def _set_wcs_choose(self, jacobian, **kw):
"""
create a galsim JacobianWCS from the input ngmix.Jacobian, as
well as pixel objects
"""
self.jacobian=jacobian
wcs_convention=kw.get("wcs_convention",None)
logger.debug(" wcs convention: %s" % wcs_convention)
if wcs_convention==1:
self.gs_wcs = galsim.JacobianWCS(jacobian.dudrow,
jacobian.dudcol,
jacobian.dvdrow,
jacobian.dvdcol)
elif wcs_convention==2:
self.gs_wcs = galsim.JacobianWCS(jacobian.dudcol,
jacobian.dudrow,
jacobian.dvdcol,
jacobian.dvdrow)
elif wcs_convention==3:
self.gs_wcs = galsim.JacobianWCS(jacobian.dvdcol,
jacobian.dvdrow,
jacobian.dudcol,
jacobian.dudrow)
else:
raise ValueError("bad wcs_convention: %s" % wcs_convention)
def exposures():
# Obtain observation list, psf list, weight from wfirst_simple_sim.py
gals_array=[fio.FITS('mcal_gal_0.fits')[-1].read(), fio.FITS('mcal_gal_1.fits')[-1].read()]
psfs_array=[fio.FITS('mcal_psf_0.fits')[-1].read(), fio.FITS('mcal_psf_1.fits')[-1].read()]
offsets=[galsim.PositionD(-0.5,-0.5), galsim.PositionD(0.48010974293083564,0.24526554339263384)]
skys_array=[fio.FITS('mcal_sky_0.fits')[-1].read(), fio.FITS('mcal_sky_1.fits')[-1].read()]
gal_true=[galsim.PositionD(31.5,31.5), galsim.PositionD(31.5,31.5)]
gal_jacobs=[galsim.JacobianWCS(0.10379201786865774, -0.037313406917181026, 0.03741492083530528, 0.1017841347351108),
galsim.JacobianWCS(0.04693577579580337, -0.09835662875798407, 0.09984826919988712, 0.045587756760917426)]
obs_list, psf_list, w = get_exp_list(gals_array, psfs_array, offsets, skys_array, gal_true, gal_jacobs, psf2=None)
return obs_list,psf_list,np.array(w)
def construct_image(self, band_index, uniform_deviate):
world_origin = self.image_parameters.world_origin.as_galsim_position()
degrees_per_pixel = self.image_parameters.degrees_per_pixel()
wcs = (
# Here we implement the confusing mapping X <-> Dec, Y <-> RA
galsim.JacobianWCS(0, degrees_per_pixel, degrees_per_pixel,
0).withOrigin(galsim.PositionI(0, 0),
world_origin=world_origin))
image = galsim.ImageF(
self.image_parameters.width_px,
self.image_parameters.height_px,
wcs=wcs,
)
for index, light_source in enumerate(self._light_sources):
sys.stdout.write('Band {} source {}\r'.format(
band_index + 1, index + 1))
sys.stdout.flush()
galsim_light_source = light_source.get_galsim_light_source(
band_index,
self.psf_sigma_pixels *
self.image_parameters.degrees_per_pixel(),
self.image_parameters,
)
galsim_light_source.drawImage(
image,
add_to_image=True,
method='phot',
max_extra_noise=self.band_sky_level_nmgy[band_index] *
self.image_parameters.band_nelec_per_nmgy[band_index] / 1000.0,
rng=uniform_deviate,
)
self._add_sky_background(image, band_index, uniform_deviate)
return image
def test_wcs():
"""Reproduce an error Erin found and reported in #834. This was never an error in a released
version, just temporarily on master, but the mistake hadn't been caught by any of our unit
tests, so this test catches the error.
"""
wcs = galsim.JacobianWCS(0.01, -0.26, -0.28, -0.03)
gal = galsim.Exponential(half_light_radius=1.1, flux=237)
psf = galsim.Moffat(beta=3.5, half_light_radius=0.9)
obs = galsim.Convolve(gal, psf)
obs_im = obs.drawImage(nx=32, ny=32, offset=(0.3, -0.2), wcs=wcs)
psf_im = psf.drawImage(nx=32, ny=32, wcs=wcs)
ii = galsim.InterpolatedImage(obs_im)
psf_ii = galsim.InterpolatedImage(psf_im)
psf_inv = galsim.Deconvolve(psf_ii)
ii_nopsf = galsim.Convolve(ii, psf_inv)
newpsf = galsim.Moffat(beta=3.5, half_light_radius=0.95)
newpsf = newpsf.dilate(1.02)
new_ii = ii_nopsf.shear(g1=0.01, g2=0.0)
new_ii = galsim.Convolve(new_ii, newpsf)
new_im = new_ii.drawImage(image=obs_im.copy(), method='no_pixel')
np.testing.assert_almost_equal(new_im.array.sum() / 237,
obs_im.array.sum() / 237,
decimal=1)
def __str__(self):
s = str(self.original)
dudx, dudy, dvdx, dvdy = self.jac.flatten()
if dudx != 1 or dudy != 0 or dvdx != 0 or dvdy != 1:
# Figure out the shear/rotate/dilate calls that are equivalent.
jac = galsim.JacobianWCS(dudx, dudy, dvdx, dvdy)
scale, shear, theta, flip = jac.getDecomposition()
single = None
if flip:
single = 0 # Special value indicating to just use transform.
if abs(theta.rad()) > 1.e-12:
if single is None:
single = '.rotate(%s)' % theta
else:
single = 0
if shear.getG() > 1.e-12:
if single is None:
single = '.shear(%s)' % shear
else:
single = 0
if abs(scale - 1.0) > 1.e-12:
if single is None:
single = '.expand(%s)' % scale
else:
single = 0
if single == 0:
# If flip or there are two components, then revert to transform as simpler.
single = '.transform(%s,%s,%s,%s)' % (dudx, dudy, dvdx, dvdy)
s += single
if self.offset.x != 0 or self.offset.y != 0:
s += '.shift(%s,%s)' % (self.offset.x, self.offset.y)
if self.flux_ratio != 1.:
#s += '.withScaledFlux(%s)'%self.flux_ratio
s += ' * %s' % self.flux_ratio
return s
def test_decam_wavefront():
file_name = 'input/Science-20121120s1-v20i2.fits'
extname = 'Science-20121120s1-v20i2'
if __name__ == '__main__':
logger = piff.config.setup_logger(verbose=2)
else:
logger = piff.config.setup_logger(log_file='output/test_decam.log')
knn = piff.des.DECamWavefront(file_name, extname, logger=logger)
n_samples = 2000
np_rng = np.random.RandomState(1234)
ccdnums = np_rng.randint(1, 63, n_samples)
star_list = []
for ccdnum in ccdnums:
# make some basic images, pass Xi as properties
# Draw the PSF onto an image. Let's go ahead and give it a non-trivial WCS.
wcs = galsim.JacobianWCS(0.26, 0.05, -0.08, -0.29)
image = galsim.Image(64,64, wcs=wcs)
# set icen and jcen
icen = np_rng.randint(100, 2048)
jcen = np_rng.randint(100, 4096)
image.setCenter(icen, jcen)
image_pos = image.center
stardata = piff.StarData(image, image_pos, properties={'chipnum': ccdnum})
star = piff.Star(stardata, None)
star_list.append(star)
# get the focal positions
star_list = piff.des.DECamInfo().pixel_to_focalList(star_list)
star_list_predicted = knn.interpolateList(star_list)
# test misalignment
misalignment = {'z04d': 10, 'z10x': 10, 'z09y': -10}
knn.misalign_wavefront(misalignment)
star_list_misaligned = knn.interpolateList(star_list)
# test the prediction algorithm
y_predicted = np.array([s.fit.params for s in star_list_predicted])
y_misaligned = np.array([s.fit.params for s in star_list_misaligned])
X = np.array([knn.getProperties(s) for s in star_list])
# check the misalignments work
np.testing.assert_array_almost_equal(y_predicted[:,0], y_misaligned[:,0] - misalignment['z04d'])
np.testing.assert_array_almost_equal(y_predicted[:,5], y_misaligned[:,5] - misalignment['z09y'] * X[:,0])
np.testing.assert_array_almost_equal(y_predicted[:,6], y_misaligned[:,6] - misalignment['z10x'] * X[:,1])
# Check shape of misalignment if array
np.testing.assert_raises(ValueError, knn.misalign_wavefront, knn.misalignment[:,:2])
np.testing.assert_raises(ValueError, knn.misalign_wavefront, knn.misalignment[:-1,:])
# empty dict is equivalent to no misalignment
knn.misalign_wavefront({})
np.testing.assert_equal(knn.misalignment, 0.)
def test_Gaussian():
"""This is about the simplest possible model I could think of. It just uses the
HSM adaptive moments routine to measure the moments, and then it models the
PSF as a Gaussian.
"""
# Here is the true PSF
sigma = 1.3
g1 = 0.23
g2 = -0.17
psf = galsim.Gaussian(sigma=sigma).shear(g1=g1, g2=g2)
# Draw the PSF onto an image. Let's go ahead and give it a non-trivial WCS.
wcs = galsim.JacobianWCS(0.26, 0.05, -0.08, -0.29)
image = galsim.Image(64,64, wcs=wcs)
# This is only going to come out right if we (unphysically) don't convolve by the pixel.
psf.drawImage(image, method='no_pixel')
# Make a StarData instance for this image
stardata = piff.StarData(image, image.true_center)
star = piff.Star(stardata, None)
# Fit the model from the image
model = piff.Gaussian(include_pixel=False)
star = model.initialize(star)
fit = model.fit(star).fit
print('True sigma = ',sigma,', model sigma = ',fit.params[0])
print('True g1 = ',g1,', model g1 = ',fit.params[1])
print('True g2 = ',g2,', model g2 = ',fit.params[2])
# This test is pretty accurate, since we didn't add any noise and didn't convolve by
# the pixel, so the image is very accurately a sheared Gaussian.
true_params = [ sigma, g1, g2 ]
np.testing.assert_almost_equal(fit.params[0], sigma, decimal=7)
np.testing.assert_almost_equal(fit.params[1], g1, decimal=7)
np.testing.assert_almost_equal(fit.params[2], g2, decimal=7)
np.testing.assert_almost_equal(fit.params, true_params, decimal=7)
# Now test running it via the config parser
config = {
'model' : {
'type' : 'Gaussian',
'include_pixel': False
}
}
if __name__ == '__main__':
logger = piff.config.setup_logger(verbose=2)
else:
logger = piff.config.setup_logger(log_file='output/test_Gaussian.log')
model = piff.Model.process(config['model'], logger)
fit = model.fit(star).fit
# Same tests.
np.testing.assert_almost_equal(fit.params[0], sigma, decimal=7)
np.testing.assert_almost_equal(fit.params[1], g1, decimal=7)
np.testing.assert_almost_equal(fit.params[2], g2, decimal=7)
np.testing.assert_almost_equal(fit.params, true_params, decimal=7)
def get_galsim_wcs(self):
"""
get a galsim.JacobianWCS object with the same contents as self
"""
import galsim
dudx = self.dudcol
dudy = self.dudrow
dvdx = self.dvdcol
dvdy = self.dvdrow
return galsim.JacobianWCS(dudx, dudy, dvdx, dvdy)
def test_table_GSInterp():
def f(x_):
return x_ + 2 * x_ * x_ + 3 * np.sin(2 * x_)
x = np.linspace(0.1, 3.3, 25)
y = np.arange(
20
) # Need something big enough to avoid having the interpolant fall off the edge
yy, xx = np.meshgrid(y, x)
interpolants = ['lanczos3', 'lanczos3F', 'lanczos7', 'sinc', 'quintic']
for interpolant in interpolants:
z = f(xx)
tab = galsim.LookupTable(x, z[:, 0], interpolant=interpolant)
do_pickle(tab)
# Use InterpolatedImage to validate
wcs = galsim.JacobianWCS(
(max(x) - min(x)) / (len(x) - 1),
0,
0,
(max(y) - min(y)) / (len(y) - 1),
)
img = galsim.Image(z.T, wcs=wcs)
ii = galsim.InterpolatedImage(
img,
use_true_center=True,
offset=(galsim.PositionD(img.xmin, img.ymin) - img.true_center),
x_interpolant=interpolant,
normalization='sb',
calculate_maxk=False,
calculate_stepk=False).shift(min(x), min(y))
# Check single value functionality.
x1 = 2.3
np.testing.assert_allclose(tab(x1),
ii.xValue(x1, 10),
atol=1e-10,
rtol=0)
# Check vectorized output
newx = np.linspace(0.2, 3.1, 15)
np.testing.assert_allclose(tab(newx),
np.array([ii.xValue(x_, 10)
for x_ in newx]),
atol=1e-10,
rtol=0)
def test_extra_interp():
# Test that specifying extra_interp_properties works properly
# TODO: This is a very bare bones test of the interface. There is basically no test of
# this functionality at all yet. TBD!
sigma = 1.3
g1 = 0.23
g2 = -0.17
psf = galsim.Gaussian(sigma=sigma).shear(g1=g1, g2=g2)
wcs = galsim.JacobianWCS(0.26, 0.05, -0.08, -0.29)
image = galsim.Image(64, 64, wcs=wcs)
psf.drawImage(image, method='no_pixel')
# use g-i color as an extra property for interpolation.
props = dict(gi_color=0.3)
print('props = ', props)
star = piff.Star(piff.StarData(image, image.true_center, properties=props),
None)
model = piff.Gaussian(fastfit=True, include_pixel=False)
interp = piff.Mean()
psf = piff.SimplePSF(model, interp, extra_interp_properties=['gi_color'])
assert psf.extra_interp_properties == ['gi_color']
# Note: Mean doesn't actually do anything useful with the extra properties, so this
# isn't really testing anything other than that the code doesn't completely break.
pointing = galsim.CelestialCoord(-5 * galsim.arcmin, -25 * galsim.degrees)
psf.fit([star], wcs={0: wcs}, pointing=pointing)
# Not much of a check here. Just check that it actually draws something with flux ~= 1
im = psf.draw(x=5, y=7, gi_color=0.3)
np.testing.assert_allclose(im.array.sum(), 1.0, rtol=1.e-3)
# Check missing or extra properties
with np.testing.assert_raises(TypeError):
psf.draw(x=5, y=7)
with np.testing.assert_raises(TypeError):
psf.draw(x=5, y=7, gi_color=0.3, ri_color=3)
# No stars raises an error. (This can happen in practice if all stars are excluded on input.)
with np.testing.assert_raises(RuntimeError):
psf.fit([], wcs={0: wcs}, pointing=pointing)
# Also for SingleChipPSf
psf2 = piff.SingleChipPSF(psf, extra_interp_properties=['gi_color'])
assert psf2.extra_interp_properties == ['gi_color']
with np.testing.assert_raises(TypeError):
psf2.draw(x=5, y=7, chipnum=0)
def wcs_approx(self, gal_stamp, psf_stamp):
#self.make_stamp()
# set a simple jacobian to the stamps before sending them to ngmix
# old center of the stamp
origin_x = gal_stamp.origin.x
origin_y = gal_stamp.origin.y
gal_stamp.setOrigin(0, 0)
psf_stamp.setOrigin(0, 0)
new_pos = galsim.PositionD(self.xy.x - origin_x, self.xy.y - origin_y)
wcs_transf = gal_stamp.wcs.affine(image_pos=new_pos)
new_wcs = galsim.JacobianWCS(wcs_transf.dudx, wcs_transf.dudy,
wcs_transf.dvdx, wcs_transf.dvdy)
gal_stamp.wcs = new_wcs
psf_stamp.wcs = new_wcs
return gal_stamp, psf_stamp
def constructModelImage(self,
params=None,
pixelScale=None,
jacobian=None,
shape=None):
"""Construct model image from parameters
@param params lmfit.Parameters object or python dictionary with
param values to use, or None to use self.params
@param pixelScale pixel scale in arcseconds to use for model image,
or None to use self.pixelScale.
@param jacobian An optional 2x2 Jacobian distortion matrix to apply
to the forward model. Note that this is relative to
the pixelScale above. Use self.jacobian if this is
None.
@param shape (nx, ny) shape for model image, or None to use
the shape of self.maskedImage
@returns numpy array image
"""
if params is None:
params = self.params
if shape is None:
shape = self.maskedImage.getImage().getArray().shape
if pixelScale is None:
pixelScale = self.pixelScale
if jacobian is None:
jacobian = self.jacobian
try:
v = params.valuesdict()
except AttributeError:
v = params
optPsf = self._getOptPsf(v)
if 'r0' in v:
atmPsf = galsim.Kolmogorov(lam=self.wavelength, r0=v['r0'])
psf = galsim.Convolve(optPsf, atmPsf)
else:
psf = optPsf
psf = psf.shift(v['dx'], v['dy']) * v['flux']
wcs = galsim.JacobianWCS(*list(pixelScale * jacobian.ravel()))
modelImg = psf.drawImage(nx=shape[0], ny=shape[1], wcs=wcs)
return modelImg.array
def generate_data(n_samples=100):
# generate as Norm(0, 1) for all parameters
np_rng = np.random.RandomState(1234)
X = np_rng.normal(0, 1, size=(n_samples, len(keys)))
y = np_rng.normal(0, 1, size=(n_samples, ntarget))
star_list = []
for Xi, yi in zip(X, y):
wcs = galsim.JacobianWCS(0.26, 0.05, -0.08, -0.29)
image = galsim.Image(64,64, wcs=wcs)
properties = {k:v for k,v in zip(keys, Xi)}
stardata = piff.StarData(image, image.true_center, properties=properties)
# params = np.array([yi[ith] for ith in attr_target])
params = yi
starfit = piff.StarFit(params)
star = piff.Star(stardata, starfit)
star_list.append(star)
return star_list
def read(cls, fits, extname):
"""Read stars from a FITS file.
:param fits: An open fitsio.FITS object
:param extname: The name of the extension to read from
:returns: a list of Star instances
"""
assert extname in fits
colnames = fits[extname].get_colnames()
for key in [
'x', 'y', 'u', 'v', 'dudx', 'dudy', 'dvdx', 'dvdy', 'xmin',
'xmax', 'ymin', 'ymax', 'flux', 'center', 'chisq'
]:
assert key in colnames
colnames.remove(key)
data = fits[extname].read()
x_list = data['x']
y_list = data['y']
u_list = data['u']
v_list = data['v']
dudx = data['dudx']
dudy = data['dudy']
dvdx = data['dvdx']
dvdy = data['dvdy']
xmin = data['xmin']
xmax = data['xmax']
ymin = data['ymin']
ymax = data['ymax']
flux = data['flux']
center = data['center']
chisq = data['chisq']
if 'params' in colnames:
params = data['params']
colnames.remove('params')
else:
params = [None] * len(data)
if 'params_var' in colnames:
params_var = data['params_var']
colnames.remove('params_var')
else:
params_var = [None] * len(data)
if 'point_ra' in colnames:
pointing_list = [
galsim.CelestialCoord(row['point_ra'] * galsim.degrees,
row['point_dec'] * galsim.degrees)
for row in data
]
colnames.remove('point_ra')
colnames.remove('point_dec')
else:
pointing_list = [None] * len(data)
fit_list = [
StarFit(p, flux=f, center=c, chisq=x, params_var=pv)
for (p, f, c, x,
pv) in zip(params, flux, center, chisq, params_var)
]
# The rest of the columns are the data properties
prop_list = [{c: row[c] for c in colnames} for row in data]
wcs_list = [
galsim.JacobianWCS(*jac) for jac in zip(dudx, dudy, dvdx, dvdy)
]
pos_list = [galsim.PositionD(*pos) for pos in zip(x_list, y_list)]
wpos_list = [galsim.PositionD(*pos) for pos in zip(u_list, v_list)]
wcs_list = [
w.withOrigin(p, wp)
for w, p, wp in zip(wcs_list, pos_list, wpos_list)
]
bounds_list = [galsim.BoundsI(*b) for b in zip(xmin, xmax, ymin, ymax)]
image_list = [
galsim.Image(bounds=b, wcs=w)
for b, w in zip(bounds_list, wcs_list)
]
weight_list = [
galsim.Image(init_value=1.0, bounds=b, wcs=w)
for b, w in zip(bounds_list, wcs_list)
]
data_list = [
StarData(im, pos, weight=w, properties=prop, pointing=point)
for im, pos, w, prop, point in zip(
image_list, pos_list, weight_list, prop_list, pointing_list)
]
stars = [Star(d, f) for (d, f) in zip(data_list, fit_list)]
return stars
def test_table2d_GSInterp():
def f(x_, y_):
return 2 * y_ * y_ + 3 * x_ * x_ + 4 * x_ * y_ - np.cos(x_)
x = np.linspace(0.1, 3.3, 25)
y = np.linspace(0.2, 10.4, 75)
yy, xx = np.meshgrid(y,
x) # Note the ordering of both input and output here!
interpolants = ['lanczos3', 'lanczos3F', 'lanczos7', 'sinc', 'quintic']
for interpolant in interpolants:
z = f(xx, yy)
tab2d = galsim.LookupTable2D(x, y, z, interpolant=interpolant)
do_pickle(tab2d)
# Make sure precomputed-hash gets covered
hash(tab2d)
# Use InterpolatedImage to validate
wcs = galsim.JacobianWCS(
(max(x) - min(x)) / (len(x) - 1),
0,
0,
(max(y) - min(y)) / (len(y) - 1),
)
img = galsim.Image(z.T, wcs=wcs)
ii = galsim.InterpolatedImage(
img,
use_true_center=True,
offset=(galsim.PositionD(img.xmin, img.ymin) - img.true_center),
x_interpolant=interpolant,
normalization='sb',
calculate_maxk=False,
calculate_stepk=False).shift(min(x), min(y))
# Check single value functionality.
x1, y1 = 2.3, 3.2
np.testing.assert_allclose(tab2d(x1, y1),
ii.xValue(x1, y1),
atol=1e-10,
rtol=0)
# Check vectorized output
newx = np.linspace(0.2, 3.1, 15)
newy = np.linspace(0.3, 10.1, 25)
newyy, newxx = np.meshgrid(newy, newx)
np.testing.assert_allclose(
tab2d(newxx, newyy).ravel(),
np.array([
ii.xValue(x_, y_)
for x_, y_ in zip(newxx.ravel(), newyy.ravel())
]).ravel(),
atol=1e-10,
rtol=0)
np.testing.assert_array_almost_equal(tab2d(newxx, newyy),
tab2d(newx, newy, grid=True))
# Check that edge_mode='wrap' works
tab2d = galsim.LookupTable2D(x, y, z, edge_mode='wrap')
ref_dfdx, ref_dfdy = tab2d.gradient(newxx, newyy)
test_dfdx, test_dfdy = tab2d.gradient(newxx + 3 * tab2d.xperiod, newyy)
np.testing.assert_array_almost_equal(ref_dfdx, test_dfdx)
np.testing.assert_array_almost_equal(ref_dfdy, test_dfdy)
test_dfdx, test_dfdy = tab2d.gradient(newxx,
newyy + 13 * tab2d.yperiod)
np.testing.assert_array_almost_equal(ref_dfdx, test_dfdx)
np.testing.assert_array_almost_equal(ref_dfdy, test_dfdy)
test_dfdx, test_dfdy = tab2d.gradient(newx,
newy + 13 * tab2d.yperiod,
grid=True)
np.testing.assert_array_almost_equal(ref_dfdx, test_dfdx)
np.testing.assert_array_almost_equal(ref_dfdy, test_dfdy)
# Test mix of inside and outside original boundary
test_dfdx, test_dfdy = tab2d.gradient(
np.dstack([newxx, newxx + 3 * tab2d.xperiod]),
np.dstack([newyy, newyy]))
np.testing.assert_array_almost_equal(ref_dfdx, test_dfdx[:, :, 0])
np.testing.assert_array_almost_equal(ref_dfdy, test_dfdy[:, :, 0])
np.testing.assert_array_almost_equal(ref_dfdx, test_dfdx[:, :, 1])
np.testing.assert_array_almost_equal(ref_dfdy, test_dfdy[:, :, 1])
def make_jacobian(dudx, dudy, dvdx, dvdy, x, y):
j = galsim.JacobianWCS(dudx, dudy, dvdx, dvdy)
return j.withOrigin(galsim.PositionD(x, y))
def test_meds():
"""
Create two objects, each with three exposures. Save them to a MEDS file.
Load the MEDS file. Compare the created objects with the one read by MEDS.
"""
# initialise empty MultiExposureObject list
objlist = []
# we will be using 2 objects for testing, each with 3 cutouts
n_obj_test = 2
n_cut_test = 3
# set the image size
box_size = 32
# first obj
img11 = galsim.Image(box_size, box_size, init_value=111)
img12 = galsim.Image(box_size, box_size, init_value=112)
img13 = galsim.Image(box_size, box_size, init_value=113)
seg11 = galsim.Image(box_size, box_size, init_value=121)
seg12 = galsim.Image(box_size, box_size, init_value=122)
seg13 = galsim.Image(box_size, box_size, init_value=123)
wth11 = galsim.Image(box_size, box_size, init_value=131)
wth12 = galsim.Image(box_size, box_size, init_value=132)
wth13 = galsim.Image(box_size, box_size, init_value=133)
psf11 = galsim.Image(box_size, box_size, init_value=141)
psf12 = galsim.Image(box_size, box_size, init_value=142)
psf13 = galsim.Image(box_size, box_size, init_value=143)
dudx = 11.1
dudy = 11.2
dvdx = 11.3
dvdy = 11.4
x0 = 11.5
y0 = 11.6
wcs11 = galsim.AffineTransform(dudx, dudy, dvdx, dvdy,
galsim.PositionD(x0, y0))
dudx = 12.1
dudy = 12.2
dvdx = 12.3
dvdy = 12.4
wcs12 = galsim.JacobianWCS(dudx, dudy, dvdx, dvdy)
wcs13 = galsim.PixelScale(13)
# create lists
images = [img11, img12, img13]
weight = [wth11, wth12, wth13]
seg = [seg11, seg12, seg13]
psf = [psf11, psf12, psf13]
wcs = [wcs11, wcs12, wcs13]
# create object
obj1 = galsim.des.MultiExposureObject(images=images,
weight=weight,
seg=seg,
psf=psf,
wcs=wcs,
id=1)
# second obj
img21 = galsim.Image(box_size, box_size, init_value=211)
img22 = galsim.Image(box_size, box_size, init_value=212)
img23 = galsim.Image(box_size, box_size, init_value=213)
seg21 = galsim.Image(box_size, box_size, init_value=221)
seg22 = galsim.Image(box_size, box_size, init_value=222)
seg23 = galsim.Image(box_size, box_size, init_value=223)
wth21 = galsim.Image(box_size, box_size, init_value=231)
wth22 = galsim.Image(box_size, box_size, init_value=332)
wth23 = galsim.Image(box_size, box_size, init_value=333)
psf21 = galsim.Image(box_size, box_size, init_value=241)
psf22 = galsim.Image(box_size, box_size, init_value=342)
psf23 = galsim.Image(box_size, box_size, init_value=343)
dudx = 21.1
dudy = 21.2
dvdx = 21.3
dvdy = 21.4
x0 = 21.5
y0 = 21.6
wcs21 = galsim.AffineTransform(dudx, dudy, dvdx, dvdy,
galsim.PositionD(x0, y0))
dudx = 22.1
dudy = 22.2
dvdx = 22.3
dvdy = 22.4
wcs22 = galsim.JacobianWCS(dudx, dudy, dvdx, dvdy)
wcs23 = galsim.PixelScale(23)
# create lists
images = [img21, img22, img23]
weight = [wth21, wth22, wth23]
seg = [seg21, seg22, seg23]
psf = [psf21, psf22, psf23]
wcs = [wcs21, wcs22, wcs23]
# create object
# This time put the wcs in the image and get it there.
img21.wcs = wcs21
img22.wcs = wcs22
img23.wcs = wcs23
obj2 = galsim.des.MultiExposureObject(images=images,
weight=weight,
seg=seg,
psf=psf,
id=2)
obj3 = galsim.des.MultiExposureObject(images=images, id=3)
# create an object list
objlist = [obj1, obj2]
# save objects to MEDS file
filename_meds = 'output/test_meds.fits'
galsim.des.WriteMEDS(objlist, filename_meds, clobber=True)
bad1 = galsim.Image(32, 48, init_value=0)
bad2 = galsim.Image(35, 35, init_value=0)
bad3 = galsim.Image(48, 48, init_value=0)
with assert_raises(TypeError):
galsim.des.MultiExposureObject(images=img11)
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=[])
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=[bad1])
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=[bad2])
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=[img11, bad3])
with assert_raises(TypeError):
galsim.des.MultiExposureObject(images=images, weight=wth11)
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=images, weight=[])
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=[img11], weight=[bad3])
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=[img11], psf=[bad1])
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=[img11], psf=[bad2])
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=[img11, img12],
psf=[bad2, psf12])
with assert_raises(TypeError):
galsim.des.MultiExposureObject(images=images, wcs=wcs11)
celestial_wcs = galsim.FitsWCS("DECam_00154912_12_header.fits",
dir='des_data')
with assert_raises(galsim.GalSimValueError):
galsim.des.MultiExposureObject(images=[img11], wcs=[celestial_wcs])
# Check the one with no psf, weight, etc.
filename_meds2 = 'output/test_meds_image_only.fits'
galsim.des.WriteMEDS([obj3], filename_meds2, clobber=True)
# Note that while there are no tests prior to this, the above still checks for
# syntax errors in the meds creation software, so it's still worth running as part
# of the normal unit tests.
# But for the rest of the tests, we'll use the meds module to make sure our code
# stays in sync with any changes there.
try:
import meds
# Meds will import this, so check for this too.
import fitsio
except ImportError:
print(
'Failed to import either meds or fitsio. Unable to do tests of meds file.'
)
return
# Run meds module's validate function
try:
meds.util.validate_meds(filename_meds)
meds.util.validate_meds(filename_meds2)
except AttributeError:
print(
'Seems to be the wrong meds package. Unable to do tests of meds file.'
)
return
m = meds.MEDS(filename_meds)
# Check the image_info extension:
ref_info = meds.util.get_image_info_dtype(1)
info = m.get_image_info()
print('info = ', info)
for name, dt in ref_info:
dt = numpy.dtype(dt)
print(name, dt, info.dtype[name], dt.char, info.dtype[name].char)
assert name in info.dtype.names, "column %s not present in image_info extension" % name
# I think S and U for this purpose are equivalent.
# But I'm finding S in the reference, and U in info.
c = info.dtype[name].char
c = 'S' if c == 'U' else c
assert dt.char == c, "column %s is the wrong type" % name
# Check the basic structure of the object_data extension
cat = m.get_cat()
ref_data = meds.util.get_meds_output_dtype(1)
for tup in ref_data:
# Some of these tuples have 3 items, not 2. The last two are the full dtype tuple.
name = tup[0]
if len(tup) == 2:
dt = tup[1]
else:
dt = tup[1:]
dt = numpy.dtype(dt)
print(name, dt, cat.dtype[name], dt.char, cat.dtype[name].char)
assert name in cat.dtype.names, "column %s not present in object_data extension" % name
assert dt.char == cat.dtype[
name].char, "column %s is the wrong type" % name
# Check that we have the right number of objects.
n_obj = len(cat)
print('number of objects is %d' % n_obj)
numpy.testing.assert_equal(n_obj,
n_obj_test,
err_msg="MEDS file has wrong number of objects")
# loop over objects and exposures - test get_cutout
for iobj in range(n_obj):
# check ID is correct
numpy.testing.assert_equal(
cat['id'][iobj],
iobj + 1,
err_msg="MEDS file has wrong id for object %d" % iobj)
# get number of cutouts and check if it's right
n_cut = cat['ncutout'][iobj]
numpy.testing.assert_equal(
n_cut,
n_cut_test,
err_msg="MEDS file has wrong ncutout for object %d" % iobj)
# loop over cutouts
for icut in range(n_cut):
# get the images etc to compare with originals
img = m.get_cutout(iobj, icut, type='image')
wth = m.get_cutout(iobj, icut, type='weight')
seg = m.get_cutout(iobj, icut, type='seg')
psf = m.get_psf(iobj, icut)
wcs_meds = m.get_jacobian(iobj, icut)
# Note: col == x, row == y.
wcs_array_meds = numpy.array([
wcs_meds['dudcol'], wcs_meds['dudrow'], wcs_meds['dvdcol'],
wcs_meds['dvdrow'], wcs_meds['col0'], wcs_meds['row0']
])
# compare
numpy.testing.assert_array_equal(
img,
objlist[iobj].images[icut].array,
err_msg="MEDS cutout has wrong img for object %d" % iobj)
numpy.testing.assert_array_equal(
wth,
objlist[iobj].weight[icut].array,
err_msg="MEDS cutout has wrong wth for object %d" % iobj)
numpy.testing.assert_array_equal(
seg,
objlist[iobj].seg[icut].array,
err_msg="MEDS cutout has wrong seg for object %d" % iobj)
numpy.testing.assert_array_equal(
psf,
objlist[iobj].psf[icut].array,
err_msg="MEDS cutout has wrong psf for object %d" % iobj)
wcs_orig = objlist[iobj].wcs[icut]
wcs_array_orig = numpy.array([
wcs_orig.dudx, wcs_orig.dudy, wcs_orig.dvdx, wcs_orig.dvdy,
wcs_orig.origin.x, wcs_orig.origin.y
])
numpy.testing.assert_array_equal(
wcs_array_meds,
wcs_array_orig,
err_msg="MEDS cutout has wrong wcs for object %d" % iobj)
# get the mosaic to compare with originals
img = m.get_mosaic(iobj, type='image')
wth = m.get_mosaic(iobj, type='weight')
seg = m.get_mosaic(iobj, type='seg')
# There is currently no get_mosaic option for the psfs.
#psf = m.get_mosaic( iobj, type='psf')
psf = numpy.concatenate(
[m.get_psf(iobj, icut) for icut in range(n_cut)], axis=0)
# get the concatenated images - create the true mosaic
true_mosaic_img = numpy.concatenate(
[x.array for x in objlist[iobj].images], axis=0)
true_mosaic_wth = numpy.concatenate(
[x.array for x in objlist[iobj].weight], axis=0)
true_mosaic_seg = numpy.concatenate(
[x.array for x in objlist[iobj].seg], axis=0)
true_mosaic_psf = numpy.concatenate(
[x.array for x in objlist[iobj].psf], axis=0)
# compare
numpy.testing.assert_array_equal(
true_mosaic_img,
img,
err_msg="MEDS mosaic has wrong img for object %d" % iobj)
numpy.testing.assert_array_equal(
true_mosaic_wth,
wth,
err_msg="MEDS mosaic has wrong wth for object %d" % iobj)
numpy.testing.assert_array_equal(
true_mosaic_seg,
seg,
err_msg="MEDS mosaic has wrong seg for object %d" % iobj)
numpy.testing.assert_array_equal(
true_mosaic_psf,
psf,
err_msg="MEDS mosaic has wrong psf for object %d" % iobj)
def test_interleaveImages():
# 1a) With galsim Gaussian
g = galsim.Gaussian(sigma=3.7, flux=1000.)
gal = galsim.Convolve([g, galsim.Pixel(1.0)])
im_list = []
offset_list = []
n = 2
for j in range(n):
for i in range(n):
im = galsim.Image(16 * n, 16 * n)
offset = galsim.PositionD(-(i + 0.5) / n + 0.5,
-(j + 0.5) / n + 0.5)
offset_list.append(offset)
gal.drawImage(image=im,
method='no_pixel',
offset=offset,
scale=0.5)
im_list.append(im)
scale = im.scale
# Input to N as an int
img = galsim.utilities.interleaveImages(im_list, n, offsets=offset_list)
im = galsim.Image(16 * n * n, 16 * n * n)
g = galsim.Gaussian(sigma=3.7, flux=1000. * n * n)
gal = galsim.Convolve([g, galsim.Pixel(1.0)])
gal.drawImage(image=im,
method='no_pixel',
offset=galsim.PositionD(0.0, 0.0),
scale=1. * scale / n)
np.testing.assert_almost_equal(
img.array,
im.array,
6,
err_msg="Interleaved Gaussian images do not match")
assert im.wcs == img.wcs
# 1b) With im_list and offsets permuted
offset_list = []
# An elegant way of generating the default offsets
DX = np.arange(0.0, -1.0, -1.0 / n)
DX -= DX.mean()
DY = DX
for dy in DY:
for dx in DX:
offset = galsim.PositionD(dx, dy)
offset_list.append(offset)
np.random.seed(42) # for generating the same random permutation everytime
rand_idx = np.random.permutation(len(offset_list))
im_list_randperm = [im_list[idx] for idx in rand_idx]
offset_list_randperm = [offset_list[idx] for idx in rand_idx]
# Input to N as a tuple
img_randperm = galsim.utilities.interleaveImages(
im_list_randperm, (n, n), offsets=offset_list_randperm)
np.testing.assert_array_equal(
img_randperm.array,
img.array,
err_msg="Interleaved images do not match when 'offsets' is supplied")
assert img_randperm.scale == img.scale
# 1c) Catching errors in offsets
offset_list = []
im_list = []
n = 5
# Generate approximate offsets
DX = np.array([-0.67, -0.33, 0., 0.33, 0.67])
DY = DX
for dy in DY:
for dx in DX:
offset = galsim.PositionD(dx, dy)
offset_list.append(offset)
im = galsim.Image(16, 16)
gal.drawImage(image=im, offset=offset, method='no_pixel')
im_list.append(im)
try:
N = (n, n)
np.testing.assert_raises(ValueError, galsim.utilities.interleaveImages,
im_list, N, offset_list)
except ImportError:
print("The assert_raises tests require nose")
offset_list = []
im_list = []
n = 5
DX = np.arange(0., 1., 1. / n)
DY = DX
for dy in DY:
for dx in DX:
offset = galsim.PositionD(dx, dy)
offset_list.append(offset)
im = galsim.Image(16, 16)
gal.drawImage(image=im, offset=offset, method='no_pixel')
im_list.append(im)
try:
N = (n, n)
np.testing.assert_raises(ValueError, galsim.utilities.interleaveImages,
im_list, N, offset_list)
except ImportError:
print("The assert_raises tests require nose")
# 2a) Increase resolution along one direction - square to rectangular images
n = 2
g = galsim.Gaussian(sigma=3.7, flux=100.)
gal1 = g.shear(g=1. * (n**2 - 1) / (n**2 + 1), beta=0.0 * galsim.radians)
im_list = []
offset_list = []
# Generating offsets in a natural way
DY = np.arange(0.0, 1.0, 1.0 / (n * n))
DY -= DY.mean()
for dy in DY:
im = galsim.Image(16, 16)
offset = galsim.PositionD(0.0, dy)
offset_list.append(offset)
gal1.drawImage(im, offset=offset, method='no_pixel', scale=2.0)
im_list.append(im)
img = galsim.utilities.interleaveImages(im_list,
N=[1, n**2],
offsets=offset_list,
add_flux=False,
suppress_warnings=True)
im = galsim.Image(16, 16 * n * n)
# The interleaved image has the total flux averaged out since `add_flux = False'
gal = galsim.Gaussian(sigma=3.7 * n, flux=100.)
gal.drawImage(image=im, method='no_pixel', scale=2.0)
np.testing.assert_array_equal(
im.array,
img.array,
err_msg="Sheared gaussian not interleaved correctly")
assert img.wcs == galsim.JacobianWCS(2.0, 0.0, 0.0, 2. / (n**2))
# 2b) Increase resolution along one direction - rectangular to square images
n = 2
g = galsim.Gaussian(sigma=3.7, flux=100.)
gal2 = g.shear(g=1. * (n**2 - 1) / (n**2 + 1), beta=90. * galsim.degrees)
im_list = []
offset_list = []
# Generating offsets in a natural way
DX = np.arange(0.0, 1.0, 1.0 / n**2)
DX -= DX.mean()
for dx in DX:
offset = galsim.PositionD(dx, 0.0)
offset_list.append(offset)
im = galsim.Image(16, 16 * n * n)
gal2.drawImage(im, offset=offset, method='no_pixel', scale=3.0)
im_list.append(im)
img = galsim.utilities.interleaveImages(im_list,
N=np.array([n**2, 1]),
offsets=offset_list,
suppress_warnings=True)
im = galsim.Image(16 * n * n, 16 * n * n)
gal = galsim.Gaussian(sigma=3.7, flux=100. * n * n)
scale = im_list[0].scale
gal.drawImage(image=im, scale=1. * scale / n, method='no_pixel')
np.testing.assert_almost_equal(
im.array,
img.array,
12,
err_msg="Sheared gaussian not interleaved correctly")
assert img.wcs == galsim.JacobianWCS(1. * scale / n**2, 0.0, 0.0, scale)
# 3) Check compatability with deInterleaveImage
n = 3
g = galsim.Gaussian(sigma=3.7, flux=100.)
# break symmetry to detect possible bugs in deInterleaveImage
gal = g.shear(g=0.2, beta=0. * galsim.degrees)
im_list = []
offset_list = []
# Generating offsets in the order they would be returned by deInterleaveImage, for convenience
for i in range(n):
for j in range(n):
im = galsim.Image(16 * n, 16 * n)
offset = galsim.PositionD(-(i + 0.5) / n + 0.5,
-(j + 0.5) / n + 0.5)
offset_list.append(offset)
gal.drawImage(image=im,
method='no_pixel',
offset=offset,
scale=0.5)
im.setOrigin(3, 3) # for non-trivial bounds
im_list.append(im)
img = galsim.utilities.interleaveImages(im_list, N=n, offsets=offset_list)
im_list_1, offset_list_1 = galsim.utilities.deInterleaveImage(img, N=n)
for k in range(n**2):
assert offset_list_1[k] == offset_list[k]
np.testing.assert_array_equal(im_list_1[k].array, im_list[k].array)
assert im_list_1[k].wcs == im_list[k].wcs
assert im_list[k].origin == img.origin
assert im_list[k].bounds == im_list_1[k].bounds
# Checking for non-default flux option
img = galsim.utilities.interleaveImages(im_list,
N=n,
offsets=offset_list,
add_flux=False)
im_list_2, offset_list_2 = galsim.utilities.deInterleaveImage(
img, N=n, conserve_flux=True)
for k in range(n**2):
assert offset_list_2[k] == offset_list[k]
np.testing.assert_array_equal(im_list_2[k].array, im_list[k].array)
assert im_list_2[k].wcs == im_list[k].wcs
def test_simple():
"""Initial simple test of Gaussian, Kolmogorov, and Moffat PSFs.
"""
# Here is the true PSF
scale = 1.3
g1 = 0.23
g2 = -0.17
du = 0.1
dv = 0.4
for fiducial in [fiducial_gaussian, fiducial_kolmogorov, fiducial_moffat]:
print()
print("fiducial = ", fiducial)
print()
psf = fiducial.dilate(scale).shear(g1=g1, g2=g2).shift(du, dv)
# Draw the PSF onto an image. Let's go ahead and give it a non-trivial WCS.
wcs = galsim.JacobianWCS(0.26, 0.05, -0.08, -0.29)
image = galsim.Image(64, 64, wcs=wcs)
# This is only going to come out right if we (unphysically) don't convolve by the pixel.
psf.drawImage(image, method='no_pixel')
# Make a StarData instance for this image
stardata = piff.StarData(image, image.true_center)
fiducial_star = piff.Star(stardata, None)
# First try fastfit.
print('Fast fit')
model = piff.GSObjectModel(fiducial, fastfit=True, include_pixel=False)
fit = model.fit(model.initialize(fiducial_star)).fit
print('True scale = ', scale, ', model scale = ', fit.params[0])
print('True g1 = ', g1, ', model g1 = ', fit.params[1])
print('True g2 = ', g2, ', model g2 = ', fit.params[2])
print('True du = ', du, ', model du = ', fit.center[0])
print('True dv = ', dv, ', model dv = ', fit.center[1])
# This test is fairly accurate, since we didn't add any noise and didn't convolve by
# the pixel, so the image is very accurately a sheared GSObject.
np.testing.assert_allclose(fit.params[0], scale, rtol=1e-4)
np.testing.assert_allclose(fit.params[1], g1, rtol=0, atol=1e-7)
np.testing.assert_allclose(fit.params[2], g2, rtol=0, atol=1e-7)
np.testing.assert_allclose(fit.center[0], du, rtol=0, atol=1e-7)
np.testing.assert_allclose(fit.center[1], dv, rtol=0, atol=1e-7)
# Now try fastfit=False.
print('Slow fit')
model = piff.GSObjectModel(fiducial,
fastfit=False,
include_pixel=False)
fit = model.fit(model.initialize(fiducial_star)).fit
print('True scale = ', scale, ', model scale = ', fit.params[0])
print('True g1 = ', g1, ', model g1 = ', fit.params[1])
print('True g2 = ', g2, ', model g2 = ', fit.params[2])
print('True du = ', du, ', model du = ', fit.center[0])
print('True dv = ', dv, ', model dv = ', fit.center[1])
np.testing.assert_allclose(fit.params[0], scale, rtol=1e-6)
np.testing.assert_allclose(fit.params[1], g1, rtol=0, atol=1e-6)
np.testing.assert_allclose(fit.params[2], g2, rtol=0, atol=1e-6)
np.testing.assert_allclose(fit.center[0], du, rtol=0, atol=1e-6)
np.testing.assert_allclose(fit.center[1], dv, rtol=0, atol=1e-6)
# Now test running it via the config parser
config = {
'model': {
'type': 'GSObjectModel',
'gsobj': repr(fiducial),
'include_pixel': False
}
}
if __name__ == '__main__':
logger = piff.config.setup_logger(verbose=3)
else:
logger = piff.config.setup_logger(verbose=1)
model = piff.Model.process(config['model'], logger)
fit = model.fit(model.initialize(fiducial_star)).fit
# Same tests.
np.testing.assert_allclose(fit.params[0], scale, rtol=1e-6)
np.testing.assert_allclose(fit.params[1], g1, rtol=0, atol=1e-6)
np.testing.assert_allclose(fit.params[2], g2, rtol=0, atol=1e-6)
np.testing.assert_allclose(fit.center[0], du, rtol=0, atol=1e-6)
np.testing.assert_allclose(fit.center[1], dv, rtol=0, atol=1e-6)
# Also need to test ability to serialize
outfile = os.path.join('output', 'gsobject_test.fits')
with fitsio.FITS(outfile, 'rw', clobber=True) as f:
model.write(f, 'psf_model')
with fitsio.FITS(outfile, 'r') as f:
roundtrip_model = piff.GSObjectModel.read(f, 'psf_model')
assert model.__dict__ == roundtrip_model.__dict__
# Finally, we should also test with pixel convolution included. This really only makes
# sense for fastfit=False, since HSM FindAdaptiveMom doesn't account for the pixel shape
# in its measurements.
# Draw the PSF onto an image. Let's go ahead and give it a non-trivial WCS.
wcs = galsim.JacobianWCS(0.26, 0.05, -0.08, -0.29)
image = galsim.Image(64, 64, wcs=wcs)
psf.drawImage(image, method='auto')
# Make a StarData instance for this image
stardata = piff.StarData(image, image.true_center)
fiducial_star = piff.Star(stardata, None)
print('Slow fit, pixel convolution included.')
model = piff.GSObjectModel(fiducial, fastfit=False, include_pixel=True)
star = model.initialize(fiducial_star)
star = model.fit(
star,
fastfit=True) # Get better results with one round of fastfit.
# Use a no op convert_func, just to touch that branch in the code.
convert_func = lambda prof: prof
fit = model.fit(star, convert_func=convert_func).fit
print('True scale = ', scale, ', model scale = ', fit.params[0])
print('True g1 = ', g1, ', model g1 = ', fit.params[1])
print('True g2 = ', g2, ', model g2 = ', fit.params[2])
print('True du = ', du, ', model du = ', fit.center[0])
print('True dv = ', dv, ', model dv = ', fit.center[1])
# Accuracy goals are a bit looser here since it's harder to fit with the pixel involved.
np.testing.assert_allclose(fit.params[0], scale, rtol=1e-6)
np.testing.assert_allclose(fit.params[1], g1, rtol=0, atol=1e-6)
np.testing.assert_allclose(fit.params[2], g2, rtol=0, atol=1e-6)
np.testing.assert_allclose(fit.center[0], du, rtol=0, atol=1e-5)
np.testing.assert_allclose(fit.center[1], dv, rtol=0, atol=1e-5)
def test_direct():
""" Simple test for directly instantiated Gaussian, Kolmogorov, and Moffat without going through
GSObjectModel explicitly.
"""
# Here is the true PSF
scale = 1.3
g1 = 0.23
g2 = -0.17
du = 0.1
dv = 0.4
gsobjs = [
galsim.Gaussian(sigma=1.0),
galsim.Kolmogorov(half_light_radius=1.0),
galsim.Moffat(half_light_radius=1.0, beta=3.0),
galsim.Moffat(half_light_radius=1.0, beta=2.5, trunc=3.0)
]
models = [
piff.Gaussian(fastfit=True, include_pixel=False),
piff.Kolmogorov(fastfit=True, include_pixel=False),
piff.Moffat(fastfit=True, beta=3.0, include_pixel=False),
piff.Moffat(fastfit=True, beta=2.5, trunc=3.0, include_pixel=False)
]
for gsobj, model in zip(gsobjs, models):
print()
print("gsobj = ", gsobj)
print()
psf = gsobj.dilate(scale).shear(g1=g1, g2=g2).shift(du, dv)
# Draw the PSF onto an image. Let's go ahead and give it a non-trivial WCS.
wcs = galsim.JacobianWCS(0.26, 0.05, -0.08, -0.29)
image = galsim.Image(64, 64, wcs=wcs)
# This is only going to come out right if we (unphysically) don't convolve by the pixel.
psf.drawImage(image, method='no_pixel')
# Make a StarData instance for this image
stardata = piff.StarData(image, image.true_center)
star = piff.Star(stardata, None)
star = model.initialize(star)
# First try fastfit.
print('Fast fit')
fit = model.fit(star).fit
print('True scale = ', scale, ', model scale = ', fit.params[0])
print('True g1 = ', g1, ', model g1 = ', fit.params[1])
print('True g2 = ', g2, ', model g2 = ', fit.params[2])
print('True du = ', du, ', model du = ', fit.center[0])
print('True dv = ', dv, ', model dv = ', fit.center[1])
# This test is fairly accurate, since we didn't add any noise and didn't convolve by
# the pixel, so the image is very accurately a sheared GSObject.
# These tests are more strict above. The truncated Moffat included here but not there
# doesn't work quite as well.
np.testing.assert_allclose(fit.params[0], scale, rtol=1e-4)
np.testing.assert_allclose(fit.params[1], g1, rtol=0, atol=1e-5)
np.testing.assert_allclose(fit.params[2], g2, rtol=0, atol=1e-5)
np.testing.assert_allclose(fit.center[0], du, rtol=0, atol=1e-5)
np.testing.assert_allclose(fit.center[1], dv, rtol=0, atol=1e-5)
# Also need to test ability to serialize
outfile = os.path.join('output', 'gsobject_direct_test.fits')
with fitsio.FITS(outfile, 'rw', clobber=True) as f:
model.write(f, 'psf_model')
with fitsio.FITS(outfile, 'r') as f:
roundtrip_model = piff.GSObjectModel.read(f, 'psf_model')
assert model.__dict__ == roundtrip_model.__dict__
# repeat with fastfit=False
models = [
piff.Gaussian(fastfit=False, include_pixel=False),
piff.Kolmogorov(fastfit=False, include_pixel=False),
piff.Moffat(fastfit=False, beta=3.0, include_pixel=False),
piff.Moffat(fastfit=False, beta=2.5, trunc=3.0, include_pixel=False)
]
for gsobj, model in zip(gsobjs, models):
print()
print("gsobj = ", gsobj)
print()
psf = gsobj.dilate(scale).shear(g1=g1, g2=g2).shift(du, dv)
# Draw the PSF onto an image. Let's go ahead and give it a non-trivial WCS.
wcs = galsim.JacobianWCS(0.26, 0.05, -0.08, -0.29)
image = galsim.Image(64, 64, wcs=wcs)
# This is only going to come out right if we (unphysically) don't convolve by the pixel.
psf.drawImage(image, method='no_pixel')
# Make a StarData instance for this image
stardata = piff.StarData(image, image.true_center)
star = piff.Star(stardata, None)
star = model.initialize(star)
print('Slow fit')
fit = model.fit(star).fit
print('True scale = ', scale, ', model scale = ', fit.params[0])
print('True g1 = ', g1, ', model g1 = ', fit.params[1])
print('True g2 = ', g2, ', model g2 = ', fit.params[2])
print('True du = ', du, ', model du = ', fit.center[0])
print('True dv = ', dv, ', model dv = ', fit.center[1])
# This test is fairly accurate, since we didn't add any noise and didn't convolve by
# the pixel, so the image is very accurately a sheared GSObject.
np.testing.assert_allclose(fit.params[0], scale, rtol=1e-5)
np.testing.assert_allclose(fit.params[1], g1, rtol=0, atol=1e-5)
np.testing.assert_allclose(fit.params[2], g2, rtol=0, atol=1e-5)
np.testing.assert_allclose(fit.center[0], du, rtol=0, atol=1e-5)
np.testing.assert_allclose(fit.center[1], dv, rtol=0, atol=1e-5)
# Also need to test ability to serialize
outfile = os.path.join('output', 'gsobject_direct_test.fits')
with fitsio.FITS(outfile, 'rw', clobber=True) as f:
model.write(f, 'psf_model')
with fitsio.FITS(outfile, 'r') as f:
roundtrip_model = piff.GSObjectModel.read(f, 'psf_model')
assert model.__dict__ == roundtrip_model.__dict__
def test_interleaveImages():
import time
t1 = time.time()
# 1a) With galsim Gaussian
g = galsim.Gaussian(sigma=3.7, flux=1000.)
gal = galsim.Convolve([g, galsim.Pixel(1.0)])
im_list = []
offset_list = []
n = 2
for j in xrange(n):
for i in xrange(n):
im = galsim.Image(16 * n, 16 * n)
offset = galsim.PositionD(-(i + 0.5) / n + 0.5,
-(j + 0.5) / n + 0.5)
offset_list.append(offset)
gal.drawImage(image=im,
method='no_pixel',
offset=offset,
scale=0.5)
im_list.append(im)
scale = im.scale
# Input to N as an int
img = galsim.utilities.interleaveImages(im_list, n, offsets=offset_list)
im = galsim.Image(16 * n * n, 16 * n * n)
g = galsim.Gaussian(sigma=3.7, flux=1000. * n * n)
gal = galsim.Convolve([g, galsim.Pixel(1.0)])
gal.drawImage(image=im,
method='no_pixel',
offset=galsim.PositionD(0.0, 0.0),
scale=1. * scale / n)
np.testing.assert_array_equal(img.array,im.array,\
err_msg="Interleaved Gaussian images do not match")
assert im.wcs == img.wcs
# 1b) With im_list and offsets permuted
offset_list = []
# An elegant way of generating the default offsets
DX = np.arange(0.0, -1.0, -1.0 / n)
DX -= DX.mean()
DY = DX
for dy in DY:
for dx in DX:
offset = galsim.PositionD(dx, dy)
offset_list.append(offset)
np.random.seed(42) # for generating the same random permutation everytime
rand_idx = np.random.permutation(len(offset_list))
im_list_randperm = [im_list[idx] for idx in rand_idx]
offset_list_randperm = [offset_list[idx] for idx in rand_idx]
# Input to N as a tuple
img_randperm = galsim.utilities.interleaveImages(
im_list_randperm, (n, n), offsets=offset_list_randperm)
np.testing.assert_array_equal(img_randperm.array,img.array,\
err_msg="Interleaved images do not match when 'offsets' is supplied")
assert img_randperm.scale == img.scale
# 1c) Catching errors in offsets
offset_list = []
im_list = []
n = 5
# Generate approximate offsets
DX = np.array([-0.67, -0.33, 0., 0.33, 0.67])
DY = DX
for dy in DY:
for dx in DX:
offset = galsim.PositionD(dx, dy)
offset_list.append(offset)
im = galsim.Image(16, 16)
gal.drawImage(image=im, offset=offset, method='no_pixel')
im_list.append(im)
try:
N = (n, n)
np.testing.assert_raises(ValueError, galsim.utilities.interleaveImages,
im_list, N, offset_list)
except ImportError:
print "The assert_raises tests require nose"
offset_list = []
im_list = []
n = 5
DX = np.arange(0., 1., 1. / n)
DY = DX
for dy in DY:
for dx in DX:
offset = galsim.PositionD(dx, dy)
offset_list.append(offset)
im = galsim.Image(16, 16)
gal.drawImage(image=im, offset=offset, method='no_pixel')
im_list.append(im)
try:
N = (n, n)
np.testing.assert_raises(ValueError, galsim.utilities.interleaveImages,
im_list, N, offset_list)
except ImportError:
print "The assert_raises tests require nose"
# 2a) Increase resolution along one direction - square to rectangular images
n = 2
g = galsim.Gaussian(sigma=3.7, flux=100.)
gal1 = g.shear(g=1. * (n**2 - 1) / (n**2 + 1), beta=0.0 * galsim.radians)
im_list = []
offset_list = []
# Generating offsets in a natural way
DY = np.arange(0.0, 1.0, 1.0 / (n * n))
DY -= DY.mean()
for dy in DY:
im = galsim.Image(16, 16)
offset = galsim.PositionD(0.0, dy)
offset_list.append(offset)
gal1.drawImage(im, offset=offset, method='no_pixel', scale=2.0)
im_list.append(im)
img = galsim.utilities.interleaveImages(im_list,
N=[1, n**2],
offsets=offset_list,
add_flux=False,
suppress_warnings=True)
im = galsim.Image(16, 16 * n * n)
# The interleaved image has the total flux averaged out since `add_flux = False'
gal = galsim.Gaussian(sigma=3.7 * n, flux=100.)
gal.drawImage(image=im, method='no_pixel', scale=2.0)
np.testing.assert_array_equal(
im.array,
img.array,
err_msg="Sheared gaussian not interleaved correctly")
assert img.wcs == galsim.JacobianWCS(2.0, 0.0, 0.0, 2. / (n**2))
# 2b) Increase resolution along one direction - rectangular to square images
n = 2
g = galsim.Gaussian(sigma=3.7, flux=100.)
gal2 = g.shear(g=1. * (n**2 - 1) / (n**2 + 1), beta=90. * galsim.degrees)
im_list = []
offset_list = []
# Generating offsets in a natural way
DX = np.arange(0.0, 1.0, 1.0 / n**2)
DX -= DX.mean()
for dx in DX:
offset = galsim.PositionD(dx, 0.0)
offset_list.append(offset)
im = galsim.Image(16, 16 * n * n)
gal2.drawImage(im, offset=offset, method='no_pixel', scale=3.0)
im_list.append(im)
img = galsim.utilities.interleaveImages(im_list,
N=np.array([n**2, 1]),
offsets=offset_list,
suppress_warnings=True)
im = galsim.Image(16 * n * n, 16 * n * n)
gal = galsim.Gaussian(sigma=3.7, flux=100. * n * n)
scale = im_list[0].scale
gal.drawImage(image=im, scale=1. * scale / n, method='no_pixel')
np.testing.assert_array_equal(
im.array,
img.array,
err_msg="Sheared gaussian not interleaved correctly")
assert img.wcs == galsim.JacobianWCS(1. * scale / n**2, 0.0, 0.0, scale)
t2 = time.time()
print 'time for %s = %.2f' % (funcname(), t2 - t1)
def deInterleaveImage(image, N, conserve_flux=False,suppress_warnings=False):
"""
The routine to do the opposite of what 'interleaveImages' routine does. It generates a
(uniform) dither sequence of low resolution images from a high resolution image.
Many pixel level detector effects, such as interpixel capacitance, persistence, charge
diffusion etc. can be included only on images drawn at the native pixel scale, which happen to
be undersampled in most cases. Nyquist-sampled images that also include the effects of detector
non-idealities can be obtained by drawing multiple undersampled images (with the detector
effects included) that are offset from each other by a fraction of a pixel. If the offsets are
uniformly spaced, then images can be combined using 'interleaveImages' into a Nyquist-sampled
image.
Drawing multiple low resolution images of a light profile can be a lot slower than drawing a
high resolution image of the same profile, even if the total number of pixels is the same. A
uniformly offset dither sequence can be extracted from a well-resolved image that is drawn by
convolving the surface brightness profile explicitly with the native pixel response and setting
a lower sampling scale (or higher sampling rate) using the `pixel_scale' argument in drawImage()
routine and setting the `method' parameter to `no_pixel'.
Here is an example script using this routine:
Interleaving four Gaussian images
---------------------------------
>>> n = 2
>>> gal = galsim.Gaussian(sigma=2.8)
>>> gal_pix = galsim.Convolve([gal,galsim.Pixel(scale=1.0)])
>>> img = gal_pix.drawImage(gal_pix,scale=1.0/n,method='no_pixel')
>>> im_list, offsets = galsim.utilities.deInterleaveImage(img,N=n)
>>> for im in im_list:
>>> im.applyNonlinearity(lambda x: x-0.01*x**2) #detector effects
>>> img_new = galsim.utilities.interleaveImages(im_list,N=n,offsets)
@param image Input image from which lower resolution images are extracted.
@param N Number of images extracted in either directions. It can be of type
'int' if equal number of images are extracted in both directions or a
list or tuple of two integers, containing the number of images in x
and y directions respectively.
@param conserve_flux Should the routine output images that have, on average, same total
pixel values as the input image (True) or should the pixel values
summed over all the images equal the sum of pixel values of the input
image (False)? [default: False]
@param suppress_warnings Suppresses the warnings about the pixel scale of the output, if True.
[default: False]
@returns a list of images and offsets to reconstruct the input image using 'interleaveImages'.
"""
if isinstance(N,int):
n1,n2 = N,N
elif hasattr(N,'__iter__'):
if len(N)==2:
n1,n2 = N
else:
raise TypeError("'N' has to be a list or a tuple of two integers")
if not (n1 == int(n1) and n2 == int(n2)):
raise TypeError("'N' has to be of type int or a list or a tuple of two integers")
n1 = int(n1)
n2 = int(n2)
else:
raise TypeError("'N' has to be of type int or a list or a tuple of two integers")
if not isinstance(image,galsim.Image):
raise TypeError("'image' has to be an instance of galsim.Image")
y_size,x_size = image.array.shape
if x_size%n1 or y_size%n2:
raise ValueError("The value of 'N' is incompatible with the dimensions of the image to "+
+"be 'deinterleaved'")
im_list, offsets = [], []
for i in range(n1):
for j in range(n2):
# The tricky part - going from array indices to Image coordinates (x,y)
# DX[i'] = -(i+0.5)/n+0.5 = -i/n + 0.5*(n-1)/n
# i = -n DX[i'] + 0.5*(n-1)
dx,dy = -(i+0.5)/n1+0.5,-(j+0.5)/n2+0.5
offset = galsim.PositionD(dx,dy)
img_arr = image.array[j::n2,i::n1].copy()
img = galsim.Image(img_arr)
if conserve_flux is True:
img *= n1*n2
im_list.append(img)
offsets.append(offset)
wcs = image.wcs
if wcs is not None and wcs.isUniform():
jac = wcs.jacobian()
for img in im_list:
img_wcs = galsim.JacobianWCS(jac.dudx*n1,jac.dudy*n2,jac.dvdx*n1,jac.dvdy*n2)
## Since pixel scale WCS is not equal to its jacobian, checking if img_wcs is a pixel
## scale
img_wcs_decomp = img_wcs.getDecomposition()
if img_wcs_decomp[1].g==0:
img.wcs = galsim.PixelScale(img_wcs_decomp[0])
else:
img.wcs = img_wcs
## Preserve the origin so that the interleaved image has the same bounds as the image
## that is being deinterleaved.
img.setOrigin(image.origin())
elif suppress_warnings is False:
import warnings
warnings.warn("Individual images could not be assigned a WCS automatically.")
return im_list, offsets
def test_var():
"""Check that the variance estimate in params_var is sane.
"""
# Here is the true PSF
scale = 1.3
g1 = 0.23
g2 = -0.17
du = 0.1
dv = 0.4
flux = 500
wcs = galsim.JacobianWCS(0.26, 0.05, -0.08, -0.29)
noise = 0.2
gsobjs = [
galsim.Gaussian(sigma=1.0),
galsim.Kolmogorov(half_light_radius=1.0),
galsim.Moffat(half_light_radius=1.0, beta=3.0),
galsim.Moffat(half_light_radius=1.0, beta=2.5, trunc=3.0)
]
# Mix of centered = True/False,
# fastfit = True/False,
# include_pixel = True/False
models = [
piff.Gaussian(fastfit=False, include_pixel=False, centered=False),
piff.Kolmogorov(fastfit=True, include_pixel=True, centered=False),
piff.Moffat(fastfit=False, beta=4.8, include_pixel=True,
centered=True),
piff.Moffat(fastfit=True,
beta=2.5,
trunc=3.0,
include_pixel=False,
centered=True)
]
names = ['Gaussian', 'Kolmogorov', 'Moffat3', 'Moffat2.5']
for gsobj, model, name in zip(gsobjs, models, names):
print()
print("gsobj = ", gsobj)
print()
psf = gsobj.dilate(scale).shear(g1=g1, g2=g2).shift(du,
dv).withFlux(flux)
image = psf.drawImage(nx=64, ny=64, wcs=wcs, method='no_pixel')
weight = image.copy()
weight.fill(1 / noise**2)
# Save this one without noise.
image1 = image.copy()
image1.addNoise(galsim.GaussianNoise(sigma=noise))
# Make a StarData instance for this image
stardata = piff.StarData(image, image.true_center, weight)
star = piff.Star(stardata, None)
star = model.initialize(star)
fit = model.fit(star).fit
file_name = 'input/test_%s_var.npz' % name
print(file_name)
if not os.path.isfile(file_name):
num_runs = 1000
all_params = []
for i in range(num_runs):
image1 = image.copy()
image1.addNoise(galsim.GaussianNoise(sigma=noise))
sd = piff.StarData(image1, image1.true_center, weight)
s = piff.Star(sd, None)
try:
s = model.initialize(s)
s = model.fit(s)
except RuntimeError as e: # Occasionally hsm fails.
print('Caught ', e)
continue
print(s.fit.params)
all_params.append(s.fit.params)
var = np.var(all_params, axis=0)
np.savez(file_name, var=var)
var = np.load(file_name)['var']
print('params = ', fit.params)
print('empirical var = ', var)
print('piff estimate = ', fit.params_var)
print('ratio = ', fit.params_var / var)
print('max ratio = ', np.max(fit.params_var / var))
print('min ratio = ', np.min(fit.params_var / var))
print('mean ratio = ', np.mean(fit.params_var / var))
# Note: The fastfit=False estimates are better -- typically better than 10%
# The fastfit=True estimates are much rougher. Especially size. Need rtol=0.3.
np.testing.assert_allclose(fit.params_var, var, rtol=0.3)
def test_jacobian_smoke(kind):
dudcol = 0.25
dudrow = 0.1
dvdcol = -0.4
dvdrow = 0.34
col = 5.6
row = -10.4
if kind == 'row-col':
jac = Jacobian(col=col,
row=row,
dudcol=dudcol,
dudrow=dudrow,
dvdcol=dvdcol,
dvdrow=dvdrow)
elif kind == 'x-y':
jac = Jacobian(x=col,
y=row,
dudx=dudcol,
dudy=dudrow,
dvdx=dvdcol,
dvdy=dvdrow)
else:
wcs = galsim.JacobianWCS(dudx=dudcol,
dudy=dudrow,
dvdx=dvdcol,
dvdy=dvdrow)
jac = Jacobian(x=col, y=row, wcs=wcs)
assert np.allclose(jac.row0, row)
assert np.allclose(jac.col0, col)
assert np.allclose(jac.dudcol, dudcol)
assert np.allclose(jac.dudrow, dudrow)
assert np.allclose(jac.dvdcol, dvdcol)
assert np.allclose(jac.dvdrow, dvdrow)
assert np.allclose(jac.det, dudcol * dvdrow - dudrow * dvdcol)
assert np.allclose(jac.sdet,
np.sqrt(np.abs(dudcol * dvdrow - dudrow * dvdcol)))
assert np.allclose(jac.scale,
np.sqrt(np.abs(dudcol * dvdrow - dudrow * dvdcol)))
r, c = 20.0, -44.5
v, u = jac.get_vu(r, c)
assert np.allclose(v, dvdrow * (r - row) + dvdcol * (c - col))
assert np.allclose(u, dudrow * (r - row) + dudcol * (c - col))
v, u = jac(r, c)
assert np.allclose(v, dvdrow * (r - row) + dvdcol * (c - col))
assert np.allclose(u, dudrow * (r - row) + dudcol * (c - col))
v, u = 20.0, -44.5
r, c = jac.get_rowcol(v, u)
assert np.allclose(r, (dudcol * v - dvdcol * u) / jac.det + row)
assert np.allclose(c, (-dudrow * v + dvdrow * u) / jac.det + col)
gs_wcs = jac.get_galsim_wcs()
assert np.allclose(gs_wcs.dudx, jac.dudcol)
assert np.allclose(gs_wcs.dudy, jac.dudrow)
assert np.allclose(gs_wcs.dvdx, jac.dvdcol)
assert np.allclose(gs_wcs.dvdy, jac.dvdrow)
cpy_jac = jac.copy()
cpy_jac.set_cen(row=-11, col=-12)
assert np.allclose(jac.row0, row)
assert np.allclose(jac.col0, col)
assert np.allclose(cpy_jac.row0, -11)
assert np.allclose(cpy_jac.col0, -12)
def _run_moments(*, n_sims, rng, dudx, dudy, dvdx, dvdy):
"""Run metacal on an image composed of stamps w/ constant noise.
Parameters
----------
n_sims : int
The number of objects to run.
rng : np.random.RandomState
An RNG to use.
dudx : float
The du/dx Jacobian component.
dudy : float
The du/dy Jacobian component.
dydx : float
The dv/dx Jacobian component.
dvdy : float
The dv/dy Jacobian component.
Returns
-------
result : dict
A dictionary with each of the metacal catalogs.
"""
method = 'no_pixel'
stamp_size = 33
psf_stamp_size = 33
cen = (stamp_size - 1) / 2
psf_cen = (psf_stamp_size - 1) / 2
s2n = 1e16
flux = 1e6
galsim_jac = galsim.JacobianWCS(dudx=dudx, dudy=dudy, dvdx=dvdx, dvdy=dvdy)
gal = galsim.Exponential(half_light_radius=0.5).withFlux(flux)
psf = galsim.Gaussian(fwhm=0.9).withFlux(1)
obj = galsim.Convolve(gal, psf)
obj_im = obj.drawImage(nx=111, ny=111).array
noise = np.sqrt(np.sum(obj_im**2)) / s2n
data = []
for ind in tqdm.trange(n_sims):
################################
# make the obs
# psf
psf_im = psf.drawImage(nx=psf_stamp_size,
ny=psf_stamp_size,
wcs=galsim_jac,
method=method).array
psf_noise = np.sqrt(np.sum(psf_im**2)) / 10000
wgt = np.ones_like(psf_im) / psf_noise**2
psf_im += (rng.normal(size=psf_im.shape) * psf_noise)
psf_jac = ngmix.Jacobian(x=psf_cen,
y=psf_cen,
dudx=dudx,
dudy=dudy,
dvdx=dvdx,
dvdy=dvdy)
psf_obs = ngmix.Observation(image=psf_im, weight=wgt, jacobian=psf_jac)
# now render object
scale = psf_jac.scale
shift = rng.uniform(low=-scale / 2, high=scale / 2, size=2)
_obj = obj.shift(dx=shift[0], dy=shift[1])
xy = galsim_jac.toImage(galsim.PositionD(shift))
im = _obj.drawImage(nx=stamp_size,
ny=stamp_size,
wcs=galsim_jac,
method=method).array
jac = ngmix.Jacobian(x=cen + xy.x,
y=cen + xy.y,
dudx=dudx,
dudy=dudy,
dvdx=dvdx,
dvdy=dvdy)
wgt = np.ones_like(im) / noise**2
nse = rng.normal(size=im.shape) * noise
im += (rng.normal(size=im.shape) * noise)
obs = ngmix.Observation(image=im,
weight=wgt,
noise=nse,
bmask=np.zeros_like(im, dtype=np.int32),
ormask=np.zeros_like(im, dtype=np.int32),
jacobian=jac,
psf=psf_obs)
# build the mbobs
mbobs = ngmix.MultiBandObsList()
obslist = ngmix.ObsList()
obslist.append(obs)
mbobs.append(obslist)
mbobs.meta['id'] = ind + 1
# these settings do not matter that much I think
mbobs[0].meta['Tsky'] = 1
mbobs[0].meta['magzp_ref'] = 26.5
mbobs[0][0].meta['orig_col'] = ind + 1
mbobs[0][0].meta['orig_row'] = ind + 1
################################
# run the fitters
try:
res = _run_moments_fitter(mbobs, rng)
except Exception as e:
print(e)
res = None
if res is not None:
data.append(res)
if len(data) > 0:
res = data
else:
res = None
return res
import numpy as np
import galsim
import pytest
from ..gauss_pix_psf import GaussPixPSF
@pytest.mark.parametrize('wcs', [
galsim.PixelScale(0.263),
galsim.PixelScale(0.5),
galsim.JacobianWCS(-0.2634420129421214, 0.0006503502840044033,
-0.0003966040125006026, -0.26354105026622404)
])
def test_gauss_pix_psf_smoke(wcs):
psf_model = GaussPixPSF()
psf = psf_model.getPSF(galsim.PositionD(x=1, y=2), wcs)
psf_im = psf.drawImage(nx=53, ny=53, wcs=wcs).array
seed = 4098
rng = np.random.RandomState(seed=seed)
g1 = rng.normal() * 0.01
g2 = rng.normal() * 0.01
fwhm = (rng.uniform(low=-0.1, high=0.1) + 1.0) * 0.9
gs = galsim.Gaussian(fwhm=fwhm).shear(g1=g1, g2=g2).withFlux(1.0)
test_im = gs.drawImage(nx=53, ny=53, wcs=wcs).array
assert np.allclose(psf_im, test_im, atol=2e-5, rtol=0)
def test_gauss_pix_psf_reproducible():
wcs = galsim.PixelScale(0.5)
def test_metacal_tracking():
"""Test that the noise tracking works for the metacal use case involving deconvolution and
reconvolution by almost the same PSF.
This test is similar to the above test_uncorrelated_noise_tracking, except the modifications
are based on what is done for the metacal procedure.
"""
import math
def check_noise(noise_image, noise, msg):
# A helper function to check that the current noise in the image is properly described
# by the given CorrelatedNoise object
noise2 = galsim.CorrelatedNoise(noise_image)
print('noise = ', noise)
print('noise2 = ', noise2)
np.testing.assert_almost_equal(noise.getVariance(),
noise2.getVariance(),
decimal=CHECKNOISE_NDECIMAL,
err_msg=msg +
': variance does not match.')
cf_im1 = galsim.Image(8, 8, wcs=noise_image.wcs)
cf_im2 = cf_im1.copy()
noise.drawImage(image=cf_im1)
noise2.drawImage(image=cf_im2)
np.testing.assert_almost_equal(cf_im1.array,
cf_im2.array,
decimal=CHECKNOISE_NDECIMAL,
err_msg=msg +
': image of cf does not match.')
def check_symm_noise(noise_image, msg):
# A helper funciton to see if a noise image has 4-fold symmetric noise.
im2 = noise_image.copy()
# Clear out any wcs to make the test simpler
im2.wcs = galsim.PixelScale(1.)
noise = galsim.CorrelatedNoise(im2)
cf = noise.drawImage(
galsim.Image(bounds=galsim.BoundsI(-1, 1, -1, 1), scale=1))
# First check the variance
print('variance: ', cf(0, 0), noise.getVariance())
np.testing.assert_almost_equal(cf(0, 0) / noise.getVariance(),
1.0,
decimal=VAR_NDECIMAL,
err_msg=msg +
':: noise variance is wrong.')
cf_plus = np.array([cf(1, 0), cf(-1, 0), cf(0, 1), cf(0, -1)])
cf_cross = np.array([cf(1, 1), cf(-1, -1), cf(-1, 1), cf(1, -1)])
print('plus pattern: ', cf_plus)
print('diff relative to dc: ', (cf_plus - np.mean(cf_plus)) / cf(0, 0))
print('cross pattern: ', cf_cross)
print('diff relative to dc: ',
(cf_cross - np.mean(cf_cross)) / cf(0, 0))
# For now, don't make these asserts. Just print whether they will pass or fail.
if True:
if np.all(np.abs((cf_plus - np.mean(cf_plus)) / cf(0, 0)) < 0.01):
print('plus test passes')
else:
print('*** FAIL ***')
print(msg + ': plus pattern is not constant')
if np.all(
np.abs((cf_cross - np.mean(cf_cross)) / cf(0, 0)) < 0.01):
print('cross test passes')
else:
print('*** FAIL ***')
print(msg + ': cross pattern is not constant')
else:
np.testing.assert_almost_equal(
(cf_plus - np.mean(cf_plus)) / cf(0, 0),
0.0,
decimal=2,
err_msg=msg + ': plus pattern is not constant')
np.testing.assert_almost_equal(
(cf_cross - np.mean(cf_cross)) / cf(0, 0),
0.0,
decimal=2,
err_msg=msg + ': cross pattern is not constant')
seed = 1234567 # For use as a unit test, we need a specific seed
#seed = 0 # During testing, it's useful to see how numbers flop around to know if
# something is systematic or random.
rng = galsim.BaseDeviate(seed)
noise_var = 1.3
im_size = 1024
dg = 0.1 # This is bigger than metacal would use, but it makes the test easier.
# Use a non-trivial wcs...
#wcs = galsim.JacobianWCS(0.26, 0.04, -0.04, -0.26) # Rotation + flip. No shear.
wcs = galsim.JacobianWCS(0.26, 0.03, 0.08, -0.21) # Fully complex
#dudx = 0.12*0.26
#dudy = 1.10*0.26
#dvdx = -0.915*0.26
#dvdy = -0.04*0.26
#wcs = galsim.JacobianWCS(dudx, dudy, dvdx, dvdy) # Even more extreme
# And an asymmetric PSF
#orig_psf = galsim.Gaussian(fwhm=0.9).shear(g1=0.05, g2=0.03)
# This one is small enough not to be fully Nyquist sampled, which makes things harder.
orig_psf = galsim.Gaussian(fwhm=0.7).shear(g1=0.05, g2=0.03)
# pixel is the pixel in world coords
pixel = wcs.toWorld(galsim.Pixel(scale=1))
pixel_inv = galsim.Deconvolve(pixel)
psf_image = orig_psf.drawImage(nx=im_size, ny=im_size, wcs=wcs)
# Metacal only has access to the PSF as an image, so use this from here on.
psf = galsim.InterpolatedImage(psf_image)
psf_nopix = galsim.Convolve([psf, pixel_inv])
psf_inv = galsim.Deconvolve(psf)
# Not what is done currently, but using a smoother target PSF helps make sure the
# zeros in the deconvolved PSF get adequately zeroed out.
def get_target_psf(psf):
dk = 0.1 # The resolution in k space for the KImage
small_kval = 1.e-2 # Find the k where the given psf hits this kvalue
smaller_kval = 3.e-3 # Target PSF will have this kvalue at the same k
kim = psf.drawKImage(scale=dk)
karr_r = kim.real.array
# Find the smallest r where the kval < small_kval
nk = karr_r.shape[0]
kx, ky = np.meshgrid(np.arange(-nk / 2, nk / 2),
np.arange(-nk / 2, nk / 2))
ksq = (kx**2 + ky**2) * dk**2
ksq_max = np.min(ksq[karr_r < small_kval * psf.flux])
# We take our target PSF to be the (round) Gaussian that is even smaller at this ksq
# exp(-0.5 * ksq_max * sigma_sq) = smaller_kval
sigma_sq = -2. * np.log(smaller_kval) / ksq_max
return galsim.Gaussian(sigma=np.sqrt(sigma_sq))
# The target PSF dilates the part without the pixel, but reconvolve by the real pixel.
#psf_target_nopix = psf_nopix.dilate(1. + 2.*dg)
#psf_target_nopix = orig_psf.dilate(1. + 4.*dg)
psf_target_nopix = get_target_psf(psf_nopix.shear(g1=dg))
print('PSF target HLR = ', psf_target_nopix.calculateHLR())
print('PSF target FWHM = ', psf_target_nopix.calculateFWHM())
psf_target = galsim.Convolve([psf_target_nopix, pixel])
# Make an image of pure (white) Gaussian noise
# Normally, there would be a galaxy in this image, but for the tests, we just have noise.
obs_image = galsim.Image(im_size, im_size, init_value=0, wcs=wcs)
obs_image.addNoise(
galsim.GaussianNoise(rng=rng, sigma=math.sqrt(noise_var)))
# The noise on this image should be describable as an UncorrelatedNoise object:
noise = galsim.UncorrelatedNoise(variance=noise_var, wcs=wcs)
check_noise(obs_image, noise, 'initial UncorrelatedNoise model is wrong')
# Make an InterpolatedImage profile to use for manipulating this image
# We can get away with no padding here, since our image is so large, but normally, you would
# probably want to pad this with noise padding.
ii = galsim.InterpolatedImage(obs_image, pad_factor=1)
ii.noise = noise
# If we draw it back, the attached noise attribute should still be correct
check_noise(ii.drawImage(obs_image.copy(), method='no_pixel'), ii.noise,
'noise model is wrong for InterpolatedImage')
# Here is the metacal process for which we want to understand the noise.
# We'll try a few different methods.
shear = galsim.Shear(g1=dg)
sheared_obj = galsim.Convolve(ii, psf_inv).shear(shear)
final_obj = galsim.Convolve(psf_target, sheared_obj)
final_image = final_obj.drawImage(obs_image.copy(), method='no_pixel')
try:
check_symm_noise(final_image, 'Initial image')
#didnt_fail = True
# This bit doesn't work while we are not actually raising exceptions in check_symm_noise
# So we expect to see **FAIL** text at this point.
print(
'The above tests are expected to **FAIL**. This is not a problem.'
)
didnt_fail = False
except AssertionError as e:
print('As expected initial image fails symmetric noise test:')
print(e)
didnt_fail = False
if didnt_fail:
assert False, 'Initial image was expected to fail symmetric noise test, but passed.'
if True:
print('\n\nStrategy 1:')
# Strategy 1: Use the noise attribute attached to ii and use it to either whiten or
# symmetrize the noise in the final image.
# Note: The check_noise tests fail. I think because the convolve and deconvolve impose
# a maxk = that of the psf. Which is too small for an accurate rendering of the
# correlation function (here just an autocorrelation of a Pixel.
# The whiten tests kind of work, but they add a lot of extra noise. Much more than
# strategy 4 below. So the level of correlation remaining is pretty well below the
# dc variance. Symmetrize doesn't add much noise, but the residual correlation is about
# the same, which means it doesn't pass the test relative to the lower dc variance.
# First, deconvolve and reconvolve by the same PSF:
test_obj = galsim.Convolve([ii, psf, psf_inv])
# This fails...
if False:
check_noise(
test_obj.drawImage(obs_image.copy(),
method='no_pixel'), test_obj.noise,
'noise model is wrong after convolve/deconvolve by psf')
# Now use a slightly dilated PSF for the reconvolution:
test_obj = galsim.Convolve([ii, psf_target, psf_inv])
if False:
check_noise(
test_obj.drawImage(obs_image.copy(), method='no_pixel'),
test_obj.noise, 'noise model is wrong for dilated target psf')
# Finally, include the shear step. This was done above with sheared_obj, final_obj.
if False:
check_noise(final_image, final_obj.noise,
'noise model is wrong when including small shear')
# If we whiten using this noise model, we should get back to white noise.
t3 = time.time()
final_image2 = final_image.copy() # Don't clobber the original
final_var = final_image2.whitenNoise(final_obj.noise)
t4 = time.time()
print('Noise tracking method with whiten: final_var = ', final_var)
print('Check: direct variance = ', np.var(final_image2.array))
check_symm_noise(final_image2, 'noise whitening does not work')
print('Time for noise tracking with whiten = ', t4 - t3)
# Using symmetrizeNoise should add less noise, but also work.
t3 = time.time()
final_image2 = final_image.copy()
final_var = final_image2.symmetrizeNoise(final_obj.noise)
t4 = time.time()
print('Noise tracking method with symmetrize: final_var = ', final_var)
print('Check: direct variance = ', np.var(final_image2.array))
check_symm_noise(final_image2, 'noise symmetrizing does not work')
print('Time for noise tracking with symmetrize = ', t4 - t3)
if True:
print('\n\nStrategy 2:')
# Strategy 2: Don't trust the noise tracking. Track a noise image through the same process
# and then measure the noise from that image. Use it to either whiten or
# symmetrize the noise in the final image.
# Note: This method doesn't work any better. The added noise for whitening is even more
# than strategy 1. And the remaining correlations are still similarly significant for the
# symmetrize version. A little smaller than strategy 1, but not enough to pass our tests.
# Make another noise image, since we don't actually have access to a pure noise image
# for real objects. But we should be able to estimate the variance in the image.
t3 = time.time()
noise_image = galsim.Image(im_size, im_size, init_value=0, wcs=wcs)
noise_image.addNoise(
galsim.GaussianNoise(rng=rng, sigma=math.sqrt(noise_var)))
noise_ii = galsim.InterpolatedImage(noise_image, pad_factor=1)
sheared_noise_obj = galsim.Convolve(noise_ii, psf_inv).shear(shear)
final_noise_obj = galsim.Convolve(psf_target, sheared_noise_obj)
final_noise_image = final_noise_obj.drawImage(obs_image.copy(),
method='no_pixel')
# Use this to construct an appropriate CorrelatedNoise object
noise = galsim.CorrelatedNoise(final_noise_image)
t4 = time.time()
final_image2 = final_image.copy()
final_var = final_image2.whitenNoise(noise)
t5 = time.time()
check_noise(
final_noise_image, noise,
'noise model is wrong when direct measuring the final noise image')
print('Direct noise method with whiten: final_var = ', final_var)
# Neither of these work currently, so maybe a bug in the whitening code?
# Or possibly in my logic here.
check_symm_noise(
final_image2,
'whitening the noise using direct noise model failed')
print('Time for direct noise with whitening = ', t5 - t3)
t6 = time.time()
final_image2 = final_image.copy()
final_var = final_image2.symmetrizeNoise(noise)
t7 = time.time()
print('Direct noise method with symmetrize: final_var = ', final_var)
check_symm_noise(
final_image2,
'symmetrizing the noise using direct noise model failed')
print('Time for direct noise with symmetrizing = ', t7 - t6 + t4 - t3)
if False:
print('\n\nStrategy 3:')
# Strategy 3: Make a noise field and do the same operations as we do to the main image
# except use the opposite shear value. Add this noise field to the final
# image to get a symmetric noise field.
# Note: This method works! But only for square pixels. However, they may be rotated
# or flipped. Just not sheared.
# Update: I think this method won't ever work for non-square pixels. The reason it works
# for square pixels is that in that case, it is equivalent to strategy 4.
t3 = time.time()
# Make another noise image
rev_image = galsim.Image(im_size, im_size, init_value=0, wcs=wcs)
rev_image.addNoise(
galsim.GaussianNoise(rng=rng, sigma=math.sqrt(noise_var)))
rev_ii = galsim.InterpolatedImage(rev_image, pad_factor=1)
rev_sheared_obj = galsim.Convolve(rev_ii, psf_inv).shear(-shear)
rev_final_obj = galsim.Convolve(psf_target, rev_sheared_obj)
rev_final_image = rev_final_obj.drawImage(obs_image.copy(),
method='no_pixel')
# Add the reverse-sheared noise image to the original image.
final_image2 = final_image + rev_final_image
t4 = time.time()
# The noise variance in the end should be 2x as large as the original
final_var = np.var(final_image2.array)
print('Reverse shear method: final_var = ', final_var)
check_symm_noise(final_image2, 'using reverse shear does not work')
print('Time for reverse shear method = ', t4 - t3)
if True:
print('\n\nStrategy 4:')
# Strategy 4: Make a noise field and do the same operations as we do to the main image,
# then rotate it by 90 degress and add it to the final image.
# This method works! Even for an arbitrarily sheared wcs.
t3 = time.time()
# Make another noise image
noise_image = galsim.Image(im_size, im_size, init_value=0, wcs=wcs)
noise_image.addNoise(
galsim.GaussianNoise(rng=rng, sigma=math.sqrt(noise_var)))
noise_ii = galsim.InterpolatedImage(noise_image, pad_factor=1)
noise_sheared_obj = galsim.Convolve(noise_ii, psf_inv).shear(shear)
noise_final_obj = galsim.Convolve(psf_target, noise_sheared_obj)
noise_final_image = noise_final_obj.drawImage(obs_image.copy(),
method='no_pixel')
# Rotate the image by 90 degrees
rot_noise_final_image = galsim.Image(
np.ascontiguousarray(np.rot90(noise_final_image.array)))
# Add the rotated noise image to the original image.
final_image2 = final_image + rot_noise_final_image
t4 = time.time()
# The noise variance in the end should be 2x as large as the original
final_var = np.var(final_image2.array)
print('Rotate image method: final_var = ', final_var)
check_symm_noise(final_image2,
'using rotated noise image does not work')
print('Time for rotate image method = ', t4 - t3)
if False:
print('\n\nStrategy 5:')
# Strategy 5: The same as strategy 3, except we target the effective net transformation
# done by strategy 4.
# I think this strategy probably can't work for non-square pixels, because the shear
# happens before the convolution by the PSF. And if the wcs is non-square, then the
# PSF is sheared relative to the pixels. That shear isn't being accounted for here,
# so the net result isn't equivalent to rotating by 90 degrees at the end.
t3 = time.time()
# Make another noise image
rev_image = galsim.Image(im_size, im_size, init_value=0, wcs=wcs)
rev_image.addNoise(
galsim.GaussianNoise(rng=rng, sigma=math.sqrt(noise_var)))
rev_ii = galsim.InterpolatedImage(rev_image, pad_factor=1)
# Find the effective transformation to apply in sky coordinates that matches what
# you would get by applying the shear in sky coords, going to image coords and then
# rotating by 90 degrees.
#
# If J is the jacobian of the wcs, and S1 is the applied shear, then we want to find
# S2 such that J^-1 S2 = R90 J^-1 S1
jac = wcs.jacobian()
J = jac.getMatrix()
Jinv = jac.inverse().getMatrix()
S1 = shear.getMatrix()
R90 = np.array([[0, -1], [1, 0]])
S2 = J.dot(R90).dot(Jinv).dot(S1)
scale, rev_shear, rev_theta, flip = galsim.JacobianWCS(
*S2.flatten()).getDecomposition()
# Flip should be False, and scale should be essentially 1.0.
assert flip == False
assert abs(scale - 1.) < 1.e-8
rev_sheared_obj = galsim.Convolve(
rev_ii, psf_inv).rotate(rev_theta).shear(rev_shear)
rev_final_obj = galsim.Convolve(psf_target, rev_sheared_obj)
rev_final_image = rev_final_obj.drawImage(obs_image.copy(),
method='no_pixel')
# Add the reverse-sheared noise image to the original image.
final_image2 = final_image + rev_final_image
t4 = time.time()
# The noise variance in the end should be 2x as large as the original
final_var = np.var(final_image2.array)
print('Alternate reverse shear method: final_var = ', final_var)
check_symm_noise(final_image2,
'using alternate reverse shear does not work')
print('Time for alternate reverse shear method = ', t4 - t3)
def interleaveImages(im_list, N, offsets, add_flux=True, suppress_warnings=False,
catch_offset_errors=True):
"""
Interleaves the pixel values from two or more images and into a single larger image.
This routine converts a list of images taken at a series of (uniform) dither offsets into a
single higher resolution image, where the value in each final pixel is the observed pixel
value from exactly one of the original images. It can be used to build a Nyquist-sampled image
from a set of images that were observed with pixels larger than the Nyquist scale.
In the original observed images, the integration of the surface brightness over the pixels is
equivalent to convolution by the pixel profile and then sampling at the centers of the pixels.
This procedure simulates an observation sampled at a higher resolution than the original images,
while retaining the original pixel convolution.
Such an image can be obtained in a fairly simple manner in simulations of surface brightness
profiles by convolving them explicitly with the native pixel response and setting a lower
sampling scale (or higher sampling rate) using the `pixel_scale' argument in drawImage()
routine and setting the `method' parameter to `no_pixel'.
However, pixel level detector effects can be included only on images drawn at the native pixel
scale, which happen to be undersampled in most cases. Nyquist-sampled images that also include
the effects of detector non-idealities can be obtained by drawing multiple undersampled images
(with the detector effects included) that are offset from each other by a fraction of a pixel.
This is similar to other procedures that build a higher resolution image from a set of low
resolution images, such as MultiDrizzle and IMCOM. A disadvantage of this routine compared to
ther others is that the images must be offset in equal steps in each direction. This is
difficult to acheive with real observations but can be precisely acheived in a series of
simulated images.
An advantage of this procedure is that the noise in the final image is not correlated as the
pixel values are each taken from just a single input image. Thus, this routine preserves the
noise properties of the pixels.
Here's an example script using this routine:
Interleaving two Gaussian images along the x-axis
-------------------------------------------------
>>> n = 2
>>> gal = galsim.Gaussian(sigma=2.8)
>>> DX = numpy.arange(0.0,1.0,1./n)
>>> DX -= DX.mean()
>>> im_list, offsets = [], []
>>> for dx in DX:
... offset = galsim.PositionD(dx,0.0)
... offsets.append(offset)
... im = galsim.Image(16,16)
... gal.drawImage(image=im,offset=offset,scale=1.0)
... im.applyNonlinearity(lambda x: x - 0.01*x**2) # detector effects
... im_list.append(im)
>>> img = galsim.utilities.interleaveImages(im_list=im_list,N=(n,1),offsets=offsets)
@param im_list A list containing the galsim.Image instances to be interleaved.
@param N Number of images to interleave in either directions. It can be of
type `int' if equal number of images are interleaved in both
directions or a list or tuple of two integers, containing the number
of images in x and y directions respectively.
@param offsets A list containing the offsets as galsim.PositionD instances
corresponding to every image in `im_list'. The offsets must be spaced
equally and must span an entire pixel area. The offset values must
be symmetric around zero, hence taking positive and negative values,
with upper and lower limits of +0.5 and -0.5 (limit values excluded).
@param add_flux Should the routine add the fluxes of all the images (True) or average
them (False)? [default: True]
@param suppress_warnings Suppresses the warnings about the pixel scale of the output, if True.
[default: False]
@param catch_offset_errors Checks for the consistency of `offsets` with `N` and raises Errors
if inconsistencies found (True). Recommended, but could slow down
the routine a little. [default: True]
@returns the interleaved image
"""
if isinstance(N,int):
n1,n2 = N,N
elif hasattr(N,'__iter__'):
if len(N)==2:
n1,n2 = N
else:
raise TypeError("'N' has to be a list or a tuple of two integers")
if not (n1 == int(n1) and n2 == int(n2)):
raise TypeError("'N' has to be of type int or a list or a tuple of two integers")
n1 = int(n1)
n2 = int(n2)
else:
raise TypeError("'N' has to be of type int or a list or a tuple of two integers")
if len(im_list)<2:
raise TypeError("'im_list' needs to have at least two instances of galsim.Image")
if (n1*n2 != len(im_list)):
raise ValueError("'N' is incompatible with the number of images in 'im_list'")
if len(im_list)!=len(offsets):
raise ValueError("'im_list' and 'offsets' must be lists of same length")
for offset in offsets:
if not isinstance(offset,galsim.PositionD):
raise TypeError("'offsets' must be a list of galsim.PositionD instances")
if not isinstance(im_list[0],galsim.Image):
raise TypeError("'im_list' must be a list of galsim.Image instances")
# These should be the same for all images in `im_list'.
y_size, x_size = im_list[0].array.shape
wcs = im_list[0].wcs
for im in im_list[1:]:
if not isinstance(im,galsim.Image):
raise TypeError("'im_list' must be a list of galsim.Image instances")
if im.array.shape != (y_size,x_size):
raise ValueError("All galsim.Image instances in 'im_list' must be of the same size")
if im.wcs != wcs:
raise ValueError(
"All galsim.Image instances in 'im_list' must have the same WCS")
img_array = np.zeros((n2*y_size,n1*x_size))
# The tricky part - going from (x,y) Image coordinates to array indices
# DX[i'] = -(i+0.5)/n+0.5 = -i/n + 0.5*(n-1)/n
# i = -n DX[i'] + 0.5*(n-1)
for k in range(len(offsets)):
dx, dy = offsets[k].x, offsets[k].y
i = int(round((n1-1)*0.5-n1*dx))
j = int(round((n2-1)*0.5-n2*dy))
if catch_offset_errors is True:
err_i = (n1-1)*0.5-n1*dx - round((n1-1)*0.5-n1*dx)
err_j = (n2-1)*0.5-n2*dy - round((n2-1)*0.5-n2*dy)
tol = 1.e-6
if abs(err_i)>tol or abs(err_j)>tol:
raise ValueError("'offsets' must be a list of galsim.PositionD instances with x "
+"values spaced by 1/{0} and y values by 1/{1} around 0 for N = ".format(n1,n2)+str(N))
if i<0 or j<0 or i>=x_size or j>=y_size:
raise ValueError("'offsets' must be a list of galsim.PositionD instances with x "
+"values spaced by 1/{0} and y values by 1/{1} around 0 for N = ".format(n1,n2)+str(N))
img_array[j::n2,i::n1] = im_list[k].array[:,:]
img = galsim.Image(img_array)
if not add_flux:
# Fix the flux normalization
img /= 1.0*len(im_list)
# Assign an appropriate WCS for the output
if wcs is not None and wcs.isUniform():
jac = wcs.jacobian()
dudx, dudy, dvdx, dvdy = jac.dudx, jac.dudy, jac.dvdx, jac.dvdy
img_wcs = galsim.JacobianWCS(1.*dudx/n1,1.*dudy/n2,1.*dvdx/n1,1.*dvdy/n2)
## Since pixel scale WCS is not equal to its jacobian, checking if img_wcs is a pixel scale
img_wcs_decomp = img_wcs.getDecomposition()
if img_wcs_decomp[1].g==0: ## getDecomposition returns scale,shear,angle,flip
img.wcs = galsim.PixelScale(img_wcs_decomp[0])
else:
img.wcs = img_wcs
elif suppress_warnings is False:
import warnings
warnings.warn("Interleaved image could not be assigned a WCS automatically.")
# Assign a possibly non-trivial origin and warn if individual image have different origins.
orig = im_list[0].origin()
img.setOrigin(orig)
for im in im_list[1:]:
if not im.origin()==orig:
import warnings
warnings.warn("Images in `im_list' have multiple values for origin. Assigning the \
origin of the first Image instance in 'im_list' to the interleaved image.")
break
return img
def test_shapelet_fit():
"""Test fitting a Shapelet decomposition of an image
"""
for method, norm in [('no_pixel','f'), ('sb','sb')]:
# We fit a shapelet approximation of a distorted Moffat profile:
flux = 20
psf = galsim.Moffat(beta=3.4, half_light_radius=1.2, flux=flux)
psf = psf.shear(g1=0.11,g2=0.07).shift(0.03,0.04)
scale = 0.2
pixel = galsim.Pixel(scale)
conv = galsim.Convolve([psf,pixel])
im1 = conv.drawImage(scale=scale, method=method)
sigma = 1.2 # Match half-light-radius as a decent first approximation.
shapelet = galsim.Shapelet.fit(sigma, 10, im1, normalization=norm)
print('fitted shapelet coefficients = ',shapelet.bvec)
# Check flux
print('flux = ',shapelet.flux,' cf. ',flux)
np.testing.assert_almost_equal(shapelet.flux / flux, 1., 1,
err_msg="Fitted shapelet has the wrong flux")
# Test centroid
print('centroid = ',shapelet.centroid,' cf. ',conv.centroid)
np.testing.assert_almost_equal(shapelet.centroid.x, conv.centroid.x, 2,
err_msg="Fitted shapelet has the wrong centroid (x)")
np.testing.assert_almost_equal(shapelet.centroid.y, conv.centroid.y, 2,
err_msg="Fitted shapelet has the wrong centroid (y)")
# Test drawing image from shapelet
im2 = im1.copy()
shapelet.drawImage(im2, method=method)
# Check that images are close to the same:
print('norm(diff) = ',np.sum((im1.array-im2.array)**2))
print('norm(im) = ',np.sum(im1.array**2))
print('max(diff) = ',np.max(np.abs(im1.array-im2.array)))
print('max(im) = ',np.max(np.abs(im1.array)))
peak_scale = np.max(np.abs(im1.array))*3 # Check agreement to within 3% of peak value.
np.testing.assert_almost_equal(im2.array/peak_scale, im1.array/peak_scale, decimal=2,
err_msg="Shapelet version not a good match to original")
# Remeasure -- should now be very close to the same.
shapelet2 = galsim.Shapelet.fit(sigma, 10, im2, normalization=norm)
np.testing.assert_equal(shapelet.sigma, shapelet2.sigma,
err_msg="Second fitted shapelet has the wrong sigma")
np.testing.assert_equal(shapelet.order, shapelet2.order,
err_msg="Second fitted shapelet has the wrong order")
np.testing.assert_almost_equal(shapelet.bvec, shapelet2.bvec, 6,
err_msg="Second fitted shapelet coefficients do not match original")
# Test drawing off center
im2 = im1.copy()
offset = galsim.PositionD(0.3,1.4)
shapelet.drawImage(im2, method=method, offset=offset)
shapelet2 = galsim.Shapelet.fit(sigma, 10, im2, normalization=norm,
center=im2.true_center + offset)
np.testing.assert_equal(shapelet.sigma, shapelet2.sigma,
err_msg="Second fitted shapelet has the wrong sigma")
np.testing.assert_equal(shapelet.order, shapelet2.order,
err_msg="Second fitted shapelet has the wrong order")
np.testing.assert_almost_equal(shapelet.bvec, shapelet2.bvec, 6,
err_msg="Second fitted shapelet coefficients do not match original")
assert_raises(ValueError, galsim.Shapelet.fit, sigma, 10, im1, normalization='invalid')
# Haven't gotten around to implementing this yet...
im2.wcs = galsim.JacobianWCS(0.2,0.01,0.01,0.2)
with assert_raises(NotImplementedError):
galsim.Shapelet.fit(sigma, 10, im2)
def main(argv):
## fixed parameters
random_seed = 314
rng = galsim.BaseDeviate(random_seed)
random_dir = galsim.UniformDeviate(rng)
poisson_noise = galsim.PoissonNoise(rng)
dither_i = 22535
use_SCA = 1
filter_ = 'H158'
stamp_size = 32
hlr = 1.0
bpass = wfirst.getBandpasses(AB_zeropoint=True)[filter_]
galaxy_sed_n = galsim.SED('Mrk_33_spec.dat',
wave_type='Ang',
flux_type='flambda')
## variable arguments
gal_num = int(sys.argv[1])
PA1 = int(sys.argv[2])
PA2 = int(sys.argv[3])
galaxy_model = sys.argv[4]
PSF_model = sys.argv[5]
shape = sys.argv[6]
output_name = sys.argv[7]
# when using more galaxies than the length of truth file.
res_noshear = np.zeros(gal_num,
dtype=[('ind', int), ('flux', float), ('g1', float),
('g2', float), ('e1', float), ('e2', float),
('snr', float), ('hlr', float),
('flags', int)])
res_1p = np.zeros(gal_num,
dtype=[('ind', int), ('flux', float), ('g1', float),
('g2', float), ('e1', float), ('e2', float),
('snr', float), ('hlr', float), ('flags', int)])
res_1m = np.zeros(gal_num,
dtype=[('ind', int), ('flux', float), ('g1', float),
('g2', float), ('e1', float), ('e2', float),
('snr', float), ('hlr', float), ('flags', int)])
res_2p = np.zeros(gal_num,
dtype=[('ind', int), ('flux', float), ('g1', float),
('g2', float), ('e1', float), ('e2', float),
('snr', float), ('hlr', float), ('flags', int)])
res_2m = np.zeros(gal_num,
dtype=[('ind', int), ('flux', float), ('g1', float),
('g2', float), ('e1', float), ('e2', float),
('snr', float), ('hlr', float), ('flags', int)])
if shape == 'metacal':
res_tot = [res_noshear, res_1p, res_1m, res_2p, res_2m]
elif shape == 'noboot':
res_tot = [res_noshear, res_1p, res_1m, res_2p, res_2m]
elif shape == 'ngmix':
res_tot = [res_noshear]
PSF = getPSF(PSF_model, use_SCA, filter_, bpass)
position_angle1 = PA1 #degrees
position_angle2 = PA2 #degrees
wcs1, sky_level1 = get_wcs(dither_i, use_SCA, filter_, stamp_size,
position_angle1)
wcs2, sky_level2 = get_wcs(dither_i, use_SCA, filter_, stamp_size,
position_angle2)
wcs = [wcs1, wcs2]
sky_level = [sky_level1, sky_level2]
t0 = time.time()
for i_gal in range(gal_num):
if i_gal % size != rank:
continue
if i_gal % 100 == 0:
print('rank', rank, 'object number, ', i_gal)
gal_model = None
st_model = None
if galaxy_model == "Gaussian":
tot_mag = np.random.choice(cat)
sed = galsim.SED('CWW_E_ext.sed', 'A', 'flambda')
sed = sed.withMagnitude(tot_mag, bpass)
flux = sed.calculateFlux(bpass)
gal_model = galsim.Gaussian(
half_light_radius=hlr, flux=1.
) # needs to normalize the flux before multiplying by sed. For bdf, there are bulge, disk, knots fractions to sum to 1.
## making galaxy sed
#knots = galsim.RandomKnots(10, half_light_radius=1.3, flux=100)
#knots = make_sed_model(galsim.ChromaticObject(knots), galaxy_sed_n, filter_, bpass)
#gal_model = galsim.Add([gal_model, knots])
gal_model = sed * gal_model
## shearing
if i_gal % 2 == 0:
gal_model = gal_model.shear(g1=0.02, g2=0)
g1 = 0.02
g2 = 0
else:
gal_model = gal_model.shear(g1=-0.02, g2=0)
g1 = -0.02
g2 = 0
elif galaxy_model == "exponential":
tot_mag = np.random.choice(cat)
sed = galsim.SED('CWW_E_ext.sed', 'A', 'flambda')
sed = sed.withMagnitude(tot_mag, bpass)
flux = sed.calculateFlux(bpass)
gal_model = galsim.Exponential(half_light_radius=hlr, flux=1.)
## making galaxy sed ## random knots should be used for bdf model
#knots = galsim.RandomKnots(10, half_light_radius=1.3, flux=1.)
#knots = make_sed_model(galsim.ChromaticObject(knots), galaxy_sed_n, filter_, bpass)
#gal_model = galsim.Add([gal_model, knots])
gal_model = sed * gal_model
## shearing
if i_gal % 2 == 0:
gal_model = gal_model.shear(g1=0, g2=0.02)
g1 = 0
g2 = 0.02
else:
gal_model = gal_model.shear(g1=0, g2=-0.02)
g1 = 0
g2 = -0.02
gal_model = gal_model * galsim.wfirst.collecting_area * galsim.wfirst.exptime
flux_ = gal_model.calculateFlux(bpass)
#mag_ = gal_model.calculateMagnitude(bpass)
# This makes the object achromatic, which speeds up drawing and convolution
gal_model = gal_model.evaluateAtWavelength(bpass.effective_wavelength)
# Reassign correct flux
gal_model = gal_model.withFlux(flux_)
gal_model = galsim.Convolve(gal_model, PSF)
st_model = galsim.DeltaFunction(flux=1.)
st_model = st_model.evaluateAtWavelength(bpass.effective_wavelength)
# reassign correct flux
starflux = 1.
st_model = st_model.withFlux(starflux)
st_model = galsim.Convolve(st_model, PSF)
stamp_size_factor = old_div(
int(gal_model.getGoodImageSize(wfirst.pixel_scale)), stamp_size)
if stamp_size_factor == 0:
stamp_size_factor = 1
# Galsim world coordinate object (ra,dec)
"""
ra = cat[i_gal]['ra']
dec = cat[i_gal]['dec']
int_e1 = cat[i_gal]['int_e1']
int_e2 = cat[i_gal]['int_e2']
radec = galsim.CelestialCoord(ra*galsim.radians, dec*galsim.radians)
# Galsim image coordinate object
xy = wcs.toImage(radec)
# Galsim integer image coordinate object
xyI = galsim.PositionI(int(xy.x),int(xy.y))
"""
#xyI = galsim.PositionI(int(stamp_size_factor*stamp_size), int(stamp_size_factor*stamp_size))
#b = galsim.BoundsI( xmin=1,
# xmax=xyI.x,
# ymin=1,
# ymax=xyI.y)
#print(xyI.x, int(stamp_size_factor*stamp_size), xyI.x-old_div(int(stamp_size_factor*stamp_size),2)+1)
#print(b)
# Create postage stamp for galaxy
#print("galaxy ", i_gal, ra, dec, int_e1, int_e2)
## translational dither check (multiple exposures)
"""
position_angle1=20*random_dir() #degrees
position_angle2=position_angle1 #degrees
wcs1, sky_level1 = get_wcs(dither_i, use_SCA, filter_, stamp_size, position_angle1)
wcs2, sky_level2 = get_wcs(dither_i, use_SCA, filter_, stamp_size, position_angle2)
wcs=[wcs1, wcs2]
sky_level=[sky_level1, sky_level2]
"""
sca_center = [
wcs[0].toWorld(
galsim.PositionI(old_div(wfirst.n_pix, 2),
old_div(wfirst.n_pix, 2))), wcs[1].toWorld(
galsim.PositionI(old_div(wfirst.n_pix, 2),
old_div(wfirst.n_pix,
2)))
]
gal_radec = sca_center[0]
thetas = [position_angle1 * (np.pi / 180) * galsim.radians]
offsets = []
gals = []
psfs = []
skys = []
for i in range(2):
gal_stamp = None
psf_stamp = None
xy = wcs[i].toImage(gal_radec) # galaxy position
xyI = galsim.PositionI(int(xy.x), int(xy.y))
b = galsim.BoundsI(
xmin=xyI.x - old_div(int(stamp_size_factor * stamp_size), 2) +
1,
ymin=xyI.y - old_div(int(stamp_size_factor * stamp_size), 2) +
1,
xmax=xyI.x + old_div(int(stamp_size_factor * stamp_size), 2),
ymax=xyI.y + old_div(int(stamp_size_factor * stamp_size), 2))
#---------------------------------------#
# if the image does not use a real wcs. #
#---------------------------------------#
#b = galsim.BoundsI( xmin=1,
# xmax=int(stamp_size_factor*stamp_size),
# ymin=1,
# ymax=int(stamp_size_factor*stamp_size))
gal_stamp = galsim.Image(b, wcs=wcs[i]) #scale=wfirst.pixel_scale)
psf_stamp = galsim.Image(b, wcs=wcs[i]) #scale=wfirst.pixel_scale)
## translational dithering test
#dx = 0 #random_dir() - 0.5
#dy = 0 #random_dir() - 0.5
#offset = np.array((dx,dy))
offset = xy - gal_stamp.true_center # original galaxy position - stamp center
gal_model.drawImage(image=gal_stamp, offset=offset)
st_model.drawImage(image=psf_stamp, offset=offset)
sigma = wfirst.read_noise
read_noise = galsim.GaussianNoise(rng, sigma=sigma)
im, sky_image = add_background(gal_stamp,
sky_level[i],
b,
thermal_backgrounds=None,
filter_='H158',
phot=False)
#im.addNoise(read_noise)
gal_stamp = add_poisson_noise(rng,
im,
sky_image=sky_image,
phot=False)
#sky_image = add_poisson_noise(rng, sky_image, sky_image=sky_image, phot=False)
gal_stamp -= sky_image
# set a simple jacobian to the stamps before sending them to ngmix
# old center of the stamp
origin_x = gal_stamp.origin.x
origin_y = gal_stamp.origin.y
gal_stamp.setOrigin(0, 0)
psf_stamp.setOrigin(0, 0)
new_pos = galsim.PositionD(xy.x - origin_x, xy.y - origin_y)
wcs_transf = gal_stamp.wcs.affine(image_pos=new_pos)
new_wcs = galsim.JacobianWCS(wcs_transf.dudx, wcs_transf.dudy,
wcs_transf.dvdx, wcs_transf.dvdy)
gal_stamp.wcs = new_wcs
psf_stamp.wcs = new_wcs
offsets.append(offset)
gals.append(gal_stamp)
psfs.append(psf_stamp)
skys.append(sky_image)
print(gals)
res_tot = get_coadd_shape(cat, gals, psfs, offsets, skys, i_gal, hlr,
res_tot, g1, g2, shape)
print(res_tot)
## send and receive objects from one processor to others
if rank != 0:
# send res_tot to rank 0 processor
comm.send(res_tot, dest=0)
else:
for i in range(comm.size):
if i == 0:
continue
# for other processors, receive res_tot.
res_ = comm.recv(source=i)
for j in range(len(res_tot)):
for col in res_tot[j].dtype.names:
res_tot[j][col] += res_[j][col]
if rank == 0:
dirr = output_name
for i in range(len(res_tot)):
fio.write(dirr + '_sim_' + str(i) + '.fits', res_tot[i])
if rank == 0:
bias = residual_bias(res_tot, shape)
#final = residual_bias_correction(res_tot,R11,R22,R12,R21)
print(time.time() - t0)
return None