stack numbering not updated in relion_image_handler

[bforsbe]

Issue description
If relion_image_handler is run with .star-file input where images reference a .mrcs-file, the output .star file images have numbers which refer to the input stack, even if the output stack is smaller.

Example: in.star has 3 lines refering to 01@in.mrcs, 02@in.mrcs, and 03@in.mrcs.

in.mrcs has 3 images.

If one edits in.star to remove any reference to 01@mrcs, running

relion_image_handler --i in.star --o out

produces an output file in_out.star which refers to 03@in_out.mrcs, even though in_out.mrcs only has 2 images. Consequently, e.g.

relion_display --i in_out.star

will fail with

ERROR: 
readMRC: Image number 3 exceeds stack size 2 of image in_out.mrcs

The image references are also incorrect, such that if a user decides to remedy the issue by removing any reference to 03@in_out.mrcs in in_out.star then 02@in_out.mrcs references image information from position 2 in the original stack, which is now in 01@in_out.mrcs.

As a result, simple manual removal of any entry in the input invalidates the references of all subsequent images. This should throw an error such as that by relion_display above, but is possible to circumvent by users in a manner that corrupts data references gracefully.

Environment:

• OS: ubuntu 22.04 LTS
• RELION version 5.0 b75b38c

Job options:

• Type of job: relion_image_handler