.. auto-generated by script ../../../../utils/nxdl2rst.py from the NXDL source NXapm_paraprobe_config_nanochem.nxdl.xml

.. index::
    ! NXapm_paraprobe_config_nanochem (application definition)
    ! apm_paraprobe_config_nanochem (application definition)
    see: apm_paraprobe_config_nanochem (application definition); NXapm_paraprobe_config_nanochem

.. _NXapm_paraprobe_config_nanochem:

===============================
NXapm_paraprobe_config_nanochem
===============================

**Status**:

  application definition, extends :ref:`NXobject`

**Description**:

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

**Symbols**:

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

  **n_ityp_deloc_cand**: How many iontypes does the delocalization filter specify.

  **n_control_pts**: How many disjoint control points are defined.

  **n_fct_filter_cand**: How many iontypes does the interface meshing iontype filter specify.

  **n_fct_iterations**: How many DCOM iterations.

  **n_ivec**: Maximum number of atoms per molecular ion.

**Groups cited**:
  :ref:`NXapm_input_ranging`, :ref:`NXapm_input_reconstruction`, :ref:`NXcg_cylinder_set`, :ref:`NXcg_ellipsoid_set`, :ref:`NXcg_face_list_data_structure`, :ref:`NXcg_hexahedron_set`, :ref:`NXcs_filter_boolean_mask`, :ref:`NXentry`, :ref:`NXmatch_filter`, :ref:`NXprocess`, :ref:`NXspatial_filter`, :ref:`NXsubsampling_filter`

.. index:: NXentry (base class); used in application definition, NXprocess (base class); used in application definition, NXapm_input_reconstruction (base class); used in application definition, NXapm_input_ranging (base class); used in application definition, NXspatial_filter (base class); used in application definition, NXcg_ellipsoid_set (base class); used in application definition, NXcg_cylinder_set (base class); used in application definition, NXcg_hexahedron_set (base class); used in application definition, NXcg_face_list_data_structure (base class); used in application definition, NXcs_filter_boolean_mask (base class); used in application definition, NXsubsampling_filter (base class); used in application definition, NXmatch_filter (base class); used in application definition

**Structure**:

  .. _/NXapm_paraprobe_config_nanochem/ENTRY-group:

  **ENTRY**: (required) :ref:`NXentry`


    .. _/NXapm_paraprobe_config_nanochem/ENTRY@version-attribute:

    .. index:: version (group attribute)

    **@version**: (required) :ref:`NX_CHAR <NX_CHAR>`

      Version specifier of this application definition.

    .. _/NXapm_paraprobe_config_nanochem/ENTRY/definition-field:

    .. index:: definition (field)

    **definition**: (required) :ref:`NX_CHAR <NX_CHAR>`

      Official NeXus NXDL schema with which this file was written.

      Obligatory value: ``NXapm_paraprobe_config_nanochem``

    .. _/NXapm_paraprobe_config_nanochem/ENTRY/program-field:

    .. index:: program (field)

    **program**: (required) :ref:`NX_CHAR <NX_CHAR>`

      Given name of the program/software/tool with which this NeXus
      (configuration) file was generated.

      .. _/NXapm_paraprobe_config_nanochem/ENTRY/program@version-attribute:

      .. index:: version (field attribute)

      **@version**: (required) :ref:`NX_CHAR <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.

    .. _/NXapm_paraprobe_config_nanochem/ENTRY/analysis_identifier-field:

    .. index:: analysis_identifier (field)

    **analysis_identifier**: (optional) :ref:`NX_CHAR <NX_CHAR>`

      Ideally, a (globally persistent) unique identifier for referring
      to this analysis.

    .. _/NXapm_paraprobe_config_nanochem/ENTRY/analysis_description-field:

    .. index:: analysis_description (field)

    **analysis_description**: (optional) :ref:`NX_CHAR <NX_CHAR>`

      Possibility for leaving a free-text description about this analysis.

    .. _/NXapm_paraprobe_config_nanochem/ENTRY/time_stamp-field:

    .. index:: time_stamp (field)

    **time_stamp**: (required) :ref:`NX_DATE_TIME <NX_DATE_TIME>`

      ISO 8601 formatted time code with local time zone offset to
      UTC information included when this configuration file was created.

    .. _/NXapm_paraprobe_config_nanochem/ENTRY/number_of_processes-field:

    .. index:: number_of_processes (field)

    **number_of_processes**: (required) :ref:`NX_UINT <NX_UINT>` {units=\ :ref:`NX_UNITLESS <NX_UNITLESS>`}

      How many individual analyses should the tool execute as part of the analysis.

    .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS-group:

    **PROCESS**: (required) :ref:`NXprocess`


      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/number_of_delocalizations-field:

      .. index:: number_of_delocalizations (field)

      **number_of_delocalizations**: (required) :ref:`NX_UINT <NX_UINT>` {units=\ :ref:`NX_UNITLESS <NX_UNITLESS>`}

        For now a support field for the tool to identify how many individual
        delocalization analyses for the above-mentioned dataset and supplementary
        files are executed as part of the high-throughput analysis.

      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset-group:

      **dataset**: (required) :ref:`NXapm_input_reconstruction`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/filename-field:

        .. index:: filename (field)

        **filename**: (required) :ref:`NX_CHAR <NX_CHAR>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/filename@version-attribute:

          .. index:: version (field attribute)

          **@version**: (required) :ref:`NX_CHAR <NX_CHAR>`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/dataset_name_reconstruction-field:

        .. index:: dataset_name_reconstruction (field)

        **dataset_name_reconstruction**: (required) :ref:`NX_CHAR <NX_CHAR>`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/dataset_name_mass_to_charge-field:

        .. index:: dataset_name_mass_to_charge (field)

        **dataset_name_mass_to_charge**: (required) :ref:`NX_CHAR <NX_CHAR>`


      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes-group:

      **iontypes**: (required) :ref:`NXapm_input_ranging`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes/filename-field:

        .. index:: filename (field)

        **filename**: (required) :ref:`NX_CHAR <NX_CHAR>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes/filename@version-attribute:

          .. index:: version (field attribute)

          **@version**: (required) :ref:`NX_CHAR <NX_CHAR>`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes/group_name_iontypes-field:

        .. index:: group_name_iontypes (field)

        **group_name_iontypes**: (required) :ref:`NX_CHAR <NX_CHAR>`


      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter-group:

      **spatial_filter**: (optional) :ref:`NXspatial_filter`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/windowing_method-field:

        .. index:: windowing_method (field)

        **windowing_method**: (required) :ref:`NX_CHAR <NX_CHAR>`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET-group:

        **CG_ELLIPSOID_SET**: (optional) :ref:`NXcg_ellipsoid_set`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/dimensionality-field:

          .. index:: dimensionality (field)

          **dimensionality**: (required) :ref:`NX_POSINT <NX_POSINT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/cardinality-field:

          .. index:: cardinality (field)

          **cardinality**: (required) :ref:`NX_POSINT <NX_POSINT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/identifier_offset-field:

          .. index:: identifier_offset (field)

          **identifier_offset**: (required) :ref:`NX_INT <NX_INT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/center-field:

          .. index:: center (field)

          **center**: (required) :ref:`NX_NUMBER <NX_NUMBER>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/half_axes_radii-field:

          .. index:: half_axes_radii (field)

          **half_axes_radii**: (required) :ref:`NX_NUMBER <NX_NUMBER>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/orientation-field:

          .. index:: orientation (field)

          **orientation**: (required) :ref:`NX_NUMBER <NX_NUMBER>`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET-group:

        **CG_CYLINDER_SET**: (optional) :ref:`NXcg_cylinder_set`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/dimensionality-field:

          .. index:: dimensionality (field)

          **dimensionality**: (required) :ref:`NX_POSINT <NX_POSINT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/cardinality-field:

          .. index:: cardinality (field)

          **cardinality**: (required) :ref:`NX_POSINT <NX_POSINT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/identifier_offset-field:

          .. index:: identifier_offset (field)

          **identifier_offset**: (required) :ref:`NX_INT <NX_INT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/center-field:

          .. index:: center (field)

          **center**: (required) :ref:`NX_NUMBER <NX_NUMBER>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/height-field:

          .. index:: height (field)

          **height**: (required) :ref:`NX_NUMBER <NX_NUMBER>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/radii-field:

          .. index:: radii (field)

          **radii**: (required) :ref:`NX_NUMBER <NX_NUMBER>`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET-group:

        **CG_HEXAHEDRON_SET**: (optional) :ref:`NXcg_hexahedron_set`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/dimensionality-field:

          .. index:: dimensionality (field)

          **dimensionality**: (required) :ref:`NX_POSINT <NX_POSINT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/cardinality-field:

          .. index:: cardinality (field)

          **cardinality**: (required) :ref:`NX_POSINT <NX_POSINT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/identifier_offset-field:

          .. index:: identifier_offset (field)

          **identifier_offset**: (required) :ref:`NX_INT <NX_INT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/hexahedra-group:

          **hexahedra**: (required) :ref:`NXcg_face_list_data_structure`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK-group:

        **CS_FILTER_BOOLEAN_MASK**: (optional) :ref:`NXcs_filter_boolean_mask`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/number_of_objects-field:

          .. index:: number_of_objects (field)

          **number_of_objects**: (required) :ref:`NX_UINT <NX_UINT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/bitdepth-field:

          .. index:: bitdepth (field)

          **bitdepth**: (required) :ref:`NX_UINT <NX_UINT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/mask-field:

          .. index:: mask (field)

          **mask**: (required) :ref:`NX_UINT <NX_UINT>`


          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/identifier-field:

          .. index:: identifier (field)

          **identifier**: (required) :ref:`NX_UINT <NX_UINT>`


      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/evaporation_id_filter-group:

      **evaporation_id_filter**: (optional) :ref:`NXsubsampling_filter`


      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontype_filter-group:

      **iontype_filter**: (optional) :ref:`NXmatch_filter`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontype_filter/method-field:

        .. index:: method (field)

        **method**: (required) :ref:`NX_CHAR <NX_CHAR>`


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontype_filter/match-field:

        .. index:: match (field)

        **match**: (required) :ref:`NX_NUMBER <NX_NUMBER>`


      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/hit_multiplicity_filter-group:

      **hit_multiplicity_filter**: (optional) :ref:`NXmatch_filter`


      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset-group:

      **edge_of_the_dataset**: (required) :ref:`NXprocess`

        The tool enables to inject a previously computed triangle soup or
        triangulated surface mesh representing a model (of the surface) of
        the edge of the dataset. This model can be used to detect and control
        various sources of bias in the analyses.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/filename-field:

        .. index:: filename (field)

        **filename**: (required) :ref:`NX_CHAR <NX_CHAR>`

          Name of the HDF5 file which contains vertex coordinates and facet
          indices to describe the desired set of triangles which represents
          the edge of the dataset.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/filename@version-attribute:

          .. index:: version (field attribute)

          **@version**: (required) :ref:`NX_CHAR <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 from which file specifically contains these data.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/dataset_name_vertices-field:

        .. index:: dataset_name_vertices (field)

        **dataset_name_vertices**: (required) :ref:`NX_CHAR <NX_CHAR>`

          Absolute path to the HDF5 dataset in the respectively specified HDF5
          file under filename which details the array of vertex positions.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/dataset_name_facet_indices-field:

        .. index:: dataset_name_facet_indices (field)

        **dataset_name_facet_indices**: (required) :ref:`NX_CHAR <NX_CHAR>`

          Absolute path to the HDF5 dataset in the respective specified HDF5
          file under filename which details the array of facet indices.

      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances-group:

      **ion_to_edge_distances**: (optional) :ref:`NXprocess`

        The tool enables to inject precomputed distance information for each
        point/ion which can be used for further post-processing and analysis.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances/filename-field:

        .. index:: filename (field)

        **filename**: (required) :ref:`NX_CHAR <NX_CHAR>`

          Name of an HDF5 file which contains the ion distances.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances/filename@version-attribute:

          .. index:: version (field attribute)

          **@version**: (required) :ref:`NX_CHAR <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 from which file specifically contains these data.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances/dataset_name-field:

        .. index:: dataset_name (field)

        **dataset_name**: (required) :ref:`NX_CHAR <NX_CHAR>`

          Absolute HDF5 path to the dataset with distance values for each ion.

      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization-group:

      **delocalization**: (optional) :ref:`NXprocess`

        Discretization of the ion point cloud on a three-dimensional grid.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/input-field:

        .. index:: input (field)

        **input**: (required) :ref:`NX_CHAR <NX_CHAR>`

          Delocalization in the field of atom probe microscopy is the process
          of discretizing a point cloud. By default the tool computes a full
          kernel density estimation of decomposed ions to create one discretized
          field for each element.

          Although, this uses an efficient multithreaded algorithm,
          the computation is costly. Therefore, it can be advantageous for users
          to load an already computed delocalization. This can be achieved with
          the load_existent option.
          When using this option the user is responsible to assure that the
          settings which were used for computing this already existent delocalization
          are specified in the same manner as they were.

          Any of these values: ``default`` | ``load_existent``

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isotope_whitelist-field:

        .. index:: isotope_whitelist (field)

        **isotope_whitelist**: (required) :ref:`NX_UINT <NX_UINT>` (Rank: 2, Dimensions: [n_ityp_deloc_cand, n_ivec]) {units=\ :ref:`NX_UNITLESS <NX_UNITLESS>`}

          Matrix of isotope vectors representing iontypes.
          The filter specifies a matrix of isotope_vectors which is the most
          general approach to define if and how many times an ion is counted.
          Currently, paraprobe_nanochem performs a so-called atomic decomposition
          of all iontypes. Specifically, the tool interprets of how many
          elements/atoms a molecular ion is composed; and thus determines the
          atoms multiplicity with respect to the iontype.

          Let's take the hydroxonium H3O+ molecular ion as an example:
          It contains hydrogen and oxygen as atoms. The multiplicity of hydrogen
          is three whereas that of oxygen is one. Therefore in an atomic
          decomposition computation of the iso-surface each H3O+ ion adds
          three hydrogen counts. This is a practical solution which accepts
          the situation that during an atom probe experiment not each bond
          of each ion/a group of neighboring atoms is broken but molecular
          ions get detected. The exact ab-initio details depend on the local
          field conditions and thus also the detailed spatial arrangement
          of the atoms and their own electronic state and that of the neighbors
          before and upon launch.
          Being able to measure the information for such sites only as
          molecular ions causes an inherent information loss with respect to the
          detailed spatial arrangement. This information loss is more relevant
          for local electrode atom probe than for field ion microscopy setting
          how precisely the atomic positions can be reconstructed.
          Accounting for multiplicities assures that at least the
          compositional information is analyzed.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/gridresolutions-field:

        .. index:: gridresolutions (field)

        **gridresolutions**: (required) :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}

          List of individual grid resolutions to analyse.
          Paraprobe discretizes on a cuboidal 3D grid with cubic cells, with
          an edge length of values in gridresolutions.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/kernel_size-field:

        .. index:: kernel_size (field)

        **kernel_size**: (required) :ref:`NX_UINT <NX_UINT>` {units=\ :ref:`NX_UNITLESS <NX_UNITLESS>`}

          Half the width of a (2n+1)^3 cubic kernel of voxel beyond
          which the Gaussian Ansatz function will be truncated.
          Intensity beyond the kernel is refactored into the kernel via
          a normalization procedure.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/kernel_variance-field:

        .. index:: kernel_variance (field)

        **kernel_variance**: (required) :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}

          Variance of the Gaussian Ansatz kernel sigma_x = sigma_y = 2*sigma_z.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/normalization-field:

        .. index:: normalization (field)

        **normalization**: (required) :ref:`NX_CHAR <NX_CHAR>`

          How should the results of the kernel-density estimation be computed
          into quantities. By default the tool computes the total number
          (intensity) of ions or elements. Alternatively the tool can compute
          the total intensity, the composition, or the concentration of the
          ions/elements specified by the white list of elements in each voxel.

          Any of these values:

            * ``total``

            * ``candidates``

            * ``composition``

            * ``concentration``


        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/has_scalar_fields-field:

        .. index:: has_scalar_fields (field)

        **has_scalar_fields**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

          Specifies if the tool should report the delocalization 3D field values.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing-group:

        **isosurfacing**: (optional) :ref:`NXprocess`

          Optional computation of iso-surfaces after each computed delocalization
          to identify for instance objects in the microstructure
          (line features, interfaces, precipitates).

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/edge_handling_method-field:

          .. index:: edge_handling_method (field)

          **edge_handling_method**: (required) :ref:`NX_CHAR <NX_CHAR>`

            As it is detailed in M. Kühbach et al. 2022 npj Comp. Mat.,
            the handling of triangles at the edge of the dataset requires
            special attention. Especially for composition-normalized
            delocalization it is possible that the composition increases
            towards the edge of the dataset because the quotient of two numbers
            which are both smaller than one is larger instead of smaller than
            the counter. By default, the tool uses a modified marching cubes
            algorithm of Lewiner et al. which detects if voxels face such a
            situation. In this case, no triangles are generated for such voxels.
            Alternatively, (via setting keep_edge_triangles) the user can
            instruct the tool to not remove these triangles at the cost of bias.

            Specifically, in this case the user should understand that all
            objects/microstructural features in contact with the edge of the
            dataset get usually artificial enlarged and their surface mesh
            often closed during the marching. This closure however is artificial!
            It can result in biased shape analyses for those objects.
            The reason why this should in general be avoided is a similar
            argument as when one analyzes grain shapes in orientation microscopy
            via e.g. SEM/EBSD. Namely, these grains, here the objects at the
            edge of the dataset, were not fully captured during e.g. limited
            field of view.
            Therefore, it is questionable if one would like to make
            substantiated quantitative statements about them.

            Thanks to collaboration with the V. V. Rielli and S. Primig, though,
            paraprobe-nanochem implements a complete pipeline to
            process even these objects at the edge of the dataset. Specifically,
            the objects are replaced by so-called proxies, i.e. replacement
            objects whose holes on the surface mesh have been closed if possible
            via iterative mesh and hole-filling procedures with fairing operations.
            In the results of each paraprobe-nanochem run, these proxy objects
            are listed separately to allow users to quantify and analyze in
            detail the differences when accounting for these objects or not.
            Especially this is relevant in atom probe microscopy are small
            in the sense that they contain few (many a few dozen) objects.
            Even though such a dataset may give statistically significant
            results for compositions this does not mean it necessarily yields
            also statistically significant and unbiased results for three-dimensional
            object analyses. Being able to quantify these effects and making
            atom probers aware of these subtleties was one of the main reasons
            why the paraprobe-nanochem tool was implemented.

            Any of these values: ``default`` | ``keep_edge_triangles``

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/edge_threshold-field:

          .. index:: edge_threshold (field)

          **edge_threshold**: (required) :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}

            The ion-to-edge-distance that is used in the analyses of objects
            (and proxies) to identify whether these are inside the dataset or
            close to the edge of the dataset. If an object has at least one ion
            with an ion-to-edge-distance below this threshold, the object is
            considered as one which lies close to the edge of the dataset.
            This implements essentially a distance-based approach to solve
            the in general complicated and involved treatment of computing
            volumetric intersections between not-necessarily convex
            closed 2-manifolds. In fact, such computational geometry analyses
            can face numerical robustness issues as a consequence of which a
            mesh can be detected as lying completely inside a dataset although
            in reality it is epsilon-close only, i.e. almost touching only
            the edge (e.g. from inside).
            Practically, humans would state in such case that the object is
            close to the edge of the dataset; however mathematically the object
            is indeed completely inside.
            In short, a distance-based approach is rigorous and more flexible.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/phi-field:

          .. index:: phi (field)

          **phi**: (required) :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_ANY <NX_ANY>`}

            Array of iso-contour values. For each value the tool computes
            an iso-surface and performs subsequent analyses.
            The unit depends on the choice for the normalization of the
            accumulated ion intensity values per voxel:

            * total, total number of ions, irrespective their iontype  
            * candidates, total number of ions with type in the isotope_whitelist.  
            * composition, candidates but normalized by composition, i.e. at.-%  
            * concentration, candidates but normalized by voxel volume, i.e. ions/nm^3

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_triangle_soup-field:

          .. index:: has_triangle_soup (field)

          **has_triangle_soup**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should report the triangle soup which represents
            each triangle of the iso-surface complex.
            Each triangle is reported with an ID specifying to which triangle
            cluster (with IDs starting at zero) the triangle belongs.
            The clustering is performed with a modified DBScan algorithm.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object-field:

          .. index:: has_object (field)

          **has_object**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should analyze for each cluster of triangles
            how they can be combinatorially processed to describe a closed
            polyhedron. Such a closed polyhedron (not-necessarily convex!)
            can be used to describe objects with relevance in the microstructure.
            Users should be aware that the resulting mesh does not necessarily
            represent the original precipitate. In fact, inaccuracies in the
            reconstructed positions cause inaccuracies in all downstream
            processing operations. Especially the effect on one-dimensional
            spatial statistics like nearest neighbor correlation functions these
            effects were discussed in the literature 
            `B. Gault et al. <https://doi.org/10.1017/S1431927621012952>`_ 
            In continuation of these thoughts this applies also to reconstructed
            objects. A well-known example is the discussion of shape deviations
            of Al3Sc precipitates in aluminium alloys which in reconstructions
            can appear as ellipsoids although they should be almost spherical,
            depending on their size.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_geometry-field:

          .. index:: has_object_geometry (field)

          **has_object_geometry**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should report a triangulated surface mesh
            for each identified closed polyhedron. It is common that a
            marching cubes algorithm creates iso-surfaces with a fraction of very
            small sub-complexes (e.g. small isolated tetrahedra).

            These can be for instance be small tetrahedra/polyhedra about the
            center of a voxel of the support grid on which marching cubes operates.
            When these objects are small, it is possible that they contain no ion;
            especially when considering that delocalization procedures smoothen
            the positions of the ions. Although these small objects are interesting
            from a numerical point of view, scientists may argue they are not worth
            to be reported:
            Physically a microstructural feature should contain at least a few
            atoms to become relevant. Therefore, paraprobe-nanochem by default
            does not report closed objects which bound not at least one ion.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_properties-field:

          .. index:: has_object_properties (field)

          **has_object_properties**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should report properties of each closed
            polyhedron, such as volume and other details.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_obb-field:

          .. index:: has_object_obb (field)

          **has_object_obb**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should report for each closed polyhedron an
            approximately optimal bounding box fitted to all triangles of the
            surface mesh of the object and ion positions inside or on the
            surface of the mesh.
            This bounding box informs about the closed object's shape 
            (aspect ratios).

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_ions-field:

          .. index:: has_object_ions (field)

          **has_object_ions**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should report for each closed polyhedron
            all evaporation IDs of those ions which lie inside or on the
            boundary of the polyhedron. This information can be used e.g.
            in the paraprobe-intersector tool to infer if two objects share
            common ions, which can be interpreted as an argument to assume
            that the two objects intersect.

            Users should be aware that two arbitrarily closed polyhedra
            in three-dimensional space can intersect but not share a common ion.
            In fact, the volume bounded by the polyhedron has sharp edges.
            When taking two objects, an edge of one object may for instance
            pierce into the surface of another object. In this case the
            objects partially overlap / intersect volumetrically; 
            however this piercing might be so small or happening in the volume
            between two ion positions and thus sharing ions is a sufficient
            but not a necessary condition for object intersections.

            Paraprobe-intersector implements a rigorous alternative to handle
            such intersections using a tetrahedralization of closed objects.
            However, in many practical cases, we found through examples that there
            are polyhedra (especially when they are non-convex and have almost
            point-like) connected channels, where tetrahedralization libraries
            have challenges dealing with. In this case checking intersections
            via shared_ions is a more practical alternative.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_edge_contact-field:

          .. index:: has_object_edge_contact (field)

          **has_object_edge_contact**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should report if a (closed) object has
            contact with the edge of the dataset. For this the tool currently
            inspects if the shortest distance between the set of triangles of the
            surface mesh and the triangles of the edge model is larger than the
            edge_threshold. If this is the case, the object is assumed to be
            deeply embedded in the interior of the dataset. Otherwise, the object
            is considered to have an edge contact, i.e. it is likely affected
            by the fact that the dataset is finite.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy-field:

          .. index:: has_proxy (field)

          **has_proxy**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should analyze a doppelganger/proxy mesh for
            each cluster of triangles whose combinatorial analysis according
            to has_object showed that the object is not a closed polyhedron.
            Such proxies are closed via iterative hole-filling, mesh refinement,
            and fairing operations.
            Users should be aware that the resulting mesh does not necessarily
            represent the original precipitate. In most cases objects,
            like precipitates in atom probe end up as open objects because
            they have been clipped by the edge of the dataset. Using a proxy is
            then a strategy to still be able to account for these objects.
            Nevertheless users should make themselves familiar with the
            potential consequences and biases which this can introduce
            into the analysis.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_geometry-field:

          .. index:: has_proxy_geometry (field)

          **has_proxy_geometry**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Like has_object_geometry but for the proxies.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_properties-field:

          .. index:: has_proxy_properties (field)

          **has_proxy_properties**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Like has_object_properties but for the proxies.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_obb-field:

          .. index:: has_proxy_obb (field)

          **has_proxy_obb**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Like has_object_obb but for the proxies.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_ions-field:

          .. index:: has_proxy_ions (field)

          **has_proxy_ions**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Like has_object_ions but for the proxies.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_edge_contact-field:

          .. index:: has_proxy_edge_contact (field)

          **has_proxy_edge_contact**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Like has_object_edge_contact but for the proxies.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_auto_proxigram-field:

          .. index:: has_object_auto_proxigram (field)

          **has_object_auto_proxigram**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should report for each closed object a 
            (cylindrical) region of interest placed, centered, and align
            with the local normal for each triangle of the object.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_auto_proxigram_edge_contact-field:

          .. index:: has_object_auto_proxigram_edge_contact (field)

          **has_object_auto_proxigram_edge_contact**: (required) :ref:`NX_BOOLEAN <NX_BOOLEAN>`

            Specifies if the tool should report for each ROI that was placed
            at a triangle of each object if this ROI intersects the edge of
            the dataset. Currently paraprobe-nanochem supports cylindrical
            ROIs. A possible intersection of these with the edge of the
            dataset, i.e. the triangulated surface mesh model for the edge
            is performed. This test checks if the cylinder intersects with
            a triangle of the surface mesh. If this is the case, the ROI is
            assumed to make edge contact, else, the ROI is assumed to have
            no edge contact.

            This approach does not work if the ROI would be completely
            outside the dataset. Also in this case there would be
            no intersection. For atom probe this case is practically
            irrelevant because for such a ROI there would also be no ion
            laying inside the ROI. Clearly it has thus to be assumed that
            the edge model culls the entire dataset. Instead, if one would
            cut a portion of the dataset, compute an edge model for this
            point cloud, it might make sense to place a ROI but in this
            case the edge contact detection is not expected to work properly.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess-group:

        **interfacial_excess**: (optional) :ref:`NXprocess`

          Analyses of interfacial excess.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/interface_model-field:

          .. index:: interface_model (field)

          **interface_model**: (required) :ref:`NX_CHAR <NX_CHAR>`

            Interfacial excess computations are performed for local regions-of-interests
            (ROIs) at selected facets or interface patch.
            For instance many scientist compute the interfacial excess for
            selected triangle facets of a created iso-surface. In this case,
            computed iso-surfaces of paraprobe could be used. An example are triangle
            facet sets about closed polyhedra, for instance to compute interfacial
            excess related to phase boundaries of second-phase precipitates.

            Another example are free-standing triangle patches of the iso-
            surfaces which paraprobe creates. These could be characterized
            for interfacial excess. The sub-routines during iso-surface
            computations already include a procedure to automatically align
            local triangle normals based on the gradients of e.g. composition
            fields. In this case, these triangulated surface patches
            could also be used as a source for computing interfacial
            excess.

            Often scientists face situations, though, in which there is no
            immediately evident composition gradient across the interface
            (grain or phase boundary) and orientation information about the
            adjoining crystal is neither available nor reliable enough.

            In this case `P. Felfer et al. <https://doi.org/10.1016/j.ultramic.2015.06.002>`_ proposed a method
            to manually place control points and run an automated tessellation-based
            algorithm to create a triangulated surface patch, i.e. a model of the
            location of the interface. In a post-processing step this triangle
            set can then be used to compute again interfacial excess in an
            automated manner by placing ROIs and aligning them with
            consistently precomputed triangle normals.

            A similar use case is conceptually the one proposed by `X. Zhou et al. <https://doi.org/10.1016/j.actamat.2022.117633>`_
            They used first a deep-learning method to locate planar triangulated
            grain boundary patches. These are eventually processed further
            with manual editing of the mesh via tools like Blender.
            Once the user is satisfied with the mesh, the computations of interfacial
            excess reduce again to an automated placing of ROIs, computations
            of the distributing of ions to respective ROIs and
            reporting the findings via plotting.

            Yet another approach for constructing an triangulated surface patch
            of an interface is to use point cloud processing methods which have
            been proposed in the laser-scanning, geoinformatics, and CAD community.
            Different computational geometry methods are available for fitting
            a parameterized surface to a set of points, using e.g. non-uniform
            rational B-splines (NURBS) and triangulating these according
            to prescribed mesh quality demands.

            The advantage of these methods is that they can be automated and
            pick up curved interface segments. The disadvantage is their often
            strong sensitivity to parameterization. As a result also such methods
            can be post-processed to yield a triangulated surface patch,
            and thus enable to run again automated ROI placement methods.
            For example like these which were explored for the use case of
            iso-surfaces with closed objects and free-standing
            surface patches that delineate regions of the dataset with a
            pronounced composition gradient normal to the interface.

            This summary of the situations which atom probers can face when
            requesting for interfacial excess computations, substantiates there
            exists a common set of settings which can describe all of these methods
            and, specifically, as here exemplified, the automated placing
            and alignment functionalities for ROIs that is an important
            step all these workflows.

            Specifically, paraprobe-nanochem operates on an already existent
            triangle set.

            Any of these values: ``isosurface`` | ``external``

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external-group:

          **external**: (optional) :ref:`NXprocess`

            The interface model is the result of a previous (set of) processing
            steps as a result of which the user has created a triangulated
            surface mesh (or a set of, eventually connected such meshes).
            These interface models are useful, if not required, in cases when
            there is no other independent approach to locate an interface.

            These are cases when insufficient crystallographic latent
            information is available and also no consistent concentration
            gradient detectable across the interface. It is then the users'
            responsibility to deliver a triangle mesh of the interface model.

            .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/file_name-field:

            .. index:: file_name (field)

            **file_name**: (required) :ref:`NX_CHAR <NX_CHAR>`

              Filename to HDF5 file which contain vertex coordinates, facet indices,
              facet unit normals. The user is responsible for the triangle
              and winding order to be consistent.
              Input is expected as a matrix of the coordinates for all disjoint
              vertices, a (Nvertices, 3)-shaped array of NX_FLOAT.
              Input is expected to include also a matrix of facet indices
              referring to these disjoint vertices. This matrix should be a
              (Nfacets, 3)-shaped array of NX_UINT. Further required input
              is a (Nfacets, 3)-shaped array of NX_FLOAT signed facet unit
              normals and a (Nvertices, 3)-shaped array of NX_FLOAT signed
              vertex unit normals. Vertex indices need to start at zero and
              must not exceed Nvertices - 1, i.e. the identifier_offset is 0
              and facet indices are indexed implicitly, i.e. [0, Nvertices-1].

              .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/file_name@version-attribute:

              .. index:: version (field attribute)

              **@version**: (required) :ref:`NX_CHAR <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 from which file specifically
                contains these data.

            .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_vertices-field:

            .. index:: dataset_name_vertices (field)

            **dataset_name_vertices**: (required) :ref:`NX_CHAR <NX_CHAR>`

              Absolute HDF5 path to the dataset which specifies the
              array of vertex positions.

            .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_facet_indices-field:

            .. index:: dataset_name_facet_indices (field)

            **dataset_name_facet_indices**: (required) :ref:`NX_CHAR <NX_CHAR>`

              Absolute HDF5 path to the dataset which specifies the
              array of facet indices.

            .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_facet_normals-field:

            .. index:: dataset_name_facet_normals (field)

            **dataset_name_facet_normals**: (required) :ref:`NX_CHAR <NX_CHAR>`

              Absolute HDF5 path to the dataset which specifies the
              array of facet signed unit normals.

            .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_facet_vertices-field:

            .. index:: dataset_name_facet_vertices (field)

            **dataset_name_facet_vertices**: (required) :ref:`NX_CHAR <NX_CHAR>`

              Absolute HDF5 path to the dataset which specifies the
              array of vertex signed unit normals.

              Users should be aware that triangulated surface meshes are
              only approximations to a given complex, eventually curved shape.
              Consequently, computations of normals show differences between
              the vertex and facet normals. Vertex normals have to be
              interpolated from normals of neighboring facets. Consequently,
              these normals are affected by the underlying parameterization
              and curvature estimation algorithms, irrespective of how
              contributions from neighboring facets are weighted. By contrast,
              facet normals are clearly defined by the associated triangle.
              Their disadvantage is that they the normal field has discontinuities
              at the edges. In general the coarser an object is triangulated
              the more significant the difference becomes between computations
              based on facet or vertex normals.
              Paraprobe-nanochem works with facet normals as it can use 
              parts of the numerical performance gained by using cutting
              edge libraries to work rather with finer meshes.

      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing-group:

      **interface_meshing**: (optional) :ref:`NXprocess`

        Create a simple principle component analysis (PCA) to mesh a
        free-standing interface patch through a point cloud of decorating solutes.
        These models can be useful for quantification of Gibbsian
        interfacial excess for interfaces where iso-surface based methods
        may fail or closed objects from iso-surfaces are not desired or
        when e.g. there are no substantial or consistently oriented
        concentration gradients across the interface patch.

        The interface_meshing functionality of paraprobe-nanochem can be useful
        when there is also insufficient latent crystallographic information
        available that could otherwise support modelling the interface,
        via e.g. ion density traces in field-desorption maps, as were used and
        discussed by `Y. Wei et al. <https://doi.org/10.1371/journal.pone.0225041>`_ 
        or are discussed by `A. Breen et al. <https://github.com/breen-aj/detector>`_

        It is noteworthy that the method here used is conceptually very similar
        in implementation to the work by `Z. Peng et al. <https://doi.org/10.1017/S1431927618016112>`_
        Noteworthy, her team uses the DCOM approach originally proposed by P. Felfer et al.
        However, both of these previous works neither discuss in detail
        nor implement inspection functionalities which enable a detection of
        potential geometric inconsistencies or self-interactions of the
        resulting DCOM mesh. This is what paraprobe-nanochem implements
        via the Computational Geometry Algorithms Library.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/initialization-field:

        .. index:: initialization (field)

        **initialization**: (required) :ref:`NX_CHAR <NX_CHAR>`

          Method how to initialize the PCA:

          * default, means based on segregated solutes in the ROI  
          * control_point_file, means based on reading an external list of  
            control points, currently coming from the Leoben APT_Analyzer.

          The control_point_file is currently expected with a specific format.
          The Leoben group lead by L. Romaner has developed a GUI tool `A. Reichmann et al. <https://github.com/areichm/APT_analyzer>`_ 
          to create a control_point_file which can be parsed by paraprobe-parmsetup
          to match the here required formatting in control_points.

          Any of these values: ``default`` | ``control_point_file``

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/filename-field:

        .. index:: filename (field)

        **filename**: (required) :ref:`NX_CHAR <NX_CHAR>`

          The name of the control point file to use.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/filename@version-attribute:

          .. index:: version (field attribute)

          **@version**: (required) :ref:`NX_CHAR <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 from which file specifically
            contains these data.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/control_points-field:

        .. index:: control_points (field)

        **control_points**: (required) :ref:`NX_FLOAT <NX_FLOAT>` (Rank: 2, Dimensions: [N, n_control_pts]) {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}

          X, Y, Z coordinates of disjoint control point read from 
          an HDF5 file named according to control_point_file.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/method-field:

        .. index:: method (field)

        **method**: (required) :ref:`NX_CHAR <NX_CHAR>`

          Method used for identifying and refining the location of the
          interface. Currently, paraprobe-nanochem implements a PCA followed
          by an iterative loop of isotropic mesh refinement and DCOM step(s),
          paired with self-intersection detection in a more robust
          implementation.

          Obligatory value: ``pca_plus_dcom``

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/number_of_iterations-field:

        .. index:: number_of_iterations (field)

        **number_of_iterations**: (required) :ref:`NX_UINT <NX_UINT>` {units=\ :ref:`NX_UNITLESS <NX_UNITLESS>`}

          How many times should the DCOM and mesh refinement be applied?

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/target_edge_length-field:

        .. index:: target_edge_length (field)

        **target_edge_length**: (required) :ref:`NX_FLOAT <NX_FLOAT>` (Rank: 1, Dimensions: [n_fct_iterations]) {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}

          Array of decreasing positive not smaller than one nanometer real values
          which specify how the initial triangles of the mesh should be iteratively
          refined by edge splitting and related mesh refinement operations.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/target_dcom_radius-field:

        .. index:: target_dcom_radius (field)

        **target_dcom_radius**: (required) :ref:`NX_FLOAT <NX_FLOAT>` (Rank: 1, Dimensions: [n_fct_iterations]) {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}

          Array of decreasing positive not smaller than one nanometer real values
          which specify the radius of the spherical region of interest within
          which the DCOM algorithm decides for each vertex how the vertex will
          be eventually relocated. The larger the DCOM radius is relative to
          the target_edge_length the more likely it is that vertices will be
          relocated so substantially that eventually triangle self-intersections
          can occur.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/target_smoothing_step-field:

        .. index:: target_smoothing_step (field)

        **target_smoothing_step**: (required) :ref:`NX_UINT <NX_UINT>` (Rank: 1, Dimensions: [n_fct_iterations]) {units=\ :ref:`NX_UNITLESS <NX_UNITLESS>`}

          Array of integers which specify for each DCOM step how many times
          the mesh should be iteratively smoothened.

          Users should be aware the three array target_edge_length, 
          target_dcom_radius, and target_smoothing_step are interpreted in the
          same sequence, i.e. the zeroth entry of each array specifies the
          values to be used in the first DCOM iteration. The first entry of
          each array those for the second DCOM iteration and so on and so forth.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/decorating_iontypes_filter-group:

        **decorating_iontypes_filter**: (required) :ref:`NXprocess`

          Specify the types of those ions which decorate the interface and
          can thus be assumed as markers for locating the interface and
          refining its local curvature.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/decorating_iontypes_filter/candidates-field:

          .. index:: candidates (field)

          **candidates**: (required) :ref:`NX_UINT <NX_UINT>` (Rank: 1, Dimensions: [n_fct_filter_cand]) {units=\ :ref:`NX_UNITLESS <NX_UNITLESS>`}

            Array of iontypes to filter. The list is interpreted as a whitelist,
            i.e. ions of these types are considered the decorating species (solutes).

      .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling-group:

      **composition_profiling**: (optional) :ref:`NXprocess`

        Functionalities for placing regions-of-interest (ROIs) in the dataset
        or at specific microstructural features to characterize composition
        profiles and cumulated profiles for quantification of interfacial excess.
        Paraprobe-nanochem currently places cylindrical ROIs. ROIs are probed
        across the triangulated surface of a user-defined mesh.
        ROIs are placed at the barycenter of the triangular facet.

        The tool can be instructed to orient the profile for each ROIs with
        the positive normal of the triangle facet normals. Profiles are
        computed for each ROI and facet triangle. The code will test which
        ROIs are completely embedded in the dataset.
        Specifically, in this test the tool evaluates if the ROI cuts at least
        one triangle of the triangulated surface mesh of the edge of the dataset.
        If this is the case the ROI will be considered close to the edge
        (of the dataset) and not analyzed further; else the ROI will be
        processed further.
        Users should be aware that the latter intersection analysis is strictly
        speaking not a volumetric intersection analysis as such one is much
        more involved because the edge model can be a closed non-convex polyhedron
        in which case one would have to test robustly if the cylinder piercing
        or laying completely inside the polyhedron. For this the polyhedron has
        to be tessellated into convex polyhedra as otherwise tests like the
        Gilbert-Johnson-Keerthi algorithm would not be applicable.

        Specifically, the tool computes atomically decomposed profiles.
        This means molecular ions are split into atoms/isotopes with respective
        multiplicity. As an example an H3O+ molecular ion contains three
        hydrogen and one oxygen atom respectively. The tool then evaluates
        how many ions are located inside the ROI or on the surface of the
        ROI respectively. All atom types and the unranged ions are distinguished.
        As a result, the analyses yield for each ROI a set of sorted lists of
        signed distance values. Currently, the distance is the projected
        distance of the ion position to the barycenter of the triangle
        and triangle plane.

        This will return a one-dimensional profile. Post-processing the set
        of atom-type-specific profiles into cumulated profiles enable the
        classical Krakauer/Seidman-style interfacial excess analyses.
        Furthermore, the tool can be instructed to compute for each
        (or a selected sub-set of facet) a set of differently oriented profiles.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/distancing_model-field:

        .. index:: distancing_model (field)

        **distancing_model**: (required) :ref:`NX_CHAR <NX_CHAR>`

          Which type of distance should be reported for the profile.

          Obligatory value: ``project_to_triangle_plane``

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/direction_model-field:

        .. index:: direction_model (field)

        **direction_model**: (required) :ref:`NX_CHAR <NX_CHAR>`

          In which directions should the tool probe for each ROI.

          Obligatory value: ``triangle_outer_unit_normal``

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/roi_cylinder_height-field:

        .. index:: roi_cylinder_height (field)

        **roi_cylinder_height**: (required) :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}

          For each ROI, how high (projected on the cylinder axis)
          should the cylindrical ROI be.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/roi_cylinder_radius-field:

        .. index:: roi_cylinder_radius (field)

        **roi_cylinder_radius**: (required) :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}

          For each ROI, how wide (radius) should the cylindrical ROI be.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh-group:

        **feature_mesh**: (required) :ref:`NXprocess`

          The feature mesh enables the injection of previously computed triangle
          soup or mesh data. Such a mesh can be the model for a grain- or phase
          boundary patch (from e.g. interface_meshing) jobs.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/filename-field:

          .. index:: filename (field)

          **filename**: (required) :ref:`NX_CHAR <NX_CHAR>`

            Name of the HDF5 file which contains vertex coordinates and facet
            indices to describe the desired set of triangles which represents
            the feature.

            .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/filename@version-attribute:

            .. index:: version (field attribute)

            **@version**: (required) :ref:`NX_CHAR <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 from which file specifically contains these data.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/dataset_name_vertices-field:

          .. index:: dataset_name_vertices (field)

          **dataset_name_vertices**: (required) :ref:`NX_CHAR <NX_CHAR>`

            Absolute path to the HDF5 dataset in the respectively specified HDF5
            file under filename which details the array of vertex positions.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/dataset_name_facet_indices-field:

          .. index:: dataset_name_facet_indices (field)

          **dataset_name_facet_indices**: (required) :ref:`NX_CHAR <NX_CHAR>`

            Absolute path to the HDF5 dataset in the respective specified HDF5
            file under filename which details the array of facet indices.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/dataset_name_facet_normals-field:

          .. index:: dataset_name_facet_normals (field)

          **dataset_name_facet_normals**: (required) :ref:`NX_CHAR <NX_CHAR>`

            Absolute path to the HDF5 dataset in the respective specified HDF5
            file under filename which details consistently oriented facet
            normals of the facets.

        .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances-group:

        **ion_to_feature_distances**: (optional) :ref:`NXprocess`

          The tool enables to inject precomputed distance information for each
          point which can be used for further post-processing and analysis.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances/filename-field:

          .. index:: filename (field)

          **filename**: (required) :ref:`NX_CHAR <NX_CHAR>`

            Name of an HDF5 file which contains ion distances.

            .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances/filename@version-attribute:

            .. index:: version (field attribute)

            **@version**: (required) :ref:`NX_CHAR <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 from which file specifically contains
              these data.

          .. _/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances/dataset_name-field:

          .. index:: dataset_name (field)

          **dataset_name**: (required) :ref:`NX_CHAR <NX_CHAR>`

            Absolute HDF5 path to the dataset with distance values for each ion.


Hypertext Anchors
-----------------

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


* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY-group </NXapm_paraprobe_config_nanochem/ENTRY-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/analysis_description-field </NXapm_paraprobe_config_nanochem/ENTRY/analysis_description-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/analysis_identifier-field </NXapm_paraprobe_config_nanochem/ENTRY/analysis_identifier-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/definition-field </NXapm_paraprobe_config_nanochem/ENTRY/definition-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/number_of_processes-field </NXapm_paraprobe_config_nanochem/ENTRY/number_of_processes-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/direction_model-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/direction_model-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/distancing_model-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/distancing_model-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/dataset_name_facet_indices-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/dataset_name_facet_indices-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/dataset_name_facet_normals-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/dataset_name_facet_normals-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/dataset_name_vertices-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/dataset_name_vertices-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/filename-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/filename-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/filename@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/feature_mesh/filename@version-attribute>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances/dataset_name-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances/dataset_name-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances/filename-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances/filename-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances/filename@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/ion_to_feature_distances/filename@version-attribute>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/roi_cylinder_height-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/roi_cylinder_height-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/roi_cylinder_radius-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/composition_profiling/roi_cylinder_radius-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/dataset_name_mass_to_charge-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/dataset_name_mass_to_charge-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/dataset_name_reconstruction-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/dataset_name_reconstruction-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/filename-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/filename-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/filename@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/dataset/filename@version-attribute>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/gridresolutions-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/gridresolutions-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/has_scalar_fields-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/has_scalar_fields-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/input-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/input-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_facet_indices-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_facet_indices-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_facet_normals-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_facet_normals-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_facet_vertices-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_facet_vertices-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_vertices-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/dataset_name_vertices-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/file_name-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/file_name-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/file_name@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/external/file_name@version-attribute>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/interface_model-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/interfacial_excess/interface_model-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/edge_handling_method-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/edge_handling_method-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/edge_threshold-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/edge_threshold-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_auto_proxigram-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_auto_proxigram-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_auto_proxigram_edge_contact-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_auto_proxigram_edge_contact-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_edge_contact-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_edge_contact-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_geometry-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_geometry-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_ions-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_ions-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_obb-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_obb-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_properties-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_object_properties-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_edge_contact-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_edge_contact-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_geometry-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_geometry-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_ions-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_ions-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_obb-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_obb-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_properties-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_proxy_properties-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_triangle_soup-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/has_triangle_soup-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/phi-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isosurfacing/phi-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isotope_whitelist-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/isotope_whitelist-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/kernel_size-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/kernel_size-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/kernel_variance-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/kernel_variance-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/normalization-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/delocalization/normalization-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/dataset_name_facet_indices-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/dataset_name_facet_indices-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/dataset_name_vertices-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/dataset_name_vertices-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/filename-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/filename-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/filename@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/edge_of_the_dataset/filename@version-attribute>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/evaporation_id_filter-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/evaporation_id_filter-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/hit_multiplicity_filter-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/hit_multiplicity_filter-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/control_points-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/control_points-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/decorating_iontypes_filter-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/decorating_iontypes_filter-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/decorating_iontypes_filter/candidates-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/decorating_iontypes_filter/candidates-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/filename-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/filename-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/filename@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/filename@version-attribute>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/initialization-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/initialization-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/method-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/method-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/number_of_iterations-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/number_of_iterations-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/target_dcom_radius-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/target_dcom_radius-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/target_edge_length-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/target_edge_length-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/target_smoothing_step-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/interface_meshing/target_smoothing_step-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances/dataset_name-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances/dataset_name-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances/filename-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances/filename-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances/filename@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/ion_to_edge_distances/filename@version-attribute>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontype_filter-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontype_filter-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontype_filter/match-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontype_filter/match-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontype_filter/method-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontype_filter/method-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes/filename-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes/filename-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes/filename@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes/filename@version-attribute>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes/group_name_iontypes-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/iontypes/group_name_iontypes-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/number_of_delocalizations-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/number_of_delocalizations-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/cardinality-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/cardinality-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/center-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/center-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/dimensionality-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/dimensionality-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/height-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/height-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/identifier_offset-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/identifier_offset-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/radii-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_CYLINDER_SET/radii-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/cardinality-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/cardinality-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/center-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/center-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/dimensionality-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/dimensionality-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/half_axes_radii-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/half_axes_radii-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/identifier_offset-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/identifier_offset-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/orientation-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_ELLIPSOID_SET/orientation-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/cardinality-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/cardinality-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/dimensionality-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/dimensionality-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/hexahedra-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/hexahedra-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/identifier_offset-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CG_HEXAHEDRON_SET/identifier_offset-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK-group </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK-group>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/bitdepth-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/bitdepth-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/identifier-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/identifier-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/mask-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/mask-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/number_of_objects-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/CS_FILTER_BOOLEAN_MASK/number_of_objects-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/windowing_method-field </NXapm_paraprobe_config_nanochem/ENTRY/PROCESS/spatial_filter/windowing_method-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/program-field </NXapm_paraprobe_config_nanochem/ENTRY/program-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/program@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY/program@version-attribute>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY/time_stamp-field </NXapm_paraprobe_config_nanochem/ENTRY/time_stamp-field>`
* :ref:`/NXapm_paraprobe_config_nanochem/ENTRY@version-attribute </NXapm_paraprobe_config_nanochem/ENTRY@version-attribute>`

**NXDL Source**:
  https://github.com/nexusformat/definitions/blob/main/applications/NXapm_paraprobe_config_nanochem.nxdl.xml