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DM-5532 #4

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merged 8 commits into from
Mar 30, 2016
Merged

DM-5532 #4

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9bc95d9
Update unit test for new star selector API
r-owen Mar 18, 2016
f0f302c
Clean up pyflakes warnings in unit test
r-owen Mar 18, 2016
bc39e70
Rename catalog to sourceCat in selectStars
r-owen Mar 18, 2016
f7e74c1
Modernize psfEx star selector
r-owen Mar 18, 2016
0d7cb93
Add documentation to psfEx star selector
r-owen Mar 18, 2016
101c2ec
Use StarSelector.run to make PSF candidates
r-owen Mar 22, 2016
ae95302
PsfExStarSelector: fix flag names
r-owen Mar 29, 2016
e6ea9ab
Fix flake8 picky errors
r-owen Mar 29, 2016
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223 changes: 122 additions & 101 deletions python/lsst/meas/extensions/psfex/psfexStarSelector.py
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Original file line number Diff line number Diff line change
@@ -1,22 +1,22 @@
#
#
# LSST Data Management System
# Copyright 2008, 2009, 2010 LSST Corporation.
#
#
# This product includes software developed by the
# LSST Project (http://www.lsst.org/).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the LSST License Statement and
# the GNU General Public License along with this program. If not,
#
# You should have received a copy of the LSST License Statement and
# the GNU General Public License along with this program. If not,
# see <http://www.lsstcorp.org/LegalNotices/>.
#
import re
Expand All @@ -29,27 +29,16 @@
except ImportError:
plt = None

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

class PsfexStarSelectorConfig(pexConfig.Config):
badFlags = pexConfig.ListField(
doc="List of flags which cause a source to be rejected as bad",
dtype=str,
default=["base_PixelFlags_flag_edge",
"base_PixelFlags_flag_saturated.center",
"base_PixelFlags_flag_cr.center",
"base_PixelFlags_flag_bad",
"base_PixelFlags_flag_suspect.center",
"base_PsfFlux_flag",
#"parent", # actually this is a test on deblend_nChild
],
)
__all__ = ["PsfexStarSelectorConfig", "PsfexStarSelectorTask"]

class PsfexStarSelectorConfig(StarSelectorTask.ConfigClass):
fluxName = pexConfig.Field(
dtype=str,
doc="Name of photometric flux key ",
Expand Down Expand Up @@ -98,16 +87,6 @@ class PsfexStarSelectorConfig(pexConfig.Config):
default=100,
check = lambda x: x >= 0.0,
)
kernelSize = pexConfig.Field(
dtype=int,
doc = "size of the Psf kernel to create",
default = 21,
)
borderWidth = pexConfig.Field(
doc = "number of pixels to ignore around the edge of PSF candidate postage stamps",
dtype = int,
default = 0,
)

def validate(self):
pexConfig.Config.validate(self)
Expand All @@ -121,6 +100,17 @@ def validate(self):
if self.minFwhm > self.maxFwhm:
raise pexConfig.FieldValidationError("minFwhm (%f) > maxFwhm (%f)" % (self.minFwhm, self.maxFwhm))

def setDefaults(self):
self.badFlags = [
"base_PixelFlags_flag_edge",
"base_PixelFlags_flag_saturatedCenter",
"base_PixelFlags_flag_crCenter",
"base_PixelFlags_flag_bad",
"base_PixelFlags_flag_suspectCenter",
"base_PsfFlux_flag",
#"parent", # actually this is a test on deblend_nChild
]

class EventHandler(object):
"""A class to handle key strokes with matplotlib displays"""
def __init__(self, axes, xs, ys, x, y, frames=[0]):
Expand All @@ -136,7 +126,7 @@ def __init__(self, axes, xs, ys, x, y, frames=[0]):
def __call__(self, ev):
if ev.inaxes != self.axes:
return

if ev.key and ev.key in ("p"):
dist = np.hypot(self.xs - ev.xdata, self.ys - ev.ydata)
dist[np.where(np.isnan(dist))] = 1e30
Expand Down Expand Up @@ -165,7 +155,7 @@ def plot(mag, width, centers, clusterId, marker="o", markersize=2, markeredgewid
if clear:
fig.clf()

axes = fig.add_axes((0.1, 0.1, 0.85, 0.80));
axes = fig.add_axes((0.1, 0.1, 0.85, 0.80))

xmin = sorted(mag)[int(0.05*len(mag))]
xmax = sorted(mag)[int(0.95*len(mag))]
Expand All @@ -192,28 +182,87 @@ def plot(mag, width, centers, clusterId, marker="o", markersize=2, markeredgewid
axes.set_ylabel(r"$\sqrt{I_{xx} + I_{yy}}$")

return fig

class PsfexStarSelector(object):

## \addtogroup LSST_task_documentation
## \{
## \page PsfexStarSelectorTask
## \ref PsfexStarSelectorTask_ "PsfexStarSelectorTask"
## \copybrief PsfexStarSelectorTask
## \}

class PsfexStarSelectorTask(StarSelectorTask):
"""!A star selector whose algorithm is not yet documented

@anchor PsfexStarSelectorTask_

@section meas_extensions_psfex_psfexStarSelectorStarSelector_Contents Contents

- @ref meas_extensions_psfex_psfexStarSelectorStarSelector_Purpose
- @ref meas_extensions_psfex_psfexStarSelectorStarSelector_Initialize
- @ref meas_extensions_psfex_psfexStarSelectorStarSelector_IO
- @ref meas_extensions_psfex_psfexStarSelectorStarSelector_Config
- @ref meas_extensions_psfex_psfexStarSelectorStarSelector_Debug

@section meas_extensions_psfex_psfexStarSelectorStarSelector_Purpose Description

A star selector whose algorithm is not yet documented

@section meas_extensions_psfex_psfexStarSelectorStarSelector_Initialize Task initialisation

@copydoc \_\_init\_\_

@section meas_extensions_psfex_psfexStarSelectorStarSelector_IO Invoking the Task

Like all star selectors, the main method is `run`.

@section meas_extensions_psfex_psfexStarSelectorStarSelector_Config Configuration parameters

See @ref PsfexStarSelectorConfig

@section meas_extensions_psfex_psfexStarSelectorStarSelector_Debug Debug variables

PsfexStarSelectorTask has a debug dictionary with the following keys:
<dl>
<dt>display
<dd>bool; if True display debug information
<dt>displayExposure
<dd>bool; if True display the exposure and spatial cells
<dt>plotFwhmHistogram
<dd>bool; if True plot histogram of FWHM
<dt>plotFlags
<dd>bool: if True plot the sources coloured by their flags
<dt>plotRejection
<dd>bool; if True plot why sources are rejected
</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("objectSizeStarSelector"):
di.display = True
di.displayExposure = True
di.plotFwhmHistogram = True

return di

lsstDebug.Info = DebugInfo
@endcode
into your `debug.py` file and run your task with the `--debug` flag.
"""
ConfigClass = PsfexStarSelectorConfig
usesMatches = False # selectStars does not use its matches argument

def __init__(self, config):
"""Construct a star selector using psfex's algorithm

@param[in] config: An instance of PsfexStarSelectorConfig
"""
self.config = config

def selectStars(self, exposure, catalog, matches=None):
"""Return a list of PSF candidates that represent likely stars

A list of PSF candidates may be used by a PSF fitter to construct a PSF.

@param[in] exposure: the exposure containing the sources
@param[in] catalog: a SourceCatalog containing sources that may be stars
@param[in] matches: astrometric matches; ignored by this star selector

@return psfCandidateList: a list of PSF candidates.
def selectStars(self, exposure, sourceCat, matches=None):
"""!Select stars from source catalog

@param[in] exposure the exposure containing the sources
@param[in] sourceCat catalog of sources that may be stars (an lsst.afw.table.SourceCatalog)
@param[in] matches astrometric matches; ignored by this star selector

@return a Struct containing:
- starCat a subset of sourceCat containing the selected stars
"""
import lsstDebug
display = lsstDebug.Info(__name__).display
Expand All @@ -226,8 +275,6 @@ def selectStars(self, exposure, catalog, matches=None):
lsstDebug.Info(__name__).plotFlags # Plot the sources coloured by their flags
plotRejection = display and plt and \
lsstDebug.Info(__name__).plotRejection # Plot why sources are rejected
# create a log for my application
logger = pexLogging.Log(pexLogging.getDefaultLog(), "meas.extensions.psfex.psfexStarSelector")

#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
#
Expand All @@ -244,21 +291,21 @@ def selectStars(self, exposure, catalog, matches=None):
maxelong = (maxellip + 1.0)/(1.0 - maxellip) if maxellip < 1.0 else 100

# Unpack the catalogue
shape = catalog.getShapeDefinition()
ixx = catalog.get("%s.xx" % shape)
iyy = catalog.get("%s.yy" % shape)
shape = sourceCat.getShapeDefinition()
ixx = sourceCat.get("%s.xx" % shape)
iyy = sourceCat.get("%s.yy" % shape)

fwhm = 2*np.sqrt(2*np.log(2))*np.sqrt(0.5*(ixx + iyy))
elong = 0.5*(ixx - iyy)/(ixx + iyy)

flux = catalog.get(fluxName)
fluxErr = catalog.get(fluxErrName)
flux = sourceCat.get(fluxName)
fluxErr = sourceCat.get(fluxErrName)
sn = flux/np.where(fluxErr > 0, fluxErr, 1)
sn[fluxErr <= 0] = -psfex.psfex.cvar.BIG

flags = 0x0
for i, f in enumerate(self.config.badFlags):
flags = np.bitwise_or(flags, np.where(catalog.get(f), 1 << i, 0))
flags = np.bitwise_or(flags, np.where(sourceCat.get(f), 1 << i, 0))
#
# Estimate the acceptable range of source widths
#
Expand Down Expand Up @@ -323,11 +370,11 @@ def selectStars(self, exposure, catalog, matches=None):
frame = 0
if displayExposure:
mi = exposure.getMaskedImage()

ds9.mtv(mi, frame=frame, title="PSF candidates")

with ds9.Buffering():
for i, source in enumerate(catalog):
for i, source in enumerate(sourceCat):
if good[i]:
ctype = ds9.GREEN # star candidate
else:
Expand Down Expand Up @@ -370,7 +417,8 @@ def selectStars(self, exposure, catalog, matches=None):

if displayExposure:
global eventHandler
eventHandler = EventHandler(plt.axes(), imag, fwhm, catalog.getX(), catalog.getY(), frames=[frame])
eventHandler = EventHandler(plt.axes(), imag, fwhm, sourceCat.getX(), sourceCat.getY(),
frames=[frame])

if plotFlags or plotRejection:
while True:
Expand All @@ -393,45 +441,18 @@ def selectStars(self, exposure, catalog, matches=None):
print """
If you put the cursor on a point in the matplotlib scatter plot and hit 'p' you'll see it in ds9."""
elif reply[0] == "p":
import pdb; pdb.set_trace()
import pdb
pdb.set_trace()
elif reply[0] == 'q':
sys.exit(1)
else:
break

#
# Time to use that stellar classification to generate psfCandidateList
#
with ds9.Buffering():
psfCandidateList = []
if True:
catalog = [s for s,g in zip(catalog, good) if g]
else:
catalog = catalog[good]
starCat = SourceCatalog(sourceCat.schema)
for source, isGood in zip(sourceCat, good):
if isGood:
starCat.append(source)

for source in catalog:
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.config.borderWidth)
psfCandidate.setWidth(self.config.kernelSize + 2*self.config.borderWidth)
psfCandidate.setHeight(self.config.kernelSize + 2*self.config.borderWidth)

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

if display and displayExposure:
ds9.dot("o", source.getX() - mi.getX0(), source.getY() - mi.getY0(),
size=4, frame=frame, ctype=ds9.CYAN)
except Exception as err:
logger.logdebug("Failed to make a psfCandidate from source %d: %s" % (source.getId(), err))

return psfCandidateList

starSelectorRegistry.register("psfex", PsfexStarSelector)
return Struct(
starCat = starCat,
)