def ObserveLens(self, noisy=True, bands=[]):
if bands == []:
bands = self.bands # if bands exists, then bands is set to be the bands
for band in bands:
if self.seeing[band] == 0:
# convolvedGalaxy and the psfForwardFourierTransform is the convolution of the galaxyModel and the psf from convolve.py and edgeCheck is True
convolvedGalaxy, self.psfFFT[band] = convolve.convolve(
self.galModel[band], self.psf[band], True)
convolvedGalaxy[convolvedGalaxy < 0] = 0
self.convolvedGal[band] = convolvedGalaxy
convolvedmodel = convolvedGalaxy * 1
convolvedsrc = {}
for sourcenumber in self.sourcenumbers:
convolvedsrc[sourcenumber] = convolve.convolve(
self.sourceModel[sourcenumber][band],
self.psfFFT[band], False)[0]
convolvedsrc[sourcenumber][
convolvedsrc[sourcenumber] < 0] = 0
self.convolvedsrc[sourcenumber][band] = convolvedsrc[
sourcenumber]
convolvedmodel += convolvedsrc[sourcenumber]
self.zeroMagCounts[band] = (10**(-(0 - self.zeropoints[band]) /
2.5))
exposurecorrection = (
(self.ET[band] * 1. /
self.zeroexposuretime)) * self.gains[band]
convolvedmodel *= exposurecorrection
#skybackground per second per square arcsecond
background = (10**(-(self.SB[band] - self.zeropoints[band]) /
2.5)) * (self.pixelsize**2)
tot_bg = background * exposurecorrection
sigma = ((convolvedmodel + tot_bg) + self.nexposures *
(self.readnoise**0.5)**2)**.5
fakeLens = convolvedmodel * 1.
if noisy:
fakeLens += (numpy.random.randn(self.side, self.side) *
(sigma))
#convert back to ADU/second:
fakeLens /= exposurecorrection
sigma /= exposurecorrection
self.image[band] = fakeLens * 1
self.fakeLens[band] = fakeLens * 1
self.sigma[band] = sigma * 1
self.fakeResidual[0][band] = fakeLens - convolvedGalaxy
for sourcenumber in self.sourcenumbers:
self.SN[sourcenumber][band]=self.SNfunc(\
convolvedsrc[sourcenumber],sigma)
self.fakeResidual[sourcenumber][band]=\
fakeLens-convolvedmodel+convolvedsrc[sourcenumber]
def optimize_amp(self):
chi2sum = 0.
for band in self.bands:
lens_models = []
for lens_model in self.lens_models:
lens_models.append(lens_model[band])
xl, yl = pylens.getDeflections(lens_models, (self.X, self.Y))
lpix = []
spix = []
for light in self.light_sb_models:
light[band].amp = 1.
lpix.append(light[band].pixeval(self.X, self.Y))
for source in self.source_sb_models:
source[band].amp = 1.
spix.append(source[band].pixeval(xl, yl))
modlist = []
for l in lpix:
modlist.append(
(convolve.convolve(l, self.convol_matrix[band], False)[0] /
self.err[band]).ravel()[self.mask_r])
for s in spix:
modlist.append(
(convolve.convolve(s, self.convol_matrix[band], False)[0] /
self.err[band]).ravel()[self.mask_r])
modarr = np.array(modlist).T
if np.isnan(modarr).any() or not np.isfinite(modarr).any():
amps = np.ones(self.nlight + self.nsource)
chi = 1e300
else:
amps, chi = nnls(modarr, (self.sci[band] /
self.err[band]).ravel()[self.mask_r])
chi2sum += chi**2
i = 0
for light, mags in zip(self.light_sb_models, self.light_mags):
if amps[i] > 0.:
light[band].amp = amps[i]
mags[band] = light[band].Mag(self.zp[band])
else:
mags[band] = 99.
i += 1
for source, mags in zip(self.source_sb_models, self.source_mags):
if amps[i] > 0.:
source[band].amp = amps[i]
mags[band] = source[band].Mag(self.zp[band])
else:
mags[band] = 99.
i += 1
self.logp = -0.5 * chi2sum
return chi2sum
def logP(value=0.,p=pars):
lp = 0.
models = []
for i in range(len(imgs)):
image, sigma,scale = imgs[i],sigs[i],scales[i]
if i == 0:
dx,dy = 0,0
xp,yp = xc+dx,yc+dy
psf = PSFs[i]
elif i ==1:
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
psf = PSFs[i]
elif i ==2:
dx = pars[2].value
dy = pars[3].value
xp,yp = xck+dx,yck+dy
psf = xpsf*0.
for obj in psfObjs:
obj.setPars()
psf += obj.pixeval(xpsf,ypsf) / (np.pi*2.*obj.pars['sigma'].value**2.)
psf = psf/psf.sum()
psf = convolve.convolve(image,psf)[1]
mask,mask2=np.ones(image.shape),np.ones(image.shape)
mask,mask2=mask==1,mask2==1
imin,sigin,xin,yin = image[mask], sigma[mask],xp[mask2],yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs)+1),imin.size))
for gal in gals:
gal.setPars()
#print gal.pars['x'].value, gal.pars['y'].value,gal.pars['q'].value, gal.pars['pa'].value,gal.pars['re'].value, gal.pars['n'].value
tmp = xp*0.
tmp[mask2] = gal.pixeval(xin,yin,scale/OVRS,csub=1)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,srcs,[xin,yin],1./OVRS,getPix=True)
for src in srcs:
src.setPars()
#print src.pars['x'].value, src.pars['y'].value,src.pars['q'].value, src.pars['pa'].value,src.pars['re'].value, src.pars['n'].value
tmp = xp*0.
tmp[mask2] = src.pixeval(x0,y0,scale/OVRS,csub=1)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
model[n] = np.ones(model[n-1].shape)
rhs = (imin/sigin)
op = (model/sigin).T
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp += -0.5*(resid**2.).sum()
models.append(model)
return lp
def GetFits(self):
bands = dict([('J0837','F606W'),('J0901','F606W'),('J0913','F555W'),('J1125','F606W'),('J1144','F606W'),('J1218','F606W'),('J1248','F555W'),('J1323','F555W'),('J1347','F606W'),('J1446','F606W'),('J1605','F555W'),('J1606','F606W'),('J1619','F606W'),('J2228','F606W')])
# not working yet - this will need us to have all the images somewhere, and all the xc,yc offsets!
# get nnls values! Ideally, these should be already saved
print "why didn't you save these before?!?"
yc,xc = iT.coords(self.img1.shape)
OVRS=1
yo,xo=iT.overSample(self.img1.shape,OVRS)
colours = [bands[self.name], 'F814W']
models = []
fits = []
for i in range(len(self.imgs)):
if i == 0:
dx,dy = 0,0
else:
dx = self.Ddic['xoffset']
dy = self.Ddic['yoffset']
xp,yp = xc+dx+self.Dx,yc+dy+self.Dx
xop,yop = xo+dy+self.Dy,yo+dy+self.Dy
image = self.imgs[i]
sigma = self.sigs[i]
psf = self.PSFs[i]
imin,sigin,xin,yin = image.flatten(), sigma.flatten(),xp.flatten(),yp.flatten()
n = 0
model = np.empty(((len(self.gals) + len(self.srcs)+1),imin.size))
for gal in self.gals:
gal.setPars()
tmp = xc*0.
tmp = gal.pixeval(xp,yp,1./OVRS,csub=11) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp.ravel()
n +=1
for lens in self.lenses:
lens.setPars()
x0,y0 = pylens.lens_images(self.lenses,self.srcs,[xp,yp],1./OVRS,getPix=True)
for src in self.srcs:
src.setPars()
tmp = xc*0.
tmp = src.pixeval(x0,y0,1./OVRS,csub=11)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp.ravel()
n +=1
model[n] = np.ones(model[n].shape)
n +=1
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
components = (model.T*fit).T.reshape((n,image.shape[0],image.shape[1]))
model = components.sum(0)
models.append(model)
#SotPleparately(image,model,sigma,colours[i])
#NotPlicely(image,model,sigma)
comps = False
if comps == True:
CotSomponents(components,colours[i])
fits.append(fit)
self.fits = fits
def ObserveLens(self, noisy=True, bands=[]):
if bands == []: bands = self.bands
for band in bands:
if self.seeing[band] != 0:
convolvedgal, self.psfFFT[band] = convolve.convolve(
self.galmodel[band], self.psf[band], True)
convolvedgal[convolvedgal < 0] = 0
self.convolvedgal[band] = convolvedgal
convolvedmodel = convolvedgal * 1
convolvedsrc = {}
for sourcenumber in self.sourcenumbers:
convolvedsrc[sourcenumber] = convolve.convolve(
self.sourcemodel[sourcenumber][band],
self.psfFFT[band], False)[0]
convolvedsrc[sourcenumber][
convolvedsrc[sourcenumber] < 0] = 0
self.convolvedsrc[sourcenumber][band] = convolvedsrc[
sourcenumber]
convolvedmodel += convolvedsrc[sourcenumber]
self.zeromagcounts[band] = (10**(-(0 - self.zeropoints[band]) /
2.5))
exposurecorrection = (
(self.ET[band] * 1. /
self.zeroexposuretime)) * self.gains[band]
convolvedmodel *= exposurecorrection
#skybackground per second per square arcsecond
background = (10**(-(self.SB[band] - self.zeropoints[band]) /
2.5)) * (self.pixelsize**2)
tot_bg = background * exposurecorrection
sigma = ((convolvedmodel + tot_bg) + self.nexposures *
(self.readnoise**0.5)**2)**.5
fakeLens = convolvedmodel * 1.
if noisy:
fakeLens += (numpy.random.randn(self.side, self.side) *
(sigma))
#convert back to ADU/second:
fakeLens /= exposurecorrection
sigma /= exposurecorrection
self.image[band] = fakeLens * 1
self.fakeLens[band] = fakeLens * 1
self.sigma[band] = sigma * 1
self.fakeResidual[0][band] = fakeLens - convolvedgal
for sourcenumber in self.sourcenumbers:
self.SN[sourcenumber][band]=self.SNfunc(\
convolvedsrc[sourcenumber],sigma)
self.fakeResidual[sourcenumber][band]=\
fakeLens-convolvedmodel+convolvedsrc[sourcenumber]
def logP(value=0.,p=pars):
lp = 0.
models = []
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
sig1 = pars[2].value.item()
q1 = pars[3].value.item()
pa1 = pars[4].value.item()
amp1 = pars[5].value.item()
sig2 = pars[6].value.item()
q2 = 1.#pars[7].value.item()
pa2 = 0#pars[7].value.item()
amp2 = pars[7].value.item()
sig3 = pars[8].value.item()
q3,pa3 = 1.,0.
amp3 = 1.-amp1-amp2
psfObj1 = SBObjects.Gauss('psf 1',{'x':0,'y':0,'sigma':sig1,'q':q1,'pa':pa1,'amp':10})
psfObj2 = SBObjects.Gauss('psf 2',{'x':0,'y':0,'sigma':sig2,'q':q2,'pa':pa2,'amp':10})
psfObj3 = SBObjects.Gauss('psf 3',{'x':0,'y':0,'sigma':sig3,'q':q3,'pa':pa3,'amp':10})
psf1 = psfObj1.pixeval(xpsf,ypsf) * amp1 / (np.pi*2.*sig1**2.)
psf2 = psfObj2.pixeval(xpsf,ypsf) * amp2 / (np.pi*2.*sig2**2.)
psf3 = psfObj3.pixeval(xpsf,ypsf) * amp3 / (np.pi*2.*sig3**2.)
psf = psf1 + psf2 + psf3
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
imin,sigin,xin,yin = image[mask], sigma[mask],xp[mask2],yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs)+1),imin.size))
for gal in gals:
gal.setPars()
tmp = xc*0.
tmp[mask2] = gal.pixeval(xin,yin,1./OVRS,csub=1) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,srcs,[xin,yin],1./OVRS,getPix=True)
for src in srcs:
src.setPars()
tmp = xc*0.
tmp[mask2] = src.pixeval(x0,y0,1./OVRS,csub=1)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
model[n] = np.ones(model[n-1].shape)
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp = -0.5*(resid**2.).sum()
return lp
def get_chi2(self):
light_ind_model = []
source_ind_model = []
xl, yl = pylens.getDeflections(self.lens_models, (self.X, self.Y))
model_array = (0. * self.scistack).ravel()[self.maskstack_r]
for light, sed in zip(self.light_sb_models, self.light_sed_models):
lmodel = 0. * self.scistack
light.setAmpFromMag(sed.mags[self.main_band],
self.zp[self.main_band])
if light.__class__.__name__ == 'PointSource':
for i in range(self.nbands):
scale = sed.scale(self.bands[i], self.main_band)
lmodel[i * self.ny:(i + 1) * self.ny, :] = light.pixeval(
self.X, self.Y, self.bands[i])
else:
lpix = light.pixeval(self.X, self.Y)
for i in range(self.nbands):
scale = sed.scale(self.bands[i], self.main_band)
lmodel[i * self.ny:(i + 1) *
self.ny, :] = scale * convolve.convolve(
lpix, self.convol_matrix[self.bands[i]],
False)[0]
model_array += lmodel.ravel()[self.maskstack_r]
for source, sed in zip(self.source_sb_models, self.source_sed_models):
smodel = 0. * self.scistack
source.setAmpFromMag(sed.mags[self.main_band],
self.zp[self.main_band])
spix = source.pixeval(xl, yl)
for i in range(self.nbands):
scale = sed.scale(self.bands[i], self.main_band)
smodel[i * self.ny:(i + 1) *
self.ny, :] = scale * convolve.convolve(
spix, self.convol_matrix[self.bands[i]], False)[0]
model_array += smodel.ravel()[self.maskstack_r]
if self.sky is not None:
skymodel = 0. * self.scistack
for i in range(self.nbands):
skymodel[i * self.ny:(i + 1) *
self.ny, :] = self.sky['amp_%s' % self.bands[i]].value
model_array += skymodel.ravel()[self.maskstack_r]
if np.isnan(model_array).any() or not np.isfinite(model_array).any():
chi2 = 1e300
else:
chi2 = (
(model_array - self.scistack.ravel()[self.maskstack_r])**2 /
(self.errstack.ravel()[self.maskstack_r])**2).sum()
self.logp = -0.5 * chi2
def logP(value=0.,p=pars):
lp = 0.
models = []
for i in range(len(imgs)):
if i == 0:
dx,dy = 0,0
xp,yp = xc+dx,yc+dy
OVRS=3
elif i ==1:
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
OVRS=3
elif i ==2:
dx = pars[0].value+pars[2].value
dy = pars[1].value +pars[3].value
xp,yp = xck+dx,yck+dy
OVRS=1
image = imgs[i]
sigma = sigs[i]
psf = PSFs[i]
mask,mask2=np.ones(image.shape),np.ones(image.shape)
mask,mask2=mask==1,mask2==1
imin,sigin,xin,yin = image[mask], sigma[mask],xp[mask2],yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs)+1),imin.size))
for gal in gals:
gal.setPars()
tmp = xp*0.
tmp[mask2] = gal.pixeval(xin,yin,1./OVRS,csub=11) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,srcs,[xin,yin],1./OVRS,getPix=True)
for src in srcs:
src.setPars()
tmp = xp*0.
tmp[mask2] = src.pixeval(x0,y0,1./OVRS,csub=11)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
model[n] = np.ones(model[n].shape)
n +=1
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp += -0.5*(resid**2.).sum()
models.append(model)
return lp #,models
def logP(value=0.,p=pars):
# read in sources - I don't think this is the best way, but...
xll,yll = pylens.getDeflections(lenses,[xind,yind])
xpeak = np.sum(xll*imgind)/np.sum(imgind)
ypeak = np.sum(yll*imgind)/np.sum(imgind)
#print 'xpeak,ypeak',xpeak, ypeak
if len(srcs)==2:
srcs[0] = SBModels.Sersic('Source 2',{'x':dics[0]['x']+xpeak,'y':dics[0]['y']+ypeak,'pa':dics[0]['pa'],'q':dics[0]['q'],'re':dics[0]['re'],'n':dics[0]['n']})
srcs[1] = SBModels.Sersic('Source 1',{'x':dics[0]['x']+xpeak,'y':dics[0]['y']+ypeak,'pa':dics[1]['pa'],'q':dics[1]['q'],'re':dics[1]['re'],'n':dics[1]['n']})
else:
srcs[0] = SBModels.Sersic('Source 1',{'x':dics[0]['x']+xpeak,'y':dics[0]['y']+ypeak,'pa':dics[0]['pa'],'q':dics[0]['q'],'re':dics[0]['re'],'n':dics[0]['n']})
lp = 0.
models = []
for i in range(len(imgs)):
if i == 0:
dx,dy = 0,0
else:
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
image = imgs[i]
sigma = sigs[i]
psf = PSFs[i]
imin,sigin,xin,yin = image[mask], sigma[mask],xp[mask2],yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs)),imin.size))
for gal in gals:
gal.setPars()
tmp = xc*0.
tmp[mask2] = gal.pixeval(xin,yin,1./OVRS,csub=1) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,srcs,[xin,yin],1./OVRS,getPix=True)
for src in srcs:
src.setPars()
tmp = xc*0.
tmp[mask2] = src.pixeval(x0,y0,1./OVRS,csub=1)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp += -0.5*(resid**2.).sum()
models.append(model)
return lp #,models
def logP(value=0.,p=pars):
lp = 0.
models = []
for i in range(len(imgs)):
if i == 0:
dx,dy = 0,0
else:
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
image = imgs[i]
sigma = sigs[i]
psf = PSFs[i]
imin,sigin,xin,yin = image[mask], sigma[mask],xp[mask2],yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs)+1),imin.size))
galaxy = np.zeros(imin.size)
for gal in gals:
gal.setPars()
tmp = xc*0.
tmp[mask2] = gal.pixeval(xin,yin,1./OVRS,csub=11) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
if gal.pars['q'].value<0.35:
galaxy += gal.pixeval(xin,yin,1,csub=11)
n +=1
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,srcs,[xin,yin],1./OVRS,getPix=True)
for src in srcs:
src.setPars()
tmp = xc*0.
tmp[mask2] = src.pixeval(x0,y0,1./OVRS,csub=11)
tmp = iT.resamp(tmp,OVRS,True)
b,std,xmid,ymid = lenses[0].pars['b'].value, lenses[0].pars['b'].value*0.5,lenses[0].pars['x'].value,lenses[0].pars['y'].value
r = np.sqrt((xin-xmid)**2. + (yin-ymid)**2.)
mask3 = np.where((r>b-std) & (r<b+std) & (galaxy>=0.05*np.amax(galaxy)))
tmp.ravel()[mask3] -= pars[-1].value#*galaxy[mask3]
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
model[n] = -1*np.ones(model[n-1].shape)
n+=1
### if galaxy light > X,
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp += -0.5*(resid**2.).sum()
models.append(model)
return lp #,models
def lensModel(inpars,
image,
sig,
gals,
lenses,
sources,
xc,
yc,
OVRS=1,
csub=11,
psf=None,
noResid=False,
verbose=False):
import pylens, numpy
import indexTricks as iT
model = xc * 0.
for gal in gals:
gal.setPars(inpars)
model += gal.pixeval(xc, yc, 1. / OVRS, csub=csub)
for src in sources:
src.setPars(inpars)
for lens in lenses:
lens.setPars(inpars)
model = model + pylens.lens_images(lenses, sources, [xc, yc], 1. / OVRS)
if numpy.isnan(model.sum()):
if verbose == True:
print 'nan model'
return -1e300
if OVRS > 1:
model = iT.resamp(model, OVRS, True)
if psf is not None:
from imageSim import convolve
global psfFFT
if psfFFT is None:
psf /= psf.sum()
model, psfFFT = convolve.convolve(model, psf)
else:
model, psfFFT = convolve.convolve(model, psfFFT, False)
if noResid is True:
return model
resid = ((model - image) / sig).ravel()
if verbose == True:
print "%f %5.2f %d %dx%d" % (
(resid**2).sum(), (resid**2).sum() / resid.size, resid.size,
image.shape[1], image.shape[0])
return -0.5 * (resid**2).sum()
def logP(value=0.,p=pars):
lp = 0.
models = []
for i in range(len(imgs)):
if i == 0:
dx,dy = 0,0
xp,yp = xc,yc
else:
dx = pars[0].value
dy = pars[1].value
xp,yp = (xck+dx)*0.2,(yck+dy)*0.2
image = imgs[i]
sigma = sigs[i]
psf = PSFs[i]
mask = np.ones(image.shape)
mask = mask==1
imin,sigin,xin,yin = image.flatten(), sigma.flatten(),xp.flatten(),yp.flatten()
n = 0
model = np.empty(((len(gals) + len(srcs)+1),imin.size))
for gal in gals:
gal.setPars()
tmp = xc*0.
if gal.pars['q'].value<0.3:
tmp = gal.boxypixeval(xp,yp,1./OVRS,csub=11,c=pars[-1].value)
else:
tmp = gal.boxypixeval(xp,yp,1./OVRS,csub=11)
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp.ravel()
n +=1
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,srcs,[xp,yp],1./OVRS,getPix=True)
for src in srcs:
src.setPars()
tmp = xp*0.
tmp = src.pixeval(x0,y0,1./OVRS,csub=11)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp.ravel()
n +=1
model[n] = np.ones(model[n-1].shape)
n+=1
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp += -0.5*(resid**2.).sum()
models.append(model)
return lp #,models
def logP(value=0.0, p=pars):
lp = 0.0
models = []
dx = pars[0].value
dy = pars[1].value
xp, yp = xc + dx, yc + dy
psf = xpsf * 0.0
for obj in psfObjs:
obj.setPars()
psf += obj.pixeval(xpsf, ypsf) / (np.pi * 2.0 * obj.pars["sigma"].value ** 2.0)
if obj.pars["amp"].value < 0:
return -1e10
psf = psf / np.sum(psf)
# print obj.pars['q'].value, obj.pars['amp'].value
psf = convolve.convolve(image, psf)[1]
imin, sigin, xin, yin = image[mask], sigma[mask], xp[mask2], yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs) + 1), imin.size))
for gal in gals:
gal.setPars()
tmp = xc * 0.0
tmp[mask2] = gal.pixeval(
xin, yin, 0.2, csub=11
) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp, OVRS, True) # convert it back to original size
tmp = convolve.convolve(tmp, psf, False)[0]
model[n] = tmp[mask].ravel()
n += 1
for lens in lenses:
lens.setPars()
x0, y0 = pylens.lens_images(lenses, srcs, [xin, yin], 1.0 / OVRS, getPix=True)
kk = 0
for src in srcs:
src.setPars()
tmp = xc * 0.0
tmp[mask2] = src.pixeval(x0, y0, 0.2, csub=11)
tmp = iT.resamp(tmp, OVRS, True)
tmp = convolve.convolve(tmp, psf, False)[0]
model[n] = tmp[mask].ravel()
n += 1
model[n] = np.ones(model[n - 1].shape)
rhs = imin / sigin # data
op = (model / sigin).T # model matrix
fit, chi = optimize.nnls(op, rhs)
model = (model.T * fit).sum(1)
resid = (model - imin) / sigin
lp = -0.5 * (resid ** 2.0).sum()
return lp
def logP(value=0.,p=pars):
#print 'calculating likelihood'
lp = 0.
models = []
for i in range(len(imgs)):
if i == 0:
dx,dy = 0,0
else:
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
image = imgs[i]
poisson = poissons[i]
noise = noises[i]
X = pars[-1].value
sigma = (poisson + noise**X)**0.5
psf = PSFs[i]
imin,sigin,xin,yin = image[mask], sigma[mask],xp[mask2],yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs)),imin.size))
for gal in gals:
gal.setPars()
tmp = xc*0.
tmp[mask2] = gal.pixeval(xin,yin,1./OVRS,csub=1) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,srcs,[xin,yin],1./OVRS,getPix=True)
for src in srcs:
src.setPars()
tmp = xc*0.
tmp[mask2] = src.pixeval(x0,y0,1./OVRS,csub=1)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp += -0.5*(resid**2.).sum()
models.append(model)
#print 'calculated likelihood', lp
return lp #,models
def logP(value=0,p=pars):
x0 = pars[0].value
y0 = pars[1].value
sig = pars[2].value
psfObj = SBObjects.Gauss('psf',{'x':0,'y':0,'sigma':sig,'q':1,'pa':0,'amp':1})
psf = psfObj.pixeval(xp,yp)
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
g1a,g2a,s1a,s2a,l1a,sha = g1.copy(),g2.copy(),s1.copy(),s2.copy(),l1.copy(),sh.copy()
g1a['x'],g2a['x'] = g1a['x']+x0,g2a['x']+x0
g1a['y'],g2a['y'] = g1a['y']+y0,g2a['y']+y0
s1a['x'] = g1a['x'] + 5*(s1a['x']-(g1a['x']-x0))
s2a['x'] = g1a['x'] + 5*(s2a['x']-(g1a['x']-x0))
s1a['y'] = g1a['y'] + 5*(s1a['y']-(g1a['y']-y0))
s2a['y'] = g1a['y'] + 5*(s2a['y']-(g1a['y']-y0))
l1a['x'] = g1a['x'] + 5*(l1a['x']-(g1a['x']-x0))
l1a['y'] = g1a['y'] + 5*(l1a['y']-(g1a['y']-y0))
s1a['re'],s2a['re'],g1a['re'],g2a['re'],l1a['b'],sha['b'] = s1a['re']*5,s2a['re']*5,g1a['re']*5,g2a['re']*5,l1a['b']*5,sha['b']*5
srcs = []
gals = []
lenses = []
srcs.append(SBModels.Sersic('Source 1',s1a))
srcs.append(SBModels.Sersic('Source 2',s2a))
gals.append(SBModels.Sersic('Galaxy 1',g1a))
gals.append(SBModels.Sersic('Galaxy 2',g2a))
lenses.append(MassModels.PowerLaw('Lens 1',l1a))
sha['x'] = lenses[0].pars['x']
sha['y'] = lenses[0].pars['y']
lenses.append(MassModels.ExtShear('shear',sha))
return lensModel.lensFit(None,image,sigma,gals,lenses,srcs,xc+x0,yc+y0,1,
verbose=False,psf=psf,csub=1)
def modelSB(inpars,
image,
sigma,
mask,
models,
xc,
yc,
OVRS=1,
csub=11,
noResid=False):
output = image * 0
for model in models:
model.setPars(inpars)
img = model.pixeval(xc, yc)
if numpy.isnan(img).any() and noResid == False:
return -1e300
if model.convolve is not None:
img = convolve.convolve(img, model.convolve, False)[0]
output += img
if noResid == True:
return output
logp = (-0.5 * ((output - image) / sigma)[mask]**2).sum()
logp -= numpy.log(sigma[mask]).sum()
return logp
def logP(value=0,p=pars):
x0 = pars[0].value
y0 = pars[1].value
sig1 = pars[2].value.item()
#q1 = pars[3].value.item()
#pa1 = pars[4].value.item()
amp1 = pars[3].value.item()
sig2 = pars[4].value.item()
#q2 = pars[7].value.item()
#pa2 = pars[8].value.item()
amp2 = pars[5].value.item()
sig3 = pars[6].value.item()
#q3 = pars[11].value.item()
#pa3 = pars[12].value.item()
amp3 = pars[7].value.item()
tamp = amp1+amp2+amp3
q1,q2,q3 = 1,1,1
pa1,pa2,pa3 = 0,0,0
amp1,amp2,amp3 = amp1/tamp, amp2/tamp, amp3/tamp
psfObj1 = SBObjects.Gauss('psf 1',{'x':0,'y':0,'sigma':sig1,'q':q1,'pa':pa1,'amp':10})
psfObj2 = SBObjects.Gauss('psf 2',{'x':0,'y':0,'sigma':sig2,'q':q2,'pa':pa2,'amp':10})
psfObj3 = SBObjects.Gauss('psf 3',{'x':0,'y':0,'sigma':sig3,'q':q3,'pa':pa3,'amp':10})
psf1 = psfObj1.pixeval(xp,yp) * amp1 / (np.pi*2.*sig1**2.)
psf2 = psfObj2.pixeval(xp,yp) * amp2 / (np.pi*2.*sig2**2.)
psf3 = psfObj3.pixeval(xp,yp) * amp3 / (np.pi*2.*sig3**2.)
psf = psf1 + psf2 + psf3
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
return lensModel.lensFit(None,image,sigma,gals,lenses,srcs,xc+x0,yc+y0,1,
verbose=False,psf=psf,csub=1)
def logP(value=0.,p=pars):
lp = 0.
models = []
for i in range(len(imgs)):
if i == 0:
dx,dy = 0,0
else:
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
image = imgs[i]
sigma = sigs[i]
psf = PSFs[i]
imin,sigin,xin,yin = image[mask], sigma[mask],xp[mask2],yp[mask2]
n = 0
model = np.empty(((len(srcs)),imin.size))
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,srcs,[xin,yin],1./OVRS,getPix=True)
for src in srcs:
src.setPars()
tmp = xc*0.
tmp[mask2] = src.pixeval(x0,y0,1./OVRS,csub=1)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp += -0.5*(resid**2.).sum()
models.append(model)
return lp #,models
def ObserveLens(self,noisy=True,bands=[]):
if bands==[]:bands=self.bands
for band in bands:
if self.seeing[band]!=0:
convolvedgal,self.psfFFT[band] = convolve.convolve(self.galmodel[band],self.psf[band],True)
convolvedgal[convolvedgal<0]=0
self.convolvedgal[band]=convolvedgal
convolvedmodel=convolvedgal*1
convolvedsrc={}
for sourcenumber in self.sourcenumbers:
convolvedsrc[sourcenumber]=convolve.convolve(self.sourcemodel[sourcenumber][band],self.psfFFT[band],False)[0]
convolvedsrc[sourcenumber][convolvedsrc[sourcenumber]<0]=0
self.convolvedsrc[sourcenumber][band]=convolvedsrc[sourcenumber]
convolvedmodel+=convolvedsrc[sourcenumber]
self.zeromagcounts[band]=(10**(-(0-self.zeropoints[band])/2.5))
exposurecorrection=((self.ET[band]*1./self.zeroexposuretime))*self.gains[band]
convolvedmodel*=exposurecorrection
#skybackground per second per square arcsecond
background=(10**(-(self.SB[band]-self.zeropoints[band])/2.5))*(self.pixelsize**2)
tot_bg=background*exposurecorrection
sigma=((convolvedmodel+tot_bg)+self.nexposures*(self.readnoise**0.5)**2)**.5
fakeLens=convolvedmodel*1.
if noisy:fakeLens+=(numpy.random.randn(self.side,self.side)*(sigma))
#convert back to ADU/second:
fakeLens/=exposurecorrection
sigma/=exposurecorrection
self.image[band]=fakeLens*1
self.fakeLens[band]=fakeLens*1
self.sigma[band]=sigma*1
self.fakeResidual[0][band]=fakeLens-convolvedgal
for sourcenumber in self.sourcenumbers:
self.SN[sourcenumber][band]=self.SNfunc(\
convolvedsrc[sourcenumber],sigma)
self.fakeResidual[sourcenumber][band]=\
fakeLens-convolvedmodel+convolvedsrc[sourcenumber]
def logP(value=0.,p=pars):
lp = 0.
models = []
for i in range(len(imgs)):
if i == 0:
dx,dy = 0,0
else:
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
image = imgs[i]
sigma = sigs[i]
psf = PSFs[i]
mask = masks[i]
mask2 = mask2s[i]
x0,y0=coords[i]
imin,sigin,xin,yin = image[mask], sigma[mask],xp[mask2],yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs)),imin.size))
for gal in gals:
gal.setPars()
tmp = xc*0.
tmp[mask2] = gal.pixeval(xin,yin,1./OVRS,csub=1) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
for src in srcs:
src.setPars()
tmp = xc*0.
tmp[mask2] = src.pixeval(x0,y0,1./OVRS,csub=1)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp += -0.5*(resid**2.).sum()
models.append(model)
return lp #,models
def logP(value=0,p=pars):
x0 = pars[0].value
y0 = pars[1].value
sig = pars[2].value.item()
q = pars[3].value.item()
pa = pars[4].value.item()
psfObj = SBObjects.Gauss('psf',{'x':0,'y':0,'sigma':sig,'q':q,'pa':pa,'amp':10})
psf = psfObj.pixeval(xp,yp)
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
return lensModel.lensFit(None,image,sigma,gals,lenses,srcs,xc+x0,yc+y0,1,
verbose=False,psf=psf,csub=1)
def lensModel(inpars,image,sig,gals,lenses,sources,xc,yc,OVRS=1,csub=11,psf=None,noResid=False,verbose=False):
import pylens,numpy
import indexTricks as iT
model = xc*0.
for gal in gals:
gal.setPars(inpars)
model += gal.pixeval(xc,yc,1./OVRS,csub=csub)
for src in sources:
src.setPars(inpars)
for lens in lenses:
lens.setPars(inpars)
model = model + pylens.lens_images(lenses,sources,[xc,yc],1./OVRS)
if numpy.isnan(model.sum()):
if verbose==True:
print 'nan model'
return -1e300
if OVRS>1:
model = iT.resamp(model,OVRS,True)
if psf is not None:
from imageSim import convolve
global psfFFT
if psfFFT is None:
psf /= psf.sum()
model,psfFFT = convolve.convolve(model,psf)
else:
model,psfFFT = convolve.convolve(model,psfFFT,False)
if noResid is True:
return model
resid = ((model-image)/sig).ravel()
if verbose==True:
print "%f %5.2f %d %dx%d"%((resid**2).sum(),(resid**2).sum()/resid.size,resid.size,image.shape[1],image.shape[0])
return -0.5*(resid**2).sum()
def logP(value=0.,p=pars):
lp = 0.
models = []
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
imin,sigin,xin,yin = image[mask], sigma[mask],xp[mask2],yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs)+1),imin.size))
for gal in gals:
gal.setPars()
tmp = xc*0.
tmp[mask2] = gal.pixeval(xin,yin,1./OVRS,csub=11) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,srcs,[xin,yin],1./OVRS,getPix=True)
kk=0
for src in srcs:
src.setPars()
tmp = xc*0.
tmp[mask2] = src.pixeval(x0,y0,1./OVRS,csub=11)
tmp = iT.resamp(tmp,OVRS,True)
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp[mask].ravel()
n +=1
model[n] = np.ones(model[n-1].shape)
rhs = (imin/sigin) # data
op = (model/sigin).T # model matrix
fit, chi = optimize.nnls(op,rhs)
model = (model.T*fit).sum(1)
resid = (model-imin)/sigin
lp = -0.5*(resid**2.).sum()
return lp
def addImg(self,name,img,sig,psf=None,scale=1.):
self.imgs.append(img)
self.sigs.append(sig)
if psf is not None:
PSF = psf/psf.sum()
self.psfImgs.append(PSF)
PSF = convolve.convolve(img,PSF)[1]
self.psfs.append(PSF)
else:
self.psfs.append(None)
self.psfImgs.append(None)
yc,xc = iT.overSample(img.shape,1.)
self.xc.append(xc*scale)
self.yc.append(yc*scale)
if len(self.imgs)>1:
self.offsets.append(pymc.Uniform('xoff_%s'%name,-5.*scale,5.*scale,value=0.))
self.offsets.append(pymc.Uniform('yoff_%s'%name,-5.*scale,5.*scale,value=0.))
self.cov += [0.1,0.1]
def AddImages(self,img1,sig1,psf1,img2,sig2,psf2,Dx=None,Dy=None):
self.img1=img1
self.sig1=sig1
self.psf1=psf1
self.img2=img2
self.sig2=sig2
self.psf2=psf2
self.Dx=Dx
self.Dy=Dy
self.imgs = [self.img1,self.img2]
self.sigs = [self.sig1,self.sig2]
self.psfs = [self.psf1,self.psf2]
self.PSFs = []
for i in range(len(self.imgs)):
psf = self.psfs[i]
image = self.imgs[i]
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
self.PSFs.append(psf)
def EasyAddImages(self):
if self.name == 'J0837':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J0837()
elif self.name == 'J0901':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J0901()
elif self.name == 'J0913':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J0913(self.srcno)
elif self.name == 'J1125':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1125()
elif self.name == 'J1144':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1144()
elif self.name == 'J1218':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1218()
elif self.name == 'J1248':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1248()
elif self.name == 'J1323':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1323(self.srcno)
elif self.name == 'J1347':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1347()
elif self.name == 'J1446':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1446()
elif self.name == 'J1605':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1605(self.srcno)
elif self.name == 'J1606':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1606()
elif self.name == 'J1619':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J1619()
elif self.name == 'J2228':
self.img1,self.sig1,self.psf1,self.img2,self.sig2,self.psf2,self.Dx,self.Dy,self.OVRS = EELsImages.J2228()
else:
print 'are you sure this is an EEL?'
return
self.imgs = [self.img1,self.img2]
self.sigs = [self.sig1,self.sig2]
self.psfs = [self.psf1,self.psf2]
self.PSFs = []
for i in range(len(self.imgs)):
psf = self.psfs[i]
image = self.imgs[i]
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
self.PSFs.append(psf)
def logP(value=0,p=pars):
x0 = pars[0].value
y0 = pars[1].value
sig1 = pars[2].value.item()
q1 = pars[3].value.item()
pa1 = pars[4].value.item()
amp1 = pars[5].value.item()
sig2 = pars[6].value.item()
q2 = pars[7].value.item()
pa2 = pars[8].value.item()
amp2 = 1.-amp1
psfObj1 = SBObjects.Gauss('psf 1',{'x':0,'y':0,'sigma':sig1,'q':q1,'pa':pa1,'amp':10})
psfObj2 = SBObjects.Gauss('psf 2',{'x':0,'y':0,'sigma':sig2,'q':q2,'pa':pa2,'amp':10})
psf1 = psfObj1.pixeval(xp,yp) * amp1 / (np.pi*2.*sig1**2.)
psf2 = psfObj2.pixeval(xp,yp) * amp2 / (np.pi*2.*sig2**2.)
psf = psf1 + psf2
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
return lensModel.lensFit(None,image,sigma,gals,lenses,srcs,xc+x0,yc+y0,1,
verbose=False,psf=psf,csub=1)
def logP(value=0,p=pars):
lp = 0.
for i in range(3):
#print i
image = imgs[i]
sigma = sigs[i]
if i == 0:
psf = PSFs[i]
x0,y0 = 0,0
xm,ym = xc,yc
#print i, x0,y0
if i == 1:
psf = PSFs[i]
x0,y0 = pars[9].value,pars[10].value
#print i, x0,y0
xm,ym = xc,yc
elif i ==2:
x0,y0 = pars[0].value,pars[1].value
#print i,x0,y0
sigma1 = pars[2].value.item()
q1 = pars[3].value.item()
pa1 = pars[4].value.item()
amp1 = pars[5].value.item()
sigma2 = pars[6].value.item()
q2 = pars[7].value.item()
pa2 = pars[8].value.item()
amp2 = 1.-amp1
psfObj1 = SBObjects.Gauss('psf 1',{'x':0,'y':0,'sigma':sigma1,'q':q1,'pa':pa1,'amp':10})
psfObj2 = SBObjects.Gauss('psf 2',{'x':0,'y':0,'sigma':sigma2,'q':q2,'pa':pa2,'amp':10})
psf1 = psfObj1.pixeval(xp,yp) * amp1 / (np.pi*2.*sigma1**2.)
psf2 = psfObj2.pixeval(xp,yp) * amp2 / (np.pi*2.*sigma2**2.)
psf = psf1 + psf2
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
xm,ym = xc3,yc3
lp += lensModel.lensFit(None,image,sigma,gals,lenses,srcs,xm+x0,ym+y0,1,
verbose=False,psf=psf,csub=1)
return lp
def logP(value=0, p=pars):
x0 = pars[0].value
y0 = pars[1].value
sig1 = pars[2].value.item()
q1 = pars[3].value.item()
pa1 = pars[4].value.item()
amp1 = pars[5].value.item()
sig2 = pars[6].value.item()
q2 = pars[7].value.item()
pa2 = pars[8].value.item()
# q2,pa2 = 1,0
amp2 = 1.0 - amp1
psfObj1 = SBObjects.Gauss("psf 1", {"x": 0, "y": 0, "sigma": sig1, "q": q1, "pa": pa1, "amp": 10})
psfObj2 = SBObjects.Gauss("psf 2", {"x": 0, "y": 0, "sigma": sig2, "q": q2, "pa": pa2, "amp": 10})
psf1 = psfObj1.pixeval(xp, yp) * amp1 / (np.pi * 2.0 * sig1 ** 2.0)
psf2 = psfObj2.pixeval(xp, yp) * amp2 / (np.pi * 2.0 * sig2 ** 2.0)
psf = psf1 + psf2
psf /= psf.sum()
psf = convolve.convolve(image, psf)[1]
return lensModel.lensFit(
None, image, sigma, gals, lenses, srcs, xc + x0, yc + y0, 1, verbose=False, psf=psf, csub=1
)
def logP(value=0,p=pars):
x0 = pars[0].value
y0 = pars[1].value
fwhm1 = pars[2].value.item()
q1 = pars[3].value.item()
pa1 = pars[4].value.item()
amp1 = pars[5].value.item()
fwhm2 = pars[6].value.item()
q2 = pars[7].value.item()
pa2 = pars[8].value.item()
index2 = pars[9].value.item()
index1 = pars[10].value.item()
amp2 = 1.-amp1
psfObj1 = SBObjects.Moffat('psf 1',{'x':0,'y':0,'fwhm':fwhm1,'q':q1,'pa':pa1,'amp':10,'index':index1})
psfObj2 = SBObjects.Moffat('psf 2',{'x':0,'y':0,'fwhm':fwhm2,'q':q2,'pa':pa2,'amp':10,'index':index2})
psf1 = psfObj1.pixeval(xp,yp) * amp1
psf2 = psfObj2.pixeval(xp,yp) * amp2
psf = psf1 + psf2
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
return lensModel.lensFit(None,image,sigma,gals,lenses,srcs,xc+x0,yc+y0,1,
verbose=False,psf=psf,csub=1)
pars[i].value = trace[a1,a2,a3,i]
print jj
jj+=1
dx = pars[0].value
dy = pars[1].value
xp,yp = xc+dx,yc+dy
psf = xpsf*0.
for obj in psfObjs:
obj.setPars()
psf += obj.pixeval(xpsf,ypsf) / (np.pi*2.*obj.pars['sigma'].value**2.)
psf = psf/np.sum(psf)
print 'ici',obj.pars['q'].value
psf = convolve.convolve(image,psf)[1]
xp,yp = xc+dx,yc+dy
xop,yop = xo+dy,yo+dy
imin,sigin,xin,yin = image.flatten(), sigma.flatten(),xp.flatten(),yp.flatten()
n = 0
model = np.empty(((len(gals) + len(srcs)+1),imin.size))
for gal in gals:
gal.setPars()
tmp = xc*0.
tmp = gal.pixeval(xp,yp,1./OVRS,csub=11) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp,OVRS,True) # convert it back to original size
tmp = convolve.convolve(tmp,psf,False)[0]
model[n] = tmp.ravel()
n +=1
for lens in lenses:
lens.setPars()
def save(self, outname, make_rgb=True):
fitsname = outname + '.fits'
rgbname = outname + '_rgb.png'
hdr = pyfits.Header()
hdr['logp'] = self.logp
light_ind_model = []
source_ind_model = []
xl, yl = pylens.getDeflections(self.lens_models, (self.X, self.Y))
n = 0
for light, mags in zip(self.light_sb_models, self.light_mags):
light_ind_dic = {}
for band in self.bands:
light[band].amp = 1.
lpix = light[band].pixeval(self.X, self.Y)
hdr['%s.mag_%s' % (light[band].name, band)] = mags[band]
scale = 10.**(-2. / 5. *
(mags[band] - light[band].Mag(self.zp[band])))
light_ind_dic[band] = scale * convolve.convolve(
lpix, self.convol_matrix[band], False)[0]
light_ind_model.append(light_ind_dic)
n += 1
xl = {}
yl = {}
for band in self.bands:
lens_models = []
for lens_model in self.lens_models:
lens_models.append(lens_model[band])
xl_here, yl_here = pylens.getDeflections(lens_models,
(self.X, self.Y))
xl[band] = xl_here
yl[band] = yl_here
for source, mags in zip(self.source_sb_models, self.source_mags):
source_ind_dic = {}
for band in self.bands:
source[band].amp = 1.
spix = source[band].pixeval(xl[band], yl[band])
hdr['%s.mag_%s' % (source[band].name, band)] = mags[band]
scale = 10.**(-2. / 5. *
(mags[band] - source[band].Mag(self.zp[band])))
source_ind_here = scale * convolve.convolve(
spix, self.convol_matrix[band], False)[0]
source_ind_dic[band] = source_ind_here
source_ind_model.append(source_ind_dic)
n += 1
phdu = pyfits.PrimaryHDU(header=hdr)
hdulist = pyfits.HDUList([phdu])
for light, light_ind_dic in zip(self.light_sb_models, light_ind_model):
for band in self.bands:
hdu_here = pyfits.ImageHDU(data=light_ind_dic[band])
hdu_here.header['EXTNAME'] = '%s_%s' % (light[band].name, band)
hdulist.append(hdu_here)
for source, source_ind_dic in zip(self.source_sb_models,
source_ind_model):
for band in self.bands:
hdu_here = pyfits.ImageHDU(data=source_ind_dic[band])
hdu_here.header['EXTNAME'] = '%s_%s' % (source[band].name,
band)
hdulist.append(hdu_here)
hdulist.writeto(fitsname, overwrite=True)
if make_rgb:
# makes model rgb
sci_list = []
light_list = []
source_list = []
for band in self.bands:
sci_list.append(self.sci[band])
lmodel = 0. * self.sci[band]
smodel = 0. * self.sci[band]
for light in light_ind_model:
lmodel += light[band]
light_list.append(lmodel)
for source in source_ind_model:
smodel += source[band]
source_list.append(smodel)
pyplz_rgbtools.make_full_rgb(sci_list,
light_list,
source_list,
outname=rgbname)
print 'schon aus Terminal'
imgs = [img1,img2]
sigs = [sig1,sig2]
psfs = [psf1,psf2]
PSFs = []
yc,xc = iT.overSample(img1.shape,1.)
yc,xc = yc-15.,xc-15.
for i in range(len(imgs)):
psf = psfs[i]
image = imgs[i]
psf /= psf.sum()
psf = convolve.convolve(image,psf)[1]
PSFs.append(psf)
OVRS = 1
G,L,S,offsets,_ = numpy.load(guiFile)
pars = []
cov = []
### first parameters need to be the offsets
xoffset = offsets[0][3]
yoffset = offsets[1][3]
print xoffset,yoffset
print offsets
pars.append(pymc.Uniform('xoffset',-5.,5.,value=offsets[0][3]))
def optimize_amp(self):
light_ind_model = []
source_ind_model = []
xl, yl = pylens.getDeflections(self.lens_models, (self.X, self.Y))
lpix = []
spix = []
for light in self.light_sb_models:
light.amp = 1.
if type(light) == SBModels.PointSource:
lpix.append(light)
else:
lpix.append(light.pixeval(self.X, self.Y))
for source in self.source_sb_models:
source.amp = 1.
spix.append(source.pixeval(xl, yl))
chi2sum = 0.
for band in self.bands:
modlist = []
for l in lpix:
if type(l) == SBModels.PointSource:
modlist.append((l.pixeval(self.X, self.Y, band) /
self.err[band]).ravel()[self.mask_r])
else:
modlist.append((convolve.convolve(
l, self.convol_matrix[band], False)[0] /
self.err[band]).ravel()[self.mask_r])
for s in spix:
modlist.append(
(convolve.convolve(s, self.convol_matrix[band], False)[0] /
self.err[band]).ravel()[self.mask_r])
modarr = np.array(modlist).T
if np.isnan(modarr).any() or not np.isfinite(modarr).any():
self.logp = -0.5e300
return 1e300
else:
amps, chi = nnls(modarr, (self.sci[band] /
self.err[band]).ravel()[self.mask_r])
print(amps)
df
chi2sum += chi**2
i = 0
for light, mags in zip(self.light_sb_models, self.light_mags):
if amps[i] > 0.:
light.amp = amps[i]
mags[band] = light.Mag(self.zp[band])
else:
mags[band] = 99.
i += 1
for source, mags in zip(self.source_sb_models, self.source_mags):
if amps[i] > 0.:
source.amp = amps[i]
mags[band] = source.Mag(self.zp[band])
else:
mags[band] = 99.
i += 1
self.logp = -0.5 * chi2sum
return chi2sum
def linearmodelSB(inpars,
simage,
sigma,
mask,
models,
xc,
yc,
OVRS=1,
csub=11,
noResid=False,
levMar=False):
def objf(x, lhs, rhs):
return ((numpy.dot(lhs, x) - rhs)**2).sum()
def objdf(x, lhs, rhs):
return numpy.dot(lhs.T, numpy.dot(lhs, x) - rhs)
nmod = len(models)
model = numpy.zeros((nmod, mask.sum()))
norm = numpy.zeros(nmod)
for n in range(nmod):
M = models[n]
M.setPars(inpars)
if M.convolve is not None:
img = M.pixeval(xc, yc, scale=1. / abs(OVRS))
img = convolve.convolve(img, M.convolve, False)[0]
if OVRS > 1:
img = iT.resamp(img, OVRS, True)
else:
img = M.pixeval(xc, yc)
if OVRS > 1:
img = iT.resamp(img, OVRS, True)
if numpy.isnan(img).any() and noResid == False:
return -1e300
model[n] = img[mask].ravel()
norm[n] = model[n].max()
model[n] /= norm[n]
op = (model / sigma).T
fit, chi = numpy.linalg.lstsq(op, simage)[:2]
fit = numpy.array(fit)
if (fit < 0).any():
sol = fit
sol[sol < 0] = 1e-11
bounds = [(1e-11, 1e11)] * nmod
result = fmin_slsqp(objf,
sol,
bounds=bounds,
full_output=1,
fprime=objdf,
acc=1e-19,
iter=2000,
args=[op.copy(), simage.copy()],
iprint=0)
fit, chi = result[:2]
fit = numpy.asarray(fit)
if (fit < 1e-11).any():
fit[fit < 1e-11] = 1e-11
for i in range(nmod):
models[i].amp = fit[i] / norm[i]
if levMar == True:
return (op * fit).sum(1) - simage
lhs = (op * fit)
print lhs.shape, simage.shape
return lhs - simage
if noResid == True:
output = []
for M in models:
if M.convolve is not None:
img = M.pixeval(xc, yc, scale=1. / abs(OVRS))
img = convolve.convolve(img, M.convolve, False)[0]
if OVRS > 1:
img = iT.resamp(img, OVRS, True)
else:
img = M.pixeval(xc, yc)
if OVRS > 1:
img = iT.resamp(img, OVRS, True)
output.append(img)
return output
logp = -0.5 * chi - numpy.log(sigma).sum()
return logp
def logP(value=0.0, p=pars):
lp = 0.0
models = []
dx = pars[0].value
dy = pars[1].value
xp, yp = xc + dx, yc + dy
sig1 = pars[2].value.item()
q1 = pars[3].value.item()
pa1 = pars[4].value.item()
amp1 = pars[5].value.item()
sig2 = pars[6].value.item()
q2 = pars[7].value.item()
pa2 = pars[8].value.item()
amp2 = pars[9].value.item()
sig3 = pars[10].value.item()
q3 = pars[11].value.item()
pa3 = pars[12].value.item()
amp3 = 1.0 - amp1 - amp2
if amp3 < 0:
return -1e10
# print dx,dy,sig1,sig2,sig3,q1,q2,q3,pa1,pa2,pa3,amp1,amp2,amp3
psfObj1 = SBObjects.Gauss("psf 1", {"x": 0, "y": 0, "sigma": sig1, "q": q1, "pa": pa1, "amp": 10})
psfObj2 = SBObjects.Gauss("psf 2", {"x": 0, "y": 0, "sigma": sig2, "q": q2, "pa": pa2, "amp": 10})
psfObj3 = SBObjects.Gauss("psf 3", {"x": 0, "y": 0, "sigma": sig3, "q": q3, "pa": pa3, "amp": 10})
psf1 = psfObj1.pixeval(xpsf, ypsf) * amp1 / (np.pi * 2.0 * sig1 ** 2.0)
psf2 = psfObj2.pixeval(xpsf, ypsf) * amp2 / (np.pi * 2.0 * sig2 ** 2.0)
psf3 = psfObj3.pixeval(xpsf, ypsf) * amp3 / (np.pi * 2.0 * sig3 ** 2.0)
psf = psf1 + psf2 + psf3
psf /= psf.sum()
psf = convolve.convolve(image, psf)[1]
imin, sigin, xin, yin = image[mask], sigma[mask], xp[mask2], yp[mask2]
n = 0
model = np.empty(((len(gals) + len(srcs) + 1), imin.size))
for gal in gals:
gal.setPars()
tmp = xc * 0.0
tmp[mask2] = gal.pixeval(
xin, yin, 1.0 / OVRS, csub=1
) # evaulate on the oversampled grid. OVRS = number of new pixels per old pixel.
tmp = iT.resamp(tmp, OVRS, True) # convert it back to original size
tmp = convolve.convolve(tmp, psf, False)[0]
model[n] = tmp[mask].ravel()
n += 1
for lens in lenses:
lens.setPars()
x0, y0 = pylens.lens_images(lenses, srcs, [xin, yin], 1.0 / OVRS, getPix=True)
kk = 0
for src in srcs:
src.setPars()
tmp = xc * 0.0
tmp[mask2] = src.pixeval(x0, y0, 1.0 / OVRS, csub=1)
tmp = iT.resamp(tmp, OVRS, True)
tmp = convolve.convolve(tmp, psf, False)[0]
model[n] = tmp[mask].ravel()
n += 1
model[n] = np.ones(model[n - 1].shape)
rhs = imin / sigin # data
op = (model / sigin).T # model matrix
fit, chi = optimize.nnls(op, rhs)
model = (model.T * fit).sum(1)
resid = (model - imin) / sigin
lp = -0.5 * (resid ** 2.0).sum()
return lp
def runInference(self,optCov=None,getModel=False):
import numpy
from SampleOpt import AMAOpt,levMar
cov = [c for c in self.cov]
pars = [o for o in self.offsets]
gals = []
srcs = []
lenses = []
self.gals = self.parent.galaxyManager.objs
self.lenses = self.parent.lensManager.objs
self.srcs = self.parent.srcManager.objs
mask = self.parent.mask
if len(self.gals)+len(self.srcs)==0:
return None
# if len(self.gals)+len(self.srcs)+len(self.lenses)==0:
# return None
for g in self.gals.keys():
gal = self.gals[g]
gal.makeModel()
gal,gpars,gcov = gal.model,gal.modelPars,gal.cov
gals.append(gal)
pars += gpars
cov += gcov
for s in self.srcs.keys():
src = self.srcs[s]
src.makeModel()
src,spars,scov = src.model,src.modelPars,src.cov
srcs.append(src)
pars += spars
cov += scov
for l in self.lenses.keys():
lens = self.lenses[l]
lens.makeModel()
lens,lpars,lcov = lens.model,lens.modelPars,lens.cov
lenses.append(lens)
pars += lpars
cov += lcov
if self.parent.shearFlag==True:
shear = self.parent.shear
shear.makeModel()
lenses.append(shear.model)
pars += shear.modelPars
cov += shear.cov
if getModel==True or len(pars)==0:
if len(pars)==0:
self.outPars = []
models = []
for i in range(len(self.imgs)):
if i==0:
x0 = 0.
y0 = 0.
else:
x0 = pars[i*2-2].value
y0 = pars[i*2-1].value
print 'x0,y0',x0,y0
img = self.imgs[i]
sig = self.sigs[i]
psf = self.psfs[i]
xc = self.xc[i]
yc = self.yc[i]
model = lensModel.lensFit(None,img,sig,gals,lenses,srcs,xc+x0,
yc+y0,1,verbose=False,psf=psf,
noResid=True,csub=1)
models.append(model)
return models
# Trim images for faster convolution if masking
xc = []
yc = []
imgs = []
sigs = []
psfs = []
if mask is not None:
Y,X = numpy.where(mask)
ylo,yhi,xlo,xhi = Y.min(),Y.max()+1,X.min(),X.max()+1
mask = mask[ylo:yhi,xlo:xhi]
for i in range(len(self.imgs)):
xc.append(self.xc[i][ylo:yhi,xlo:xhi].copy())
yc.append(self.yc[i][ylo:yhi,xlo:xhi].copy())
imgs.append(self.imgs[i][ylo:yhi,xlo:xhi].copy())
sigs.append(self.sigs[i][ylo:yhi,xlo:xhi].copy())
if self.psfs[i] is not None:
PSF = self.psfImgs[i]
psfs.append(convolve.convolve(imgs[-1],PSF)[1])
else:
xc = [i for i in self.xc]
yc = [i for i in self.yc]
imgs = [i for i in self.imgs]
sigs = [i for i in self.sigs]
psfs = [i for i in self.psfs]
@pymc.deterministic
def logP(value=0.,p=pars):
lp = 0.
for i in range(len(imgs)):
if i==0:
x0 = 0.
y0 = 0.
else:
x0 = pars[i*2-2].value
y0 = pars[i*2-1].value
img = imgs[i]
sig = sigs[i]
psf = psfs[i]
lp += lensModel.lensFit(None,img,sig,gals,lenses,srcs,xc[i]+x0,
yc[i]+y0,1,verbose=False,psf=psf,
mask=mask,csub=1)
return lp
@pymc.observed
def likelihood(value=0.,lp=logP):
return lp
def resid(p):
lp = -2*logP.value
return self.imgs[0].ravel()*0 + lp
if optCov is None:
optCov = numpy.array(cov)
#S = levMar(pars,resid)
#self.outPars = pars
#return
niter = 2*len(pars)**2
if niter<20:
niter = 20
S = AMAOpt(pars,[likelihood],[logP],cov=optCov)
S.set_minprop(10*len(pars))
S.sample(niter)
self.Sampler = S
self.outPars = pars
return self.getModel()
def optimize_amp(self):
light_ind_model = []
source_ind_model = []
xl, yl = pylens.getDeflections(self.lens_models, (self.X, self.Y))
modlist = []
for light, sed, mags in zip(self.light_sb_models,
self.light_sed_models, self.light_mags):
lmodel = 0. * self.scistack
light.amp = 1.
if light.__class__.__name__ == 'PointSource':
for i in range(self.nbands):
scale = sed.scale(self.bands[i], self.reference_band)
lmodel[i * self.ny:(i + 1) * self.ny, :] = light.pixeval(
self.X, self.Y, self.bands[i])
mags[self.bands[i]] = -2.5 * np.log10(scale) + self.zp[
self.bands[i]] - self.zp[self.reference_band]
else:
lpix = light.pixeval(self.X, self.Y)
for i in range(self.nbands):
scale = sed.scale(self.bands[i], self.reference_band)
lmodel[i * self.ny:(i + 1) *
self.ny, :] = scale * convolve.convolve(
lpix, self.convol_matrix[self.bands[i]],
False)[0]
mags[self.bands[i]] = -2.5 * np.log10(scale) + self.zp[
self.bands[i]] - self.zp[self.reference_band]
modlist.append((lmodel / self.errstack).ravel()[self.maskstack_r])
for source, sed, mags in zip(self.source_sb_models,
self.source_sed_models, self.source_mags):
smodel = 0. * self.scistack
source.amp = 1.
spix = source.pixeval(xl, yl)
for i in range(self.nbands):
scale = sed.scale(self.bands[i], self.reference_band)
smodel[i * self.ny:(i + 1) *
self.ny, :] = scale * convolve.convolve(
spix, self.convol_matrix[self.bands[i]], False)[0]
mags[self.bands[i]] = -2.5 * np.log10(scale) + self.zp[
self.bands[i]] - self.zp[self.reference_band]
modlist.append((smodel / self.errstack).ravel()[self.maskstack_r])
modarr = np.array(modlist).T
if np.isnan(modarr).any() or not np.isfinite(modarr).any():
amps = np.ones(self.nlight + self.nsource)
chi = 1e300
else:
amps, chi = nnls(modarr, (self.scistack /
self.errstack).ravel()[self.maskstack_r])
i = 0
for light, sed, mags in zip(self.light_sb_models,
self.light_sed_models, self.light_mags):
if amps[i] > 0.:
light.amp *= amps[i]
mainmag = light.Mag(self.zp[self.reference_band])
for band in self.bands:
mags[band] += mainmag
if sed.__class__.__name__ == 'SPS':
mags['mstar'] = 10.**(
-2. / 5. * (mainmag - sed.mags[self.reference_band]))
else:
for band in self.bands:
mags[band] = 99.
if sed.__class__.__name__ == 'SPS':
mags['mstar'] = 0.
i += 1
for source, mags in zip(self.source_sb_models, self.source_mags):
if amps[i] > 0.:
source.amp *= amps[i]
mainmag = source.Mag(self.zp[self.reference_band])
for band in self.bands:
mags[band] = mags[band] + mainmag
else:
for band in self.bands:
mags[band] = 99.
i += 1
self.logp = -0.5 * chi**2
return chi**2
def save(self, outname, config, make_rgb=True):
fitsname = outname + '.fits'
rgbname = outname + '_rgb.png'
hdr = pyfits.Header()
hdr['logp'] = self.logp
light_ind_model = []
source_ind_model = []
xl, yl = pylens.getDeflections(self.lens_models, (self.X, self.Y))
n = 0
for light, sed, mags in zip(self.light_sb_models,
self.light_sed_models, self.light_mags):
light_ind_dic = {}
if light.__class__.__name__ == 'PointSource':
for band in self.bands:
hdr['%s.mag_%s' % (light.name, band)] = mags[band]
scale = sed.scale(band, self.reference_band)
light_ind_dic[band] = scale * light.pixeval(
self.X, self.Y, band)
else:
lpix = light.pixeval(self.X, self.Y)
for band in self.bands:
hdr['%s.mag_%s' % (light.name, band)] = mags[band]
scale = sed.scale(band, self.reference_band)
light_ind_dic[band] = scale * convolve.convolve(
lpix, self.convol_matrix[band], False)[0]
light_ind_model.append(light_ind_dic)
n += 1
for source, sed, mags in zip(self.source_sb_models,
self.source_sed_models, self.source_mags):
source_ind_dic = {}
spix = source.pixeval(xl, yl)
for band in self.bands:
hdr['%s.mag_%s' % (source.name, band)] = mags[band]
scale = sed.scale(band, self.reference_band)
source_ind_here = scale * convolve.convolve(
spix, self.convol_matrix[band], False)[0]
source_ind_dic[band] = source_ind_here
source_ind_model.append(source_ind_dic)
n += 1
phdu = pyfits.PrimaryHDU(header=hdr)
hdulist = pyfits.HDUList([phdu])
for light, light_ind_dic in zip(self.light_sb_models, light_ind_model):
for band in self.bands:
hdu_here = pyfits.ImageHDU(data=light_ind_dic[band])
hdu_here.header['EXTNAME'] = '%s_%s' % (light.name, band)
hdulist.append(hdu_here)
for source, source_ind_dic in zip(self.source_sb_models,
source_ind_model):
for band in self.bands:
hdu_here = pyfits.ImageHDU(data=source_ind_dic[band])
hdu_here.header['EXTNAME'] = '%s_%s' % (source.name, band)
hdulist.append(hdu_here)
hdulist.writeto(fitsname, overwrite=True)
if make_rgb:
# makes model rgb
sci_list = []
model_list = []
for band in self.bands:
sci_list.append(self.sci[band])
comp_list = []
for light in light_ind_model:
comp_list.append(light[band])
for source in source_ind_model:
comp_list.append(source[band])
model_list.append(comp_list)
pyplz_rgbtools.make_full_rgb(sci_list,
model_list,
outname=rgbname,
scheme=config['rgbscheme'],
cuts=config['rgbcuts'],
scales=config['rgbscales'])
def __init__(self, config):
self.pars = []
self.par2index = {}
self.index2par = {}
self.sci = {}
self.err = {}
self.convol_matrix = {}
self.zp = {}
self.light_sb_models = []
self.source_sb_models = []
self.light_sed_models = []
self.source_sed_models = []
self.light_mags = []
self.source_mags = []
self.lens_models = []
self.logp = None
# defines bands
self.bands = []
self.reference_band = config['reference_band']
for band in config['filters']:
self.bands.append(band)
self.nbands = len(self.bands)
# reads in data
filtnames = {}
psfdic = {}
for i in range(self.nbands):
band = self.bands[i]
self.zp[band] = config['zeropoints'][i]
filtname = config['filter_prefix'] + band + config['filter_suffix']
filtnames[band] = filtname
hdu = pyfits.open(
os.path.expandvars(config['data_dir']) + '/' +
config['filename'] + '_%s' % band + config['science_tag'])[0]
img = hdu.data.copy()
subimg = img.copy()
self.sci[band] = subimg
suberr = pyfits.open(
os.path.expandvars(config['data_dir']) + '/' +
config['filename'] + '_%s' % band +
config['err_tag'])[0].data.copy()
if config['err_type'] == 'VAR':
self.err[band] = suberr**0.5
elif config['err_type'] == 'SIGMA':
self.err[band] = suberr.copy()
else:
df
psf_file = pyfits.open(
os.path.expandvars(config['data_dir']) + '/' +
config['filename'] + '_%s' % band + config['psf_tag'])
nhdu = len(psf_file)
found = False
n = 0
while not found and n < nhdu:
if psf_file[n].data is not None:
psf = psf_file[n].data.copy()
found = True
else:
n += 1
if not found:
df
m = (psf[:2].mean() + psf[-2:].mean() + psf[:, :2].mean() +
psf[:, -2:].mean()) / 4.
psf -= m
psf /= psf.sum()
psfdic[band] = psf
self.convol_matrix[band] = convolve.convolve(self.sci[band],
psf)[1]
# prepares mask and data array
ny, nx = self.sci[self.bands[0]].shape
X, Y = np.meshgrid(np.arange(1. * nx), np.arange(1. * ny))
self.ny = ny
self.nx = nx
self.X = X
self.Y = Y
self.R = ((X - nx / 2)**2 + (Y - ny / 2)**2)**0.5
if config['mask_dir'] is None:
mask_dir = './'
else:
mask_dir = os.path.expandvars(config['mask_dir'])
if config['maskname'] is not None:
MASK = pyfits.open(mask_dir + config['maskname'])[0].data.copy()
else:
MASK = np.ones(X.shape, dtype=int)
if config['rmax'] is not None:
MASK[self.R > config['rmax']] = 0
mask = MASK > 0
mask_r = mask.ravel()
self.modelstack = np.zeros((self.nbands * ny, nx))
self.scistack = 0. * self.modelstack
self.errstack = 0. * self.modelstack
self.maskstack = np.zeros((self.nbands * ny, nx), dtype=bool)
for i in range(self.nbands):
self.scistack[i * ny:(i + 1) * ny, :] = self.sci[self.bands[i]]
self.errstack[i * ny:(i + 1) * ny, :] = self.err[self.bands[i]]
self.maskstack[i * ny:(i + 1) * ny, :] = mask
self.maskstack_r = self.maskstack.ravel()
#defines model parameters
ncomp = 0
npar = 0
for comp in config['light_components']:
ncomp += 1
for par in comp['pars']:
parpar = comp['pars'][par]
if parpar['link'] is None and parpar['var'] == 1:
self.pars.append(
Par(par + str(ncomp),
lower=parpar['low'],
upper=parpar['up'],
value=parpar['value'],
step=parpar['step']))
self.par2index['light' + str(ncomp) + '.' + par] = npar
self.index2par[npar] = 'light' + str(ncomp) + '.' + par
npar += 1
ncomp = 0
for comp in config['source_components']:
ncomp += 1
for par in comp['pars']:
parpar = comp['pars'][par]
if parpar['link'] is None and parpar['var'] == 1:
self.pars.append(
Par(par + str(ncomp),
lower=parpar['low'],
upper=parpar['up'],
value=parpar['value'],
step=parpar['step']))
self.par2index['source' + str(ncomp) + '.' + par] = npar
self.index2par[npar] = 'source' + str(ncomp) + '.' + par
npar += 1
ncomp = 0
for comp in config['lens_components']:
ncomp += 1
for par in comp['pars']:
parpar = comp['pars'][par]
if parpar['link'] is None and parpar['var'] == 1:
self.pars.append(
Par(par + str(ncomp),
lower=parpar['low'],
upper=parpar['up'],
value=parpar['value'],
step=parpar['step']))
self.par2index['lens' + str(ncomp) + '.' + par] = npar
self.index2par[npar] = 'lens' + str(ncomp) + '.' + par
npar += 1
i = 0
filtnames = {}
for band in config['filters']:
filtname = config['filter_prefix'] + band + config['filter_suffix']
filtnames[band] = filtname
ncomp = 1
for comp in config['lens_components']:
name = 'lens%d' % ncomp
pars_here = {}
for par in comp['pars']:
if comp['pars'][par]['link'] is None:
if comp['pars'][par]['var'] == 1:
pars_here[par] = self.pars[self.par2index[name + '.' +
par]]
elif comp['pars'][par]['var'] == 0:
pars_here[par] = Par(par,
lower=comp['pars'][par]['value'],
upper=comp['pars'][par]['value'],
value=comp['pars'][par]['value'])
else:
df
else:
pars_here[par] = self.pars[self.par2index[comp['pars'][par]
['link']]]
ncomp += 1
lens = MassModels.PowerLaw(name, pars_here)
self.lens_models.append(lens)
self.nlens = len(self.lens_models)
ncomp = 1
for comp in config['light_components']:
name = 'light%d' % ncomp
pars_here = {}
sed_here = {}
for par in comp['pars']:
if par in SBModels.parlists[comp['class']]:
if comp['pars'][par]['link'] is None:
if comp['pars'][par]['var'] == 1:
pars_here[par] = self.pars[self.par2index[name +
'.' +
par]]
else:
pars_here[par] = Par(
par,
lower=comp['pars'][par]['value'],
upper=comp['pars'][par]['value'],
value=comp['pars'][par]['value'])
else:
pars_here[par] = self.pars[self.par2index[
comp['pars'][par]['link']]]
else:
if comp['pars'][par]['link'] is None:
if comp['pars'][par]['var'] == 1:
sed_here[par] = self.pars[self.par2index[name +
'.' +
par]]
else:
sed_here[par] = Par(
par,
lower=comp['pars'][par]['value'],
upper=comp['pars'][par]['value'],
value=comp['pars'][par]['value'])
else:
sed_here[par] = self.pars[self.par2index[
comp['pars'][par]['link']]]
if comp['class'] == 'Sersic':
light = SBModels.Sersic('light%d' % ncomp, pars_here)
elif comp['class'] == 'PointSource':
light = SBModels.PointSource('light%d' % ncomp, psfdic,
pars_here)
else:
df
self.light_sb_models.append(light)
if comp['sed'] == 'colorpars':
sed = SEDModels.Colors('light_sed%d' % ncomp, sed_here,
self.bands, self.reference_band,
self.zp)
elif comp['sed'] == 'template':
sed = SEDModels.Template('light_sed%d' % ncomp, sed_here,
filtnames, self.zp)
elif comp['sed'] == 'sps':
modelname = config['sps_model_dir'] + comp['sps_model']
sed = SEDModels.SPS('light_sed%d' % ncomp, sed_here,
self.bands, self.zp, modelname)
else:
df
self.light_sed_models.append(sed)
self.light_mags.append({})
ncomp += 1
self.nlight = len(self.light_sb_models)
ncomp = 1
for comp in config['source_components']:
name = 'source%d' % ncomp
pars_here = {}
sed_here = {}
for par in comp['pars']:
if par in SBModels.parlists['Sersic']:
if comp['pars'][par]['link'] is None:
if comp['pars'][par]['var'] == 1:
pars_here[par] = self.pars[self.par2index[name +
'.' +
par]]
else:
pars_here[par] = comp['pars'][par]['value']
else:
pars_here[par] = self.pars[self.par2index[
comp['pars'][par]['link']]]
else:
if comp['pars'][par]['link'] is None:
if comp['pars'][par]['var'] == 1:
sed_here[par] = self.pars[self.par2index[name +
'.' +
par]]
else:
sed_here[par] = Par(
par,
lower=comp['pars'][par]['value'],
upper=comp['pars'][par]['value'],
value=comp['pars'][par]['value'])
else:
sed_here[par] = self.pars[self.par2index[
comp['pars'][par]['link']]]
if comp['class'] == 'Sersic':
source = SBModels.Sersic('source%d' % ncomp, pars_here)
else:
df
self.source_sb_models.append(source)
if comp['sed'] == 'colorpars':
sed = SEDModels.Colors('light_sed%d' % ncomp,
sed_here,
self.bands,
self.reference_band,
zp=self.zp)
elif comp['sed'] == 'template':
sed = SEDModels.Template('light_sed%d' % ncomp,
sed_here,
filtnames,
zp=self.zp)
self.source_sed_models.append(sed)
self.source_mags.append({})
ncomp += 1
self.nsource = len(self.source_sb_models)
pl.subplot(223)
pl.imshow(image-im,origin='lower',interpolation='nearest',extent=ext,vmin=-0.25,vmax=0.25)
pl.colorbar()
pl.title('data-model')
pl.subplot(224)
pl.imshow((image-im)/sigma,origin='lower',interpolation='nearest',extent=ext,vmin=-5,vmax=5)
pl.title('signal-to-noise residuals')
pl.colorbar()
img2 = pyfits.open('/data/ljo31/Lens/J1605/SDSSJ1605+3811_F814W_sci_cutout2.fits')[0].data.copy()
sig2 = pyfits.open('/data/ljo31/Lens/J1605/SDSSJ1605+3811_F814W_noisemap2_masked.fits')[0].data.copy()
psf2 = pyfits.open('/data/ljo31/Lens/J1605/F814W_psf_#2.fits')[0].data.copy()
psf2= psf2[15:-16,14:-16]
psf2 /= psf2.sum()
psf = convolve.convolve(img2,psf2)[1]
OVRS=1.
fchain = np.load('/data/ljo31/Lens/J1605/fchain_PixFit_2src.npy')
flnprob = np.load('/data/ljo31/Lens/J1605/flnprob_PixFit_2src.npy')
fit = np.load('/data/ljo31/Lens/J1605/fit_PixFit_2src.npy')
ii = np.argmax(flnprob)
XX = fchain[ii]
x,y,pa,q,re,n,pa2,q2,re2,n2 = fchain[ii]
srcs = []
src1 = SBModels.Sersic('Source 1', {'x':0.1196461*x+10.91,'y':0.11966*y + 5.877,'pa':pa,'q':q,'re':re*0.1196461,'n':n,'amp':fit[0]})
src2 = SBModels.Sersic('Source 2', {'x':0.1196461*x+10.91,'y':0.11966*y + 5.877,'pa':pa2,'q':q2,'re':re2*0.1196461,'n':n2,'amp':fit[1]})
srcs = [src1,src2]
def save(self, outname, make_rgb=True):
fitsname = outname + '.fits'
rgbname = outname + '_rgb.png'
hdr = pyfits.Header()
hdr['logp'] = self.logp
light_ind_model = []
source_ind_model = []
xl, yl = pylens.getDeflections(self.lens_models, (self.X, self.Y))
n = 0
for light, sed in zip(self.light_sb_models, self.light_sed_models):
light_ind_dic = {}
if light.__class__.__name__ == 'PointSource':
for band in self.bands:
hdr['%s.mag_%s' % (light.name, band)] = sed.mags[band]
scale = sed.scale(band, self.main_band)
light_ind_dic[band] = scale * light.pixeval(
self.X, self.Y, band)
else:
lpix = light.pixeval(self.X, self.Y)
for band in self.bands:
hdr['%s.mag_%s' % (light.name, band)] = sed.mags[band]
scale = sed.scale(band, self.main_band)
light_ind_dic[band] = scale * convolve.convolve(
lpix, self.convol_matrix[band], False)[0]
light_ind_model.append(light_ind_dic)
n += 1
for source, sed in zip(self.source_sb_models, self.source_sed_models):
source_ind_dic = {}
spix = source.pixeval(xl, yl)
for band in self.bands:
hdr['%s.mag_%s' % (source.name, band)] = sed.mags[band]
scale = sed.scale(band, self.main_band)
source_ind_here = scale * convolve.convolve(
spix, self.convol_matrix[band], False)[0]
source_ind_dic[band] = source_ind_here
source_ind_model.append(source_ind_dic)
n += 1
phdu = pyfits.PrimaryHDU(header=hdr)
hdulist = pyfits.HDUList([phdu])
for light, light_ind_dic in zip(self.light_sb_models, light_ind_model):
for band in self.bands:
hdu_here = pyfits.ImageHDU(data=light_ind_dic[band])
hdu_here.header['EXTNAME'] = '%s_%s' % (light.name, band)
hdulist.append(hdu_here)
for source, source_ind_dic in zip(self.source_sb_models,
source_ind_model):
for band in self.bands:
hdu_here = pyfits.ImageHDU(data=source_ind_dic[band])
hdu_here.header['EXTNAME'] = '%s_%s' % (source.name, band)
hdulist.append(hdu_here)
if self.sky is not None:
for band in self.bands:
hdu_here = pyfits.ImageHDU(
data=self.sky['amp_%s' % band].value + 0. * self.sci[band])
hdu_here.header['EXTNAME'] = 'sky_%s' % band
hdulist.append(hdu_here)
hdulist.writeto(fitsname, overwrite=True)
if make_rgb:
# makes model rgb
sci_list = []
light_list = []
source_list = []
for band in self.bands:
sci_list.append(self.sci[band])
lmodel = 0. * self.sci[band]
smodel = 0. * self.sci[band]
for light in light_ind_model:
lmodel += light[band]
if self.sky is not None:
lmodel += self.sky['amp_%s' % band].value
light_list.append(lmodel)
for source in source_ind_model:
smodel += source[band]
source_list.append(smodel)
pyplz_rgbtools.make_full_rgb(sci_list,
light_list,
source_list,
outname=rgbname)
def lensFit(inpars,
image,
sig,
gals,
lenses,
sources,
xc,
yc,
OVRS=1,
csub=5,
psf=None,
mask=None,
noResid=False,
verbose=False,
getModel=False,
showAmps=False,
allowNeg=False):
import pylens, numpy
import indexTricks as iT
from imageSim import convolve
from scipy import optimize
"""
if psf is not None:
from imageSim import convolve
global psfFFT
if psfFFT is None:
psf /= psf.sum()
#if OVRS>1:
# from scipy import ndimage
# psf = ndimage.zoom(psf,OVRS)
tmp,psfFFT = convolve.convolve(image,psf)
"""
if noResid == True or getModel == True:
mask = None
if mask is None:
xin = xc.copy()
yin = yc.copy()
imin = image.flatten()
sigin = sig.flatten()
else:
xin = xc[mask].copy()
yin = yc[mask].copy()
imin = image[mask].flatten()
sigin = sig[mask].flatten()
n = 0
model = numpy.empty((len(gals) + len(sources), imin.size))
for gal in gals:
gal.setPars()
gal.amp = 1
if mask is None:
tmp = gal.pixeval(xin, yin, 1. / OVRS, csub=csub)
else:
tmp = xc * 0.
tmp[mask] = gal.pixeval(xin, yin, 1. / OVRS, csub=csub)
if numpy.isnan(tmp).any():
if verbose == True:
print 'nan model'
return -1e300
# if psf is not None:
# tmp = convolve.convolve(tmp,psfFFT,False)[0]
if OVRS > 1:
tmp = iT.resamp(tmp, OVRS, True)
if psf is not None and gal.convolve is not None:
tmp = convolve.convolve(tmp, psf, False)[0]
if mask is None:
model[n] = tmp.ravel()
else:
model[n] = tmp[mask].ravel()
n += 1
for lens in lenses:
lens.setPars()
x0, y0 = pylens.lens_images(lenses,
sources, [xin, yin],
1. / OVRS,
getPix=True)
for src in sources:
src.setPars()
src.amp = 1
if mask is None:
tmp = src.pixeval(x0, y0, 1. / OVRS, csub=csub)
else:
tmp = xc * 0.
tmp[mask] = src.pixeval(x0, y0, 1. / OVRS, csub=csub)
if numpy.isnan(tmp).any():
if verbose == True:
print 'nan model'
return -1e300
# if psf is not None:
# tmp = convolve.convolve(tmp,psfFFT,False)[0]
if OVRS > 1:
tmp = iT.resamp(tmp, OVRS, True)
if psf is not None:
tmp = convolve.convolve(tmp, psf, False)[0]
if mask is None:
model[n] = tmp.ravel()
else:
model[n] = tmp[mask].ravel()
n += 1
rhs = (imin / sigin)
op = (model / sigin).T
fit, chi = optimize.nnls(op, rhs)
#print fit
#exit()
if getModel is True:
j = 0
for m in gals + sources:
m.amp = fit[j]
j += 1
return (model.T * fit).T.reshape((n, image.shape[0], image.shape[1]))
elif noResid is True:
model = (model.T * fit).sum(1).reshape(image.shape)
j = 0
for m in gals + sources:
m.amp = fit[j]
j += 1
return model
model = (model.T * fit).sum(1)
if mask is None:
model = model.reshape(image.shape)
resid = ((model - image) / sig).ravel()
else:
resid = (model - imin) / sigin
if verbose == True:
print "%f %5.2f %d %dx%d" % (
(resid**2).sum(), (resid**2).sum() / resid.size, resid.size,
image.shape[1], image.shape[0])
return -0.5 * (resid**2).sum()
def lensFit(inpars,image,sig,gals,lenses,sources,xc,yc,OVRS=1,csub=5,psf=None,mask=None,noResid=False,verbose=False,getModel=False,showAmps=False,allowNeg=False):
import pylens,numpy
import indexTricks as iT
from imageSim import convolve
from scipy import optimize
if noResid==True or getModel==True:
mask = None
if mask is None:
xin = xc.copy()
yin = yc.copy()
imin = image.flatten()
sigin = sig.flatten()
else:
xin = xc[mask].copy()
yin = yc[mask].copy()
imin = image[mask].flatten()
sigin = sig[mask].flatten()
n = 0
model = numpy.empty((len(gals)+len(sources),imin.size))
for gal in gals:
gal.setPars()
gal.amp = 1
if mask is None:
tmp = gal.pixeval(xin,yin,1./OVRS,csub=csub)
else:
tmp = xc*0.
tmp[mask] = gal.pixeval(xin,yin,1./OVRS,csub=csub)
if numpy.isnan(tmp).any():
if verbose==True:
print 'nan model'
return -1e300
# if psf is not None:
# tmp = convolve.convolve(tmp,psfFFT,False)[0]
if OVRS>1:
tmp = iT.resamp(tmp,OVRS,True)
if psf is not None and gal.convolve is not None:
tmp = convolve.convolve(tmp,psf,False)[0]
if mask is None:
model[n] = tmp.ravel()
else:
model[n] = tmp[mask].ravel()
n += 1
for lens in lenses:
lens.setPars()
x0,y0 = pylens.lens_images(lenses,sources,[xin,yin],1./OVRS,getPix=True)
for src in sources:
src.setPars()
src.amp = 1
if mask is None:
tmp = src.pixeval(x0,y0,1./OVRS,csub=csub)
else:
tmp = xc*0.
tmp[mask] = src.pixeval(x0,y0,1./OVRS,csub=csub)
if numpy.isnan(tmp).any():
if verbose==True:
print 'nan model'
return -1e300
# if psf is not None:
# tmp = convolve.convolve(tmp,psfFFT,False)[0]
if OVRS>1:
tmp = iT.resamp(tmp,OVRS,True)
if psf is not None:
tmp = convolve.convolve(tmp,psf,False)[0]
if mask is None:
model[n] = tmp.ravel()
else:
model[n] = tmp[mask].ravel()
n += 1
rhs = (imin/sigin)
op = (model/sigin).T
fit,chi = optimize.nnls(op,rhs)
if getModel is True:
j = 0
for m in gals+sources:
m.amp = fit[j]
j += 1
return (model.T*fit).T.reshape((n,image.shape[0],image.shape[1]))
elif noResid is True:
model = (model.T*fit).sum(1).reshape(image.shape)
j = 0
for m in gals+sources:
m.amp = fit[j]
j += 1
return model
model = (model.T*fit).sum(1)
if mask is None:
model = model.reshape(image.shape)
resid = ((model-image)/sig).ravel()
else:
resid = (model-imin)/sigin
if verbose==True:
print "%f %5.2f %d %dx%d"%((resid**2).sum(),(resid**2).sum()/resid.size,resid.size,image.shape[1],image.shape[0])
return -0.5*(resid**2).sum()