Source code for refstis.basedark

"""Functions to create a BaseDark for the STIS instrument

#. If not already done, perform bias subtraction
#. If after switch to side-2 electronics, perform temperature scaling
#. Join all imsets from input list into single file
#. combine and cr-reject
#. normalize to e/s by dividing by (exptime/gain)
#. update DQ array with hot pixel information

.. note::

  * Side 1 operations ended on May 16, 2001.
  * Side 2 operations started on July 10, 2001.
  * The dark correction will only be applied to datasets after July 1, 2001 (MJD 52091.0).
"""



from astropy.io import fits
from astropy.stats import sigma_clipped_stats
import numpy as np
from scipy.ndimage.filters import median_filter
import shutil

from . import functions

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[docs]def update_sci(filename): """Create the science extension of the baseline dark .. note:: The input file will be updated in-place. Parameters ---------- filename: str name of the file to be updated """ with fits.open(filename, mode='update') as hdu: im_mean, im_median, im_std = sigma_clipped_stats(hdu[('sci', 1)].data, sigma=5, maxiters=50) fivesig = im_mean + 5.0 * im_std only_hotpix = np.where(hdu[('sci', 1)].data >= fivesig, hdu[('sci', 1)].data - im_mean, 0) #-- I don't see this being used med_im = median_filter(hdu[('sci', 1)].data, (3, 3)) only_baseline = np.where(hdu[('sci', 1)].data >= fivesig, med_im, hdu[('sci', 1)].data) hdu[('dq', 1)].data = np.where(only_hotpix >= .1, 16, hdu[('dq', 1)].data)
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[docs]def find_hotpix(filename): """Find hotpixels and update DQ array Pixels hotter that median + 5*sigma will be updated to have a DQ value of 16. .. note:: The input file will be updated in-place. Parameters ---------- filename: str filename of the input biasfile """ with fits.open(filename, mode='update') as hdu: im_mean, im_median, im_std = sigma_clipped_stats(hdu[('sci', 1)].data, sigma=3, maxiters=40) five_sigma = im_median + 5 * im_std index = np.where((hdu[('SCI', 1)].data > five_sigma) & (hdu[('SCI', 1)].data > im_mean + 0.1)) hdu[('DQ', 1)].data[index] = 16
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[docs]def make_basedark(input_list, refdark_name='basedark.fits', bias_file=None): """Make a monthly baseline dark from the input list. Parameters ---------- input_list: list list of input dark files refdark_name: str name of the output reference file bias_file: str or None bias file to be used in calibration (optional) """ print('#-------------------------------#') print('# Running basedark #') print('#-------------------------------#') print('output to: %s' % refdark_name) print('with biasfile %s' % bias_file) #-- bias subtract data if not already done if bias_file: flt_list = [functions.bias_subtract_data(item, bias_file) for item in input_list] else: flt_list = input_list for filename in flt_list: texpstrt = fits.getval(filename, 'texpstrt', 0) if texpstrt > 52091.0: functions.apply_dark_correction(filename, texpstrt) joined_filename = refdark_name.replace('.fits', '_joined.fits') crj_filename = joined_filename.replace('.fits', '_crj.fits') #if not bias_file: # raise IOError('No biasfile specified, this task needs one to run') print('Joining images') functions.msjoin(flt_list, joined_filename) print('Performing CRREJECT') crdone = functions.bd_crreject(joined_filename) if not crdone: functions.bd_calstis(joined_filename, bias_file) functions.normalize_crj(crj_filename) shutil.copy(crj_filename, refdark_name) update_sci(refdark_name) find_hotpix(refdark_name) functions.update_header_from_input(refdark_name, input_list) fits.setval(refdark_name, 'TASKNAME', ext=0, value='BASEDARK') print('Cleaning...') functions.RemoveIfThere(crj_filename) functions.RemoveIfThere(joined_filename) #map(functions.RemoveIfThere, flt_list) print('basedark done for {}'.format(refdark_name))
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