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EM refactoring / EMv2#136

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sanbrock merged 69 commits intofairmatFAIRmat-NFDI/nexus_definitions:fairmatfrom em_refactoringFAIRmat-NFDI/nexus_definitions:em_refactoringCopy head branch name to clipboardMar 1, 2024

+18,502-35,911

Commits

Commits on Dec 13, 2023

• Fixed missing references to EM/CGMS/ICME-related base classes in the documentation, adding first round of changes relevant for the implementation of the refactoring of the em-related readers in pyn…

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• Refactoring storage of images and spectra

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• Minor edit

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Commits on Jan 3, 2024

• Refactoring apm has three aims: i) extent NXapm appdef to take advantage of more general base classes NXserialized, NXidentifier, and CG base classes, also incorporate feedback from discussions wit…

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• Testing the use of NXapm_paraprobe_tool_config/results base classes on a minimum example, next steps i) apply to paraprobe_ranger, ii) refactor NXapm appdef, iii) update pynxtools, iv) discuss

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• Applied to i)

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Commits on Jan 4, 2024

• Working on ii) mirrored concept used for NXem with NXapm_msr and NXapm_sim to enable a description of simulation and measurement the work on NXapm is not yet finished, NXapm_new is the constraint s…

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Commits on Jan 5, 2024

• Implemented design of event_data_apm, correlated signals with keyword logged_against, and base classes for processing of results

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• Editing NXapm_ranging remains and a final check of the NXapm_new, then NXapm can be removed

  

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• Refactored NXapm_ranging, renamed NXapm_new, a through and complete check remains, NXsimilarity_grouping to edit

  

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Commits on Jan 6, 2024

• Reviewing, fixing typos, a minor glitches

  

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• Further reviewing and corrections

  

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Commits on Jan 7, 2024

• NXapm reviewing and typos

  

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Commits on Jan 8, 2024

• Fixed issues detected during make local, manual builds successfully, open issue: appdefs require redefinition of properties from inherited base classes violates single source principle

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Commits on Jan 10, 2024

• Added changes relevant to use the refactored NXapm parser of pynxtools 0572bfa9df6f513325024185ed1f1c1901d0758c

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Commits on Jan 17, 2024

• Fixes and additions revealed from implementing parser functionalities in pynxtools

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• Placed version as child of definition

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• Added version as a child of definition, spotted what could be a bug though, if the NXDL contains only field defintion with attribute version, no docstrings for both and an enumeration make local su…

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• Fixes and modifications revealed during implementation of imgs, apex readers

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• Added suggestions from @lukaspie on NXpeak

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Commits on Jan 19, 2024

• Fixes introduced for Velox EMD file parser

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Commits on Jan 23, 2024

• Fixed definitions and version

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• Fixed definitions and version

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• Removed unfortunated row vector style matrix isotope_vector and nuclid list and made clarified that isotope_vector means indeed nuclid hashes and not isotopes (i.e. nuclids of same element)

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• Updated apm-specific documentation for new base classes and refactoring changes, plus add consistency changes for deprecated isotope_vector

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Commits on Jan 25, 2024

• Fixes and modifications specifically for paraprobe-toolbox tools: parmsetup-transcoder, parmsetup-ranger, parmsetup-selector, transcoder, ranger, reporter-transcoder, reporter-ranger

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• Added appdef for selector_results, reorganized where to place common configuration information to take advantage of base class inheritance in more places, fixed incorrect handling of definition and…

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Commits on Jan 26, 2024

• Reorganized transcoder, ranger, selector

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• Refactored surfacer to use APMv2

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Commits on Jan 27, 2024

• Refactored appdefs for distancer and tessellator to use APMv2

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• Fixes added in the process of refactoring parmsetup-distancer and parmsetup-tessellator

  

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Commits on Jan 28, 2024

• Fixes to complete distancer and tessellator APMv2 refactoring

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• Refactored appdefs for paraprobe-spatstat, specified symbol to use for NXcoordinate_system_set and NXuser

  

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Commits on Feb 9, 2024

• Minor editing of spatstat

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Commits on Feb 10, 2024

• Refactored paraprobe-clusterer definitions to use APM v2

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• Added missing profiling and program for results appdefs of tools where missing

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Commits on Feb 13, 2024

• Renaming the last two missing appdefs for tools nanochem and intersector in preparation for their refactoring for APM v2

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Commits on Feb 16, 2024

• Refactored config files for nanochem and intersector to use APMv2

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• Updated apm-specific landing page

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• Minor edits and fixes apm-structure

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• Fixing a copy-paste error

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• Fixed inconsistence

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• Refactored NXapm_paraprobe_nanochem_results and delocalization

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• Refactored NXapm_paraprobe_intersector_results, fixed formatting issues with math envs, removed obsolete FAIRmat Area B numbering schemes

  

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Commits on Feb 18, 2024

• Proposal to move common data nicely out, fixes on nanochem config, next step test properly

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Commits on Feb 26, 2024

• Moved profiling and other common information out of task specific groups as this was cumbersome to use. This essentially concludes the refactoring for appdefs for the paraprobe-toolbox, the remaini…

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• Resolved logical problem that status was not always present

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• Moving of analysis_identifier and config

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Commits on Feb 27, 2024

• First round of fixes for appdefs of nanochem tool for delocalization mode

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• Fixes intersector config

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Commits on Feb 28, 2024

• Changes due to comments from colleagues

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• Final changes prior merge

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• Merge pull request #151 from FAIRmat-NFDI/composing-v0.5

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• Round 1, implementation feedback from colleagues

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• Recompiled NXDLs from YAML using nyaml==0.0.9

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• Recompiled NXDLs from yaml using nyaml==0.0.9

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• Manually merged em into apm

  

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• Deactivated use of NXactuator for now because em_refactoring branch does not yet know this exists

  

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• Constrained name of ions in NXapm

  

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Commits on Feb 29, 2024

• Merge pull request #140 from FAIRmat-NFDI/apm_refactoring

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• Manual merge of fairmat into em_refactoring

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• Recompiled NXdata and NXsensor with nyaml==0.0.9 as they showed issues in the catchen test

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• Clarifying situation with NXem_base

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• Dropped NXem_base to not immediately be a competitor to NXem, all suggestions and reviews and feedback from community should target NXem first before thinking about offsprings

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• Cleanly removed NXem_base class

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• Merge pull request #187 from FAIRmat-NFDI/em_refactoring_em_base_removal

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Commits on Mar 1, 2024

• Changes suggested by @domna

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• Reverted unintentional change NXsensor.nxdl.xml

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• Revert that was unintentionally changed NXdata.nxdl.xml

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