vitrio

vitrio is a high-throughput image I/O library tailored to the access patterns and file formats common in Cryo-Electron Microscopy (CryoEM). This is the reference of its Python package. The C++ library it is made on has its own, at ../cpp/, and the README and the examples show how the two are used.

import vitrio as vio

micrograph = vio.read("micrograph.mrc")
vio.write_single(micrograph, "copy.tif")

Anywhere an array is asked for, so is whatever hands out host memory through DLPack or the buffer protocol: a numpy array, a tensor of PyTorch or JAX, a memoryview. It is read or written where it is, and nothing is copied. What a read returns is a vitrio.Array, which those use in turn.

The functions that are _async return before the work is done, with a vitrio.Completion to wait on. Anything that reads, writes or waits releases the GIL meanwhile.

Reference

• Reading and writing
• Arrays and locations
• Loaders, savers and providers
• Scratches
• Detector events
• Feeding a model