mjo22 / cryojax

Cryo electron microscopy image simulation and analysis built on JAX.
https://mjo22.github.io/cryojax/
GNU Lesser General Public License v2.1
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Add envelope function to RelionDataset #252

Closed DSilva27 closed 2 weeks ago

mjo22 commented 1 month ago

See the cryojax.image.operators.FourierGaussian function. This can be added as an optional field to the RelionParticleStack and loaded in if the b factor is in the STAR file, and left as None otherwise. For example the particle stack can be updated to be:

from typing import Optional
from cryojax.image.operators import FourierGaussian

class RelionParticleStack(AbstractParticleStack):

    # ... other fields
    envelope: Optional[FourierGaussian]

    def __init__(..., envelope: Optional[FourierGaussian] = None):  # plus other arguments
        # ... other stuff
        self.envelope = envelope
DSilva27 commented 1 month ago

Yes, this is exactly what I was thinking!