def test_fix_inputs_compound_bounding_box():
base_model = models.Gaussian2D(1, 2, 3, 4, 5)
bbox = {2.5: (-1, 1), 3.14: (-7, 3)}
model = fix_inputs(base_model, {'y': 2.5}, bounding_boxes=bbox)
assert model.bounding_box == (-1, 1)
model = fix_inputs(base_model, {'x': 2.5}, bounding_boxes=bbox)
assert model.bounding_box == (-1, 1)
model = fix_inputs(base_model, {'y': 2.5},
bounding_boxes=bbox,
selector_args=(('y', True), ))
assert model.bounding_box == (-1, 1)
model = fix_inputs(base_model, {'x': 2.5},
bounding_boxes=bbox,
selector_args=(('x', True), ))
assert model.bounding_box == (-1, 1)
model = fix_inputs(base_model, {'x': 2.5},
bounding_boxes=bbox,
selector_args=((0, True), ))
assert model.bounding_box == (-1, 1)
base_model = models.Identity(4)
bbox = {(2.5, 1.3): ((-1, 1), (-3, 3)), (2.5, 2.71): ((-3, 3), (-1, 1))}
model = fix_inputs(base_model, {'x0': 2.5, 'x1': 1.3}, bounding_boxes=bbox)
assert model.bounding_box == ((-1, 1), (-3, 3))
model = fix_inputs(base_model, {
'x0': 2.5,
'x1': 1.3
},
bounding_boxes=bbox,
selector_args=(('x0', True), ('x1', True)))
assert model.bounding_box == ((-1, 1), (-3, 3))
model = fix_inputs(base_model, {
'x0': 2.5,
'x1': 1.3
},
bounding_boxes=bbox,
selector_args=((0, True), (1, True)))
assert model.bounding_box == ((-1, 1), (-3, 3))
def test_with_fitters_and_sigma_clip(self):
import scipy.stats as stats
np.random.seed(0)
c = stats.bernoulli.rvs(0.25, size=self.z.shape)
self.z += (np.random.normal(0., 0.2, self.z.shape) +
c * np.random.normal(self.z, 2.0, self.z.shape))
guess = self.initial_guess(self.z, np.array([self.y, self.x]))
g2_init = models.Gaussian2D(amplitude=guess[0],
x_mean=guess[1],
y_mean=guess[2],
x_stddev=0.75,
y_stddev=1.25)
# test with Levenberg-Marquardt Least Squares fitter
fit = FittingWithOutlierRemoval(LevMarLSQFitter(),
sigma_clip,
niter=3,
sigma=3.)
fitted_model, _ = fit(g2_init, self.x, self.y, self.z)
assert_allclose(fitted_model.parameters[0:5],
self.model_params,
atol=1e-1)
# test with Sequential Least Squares Programming fitter
fit = FittingWithOutlierRemoval(SLSQPLSQFitter(),
sigma_clip,
niter=3,
sigma=3.)
fitted_model, _ = fit(g2_init, self.x, self.y, self.z)
assert_allclose(fitted_model.parameters[0:5],
self.model_params,
atol=1e-1)
# test with Simplex LSQ fitter
fit = FittingWithOutlierRemoval(SimplexLSQFitter(),
sigma_clip,
niter=3,
sigma=3.)
fitted_model, _ = fit(g2_init, self.x, self.y, self.z)
assert_allclose(fitted_model.parameters[0:5],
self.model_params,
atol=1e-1)
def test_2d_model():
# 2D model with LevMarLSQFitter
gauss2d = models.Gaussian2D(10.2, 4.3, 5, 2, 1.2, 1.4)
fitter = fitting.LevMarLSQFitter()
X = np.linspace(-1, 7, 200)
Y = np.linspace(-1, 7, 200)
x, y = np.meshgrid(X, Y)
z = gauss2d(x, y)
w = np.ones(x.size)
w.shape = x.shape
from astropy.utils import NumpyRNGContext
with NumpyRNGContext(1234567890):
n = np.random.randn(x.size)
n.shape = x.shape
m = fitter(gauss2d, x, y, z + 2 * n, weights=w)
assert_allclose(m.parameters, gauss2d.parameters, rtol=0.05)
m = fitter(gauss2d, x, y, z + 2 * n, weights=None)
assert_allclose(m.parameters, gauss2d.parameters, rtol=0.05)
# 2D model with LevMarLSQFitter, fixed constraint
gauss2d.x_stddev.fixed = True
m = fitter(gauss2d, x, y, z + 2 * n, weights=w)
assert_allclose(m.parameters, gauss2d.parameters, rtol=0.05)
m = fitter(gauss2d, x, y, z + 2 * n, weights=None)
assert_allclose(m.parameters, gauss2d.parameters, rtol=0.05)
# Polynomial2D, col_fit_deriv=False
p2 = models.Polynomial2D(1, c0_0=1, c1_0=1.2, c0_1=3.2)
z = p2(x, y)
m = fitter(p2, x, y, z + 2 * n, weights=None)
assert_allclose(m.parameters, p2.parameters, rtol=0.05)
m = fitter(p2, x, y, z + 2 * n, weights=w)
assert_allclose(m.parameters, p2.parameters, rtol=0.05)
# Polynomial2D, col_fit_deriv=False, fixed constraint
p2.c1_0.fixed = True
m = fitter(p2, x, y, z + 2 * n, weights=w)
assert_allclose(m.parameters, p2.parameters, rtol=0.05)
m = fitter(p2, x, y, z + 2 * n, weights=None)
assert_allclose(m.parameters, p2.parameters, rtol=0.05)
def corr_shift_determination(corr):
#Measure shift between the check and master images by fitting a 2D gaussian to corr. This gives sub-pixel accuracy.
y_max, x_max = np.unravel_index(
np.argmax(corr), corr.shape
) #Find the pixel with highest correlation, then use this as estimate for gaussian fit.
y, x = np.mgrid[y_max - 10:y_max + 10, x_max - 10:x_max + 10]
try:
corr_cut = corr[y, x]
gaussian_init = models.Gaussian2D(np.max(corr_cut), x_max, y_max,
8 / 2.355, 8 / 2.355, 0)
fit_gauss = fitting.LevMarLSQFitter()
gaussian = fit_gauss(gaussian_init, x, y, corr_cut)
fit_x = gaussian.x_mean.value
fit_y = gaussian.y_mean.value
x_shift = fit_x - 512
y_shift = 512 - fit_y
return (x_shift, y_shift)
except:
print('Problem with corr indexing, returning 0 shifts.')
return (0, 0)
def test_with_fitters_and_sigma_clip(self, fitter):
import scipy.stats as stats
fitter = fitter()
np.random.seed(0)
c = stats.bernoulli.rvs(0.25, size=self.z.shape)
z = self.z + (np.random.normal(0., 0.2, self.z.shape) +
c*np.random.normal(self.z, 2.0, self.z.shape))
guess = self.initial_guess(self.z, np.array([self.y, self.x]))
g2_init = models.Gaussian2D(amplitude=guess[0], x_mean=guess[1],
y_mean=guess[2], x_stddev=0.75,
y_stddev=1.25)
fit = FittingWithOutlierRemoval(fitter, sigma_clip,
niter=3, sigma=3.)
fitted_model, _ = fit(g2_init, self.x, self.y, z)
assert_allclose(fitted_model.parameters[0:5], self.model_params,
atol=1e-1)
def test_print_special_operator_CompoundModel(capsys):
"""
Test that issue #11310 has been fixed
"""
model = convolve_models(models.Sersic2D(), models.Gaussian2D())
with astropy.conf.set_temp('max_width', 80):
assert str(model) == "Model: CompoundModel\n" +\
"Inputs: ('x', 'y')\n" +\
"Outputs: ('z',)\n" +\
"Model set size: 1\n" +\
"Expression: convolve_fft (([0]), ([1]))\n" +\
"Components: \n" +\
" [0]: <Sersic2D(amplitude=1., r_eff=1., n=4., x_0=0., y_0=0., ellip=0., theta=0.)>\n" +\
"\n" +\
" [1]: <Gaussian2D(amplitude=1., x_mean=0., y_mean=0., x_stddev=1., y_stddev=1., theta=0.)>\n" +\
"Parameters:\n" +\
" amplitude_0 r_eff_0 n_0 x_0_0 y_0_0 ... y_mean_1 x_stddev_1 y_stddev_1 theta_1\n" +\
" ----------- ------- --- ----- ----- ... -------- ---------- ---------- -------\n" +\
" 1.0 1.0 4.0 0.0 0.0 ... 0.0 1.0 1.0 0.0"
def lp(p,data,error,fixp,guess,pixsize,types):
'''Log probability for 2D Gaussian models
INPUT: p - parameter array of floats consisting of [amp, x, y, bmaj(fwhm), bmin(fwhm), bpa] (units mJy, pix, pix, arcsec, arcsec, deg)
data - 2D fits image (array)
error - 2D fits image variance (array)
fixp - boolean array indicating which parameters are fixed in fit; same dimensions as p
guess - array of floats of initial guesses for parameters; same dimensions as p
pixsize - pixel size in the image in arcsec (float)
types - 'toti' or 'pol' (str)
OUTPUT: log probability
'''
amp,xx,yy,bmaj,bmin,bpa=p[0],p[1],p[2],p[3],p[4],p[5]
mod0=models.Gaussian2D(amp,xx,yy,bmaj/(2.*pixsize),bmin/(2.*pixsize),bpa)
xval=np.arange(0,len(data[0,:]))
yval=np.arange(0,len(data[:,0]))
Xval, Yval = np.meshgrid(xval, yval)
mod1=mod0(Xval,Yval)
re=-0.5*np.nansum(np.log(2*np.pi*error**2))-np.nansum((mod1-data)**2/(2*error**2))
prior=prior_func(p,fixp,guess,types)
return(re+prior)
def guess_2d_gaussian(x, y, z, ok=None):
'''
Make a guess to initialize the baseline + 2D Gaussian model,
based on medians and weighted moments of the image.
'''
if ok == None:
ok = np.ones_like(z).astype(np.bool)
# estimate a baseline flux, from the median of the good pixels
baseline_guess = np.median(z[ok])
# do a *veyr* coarse subtraction, to focus on just the blob
crudelysubtracted = np.maximum((z-baseline_guess), 0)
amplitude_guess = np.sum(crudelysubtracted)
def moment(q):
'''
Take the weighted moment of a quantity.
'''
return np.sum(q[ok]*crudelysubtracted[ok])/np.sum(crudelysubtracted[ok])
# calculate flux-weighted centroids of the blob
x_guess = moment(x)
y_guess = moment(y)
# calculate flux-weighted widths of the blob
x_width_guess = np.sqrt(moment((x - x_guess)**2))
y_width_guess = np.sqrt(moment((y - y_guess)**2))
# create an initial model, with the initial guesses
initial = ( models.Const2D(amplitude=baseline_guess) +
models.Gaussian2D(amplitude=amplitude_guess,
x_mean=x_guess, y_mean=y_guess,
x_stddev=x_width_guess, y_stddev=y_width_guess,
theta=0.0))
return initial
def fit_2dgaussian(data, uncertainty=None, mask=None):
"""
Fit a 2D Gaussian to a 2D image.
Parameters
----------
data : array_like or `~astropy.nddata.NDData`
The 2D array of the image.
uncertainty : array_like, optional
The 2D array of the 1-sigma errors of the input ``data``.
mask : array_like, bool, optional
(Not yet implemented).
A boolean mask with the same shape as ``data``, where a `True`
value indicates the corresponding element of ``data`` is
invalid. If ``mask`` is input it will override ``data.mask``
for `~astropy.nddata.NDData` inputs.
Returns
-------
centroid : tuple
(x, y) coordinates of the centroid.
"""
if uncertainty is None:
weights = None
else:
weights = 1.0 / uncertainty
init_param = shape_params(data, mask=mask)
init_amplitude = np.ptp(data)
g_init = models.Gaussian2D(init_amplitude,
init_param['xcen'],
init_param['ycen'],
init_param['major_axis'],
init_param['minor_axis'],
theta=init_param['angle'])
fitter = LevMarLSQFitter()
y, x = np.indices(data.shape)
gfit = fitter(g_init, x, y, data, weights=weights)
return gfit
def test_gaussian_fwhm_after_convolution(self):
"""Convolve a Gaussian image with a Gaussian kernel, and measure
the sigma of the final image. A Gaussian convolved with a Gaussian
is a Gaussian with a variance that is the sum of the two:
http://www.tina-vision.net/docs/memos/2003-003.pdf
"""
nx, ny = 31, 61
fwhmi = 7
fwhmk = 5
factor = 5
x, y = testimage.xy_data(nx, ny)
m = guassian_convolved_with_gaussian(nx,
ny,
amplitude=1.0,
x0=None,
y0=None,
fwhmi=fwhmi,
fwhmk=fwhmk,
factor=factor)
x, y = testimage.xy_data(nx, ny)
# fit Gaussian2D to the convolved model
g_init = models.Gaussian2D(amplitude=m.max(),
x_mean=(ny - 1) / 2,
y_mean=(nx - 1) / 2,
x_stddev=fwhmi,
y_stddev=fwhmi)
fit_g = fitting.LevMarLSQFitter()
g = fit_g(g_init, x, y, m)
# calculate the the theoretical standard deviation for convolution
# of two Gaussians in 1D.
stddevi, stddevk = fwhmi / 2.35, fwhmk / 2.35
stddevt = np.sqrt(stddevi**2 + stddevk**2)
# make sure that it is within 10%
rel_dev = (g.x_stddev.value - stddevt) / stddevt
return self.assertTrue(np.abs(rel_dev) < 0.1)
def single_source_side():
# Large shape to allow for psf fitting
# as beam needs to be much smaller than the map at some point..
shape = (27, 27)
pixsize = 1 / 3
data = np.zeros(shape)
wcs = WCS()
wcs.wcs.crpix = np.asarray(shape) / 2 - 0.5 # Center of pixel
wcs.wcs.cdelt = np.asarray([-1, 1]) * pixsize
wcs.wcs.ctype = ("RA---TAN", "DEC--TAN")
fake_sources = Table(masked=True)
fake_sources["fake_id"] = [1]
fake_sources["x_mean"] = [0]
fake_sources["y_mean"] = [13]
ra, dec = wcs.wcs_pix2world(fake_sources["x_mean"], fake_sources["y_mean"],
0)
fake_sources["ra"] = ra * u.deg
fake_sources["dec"] = dec * u.deg
fake_sources["_ra"] = fake_sources["ra"]
fake_sources["_dec"] = fake_sources["dec"]
xx, yy = np.indices(shape)
stddev = 1 / pixsize * gaussian_fwhm_to_sigma
g = models.Gaussian2D(1, fake_sources["y_mean"], fake_sources["x_mean"],
stddev, stddev)
data += g(xx, yy)
nm = NikaMap(data,
uncertainty=np.ones_like(data) / 4,
wcs=wcs,
unit=u.Jy / u.beam,
fake_sources=fake_sources)
nm.x = fake_sources["x_mean"]
nm.y = fake_sources["y_mean"]
return nm
def test_custom_bounding_box_1d():
"""
Tests that the bounding_box setter works.
"""
# 1D models
g1 = models.Gaussian1D()
bb = g1.bounding_box
expected = g1.render()
# assign the same bounding_box, now through the bounding_box setter
g1.bounding_box = bb
assert_allclose(g1.render(), expected)
# 2D models
g2 = models.Gaussian2D()
bb = g2.bounding_box
expected = g2.render()
# assign the same bounding_box, now through the bounding_box setter
g2.bounding_box = bb
assert_allclose(g2.render(), expected)
def fakeData():
"""
Generate some fake data i.e. a 2D Gaussian with noise.
"""
#Create the coordinates x and y
x = np.arange(0, 256)
y = np.arange(0, 256)
#Put the coordinates in a mesh
xx, yy = np.meshgrid(x, y)
#get Gaussian with fixed params
model = models.Gaussian2D(50, 123, 135, 20, 35.5)
zz = model.eval(xx, yy, 50, 123, 135, 20, 35.5, 0)
#Flatten the arrays
xx = xx.flatten()
yy = yy.flatten()
#add some noise to zz
zz = zz.flatten() + np.random.normal(0.0, 2., len(xx))
sigma = np.ones(len(xx))
return xx, yy, zz, sigma
def hclean(dirtyim, psf, thresh, niter, lpgain, window=None):
"""
Hogbom CLEAN alogrithm
:dirtyim:
:psf:
:thresh:
:niter:
:lpgain:
:window:
"""
clmodel = np.zeros_like(dirtyim)
res = np.copy(dirtyim)
for n in range(niter):
[mx, my] = np.unravel_index(np.fabs(res).argmax(), res.shape)
clmodel[mx, my] += lpgain * res[mx, my]
okxy, osxy = effregion(psf, res, mx, my)
res[osxy[0]:osxy[1] + 1,
osxy[2]:osxy[3] + 1] -= psf[okxy[0]:okxy[1] + 1, okxy[2]:okxy[3] +
1] * lpgain * res[mx, my]
if (np.fabs(res).max() < thresh):
break
xg, yg = np.arange(-3, 4), np.arange(-3, 4)
xpg, ypg = np.meshgrid(xg, yg)
g_init = models.Gaussian2D(amplitude=1.,
x_mean=0,
x_stddev=1.,
y_mean=0,
y_stddev=1.,
theta=0)
fitg = fitting.LevMarLSQFitter()
g2d = fitg(g_init, xpg, ypg, psf)
# Using 2-d Gaussian beam as clean beam to fit psf
clbeam = g2d(xpg, ypg)
clmap = signal.fftconvolve(clmodel, clbeam, 'same')
return clmap, res
def astropy_Psf(N, FWHM):
"""Psf es una funcion que proporciona una matriz 2D con una gaussiana
simétrica en ambos ejes. con N se especifica el tamaño en pixeles que
necesitamos y con FWHM el ancho sigma de la gaussiana en pixeles
%timeit simtools.astropy_Psf(128, 10)
1 loops, best of 3: 338 ms per loop
"""
psf = np.zeros((N, N))
mu = (N - 1) / 2.
sigma = FWHM / 2.335
model = models.Gaussian2D(amplitude=1.,
x_mean=mu,
y_mean=mu,
x_stddev=sigma,
y_stddev=sigma)
tail_len = int(7 * sigma)
mu_int = int(mu)
i = range(mu_int - tail_len, mu_int + tail_len, 1)
for ii, jj in cartesian_product([i, i]):
psf[ii, jj] = model(ii, jj)
return psf / np.sum(psf)
def test_render_model_2d():
imshape = (71, 141)
image = np.zeros(imshape)
coords = y, x = np.indices(imshape)
model = models.Gaussian2D(x_stddev=6.1, y_stddev=3.9, theta=np.pi / 3)
# test points for edges
ye, xe = [0, 35, 70], [0, 70, 140]
# test points for floating point positions
yf, xf = [35.1, 35.5, 35.9], [70.1, 70.5, 70.9]
test_pts = [(a, b) for a in xe for b in ye]
test_pts += [(a, b) for a in xf for b in yf]
for x0, y0 in test_pts:
model.x_mean = x0
model.y_mean = y0
expected = model(x, y)
for xy in [coords, None]:
for im in [image.copy(), None]:
if (im is None) & (xy is None):
# this case is tested in Fittable2DModelTester
continue
actual = model.render(out=im, coords=xy)
if im is None:
assert_allclose(actual, model.render(coords=xy))
# assert images match
assert_allclose(expected, actual, atol=3e-7)
# assert model fully captured
if (x0, y0) == (70, 35):
boxed = model.render()
flux = np.sum(expected)
assert ((flux - np.sum(boxed)) / flux) < 1e-7
# test an error is raised when the bounding box is larger than the input array
try:
actual = model.render(out=np.zeros((1, 1)))
except ValueError:
pass
def measure_fwhm(array):
"""Fit a Gaussian2D model to a PSF and return the FWHM
Parameters
----------
array : numpy.ndarray
Array containing PSF
Returns
-------
x_fwhm : float
FWHM in x direction in units of pixels
y_fwhm : float
FWHM in y direction in units of pixels
"""
yp, xp = array.shape
y, x, = np.mgrid[:yp, :xp]
p_init = models.Gaussian2D()
fit_p = fitting.LevMarLSQFitter()
fitted_psf = fit_p(p_init, x, y, array)
return fitted_psf.x_fwhm, fitted_psf.y_fwhm
def log_likelihood(theta, x, y, data, var, size):
"""
Logarithm of the likelihood function.
"""
#unpack the parameters
peak, center_x, center_y, radius, focus, width_x, width_y = theta
#1)Generate a model Airy disc
amplitude = _amplitudeFromPeak(peak,
center_x,
center_y,
radius,
x_0=int(size[0] / 2. - 0.5),
y_0=int(size[1] / 2. - 0.5))
airy = models.AiryDisk2D(amplitude, center_x, center_y, radius)
adata = airy.eval(x, y, amplitude, center_x, center_y,
radius).reshape(size)
#2)Apply Focus
f = models.Gaussian2D(1., center_x, center_y, focus, focus, 0.)
focusdata = f.eval(x, y, 1., center_x, center_y, focus, focus,
0.).reshape(size)
model = signal.convolve2d(adata, focusdata, mode='same')
#3)Apply CCD diffusion, approximated with a Gaussian
CCDdata = np.array(
[[0.0, width_y, 0.0],
[width_x, (1. - width_y - width_y - width_x - width_x), width_x],
[0.0, width_y, 0.0]])
model = signal.convolve2d(model, CCDdata, mode='same').flatten()
#true for Gaussian errors
#lnL = - 0.5 * np.sum((data - model)**2 / var)
#Gary B. said that this should be from the model not data so recompute var (now contains rn**2)
var += model.copy()
lnL = -(np.size(var) * np.sum(np.log(var))) - (0.5 * np.sum(
(data - model)**2 / var))
return lnL
def fit_2D_gaussian(xmat, ymat, z):
'''
Return fitted model parameters
'''
g = astropy_models.Gaussian2D(x_mean=[0], y_mean=[0], x_stddev=[1],
y_stddev=[1], amplitude=z.max(),
theta=[0],
fixed={'amplitude': True,
'x_mean': True,
'y_mean': True}) + \
astropy_models.Const2D(amplitude=[np.percentile(z, 10)])
fit_g = fitting.LevMarLSQFitter()
output = fit_g(g, xmat, ymat, z)
cov = fit_g.fit_info['param_cov']
if cov is None:
warn("Fitting failed.")
cov = np.zeros((4, 4)) * np.NaN
return output, cov
def test_Gaussian2D():
"""
Test rotated elliptical Gaussian2D model.
https://github.com/astropy/astropy/pull/2038
"""
model = models.Gaussian2D(4.2,
1.7,
3.1,
x_stddev=5.1,
y_stddev=3.3,
theta=np.pi / 6.)
y, x = np.mgrid[0:5, 0:5]
g = model(x, y)
g_ref = [[3.01907812, 2.99051889, 2.81271552, 2.5119566, 2.13012709],
[3.55982239, 3.6086023, 3.4734158, 3.17454575, 2.75494838],
[3.88059142, 4.0257528, 3.96554926, 3.70908389, 3.29410187],
[3.91095768, 4.15212857, 4.18567526, 4.00652015, 3.64146544],
[3.6440466, 3.95922417, 4.08454159, 4.00113878, 3.72161094]]
assert_allclose(g, g_ref, rtol=0, atol=1e-6)
assert_allclose([model.x_fwhm, model.y_fwhm],
[12.009582229657841, 7.7709061486021325])
def FitGaussian(img, amp, stddev, center, theta=0, FWHM=False):
if FWHM:
stddev[:] = [x / 1.17741 / 2 for x in stddev]
xy = np.where(img > 0)
# Fit the data using astropy.modeling
p_init = models.Gaussian2D(amplitude=amp,
x_mean=center[1],
y_mean=center[0],
x_stddev=stddev[0],
y_stddev=stddev[1],
theta=np.radians(theta))
fit_p = fitting.LevMarLSQFitter()
with warnings.catch_warnings():
# Ignore model linearity warning from the fitter
warnings.simplefilter('ignore')
p = fit_p(p_init, xy[0], xy[1], img[xy])
return p
def setup(self):
# create temporary directory
self.tmpdir_in = tempfile.TemporaryDirectory()
# Create image data
in_array = np.zeros([1, 1, 100, 100])
# Add noise
np.random.seed(10)
in_array += np.random.normal(0.0, 1e-5, [1, 1, 100, 100])
# Add a gaussian source to fit (otherwise QA code will fail)
y, x = np.mgrid[:100, :100]
gaus_mod = models.Gaussian2D(0.001, 50, 50, 2.5, 6, 0.6)
gaus_data = gaus_mod(y, x)
# Leave in extra axes as QA code will try to drop extra axes
# inferred from the header
in_array += gaus_data[np.newaxis, np.newaxis, :, :]
hdu = fits.PrimaryHDU(in_array, header=fits.Header(HDR_KEYS))
# QA code expects a frequency axis
hdu.header['CTYPE3'] = 'FREQ '
# Construct 4 targets
target_names = ['Gunther Lord of the Gibichungs',
'Gutrune', 'Hagen', 'Gutrune']
self.metadata = _create_test_metadata(target_names)
# Create input images per target
self.dir_base = []
for f, t in zip(self.metadata['FITSImageFilename'], self.metadata['Targets']):
pipe_dirname = os.path.join(self.tmpdir_in.name, '1234')
# Expected base name of new directories containing QA products
outDirName = pipe_dirname + '_' + t + '_' + self.metadata['Run']
self.dir_base.append(outDirName)
os.mkdir(outDirName + '_PB.writing')
file_base = os.path.splitext(f)[0]
inFileName = os.path.join(outDirName + '_PB.writing', file_base + '_PB' + FITS_EXT)
hdu.writeto(inFileName)
def guide_star_seeing(subframe):
# subframe = subframe - np.median(subframe)
subframe = subframe - np.percentile(subframe, 5)
sub_frame_l = int(np.shape(subframe)[0])
y, x = np.mgrid[:sub_frame_l, :sub_frame_l]
# gaussian_init = models.Gaussian2D(subframe[int(sub_frame_l/2),int(sub_frame_l/2)],int(sub_frame_l/2),int(sub_frame_l/2),8/2.355,8/2.355,0)
# fit_gauss = fitting.LevMarLSQFitter()
# gaussian = fit_gauss(gaussian_init, x, y, subframe)
# fwhm_x = 2.355*gaussian.x_stddev.value
# fwhm_y = 2.355*gaussian.y_stddev.value
# Fit with constant, bounds, tied x and y sigmas and outlier rejection:
gaussian_init = models.Const2D(0.0) + models.Gaussian2D(
subframe[int(sub_frame_l / 2),
int(sub_frame_l / 2)], int(sub_frame_l / 2),
int(sub_frame_l / 2), 8 / 2.355, 8 / 2.355, 0)
gaussian_init.x_stddev_1.min = 1.0 / 2.355
gaussian_init.x_stddev_1.max = 20.0 / 2.355
gaussian_init.y_stddev_1.min = 1.0 / 2.355
gaussian_init.y_stddev_1.max = 20.0 / 2.355
gaussian_init.y_stddev_1.tied = tie_sigma
gaussian_init.theta_1.fixed = True
fit_gauss = fitting.FittingWithOutlierRemoval(
fitting.LevMarLSQFitter(), sigma_clip, niter=3, sigma=3.0)
# gaussian, mask = fit_gauss(gaussian_init, x, y, subframe)
gain = 8.21 #e per ADU
read_noise = 2.43 #ADU
weights = gain / np.sqrt(
np.absolute(subframe) * gain +
(read_noise * gain)**2) #1/sigma for each pixel
gaussian, mask = fit_gauss(gaussian_init, x, y, subframe, weights)
fwhm_x = 2.355 * gaussian.x_stddev_1.value
fwhm_y = 2.355 * gaussian.y_stddev_1.value
x_seeing = fwhm_x * 0.579
y_seeing = fwhm_y * 0.579
return (x_seeing, y_seeing)
diagnostic_plot = 0 #Set to true to plot master and check images with sources.
def GetFitsForSigma(x_c, y_c, factor, fo, sigma, plot_name, bmaj, bmin, bpa,
fijo, pix_size):
ancho = int(round(0.5 * (5.0 * bmaj / pix_size)) * 2)
center = int(ancho / 2.0)
z = fo[max(int(y_c) - center, 0):min(int(y_c) + center, len(fo)),
max(int(x_c) - center, 0):min(int(x_c) + center, len(fo[0]))]
y, x = np.mgrid[0:len(z), 0:len(z[0])]
p_init = models.Gaussian2D(amplitude=np.nanmax(z.flatten()),
x_mean=center,
y_mean=center,
x_stddev=(bmaj / 2.355) / pix_size,
y_stddev=(bmin / 2.355) / pix_size,
theta=(bpa * 2.0 * np.pi / 360.0) + np.pi / 2)
if fijo:
p_init.x_stddev.fixed = True
p_init.y_stddev.fixed = True
p_init.theta.fixed = True
fit_p = fitting.LevMarLSQFitter()
with warnings.catch_warnings():
warnings.simplefilter('ignore')
p = fit_p(p_init, x, y, z)
model_flat = p(x, y).flatten()
model2 = model_flat[model_flat >= 0.135 * max(model_flat)]
peak_model = np.max(model_flat)
fo[max(int(y_c) - center, 0):min(int(y_c) + center, len(fo)),
max(int(x_c) - center, 0):min(int(x_c) + center, len(fo[0]))] = fo[
max(int(y_c) - center, 0):min(int(y_c) + center, len(fo)),
max(int(x_c) - center, 0):min(int(x_c) +
center, len(fo[0]))] - np.nan_to_num(
p(x, y))
# plt.imshow(fo[max(int(y_c)-center,0):min(int(y_c)+center,len(fo)),max(int(x_c)-center,0):min(int(x_c)+center,len(fo[0]))],origin='lower')
# plt.contour(p(x, y),origin='lower')
# plt.show()
return np.sum(model_flat) * factor, np.sqrt(
len(model2) * factor) * sigma, peak_model, np.std(
z - p(x, y)), p.x_stddev.value, p.y_stddev.value, p.theta.value, fo
def ClassicalOptimization():
fit_LSQ = fitting.LevMarLSQFitter()
ring1 = FFRing(i0=0.0036,
i1=0.0036,
sig0=1.,
sig1=0.1,
gam=1.6,
xc=0.,
yc=0.,
a=50.,
b=50.,
theta=0.)
ring2 = GaussianRing(amplitude=0.0005, a=230., b=230., width=20.)
ring3 = GaussianRing(amplitude=0.0004, a=270., b=270., width=20.)
ring4 = GaussianRing(amplitude=0.0005, a=40., b=40., width=5.)
centralgauss = models.Gaussian2D(amplitude=0.0035,
x_mean=0.,
y_mean=0.,
x_stddev=5.,
y_stddev=5.,
theta=0.)
ring1.theta.fixed = True
ring2.theta.fixed = True
ring3.theta.fixed = True
ring4.theta.fixed = True
centralgauss.theta.fixed = True
model = centralgauss + ring1 + ring2 + ring3 + ring4
modelend = fit_LSQ(model, xx, yy, image)
#showi(modelend(xx,yy))
modelend.theta_0.fixed = False
modelend.theta_2.fixed = False
modelend.theta_1.fixed = False
modelend.theta_3.fixed = False
modelend.theta_4.fixed = False
modelend = fit_LSQ(modelend, xx, yy, image)
modelend = fit_LSQ(modelend, xx, yy, image)
#showi(modelend(xx,yy))
return (modelend.parameters)
def _initialize_model(self):
"""Initialize a model with first guesses for the parameters.
The user can select between several astropy models, e.g., 'Gaussian2D', 'Moffat2D'. We will use the data to get
the first estimates of the parameters of each model. Finally, a Constant2D model is added to account for the
background or sky level around the star.
"""
max_value = self.data.max()
if self.model_type == self._GAUSSIAN2D:
model = models.Gaussian2D(x_mean=self.x,
y_mean=self.y,
x_stddev=1,
y_stddev=1)
model.amplitude = max_value
# Establish reasonable bounds for the fitted parameters
model.x_stddev.bounds = (0, self._box / 4)
model.y_stddev.bounds = (0, self._box / 4)
model.x_mean.bounds = (self.x - 5, self.x + 5)
model.y_mean.bounds = (self.y - 5, self.y + 5)
elif self.model_type == self._MOFFAT2D:
model = models.Moffat2D()
model.x_0 = self.x
model.y_0 = self.y
model.gamma = 2
model.alpha = 2
model.amplitude = max_value
# Establish reasonable bounds for the fitted parameters
model.alpha.bounds = (1, 6)
model.gamma.bounds = (0, self._box / 4)
model.x_0.bounds = (self.x - 5, self.x + 5)
model.y_0.bounds = (self.y - 5, self.y + 5)
model += models.Const2D(self.fit_sky())
model.amplitude_1.fixed = True
return model
def centroid(data, coords, rad=30, returnFit=False):
if isinstance(data, str):
data = pyfits.getdata(data)
# Transpose x and y b/c reasons
center_y, center_x = coords
dslice = data[center_x - rad:center_x + rad, center_y - rad:center_y + rad]
x, y = np.mgrid[0:dslice.shape[0], 0:dslice.shape[1]]
x -= dslice.shape[0] / 2.
y -= dslice.shape[1] / 2.
p_init = models.Gaussian2D(np.max(dslice), 0, 0, rad, rad)
p = fitter(p_init, x, y, dslice)
# Rescale coordinates to match data
p.x_mean = center_y - p.x_mean
p.y_mean = center_x - p.y_mean
if returnFit:
return p.x_mean.value, p.y_mean.value, p
else:
return p.x_mean.value, p.y_mean.value
def test_bounds_gauss2d_lsq(self):
X, Y = np.meshgrid(np.arange(11), np.arange(11))
bounds = {"x_mean": [0., 11.],
"y_mean": [0., 11.],
"x_stddev": [1., 4],
"y_stddev": [1., 4]}
gauss = models.Gaussian2D(amplitude=10., x_mean=5., y_mean=5.,
x_stddev=4., y_stddev=4., theta=0.5,
bounds=bounds)
gauss_fit = fitting.LevMarLSQFitter()
model = gauss_fit(gauss, X, Y, self.data)
x_mean = model.x_mean.value
y_mean = model.y_mean.value
x_stddev = model.x_stddev.value
y_stddev = model.y_stddev.value
assert x_mean + 10 ** -5 >= bounds['x_mean'][0]
assert x_mean - 10 ** -5 <= bounds['x_mean'][1]
assert y_mean + 10 ** -5 >= bounds['y_mean'][0]
assert y_mean - 10 ** -5 <= bounds['y_mean'][1]
assert x_stddev + 10 ** -5 >= bounds['x_stddev'][0]
assert x_stddev - 10 ** -5 <= bounds['x_stddev'][1]
assert y_stddev + 10 ** -5 >= bounds['y_stddev'][0]
assert y_stddev - 10 ** -5 <= bounds['y_stddev'][1]
def measure_psf_fwhm(psf, fwhm_guess):
"""
Fit a 2D Gaussian to observed psf to estimate the FWHM
Parameters
----------
psf : ndarray
Observed psf
fwhm_guess : float
Guess for fwhm in pixels
Returns
-------
mean_fwhm : float
Mean x & y FWHM
"""
sigma = fwhm_guess * gaussian_fwhm_to_sigma
g_init = models.Gaussian2D(psf.max() * 0.3, psf.shape[1] / 2,
psf.shape[0] / 2, sigma)
fit_g = fitting.LevMarLSQFitter()
xx, yy = np.meshgrid(np.arange(psf.shape[1]), np.arange(psf.shape[0]))
best_fit = fit_g(g_init, xx, yy, psf)
mean_fwhm = np.mean([best_fit.x_fwhm, best_fit.y_fwhm])
return mean_fwhm
def fit_gauss(sci):
from astropy.modeling import models, fitting
sh = sci.shape
gau = models.Gaussian2D(amplitude=sci.max(),
x_mean=sh[0] / 2,
y_mean=sh[0] / 2.,
x_stddev=None,
y_stddev=None,
theta=None,
cov_matrix=None)
lm = fitting.LevMarLSQFitter()
yp, xp = np.indices(sh)
fit = lm(gau, xp, yp, sci)
q = (fit.x_stddev / fit.y_stddev)**2
theta = fit.theta.value
if q > 1:
q = 1. / q
theta += np.pi / 2.
return fit, q, theta