CTF

class CTF(shape=None, defocus_x=None, angles=None, opening_axis=None, tilt_axis=None, correct_defocus_gradient=False, sampling_rate=1, acceleration_voltage=300000.0, spherical_aberration=27000000.0, amplitude_contrast=0.07, phase_shift=0, defocus_angle=0, defocus_y=None, flip_phase=True, return_real_fourier=False, no_reconstruction=True)

Bases: ComposableFilter

Generate a contrast transfer function mask.

References

[1]

CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Alexis Rohou and Nikolaus Grigorieff. Journal of Structural Biology 2015.

Attributes

CTF.acceleration_voltage	The acceleration voltage in Volts, defaults to 300e3.
CTF.amplitude_contrast	The amplitude contrast, defaults to 0.07.
CTF.angles	The tilt angles.
CTF.correct_defocus_gradient	Whether to correct defocus gradient, defaults to False.
CTF.defocus_angle	The defocus angle, defaults to 0.
CTF.defocus_x	The defocus value in x direction.
CTF.defocus_y	The defocus value in y direction, defaults to None.
CTF.flip_phase	Whether the returned CTF should be phase-flipped.
CTF.no_reconstruction	Whether the output should not be used for n+1 dimensional reconstruction
CTF.opening_axis	The axis around which the wedge is opened, defaults to None.
CTF.phase_shift	The phase shift, defaults to 0.
CTF.return_real_fourier	Whether to return a format compliant with rfft.
CTF.sampling_rate	The sampling rate, defaults to 1 Angstrom / Voxel.
CTF.shape	The shape of the to-be reconstructed volume.
CTF.spherical_aberration	The spherical aberration coefficient, defaults to 2.7e7.
CTF.tilt_axis	The axis along which the tilt is applied, defaults to None.

Methods

CTF.__call__(**kwargs)
CTF.from_file(filename)	Initialize CTF from file.
CTF.weight(shape, defocus_x, angles[, ...])	Compute the CTF weight tilt stack.