Add the option to provide a reference file for txrm processing - #271
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stephen-riggs
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Jun 16, 2026
If a txrm does not have an internal reference, instead of dismissing it search for a reference file in xrm format. Takes the most recent xrm which is not a mosaic image. Still skips processing for txrms with less than 20 frames as these will be reference stacks. Also changes the tilt series tags to remove angle naming, and skips transfer of "New folder" Pairs with DiamondLightSource/cryoem-services#271
tieneupin
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Looks good. Nice work!
tieneupin
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Jun 16, 2026
| tifftomo = Path(stack_file).with_suffix(".tiff") | ||
| convert_and_save(txrm_file, str(tifftomo), custom_reference=None) | ||
| convert_and_save( | ||
| txrm_file, str(tifftomo), custom_reference=xrm_reference or None |
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This is fine, but did you write it this way to also guard against empty strings? If not, passing xrm_reference directly should already be fine, since it's meant to be a string or None already.
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Allow an xrm file to be provided as an external reference for txrm processing.
Also converts from using Optional to |
Pairs with DiamondLightSource/python-murfey#826