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NXapm_paraprobe_config_distancer.nxdl.xml
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NXapm_paraprobe_config_distancer.nxdl.xml
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<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
<!--
# NeXus - Neutron and X-ray Common Data Format
#
# Copyright (C) 2014-2024 NeXus International Advisory Committee (NIAC)
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 3 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# For further information, see http://www.nexusformat.org
-->
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="application" name="NXapm_paraprobe_config_distancer" extends="NXobject" type="group" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<symbols>
<doc>
The symbols used in the schema to specify e.g. dimensions of arrays.
</doc>
</symbols>
<doc>
Configuration/settings of a paraprobe-distancer software tool run.
</doc>
<group type="NXentry">
<attribute name="version">
<doc>
Version specifier of this application definition.
</doc>
</attribute>
<field name="definition">
<doc>
Official NeXus NXDL schema with which this file was written.
</doc>
<enumeration>
<item value="NXapm_paraprobe_config_distancer"/>
</enumeration>
</field>
<field name="program">
<doc>
Given name of the program/software/tool with which this NeXus
(configuration) file was generated.
</doc>
<attribute name="version">
<doc>
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.
</doc>
</attribute>
</field>
<field name="time_stamp" type="NX_DATE_TIME">
<doc>
ISO 8601 formatted time code with local time zone offset to UTC
information included when this configuration file was created.
</doc>
</field>
<field name="analysis_identifier">
<doc>
Ideally, a (globally persistent) unique identifier for referring
to this analysis.
</doc>
</field>
<field name="analysis_description" optional="true">
<doc>
Possibility for leaving a free-text description about this analysis.
</doc>
</field>
<field name="results_path" optional="true">
<doc>
Path to the directory where the tool should store NeXus/HDF5 results
of this analysis. If not specified results will be stored in the
current working directory.
</doc>
</field>
<field name="number_of_processes" type="NX_UINT" units="NX_UNITLESS">
<doc>
How many individual analyses should the tool execute.
</doc>
</field>
<group type="NXprocess">
<group name="dataset" type="NXapm_input_reconstruction">
<field name="filename">
<attribute name="version"/>
</field>
<field name="dataset_name_reconstruction"/>
<field name="dataset_name_mass_to_charge"/>
</group>
<group name="iontypes" type="NXapm_input_ranging">
<field name="filename">
<attribute name="version"/>
</field>
<field name="group_name_iontypes"/>
</group>
<group name="spatial_filter" type="NXspatial_filter" optional="true">
<field name="windowing_method"/>
<group type="NXcg_ellipsoid_set" optional="true">
<field name="dimensionality" type="NX_POSINT"/>
<field name="cardinality" type="NX_POSINT"/>
<field name="identifier_offset" type="NX_INT"/>
<field name="center" type="NX_NUMBER"/>
<field name="half_axes_radii" type="NX_NUMBER"/>
<field name="orientation" type="NX_NUMBER"/>
</group>
<group type="NXcg_cylinder_set" optional="true">
<field name="dimensionality" type="NX_POSINT"/>
<field name="cardinality" type="NX_POSINT"/>
<field name="identifier_offset" type="NX_INT"/>
<field name="center" type="NX_NUMBER"/>
<field name="height" type="NX_NUMBER"/>
<field name="radii" type="NX_NUMBER"/>
</group>
<group type="NXcg_hexahedron_set" optional="true">
<field name="dimensionality" type="NX_POSINT"/>
<field name="cardinality" type="NX_POSINT"/>
<field name="identifier_offset" type="NX_INT"/>
<group name="hexahedra" type="NXcg_face_list_data_structure"/>
</group>
<group type="NXcs_filter_boolean_mask" optional="true">
<field name="number_of_objects" type="NX_UINT"/>
<field name="bitdepth" type="NX_UINT"/>
<field name="mask" type="NX_UINT"/>
<field name="identifier" type="NX_UINT"/>
</group>
</group>
<group name="evaporation_id_filter" type="NXsubsampling_filter" optional="true"/>
<group name="iontype_filter" type="NXmatch_filter" optional="true"/>
<group name="hit_multiplicity_filter" type="NXmatch_filter" optional="true"/>
<group name="point_to_triangle" type="NXprocess">
<doc>
Compute for all filtered points, e.g. ions of the point set
the shortest Euclidean distance to the closest triangle of the
set of triangles. The triangles can formed a closed surface mesh.
Distances are not simple distances based on normal projections but
giving an exact solution.
</doc>
<group name="triangle_soup" type="NXprocess">
<!--NEW ISSUE NXtriangle_soup-->
<doc>
Paraprobe-distancer enables the computation of the Euclidean shortest
distance for each member of a set of points against a set of triangles.
In contrast to comparable methods used in atom probe the here computed
distance is not simply the projected distance to one of the triangles
but the more costly but robust computation of the distance between
a point and a triangle.
The triangles can represent for instance the facets of a triangulated
surface mesh of a model for the edge of the dataset. Such a model can
be computed with paraprobe-surfacer. Alternatively, the triangles can
be those from the set of all facets for a set of convex hulls, alpha-shapes,
or alpha wrappings about three-dimensional objects like precipitates
(computed with e.g. paraprobe-nanochem).
Currently, the tool does not check if the respectively specified
triangle sets are consistent, what their topology is, or whether or
not they are consistently oriented.
Each dataset that is referred to in the list_of _dataset_names_vertices
should be an (Nvertices, 3) array of NX_FLOAT. Each dataset referred
to in the list_of_dataset_names_facet_indices should be an
(Nfacets, 3) array of NX_UINT.
Facet indices refer to vertex indices. These need to start at zero
and must not exceed Nvertices - 1, i.e. the identifier_offset is 0
and vertices are indexed thus implicitly.
Facet normal vectors have to be also an array
of shape (Nfacets, 3) of NX_FLOAT.
</doc>
<field name="number_of_files" type="NX_UINT" units="NX_UNITLESS">
<doc>
How many triangle sets to consider.
</doc>
</field>
<group type="NXprocess">
<doc>
List of triangle sets. This design allows users to combine
multiple triangle sets.
</doc>
<field name="filename">
<doc>
Name of the HDF5 file(s) which contain(s) vertex coordinates
and facet indices to describe the desired set of triangles.
</doc>
<attribute name="version">
<doc>
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.
</doc>
</attribute>
</field>
<field name="dataset_name_vertices">
<doc>
Absolute HDF5 path to the dataset which
specifies the array of vertex positions.
</doc>
</field>
<field name="dataset_name_facet_indices">
<doc>
Absolute HDF5 path to the dataset which
specifies the array of facet indices.
</doc>
</field>
<field name="dataset_name_facet_normals" optional="true">
<doc>
Absolute HDF5 path to the dataset which
specifies the array of facet normal vectors.
</doc>
</field>
</group>
</group>
<field name="method">
<doc>
Specifies for which ions/points the tool will compute distances.
The purpose of this setting is to avoid unnecessary computations
when the user requests to only compute distances of ions within a
threshold distance to the triangle soup.
By default the distances are computed for all ions; however
the setting skin enables to compute distances only for those
ions which are not farther away located to a triangle
than threshold_distance.
</doc>
<enumeration>
<item value="default"/>
<item value="skin"/>
</enumeration>
</field>
<field name="threshold_distance" type="NX_FLOAT" units="NX_LENGTH">
<!--##MK::only required when method is skin-->
<doc>
Maximum distance for which distances are computed when method is skin.
</doc>
</field>
</group>
</group>
<!--\@units: nm-->
<!--point_set_to_polyline_set(NXprocess):
doc: |
Compute the shortest Euclidean distance of all filtered points/ions
of a point set to the closest point on the closest polyline.
polyhedra_set_to_triangle_set(NXprocess):
doc: |
Compute the (shortest Euclidean) distance of all polyhedra of a set-->
<group name="performance" type="NXcs_profiling">
<field name="current_working_directory"/>
</group>
</group>
</definition>