2.3.3.3.91. NXem_calorimetry

Status:

application definition (contribution), extends NXobject

Description:

Application definition for minimal example in-situ calorimetry. ...

Application definition for minimal example in-situ calorimetry.

TODO:

  • What is the technique about.

  • General context.

  • Literature references.

Symbols:

The symbols used in the schema to specify e.g. dimensions of arrays.

n_p: Number of diffraction pattern.

n_f: Number of radial integration bins.

n_i: Number of coordinates along i axis.

n_j: Number of coordinates along j axis.

Groups cited:

NXcite, NXcoordinate_system, NXcs_profiling, NXdata, NXentry, NXnote, NXobject, NXprocess, NXprogram, NXsample, NXuser

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

Obligatory value: NXem_calorimetry

profiling: (optional) NXcs_profiling

Details about performance, profiling, etc.

start_time: (recommended) NX_DATE_TIME ⤆

end_time: (recommended) NX_DATE_TIME ⤆

total_elapsed_time: (required) NX_NUMBER ⤆

program1: (recommended) NXprogram

Name of the program whereby this config file was created.

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

environment: (recommended) NXobject

Programs and libraries representing the computational environment

PROGRAM: (required) NXprogram

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

USER: (optional) NXuser ⤆

sample: (recommended) NXsample ⤆

type: (required) NX_CHAR ⤆

A qualifier whether the sample is a real one or a virtual one. ...

A qualifier whether the sample is a real one or a virtual one.

Any of these values: experiment | simulation

atom_types: (required) 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 specimen. If the specimen substance has multiple components, all elements from each component must be included in atom_types.

The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret these from the resources pointed to by identifier_parent or walk through eventually deeply nested groups in data instances.

CITE: (optional) NXcite

diffraction_space: (optional) NXcoordinate_system

diffraction: (required) NXnote ⤆

Reference to the resource which stores acquired pattern from the ...

Reference to the resource which stores acquired pattern from the experiment or simulation that are analyzed in this workflow.

Can refer to the original EMD or MRC files or the parsed NXem in RDM e.g. NOMAD OASIS.

file_name: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

actuator: (required) NXnote ⤆

Reference to the resource which stores actuator log file from the experiment.

file_name: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

config: (required) NXnote ⤆

Configuration file that was used for parametrizing this analysis workflow.

file_name: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

synchronization: (required) NXprocess ⤆

Assumptions and computations whereby timestamping data from ...

Assumptions and computations whereby timestamping data from the detector and actuator (e.g. heating chip) were synchronized.

sequence_index: (required) NX_POSINT ⤆

start_time: (required) NX_DATE_TIME

ISO8601 with local time zone reference timestamp that tells ...

ISO8601 with local time zone reference timestamp that tells with which delta_time can be converted in timestamp. The reference timestamp is defined as the time when the actuator started acting on the sample.

Time differences to this timestamp when correlated signals such as diffraction pattern matching with a specific state of the sample (e.g. obtained temperature via the actuator) are reported through delta_time.

identifier_pattern: (required) NX_UINT (Rank: 1, Dimensions: [n_p]) {units=NX_UNITLESS}

delta_time: (required) NX_FLOAT (Rank: 1, Dimensions: [n_p]) {units=NX_TIME}

Time difference to start_time. ...

Time difference to start_time.

Collecting diffraction pattern also takes some time. It is assumed that the acquisition time for each pattern is substantial shorter than the time it takes the actuator to cause a change in stimulus (e.g. temperature).

pattern_center: (required) NXprocess ⤆

Computation of the centre for each pattern using e.g. a Circular Hough ...

Computation of the centre for each pattern using e.g. a Circular Hough Transformation.

sequence_index: (required) NX_POSINT ⤆

position: (required) NX_FLOAT (Rank: 2, Dimensions: [n_p, 2]) {units=NX_LENGTH}

Computed centre for each pattern.

distortion_correction: (optional) NXprocess ⤆

Elliptical distortion correction as a step when computing the centre for ...

Elliptical distortion correction as a step when computing the centre for patterns.

sequence_index: (required) NX_POSINT ⤆

center: (required) NX_NUMBER (Rank: 2, Dimensions: [n_p, 2]) {units=NX_LENGTH}

Computed centre for each pattern.

integration: (required) NXprocess ⤆

Integrated diffraction pattern intensity as a function of radial distance fr ...

Integrated diffraction pattern intensity as a function of radial distance from the centre azimuthally integrated as a function of time.

sequence_index: (required) NX_POSINT ⤆

resultBACKGROUND: (optional) NXdata ⤆

The integrated intensities: ...

The integrated intensities:

  • result_with_background

  • result_without_background

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_UINT

title: (required) NX_CHAR ⤆

intensity: (required) NX_FLOAT (Rank: 2, Dimensions: [n_p, n_f]) {units=NX_UNITLESS}

Integrated intensity as a function of time and the radial distance from ...

Integrated intensity as a function of time and the radial distance from the pattern centre.

@long_name: (required) NX_CHAR

identifier_pattern: (optional) NX_UINT (Rank: 1, Dimensions: [n_p]) {units=NX_UNITLESS}

Identifier for each pattern.

@long_name: (required) NX_CHAR

s: (required) NX_FLOAT (Rank: 1, Dimensions: [n_f]) {units=NX_ANY}

Positions in reciprocal space.

@long_name: (required) NX_CHAR

time: (required) NX_FLOAT (Rank: 1, Dimensions: [n_p]) {units=NX_TIME}

Time since start of the in-situ experiment

background_subtraction: (optional) NXprocess ⤆

sequence_index: (required) NX_POSINT ⤆

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/NXem_calorimetry.nxdl.xml