2.3.3.3.33. NXapm_paraprobe_spatstat_config

Status:

application definition, extends NXobject

Description:

Application definition for a configuration file of the paraprobe-spatstat tool. ...

Application definition for a configuration file of the paraprobe-spatstat tool.

This tool is part of the paraprobe-toolbox. Inspect NXapm_paraprobe_tool_config for details.

Symbols:

The symbols used in the schema to specify e.g. dimensions of arrays.

n_ivec_max: Maximum number of atoms per molecular ion. Should be 32 for paraprobe.

n_ion_source: Number of different source iontypes to distinguish.

n_ion_target: Number of different target iontypes to distinguish.

Groups cited:

NXapm_paraprobe_tool_common, NXapm_paraprobe_tool_config, NXcg_cylinder_set, NXcg_ellipsoid_set, NXcg_face_list_data_structure, NXcg_hexahedron_set, NXcg_polyhedron_set, NXcs_filter_boolean_mask, NXcs_prng, NXcs_profiling, NXentry, NXidentifier, NXmatch_filter, NXprocess, NXprogram, NXserialized, NXspatial_filter, NXsubsampling_filter

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

Obligatory value: NXapm_paraprobe_spatstat_config

@version: (required) NX_CHAR ⤆

number_of_tasks: (required) NX_UINT {units=NX_UNITLESS}

How many spatial_statistics tasks should the tool execute.

spatial_statisticsID: (required) NXapm_paraprobe_tool_config

analysis_identifier: (recommended) NX_UINT ⤆

randomize_iontypes: (required) NX_BOOLEAN

Specifies, if the iontypes are randomized for the point cloud or not. ...

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 iontypes randomly across the entire set of ions. That is the total number of ions of either type remain the same but the information about their location is randomized.

ion_query_type_source: (required) NX_CHAR

How should the iontype be interpreted on the source-side, i.e. ...

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. Each active ion is accounted for once.

The value resolve_unknown will set an ion active when the ion is of the UNKNOWNTYPE type. Each active ion is accounted for once.

The value resolve_ion will set an ion active if it is of the specific iontype, irregardless of its elemental or isotopic details. Each active ion is counted once.

The value resolve_element will set an ion active, and most importantly, account for each as many times 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 for each as many times 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, i.e. how often it is accounted for.

Any of these values:

  • resolve_all

  • resolve_unknown

  • resolve_ion

  • resolve_element

  • resolve_isotope

ion_query_nuclide_source: (required) NX_UINT (Rank: 2, Dimensions: [n_ion_source, n_ivec_max]) {units=NX_UNITLESS}

Matrix of isotope vectors, as many as rows as different candidates ...

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 ...

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_nuclide_target: (required) NX_UINT (Rank: 2, Dimensions: [n_ion_target, n_ivec_max]) {units=NX_UNITLESS}

Matrix of isotope vectors, as many as rows as different candidates for ...

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.

IDENTIFIER: (optional) NXidentifier ⤆

reconstruction: (required) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

position: (required) NX_CHAR ⤆

mass_to_charge: (required) NX_CHAR ⤆

ranging: (required) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

ranging_definitions: (required) NX_CHAR ⤆

surface_distance: (optional) NXserialized ⤆

Distance between each ion and triangulated surface mesh.

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

distance: (required) NX_CHAR ⤆

edge_distance: (required) NX_FLOAT {units=NX_LENGTH}

Threshold to define how far an ion has to lay at least from the edge ...

Threshold to define how far an ion has to lay at least from the edge of the dataset so that the ion can act as a source. This means that an ROI is placed at the location of the ion and its neighbors are analyzed how they contribute to the computed statistics.

The edge_distance threshold can be combined with the feature_distance threshold. This threshold defines defines up to which distance to a microstructural feature an ROI is placed.

The threshold is useful to process the dataset such that ROIs do not protrude out of the dataset as this would add bias.

feature_distance: (optional) NXserialized

Distance between each ion and triangulated mesh of microstructural feature ...

Distance between each ion and triangulated mesh of microstructural features. 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 the feature_distance threshold value.

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

distance: (required) NX_CHAR

Absolute path in the (HDF5) file which points to the distance of each ...

Absolute path in the (HDF5) file which points to the distance of each ion to the closest feature.

feature_distance: (required) NX_FLOAT {units=NX_LENGTH}

Threshold to define how close an ion has to lay to a feature so that ...

Threshold to define how close an ion has to lay to a feature so that the ion can at all qualify as a source, i.e. that an ROI is placed at the location of the ion and its neighbors are then analyzed how they contribute to the computed statistics.

Recall that this feature_distance threshold is used in combination with the edge_distance threshold when placing ROI about source ions.

spatial_filter: (required) NXspatial_filter ⤆

windowing_method: (required) NX_CHAR ⤆

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 ⤆

vertices: (required) NX_UINT

cylinder_set: (optional) NXcg_cylinder_set ⤆

dimensionality: (required) NX_POSINT ⤆

cardinality: (required) NX_POSINT ⤆

identifier_offset: (required) NX_INT ⤆

center: (required) NX_NUMBER ⤆

height: (required) NX_NUMBER ⤆

radii: (required) NX_NUMBER ⤆

ellipsoid_set: (optional) NXcg_ellipsoid_set ⤆

dimensionality: (required) NX_POSINT ⤆

cardinality: (required) NX_POSINT ⤆

identifier_offset: (required) NX_INT ⤆

center: (required) NX_NUMBER ⤆

half_axes_radii: (required) NX_NUMBER ⤆

orientation: (required) NX_NUMBER ⤆

polyhedron_set: (optional) NXcg_polyhedron_set ⤆

bitmask: (optional) NXcs_filter_boolean_mask ⤆

number_of_objects: (required) NX_UINT ⤆

bitdepth: (required) NX_UINT ⤆

mask: (required) NX_UINT ⤆

evaporation_id_filter: (optional) NXsubsampling_filter ⤆

min_incr_max: (required) NX_INT ⤆

iontype_filter: (optional) NXmatch_filter ⤆

method: (required) NX_CHAR ⤆

match: (required) NX_NUMBER ⤆

hit_multiplicity_filter: (optional) NXmatch_filter ⤆

method: (required) NX_CHAR ⤆

match: (required) NX_NUMBER ⤆

random_number_generator: (recommended) NXcs_prng

type: (required) NX_CHAR ⤆

seed: (required) NX_NUMBER

warmup: (required) NX_NUMBER

statistics: (required) NXprocess

Specifies which spatial statistics to compute.

knn: (optional) NXprocess

Compute k-th nearest neighbour statistics.

kth: (required) NX_UINT {units=NX_UNITLESS}

Order k.

min_incr_max: (required) NX_FLOAT (Rank: 1, Dimensions: [3]) {units=NX_LENGTH}

Minimum value, increment, and maximum value of the histogram binning.

rdf: (optional) NXprocess

Compute radial distribution function.

min_incr_max: (required) NX_FLOAT (Rank: 1, Dimensions: [3]) {units=NX_LENGTH}

Minimum value, increment, and maximum value of the histogram binning.

common: (required) NXapm_paraprobe_tool_common

status: (required) NX_CHAR ⤆

programID: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

profiling: (recommended) NXcs_profiling ⤆

start_time: (required) NX_DATE_TIME ⤆

end_time: (required) NX_DATE_TIME ⤆

total_elapsed_time: (required) NX_FLOAT ⤆

current_working_directory: (required) NX_CHAR ⤆

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_spatstat_config.nxdl.xml