Failed to load mrc about blik HOT 9 CLOSED

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ccpem/mrcfile#47

from blik.

Hi! This seems to be unrelated to #130. The issue is deeper (with mrcfile):

ValueError: Unrecognised machine stamp: 0x44 0x20 0x20 0x20

Something seems to be off with the header of your mrc file, which is not recognized by mrcfile. Can you try to manually open the file by doing this in ipython?:

with mrcfile.open('/path/to/file.mrc', 'r', header_only=True) as mrc:
    print(mrc.header)

If this fails again, try:

with mrcfile.open('/path/to/file.mrc', 'r', header_only=True, permissive=True) as mrc:
    print(mrc.header)

I didn't add any machinery to allow permissive=True for now; if that solves it, maybe I should consider setting it to True by default.

from blik.

It fails without permissive=True, but loads with it:

/home/joran.deschamps/miniconda3/envs/blik/lib/python3.9/site-packages/mrcfile/mrcinterpreter.py:219: 
RuntimeWarning: Unrecognised machine stamp: 0x44 0x20 0x20 0x20
  warnings.warn(str(err), RuntimeWarning)
(1024, 1024, 512, 2, 0, 0, 0, 1024, 1024, 512, (1024., 1024., 512.), (90., 90., 90.), 1, 2, 3, -995.9688, 480.2282, 
-2.2351742e-07, 0, 0, b'\x00\x00\x00\x00\x00\x00\x00\x00', b'', 0, b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00', (0., 0., 0.), b'MAP ', [68, 32, 32, 32], -1., 0, 
[b'', b'', b'', b'', b'', b'', b'', b'', b'', b''])

from blik.

Yeah, this happens if the header is a bit messed up for some reason. Corrupted file, or maybe it was written by a software that wasn't very careful about writing correct information in the header. If you want a quick fix, you can edit the code in naaf for the mrc reader function and add the permissive=True argument to the mrcfile.mmap call. I will try to release a half update to naaf and blik to fix both this issue and the other you raised.

from blik.

Thanks a lot! I will let you be the judge of whether to keep this issue open!

FYI the file was saved using imod, and there is no issue opening it there.

from blik.

You might want to bring this issue up to the mrcfile repo then, since this can only be solved there.

In my experience, imod is super resilient to broken headers, but because of this it might be less careful in writing correct ones :P

from blik.

@jdeschamps I just released v0.3.2 as an intermediate version before napari 0.4.17. Feel free to try it out and let me know if things work :)

from blik.

@jdeschamps update: v0.3.3 is actually fixed, sorry :P

from blik.

Awesome thanks, I'll let you know if anything arises!

from blik.