def __init__(self, config, *, display=None, **kwargs):
super().__init__(config=config, **kwargs)
self.makeSubtask("installPsf")
self.display = None
if display:
self.display = display
self.centroidName = "base_SdssCentroid"
self.shapeName = "base_SdssShape"
self.schema = afwTable.SourceTable.makeMinimalSchema()
self.schema.getAliasMap().set("slot_Centroid", self.centroidName)
self.schema.getAliasMap().set("slot_Shape", self.shapeName)
self.control = measBase.SdssCentroidControl()
self.centroider = measBase.SdssCentroidAlgorithm(
self.control, self.centroidName, self.schema)
self.sdssShape = measBase.SdssShapeControl()
self.shaper = measBase.SdssShapeAlgorithm(self.sdssShape,
self.shapeName, self.schema)
self.apFluxControl = measBase.ApertureFluxControl()
md = dafBase.PropertySet()
self.apFluxer = measBase.CircularApertureFluxAlgorithm(
self.apFluxControl, "aperFlux", self.schema, md)
self.table = afwTable.SourceTable.make(
self.schema) # make sure to call this last!
def showPsfMosaic(exposure, psf=None, nx=7, ny=None, showCenter=True, showEllipticity=False,
showFwhm=False, stampSize=0, display=None, title=None):
"""Show a mosaic of Psf images. exposure may be an Exposure (optionally with PSF),
or a tuple (width, height)
If stampSize is > 0, the psf images will be trimmed to stampSize*stampSize
"""
scale = 1.0
if showFwhm:
showEllipticity = True
scale = 2*math.log(2) # convert sigma^2 to HWHM^2 for a Gaussian
mos = displayUtils.Mosaic()
try: # maybe it's a real Exposure
width, height = exposure.getWidth(), exposure.getHeight()
x0, y0 = exposure.getXY0()
if not psf:
psf = exposure.getPsf()
except AttributeError:
try: # OK, maybe a list [width, height]
width, height = exposure[0], exposure[1]
x0, y0 = 0, 0
except TypeError: # I guess not
raise RuntimeError("Unable to extract width/height from object of type %s" % type(exposure))
if not ny:
ny = int(nx*float(height)/width + 0.5)
if not ny:
ny = 1
centroidName = "SdssCentroid"
shapeName = "base_SdssShape"
schema = afwTable.SourceTable.makeMinimalSchema()
schema.getAliasMap().set("slot_Centroid", centroidName)
schema.getAliasMap().set("slot_Centroid_flag", centroidName+"_flag")
control = measBase.SdssCentroidControl()
centroider = measBase.SdssCentroidAlgorithm(control, centroidName, schema)
sdssShape = measBase.SdssShapeControl()
shaper = measBase.SdssShapeAlgorithm(sdssShape, shapeName, schema)
table = afwTable.SourceTable.make(schema)
table.defineCentroid(centroidName)
table.defineShape(shapeName)
bbox = None
if stampSize > 0:
w, h = psf.computeImage(lsst.geom.PointD(0, 0)).getDimensions()
if stampSize <= w and stampSize <= h:
bbox = lsst.geom.BoxI(lsst.geom.PointI((w - stampSize)//2, (h - stampSize)//2),
lsst.geom.ExtentI(stampSize, stampSize))
centers = []
shapes = []
for iy in range(ny):
for ix in range(nx):
x = int(ix*(width-1)/(nx-1)) + x0
y = int(iy*(height-1)/(ny-1)) + y0
im = psf.computeImage(lsst.geom.PointD(x, y)).convertF()
imPeak = psf.computePeak(lsst.geom.PointD(x, y))
im /= imPeak
if bbox:
im = im.Factory(im, bbox)
lab = "PSF(%d,%d)" % (x, y) if False else ""
mos.append(im, lab)
exp = afwImage.makeExposure(afwImage.makeMaskedImage(im))
exp.setPsf(psf)
w, h = im.getWidth(), im.getHeight()
centerX = im.getX0() + w//2
centerY = im.getY0() + h//2
src = table.makeRecord()
spans = afwGeom.SpanSet(exp.getBBox())
foot = afwDet.Footprint(spans)
foot.addPeak(centerX, centerY, 1)
src.setFootprint(foot)
try:
centroider.measure(src, exp)
centers.append((src.getX() - im.getX0(), src.getY() - im.getY0()))
shaper.measure(src, exp)
shapes.append((src.getIxx(), src.getIxy(), src.getIyy()))
except Exception:
pass
if not display:
display = afwDisplay.Display()
mos.makeMosaic(display=display, title=title if title else "Model Psf", mode=nx)
if centers and display:
with display.Buffering():
for i, (cen, shape) in enumerate(zip(centers, shapes)):
bbox = mos.getBBox(i)
xc, yc = cen[0] + bbox.getMinX(), cen[1] + bbox.getMinY()
if showCenter:
display.dot("+", xc, yc, ctype=afwDisplay.BLUE)
if showEllipticity:
ixx, ixy, iyy = shape
ixx *= scale
ixy *= scale
iyy *= scale
display.dot("@:%g,%g,%g" % (ixx, ixy, iyy), xc, yc, ctype=afwDisplay.RED)
return mos
def showKernelMosaic(bbox, kernel, nx=7, ny=None, frame=None, title=None,
showCenter=True, showEllipticity=True):
"""Show a mosaic of Kernel images.
"""
mos = afwDisplay.utils.Mosaic()
x0 = bbox.getBeginX()
y0 = bbox.getBeginY()
width = bbox.getWidth()
height = bbox.getHeight()
if not ny:
ny = int(nx*float(height)/width + 0.5)
if not ny:
ny = 1
schema = afwTable.SourceTable.makeMinimalSchema()
centroidName = "base_SdssCentroid"
shapeName = "base_SdssShape"
control = measBase.SdssCentroidControl()
schema.getAliasMap().set("slot_Centroid", centroidName)
schema.getAliasMap().set("slot_Centroid_flag", centroidName + "_flag")
centroider = measBase.SdssCentroidAlgorithm(control, centroidName, schema)
sdssShape = measBase.SdssShapeControl()
shaper = measBase.SdssShapeAlgorithm(sdssShape, shapeName, schema)
table = afwTable.SourceTable.make(schema)
table.defineCentroid(centroidName)
table.defineShape(shapeName)
centers = []
shapes = []
for iy in range(ny):
for ix in range(nx):
x = int(ix*(width - 1)/(nx - 1)) + x0
y = int(iy*(height - 1)/(ny - 1)) + y0
im = afwImage.ImageD(kernel.getDimensions())
ksum = kernel.computeImage(im, False, x, y)
lab = "Kernel(%d,%d)=%.2f" % (x, y, ksum) if False else ""
mos.append(im, lab)
# SdssCentroidAlgorithm.measure requires an exposure of floats
exp = afwImage.makeExposure(afwImage.makeMaskedImage(im.convertF()))
w, h = im.getWidth(), im.getHeight()
centerX = im.getX0() + w//2
centerY = im.getY0() + h//2
src = table.makeRecord()
spans = afwGeom.SpanSet(exp.getBBox())
foot = afwDet.Footprint(spans)
foot.addPeak(centerX, centerY, 1)
src.setFootprint(foot)
try: # The centroider requires a psf, so this will fail if none is attached to exp
centroider.measure(src, exp)
centers.append((src.getX(), src.getY()))
shaper.measure(src, exp)
shapes.append((src.getIxx(), src.getIxy(), src.getIyy()))
except Exception:
pass
disp = afwDisplay.Display(frame=frame)
mos.makeMosaic(display=disp, title=title if title else "Model Kernel", mode=nx)
if centers and frame is not None:
disp = afwDisplay.Display(frame=frame)
i = 0
with disp.Buffering():
for cen, shape in zip(centers, shapes):
bbox = mos.getBBox(i)
i += 1
xc, yc = cen[0] + bbox.getMinX(), cen[1] + bbox.getMinY()
if showCenter:
disp.dot("+", xc, yc, ctype=afwDisplay.BLUE)
if showEllipticity:
ixx, ixy, iyy = shape
disp.dot("@:%g,%g,%g" % (ixx, ixy, iyy), xc, yc, ctype=afwDisplay.RED)
return mos
def do_testmeasureShape(self):
"""Test that we can instantiate and play with a measureShape"""
im = afwImage.ImageF(afwGeom.ExtentI(100))
msk = afwImage.MaskU(im.getDimensions())
msk.set(0)
var = afwImage.ImageF(im.getDimensions())
var.set(10)
mi = afwImage.MaskedImageF(im, msk, var)
del im
del msk
del var
exp = afwImage.makeExposure(mi)
bkgd = 100.0
control = measBase.SdssShapeControl()
control.background = bkgd
control.maxShift = 2
plugin, cat = makePluginAndCat(measBase.SdssShapeAlgorithm,
"test",
control,
centroid="centroid")
#cat.defineCentroid("test")
cat.defineShape("test")
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
#
# Add a Gaussian to the image
#
for a, b, phi, tol in [ # n.b. phi in degrees
(2.5, 1.5, 90.0, 1e-3),
(1.5, 2.5, 0.0, 1e-3),
(1.5, 2.5, 45.0, 1e-3),
(1.5, 2.5, 90.0, 1e-3),
(3.0, 2.5, 0.0, 1e-3),
(3.0, 12.5, 0.0, 1e-3),
(3.0, 12.5, 0.0, 2e-4),
(1.0, 1.0, 0.0, 4e-3),
(1.0, 0.75, 0.0, 2e-2),
#(0.75, 0.75, 0.0, 1e-1),
]:
if b > a:
a, b = b, a
phi -= 90
a, b, phi = float(a), float(b), math.radians(phi)
im = mi.getImage()
x, y = 30, 40 # centre of object
im[:] = bkgd
axes = afwGeom.ellipses.Axes(a, b, phi, True)
quad = afwGeom.ellipses.Quadrupole(axes)
if False:
a0, b0 = a, b
pixellatedAxes = axes.convolve(
afwGeom.ellipses.Quadrupole(1 / 6.0, 1 / 6.0))
a, b = pixellatedAxes.getA(), pixellatedAxes.getB()
print a, b, a0, b0
sigma_xx, sigma_yy, sigma_xy = quad.getIxx(), quad.getIyy(
), quad.getIxy()
ksize = 2 * int(4 * max(a, b)) + 1
c, s = math.cos(phi), math.sin(phi)
sum, sumxx, sumxy, sumyy = 4 * [0.0] if False else 4 * [None]
for dx in range(-ksize / 2, ksize / 2 + 1):
for dy in range(-ksize / 2, ksize / 2 + 1):
u, v = c * dx + s * dy, s * dx - c * dy
I = 1000 * math.exp(-0.5 * ((u / a)**2 + (v / b)**2))
im[x + dx, y + dy] += I
if sum is not None:
sum += I
sumxx += I * dx * dx
sumxy += I * dx * dy
sumyy += I * dy * dy
if sum is not None:
sumxx /= sum
sumxy /= sum
sumyy /= sum
print "RHL %g %g %g" % (sumxx, sumyy, sumxy)
if display:
ds9.mtv(im)
footprint = afwDetection.FootprintSet(
im, afwDetection.Threshold(110)).getFootprints()[0]
source = cat.addNew()
source.setFootprint(footprint)
source.set("centroid_x",
footprint.getPeaks()[0].getCentroid().getX())
source.set("centroid_y",
footprint.getPeaks()[0].getCentroid().getY())
plugin.measure(source, exp)
if False:
Ixx, Iyy, Ixy = source.getIxx(), source.getIyy(
), source.getIxy()
A2 = 0.5 * (Ixx + Iyy) + math.sqrt((0.5 *
(Ixx - Iyy))**2 + Ixy**2)
B2 = 0.5 * (Ixx + Iyy) - math.sqrt((0.5 *
(Ixx - Iyy))**2 + Ixy**2)
print "I_xx: %.5f %.5f" % (Ixx, sigma_xx)
print "I_xy: %.5f %.5f" % (Ixy, sigma_xy)
print "I_yy: %.5f %.5f" % (Iyy, sigma_yy)
print "A2, B2 = %.5f, %.5f" % (A2, B2)
print source.getX(), source.getY(), x, y
print source.getIxx(), sigma_xx, source.getIyy(
), sigma_yy, source.getIxy(), sigma_xy
self.assertTrue(
abs(x - source.getX()) < 1e-4, "%g v. %g" % (x, source.getX()))
self.assertTrue(
abs(y - source.getY()) < 1e-4, "%g v. %g" % (y, source.getY()))
self.assertTrue(
abs(source.getIxx() - sigma_xx) < tol * (1 + sigma_xx),
"%g v. %g" % (sigma_xx, source.getIxx()))
self.assertTrue(
abs(source.getIxy() - sigma_xy) < tol * (1 + abs(sigma_xy)),
"%g v. %g" % (sigma_xy, source.getIxy()))
self.assertTrue(
abs(source.getIyy() - sigma_yy) < tol * (1 + sigma_yy),
"%g v. %g" % (sigma_yy, source.getIyy()))