer (the one on the front surface, on which the light incident). The order must be consistent with layer_structure

atom_types: (optional) NX_CHAR

List of comma-separated elements from the periodic table that are ...

List of comma-separated elements from the periodic table that are contained in the sample. If the sample substance has multiple components, all elements from each component must be included in ‘atom_types’.

preparation_date: (recommended) NX_DATE_TIME ⤆

ISO 8601 time code with local time zone offset to UTC information ...

ISO 8601 time code with local time zone offset to UTC information when the specimen was prepared.

Ideally, report the end of the preparation, i.e. the last known timestamp when the measured specimen surface was actively prepared.

thickness: (optional) NX_NUMBER {units=NX_LENGTH}

(Measured) sample thickness. ...

(Measured) sample thickness.

The information is recorded to qualify if the light used was likely able to shine through the sample.

In this case the value should be set to the actual thickness of the specimen viewed for an illumination situation where the nominal surface normal of the specimen is parallel to the optical axis.

thickness_determination: (optional) NX_CHAR

If a thickness if given, please specify how this thickness was estimated o ...

If a thickness if given, please specify how this thickness was estimated or determined.

layer_structure: (optional) NX_CHAR

Qualitative description of the layer structure for the sample, ...

Qualitative description of the layer structure for the sample, starting with the top layer (i.e. the one on the front surface, on which the light incident), e.g. native oxide/bulk substrate, or Si/native oxide/thermal oxide/polymer/peptide.

sample_orientation: (optional) NX_CHAR

Specify the sample orientation, how is its sample normal oriented ...

Specify the sample orientation, how is its sample normal oriented relative in the laboratory reference frame, incident beam reference frame.

substrate: (recommended) NX_CHAR

If the sample is grown or fixed on a substrate, specify this here by ...

If the sample is grown or fixed on a substrate, specify this here by a free text description.

history: (recommended) NXhistory ⤆

A set of activities that occurred to the sample prior to/during the experiment.

temperature: (recommended) NXenvironment

Sample temperature (either controlled or just measured).

temperature_nominal: (optional) NX_CHAR

If no sensor was available for the determination of temperature, selecte ...

If no sensor was available for the determination of temperature, selected a nominal value which represents approximately the situation of sample temperature.

Any of these values:

  • room temperature

  • liquid helium temperature

  • liquid nitrogen temperature

  • other

temperature_nominal_other: (optional) NX_NUMBER {units=NX_TEMPERATURE}

If temperature_nominal is "other", enter here a nominal/assumed/estimate ...

If temperature_nominal is “other”, enter here a nominal/assumed/estimated sample temperature.

temperature_sensor: (recommended) NXsensor ⤆

Temperature sensor measuring the sample temperature. ...

Temperature sensor measuring the sample temperature. This should be a link to /entry/instrument/manipulator/temperature_sensor.

sample_heater: (optional) NXactuator ⤆

Device to heat the sample. ...

Device to heat the sample. This should be a link to /entry/instrument/manipulator/sample_heater.

sample_cooler: (optional) NXactuator ⤆

Device for cooling the sample (Cryostat, Airflow cooler, etc.). ...

Device for cooling the sample (Cryostat, Airflow cooler, etc.). This should be a link to /entry/instrument/manipulator/cryostat.

ENVIRONMENT: (optional) NXenvironment ⤆

Arbirary sample property which may be varied during the experiment ...

Arbirary sample property which may be varied during the experiment and controlled by a device. Examples are pressure, voltage, magnetic field etc. Similar to the temperautre description of the sample.

sample_medium: (recommended) NX_CHAR

Medium, in which the sample is placed. ...

Medium, in which the sample is placed.

Any of these values:

  • air

  • vacuum

  • inert atmosphere

  • oxidising atmosphere

  • reducing atmosphere

  • sealed can

  • water

  • other

DATA: (required) NXdata ⤆

Here generic types of data may be saved.. This may refer to data derived ...

Here generic types of data may be saved.. This may refer to data derived from single or multiple raw measurements (i.e. several intensities are evaluated for different parameters: ellipsometry -> psi and delta) - i.e. non-raw data. As well plotable data may be stored/linked here, which provides the most suitable representation of the data (for the respective community).

You may provide multiple instances of NXdata

@axes: (required) NX_CHAR ⤆

Spectrum, i.e. x-axis of the data (e.g. wavelength, energy etc.)

@signal: (required) NX_CHAR ⤆

Spectrum, i.e. y-axis of the data (e.g. counts, intensity)

measurement_data_calibration_TYPE: (recommended) NXprocess ⤆

wavelength_calibration: (optional) NXcalibration ⤆

calibrated_axis: (recommended) NX_FLOAT ⤆

Location to save the calibrated wavelength data.

derived_parameters: (optional) NXprocess ⤆

Parameters that are derived from the measured data.

depolarization: (optional) NX_NUMBER (Rank: 3, Dimensions: [N_measurements, 1, N_spectrum]) {units=NX_UNITLESS}

Light loss due to depolarization as a value in [0-1].

jones_quality_factor: (optional) NX_NUMBER (Rank: 3, Dimensions: [N_measurements, 1, N_spectrum]) {units=NX_UNITLESS}

Jones quality factor.

reflectivity: (optional) NX_NUMBER (Rank: 3, Dimensions: [N_measurements, 1, N_spectrum]) {units=NX_UNITLESS}

Reflectivity.

transmittance: (optional) NX_NUMBER (Rank: 3, Dimensions: [N_measurements, 1, N_spectrum]) {units=NX_UNITLESS}

Transmittance.

ANALYSIS_program: (optional) NXprocess

program: (required) NX_CHAR ⤆

Commercial or otherwise defined given name of the program that was ...

Commercial or otherwise defined given name of the program that was used to generate or calculate the derived parameters. If home written, one can provide the actual steps in the NOTE subfield here.

version: (required) NX_CHAR ⤆

Either version with build number, commit hash, or description of a ...

Either version with build number, commit hash, or description of a (online) repository where the source code of the program and build instructions can be found so that the program can be configured in such a way that result files can be created ideally in a deterministic manner.

Hypertext Anchors

List of hypertext anchors for all groups, fields, attributes, and links defined in this class.

NXDL Source:

https://github.com/FAIRmat-NFDI/nexus_definitions/tree/fairmat/contributed_definitions/NXoptical_spectroscopy.nxdl.xml