CTFReconstructed#

class CTFReconstructed(shape=None, defocus_x=None, angles=None, opening_axis=2, tilt_axis=0, 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)[source]#

Bases: CTF

Create a simple contrast transfer function mask without the ability to specify per-tilt parameters like in CTF.

Attributes

CTFReconstructed.acceleration_voltage

The acceleration voltage in Volts, defaults to 300e3.

CTFReconstructed.amplitude_contrast

The amplitude contrast, defaults to 0.07.

CTFReconstructed.angles

The tilt angles.

CTFReconstructed.correct_defocus_gradient

Whether to correct defocus gradient, defaults False.

CTFReconstructed.defocus_angle

The defocus angle in degrees, defaults to 0.

CTFReconstructed.defocus_x

The defocus value in x direction (in units of sampling rate).

CTFReconstructed.defocus_y

The defocus value in y direction, defaults to None (in units of sampling rate).

CTFReconstructed.flip_phase

Whether the returned CTF should be phase-flipped, defaults to True.

CTFReconstructed.opening_axis

The microscope projection axis, defaults to 2 (z).

CTFReconstructed.phase_shift

The phase shift in degrees, defaults to 0.

CTFReconstructed.return_real_fourier

Whether to return a ctf mask for rfft (for CTFReconstructed).

CTFReconstructed.sampling_rate

The sampling rate, defaults to 1 Ångstrom / voxel.

CTFReconstructed.shape

The shape of the to-be created mask.

CTFReconstructed.spherical_aberration

The spherical aberration, defaults to 2.7e7 (in units of sampling rate).

CTFReconstructed.tilt_axis

The axis along which the tilt is applied, defaults to 0 (x).

Methods

CTFReconstructed.__call__(**kwargs)

Returns a CTF stack of chosen parameters with DC component in the center.

CTFReconstructed.from_file(filename, **kwargs)

Initialize CTF from file.

CTFReconstructed.weight(shape, defocus_x[, ...])

Compute the CTF weight tilt stack.