shampoo Package


cluster_focus_peaks(xyz[, eps, min_samples]) Use DBSCAN to identify single particles through multiple focus planes.
create_hdf5_archive(hdf5_path, ...[, ...]) Create HDF5 file structure for holograms and phase/intensity reconstructions.
fftshift(x[, additional_shift, axes]) Shift the zero-frequency component to the center of the spectrum, or with some additional offset from the center.
find_focus_plane(roi_cube[, focus_on, plot]) Find focus plane in a cube of reconstructed waves at different propagation distances.
glue_focus(xyz, labels) Launch a glue session with focusing results.
locate_specimens(wave_cube, positions, ...) Identify the (x, y, z) coordinates of a specimen.
open_hdf5_archive(hdf5_path) Load and return a shampoo HDF5 archive.
save_scaled_image(image, filename[, margin, ...]) Save an image to png.
test([package, test_path, args, plugins, ...]) Run the tests using py.test.
unwrap_phase(reconstructed_wave[, seed]) 2D phase unwrap a complex reconstructed wave.


FFT(shape, float_precision, complex_precision) Convenience wrapper around
Hologram(hologram[, crop_fraction, ...]) Container for holograms and methods to reconstruct them.
ReconstructedWave(reconstructed_wave) Container for reconstructed waves and their intensity and phase arrays.

Class Inheritance Diagram

Inheritance diagram of shampoo.fftutils.FFT, shampoo.reconstruction.Hologram, shampoo.reconstruction.ReconstructedWave