juglab/cryoCARE_pip

Failing to read tomograms written out by cryoCARE

alisterburt opened this issue · 2 comments

alisterburt commented

Came across an issue with cryoCARE generated tomograms with @AndrikovonKugelgen - they are also misinterpreted by IMOD

/Users/alisterburt/mambaforge/envs/py/lib/python3.10/site-packages/mrcfile/mrcinterpreter.py:342: RuntimeWarning: Expected 2649024000 bytes in data block but limit is 2648966400

This is probably a problem with mrcfile and the headers that cryoCARE is writing, checking in detail now and will report over there if I can reproduce outside of cryoCARE

alisterburt commented

@AndrikovonKugelgen found the issue - the extended header was not copied into the output file and the header contains a reference to the number of bytes found in the extended header. This led to an offset in where the data was expected to start within the file.

jychoi0616 commented

Sorry to ask here again when this issue was already closed.
I have a feeling that the still opened issue (#29) may be related to this.

So how would you get around this in the end? And could cryoCARE code be fixed about "possibility of writing invalid headers" please?