calexpCutout.py

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# This file is part of pipe_tasks.
#
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# (https://www.lsst.org).
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__all__ = ['CalexpCutoutTaskConfig', 'CalexpCutoutTask']
 
import lsst.pipe.base as pipeBase
import lsst.geom as geom
from lsst.pex.config import Field
from lsst.meas.algorithms import Stamp, Stamps
 
DETECTOR_DIMENSIONS = ('instrument', 'visit', 'detector')
 
 
class CalexpCutoutTaskConnections(pipeBase.PipelineTaskConnections,
                                  dimensions=DETECTOR_DIMENSIONS,
                                  defaultTemplates={}):
    """Connections class for CalexpCutoutTask
    """
    in_table = pipeBase.connectionTypes.Input(
        doc="Locations for cutouts",
        name="cutout_positions",
        storageClass="AstropyQTable",
        dimensions=DETECTOR_DIMENSIONS,
    )
    calexp = pipeBase.connectionTypes.Input(
        doc="Calexp objects",
        name="calexp",
        storageClass="ExposureF",
        dimensions=DETECTOR_DIMENSIONS,
    )
    cutouts = pipeBase.connectionTypes.Output(
        doc="Cutouts",
        name="calexp_cutouts",
        storageClass="Stamps",
        dimensions=DETECTOR_DIMENSIONS,
    )
 
 
class CalexpCutoutTaskConfig(pipeBase.PipelineTaskConfig,
                             pipelineConnections=CalexpCutoutTaskConnections):
    """Configuration for CalexpCutoutTask
    """
    max_cutouts = Field(dtype=int, default=100, doc='Maximum number of entries to process. '
                                                    'The result will be the first N in the input table.')
    skip_bad = Field(dtype=bool, default=True, doc='Skip cutouts that do not fall completely within'
                                                   ' the calexp bounding box?  If set to False a ValueError'
                                                   ' is raised instead.')
 
 
class CalexpCutoutTask(pipeBase.PipelineTask):
    """Task for computing cutouts on a specific calexp given
    positions, xspans, and yspans of the stamps.
    """
    ConfigClass = CalexpCutoutTaskConfig
    _DefaultName = "calexpCutoutTask"
 
    def run(self, in_table, calexp):
        """Compute and return the cutouts.
 
        Parameters
        ----------
        in_table : `astropy.QTable`
            A table containing at least the following columns: position, xspan
            and yspan.  The position should be an `astropy.SkyCoord`.  The
            xspan and yspan are the extent of the cutout in x and y in pixels.
        calexp : `lsst.afw.image.ExposureF`
            The calibrated exposure from which to extract cutouts
 
        Returns
        -------
        output : `lsst.pipe.base.Struct`
            A struct containing:
 
            * cutouts: an `lsst.meas.algorithms.Stamps` object
                       that wraps a list of masked images of the cutouts and a
                       `PropertyList` containing the metadata to be persisted
                       with the cutouts.  The exposure metadata is preserved and,
                       in addition, arrays holding the RA and Dec of each stamp
                       in degrees are added to the metadata.  Note: the origin
                       of the output stamps is `lsst.afw.image.PARENT`.
            * skipped_positions: a `list` of `lsst.geom.SpherePoint` objects for
                                 stamps that were skiped for being off the image
                                 or partially off the image
 
        Raises
        ------
        ValueError
            If the input catalog doesn't have the required columns,
            a ValueError is raised
        """
        cols = in_table.colnames
        if 'position' not in cols or 'xspan' not in cols or 'yspan' not in cols:
            raise ValueError('Required column missing from the input table.  '
                             'Required columns are "position", "xspan", and "yspan".  '
                             f'The column names are: {in_table.colnames}')
        wcs = calexp.getWcs()
        if wcs is None:
            raise RuntimeError("Calexp has no WCS, so cannot compute sky positions.")
        max_idx = self.config.max_cutouts
        cutout_list = []
        mim = calexp.getMaskedImage()
        ras = []
        decs = []
        skipped_positions = []
        for rec in in_table[:max_idx]:
            ra = rec['position'].ra.degree
            dec = rec['position'].dec.degree
            ras.append(ra)
            decs.append(dec)
            pt = geom.SpherePoint(geom.Angle(ra, geom.degrees),
                                  geom.Angle(dec, geom.degrees))
            pix = wcs.skyToPixel(pt)
            xspan = rec['xspan'].value
            yspan = rec['yspan'].value
            # Clamp to LL corner of the LL pixel and draw extent from there
            box = geom.Box2I(geom.Point2I(int(pix.x-xspan/2), int(pix.y-yspan/2)),
                             geom.Extent2I(xspan, yspan))
            if not mim.getBBox().contains(box):
                if not self.config.skip_bad:
                    raise ValueError(f'Cutout bounding box is not completely contained in the image: {box}')
                else:
                    skipped_positions.append(pt)
                    continue
            sub = mim.Factory(mim, box)
            stamp = Stamp(stamp_im=sub, position=pt)
            cutout_list.append(stamp)
        metadata = calexp.getMetadata()
        metadata['RA_DEG'] = ras
        metadata['DEC_DEG'] = decs
        return pipeBase.Struct(cutouts=Stamps(cutout_list, metadata=metadata),
                               skipped_positions=skipped_positions)