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DM-5532 #24

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merged 8 commits into from
Mar 30, 2016
Merged

DM-5532 #24

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11fe4c2
Stop copying the config fields in catalogStarSelector
r-owen Mar 18, 2016
f36a132
Standardize config param badStarPixelFlags to badFlags
r-owen Mar 18, 2016
9c2adc2
Update catalog star selector to new API
r-owen Mar 18, 2016
8caf1d7
Use RangeField in catalog star selector
r-owen Mar 18, 2016
4c973f2
Stop using star selector registry
r-owen Mar 18, 2016
ebe0aa4
Standardize bad flags name in catalog star selector
r-owen Mar 18, 2016
8210d76
Simplify catalog star selector debug variables
r-owen Mar 18, 2016
dd07098
Add documentation to catalog star selector
r-owen Mar 18, 2016
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3 changes: 1 addition & 2 deletions python/lsst/meas/astrom/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,6 @@
from .approximateWcs import *
from .createMatchMetadata import *
from .astromLib import *

from . import catalogStarSelector
from .catalogStarSelector import *

from .version import *
196 changes: 101 additions & 95 deletions python/lsst/meas/astrom/catalogStarSelector.py
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Expand Up @@ -19,49 +19,39 @@
# the GNU General Public License along with this program. If not,
# see <http://www.lsstcorp.org/LegalNotices/>.
#
import numpy

from lsst.afw.table import SourceCatalog
from lsst.meas.algorithms import StarSelectorTask
from lsst.pipe.base import Struct
import lsst.pex.config as pexConfig
import lsst.afw.display.ds9 as ds9
import lsst.afw.math as afwMath
import lsst.meas.algorithms as measAlg

class CatalogStarSelectorConfig(pexConfig.Config):
fluxLim = pexConfig.Field(
class CatalogStarSelectorConfig(StarSelectorTask.ConfigClass):
fluxLim = pexConfig.RangeField(
doc = "specify the minimum psfFlux for good Psf Candidates",
dtype = float,
default = 0.0,
check = lambda x: x >= 0.0,
min = 0.0,
)
fluxMax = pexConfig.Field(
fluxMax = pexConfig.RangeField(
doc = "specify the maximum psfFlux for good Psf Candidates (ignored if == 0)",
dtype = float,
default = 0.0,
# minValue = 0.0,
check = lambda x: x >= 0.0,
)
badStarPixelFlags = pexConfig.ListField(
doc = "PSF candidate objects may not have any of these bits set",
dtype = str,
default = ["base_PixelFlags_flag_edge", "base_PixelFlags_flag_interpolatedCenter",
"base_PixelFlags_flag_saturatedCenter"],
)
kernelSize = pexConfig.Field(
doc = "size of the kernel to create",
dtype = int,
default = 21,
)
borderWidth = pexConfig.Field(
doc = "number of pixels to ignore around the edge of PSF candidate postage stamps",
dtype = int,
default = 0,
min = 0.0,
)

def setDefaults(self):
StarSelectorTask.ConfigClass.setDefaults(self)
self.badFlags = [
"base_PixelFlags_flag_edge",
"base_PixelFlags_flag_interpolatedCenter",
"base_PixelFlags_flag_saturatedCenter",
]

class CheckSource(object):
"""A functor to check whether a source has any flags set that should cause it to be labeled bad."""

def __init__(self, table, fluxLim, fluxMax, badStarPixelFlags):
self.keys = [table.getSchema().find(name).key for name in badStarPixelFlags]
def __init__(self, table, fluxLim, fluxMax, badFlags):
self.keys = [table.getSchema().find(name).key for name in badFlags]
self.keys.append(table.getCentroidFlagKey())
self.fluxLim = fluxLim
self.fluxMax = fluxMax
Expand All @@ -76,25 +66,73 @@ def __call__(self, source):
return False
return True

class CatalogStarSelector(object):
ConfigClass = CatalogStarSelectorConfig
usesMatches = True # selectStars uses (requires) its matches argument
## \addtogroup LSST_task_documentation
## \{
## \page CatalogStarSelectorTask
## \ref CatalogStarSelectorTask_ "CatalogStarSelectorTask"
## \copybrief CatalogStarSelectorTask
## \}

def __init__(self, config=None):
"""Construct a star selector that uses second moments
class CatalogStarSelectorTask(object):
"""!Select stars based on a reference catalog

This is a naive algorithm and should be used with caution.
@anchor CatalogStarSelectorTask_

@section meas_astrom_catalogStarSelector_Contents Contents

@param[in] config: An instance of CatalogStarSelectorConfig
"""
if not config:
config = CatalogStarSelector.ConfigClass()
- @ref meas_astrom_catalogStarSelector_Purpose
- @ref meas_astrom_catalogStarSelector_Initialize
- @ref meas_astrom_catalogStarSelector_IO
- @ref meas_astrom_catalogStarSelector_Config
- @ref meas_astrom_catalogStarSelector_Debug

@section meas_astrom_catalogStarSelector_Purpose Description

Select stars using a match list: select sources where the matching reference object is unresolved,
plus the source passes the following tests:
- no flag from config.badFlags is set
- psf flux >= config.fluxLim
- psf flux <= config.fluxMax (not checked if fluxMax == 0)

@section meas_astrom_catalogStarSelector_Initialize Task initialisation

@copydoc \_\_init\_\_

@section meas_astrom_catalogStarSelector_IO Invoking the Task

Like all star selectors, the main method is `run`. Unlike most star selectors,
this one requires the `matches` argument (the `usesMatches` property is true).

self._kernelSize = config.kernelSize
self._borderWidth = config.borderWidth
self._fluxLim = config.fluxLim
self._fluxMax = config.fluxMax
self._badStarPixelFlags = config.badStarPixelFlags
@section meas_astrom_catalogStarSelector_Config Configuration parameters

See @ref CatalogStarSelectorConfig

@section meas_astrom_catalogStarSelector_Debug Debug variables

CatalogStarSelectorTask has a debug dictionary with the following keys:
<dl>
<dt>display
<dd>bool; if True display debug information
<dt>pauseAtEnd
<dd>bool; if True wait after displaying everything and wait for user input
</dl>

For example, put something like:
@code{.py}
import lsstDebug
def DebugInfo(name):
di = lsstDebug.getInfo(name) # N.b. lsstDebug.Info(name) would call us recursively
if name.endswith("catalogStarSelector"):
di.display = True

return di

lsstDebug.Info = DebugInfo
@endcode
into your `debug.py` file and run your task with the `--debug` flag.
"""
ConfigClass = CatalogStarSelectorConfig
usesMatches = True # `run` and `selectStars` require the `matches` argument

def selectStars(self, exposure, sourceCat, matches=None):
"""!Return a list of PSF candidates that represent likely stars
Expand All @@ -106,74 +144,42 @@ def selectStars(self, exposure, sourceCat, matches=None):
@param[in] matches a match vector as produced by meas_astrom; required
(defaults to None to match the StarSelector API and improve error handling)

@return psfCandidateList: a list of PSF candidates.
@return an lsst.pipe.base.Struct containing:
- starCat catalog of selected stars (a subset of sourceCat)
"""
import lsstDebug
display = lsstDebug.Info(__name__).display
displayExposure = lsstDebug.Info(__name__).displayExposure # display the Exposure + spatialCells
pauseAtEnd = lsstDebug.Info(__name__).pauseAtEnd # pause when done
debugInfo = lsstDebug.Info(__name__)
display = debugInfo.display
pauseAtEnd = debugInfo.pauseAtEnd # pause when done

if matches is None:
raise RuntimeError("CatalogStarSelector requires matches")
raise RuntimeError("CatalogStarSelectorTask requires matches")

mi = exposure.getMaskedImage()

if display:
frames = {}
if displayExposure:
frames["displayExposure"] = 1
ds9.mtv(mi, frame=frames["displayExposure"], title="PSF candidates")
#
# Read the reference catalogue
#
isGoodSource = CheckSource(sourceCat, self._fluxLim, self._fluxMax, self._badStarPixelFlags)

#
# Go through and find all the PSFs in the catalogue
#
# We'll split the image into a number of cells, each of which contributes only
# one PSF candidate star
#
psfCandidateList = []
frame = 1
ds9.mtv(mi, frame=frame, title="PSF candidates")

isGoodSource = CheckSource(sourceCat, self.config.fluxLim, self.config.fluxMax, self.config.badFlags)

starCat = SourceCatalog(sourceCat.schema)
with ds9.Buffering():
for ref, source, d in matches:
if not ref.get("resolved"):
if not isGoodSource(source):
symb, ctype = "+", ds9.RED
else:
try:
psfCandidate = measAlg.makePsfCandidate(source, exposure)

# The setXXX methods are class static, but it's convenient to call them on
# an instance as we don't know Exposure's pixel type
# (and hence psfCandidate's exact type)
if psfCandidate.getWidth() == 0:
psfCandidate.setBorderWidth(self._borderWidth)
psfCandidate.setWidth(self._kernelSize + 2*self._borderWidth)
psfCandidate.setHeight(self._kernelSize + 2*self._borderWidth)

im = psfCandidate.getMaskedImage().getImage()
max = afwMath.makeStatistics(im, afwMath.MAX).getValue()
if not numpy.isfinite(max):
continue
psfCandidateList.append(psfCandidate)

symb, ctype = "+", ds9.GREEN
except Exception as err:
symb, ctype = "o", ds9.RED
print "RHL", err
pass # FIXME: should log this!
else:
symb, ctype = "o", ds9.BLUE

if display and displayExposure:
ds9.dot(symb, source.getX() - mi.getX0(), source.getY() - mi.getY0(),
size=4, frame=frames["displayExposure"], ctype=ctype)
starCat.append(source)
symb, ctype = "+", ds9.GREEN

if display:
ds9.dot(symb, source.getX() - mi.getX0(), source.getY() - mi.getY0(),
size=4, frame=frame, ctype=ctype)

if display and pauseAtEnd:
raw_input("Continue? y[es] p[db] ")

return psfCandidateList

measAlg.starSelectorRegistry.register("catalog", CatalogStarSelector)
return Struct(
starCat = starCat,
)