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Merge pull request #247 from lsst/tickets/DM-26651
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DM-26651: Change BrightStarStamp to save archive elements, positions, and number of rotations
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@MorganSchmitz
MorganSchmitz committed Jul 1, 2021
2 parents bc33d95 + e624689 commit 8474ae8
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Showing 2 changed files with 60 additions and 15 deletions.
52 changes: 41 additions & 11 deletions python/lsst/meas/algorithms/brightStarStamps.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,8 @@
from lsst.afw import geom as afwGeom
from lsst.afw import math as afwMath
from lsst.afw import table as afwTable
from .stamps import StampsBase, AbstractStamp, readFitsWithOptions
from lsst.geom import Point2I
from .stamps import Stamps, AbstractStamp, readFitsWithOptions


@dataclass
Expand All @@ -46,6 +47,8 @@ class BrightStarStamp(AbstractStamp):
----------
stamp_im : `lsst.afw.image.MaskedImage`
Pixel data for this postage stamp
position : `lsst.geom.Point2I`
Origin of the stamps in its origin exposure (pixels)
gaiaGMag : `float`
Gaia G magnitude for the object in this stamp
gaiaId : `int`
Expand All @@ -56,6 +59,7 @@ class BrightStarStamp(AbstractStamp):
stamp_im: MaskedImageF
gaiaGMag: float
gaiaId: int
position: Point2I
archive_element: Optional[afwTable.io.Persistable] = None
annularFlux: Optional[float] = None

Expand Down Expand Up @@ -86,9 +90,16 @@ def factory(cls, stamp_im, metadata, idx, archive_element=None):
brightstarstamp : `BrightStarStamp`
An instance of this class
"""
if 'X0S' in metadata and 'Y0S' in metadata:
x0 = metadata.getArray('X0S')[idx]
y0 = metadata.getArray('Y0S')[idx]
position = Point2I(x0, y0)
else:
position = None
return cls(stamp_im=stamp_im,
gaiaGMag=metadata.getArray('G_MAGS')[idx],
gaiaId=metadata.getArray('GAIA_IDS')[idx],
position=position,
archive_element=archive_element,
annularFlux=metadata.getArray('ANNULAR_FLUXES')[idx])

Expand Down Expand Up @@ -137,7 +148,7 @@ def measureAndNormalize(self, annulus, statsControl=afwMath.StatisticsControl(),
return None


class BrightStarStamps(StampsBase):
class BrightStarStamps(Stamps):
"""Collection of bright star stamps and associated metadata.
Parameters
Expand All @@ -153,6 +164,9 @@ class BrightStarStamps(StampsBase):
Outer radius value, in pixels. This and ``innerRadius`` define the
annulus used to compute the ``"annularFlux"`` values within each
``starStamp``. Must be provided if ``normalize`` is True.
nb90Rots : `int`, optional
Number of 90 degree rotations required to compensate for detector
orientation.
metadata : `lsst.daf.base.PropertyList`, optional
Metadata associated with the bright stars.
use_mask : `bool`
Expand Down Expand Up @@ -184,7 +198,7 @@ class BrightStarStamps(StampsBase):
>>> starSubregions = butler.get("brightStarStamps", dataId, parameters={'bbox': bbox})
"""

def __init__(self, starStamps, innerRadius=None, outerRadius=None,
def __init__(self, starStamps, innerRadius=None, outerRadius=None, nb90Rots=None,
metadata=None, use_mask=True, use_variance=False, use_archive=False):
super().__init__(starStamps, metadata, use_mask, use_variance, use_archive)
# Ensure stamps contain a flux measurement if and only if they are
Expand All @@ -195,11 +209,13 @@ def __init__(self, starStamps, innerRadius=None, outerRadius=None,
self.normalized = True
else:
self.normalized = False
self.nb90Rots = nb90Rots

@classmethod
def initAndNormalize(cls, starStamps, innerRadius, outerRadius,
def initAndNormalize(cls, starStamps, innerRadius, outerRadius, nb90Rots=None,
metadata=None, use_mask=True, use_variance=False,
imCenter=None, discardNanFluxObjects=True,
use_archive=False, imCenter=None,
discardNanFluxObjects=True,
statsControl=afwMath.StatisticsControl(),
statsFlag=afwMath.stringToStatisticsProperty("MEAN"),
badMaskPlanes=('BAD', 'SAT', 'NO_DATA')):
Expand All @@ -224,12 +240,20 @@ def initAndNormalize(cls, starStamps, innerRadius, outerRadius,
Outer radius value, in pixels. This and ``innerRadius`` define the
annulus used to compute the ``"annularFlux"`` values within each
``starStamp``.
nb90Rots : `int`, optional
Number of 90 degree rotations required to compensate for detector
orientation.
metadata : `lsst.daf.base.PropertyList`, optional
Metadata associated with the bright stars.
use_mask : `bool`
If `True` read and write mask data. Default `True`.
use_variance : `bool`
If ``True`` read and write variance data. Default ``False``.
use_archive : `bool`
If ``True`` read and write an Archive that contains a Persistable
associated with each stamp. In the case of bright stars, this is
usually a ``TransformPoint2ToPoint2``, used to warp each stamp
to the same pixel grid before stacking.
imCenter : `collections.abc.Sequence`, optional
Center of the object, in pixels. If not provided, the center of the
first stamp's pixel grid will be used.
Expand Down Expand Up @@ -263,9 +287,9 @@ def initAndNormalize(cls, starStamps, innerRadius, outerRadius,
innerCircle = afwGeom.SpanSet.fromShape(innerRadius, afwGeom.Stencil.CIRCLE, offset=imCenter)
annulus = outerCircle.intersectNot(innerCircle)
# Initialize (unnormalized) brightStarStamps instance
bss = cls(starStamps, innerRadius=None, outerRadius=None,
bss = cls(starStamps, innerRadius=None, outerRadius=None, nb90Rots=nb90Rots,
metadata=metadata, use_mask=use_mask,
use_variance=use_variance)
use_variance=use_variance, use_archive=use_archive)
# Ensure no stamps had already been normalized
bss._checkNormalization(True, innerRadius, outerRadius)
bss._innerRadius, bss._outerRadius = innerRadius, outerRadius
Expand All @@ -289,14 +313,19 @@ def _refresh_metadata(self):
"""Refresh the metadata. Should be called before writing this object
out.
"""
# add full list of Gaia magnitudes, IDs and annularFlxes to shared
# metadata
# add full list of positions, Gaia magnitudes, IDs and annularFlxes to
# shared metadata
self._metadata["G_MAGS"] = self.getMagnitudes()
self._metadata["GAIA_IDS"] = self.getGaiaIds()
positions = self.getPositions()
self._metadata["X0S"] = [xy0[0] for xy0 in positions]
self._metadata["Y0S"] = [xy0[1] for xy0 in positions]
self._metadata["ANNULAR_FLUXES"] = self.getAnnularFluxes()
self._metadata["NORMALIZED"] = self.normalized
self._metadata["INNER_RADIUS"] = self._innerRadius
self._metadata["OUTER_RADIUS"] = self._outerRadius
if self.nb90Rots is not None:
self._metadata["NB_90_ROTS"] = self.nb90Rots
return None

@classmethod
Expand All @@ -322,13 +351,14 @@ def readFitsWithOptions(cls, filename, options):
Collection of metadata parameters
"""
stamps, metadata = readFitsWithOptions(filename, BrightStarStamp.factory, options)
nb90Rots = metadata["NB_90_ROTS"] if "NB_90_ROTS" in metadata else None
if metadata["NORMALIZED"]:
return cls(stamps,
innerRadius=metadata["INNER_RADIUS"], outerRadius=metadata["OUTER_RADIUS"],
metadata=metadata, use_mask=metadata['HAS_MASK'],
nb90Rots=nb90Rots, metadata=metadata, use_mask=metadata['HAS_MASK'],
use_variance=metadata['HAS_VARIANCE'], use_archive=metadata['HAS_ARCHIVE'])
else:
return cls(stamps, metadata=metadata, use_mask=metadata['HAS_MASK'],
return cls(stamps, nb90Rots=nb90Rots, metadata=metadata, use_mask=metadata['HAS_MASK'],
use_variance=metadata['HAS_VARIANCE'], use_archive=metadata['HAS_ARCHIVE'])

def append(self, item, innerRadius=None, outerRadius=None):
Expand Down
23 changes: 19 additions & 4 deletions tests/test_brightStarStamps.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@

from lsst.meas.algorithms import brightStarStamps
from lsst.afw import image as afwImage
from lsst.geom import Point2I
from lsst.daf.base import PropertyList
import lsst.utils.tests

Expand All @@ -42,6 +43,8 @@ def setUp(self):
starImArray = starIm.image.array
starImArray += np.random.rand(*stampSize)
ids = ["111", "aaa", "bbb"]
positions = [Point2I(x0, y0)
for x0, y0 in zip(np.random.randint(11, size=3), np.random.randint(11, size=3))]
mags = np.random.rand(3)
# faint object to test magnitude cuts
self.faintObjIdx = 1
Expand All @@ -50,22 +53,30 @@ def setUp(self):
fluxes = np.random.rand(3)
self.starStamps = [brightStarStamps.BrightStarStamp(stamp_im=starIm,
gaiaGMag=mag,
position=pos,
gaiaId=gaiaId,
annularFlux=flux)
for starIm, mag, gaiaId, flux in zip(starImages, mags, ids, fluxes)]
for starIm, mag, gaiaId, pos, flux in
zip(starImages, mags, ids, positions, fluxes)]
self.unnormalizedStarStamps = [brightStarStamps.BrightStarStamp(stamp_im=starIm,
gaiaGMag=mag,
position=pos,
gaiaId=gaiaId)
for starIm, mag, gaiaId, flux in zip(starImages, mags, ids, fluxes)]
for starIm, mag, gaiaId, pos, flux in
zip(starImages, mags, ids, positions, fluxes)]
self.toBeNormalizedStarStamps = [brightStarStamps.BrightStarStamp(stamp_im=starIm,
gaiaGMag=mag,
position=pos,
gaiaId=gaiaId)
for starIm, mag, gaiaId, flux in zip(starImages, mags, ids, fluxes)]
for starIm, mag, gaiaId, pos, flux in
zip(starImages, mags, ids, positions, fluxes)]
self.innerRadius = 5
self.outerRadius = 10
self.nb90Rots = 2
self.bss = brightStarStamps.BrightStarStamps(self.starStamps,
innerRadius=self.innerRadius,
outerRadius=self.outerRadius)
outerRadius=self.outerRadius,
nb90Rots=self.nb90Rots)

def tearDown(self):
del self.bss
Expand Down Expand Up @@ -94,6 +105,10 @@ def testIO(self):
np.testing.assert_almost_equal(self.bss.getAnnularFluxes(), bss2.getAnnularFluxes())
for id1, id2 in zip(self.bss.getGaiaIds(), bss2.getGaiaIds()):
self.assertEqual(id1, id2)
for pos1, pos2 in zip(self.bss.getPositions(), bss2.getPositions()):
self.assertEqual(pos1[0], pos2[0])
self.assertEqual(pos1[1], pos2[1])
self.assertEqual(bss2.nb90Rots, self.nb90Rots)

def testMagnitudeSelection(self):
brightOnly = self.bss.selectByMag(magMax=7)
Expand Down

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