added minutes from the microstructure workshop 2022/04/12, 1-4pm

microstructure/executive_summary_20220412_workshop.md

+# Executive summary:
+Workshop on Tuesday April 12 between 13:00 and 16:00
+Present: Yue, Carola, Sebastian, Laurenz, Sherjeel, Tommaso, Sandor, Andrea, Tamás, MarkusK
+
+# Individual task
+> For each we defined, all capital summary, urgency (1 high, 3 lower), coordinating responsible person.
+
+> What are our clear expectations why we invest time into describing materials (structure) at all with NeXus?
+  (Relevant for paper and scientific communication)
+  How should we extend NeXus to describe their (skeptical people) needs, self-evident that each experiment and material 
+  should be described to relevant detail, we are convinced about it in FAIRmat, pros: open to extension, long-standing processes,
+  community standardization, automated documentation, ontology, verification, visualization tools
+  WHY NEXUS?, 1, done!
+
+> Description of elements and molecules (starting from smiles and inchi, mapping of atom type and position, binding topology
+  to string representations), how to integrate area A, expected time frame, people, coarse-grained molecular dynamics, integration of area C?
+  component, ionic, radical, elements, and molecules
+  CHEMICAL SPECIES, CROSS-AREA EXCHANGE -> make base classes out of it, 1, area A activity, Tamás, Andrea, (Sebastian) 
+
+> Description of the sample geometry, including the geometry of individual "features" (objects) in the sample?
+  Description of multi-layers (which level of detail to begin with, qualitative, stacking of e.g. NXlayer base classes, or
+  detailed computational geometry description, i.e. a layer is a space in between two surfaces ...?
+  surface roughness long term perspective
+  SHAPE, GEOMETRY, MORPHOLOGY, 1, MarkusK
+
+> NXbase classes to model graph relations between elements inside NeXus or is it sufficient what comes shipped with NeXus?
+  NEXUS FILE CONTENT, 1, Sandor, kick-off meeting
+
+> Beyond crystallinity (amorphous, thermodynamic state (liquid, etc.) interfacing and/or using NeXus to describe crystal, new base classes to
+  describe beyond crystallinity?, information at which level, example amorphous (macroscale SAXS, atomic scale, amorphized layers STEM measurements)
+  use cases, different examples of collodial systems in Tamás backpack, these are statistically described
+  STATE OF MATTER, CONSTITUTION, 1
+> (e.g. lamellar structures, grain boundary energy), domain classification, dimensionality, all descriptors packed together
+  "representation of structural units, representing the organization of the units via a individual hierarchies", 
+  (i.e. volume1 grain1, grain2 > atom_set for grain 1, etc...?
+  DOMAIN DESCRIPTORS, 1, Támas
+
+> Position of objects/illumination/beam wrt to regions-of-interest, learn and build upon the mpes or NXmx examples how to use NXtransformations,
+  need and how to of more abstract (geometrical?) description how objects (beam) and e.g. specimen/detector are arranged in space.
+  strategies how to avoid manually-written docstrings which describe the context of an NXtransformation. "super-base line depends_on" ?
+  CONTEXT FOR AND USE OF NXTRANSFORMATIONS, 1, Laurenz, request to have a follow up meeting
+
+> How to represent the length and time scales of observations, synchronicity, asynchronous, time series data not fully-overlapping,
+  several records monitoring the same experiment not synced via a common clock.
+  NXsnapshot base class for enabling collections of snapshot data, whose childs again then branch further
+  HANDLING TIME SERIES DATA, 3, Pepe?
+ 
+> Integration of descriptors for spatio-temporal mechanisms/phenomena during the experiment 
+  which lead alter the state of the sample and its structure "damage" accounting, radiation damage work group, 
+  is damage monitoring not just a case of time series data?, for sample-based description (indeed connection to HANDLING TIME SERIES),
+  however, in the documentation domain specific extra information can be relevant and thus should be detected (dose history, overall dose
+  history, or point-by-point), very experiment-specific, (Yue Sun/Sandor, pressure change history, maybe adding it to NXmonitor?).
+  TIME-DEPENDENT DOMAIN DESCRIPTION OF E.G. DAMAGE, 3 / CHANGE HISTORY, Sandor, (Laurenz)
+
+PROCEDURAL ASPECTS / ACTION POINTS / HOW TO PROCEED
+> When to discuss the individual points in more detail and how to sync with implementation, half-year perspective
+  
+> Begin with implementing NXbase classes or method-specific application definitions?
+  i.e. how to implement our definitions, how important to build then, when to start building them?
+  IMPLEMENTATION, starting from base class
+
+> Who would like to/should like to contribute how much to the implementation?
+
+> How to discuss: weekly 1pm meeting task force meeting should not be polluted with detailed discussion
+  about the above-mentioned points, responsible persons should invite (have a Thursday morning e.g.?), use slack
+
+> Use areab-appdef gitlab for storage of results and codes
+
+FYI:
+> Next NIAC meeting, April 26th, new file formats, please come, tell how you can contribute
+