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rosalindfranklininstitute / parakeet

Phantom generator
GNU General Public License v3.0
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Problem with "extended_header" in parakeet.export #49

Closed majtner closed 1 year ago

majtner commented 1 year ago

Hi James,

I am using parakeet v.0.4.3. and I have issues converting .h5 file to .mrc file using parakeet.export. I am getting an error in "io.py", line 606, in init self.handle = mrcfile.new_mmap( TypeError: new_mmap() got an unexpected keyword argument 'extended_header'

When I tried to run the same script (from parakeet.sample.new until parakeet.export) using parakeet v.0.3.0., it worked fine for me. But for this new version, even when I tried converting with eman2, it fails with a RuntimeError. Do you have any idea, how can I export it to .mrc?

Thanks in advance! Tomas

jmp1985 commented 1 year ago

Hi @majtner

There was an update to the ccpem mrcfile library that allows more efficient creation of large files by passing the extended_header keyword to the new_mmap function. I believe that this functionality was added in v1.4.0 of the mrcfile library.

To fix this issue try updating the mrcfile package. You can probably do this by typing "pip install -U mrcfile".

Let me know if that works!

Best wishes James

majtner commented 1 year ago

Thank you @jmp1985 you are right, there was by mistake a dependency to an older version of mrcfile library, now it works fine! Thanks again and sorry for this basic question.

Cheers, Tomas