naaf

naaf is a library for reading and writing Cryo-ET data.

Installation

pip install naaf

Usage

This command will land in an ipython shell with the loaded data collected in a list called data:

naaf path/to/files/ /other/path/to/file.star

Features

Currently naaf is capable of reading images in the following formats:

• .mrc
• Dynamo .em

and particle data in the following formats:

• Relion .star
• Dynamo .tbl
• Cryolo .cbox and .box

Data structures

Data is loaded into simple data objects called Particles or Image. They have the following attributes:

Data.name  # name guessed from the data or file path
Data.source  # path to the file containing this data
Data.pixel_size  # pixel size information extracted from the data. None if absent.

Particles.data  # pandas DataFrame with coordinates, rotations and arbitary particle features

Image.data  # data array with pixel intensities

Particle orientations

Orientations are scipy Rotation objects. They can be handled normally in a pandas dataframe. They also provide useful batch tools:

• Rotation.concatenate(array_of_rotations) will merge all the rotation objects into one
• rotation_object.apply(vectors) will apply the rotation(s) (following numpy broadcasting rules) to vector(s)

Image data

When possible (and unless disabled), naaf loads images lazily using dask. The resulting objects can be treated as normal numpy array, except one needs to call array.compute() to apply any pending operations and return the result.