Density.to_file#

Density.to_file(filename, gzip=False)[source]#

Writes class instance to disk.

Parameters:

filenamestr: Path to write to.
gzipbool, optional: Gzip compress the output and add corresponding suffix to filename if not present. False by default.

See also

Density.from_file()

Notes

If filename endswith “.em” or “.h5” a EM file or HDF5 file will be created. The default output format is CCP4/MRC and on failure, skimage.io.imsave is used.

References

[1]

Burnley T et al., Acta Cryst. D, 2017

[2]

Nickell S. et al, Journal of Structural Biology, 2005

[3]

https://scikit-image.org/docs/stable/api/skimage.io.html

Examples

The following creates a Density instance dens holding random data values and writes it to disk:

>>> import numpy as np
>>> from tme import Density
>>> data = np.random.rand(50,50,50)
>>> dens = Density(data=data, origin=(0, 0, 0), sampling_rate=(1, 1, 1))
>>> dens.to_file("example.mrc")

The output file can also be directly gzip compressed. The corresponding “.gz” extension will be automatically added if absent [1].

>>> dens.to_file("example.mrc", gzip=True)

The Density.to_file() method also supports writing EM files [2]:

>>> dens.to_file("example.em")

In addition, a variety of image file formats are supported [3]:

>>> data = np.random.rand(50,50)
>>> dens = Density(data=data, origin=(0, 0), sampling_rate=(1, 1))
>>> dens.to_file("example.tiff")