def main():
import optparse
parser = optparse.OptionParser(usage='%prog [options] <NGC-number>')
parser.add_option('--threads', dest='threads', type=int, help='use multiprocessing')
parser.add_option('--itune1',dest='itune1',type=int,help='Individual tuning, first stage',default=5)
parser.add_option('--itune2',dest='itune2',type=int,help='Individual tuning, second stage',default=5)
parser.add_option('--ntune',dest='ntune',type=int,help='All objects tuning',default=0)
parser.add_option('--nocache',dest='nocache',action='store_true',default=False,help='Disable caching for memory reasons')
opt,args = parser.parse_args()
if len(args) != 1:
parser.print_help()
sys.exit(-1)
if opt.threads:
mp = multiproc(nthreads=opt.threads)
else:
mp = multiproc()
ngc = int(args[0])
j = getNGC(ngc)
print j
ra = float(j['RA'][0])
dec = float(j['DEC'][0])
itune1 = opt.itune1
itune2 = opt.itune2
ntune = opt.ntune
IRLS_scale = 25.
radius = (10.**j['LOG_D25'][0])/10.
dr8 = True
noarcsinh = False
print 'Radius', radius
print 'RA,Dec', ra, dec
sras, sdecs, smags = tychoMatch(ra,dec,(radius*1.5)/60.)
for sra,sdec,smag in zip(sras,sdecs,smags):
print sra,sdec,smag
rcfs = radec_to_sdss_rcf(ra,dec,radius=math.hypot(radius,13./2.),tablefn="dr8fields.fits")
print rcfs
#fieldPlot(ra,dec,radius,ngc)
imkw = dict(psf='dg')
if dr8:
getim = st.get_tractor_image_dr8
getsrc = st.get_tractor_sources_dr8
imkw.update(zrange=[-3,100])
else:
getim = st.get_tractor_image
getsrc = st.get_tractor_sources_dr8
imkw.update(useMags=True)
bands=['u','g','r','i','z']
#bands=['r']
bandname = 'r'
flipBands = ['r']
imsrcs = mp.map(get_ims_and_srcs, [(rcf + (bands, ra, dec, radius*60./0.396, imkw, getim, getsrc))
for rcf in rcfs])
timgs = []
sources = []
allsources = []
for ims,s in imsrcs:
if ims is None:
continue
if s is None:
continue
timgs.extend(ims)
allsources.extend(s)
sources.append(s)
#rds = [rcf[3:5] for rcf in rcfs]
plotarea(ra, dec, radius, ngc, timgs) #, rds)
lvl = logging.DEBUG
logging.basicConfig(level=lvl,format='%(message)s',stream=sys.stdout)
tractor = st.Tractor(timgs, allsources, mp=mp)
sa = dict(debug=True, plotAll=False,plotBands=False)
if noarcsinh:
sa.update(nlscale=0)
elif dr8:
sa.update(chilo=-8.,chihi=8.)
if opt.nocache:
tractor.cache = NullCache()
sg.disable_galaxy_cache()
zr = timgs[0].zr
print "zr is: ",zr
print bands
print "Number of images: ", len(timgs)
# for timg,band in zip(timgs,bands):
# data = timg.getImage()/np.sqrt(timg.getInvvar())
# plt.hist(data,bins=100)
# plt.savefig('hist-%s.png' % (band))
prefix = 'ngc%d' % (ngc)
saveAll('initial-'+prefix, tractor,**sa)
#plotInvvar('initial-'+prefix,tractor)
for sra,sdec,smag in zip(sras,sdecs,smags):
print sra,sdec,smag
for img in tractor.getImages():
wcs = img.getWcs()
starx,stary = wcs.positionToPixel(RaDecPos(sra,sdec))
starr=25*(2**(max(11-smag,0.)))
if starx+starr<0. or starx-starr>img.getWidth() or stary+starr <0. or stary-starr>img.getHeight():
continue
X,Y = np.meshgrid(np.arange(img.getWidth()), np.arange(img.getHeight()))
R2 = (X - starx)**2 + (Y - stary)**2
img.getStarMask()[R2 < starr**2] = 0
#star = [(x,y) for x in range(img.getWidth()) for y in range(img.getHeight()) if (x-starx)**2+(y-stary)**2 <= starr**2]
#for (x,y) in star:
# img.getStarMask()[y][x] = 0
for timgs,sources in imsrcs:
timg = timgs[0]
wcs = timg.getWcs()
xtr,ytr = wcs.positionToPixel(RaDecPos(ra,dec))
print xtr,ytr
xt = xtr
yt = ytr
r = ((radius*60.))/.396 #radius in pixels
for src in sources:
xs,ys = wcs.positionToPixel(src.getPosition(),src)
if (xs-xt)**2+(ys-yt)**2 <= r**2:
print "Removed:", src
print xs,ys
tractor.removeSource(src)
#saveAll('removed-'+prefix, tractor,**sa)
newShape = sg.GalaxyShape(30.,1.,0.)
newBright = ba.Mags(r=15.0,g=15.0,u=15.0,z=15.0,i=15.0,order=['u','g','r','i','z'])
EG = st.ExpGalaxy(RaDecPos(ra,dec),newBright,newShape)
print EG
tractor.addSource(EG)
saveAll('added-'+prefix,tractor,**sa)
print 'Tractor has', tractor.getParamNames()
for im in tractor.images:
im.freezeAllParams()
im.thawParam('sky')
tractor.catalog.freezeAllBut(EG)
print 'Tractor has', tractor.getParamNames()
print 'values', tractor.getParams()
for i in range(itune1):
tractor.optimize()
print resource.getpagesize()
print resource.getrusage(resource.RUSAGE_SELF)[2]
tractor.changeInvvar(IRLS_scale)
print resource.getpagesize()
print resource.getrusage(resource.RUSAGE_SELF)[2]
saveAll('itune1-%d-' % (i+1)+prefix,tractor,**sa)
print resource.getpagesize()
print resource.getrusage(resource.RUSAGE_SELF)[2]
tractor.clearCache()
sg.get_galaxy_cache().clear()
gc.collect()
print resource.getpagesize()
print resource.getrusage(resource.RUSAGE_SELF)[2]
CGPos = EG.getPosition()
CGShape1 = EG.getShape().copy()
CGShape2 = EG.getShape().copy()
EGBright = EG.getBrightness()
CGu = EGBright[0] + 0.75
CGg = EGBright[1] + 0.75
CGr = EGBright[2] + 0.75
CGi = EGBright[3] + 0.75
CGz = EGBright[4] + 0.75
CGBright1 = ba.Mags(r=CGr,g=CGg,u=CGu,z=CGz,i=CGi,order=['u','g','r','i','z'])
CGBright2 = ba.Mags(r=CGr,g=CGg,u=CGu,z=CGz,i=CGi,order=['u','g','r','i','z'])
print EGBright
print CGBright1
CG = st.CompositeGalaxy(CGPos,CGBright1,CGShape1,CGBright2,CGShape2)
tractor.removeSource(EG)
tractor.addSource(CG)
tractor.catalog.freezeAllBut(CG)
print resource.getpagesize()
print resource.getrusage(resource.RUSAGE_SELF)[2]
for i in range(itune2):
tractor.optimize()
tractor.changeInvvar(IRLS_scale)
saveAll('itune2-%d-' % (i+1)+prefix,tractor,**sa)
print resource.getpagesize()
print "RUsage is: ",resource.getrusage(resource.RUSAGE_SELF)[2]
tractor.clearCache()
sg.get_galaxy_cache().clear()
print resource.getpagesize()
print resource.getrusage(resource.RUSAGE_SELF)[2]
tractor.catalog.thawAllParams()
for i in range(ntune):
tractor.optimize()
tractor.changeInvvar(IRLS_scale)
saveAll('ntune-%d-' % (i+1)+prefix,tractor,**sa)
#plotInvvar('final-'+prefix,tractor)
sa.update(plotBands=True)
saveAll('allBands-' + prefix,tractor,**sa)
print CG
print CG.getPosition()
print CGBright1
print CGBright2
print CGShape1
print CGShape2
print CGBright1+CGBright2
print CG.getBrightness()
pfn = 'ngc-%d.pickle' % ngc
pickle_to_file(CG,pfn)
makeflipbook(prefix,len(tractor.getImages()),itune1,itune2,ntune)
def main():
# In LSST meas-deblend (on lsst6):
# python examples/suprimePlot.py --data ~dstn/lsst/ACT-data -v 126969 -c 5 --data-range -100 300 --roi 0 500 0 500 --psf psf.fits --image img.fits --sources srcs.fits
from optparse import OptionParser
import sys
parser = OptionParser(usage=('%prog <img> <psf> <srcs>'))
parser.add_option('-v',
'--verbose',
dest='verbose',
action='count',
default=0,
help='Make more verbose')
opt, args = parser.parse_args()
if len(args) != 3:
parser.print_help()
sys.exit(-1)
if opt.verbose == 0:
lvl = logging.INFO
else:
lvl = logging.DEBUG
logging.basicConfig(level=lvl, format='%(message)s', stream=sys.stdout)
imgfn, psffn, srcfn = args
pimg = pyfits.open(imgfn)
if len(pimg) != 4:
print('Image must have 3 extensions')
sys.exit(-1)
img = pimg[1].data
mask = pimg[2].data
maskhdr = pimg[2].header
var = pimg[3].data
del pimg
print('var', var.shape)
#print var
print('mask', mask.shape)
#print mask
print('img', img.shape)
#print img
mask = mask.astype(np.int16)
for bit in range(16):
on = ((mask & (1 << bit)) != 0)
print('Bit', bit, 'has', np.sum(on), 'pixels set')
'''
MP_BAD = 0
Bit 0 has 2500 pixels set
MP_SAT = 1
Bit 1 has 5771 pixels set
MP_INTRP= 2
Bit 2 has 11269 pixels set
MP_CR = 3
Bit 3 has 136 pixels set
MP_EDGE = 4
Bit 4 has 11856 pixels set
HIERARCH MP_DETECTED = 5
Bit 5 has 37032 pixels set
'''
print('Mask header:', maskhdr)
maskplanes = {}
print('Mask planes:')
for card in maskhdr.ascardlist():
if not card.key.startswith('MP_'):
continue
print(card.value, card.key)
maskplanes[card.key[3:]] = card.value
print('Variance range:', var.min(), var.max())
print('Image median:', np.median(img.ravel()))
invvar = 1. / var
invvar[var == 0] = 0.
invvar[var < 0] = 0.
sig = np.sqrt(np.median(var))
H, W = img.shape
for k, v in maskplanes.items():
plt.clf()
I = ((mask & (1 << v)) != 0)
rgb = np.zeros((H, W, 3))
clipimg = np.clip((img - (-3. * sig)) / (13. * sig), 0, 1)
cimg = clipimg.copy()
cimg[I] = 1
rgb[:, :, 0] = cimg
cimg = clipimg.copy()
cimg[I] = 0
rgb[:, :, 1] = cimg
rgb[:, :, 2] = cimg
plt.imshow(rgb, interpolation='nearest', origin='lower')
plt.title(k)
plt.savefig('mask-%s.png' % k.lower())
badmask = sum([(1 << maskplanes[k])
for k in ['BAD', 'SAT', 'INTRP', 'CR']])
# HACK -- left EDGE sucks
badmask += (1 << maskplanes['EDGE'])
#badmask = (1 << 0) | (1 << 1) | (1 << 2) | (1 << 3)
#badmask |= (1 << 4)
print('Masking out: 0x%x' % badmask)
invvar[(mask & badmask) != 0] = 0.
assert (all(np.isfinite(img.ravel())))
assert (all(np.isfinite(invvar.ravel())))
psf = pyfits.open(psffn)[0].data
print('psf', psf.shape)
psf /= psf.sum()
from tractor.emfit import em_fit_2d
from tractor.fitpsf import em_init_params
# Create Gaussian mixture model PSF approximation.
S = psf.shape[0]
# number of Gaussian components
K = 3
w, mu, sig = em_init_params(K, None, None, None)
II = psf.copy()
II /= II.sum()
# HIDEOUS HACK
II = np.maximum(II, 0)
print('Multi-Gaussian PSF fit...')
xm, ym = -(S / 2), -(S / 2)
em_fit_2d(II, xm, ym, w, mu, sig)
print('w,mu,sig', w, mu, sig)
mypsf = tractor.GaussianMixturePSF(w, mu, sig)
P = mypsf.getPointSourcePatch(S / 2, S / 2)
mn, mx = psf.min(), psf.max()
ima = dict(interpolation='nearest', origin='lower', vmin=mn, vmax=mx)
plt.clf()
plt.subplot(1, 2, 1)
plt.imshow(psf, **ima)
plt.subplot(1, 2, 2)
pimg = np.zeros_like(psf)
P.addTo(pimg)
plt.imshow(pimg, **ima)
plt.savefig('psf.png')
sig = np.sqrt(np.median(var))
plt.clf()
plt.hist(img.ravel(), 100, range=(-3. * sig, 3. * sig))
plt.savefig('imghist.png')
srcs = fits_table(srcfn)
print('Initial:', len(srcs), 'sources')
# Trim sources with x=0 or y=0
srcs = srcs[(srcs.x != 0) * (srcs.y != 0)]
print('Trim on x,y:', len(srcs), 'sources left')
# Zero out nans & infs
for c in ['theta', 'a', 'b']:
I = np.logical_not(np.isfinite(srcs.get(c)))
srcs.get(c)[I] = 0.
# Set sources with flux=NaN to something more sensible...
I = np.logical_not(np.isfinite(srcs.flux))
srcs.flux[I] = 1.
# Sort sources by flux.
srcs = srcs[np.argsort(-srcs.flux)]
# Trim sources that are way outside the image.
margin = 8. * np.maximum(srcs.a, srcs.b)
H, W = img.shape
srcs = srcs[(srcs.x > -margin) * (srcs.y > -margin) *
(srcs.x < (W + margin) * (srcs.y < (H + margin)))]
print('Trim out-of-bounds:', len(srcs), 'sources left')
wcs = tractor.FitsWcs(Sip(imgfn, 1))
#wcs = tractor.NullWCS()
timg = tractor.Image(data=img,
invvar=invvar,
psf=mypsf,
wcs=wcs,
sky=tractor.ConstantSky(0.),
photocal=tractor.NullPhotoCal(),
name='image')
inverr = timg.getInvError()
assert (all(np.isfinite(inverr.ravel())))
tsrcs = []
for s in srcs:
#pos = tractor.PixPos(s.x, s.y)
pos = tractor.RaDecPos(s.ra, s.dec)
if s.a > 0 and s.b > 0:
eflux = tractor.Flux(s.flux / 2.)
dflux = tractor.Flux(s.flux / 2.)
re, ab, phi = s.a, s.b / s.a, 90. - s.theta
eshape = gal.GalaxyShape(re, ab, phi)
dshape = gal.GalaxyShape(re, ab, phi)
print('Fluxes', eflux, dflux)
tsrc = gal.CompositeGalaxy(pos, eflux, eshape, dflux, dshape)
else:
flux = tractor.Flux(s.flux)
print('Flux', flux)
tsrc = tractor.PointSource(pos, flux)
tsrcs.append(tsrc)
chug = tractor.Tractor([timg])
for src in tsrcs:
if chug.getModelPatch(timg, src) is None:
print('Dropping non-overlapping source:', src)
continue
chug.addSource(src)
print('Kept a total of', len(chug.catalog), 'sources')
ima = dict(interpolation='nearest',
origin='lower',
vmin=-3. * sig,
vmax=10. * sig)
chia = dict(interpolation='nearest', origin='lower', vmin=-5., vmax=5.)
plt.clf()
plt.imshow(img, **ima)
plt.colorbar()
plt.savefig('img.png')
plt.clf()
plt.imshow(invvar, interpolation='nearest', origin='lower')
plt.colorbar()
plt.savefig('invvar.png')
mod = chug.getModelImages()[0]
plt.clf()
plt.imshow(mod, **ima)
plt.colorbar()
plt.savefig('mod-0.png')
chi = chug.getChiImage(0)
plt.clf()
plt.imshow(chi, **chia)
plt.colorbar()
plt.savefig('chi-0.png')
for step in range(5):
cat = chug.getCatalog()
for src in cat:
if chug.getModelPatch(timg, src) is None:
print('Dropping non-overlapping source:', src)
chug.removeSource(src)
print('Kept a total of', len(chug.catalog), 'sources')
#cat = chug.getCatalog()
#for i,src in enumerate([]):
#for i,src in enumerate(chug.getCatalog()):
#for i in range(len(cat)):
i = 0
while i < len(cat):
src = cat[i]
#print 'Step', i
#for j,s in enumerate(cat):
# x,y = timg.getWcs().positionToPixel(s, s.getPosition())
# print ' ',
# if j == i:
# print '*',
# print '(%6.1f, %6.1f)'%(x,y), s
print('Optimizing source', i, 'of', len(cat))
x, y = timg.getWcs().positionToPixel(src.getPosition(), src)
print('(%6.1f, %6.1f)' % (x, y), src)
# pre = src.getModelPatch(timg)
s1 = str(src)
print('src1 ', s1)
dlnp1, X, a = chug.optimizeCatalogFluxes(srcs=[src])
s2 = str(src)
dlnp2, X, a = chug.optimizeCatalogAtFixedComplexityStep(srcs=[src],
sky=False)
s3 = str(src)
#post = src.getModelPatch(timg)
print('src1 ', s1)
print('src2 ', s2)
print('src3 ', s3)
print('dlnp', dlnp1, dlnp2)
if chug.getModelPatch(timg, src) is None:
print('After optimizing, no overlap!')
print('Removing source', src)
chug.removeSource(src)
i -= 1
i += 1
# plt.clf()
# plt.subplot(2,2,1)
# img = timg.getImage()
# (x0,x1,y0,y1) = pre.getExtent()
# plt.imshow(img, **ima)
# ax = plt.axis()
# plt.plot([x0,x0,x1,x1,x0], [y0,y1,y1,y0,y0], 'k-', lw=2)
# plt.axis(ax)
# plt.subplot(2,2,3)
# plt.imshow(pre.getImage(), **ima)
# plt.subplot(2,2,4)
# plt.imshow(post.getImage(), **ima)
# plt.savefig('prepost-s%i-s%03i.png' % (step, i))
#
# mod = chug.getModelImages()[0]
# plt.clf()
# plt.imshow(mod, **ima)
# plt.colorbar()
# plt.savefig('mod-s%i-s%03i.png' % (step, i))
# chi = chug.getChiImage(0)
# plt.clf()
# plt.imshow(chi, **chia)
# plt.colorbar()
# plt.savefig('chi-s%i-s%03i.png' % (step, i))
#dlnp,x,a = chug.optimizeCatalogFluxes()
#print 'fluxes: dlnp', dlnp
#dlnp,x,a = chug.optimizeCatalogAtFixedComplexityStep()
#print 'opt: dlnp', dlnp
mod = chug.getModelImages()[0]
plt.clf()
plt.imshow(mod, **ima)
plt.colorbar()
plt.savefig('mod-%i.png' % (step + 1))
chi = chug.getChiImage(0)
plt.clf()
plt.imshow(chi, **chia)
plt.colorbar()
plt.savefig('chi-%i.png' % (step + 1))
return
for step in range(5):
chug.optimizeCatalogFluxes()
mod = chug.getModelImages()[0]
plt.clf()
plt.imshow(mod, **ima)
plt.colorbar()
plt.savefig('mod-s%i.png' % step)
chi = chug.getChiImage(0)
plt.clf()
plt.imshow(chi, **chia)
plt.colorbar()
plt.savefig('chi-s%i.png' % step)
def main():
ra = 126.925
dec = 21.4833
itune1 = 5
itune2 = 5
ntune = 2
run = [4517, 4576, 4576]
field = [103, 99, 100]
camcol = [2, 6, 6]
bands = ['r']
bandname = 'r'
flipBands = ['r']
rerun = 0
TI = []
sources = []
table = pyfits.open("J082742.02+212844.7-r.fits")
table.info()
header = table[0].header
data = table[0].data
invvar = table[1].data
skyobj = ba.ConstantSky(header['skyval'])
psffn = 'J082742.02+212844.7-r-bpsf.fits.gz'
psfimg = pyfits.open(psffn)[0].data
print('PSF image shape', psfimg.shape)
# number of Gaussian components
PS = psfimg.shape[0]
K = 3
w, mu, sig = em_init_params(K, None, None, None)
II = psfimg.copy()
II /= II.sum()
# HACK
II = np.maximum(II, 0)
print('Multi-Gaussian PSF fit...')
xm, ym = -(PS / 2), -(PS / 2)
em_fit_2d(II, xm, ym, w, mu, sig)
print('w,mu,sig', w, mu, sig)
psf = GaussianMixturePSF(w, mu, sig)
sources = []
# for run,camcol,field in zip(run,camcol,field):
# sources.append(st.get_tractor_sources(run,camcol,field,bandname,bands=bands))
wcs = Tan("J082742.02+212844.7-r.fits", 0)
wcs = FitsWcs(wcs)
wcs.setX0Y0(1., 1.)
photocal = ba.NasaSloanPhotoCal(bandname) #Also probably not right
TI.append(
en.Image(data=data,
invvar=invvar,
sky=skyobj,
psf=psf,
wcs=wcs,
photocal=photocal,
name="NASA-Sloan Test"))
lvl = logging.DEBUG
logging.basicConfig(level=lvl, format='%(message)s', stream=sys.stdout)
tims = [TI[0]]
tractor = st.SDSSTractor(tims)
for source in sources:
tractor.addSources(source)
zr = np.array([-5., +5.]) # * info['skysig']
print(bands)
prefix = 'ngc2595'
# saveAll('initial-'+prefix, tractor,zr,flipBands,debug=True)
bright = None
lowbright = 1000
sources = []
for timg, sources in zip(tims, sources):
wcs = timg.getWcs()
xtr, ytr = wcs.positionToPixel(RaDecPos(ra, dec))
print(xtr, ytr)
xt = xtr
yt = ytr
r = 250.
for src in sources:
xs, ys = wcs.positionToPixel(src.getPosition(), src)
if (xs - xt)**2 + (ys - yt)**2 <= r**2:
print("Removed:", src)
print(xs, ys)
tractor.removeSource(src)
# saveAll('removed-'+prefix, tractor,zr,flipBands,debug=True)
newShape = sg.GalaxyShape(30., 1., 0.)
newBright = ba.Mags(r=15.0, g=15.0, u=15.0, z=15.0, i=15.0)
EG = st.ExpGalaxy(RaDecPos(ra, dec), newBright, newShape)
print(EG)
tractor.addSource(EG)
saveAll('added-' + prefix, tractor, zr, flipBands, debug=True)
plotInvvar('added-' + prefix, tractor)
for i in range(itune1):
if (i % 5 == 0):
tractor.optimizeCatalogLoop(nsteps=1, srcs=[EG], sky=True)
else:
tractor.optimizeCatalogLoop(nsteps=1, srcs=[EG], sky=False)
tractor.changeInvvar(9.)
tractor.clearCache()
saveAll('itune1-%d-' % (i + 1) + prefix,
tractor,
zr,
flipBands,
debug=True)
plotInvvar('itune1-%d-' % (i + 1) + prefix, tractor)
CGPos = EG.getPosition()
CGShape = EG.getShape()
EGBright = EG.getBrightness()
print(EGBright)
CGg = EGBright[0] * 1.25
CGi = EGBright[1] * 1.25
CGr = EGBright[2] * 1.25
CGu = EGBright[3] * 1.25
CGz = EGBright[4] * 1.25
CGBright = ba.Mags(r=CGr, g=CGg, u=CGu, z=CGz, i=CGi)
print(EGBright)
print(CGBright)
CG = st.CompositeGalaxy(CGPos, CGBright, CGShape, CGBright, CGShape)
tractor.removeSource(EG)
tractor.addSource(CG)
for i in range(itune2):
if (i % 5 == 0):
tractor.optimizeCatalogLoop(nsteps=1, srcs=[CG], sky=True)
else:
tractor.optimizeCatalogLoop(nsteps=1, srcs=[CG], sky=False)
tractor.changeInvvar(9.)
tractor.clearCache()
saveAll('itune2-%d-' % (i + 1) + prefix,
tractor,
zr,
flipBands,
debug=True)
plotInvvar('itune2-%d-' % (i + 1) + prefix, tractor)
for i in range(ntune):
tractor.optimizeCatalogLoop(nsteps=1, sky=True)
saveAll('ntune-%d-' % (i + 1) + prefix,
tractor,
zr,
flipBands,
debug=True)
tractor.clearCache()
makeflipbook(prefix, len(tractor.getImages()), itune1, itune2, ntune)
def twogalaxies(name1, ra1, dec1, name2, ra2, dec2):
name = "%s %s" % (name1, name2)
ra = float(ra1)
dec = float(dec1)
ra2 = float(ra2)
dec2 = float(dec2)
remradius = 6.
fieldradius = 6.
threads = None
itune1 = 5
itune2 = 5
ntune = 0
nocache = True
#Radius should be in arcminutes
if threads:
mp = multiproc(nthreads=threads)
else:
mp = multiproc()
IRLS_scale = 25.
dr9 = True
dr8 = False
noarcsinh = False
print(name)
prefix = '%s' % (name.replace(' ', '_'))
prefix1 = '%s' % (name1.replace(' ', '_'))
prefix2 = '%s' % (name2.replace(' ', '_'))
print('Removal Radius', remradius)
print('Field Radius', fieldradius)
print('RA,Dec', ra, dec)
print(os.getcwd())
rcfs = radec_to_sdss_rcf(ra,
dec,
radius=math.hypot(fieldradius, 13. / 2.),
tablefn="dr9fields.fits")
print(rcfs)
assert (len(rcfs) > 0)
assert (len(rcfs) < 15)
sras, sdecs, smags = tychoMatch(ra, dec, (fieldradius * 1.5) / 60.)
for sra, sdec, smag in zip(sras, sdecs, smags):
print(sra, sdec, smag)
imkw = dict(psf='dg')
if dr9:
getim = st.get_tractor_image_dr9
getsrc = st.get_tractor_sources_dr9
imkw.update(zrange=[-3, 100])
elif dr8:
getim = st.get_tractor_image_dr8
getsrc = st.get_tractor_sources_dr8
imkw.update(zrange=[-3, 100])
else:
getim = st.get_tractor_image
getsrc = st.get_tractor_sources_dr8
imkw.update(useMags=True)
bands = ['u', 'g', 'r', 'i', 'z']
bandname = 'r'
flipBands = ['r']
print(rcfs)
imsrcs = mp.map(
get_ims_and_srcs,
[(rcf +
(bands, ra, dec, fieldradius * 60. / 0.396, imkw, getim, getsrc))
for rcf in rcfs])
timgs = []
sources = []
allsources = []
for ims, s in imsrcs:
if ims is None:
continue
if s is None:
continue
timgs.extend(ims)
allsources.extend(s)
sources.append(s)
#rds = [rcf[3:5] for rcf in rcfs]
plotarea(ra, dec, fieldradius, name, prefix, timgs) #, rds)
lvl = logging.DEBUG
logging.basicConfig(level=lvl, format='%(message)s', stream=sys.stdout)
tractor = st.Tractor(timgs, allsources, mp=mp)
sa = dict(debug=True, plotAll=False, plotBands=False)
if noarcsinh:
sa.update(nlscale=0)
elif dr8 or dr9:
sa.update(chilo=-8., chihi=8.)
if nocache:
tractor.cache = NullCache()
sg.disable_galaxy_cache()
zr = timgs[0].zr
print("zr is: ", zr)
print(bands)
print("Number of images: ", len(timgs))
# for timg,band in zip(timgs,bands):
# data = timg.getImage()/np.sqrt(timg.getInvvar())
# plt.hist(data,bins=100)
# plt.savefig('hist-%s.png' % (band))
saveAll('initial-' + prefix, tractor, **sa)
#plotInvvar('initial-'+prefix,tractor)
for sra, sdec, smag in zip(sras, sdecs, smags):
print(sra, sdec, smag)
for img in tractor.getImages():
wcs = img.getWcs()
starx, stary = wcs.positionToPixel(RaDecPos(sra, sdec))
starr = 25 * (2**(max(11 - smag, 0.)))
if starx + starr < 0. or starx - starr > img.getWidth(
) or stary + starr < 0. or stary - starr > img.getHeight():
continue
X, Y = np.meshgrid(np.arange(img.getWidth()),
np.arange(img.getHeight()))
R2 = (X - starx)**2 + (Y - stary)**2
img.getStarMask()[R2 < starr**2] = 0
for timgs, sources in imsrcs:
timg = timgs[0]
wcs = timg.getWcs()
xtr, ytr = wcs.positionToPixel(RaDecPos(ra, dec))
print(xtr, ytr)
xt = xtr
yt = ytr
r = ((remradius * 60.)) / .396 #radius in pixels
for src in sources:
xs, ys = wcs.positionToPixel(src.getPosition(), src)
if (xs - xt)**2 + (ys - yt)**2 <= r**2:
#print "Removed:", src
#print xs,ys
tractor.removeSource(src)
#saveAll('removed-'+prefix, tractor,**sa)
newShape = sg.GalaxyShape((remradius * 60.) / 10., 1., 0.)
newBright = ba.Mags(r=15.0,
g=15.0,
u=15.0,
z=15.0,
i=15.0,
order=['u', 'g', 'r', 'i', 'z'])
EG = st.ExpGalaxy(RaDecPos(ra, dec), newBright, newShape)
newShape2 = sg.GalaxyShape((remradius * 60.) / 10., 1., 0.)
newBright2 = ba.Mags(r=15.0,
g=15.0,
u=15.0,
z=15.0,
i=15.0,
order=['u', 'g', 'r', 'i', 'z'])
EG2 = st.ExpGalaxy(RaDecPos(ra2, dec2), newBright2, newShape2)
print(EG)
print(EG2)
tractor.addSource(EG)
tractor.addSource(EG2)
saveAll('added-' + prefix, tractor, **sa)
#print 'Tractor has', tractor.getParamNames()
for im in tractor.images:
im.freezeAllParams()
im.thawParam('sky')
tractor.catalog.freezeAllBut(EG)
tractor.catalog.thawParams(EG2)
#print 'Tractor has', tractor.getParamNames()
#print 'values', tractor.getParams()
for i in range(itune1):
tractor.optimize()
tractor.changeInvvar(IRLS_scale)
saveAll('itune1-%d-' % (i + 1) + prefix, tractor, **sa)
tractor.clearCache()
sg.get_galaxy_cache().clear()
gc.collect()
print(resource.getpagesize())
print(resource.getrusage(resource.RUSAGE_SELF)[2])
CGPos = EG.getPosition()
CGShape1 = EG.getShape().copy()
CGShape2 = EG.getShape().copy()
EGBright = EG.getBrightness()
CGu = EGBright[0] + 0.75
CGg = EGBright[1] + 0.75
CGr = EGBright[2] + 0.75
CGi = EGBright[3] + 0.75
CGz = EGBright[4] + 0.75
CGBright1 = ba.Mags(r=CGr,
g=CGg,
u=CGu,
z=CGz,
i=CGi,
order=['u', 'g', 'r', 'i', 'z'])
CGBright2 = ba.Mags(r=CGr,
g=CGg,
u=CGu,
z=CGz,
i=CGi,
order=['u', 'g', 'r', 'i', 'z'])
print(EGBright)
print(CGBright1)
CG = st.CompositeGalaxy(CGPos, CGBright1, CGShape1, CGBright2, CGShape2)
CG2Pos = EG2.getPosition()
CG2Shape1 = EG2.getShape().copy()
CG2Shape2 = EG2.getShape().copy()
EG2Bright = EG2.getBrightness()
CG2u = EG2Bright[0] + 0.75
CG2g = EG2Bright[1] + 0.75
CG2r = EG2Bright[2] + 0.75
CG2i = EG2Bright[3] + 0.75
CG2z = EG2Bright[4] + 0.75
CG2Bright1 = ba.Mags(r=CG2r,
g=CG2g,
u=CG2u,
z=CG2z,
i=CG2i,
order=['u', 'g', 'r', 'i', 'z'])
CG2Bright2 = ba.Mags(r=CG2r,
g=CG2g,
u=CG2u,
z=CG2z,
i=CG2i,
order=['u', 'g', 'r', 'i', 'z'])
CG2 = st.CompositeGalaxy(CG2Pos, CG2Bright1, CG2Shape1, CG2Bright2,
CG2Shape2)
tractor.removeSource(EG)
tractor.removeSource(EG2)
tractor.addSource(CG)
tractor.addSource(CG2)
tractor.catalog.freezeAllBut(CG)
tractor.catalog.thawParams(CG2)
print(resource.getpagesize())
print(resource.getrusage(resource.RUSAGE_SELF)[2])
for i in range(itune2):
tractor.optimize()
tractor.changeInvvar(IRLS_scale)
saveAll('itune2-%d-' % (i + 1) + prefix, tractor, **sa)
tractor.clearCache()
sg.get_galaxy_cache().clear()
print(resource.getpagesize())
print(resource.getrusage(resource.RUSAGE_SELF)[2])
tractor.catalog.thawAllParams()
for i in range(ntune):
tractor.optimize()
tractor.changeInvvar(IRLS_scale)
saveAll('ntune-%d-' % (i + 1) + prefix, tractor, **sa)
#plotInvvar('final-'+prefix,tractor)
sa.update(plotBands=True)
saveAll('allBands-' + prefix, tractor, **sa)
print(CG)
print(CG.getPosition())
print(CGBright1)
print(CGBright2)
print(CGShape1)
print(CGShape2)
print(CGBright1 + CGBright2)
print(CG.getBrightness())
pfn = '%s.pickle' % prefix
pickle_to_file([CG, CG2], pfn)
makeflipbook(prefix, len(tractor.getImages()), itune1, itune2, ntune)
pickle_to_file(CG, "%s.pickle" % prefix1)
pickle_to_file(CG2, "%s.pickle" % prefix2)
os.system('cp %s.pickle RC3_Output' % prefix1)
os.system('cp %s.pickle RC3_Output' % prefix2)
def general(name,
ra,
dec,
remradius,
fieldradius,
threads=None,
itune1=5,
itune2=5,
ntune=0,
nocache=False,
scale=1,
ab=1.,
angle=0.):
#Radius should be in arcminutes
if threads:
mp = multiproc(nthreads=threads)
else:
mp = multiproc()
IRLS_scale = 25.
dr9 = True
dr8 = False
noarcsinh = False
print name
prefix = 'swapCG_%s' % (name.replace(' ', '_'))
print 'Removal Radius', remradius
print 'Field Radius', fieldradius
print 'RA,Dec', ra, dec
print os.getcwd()
print ra, dec, math.hypot(fieldradius, 13. / 2.)
rcfs = radec_to_sdss_rcf(ra,
dec,
radius=math.hypot(fieldradius, 13. / 2.),
tablefn="dr9fields.fits")
print 'RCFS:', rcfs
print len(rcfs)
assert (len(rcfs) > 0)
if 10 <= len(rcfs) < 20:
scale = 2
elif 20 <= len(rcfs) < 40:
scale = 4
elif 40 <= len(rcfs) < 80:
scale = 8
assert (len(rcfs) < 80)
sras, sdecs, smags = tychoMatch(ra, dec, (fieldradius * 1.5) / 60.)
imkw = dict(psf='kl-gm')
if dr9:
getim = st.get_tractor_image_dr9
getsrc = st.get_tractor_sources_dr9
imkw.update(zrange=[-3, 100])
elif dr8:
getim = st.get_tractor_image_dr8
getsrc = st.get_tractor_sources_dr8
imkw.update(zrange=[-3, 100])
else:
getim = st.get_tractor_image
getsrc = st.get_tractor_sources_dr8
imkw.update(useMags=True)
bands = ['u', 'g', 'r', 'i', 'z']
#bands=['r']
bandname = 'r'
flipBands = ['r']
print rcfs
imsrcs = mp.map(
get_ims_and_srcs,
[(rcf +
(bands, ra, dec, fieldradius * 60. / 0.396, imkw, getim, getsrc))
for rcf in rcfs])
timgs = []
sources = []
allsources = []
for ims, s in imsrcs:
if ims is None:
continue
if s is None:
continue
if scale > 1:
for im in ims:
timgs.append(st.scale_sdss_image(im, scale))
else:
timgs.extend(ims)
allsources.extend(s)
sources.append(s)
#rds = [rcf[3:5] for rcf in rcfs]
#plotarea(ra, dec, fieldradius, name, prefix, timgs) #, rds)
#lvl = logging.DEBUG
#logging.basicConfig(level=lvl,format='%(message)s',stream=sys.stdout)
tractor = st.Tractor(timgs, allsources, mp=mp)
sa = dict(debug=True, plotAll=False, plotBands=False)
if noarcsinh:
sa.update(nlscale=0)
elif dr8 or dr9:
sa.update(chilo=-8., chihi=8.)
if nocache:
tractor.cache = NullCache()
sg.disable_galaxy_cache()
zr = timgs[0].zr
print "zr is: ", zr
print bands
print "Number of images: ", len(timgs)
#for timg,band in zip(timgs,bands):
# data = timg.getImage()/np.sqrt(timg.getInvvar())
# plt.hist(data,bins=100)
# plt.savefig('hist-%s.png' % (band))
saveAll('initial-' + prefix, tractor, **sa)
#plotInvvar('initial-'+prefix,tractor)
for sra, sdec, smag in zip(sras, sdecs, smags):
for img in tractor.getImages():
wcs = img.getWcs()
starx, stary = wcs.positionToPixel(RaDecPos(sra, sdec))
starr = 25 * (2**(max(11 - smag, 0.)))
if starx + starr < 0. or starx - starr > img.getWidth(
) or stary + starr < 0. or stary - starr > img.getHeight():
continue
X, Y = np.meshgrid(np.arange(img.getWidth()),
np.arange(img.getHeight()))
R2 = (X - starx)**2 + (Y - stary)**2
img.getStarMask()[R2 < starr**2] = 0
for timgs, sources in imsrcs:
timg = timgs[0]
wcs = timg.getWcs()
xtr, ytr = wcs.positionToPixel(RaDecPos(ra, dec))
xt = xtr
yt = ytr
r = ((remradius * 60.)) / .396 #radius in pixels
for src in sources:
xs, ys = wcs.positionToPixel(src.getPosition(), src)
if (xs - xt)**2 + (ys - yt)**2 <= r**2:
#print "Removed:", src
#print xs,ys
tractor.removeSource(src)
#saveAll('removed-'+prefix, tractor,**sa)
newShape = sg.GalaxyShape((remradius * 60.) / 10., ab, angle)
newBright = ba.Mags(r=15.0,
g=15.0,
u=15.0,
z=15.0,
i=15.0,
order=['u', 'g', 'r', 'i', 'z'])
EG = st.ExpGalaxy(RaDecPos(ra, dec), newBright, newShape)
print EG
tractor.addSource(EG)
saveAll('added-' + prefix, tractor, **sa)
#print 'Tractor has', tractor.getParamNames()
for im in tractor.images:
im.freezeAllParams()
im.thawParam('sky')
tractor.catalog.freezeAllBut(EG)
#print 'Tractor has', tractor.getParamNames()
#print 'values', tractor.getParams()
for i in range(itune1):
tractor.optimize()
tractor.changeInvvar(IRLS_scale)
saveAll('itune1-%d-' % (i + 1) + prefix, tractor, **sa)
tractor.clearCache()
sg.get_galaxy_cache().clear()
gc.collect()
print resource.getpagesize()
print resource.getrusage(resource.RUSAGE_SELF)[2]
CGPos = EG.getPosition()
CGShape1 = EG.getShape().copy()
CGShape2 = EG.getShape().copy()
EGBright = EG.getBrightness()
CGu = EGBright[0] + 0.75
CGg = EGBright[1] + 0.75
CGr = EGBright[2] + 0.75
CGi = EGBright[3] + 0.75
CGz = EGBright[4] + 0.75
CGBright1 = ba.Mags(r=CGr,
g=CGg,
u=CGu,
z=CGz,
i=CGi,
order=['u', 'g', 'r', 'i', 'z'])
CGBright2 = ba.Mags(r=CGr,
g=CGg,
u=CGu,
z=CGz,
i=CGi,
order=['u', 'g', 'r', 'i', 'z'])
print EGBright
print CGBright1
CG = st.CompositeGalaxy(CGPos, CGBright1, CGShape1, CGBright2, CGShape2)
tractor.removeSource(EG)
tractor.addSource(CG)
tractor.catalog.freezeAllBut(CG)
print resource.getpagesize()
print resource.getrusage(resource.RUSAGE_SELF)[2]
for i in range(itune2):
tractor.optimize()
tractor.changeInvvar(IRLS_scale)
saveAll('itune2-%d-' % (i + 1) + prefix, tractor, **sa)
tractor.clearCache()
sg.get_galaxy_cache().clear()
print resource.getpagesize()
print resource.getrusage(resource.RUSAGE_SELF)[2]
tractor.catalog.thawAllParams()
for i in range(ntune):
tractor.optimize()
tractor.changeInvvar(IRLS_scale)
saveAll('ntune-%d-' % (i + 1) + prefix, tractor, **sa)
#plotInvvar('final-'+prefix,tractor)
sa.update(plotBands=True)
saveAll('allBands-' + prefix, tractor, **sa)
print "end of first round of optimization:", tractor.getLogLikelihood()
print CG
print CG.getPosition()
print CGBright1
print CGBright2
print CGShape1
print CGShape2
print CGBright1 + CGBright2
print CG.getBrightness()
pfn = '%s.pickle' % prefix
pickle_to_file(CG, pfn)
makeflipbook(prefix, len(tractor.getImages()), itune1, itune2, ntune)
# now SWAP exp and dev and DO IT AGAIN
newCG = st.CompositeGalaxy(CG.getPosition, CG.brightnessDev.copy(),
CG.shapeDev.copy(), CG.brightnessExp.copy(),
CG.shapeExp.copy())
tractor.removeSource(CG)
tractor.addSource(newCG)
tractor.catalog.thawAllParams()
for i in range(ntune):
tractor.optimize()
tractor.changeInvvar(IRLS_scale)
saveAll('ntune-swap-%d-' % (i + 1) + prefix, tractor, **sa)
#plotInvvar('final-'+prefix,tractor)
sa.update(plotBands=True)
saveAll('allBands-swap-' + prefix, tractor, **sa)
print "end of second (swapped) round of optimization:", tractor.getLogLikelihood(
)
print newCG
print newCG.getPosition()
print newCG.getBrightness()
pfn = '%s-swap.pickle' % prefix
pickle_to_file(newCG, pfn)
makeflipbook(prefix + "-swap", len(tractor.getImages()), itune1, itune2,
ntune)