def _fit_simple_lm(self, obs, model, guesser):
from ngmix.fitting import LMSimple
max_pars = self['max_pars']
prior = self['search_prior']
#if obs.has_psf():
# print("psf _data:",obs.psf.gmix._data)
# print("psf copy _data:",obs.psf.gmix.copy()._data)
fitter = LMSimple(obs,
model,
prior=prior,
use_logpars=self['use_logpars'],
lm_pars=max_pars['lm_pars'])
for i in xrange(max_pars['ntry']):
guess = guesser(prior=prior)
print_pars(guess, front=' lm_guess: ')
fitter.run_max(guess)
res = fitter.get_result()
if res['flags'] == 0:
break
return fitter
def _fit_simple_lm(self, mb_obs_list, model, params, use_prior=True):
"""
Fit one of the "simple" models, e.g. exp or dev
use flat g prior
"""
from ngmix.fitting import LMSimple
if use_prior:
prior=self['model_pars'][model]['gflat_prior']
else:
prior=None
ok=False
ntry=params['lm_ntry']
for i in xrange(ntry):
guess=self.guesser(prior=prior)
fitter=LMSimple(mb_obs_list,
model,
prior=prior,
lm_pars=params['lm_pars'])
fitter.run_lm(guess)
res=fitter.get_result()
if res['flags']==0:
ok=True
break
res['ntry']=i+1
return fitter
def _fit_simple_lm(self, obs, model, guesser):
from ngmix.fitting import LMSimple
max_pars=self['max_pars']
prior=self['search_prior']
#if obs.has_psf():
# print("psf _data:",obs.psf.gmix._data)
# print("psf copy _data:",obs.psf.gmix.copy()._data)
fitter=LMSimple(obs,
model,
prior=prior,
use_logpars=self['use_logpars'],
lm_pars=max_pars['lm_pars'])
for i in xrange(max_pars['ntry']):
guess=guesser(prior=prior)
print_pars(guess,front=' lm_guess: ')
fitter.run_max(guess)
res=fitter.get_result()
if res['flags']==0:
break
return fitter
def go(self, ntry=1):
from ngmix.fitting import LMSimple
for i in xrange(ntry):
guess=self.get_guess()
fitter=LMSimple(self.obs,self.model,lm_pars=self.lm_pars)
fitter.go(guess)
res=fitter.get_result()
if res['flags']==0:
break
self.fitter=fitter
def go(self, ntry=1):
from ngmix.fitting import LMSimple
for i in xrange(ntry):
guess = self.get_guess()
fitter = LMSimple(self.obs, self.model, lm_pars=self.lm_pars)
fitter.go(guess)
res = fitter.get_result()
if res['flags'] == 0:
break
self.fitter = fitter
def _go_lm(self, ntry=1):
from ngmix.fitting import LMSimple
for i in xrange(ntry):
guess=self.guesser()
fitter=LMSimple(self.obs,
self.model,
lm_pars=self.send_pars,
use_logpars=self.use_logpars,
prior=self.prior)
fitter.go(guess)
res=fitter.get_result()
if res['flags']==0:
break
self.fitter=fitter
def _run_ml_fitter(mbobs, rng):
# fit the PSF
_fit_psf(mbobs[0][0].psf)
# overall flags, or'ed from each moments fit
res = {'mcal_flags': 0}
try:
fitter = LMSimple(mbobs[0][0], 'exp')
fitter.go(np.array([0, 0, 0, 0, 1, 10]))
fres = fitter.get_result()
except Exception as err:
print('err:', err)
fres = {'flags': np.ones(1, dtype=[('flags', 'i4')])}
res['mcal_flags'] |= fres['flags']
if not res['mcal_flags']:
res['g'] = fres['g']
return res
def _go_lm(self, ntry=1):
from ngmix.fitting import LMSimple
for i in xrange(ntry):
guess = self.guesser()
fitter = LMSimple(self.obs,
self.model,
lm_pars=self.send_pars,
use_logpars=self.use_logpars,
prior=self.prior)
fitter.go(guess)
res = fitter.get_result()
if res['flags'] == 0:
break
self.fitter = fitter
def _fit_simple_lm(self, mb_obs_list, model, max_pars, prior):
"""
Fit one of the "simple" models, e.g. exp or dev
use flat g prior
"""
from ngmix.fitting import LMSimple
ntry=max_pars['ntry']
for i in xrange(ntry):
guess=self.guesser(prior=prior)
# catch case where guess is just no good...
try:
fitter=LMSimple(mb_obs_list,
model,
prior=prior,
lm_pars=max_pars['lm_pars'])
fitter.go(guess)
res=fitter.get_result()
if res['flags']==0:
break
except GMixRangeError:
# probably bad guesser
print(" caught gmix range, using psf guesser")
self.guesser=self._get_guesser_from_me_psf()
res={'flags': GAL_FIT_FAILURE}
fitter=None
if res['flags']==0 and max_pars['replace_cov']:
self._try_replace_cov(fitter)
res['ntry']=i+1
return fitter
def _fit_psf_max(self, obs):
from ngmix.fitting import MaxSimple, LMSimple
assert self['psf_model'] in ["turb",
"gauss"], "gauss,turb only for now"
max_pars = self['psf_max_pars']
if self['psf_method'] == 'Nelder-Mead':
fitter = MaxSimple(obs,
self['psf_model'],
method=self['psf_method'])
else:
fitter = LMSimple(obs, self['psf_model'], lm_pars=max_pars)
Tguess = 2 * self['psf_sigma_guess']**2
Fguess = obs.image.sum()
guess0 = array([0.0, 0.0, 0.0, 0.0, Tguess, Fguess])
for i in xrange(self['psf_ntry']):
guess = guess0.copy()
guess[0:0 + 2] += 0.01 * srandu(2)
guess[2:2 + 2] += 0.1 * srandu(2)
guess[4] *= (1.0 + 0.1 * srandu())
guess[5] *= (1.0 + 0.1 * srandu())
print_pars(guess, front=' guess: ')
if self['psf_method'] == 'lm':
fitter.run_max(guess)
else:
fitter.run_max(guess, **max_pars)
res = fitter.get_result()
if res['flags'] == 0:
print(" max_nfev:", res['nfev'])
break
return fitter
def test_ml_fitting_exp_obj_gauss_psf_smoke(g1_true, g2_true, wcs_g1, wcs_g2):
rng = np.random.RandomState(seed=10)
image_size = 33
cen = (image_size - 1) / 2
gs_wcs = galsim.ShearWCS(0.25, galsim.Shear(g1=wcs_g1,
g2=wcs_g2)).jacobian()
scale = np.sqrt(gs_wcs.pixelArea())
g_prior = ngmix.priors.GPriorBA(0.1)
cen_prior = ngmix.priors.CenPrior(0, 0, scale, scale)
T_prior = ngmix.priors.FlatPrior(0.01, 2)
F_prior = ngmix.priors.FlatPrior(1e-4, 1e9)
prior = ngmix.joint_prior.PriorSimpleSep(cen_prior, g_prior, T_prior,
F_prior)
gal = galsim.Exponential(half_light_radius=0.5).shear(
g1=g1_true, g2=g2_true).withFlux(400)
obj = galsim.Convolve([gal, galsim.Gaussian(fwhm=0.5)])
psf_im = galsim.Gaussian(fwhm=0.5).drawImage(nx=33,
ny=33,
wcs=gs_wcs,
method='no_pixel').array
psf_gmix = ngmix.gmix.make_gmix_model(
[0, 0, 0, 0, fwhm_to_T(0.5), 1], "gauss")
psf_obs = Observation(image=psf_im, gmix=psf_gmix)
im = obj.drawImage(nx=image_size,
ny=image_size,
wcs=gs_wcs,
method='no_pixel').array
noise = np.sqrt(np.sum(im**2)) / 1e16
wgt = np.ones_like(im) / noise**2
guess = np.ones(6) * 0.1
guess[0] = 0
guess[1] = 0
guess[2] = g1_true
guess[3] = g2_true
guess[4] = fwhm_to_T(0.5)
guess[5] = 400
g1arr = []
g2arr = []
farr = []
xarr = []
yarr = []
for _ in range(50):
shift = rng.uniform(low=-scale / 2, high=scale / 2, size=2)
xy = gs_wcs.toImage(galsim.PositionD(shift))
im = obj.shift(dx=shift[0],
dy=shift[1]).drawImage(nx=image_size,
ny=image_size,
wcs=gs_wcs,
method='no_pixel',
dtype=np.float64).array
jac = Jacobian(y=cen + xy.y,
x=cen + xy.x,
dudx=gs_wcs.dudx,
dudy=gs_wcs.dudy,
dvdx=gs_wcs.dvdx,
dvdy=gs_wcs.dvdy)
_im = im + (rng.normal(size=im.shape) * noise)
obs = Observation(image=_im, weight=wgt, jacobian=jac, psf=psf_obs)
fitter = LMSimple(obs, 'exp', prior=prior)
fitter.go(guess + rng.normal(size=6) * 0.01)
res = fitter.get_result()
if res['flags'] == 0:
_g1, _g2, _ = res['g'][0], res['g'][1], res['pars'][4]
g1arr.append(_g1)
g2arr.append(_g2)
farr.append(res['pars'][5])
xarr.append(res['pars'][1])
yarr.append(res['pars'][0])
g1 = np.mean(g1arr)
g2 = np.mean(g2arr)
gtol = 1e-5
assert np.abs(g1 - g1_true) < gtol
assert np.abs(g2 - g2_true) < gtol
xerr = np.std(xarr) / np.sqrt(len(xarr))
assert np.abs(np.mean(xarr)) < xerr * 5
yerr = np.std(yarr) / np.sqrt(len(yarr))
assert np.abs(np.mean(yarr)) < yerr * 5
def measure(self, measRecord, exposure):
psf = exposure.getPsf()
if psf is None:
raise MeasurementError(
self.flagHandler.getDefinition(
SingleFrameLMSimpleShapePlugin.ErrEnum.flag_noPsf).doc,
SingleFrameLMSimpleShapePlugin.ErrEnum.flag_noPsf)
# make an observation for the psf image
psfArray = psf.computeKernelImage().getArray()
psfJacob = ngmix.UnitJacobian(row=psfArray.shape[0] / 2.0,
col=psfArray.shape[1] / 2.0)
psfObs = Observation(psfArray, jacobian=psfJacob)
# Fallback code if no psf algorithm is requested. Then just do an LM single gaussian fit
if self.config.psfName is None:
pfitter = LMSimple(psfObs, 'gauss')
# gues parameters for a simple Gaussian
psfPars = [0.0, 0.0, -0.03, 0.02, 8.0, 1.0]
pfitter.go(psfPars)
psfGMix = pfitter.get_gmix()
else:
shape = psfArray.shape
image = lsst.afw.image.ImageD(shape[1], shape[0])
evaluate = measRecord.get(self.psfMsfKey).evaluate()
evaluate.addToImage(
image.getArray(),
lsst.afw.geom.Point2I(-(shape[0] - 1) // 2,
-(shape[1] - 1) // 2))
psfObs = Observation(image.getArray(), jacobian=psfJacob)
# Now create a gmix directly from what the PsfApprox algorithm produced
multiShapeletFunction = measRecord.get(self.psfMsfKey)
shapeletFunctions = multiShapeletFunction.getComponents()
psfPars = []
# add pars in the order flux, y, x, yy, xy, xx
for sf in shapeletFunctions:
psfPars.append(sf.getCoefficients()[0])
psfPars.append(sf.getEllipse().getCenter().getY())
psfPars.append(sf.getEllipse().getCenter().getX())
psfPars.append(sf.getEllipse().getCore().getIyy())
psfPars.append(sf.getEllipse().getCore().getIxy())
psfPars.append(sf.getEllipse().getCore().getIxx())
psfGMix = ngmix.gmix.GMix(len(shapeletFunctions), psfPars)
psfObs.set_gmix(psfGMix)
# Now create an obs for the galaxy itself, including the weight plane
galArray = exposure.getMaskedImage().getImage().getArray()
galShape = galArray.shape
galJacob = ngmix.UnitJacobian(row=galShape[1] / 2.0,
col=galShape[0] / 2.0)
variance = exposure.getMaskedImage().getVariance().getArray()
gal_weight = 1 / variance
obs = Observation(galArray,
weight=gal_weight,
jacobian=galJacob,
psf=psfObs)
fp = measRecord.getFootprint()
bbox = fp.getBBox()
ymin = bbox.getBeginY() - exposure.getXY0().getY()
ymax = bbox.getEndY() - exposure.getXY0().getY()
xmin = bbox.getBeginX() - exposure.getXY0().getX()
xmax = bbox.getEndX() - exposure.getXY0().getX()
flux = exposure.getMaskedImage().getImage().getArray()[
ymin:ymax, xmin:xmax].sum()
xx = fp.getShape().getIxx()
yy = fp.getShape().getIyy()
xy = fp.getShape().getIxy()
# Now run the shape algorithm, using the config parameters
lmPars = {
'maxfev': self.config.maxfev,
'ftol': self.config.ftol,
'xtol': self.config.xtol
}
maxPars = {'method': 'lm', 'lm_pars': lmPars}
guesser = ngmix.guessers.TFluxGuesser(xx + yy, flux)
runner = ngmix.bootstrap.MaxRunner(obs, self.config.model, maxPars,
guesser)
runner.go(ntry=4)
fitter = runner.fitter
res = fitter.get_result()
# Set the results, including the fit info returned by MaxRunner
if res['flags'] != 0:
if res['flags'] & LM_SINGULAR_MATRIX:
raise MeasurementError(
self.flagHandler.getDefinition(
SingleFrameLMSimpleShapePlugin.ErrEnum.
flag_singularMatrix).doc,
SingleFrameLMSimpleShapePlugin.ErrEnum.flag_singularMatrix)
if res['flags'] & LM_NEG_COV_EIG:
raise MeasurementError(
self.flagHandler.getDefinition(
SingleFrameLMSimpleShapePlugin.ErrEnum.
flag_negativeCovEig).doc,
SingleFrameLMSimpleShapePlugin.ErrEnum.flag_negativeCovEig)
if res['flags'] & LM_NEG_COV_DIAG:
raise MeasurementError(
self.flagHandler.getDefinition(
SingleFrameLMSimpleShapePlugin.ErrEnum.
flag_negativeCovDiag).doc,
SingleFrameLMSimpleShapePlugin.ErrEnum.flag_negativeCovDiag
)
if res['flags'] & EIG_NOTFINITE:
raise MeasurementError(
self.flagHandler.getDefinition(
SingleFrameLMSimpleShapePlugin.ErrEnum.
flag_eigNotFinite).doc,
SingleFrameLMSimpleShapePlugin.ErrEnum.flag_eigNotFinite)
if res['flags'] & LM_FUNC_NOTFINITE:
raise MeasurementError(
self.flagHandler.getDefinition(
SingleFrameLMSimpleShapePlugin.ErrEnum.
flag_funcNotFinite).doc,
SingleFrameLMSimpleShapePlugin.ErrEnum.flag_funcNotFinite)
if res['flags'] & DIV_ZERO:
raise MeasurementError(
self.flagHandler.getDefinition(
SingleFrameLMSimpleShapePlugin.ErrEnum.flag_divZero).
doc, SingleFrameLMSimpleShapePlugin.ErrEnum.flag_divZero)
if res['nfev'] >= self.config.maxfev:
raise MeasurementError(
self.flagHandler.getDefinition(
SingleFrameLMSimpleShapePlugin.ErrEnum.flag_maxFev).
doc, SingleFrameLMSimpleShapePlugin.ErrEnum.flag_maxFev)
# Unknown error, but there should be an errmsg set by ngmix
raise RuntimeError(res['errmsg'])
# Convert the nGauss Gaussians to ShapeletFunction's. Zeroth order HERMITES are Gaussians.
# There are always 6 parameters for each Gaussian.
galGMix = fitter.get_gmix()
galPars = galGMix.get_full_pars()
# convert the center in row,col coordinates to pixel coordinates and save
cen = galGMix.get_cen()
measRecord.set(self.xKey, cen[1] + galShape[1] / 2.0)
measRecord.set(self.yKey, cen[0] + galShape[0] / 2.0)
# save the model flux
measRecord.set(self.fluxKey, galGMix.get_flux())
# save the model T=xx+yy, e1, and e2
(e1, e2, T) = galGMix.get_e1e2T()
measRecord.set(self.e1Key, e1)
measRecord.set(self.e2Key, e2)
measRecord.set(self.TKey, T)
for i in range(self.nGauss):
flux, y, x, iyy, ixy, ixx = galPars[i *
self._gaussian_pars_len:(i +
1) *
self._gaussian_pars_len]
quad = lsst.afw.geom.ellipses.Quadrupole(ixx, iyy, ixy)
ellipse = lsst.afw.geom.ellipses.Ellipse(
quad, lsst.afw.geom.Point2D(x, y))
# create a 0th order (gaussian) shapelet function.
sf = ShapeletFunction(0, HERMITE, ellipse)
sf.getCoefficients()[0] = flux / ShapeletFunction.FLUX_FACTOR
measRecord.set(self.keys[i], sf)
def _fit_smooth_model(self):
dxy = 256
ny = 4096 // dxy + 1
nx = 2048 // dxy + 1
xloc = np.empty((ny, nx), dtype=np.float64)
yloc = np.empty((ny, nx), dtype=np.float64)
pars = np.empty((ny, nx, 3), dtype=np.float64)
for yi, yl in enumerate(np.linspace(1, 4096, ny)):
for xi, xl in enumerate(np.linspace(1, 2048, nx)):
rng = np.random.RandomState(seed=yi + nx * xi)
xloc[yi, xi] = xl
yloc[yi, xi] = yl
pos = galsim.PositionD(x=xl, y=yl)
img = self._draw(pos).drawImage(
nx=19, ny=19, scale=0.25, method='sb').array
nse = np.std(
np.concatenate([img[0, :], img[-1, :]]))
obs = ngmix.Observation(
image=img,
weight=np.ones_like(img)/nse**2,
jacobian=ngmix.jacobian.DiagonalJacobian(
x=9, y=9, scale=0.25))
_g1 = np.nan
_g2 = np.nan
_T = np.nan
for _ in range(5):
try:
am = Admom(obs, rng=rng)
am.go(0.3)
res = am.get_result()
if res['flags'] != 0:
continue
lm = LMSimple(obs, 'turb')
lm.go(res['pars'])
lm_res = lm.get_result()
if lm_res['flags'] == 0:
_g1 = lm_res['pars'][2]
_g2 = lm_res['pars'][3]
_T = lm_res['pars'][4]
break
except ngmix.gexceptions.GMixRangeError:
pass
pars[yi, xi, 0] = _g1
pars[yi, xi, 1] = _g2
pars[yi, xi, 2] = _T
xloc = xloc.ravel()
yloc = yloc.ravel()
pos = np.stack([xloc, yloc], axis=1)
assert pos.shape == (xloc.shape[0], 2)
# make interps
g1 = pars[:, :, 0].ravel()
msk = np.isfinite(g1)
if len(msk) < 10:
raise ValueError('DES Piff fitting failed too much!')
if np.any(~msk):
g1[~msk] = np.mean(g1[msk])
self._g1int = CloughTocher2DInterpolator(pos, g1)
g2 = pars[:, :, 1].ravel()
msk = np.isfinite(g2)
if len(msk) < 10:
raise ValueError('DES Piff fitting failed too much!')
if np.any(~msk):
g2[~msk] = np.mean(g2[msk])
self._g2int = CloughTocher2DInterpolator(pos, g2)
T = pars[:, :, 2].ravel()
msk = np.isfinite(T)
if len(msk) < 10:
raise ValueError('DES Piff fitting failed too much!')
if np.any(~msk):
T[~msk] = np.mean(T[msk])
self._Tint = CloughTocher2DInterpolator(pos, T)
self._did_fit = True
def test_ml_fitting_gauss_smoke(g1_true, g2_true, wcs_g1, wcs_g2):
rng = np.random.RandomState(seed=42)
# allow some small relative bias due to approximate exp function
tol = 1.0e-5
image_size = 33
cen = (image_size - 1) / 2
gs_wcs = galsim.ShearWCS(0.25, galsim.Shear(g1=wcs_g1,
g2=wcs_g2)).jacobian()
scale = np.sqrt(gs_wcs.pixelArea())
g_prior = ngmix.priors.GPriorBA(0.2)
cen_prior = ngmix.priors.CenPrior(0, 0, scale, scale)
T_prior = ngmix.priors.FlatPrior(0.1, 2)
F_prior = ngmix.priors.FlatPrior(1e-4, 1e9)
prior = ngmix.joint_prior.PriorSimpleSep(cen_prior, g_prior, T_prior,
F_prior)
obj = galsim.Gaussian(fwhm=0.9).shear(g1=g1_true, g2=g2_true).withFlux(400)
im = obj.drawImage(nx=image_size,
ny=image_size,
wcs=gs_wcs,
method='no_pixel').array
noise = np.sqrt(np.sum(im**2)) / 1e16
wgt = np.ones_like(im) / noise**2
g1arr = []
g2arr = []
Tarr = []
farr = []
xarr = []
yarr = []
for _ in range(100):
shift = rng.uniform(low=-scale / 2, high=scale / 2, size=2)
xy = gs_wcs.toImage(galsim.PositionD(shift))
im = obj.shift(dx=shift[0],
dy=shift[1]).drawImage(nx=image_size,
ny=image_size,
wcs=gs_wcs,
method='no_pixel',
dtype=np.float64).array
jac = Jacobian(y=cen + xy.y,
x=cen + xy.x,
dudx=gs_wcs.dudx,
dudy=gs_wcs.dudy,
dvdx=gs_wcs.dvdx,
dvdy=gs_wcs.dvdy)
_im = im + (rng.normal(size=im.shape) * noise)
obs = Observation(image=_im, weight=wgt, jacobian=jac)
fitter = LMSimple(obs, 'gauss', prior=prior)
guess = np.ones(6) * 0.1
guess[0] = 0
guess[1] = 0
guess[2] = g1_true
guess[3] = g2_true
guess[4] = fwhm_to_T(0.9)
guess[5] = 400 * scale * scale
fitter.go(guess + rng.normal(size=6) * 0.01)
res = fitter.get_result()
if res['flags'] == 0:
_g1, _g2, _T = res['g'][0], res['g'][1], res['pars'][4]
g1arr.append(_g1)
g2arr.append(_g2)
Tarr.append(_T)
farr.append(res['pars'][5])
xarr.append(res['pars'][1])
yarr.append(res['pars'][0])
g1 = np.mean(g1arr)
g2 = np.mean(g2arr)
assert np.abs(g1 - g1_true) < tol
assert np.abs(g2 - g2_true) < tol
if g1_true == 0 and g2_true == 0:
T = np.mean(Tarr)
Ttrue = fwhm_to_T(0.9)
assert T / Ttrue - 1 < tol
fmn = np.mean(farr) / scale / scale
assert np.abs(fmn / 400 - 1) < tol
xerr = np.std(xarr) / np.sqrt(len(xarr))
assert np.abs(np.mean(xarr)) < xerr * 5
yerr = np.std(yarr) / np.sqrt(len(yarr))
assert np.abs(np.mean(yarr)) < yerr * 5