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Check name Status Explanation Title check The title clearly describes the main change: improved fibsemOS microscope state handling. Description check The description directly explains microscope-state recording, metadata preservation, vendor differences, and state restoration. Linked Issues check Check skipped because no linked issues were found for this pull request. Out of Scope Changes check Check skipped because no linked issues were found for this pull request.
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Only relatively minor comments.
BTW, I don't know how useful is migrate_system_state(). That would be in case you start a project with an old version of Odemis, update Odemis, and continue the milling? Or are there other use cases? I am mostly asking because if that the only case, it seems pretty unlikely and if we dropped support for this, it would simplify the code.
@pieleric Indeed, reusing an old reference after remounting the sample would require a new acquisition anyway. I'll remove automatic migration and keep older projects readable. If milling is requested for a feature without recorded state, let's show a message asking the user to acquire a new reference through "Save Position". |
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Actionable comments posted: 1
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Inline comments:
Review comments at @src/odemis/driver/test/tescan_test.py:
- Around line 1026-1028: Update the expected-preset logic in test_load_presets
to apply the driver’s membership check: use the reported preset only when it
appears in self.scanner.beamPreset.choices; otherwise expect
tescan.DEFAULT_ION_PRESET. Assert beamPreset.value against that expected value.
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📒 Files selected for processing: 14
src/odemis/acq/feature.pysrc/odemis/acq/milling/fibsemos.pysrc/odemis/acq/milling/system_state.pysrc/odemis/acq/milling/test/fibsemos_millmng_test.pysrc/odemis/acq/milling/test/fibsemos_test.pysrc/odemis/acq/test/feature_test.pysrc/odemis/driver/tescan.pysrc/odemis/driver/test/tescan_test.pysrc/odemis/gui/cont/cryo_project.pysrc/odemis/gui/cont/features.pysrc/odemis/gui/cont/milling.pysrc/odemis/gui/cont/test/cryo_project_test.pysrc/odemis/gui/test/comp_milling_test.pysrc/odemis/gui/test/cont_features_test.py
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Record microscope settings by component role and pass them to fibsemOS without modifying the original image metadata. Support Thermo and Tescan differences, preserve reference acquisition settings, and restore pre-milling imaging conditions afterward.
This PR builds on #3616 and includes its API compatibility commit 2d23ecee64bc9c2a5ba94eade48f4f6bfa1be92e. Please review the microscope-state and metadata changes here. #3616 should merge first, then I'll update this branch so the shared commit no longer appears in the diff.