Further working on em-specific base classes, next up: i) NXscanbox_em…

…, ii) NXstage_lab consolidation with NXmanipulator, and NXem appdef

base_classes/NXprocessing_reference_frame.nxdl.xml

@@ -39,7 +39,7 @@
         If any of these assumptions is not met, the user is required to
         explicitly state this.
 
-        `Reference <https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggest to label the base
+        `Reference <https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the base
         the base vectors of this coordinate system as :math:`X_p, Y_p, Z_p`.
     </doc>
     <field name="x_alias" type="NX_CHAR">

base_classes/NXsample_reference_frame.nxdl.xml

@@ -34,22 +34,22 @@
         If any of these assumptions is not met, the user is required to
         explicitly state this.
 
-        Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the base
-        vectors of this coordinate system as Xs, Ys, Zs.
+        `Reference <https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the base
+        vectors of this coordinate system as :math:`X_s, Y_s, Z_s`.
     </doc>
     <field name="x_alias" type="NX_CHAR">
-        <enumeration>
+        <!--<enumeration>
              <item value="Xs"/>
-        </enumeration>
+        </enumeration>-->
     </field>
     <field name="y_alias" type="NX_CHAR">
-        <enumeration>
+        <!--<enumeration>
              <item value="Ys"/>
-        </enumeration>
+        </enumeration>-->
     </field>
     <field name="z_alias" type="NX_CHAR">
-        <enumeration>
+        <!--<enumeration>
              <item value="Zs"/>
-        </enumeration>
-    </field>        
+        </enumeration>-->
+    </field>
 </definition>

base_classes/NXscanbox_em.nxdl.xml

@@ -21,26 +21,26 @@
 #
 # 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="base" type="group" name="NXscanbox_em" extends="NXcomponent" 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" type="group" name="NXscanbox_em" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <doc>
          Scan box and coils which deflect a beam of charged particles in a controlled manner.
 
          The scan box is instructed by an instance of :ref:`NXprogram`, some control software,
-         which is not necessarily the same program as for all components of a microscope.
+         which is not necessarily the same program as for all components of an instrument.
 
          The scanbox directs the probe of charged particles (electrons, ions)
          to controlled locations according to a scan scheme and plan.
     </doc>
     <!--user perspective-->
     <field name="scan_schema" type="NX_CHAR">
         <doc>
-             Name of the typically tech-partner-specific term that specifies
-             an automated protocol which controls the details how the components
-             of the microscope work together to achieve a controlled scanning of the
-             beam over the sample surface.
+             Name of the typically tech-partner-specific term that specifies an
+             automated protocol which controls the details how the components
+             of the scan_box and instrument work together to achieve a controlled
+             scanning of the beam over the sample surface.
 
              In most cases users do not know, have to care, or are able to disentangle the
-             details of the spatiotemporal dynamics of the components of the microscope.
+             details of the spatiotemporal dynamics of the components of the instrument.
              Instead, they rely on the assumption that the microscope and control software
              work as expected. Selecting then a specific scan_schema assures some level
              of reproducibility in the way how the beam is scanned over the surface.
@@ -101,11 +101,7 @@
              TODO discuss with the electron microscopists.
         </doc>
     </field>
-    <!--technical design perspective
-(NXlens_em):-->
+    <!--technical design perspective-->
     <group type="NXdeflector"/>
     <group type="NXcircuit"/>
-    <!--(NXcg_point_set):
-NEW ISSUE: build on work of EMglossary with HMC and use duty cycle instead
-NEW ISSUE: make use of and define duty cycle-->
 </definition>

base_classes/NXsingle_crystal.nxdl.xml

@@ -59,7 +59,7 @@
             <dim index="2" value="3"/>
         </dimensions>
     </field>
-    <group name="rotation_set" type="NXrotation_set">
+    <group name="rotation" type="NXrotation">
         <doc>
              Detailed description of single crystal orientation and misorientation.
         </doc>

base_classes/NXstage_lab.nxdl.xml

@@ -21,7 +21,7 @@
 #
 # 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="base" type="group" name="NXstage_lab" extends="NXcomponent" 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" type="group" name="NXstage_lab" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <doc>
          Base class for a stage (lab) used to hold, orient, and prepare a specimen.