Failing to read tomograms written out by cryoCARE

juglab / cryoCARE_pip

PIP package of cryoCARE

BSD 3-Clause "New" or "Revised" License

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Failing to read tomograms written out by cryoCARE #43

Closed alisterburt closed 1 year ago

alisterburt commented 1 year ago

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 1 year ago

@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 8 months ago

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?