Coverage for python/lsst/pipe/tasks/calexpCutout.py : 31%

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1import lsst.pipe.base as pipeBase
2import lsst.geom as geom
3from lsst.pex.config import Field
4from lsst.meas.algorithms import Stamp, Stamps
6__all__ = ['CalexpCutoutTaskConfig', 'CalexpCutoutTask']
7DETECTOR_DIMENSIONS = ('instrument', 'visit', 'detector')
10class CalexpCutoutTaskConnections(pipeBase.PipelineTaskConnections,
11 dimensions=DETECTOR_DIMENSIONS,
12 defaultTemplates={}):
13 """Connections class for CalexpCutoutTask
14 """
15 in_table = pipeBase.connectionTypes.Input(
16 doc="Locations for cutouts",
17 name="cutout_positions",
18 storageClass="AstropyQTable",
19 dimensions=DETECTOR_DIMENSIONS,
20 )
21 calexp = pipeBase.connectionTypes.Input(
22 doc="Calexp objects",
23 name="calexp",
24 storageClass="ExposureF",
25 dimensions=DETECTOR_DIMENSIONS,
26 )
27 cutouts = pipeBase.connectionTypes.Output(
28 doc="Cutouts",
29 name="calexp_cutouts",
30 storageClass="Stamps",
31 dimensions=DETECTOR_DIMENSIONS,
32 )
35class CalexpCutoutTaskConfig(pipeBase.PipelineTaskConfig,
36 pipelineConnections=CalexpCutoutTaskConnections):
37 """Configuration for CalexpCutoutTask
38 """
39 max_cutouts = Field(dtype=int, default=100, doc='Maximum number of entries to process. '
40 'The result will be the first N in the input table.')
41 skip_bad = Field(dtype=bool, default=True, doc='Skip cutouts that do not fall completely within'
42 ' the calexp bounding box? If set to False a ValueError'
43 ' is raised instead.')
46class CalexpCutoutTask(pipeBase.PipelineTask):
47 """Task for computing cutouts on a specific calexp given
48 positions and sizes of the stamps.
49 """
50 ConfigClass = CalexpCutoutTaskConfig
51 _DefaultName = "calexpCutoutTask"
53 def run(self, in_table, calexp):
54 """Compute and return the cutouts.
56 Parameters
57 ----------
58 in_table : `astropy.QTable`
59 A table containing at least the following columns: position, size.
60 The position should be an `astropy.SkyCoord`. The size is
61 the size of the cutout in pixels. All cutouts are square in pixel
62 space.
63 calexp : `lsst.afw.image.ExposureF`
64 The calibrated exposure from which to extract cutouts
66 Returns
67 -------
68 output : `lsst.pipe.base.Struct`
69 A struct containing:
71 * cutouts: an `lsst.meas.algorithms.Stamps` object
72 that wraps a list of masked images of the cutouts and a
73 `PropertyList` containing the metadata to be persisted
74 with the cutouts. The exposure metadata is preserved and,
75 in addition, arrays holding the RA and Dec of each stamp
76 in degrees are added to the metadata. Note: the origin
77 of the output stamps is `lsst.afw.image.PARENT`.
78 * skipped_positions: a `list` of `lsst.geom.SpherePoint` objects for
79 stamps that were skiped for being off the image
80 or partially off the image
82 Raises
83 ------
84 ValueError
85 If the input catalog doesn't have the required columns,
86 a ValueError is raised
87 """
88 if 'position' not in in_table.colnames or 'size' not in in_table.colnames:
89 raise ValueError('Required column missing from the input table. '
90 'Required columns are "position" and "size".'
91 f'The column names are: {in_table.colnames}')
92 max_idx = self.config.max_cutouts
93 cutout_list = []
94 wcs = calexp.getWcs()
95 mim = calexp.getMaskedImage()
96 ras = []
97 decs = []
98 skipped_positions = []
99 for rec in in_table[:max_idx]:
100 ra = rec['position'].ra.degree
101 dec = rec['position'].dec.degree
102 ras.append(ra)
103 decs.append(dec)
104 pt = geom.SpherePoint(geom.Angle(ra, geom.degrees),
105 geom.Angle(dec, geom.degrees))
106 pix = wcs.skyToPixel(pt)
107 size = rec['size'].value
108 # Clamp to LL corner of the LL pixel and draw extent from there
109 box = geom.Box2I(geom.Point2I(int(pix.x-size/2), int(pix.y-size/2)),
110 geom.Extent2I(size, size))
111 if not mim.getBBox().contains(box):
112 if not self.config.skip_bad:
113 raise ValueError(f'Cutout bounding box is not completely contained in the image: {box}')
114 else:
115 skipped_positions.append(pt)
116 continue
117 sub = mim.Factory(mim, box)
118 stamp = Stamp(stamp_im=sub, position=pt)
119 cutout_list.append(stamp)
120 metadata = calexp.getMetadata()
121 metadata['RA_DEG'] = ras
122 metadata['DEC_DEG'] = decs
123 return pipeBase.Struct(cutouts=Stamps(cutout_list, metadata=metadata),
124 skipped_positions=skipped_positions)