3.3.3.18. NXapm_paraprobe_config_distancer

Status:

application definition, extends NXobject

Description:

Configuration/settings of a paraprobe-distancer software tool run.

Symbols:

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

Groups cited:

NXapm_input_ranging, NXapm_input_reconstruction, NXcg_cylinder_set, NXcg_ellipsoid_set, NXcg_face_list_data_structure, NXcg_hexahedron_set, NXcs_filter_boolean_mask, NXcs_profiling, NXentry, NXmatch_filter, NXprocess, NXspatial_filter, NXsubsampling_filter

Structure:

ENTRY: (required) NXentry

@version: (required) NX_CHAR

Version specifier of this application definition.

definition: (required) NX_CHAR ⤆

Official NeXus NXDL schema with which this file was written. ...

Official NeXus NXDL schema with which this file was written.

Obligatory value: NXapm_paraprobe_config_distancer

program: (required) NX_CHAR

Given name of the program/software/tool with which this NeXus ...

Given name of the program/software/tool with which this NeXus (configuration) file was generated.

@version: (required) NX_CHAR

Ideally program version plus build number, or commit hash or description ...

Ideally program version plus build number, or commit hash or description of ever persistent resources where the source code of the program and build instructions can be found so that the program can be configured ideally in such a manner that the result of this computational process is recreatable in the same deterministic manner.

time_stamp: (required) NX_DATE_TIME

ISO 8601 formatted time code with local time zone offset to UTC ...

ISO 8601 formatted time code with local time zone offset to UTC information included when this configuration file was created.

analysis_identifier: (required) NX_CHAR

Ideally, a (globally persistent) unique identifier for referring ...

Ideally, a (globally persistent) unique identifier for referring to this analysis.

analysis_description: (optional) NX_CHAR

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

results_path: (optional) NX_CHAR

Path to the directory where the tool should store NeXus/HDF5 results ...

Path to the directory where the tool should store NeXus/HDF5 results of this analysis. If not specified results will be stored in the current working directory.

number_of_processes: (required) NX_UINT {units=NX_UNITLESS}

How many individual analyses should the tool execute.

PROCESS: (required) NXprocess ⤆

dataset: (required) NXapm_input_reconstruction

filename: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

dataset_name_reconstruction: (required) NX_CHAR ⤆

dataset_name_mass_to_charge: (required) NX_CHAR ⤆

iontypes: (required) NXapm_input_ranging

filename: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

group_name_iontypes: (required) NX_CHAR ⤆

spatial_filter: (optional) NXspatial_filter

windowing_method: (required) NX_CHAR ⤆

CG_ELLIPSOID_SET: (optional) NXcg_ellipsoid_set ⤆

dimensionality: (required) NX_POSINT ⤆

cardinality: (required) NX_POSINT ⤆

identifier_offset: (required) NX_INT ⤆

center: (required) NX_NUMBER ⤆

half_axes_radii: (required) NX_NUMBER ⤆

orientation: (required) NX_NUMBER ⤆

CG_CYLINDER_SET: (optional) NXcg_cylinder_set ⤆

dimensionality: (required) NX_POSINT ⤆

cardinality: (required) NX_POSINT ⤆

identifier_offset: (required) NX_INT ⤆

center: (required) NX_NUMBER ⤆

height: (required) NX_NUMBER ⤆

radii: (required) NX_NUMBER ⤆

CG_HEXAHEDRON_SET: (optional) NXcg_hexahedron_set ⤆

dimensionality: (required) NX_POSINT ⤆

cardinality: (required) NX_POSINT ⤆

identifier_offset: (required) NX_INT ⤆

hexahedra: (required) NXcg_face_list_data_structure ⤆

CS_FILTER_BOOLEAN_MASK: (optional) NXcs_filter_boolean_mask ⤆

number_of_objects: (required) NX_UINT ⤆

bitdepth: (required) NX_UINT ⤆

mask: (required) NX_UINT ⤆

identifier: (required) NX_UINT ⤆

evaporation_id_filter: (optional) NXsubsampling_filter

iontype_filter: (optional) NXmatch_filter

hit_multiplicity_filter: (optional) NXmatch_filter

point_to_triangle: (required) NXprocess

Compute for all filtered points, e.g. ions of the point set ...

Compute for all filtered points, e.g. ions of the point set the shortest Euclidean distance to the closest triangle of the set of triangles. The triangles can formed a closed surface mesh. Distances are not simple distances based on normal projections but giving an exact solution.

method: (required) NX_CHAR

Specifies for which ions/points the tool will compute distances. ...

Specifies for which ions/points the tool will compute distances. The purpose of this setting is to avoid unnecessary computations when the user requests to only compute distances of ions within a threshold distance to the triangle soup.

By default the distances are computed for all ions; however the setting skin enables to compute distances only for those ions which are not farther away located to a triangle than threshold_distance.

Any of these values: default | skin

threshold_distance: (required) NX_FLOAT {units=NX_LENGTH}

Maximum distance for which distances are computed when method is skin.

triangle_soup: (required) NXprocess

Paraprobe-distancer enables the computation of the Euclidean shortest ...

Paraprobe-distancer enables the computation of the Euclidean shortest distance for each member of a set of points against a set of triangles. In contrast to comparable methods used in atom probe the here computed distance is not simply the projected distance to one of the triangles but the more costly but robust computation of the distance between a point and a triangle.

The triangles can represent for instance the facets of a triangulated surface mesh of a model for the edge of the dataset. Such a model can be computed with paraprobe-surfacer. Alternatively, the triangles can be those from the set of all facets for a set of convex hulls, alpha-shapes, or alpha wrappings about three-dimensional objects like precipitates (computed with e.g. paraprobe-nanochem).

Currently, the tool does not check if the respectively specified triangle sets are consistent, what their topology is, or whether or not they are consistently oriented. Each dataset that is referred to in the list_of _dataset_names_vertices should be an (Nvertices, 3) array of NX_FLOAT. Each dataset referred to in the list_of_dataset_names_facet_indices should be an (Nfacets, 3) array of NX_UINT. Facet indices refer to vertex indices. These need to start at zero and must not exceed Nvertices - 1, i.e. the identifier_offset is 0 and vertices are indexed thus implicitly. Facet normal vectors have to be also an array of shape (Nfacets, 3) of NX_FLOAT.

number_of_files: (required) NX_UINT {units=NX_UNITLESS}

How many triangle sets to consider.

PROCESS: (required) NXprocess

List of triangle sets. This design allows users to combine ...

List of triangle sets. This design allows users to combine multiple triangle sets.

filename: (required) NX_CHAR

Name of the HDF5 file(s) which contain(s) vertex coordinates ...

Name of the HDF5 file(s) which contain(s) vertex coordinates and facet indices to describe the desired set of triangles.

@version: (required) NX_CHAR

Version identifier of the file such as a secure hash which ...

Version identifier of the file such as a secure hash which documents the binary state of the file to add an additional layer of reproducibility.

dataset_name_vertices: (required) NX_CHAR

Absolute HDF5 path to the dataset which ...

Absolute HDF5 path to the dataset which specifies the array of vertex positions.

dataset_name_facet_indices: (required) NX_CHAR

Absolute HDF5 path to the dataset which ...

Absolute HDF5 path to the dataset which specifies the array of facet indices.

dataset_name_facet_normals: (optional) NX_CHAR

Absolute HDF5 path to the dataset which ...

Absolute HDF5 path to the dataset which specifies the array of facet normal vectors.

performance: (required) NXcs_profiling

current_working_directory: (required) NX_CHAR ⤆

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/NXapm_paraprobe_config_distancer.nxdl.xml