Fix #82 #89
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Fix #82 #89
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* Fix #80, which is a temporary fix until the hyperspy developers fix #71 on their side * Tecnai and fei legacy issue84 (#91) * Configuration table and logic to identify Tecnai, next steps: i) test, ii) implement for Helios NanoLab, merge * Testing and fixing FEI Tiff Tecnai example * Fixed logic bug in mapping_functor that caused some quantities to become skipped * Cleaner handling of FEI concepts that have no values * Reading legacy FEI Helios NanoLab metadata correctly, mapping remains * Completed reading of legacy FEI XML metadata with exemplar mapping for FEI Helios NanoLab instrument. It turned out though that already the first example TIFF file from a real world study on such instrument revealed that TFS/FEI may store metadata in at least two places, on the one hand in a structure text under TIFF tag 30482 - which the image_tiff_tfs parser picks up on already - on the other hand as text XML within a Metadata XML-formatted block which this the image_tiff_fei_legacy parser picks up on. For this reason the example populates unexpectedly currently not only in the dynamic but also fields in the static detector group. In summary, for at least these Helios NanoLab examples the image_tiff_tfs parser is sufficient and the implementation of an additional FEI_HELIOS_MODE in the image_tiff_fei_legacy parser is not required. Consequently, the FEI_HELIOS_MODE is switched off with a log information to the user instructing to check if content has not already been picked up by the image_tiff_tfs parser. The commit here is therefore made only to keep working code snippets to eventually cover cases from the likely transition period between TFS acquisition of FEI where customers might have files that keep the metadata in only one place. Another argument for keeping the FEI_HELIOS configuration for now is that it covers a few more metadata than the current image_tiff_tfs parser. * Deactivated FEI_LEGACY_HELIOS mode and updated docs * Added citation.cff file to prepare task Zenodo/DOI/publishing of the … (#93) * Added citation.cff file to prepare task Zenodo/DOI/publishing of the pynxtools-em plugin related to issue #87 * Temporarily removed the yet unknown DOI for the software artifact --------- Co-authored-by: mkuehbach <[email protected]> --------- Co-authored-by: mkuehbach <[email protected]> --------- Co-authored-by: mkuehbach <[email protected]>
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