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, 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.
Obligatory value:
NXapm_paraprobe_config_distancer
program: (required) NX_CHAR
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 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 information included when this configuration file was created.
analysis_identifier: (optional) NX_CHAR
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.
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
iontypes: (required) NXapm_input_ranging
spatial_filter: (optional) NXspatial_filter
windowing_method: (required) NX_CHAR
CG_ELLIPSOID_SET: (optional) NXcg_ellipsoid_set
CG_CYLINDER_SET: (optional) NXcg_cylinder_set
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
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 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. 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 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 multiple triangle sets.
filename: (required) NX_CHAR
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 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 specifies the array of vertex positions.
dataset_name_facet_indices: (required) NX_CHAR
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 specifies the array of facet normal vectors.
Hypertext Anchors¶
List of hypertext anchors for all groups, fields, attributes, and links defined in this class.
/NXapm_paraprobe_config_distancer/ENTRY/analysis_description-field
/NXapm_paraprobe_config_distancer/ENTRY/analysis_identifier-field
/NXapm_paraprobe_config_distancer/ENTRY/number_of_processes-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/dataset-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/dataset/dataset_name_mass_to_charge-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/dataset/dataset_name_reconstruction-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/dataset/filename-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/dataset/filename@version-attribute
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/evaporation_id_filter-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/hit_multiplicity_filter-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/iontype_filter-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/iontypes-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/iontypes/filename-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/iontypes/filename@version-attribute
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/iontypes/group_name_iontypes-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/point_to_triangle-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/point_to_triangle/method-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/point_to_triangle/threshold_distance-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/point_to_triangle/triangle_soup-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/point_to_triangle/triangle_soup/PROCESS-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/cardinality-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/center-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/dimensionality-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/height-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/radii-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/cardinality-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/center-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/dimensionality-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/orientation-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/cardinality-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/hexahedra-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK-group
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/bitdepth-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/mask-field
/NXapm_paraprobe_config_distancer/ENTRY/PROCESS/spatial_filter/windowing_method-field
/NXapm_paraprobe_config_distancer/ENTRY/program@version-attribute