Simplified base class design for documenting aberrations

contributed_definitions/NXaberration_model.nxdl.xml

@@ -36,5 +36,86 @@
             <item value="nion"/>
         </enumeration>
     </field>
-    <group type="NXaberration"/>
+    <!--(NXaberration):-->
+    <!--specifically-named aberrations following the CEOS convention-->
+    <group name="c_1" type="NXaberration"/>
+    <group name="a_1" type="NXaberration"/>
+    <group name="b_2" type="NXaberration"/>
+    <group name="a_2" type="NXaberration"/>
+    <group name="c_3" type="NXaberration"/>
+    <group name="s_3" type="NXaberration"/>
+    <group name="a_3" type="NXaberration"/>
+    <!--based on feedback from Thilo Remmele the following aberrations could be measured
+(enhanced mode, tilt angle > 30 mrad) but are not corrected-->
+    <group name="b_4" type="NXaberration"/>
+    <group name="d_4" type="NXaberration"/>
+    <group name="a_4" type="NXaberration"/>
+    <group name="c_5" type="NXaberration"/>
+    <group name="s_5" type="NXaberration"/>
+    <group name="r_5" type="NXaberration"/>
+    <group name="a_6" type="NXaberration"/>
+    <!--further comments from Thilo Remmele (Leibniz-Institut für Kristallzüchtung)
+ThermoFisher uses CEOS correctors but makes customizations to these in their microscopes
+Aberration naming schema: C_order_multiplicity (similar to NXem, but with
+another coordinate system and in addition with a confidence entry.
+Aberrations with multiplicity 0 have no angle entry (C1,C3,C5,.., CEOS notation)
+contrast transferfuntion: ctf = e^(-i*Xi(g)) in Fourier space
+aberration function:
+Xi(g) = 2*pi/lamda{ 1/2 * (lamda*g)^2 (C20 + C22 cos[2(phi-phi_22)]
++1/3 * (lamda*g)^3 (C31 cos[(phi-phi_31) + C33 cos[3(phi-phi_33)
++1/4 * (lamda*g)^4 (C40 + C42 cos[2(phi-phi_42)] + C44 cos[4(phi-phi_42)]
++1/f * (lamda*g)^f Sum (Cfm cos[m(phi-phi_fm)] where m=[0,2,..f] for even f and m=[1,3,..,f] for odd f-->
+    <!--Thilo Remmele also mentions that there is a mapping of aberration coefficient names:
+C_2_0 -> C1 Defocus
+C_2_2 -> A1 2-fold astigmatism
+C_3_3 -> A2 3-fold astigmatism
+C_3_1 -> B2 axial coma
+C_4_0 -> C3 spherical aberration
+C_4_4 -> A3 4-fold astigmatism
+C_4_2 -> S3 star aberration
+C_5_5 -> A4 5-fold astigmatism-->
+    <!--C_5_1 -> B4 axial coma
+C_5_3 -> D4 three lobe aberration
+C_6_0 -> C5 spherical aberration
+C_6_2 -> S5 star aberration
+C_6_4 -> R5 rosette aberration
+C_6_6 -> A5 6-fold astigmatism-->
+    <!--In a session with HRTEM images the corrector is commonly aligned.
+The final measurement with the estimated residual aberrations
+should be saved in a corrector.html file (an example is appended
+at the end of this file. Unfortunately the datetime is not included
+in that html output, nor is the used outer tilt angle and exposure time.
+The datetime may be estimated from the file datetime and the Delta t entry,
+but caution if that datetime is not preserved on file transfers!
+More than one detector entry could occure but is not common.
+A seperate corrector schema, so it can be easily exchanged to other correctors if necessary.
+It might be useful to collect all the corrector entries in one table, for example to analyse the performance of the corrector.
+The corrector entry of the nexus em definition lacks the confidence information and the
+parameter settings for the estimation oft the aberrations.-->
+    <!--specifically-named aberrations following the Nion convention-->
+    <group name="c_1_0" type="NXaberration"/>
+    <group name="c_1_2_a" type="NXaberration"/>
+    <group name="c_1_2_b" type="NXaberration"/>
+    <group name="c_2_1_a" type="NXaberration"/>
+    <group name="c_2_1_b" type="NXaberration"/>
+    <group name="c_2_3_a" type="NXaberration"/>
+    <group name="c_2_3_b" type="NXaberration"/>
+    <group name="c_3_0" type="NXaberration"/>
+    <group name="c_3_2_a" type="NXaberration"/>
+    <group name="c_3_2_b" type="NXaberration"/>
+    <group name="c_3_4_a" type="NXaberration"/>
+    <group name="c_3_4_b" type="NXaberration"/>
+    <group name="c_4_1_a" type="NXaberration"/>
+    <group name="c_4_1_b" type="NXaberration"/>
+    <group name="c_4_3_a" type="NXaberration"/>
+    <group name="c_4_3_b" type="NXaberration"/>
+    <group name="c_4_5_a" type="NXaberration"/>
+    <group name="c_4_5_b" type="NXaberration"/>
+    <group name="c_5_0" type="NXaberration"/>
+    <group name="c_5_2_a" type="NXaberration"/>
+    <group name="c_5_2_b" type="NXaberration"/>
+    <group name="c_5_4_a" type="NXaberration"/>
+    <group name="c_5_4_b" type="NXaberration"/>
+    <group name="c_5_6_a" type="NXaberration"/>
+    <group name="c_5_6_b" type="NXaberration"/>
 </definition>

contributed_definitions/NXapm.nxdl.xml

@@ -664,7 +664,7 @@ NEW ISSUE: add section for propagation_delay(NXprocess) ?
 NEW ISSUE: make recon an own subentry NXapm_reconstruction
 NEW ISSUE: different algorithms used one could create a class for each reconstruction method
 NEW ISSUE: make this rather an own subentry NXapm_ranging-->
-            <group name="initial_specimen" type="NXimage_r_set" recommended="true">
+            <group name="initial_specimen" type="NXimage_set" recommended="true">
                 <doc>
                      SEM or TEM image of the initial specimen i.e.
                      ideally taken prior to the data acquisition.
@@ -673,16 +673,16 @@ NEW ISSUE: make this rather an own subentry NXapm_ranging-->
                     <attribute name="signal" type="NX_CHAR"/>
                     <attribute name="axes" type="NX_CHAR"/>
                     <attribute name="AXISNAME_indices" type="NX_CHAR"/>
-                    <field name="intensity" type="NX_NUMBER"/>
-                    <field name="axis_y" type="NX_NUMBER">
+                    <field name="real" type="NX_NUMBER"/>
+                    <field name="axis_j" type="NX_NUMBER">
                         <dimensions rank="1">
-                            <dim index="1" value="n_y"/>
+                            <dim index="1" value="n_j"/>
                         </dimensions>
                         <attribute name="long_name" type="NX_CHAR"/>
                     </field>
                     <field name="axis_x" type="NX_NUMBER">
                         <dimensions rank="1">
-                            <dim index="1" value="n_x"/>
+                            <dim index="1" value="n_i"/>
                         </dimensions>
                         <attribute name="long_name" type="NX_CHAR"/>
                     </field>

contributed_definitions/NXcomponent_em.nxdl.xml → contributed_definitions/NXcomponent.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="NXcomponent_em" extends="NXobject" 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="NXcomponent" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <doc>
          Base class for components of an instrument - real ones or a simulated ones.
     </doc>

contributed_definitions/NXcorrector_cs.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="NXcorrector_cs" extends="NXcomponent_em" 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="NXcorrector_cs" extends="NXcomponent" 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.
@@ -43,7 +43,7 @@
          and microscope. Many of their technical details is proprietary knowledge.
 
          If functionalities for correcting multiple aberrations are included in
-         one :ref:`NXcomponent_em` `like it is reported here &lt;https://www.ceos-gmbh.de/en/research/electrostat&gt;`_ 
+         one :ref:`NXcomponent` `like it is reported here &lt;https://www.ceos-gmbh.de/en/research/electrostat&gt;`_ 
          use multiple groups:
 
          * :ref:`NXcorrector_cs` for spherical aberration
@@ -109,12 +109,11 @@
             <doc>
                  Place for storing measured or estimated aberrations (for each image or final).
             </doc>
-            <group name="ceos" type="NXaberration_model_ceos"/>
-            <group name="nion" type="NXaberration_model_nion"/>
+            <group type="NXaberration_model"/>
         </group>
     </group>
     <!--technical design perspective-->
     <group type="NXlens_em"/>
-    <group type="NXaperture_em"/>
+    <group type="NXaperture"/>
     <!--(NXdeflector):-->
 </definition>

contributed_definitions/NXebeam_column.nxdl.xml

@@ -22,7 +22,7 @@
 # For further information, see http://www.nexusformat.org
 -->
 <!--
-NXebeam_column is an NXobject instead of an NXcomponent_em to make that
+NXebeam_column is an NXobject instead of an NXcomponent to make that
 part "an electron gun" reusable in other context-->
 <definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXebeam_column" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <doc>
@@ -98,10 +98,10 @@ relevant from maintenance point of view-->
         </group>
     </group>
     <group type="NXlens_em"/>
-    <group type="NXaperture_em"/>
+    <group type="NXaperture"/>
     <group type="NXmonochromator"/>
     <group type="NXcorrector_cs"/>
-    <group type="NXcomponent_em"/>
+    <group type="NXcomponent"/>
     <group type="NXsensor"/>
     <group type="NXactuator"/>
     <group type="NXbeam">