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Output Bitmasks

PypeIt uses bitmasks to flag data for various reasons. For a primer on the general use of bitmasks, see the `SDSS bitmasks`_ primer.

For the underlying bitmask utility class used by PypeIt, see :doc:`bitmasks`.

Spec2D Bits

In terms of the output data, the main bitmask you will encounter is in the :ref:`spec-2d-output`. The BPMMASK extension in these files contain the bad-pixel bitmask values accrued during the processing and reduction of the data. The main object that manages the bitmasks is :class:`~pypeit.images.imagebitmask.ImageBitMask`, which defines the following bits:

Interpreting the bit values

You can construct the appropriate bitmask in two ways:

  • (Recommended) Instantiate the bitmask directly:

    from pypeit.images.imagebitmask import ImageBitMask
bm = ImageBitMask()

  • Specifically for the spec2d* files, the names of the bits and their order is saved to the header. You can instantiate a generic :class:`~pypeit.bitmask.BitMask` from the header; however, it's not clear how long this behavior will remain. To instantiate the relevant :class:`~pypeit.bitmask.BitMask` from the header:

    from astropy.io import fits
from pypeit.bitmask import BitMask
hdu = fits.open('spec2d_DE.20100913.22358-CFHQS1_DEIMOS_20100913T061231.334.fits')
bm = BitMask(hdu[1].header['IMGBITM'].split(','))

With the :class:`~pypeit.bitmask.BitMask` or :class:`~pypeit.images.imagebitmask.ImageBitMask` instantiated, you can interpret the meaning of the BPMMASK extensions as follows:

  • Use the :func:`~pypeit.bitmask.BitMask.flagged` method to produce a boolean array that selects pixels flagged with a given bit:

    extract_flag = bm.flagged(hdu['DET01-BPMMASK'].data, flag='EXTRACT')

  • Use the same method to select multiple bits:

    process_flag = bm.flagged(hdu['DET01-BPMMASK'].data, flag=['BPM', 'CR', 'SATURATION'])

  • Or select bits that are flagged for any reason:

    # You can use the `flagged` method for this
any_flag = bm.flagged(hdu['DET01-BPMMASK'].data)
# or equivalently
_any_flag = hdu['DET01-BPMMASK'].data > 0

  • To get the human-readable reason that any given value is flagged, use the :func:`~pypeit.bitmask.BitMask.flagged_bits` method. Currently this can only be used with a single bit value:

    print(bm.flagged_bits(hdu['DET01-BPMMASK'].data[0,0]))