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tickets/DM-12404: Update stack with new deblender API #48

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merged 3 commits into from
Apr 13, 2018
Merged

tickets/DM-12404: Update stack with new deblender API #48

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9395817
Integrate changes from user branch
Mar 26, 2018
f30d2d7
Update multiband deblender API
Mar 29, 2018
718963b
Fixed based on reviewer comments
Apr 10, 2018
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
.sconf_temp
.sconsign.dblite
_build.*
.cache
*.o
*.pyc
*.so
Expand Down Expand Up @@ -38,3 +39,4 @@ im1[0-9]m.png
foot2.png
sfoot3.png
img.png
examples/.ipynb_checkpoints/
4 changes: 4 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
meas_deblender
--------------

Deblending algorithms for the [LSST pipeline](https://github.com/lsst).
104 changes: 59 additions & 45 deletions python/lsst/meas/deblender/baseline.py
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Expand Up @@ -48,18 +48,21 @@
class DeblenderResult(object):
"""Collection of objects in multiple bands for a single parent footprint
"""
def __init__(self, footprints, maskedImages, psfs, psffwhms, log, filters=None,

def __init__(self, footprint, maskedImages, psfs, psffwhms, log, filters=None,
maxNumberOfPeaks=0, avgNoise=None):
""" Initialize a DeblededParent

Parameters
----------
footprint: list of `afw.detection.Footprint`s
Parent footprint to deblend in each band.
footprint: `afw.detection.Footprint`
Parent footprint to deblend. While `maskedImages`, `psfs`,
and `psffwhms` are lists of objects, one for each band,
`footprint` is a single parent footprint (from a `mergedDet`)
this is used for all bands.
maskedImages: list of `afw.image.MaskedImageF`s
Masked image containing the ``footprint`` in each band.
psf: list of `afw.detection.Psf`s
psfs: list of `afw.detection.Psf`s
Psf of the ``maskedImage`` for each band.
psffwhm: list of `float`s
FWHM of the ``maskedImage``'s ``psf`` in each band.
Expand All @@ -79,10 +82,6 @@ def __init__(self, footprints, maskedImages, psfs, psffwhms, log, filters=None,
None
"""
# Check if this is collection of footprints in multiple bands or a single footprint
try:
len(footprints)
except TypeError:
footprints = [footprints]
try:
len(maskedImages)
except TypeError:
Expand All @@ -103,42 +102,48 @@ def __init__(self, footprints, maskedImages, psfs, psffwhms, log, filters=None,
else:
avgNoise = [avgNoise]
# Now check that all of the parameters have the same number of entries
if any([len(footprints)!=len(p) for p in [maskedImages, psfs, psffwhms, avgNoise]]):
if any([len(maskedImages)!=len(p) for p in [psfs, psffwhms, avgNoise]]):
raise ValueError("To use the multi-color deblender, "
"'footprint', 'maskedImage', 'psf', 'psffwhm', 'avgNoise'"
"'maskedImage', 'psf', 'psffwhm', 'avgNoise'"
"must have the same length, but instead have lengths: "
"{0}".format([len(p) for p in [footprints,
maskedImages,
"{0}".format([len(p) for p in [maskedImages,
psfs,
psffwhms,
avgNoise]]))

self.log = log
self.filterCount = len(footprints)
self.filterCount = len(maskedImages)
self.maskedImages = maskedImages
self.footprint = footprint
self.psfs = psfs

self.peakCount = len(footprints[0].getPeaks())
self.peakCount = len(footprint.getPeaks())
if maxNumberOfPeaks>0 and maxNumberOfPeaks<self.peakCount:
self.peakCount = maxNumberOfPeaks

if filters is None:
filters = range(len(footprints))
filters = range(self.filterCount)
self.filters = filters

# Create a DeblendedParent for the Footprint in every filter
self.deblendedParents = OrderedDict([])
for n in range(self.filterCount):
f = self.filters[n]
dp = DeblendedParent(f, footprints[n], maskedImages[n], psfs[n],
dp = DeblendedParent(f, footprint, maskedImages[n], psfs[n],
psffwhms[n], avgNoise[n], maxNumberOfPeaks, self)
self.deblendedParents[self.filters[n]] = dp

# Group the peaks in each color
self.peaks = []
for idx in range(self.peakCount):
peakDict = {f: dp.peaks[idx] for f,dp in self.deblendedParents.items()}
peakDict = OrderedDict([(f, dp.peaks[idx]) for f,dp in self.deblendedParents.items()])
multiPeak = MultiColorPeak(peakDict, idx, self)
self.peaks.append(multiPeak)

# Result from multiband debender (if used)
self.blend = None
self.failed = False

def getParentProperty(self, propertyName):
"""Get the footprint in each filter"""
return [getattr(fp, propertyName) for dp in self.deblendedParents]
Expand All @@ -152,14 +157,14 @@ def setTemplateSums(self, templateSums, fidx=None):

class DeblendedParent(object):
"""Deblender result of a single parent footprint, in a single band

Convenience class to store useful objects used by the deblender for a single band,
such as the maskedImage, psf, etc as well as the results from the deblender.
"""
def __init__(self, filterName, footprint, maskedImage, psf, psffwhm, avgNoise,
def __init__(self, filterName, footprint, maskedImage, psf, psffwhm, avgNoise,
maxNumberOfPeaks, debResult):
"""Create a DeblendedParent to store a deblender result

Parameters
----------
filterName: `str`
Expand Down Expand Up @@ -198,14 +203,14 @@ def __init__(self, filterName, footprint, maskedImage, psf, psffwhm, avgNoise,
self.debResult = debResult
self.peakCount = debResult.peakCount
self.templateSum = None

# avgNoise is an estiamte of the average noise level for the image in this filter
if avgNoise is None:
stats = afwMath.makeStatistics(self.varimg, self.mask, afwMath.MEDIAN)
avgNoise = np.sqrt(stats.getValue(afwMath.MEDIAN))
debResult.log.trace('Estimated avgNoise for filter %s = %f', self.filter, avgNoise)
self.avgNoise = avgNoise

# Store all of the peak information in a single object
self.peaks = []
peaks = self.fp.getPeaks()
Expand All @@ -215,7 +220,7 @@ def __init__(self, filterName, footprint, maskedImage, psf, psffwhm, avgNoise,

def updateFootprintBbox(self):
"""Update the bounding box of the parent footprint

If the parent Footprint is resized it will be necessary to update the bounding box of the footprint.
"""
# Pull out the image bounds of the parent Footprint
Expand All @@ -229,13 +234,13 @@ def updateFootprintBbox(self):

class MultiColorPeak(object):
"""Collection of single peak deblender results in multiple bands.

There is one of these objects for each Peak in the footprint.
"""

def __init__(self, peaks, pki, parent):
"""Create a collection for deblender results in each band.

Parameters
----------
peaks: `dict` of `afw.detection.PeakRecord`
Expand All @@ -244,11 +249,11 @@ def __init__(self, peaks, pki, parent):
Index of the peak in `parent.peaks`
parent: `DeblendedParent`
DeblendedParent object that contains the peak as a child.

Returns
-------
None

"""
self.filters = list(peaks.keys())
self.deblendedPeaks = peaks
Expand All @@ -262,6 +267,8 @@ def __init__(self, peaks, pki, parent):
self.pki = pki
self.skip = False
self.deblendedAsPsf = False
self.x = self.deblendedPeaks[self.filters[0]].peak.getFx()
self.y = self.deblendedPeaks[self.filters[0]].peak.getFy()

class DeblendedPeak(object):
"""Result of deblending a single Peak within a parent Footprint.
Expand All @@ -271,7 +278,7 @@ class DeblendedPeak(object):

def __init__(self, peak, pki, parent, multiColorPeak=None):
"""Initialize a new deblended peak in a single filter band

Parameters
----------
peak: `afw.detection.PeakRecord`
Expand All @@ -282,7 +289,7 @@ def __init__(self, peak, pki, parent, multiColorPeak=None):
Parent in the same filter that contains the peak
multiColorPeak: `MultiColorPeak`
Object containing the same peak in multiple bands

Returns
-------
None
Expand Down Expand Up @@ -455,7 +462,7 @@ def deblend(footprint, maskedImage, psf, psffwhm, filters=None,
removeDegenerateTemplates=False, maxTempDotProd=0.5
):
"""Deblend a parent ``Footprint`` in a ``MaskedImageF``.

Deblending assumes that ``footprint`` has multiple peaks, as it will still create a
`PerFootprint` object with a list of peaks even if there is only one peak in the list.
It is recommended to first check that ``footprint`` has more than one peak, similar to the
Expand Down Expand Up @@ -509,12 +516,12 @@ def deblend(footprint, maskedImage, psf, psffwhm, filters=None,
otherwise the one with the maximum template value is kept.
* Relevant parameters: ``maxTempDotProduct``
# Apportion flux to all of the peak templates
* Divide the ``maskedImage`` flux amongst all of the templates based on the fraction of
* Divide the ``maskedImage`` flux amongst all of the templates based on the fraction of
flux assigned to each ``tempalteFootprint``.
* Leftover "stray flux" is assigned to peaks based on the other parameters.
* Relevant parameters: ``clipStrayFluxFraction``, ``strayFluxAssignment``,
``strayFluxToPointSources``, ``assignStrayFlux``

Parameters
----------
footprint: `afw.detection.Footprint`
Expand Down Expand Up @@ -620,7 +627,7 @@ def deblend(footprint, maskedImage, psf, psffwhm, filters=None,
All dot products between templates greater than ``maxTempDotProduct`` will result in one
of the templates removed. This parameter is only used when ``removeDegenerateTempaltes==True``.
The default is 0.5.

Returns
-------
res: `PerFootprint`
Expand All @@ -633,7 +640,7 @@ def deblend(footprint, maskedImage, psf, psffwhm, filters=None,

# Add activated deblender plugins
if fitPsfs:
debPlugins.append(plugins.DeblenderPlugin(plugins.fitPsfs,
debPlugins.append(plugins.DeblenderPlugin(plugins.fitPsfs,
psfChisqCut1=psfChisqCut1,
psfChisqCut2=psfChisqCut2,
psfChisqCut2b=psfChisqCut2b,
Expand Down Expand Up @@ -669,10 +676,10 @@ def deblend(footprint, maskedImage, psf, psffwhm, filters=None,

return debResult

def newDeblend(debPlugins, footprint, maskedImage, psf, psffwhm, filters=None,
def newDeblend(debPlugins, footprint, maskedImages, psfs, psfFwhms, filters=None,
log=None, verbose=False, avgNoise=None, maxNumberOfPeaks=0):
"""Deblend a parent ``Footprint`` in a ``MaskedImageF``.

Deblending assumes that ``footprint`` has multiple peaks, as it will still create a
`PerFootprint` object with a list of peaks even if there is only one peak in the list.
It is recommended to first check that ``footprint`` has more than one peak, similar to the
Expand All @@ -687,11 +694,11 @@ def newDeblend(debPlugins, footprint, maskedImage, psf, psffwhm, filters=None,
Plugins to execute (in order of execution) for the deblender.
footprint: `afw.detection.Footprint` or list of Footprints
Parent footprint to deblend.
maskedImage: `afw.image.MaskedImageF` or list of MaskedImages
maskedImages: `afw.image.MaskedImageF` or list of MaskedImages
Masked image containing the ``footprint``.
psf: `afw.detection.Psf` or list of Psfs
psfs: `afw.detection.Psf` or list of Psfs
Psf of the ``maskedImage``.
psffwhm: `float` or list of floats
psfFwhms: `float` or list of floats
FWHM of the ``maskedImage``'s ``psf``.
filters: list of `string`s, optional
Names of the filters when ``footprint`` is a list instead of a single ``footprint``.
Expand Down Expand Up @@ -721,7 +728,7 @@ def newDeblend(debPlugins, footprint, maskedImage, psf, psffwhm, filters=None,
# Import C++ routines
import lsst.meas.deblender as deb
butils = deb.BaselineUtilsF

if log is None:
import lsst.log as lsstLog

Expand All @@ -732,12 +739,19 @@ def newDeblend(debPlugins, footprint, maskedImage, psf, psffwhm, filters=None,
log.setLevel(lsstLog.Log.TRACE)

# get object that will hold our results
debResult = DeblenderResult(footprint, maskedImage, psf, psffwhm, log, filters=filters,
debResult = DeblenderResult(footprint, maskedImages, psfs, psfFwhms, log, filters=filters,
maxNumberOfPeaks=maxNumberOfPeaks, avgNoise=avgNoise)

step = 0
while step < len(debPlugins):
reset = debPlugins[step].run(debResult, log)
# If a failure occurs at any step,
# the result is flagged as `failed`
# and the remaining steps are skipped
if not debResult.failed:
reset = debPlugins[step].run(debResult, log)
else:
log.warn("Skipping steps {0}".format(debPlugins[step:]))
return debResult
if reset:
step = debPlugins[step].onReset
else:
Expand Down