2.3.3.3.23. NXapm_paraprobe_distancer_results

Status:

application definition, extends NXobject

Description:

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

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

This tool is part of the paraprobe-toolbox. Inspect the base class NXapm_paraprobe_tool_results. The paraprobe-distancer tool can be used for the computing of the shortest Euclidean distance for each member of a set of points against a set of triangles. In contrast to most approaches in atom probe where the distance is computed as the projected distance, this tool evaluates robustly the exact distance between a point and a triangle.

Triangles can represent for instance the facets of a triangulated surface mesh like those returned by paraprobe-surfacer or any other set of triangles. Triangles do not have to be connected.

Currently, paraprobe-distancer does not check if the respectively specified triangle sets are consistent, what their topology is, or whether or not these triangles are consistently oriented.

Symbols:

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

n_ions: The total number of points, i.e. ions in the reconstruction.

n_tri: The total number of triangles in the set.

Groups cited:

NXapm_paraprobe_tool_common, NXapm_paraprobe_tool_results, NXcoordinate_system_set, NXcoordinate_system, NXcs_filter_boolean_mask, NXcs_profiling, NXentry, NXprogram, NXserialized, NXuser

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

Obligatory value: NXapm_paraprobe_distancer_results

@version: (required) NX_CHAR ⤆

point_to_triangle: (required) NXapm_paraprobe_tool_results

analysis_identifier: (required) NX_UINT

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

The shortest analytical distance of each point to their ...

The shortest analytical distance of each point to their respectively closest triangle from the joint triangle set.

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

For each point the identifier of the triangle for which the ...

For each point the identifier of the triangle for which the shortest distance was found

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

A support field to enable the visualization of each point ...

A support field to enable the visualization of each point by an explicit identifier on the interval [0, n_ions - 1]. The field can be used to visualize the points as a function of their distance to the triangle set (e.g. via XDMF/Paraview).

config: (required) NXserialized

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

window: (required) NXcs_filter_boolean_mask ⤆

number_of_ions: (required) NX_UINT ⤆

bitdepth: (required) NX_UINT ⤆

mask: (required) NX_UINT ⤆

sign_valid: (optional) NXcs_filter_boolean_mask

A bitmask that identifies which of the distance values is ...

A bitmask that identifies which of the distance values is assumed to have a consistent sign because the closest triangle had a consistent outer unit normal defined.

For points whose bit is set to 0 the distance is correct but the sign is not reliable.

number_of_triangles: (required) NX_UINT {units=NX_UNITLESS}

Number of triangles covered by the mask.

bitdepth: (required) NX_UINT {units=NX_UNITLESS} ⤆

Bitdepth of the elementary datatype that is used to store ...

Bitdepth of the elementary datatype that is used to store the information content of the mask (typically 8 bit, uint8).

mask: (required) NX_UINT (Rank: 1, Dimensions: [n_ions]) {units=NX_UNITLESS} ⤆

The content of the mask. Like for all masks used in the tools ...

The content of the mask. Like for all masks used in the tools of the paraprobe-toolbox, padding is used when number_of_objects is not an integer multiple of bitdepth. If padding is used, padded bits are set to 0.

window_triangles: (optional) NXcs_filter_boolean_mask

A bitmask that identifies which of the triangles in the set were ...

A bitmask that identifies which of the triangles in the set were considered when certain triangles have been filtered out.

number_of_objects: (required) NX_UINT ⤆

bitdepth: (required) NX_UINT ⤆

mask: (required) NX_UINT (Rank: 1, Dimensions: [n_tri]) ⤆

common: (required) NXapm_paraprobe_tool_common

status: (required) NX_CHAR ⤆

programID: (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_POSINT

number_of_threads: (required) NX_POSINT

number_of_gpus: (required) NX_POSINT

userID: (optional) NXuser ⤆

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

name: (required) NX_CHAR ⤆

coordinate_system_set: (required) NXcoordinate_system_set ⤆

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_distancer_results.nxdl.xml