"""
This script enables the viewing of a raw FITS file
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
from IPython import embed
from pypeit.scripts import scriptbase
from pypeit import utils
[docs]class ViewFits(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
from pypeit.spectrographs import available_spectrographs
parser = super().get_parser(description='View FITS files with ginga', width=width)
parser.add_argument('spectrograph', type=str,
help='A valid spectrograph identifier: {0}'.format(
', '.join(available_spectrographs)))
parser.add_argument('file', type=str, default=None, help='FITS file')
parser.add_argument('--list', default=False, action='store_true',
help='List the extensions only?')
parser.add_argument('--proc', default=False, action='store_true',
help='Process the image (i.e. orient, overscan subtract, multiply by '
'gain) using pypeit.images.buildimage.')
parser.add_argument('--bkg_file', type=str, default=None, help='FITS file to be subtracted from the image in file.'
'--proc must be set in order for this option to work.')
parser.add_argument('--exten', type=int, default=None,
help='Show a FITS extension in the raw file. Note --proc and --mosaic '
'will not work with this option.')
parser.add_argument('--det', type=str, default='1', nargs='*',
help='Detector(s) to show. If more than one, the list of detectors, i.e. --det 4 8 '
'to show detectors 4 and 8. This combination must be one of the allowed '
'mosaics hard-coded for the selected '
'spectrograph. Using "mosaic" for gemini_gmos, keck_deimos, or '
'keck_lris will show the mosaic of all detectors.')
parser.add_argument('--chname', type=str, default='Image', help='Name of Ginga tab')
parser.add_argument('--showmask', default=False, help='Overplot masked pixels',
action='store_true')
parser.add_argument('--embed', default=False, action='store_true',
help='Upon completion embed in ipython shell')
return parser
[docs] @staticmethod
def main(args):
from pypeit import msgs
from pypeit.display import display
from pypeit.spectrographs import util
from pypeit import io
from pypeit.images import buildimage
# List only?
if args.list:
hdu = io.fits_open(args.file)
print(hdu.info())
return
# Setup for PYPIT imports
msgs.reset(verbosity=2)
if args.proc and args.exten is not None:
msgs.error('You cannot specify --proc and --exten, since --exten shows the raw image')
if args.exten is not None and args.det == 'mosaic':
msgs.error('You cannot specify --exten and --det mosaic, since --mosaic displays '
'multiple extensions by definition')
if args.exten is not None:
hdu = io.fits_open(args.file)
img = hdu[args.exten].data
hdu.close()
else:
spectrograph = util.load_spectrograph(args.spectrograph)
bad_read_message = 'Unable to construct image due to a read or image processing ' \
'error. Use case interpreted from command-line inputs requires ' \
'a raw image, not an output image product from pypeit. To show ' \
'a pypeit output image, specify the extension using --exten. ' \
'Use --list to show the extension names.'
if 'mosaic' in args.det:
mosaic = True
_det = spectrograph.default_mosaic
if _det is None:
msgs.error(f'{args.spectrograph} does not have a known mosaic')
else:
try:
_det = tuple(int(d) for d in args.det)
except:
msgs.error(f'Could not convert detector input to integer.')
mosaic = len(_det) > 1
if not mosaic:
_det = _det[0]
if args.proc:
# Use the biasframe processing parameters because processing
# these frames is independent of any other frames (ie., does not
# perform bias subtraction or flat-fielding)
par = spectrograph.default_pypeit_par()['calibrations']['biasframe']
try:
Img = buildimage.buildimage_fromlist(spectrograph, _det, par,
[args.file], mosaic=mosaic)
except Exception as e:
msgs.error(bad_read_message
+ f' Original exception -- {type(e).__name__}: {str(e)}')
if args.bkg_file is not None:
try:
bkgImg = buildimage.buildimage_fromlist(spectrograph, _det, par,
[args.bkg_file], mosaic=mosaic)
except Exception as e:
msgs.error(bad_read_message
+ f' Original exception -- {type(e).__name__}: {str(e)}')
Img = Img.sub(bkgImg)
img = Img.image
else:
try:
img = spectrograph.get_rawimage(args.file, _det)[1]
except Exception as e:
msgs.error(bad_read_message
+ f' Original exception -- {type(e).__name__}: {str(e)}')
display.connect_to_ginga(raise_err=True, allow_new=True)
display.show_image(img, chname=args.chname)
if args.showmask:
if not args.proc:
msgs.info("You need to use --proc with --showmask to show the mask. Ignoring your argument")
else:
viewer, ch_mask = display.show_image(Img.bpm, chname="BPM")
if args.embed:
embed(header=utils.embed_header())