2.3.3.3.36. NXapm_paraprobe_transcoder_results

Status:

application definition (contribution), extends NXobject

Description:

Application definition for results files of the paraprobe-transcoder tool. ...

Application definition for results files of the paraprobe-transcoder tool.

This tool is part of the paraprobe-toolbox. Inspect the base class NXapm_paraprobe_tool_results. The purpose and need of the paraprobe-transcoder tool is to create a standardized representation of reconstructed position and mass-to-charge-state-ratio values surplus other pieces of information to enable working with atom probe data in reconstruction space in the paraprobe-toolbox. This includes ranging definitions which map mass-to-charge-state ratio values onto iontypes.

So far the atom probe community has not yet agreed upon a comprehensive standardization on how to exchange information especially when it comes to the communication of configurations and results from analyses of atom probe data. Instead, different simplistic file formats are used, such as POS, ePOS, APT, or RNG and RRNG. None of these formats, though, are self-descriptive, standardize, or document their origin and thus the sequence in which the file was generated during an analysis.

Paraprobe-transcoder solves this limitation by interpreting the information content in such files and standardize the representation prior injection into the scientific data analysis tools of the toolbox. Therefore, the here proposed set of NeXus base classes and application definitions can be a useful starting point for the atom probe community to take advantage of standardized information exchange and improve the here proposed classes and concepts to become more inclusive.

Paraprobe-transcoder uses a Python library developed based on efforts by members of the global atom probe community International Field Emission Society (IFES) Atom Probe Technical Committee (APT TC). This library offers the actual low-level I/O operations and respective information interpretation of above-mentioned file formats.

Symbols:

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

n_ions: The total number of ions in the reconstruction.

n_ivec_max: Maximum number of allowed atoms per (molecular) ion (fragment). Needs to match maximum_number_of_atoms_per_molecular_ion.

n_topology: Total number of integers in the supplementary XDMF topology array.

n_variable: Number of entries

Groups cited:

NXapm_paraprobe_tool_common, NXapm_paraprobe_tool_results, NXatom, NXcoordinate_system, NXcs_filter_boolean_mask, NXcs_profiling, NXentry, NXnote, NXprocess, NXprogram, NXuser

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

Obligatory value: NXapm_paraprobe_transcoder_results

@version: (required) NX_CHAR ⤆

atom_probe: (required) NXapm_paraprobe_tool_results

identifier_analysis: (required) NX_UINT

config: (required) NXnote ⤆

type: (required) NX_CHAR ⤆

file_name: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

window: (optional) NXcs_filter_boolean_mask ⤆

By default the entire reconstructed volume is processed. ...

By default the entire reconstructed volume is processed. In this case, using window is also equivalent to an NXspatial_filter that specified a window entire_dataset.

number_of_ions: (required) NX_UINT ⤆

bitdepth: (required) NX_UINT ⤆

mask: (required) NX_UINT ⤆

mass_to_charge_conversion: (required) NXprocess

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

Mass-to-charge-state-ratio values.

reconstruction: (required) NXprocess

reconstructed_positions: (required) NX_FLOAT (Rank: 2, Dimensions: [n_ions, 3]) {units=NX_LENGTH}

Three-dimensional reconstructed positions of the ions. ...

Three-dimensional reconstructed positions of the ions. Interleaved array of x, y, z positions in the specimen space.

@depends_on: (required) NX_CHAR

Defines in which reference frame the positions are defined.

visualization: (recommended) NXprocess

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

An array of triplets of integers which can serve as a supplementary ...

An array of triplets of integers which can serve as a supplementary array for Paraview to display the reconstruction. The XDMF datatype is here 1, the number of primitives 1 per triplet, the last integer in each triplet is the identifier of each point starting from zero.

ranging: (required) NXprocess

peak_identification: (required) NXprocess

Details about how peaks are interpreted as ion types or not.

ATOM: (required) NXatom

nuclide_hash: (required) NX_UINT ⤆

nuclide_list: (recommended) NX_UINT ⤆

charge_state: (required) NX_INT

mass_to_charge_range: (required) NX_FLOAT (Rank: 2, Dimensions: [n_variable, 2]) {units=NX_ANY}

common: (required) NXapm_paraprobe_tool_common

status: (required) NX_CHAR ⤆

identifier_analysis: (required) NX_UINT ⤆

config: (required) NXnote ⤆

type: (required) NX_CHAR ⤆

file_name: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

PROGRAM: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

profiling: (recommended) NXcs_profiling ⤆

start_time: (required) NX_DATE_TIME ⤆

end_time: (required) NX_DATE_TIME ⤆

total_elapsed_time: (required) NX_FLOAT ⤆

current_working_directory: (required) NX_CHAR ⤆

number_of_processes: (required) NX_UINT

number_of_threads: (required) NX_UINT

number_of_gpus: (required) NX_UINT

USER: (optional) NXuser ⤆

If used, metadata of at least the person who performed this analysis.

name: (required) NX_CHAR ⤆

paraprobe: (required) NXcoordinate_system ⤆

type: (required) NX_CHAR ⤆

handedness: (required) NX_CHAR

x: (required) NX_NUMBER (Rank: 1, Dimensions: [3]) {units=NX_LENGTH} ⤆

y: (required) NX_NUMBER (Rank: 1, Dimensions: [3]) {units=NX_LENGTH} ⤆

z: (required) NX_NUMBER (Rank: 1, Dimensions: [3]) {units=NX_LENGTH} ⤆

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/NXapm_paraprobe_transcoder_results.nxdl.xml