Composable Filters#

Composable filters in pytme are inspired by the similarly named Compose operation used in deep learning frameworks. Composable filters are an explicit solution to defining complex filtering procedures and can be lazily evaluated.

To demonstrate the use of composable filters, let’s walk through a basic example showcasing how to combine BandPassFilter and WedgeReconstructed

import numpy as np
from tme.filters import Compose, BandPassFilter, WedgeReconstructed

sampling_rate = (5,5,5)           # Sampling rate, typically Å/voxel

# Setup BandPassFilter
bandpass = BandPassFilter(
    lowpass=30,                   # Resolution to lowpass filter to
    highpass=5,                   # Resolution to highpass filter to
    sampling_rate=sampling_rate
)

# Setup WedgeReconstructed
wedge = WedgeReconstructed(
    angles=[60, 60],              # Start, stop tilt angle
    opening_axis=0,               # Wedge is open in z-axis
    tilt_axis=1,                  # Sample is tilted over y-axis
    create_continuous_wedge=True, # Include all angles from -60 to 60
    sampling_rate=sampling_rate,
)

# Combine bandpass and wedge mask into a single filter
composed_filter = Compose([bandpass, wedge])

data_shape = (50,50,50)
filter_mask = composed_filter(
   shape=data_shape, return_real_fourier=False
)["data"]

# Apply the filter mask
data = np.random.rand(*data_shape)
data_filtered = np.fft.ifftn(np.fft.fftn(data * filter_mask)).real

Specification#

ComposableFilter serves as specification for new composable filters.

ComposableFilter

Strategy class for composable filters.

Aggregator#

Compose allows for combining the operations described by multiple objects of type ComposableFilter.

Compose

Compose a series of transformations.

Frequency Filters#

`BandPassFilter`	Generate bandpass filters in Fourier space.
`LinearWhiteningFilter`	Compute Fourier power spectrums and perform whitening.

Cryo-EM Filters#

`CTF`	Generate a contrast transfer function mask.
`Wedge`	Generate wedge mask for tomographic data.
`WedgeReconstructed`	Initialize `WedgeReconstructed`.

Reconstruction#

ReconstructFromTilt

Reconstruct a volume from a tilt series.