NXapm_paraprobe_config_spatstat¶
Status:
application definition, extends NXobject
Description:
Configuration of a paraprobe-spatstat tool run in atom probe microscopy.
Symbols:
The symbols used in the schema to specify e.g. dimensions of arrays.
n_ivecmax: Maximum number of atoms per molecular ion. Should be 32 for paraprobe.
n_ion_source: Number of different sources iontypes to distinguish.
n_ion_target: Number of different target iontypes to distinguish.
- Groups cited:
NXapm_input_ranging, NXapm_input_reconstruction, NXcg_cylinder_set, NXcg_ellipsoid_set, NXcg_face_list_data_structure, NXcg_hexahedron_set, NXcollection, NXcs_filter_boolean_mask, NXcs_prng, 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_spatstat
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.
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.
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.
number_of_processes: (required) NX_UINT {units=NX_UNITLESS}
How many range_with_existent_iontypes processes should the tool execute as part of the analysis.
spatial_statistics: (optional) 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
ion_to_edge_distances: (optional) NXprocess
The tool enables to inject precomputed distances of each ion to a representation of the edge of the dataset which can be used to control and substantially reduce edge effects when computing spatial statistics.
filename: (required) NX_CHAR
Name of an HDF5 file which contains ion-to-edge distances.
dataset_name_distances: (required) NX_CHAR
Absolute HDF5 path to the dataset with the ion-to-edge distance values for each ion. The shape of the distance values has to match the length of the ion positions array in dataset/dataset_name_reconstruction and dataset_name_mass_to_charge respectively.
ion_to_feature_distances: (optional) NXprocess
In addition to spatial filtering, and considering how far ions lie to the edge of the dataset, it is possible to restrict the analyses to a sub-set of ions within a distance not farther away to a feature than a threshold value.
filename: (required) NX_CHAR
Name of an HDF5 file which contains ion-to-feature distances.
dataset_name_distances: (required) NX_CHAR
Absolute HDF5 path to the dataset with the ion-to-feature distance values for each ion.
randomize_labels: (required) NX_BOOLEAN
Specifies if the iontypes are randomized for the point cloud or not. Internally paraprobe uses a sequentially executed deterministic MT19987 (MersenneTwister) pseudo-random number generator to shuffle the iontype labels randomly across the entire set of ions.
ion_query_type_source: (required) NX_CHAR
How should the iontype be interpreted on the source-side, i.e. all these ion positions where a regions-of-interest (ROI) around so-called source ions will be placed. Different options exist how iontypes are interpreted given an iontype represents in general a (molecular) ion with different isotopes that have individually different multiplicity.
The value resolve_all will set an ion active in the analysis regardless of which iontype it is. The value resolve_unknown will set an ion active when it is of the UNKNOWNTYPE. The value resolve_ion will set an ion active if it is of the specific iontype, irregardless of its elemental or isotopic details. The value resolve_element will set an ion active, and most importantly, account as many times for it, as the (molecular) ion contains atoms of elements in the whitelist ion_query_isotope_vector. The value resolve_isotope will set an ion active, and most importantly, account as many times for it, as the (molecular) ion contains isotopes in the whitelist ion_query_isotope_vector.
In effect, ion_query_isotope_vector acts as a whitelist to filter which ions are considered as source ions of the correlation statistics and how the multiplicity of each ion will be factorized.
Any of these values:
resolve_all
resolve_unknown
resolve_ion
resolve_element
resolve_isotope
ion_query_isotope_vector_source: (required) NX_UINT (Rank: 2, Dimensions: [n_ion_source, n_ivecmax]) {units=NX_UNITLESS}
Matrix of isotope vectors, as many as rows as different candidates for iontypes should be distinguished as possible source iontypes. In the simplest case, the matrix contains only the proton number of the element in the row, all other values set to zero. Combined with ion_query_type_source set to resolve_element this will recover usual spatial correlation statistics like the 1NN C-C spatial statistics.
ion_query_type_target: (required) NX_CHAR
Similarly as ion_query_type_source how should iontypes be interpreted on the target-side, i.e. how many counts will be bookkept for ions which are neighbors of source ions within or on the surface of each inspection/ROI about each source ion. Source ion in the center of the ROI are not accounted for during counting the summary statistics. For details about the resolve values consider the explanations in ion_query_type_source. These account for ion_query_type_target as well.
Any of these values:
resolve_all
resolve_unknown
resolve_ion
resolve_element
resolve_isotope
ion_query_isotope_vector_target: (required) NX_UINT (Rank: 2, Dimensions: [n_ion_target, n_ivecmax]) {units=NX_UNITLESS}
Matrix of isotope vectors, as many as rows as different candidates for iontypes to distinguish as possible targets. See additional comments under ion_query_isotope_vector_source.
random_number_generator: (recommended) NXcs_prng
statistics: (required) NXprocess
Specifies which spatial statistics to compute.
knn: (optional) NXcollection
Compute k-th nearest neighbour statistics.
nth: (required) NX_UINT {units=NX_UNITLESS}
Order k.
histogram_min_incr_max: (required) NX_FLOAT (Rank: 1, Dimensions: [3]) {units=NX_LENGTH}
Minimum value, increment, and maximum value of the histogram binning.
Hypertext Anchors¶
List of hypertext anchors for all groups, fields, attributes, and links defined in this class.
/NXapm_paraprobe_config_spatstat/ENTRY/analysis_description-field
/NXapm_paraprobe_config_spatstat/ENTRY/analysis_identifier-field
/NXapm_paraprobe_config_spatstat/ENTRY/number_of_processes-field
/NXapm_paraprobe_config_spatstat/ENTRY/program@version-attribute
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/dataset-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/dataset/dataset_name_mass_to_charge-field
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/dataset/dataset_name_reconstruction-field
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/dataset/filename-field
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/dataset/filename@version-attribute
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/evaporation_id_filter-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/hit_multiplicity_filter-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/ion_to_edge_distances-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/ion_to_edge_distances/filename-field
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/ion_to_feature_distances-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/ion_to_feature_distances/filename-field
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/ion_to_feature_distances/statistics-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/iontype_filter-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/iontypes-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/iontypes/filename-field
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/iontypes/filename@version-attribute
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/iontypes/group_name_iontypes-field
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/spatial_filter-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/spatial_filter/CG_CYLINDER_SET-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/spatial_filter/CG_CYLINDER_SET/radii-field
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/spatial_filter/CG_ELLIPSOID_SET-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/spatial_filter/CG_HEXAHEDRON_SET-group
/NXapm_paraprobe_config_spatstat/ENTRY/spatial_statistics/spatial_filter/windowing_method-field