NXapm_paraprobe_config_clusterer

Status:

application definition, extends NXobject

Description:

Configuration of a paraprobe-clusterer tool run in atom probe microscopy.

Symbols:

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

n_positions: Number of position values.

n_disjoint_clusters: Number of disjoint cluster.

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_clusterer

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 clustering processes should the tool execute.

cameca_to_nexus: (optional) NXprocess

This process maps results from cluster analyses performed with IVAS/APSuite into an interoperable representation. Specifically in this process paraprobe-clusterer takes results from clustering methods from other tools of the APM community, like IVAS/APSuite. These results are usually reported in two ways. Either as an explicit list of reconstructed ion positions. In the case of IVAS these positions are reported through a text file with a cluster label for each position.

Alternatively, the list of positions is reported, as it is the case for AMETEK (IVAS/AP Suite) but the cluster labels are specified implicitly only in the following way: The mass-to-charge-state ratio column of a what is effectively a file formatted like POS is used to assign a hypothetical mass-to-charge value which resolves a floating point representation of the cluster ID.

Another case can occur where all disjoint floating point values, i.e. here cluster labels, are reported and then a dictionary is created how each value matches to a cluster ID.

In general the cluster ID zero is reserved for marking the dataset as to not be assigned to any cluster. Therefore, indices of disjoint clusters start at 1.

ion_position_filename: (required) NX_CHAR

Name of HDF5 file which stores reconstructed ion positions. This file should have been generated by from the community or vendor format. This file not necessarily contains all the of the dataset because spatial filters might have been applied in commercial software prior to executing the cluster analysis so that e.g. only positions within a ROI are reported by the commercial software. POS files from IVAS have to be converted first.

dataset_name_positions: (required) NX_CHAR

Name of the dataset inside the HDF5 file ion_position_filename which refers to the specific positions to use for this analysis. The referred to dataset has to be formatted as an array of shape (n_positions, 3).

cluster_indices_filename: (required) NX_CHAR

Name of the HDF5 file which stores mass-to-charge-state-ratio values (in the case of IVAS/APSuite) or other numbers which can be interpreted as cluster labels.

dataset_name_cluster_indices: (required) NX_CHAR

Name of the dataset inside the HDF5 file cluster_indices_filename which refers to the specifically encoded cluster indices. The referred to dataset has to be formatted as an array of shape (n_positions, 1).

mapping_dictionary_keyword: (required) NX_NUMBER (Rank: 1, Dimensions: [n_disjoint_clusters]) {units=NX_UNITLESS}

The list of all keywords of a dictionary which maps implicit cluster indices like those from IVAS/APSuite which were0ass-to-charge-state ratios.

mapping_dictionary_value: (required) NX_UINT (Rank: 1, Dimensions: [n_disjoint_clusters]) {units=NX_UNITLESS}

The list of all values of a dictionary which maps implicit cluster indices like those from IVAS/APSuite which were0ass-to-charge-state ratios. The sequences of mapping_dictionary_keyword and mapping_dictionary_value have to match.

recover_evaporation_id: (required) NX_BOOLEAN {units=NX_UNITLESS}

Specifies if the tool should try to recover for each position the closest matching position from dataset/dataset_name_reconstruction (within floating point accuracy). This can be useful for instance when users wish to recover the original evaporation ID which IVAS/AP Suite drops for instance when writing their .indexed. cluster results files.

recover_bitmask: (required) NX_BOOLEAN {units=NX_UNITLESS}

Specifies if the tool should try to recover, after a recovery of the evaporation IDs a bitmask which identifies which of the positions in dataset/dataset/dataset_name_reconstruction where covered by the IVAS/APSuite cluster analysis. This can be useful to recover the region of interest.

dataset: (required) NXapm_input_reconstruction

filename: (required) NX_CHAR

@version: (required) NX_CHAR

dataset_name_reconstruction: (required) NX_CHAR

dataset_name_mass_to_charge: (required) NX_CHAR

iontypes: (required) NXapm_input_ranging

filename: (required) NX_CHAR

@version: (required) NX_CHAR

group_name_iontypes: (required) NX_CHAR

spatial_filter: (optional) NXspatial_filter

windowing_method: (required) NX_CHAR

CG_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

CG_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

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

number_of_objects: (required) NX_UINT

bitdepth: (required) NX_UINT

mask: (required) NX_UINT

identifier: (required) NX_UINT

evaporation_id_filter: (optional) NXsubsampling_filter

iontype_filter: (optional) NXmatch_filter

hit_multiplicity_filter: (optional) NXmatch_filter

cluster_analysis: (optional) NXprocess

This process performs a cluster analysis on a reconstructed dataset or a portion of the reconstruction.

clustering_algorithm: (required) NX_CHAR

Name of the algorithm.

clustering_parameter: (required) NX_CHAR

A text representation like a JSON/YAML dictionary with the parameter of the clustering_algorithm.

dataset: (required) NXapm_input_reconstruction

filename: (required) NX_CHAR

@version: (required) NX_CHAR

dataset_name_reconstruction: (required) NX_CHAR

dataset_name_mass_to_charge: (required) NX_CHAR

iontypes: (required) NXapm_input_ranging

filename: (required) NX_CHAR

@version: (required) NX_CHAR

group_name_iontypes: (required) NX_CHAR

spatial_filter: (optional) NXspatial_filter

windowing_method: (required) NX_CHAR

CG_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

CG_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

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

number_of_objects: (required) NX_UINT

bitdepth: (required) NX_UINT

mask: (required) NX_UINT

identifier: (required) NX_UINT

evaporation_id_filter: (optional) NXsubsampling_filter

iontype_filter: (optional) NXmatch_filter

hit_multiplicity_filter: (optional) NXmatch_filter

Hypertext Anchors

List of hypertext anchors for all groups, fields, attributes, and links defined in this class.

NXDL Source:

https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat/contributed_definitions/NXapm_paraprobe_config_clusterer.nxdl.xml