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APM refactoring / APMv2#204

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mkuehbach wants to merge 15 commits intoem_refactoringFAIRmat-NFDI/pynxtools:em_refactoringfrom apm_refactoringFAIRmat-NFDI/pynxtools:apm_refactoringCopy head branch name to clipboard

+1,404-560

Commits

Commits on Dec 31, 2023

• Starting the refactoring of the apm reader, added support for ATO, ENV, FAU/Erlangen's pyccapt calibration and ranging, and FAU/Erlangen's Matlab Atom probe Toolbox fig ranging definitions, current…

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Commits on Jan 2, 2024

• First round of fixes detected and solved when working through the large 176 dataset example case

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• Fixed steps i), ii), all 176 examples processed successfully, PSE coverage 58 elements, 5.9 billions ions in total, 77 projects from research of all major groups worldwide, next steps: iii) move to…

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• Deactivate synthesizer because that needs refactoring and because we have now plenty of real world examples to show and run these tools with

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Commits on Jan 8, 2024

• Switched nxdefs from working fairmat 615ff37cbafd2ca017fb61c119c0f5c0cf052a34 to not tested developmental apm_refactoring

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• Reactivated NOMAD OASIS deployment specific parsing

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• Reactivated default plots for m_z, xyz and path to default plot

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• Refactoring the exemplar NOMAD-OASIS-custom-ELN-schema-to-NXapm mapping, incomplete

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Commits on Jan 9, 2024

• Added support for adding references to proprietary/Cameca/non-Cameca workflow-related files in the NeXus file so that NOMAD is available could use them further, also added feedback of best practice…

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Commits on Jan 10, 2024

• Added support for being able to incorporate D. R. Diercks et al. APT mass spectrum database which is currently hosted on an AirTable (but no longer maintained), added ELN and I/O logic parsing to p…

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• User parsing also fixed, therewith i) completed

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• Added citations for 176case study and fixed NX_CLASS decoration bug for charge_state_model

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• pycodestyle, pylint, mypy, ready for runthroughs and nomad integration

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• Synced nxdefs with FAIRmat-NFDI/nexus_definitions/apm_refactoring branch 5c7d197

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Commits on Jan 23, 2024

• Hooked in the correct NeXus definitions branch to use for the em_refactoring feature branch

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