move new definitions to application and base_classes

# Conflicts:
#	applications/NXellipsometry.nxdl.xml
#	applications/NXmpes_arpes.nxdl.xml
#	applications/NXoptical_spectroscopy.nxdl.xml
#	applications/NXraman.nxdl.xml
#	applications/NXxps.nxdl.xml
#	applications/xps/xps_cs.png
#	base_classes/NXactivity.nxdl.xml
#	base_classes/NXactuator.nxdl.xml
#	base_classes/NXapm_charge_state_analysis.nxdl.xml
#	base_classes/NXapm_hit_finding.nxdl.xml
#	base_classes/NXapm_msr.nxdl.xml
#	base_classes/NXapm_ranging.nxdl.xml
#	base_classes/NXapm_reconstruction.nxdl.xml
#	base_classes/NXapm_sim.nxdl.xml
#	base_classes/NXapm_volt_and_bowl.nxdl.xml
#	base_classes/NXbeam_device.nxdl.xml
#	base_classes/NXbeam_transfer_matrix_table.nxdl.xml
#	base_classes/NXcg_cylinder_set.nxdl.xml
#	base_classes/NXcg_ellipsoid_set.nxdl.xml
#	base_classes/NXcg_face_list_data_structure.nxdl.xml
#	base_classes/NXcg_hexahedron_set.nxdl.xml
#	base_classes/NXcg_parallelogram_set.nxdl.xml
#	base_classes/NXcg_point_set.nxdl.xml
#	base_classes/NXcg_polygon_set.nxdl.xml
#	base_classes/NXcg_polyhedron_set.nxdl.xml
#	base_classes/NXcg_primitive_set.nxdl.xml
#	base_classes/NXcg_sphere_set.nxdl.xml
#	base_classes/NXcg_tetrahedron_set.nxdl.xml
#	base_classes/NXcg_triangle_set.nxdl.xml
#	base_classes/NXchemical_process.nxdl.xml
#	base_classes/NXcircuit.nxdl.xml
#	base_classes/NXcollectioncolumn.nxdl.xml
#	base_classes/NXcomponent.nxdl.xml
#	base_classes/NXdata_mpes.nxdl.xml
#	base_classes/NXdata_mpes_detector.nxdl.xml
#	base_classes/NXelectron_level.nxdl.xml
#	base_classes/NXem_eds.nxdl.xml
#	base_classes/NXevent_data_apm.nxdl.xml
#	base_classes/NXevent_data_apm_set.nxdl.xml
#	base_classes/NXfit.nxdl.xml
#	base_classes/NXfit_background.nxdl.xml
#	base_classes/NXfit_function.nxdl.xml
#	base_classes/NXfit_parameter.nxdl.xml
#	base_classes/NXhistory.nxdl.xml
#	base_classes/NXidentifier.nxdl.xml
#	base_classes/NXmanipulator.nxdl.xml
#	base_classes/NXopt_window.nxdl.xml
#	base_classes/NXphysical_process.nxdl.xml
#	base_classes/NXprocess_mpes.nxdl.xml
#	base_classes/NXprogram.nxdl.xml
#	base_classes/NXregistration.nxdl.xml
#	base_classes/NXresolution.nxdl.xml
#	base_classes/NXrotation_set.nxdl.xml
#	base_classes/NXsample_component_set.nxdl.xml
#	base_classes/NXserialized.nxdl.xml
#	base_classes/NXsingle_crystal.nxdl.xml
#	base_classes/NXspindispersion.nxdl.xml
#	base_classes/NXsubstance.nxdl.xml
#	base_classes/NXunit_cell.nxdl.xml
#	contributed_definitions/NXactivity.nxdl.xml
#	contributed_definitions/NXadc.nxdl.xml
#	contributed_definitions/NXaperture_em.nxdl.xml
#	contributed_definitions/NXapm_sim.nxdl.xml
#	contributed_definitions/NXcs_cpu_obj.nxdl.xml
#	contributed_definitions/NXcs_cpu_sys.nxdl.xml
#	contributed_definitions/NXcs_mm_obj.nxdl.xml
#	contributed_definitions/NXem_ebsd_crystal_structure_model.nxdl.xml
#	contributed_definitions/NXfit_function.nxdl.xml
#	contributed_definitions/NXfit_parameter.nxdl.xml
#	contributed_definitions/NXidentifier.nxdl.xml
#	contributed_definitions/NXms_ipf_set.nxdl.xml
#	contributed_definitions/NXms_snapshot.nxdl.xml
#	contributed_definitions/NXprogram.nxdl.xml
#	contributed_definitions/NXregistration.nxdl.xml
#	contributed_definitions/NXunit_cell.nxdl.xml
#	contributed_definitions/nyaml/NXcg_primitive_set.yaml
#	contributed_definitions/nyaml/NXcoordinate_system.yaml
#	contributed_definitions/nyaml/NXcrystal_structure.yaml
#	contributed_definitions/nyaml/NXem_correlation.yaml
#	contributed_definitions/nyaml/NXem_eds.yaml
#	contributed_definitions/nyaml/NXem_eels.yaml
#	contributed_definitions/nyaml/NXem_img.yaml
#	contributed_definitions/nyaml/NXem_method.yaml
#	contributed_definitions/nyaml/NXem_msr.yaml
#	contributed_definitions/nyaml/NXem_sim.yaml
#	contributed_definitions/nyaml/NXroi.yaml

base_classes/NXcg_cylinder_set.nxdl.xml

@@ -1,10 +1,10 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?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
@@ -21,119 +21,139 @@
 #
 # For further information, see http://www.nexusformat.org
 -->
-<!--
-redundant as there is NXcsg, NXquadric, NXsolid_geometry with which
+<!--redundant as there is NXcsg, NXquadric, NXsolid_geometry with which
 cylinder could be constructed, but NXcylinder is easier to understand-->
-<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_cylinder_set" extends="NXcg_primitive_set" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" name="NXcg_cylinder_set" 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>
-        <symbol name="d">
-            <doc>
-                 The dimensionality of the space in which the members are assumed embedded.
-            </doc>
-        </symbol>
         <symbol name="c">
             <doc>
-                 The cardinality of the set, i.e. the number of members.
+                 The cardinality of the set, i.e. the number of cylinders or cones.
             </doc>
         </symbol>
     </symbols>
     <doc>
-         Computational geometry description of a set of cylinders.
+         Computational geometry description of a set of cylinders in Euclidean space.
 
-         The radius can either be defined in the radii field or by filling both
-         the upper_cap_radii or lower_cap_radii field. The latter field case can
-         thus be used to represent truncated cones.
+         The members of the set can have different size. For each member the position
+         of the center and the height is mandatory. The radius can either be defined
+         in the radius field or by filling both the upper and the lower radius field.
+         The latter case can be used to represent truncated cones.
     </doc>
-    <field name="height" type="NX_NUMBER" units="NX_LENGTH">
+    <field name="dimensionality" type="NX_POSINT" units="NX_UNITLESS">
+        <enumeration>
+            <item value="3"/>
+        </enumeration>
+    </field>
+    <field name="cardinality" type="NX_POSINT" units="NX_UNITLESS"/>
+    <field name="identifier_offset" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             A direction vector which is parallel to the cylinder/cone axis
-             and whose magnitude is the height of the cylinder/cone.
+             Integer which specifies the first index to be used for distinguishing
+             identifiers for cylinders. Identifiers are defined either implicitly
+             or explicitly. For implicit indexing the identifiers are defined on the
+             interval [identifier_offset, identifier_offset+c-1].
+             For explicit indexing the identifier array has to be defined.
+
+             The identifier_offset field can for example be used to communicate if the
+             identifiers are expected to start from 1 (referred to as Fortran-/Matlab-)
+             or from 0 (referred to as C-, Python-style index notation) respectively.
         </doc>
-        <dimensions>
+    </field>
+    <field name="identifier" type="NX_INT">
+        <doc>
+             Integer used to distinguish members for explicit indexing.
+        </doc>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
-            <dim index="2" value="d"/>
         </dimensions>
     </field>
-    <!--observe that although we claim that d is the dimensionality we have
-currently no strategy to tell it must not be d but the actual value
-equally so the symbol c, currently all we say that in the specialization
-defined here the fields radii, upper_cap_radius, and others are all having
-value arguments of the same shape, i.e. these are arrays of rank one with some length c!
-behind the dimensionality field defined either in the here defined specialization
-of NXcg_primitive_set or otherwise that variable is undefined
-alternatively one could store the center of the lower and upper cap but
-these are then no longer necessarily on the same axis
-maybe a future feature for representing skewed cylinder, but then
-one should really better use NXquadric...-->
-    <field name="radius" type="NX_NUMBER" units="NX_LENGTH">
+    <field name="center" type="NX_NUMBER" units="NX_LENGTH">
         <doc>
-             Radius of the cylinder if all have the same radius.
+             The geometric center of each member.
         </doc>
+        <dimensions rank="2">
+            <dim index="1" value="c"/>
+            <dim index="2" value="3"/>
+        </dimensions>
     </field>
-    <field name="radii" type="NX_NUMBER" units="NX_LENGTH">
+    <field name="height" type="NX_NUMBER" units="NX_LENGTH">
         <doc>
-             Radii of the cylinder.
+             A direction vector which is parallel to the cylinder/cone axis and
+             whose magnitude is the height of the cylinder/cone.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
+            <dim index="1" value="c"/>
+            <dim index="2" value="3"/>
+        </dimensions>
+    </field>
+    <!--alternatively one could store the center of the lower and upper cap but
+these are then no longer necessarily on the same axis
+maybe a future feature for representing skewed cylinder, but then
+one should really better use NXquadric...-->
+    <field name="radii" type="NX_NUMBER" units="NX_LENGTH">
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
-    <field name="upper_cap_radii" type="NX_NUMBER" units="NX_LENGTH">
+    <field name="upper_cap_radius" type="NX_NUMBER" units="NX_LENGTH">
         <doc>
-             Radii of the upper circular cap.
-
-             This field, combined with lower_cap_radius can be used to describe
-             (eventually truncated) circular cones.
+             The radius of the upper circular cap.
+             This field, combined with lower_cap_radius can be used to
+             describe (eventually truncated) circular cones.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
-    <field name="lower_cap_radii" type="NX_NUMBER" units="NX_LENGTH">
+    <field name="lower_cap_radius" type="NX_NUMBER" units="NX_LENGTH">
         <doc>
-             Radii of the upper circular cap.
-
-             This field, combined with upper_cap_radius can be used to describe
-             (eventually truncated) circular cones.
+             The radius of the upper circular cap.
+             This field, combined with lower_cap_radius can be used to
+             describe (eventually truncated) circular cones.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
+    <group type="NXtransformations">
+        <doc>
+             Reference to or definition of a coordinate system with
+             which the positions and directions are interpretable.
+        </doc>
+    </group>
     <!--properties of the cylinder-->
-    <field name="lateral_surface_area" type="NX_NUMBER" units="NX_AREA">
+    <field name="volume" type="NX_NUMBER" units="NX_VOLUME">
         <doc>
-             Lateral surface area
+             Interior volume of each cylinder
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
-    <field name="upper_cap_surface_area" type="NX_NUMBER" units="NX_AREA">
+    <field name="lateral_surface_area" type="NX_NUMBER" units="NX_AREA">
         <doc>
-             Area of the upper cap of each cylinder.
+             Lateral surface area
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
-    <field name="lower_cap_surface_area" type="NX_NUMBER" units="NX_AREA">
+    <field name="cap_surface_area" type="NX_NUMBER" units="NX_AREA">
         <doc>
-             Area of the lower cap of each cylinder.
+             Area of the upper and the lower cap of each cylinder respectively.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
+            <dim index="2" value="2"/>
         </dimensions>
     </field>
-    <field name="total_surface_area" type="NX_NUMBER" units="NX_AREA">
+    <field name="surface_area" type="NX_NUMBER" units="NX_AREA">
         <doc>
-             Sum of upper and lower cap areas and lateral surface area
-             of each cylinder.
+             Cap and lateral surface area for each cylinder.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>

base_classes/NXcg_ellipsoid_set.nxdl.xml

@@ -1,10 +1,10 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?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
@@ -21,45 +21,115 @@
 #
 # For further information, see http://www.nexusformat.org
 -->
-<!--
-redundant as there is NXcsg, and NXquadric but easier to understand-->
-<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_ellipsoid_set" extends="NXcg_primitive_set" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+<!--redundant as there is NXcsg, and NXquadric but easier to understand-->
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" name="NXcg_ellipsoid_set" 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>
         <symbol name="d">
             <doc>
-                 The dimensionality of the space in which the members are assumed embedded.
+                 The dimensionality, which has to be at least 2.
             </doc>
         </symbol>
         <symbol name="c">
             <doc>
-                 The cardinality of the set, i.e. the number of members.
+                 The cardinality of the set, i.e. the number of ellipses, or ellipsoids.
             </doc>
         </symbol>
     </symbols>
     <doc>
-         Computational geometry description of a set of ellipsoids.
+         Computational geometry description of a set of ellipsoids in Euclidean space.
+
+         Individual ellipsoids can have different half axes.
     </doc>
-    <field name="half_axes_radius" type="NX_NUMBER" units="NX_LENGTH">
+    <field name="dimensionality" type="NX_POSINT" units="NX_UNITLESS"/>
+    <field name="cardinality" type="NX_POSINT" units="NX_UNITLESS"/>
+    <field name="identifier_offset" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             Radius of the half axes.
+             Integer which specifies the first index to be used for distinguishing
+             identifiers for ellipsoids. Identifiers are defined either implicitly
+             or explicitly. For implicit indexing the identifiers are defined on the
+             interval [identifier_offset, identifier_offset+c-1].
+             For explicit indexing the identifier array has to be defined.
 
-             Use if all ellipsoids in the set have the same half-axes.
+             The identifier_offset field can for example be used to communicate if the
+             identifiers are expected to start from 1 (referred to as Fortran-/Matlab-)
+             or from 0 (referred to as C-, Python-style index notation) respectively.
+        </doc>
+    </field>
+    <field name="identifier" type="NX_INT" units="NX_UNITLESS">
+        <doc>
+             Integer used to distinguish ellipsoids for explicit indexing.
+        </doc>
+        <dimensions rank="1">
+            <dim index="1" value="c"/>
+        </dimensions>
+    </field>
+    <field name="center" type="NX_NUMBER" units="NX_LENGTH">
+        <doc>
+             Geometric center of the ellipsoids. This can be the center of mass.
+             Dimensionality and cardinality of the point and ellipsoid set have to match.
+             The identifier_offset and identifier field of NXcg_point_set do not need
+             to be used as they should be same as the identifier_offset and the
+             identifier for the ellipsoids.
+        </doc>
+        <dimensions rank="2">
+            <dim index="1" value="c"/>
+            <dim index="2" value="d"/>
+        </dimensions>
+    </field>
+    <field name="half_axes_radius" type="NX_NUMBER" units="NX_LENGTH">
+        <doc>
+             If all ellipsoids in the set have the same half-axes.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="d"/>
         </dimensions>
     </field>
     <field name="half_axes_radii" type="NX_NUMBER" units="NX_LENGTH">
         <doc>
-             Half-axes radii of each ellipsoid.
+             In the case that ellipsoids have different radii use this field
+             instead of half_axes_radius.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
             <dim index="2" value="d"/>
         </dimensions>
     </field>
+    <group type="NXtransformations">
+        <doc>
+             Reference to or definition of a coordinate system with
+             which the positions and directions are interpretable.
+        </doc>
+    </group>
     <!--properties of ellipsoids-->
+    <field name="is_closed" type="NX_BOOLEAN">
+        <doc>
+             Are the ellipsoids closed or hollow?
+        </doc>
+        <dimensions rank="1">
+            <dim index="1" value="c"/>
+        </dimensions>
+    </field>
+    <field name="volume" type="NX_NUMBER" units="NX_ANY">
+        <dimensions rank="1">
+            <dim index="1" value="c"/>
+        </dimensions>
+    </field>
+    <field name="surface_area" type="NX_NUMBER" units="NX_ANY">
+        <dimensions rank="1">
+            <dim index="1" value="c"/>
+        </dimensions>
+    </field>
+    <!--NXcg_orientation_set-->
+    <field name="orientation" type="NX_NUMBER" units="NX_DIMENSIONLESS">
+        <doc>
+             Direction unit vector which points along the largest half-axes.
+        </doc>
+        <dimensions rank="2">
+            <dim index="1" value="c"/>
+            <dim index="2" value="d"/>
+        </dimensions>
+    </field>
 </definition>