Completing first round of edits on base classes for NXem

nexusformat · Jan 17, 2025 · 866d624 · 866d624
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diff --git a/base_classes/NXoptical_system_em.nxdl.xml b/base_classes/NXoptical_system_em.nxdl.xml
@@ -99,6 +99,31 @@
             The unit of the nominal dose rate is e-/(angstrom^2*s).
         </doc>
     </field>
+    <field name="dose_rate" type="NX_NUMBER" units="e-/(angstrom^2*s)">
+        <doc>Nominal dose rate.</doc>
+    </field>
+    <field name="rotation" type="NX_NUMBER" units="NX_ANGLE">
+        <doc>
+            In the process of passing through an :ref:`NXlens_em` electrons are typically accelerated
+            on a helical path about the optical axis. This causes an image rotation whose strength
+            is affected by the magnification.
+
+            Microscopes may be equipped with compensation methods (implemented in hardware
+            or software) that reduce but not necessarily eliminate this rotation.
+
+            See  `L. Reimer &lt;https://doi.org/10.1007/978-3-540-38967-5&gt;`_ for details.
+        </doc>
+    </field>
+    <field name="focal_length" type="NX_NUMBER" units="NX_LENGTH">
+        <doc>
+             Distance which lies between the principal plane of the lens and the focal point
+             along the optical axis.
+
+             This concept is related to term `Focal Length`_ of the EMglossary standard.
+
+             .. _Focal Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000029
+        </doc>
+    </field>
     <field name="tilt_correction" type="NX_BOOLEAN">
         <doc>
              Details about an imaging setting used during acquisition to correct perspective
@@ -127,14 +152,5 @@
              .. _Dynamic Refocusing: https://purls.helmholtz-metadaten.de/emg/EMG_00000017
         </doc>
     </field>
-    <field name="focal_length" type="NX_NUMBER" units="NX_LENGTH">
-        <doc>
-             Distance which lies between the principal plane of the lens and the focal point
-             along the optical axis.
-
-             This concept is related to term `Focal Length`_ of the EMglossary standard.
-
-             .. _Focal Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000029
-        </doc>
-    </field>
+
 </definition>
diff --git a/base_classes/NXprocessing_reference_frame.nxdl.xml b/base_classes/NXprocessing_reference_frame.nxdl.xml
@@ -23,12 +23,17 @@
 -->
 <definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXprocessing_reference_frame" extends="NXcoordinate_system" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <doc>
-        Details about eventually relevant named directions that may give
-        reasons for anisotropies.
+        Base class to document details about processing reference frames.
 
-        The classical example is mechanical processing where one has to 
-        specify which directions (e.g. rolling, transverse, and normal
-        direction) align how with the direction of the base vectors of the 
+        Directional differences in processing materials can cause anisotropies
+        of material properties. Mechanical processing is one example where
+        the rotation of the NXsample_reference_frame with respect to another
+        processing_reference_frame is relevant.
+
+        Fields with suffix alias should be used to specify 
+
+        how the base vectors of the reference frame for the (macroscopic) sampleare aligned different
+        directions (e.g. rolling, transverse, and normal direction) align how with the direction of the base vectors of the 
         :ref:`NXsample_reference_frame`.
 
         It is assumed that the configuration is inspected by looking towards
@@ -43,6 +48,7 @@
         the base vectors of this coordinate system as :math:`X_p, Y_p, Z_p`.
     </doc>
     <field name="x_alias" type="NX_CHAR">
+        <doc>Alias 
         <!--<enumeration>
              <item value="Xp"/>
         </enumeration>-->

diff --git a/base_classes/NXscanbox_em.nxdl.xml b/base_classes/NXscanbox_em.nxdl.xml
@@ -46,16 +46,6 @@
              of reproducibility in the way how the beam is scanned over the surface.
         </doc>
     </field>
-    <field name="calibration_style" type="NX_CHAR">
-        <doc>
-             TODO discuss with the electron microscopists.
-        </doc>
-    </field>
-    <field name="center" type="NX_NUMBER" units="NX_ANY">
-        <doc>
-             TODO discuss with the electron microscopists.
-        </doc>
-    </field>
     <!--descriptors relevant from economic usage and dose management perspective-->
     <field name="dwell_time" type="NX_NUMBER" units="NX_TIME">
         <doc>
@@ -76,31 +66,6 @@
              .. _Flyback Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000028
         </doc>
     </field>
-    <field name="line_time" type="NX_NUMBER" units="NX_TIME">
-        <doc>
-             TODO discuss with the electron microscopists.
-        </doc>
-    </field>
-    <field name="pixel_time" type="NX_NUMBER" units="NX_TIME">
-        <doc>
-             TODO discuss with the electron microscopists.
-        </doc>
-    </field>
-    <field name="requested_pixel_time" type="NX_NUMBER" units="NX_TIME">
-        <doc>
-             TODO discuss with the electron microscopists.
-        </doc>
-    </field>
-    <field name="ac_line_sync" type="NX_BOOLEAN">
-        <doc>
-             TODO discuss with the electron microscopists.
-        </doc>
-    </field>
-    <field name="rotation" type="NX_NUMBER" units="NX_ANGLE">
-        <doc>
-             TODO discuss with the electron microscopists.
-        </doc>
-    </field>
     <!--technical design perspective-->
     <group type="NXdeflector"/>
     <group type="NXcircuit"/>

diff --git a/base_classes/NXstage_lab.nxdl.xml b/base_classes/NXstage_lab.nxdl.xml
@@ -100,48 +100,45 @@
          * `Specimens in atom probe &lt;https://doi.org/10.1007/978-1-4614-8721-0&gt;`_ (page 47ff)
          * `Exemplar micro-manipulators &lt;https://nano.oxinst.com/products/omniprobe/omniprobe-200&gt;`_
 
-         We are looking forward to suggestions from the scientists.
     </doc>
     <field name="design" type="NX_CHAR">
         <doc>
-             Principal design of the stage.
-
-             Exemplar terms could be side_entry, top_entry,
+             Principal design of the stage. Exemplar terms could be
+             side_entry, top_entry,
              single_tilt, quick_change, multiple_specimen,
              bulk_specimen, double_tilt, tilt_rotate,
              heating_chip, atmosphere_chip,
-             electrical_biasing_chip, liquid_cell_chip
+             electrical_biasing_chip, or liquid_cell_chip.
         </doc>
     </field>
     <field name="alias" type="NX_CHAR">
         <doc>
-             Free-text field to give a term how that a stage_lab at this level of the
-             stage_lab hierarchy is commonly referred to. Examples could be stub,
-             puck, carousel, microtip, clip, holder, etc.
+             Free-text field to give a term how that stage_lab instance is commonly referred to.
+             Examples could be stub, puck, carousel, microtip, clip, holder, etc.
         </doc>
     </field>
     <field name="tilt_1" type="NX_NUMBER" units="NX_ANGLE">
         <doc>
              The interpretation of this tilt should be specialized
-             and thus detailed via the application definition.
+             via an application definition.
         </doc>
     </field>
     <field name="tilt_2" type="NX_NUMBER" units="NX_ANGLE">
         <doc>
              The interpretation of this tilt should be specialized
-             and thus detailed via the application definition.
+             via an application definition.
         </doc>
     </field>
     <field name="rotation" type="NX_NUMBER" units="NX_ANGLE">
         <doc>
              The interpretation of this rotation should be specialized
-             and thus detailed via the application definition.
+             via an application definition.
         </doc>
     </field>
     <field name="position" type="NX_NUMBER" units="NX_LENGTH">
         <doc>
              The interpretation of this position should be specialized
-             and thus detailed via the application definition.
+             via an application definition.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="3"/>
@@ -155,19 +152,5 @@
     <!--NEW ISSUE: rather the field if possible should be specified-->
     <group type="NXpositioner"/>
     <group type="NXsensor"/>
-    <!--(NXactuator):
-see for complicated positioning tools like an eucentric five-axis table stage in an SEM
-https://www.nanotechnik.com/e5as.html
-shipswing_tilt(NXpositioner):
-normal_rotate(NXpositioner):
-normal_height(NXpositioner):
-inplane_translate1(NXpositioner):
-inplane_translate2(NXpositioner):
-NEW ISSUE: add temperature control units and components to apply external stimuli
-NEW ISSUE: on the specimen such as NXmech_testing_unit and NXfurnace, NXreaction_cell
-NEW ISSUE: by contrast, the purpose and design of so-called nano/or micromanipulators,
-i.e. automatable devices to perform e.g. site-specific lift out, procedures warrants
-to define an own class NXspecimen_manipulator given this is nothing else than
-miniature robot arm essential one could also think about creating an own NXrobotarm class,
-below are two examples of such tools as they are used in FIB and SEMs-->
+    <group type="NXactuator"/>
 </definition>