2.3.3.3.34. NXapm_paraprobe_surfacer_config

Status:

application definition, extends NXobject

Description:

Application definition for a configuration file of the paraprobe-surfacer tool. ...

Application definition for a configuration file of the paraprobe-surfacer tool.

This tool is part of the paraprobe-toolbox. Inspect NXapm_paraprobe_tool_config for details.

Symbols:

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

n_alpha_values: Number of alpha values (and offset values) to probe.

n_values: How many different match values does the filter specify.

Groups cited:

NXapm_paraprobe_tool_common, NXapm_paraprobe_tool_config, NXcg_cylinder_set, NXcg_ellipsoid_set, NXcg_face_list_data_structure, NXcg_hexahedron_set, NXcg_polyhedron_set, NXcs_filter_boolean_mask, NXcs_profiling, NXentry, NXidentifier, NXmatch_filter, NXprocess, NXprogram, NXserialized, NXspatial_filter, NXsubsampling_filter

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

Obligatory value: NXapm_paraprobe_surfacer_config

@version: (required) NX_CHAR ⤆

surface_meshing: (required) NXapm_paraprobe_tool_config

analysis_identifier: (recommended) NX_UINT ⤆

alpha_value_choice: (required) NX_CHAR

Specifies which method to use to define the alpha value. ...

Specifies which method to use to define the alpha value.

The value convex_hull_naive is the default. The setting instructs the tool to use a fast specialized algorithm for computing only the convex hull. The resulting triangles can be skinny.

The value convex_hull_refine instructs to tool to refine the quality of the mesh resulting from convex_hull_naive via triangle flipping and splitting.

The value smallest_solid instructs the CGAL library to choose a value which realizes an alpha-shape that is the smallest solid.

The value cgal_optimal instructs the CGAL library to choose a value which the library considers as to be an optimal value. Details are defined in the respective section of the CGAL library on 3D alpha shapes.

The value set_of_values instructs the tool to compute a list collection of alpha-shapes for the specified alpha-values.

The value set_of_alpha_wrappings instructs the tool to generate a set of so-called alpha wrappings. These are similar to alpha-shapes but provide additional guarantees (such as watertightness and proximity constraints) on the resulting wrapping.

Any of these values:

  • convex_hull_naive

  • convex_hull_refine

  • smallest_solid

  • cgal_optimal

  • set_of_values

  • set_of_alpha_wrappings

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

Array of alpha values to use when alpha_value_choice is ...

Array of alpha values to use when alpha_value_choice is set_of_values or when alpha_value_choice is set_of_alpha_wrappings.

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

Array of offset values to use when alpha_value_choice is set_of_alpha_wrap ...

Array of offset values to use when alpha_value_choice is set_of_alpha_wrappings. The array of alpha_values and offset_values define a sequence of (alpha and offset value).

has_exterior_facets: (required) NX_BOOLEAN

Specifies if the tool should compute the set of exterior triangle facets ...

Specifies if the tool should compute the set of exterior triangle facets for each alpha complex (for convex hull, alpha shapes, and wrappings).

has_closure: (required) NX_BOOLEAN

Specifies if the tool should check if the alpha complex of ...

Specifies if the tool should check if the alpha complex of exterior triangular facets is a closed polyhedron.

has_interior_tetrahedra: (required) NX_BOOLEAN

Specifies if the tool should compute all interior tetrahedra ...

Specifies if the tool should compute all interior tetrahedra of the alpha complex (currently only for alpha shapes).

IDENTIFIER: (optional) NXidentifier ⤆

reconstruction: (required) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

position: (required) NX_CHAR ⤆

mass_to_charge: (required) NX_CHAR ⤆

ranging: (required) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

ranging_definitions: (required) NX_CHAR ⤆

spatial_filter: (required) NXspatial_filter ⤆

windowing_method: (required) NX_CHAR ⤆

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 ⤆

vertices: (required) NX_UINT

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 ⤆

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 ⤆

polyhedron_set: (optional) NXcg_polyhedron_set ⤆

bitmask: (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 ⤆

min_incr_max: (required) NX_INT ⤆

iontype_filter: (optional) NXmatch_filter ⤆

method: (required) NX_CHAR ⤆

match: (required) NX_NUMBER ⤆

hit_multiplicity_filter: (optional) NXmatch_filter ⤆

method: (required) NX_CHAR ⤆

match: (required) NX_NUMBER ⤆

preprocessing: (required) NXprocess

method: (required) NX_CHAR

Specifies the method that is used to preprocess the point cloud ...

Specifies the method that is used to preprocess the point cloud prior to the alpha-shape computation.

The option default specifies that no such filtering is applied. The option kuehbach specifies that a Hoshen-Kopelman percolation analysis is used to identify points that lie closer to the edge of the dataset. Details about the methods are reported in M. Kühbach et al..

Any of these values: default | kuehbach

kernel_width: (required) NX_UINT {units=NX_UNITLESS}

When using the kuehbach preprocessing, this is the width of the ...

When using the kuehbach preprocessing, this is the width of the kernel for identifying which ions are in voxels close to the edge of the point cloud.

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 ⤆

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_surfacer_config.nxdl.xml