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]
# 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)
def create_test_image(gap=3, N=25):
'''
Create one random stitched camera, with a Gaussian-ish background to it.
'''
# generate a random model
p_generate = (models.Const2D(amplitude=10**np.random.uniform(0, 1)) +
models.Gaussian2D(amplitude=10**np.random.uniform(.5, 2),
x_mean=np.random.uniform(-N, N),
y_mean=np.random.uniform(-N, N),
x_stddev=np.random.uniform(2, N),
y_stddev=np.random.uniform(2, N),
theta=np.random.uniform(0, 2*np.pi)))
# create fake x and y arrays
x, y = np.meshgrid(np.arange(-N-gap, N+gap+1), np.arange(-N-gap, N+gap+1))
# create the model
perfect = p_generate(x, y)
z = np.random.normal(perfect, 1)
# find the gaps, replace them with zeros, and mark them as bad
bad = (np.abs(x) < gap) | (np.abs(y) < gap)
z[bad] = 0
ok = bad == False
return x, y, z, ok, p_generate
def test_get_bounding_box():
model = models.Const2D(2)
# No with_bbox
assert model.get_bounding_box(False) is None
# No bounding_box
with pytest.raises(NotImplementedError):
model.bounding_box
assert model.get_bounding_box(True) is None
# Normal bounding_box
model.bounding_box = ((0, 1), (0, 1))
assert not isinstance(model.bounding_box, CompoundBoundingBox)
assert model.get_bounding_box(True) == ((0, 1), (0, 1))
# CompoundBoundingBox with no removal
bbox = CompoundBoundingBox.validate(model, {(1,): ((-1, 0), (-1, 0)), (2,): ((0, 1), (0, 1))},
selector_args=[('y', False)])
model.bounding_box = bbox
assert isinstance(model.bounding_box, CompoundBoundingBox)
# Get using argument not with_bbox
assert model.get_bounding_box(True) == bbox
# Get using with_bbox not argument
assert model.get_bounding_box((1,)) == ((-1, 0), (-1, 0))
assert model.get_bounding_box((2,)) == ((0, 1), (0, 1))
def test_legacy_const(tmpdir):
model = astropy_models.Const1D(amplitude=5.)
assert_model_roundtrip(model, tmpdir, version="1.3.0")
model = astropy_models.Const2D(amplitude=5.)
with pytest.raises(TypeError,
match="does not support models with > 1 dimension"):
assert_model_roundtrip(model, tmpdir, version="1.3.0")
def from_tree_transform(self, node):
if self.version < AsdfVersion('1.4.0'):
# The 'dimensions' property was added in 1.4.0,
# previously all values were 1D.
return models.Const1D(node['value'])
elif node['dimensions'] == 1:
return models.Const1D(node['value'])
elif node['dimensions'] == 2:
return models.Const2D(node['value'])
def FitGaussian2D(B, reconstruct_model=False):
'''
Fits a 2D gaussian model to a vignette using Levenberg-Marquardt algorithm and least squares statistic.
input:
B: Vignette with the object
reconstruct_model: Boolean flag. Indicates if the reconstructed model and its residuals should be computed
output:
params: Dictionary with the 6 fitted parameters. Keys = ['amp', 'ab', 'ellip', 'theta', 'x0', 'y0']
*rec_model: Vignette with the fitted model. Only if reconstruct_model=True
*rec_resi: Vignette with the residuals, ie: rec_resi=B-rec_model. Only if reconstruct_model=True
Notes: Given the polar nature of the ellipticity definition, the fit can be confusing. For ex., given a
gaussian with ellip = 0.1 and theta = 0 (where theta is measured from the y axis), it is posible that the
fitter returns ellip = -0.1 and theta = pi/2. This time the minus sign in ellip indicates that it is meassuring
it on the oposite axis, thus theta is being measured from the x axis.
We fix the position x0,y0 of the model at the center of the stamp. There is no need to fit them
Notes 2: Add the posibility of fitting a sum of gaussians instead of just one.
'''
p = model_Gaussian2D(amp=B.max()-B.min(), ab=5, e1=0., e2=0.2,x0=B.shape[0]/2,y0=B.shape[1]/2) + \
models.Const2D(amplitude=B.min())
# Constraints on some parameters
p.x0_0.fixed = True
p.y0_0.fixed = True
x, y = np.meshgrid(range(B.shape[0]), range(B.shape[1]), indexing='ij')
out_gauss, out_const = fitter(p, x, y, B, maxiter=10000,
acc=1e-16) # fitter() is defined globally
# retrieves the 6 gaussian parameters
params = {
'amp': out_gauss.amp.value,
'ab': out_gauss.ab.value,
'x0': out_gauss.x0.value,
'y0': out_gauss.y0.value,
'e1': out_gauss.e1.value,
'e2': out_gauss.e2.value
}
# generates a vignette with the model and computes residuals
if reconstruct_model:
rec_model = Gauss2D_stamp(amp=params['amp'],
ab=params['ab'],
e1=params['e1'],
e2=params['e2'],
x0=params['x0'],
y0=params['y0'],
noise=0,
zerolevel=out_const.amplitude,
shape=B.shape)
resi = B - rec_model
return params, rec_model, resi
else:
return params
def models_with_input_eq():
# 1D model
m1 = astmodels.Shift(1*u.kg)
m1.input_units_equivalencies = {'x': u.mass_energy()}
# 2D model
m2 = astmodels.Const2D(10*u.Hz)
m2.input_units_equivalencies = {'x': u.dimensionless_angles(),
'y': u.dimensionless_angles()}
# 2D model with only one input equivalencies
m3 = astmodels.Const2D(10*u.Hz)
m3.input_units_equivalencies = {'x': u.dimensionless_angles()}
# model using equivalency that has args using units
m4 = astmodels.PowerLaw1D(amplitude=1*u.m, x_0=10*u.pix, alpha=7)
m4.input_units_equivalencies = {'x': u.equivalencies.pixel_scale(0.5*u.arcsec/u.pix)}
return[m1, m2, m3, m4]
def FitSersic2D(B, reconstruct_model=False):
'''
Fits a 2D sersic model to a vignette using Levenberg-Marquardt algorithm and least squares statistic.
input:
B: Vignette with the object
reconstruct_model: Boolean flag. Indicates if the reconstructed model and its residuals should be computed
output:
params: Dictionary with the 7 fitted parameters. Keys = ['amp', 'radius', 'sersic_n', 'e1', 'e2', 'x0', 'y0']
*rec_model: Vignette with the fitted model. Only if reconstruct_model=True
*rec_resi: Vignette with the residuals, ie: rec_resi=B-rec_model. Only if reconstruct_model=True
Notes: We fix the position x0,y0 of the model at the center of the stamp. There is no need to fit them
'''
p = model_Sersic2D(amp=B.max()-B.min(), radius=10, sersic_n=4, x0=B.shape[0]/2,y0=B.shape[1]/2,e1=0.1, e2=0.1) + \
models.Const2D(amplitude=B.min())
# Constraints on some parameters
p.x0_0.fixed = True
p.y0_0.fixed = True
x, y = np.meshgrid(range(B.shape[0]), range(B.shape[1]), indexing='ij')
out_sersic, out_const = fitter(p, x, y, B, maxiter=10000,
acc=1e-16) # fitter() is defined globally
# retrieves sersic parameters
params = {
'amp': out_sersic.amp.value,
'sersic_n': out_sersic.sersic_n.value,
'radius': out_sersic.radius.value,
'x0': out_sersic.x0.value,
'y0': out_sersic.y0.value,
'e1': out_sersic.e1.value,
'e2': out_sersic.e2.value
}
# generates a vignette with the model and computes residuals
if reconstruct_model:
rec_model = Sersic2D_stamp(amp=out_sersic.amp,
radius=out_sersic.radius,
sersic_n=out_sersic.sersic_n,
x0=out_sersic.x0,
y0=out_sersic.y0,
e1=out_sersic.e1,
e2=out_sersic.e2,
noise=0,
zerolevel=out_const.amplitude,
shape=B.shape)
resi = B - rec_model
return params, rec_model, resi
else:
return params
def FitMoffat2D(B, reconstruct_model=False):
'''
Fits a 2D moffat model to a vignette using Levenberg-Marquardt algorithm and least squares statistic.
input:
B: Vignette with the object
reconstruct_model: Boolean flag. Indicates if the reconstructed model and its residuals should be computed
output:
params: Dictionary with the 6 fitted parameters. Keys = ['beta', 'fwhm', 'e1', 'e2', 'x0', 'y0']
*rec_model: Vignette with the fitted model. Only if reconstruct_model=True
*rec_resi: Vignette with the residuals, ie: rec_resi=B-rec_model. Only if reconstruct_model=True
Notes: We fix the position x0,y0 of the model at the center of the stamp. There is no need to fit them
'''
p = model_Moffat2D(fwhm=5, beta=1, x0=B.shape[0]/2,y0=B.shape[1]/2,e1=0.1, e2=0.1) + \
models.Const2D(amplitude=B.min())
# Constraints on some parameters
p.x0_0.fixed = True
p.y0_0.fixed = True
x, y = np.meshgrid(range(B.shape[0]), range(B.shape[1]), indexing='ij')
out_moffat, out_const = fitter(p, x, y, B, maxiter=10000,
acc=1e-16) # fitter() is defined globally
# retrieves the 6 moffat parameters
params = {
'beta': out_moffat.beta.value,
'fwhm': out_moffat.fwhm.value,
'x0': out_moffat.x0.value,
'y0': out_moffat.y0.value,
'e1': out_moffat.e1.value,
'e2': out_moffat.e2.value
}
# generates a vignette with the model and computes residuals
if reconstruct_model:
rec_model = Moffat2D_stamp(beta=out_moffat.beta,
fwhm=out_moffat.fwhm,
x0=out_moffat.x0,
y0=out_moffat.y0,
e1=out_moffat.e1,
e2=out_moffat.e2,
noise=0,
zerolevel=out_const.amplitude,
shape=B.shape)
resi = B - rec_model
return params, rec_model, resi
else:
return params
def fit_gaussian2d(b, fitter=None):
if fitter is None:
fitter = fitting.LevMarLSQFitter()
y2, x2 = np.mgrid[:b.shape[0], :b.shape[1]]
ampl = b.max() - b.min()
p = models.Gaussian2D(
x_mean=b.shape[1] / 2.0,
y_mean=b.shape[0] / 2.0,
x_stddev=1.0,
y_stddev=1.0,
theta=np.pi / 4.0,
amplitude=ampl,
)
p += models.Const2D(amplitude=b.min())
out = fitter(p, x2, y2, b, maxiter=1000)
return out
def fitpsf(psf, *center):
fixed = {}
bounds = {}
if not center:
amplitude = psf.max()
y_center, x_center = numpy.unravel_index(psf.argmax(), psf.shape)
fixed['x_mean'] = False
fixed['y_mean'] = False
bounds['x_stddev'] = [0., psf.shape[1]]
bounds['y_stddev'] = [0., psf.shape[0]]
else:
amplitude = psf[center[1], center[0]]
x_center = center[0]
y_center = center[1]
fixed['x_mean'] = True
fixed['y_mean'] = True
bounds['x_stddev'] = [0., psf.shape[1]]
bounds['y_stddev'] = [0., psf.shape[0]]
x_stddev = 3. / 2.35
y_stddev = 3. / 2.35
theta = 0
p_init = models.Gaussian2D(amplitude = amplitude, x_mean = x_center, \
y_mean = y_center, x_stddev = x_stddev, y_stddev = y_stddev, \
theta = theta, fixed = fixed, bounds = bounds)
p_const_init = models.Const2D(amplitude=0.)
fit_p = fitting.LevMarLSQFitter()
gridy, gridx = numpy.mgrid[0:psf.shape[0]:1, 0:psf.shape[1]:1]
p = fit_p(p_init + p_const_init, gridx, gridy, psf, maxiter=200)
if not numpy.any(fit_p.fit_info['param_cov']):
p = None
return p
def fit_plane(image, maxiter=5000, epsilon=1e-10):
model = models.Planar2D(slope_x=0., slope_y=0,
intercept=0) + models.Const2D(0)
# Make x and y grid to fit to
y_arange, x_arange = np.where(~(np.isnan(image)))
z = image[(y_arange, x_arange)]
# Fit model to grid
fit = fitting.LevMarLSQFitter() # fitting.LinearLSQFitter()
fitted_line = fit(model,
x_arange,
y_arange,
z,
maxiter=5000,
epsilon=1e-10)
return fitted_line, fit
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_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 _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 gfit(data,
x0,
y0,
size=5,
fwhm=3,
sub=True,
plot=None,
fig=1,
scale=1,
pafixed=False):
"""
Does gaussian fit to input data given initial xcen,ycen
"""
fit = fitting.LevMarLSQFitter()
#fit=fitting.SLSQPLSQFitter()
z = data[int(y0) - size:int(y0) + size, int(x0) - size:int(x0) + size]
xcen, ycen = np.unravel_index(np.argmax(z), z.shape)
xcen += (int(x0) - size)
ycen += (int(y0) - size)
y, x = np.mgrid[ycen - size:ycen + size, xcen - size:xcen + size]
z = data[ycen - size:ycen + size, xcen - size:xcen + size]
g_init = models.Gaussian2D(x_mean=xcen,
y_mean=ycen,
x_stddev=fwhm / 2.354,
y_stddev=fwhm / 2.354,
amplitude=data[ycen, xcen],
theta=0.,
fixed={'theta': pafixed}) + models.Const2D(0.)
g = fit(g_init, x, y, z)
xfwhm = g[0].x_stddev * 2.354 * scale
yfwhm = g[0].y_stddev * 2.354 * scale
fwhm = np.sqrt(xfwhm * yfwhm)
xcen = g[0].x_mean.value
ycen = g[0].y_mean.value
theta = (g[0].theta.value % (2 * np.pi)) * 180. / np.pi
print(
'xFWHM:{:8.2f} yFWHM:{:8.2f} FWHM:{:8.2f} SCALE:{:8.2f} PA:{:8.2f}'
.format(xfwhm, yfwhm, fwhm, scale, theta))
if plot is not None:
r = np.sqrt((y - ycen)**2 + (x - xcen)**2)
plots.plotp(plot, r, z, xt='R(pixels)', yt='Intensity')
r = np.arange(0., 5 * fwhm / 2.354 / scale, 0.1)
peak = g[0].amplitude
plot.plot(
r,
peak * np.exp(-np.power(r, 2.) /
(2 * np.power(g[0].x_stddev, 2.))) + g[1].amplitude)
plot.plot(
r,
peak * np.exp(-np.power(r, 2.) /
(2 * np.power(g[0].y_stddev, 2.))) + g[1].amplitude)
plot.text(0.9,
0.9,
'x: {:7.1f} y: {:7.1f} fw: {:8.2f}'.format(xcen, ycen, fwhm),
transform=plot.transAxes,
ha='right')
plt.draw()
if sub:
out = data
out[ycen - size:ycen + size, xcen - size:xcen + size] -= g[0](x, y)
return out
return g
def model_plot(model,
image,
amp,
x_wid=5,
y_wid=5,
angle=0,
fignumber=1,
title=None):
cutout_size = np.shape(image)[0]
# Open Fit
y_o, x_o = np.mgrid[:cutout_size, :cutout_size]
z_o = image
if model == "Gaussian":
g2d_model = models.Gaussian2D(np.amax(z_o),
cutout_size / 2,
cutout_size / 2,
x_stddev=x_wid,
y_stddev=y_wid,
theta=angle)
c2d_model = models.Const2D(0.0)
p_init_o = g2d_model + c2d_model
elif model == "Moffat":
g2d_model = Elliptical_Moffat2D(amplitude=np.amax(z_o),
x_0=cutout_size / 2,
y_0=cutout_size / 2,
width_x=x_wid,
width_y=y_wid)
c2d_model = models.Const2D(0.0)
p_init_o = g2d_model + c2d_model
fit_p_o = fitting.LevMarLSQFitter()
# weights = 1.0 / z_o**0.5
# weights = z_o**0.5
# weights = np.ones(z_o.shape, dtype=float)
p_o = fit_p_o(p_init_o,
x_o,
y_o,
z_o,
epsilon=1e-12,
acc=1e-12,
maxiter=300,
weights=None)
# FWHM values?
if model == "Gaussian":
x_fwhm = p_o.x_stddev_0.value / gaussian_fwhm_to_sigma
y_fwhm = p_o.y_stddev_0.value / gaussian_fwhm_to_sigma
elif model == "Moffat":
# BUG this isn't quite right for a moffat fit...
x_fwhm = p_o.width_x_0.value
y_fwhm = p_o.width_y_0.value
#Images
model_img = p_o(x_o, y_o)
diff_img = z_o - model_img
#Images cut:
half_size = image.shape[0] / 2
x_lo = int(round(half_size - x_fwhm))
x_hi = x_lo + int(round(x_fwhm * 2))
y_lo = int(round(half_size - y_fwhm))
y_hi = y_lo + int(round(y_fwhm * 2))
#cut size for metrics
z_o_cut = z_o[y_lo:y_hi, x_lo:x_hi].astype(float)
diff_img_cut = diff_img[y_lo:y_hi, x_lo:x_hi].astype(float)
# Fit metrics
residual_o = np.sum(diff_img_cut**2)
PSF_mean = np.mean(z_o_cut)
fresid = np.median(np.abs(diff_img_cut /
z_o_cut)) # mean fractional residual
FVU = np.sum(diff_img**2) / np.sum(
(z_o_cut - PSF_mean)**2) # fraction of variance unexplained
# Plotting
plt.figure(fignumber, figsize=(12, 3))
plt.suptitle(title)
vmin = z_o.min()
vmax = z_o.max()
# left panel
plt.subplot(1, 4, 1)
plt.imshow(z_o, origin='lower', vmin=vmin, vmax=vmax)
plt.gca().add_patch(
Rectangle((x_lo, y_lo),
x_hi - x_lo,
y_hi - y_lo,
edgecolor='red',
facecolor='none',
lw=2))
plt.colorbar(fraction=0.046, pad=0.05)
plt.title("Data")
# left middle panel
plt.subplot(1, 4, 2)
plt.imshow(model_img, origin='lower', vmin=vmin, vmax=vmax)
plt.gca().add_patch(
Rectangle((x_lo, y_lo),
x_hi - x_lo,
y_hi - y_lo,
edgecolor='red',
facecolor='none',
lw=2))
plt.colorbar(fraction=0.046, pad=0.04)
plt.title("Model")
# right middle panel
plt.subplot(1, 4, 3)
plt.imshow(z_o - model_img, origin='lower', vmin=-vmax / 6, vmax=vmax / 6)
plt.gca().add_patch(
Rectangle((x_lo, y_lo),
x_hi - x_lo,
y_hi - y_lo,
edgecolor='red',
facecolor='none',
lw=1))
plt.colorbar(fraction=0.046, pad=0.04)
plt.title("Data-Model")
# right panel
plt.subplot(1, 4, 4)
plt.imshow((z_o - model_img) / z_o, origin='lower', vmax=1, vmin=-1)
plt.gca().add_patch(
Rectangle((x_lo, y_lo),
x_hi - x_lo,
y_hi - y_lo,
edgecolor='red',
facecolor='none',
lw=1))
plt.colorbar(fraction=0.046, pad=0.04)
plt.title("Fract. Resid.")
plt.tight_layout()
print("Residuals Squared Summed - ", title, ": ",
'{:.2e}'.format(residual_o))
print("Fraction of Variance Unexplained (FVU) - ", title, ": ",
'{:.2e}'.format(FVU))
print("Median Fractional Residual Per Pix - ", title, ": ",
'{:.2e}'.format(fresid))
if model == "Moffat":
print("beta: ", p_o.power_0.value)
print('\nFit Info:')
print('nfev = ', fit_p_o.fit_info['nfev'])
print('ierr = ', fit_p_o.fit_info['ierr'])
print('mesg = ', fit_p_o.fit_info['message'])
print('\nParams:')
for k, v in p_o._parameters_.items():
val = v.value
unit = 'pix'
if 'phi' in k:
val = val % 360.0
unit = 'deg'
if 'theta' in k:
val = np.rad2deg(val) % 360.0
unit = 'deg'
if 'amp' in k:
unit = 'flux'
print(f'{k:15s} = {val:10.6f} {unit:5s}')
print('\n')
return p_o
def find_source(im, guesspos=None, searchbox=None, fitbox=None,
guessmeth='max', smooth=0, searchsmooth=3,
guessFWHM=None, guessamp=None, guessbg=None,
method='fast', sign=1, verbose=False, fixFWHM=False,
fixpos=False, minamp=0.01, maxamp=None, plot=False,
maxFWHM=None, minFWHM=None, posradius=None, silent=False):
"""
find the point source in an image and provide its best fit parameters from
a Gaussian fit
Parameters:
- im: image to be searched
- guesspos: 2D array with the (y, x) guessed position for the point
source position. If None, use the middle of the whole image
- searchbox: int or 2D array with (y, x) size, size of box to be
searched centered on the guesspos. If None, search the
whole image
- fitbox: int or 2D array with (y, x) size, size of box used for the
fit. If None, use searchbox
- guessmeth: method for guesstimating the point source position
(currently only 'max' and other). For 'max' use the
maximum brightness pixel in the searchbox. Other: use
centre of the searchbox
- smooth: optional smoothing with a Gaussian. The value specifies the
width of the Gaussian used for the smoothing
- searchsmooth: optional smoothing only for guesstimating source
position
- guessFWHM: guess for the FWHM of the source. If None, use middle
between minFWHM and maxFWHM or 5 if the former are not
provided
- guessamp: guess for the amplitude of the source. If None, use the
pixel brightness at the guess position
- guessbg: guess for the background level in the image. If None, use
the median of the image.
- method: method used for the fitting: 'fast': use LevMarLSQFitter
from astropy, 'mpfit': use the MPFIT package
- sign: sign of the point source to be searched
- fixFWHM: fix the FWHM of the source to the guess value
- fixpos: fix the position of the source to the guess value
- minamp, maxamp: minimum and maximum allowed values for the amplitude
of the source
- minFWHM, maxFWHM: minimum and maximum allowed values for the FWHM
of the source
- posradius: maximum allowed radius in pix around the guess position
for the source location. If None, the whole searchbox is
allowed
"""
funname = "FIND_SOURCE"
s2f = (2.0 * np.sqrt(2.0*np.log(2.0)))
f2s = 1.0/s2f
s = np.shape(im)
if sign < 0:
im = -im
if smooth > 0:
im = gaussian_filter(im, sigma=smooth)
if guesspos is None :
guesspos = 0.5*np.array(s)
if verbose:
print(funname + ": method: ", method)
print(funname + ": s: ", s)
print(funname + ": sign: ", sign)
print(funname + ": searchsmooth: ", searchsmooth)
print(funname + ": guessmeth: ", guessmeth)
print(funname + ": initial guessamp: ", guessamp)
print(funname + ": initial guessbg: ", guessbg)
print(funname + ": intial guesspos: ", guesspos)
print(funname + ": intial searchbox: ", searchbox)
# --- define the search box
if searchbox is not None :
# test if the box provided is an integer, in which case blow up to array
if not hasattr(searchbox, "__len__"):
searchbox = np.array([searchbox, searchbox])
searchbox = np.array(searchbox, dtype=int)
sx0 = np.max([0, int(np.round(guesspos[1] - 0.5 * searchbox[1]))])
sx1 = np.min([s[1], int(np.round(guesspos[1] + 0.5 * searchbox[1]))])
sy0 = np.max([0, int(np.round(guesspos[0] - 0.5 * searchbox[0]))])
sy1 = np.min([s[0], int(np.round(guesspos[0] + 0.5 * searchbox[0]))])
searchim = im[sy0:sy1, sx0:sx1]
if verbose:
print(funname + ": sy0, sy1, sx0, sx1 ", sy0, sy1, sx0, sx1)
searchbox = np.array(np.shape(searchim))
# print(funname + ": ss: ", np.shape(searchim))
else:
searchbox = np.array(s, dtype=int)
sx0 = 0
sy0 = 0
searchim = im
if verbose:
print(funname + ": final searchbox: ", searchbox)
# --- should the first guess be based on the max or on the position?
if guessmeth == 'max':
if searchsmooth > 0:
# smoothing is quick and thus on by default
ssim = gaussian_filter(searchim, sigma=searchsmooth,
mode='nearest')
guesspos = np.array(np.unravel_index(np.nanargmax(ssim),
searchbox))
if plot is True:
plt.figure(1, figsize=(3,3))
plt.imshow(ssim, origin='bottom', interpolation='nearest')
plt.title('Smoothed Search image')
plt.show()
# print(funname + ": guesspos: ", guesspos)
else:
guesspos = np.array(np.unravel_index(np.nanargmax(searchim),
searchbox))
else:
guesspos = 0.5*searchbox
if verbose:
print(funname + ": guesspos in searchbox: ", guesspos)
print(funname + ": guesspos in total image: ", guesspos[0] + sy0, guesspos[1] + sx0)
# print(funname + ": guesspos: ", guesspos)
guesspos = np.array([guesspos[0] + sy0, guesspos[1] + sx0])
if plot is True:
plt.clf()
plt.close(1)
plt.figure(1, figsize=(3,3))
plt.imshow(searchim, origin='bottom', interpolation='nearest')
plt.title('Search image')
plt.show()
if verbose:
print(funname + ": intial fitbox: ", fitbox)
# --- define the fit box
if fitbox is not None:
# test if the box provided is an integer, in which case blow up to array
if not hasattr(fitbox, "__len__"):
fitbox = np.array([fitbox, fitbox])
fitbox = np.array(fitbox, dtype=int)
fx0 = int(np.round(guesspos[1] - 0.5 * fitbox[1]))
fx1 = int(np.round(guesspos[1] + 0.5 * fitbox[1]))
fy0 = int(np.round(guesspos[0] - 0.5 * fitbox[0]))
fy1 = int(np.round(guesspos[0] + 0.5 * fitbox[0]))
guesspos = 0.5*fitbox
# print('guesspos, fx0, fx1, fy0, fy1 ', guesspos, fx0, fx1, fy0, fy1)
# for the new guess position, we have to take into account if the
# fitbox is smaller than expected because being close to the edge
if fx0 < 0:
guesspos[1] = guesspos[1] + fx0
fx0 = 0
# if fx1 > s[1]:
# guesspos[1] = guesspos[1] - (fx1 - s[1])
# fx1 = s[1]
if fy0 < 0:
guesspos[0] = guesspos[0] + fy0
fy0 = 0
# if fy1 > s[0]:
# guesspos[0] = guesspos[0] - (fy1 - s[0])
# fy1 = s[0]
fitim = im[fy0:fy1, fx0:fx1]
fs = np.array(np.shape(fitim))
else:
fitim = im
fx0 = 0
fy0 = 0
fs = np.shape(fitim)
fitbox = fs
if verbose:
print(funname + ": final fitbox: ", fitbox)
print(funname + ": final guesspos in fitbox: ", guesspos)
if plot is True:
plt.figure(1, figsize=(3,3))
plt.imshow(fitim, origin='bottom', interpolation='nearest')
plt.title('(Sub)image to be fitted')
plt.show()
if guessFWHM is None:
if maxFWHM is not None and minFWHM is not None:
guessFWHM = 0.5 * (maxFWHM + minFWHM)
elif maxFWHM is not None:
guessFWHM = 0.5 * maxFWHM
elif minFWHM is not None:
guessFWHM = 2 * minFWHM
else:
guessFWHM = 5
# --- estimate the BG with ignoring central source (use either 3*FWHM or
# 80% of image whatever is smaller). First generate a background image
# of sufficient size
bgbox = int(np.round(6*guessFWHM))
if verbose:
print('bgbox:', bgbox)
print("bgcenpos: ", [fy0 + 0.5*fitbox[0], fx0 + 0.5*fitbox[1]])
bgim = _crop_image(im, box=bgbox,
cenpos=[fy0 + 0.5*fitbox[0], fx0 + 0.5*fitbox[1]],
exact=False)
ignore_aper = np.min([3*guessFWHM, 0.8*np.max(s)])
bgval, bgstd = _measure_bkg(bgim, ignore_aper=ignore_aper)
if guessbg is None:
guessbg = bgval
if guessamp is None:
guessamp = fitim[int(guesspos[0]), int(guesspos[1])] - guessbg
if maxFWHM is None:
maxFWHM = np.max(s)
if minFWHM is None:
minFWHM = 1
maxsigma = maxFWHM * f2s
minsigma = minFWHM * f2s
if posradius is not None:
minx = guesspos[1] - posradius
maxx = guesspos[1] + posradius
miny = guesspos[0] - posradius
maxy = guesspos[0] + posradius
else:
minx = 0
maxx = fs[1]
miny = 0
maxy = fs[0]
sigma = guessFWHM * f2s
guess = [guessbg, guessamp , guesspos[1],
guesspos[0], sigma, sigma, 0]
if verbose:
print(' - Guess: ', guess)
print(' - minFWHM: ', minFWHM)
print(' - maxFWHM: ', maxFWHM)
print(' - minsigma: ', minsigma)
print(' - maxsigma: ', maxsigma)
print(' - minamp: ', minamp)
print(' - maxamp: ', maxamp)
print(' - minx,maxx, miny,maxy: ', minx, maxx, miny, maxy)
y, x = np.mgrid[:fs[0], :fs[1]]
g_init = models.Gaussian2D(amplitude=guessamp, x_mean=guesspos[1],
y_mean=guesspos[0], x_stddev=sigma,
y_stddev=sigma)
c_init = models.Const2D(amplitude=guessbg)
init = g_init + c_init
gim = init(x, y)
if plot is True:
plt.figure(1, figsize=(3,3))
plt.imshow(gim, origin='bottom', interpolation='nearest')
plt.title('Guess')
plt.show()
if np.isnan(fitim).any():
if not silent:
print(funname + ": WARNING: image to be cropped contains NaNs!")
fitim[np.isnan(fitim)] = guessbg # set any NaNs to 0 for crop to work
if ('mpfit' in method) :
# params=[] - initial input parameters for Gaussian function.
# (height, amplitude, x, y, width_x, width_y, rota)
# parameter limits
minpars = [0, minamp, minx, miny, minsigma, minsigma, 0]
maxpars = [0, maxamp, maxx, maxy, maxsigma, maxsigma, 0]
limitedmin = [False, True, True, True, True, True, False]
limitedmax = [False, False, True, True, True, True, False]
# ensure that the fit is positive if the sign is 1
# (or negative if the sign is -1)
if minamp is None:
limitedmin[1] = False
if maxamp:
limitedmax[1] = True
if fixFWHM:
limitedmin[4] = True
limitedmax[4] = True
minpars[4] = sigma-0.001
maxpars[4] = sigma+0.001
limitedmin[5] = True
limitedmax[5] = True
minpars[5] = sigma-0.001
maxpars[5] = sigma+0.001
if fixpos:
limitedmin[2] = True
limitedmax[2] = True
minpars[2] = guesspos[1]-0.001
maxpars[2] = guesspos[1]+0.001
limitedmin[3] = True
limitedmax[3] = True
minpars[3] = guesspos[0]-0.001
maxpars[3] = guesspos[0]+0.001
res = _gaussfit(fitim, err=None, params=guess, returnfitimage=True,
return_all=1, minpars=minpars, maxpars=maxpars,
limitedmin=limitedmin, limitedmax=limitedmax)
params = res[0][0]
perrs = res[0][1]
if perrs is None:
perrs = np.full(6,-1, dtype=float)
fit = res[1]
elif 'fast' in method:
# ensure that the fit is positive
init.amplitude_0.bounds = (minamp, maxamp)
init.x_mean_0.bounds = (minx, maxx)
init.y_mean_0.bounds = (miny, maxy)
init.x_stddev_0.bounds = (minsigma, maxsigma)
# --- ensure that angle stays in useful pounds
#init.theta_0.bounds = (-2*np.pi, 2*np.pi) # somehow fixing the angle does not work
if fixFWHM:
init.x_stddev_0.fixed = True
init.y_stddev_0.fixed = True
if fixpos:
init.x_mean_0.fixed = True
init.y_mean_0.fixed = True
fit_meth = fitting.LevMarLSQFitter()
# fit_meth = fitting.SimplexLSQFitter() # very slow
# fit_meth = fitting.SLSQPLSQFitter() # not faster than LevMar
g_fit = fit_meth(init, x, y, fitim, acc=1e-8)
fit = g_fit(x, y)
params = np.array([g_fit.amplitude_1.value, g_fit.amplitude_0.value,
g_fit.x_mean_0.value, g_fit.y_mean_0.value,
g_fit.x_stddev_0.value, g_fit.y_stddev_0.value,
g_fit.theta_0.value])
perrs = params * 0 # this method does not provide uncertainty estimates
# --- convert theta to deg:
params[6] = params[6]/np.pi*180.0
# --- theta measures the angle from the x-axis, so we need to add 90
params[6] = params[6] + 90.0
# print(init.x_stddev_0.fixed, init.x_stddev_0.bounds)
# print(g_fit.x_stddev_0.fixed, g_fit.x_stddev_0.bounds)
else:
print(funname + ": ERROR: non-valid method requested: " + method
+"\n returning None")
return(None, None, None)
# --- use the STD of the BG for the BG level uncertainty if larger than
# error estimate
if bgstd > perrs[0]:
perrs[0] = bgstd
if verbose:
print(funname + ": uncorrected fit params: ", params)
print(funname + ": uncorrected fit errs: ", perrs)
# --- compute the position in the total image and switch x and y to agree
# with the numpy convention
temp = np.copy(params)
params[2] = temp[3] + fy0
params[3] = temp[2] + fx0
temp = np.copy(perrs)
perrs[2] = temp[3]
perrs[3] = temp[2]
# --- if the y FWHM is larger than the one in x direction, switch them so
# that the first FWHM is the major axis one.
if params[5] > params[4]:
temp = params[4]
params[4] = params[5]
params[5] = temp
temp = perrs[4]
perrs[4] = perrs[5]
perrs[5] = temp
params[6] = params[6] + 90.0
# --- normalise the angle
params[6] = params[6] % 180
if params[6] < 0:
params[6] = params[6] + 180
#
if sign < 0:
params[0] = - params[0]
params[1] = - params[1]
fit = - fit
fitim = - fitim
if verbose:
print(" - GET_POINTSOURCE: fitted params: ", params)
# convert sigma to FWHM for the output:
params[4:6] = params[4:6] * s2f
if plot is True:
plt.figure(1, figsize=(3,3))
plt.imshow(fit, origin='bottom', interpolation='nearest')
plt.title('Fit with sign')
plt.show()
plt.close(1)
plt.figure(1, figsize=(3,3))
plt.imshow(fitim-fit, origin='bottom', interpolation='nearest')
plt.title('Residual')
plt.show()
plt.close(1)
ims = [fitim, fit, fitim-fit]
return(params, perrs, ims)
astmodels.Multiply(3),
astmodels.Multiply(10 * u.m),
astmodels.RotateCelestial2Native(5.63, -72.5, 180),
astmodels.EulerAngleRotation(23, 14, 2.3, axes_order='xzx'),
astmodels.Mapping((0, 1), n_inputs=3),
astmodels.Shift(2. * u.deg),
astmodels.Scale(3.4 * u.deg),
astmodels.RotateNative2Celestial(5.63 * u.deg, -72.5 * u.deg, 180 * u.deg),
astmodels.RotateCelestial2Native(5.63 * u.deg, -72.5 * u.deg, 180 * u.deg),
astmodels.RotationSequence3D([1.2, 2.3, 3.4, .3], 'xyzx'),
astmodels.SphericalRotationSequence([1.2, 2.3, 3.4, .3], 'xyzy'),
astmodels.AiryDisk2D(amplitude=10., x_0=0.5, y_0=1.5),
astmodels.Box1D(amplitude=10., x_0=0.5, width=5.),
astmodels.Box2D(amplitude=10., x_0=0.5, x_width=5., y_0=1.5, y_width=7.),
astmodels.Const1D(amplitude=5.),
astmodels.Const2D(amplitude=5.),
astmodels.Disk2D(amplitude=10., x_0=0.5, y_0=1.5, R_0=5.),
astmodels.Ellipse2D(amplitude=10., x_0=0.5, y_0=1.5, a=2., b=4.,
theta=0.1),
astmodels.Exponential1D(amplitude=10., tau=3.5),
astmodels.Gaussian1D(amplitude=10., mean=5., stddev=3.),
astmodels.Gaussian2D(amplitude=10.,
x_mean=5.,
y_mean=5.,
x_stddev=3.,
y_stddev=3.),
astmodels.KingProjectedAnalytic1D(amplitude=10., r_core=5., r_tide=2.),
astmodels.Logarithmic1D(amplitude=10., tau=3.5),
astmodels.Lorentz1D(amplitude=10., x_0=0.5, fwhm=2.5),
astmodels.Moffat1D(amplitude=10., x_0=0.5, gamma=1.2, alpha=2.5),
astmodels.Moffat2D(amplitude=10., x_0=0.5, y_0=1.5, gamma=1.2, alpha=2.5),
def star_centers_from_waffle_cube(cube,
wave,
instrument,
waffle_orientation,
high_pass=False,
center_offset=(0, 0),
smooth=0,
coro=True,
display=False,
save_path=None):
'''
Compute star center from waffle images
Parameters
----------
cube : array_like
Waffle IRDIS cube
wave : array_like
Wavelength values, in nanometers
instrument : str
Instrument, IFS or IRDIS
waffle_orientation : str
String giving the waffle orientation '+' or 'x'
high_pass : bool
Apply high-pass filter to the image before searching for the
satelitte spots
smooth : int
Apply a gaussian smoothing to the images to reduce noise. The
value is the sigma of the gaussian in pixel. Default is no
smoothing
center_offset : tuple
Apply an (x,y) offset to the default center position. Default is no offset
coro : bool
Observation was performed with a coronagraph. Default is True
display : bool
Display the fit of the satelitte spots
save_path : str
Path where to save the fit images
Returns
-------
spot_center : array_like
Centers of each individual spot in each frame of the cube
spot_dist : array_like
The 6 possible distances between the different spots
img_center : array_like
The star center in each frame of the cube
'''
# instrument
if instrument == 'IFS':
pixel = 7.46
offset = 102
elif instrument == 'IRDIS':
pixel = 12.25
offset = 0
else:
raise ValueError('Unknown instrument {0}'.format(instrument))
# standard parameters
dim = cube.shape[-1]
nwave = wave.size
loD = wave * 1e-6 / 8 * 180 / np.pi * 3600 * 1000 / pixel
# waffle parameters
freq = 10 * np.sqrt(2) * 0.97
box = 8
if waffle_orientation == '+':
orient = offset * np.pi / 180
elif waffle_orientation == 'x':
orient = offset * np.pi / 180 + np.pi / 4
# spot fitting
xx, yy = np.meshgrid(np.arange(2 * box), np.arange(2 * box))
# multi-page PDF to save result
if save_path is not None:
pdf = PdfPages(save_path)
# center guess
if instrument == 'IFS':
center_guess = np.full((nwave, 2), ((dim // 2) + 3, (dim // 2) - 1))
elif instrument == 'IRDIS':
center_guess = np.array(((485, 520), (486, 508)))
# loop over images
spot_center = np.zeros((nwave, 4, 2))
spot_dist = np.zeros((nwave, 6))
img_center = np.zeros((nwave, 2))
for idx, (wave, img) in enumerate(zip(wave, cube)):
print(' wave {0:2d}/{1:2d} ({2:.3f} micron)'.format(
idx + 1, nwave, wave))
# remove any NaN
img = np.nan_to_num(img)
# center guess (+offset)
cx_int = int(center_guess[idx, 0]) + center_offset[0]
cy_int = int(center_guess[idx, 1]) + center_offset[1]
# optional high-pass filter
if high_pass:
img = img - ndimage.median_filter(img, 15, mode='mirror')
# optional smoothing
if smooth > 0:
img = ndimage.gaussian_filter(img, smooth)
# mask for non-coronagraphic observations
if not coro:
mask = aperture.disc(cube[0].shape[-1],
5 * loD[idx],
diameter=False,
center=(cx_int, cy_int),
invert=True)
img *= mask
# create plot if needed
if save_path or display:
fig = plt.figure(0, figsize=(8, 8))
plt.clf()
col = ['red', 'blue', 'magenta', 'purple']
ax = fig.add_subplot(111)
ax.imshow(img / img.max(),
aspect='equal',
vmin=1e-2,
vmax=1,
norm=colors.LogNorm(),
interpolation='nearest')
ax.set_title(r'Image #{0} - {1:.3f} $\mu$m'.format(idx + 1, wave))
# satelitte spots
for s in range(4):
cx = int(cx_int + freq * loD[idx] * np.cos(orient + np.pi / 2 * s))
cy = int(cy_int + freq * loD[idx] * np.sin(orient + np.pi / 2 * s))
sub = img[cy - box:cy + box, cx - box:cx + box]
# fit: Gaussian + constant
imax = np.unravel_index(np.argmax(sub), sub.shape)
g_init = models.Gaussian2D(amplitude=sub.max(), x_mean=imax[1], y_mean=imax[0],
x_stddev=loD[idx], y_stddev=loD[idx]) + \
models.Const2D(amplitude=sub.min())
fitter = fitting.LevMarLSQFitter()
par = fitter(g_init, xx, yy, sub)
fit = par(xx, yy)
cx_final = cx - box + par[0].x_mean
cy_final = cy - box + par[0].y_mean
spot_center[idx, s, 0] = cx_final
spot_center[idx, s, 1] = cy_final
# plot sattelite spots and fit
if save_path or display:
ax.plot([cx_final], [cy_final], marker='D', color=col[s])
ax.add_patch(
patches.Rectangle((cx - box, cy - box),
2 * box,
2 * box,
ec='white',
fc='none'))
axs = fig.add_axes((0.17 + s * 0.2, 0.17, 0.1, 0.1))
axs.imshow(sub,
aspect='equal',
vmin=0,
vmax=sub.max(),
interpolation='nearest')
axs.plot([par[0].x_mean], [par[0].y_mean],
marker='D',
color=col[s])
axs.set_xticks([])
axs.set_yticks([])
axs = fig.add_axes((0.17 + s * 0.2, 0.06, 0.1, 0.1))
axs.imshow(fit,
aspect='equal',
vmin=0,
vmax=sub.max(),
interpolation='nearest')
axs.set_xticks([])
axs.set_yticks([])
# lines intersection
intersect = lines_intersect(spot_center[idx, 0, :], spot_center[idx,
2, :],
spot_center[idx, 1, :], spot_center[idx,
3, :])
img_center[idx] = intersect
# scaling
spot_dist[idx, 0] = np.sqrt(
np.sum((spot_center[idx, 0, :] - spot_center[idx, 2, :])**2))
spot_dist[idx, 1] = np.sqrt(
np.sum((spot_center[idx, 1, :] - spot_center[idx, 3, :])**2))
spot_dist[idx, 2] = np.sqrt(
np.sum((spot_center[idx, 0, :] - spot_center[idx, 1, :])**2))
spot_dist[idx, 3] = np.sqrt(
np.sum((spot_center[idx, 0, :] - spot_center[idx, 3, :])**2))
spot_dist[idx, 4] = np.sqrt(
np.sum((spot_center[idx, 1, :] - spot_center[idx, 2, :])**2))
spot_dist[idx, 5] = np.sqrt(
np.sum((spot_center[idx, 2, :] - spot_center[idx, 3, :])**2))
# finalize plot
if save_path or display:
ax.plot([spot_center[idx, 0, 0], spot_center[idx, 2, 0]],
[spot_center[idx, 0, 1], spot_center[idx, 2, 1]],
color='w',
linestyle='dashed')
ax.plot([spot_center[idx, 1, 0], spot_center[idx, 3, 0]],
[spot_center[idx, 1, 1], spot_center[idx, 3, 1]],
color='w',
linestyle='dashed')
ax.plot([intersect[0]], [intersect[1]],
marker='+',
color='w',
ms=15)
ext = 1000 / pixel
ax.set_xlim(intersect[0] - ext, intersect[0] + ext)
ax.set_ylim(intersect[1] - ext, intersect[1] + ext)
plt.tight_layout()
if save_path:
pdf.savefig()
if display:
plt.pause(1e-3)
if save_path:
pdf.close()
return spot_center, spot_dist, img_center
def iraf_style_photometry(phot_apertures,
bg_apertures,
data,
dark_std_data,
header,
seeing,
bg_method='mean',
epadu=1.0,
gain=8.21,
non_linear_threshold=4000):
"""Computes photometry with PhotUtils apertures, with IRAF formulae
Parameters
----------
phot_apertures : photutils PixelAperture object (or subclass)
The PhotUtils apertures object to compute the photometry.
i.e. the object returned via CircularAperture.
bg_apertures : photutils PixelAperture object (or subclass)
The phoutils aperture object to measure the background in.
i.e. the object returned via CircularAnnulus.
data : array
The data for the image to be measured.
bg_method: {'mean', 'median', 'mode'}, optional
The statistic used to calculate the background.
All measurements are sigma clipped.
NOTE: From DAOPHOT, mode = 3 * median - 2 * mean.
epadu: float, optional
Gain in electrons per adu (only use if image units aren't e-).
Returns
-------
final_tbl : astropy.table.Table
An astropy Table with the colums X, Y, flux, flux_error, mag,
and mag_err measurements for each of the sources.
"""
exptime = header['EXPTIME']
if bg_method not in ['mean', 'median', 'mode']:
raise ValueError(
'Invalid background method, choose either mean, median, or mode')
#Create a list to hold the flux for each source.
aperture_sum = []
interpolation_flags = np.zeros(len(phot_apertures.positions), dtype='bool')
for i in range(len(phot_apertures.positions)):
pos = phot_apertures.positions[i]
#Cutout around the source position
cutout_w = 15
x_pos = pos[0]
y_pos = pos[1]
cutout = data[int((y_pos - cutout_w)):int(y_pos + cutout_w) + 1,
int(x_pos - cutout_w):int(x_pos + cutout_w) + 1]
x_cutout = x_pos - np.floor(x_pos - cutout_w)
y_cutout = y_pos - np.floor(y_pos - cutout_w)
ap = CircularAperture((x_cutout, y_cutout), r=phot_apertures.r)
#Cut out the pixels JUST inside the aperture, and check if there are NaNs there. If so, interpolate over NaNs in the cutout.
ap_mask = ap.to_mask(method='exact')
ap_cut = ap_mask.cutout(cutout)
non_linear_sum = np.sum(ap_cut / gain > non_linear_threshold)
# if non_linear_sum > 0:
# print('Pixels in the non-linear range!')
# breakpoint()
bad_sum = np.sum(np.isnan(ap_cut))
if bad_sum > 0:
bads = np.where(np.isnan(cutout))
bad_dists = np.sqrt((bads[0] - y_cutout)**2 +
(bads[1] - x_cutout)**2)
#Check if any bad pixels fall within the aperture. If so, set the interpolation flag to True for this source.
if np.sum(bad_dists < phot_apertures.r + 1):
# if np.sum(bad_dists < 1) == 0:
# #ONLY interpolate if bad pixels lay away from centroid position by at least a pixel.
# #2D gaussian fitting approach
# #Set up a 2D Gaussian model to interpolate the bad pixel values in the cutout.
# model_init = models.Const2D(amplitude=np.nanmedian(cutout))+models.Gaussian2D(amplitude=np.nanmax(cutout), x_mean=x_cutout, y_mean=y_cutout, x_stddev=seeing, y_stddev=seeing)
# xx, yy = np.indices(cutout.shape) #2D grids of x and y coordinates
# mask = ~np.isnan(cutout) #Find locations where the cutout has *good* values (i.e. not NaNs).
# x = xx[mask] #Only use coordinates at these good values.
# y = yy[mask]
# cutout_1d = cutout[mask] #Make a 1D cutout using only the good values.
# fitter = fitting.LevMarLSQFitter()
# model_fit = fitter(model_init, x, y, cutout_1d) #Fit the model to the 1d cutout.
# cutout[~mask] = model_fit(xx,yy)[~mask] #Interpolate the pixels in the cutout using the 2D Gaussian fit.
# pdb.set_trace()
# #TODO: interpolate_replace_nans with 2DGaussianKernel probably gives better estimation of *background* pixels.
# else:
# interpolation_flags[i] = True
#2D gaussian fitting approach
#Set up a 2D Gaussian model to interpolate the bad pixel values in the cutout.
model_init = models.Const2D(
amplitude=np.nanmedian(cutout)) + models.Gaussian2D(
amplitude=np.nanmax(cutout),
x_mean=x_cutout,
y_mean=y_cutout,
x_stddev=seeing,
y_stddev=seeing)
xx, yy = np.indices(
cutout.shape) #2D grids of x and y coordinates
mask = ~np.isnan(
cutout
) #Find locations where the cutout has *good* values (i.e. not NaNs).
x = xx[mask] #Only use coordinates at these good values.
y = yy[mask]
cutout_1d = cutout[
mask] #Make a 1D cutout using only the good values.
fitter = fitting.LevMarLSQFitter()
model_fit = fitter(model_init, x, y,
cutout_1d) #Fit the model to the 1d cutout.
# #Uncomment this block to show inerpolation plots.
# norm = ImageNormalize(cutout, interval=ZScaleInterval())
# plt.ion()
# fig, ax = plt.subplots(1, 4, figsize=(10,4), sharex=True, sharey=True)
# ax[0].imshow(cutout, origin='lower', norm=norm)
# ax[0].set_title('Data')
# ax[1].imshow(model_fit(xx,yy), origin='lower', norm=norm)
# ax[1].set_title('2D Gaussian Model')
cutout[~mask] = model_fit(
xx, yy
)[~mask] #Interpolate the pixels in the cutout using the 2D Gaussian fit.
# ax[2].imshow(cutout, origin='lower', norm=norm)
# ax[2].set_title('Data w/ Bad\nPixels Replaced')
# ax[3].imshow(cutout-model_fit(xx,yy), origin='lower')
# ax[3].set_title('Residuals')
# pdb.set_trace()
interpolation_flags[i] = True
# #Gaussian convolution approach.
# cutout = interpolate_replace_nans(cutout, kernel=Gaussian2DKernel(x_stddev=0.5))
phot_source = aperture_photometry(cutout, ap)
# if np.isnan(phot_source['aperture_sum'][0]):
# pdb.set_trace()
aperture_sum.append(phot_source['aperture_sum'][0])
#Add positions/fluxes to a table
xcenter = phot_apertures.positions[:, 0] * u.pix
ycenter = phot_apertures.positions[:, 1] * u.pix
phot = QTable([xcenter, ycenter, aperture_sum],
names=('xcenter', 'ycenter', 'aperture_sum'))
#Now measure the background around each source.
mask = make_source_mask(
data, nsigma=3, npixels=5, dilate_size=7
) #Make a mask to block out any sources that might show up in the annuli and bias them.
bg_phot = aperture_stats_tbl(
~mask * data, bg_apertures, sigma_clip=True
) #Pass the data with sources masked out to the bg calculator.
ap_area = phot_apertures.area
bg_method_name = 'aperture_{}'.format(bg_method)
background = bg_phot[bg_method_name]
flux = phot['aperture_sum'] - background * ap_area
# Need to use variance of the sources for Poisson noise term in error computation.
flux_error = compute_phot_error(flux, bg_phot, bg_method, ap_area, exptime,
dark_std_data, phot_apertures, epadu)
mag = -2.5 * np.log10(flux)
mag_err = 1.0857 * flux_error / flux
# Make the final table
X, Y = phot_apertures.positions.T
stacked = np.stack([
X, Y, flux, flux_error, mag, mag_err, background, interpolation_flags
],
axis=1)
names = [
'X', 'Y', 'flux', 'flux_error', 'mag', 'mag_error', 'background',
'interpolation_flag'
]
final_tbl = Table(data=stacked, names=names)
#Check for nans
if sum(np.isnan(final_tbl['flux'])) > 0:
bad_locs = np.where(np.isnan(final_tbl['flux']))[0]
#pdb.set_trace()
return final_tbl
def simulate_image(psffits=None,
theofits=None,
obsfits=None,
distance=None,
extfits=None,
wlen=None,
pfov=None,
filt=None,
psfext=0,
obsext=0,
bgstd=0,
bgmed=0,
silent=False,
posang=0,
foi_as=4,
outname=None,
manscale=None,
fnucdiam_as=0.45,
suffix=None,
fitsize=None,
outfolder='.',
writesimfits=False,
writetheofits=False,
writeallfits=False,
writefitplot=False,
debug=False,
returncmod=True,
fitpsf=False,
saveplot=False,
meastime=False):
"""
Simulate a (VISIR) imaging observaion given a real image, a PSF reference
image and a model image for a provided object distance and position angle
Current constraints:
- The routine assumes that the images are squares (x = y)
"""
if meastime:
tstart = time.time()
psfim = fits.getdata(psffits, ext=psfext)
psfhead = fits.getheader(psffits)
# print(obsfits, obsext)
# ==== 1. Load Observational and PSF data ====
if obsfits is not None:
obsim = fits.getdata(obsfits, ext=obsext)
obshead = fits.getheader(obsfits)
if wlen is None:
wlen = float(obshead['WAVELEN'])
if pfov is None:
pfov = obshead['PFOV']
if filt is None:
filt = obshead['Filter']
else:
if wlen is None:
wlen = float(psfhead['WAVELEN'])
if pfov is None:
pfov = psfhead['PFOV']
if filt is None:
filt = psfhead['Filter']
wlenstr = "{:.1f}".format(wlen)
diststr = "{:.1f}".format(distance)
pastr = "{:.0f}".format(posang)
# --- optinal cropping of the PSF image
if fitsize is not None:
psfim = _crop_image(psfim,
box=fitsize,
cenpos=_get_pointsource(psfim)[0][2:4])
psfsize = np.array(np.shape(psfim))
psfsize_as = psfsize[0] * pfov
if not silent:
print("Obs. wavelength [um]: " + wlenstr)
# ==== 2. Prepare theoretical image for convolution ====
theohdu = fits.open(theofits)
theohead = theohdu[0].header
# --- check if provided file is the full cube
if 'NAXIS3' in theohead:
# find the right frame to be extracted
mind, mwlen = find_wlen_match(theofits, wlen)
theoim = theohdu[0].data[mind]
if not silent:
print(" - Model wavelength [um] | frame no: " + str(mwlen) +
" | " + str(mind))
else:
theoim = theohdu[0].data
theohdu.close()
if meastime:
print(" - All files read. Elapsed time: ", time.time() - tstart)
if debug is True:
print("THEOIM: ")
plt.imshow(theoim,
origin='bottom',
norm=LogNorm(),
interpolation='nearest')
plt.show()
# --- if a manual scaling (fudge) factor was provided, apply to the model
if manscale:
theoim = theoim * manscale
# --- rotate the model image (this changes its extent and thus has to be
# done first)
# unrot = np.copy(theoim)
if np.abs(posang - 0) > 0.01:
theoim = ndimage.interpolation.rotate(theoim, 180 - posang, order=0)
if meastime:
print(" - Model rotated. Elapsed time: ", time.time() - tstart)
if debug is True:
print("THEOIM_ROT: ")
plt.imshow(theoim,
origin='bottom',
norm=LogNorm(),
interpolation='nearest')
plt.show()
# --- size units of the theoretical image
theopixsize_pc = theohead['CDELT1']
theosize = np.array(np.shape(theoim))
theosize_pc = theopixsize_pc * theosize[0] # pc
theosize_as = 2 * np.arctan(
theosize_pc / distance / 2.0e6) * 180 / np.pi * 3600
theopixsize_as = (2 * np.arctan(theopixsize_pc / distance / 2.e6) * 180 /
np.pi * 3600)
# plt.imshow(unrot, origin='bottom', norm=LogNorm())
# plt.imshow(theoim, origin='bottom', norm=LogNorm())
# plt.imshow(theoim, origin='bottom')
# theopfov = angsize/theosize[0]
# normalize image to flux = 1
# theoim = theoim/np.sum(theoim)
# theoim = theoim/np.max(theoim)
# --- convert to the right flux units
# surface brightness unit in cube is W/m^2/arcsec2
# -> convert to flux density in mJy
# print(np.sum(theoim))
freq = 2.99793e8 / (1e-6 * wlen)
# print(freq)
theoim = theoim * 1.0e29 / freq * theopixsize_as**2
theototflux = np.sum(theoim)
# --- resample to the same pixel size as the observation
# print( "- Resampling the model image to instrument pixel size...")
# --- the ndimage.zoom sometimes creates weird artifacts and thus might not
# be a good choice. Instead, use the self-made routine
# theoim_resres = ndimage.zoom(theoim_res, theopixsize_as/pfov, order=0)
# --- do the rasmpling before scaling it to the size of the observation to
# save computing time
theoim_res, sizerat = _increase_pixelsize(theoim,
oldpfov=theopixsize_as,
newpfov=pfov,
meastime=False)
if meastime:
print(" - Pixelsize increased. Elapsed time: ", time.time() - tstart)
if debug is True:
print("sizerat: ", sizerat)
print("THEOIM_RESRES: ")
plt.imshow(theoim_res,
origin='bottom',
norm=LogNorm(),
interpolation='nearest')
plt.show()
# --- if the PSF frame size is larger than the model extend the model frame
framerat = psfsize_as / theosize_as
if debug is True:
print("psfsize_as: ", psfsize_as)
print("theosize_as: ", theosize_as)
print("theopixsize_as: ", theopixsize_as)
print("theosize_pc: ", theosize_pc)
print("theosize: ", theosize)
print("framerat: ", framerat)
#print("newsize: ", newsize)
if framerat > 1.0:
theoim_resres = _extend_image(theoim_res, fac=framerat)
if meastime:
print(" - Frame extended. Elapsed time: ", time.time() - tstart)
if debug is True:
print("thesize_ext: ", np.shape(theoim_resres))
print("THEOIM_RESRES: ")
plt.imshow(theoim_resres,
origin='bottom',
norm=LogNorm(),
interpolation='nearest')
plt.show()
# plt.imshow(theoim_res, origin='bottom')
else:
theoim_resres = np.copy(theoim_res)
theosize_new = np.array(np.shape(theoim_resres))
if debug is True:
print("theosize_new: ", theosize_new)
print("new theosize_as: ", theosize_new * pfov)
# print(np.sum(theoim_resres))
# --- after resampling we need to re-establish the right flux levels
theoim_resres = theoim_resres / np.sum(theoim_resres) * theototflux
# plt.imshow(theoim_resres, origin='bottom', norm=LogNorm())
# plt.imshow(theoim_resres, origin='bottom')
# ==== 4. Optionally, apply a foreground extinction map if provided ====
if extfits:
exthdu = fits.open(extfits)
exthead = exthdu[0].header
extpfov = exthead["PFOV"]
# check if provided file is the full cube
if 'NAXIS3' in exthead:
# find the right frame to be extracted
if not mind:
mind, mwlen = find_wlen_match(theofits, wlen)
extim = exthdu[0].data[mind]
else:
extim = exthdu[0].data
# plt.imshow(extim,origin='bottom')
# plt.show()
exthdu.close()
# --- Do we have to resample the extinction map
if np.abs(extpfov - pfov) > 0.001:
# print("Resampling extinction map... ")
extim = ndimage.zoom(extim, 1.0 * pfov / extpfov, order=0)
# --- match the size of the extinction map to the one of the model
# image
extsize = np.array(np.shape(extim))
if theosize_new[0] > extsize[0]:
print(" - ERROR: provided extinction map is too small to cover \
the imaged region. Abort...")
return ()
if extsize[0] > theosize_new[0]:
# print("Cuttting exctinction map...")
extim = _crop_image(extim, box=theosize_new)
# --- finally apply the extinction map
theoim_resres = theoim_resres * extim
# print('Maximum extinction: ',np.min(extim))
# ==== 5. Obtain the Airy function from the calibrator ====
if debug is True:
print("PSF_IM: ")
plt.imshow(psfim,
origin='bottom',
norm=LogNorm(),
interpolation='nearest')
plt.show()
# --- set up the fitting of the STD star image
# --- assume that the maximum of the (cropped) image is the STD star
if fitpsf is True:
psfmax = np.max(psfim)
psfmaxpos = np.unravel_index(np.argmax(psfim), psfsize)
# print(im_bg, im_max, im_size, im_maxpos)
# --- Use an Airy plus a Moffat + constant as PSF model
c_init = models.Const2D(amplitude=np.median(psfim))
oa_init = obsc_AiryDisk2D(amplitude=psfmax,
x_0=psfmaxpos[1],
y_0=psfmaxpos[0],
radius=5,
obsrat=0.15)
m_init = models.Moffat2D(amplitude=psfmax,
x_0=psfmaxpos[1],
y_0=psfmaxpos[0],
gamma=5,
alpha=1)
a_plus_m = oa_init + m_init + c_init
# print(psfmax, psfmaxpos)
# --- Selection of fitting method
fit_meth = fitting.LevMarLSQFitter()
# --- Do the Fitting:
y, x = np.mgrid[:psfsize[0], :psfsize[1]]
am_fit = fit_meth(a_plus_m, x, y, psfim)
# print(am_fit.radius_0.value, am_fit.obsrat_0.value)
# then refine the fit by subtracting another Moffat
# a_plus_m_minus_m = am_fit - m_init
# amm_fit = fit_meth(a_plus_m_minus_m, x, y, psfim)
# z_amm = amm_fit(x, y)
# res = psfim - z_amm
#print(amm_fit.radius_0.value, amm_fit.obsrat_0.value)
if meastime:
print(" - PSf fit. Elapsed time: ", time.time() - tstart)
if debug is True:
print("PSF_FIT: ")
plt.imshow(am_fit(x, y),
origin='bottom',
norm=LogNorm(),
interpolation='nearest')
plt.show()
# --- Genarate the PSF image with the fitted model
# --- check whether the model image is on sky larger than the PSF image
# and if this is the case increase the grid and adjust the positions
# of the fits
size_diff = theosize_new[0] - psfsize[0]
if size_diff > 0:
y, x = np.mgrid[:theosize_new[0], :theosize_new[1]]
am_fit.x_0_0 = am_fit.x_0_0 + 0.5 * size_diff
am_fit.y_0_0 = am_fit.y_0_0 + 0.5 * size_diff
am_fit.x_0_1 = am_fit.x_0_1 + 0.5 * size_diff
am_fit.y_0_1 = am_fit.y_0_1 + 0.5 * size_diff
# --- create the final PSF image by subtracting the constant terms
# and normalise by its area
psf = am_fit(x, y) - am_fit.amplitude_2.value
psf = psf / np.sum(psf)
if debug is True:
print("PSF_FINAL: ")
plt.imshow(psf,
origin='bottom',
norm=LogNorm(),
interpolation='nearest')
plt.show()
# plt.imshow(psf, origin='bottom', norm=LogNorm())
# plt.show()
if writeallfits is True:
fout = psffits.replace('.fits', '_fit.fits')
if 'OBS NAME' in psfhead:
psfhead.remove('OBS NAME')
fits.writeto(fout, psf, psfhead, overwrite=True)
# --- optinally, write the a plot documenting the quality of the PSF fit
if writefitplot:
fitplotfname = psffits.split('/')[-1]
fitplotfname = fitplotfname.replace('.fits', '_fitplot.pdf')
fitplotfname = outfolder + '/' + fitplotfname
maxrad = int(0.5 * np.sqrt(0.5) * np.min(psfsize))
_make_fit_plots(psfim,
am_fit(x, y),
fitplotfname,
am_fit.x_0_0,
am_fit.y_0_0,
maxrad,
inv=True,
cmap='gist_heat',
labelcolor='black')
# --- alternatively the PSF can also be direclty provided so that no fit is
# necessary
else:
# normalise the provided psf
psf = psfim - np.nanmin(psfim)
psf = psf / np.nansum(psf)
psf[np.argwhere(np.isnan(psf))] = 0
# ==== 6. Convolution of the model image with the PSF ====
simim = scipy.signal.convolve2d(theoim_resres, psf, mode='same')
# print(np.sum(simim))
if meastime:
print(" - Model convolved. Elapsed time: ", time.time() - tstart)
if debug is True:
print("SIMIM:")
plt.imshow(simim,
origin='bottom',
norm=LogNorm(),
interpolation='nearest')
plt.show()
# ==== 7. Flux measurements and application of noise ====
# --- Flux measurement on the model image before applying noise
ftotmod = int(np.nansum(simim))
apos = 0.5 * np.array(theosize_new)
nucrad_px = 0.5 * fnucdiam_as / pfov
from aper import aper
(mag, magerr, flux, fluxerr, sky, skyerr, badflag,
outstr) = aper(simim,
apos[1],
apos[0],
apr=nucrad_px,
exact=True,
setskyval=0)
fnucmod = int(flux)
if not silent:
print(' - Model total | nuclear flux [mJy]: ' + str(ftotmod) +
' | ' + str(fnucmod))
plotsize_px = int(1.0 * foi_as / pfov)
# --- Measure the background noise from the real observation
if obsfits is not None:
bg = np.copy(obsim)
# bgsize = np.shape(bg)
params, _, _ = _get_pointsource(obsim)
xpos = params[2]
ypos = params[3]
bg[int(ypos - 0.5 * plotsize_px):int(ypos + 0.5 * plotsize_px),
int(xpos - 0.5 * plotsize_px):int(xpos + 0.5 * plotsize_px)] = 0
if bgstd == 0:
bgstd = np.std(bg[bg != 0])
if bgmed == 0:
bgmed = np.median(bg[bg != 0])
# plt.imshow(bg, origin='bottom', norm=LogNorm(), cmap='gist_heat')
# --- crop the observational image to the requested plot size
cim = _crop_image(obsim,
box=plotsize_px,
cenpos=_get_pointsource(obsim)[0][2:4])
newsize = np.shape(cim)
# --- make flux measurements on the nucleus and total
ftotobs = int(np.sum(cim - bgmed))
apos = 0.5 * np.array(newsize)
(mag, magerr, flux, fluxerr, sky, skyerr, badflag,
outstr) = aper(cim,
apos[1],
apos[0],
apr=nucrad_px,
exact=True,
setskyval=0)
fnucobs = int(flux)
if not silent:
print(' - Observed total | nuclear flux [mJy]: ' + str(ftotobs) +
' | ' + str(fnucobs))
else:
cim = None
if meastime:
print(" - Fluxes measured. Elapsed time: ", time.time() - tstart)
# pdb.set_trace()
# --- crop the simulated image to the requested plot size
params, _, _ = _get_pointsource(simim)
csimim = _crop_image(simim,
box=plotsize_px,
cenpos=_get_pointsource(simim)[0][2:4])
if debug is True:
plt.imshow(simim, origin='bottom', cmap='gist_heat', norm=LogNorm())
plt.title('simim')
plt.show()
print(plotsize_px, np.shape(csimim))
plt.imshow(csimim, origin='bottom', cmap='gist_heat', norm=LogNorm())
plt.title('csimim')
plt.show()
if meastime:
print(" - Obs cropped. Elapsed time: ", time.time() - tstart)
# --- generate an artifical noise frame with same properties as in real
# image
if bgstd > 0:
artbg = np.random.normal(scale=bgstd,
size=(plotsize_px, plotsize_px)) + bgmed
# artbg = 0
# --- apply the artificial background
# csimim = csimim/np.max(csimim)*(np.max(cim)-bgmed)+bgmed+artbg
csimim = csimim + artbg
# --- crop the PSF image to the requested plot size
cpsf = _crop_image(psf,
box=plotsize_px,
cenpos=_get_pointsource(psf)[0][2:4])
# print(bgmed, bgstd, np.std(artbg), np.median(cim), np.median(csimim),
# np.std(cim), np.std(csimim), np.max(cim), np.min(cim), np.max(csimim),
# np.min(csimim))
if meastime:
print(" - PSF cropped. Elapsed time: ", time.time() - tstart)
theopfov = theopixsize_as
theobox = int(np.round(plotsize_px * pfov / theopfov))
if returncmod:
# --- crop the model imae to the requested plot size
if framerat > 1.0:
theoim_res_0 = _extend_image(theoim, fac=framerat)
else:
theoim_res_0 = theoim
cmod = _crop_image(theoim_res_0, box=theobox, exact=False)
# plt.imshow(cmod, origin='bottom', norm=LogNorm(), cmap='gist_heat')
if meastime:
print(" - Theo cropped. Elapsed time: ", time.time() - tstart)
else:
cmod = None
# --- write out the simulated image as a fits file
if not outname:
theofitsfile = theofits.split("/")[-1]
out_str = theofitsfile.replace("_total.fits", "")
out_str = (out_str + "_pa" + pastr + "_dist" + diststr + "_wlen" +
wlenstr)
if suffix:
out_str = out_str + "_" + suffix
else:
out_str = outname
out_str = outfolder + '/' + out_str
if writeallfits or writetheofits:
fout = out_str + '_mod.fits'
theohead["Filter"] = filt
theohead["WAVELEN"] = wlen
theohead["PFOV"] = theopixsize_as
fits.writeto(fout, cmod, theohead, overwrite=True)
if saveplot:
_simple_image_plot(cmod, fout.replace(".fits", ".png"), log=True)
if writeallfits or writesimfits:
fout = out_str + '_sim.fits'
theohead["PFOV"] = pfov
theohead["BUNIT"] = 'mJy'
ts = np.shape(simim)
theohead["CRPIX1"] = 0.5 * ts[1]
theohead["CDELT1"] = pfov
theohead["CTYPE1"] = 'arcsec'
theohead["CRPIX2"] = 0.5 * ts[0]
theohead["CDELT2"] = pfov
theohead["CTYPE2"] = 'arcsec'
fits.writeto(fout, csimim, theohead, overwrite=True)
if saveplot:
_simple_image_plot(csimim, fout.replace(".fits", ".png"), log=True)
if meastime:
print(" - All finished: ", time.time() - tstart)
return (cpsf, cmod, cim, csimim, wlen, pfov, theopfov)
def star_centers_from_PSF_cube(cube,
wave,
pixel,
display=False,
save_path=None):
'''
Compute star center from PSF images
Parameters
----------
cube : array_like
PSF IFS cube
wave : array_like
Wavelength values, in nanometers
pixel : float
Pixel scale, in mas/pixel
display : bool
Display the fit of the satelitte spots
save_path : str
Path where to save the fit images
Returns
-------
img_center : array_like
The star center in each frame of the cube
'''
# standard parameters
nwave = wave.size
loD = wave * 1e-6 / 8 * 180 / np.pi * 3600 * 1000 / pixel
box = 30
# spot fitting
xx, yy = np.meshgrid(np.arange(2 * box), np.arange(2 * box))
# multi-page PDF to save result
if save_path is not None:
pdf = PdfPages(save_path)
# loop over images
img_center = np.zeros((nwave, 2))
for idx, (wave, img) in enumerate(zip(wave, cube)):
print(' wave {0:2d}/{1:2d} ({2:.3f} micron)'.format(
idx + 1, nwave, wave))
# remove any NaN
img = np.nan_to_num(img)
# center guess
cy, cx = np.unravel_index(np.argmax(img), img.shape)
# sub-image
sub = img[cy - box:cy + box, cx - box:cx + box]
# fit peak with Gaussian + constant
imax = np.unravel_index(np.argmax(sub), sub.shape)
g_init = models.Gaussian2D(amplitude=sub.max(), x_mean=imax[1], y_mean=imax[0],
x_stddev=loD[idx], y_stddev=loD[idx]) + \
models.Const2D(amplitude=sub.min())
fitter = fitting.LevMarLSQFitter()
par = fitter(g_init, xx, yy, sub)
cx_final = cx - box + par[0].x_mean
cy_final = cy - box + par[0].y_mean
img_center[idx, 0] = cx_final
img_center[idx, 1] = cy_final
if save_path or display:
fig = plt.figure(0, figsize=(8, 8))
plt.clf()
ax = fig.add_subplot(111)
ax.imshow(img / img.max(),
aspect='equal',
vmin=1e-6,
vmax=1,
norm=colors.LogNorm(),
interpolation='nearest')
ax.plot([cx_final], [cy_final], marker='D', color='red')
ax.add_patch(
patches.Rectangle((cx - box, cy - box),
2 * box,
2 * box,
ec='white',
fc='none'))
ax.set_title(r'Image #{0} - {1:.3f} $\mu$m'.format(idx + 1, wave))
ext = 1000 / pixel
ax.set_xlim(cx_final - ext, cx_final + ext)
ax.set_ylim(cy_final - ext, cy_final + ext)
plt.tight_layout()
if save_path:
pdf.savefig()
if display:
plt.pause(1e-3)
if save_path:
pdf.close()
return img_center
def autocorrelation_fit(im2, rough_sep = 44.93, rough_pa=0., cutout_sz=5, background_subtracted=False,
plot_cutout=False, plot_resids=False):
""" Fits to the distance of the second peak in the autocorrelation (i.e. the binary separation).
This will perform a Levenberg-Marquardt fit over a small, fixed region around the peak.
The model used for the fit will depend on the options set.
rough_sep, rough_pa: Defaults 44.93 pixels and 0 degrees
These define the position of the region used for the fit.
cutout_sz: Default 5 pixels
The radius of the box used for the fit.
background_subtracted: Default False
If True, the model used for the fit will be an Airy Disk + constant background.
If False, the model will be a Gaussian + planar background.
These seemed to work best.
"""
rough_pos = np.round([rough_sep*np.sin(rough_pa),rough_sep*np.cos(rough_pa)]).astype(int)
calc_pos = [rough_sep*np.sin(rough_pa),rough_sep*np.cos(rough_pa)]
cutout = np.copy(im2[im2.shape[0]//2+rough_pos[0]-cutout_sz:im2.shape[0]//2+rough_pos[0]+cutout_sz,
im2.shape[1]//2+rough_pos[1]-cutout_sz:im2.shape[1]//2+rough_pos[1]+cutout_sz])
cutout /= np.max(cutout)
if plot_cutout:
plt.imshow(cutout)
x,y = np.indices(cutout.shape)
x = x + rough_pos[0] - cutout_sz
y = y + rough_pos[1] - cutout_sz
# Fit a Gaussian
fit = fitting.LevMarLSQFitter()
if background_subtracted:
gauss = models.AiryDisk2D(amplitude=cutout.max(),x_0=calc_pos[0],y_0=calc_pos[1],radius=3.54)
bckgd = models.Const2D(amplitude=0.6)
else:
gauss = models.Gaussian2D(amplitude = cutout.max(),x_stddev=1.36,y_stddev=1.36,
x_mean=calc_pos[0],y_mean=calc_pos[1])
bckgd = models.Planar2D(slope_x = -0.00564816,slope_y=-0.02378304,intercept=1.01)
gauss.fixed['theta']=True
cutout_model = gauss + bckgd
# fit the data with the fitter
fitted_model = fit(cutout_model,x,y,cutout,maxiter=100000,acc=1e-7);
# Rename the parameters so the output looks the same
if background_subtracted:
fitted_model.x_mean_0 = fitted_model.x_0_0
fitted_model.y_mean_0 = fitted_model.y_0_0
if plot_resids:
test = fitted_model(x,y)
plt.figure(figsize=(12,4))
plt.clf()
plt.subplot(131)
plt.imshow(cutout,origin='lowerleft',vmin=0.7,vmax=1);plt.colorbar()
plt.subplot(132)
plt.imshow(test,origin='lowerleft',vmin=0.7,vmax=1);plt.colorbar()
plt.subplot(133)
plt.imshow(cutout-test,origin='lowerleft',vmin=-0.05,vmax=0.05);plt.colorbar()
return fitted_model
def _do_fitting(self):
"""Performs 1-D and 2-G gaussian fits to the stars in the
internal fit_table.
A 2-dimensional Gaussian plus flat background model is fit to
each cut-out image. The model is initialized with the global
background level, and source centroid and peak value from the
input photometry list. The Levenberg-Marquardt non-linear
least squares fitting algorithm is used to fit the data.
The data is assumed to have Gaussian errors that are the square
root of the pixel counts.
There are some limitations to this at present:
- The reduced chi-squared values obtained are unrealistic. It is
not clear whether the errors are underestimated and/or the
fitting has trouble converging to the true solution.
"""
# Setup
num_stars = len(self._fit_table)
sigma_to_fwhm = 2.35482
fwhm_to_sigma = 1.0 / sigma_to_fwhm
max_iterations = 500
# Fit for x and y after initially just fitting for amplitude,
# fwhm, and theta?
is_pos_fitted_for = True
# Extract data from main image, stores in _pixel_array.
self._extract_cutouts()
# Add extra columns to the output table for the fit results
self._prepare_fit_columns()
self._logger.info(
f'Starting to fit Const2D+XX models to {num_stars} star cutouts.')
perf_time_start = time.perf_counter(
) # highest res timer, counts sleeps
# X and Y pixel index grids needed by the fitter
x_grid, y_grid = np.mgrid[0:self._box_width_pix, 0:self._box_width_pix]
# We initialize the 2-D Gaussians based on the initial FWHM
# but with a slight asymmetry sig_x/sig_y = 1.1, theta approx 30 degrees.
def_axrat = 1.05
sig_y = self._init_fwhm * fwhm_to_sigma
sig_x = def_axrat * sig_y
rotang = 1.1 # radians, approx 60 degrees.
xpos = self._box_width_pix / 2
ypos = self._box_width_pix / 2
ampl = 1
num_fit_pars = 0
# The background model starts off fixed.
bg_mod = models.Const2D(amplitude=self._init_bglvl)
bg_mod.amplitude.fixed = True
# 2-D gaussian model for the star.
star_mod = models.Gaussian2D(amplitude=ampl,
x_mean=xpos,
y_mean=ypos,
x_stddev=sig_x,
y_stddev=sig_y,
theta=rotang)
# Constraint theta to -pi/2 to pi/2
# NOTE Disabled as it results in the fitter failing very often
##half_pi = 0.5 * math.pi
##star_mod.theta.bounds = (-half_pi, half_pi)
# Start fits at the initial centroid positions
star_mod.x_mean.fixed = True
star_mod.y_mean.fixed = True
num_fit_pars += 4 # 4 free fit parameters
comb_mod = star_mod + bg_mod
fitter = fitting.LevMarLSQFitter()
# Iterate over stars, first updating initial values, then fitting,
# then storing the fit results.
for idx in range(num_stars):
# Get better estimate for initial parameters, in particular
# the amplitude.
# Note: you can set a Parameter object by value directly,
# (e.g. "bob=3") but to access it you must access its value
# attribute (e.g. "x = bob.value")
starid = self._fit_table['id'][idx]
xpos = self._fit_table['xcenter'][idx] - self._fit_table['xmin'][
idx]
ypos = self._fit_table['ycenter'][idx] - self._fit_table['ymin'][
idx]
ampl = self._fit_table['peak_adu'][idx]
bglvl = self._fit_table['bgmed_per_pix'][idx]
comb_mod[0].x_mean = xpos
comb_mod[0].y_mean = ypos
comb_mod[0].amplitude = ampl
comb_mod[1].amplitude = bglvl
current_num_fit_pars = num_fit_pars
# Estimated standard devation of the data.
var_arr = np.where(self._pixel_array[idx] > 0,
self._pixel_array[idx], 1)
mean_variance = np.mean(var_arr[var_arr != 1])
rms_stddev = math.sqrt(mean_variance)
std_arr = np.where(var_arr != 1, np.sqrt(var_arr), rms_stddev)
# If used, the weight array should have values of 1/sigma
if self._use_weights:
weights_arr = 1.0 / std_arr
else:
weights_arr = None
# Fit
self._logger.debug(
f'Fitting star #{idx} (id={starid}) at fixed xpos={xpos:.2f}, ypos={ypos:.2f}'
)
fitted_mod, fit_status, fit_message, fit_ok, uncert_vals = self._do_single_fit(
fitter, comb_mod, self._pixel_array[idx], weights_arr, x_grid,
y_grid, max_iterations, current_num_fit_pars, idx)
# If the ift is OK, and fit_for_bg is true, then fit for the BG level.
if (fit_ok) and (self._fit_for_bg is True):
fitted_mod[1].amplitude.fixed = False
current_num_fit_pars += 1
fitted_mod, fit_status, fit_message, fit_ok, uncert_vals = self._do_single_fit(
fitter, fitted_mod, self._pixel_array[idx], weights_arr,
x_grid, y_grid, max_iterations, current_num_fit_pars, idx)
# If the fit did NOT fail we can relax the constraints on the
# position of the gaussian.
if fit_ok and is_pos_fitted_for:
fitted_mod[0].x_mean.fixed = False
fitted_mod[0].y_mean.fixed = False
current_num_fit_pars += 2
fitted_mod, fit_status, fit_message, fit_ok, uncert_vals = self._do_single_fit(
fitter, fitted_mod, self._pixel_array[idx], weights_arr,
x_grid, y_grid, max_iterations, current_num_fit_pars, idx)
# Calculate reduced chi squared.
rchisq = self._calculate_rchisq(self._pixel_array[idx], x_grid,
y_grid, std_arr, fitted_mod,
current_num_fit_pars)
# Extract fit parameters
# Unfortunately we have to hardcode the parameter order. :(
# And which columns they should go into.
fit_par_dict = {
'xc_fit': 1, # Not used.
'yc_fit': 2,
'ampl': 0,
'fwhm_x': 3,
'fwhm_y': 4,
'theta': 5
}
if is_pos_fitted_for:
# Error par dict if xc and yc are fitted for
err_par_dict = {
'xc_err': 1,
'yc_err': 2,
'ampl_err': 0,
'fwhm_x_err': 3,
'fwhm_y_err': 4,
'theta_err': 5
}
else:
# Error par dict if xc and yc are fixed
err_par_dict = {
'ampl_err': 0,
'fwhm_x_err': 1,
'fwhm_y_err': 2,
'theta_err': 3
}
self._fit_table['ampl'][idx] = fitted_mod[0].amplitude.value
self._fit_table['xc_fit'][idx] = fitted_mod[0].x_mean.value
self._fit_table['yc_fit'][idx] = fitted_mod[0].y_mean.value
self._fit_table['fwhm_x'][
idx] = sigma_to_fwhm * fitted_mod[0].x_stddev.value
self._fit_table['fwhm_y'][
idx] = sigma_to_fwhm * fitted_mod[0].y_stddev.value
self._fit_table['theta'][idx] = fitted_mod[0].theta.value
self._fit_table['fit_ok'][idx] = fit_ok
self._fit_table['rchisq'][idx] = rchisq
# Get the errors.
if fit_ok:
for col in err_par_dict:
paridx = err_par_dict[col]
if 'fwhm' in col:
self._fit_table[col][
idx] = sigma_to_fwhm * uncert_vals[paridx]
else:
self._fit_table[col][idx] = uncert_vals[paridx]
# Calculate axis ratio and circularity.
# Note this calculation is not quite right because the two
# parameters are NOT independent.
fwhm_x = self._fit_table['fwhm_x'][idx]
fwhm_y = self._fit_table['fwhm_y'][idx]
axrat = max(fwhm_x, fwhm_y) / min(fwhm_x, fwhm_y)
axrat_err = 0
if fit_ok:
fwhm_xerr = self._fit_table['fwhm_x_err'][idx]
fwhm_yerr = self._fit_table['fwhm_y_err'][idx]
axrat_err = axrat * math.sqrt((fwhm_xerr / fwhm_x)**2 +
(fwhm_yerr / fwhm_y)**2)
circular = self.is_circular(fwhm_x, fwhm_y, fwhm_xerr,
fwhm_yerr)
self._fit_table['circular'][idx] = circular
self._fit_table['axrat'][idx] = axrat
self._fit_table['axrat_err'][idx] = axrat_err
perf_time_end = time.perf_counter() # highest res timer, counts sleeps
perf_time = perf_time_end - perf_time_start # seconds
avg_time_ms = 1000.0 * perf_time / num_stars # milliseconds
self._logger.debug(
f'Fitting completed in {perf_time:.3f} s (average {avg_time_ms:.1f} ms/star)'
)
if not self._quiet:
print('Fit results:')
print(self._fit_table)
print('')
return
def peak_center(img, window=0, edges=0, mask=None):
'''Determine the center position of a peak
Parameters
----------
img : array
Image where the peak must be found
window : int
Half-size of sub-window in which to do the fit. If 0, then the fit
is performed over the full image. Default is 0
edges : int
Number of pixels to hide on the edges. Default is 0
mask : array
Mask to apply to the data. Default is None
Returns
-------
cx, cy : tuple
Center of the peak
'''
img = img.copy()
# hide edges
if edges > 0:
img[:edges, :] = 0
img[:, :edges] = 0
img[edges:, :] = 0
img[:, edges:] = 0
# apply mask
if mask is not None:
img *= mask
# estimate peak position
imax = np.unravel_index(np.argmax(img), img.shape)
cx_int = imax[1]
cy_int = imax[0]
# sub-window
win = window // 2
if window > 0:
if (window % 2):
raise ValueError('window parameter must be even')
sub = img[cy_int - win:cy_int + win, cx_int - win:cx_int + win]
cx_init = win
cy_init = win
else:
sub = img
cx_init = cx_int
cy_init = cy_int
# fit
x, y = np.meshgrid(np.arange(sub.shape[1]), np.arange(sub.shape[0]))
g_init = models.Gaussian2D(amplitude=sub.max(), x_mean=cx_init, y_mean=cy_init) + \
models.Const2D(amplitude=0)
fit_g = fitting.LevMarLSQFitter()
g = fit_g(g_init, x, y, sub)
cx = g[0].x_mean.value - cx_init + cx_int
cy = g[0].y_mean.value - cy_init + cy_int
return cx, cy
def star_centers_from_waffle_img_cube(cube_cen,
wave,
waffle_orientation,
center_guess,
pixel,
orientation_offset,
high_pass=False,
center_offset=(0, 0),
box_size=16,
smooth=0,
coro=True,
save_path=None,
logger=_log):
'''
Compute star center from waffle images (IRDIS CI, IRDIS DBI, IFS)
Parameters
----------
cube_cen : array_like
IRDIFS waffle cube
wave : array_like
Wavelength values, in nanometers
waffle_orientation : str
String giving the waffle orientation '+' or 'x'
center_guess : array
Estimation of the image center as a function of wavelength.
This should be an array of shape nwave*2.
pixel : float
Pixel scale, in mas/pixel
orientation_offset : float
Field orientation offset, in degrees
high_pass : bool
Apply high-pass filter to the image before searching for the
satelitte spots. Default is False
smooth : int
Apply a gaussian smoothing to the images to reduce noise. The
value is the sigma of the gaussian in pixel. Default is no
smoothing
center_offset : tuple
Apply an (x,y) offset to the default center position. The offset
will move the search box of the waffle spots by the amount of
specified pixels in each direction. Default is no offset
box_size : int
Size of the box in which the fit is performed. Default is 16 pixels
coro : bool
Observation was performed with a coronagraph. Default is True
save_path : str
Path where to save the fit images. Default is None, which means
that the plot is not produced
logger : logHandler object
Log handler for the reduction. Default is root logger
Returns
-------
spot_centers : array_like
Centers of each individual spot in each frame of the cube
spot_dist : array_like
The 6 possible distances between the different spots
img_centers : array_like
The star center in each frame of the cube
'''
# standard parameters
nwave = wave.size
loD = wave * 1e-9 / 8 * 180 / np.pi * 3600 * 1000 / pixel
# waffle parameters
freq = 10 * np.sqrt(2) * 0.97
box = box_size // 2
if waffle_orientation == '+':
orient = orientation_offset * np.pi / 180
elif waffle_orientation == 'x':
orient = orientation_offset * np.pi / 180 + np.pi / 4
# spot fitting
xx, yy = np.meshgrid(np.arange(2 * box), np.arange(2 * box))
# multi-page PDF to save result
if save_path is not None:
pdf = PdfPages(save_path)
# loop over images
spot_centers = np.zeros((nwave, 4, 2))
spot_dist = np.zeros((nwave, 6))
img_centers = np.zeros((nwave, 2))
for idx, (wave, img) in enumerate(zip(wave, cube_cen)):
logger.info(' ==> wave {0:2d}/{1:2d} ({2:4.0f} nm)'.format(
idx + 1, nwave, wave))
# remove any NaN
img = np.nan_to_num(img)
# center guess (+offset)
cx_int = int(center_guess[idx, 0]) + center_offset[0]
cy_int = int(center_guess[idx, 1]) + center_offset[1]
# optional high-pass filter
if high_pass:
img = img - ndimage.median_filter(img, 15, mode='mirror')
# optional smoothing
if smooth > 0:
img = ndimage.gaussian_filter(img, smooth)
# mask for non-coronagraphic observations
if not coro:
mask = aperture.disc(cube_cen[0].shape[-1],
5 * loD[idx],
diameter=False,
center=(cx_int, cy_int),
invert=True)
img *= mask
# create plot if needed
if save_path:
fig = plt.figure('Waffle center - imaging', figsize=(8.3, 8))
plt.clf()
if high_pass:
norm = colors.PowerNorm(gamma=1, vmin=-1e-1, vmax=1e-1)
else:
norm = colors.LogNorm(vmin=1e-2, vmax=1)
col = ['green', 'blue', 'deepskyblue', 'purple']
ax = fig.add_subplot(111)
ax.imshow(img / img.max(),
aspect='equal',
norm=norm,
interpolation='nearest',
cmap=global_cmap)
ax.set_title(r'Image #{0} - {1:.0f} nm'.format(idx + 1, wave))
ax.set_xlabel('x position [pix]')
ax.set_ylabel('y position [pix]')
# satelitte spots
for s in range(4):
cx = int(cx_int + freq * loD[idx] * np.cos(orient + np.pi / 2 * s))
cy = int(cy_int + freq * loD[idx] * np.sin(orient + np.pi / 2 * s))
sub = img[cy - box:cy + box, cx - box:cx + box]
# bounds for fitting: spots slightly outside of the box are allowed
gbounds = {
'amplitude': (0.0, None),
'x_mean': (-2.0, box * 2 + 2),
'y_mean': (-2.0, box * 2 + 2),
'x_stddev': (1.0, 20.0),
'y_stddev': (1.0, 20.0)
}
# fit: Gaussian + constant
imax = np.unravel_index(np.argmax(sub), sub.shape)
g_init = models.Gaussian2D(amplitude=sub.max(), x_mean=imax[1], y_mean=imax[0],
x_stddev=loD[idx], y_stddev=loD[idx], bounds=gbounds) + \
models.Const2D(amplitude=sub.min())
fitter = fitting.LevMarLSQFitter()
par = fitter(g_init, xx, yy, sub)
fit = par(xx, yy)
cx_final = cx - box + par[0].x_mean
cy_final = cy - box + par[0].y_mean
spot_centers[idx, s, 0] = cx_final
spot_centers[idx, s, 1] = cy_final
# plot sattelite spots and fit
if save_path:
ax.plot([cx_final], [cy_final],
marker='D',
color=col[s],
zorder=1000)
ax.add_patch(
patches.Rectangle((cx - box, cy - box),
2 * box,
2 * box,
ec='white',
fc='none'))
axs = fig.add_axes((0.17 + s * 0.2, 0.17, 0.1, 0.1))
axs.imshow(sub,
aspect='equal',
vmin=0,
vmax=sub.max(),
interpolation='nearest',
cmap=global_cmap)
axs.plot([par[0].x_mean.value], [par[0].y_mean.value],
marker='D',
color=col[s])
axs.set_xticks([])
axs.set_yticks([])
axs = fig.add_axes((0.17 + s * 0.2, 0.06, 0.1, 0.1))
axs.imshow(fit,
aspect='equal',
vmin=0,
vmax=sub.max(),
interpolation='nearest',
cmap=global_cmap)
axs.set_xticks([])
axs.set_yticks([])
# lines intersection
intersect = lines_intersect(spot_centers[idx, 0, :],
spot_centers[idx, 2, :],
spot_centers[idx,
1, :], spot_centers[idx,
3, :])
img_centers[idx] = intersect
# scaling
spot_dist[idx, 0] = np.sqrt(
np.sum((spot_centers[idx, 0, :] - spot_centers[idx, 2, :])**2))
spot_dist[idx, 1] = np.sqrt(
np.sum((spot_centers[idx, 1, :] - spot_centers[idx, 3, :])**2))
spot_dist[idx, 2] = np.sqrt(
np.sum((spot_centers[idx, 0, :] - spot_centers[idx, 1, :])**2))
spot_dist[idx, 3] = np.sqrt(
np.sum((spot_centers[idx, 0, :] - spot_centers[idx, 3, :])**2))
spot_dist[idx, 4] = np.sqrt(
np.sum((spot_centers[idx, 1, :] - spot_centers[idx, 2, :])**2))
spot_dist[idx, 5] = np.sqrt(
np.sum((spot_centers[idx, 2, :] - spot_centers[idx, 3, :])**2))
# finalize plot
if save_path:
ax.plot([spot_centers[idx, 0, 0], spot_centers[idx, 2, 0]],
[spot_centers[idx, 0, 1], spot_centers[idx, 2, 1]],
color='w',
linestyle='dashed',
zorder=900)
ax.plot([spot_centers[idx, 1, 0], spot_centers[idx, 3, 0]],
[spot_centers[idx, 1, 1], spot_centers[idx, 3, 1]],
color='w',
linestyle='dashed',
zorder=900)
ax.plot([intersect[0]], [intersect[1]],
marker='+',
color='w',
ms=15)
ext = 1000 / pixel
ax.set_xlim(intersect[0] - ext, intersect[0] + ext)
ax.set_ylim(intersect[1] - ext, intersect[1] + ext)
plt.subplots_adjust(left=0.1, right=0.98, bottom=0.1, top=0.95)
if save_path:
pdf.savefig()
if save_path:
pdf.close()
return spot_centers, spot_dist, img_centers
def prepare_psf_model(psfmodel,
xname=None,
yname=None,
fluxname=None,
renormalize_psf=True):
"""
Convert a 2D PSF model to one suitable for use with
`BasicPSFPhotometry` or its subclasses.
The resulting model may be a composite model, but should have only
the x, y, and flux related parameters un-fixed.
Parameters
----------
psfmodel : a 2D model
The model to assume as representative of the PSF.
xname : str or None
The name of the ``psfmodel`` parameter that corresponds to the
x-axis center of the PSF. If None, the model will be assumed to
be centered at x=0, and a new parameter will be added for the
offset.
yname : str or None
The name of the ``psfmodel`` parameter that corresponds to the
y-axis center of the PSF. If None, the model will be assumed to
be centered at y=0, and a new parameter will be added for the
offset.
fluxname : str or None
The name of the ``psfmodel`` parameter that corresponds to the
total flux of the star. If None, a scaling factor will be added
to the model.
renormalize_psf : bool
If True, the model will be integrated from -inf to inf and
re-scaled so that the total integrates to 1. Note that this
renormalization only occurs *once*, so if the total flux of
``psfmodel`` depends on position, this will *not* be correct.
Returns
-------
outmod : a model
A new model ready to be passed into `BasicPSFPhotometry` or its
subclasses.
"""
if xname is None:
xinmod = models.Shift(0, name='x_offset')
xname = 'offset_0'
else:
xinmod = models.Identity(1)
xname = xname + '_2'
xinmod.fittable = True
if yname is None:
yinmod = models.Shift(0, name='y_offset')
yname = 'offset_1'
else:
yinmod = models.Identity(1)
yname = yname + '_2'
yinmod.fittable = True
outmod = (xinmod & yinmod) | psfmodel
if fluxname is None:
outmod = outmod * models.Const2D(1, name='flux_scaling')
fluxname = 'amplitude_3'
else:
fluxname = fluxname + '_2'
if renormalize_psf:
# we do the import here because other machinery works w/o scipy
from scipy import integrate
integrand = integrate.dblquad(psfmodel, -np.inf, np.inf,
lambda x: -np.inf, lambda x: np.inf)[0]
normmod = models.Const2D(1. / integrand, name='renormalize_scaling')
outmod = outmod * normmod
# final setup of the output model - fix all the non-offset/scale
# parameters
for pnm in outmod.param_names:
outmod.fixed[pnm] = pnm not in (xname, yname, fluxname)
# and set the names so that BasicPSFPhotometry knows what to do
outmod.xname = xname
outmod.yname = yname
outmod.fluxname = fluxname
# now some convenience aliases if reasonable
outmod.psfmodel = outmod[2]
if 'x_0' not in outmod.param_names and 'y_0' not in outmod.param_names:
outmod.x_0 = getattr(outmod, xname)
outmod.y_0 = getattr(outmod, yname)
if 'flux' not in outmod.param_names:
outmod.flux = getattr(outmod, fluxname)
return outmod
def fit_alignment_box(region, box_size=30, verbose=False, seeing=None,
medfilt=False):
pixelscale = u.pixel_scale(0.1798*u.arcsec/u.pixel)
if medfilt is True:
region = median_filter(region, size=(3,3))
# Estimate center of alignment box
threshold_pct = 80
window = region.data > np.percentile(region.data, threshold_pct)
alignment_box_position = ndimage.measurements.center_of_mass(window)
offset_val = np.median(region.data[~window])
offset = models.Const2D(offset_val)
# Determine fluctuations in sky
sky_amplitude = np.median(region.data[window])
sky_fluctuations = np.std(region.data[window])
# Detect box edges
gradx = np.gradient(region.data, axis=1)
horizontal_profile = np.sum(gradx, axis=0)
h_edges = fit_CSU_edges(horizontal_profile)
grady = np.gradient(region.data, axis=0)
vertical_profile = np.sum(grady, axis=1)
v_edges = fit_CSU_edges(vertical_profile)
# Estimate stellar position
maxr = np.max(region.data)
starloc = (np.where(region == maxr)[0][0],
np.where(region == maxr)[1][0])
# Build model of sky, star, & box
boxamplitude = 1
box = mosfireAlignmentBox(boxamplitude, alignment_box_position[1], alignment_box_position[0],\
abs(h_edges[0]-h_edges[1]), abs(v_edges[0]-v_edges[1]))
box.amplitude.fixed = True
box.x_width.min = 10
box.y_width.min = 10
sky = models.Const2D(sky_amplitude)
sky.amplitude.min = 0
star_amplitude = maxr - sky_amplitude
star_sigma = star_amplitude / sky_fluctuations
if star_sigma < 5:
if verbose: print(f'No star detected. sigma={star_sigma:.1f}')
return [None]*4
else:
if verbose: print(f'Detected peak pixel {star_sigma:.1f} sigma above sky.')
star = models.Gaussian2D(amplitude=star_amplitude,
x_mean=starloc[1], y_mean=starloc[0],
x_stddev=2, y_stddev=2)
# print(h_edges)
# print(v_edges)
# star.y_mean.min = v_edges[0]
# star.y_mean.max = v_edges[1]
# star.x_mean.min = h_edges[0]
# star.x_mean.max = h_edges[1]
star.amplitude.min = 5*sky_fluctuations
star.x_stddev.min = 1 # FWHM = 2.355*stddev = 0.42 arcsec FWHM
star.x_stddev.max = 4 # FWHM = 2.355*stddev = 1.47 arcsec FWHM
star.y_stddev.min = 1
star.y_stddev.max = 4
if seeing is not None and seeing > 0:
sigma = (seeing / 2.355 * u.arcsec).to(u.pixel, equivalencies=pixelscale)
star.x_stddev.min = max(2, sigma.value-1)
star.y_stddev.min = max(2, sigma.value-1)
star.x_stddev.max = min(sigma.value+1, 4)
star.y_stddev.max = min(sigma.value+1, 4)
# print(f"Using seeing value {seeing} arcsec. sigma limits {star.x_stddev.min}, {star.x_stddev.max} pix")
model = box*(sky + star) + offset
# modelim = np.zeros((61,61))
# fitim = np.zeros((61,61))
# for i in range(0,60):
# for j in range(0,60):
# modelim[j,i] = model(i,j)
# fitim[j,i] = model(i,j)
# residuals = region.data-fitim
# residualsum = np.sum(residuals)
# import pdb ; pdb.set_trace()
fitter = fitting.LevMarLSQFitter()
y, x = np.mgrid[:2*box_size+1, :2*box_size+1]
fit = fitter(model, x, y, region.data)
FWHMx = 2*(2*np.log(2))**0.5*fit.x_stddev_2.value * u.pix
FWHMy = 2*(2*np.log(2))**0.5*fit.y_stddev_2.value * u.pix
FWHM = (FWHMx**2 + FWHMy**2)**0.5/2**0.5
FWHMarcsec = FWHM.to(u.arcsec, equivalencies=pixelscale)
sky_amplitude = fit.amplitude_1.value
star_flux = 2*np.pi*fit.amplitude_2.value*fit.x_stddev_2.value*fit.y_stddev_2.value
star_amplitude = fit.amplitude_2.value
boxpos_x = fit.x_0_0.value
boxpos_y = fit.y_0_0.value
star_x = fit.x_mean_2.value
star_y = fit.y_mean_2.value
if verbose: print(f" Box X Center = {boxpos_x:.0f}")
if verbose: print(f" Box Y Center = {boxpos_y:.0f}")
if verbose: print(f" Sky Brightness = {fit.amplitude_1.value:.0f} ADU")
if verbose: print(f" Stellar FWHM = {FWHMarcsec:.2f}")
if verbose: print(f" Stellar Xpos = {star_x:.0f}")
if verbose: print(f" Stellar Xpos = {star_y:.0f}")
if verbose: print(f" Stellar Amplitude = {star_amplitude:.0f} ADU")
if verbose: print(f" Stellar Flux (fit) = {star_flux:.0f} ADU")
result = {'Star X': star_x,
'Star Y': star_y,
'Star Amplitude': star_amplitude,
'Sky Amplitude': sky_amplitude,
'FWHM pix': FWHM.value,
'FWHM arcsec': FWHMarcsec,
'Box X': boxpos_x,
'Box Y': boxpos_y,
# 'Residuals': residuals,
}
return result
def star_centers_from_PSF_img_cube(cube,
wave,
pixel,
exclude_fraction=0.1,
high_pass=False,
box_size=60,
save_path=None,
logger=_log):
'''
Compute star center from PSF images (IRDIS CI, IRDIS DBI, IFS)
Parameters
----------
cube : array_like
IRDIFS PSF cube
wave : array_like
Wavelength values, in nanometers
pixel : float
Pixel scale, in mas/pixel
exclude_fraction : float
Exclude a fraction of the image borders to avoid getting
biased by hot pixels close to the edges. Default is 10%
high_pass : bool
Apply high-pass filter to the PSF image before searching for the center.
Default is False
box_size : int
Size of the box in which the fit is performed. Default is 60 pixels
save_path : str
Path where to save the fit images. Default is None, which means
that the plot is not produced
logger : logHandler object
Log handler for the reduction. Default is root logger
Returns
-------
img_centers : array_like
The star center in each frame of the cube
'''
# standard parameters
nwave = wave.size
loD = wave * 1e-9 / 8 * 180 / np.pi * 3600 * 1000 / pixel
box = box_size // 2
# spot fitting
xx, yy = np.meshgrid(np.arange(2 * box), np.arange(2 * box))
# loop over images
img_centers = np.zeros((nwave, 2))
failed_centers = np.zeros(nwave, dtype=np.bool)
for idx, (cwave, img) in enumerate(zip(wave, cube)):
logger.info(' ==> wave {0:2d}/{1:2d} ({2:4.0f} nm)'.format(
idx + 1, nwave, cwave))
# remove any NaN
img = np.nan_to_num(cube[idx])
# optional high-pass filter
if high_pass:
img = img - ndimage.median_filter(img, 15, mode='mirror')
cube[idx] = img
# center guess
cy, cx = np.unravel_index(np.argmax(img), img.shape)
# check if we are really too close to the edge
dim = img.shape
lf = exclude_fraction
hf = 1 - exclude_fraction
if (cx <= lf*dim[-1]) or (cx >= hf*dim[-1]) or \
(cy <= lf*dim[0]) or (cy >= hf*dim[0]):
nimg = img.copy()
nimg[:, :int(lf * dim[-1])] = 0
nimg[:, int(hf * dim[-1]):] = 0
nimg[:int(lf * dim[0]), :] = 0
nimg[int(hf * dim[0]):, :] = 0
cy, cx = np.unravel_index(np.argmax(nimg), img.shape)
# sub-image
sub = img[cy - box:cy + box, cx - box:cx + box]
# fit peak with Gaussian + constant
imax = np.unravel_index(np.argmax(sub), sub.shape)
g_init = models.Gaussian2D(amplitude=sub.max(), x_mean=imax[1], y_mean=imax[0],
x_stddev=loD[idx], y_stddev=loD[idx]) + \
models.Const2D(amplitude=sub.min())
fitter = fitting.LevMarLSQFitter()
par = fitter(g_init, xx, yy, sub)
cx_final = cx - box + par[0].x_mean
cy_final = cy - box + par[0].y_mean
img_centers[idx, 0] = cx_final
img_centers[idx, 1] = cy_final
# look for outliers and replace by a linear fit to all good ones
# Ticket #81
ibad = []
if nwave > 2:
c_med = np.median(img_centers, axis=0)
c_std = np.std(img_centers, axis=0)
bad = np.any(np.logical_or(img_centers < (c_med - 3 * c_std),
img_centers > (c_med + 3 * c_std)),
axis=1)
ibad = np.where(bad)[0]
igood = np.where(np.logical_not(bad))[0]
if len(ibad) != 0:
logger.info(
f' ==> found {len(ibad)} outliers. Will replace them with a linear fit.'
)
idx = np.arange(nwave)
# x
lin = np.polyfit(idx[igood], img_centers[igood, 0], 1)
pol = np.poly1d(lin)
img_centers[ibad, 0] = pol(idx[ibad])
# y
lin = np.polyfit(idx[igood], img_centers[igood, 1], 1)
pol = np.poly1d(lin)
img_centers[ibad, 1] = pol(idx[ibad])
#
# Generate summary plot
#
# multi-page PDF to save result
if save_path is not None:
pdf = PdfPages(save_path)
for idx, (cwave, img) in enumerate(zip(wave, cube)):
cx_final = img_centers[idx, 0]
cy_final = img_centers[idx, 1]
failed = (idx in ibad)
if failed:
mcolor = 'r'
bcolor = 'r'
else:
mcolor = 'b'
bcolor = 'w'
plt.figure('PSF center - imaging', figsize=(8.3, 8))
plt.clf()
plt.subplot(111)
plt.imshow(img / np.nanmax(img),
aspect='equal',
norm=colors.LogNorm(vmin=1e-6, vmax=1),
interpolation='nearest',
cmap=global_cmap)
plt.plot([cx_final], [cy_final], marker='D', color=mcolor)
plt.gca().add_patch(
patches.Rectangle((cx - box, cy - box),
2 * box,
2 * box,
ec=bcolor,
fc='none'))
if failed:
plt.text(cx,
cy + box,
'Fit failed',
color='r',
weight='bold',
fontsize='x-small',
ha='center',
va='bottom')
plt.title(r'Image #{0} - {1:.0f} nm'.format(idx + 1, cwave))
ext = 1000 / pixel
plt.xlim(cx_final - ext, cx_final + ext)
plt.xlabel('x position [pix]')
plt.ylim(cy_final - ext, cy_final + ext)
plt.ylabel('y position [pix]')
plt.subplots_adjust(left=0.1, right=0.98, bottom=0.1, top=0.95)
pdf.savefig()
pdf.close()
return img_centers