noao.imred.crutil¶

The noao.imred.crutil package contains various algorithims for finding and replacing comsic rays in single images or image sets.

Notes¶

For questions or comments please see our github page. We encourage and appreciate user feedback.

Contents:

cosmicrays
craverage
crfix
crgrow
crmedian
crnebula

cosmicrays¶

craverage¶

crfix¶

crgrow¶

Please review the Notes section above before running any examples in this notebook

The crgrow replacement uses the skimage.morphology package to grow the values in any numpy array. The dilation task is a wrapper around scipy.ndimage.grey_dilation. You can insert any kernal type where disk is called in this example.

# Standard Imports
from skimage.morphology import disk,dilation

# Astronomy Specific Imports
from astropy.io import fits

# Change this value to your desired data file
test_data = '/eng/ssb/iraf_transition/test_data/id0k16pdq_blv_tmp.fits'

# Read in your fits file, when using a fits file, the bytesway call is required to
# make sure your arry data type is correct.
hdu = fits.open(test_data,mode='update')
dq1 = hdu[3].data.byteswap().newbyteorder('=')

# Dilation used to grow the CR flags
grownDQ = dilation(dq1, disk(2))

# Re-assign the changed array to our original fits file and close the file to save.
hdu[3].data = grownDQ
hdu.close()

crmedian¶

Please review the Notes section above before running any examples in this notebook

The crmedian task is a way to indentify and replace cosmic rays in a single image by detecting pixels that deviate a statistically significant amount from the median by comparing to a median filtered version of the image. The indentfied cosmic rays can then be replaced by the median filtered value. A similar algorithim has been used in ccdproc.cosmicray_median. In ccdproc.cosmicray_median you also have the option of using an error array. If none is provided the standard deviation of the data is used.

# Astronomy Specific Imports
from astropy.io import fits
from astropy import units
from ccdproc import cosmicray_median, fits_ccddata_reader

# Change these values to your desired data files
test_data = '/eng/ssb/iraf_transition/test_data/iczgs3y5q_flt.fits'

# First we need to pull out the science arrays to create CCDData objects
# Our acutal unit is electrons/sec, this is not accepted by the current
# set of units
image_data = fits_ccddata_reader(test_data, hdu=1, unit=units.electron/units.s, hdu_uncertainty=2)
error_data = image_data.uncertainty.array

# Now we run cosmicray_median, since we input a CCDData type, a CCDData type is returned
# If a numpy.ndarray if the input data type, it will return a numpy.ndarray
newdata = cosmicray_median(image_data, error_image=error_data, thresh=5, mbox=11, rbox=11, gbox=3)

INFO: using the unit electron / s passed to the FITS reader instead of the unit ELECTRONS/S in the FITS file. [ccdproc.ccddata]

crnebula¶

Not Replacing¶

crcombine - see ctio.immatch.imcombine, work in progress
credit - see images.tv.imedit, work in progress