CTF Simulation Data

Multidistance CFT phase retrieval

This notebook runs an example of multi-distance CTF phase retrieval on simulation data in edf format.

Dataset setup

Install pyPhase. Then:

from pyphase import dataset
from pyphase import phaseretrieval
from pyphase import utilities 

import matplotlib.pyplot as plt # for visualization purposes
from skimage import io

Define the project's name

name = 'holosim'

and set the path to the data

path = '/data/staff/tomograms/HoloSim'

Make sure that the data folders and files have the right format and structure.

You can have a look at the data

fig, ax = plt.subplots(nrows = 2, ncols = 2, figsize = (22, 15))

for i,row in enumerate(ax):
    for j,col in enumerate(row):
        file = '/home/d/PhasingProj/Data/HoloSimT/holosimt_{proj}_/holosimt_{proj2}_0001.tif'.format(proj=(i+1)*(j+1),proj2=(i+1)*(j+1))
        im = io.imread(file)
        col.imshow(im, cmap='gray')

Projections

Create a DataSet object

ds = dataset.ESRFID19(path,name)

Phase retrieval

Choose a phase retreival algorithm(link to list of algorithms) and create a retriever for the dataset, with the appropriate arguments

alpha =  1e-8
retriever = phaseretrieval.CTF(ds,alpha)

Select range of projections for which to retrieve phase

start = 0 
end = 3

Run the phase retreival

retriever.ReconstructProjections(ds, start, end)

For each projection, a file named holosim_[version_predix]_000[n].edf with the retrieved phase and and a file named holosim_att__000[n].edf, with the retrieved attenuation, is created in the [path]/myProject_

Visualizing the results

Look at the results by plotting the retrieved phase and retrieved attenuation for one projection

plt.figure(figsize = [8,8])
im = io.imread(path + 'holosim_/holosim_PP_0001.tif')
plt.imshow(imm, cmap = 'gray')

Projections

plt.figure(figsize = [8,8])
im = io.imread(path + 'holosim_/holosim_PP_att_0000.tif')
plt.imshow(imm, cmap = 'gray')

Projections