"""
This script prints a user-friendly description of the bad pixel mask
based on a spec2d file.
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
from IPython import embed
from astropy.io import fits
from pypeit import __version__
from pypeit import msgs, spec2dobj
from pypeit.images.detector_container import DetectorContainer
from pypeit.images.imagebitmask import ImageBitMask
from pypeit.pypmsgs import PypeItDataModelError
from pypeit.scripts import scriptbase
[docs]class PrintBPM(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Print out an informative description of a '
'bad pixel masked value. Usually, you should '
'run pypeit_show_2dspec --showmask first to '
'see the bad pixel mask values. Then, call this '
'script with the BPM value that you want to find'
'more information about.',
width=width)
parser.add_argument('bit', type=int, default=None, help='Bad pixel mask value to describe in plain text')
parser.add_argument('--file', type=str, default=None, help='PypeIt spec2d file to use for the description'
'(optional). If provided, the bitmask contained '
'in the spec2d file will be used to describe the '
'bad pixel mask value. If not provided, the default '
'pypeit bad pixel mask will be used.')
parser.add_argument('--det', default='1', type=str,
help='Detector name or number. If a number, the name is constructed '
'assuming the reduction is for a single detector. If a string, '
'it must match the name of the detector object (e.g., DET01 for '
'a detector, MSC01 for a mosaic). This is not required, and the '
'value is acceptable. Default is 1.')
return parser
[docs] @staticmethod
def main(args):
# Convert the integer bitmask value to a list of binary numbers
binvals = [int(x) for x in bin(args.bit)[2:]][::-1]
if args.file is None:
msgs.info("Using the default PypeIt bad pixel mask.")
# Generate an Image BitMask object
bpm = ImageBitMask()
descr = bpm.descr
else:
# Read the spec2d file
msgs.info("Using the bad pixel mask from the following spec2d file:" + msgs.newline() + f"{args.file}.")
spec2d_file = args.file
# Parse the detector name
try:
det = int(args.det)
except:
detname = args.det
else:
detname = DetectorContainer.get_name(det)
# Try to read the Spec2DObj using the current datamodel, but allowing
# for the datamodel version to be different
try:
spec2DObj = spec2dobj.Spec2DObj.from_file(args.file, detname, chk_version=False)
except PypeItDataModelError:
try:
# Try to get the pypeit version used to write this file
file_pypeit_version = fits.getval(args.file, 'VERSPYP', 0)
except KeyError:
file_pypeit_version = '*unknown*'
msgs.warn(f'Your installed version of PypeIt ({__version__}) cannot be used to parse '
f'{args.file}, which was reduced using version {file_pypeit_version}. You '
'are strongly encouraged to re-reduce your data using this (or, better yet, '
'the most recent) version of PypeIt. Script will try to parse only the '
'relevant bits from the spec2d file and continue (possibly with more '
'limited functionality).')
# Generate an Image BitMask object
msgs.info("Using the default PypeIt bad pixel mask.")
bpm = ImageBitMask()
descr = bpm.descr
else:
bpm = spec2DObj.bpmmask
descr = bpm.bitmask.descr
# Print the description of the bad pixel mask value
outstr = f"The bad pixel mask value ({args.bit}) corresponds to the following:" \
+ msgs.newline() + msgs.newline()
bitkeys = list(bpm.bits.keys())
# Pad the bit keys with spaces so that they all have the same length
bitlen = len(max(bitkeys, key=len))
for i in range(len(binvals)):
if binvals[i] == 1:
outstr += f"* {bitkeys[i].ljust(bitlen)} : {descr[i]}" + msgs.newline()
# Print the message to the user
msgs.info(outstr)
# Finally, print out a message to point users to the online documentation
msgs.info("Please see the following website for more information:" + msgs.newline() +
"https://pypeit.readthedocs.io/en/release/out_masks.html")