Fixing of references in the manual to classes that were removed durin…

…g the discussions with NIAC

manual/source/classes/contributed_definitions/apm-structure.rst

@@ -61,7 +61,7 @@ The following base classes are proposed to support modularizing the storage of p
     :ref:`NXpump`:
         A base class to describe details about pump(s) used as components of an instrument.
 
-    :ref:`NXstage_lab`:
+    :ref:`NXmanipulator`:
         A base class to describe the specimen fixture including the cryo-head.
         Nowadays, stages of microscopes represent small-scale laboratory platforms.
         Therefore, there is a need to define the characteristics of such stages in more detail,
@@ -86,8 +86,8 @@ data revealed that it is better to define atom-probe-agnostic reusable concepts
 
     :ref:`NXspatial_filter`:
         A base class proposing how a point cloud can be spatially filtered in a specific yet general manner.
-        This base class takes advantage of :ref:`NXcg_ellipsoid_set`, :ref:`NXcg_cylinder_set`,
-        and :ref:`NXcg_hexahedron_set` to cater for commonly used geometric primitives in atom probe.
+        This base class takes advantage of :ref:`NXcg_ellipsoid`, :ref:`NXcg_cylinder`, and :ref:`NXcg_hexahedron`
+        to cater for commonly used geometric primitives in atom probe.
         The primitives are used for defining the shape and extent of a region of interest (ROI).
 
     :ref:`NXsubsampling_filter`:

manual/source/classes/contributed_definitions/cgms-structure.rst

@@ -1,8 +1,8 @@
 .. _CgmsFeatures-Structure:
 
-=========================
+====================
 Geometry & Microstructure
-=========================
+====================
 
 .. index::
    CgmsBC
@@ -85,9 +85,6 @@ of material (area or volume) which can be useful not only for stencil-based meth
         is smoothed in a controlled manner.
 
     :ref:`NXsimilarity_grouping`:
-        An alternative for NXclustering.
-
-    :ref:`NXclustering`:
         A description for clustering of objects (such as atoms or features).
 
 TODO CHECK THAT MICROSTRUCTURE PART IS COVERED IN ICME WHEN MICROSTRUCTURE PROPOSAL SYNCED UP

manual/source/classes/contributed_definitions/em-structure.rst

@@ -1,19 +1,20 @@
 .. _Em-Structure:
 
-===================
+===============
 Electron microscopy
-===================
+===============
 
 .. index::
    IntroductionEm
    EmAppDef
    EmBC
    EmAnalysisClasses
+   EmExamples
 
 .. _IntroductionEm:
 
 Introduction
-############
+##########
 
 A set of data schemas is proposed to describe components of an electron microscope and its eventually available focused-ion beam functionalities.
 The data schemas were designed from the perspective of how electron microscopes are used by colleagues in the materials-science-branch of electron microscopy.
@@ -27,8 +28,8 @@ Electron microscopes are functionally very customizable tools: Examples include
 
 .. _EmAppDef:
 
-Application Definitions
-#######################
+Application Definition NXem
+######################
 
 We acknowledge that it can be difficult to agree on a single application definition which is generally enough applicable yet not unnecessarily complex and useful for applications across a variety of instruments, technology partners, and instrument use cases. In what follows, the proposal conceptualizes first the basic components of an electron microscope and the usual workflow of how an electron microscope is used for collecting data with detectors via probing radiation-specimen-matter interaction mechanisms.
 
@@ -37,25 +38,24 @@ In summary, scientists place a specimen/sample into the microscope, calibrate th
 A microscope session ends with the scientist removing the specimen from the instrument or parking it so that the next user can start a session. Occasionally, service technicians perform calibrations and maintenance which also can be described as a session on the microscope. We have provided base classes to describe these steps and events and an application definition for electron microscopy:
 
     :ref:`NXem`:
-        An application definition which explores the possibilities of electron microscopes.
+        An application definition which explores the possibilities of research on electron-beam matter interaction with (real or simulated) electron microscopes.
 
 
 .. _EmBC:
 
 Base Classes
-############
+###########
 
 The following base classes are proposed to support modularizing the storage of pieces of information related to electron microscopy research:
 
-    :ref:`NXem_msr`, :ref:`NXem_sim`:
-        Base classes to distinguish descriptions relevant for an experiment that is performed with a real microscope or a computer simulation of
-        electron matter interaction. Through these base classes NeXus supports to serialize details of a measurement and a related computer simulation
-        into one data artifact.
+    :ref:`NXcomponent`:
+        A base class to describe components aka devices to building an instrument like a microscope irrespective whether that is a real one or a simulated one.
 
-    :ref:`NXidentifier`, :ref:`NXserialized`:
-        Base classes to support storage of metadata whereby the source of information stored in a NeXus data artifact or class instances can be
-        documented especially when one does not store all relevant information using NeXus but one would like to refer to a specific other resource
-        where these pieces of information are stored.
+    :ref:`NXfabrication`:
+        A base class to bundle manufacturer/technology-partner-specific details about a component or device of an instrument.
+
+    :ref:`NXcircuit`:
+        A base class to describe a logical unit of at least one integrated circuit.
 
     :ref:`NXebeam_column`:
         A base class serving the possibility to group the components relevant for generating
@@ -65,29 +65,15 @@ The following base classes are proposed to support modularizing the storage of p
         A base class serving the possibility to group the components relevant for generating
         and shaping an ion beam of an instrument to offer focused-ion beam (milling) capabilities.
 
-    :ref:`NXcomponent`:
-        A base class to describe components aka devices to building an instrument like a microscope irrespective whether that is a real one or a simulated one.
-
     :ref:`NXlens_em`:
         A base class to detail an electro-magnetic lens. In practice, an electron microscope has many such lenses. It is possible to specify as many lenses as necessary to represent eventually each single lens of the microscope and thus describe how the lenses are affecting the electron beam. This can offer opportunities for developers of software tools which strive to model the instrument e.g. to create digital twins of the instrument. We understand there is still a way to go with this to arrive there though. Consequently, we suggest to focus first on which details should be collected for a lens as a component so that developers of application definitions can take immediate advantage of this work.
 
     :ref:`NXdeflector`:
         A base class to describe a component to deflect a beam of charged particles.
 
-    :ref:`NXchamber`:
-        A base class to describe the chamber as a part of the microscope or storage unit
-        for transferring specimens in between or within an instrument.
-
     :ref:`NXpump`:
         A base class to describe details about pump(s) as components of an electron microscope.
 
-    :ref:`NXfabrication`:
-        A base class to bundle manufacturer/technology-partner-specific details about a component or device of an instrument.
-
-    :ref:`NXcoordinate_system_set`, :ref:`NXcoordinate_system`, :ref:`NXtransformations`:
-        Base classes to describe different coordinate systems used and/or to be harmonized
-        or transformed into one another and respective transformations.
-
     :ref:`NXcorrector_cs`, :ref:`NXaberration`:
         Base classes to describe procedures and values for the calibration of aberrations based on
         conventions of different companies active in the field of aberration correction including a base class
@@ -101,27 +87,30 @@ The following base classes are proposed to support modularizing the storage of p
         is a component in a microscope which controls eventually multiple other components such as beam deflectors to achieve deflection
         and thus a controlled scanning of the beam over the sample/specimen surface.
 
-    :ref:`NXstage_lab`:
+    :ref:`NXmanipulator`:
         A base class to describe the stage/specimen holder which offers place for the documentation of the small-scale laboratory functionalities
         which modern stages of electron microscopes typically offer.
 
+    :ref:`NXinstrument_em`:
+        A base class to group the components that make up an electron microscope.
+
+Contextualizing and defining definitions of reference frames and transformations of these and rotations and orientations defined within such reference frames:
+
+    :ref:`NXcoordinate_system_set`, :ref:`NXcoordinate_system`, :ref:`NXtransformations`:
+        Base classes to describe different coordinate systems used and/or to be harmonized
+        or transformed into one another and respective transformations.
+
     :ref:`NXevent_data_em`:
         A base class representing a container to hold time-stamped and microscope-state-annotated
         data during a session at an electron microscope.
 
-    :ref:`NXevent_data_em_set`:
-        A base class to group all :ref:`NXevent_data_em` instances.
-
-    :ref:`NXimage_set`:
+    :ref:`NXimage`:
         Base classes for storing acquisition details for individual images or stacks of images.
 
-    :ref:`NXspectrum_set`:
+    :ref:`NXspectrum`:
         A base class and specializations comparable to :ref:`NXimage_set` but for storing spectra.
 
-    :ref:`NXinteraction_vol_em`:
-        A base class to describe details about e.g. the assumed or simulated volume of interaction of the electrons with the specimen.
-
-    :ref:`NXion`:
+    :ref:`NXion` (about to become replaced by :ref:`NXatom`):
         A base class to describe molecular ions with an adjustable number of atoms/isotopes building each ion. Right now the maximum number of atoms supported building a molecular ion is 32. Suggestions made in reference `DOI: 10.1017/S1431927621012241 <https://doi.org/10.1017/S1431927621012241>`_ are used to map isotope to hash values with which all possible isotopes can be described.
 
     :ref:`NXoptical_system_em`:
@@ -132,12 +121,12 @@ The following base classes are proposed to support modularizing the storage of p
     :ref:`NXpeak`:
         A base class to describe peaks mathematically.
 
-    :ref:`NXcircuit`:
-        A base class to describe a logical unit of at least one integrated circuit.
-
 
 .. _EmAnalysisClasses:
 
+Storage of event-base data and results of post-processing
+###############################################
+
 We provide specific base classes which granularize frequently collected or analyzed quantities in specific application fields of electron microscopy to deal
 with the situation that there are cases were logical connections between generated data artifacts mainly exist for the fact that the data artifacts were
 collected during a workflow of electron microscopy research (e.g. taking measurements and then performing method-specific analyses generating new data and conclusions).
@@ -154,11 +143,20 @@ storage (i.e. serialization) using NeXus.
 
 More consolidation through the use of NXsubentry classes should be considered in the future. For now we use an approach whereby base classes are combined to reuse vocabulary and a hierarchical organization of pieces of information with specific constraints which are relevant only for specific usage of such data by specific tools used by an eventually smaller circle of users.
 
-    :ref:`NXem_method`, :ref:`NXem_ebsd`, :ref:`NXem_eds`, :ref:`NXem_eels`, :ref:`NXem_img`, :ref:`NXem_correlation`:
+    :ref:`NXem_ebsd`, :ref:`NXem_eds`, :ref:`NXem_eels`, :ref:`NXem_img`:
         Base classes with method-specific details especially when it comes to reporting post-processed data within electron microscopy.
 
-    :ref:`NXcrystal_structure`:
-        A base class to store crystalline phase/structure used for a simulation of diffraction pattern and comparison of these pattern against patterns to support indexing.
+    :ref:`NXphase`, :ref:`NXunit_cell`, :ref:`NXatom`:
+        Base classes to store crystal structure specific details e.g. to support simulation of and post-processing of diffraction patterns.
 
-    :ref:`NXroi`:
+    :ref:`NXcg_roi`:
         A base class to granularize information collected and relevant for the characterization of a region-of-interest.
+
+
+.. _EMExamples:
+
+Domain-specific data analysis
+########################
+
+    :ref:`NXem_calorimetry`:
+        Example together with the IKZ in Berlin and FAIRmat, in-situ (transmission) electron microscopy with a heating stage.