3.3.3.34. NXapm_paraprobe_results_surfacer

Status:

application definition, extends NXobject

Description:

Results of a paraprobe-surfacer tool run.

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:

NXcg_alpha_complex, NXcg_face_list_data_structure, NXcg_tetrahedron_set, NXcg_triangle_set, NXcoordinate_system_set, NXcs_computer, NXcs_cpu, NXcs_filter_boolean_mask, NXcs_gpu, NXcs_io_obj, NXcs_io_sys, NXcs_mm_sys, NXcs_profiling_event, NXcs_profiling, NXentry, NXfabrication, NXprocess, NXtransformations, NXuser

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_results_surfacer

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.

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.

start_time: (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 the analysis behind this results file was started, i.e. the paraprobe-tool executable started as a process.

end_time: (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 the analysis behind this results file were completed and the paraprobe-tool executable exited as a process.

config_filename: (required) NX_CHAR

The absolute path and name of the config file for this analysis.

@version: (required) NX_CHAR

At least SHA256 strong hash of the specific config_file for ...

At least SHA256 strong hash of the specific config_file for tracking provenance.

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.

status: (required) NX_CHAR

A statement whether the paraprobe-tool executable managed to ...

A statement whether the paraprobe-tool executable managed to process the analysis or failed prematurely.

This status is written to the results file after the end_time at which point the executable must not compute any analysis. Only when this status message is present and shows success, the user should consider the results. In all other cases it might be that the executable has terminated prematurely or another error occurred.

Any of these values: success | failure

USER: (recommended) NXuser ⤆

If used, contact information and eventually details ...

If used, contact information and eventually details of at least the person who performed this analysis.

name: (required) NX_CHAR ⤆

affiliation: (recommended) NX_CHAR ⤆

address: (optional) NX_CHAR ⤆

email: (recommended) NX_CHAR ⤆

orcid: (recommended) NX_CHAR ⤆

orcid_platform: (recommended) NX_CHAR ⤆

telephone_number: (optional) NX_CHAR ⤆

role: (recommended) NX_CHAR ⤆

social_media_name: (optional) NX_CHAR ⤆

social_media_platform: (optional) NX_CHAR ⤆

COORDINATE_SYSTEM_SET: (required) NXcoordinate_system_set

Details about the coordinate system conventions used.

TRANSFORMATIONS: (required) NXtransformations ⤆

The individual coordinate systems which should be used. ...

The individual coordinate systems which should be used. Field names should be prefixed with the following controlled terms indicating which individual coordinate system is described:

  • paraprobe

  • lab

  • specimen

  • laser

  • leap

  • detector

  • recon

PROCESS: (optional) NXprocess ⤆

window: (required) NXcs_filter_boolean_mask

A bitmask which identifies which of the ions in the dataset were ...

A bitmask which identifies which of the ions in the dataset were analyzed. Computations of alpha complexes may have filtered this ion set further but this process is deterministic.

number_of_ions: (required) NX_UINT {units=NX_UNITLESS}

Number of ions covered by the mask. The mask may be 0 for most.

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

Number of bits assumed matching on a default datatype. ...

Number of bits assumed matching on a default datatype. (e.g. 8 bits for a C-style uint8).

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

The unsigned integer array representing the content of the mask. ...

The unsigned integer array representing the content of the mask. If padding is used the padded bits are set to 0. The mask is for convenience always as large as the entire dataset as it will be stored compressed anyway. The convenience feature with this is that then the mask can be decoded with numpy and mirrored against the evaporation_id array and one immediately can filter out all points that were used by the paraprobe. The length of the array adds to the next unsigned integer if the number of ions in the dataset is not an integer multiple of the bitdepth.

POINT_SET_WRAPPING: (optional) NXprocess

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_complex: (optional) NXcg_alpha_complex

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

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_LENGTH} ⤆

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 the alpha complex was then in fact computed. This window can be different to the entire window as irrelevant ions might have been filtered out to reduce the computational costs of the alpha complex analysis.

number_of_ions: (required) NX_UINT {units=NX_UNITLESS}

Number of ions covered by the mask. ...

Number of ions covered by the mask. The mask value for most may be 0.

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

Number of bits assumed matching on a default datatype. ...

Number of bits assumed matching on a default datatype. (e.g. 8 bits for a C-style uint8).

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

The unsigned integer array representing the content of the mask. ...

The unsigned integer array representing the content of the mask. If padding is used the padded bits are set to 0. The mask is for convenience always as large as the entire dataset as it will be stored compressed anyway. The convenience feature with this is that then the mask can be decoded with numpy and mirrored against the evaporation_id array and one immediately can filter out all points that were used by the paraprobe. The length of the array adds to the next unsigned integer if the number of ions in the dataset is not an integer multiple of the bitdepth.

triangle_set: (optional) NXcg_triangle_set ⤆

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.

identifier_offset: (required) NX_INT {units=NX_UNITLESS} ⤆

Integer which specifies the first index to be used for distinguishin ...

Integer which specifies the first index to be used for distinguishing triangles. Identifiers are defined either implicitly or explicitly. For implicit indexing the identifiers are defined on the interval [identifier_offset, identifier_offset+c-1].

is_watertight: (optional) NX_BOOLEAN

Do the triangles define a triangulated surface mesh which ...

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

volume: (optional) NX_FLOAT {units=NX_VOLUME}

The volume which the triangulated surface mesh encloses ...

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

triangles: (required) NXcg_face_list_data_structure ⤆

dimensionality: (required) NX_POSINT {units=NX_UNITLESS} ⤆

number_of_vertices: (required) NX_POSINT {units=NX_UNITLESS} ⤆

Number of vertices.

number_of_faces: (required) NX_POSINT {units=NX_UNITLESS} ⤆

Number of faces.

vertex_identifier_offset: (required) NX_INT {units=NX_UNITLESS} ⤆

face_identifier_offset: (required) NX_INT {units=NX_UNITLESS} ⤆

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]) {units=NX_UNITLESS}

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).

interior_tetrahedra: (optional) NXcg_tetrahedron_set

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

The set of tetrahedra which represent the interior volume of the complex if that is a closed 2-manifold.

identifier_offset: (required) NX_INT {units=NX_UNITLESS} ⤆

Integer which specifies the first index to be used for distin- ...

Integer which specifies the first index to be used for distin- guishing tetrahedra. Identifiers are defined either implicitly or explicitly. For implicit indexing the identifiers are defined on the interval [identifier_offset, identifier_offset+c-1]. For explicit indexing the identifier array has to be defined.

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_POSINT {units=NX_UNITLESS} ⤆

Number of vertices.

number_of_faces: (required) NX_POSINT {units=NX_UNITLESS} ⤆

Number of faces.

vertex_identifier_offset: (required) NX_INT {units=NX_UNITLESS} ⤆

face_identifier_offset: (required) NX_INT {units=NX_UNITLESS} ⤆

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).

TRIANGLE_SET_WRAPPING: (optional) NXprocess

In the future we may want to wrap other primitives ...

In the future we may want to wrap other primitives like triangles or polylines.

performance: (recommended) NXcs_profiling

current_working_directory: (required) NX_CHAR ⤆

command_line_call: (optional) NX_CHAR ⤆

start_time: (recommended) NX_DATE_TIME ⤆

end_time: (recommended) NX_DATE_TIME ⤆

total_elapsed_time: (required) NX_NUMBER ⤆

number_of_processes: (required) NX_POSINT ⤆

number_of_threads: (required) NX_POSINT ⤆

number_of_gpus: (required) NX_POSINT ⤆

CS_COMPUTER: (recommended) NXcs_computer ⤆

name: (recommended) NX_CHAR ⤆

operating_system: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

uuid: (optional) NX_CHAR ⤆

CS_CPU: (optional) NXcs_cpu ⤆

name: (optional) NX_CHAR ⤆

FABRICATION: (recommended) NXfabrication ⤆

identifier: (optional) NX_CHAR ⤆

capabilities: (optional) NX_CHAR

CS_GPU: (optional) NXcs_gpu ⤆

name: (optional) NX_CHAR ⤆

FABRICATION: (recommended) NXfabrication ⤆

identifier: (optional) NX_CHAR ⤆

capabilities: (optional) NX_CHAR

CS_MM_SYS: (optional) NXcs_mm_sys ⤆

total_physical_memory: (required) NX_NUMBER ⤆

CS_IO_SYS: (optional) NXcs_io_sys ⤆

CS_IO_OBJ: (required) NXcs_io_obj ⤆

technology: (required) NX_CHAR ⤆

max_physical_capacity: (required) NX_NUMBER ⤆

name: (optional) NX_CHAR ⤆

FABRICATION: (recommended) NXfabrication ⤆

identifier: (optional) NX_CHAR ⤆

capabilities: (optional) NX_CHAR

CS_PROFILING_EVENT: (required) NXcs_profiling_event

start_time: (optional) NX_DATE_TIME ⤆

end_time: (optional) NX_DATE_TIME ⤆

description: (required) NX_CHAR ⤆

elapsed_time: (required) NX_NUMBER ⤆

number_of_processes: (required) NX_POSINT ⤆

Specify if it was different from the number_of_processes ...

Specify if it was different from the number_of_processes in the NXcs_profiling super class.

number_of_threads: (required) NX_POSINT ⤆

Specify if it was different from the number_of_threads ...

Specify if it was different from the number_of_threads in the NXcs_profiling super class.

number_of_gpus: (required) NX_POSINT ⤆

Specify if it was different from the number_of_threads ...

Specify if it was different from the number_of_threads in the NXcs_profiling super class.

max_virtual_memory_snapshot: (recommended) NX_NUMBER ⤆

max_resident_memory_snapshot: (recommended) NX_NUMBER ⤆

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_results_surfacer.nxdl.xml