In [1]:

    

import time
import os
import sys

from pathlib import Path

import numpy as np
import matplotlib
matplotlib.use('nbagg')
#from matplotlib import style
#style.use('ggplot')
import matplotlib.pyplot as plt

from astroscrappy import detect_cosmics
import photutils 

from scipy.ndimage import median_filter

import astropy.units as u
from astropy import stats
from astropy.io import fits


    

In [2]:

    

%load_ext autoreload
%autoreload 2


    

In [3]:

    

p = Path(".")


    

In [31]:

    

im = fits.open("f9_bad_pixel.fits")[0].data
im -= np.median(im)
plt.imshow(im, origin="lower")
plt.show()


    

In [44]:

    

cr_mask, data = detect_cosmics(im, gain=2, readnoise=9.3, sigclip=100, cleantype='medmask')
plt.imshow(data, origin="lower")
plt.show()


    

In [45]:

    

plt.imshow(cr_mask, origin="lower")
plt.show()


    

In [46]:

    

cr_mask


    

    
Out[46]:





array([[False, False, False, ..., False, False, False],
       [False, False, False, ..., False, False, False],
       [False, False, False, ..., False, False, False],
       ..., 
       [False, False, False, ..., False, False, False],
       [False, False, False, ..., False, False, False],
       [False, False, False, ..., False, False, False]], dtype=bool)

In [54]:

    

test_im = fits.open("/Users/tim/MMT/wfsdat/20171231/f9wfs_20171230-182343.fits")[-1].data
#test_im = fits.open("f9_bad_pixel.fits")[-1].data
blurred = median_filter(test_im, size=5)
test_im[cr_mask] = blurred[cr_mask]
plt.imshow(test_im, origin="lower")
plt.show()


    

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fits.writeto("f9_mask.fits", cr_mask.astype(int))


    

In [61]:

    

m = fits.open("mask.fits")[-1].data.astype(bool)


    

In [62]:

    

m


    

    
Out[62]:





array([[False, False, False, ..., False, False, False],
       [False, False, False, ..., False, False, False],
       [False, False, False, ..., False, False, False],
       ..., 
       [False, False, False, ..., False, False, False],
       [False, False, False, ..., False, False, False],
       [False, False, False, ..., False, False, False]], dtype=bool)

In [29]:

    

detect_cosmics?


    

In [55]:

    

cr_mask.sum()


    

    
Out[55]:





83

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