ctffind_runner fails with tiff images

[gruchalla]

CTFFIND can process tiff images. Relion launches CTFFIND and executes correctly, but the ctffind_runner fails with warning messages:

WARNING: skipping, since cannot get CTF values for images/4_bl.000.tif

The issue is cttfind_runner is hard-coded to strip ".mrc" off the image filenames when looking for ctf files, so it cannot find them. For the above example, instead of looking for the 4_bl.000.ctf that ctffind created, it is looking for 4_bl.000.tif.ctf which doesn’t exist. See ctffind_runner.cpp line 252:
FileName fn_microot = fn_mic_ctf_given_all[imic].without(".mrc");
and line 431:
FileName fn_microot = fn_micrographs_ctf_all[imic].without(".mrc")

replacing these lines with
FileName fn_microot = fn_mic_ctf_given_all[imic].withoutExtension();
and
FileName fn_microot = fn_micrographs_ctf_all[imic].withoutExtension();

respectively, appears to resolve the problem with tiff images.

[biochem-fan]

This makes sense. I applied your suggestion in commit 319cd1b. Thank you very much for feedback.