2.3.3.3.29. NXapm_paraprobe_surfacer_results

Status:

application definition (contribution), extends NXapm_paraprobe_tool_results

Description:

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

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_v_tri: The number of vertices of the alpha complex.

n_f_tri: The number of faces of the alpha complex.

n_f_tri_xdmf: The total number of XDMF values to represent all faces of triangles via XDMF.

n_f_tet_xdmf: The total number of XDMF values to represent all faces of tetrahedra via XDMF.

Groups cited:

NXapm_paraprobe_tool_process, NXcg_alpha_complex, NXcg_face_list_data_structure, NXcg_tetrahedron, NXcg_triangle, NXcs_filter_boolean_mask, NXentry

Structure:

ENTRY: (required) NXentry ⤆

definition: (required) NX_CHAR ⤆

Obligatory value: NXapm_paraprobe_surfacer_results

point_set_wrappingID: (required) NXapm_paraprobe_tool_process ⤆

Paraprobe-surfacer can be used to load a ROI that is the entire or a ...

Paraprobe-surfacer can be used to load a ROI that is the entire or a sub-set of the ion point cloud. In the point_cloud_wrapping process the tool computes a triangulated surface mesh which encloses the ROI/point cloud. This mesh can be seen as a model for the edge of the dataset.

Different algorithms can be used with paraprobe-surfacer to create this mesh such as convex hulls, alpha-shapes as their generalization, or alpha wrappings.

Ideally, the resulting mesh should be a watertight polyhedron. This polyhedron is not necessarily convex. For some algorithms there is no guarantee that the resulting mesh yields a watertight mesh.

alpha_complexID: (optional) NXcg_alpha_complex

dimensionality: (required) NX_POSINT ⤆

Any of these values: 2 | 3

type: (required) NX_CHAR ⤆

Any of these values:

  • convex_hull

  • alpha_shape

  • alpha_wrapping

  • other

  • undefined

mode: (required) NX_CHAR

Any of these values: general | regularized

alpha: (required) NX_NUMBER {units=NX_ANY} ⤆

offset: (optional) NX_NUMBER {units=NX_LENGTH} ⤆

window: (required) NXcs_filter_boolean_mask

A bitmask which identifies exactly all those ions whose positions ...

A bitmask which identifies exactly all those ions whose positions were considered when defining the filtered point set from which that alpha_complex instance was computed.

This window can be different to the window of the point_set_wrapping parent group because irrelevant ions might have been filtered out in addition to the window defined in point_set_wrapping to reduce e.g. computational costs of the alpha complex computation.

number_of_ions: (required) NX_UINT {units=NX_UNITLESS}

Number of ions covered by the mask.

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

Number of bits assumed matching on a default datatype.

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

The bitfield of the mask. See :ref:`NXcs_filter_boolean_mask` for ...

The bitfield of the mask. See NXcs_filter_boolean_mask for how this bitfield is to be interpreted.

triangle_set: (optional) NXcg_triangle ⤆

The set of triangles in the coordinate system paraprobe ...

The set of triangles in the coordinate system paraprobe which discretizes the exterior surface of the alpha complex.

index_offset: (required) NX_INT ⤆

triangles: (required) NXcg_face_list_data_structure ⤆

dimensionality: (required) NX_POSINT ⤆

number_of_vertices: (required) NX_UINT ⤆

number_of_faces: (required) NX_UINT ⤆

indices_offset_vertex: (required) NX_INT

indices_offset_face: (required) NX_INT

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

faces: (required) NX_UINT (Rank: 2, Dimensions: [n_f_tri, 3])

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

A list of as many tuples of XDMF topology key, XDMF number ...

A list of as many tuples of XDMF topology key, XDMF number of vertices and a triple of vertex indices specifying each triangle. The total number of entries is n_f_tri * (1+1+3).

is_watertight: (optional) NX_BOOLEAN

Do the triangles define a triangulated surface mesh that is watertight?

volume: (optional) NX_FLOAT {units=NX_VOLUME}

The volume which the triangulated surface mesh ...

The volume which the triangulated surface mesh encloses if that mesh is watertight.

interior_tetrahedra: (optional) NXcg_tetrahedron ⤆

The set of tetrahedra which represent the interior volume ...

The set of tetrahedra which represent the interior volume of the complex if that is a closed two-manifold.

index_offset: (required) NX_INT ⤆

volume: (optional) NX_FLOAT {units=NX_VOLUME}

The accumulated volume of all interior tetrahedra.

tetrahedra: (optional) NXcg_face_list_data_structure ⤆

number_of_vertices: (required) NX_UINT ⤆

number_of_faces: (required) NX_UINT ⤆

indices_offset_vertex: (required) NX_INT

indices_offset_face: (required) NX_INT

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

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

A list of as many tuples of XDMF topology key, XDMF number ...

A list of as many tuples of XDMF topology key, XDMF number of vertices and a triple of vertex indices specifying each triangle. The total number of entries is n_f_tet * (1+1+4).

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_results.nxdl.xml