2.3.3.3.34. NXapm_paraprobe_tool_parameters

Status:

base class (contribution), extends NXparameters

Description:

Base class documenting parameters for processing used by all tools of the ...

Base class documenting parameters for processing used by all tools of the paraprobe-toolbox.

Symbols:

No symbol table

Groups cited:

NXmatch_filter, NXnote, NXspatial_filter, NXsubsampling_filter

Structure:

identifier_analysis: (optional) NX_UINT {units=NX_UNITLESS}

Internal identifier used by the tool to refer to an analysis. ...

Internal identifier used by the tool to refer to an analysis. Simulation ID an alias.

description: (optional) NX_CHAR

Possibility for leaving a free-text description about this analysis. ...

Possibility for leaving a free-text description about this analysis.

Although offered here for convenience, we strongly encourage to parameterize such descriptions as much as possible to support reusage and clearer communication.

reconstruction: (optional) NXnote ⤆

Specification of the tomographic reconstruction to use for this analysis. ...

Specification of the tomographic reconstruction to use for this analysis.

Typically, reconstructions in the field of atom probe tomography are communicated via files which store at least reconstructed ion positions and mass-to-charge-state-ratio values. Container files like HDF5 though can store multiple reconstructions. Therefore, the position and mass_to_charge concepts point to specific instances to use for this analysis.

position: (optional) NX_CHAR

Name of the node which resolves the reconstructed ion position ...

Name of the node which resolves the reconstructed ion position values to use for this analysis.

mass_to_charge: (optional) NX_CHAR

Name of the node which resolves the mass-to-charge-state-ratio ...

Name of the node which resolves the mass-to-charge-state-ratio values to use for this analysis.

ranging: (optional) NXnote ⤆

Specification of the ranging definitions to use for this analysis. ...

Specification of the ranging definitions to use for this analysis.

Ranging is the process of labeling time-of-flight data with so-called iontypes (aka ion species). Ideally, iontypes specify the most likely (molecular) ion that is assumed to have been evaporated given that its mass-to-charge-state ratio lies within the specific mass-to-charge-state-ratio value interval of the iontype.

The so-called unknown_type iontype represents the null model of an ion that has not been ranged (for whatever reasons) or is not rangeable. The identifier of this special iontype is always the reserved value 0.

ranging_definitions: (optional) NX_CHAR

Name of the (parent) node directly below which (in the hierarchy) ...

Name of the (parent) node directly below which (in the hierarchy) the ranging definition for (molecular) ions are stored.

surface: (optional) NXnote ⤆

Specification of the triangulated surface mesh to use for this analysis. ...

Specification of the triangulated surface mesh to use for this analysis.

Such a surface mesh can be used to define the edge of the reconstructed volume to account for finite size effects.

surface_distance: (optional) NXnote ⤆

Specification of the point-to-triangulated-surface-mesh distances to ...

Specification of the point-to-triangulated-surface-mesh distances to use for this analysis.

distance: (optional) NX_CHAR

Absolute path in the (HDF5) file that points to the distance values. ...

Absolute path in the (HDF5) file that points to the distance values. The tool assumes that the values are stored in the same order as points (ions).

spatial_filter: (optional) NXspatial_filter

evaporation_id_filter: (optional) NXsubsampling_filter

iontype_filter: (optional) NXmatch_filter

hit_multiplicity_filter: (optional) NXmatch_filter

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_tool_parameters.nxdl.xml