fix links in manual

Author: lukaspie

dev_tools/docs/nxdl_index.py

@@ -80,6 +80,7 @@ def nxdl_indices() -> Dict[str, dict]:
         if file.endswith("contributed_definitions/index.rst"):
             rst_lines.append(f"{indentation}apm-structure\n")
             rst_lines.append(f"{indentation}optical-spectroscopy-structure\n")
+            rst_lines.append(f"{indentation}spm-structure\n")
             rst_lines.append(f"{indentation}transport-structure\n")
         for cname in sorted(classes):
             rst_lines.append(f"{indentation}{cname}\n")

manual/source/apm-structure.rst

@@ -6,4 +6,5 @@ Atom-probe tomography
 
 Atom probe tomography and related field-ion microscopy, aka atom probe microscopy (techniques) cover metrology methods with an origin in the materials science and condensed-matter physics communities. With its maturation and commercialization in the last two decades atom probe is increasingly being used for characterization of bio materials and fundamental science of field evaporation physics.
 
-A status report of the ongoing work on data schemas for atom probe using NeXus is available here: :ref:`Apm-Structure`.
+The list of standardized data schemas for atom probe in NeXus is available here: :ref:`Appdef-Apm-Structure`.
+A status report of additional ongoing work on NeXus data schemas for atom probe is available here: :ref:`Contributed-Apm-Structure`.

manual/source/cgms-structure.rst

@@ -8,6 +8,6 @@ Computational geometry is a frequently used tool for describing the shape and ge
 NeXus has a long history of base classes which serve specifically the former tasks. Upon closer inspection during the first year of the FAIRmat project we found though that the collection of
 base classes could profit from an extension to make working with computational geometry data in NeXus simpler and more fine-grained.
 
-A status report of this ongoing work is available here: :ref:`CgmsFeatures-Structure`.
+A status report of this ongoing work is available here: :ref:`BC-Cgms-Structure`.
 
-A status report of how these definitions can be of value for the field of Integrated Materials Engineering (ICME) is available here: :ref:`Icme-Structure`.
+A status report of how these definitions can be of value for the field of Integrated Materials Engineering (ICME) is available here: :ref:`BC-Cgms-Introduction-IcmeMsModels`.

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

@@ -46,15 +46,15 @@ Base Classes
     :ref:`NXcircuit`:
        Base class to describe electronic circuits.
 
-    :ref:`NXinstrument_apm`:
+    :ref:`NXapm_instrument`:
         A base class which defines all modular parts that make up an instrument (real or simulated) for studying
         ion extraction as performed in atom probe and related field-ion microscopy. This base class is used in NXapm in two places:
         One that is placed inside an ENTRY.measurement.instrument
         group. This group holds all those (meta)data which do not change during a session, i.e. instrument name, typically identifier of 
         hardware components or version of control software. Another one that is placed inside an ENTRY.measurements.eventID group.
         This group holds all those (meta)data data change when collecting data during a session.
 
-    :ref:`NXevent_data_apm`:
+    :ref:`NXapm_event_data`:
         A base class representing a container to hold time-stamped and instrument-specific-state-
         annotated data during a session at an electron microscope.
 

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

@@ -162,27 +162,11 @@ of material (area or volume) which can be useful not only for stencil-based meth
     :ref:`NXsimilarity_grouping`:
         An alternative for NXclustering.
 
-    :ref:`NXclustering`:
-        A description for clustering of objects (such as atoms or features).
-
-    :ref:`NXorientation_set`:
-        A set of parameters to describe the relative orientation of members of a set of features/objects.
-
-    :ref:`NXslip_system_set`:
-        Metadata for a set of slip systems in a given crystal structure.
-
-    :ref:`NXms_feature_set`:
-        Generic base class to describe any nested set of features
+    :ref:`NXmicrostructure_feature`:
+        Generic base class to describe any nested features
         of a microstructure at the continuum-, micron-, nano-scale, or
         to represent a topology of molecules and atoms.
 
-    :ref:`NXms_snapshot`:
-        A container to describe the state of microstructural features
-        at a given point in time.
-
-    :ref:`NXms_snapshot_set`:
-        The corresponding class to hold a set of :ref:`NXms_snapshot` objects.
-
     :ref:`NXchemical_composition`:
         (Chemical) composition of a sample or a set of things.
 
@@ -205,21 +189,6 @@ parameters and to summarize its performance statistics:
     :ref:`NXcs_computer`:
         Metadata of a computer.
 
-    :ref:`NXcs_cpu`:
-        Metadata of a central processing unit.
-
-    :ref:`NXcs_gpu`:
-        Metadata of a graphical processing unit / accelerator.
-
-    :ref:`NXcs_mm_sys`:
-        Metadata of the (main) memory (sub-)system.
-
-    :ref:`NXcs_io_sys`:
-        Metadata of the input/output system.
-
-    :ref:`NXcs_io_obj`:
-        Metadata of a component storing data of an :ref:`NXcs_io_sys` instance.
-
     :ref:`NXprogram`:
         A named and version of a program of library/component.
 
@@ -241,18 +210,18 @@ The following application definitions are proposed to support discussion on
 how materials engineering-specific data models connect to or can be mapped on
 concepts which are equally modellable with NeXus:
 
-    :ref:`NXms`:
+    :ref:`NXmicrostructure`:
         An application definition for arbitrary spatiotemporally resolved simulations.
 
-    :ref:`NXms_feature_set`:
+    :ref:`NXmicrostructure_feature`:
         Set of topological/spatial features in materials build from other features.       
 
-    :ref:`NXms_score_config`:
-        A specific example of how :ref:`NXapm_paraprobe_config_ranger` can be
+    :ref:`NXmicrostructure_score_config`:
+        A specific example of how :ref:`NXapm_paraprobe_ranger_config` can be
         specialized for documenting the configuration of a computer simulation
         with the static recrystallization cellular automata model SCORE.
 
-    :ref:`NXms_score_results`:
-        A specific example of how :ref:`NXms` can be specialized for documenting
+    :ref:`NXmicrostructure_score_results`:
+        A specific example of how :ref:`NXmicrostructure` can be specialized for documenting
         results of computer simulations with the static recrystallization
         cellular automata model SCORE.

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

@@ -33,7 +33,7 @@ applicable for the field of electron microscopy (:ref:`NXactuator`, :ref:`NXaper
 :ref:`NXsample`, :ref:`NXsensor`, :ref:`NXsource`, and :ref:`NXuser`).
 
 Many design decisions of the application definitions :ref:`NXem` and :ref:`NXapm` are aligned. Examples are the use of base 
-classes for instrument-specific events :ref:`NXevent_data_em`, the grouping of measurements :ref:`NXem_measurement` and simulations
+classes for instrument-specific events :ref:`NXem_event_data`, the grouping of measurements :ref:`NXem_measurement` and simulations
 :ref:`NXem_simulation`, and the encapsulating of :ref:`NXparameters` and :ref:`NXdata` in :ref:`NXprocess` instances to describe
 workflows of processing. The base classes :ref:`NXatom`, :ref:`NXunit_cell`, and :ref:`NXphase` were introduced to document sets
 of atoms, the spatial arrangement of atoms, and offer concepts for documenting when regions-of-interest in a material represent
@@ -56,7 +56,7 @@ In addition to these considerations, there exists a set of base classes to defin
     :ref:`NXimage`:
         A base class to store individual images or stacks of images.
 
-    :ref:`NXinstrument_em`:
+    :ref:`NXem_instrument`:
         A base class to document all components that make up an instrument (real or simulated) when using it for studying
         electron matter interaction. This base class is used in NXem in two places:
         Firstly, inside an ENTRY/measurement/instrument group. This group holds all those (meta)data which do not change

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

@@ -109,7 +109,7 @@ Data and metadata between the tools are exchanged with NeXus/HDF5 files. This me
 inside HDF5 binary containers are named, formatted, and hierarchically structured according
 to application definitions.
 
-For example the application definition :ref:`NXapm_paraprobe_config_surfacer`: specifies
+For example the application definition :ref:`NXapm_paraprobe_surfacer_config`: specifies
 how a configuration file for the paraprobe-surfacer tool should be formatted
 and which parameters it contains including optionality and cardinality constraints.
 
@@ -148,47 +148,47 @@ NXapm_paraprobe application definitions are in fact pairs of application definit
 One for the configuration (input) side and one for the results (output) side. For each
 tool one such pair is proposed:
 
-    :ref:`NXapm_paraprobe_config_transcoder`, :ref:`NXapm_paraprobe_results_transcoder`:
+    :ref:`NXapm_paraprobe_transcoder_config`, :ref:`NXapm_paraprobe_transcoder_results`:
         Configuration and the results respectively of the paraprobe-transcoder tool.
         Load POS, ePOS, APSuite APT, RRNG, RNG, and NeXus NXapm files.
         Store reconstructed positions, ions, and charge states.
 
-    :ref:`NXapm_paraprobe_config_ranger`, :ref:`NXapm_paraprobe_results_ranger`:
+    :ref:`NXapm_paraprobe_ranger_config`, :ref:`NXapm_paraprobe_ranger_results`:
         Configuration and results respectively of the paraprobe-ranger tool.
         Apply ranging definitions and explore possible molecular ions.
         Store applied ranging definitions and combinatorial analyses of possible iontypes.
 
-    :ref:`NXapm_paraprobe_config_selector`, :ref:`NXapm_paraprobe_results_selector`:
+    :ref:`NXapm_paraprobe_selector_config`, :ref:`NXapm_paraprobe_selector_results`:
         Configuration and results respectively of the paraprobe-selector tool.
         Defining complex spatial regions-of-interest to filter reconstructed datasets.
         Store which points are inside or on the boundary of complex spatial regions-of-interest.
 
-    :ref:`NXapm_paraprobe_config_surfacer`, :ref:`NXapm_paraprobe_results_surfacer`:
+    :ref:`NXapm_paraprobe_surfacer_config`, :ref:`NXapm_paraprobe_surfacer_results`:
         Configuration and results respectively of the paraprobe-surfacer tool.
         Create a model for the edge of a point cloud via convex hulls, alpha shapes, or alpha-wrappings.
         Store triangulated surface meshes of models for the edge of a dataset.
 
-    :ref:`NXapm_paraprobe_config_distancer`, :ref:`NXapm_paraprobe_results_distancer`:
+    :ref:`NXapm_paraprobe_distancer_config`, :ref:`NXapm_paraprobe_distancer_results`:
         Configuration and results respectively of the paraprobe-distancer tool.
         Compute and store analytical distances between ions to a set of triangles.
 
-    :ref:`NXapm_paraprobe_config_tessellator`, :ref:`NXapm_paraprobe_results_tessellator`:
+    :ref:`NXapm_paraprobe_tessellator_config`, :ref:`NXapm_paraprobe_tessellator_results`:
         Configuration and results respectively of the paraprobe-tessellator tool.
         Compute and store Voronoi cells and properties of these for all ions in a dataset.
 
-    :ref:`NXapm_paraprobe_config_spatstat`, :ref:`NXapm_paraprobe_results_spatstat`:
+    :ref:`NXapm_paraprobe_spatstat_config`, :ref:`NXapm_paraprobe_spatstat_results`:
         Configuration and results respectively of the paraprobe-spatstat tool.
         Compute spatial statistics on the entire or selected regions of the reconstructed dataset.
 
-    :ref:`NXapm_paraprobe_config_clusterer`, :ref:`NXapm_paraprobe_results_clusterer`:
+    :ref:`NXapm_paraprobe_clusterer_config`, :ref:`NXapm_paraprobe_clusterer_results`:
         Configuration and results resepctively of the paraprobe-clusterer tool.
         Compute cluster analyses with established machine learning algorithms using CPU or GPUs.
 
-    :ref:`NXapm_paraprobe_config_nanochem`, :ref:`NXapm_paraprobe_results_nanochem`:
+    :ref:`NXapm_paraprobe_nanochem_config`, :ref:`NXapm_paraprobe_nanochem_results`:
         Configuration and results resepctively of the paraprobe-nanochem tool.
         Compute delocalization, iso-surfaces, analyze 3D objects, composition profiles, and mesh interfaces.
 
-    :ref:`NXapm_paraprobe_config_intersector`, :ref:`NXapm_paraprobe_results_intersector`:
+    :ref:`NXapm_paraprobe_intersector_config`, :ref:`NXapm_paraprobe_intersector_results`:
         Configuration and results resepctively of the paraprobe-intersector tool.
         Analyze volumetric intersections and proximity of 3D objects discretized as triangulated surface meshes
         in continuum space to study the effect the parameterization of surface extraction algorithms on the resulting shape,