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# 

# LSST Data Management System 

# 

# Copyright 2008-2017 AURA/LSST. 

# 

# 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, 

# see <https://www.lsstcorp.org/LegalNotices/>. 

# 

import sys 

 

import numpy 

import warnings 

from functools import reduce 

 

from lsst.log import Log 

from lsst.pipe.base import Struct 

import lsst.geom 

from lsst.afw.cameraGeom import PIXELS, TAN_PIXELS 

import lsst.afw.geom as afwGeom 

import lsst.pex.config as pexConfig 

import lsst.afw.display.ds9 as ds9 

from .sourceSelector import BaseSourceSelectorTask, sourceSelectorRegistry 

 

 

class ObjectSizeStarSelectorConfig(BaseSourceSelectorTask.ConfigClass): 

fluxMin = pexConfig.Field( 

doc="specify the minimum psfFlux for good Psf Candidates", 

dtype=float, 

default=12500.0, 

check=lambda x: x >= 0.0, 

) 

fluxMax = pexConfig.Field( 

doc="specify the maximum psfFlux for good Psf Candidates (ignored if == 0)", 

dtype=float, 

default=0.0, 

check=lambda x: x >= 0.0, 

) 

widthMin = pexConfig.Field( 

doc="minimum width to include in histogram", 

dtype=float, 

default=0.0, 

check=lambda x: x >= 0.0, 

) 

widthMax = pexConfig.Field( 

doc="maximum width to include in histogram", 

dtype=float, 

default=10.0, 

check=lambda x: x >= 0.0, 

) 

sourceFluxField = pexConfig.Field( 

doc="Name of field in Source to use for flux measurement", 

dtype=str, 

default="base_GaussianFlux_instFlux", 

) 

widthStdAllowed = pexConfig.Field( 

doc="Standard deviation of width allowed to be interpreted as good stars", 

dtype=float, 

default=0.15, 

check=lambda x: x >= 0.0, 

) 

nSigmaClip = pexConfig.Field( 

doc="Keep objects within this many sigma of cluster 0's median", 

dtype=float, 

default=2.0, 

check=lambda x: x >= 0.0, 

) 

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_interpolatedCenter", 

"base_PixelFlags_flag_saturatedCenter", 

"base_PixelFlags_flag_crCenter", 

"base_PixelFlags_flag_bad", 

"base_PixelFlags_flag_interpolated", 

], 

) 

 

def validate(self): 

BaseSourceSelectorTask.ConfigClass.validate(self) 

if self.widthMin > self.widthMax: 

raise pexConfig.FieldValidationError("widthMin (%f) > widthMax (%f)" 

% (self.widthMin, self.widthMax)) 

 

 

class EventHandler: 

"""A class to handle key strokes with matplotlib displays""" 

 

def __init__(self, axes, xs, ys, x, y, frames=[0]): 

self.axes = axes 

self.xs = xs 

self.ys = ys 

self.x = x 

self.y = y 

self.frames = frames 

 

self.cid = self.axes.figure.canvas.mpl_connect('key_press_event', self) 

 

def __call__(self, ev): 

if ev.inaxes != self.axes: 

return 

 

if ev.key and ev.key in ("p"): 

dist = numpy.hypot(self.xs - ev.xdata, self.ys - ev.ydata) 

dist[numpy.where(numpy.isnan(dist))] = 1e30 

 

which = numpy.where(dist == min(dist)) 

 

x = self.x[which][0] 

y = self.y[which][0] 

for frame in self.frames: 

ds9.pan(x, y, frame=frame) 

ds9.cmdBuffer.flush() 

else: 

pass 

 

 

def _assignClusters(yvec, centers): 

"""Return a vector of centerIds based on their distance to the centers""" 

assert len(centers) > 0 

 

minDist = numpy.nan*numpy.ones_like(yvec) 

clusterId = numpy.empty_like(yvec) 

clusterId.dtype = int # zeros_like(..., dtype=int) isn't in numpy 1.5 

dbl = Log.getLogger("objectSizeStarSelector._assignClusters") 

dbl.setLevel(dbl.INFO) 

 

# Make sure we are logging aall numpy warnings... 

oldSettings = numpy.seterr(all="warn") 

with warnings.catch_warnings(record=True) as w: 

warnings.simplefilter("always") 

for i, mean in enumerate(centers): 

dist = abs(yvec - mean) 

if i == 0: 

update = dist == dist # True for all points 

else: 

update = dist < minDist 

if w: # Only do if w is not empty i.e. contains a warning message 

dbl.trace(str(w[-1])) 

 

minDist[update] = dist[update] 

clusterId[update] = i 

numpy.seterr(**oldSettings) 

 

return clusterId 

 

 

def _kcenters(yvec, nCluster, useMedian=False, widthStdAllowed=0.15): 

"""A classic k-means algorithm, clustering yvec into nCluster clusters 

 

Return the set of centres, and the cluster ID for each of the points 

 

If useMedian is true, use the median of the cluster as its centre, rather than 

the traditional mean 

 

Serge Monkewitz points out that there other (maybe smarter) ways of seeding the means: 

"e.g. why not use the Forgy or random partition initialization methods" 

however, the approach adopted here seems to work well for the particular sorts of things 

we're clustering in this application 

""" 

 

assert nCluster > 0 

 

mean0 = sorted(yvec)[len(yvec)//10] # guess 

delta = mean0 * widthStdAllowed * 2.0 

centers = mean0 + delta * numpy.arange(nCluster) 

 

func = numpy.median if useMedian else numpy.mean 

 

clusterId = numpy.zeros_like(yvec) - 1 # which cluster the points are assigned to 

clusterId.dtype = int # zeros_like(..., dtype=int) isn't in numpy 1.5 

while True: 

oclusterId = clusterId 

clusterId = _assignClusters(yvec, centers) 

 

if numpy.all(clusterId == oclusterId): 

break 

 

for i in range(nCluster): 

# Only compute func if some points are available; otherwise, default to NaN. 

pointsInCluster = (clusterId == i) 

if numpy.any(pointsInCluster): 

centers[i] = func(yvec[pointsInCluster]) 

else: 

centers[i] = numpy.nan 

 

return centers, clusterId 

 

 

def _improveCluster(yvec, centers, clusterId, nsigma=2.0, nIteration=10, clusterNum=0, widthStdAllowed=0.15): 

"""Improve our estimate of one of the clusters (clusterNum) by sigma-clipping around its median""" 

 

nMember = sum(clusterId == clusterNum) 

if nMember < 5: # can't compute meaningful interquartile range, so no chance of improvement 

return clusterId 

211 ↛ 237line 211 didn't jump to line 237, because the loop on line 211 didn't complete for iter in range(nIteration): 

old_nMember = nMember 

 

inCluster0 = clusterId == clusterNum 

yv = yvec[inCluster0] 

 

centers[clusterNum] = numpy.median(yv) 

stdev = numpy.std(yv) 

 

syv = sorted(yv) 

stdev_iqr = 0.741*(syv[int(0.75*nMember)] - syv[int(0.25*nMember)]) 

median = syv[int(0.5*nMember)] 

 

sd = stdev if stdev < stdev_iqr else stdev_iqr 

 

if False: 

print("sigma(iqr) = %.3f, sigma = %.3f" % (stdev_iqr, numpy.std(yv))) 

newCluster0 = abs(yvec - centers[clusterNum]) < nsigma*sd 

clusterId[numpy.logical_and(inCluster0, newCluster0)] = clusterNum 

clusterId[numpy.logical_and(inCluster0, numpy.logical_not(newCluster0))] = -1 

 

nMember = sum(clusterId == clusterNum) 

# 'sd < widthStdAllowed * median' prevents too much rejections 

234 ↛ 211line 234 didn't jump to line 211, because the condition on line 234 was never false if nMember == old_nMember or sd < widthStdAllowed * median: 

break 

 

return clusterId 

 

 

def plot(mag, width, centers, clusterId, marker="o", markersize=2, markeredgewidth=0, ltype='-', 

magType="model", clear=True): 

 

log = Log.getLogger("objectSizeStarSelector.plot") 

try: 

import matplotlib.pyplot as plt 

except ImportError as e: 

log.warn("Unable to import matplotlib: %s", e) 

return 

 

global fig 

if not fig: 

fig = plt.figure() 

else: 

if clear: 

fig.clf() 

 

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))] 

 

axes.set_xlim(-17.5, -13) 

axes.set_xlim(xmin - 0.1*(xmax - xmin), xmax + 0.1*(xmax - xmin)) 

axes.set_ylim(0, 10) 

 

colors = ["r", "g", "b", "c", "m", "k", ] 

for k, mean in enumerate(centers): 

if k == 0: 

axes.plot(axes.get_xlim(), (mean, mean,), "k%s" % ltype) 

 

li = (clusterId == k) 

axes.plot(mag[li], width[li], marker, markersize=markersize, markeredgewidth=markeredgewidth, 

color=colors[k % len(colors)]) 

 

li = (clusterId == -1) 

axes.plot(mag[li], width[li], marker, markersize=markersize, markeredgewidth=markeredgewidth, 

color='k') 

 

if clear: 

axes.set_xlabel("Instrumental %s mag" % magType) 

axes.set_ylabel(r"$\sqrt{(I_{xx} + I_{yy})/2}$") 

 

return fig 

 

## @addtogroup LSST_task_documentation 

## @{ 

## @page ObjectSizeStarSelectorTask 

## @ref ObjectSizeStarSelectorTask_ "ObjectSizeStarSelectorTask" 

## @copybrief ObjectSizeStarSelectorTask 

## @} 

 

 

@pexConfig.registerConfigurable("objectSize", sourceSelectorRegistry) 

class ObjectSizeStarSelectorTask(BaseSourceSelectorTask): 

"""!A star selector that looks for a cluster of small objects in a size-magnitude plot 

 

@anchor ObjectSizeStarSelectorTask_ 

 

@section meas_algorithms_objectSizeStarSelector_Contents Contents 

 

- @ref meas_algorithms_objectSizeStarSelector_Purpose 

- @ref meas_algorithms_objectSizeStarSelector_Initialize 

- @ref meas_algorithms_objectSizeStarSelector_IO 

- @ref meas_algorithms_objectSizeStarSelector_Config 

- @ref meas_algorithms_objectSizeStarSelector_Debug 

 

@section meas_algorithms_objectSizeStarSelector_Purpose Description 

 

A star selector that looks for a cluster of small objects in a size-magnitude plot. 

 

@section meas_algorithms_objectSizeStarSelector_Initialize Task initialisation 

 

@copydoc \_\_init\_\_ 

 

@section meas_algorithms_objectSizeStarSelector_IO Invoking the Task 

 

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

 

@section meas_algorithms_objectSizeStarSelector_Config Configuration parameters 

 

See @ref ObjectSizeStarSelectorConfig 

 

@section meas_algorithms_objectSizeStarSelector_Debug Debug variables 

 

ObjectSizeStarSelectorTask 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>plotMagSize 

<dd>bool: if True display the magnitude-size relation using matplotlib 

<dt>dumpData 

<dd>bool; if True dump data to a pickle file 

</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.plotMagSize = True 

 

return di 

 

lsstDebug.Info = DebugInfo 

@endcode 

into your `debug.py` file and run your task with the `--debug` flag. 

""" 

ConfigClass = ObjectSizeStarSelectorConfig 

usesMatches = False # selectStars does not use its matches argument 

 

def selectSources(self, sourceCat, matches=None, exposure=None): 

"""Return a selection of PSF candidates that represent likely stars. 

 

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

 

Parameters: 

----------- 

sourceCat : `lsst.afw.table.SourceCatalog` 

Catalog of sources to select from. 

This catalog must be contiguous in memory. 

matches : `list` of `lsst.afw.table.ReferenceMatch` or None 

Ignored in this SourceSelector. 

exposure : `lsst.afw.image.Exposure` or None 

The exposure the catalog was built from; used to get the detector 

to transform to TanPix, and for debug display. 

 

Return 

------ 

struct : `lsst.pipe.base.Struct` 

The struct contains the following data: 

 

- selected : `array` of `bool`` 

Boolean array of sources that were selected, same length as 

sourceCat. 

""" 

import lsstDebug 

display = lsstDebug.Info(__name__).display 

displayExposure = lsstDebug.Info(__name__).displayExposure # display the Exposure + spatialCells 

plotMagSize = lsstDebug.Info(__name__).plotMagSize # display the magnitude-size relation 

dumpData = lsstDebug.Info(__name__).dumpData # dump data to pickle file? 

 

detector = exposure.getDetector() 

pixToTanPix = None 

389 ↛ 394line 389 didn't jump to line 394, because the condition on line 389 was never false if detector is not None: 

pixToTanPix = detector.getTransform(PIXELS, TAN_PIXELS) 

# 

# Look at the distribution of stars in the magnitude-size plane 

# 

flux = sourceCat.get(self.config.sourceFluxField) 

 

xx = numpy.empty(len(sourceCat)) 

xy = numpy.empty_like(xx) 

yy = numpy.empty_like(xx) 

for i, source in enumerate(sourceCat): 

Ixx, Ixy, Iyy = source.getIxx(), source.getIxy(), source.getIyy() 

401 ↛ 408line 401 didn't jump to line 408, because the condition on line 401 was never false if pixToTanPix: 

p = lsst.geom.Point2D(source.getX(), source.getY()) 

linTransform = afwGeom.linearizeTransform(pixToTanPix, p).getLinear() 

m = afwGeom.Quadrupole(Ixx, Iyy, Ixy) 

m.transform(linTransform) 

Ixx, Iyy, Ixy = m.getIxx(), m.getIyy(), m.getIxy() 

 

xx[i], xy[i], yy[i] = Ixx, Ixy, Iyy 

 

width = numpy.sqrt(0.5*(xx + yy)) 

with numpy.errstate(invalid="ignore"): # suppress NAN warnings 

bad = reduce(lambda x, y: numpy.logical_or(x, sourceCat.get(y)), self.config.badFlags, False) 

bad = numpy.logical_or(bad, flux < self.config.fluxMin) 

bad = numpy.logical_or(bad, numpy.logical_not(numpy.isfinite(width))) 

bad = numpy.logical_or(bad, numpy.logical_not(numpy.isfinite(flux))) 

bad = numpy.logical_or(bad, width < self.config.widthMin) 

bad = numpy.logical_or(bad, width > self.config.widthMax) 

418 ↛ 419line 418 didn't jump to line 419, because the condition on line 418 was never true if self.config.fluxMax > 0: 

bad = numpy.logical_or(bad, flux > self.config.fluxMax) 

good = numpy.logical_not(bad) 

 

422 ↛ 423line 422 didn't jump to line 423, because the condition on line 422 was never true if not numpy.any(good): 

raise RuntimeError("No objects passed our cuts for consideration as psf stars") 

 

mag = -2.5*numpy.log10(flux[good]) 

width = width[good] 

# 

# Look for the maximum in the size histogram, then search upwards for the minimum that separates 

# the initial peak (of, we presume, stars) from the galaxies 

# 

431 ↛ 432line 431 didn't jump to line 432, because the condition on line 431 was never true if dumpData: 

import os 

import pickle as pickle 

_ii = 0 

while True: 

pickleFile = os.path.expanduser(os.path.join("~", "widths-%d.pkl" % _ii)) 

if not os.path.exists(pickleFile): 

break 

_ii += 1 

 

with open(pickleFile, "wb") as fd: 

pickle.dump(mag, fd, -1) 

pickle.dump(width, fd, -1) 

 

centers, clusterId = _kcenters(width, nCluster=4, useMedian=True, 

widthStdAllowed=self.config.widthStdAllowed) 

 

448 ↛ 449line 448 didn't jump to line 449, because the condition on line 448 was never true if display and plotMagSize: 

fig = plot(mag, width, centers, clusterId, 

magType=self.config.sourceFluxField.split(".")[-1].title(), 

marker="+", markersize=3, markeredgewidth=None, ltype=':', clear=True) 

else: 

fig = None 

 

clusterId = _improveCluster(width, centers, clusterId, 

nsigma=self.config.nSigmaClip, 

widthStdAllowed=self.config.widthStdAllowed) 

 

459 ↛ 460line 459 didn't jump to line 460, because the condition on line 459 was never true if display and plotMagSize: 

plot(mag, width, centers, clusterId, marker="x", markersize=3, markeredgewidth=None, clear=False) 

 

stellar = (clusterId == 0) 

# 

# We know enough to plot, if so requested 

# 

frame = 0 

 

468 ↛ 469line 468 didn't jump to line 469, because the condition on line 468 was never true if fig: 

if display and displayExposure: 

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

 

global eventHandler 

eventHandler = EventHandler(fig.get_axes()[0], mag, width, 

sourceCat.getX()[good], sourceCat.getY()[good], frames=[frame]) 

 

fig.show() 

 

while True: 

try: 

reply = input("continue? [c h(elp) q(uit) p(db)] ").strip() 

except EOFError: 

reply = None 

if not reply: 

reply = "c" 

 

if reply: 

if reply[0] == "h": 

print("""\ 

We cluster the points; red are the stellar candidates and the other colours are other clusters. 

Points labelled + are rejects from the cluster (only for cluster 0). 

 

At this prompt, you can continue with almost any key; 'p' enters pdb, and 'h' prints this text 

 

If displayExposure is true, you can put the cursor on a point and hit 'p' to see it in ds9. 

""") 

elif reply[0] == "p": 

import pdb 

pdb.set_trace() 

elif reply[0] == 'q': 

sys.exit(1) 

else: 

break 

 

504 ↛ 505line 504 didn't jump to line 505, because the condition on line 504 was never true if display and displayExposure: 

mi = exposure.getMaskedImage() 

 

with ds9.Buffering(): 

for i, source in enumerate(sourceCat): 

if good[i]: 

ctype = ds9.GREEN # star candidate 

else: 

ctype = ds9.RED # not star 

 

ds9.dot("+", source.getX() - mi.getX0(), 

source.getY() - mi.getY0(), frame=frame, ctype=ctype) 

 

# stellar only applies to good==True objects 

mask = good == True # noqa (numpy bool comparison): E712 

good[mask] = stellar 

 

return Struct(selected=good)