.. auto-generated by dev_tools.docs.nxdl from the NXDL source contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml -- DO NOT EDIT .. index:: ! NXapm_paraprobe_surfacer_results (application definition) ! apm_paraprobe_surfacer_results (application definition) see: apm_paraprobe_surfacer_results (application definition); NXapm_paraprobe_surfacer_results .. _NXapm_paraprobe_surfacer_results: ================================ NXapm_paraprobe_surfacer_results ================================ **Status**: *application definition* (contribution), extends :ref:`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**: :ref:`NXapm_paraprobe_tool_process`, :ref:`NXcg_alpha_complex`, :ref:`NXcg_face_list_data_structure`, :ref:`NXcg_tetrahedron`, :ref:`NXcg_triangle`, :ref:`NXcs_filter_boolean_mask`, :ref:`NXentry` .. index:: NXentry (base class); used in application definition, NXapm_paraprobe_tool_process (base class); used in application definition, NXcg_alpha_complex (base class); used in application definition, NXcs_filter_boolean_mask (base class); used in application definition, NXcg_triangle (base class); used in application definition, NXcg_face_list_data_structure (base class); used in application definition, NXcg_tetrahedron (base class); used in application definition **Structure**: .. _/NXapm_paraprobe_surfacer_results/ENTRY-group: :bolditalic:`ENTRY`: (required) :ref:`NXentry` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/definition-field: .. index:: definition (field) **definition**: (required) :ref:`NX_CHAR ` :ref:`⤆ ` Obligatory value: ``NXapm_paraprobe_surfacer_results`` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID-group: **point_set_wrapping**\ :bolditalic:`ID`: (required) :ref:`NXapm_paraprobe_tool_process` :ref:`⤆ ` .. collapse:: 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. .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID-group: **alpha_complex**\ :bolditalic:`ID`: (optional) :ref:`NXcg_alpha_complex` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/dimensionality-field: .. index:: dimensionality (field) **dimensionality**: (required) :ref:`NX_POSINT ` :ref:`⤆ ` Any of these values: ``2`` | ``3`` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/type-field: .. index:: type (field) **type**: (required) :ref:`NX_CHAR ` :ref:`⤆ ` Any of these values: * ``convex_hull`` * ``alpha_shape`` * ``alpha_wrapping`` * ``other`` * ``undefined`` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/mode-field: .. index:: mode (field) **mode**: (required) :ref:`NX_CHAR ` Any of these values: ``general`` | ``regularized`` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/alpha-field: .. index:: alpha (field) **alpha**: (required) :ref:`NX_NUMBER ` {units=\ :ref:`NX_ANY `} :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/offset-field: .. index:: offset (field) **offset**: (optional) :ref:`NX_NUMBER ` {units=\ :ref:`NX_LENGTH `} :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/window-group: **window**: (required) :ref:`NXcs_filter_boolean_mask` .. collapse:: 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. .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/window/number_of_ions-field: .. index:: number_of_ions (field) **number_of_ions**: (required) :ref:`NX_UINT ` {units=\ :ref:`NX_UNITLESS `} Number of ions covered by the mask. .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/window/bitdepth-field: .. index:: bitdepth (field) **bitdepth**: (required) :ref:`NX_UINT ` {units=\ :ref:`NX_UNITLESS `} :ref:`⤆ ` Number of bits assumed matching on a default datatype. .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/window/mask-field: .. index:: mask (field) **mask**: (required) :ref:`NX_UINT ` (Rank: 1, Dimensions: [n_ions]) {units=\ :ref:`NX_UNITLESS `} :ref:`⤆ ` .. collapse:: The bitfield of the mask. See :ref:`NXcs_filter_boolean_mask` for ... The bitfield of the mask. See :ref:`NXcs_filter_boolean_mask` for how this bitfield is to be interpreted. .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set-group: **triangle_set**: (optional) :ref:`NXcg_triangle` :ref:`⤆ ` .. collapse:: 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. .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/index_offset-field: .. index:: index_offset (field) **index_offset**: (required) :ref:`NX_INT ` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles-group: **triangles**: (required) :ref:`NXcg_face_list_data_structure` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/dimensionality-field: .. index:: dimensionality (field) **dimensionality**: (required) :ref:`NX_POSINT ` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/number_of_vertices-field: .. index:: number_of_vertices (field) **number_of_vertices**: (required) :ref:`NX_UINT ` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/number_of_faces-field: .. index:: number_of_faces (field) **number_of_faces**: (required) :ref:`NX_UINT ` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/indices_offset_vertex-field: .. index:: indices_offset_vertex (field) **indices_offset_vertex**: (required) :ref:`NX_INT ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/indices_offset_face-field: .. index:: indices_offset_face (field) **indices_offset_face**: (required) :ref:`NX_INT ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/vertices-field: .. index:: vertices (field) **vertices**: (required) :ref:`NX_FLOAT ` (Rank: 2, Dimensions: [n_v_tri, 3]) {units=\ :ref:`NX_LENGTH `} .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/faces-field: .. index:: faces (field) **faces**: (required) :ref:`NX_UINT ` (Rank: 2, Dimensions: [n_f_tri, 3]) .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/xdmf_topology-field: .. index:: xdmf_topology (field) **xdmf_topology**: (required) :ref:`NX_UINT ` (Rank: 1, Dimensions: [n_f_tri_xdmf]) {units=\ :ref:`NX_UNITLESS `} .. collapse:: 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). .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/is_watertight-field: .. index:: is_watertight (field) **is_watertight**: (optional) :ref:`NX_BOOLEAN ` Do the triangles define a triangulated surface mesh that is watertight? .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/volume-field: .. index:: volume (field) **volume**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_VOLUME `} .. collapse:: The volume which the triangulated surface mesh ... The volume which the triangulated surface mesh encloses if that mesh is watertight. .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra-group: **interior_tetrahedra**: (optional) :ref:`NXcg_tetrahedron` :ref:`⤆ ` .. collapse:: 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. .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/index_offset-field: .. index:: index_offset (field) **index_offset**: (required) :ref:`NX_INT ` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/volume-field: .. index:: volume (field) **volume**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_VOLUME `} The accumulated volume of all interior tetrahedra. .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra-group: **tetrahedra**: (optional) :ref:`NXcg_face_list_data_structure` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/number_of_vertices-field: .. index:: number_of_vertices (field) **number_of_vertices**: (required) :ref:`NX_UINT ` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/number_of_faces-field: .. index:: number_of_faces (field) **number_of_faces**: (required) :ref:`NX_UINT ` :ref:`⤆ ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/indices_offset_vertex-field: .. index:: indices_offset_vertex (field) **indices_offset_vertex**: (required) :ref:`NX_INT ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/indices_offset_face-field: .. index:: indices_offset_face (field) **indices_offset_face**: (required) :ref:`NX_INT ` .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/vertices-field: .. index:: vertices (field) **vertices**: (required) :ref:`NX_FLOAT ` (Rank: 2, Dimensions: [n_v_tet, 3]) {units=\ :ref:`NX_LENGTH `} .. _/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/xdmf_topology-field: .. index:: xdmf_topology (field) **xdmf_topology**: (required) :ref:`NX_UINT ` (Rank: 1, Dimensions: [n_f_tet_xdmf]) {units=\ :ref:`NX_UNITLESS `} .. collapse:: 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. * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY-group ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/definition-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID-group ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID-group ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/alpha-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/dimensionality-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra-group ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/index_offset-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra-group ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/indices_offset_face-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/indices_offset_vertex-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/number_of_faces-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/number_of_vertices-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/vertices-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/tetrahedra/xdmf_topology-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/interior_tetrahedra/volume-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/mode-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/offset-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set-group ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/index_offset-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles-group ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/dimensionality-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/faces-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/indices_offset_face-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/indices_offset_vertex-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/is_watertight-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/number_of_faces-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/number_of_vertices-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/vertices-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/volume-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/triangle_set/triangles/xdmf_topology-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/type-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/window-group ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/window/bitdepth-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/window/mask-field ` * :ref:`/NXapm_paraprobe_surfacer_results/ENTRY/point_set_wrappingID/alpha_complexID/window/number_of_ions-field ` **NXDL Source**: https://github.com/FAIRmat-NFDI/nexus_definitions/tree/fairmat/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml