class MedsFitBase(dict):
def __init__(self, meds_file, truth_file, psf_file, **keys):
self['meds_file'] = meds_file
self['truth_file'] = truth_file
self['psf_file'] = psf_file
self.update(keys)
self.set_true_shear()
self.set_defaults()
self.load_data()
self.set_indices()
self.make_struct()
def set_defaults(self):
"""
deal with default parameters and conversions
"""
# in arcsec
sigma_guess = self['psf_pars']['fwhm_guess'] / 2.35
self['psf_Tguess'] = 2 * sigma_guess**2
self['make_plots'] = self.get('make_plots', False)
self['randomize_psf'] = self.get('randomize_psf', False)
self['fix_centroid_bug'] = self.get('fix_centroid_bug', False)
def set_true_shear(self):
from . import analyze
if 'gnum' in self:
self.true_shear = analyze.SHEARS[self['gnum']]
def get_data(self):
"""
get a reference to the data structure
"""
return self.data
def do_fits(self):
"""
loop and fit all objects
"""
t0 = time.time()
last = self.indices.size - 1
for dindex, mindex in enumerate(self.indices):
self.dindex = dindex
self.mindex = mindex
print("%d:%d %d:%d" % (dindex, last, mindex, self['end']))
#print(self.data.size, self.meds.size)
#print(dindex, mindex)
self.data['number'][dindex] = self.meds['number'][mindex]
self.make_psf_observation()
self.make_galaxy_observation()
self.run_fitters()
if self['make_plots']:
self.compare_psf()
self.do_gal_plots()
tm = time.time() - t0
num = len(self.indices)
print("time:", tm)
print("time per:", tm / num)
def run_fitters(self):
from great3.generic import PSFFailure, GalFailure
dindex = self.dindex
boot = self.get_bootstrapper()
# find the center and reset the jacobian
#boot.find_cen()
self.boot = boot
try:
self.fit_psf()
self.fit_psf_flux()
try:
self.fit_galaxy()
self.copy_galaxy_result()
self.print_galaxy_result()
except BootGalFailure:
print(" galaxy fitting failed")
self.data['flags'][dindex] = GAL_FIT_FAILURE
except BootPSFFailure:
print(" psf fitting failed")
self.data['flags'][dindex] = PSF_FIT_FAILURE
def fit_psf(self):
dindex = self.dindex
boot = self.boot
psf_pars = self['psf_pars']
boot.fit_psfs(psf_pars['model'],
Tguess=self['psf_Tguess'],
ntry=psf_pars['ntry'])
#self.psf_fitter=self.boot.get_psf_fitter()
# for multi-obs this will be the latest
self.psf_fitter = self.boot.psf_fitter
self.copy_psf_result()
def fit_psf_flux(self):
"""
fit psf model to galaxy with one free parameter for flux
"""
boot = self.boot
dindex = self.dindex
boot.fit_gal_psf_flux()
data = self.data
pres = boot.get_psf_flux_result()
data['psf_flux'][dindex] = pres['psf_flux'][0]
data['psf_flux_err'][dindex] = pres['psf_flux_err'][0]
def fit_galaxy(self):
"""
over-ride for different fitters
"""
raise RuntimeError("over-ride me")
def fit_max(self):
"""
do a maximum likelihood fit
"""
boot = self.boot
model = self['model_pars']['model']
max_pars = self['max_pars']
cov_pars = self['cov_pars']
# now with prior
boot.fit_max(model,
max_pars,
prior=self['prior'],
ntry=max_pars['ntry'])
boot.try_replace_cov(cov_pars)
def do_round_measures(self):
rpars = self['round_pars']
self.boot.set_round_s2n(fitter_type=rpars['fitter_type'])
def get_bootstrapper(self):
"""
get the bootstrapper for fitting psf through galaxy
"""
boot = get_bootstrapper(self.obs)
return boot
def make_psf_observation(self):
"""
read the image and weight data
"""
ext = self.get_psf_ext()
self['psf_id'] = ext
self.data['psf_id'][self.dindex] = ext
image0 = self.psf_obj[ext][:, :]
noise = self['psf_pars']['addnoise']
image = image0 + numpy.random.normal(scale=noise, size=image0.shape)
weight = image.copy()
weight *= 0
weight += 1.0 / noise**2
jacob = self.get_jacobian(type='psf')
row, col = jacob.get_cen()
jacob.set_cen(row - 1, col - 1)
self.psf_obs = Observation(image, weight=weight, jacobian=jacob)
def get_psf_ext(self):
if self['randomize_psf']:
ext = numpy.random.randint(0, self.npsf)
print("getting random psf:", ext)
else:
ext = self.truth['id_psf'][self.mindex]
return ext
def make_galaxy_observation(self):
"""
read the image and weight data
"""
image = self.meds.get_cutout(self.mindex, 0)
calc_weight = self.get('calc_weight', False)
if calc_weight:
import esutil as eu
border = 5
nrow, ncol = image.shape
row, col = numpy.mgrid[0:nrow, 0:ncol]
w = numpy.where((row < 5) | (row > (nrow - 5 - 1))
| (col < 5) | (col > (ncol - 5 - 1)))
mn, skysig_meas = eu.stat.sigma_clip(image[w].ravel())
print(" skysig_meas: %g" % skysig_meas)
weight = 0 * image + 1.0 / skysig_meas**2
else:
if self['noisefree']:
weight = image * 0 + 1.0 / self['skynoise']**2
else:
weight = self.meds.get_cutout(self.mindex, 0, type='weight')
jacob = self.get_jacobian()
self.obs = Observation(image,
weight=weight,
jacobian=jacob,
psf=self.psf_obs)
def get_psf_guesser(self):
"""
get guesser based of size of psf and psf flux
"""
from gmix_meds.util import FromPSFGuesser
data = self.data
T = data['psf_T'][self.dindex]
flux = data['psf_flux'][self.dindex]
if self['use_logpars']:
scaling = 'log'
else:
scaling = 'linear'
guesser = FromPSFGuesser(T, flux, scaling=scaling)
return guesser
def get_flux_and_prior_guesser(self):
"""
from the psf flux and the prior
"""
from gmix_meds.util import FluxAndPriorGuesser
psf_flux = self.data['psf_flux'][self.dindex]
psf_flux = psf_flux.clip(min=0.1, max=1.0e9)
if self['use_logpars']:
scaling = 'log'
else:
scaling = 'linear'
guesser = FluxAndPriorGuesser(psf_flux, self['prior'], scaling=scaling)
return guesser
def get_T_flux_and_prior_guesser(self):
"""
from the psf flux and the prior
"""
from gmix_meds.util import TFluxAndPriorGuesser
psf_gmix = self.psf_obs.get_gmix()
psf_T = psf_gmix.get_T()
psf_flux = self.data['psf_flux'][self.dindex]
psf_flux = psf_flux.clip(min=0.1, max=1.0e9)
if self['use_logpars']:
scaling = 'log'
else:
scaling = 'linear'
guesser = TFluxAndPriorGuesser(psf_T,
psf_flux,
self['prior'],
scaling=scaling)
return guesser
def try_replace_cov(self, fitter):
"""
the lm cov sucks, try to replace it
"""
# reference to res
res = fitter.get_result()
print(" replacing cov")
max_pars = self['max_pars']
fitter.calc_cov(max_pars['cov_h'], max_pars['cov_m'])
if res['flags'] != 0:
print(" replacement failed")
res['flags'] = 0
def compare_psf(self):
"""
compare psf image to best fit model
"""
import images
fitter = self.psf_fitter
model = self['psf_pars']['model']
obs = self.psf_obs
if 'em' in model:
model_image = fitter.make_image(counts=obs.image.sum())
else:
gm = fitter.get_gmix()
j = obs.get_jacobian()
model_image = gm.make_image(obs.image.shape, jacobian=j)
plt = images.compare_images(obs.image,
model_image,
label1='psf',
label2=model,
show=False)
pname = 'psf-resid-%s-%06d.png' % (model, self.mindex)
print(" ", pname)
plt.write_img(1400, 800, pname)
def do_gal_plots(self):
"""
Make residual plot and trials plot
"""
res = self.gal_fitter.get_result()
if res['flags'] != 0:
return
self.compare_gal()
#self.make_trials_plot()
#self.plot_autocorr()
def compare_gal(self):
"""
compare psf image to best fit model
"""
import images
fitter = self.gal_fitter
model = self['model_pars']['model']
title = '%d %s' % (self.mindex, model)
gmix = fitter.get_gmix()
obs = self.obs
res = fitter.get_result()
psf_gmix = self.psf_obs.get_gmix()
gmix_conv = gmix.convolve(psf_gmix)
image = obs.image
model_image = gmix_conv.make_image(image.shape,
jacobian=obs.get_jacobian())
plt = images.compare_images(image,
model_image,
label1='galaxy',
label2=model,
show=False)
plt.title = title
pname = 'gal-resid-%06d-%s.png' % (self.mindex, model)
resid_std = (image - model_image).std()
print(" residual std:", resid_std)
print(" ", pname)
plt.write_img(1400, 800, pname)
def get_jacobian(self, type='galaxy'):
"""
get the jacobian and return a Jacobian object
"""
jdict = self.meds.get_jacobian(self.mindex, 0)
row0 = jdict['row0']
col0 = jdict['col0']
if self['fix_centroid_bug'] and type == 'galaxy':
print("fixing centroid bug")
row0 = row0 - 1
col0 = col0 - 1
jacob = Jacobian(row0, col0, jdict['dudrow'], jdict['dudcol'],
jdict['dvdrow'], jdict['dvdcol'])
return jacob
def load_data(self):
"""
read or load all data
"""
print("loading:", self['meds_file'])
self.meds = meds.MEDS(self['meds_file'])
print("reading:", self['truth_file'])
self.truth = fitsio.read(self['truth_file'])
print("loading:", self['psf_file'])
self.psf_obj = fitsio.FITS(self['psf_file'])
self.npsf = len(self.psf_obj)
def set_indices(self):
"""
this version we don't support work dir
"""
obj_range = self.get('obj_range', None)
if obj_range is not None:
self['start'] = obj_range[0]
self['end'] = obj_range[1]
self.indices = arange(obj_range[0], obj_range[1] + 1)
else:
self['start'] = 0
self['end'] = self.meds.size - 1
self.indices = arange(self.meds.size)
def copy_psf_result(self):
"""
copy some subset of the psf parameters
"""
ppars = self['psf_pars']
data = self.data
fitter = self.psf_fitter
res = fitter.get_result()
data['psf_flags'][self.dindex] = res['flags']
if 'nfev' in res:
data['psf_nfev'][self.dindex] = res['nfev']
elif 'numiter' in res:
data['psf_nfev'][self.dindex] = res['numiter']
if res['flags'] != 0:
return
psf_gmix = fitter.get_gmix()
g1, g2, T = psf_gmix.get_g1g2T()
print(" psf_id: %d psf_fwhm: %.3f g: %.3g %.3g" %
(self['psf_id'], sqrt(T / 2) * 2.35, g1, g2))
if 'em' in ppars['model']:
print(" niter: %d fdiff: %g" % (res['numiter'], res['fdiff']))
else:
print_pars(res['pars'], front=' psf_pars: ')
print_pars(res['pars_err'], front=' psf_perr: ')
data['psf_g'][self.dindex, 0] = g1
data['psf_g'][self.dindex, 1] = g2
data['psf_T'][self.dindex] = T
def get_namer(self):
from great3.generic import Namer
if self['use_logpars']:
n = Namer('log')
else:
n = Namer()
return n
def copy_galaxy_result(self):
"""
copy some subset of the psf parameters
"""
n = self.get_namer()
data = self.data
dindex = self.dindex
fitter = self.gal_fitter
mres = self.boot.get_max_fitter().get_result()
res = fitter.get_result()
if res['flags'] != 0:
print(" galaxy fit failure")
data['flags'][dindex] = GAL_FIT_FAILURE
return
else:
data['flags'][dindex] = 0
jacob = self.boot.mb_obs_list[0][0].jacobian
jrow, jcol = jacob.get_cen()
scale = jacob.get_scale()
row = jrow + res['pars'][0] / scale
col = jcol + res['pars'][1] / scale
data['pars'][dindex] = res['pars']
data['pars_cov'][dindex] = res['pars_cov']
data['cen_pix'][dindex] = array([row, col])
data['g'][dindex] = res['g']
data['g_cov'][dindex] = res['g_cov']
data[n('flux')][dindex] = res['pars'][5]
data[n('flux_err')][dindex] = sqrt(res['pars_cov'][5, 5])
data[n('T')][dindex] = res['pars'][4]
data[n('T_err')][dindex] = sqrt(res['pars_cov'][4, 4])
if self['use_logpars']:
Ts2n = 1.0 / data[n('T_err')][dindex]
else:
Ts2n = data[n('T')][dindex] / data[n('T_err')][dindex]
data['T_s2n'][dindex] = Ts2n
rres = self.boot.get_round_result()
data['flags_r'][dindex] = rres['flags']
data['T_r'][dindex] = rres['T_r']
data['s2n_r'][dindex] = rres['s2n_r']
data['psf_T_r'][self.dindex] = rres['psf_T_r']
# from the max like result
if 'max_flags' in data.dtype.names:
data['max_flags'][dindex] = mres['flags']
data['s2n_w'][dindex] = mres['s2n_w']
data['chi2per'][dindex] = mres['chi2per']
data['dof'][dindex] = mres['dof']
def print_galaxy_result(self):
res = self.gal_fitter.get_result()
if 'pars' in res:
print_pars(res['pars'], front=' gal_pars: ')
if 'pars_err' in res:
print_pars(res['pars_err'], front=' gal_perr: ')
def make_dtype(self):
"""
make the output data type
"""
n = self.get_namer()
np = ngmix.gmix.get_model_npars(self['model_pars']['model'])
dt = [
('number', 'i4'),
('flags', 'i4'),
('psf_id', 'i4'),
('psf_flags', 'i4'),
('psf_nfev', 'i4'),
('psf_g', 'f8', 2),
('psf_T', 'f8'),
('psf_flux', 'f8'),
('psf_flux_err', 'f8'),
('pars', 'f8', np),
('pars_cov', 'f8', (np, np)),
('cen_pix', 'f8', 2),
(n('flux'), 'f8'),
(n('flux_err'), 'f8'),
(n('T'), 'f8'),
(n('T_err'), 'f8'),
('g', 'f8', 2),
('g_cov', 'f8', (2, 2)),
('s2n_w', 'f8'),
('T_s2n', 'f8'),
('flags_r', 'i4'),
('T_r', 'f8'),
('s2n_r', 'f8'),
('psf_T_r', 'f8'),
('chi2per', 'f8'),
('dof', 'f8'),
]
self.dtype = dt
def make_struct(self):
self.make_dtype()
n = self.get_namer()
num = self.indices.size
data = zeros(num, dtype=self.dtype)
data['flags'] = NO_ATTEMPT
data['psf_g'] = DEFVAL
data['psf_T'] = DEFVAL
data['psf_flux'] = DEFVAL
data['psf_flux_err'] = PDEFVAL
data['pars'] = DEFVAL
data['pars_cov'] = PDEFVAL
data[n('flux')] = DEFVAL
data[n('flux_err')] = PDEFVAL
data[n('T')] = DEFVAL
data[n('T_err')] = PDEFVAL
data['T_s2n'] = PDEFVAL
data['flags_r'] = NO_ATTEMPT
data['T_r'] = DEFVAL
data['s2n_r'] = DEFVAL
data['psf_T_r'] = DEFVAL
data['g'] = DEFVAL
data['g_cov'] = PDEFVAL
data['s2n_w'] = DEFVAL
data['chi2per'] = PDEFVAL
self.data = data
def set_fracdev_stuff(self):
self['fracdev_grid'] = self.get('fracdev_grid', None)
self['fracdev_prior'] = self.get('fracdev_prior', None)
class MedsFitBase(dict):
def __init__(self, meds_file, truth_file, psf_file, **keys):
self['meds_file']=meds_file
self['truth_file']=truth_file
self['psf_file']=psf_file
self.update(keys)
self.set_defaults()
self.load_data()
self.set_indices()
self.make_struct()
def set_defaults(self):
"""
deal with default parameters and conversions
"""
# in arcsec
sigma_guess=self['psf_pars']['fwhm_guess']/2.35
self['psf_Tguess'] = 2*sigma_guess**2
self['make_plots']=self.get('make_plots',False)
self['randomize_psf'] = self.get('randomize_psf',False)
def get_data(self):
"""
get a reference to the data structure
"""
return self.data
def do_fits(self):
"""
loop and fit all objects
"""
t0=time.time()
last=self.indices.size-1
for dindex,mindex in enumerate(self.indices):
self.dindex=dindex
self.mindex=mindex
print("%d:%d %d:%d" % (dindex, last, mindex, self['end']))
self.data['number'][dindex] = self.meds['number'][mindex]
self.make_psf_observation()
self.make_galaxy_observation()
self.run_fitters()
if self['make_plots']:
self.compare_psf()
self.do_gal_plots()
tm=time.time()-t0
num=len(self.indices)
print("time:",tm)
print("time per:",tm/num)
def run_fitters(self):
from great3.generic import PSFFailure,GalFailure
dindex=self.dindex
boot=self.get_bootstrapper()
# find the center and reset the jacobian
boot.find_cen()
self.boot=boot
try:
self.fit_psf()
self.fit_psf_flux()
try:
self.fit_galaxy()
self.copy_galaxy_result()
self.print_galaxy_result()
except GalFailure:
print(" galaxy fitting failed")
self.data['flags'][dindex] = GAL_FIT_FAILURE
except PSFFailure:
print(" psf fitting failed")
self.data['flags'][dindex] = PSF_FIT_FAILURE
def fit_psf(self):
dindex=self.dindex
boot=self.boot
psf_pars=self['psf_pars']
boot.fit_psf(psf_pars['model'],
Tguess=self['psf_Tguess'],
ntry=psf_pars['ntry'])
self.psf_fitter=self.boot.get_psf_fitter()
self.copy_psf_result()
def fit_psf_flux(self):
"""
fit psf model to galaxy with one free parameter for flux
"""
boot=self.boot
dindex=self.dindex
boot.fit_gal_psf_flux()
data=self.data
data['psf_flux'][dindex] = boot.psf_flux
data['psf_flux_err'][dindex] = boot.psf_flux_err
def fit_galaxy(self):
"""
over-ride for different fitters
"""
raise RuntimeError("over-ride me")
def fit_max(self):
"""
do a maximum likelihood fit
"""
boot=self.boot
model=self['model_pars']['model']
max_pars=self['max_pars']
boot.fit_max(model,
max_pars,
prior=self['prior'],
ntry=max_pars['ntry'])
def get_bootstrapper(self):
"""
get the bootstrapper for fitting psf through galaxy
"""
from great3.sfit import get_bootstrapper
boot = get_bootstrapper(self.psf_obs, self.obs)
return boot
def make_psf_observation(self):
"""
read the image and weight data
"""
ext=self.get_psf_ext()
self['psf_id'] = ext
self.data['psf_id'][self.dindex] = ext
image0 = self.psf_obj[ext][:,:]
noise=self['psf_pars']['addnoise']
image = image0 + numpy.random.normal(scale=noise,
size=image0.shape)
weight = image.copy()
weight *= 0
weight += 1.0/noise**2
jacob=self.get_jacobian()
self.psf_obs = Observation(image, weight=weight, jacobian=jacob)
def get_psf_ext(self):
if self['randomize_psf']:
ext=numpy.random.randint(0,self.npsf)
print("getting random psf:",ext)
else:
ext=self.truth['id_psf'][self.mindex]
return ext
def make_galaxy_observation(self):
"""
read the image and weight data
"""
image = self.meds.get_cutout(self.mindex, 0)
calc_weight=self.get('calc_weight',False)
if calc_weight:
import esutil as eu
border=5
nrow,ncol=image.shape
row,col=numpy.mgrid[0:nrow, 0:ncol]
w=numpy.where((row < 5) | (row > (nrow-5-1))
| (col < 5) | (col > (ncol-5-1)) )
mn, skysig_meas = eu.stat.sigma_clip(image[w].ravel())
print(" skysig_meas: %g" % skysig_meas)
weight = 0*image + 1.0/skysig_meas**2
else:
if self['noisefree']:
weight = image*0 + 1.0/self['skynoise']**2
else:
weight = self.meds.get_cutout(self.mindex, 0, type='weight')
jacob=self.get_jacobian()
self.obs = Observation(image, weight=weight, jacobian=jacob)
def get_psf_guesser(self):
"""
get guesser based of size of psf and psf flux
"""
from gmix_meds.util import FromPSFGuesser
data=self.data
T=data['psf_T'][self.dindex]
flux=data['psf_flux'][self.dindex]
if self['use_logpars']:
scaling='log'
else:
scaling='linear'
guesser=FromPSFGuesser(T, flux, scaling=scaling)
return guesser
def get_flux_and_prior_guesser(self):
"""
from the psf flux and the prior
"""
from gmix_meds.util import FluxAndPriorGuesser
psf_flux=self.data['psf_flux'][self.dindex]
psf_flux=psf_flux.clip(min=0.1, max=1.0e9)
if self['use_logpars']:
scaling='log'
else:
scaling='linear'
guesser=FluxAndPriorGuesser(psf_flux, self['prior'],scaling=scaling)
return guesser
def get_T_flux_and_prior_guesser(self):
"""
from the psf flux and the prior
"""
from gmix_meds.util import TFluxAndPriorGuesser
psf_gmix = self.psf_obs.get_gmix()
psf_T = psf_gmix.get_T()
psf_flux=self.data['psf_flux'][self.dindex]
psf_flux=psf_flux.clip(min=0.1, max=1.0e9)
if self['use_logpars']:
scaling='log'
else:
scaling='linear'
guesser=TFluxAndPriorGuesser(psf_T,
psf_flux,
self['prior'],
scaling=scaling)
return guesser
def try_replace_cov(self, fitter):
"""
the lm cov sucks, try to replace it
"""
# reference to res
res=fitter.get_result()
print(" replacing cov")
max_pars=self['max_pars']
fitter.calc_cov(max_pars['cov_h'], max_pars['cov_m'])
if res['flags'] != 0:
print(" replacement failed")
res['flags']=0
def compare_psf(self):
"""
compare psf image to best fit model
"""
import images
fitter=self.psf_fitter
model=self['psf_pars']['model']
obs=self.psf_obs
if 'em' in model:
model_image = fitter.make_image(counts=obs.image.sum())
else:
gm=fitter.get_gmix()
j=obs.get_jacobian()
model_image = gm.make_image(obs.image.shape,
jacobian=j)
plt=images.compare_images(obs.image,
model_image,
label1='psf',
label2=model,
show=False)
pname='psf-resid-%s-%06d.png' % (model, self.mindex)
print(" ",pname)
plt.write_img(1400,800,pname)
def do_gal_plots(self):
"""
Make residual plot and trials plot
"""
res=self.gal_fitter.get_result()
if res['flags'] != 0:
return
self.compare_gal()
#self.make_trials_plot()
#self.plot_autocorr()
def compare_gal(self):
"""
compare psf image to best fit model
"""
import images
fitter=self.gal_fitter
model=self['model_pars']['model']
title = '%d %s' % (self.mindex, model)
gmix = fitter.get_gmix()
obs = self.obs
res=fitter.get_result()
psf_gmix = self.psf_obs.get_gmix()
gmix_conv = gmix.convolve(psf_gmix)
image=obs.image
model_image = gmix_conv.make_image(image.shape,
jacobian=obs.get_jacobian())
plt=images.compare_images(image,
model_image,
label1='galaxy',
label2=model,
show=False)
plt.title=title
pname='gal-resid-%06d-%s.png' % (self.mindex,model)
resid_std = (image-model_image).std()
print(" residual std:",resid_std)
print(" ",pname)
plt.write_img(1400,800,pname)
def get_jacobian(self):
"""
get the jacobian and return a Jacobian object
"""
jdict = self.meds.get_jacobian(self.mindex,0)
jacob = Jacobian(jdict['row0']-1,
jdict['col0']-1,
jdict['dudrow'],
jdict['dudcol'],
jdict['dvdrow'],
jdict['dvdcol'])
return jacob
def load_data(self):
"""
read or load all data
"""
print("loading:",self['meds_file'])
self.meds=meds.MEDS(self['meds_file'])
print("reading:",self['truth_file'])
self.truth=fitsio.read(self['truth_file'])
print("loading:",self['psf_file'])
self.psf_obj = fitsio.FITS(self['psf_file'])
self.npsf = len(self.psf_obj)
def set_indices(self):
"""
this version we don't support work dir
"""
obj_range = self.get('obj_range',None)
if obj_range is not None:
self['start'] = obj_range[0]
self['end'] = obj_range[1]
self.indices = arange(obj_range[0], obj_range[1]+1)
else:
self['start']=0
self['end']=self.meds.size-1
self.indices = arange(self.meds.size)
def copy_psf_result(self):
"""
copy some subset of the psf parameters
"""
ppars=self['psf_pars']
data=self.data
fitter=self.psf_fitter
res=fitter.get_result()
data['psf_flags'][self.dindex] = res['flags']
if 'nfev' in res:
data['psf_nfev'][self.dindex] = res['nfev']
elif 'numiter' in res:
data['psf_nfev'][self.dindex] = res['numiter']
if res['flags'] != 0:
return
psf_gmix=fitter.get_gmix()
g1,g2,T=psf_gmix.get_g1g2T()
print(" psf_id: %d psf_fwhm: %.3f g: %.3g %.3g" % (self['psf_id'],sqrt(T/2)*2.35,g1,g2) )
if 'em' in ppars['model']:
print(" niter: %d fdiff: %g" % (res['numiter'],res['fdiff']))
else:
print_pars(res['pars'], front=' psf_pars: ')
print_pars(res['pars_err'],front=' psf_perr: ')
data['psf_g'][self.dindex, 0] = g1
data['psf_g'][self.dindex, 1] = g2
data['psf_T'][self.dindex] = T
def get_namer(self):
from great3.generic import Namer
if self['use_logpars']:
n=Namer('log')
else:
n=Namer()
return n
def copy_galaxy_result(self):
"""
copy some subset of the psf parameters
"""
from pprint import pprint
n=self.get_namer()
data=self.data
dindex=self.dindex
fitter=self.gal_fitter
res=fitter.get_result()
#pprint(res)
if res['flags'] != 0:
print(" galaxy fit failure")
data['flags'][dindex] = GAL_FIT_FAILURE
return
else:
data['flags'][dindex]=0
jacob=self.boot.gal_obs.jacobian
jrow, jcol = jacob.get_cen()
scale = jacob.get_scale()
row = jrow + res['pars'][0]/scale
col = jcol + res['pars'][1]/scale
data['pars'][dindex] = res['pars']
data['pars_cov'][dindex] = res['pars_cov']
data['cen_pix'][dindex] = array([row,col])
data['g'][dindex] = res['g']
data['g_cov'][dindex] = res['g_cov']
data[n('flux')][dindex] = res['pars'][5]
data[n('flux_err')][dindex] = sqrt(res['pars_cov'][5,5])
data[n('T')][dindex] = res['pars'][4]
data[n('T_err')][dindex] = sqrt(res['pars_cov'][4,4])
if self['use_logpars']:
Ts2n = 1.0/data[n('T_err')][dindex]
else:
Ts2n = data[n('T')][dindex]/data[n('T_err')][dindex]
data['T_s2n'][dindex] = Ts2n
data['s2n_w'][dindex] = res['s2n_w']
data['chi2per'][dindex] = res['chi2per']
data['dof'][dindex] = res['dof']
def print_galaxy_result(self):
res=self.gal_fitter.get_result()
if 'pars' in res:
print_pars(res['pars'], front=' gal_pars: ')
if 'pars_err' in res:
print_pars(res['pars_err'],front=' gal_perr: ')
def make_dtype(self):
"""
make the output data type
"""
n=self.get_namer()
np=ngmix.gmix.get_model_npars(self['model_pars']['model'])
dt=[
('number','i4'),
('flags','i4'),
('psf_id','i4'),
('psf_flags','i4'),
('psf_nfev','i4'),
('psf_g','f8',2),
('psf_T','f8'),
('psf_flux','f8'),
('psf_flux_err','f8'),
('pars','f8',np),
('pars_cov','f8',(np,np)),
('cen_pix','f8',2),
(n('flux'),'f8'),
(n('flux_err'),'f8'),
(n('T'),'f8'),
(n('T_err'),'f8'),
('T_s2n','f8'),
('g','f8',2),
('g_cov','f8',(2,2)),
('s2n_w','f8'),
('chi2per','f8'),
('dof','f8'),
]
self.dtype=dt
def make_struct(self):
self.make_dtype()
n=self.get_namer()
num=self.indices.size
data=zeros(num, dtype=self.dtype)
data['flags'] = NO_ATTEMPT
data['psf_g'] = DEFVAL
data['psf_T'] = DEFVAL
data['psf_flux'] = DEFVAL
data['psf_flux_err'] = PDEFVAL
data['pars'] = DEFVAL
data['pars_cov'] = PDEFVAL
data[n('flux')] = DEFVAL
data[n('flux_err')] = PDEFVAL
data[n('T')] = DEFVAL
data[n('T_err')] = PDEFVAL
data['g'] = DEFVAL
data['g_cov'] = PDEFVAL
data['s2n_w'] = DEFVAL
data['chi2per'] = PDEFVAL
self.data=data
def set_fracdev_stuff(self):
self['fracdev_grid']=self.get('fracdev_grid',None)
self['fracdev_prior'] = self.get('fracdev_prior',None)
def test_observation_set(image_data):
obs = Observation(image=image_data['image'],
weight=image_data['weight'],
bmask=image_data['bmask'],
ormask=image_data['ormask'],
noise=image_data['noise'],
jacobian=image_data['jacobian'],
gmix=image_data['gmix'],
psf=image_data['psf'],
meta=image_data['meta'])
rng = np.random.RandomState(seed=11)
new_arr = rng.normal(size=image_data['image'].shape)
assert np.all(obs.image != new_arr)
obs.image = new_arr
assert np.all(obs.image == new_arr)
new_arr = np.exp(rng.normal(size=image_data['image'].shape))
assert np.all(obs.weight != new_arr)
obs.weight = new_arr
assert np.all(obs.weight == new_arr)
new_arr = (np.exp(rng.normal(size=image_data['image'].shape)) *
100).astype(np.int32)
assert np.all(obs.bmask != new_arr)
obs.bmask = new_arr
assert np.all(obs.bmask == new_arr)
obs.bmask = None
assert not obs.has_bmask()
new_arr = (np.exp(rng.normal(size=image_data['image'].shape)) *
100).astype(np.int32)
assert np.all(obs.ormask != new_arr)
obs.ormask = new_arr
assert np.all(obs.ormask == new_arr)
obs.ormask = None
assert not obs.has_ormask()
new_arr = rng.normal(size=image_data['image'].shape)
assert np.all(obs.noise != new_arr)
obs.noise = new_arr
assert np.all(obs.noise == new_arr)
obs.noise = None
assert not obs.has_noise()
new_jac = DiagonalJacobian(x=8, y=13, scale=1.2)
assert new_jac.get_galsim_wcs() != obs.jacobian.get_galsim_wcs()
obs.jacobian = new_jac
assert new_jac.get_galsim_wcs() == obs.jacobian.get_galsim_wcs()
new_meta = {'new': 5}
assert obs.meta != new_meta
obs.meta = new_meta
assert obs.meta == new_meta
with pytest.raises(TypeError):
obs.meta = [10]
obs.meta = None
assert len(obs.meta) == 0
new_meta = {'blue': 10}
new_meta.update(obs.meta)
assert obs.meta != new_meta
obs.update_meta_data({'blue': 10})
assert obs.meta == new_meta
with pytest.raises(TypeError):
obs.update_meta_data([10])
new_gmix = GMix(pars=rng.uniform(size=6))
assert np.all(obs.gmix.get_full_pars() != new_gmix.get_full_pars())
obs.gmix = new_gmix
assert np.all(obs.gmix.get_full_pars() == new_gmix.get_full_pars())
obs.gmix = None
assert not obs.has_gmix()
with pytest.raises(RuntimeError):
obs.get_gmix()
new_psf = Observation(image=rng.normal(size=obs.psf.image.shape),
meta={'ispsf': True})
assert np.all(obs.psf.image != new_psf.image)
obs.psf = new_psf
assert np.all(obs.psf.image == new_psf.image)
assert np.all(obs.get_psf().image == new_psf.image)
obs.psf = None
assert not obs.has_psf()
with pytest.raises(RuntimeError):
obs.get_psf()
with pytest.raises(RuntimeError):
obs.get_psf_gmix()