In [1]:

    

%pylab inline

import tqdm

%load_ext autoreload
%autoreload 2
from pyotf.microscope import WidefieldMicroscope, ConfocalMicroscope
from easy_plot import easy_plot


    

    




Populating the interactive namespace from numpy and matplotlib

In [2]:

    

plt.set_cmap("inferno");


    

    






<Figure size 432x288 with 0 Axes>

In [3]:

    

# We'll use a 1.27 NA water dipping objective imaging in water
psf_params = dict(
    na=1.27,
    ni=1.33,
    wl=0.585,
    size=128,
    vec_corr="none"
)

# Set the Nyquist sampling rate
nyquist_sampling = psf_params["wl"] / psf_params["na"] / 4


    

In [4]:

    

# calculate infocus part only
psfs = [WidefieldMicroscope(**psf_params, model='sheppard', pixel_size=0.99 * nyquist_sampling, oversample_factor=oversample_factor)
       for oversample_factor in (1, 3, 5, 7, 9)]


    

In [5]:

    

easy_plot([p.PSF for p in tqdm.tqdm_notebook(psfs)], (1, 3, 5, 7, 9))


    

    




/Users/david/miniconda3/envs/sandbox/lib/python3.6/site-packages/ipykernel_launcher.py:1: TqdmDeprecationWarning: This function will be removed in tqdm==5.0.0
Please use `tqdm.notebook.tqdm` instead of `tqdm.tqdm_notebook`
  """Entry point for launching an IPython kernel.






    






 
 










    










    













    

In [6]:

    

p = psfs[-1].PSF / psfs[-1].PSF.max() - psfs[0].PSF / psfs[0].PSF.max()


    

In [7]:

    

matshow(p.max(0))
colorbar()


    

    
Out[7]:





<matplotlib.colorbar.Colorbar at 0x1a17f9a0f0>






    

In [8]:

    

matshow(p.max(1))
colorbar()


    

    
Out[8]:





<matplotlib.colorbar.Colorbar at 0x1a17f87a58>






    

In [9]:

    

# calculate infocus part only
con_psfs = [ConfocalMicroscope(**psf_params, oversample_factor=1,
                               model='sheppard', pixel_size=0.45 * nyquist_sampling,
                               wl_exc=0.561, pinhole_size=pinhole_size)
       for pinhole_size in (0, 0.1, 1, 10)]


    

In [10]:

    

easy_plot([p.PSF for p in tqdm.notebook.tqdm_notebook(con_psfs)], (0, 0.1, 1, 10))


    

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