3.3.3.101. NXxas

Status:

application definition (contribution), extends NXobject

Description:

This is a generic application definition for X-ray absorption …

This is a generic application definition for X-ray absorption spectroscopy. Technique-specific application definitions extend this base definition.

Symbols:

The symbol(s) listed here will be used below to coordinate datasets …

The symbol(s) listed here will be used below to coordinate datasets with the same shape.

nP: Number of spectra (scan points). For a stack, this is the growable first dimension of intensity: data could be appended along it during acquisition. For a single spectrum, nP is 1, but intensity has no nP dimension.

nEnergy: Number of energy data points

dataRank: Rank of the intensity field: 1 for a single spectrum [nEnergy] or 2 for a stack of spectra [nP, nEnergy].

Groups cited:

NXabsorption_edge, NXcollection, NXdata, NXelement, NXentry, NXnote, NXparameters, NXprocess, NXsample, NXsubentry

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

Official NeXus NXDL schema to which this file conforms. …

Official NeXus NXDL schema to which this file conforms.

Obligatory value: NXxas

title: (recommended) NX_CHAR ⤆

Human-readable title for the measurement or calculation.

start_time: (optional) NX_DATE_TIME ⤆

Start time of the measurement. Omit for calculated or …

Start time of the measurement. Omit for calculated or reconstructed spectra.

end_time: (optional) NX_DATE_TIME ⤆

End time of the measurement.

is_experimental: (required) NX_BOOLEAN

Specify if the data comes from an experiment. Use true for …

Specify if the data comes from an experiment. Use true for data acquired at a beamline or laboratory instrument, and false for spectra calculated/simulated using a computational tool, reconstructed from a linear combination of reference components, etc. Record provenance in the processing group.

element: (required) NXelement

The element being probed by the incident X-rays.

symbol: (required) NX_CHAR ⤆

edge: (required) NXabsorption_edge

The absorption edge being probed, defined by the principal …

The absorption edge being probed, defined by the principal quantum number and orbital symmetry of the photoionized electron (for example K, L1, L2, or L3). Together with the element, it uniquely identifies the probed electronic transition.

name: (required) NX_CHAR ⤆

energy: (required) NX_FLOAT (Rank: 1, Dimensions: [nEnergy]) {units=NX_ENERGY}

The energy axis of the spectrum.

intensity: (required) NX_FLOAT (Rank: dataRank) {units=NX_ANY}

The intensity of the spectrum. The precise definition of what is …

The intensity of the spectrum. The precise definition of what is meant by intensity depends on the acquisition mode, and will be specified by each subclass application definition.

intensity_errors: (optional) NX_FLOAT (Rank: dataRank) {units=NX_ANY}

The estimated uncertainty associated with each intensity value, …

The estimated uncertainty associated with each intensity value, expressed as a standard deviation.

SAMPLE: (required) NXsample ⤆

name: (required) NX_CHAR ⤆

Descriptive name of the sample

temperature: (optional) NX_FLOAT (Rank: 1, Dimensions: [nP]) {units=NX_TEMPERATURE} ⤆

Sample temperature, one value per spectrum.

DATA: (required) NXdata ⤆

Plot of the X-ray absorption intensity versus energy. …

Plot of the X-ray absorption intensity versus energy. The energy and intensity links are required. Additional coordinate links are allowed.

For a single spectrum, energy spans dimension 0 (@energy_indices = 0). For a stack, energy has @energy_indices = 1 and the quantity that varies across the stack (a time series, a spatial map, an operando series, …) is the leading axis with @AXISNAME_indices = 0.

That quantity is stored in its standard NeXus location (for example NXsample/temperature, NXsample/electric_field, an NXsample/NXtransformations axis, or an NXbeam polarization field) and linked here. The application definition does not enumerate these coordinates: any of them, including ones not listed, is declared by adding the field in its base-class location and wiring it into this group.

@signal: (required) NX_CHAR ⤆

Name of the field to plot: the absorption intensity. …

Name of the field to plot: the absorption intensity.

Obligatory value: intensity

energy: (required) NX_CHAR

intensity: (required) NX_CHAR

raw_data: (optional) NXcollection ⤆

Raw data as written by the acquisition or simulation …

Raw data as written by the acquisition or simulation software, preserved without modification.

processing: (optional) NXprocess ⤆

Provenance of …

Provenance of intensity.

For measured spectra, include all processing steps from measured data to the reported spectrum. For calculated spectra, describe the calculation. For linear combinations, identify the reference components and their weights.

program: (optional) NX_CHAR ⤆

Name of the processing program.

version: (optional) NX_CHAR ⤆

Version of the program identified by program.

date: (optional) NX_DATE_TIME ⤆

Date and time of processing.

parameters: (optional) NXparameters ⤆

Processing parameter values. …

Processing parameter values. Include a units attribute for each parameter where applicable.

note: (optional) NXnote ⤆

Description of the processing. Identify the input data …

Description of the processing. Identify the input data and give the processing steps in order.

data: (required) NX_CHAR

Description of the processing as plain text.

reference: (optional) NXsubentry ⤆

An independent reference spectrum, for example a metal-foil …

An independent reference spectrum, for example a metal-foil standard used for energy calibration. Store the reference here when it is a complete spectrum in its own right, in particular when it probes a different absorbing element or absorption edge, or when it is measured in a different acquisition mode than the main spectrum (for example a foil measured in transmission while the sample is measured in fluorescence).

definition: (required) NX_CHAR ⤆

NeXus NXDL schema to which this file conforms …

NeXus NXDL schema to which this file conforms

Obligatory value: NXxas

Hypertext Anchors

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

NXDL Source:

https://github.com/nexusformat/definitions/blob/main/contributed_definitions/NXxas.nxdl.xml