import astropy.io.fits as iofits
from scipy.stats import norm
from astropy.modeling import models, fitting #A
# Params
fmax, fmin, nbin = 3000, 0, 300 #A
fits = iofits.open('data/fits/fpC-001729-r3-0083.fit.gz')
img = fits[0].data
param = norm.fit(img.flatten())
print(param[0], param[1])
print('中央値：{}, 平均値：{}'.format(np.median(img), img.mean()))
x = np.linspace(fmin, fmax, nbin + 1) + (fmax - fmin) / nbin / 2 #A
x = x[:-1] #A
pdf_fitted = norm.pdf(x, loc=param[0], scale=param[1]) #A
fit = fitting.LevMarLSQFitter() #A
gauss_init = models.Gaussian1D(mean=x[np.argmax(pdf_fitted)],
stddev=100,
amplitude=max(pdf_fitted)) #A
result = fit(gauss_init, x, pdf_fitted) #A
print(result, result.mean[0])
print(gauss_init)
plt.plot(x, pdf_fitted, 'r-')
plt.plot(x, result(x), 'b.')
plt.xlim([0, fmax]) #A
plt.show()
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
"""
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("GET_POINTSOURCE: method: ", method)
print("GET_POINTSOURCE: s: ", s)
print("GET_POINTSOURCE: sign: ", sign)
print("GET_POINTSOURCE: searchsmooth: ", searchsmooth)
print("GET_POINTSOURCE: guessmeth: ", guessmeth)
print("GET_POINTSOURCE: initial guessamp: ", guessamp)
print("GET_POINTSOURCE: initial guessbg: ", guessbg)
print("GET_POINTSOURCE: intial guesspos: ", guesspos)
print("GET_POINTSOURCE: 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("GET_POINTSOURCE: sy0, sy1, sx0, sx1 ", sy0, sy1, sx0, sx1)
searchbox = np.array(np.shape(searchim))
# print("GET_POINTSOURCE: ss: ", np.shape(searchim))
else:
searchbox = np.array(s, dtype=int)
sx0 = 0
sy0 = 0
searchim = im
if verbose:
print("GET_POINTSOURCE: 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("GET_POINTSOURCE: guesspos: ", guesspos)
else:
guesspos = np.array(
np.unravel_index(np.nanargmax(searchim), searchbox))
else:
guesspos = 0.5 * searchbox
if verbose:
print("GET_POINTSOURCE: guesspos in searchbox: ", guesspos)
print("GET_POINTSOURCE: guesspos in total image: ", guesspos[0] + sy0,
guesspos[1] + sx0)
# print("GET_POINTSOURCE: 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("GET_POINTSOURCE: 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("GET_POINTSOURCE: final fitbox: ", fitbox)
print("GET_POINTSOURCE: 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(' - GET_POINTSOURCE: Guess: ', guess)
print(' - GET_POINTSOURCE: minFWHM: ', minFWHM)
print(' - GET_POINTSOURCE: maxFWHM: ', maxFWHM)
print(' - GET_POINTSOURCE: minsigma: ', minsigma)
print(' - GET_POINTSOURCE: maxsigma: ', maxsigma)
print(' - GET_POINTSOURCE: minamp: ', minamp)
print(' - GET_POINTSOURCE: maxamp: ', maxamp)
print(' - GET_POINTSOURCE: 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(
"GET_POINTSOURCE: 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("GET_POINTSOURCE: 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("GET_POINTSOURCE: uncorrected fit params: ", params)
print("GET_POINTSOURCE: 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)
def _fit_lines(spectrum, model, fitter=fitting.LevMarLSQFitter(),
exclude_regions=None, weights=None, window=None,
ignore_units=False, **kwargs):
"""
Fit the input model (initial conditions) to the spectrum. Output will be
the same model with the parameters set based on the fitting.
spectrum, model -> model
"""
#
# If we are to exclude certain regions, then remove them.
#
if exclude_regions is not None:
spectrum = excise_regions(spectrum, exclude_regions)
if isinstance(weights, str):
if weights == 'unc':
uncerts = spectrum.uncertainty
if uncerts is not None:
weights = uncerts.array ** -2
else:
logging.warning("Uncertainty values are not defined, but are "
"trying to be used in model fitting.")
else:
raise ValueError("Unrecognized value `%s` in keyword argument.",
weights)
elif weights is not None:
# Assume that the weights argument is list-like
weights = np.array(weights)
dispersion = spectrum.spectral_axis
dispersion_unit = spectrum.spectral_axis.unit
flux = spectrum.flux
flux_unit = spectrum.flux.unit
#
# Determine the window if it is not None. There
# are several options here:
# window = 4 * u.Angstrom -> Quantity
# window = (4*u.Angstrom, 6*u.Angstrom) -> tuple
# window = (4, 6)*u.Angstrom -> Quantity
#
#
# Determine the window if there is one
#
# In this case the window defines the area around the center of each model
if window is not None and isinstance(window, (float, int)):
center = model.mean
indices = np.nonzero((spectrum.spectral_axis >= center-window) &
(spectrum.spectral_axis < center+window))
dispersion = dispersion[indices]
flux = flux[indices]
if weights is not None:
weights = weights[indices]
# In this case the window is the start and end points of where we
# should fit
elif window is not None and isinstance(window, tuple):
indices = np.nonzero((dispersion >= window[0]) &
(dispersion < window[1]))
dispersion = dispersion[indices]
flux = flux[indices]
if weights is not None:
weights = weights[indices]
elif window is not None and isinstance(window, SpectralRegion):
try:
idx1, idx2 = window.bounds
if idx1 == idx2:
raise Exception("Bad selected region.")
extracted_regions = extract_region(spectrum, window)
dispersion, flux = _combined_region_data(extracted_regions)
dispersion = dispersion * dispersion_unit
flux = flux * flux_unit
except ValueError as e:
return
if flux is None or len(flux) == 0:
raise Exception("Spectrum flux is empty or None.")
input_spectrum = spectrum
spectrum = Spectrum1D(
flux=flux.value * flux_unit,
spectral_axis=dispersion.value * dispersion_unit,
wcs=input_spectrum.wcs,
velocity_convention=input_spectrum.velocity_convention,
rest_value=input_spectrum.rest_value)
#
# Compound models with units can not be fit.
#
# Convert the model initial guess to the spectral
# units and then remove the units
#
model_unitless, dispersion_unitless, flux_unitless = \
_strip_units_from_model(model, spectrum, convert=not ignore_units)
#
# Do the fitting of spectrum to the model.
#
fit_model_unitless = fitter(model_unitless, dispersion_unitless,
flux_unitless, weights=weights, **kwargs)
#
# Now add the units back onto the model....
#
if not ignore_units:
fit_model = _add_units_to_model(fit_model_unitless, model, spectrum)
else:
fit_model = QuantityModel(fit_model_unitless,
spectrum.spectral_axis.unit,
spectrum.flux.unit)
return fit_model
def gen_center_g2d(image,
center_x,
center_y,
box_width,
amp,
x_std,
y_std,
Theta,
model_plotting=False):
"""
PARAMETERS:
center_x = x coordinate of the circular aperture; Type = float
center_y = y coordinate of the circular aperture; Type = float
amp = amplitude of the gaussian. Find from the projection curve along the center; Type = float
x_std = Standard deviation of the Gaussian in x before rotating by theta; Type = float
y_std = Standard deviation of the Gaussian in y before rotating by theta; Type = float
Theta = Rotation angle in radians. The rotation angle increases counterclockwise; Type = float
RETURNS:
seperate_centers = Center of each image; Type = Array [of tuples]
x_values = x_value of center of each image; Type = Array
y_values = y_value of center of each image; Type = Array
"""
#Creating a mesh grid with the shape of image to create model
y_pos, x_pos = np.mgrid[:image.shape[0], :image.shape[1]]
#defining starting and stopping points for drawing a box to fit the gaussian to
xA, yA = int(center_x - box_width), int(center_y - box_width)
xB, yB = int(center_x + box_width), int(center_y + box_width)
# fitting the gaussian model
fit_g = fitting.LevMarLSQFitter()
gauss2D = models.Gaussian2D(amplitude=amp,
x_mean=center_x,
y_mean=center_y,
x_stddev=x_std,
y_stddev=y_std,
theta=Theta)
g = fit_g(gauss2D, x_pos[yA:yB, xA:xB], y_pos[yA:yB, xA:xB], image[yA:yB,
xA:xB])
g1 = fit_g(g, x_pos[yA:yB, xA:xB], y_pos[yA:yB, xA:xB], image[yA:yB,
xA:xB])
#pdb.set_trace()
new_xCen = g1.x_mean[0]
new_yCen = g1.y_mean[0]
fwhm_x = g1.x_fwhm
fwhm_y = g1.y_fwhm
if model_plotting == True:
plt.subplot(131)
plt.imshow(image[yA:yB, xA:xB])
plt.title('Data')
plt.subplot(132)
plt.imshow(g1(x_pos[yA:yB, xA:xB], y_pos[yA:yB, xA:xB]))
plt.title('Model')
plt.subplot(133)
plt.imshow(image[yA:yB, xA:xB] -
g1(x_pos[yA:yB, xA:xB], y_pos[yA:yB, xA:xB]))
plt.title('Residual')
#Results
return new_xCen, new_yCen, fwhm_x, fwhm_y
def test_deriv_2D(self, model_class, test_parameters):
"""
Test the derivative of a model by fitting with an estimated and
analytical derivative.
"""
x_lim = test_parameters['x_lim']
y_lim = test_parameters['y_lim']
if model_class.fit_deriv is None or issubclass(model_class,
PolynomialBase):
return
if "log_fit" in test_parameters:
if test_parameters['log_fit']:
x = np.logspace(x_lim[0], x_lim[1], self.N)
y = np.logspace(y_lim[0], y_lim[1], self.M)
x_test = np.logspace(x_lim[0], x_lim[1], self.N * 10)
y_test = np.logspace(y_lim[0], y_lim[1], self.M * 10)
else:
x = np.linspace(x_lim[0], x_lim[1], self.N)
y = np.linspace(y_lim[0], y_lim[1], self.M)
x_test = np.linspace(x_lim[0], x_lim[1], self.N * 10)
y_test = np.linspace(y_lim[0], y_lim[1], self.M * 10)
xv, yv = np.meshgrid(x, y)
xv_test, yv_test = np.meshgrid(x_test, y_test)
try:
model_with_deriv = create_model(model_class,
test_parameters,
use_constraints=False,
parameter_key='deriv_initial')
model_no_deriv = create_model(model_class,
test_parameters,
use_constraints=False,
parameter_key='deriv_initial')
model = create_model(model_class,
test_parameters,
use_constraints=False,
parameter_key='deriv_initial')
except KeyError:
model_with_deriv = create_model(model_class,
test_parameters,
use_constraints=False)
model_no_deriv = create_model(model_class,
test_parameters,
use_constraints=False)
model = create_model(model_class,
test_parameters,
use_constraints=False)
# add 10% noise to the amplitude
rsn = np.random.default_rng(0)
amplitude = test_parameters['parameters'][0]
n = 0.1 * amplitude * (rsn.random((self.M, self.N)) - 0.5)
data = model(xv, yv) + n
fitter_with_deriv = fitting.LevMarLSQFitter()
new_model_with_deriv = fitter_with_deriv(model_with_deriv, xv, yv,
data)
fitter_no_deriv = fitting.LevMarLSQFitter()
new_model_no_deriv = fitter_no_deriv(model_no_deriv,
xv,
yv,
data,
estimate_jacobian=True)
assert_allclose(new_model_with_deriv(xv_test, yv_test),
new_model_no_deriv(xv_test, yv_test),
rtol=1e-2)
if model_class != Gaussian2D:
assert_allclose(new_model_with_deriv.parameters,
new_model_no_deriv.parameters,
rtol=0.1)
linepad_left = 25
if i == 47 and j == 26:
linepad_left = 75
if i == 48 and j == 26:
linepad_left = 75
line_y_arr_comp1 = line_comp1[line_idx-linepad_left:line_idx+linepad_right, i, j]
line_x_arr_comp1 = np.linspace(line_idx-linepad_left, line_idx+linepad_right, len(line_y_arr_comp1))
line_y_arr_comp2 = line_comp2[line_idx-linepad_left:line_idx+linepad_right, i, j]
line_x_arr_comp2 = np.linspace(line_idx-linepad_left, line_idx+linepad_right, len(line_y_arr_comp2))
# fitting
gauss_init_lowcomp = models.Gaussian1D(amplitude=5.0, mean=line_idx-10, stddev=5.0)
gauss_init_highcomp = models.Gaussian1D(amplitude=5.0, mean=line_idx+10, stddev=5.0)
fit_gauss = fitting.LevMarLSQFitter()
g1 = fit_gauss(gauss_init_lowcomp, line_x_arr_comp1, line_y_arr_comp1)
g2 = fit_gauss(gauss_init_highcomp, line_x_arr_comp2, line_y_arr_comp2)
# save lzifu total fit to array for plotting
line_y_arr_total = line_total[line_idx-linepad_left:line_idx+linepad_right, i, j]
# also fit raw data by a single gaussian
if (i,j) in force_onecomp_arr:
linepad_left = 25
linepad_right = 25
line_y_arr_data = obs_data[line_idx-linepad_left:line_idx+linepad_right, i, j]
line_x_arr_data = np.linspace(line_idx-linepad_left, line_idx+linepad_right, len(line_y_arr_data))
def calc_rv_todcor(spect,wave,sig, template_fns,bad_intervals=[],fig_fn='',\
smooth_distance=201,convolve_template=True, alpha=0.3,\
nwave_log=int(1e4),ncor=1000, return_fitted=False,jd=0.0,out_fn='',\
heliocentric_correction=0, plotit=False):
"""Compute a radial velocity based on an best fitting template spectrum.
Teff is estimated at the same time.
Parameters
----------
spect: array-like
The reduced WiFeS spectrum
wave: array-like
The wavelengths corresponding to the reduced WiFeS spectrum
template_fns: string
Spectral template for star 1 and star 2 that can be read in by np.loadtxt
bad_intervals:
List of wavelength intervals where e.g. telluric absorption is bad. For todcor,
These can only be smoothed over.
smooth_distance: float
Distance to smooth for "continuum" correction
Returns
-------
rv1: float
Radial velocity of star 1 in km/s
rv_sig1: float
Uncertainty in radial velocity (NB assumes good model fit)
rv2: float
Radial velocity of star 2 in km/s
rv_sig2: float
Uncertainty in radial velocity (NB assumes good model fit)
corpeak: float
Correlation peak
"""
(wave_log, spect_int, sig_int, template_ints) = \
interpolate_spectra_onto_log_grid(spect,wave,sig, template_fns,\
bad_intervals=bad_intervals, smooth_distance=smooth_distance, \
convolve_template=convolve_template, nwave_log=nwave_log)
rvs = np.zeros(len(template_fns))
peaks = np.zeros(len(template_fns))
drv = np.log(wave_log[1] / wave_log[0]) * 2.998e5
#*** Next (hopefully with two templates only!) we continue and apply the TODCOR algorithm.
window_width = nwave_log // 20
ramp = np.arange(1, window_width + 1, dtype=float) / window_width
window = np.ones(nwave_log)
window[:window_width] *= ramp
window[-window_width:] *= ramp[::-1]
template_ints[0] *= window
template_ints[1] *= window
spect_int *= window
norm1 = np.sqrt(np.sum(template_ints[0]**2))
norm2 = np.sqrt(np.sum(template_ints[1]**2))
norm_tgt = np.sqrt(np.sum(spect_int**2))
#pdb.set_trace()
c1 = np.fft.irfft(
np.conj(np.fft.rfft(template_ints[0] / norm1)) *
np.fft.rfft(spect_int / norm_tgt))
c1 = np.roll(c1, ncor // 2)[:ncor]
c2 = np.fft.irfft(
np.conj(np.fft.rfft(template_ints[1] / norm2)) *
np.fft.rfft(spect_int / norm_tgt))
c2 = np.roll(c2, ncor // 2)[:ncor]
#Unclear which way around this line should be. ix_c12 sign was corrected in order to
#give the right result with simulated data.
c12 = np.fft.irfft(
np.fft.rfft(template_ints[1] / norm2) *
np.conj(np.fft.rfft(template_ints[0] / norm1)))
c12 = np.roll(c12, ncor // 2)[:ncor]
ix = np.arange(ncor).astype(int)
xy = np.meshgrid(ix, ix)
#Correct the flux ratio for the RMS spectral variation. Is this needed???
alpha_norm = alpha * norm2 / norm1
ix_c12 = np.minimum(np.maximum(xy[0] - xy[1] + ncor // 2, 0),
ncor - 1) #!!!This was the old line !!!
#ix_c12 = np.minimum(np.maximum(xy[1]-xy[0]+ncor//2,0),ncor-1) #XXX New (temporary?) line XXX
todcor = (c1[xy[0]] + alpha_norm * c2[xy[1]]
) / np.sqrt(1 + 2 * alpha_norm * c12[ix_c12] + alpha_norm**2)
#print("Max correlation: {0:5.2f}".format(np.max(todcor)))
#print(alpha_norm)
#plt.plot(drv*(np.arange(nwave_log)-nwave_log//2),np.roll(c1,nwave_log//2))
#Figure like TODCOR paper:
#fig = plt.figure()
#ax = fig.gca(projection='3d')
#ax.plot_surface(xy[0],xy[1],todcor)
plt.clf()
plt.imshow(todcor,
cmap=cm.gray,
interpolation='nearest',
extent=[
-drv * ncor / 2, drv * ncor / 2, -drv * ncor / 2,
drv * ncor / 2
])
xym = np.unravel_index(np.argmax(todcor), todcor.shape)
hw_fit = 2
if (xym[0] < hw_fit) | (xym[1] < hw_fit) | (xym[0] >= ncor - hw_fit) | (
xym[1] >= ncor - hw_fit):
print("Error: TODCOR peak to close to edge!")
raise UserWarning
ix_fit = np.arange(-hw_fit, hw_fit + 1).astype(int)
xy_fit = np.meshgrid(ix_fit, ix_fit)
p_init = models.Gaussian2D(amplitude=np.max(todcor),
x_mean=0,
y_mean=0,
x_stddev=50.0 / drv,
y_stddev=50.0 / drv)
fit_p = fitting.LevMarLSQFitter()
p = fit_p(
p_init, xy_fit[0], xy_fit[1],
todcor[xym[0] - hw_fit:xym[0] + hw_fit + 1,
xym[1] - hw_fit:xym[1] + hw_fit + 1])
#import pdb; pdb.set_trace()
rv_x = drv * ((p.parameters[1] + xym[1]) - ncor // 2)
rv_y = drv * ((p.parameters[2] + xym[0]) - ncor // 2)
model_spect = rv_shift_binary(rv_x / drv, rv_y / drv, alpha,
np.fft.rfft(template_ints[0]),
np.fft.rfft(template_ints[1]))
if plotit:
(wave_log, spect_int_norm, sig_int, template_int_norm) = \
interpolate_spectra_onto_log_grid(spect,wave,sig, template_fns,\
bad_intervals=bad_intervals, smooth_distance=smooth_distance, \
convolve_template=convolve_template, nwave_log=nwave_log, \
subtract_smoothed=False)
model_spect_norm = rv_shift_binary(rv_x/drv, rv_y/drv, alpha, \
np.fft.rfft(template_int_norm[0]), np.fft.rfft(template_int_norm[1]))
model_spect_prim = rv_shift_binary(rv_x/drv, rv_y/drv, 0, \
np.fft.rfft(template_int_norm[0]), np.fft.rfft(template_int_norm[1]))
model_spect_sec = rv_shift_binary(rv_x/drv, rv_y/drv, 1e6, \
np.fft.rfft(template_int_norm[0]), np.fft.rfft(template_int_norm[1]))
ss = np.ones(5e2) / 5e2
model_ss = np.convolve(model_spect_norm, ss, mode='same')
spect_ss = np.convolve(spect_int_norm, ss, mode='same')
plt.clf()
plt.plot(wave_log, model_spect_norm / model_ss, label='Joint Model')
plt.plot(wave_log,
model_spect_prim / model_ss / (1 + alpha),
label='Primary')
plt.plot(wave_log,
model_spect_sec / model_ss * alpha / (1 + alpha),
label='Secondary')
plt.plot(wave_log, spect_int_norm / spect_ss, label='Data')
plt.legend()
plt.axis([3810, 5610, 0, 1.45])
plt.xlabel(r'Wavelength ($\AA$)')
plt.ylabel('Flux (normalised)')
plt.draw()
#pdb.set_trace() #XXX
#Compute theoretical RV uncertainties from the "Q" factors...
errors = []
for i, template_int in enumerate(template_ints):
if (i == 0):
ti = template_int / (1 + alpha)
else:
ti = template_int * alpha / (1 + alpha)
model_spect_deriv = (ti[1:] - ti[:-1]) / (wave_log[1:] - wave_log[:-1])
wave2_on_s = (0.5 * (wave_log[1:] + wave_log[:-1]))**2 / (
0.5 * (ti[1:] + ti[:-1] + 2))
q_factor = np.sqrt(np.mean(wave2_on_s * model_spect_deriv**2))
photon_rv_error = 3e5 / q_factor * np.median(sig_int) / np.sqrt(
len(spect))
errors.append(photon_rv_error)
#ISSUES:
#1) Error (below) not computed.
#errors = np.sqrt(np.diag(fit_p.fit_info['cov_x']))
if len(out_fn) > 0:
outfile = open(out_fn, 'a')
outfile.write(
'{0:12.4f}, {1:8.2f}, {2:8.2f}, {3:8.2f}, {4:8.2f}, {5:8.3f}\n'.
format(jd, rv_x + heliocentric_correction, errors[0],
rv_y + heliocentric_correction, errors[1], np.max(todcor)))
outfile.close()
if return_fitted:
return wave_log, spect_int, model_spect
else:
return rv_x, errors[0], rv_y, errors[1], np.max(todcor)
def findHalfLightSersicdf(pgcs,df1,df2):
#df1 is galbasedf with including r25- get pgc names from this file
#df2 is pickle file
halflights = []
amps = []
ns = []
mses = []
#print('0')
for i in np.arange(len(pgcs)):
print(len(pgcs)-i)
galmask = df2.PGC.isin([pgcs[i]])
rp = df2.loc[galmask]
#print(rp)
pgc=pgcs[i]
if np.isnan(rp.r_arcsec).all()==True:
halflights.append(np.nan)
amps.append(np.nan)
ns.append(np.nan)
mses.append(np.nan)
#print('1')
elif rp.r_arcsec.min()>200:
halflights.append(np.nan)
amps.append(np.nan)
ns.append(np.nan)
mses.append(np.nan)
#print('2')
else:
try:
#print('3')
rp.r_arcsec/=3600.
r25 = df1.loc[i].R25_DEG
#print(r25)`=-0
#r25= r25.tolist()[0]
#print(r25)
mask = rp.r_arcsec<2*r25
#print(mask)
rp = rp[mask]
#mask = rp.I>0
#rp = rp[mask]
ind = np.where(rp.r_arcsec<.5*r25)[0][-1]
sersic = models.Sersic1D(bounds = {'n':(0,14)})
outlier_fit = fitting.FittingWithOutlierRemoval(fitting.LevMarLSQFitter(),sigma_clip, niter=3, sigma=2.5)
fitted_model,filtered_data = outlier_fit(sersic,rp.r_arcsec,rp.I)#,weights=0.1*rp.I)
filtered_data[:ind]=False
fit = fitting.LevMarLSQFitter()
fitted_model = fit(sersic,rp.r_arcsec[~filtered_data],rp.I[~filtered_data])#,weights=(0.1*rp.I[~filtered_data]))
mse = np.nanmean((rp.I[~filtered_data] - fitted_model(rp.I[~filtered_data]))**2)
print('')
print(pgc)
#print(np.round(mse,decimals=2))
"""
if mse>3.:
ns_mse = []
for n in nrange:
sersic = models.Sersic1D(bounds = {'n':(n,n+1)})
outlier_fit = fitting.FittingWithOutlierRemoval(fitting.LevMarLSQFitter(),sigma_clip, niter=3, sigma=3)
fitted_model,filtered_data_chisq = outlier_fit(sersic,rp.r_arcsec[~filtered_data],rp.I[~filtered_data])#,weights=(0.1*rp.I[~filtered_data]))
m = np.nanmean((rp.I[~filtered_data] - fitted_model(rp.I[~filtered_data]))**2)
if m<mse:
mse=m
ns_mse.append(n)
print(mse,n)
else:
pass
if len(ns_mse)==0:
print(ns_mse)
print('none better')
pass
else:
sersic = models.Sersic1D(bounds = {'n':(ns_mse[-1]-1,ns_mse[-1]+1)})
fitted_model = fit(sersic,rp.r_arcsec[~filtered_data],rp.I[~filtered_data])
"""
re = np.round(fitted_model.r_eff.value*3600*0.9,decimals=3)
#re*=0.9
#re = np.round(re,decimals=3)
n = np.round(fitted_model.n.value,decimals=3)
#print(re,saloratio,mm15ratio)
#print(n,mmres.n[i],np.round(mmres['T'][i],decimals=2))
print(re)
if re>250.:
halflights.append(np.nan)
amps.append('fit fail')
ns.append('fit fail')
mses.append('fit fail')
elif re<5.:
halflights.append(np.nan)
amps.append('fit fail')
ns.append('fit fail')
mses.append('fit fail')
else:
halflights.append(re)
amps.append(fitted_model.amplitude.value)
ns.append(n)
mses.append(mse)
except:
halflights.append(np.nan)
amps.append('fit fail')
ns.append('fit fail')
mses.append('fit fail')
redf = pd.DataFrame({'PGC':pgcs,'re':halflights,'amp': amps,'n':ns})
#pgcs = np.asarray(pgcs)
#halflights = np.asarray(halflights,dtype='float')
#amps = np.asarray(amps)
#ns = np.asarray(ns)
#return(pgcs,halflights,amps,ns,datamasks,nummasked)
return(redf)
def photometry(image_paths, master_dark_path, master_flat_path,
target_centroid, comparison_flux_threshold, aperture_radii,
centroid_stamp_half_width, psf_stddev_init,
aperture_annulus_radius, output_path):
"""
Parameters
----------
master_dark_path : str
Path to master dark frame
master_flat_path :str
Path to master flat field
target_centroid : `~numpy.ndarray`
position of centroid, with shape (2, 1)
comparison_flux_threshold : float
Minimum fraction of the target star flux required to accept for a
comparison star to be included
aperture_radii : `~numpy.ndarray`
Range of aperture radii to use
centroid_stamp_half_width : int
Centroiding is done within image stamps centered on the stars. This
parameter sets the half-width of the image stamps.
psf_stddev_init : float
Initial guess for the width of the PSF stddev parameter, used for
fitting 2D Gaussian kernels to the target star's PSF.
aperture_annulus_radius : int
For each aperture in ``aperture_radii``, measure the background in an
annulus ``aperture_annulus_radius`` pixels bigger than the aperture
radius
output_path : str
Path to where outputs will be saved.
"""
master_dark = fits.getdata(master_dark_path)
master_flat = fits.getdata(master_flat_path)
star_positions = init_centroids(image_paths[0],
master_flat,
master_dark,
target_centroid,
plots=True,
min_flux=comparison_flux_threshold).T
# Initialize some empty arrays to fill with data:
times = np.zeros(len(image_paths))
fluxes = np.zeros(
(len(image_paths), len(star_positions), len(aperture_radii)))
errors = np.zeros(
(len(image_paths), len(star_positions), len(aperture_radii)))
xcentroids = np.zeros((len(image_paths), len(star_positions)))
ycentroids = np.zeros((len(image_paths), len(star_positions)))
airmass = np.zeros(len(image_paths))
airpress = np.zeros(len(image_paths))
humidity = np.zeros(len(image_paths))
telfocus = np.zeros(len(image_paths))
psf_stddev = np.zeros(len(image_paths))
medians = np.zeros(len(image_paths))
with ProgressBar(len(image_paths)) as bar:
for i in range(len(image_paths)):
bar.update()
# Subtract image by the dark frame, normalize by flat field
#imagedata = (rebin_image(fits.getdata(image_paths[i]), 2) - master_dark[:-1, :-1]) / master_flat[:-1, :-1]
imagedata = (fits.getdata(image_paths[i]) -
master_dark) / master_flat
# Collect information from the header
imageheader = fits.getheader(image_paths[i])
exposure_duration = imageheader['EXPTIME']
times[i] = Time(imageheader['DATE-OBS'],
format='isot',
scale='utc').jd
medians[i] = np.median(imagedata)
airmass[i] = imageheader['AIRMASS']
airpress[i] = imageheader['AIRPRESS']
humidity[i] = imageheader['HUMIDITY']
telfocus[i] = imageheader['TELFOCUS']
# Initial guess for each stellar centroid informed by previous centroid
for j in range(len(star_positions)):
if i == 0:
init_x = star_positions[j][0]
init_y = star_positions[j][1]
else:
init_x = ycentroids[i - 1][j]
init_y = xcentroids[i - 1][j]
# Cut out a stamp of the full image centered on the star
image_stamp = imagedata[init_y -
centroid_stamp_half_width:init_y +
centroid_stamp_half_width, init_x -
centroid_stamp_half_width:init_x +
centroid_stamp_half_width]
# Measure stellar centroid with 2D gaussian fit
x_stamp_centroid, y_stamp_centroid = centroid_com(image_stamp)
y_centroid = x_stamp_centroid + init_x - centroid_stamp_half_width
x_centroid = y_stamp_centroid + init_y - centroid_stamp_half_width
xcentroids[i, j] = x_centroid
ycentroids[i, j] = y_centroid
# import matplotlib.pyplot as plt
# plt.figure()
# plt.imshow(np.log(image_stamp), origin='lower', cmap=plt.cm.viridis)
# plt.scatter(x_stamp_centroid, y_stamp_centroid, s=30)
# plt.show()
#
# plt.figure()
# s = np.std(imagedata)
# m = np.median(imagedata)
# plt.imshow(imagedata, origin='lower', cmap=plt.cm.viridis,
# vmin=m-2*s, vmax=m+2*s)
# plt.show()
# For the target star, measure PSF:
if j == 0:
psf_model_init = models.Gaussian2D(
amplitude=np.max(image_stamp),
x_mean=centroid_stamp_half_width,
y_mean=centroid_stamp_half_width,
x_stddev=psf_stddev_init,
y_stddev=psf_stddev_init)
fit_p = fitting.LevMarLSQFitter()
y, x = np.mgrid[:image_stamp.shape[0], :image_stamp.
shape[1]]
best_psf_model = fit_p(
psf_model_init, x, y,
image_stamp - np.median(image_stamp))
psf_stddev[i] = 0.5 * (best_psf_model.x_stddev.value +
best_psf_model.y_stddev.value)
positions = np.vstack([ycentroids[i, :], xcentroids[i, :]])
for k, aperture_radius in enumerate(aperture_radii):
target_apertures = CircularAperture(positions, aperture_radius)
background_annuli = CircularAnnulus(
positions,
r_in=aperture_radius + aperture_annulus_radius,
r_out=aperture_radius + 2 * aperture_annulus_radius)
flux_in_annuli = aperture_photometry(
imagedata, background_annuli)['aperture_sum'].data
background = flux_in_annuli / background_annuli.area()
flux = aperture_photometry(
imagedata, target_apertures)['aperture_sum'].data
background_subtracted_flux = (
flux - background * target_apertures.area())
fluxes[i, :,
k] = background_subtracted_flux / exposure_duration
errors[i, :, k] = np.sqrt(flux)
## Save some values
results = PhotometryResults(times, fluxes, errors, xcentroids, ycentroids,
airmass, airpress, humidity, medians,
psf_stddev, aperture_radii)
results.save(output_path)
return results
# Build psf basis
N_psf_basis = abs(cut)
lambdas = valh[cut:]
xs = vech[:, cut:]
psf_basis = []
for i in range(N_psf_basis):
psf_basis.append(np.tensordot(xs[:, i], renders, axes=[0, 0]))
# =============================================================================
# Manual test
# =============================================================================
runtest = False #input('Run Manual test?')
if runtest:
prf_model = models.Gaussian2D(x_stddev=1, y_stddev=1)
fitter = fitting.LevMarLSQFitter()
indices = np.indices(sim.bkg_sub_img.shape)
model_fits = []
best_big = srcs['tnpix'] >= p_sizes[0]**2.
best_small = srcs['tnpix'] <= p_sizes[2]**2.
best_flag = srcs['flag'] < 31
best_srcs = srcs[best_big & best_flag & best_small]
fitshape = (4 * FWHM, 4 * FWHM)
prf_model.x_mean = fitshape[0] / 2.
prf_model.y_mean = fitshape[1] / 2.
for row in best_srcs:
position = (row['y'], row['x'])
y = extract_array(indices[0], fitshape, position)
x = extract_array(indices[1], fitshape, position)
sub_array_data = extract_array(sim.bkg_sub_img,
def ajusta(x_cube, y_cube, imagen_in, l_min_izq, l_max_izq, l_min_der,
l_max_der, guess_line, guess_FWHM, orden_pol):
#def ajusta(x_cube,y_cube,orden_pol):
#scientific packages
import pyfits
import scipy
from scipy.optimize import curve_fit, leastsq
import numpy as np
from numpy import random, exp, sqrt
import matplotlib.pyplot as plt
from astropy.modeling import models, fitting, polynomial
# global imagen_in
# imagen_in=sys.argv[1]
# l_min_izq=float(sys.argv[2])
# l_max_izq=float(sys.argv[3])
# l_min_der=float(sys.argv[4])
# l_max_der=float(sys.argv[5])
# guess_line=float(sys.argv[6])
# guess_FWHM=float(sys.argv[7])
# orden_pol=float(sys.argv[8])
def Lee_cubo(spectra, XX, YY):
global imagen
imagen = pyfits.getdata(spectra, header=False)
header = pyfits.getheader(spectra)
#print len(imagen)
#empty array
Lambda_t = []
Flux_t = []
for i in range(len(imagen)):
y = imagen[i][XX][YY]
# x=i*header['CDELT1']+header['CRVAL1']
x = i * header['CD3_3'] + header['CRVAL3']
Lambda_t.append(float(imagen[i][XX][YY]))
#Flux_t.append(float(i*header['CDELT1']+header['CRVAL1']))
Flux_t.append(float(i * header['CD3_3'] + header['CRVAL3']))
#print x,y
Flux = np.array(Lambda_t)
Lambda = np.array(Flux_t)
x = Lambda
y = Flux
return x, y
##########################
##
## Funcion Region
## Toma una region de un espectro entre
## un minimo lambda y un maximo lambda
## x e y corresponden a lamba y cuentas o flujo
##
###########################
#
def region(minimo, maximo, x, y):
xar = []
yar = []
for i in range(len(x)):
if (x[i] > minimo) and (x[i] < maximo):
xar.append(float(x[i]))
yar.append(float(y[i]))
xar = np.array(xar)
yar = np.array(yar)
return xar, yar
#########################
#
# Funcion Region_discontinuo
# Toma dos regiones de un espectro separadoas entre
# un minimo lambda y un maximo lambda a la izquierda y un
# un minimo lambda y un maximo lambda a la deracha de la emission o obsorption
# x e y corresponden a lamba y cuentas (o flujo)
#
##########################
def region_discontinua(minimo1, maximo1, minimo2, maximo2, x, y):
xar = []
yar = []
for i in range(len(x)):
if ((x[i] > minimo1) and (x[i] < maximo1)) or ((x[i] > minimo2) and
(x[i] < maximo2)):
xar.append(float(x[i]))
yar.append(float(y[i]))
xar = np.array(xar)
yar = np.array(yar)
return xar, yar
#######
# poly_fit, fitea un polinomio a datos
# xp e yp correspondend a x e y a ser fiteado
#
# en este caso corresponden al x e y del output de la
# region discontinua
#
#
#######
def poly_fit(xp, yp, grado_pol):
t_init = polynomial.Polynomial1D(degree=int(grado_pol))
fit_t = fitting.LevMarLSQFitter()
t = fit_t(t_init, xp, yp)
return t
#calclulo original
x_sci, y_sci = Lee_cubo(imagen_in, x_cube, y_cube)
x = x_sci
y = y_sci
xspec_o, yspec_o = region(l_min_izq, l_max_der, x, y)
#################
###Fitting regions with a polynomio
x_cont_o, y_cont_o = region_discontinua(l_min_izq, l_max_izq, l_min_der,
l_max_der, x, y)
#cont1=poly_fit(xa1,ya1,12)
#cont2=poly_fit(xa2,ya2,12)
cont3_o = poly_fit(x_cont_o, y_cont_o, orden_pol)
#print cont1
#print cont2
#res1= -cont1(xa1)+ ya1
#res2= -cont2(xa2)+ ya2
res3_o = -cont3_o(x_cont_o) + y_cont_o
#se aplica el polinomio al espectro en la zona de interes
res4_o = -cont3_o(xspec_o) + yspec_o
#####################
#
# Normalization!!!
#
######################
res4_oN = yspec_o / cont3_o(xspec_o)
######################
################
#iteracion 1
t_init4_o = models.Gaussian1D(amplitude=1,
mean=guess_line,
stddev=guess_FWHM)
fit_t4_o = fitting.LevMarLSQFitter()
t4_o = fit_t4_o(t_init4_o, xspec_o, res4_o)
a_science = t4_o.mean.value
b_science = t4_o.stddev.value
Amplitud = t4_o.amplitude.value
# Redefiniendo: de acuerdo al FWHM
#xspec_o,yspec_o=region(l_min_izq,l_max_der,x,y)
#x_cont_o,y_cont_o=region_discontinua(l_min_izq,l_max_izq,l_min_der,l_max_der,x,y)
#cont3_o=poly_fit(x_cont_o,y_cont_o,orden_pol)
#res4_o= -cont3_o(xspec_o)+yspec_o
import numpy
from scipy.optimize import curve_fit
import matplotlib.pyplot as plt
import math
CWt = t4_o.mean.value
FWHMt = 2 * sqrt(2 * math.log(2)) * t4_o.stddev.value
At = t4_o.amplitude.value
xspec_o, yspec_o = region(CWt - 5 * FWHMt, CWt + 5 * FWHMt, x, y)
x_cont_o, y_cont_o = region_discontinua(CWt - 5 * FWHMt, CWt - 3 * FWHMt,
CWt + 3 * FWHMt, CWt + 5 * FWHMt,
x, y)
cont3_o = poly_fit(x_cont_o, y_cont_o, orden_pol)
res4_o = -cont3_o(xspec_o) + yspec_o
#iteracion 1
t_init4_o = models.Gaussian1D(amplitude=Amplitud,
mean=a_science,
stddev=b_science)
fit_t4_o = fitting.LevMarLSQFitter()
t4_o = fit_t4_o(t_init4_o, xspec_o, res4_o)
a_science = t4_o.mean.value
b_science = t4_o.stddev.value
Amplitud = t4_o.amplitude.value
#iteracion 2 para gaussiana
t_init4_o = models.Gaussian1D(amplitude=Amplitud,
mean=a_science,
stddev=b_science)
fit_t4_o = fitting.LevMarLSQFitter()
t4_o = fit_t4_o(t_init4_o, xspec_o, res4_o)
residuo_o = -t4_o(xspec_o) + res4_o
#print "resultados",t_init4,t4
#print "resultados",t4_o
a_science = t4_o.mean.value
b_science = t4_o.stddev.value
c_science_amplitude = t4_o.amplitude.value
#Aplicando FWHM guess
guess_FWHM_gauss = -float(-b_science)
#print guess_FWHM_gauss
#exit(0)
##print t4.mean
Lambda_gauss_fit_sci = "{:10.3f}".format(a_science)
Sigma_gauss_fit_sci = "{:10.3f}".format(b_science)
#print Lambda_gauss_fit_sci, Sigma_gauss_fit_sci
#print a ,b
central_wavelenght = t4_o.mean.value
FWHM = t4_o.stddev.value
Amplitude = t4_o.amplitude.value
import numpy
from scipy.optimize import curve_fit
import matplotlib.pyplot as plt
import math
# Define model function to be used to fit to the data above:
def gauss(x, *p):
A, mu, sigma = p
return A * numpy.exp(-(x - mu)**2 / (2. * sigma**2))
CW = t4_o.mean.value
FWHM = 2 * sqrt(2 * math.log(2)) * t4_o.stddev.value
A = t4_o.amplitude.value
# def Momentos(x,*p)
#INTEGRAL
from scipy import integrate
#def myfunc(x, a, b):
# return (x**b) + a
#
## These are the arguments that will be passed as a and b to myfunc()
args = A, CW, FWHM
#print args
#
## Integrate myfunc() from 0.5 to 1.5
#print CW,CW-4*FWHM, CW+4*FWHM,FWHM
#results = integrate.quad(gauss, min(x_sci), max(x_sci), args)
results = integrate.romberg(gauss, CW - 5 * FWHM, CW + 5 * FWHM, args)
#print results, gauss(CW-4*FWHM,A,CW,FWHM), gauss(CW+4*FWHM,A,CW,FWHM), gauss(CW+4*FWHM,A,CW,FWHM)*(CW+4*FWHM-(CW-4*FWHM))
#print x_cube,y_cube,A,CW,FWHM,results
# print Lambda_gauss_fit_sci, Sigma_gauss_fit_sci
#plt.plot(xspec_o,res4_o, 'c-',lw=1,label='gaus')
#plt.plot(xspec_o,t4_o(xspec_o),'r-', lw=2,label='gauss')
#plt.pause(0.005)
#plt.clf()
RESULTADO = int(x_cube), int(y_cube), float(A), float(CW), float(
FWHM), float(results)
return RESULTADO[0], RESULTADO[1], RESULTADO[2], RESULTADO[3], RESULTADO[
4], RESULTADO[5]
def Flux_line(
source_name, instru, line, row, column
): #row/colonne définit la position d'un pixel instru=MAPS/SPIRE_Map
fit_g = fitting.LevMarLSQFitter()
if instru == 'PACS':
Wave_red, Flux_red = flux_PACS(source_name,
'R')[2], flux_PACS(source_name, 'R')[4]
Wave_blue, Flux_blue = flux_PACS(source_name,
'B')[2], flux_PACS(source_name,
'B')[4]
fit_g = fitting.LevMarLSQFitter()
if line == 'NII_122_em' or line == 'OH_119' or line == 'OI_145' or line == 'NII_122_abs' or line == 'Thing_123':
cond = np.where(np.isfinite(Flux_red[:, row, column]))
Wave_R, Flux_R = Wave_red[cond], Flux_red[:, row, column][cond]
if line == 'NIII_57' or line == 'OI_63':
cond = np.where(np.isfinite(Flux_blue[:, row, column]))
Wave_B, Flux_B = Wave_blue[cond], Flux_blue[:, row, column][cond]
if np.shape(cond)[1] != 0:
if line == 'NII_122_em':
NII = Flux_R[np.where((Wave_R > 121.5) & (Wave_R < 122.5))]
fit_line = fit_lines_gauss(Wave_R, Flux_R, NII, 'Em')[2]
if line == 'NII_122_abs':
NII = Flux_R[np.where((Wave_R > 121.5) & (Wave_R < 122.5))]
fit_line = fit_lines_gauss(Wave_R, Flux_R, NII, 'Abs')[2]
if line == 'Thing_123':
Thing_123 = Flux_R[np.where((Wave_R > 122.5)
& (Wave_R < 123.5))]
fit_line = fit_lines_gauss(Wave_R, Flux_R, Thing_123, 'Em')[2]
if line == 'NIII_57':
NIII = Flux_B[np.where((Wave_B > 56) & (Wave_B < 58))]
fit_line = fit_lines_gauss(Wave_B, Flux_B, NIII, 'Em')[2]
if line == 'OH_119':
OH_1 = Flux_R[np.where((Wave_R > 119.21) & (Wave_R < 119.25))]
OH_2 = Flux_R[np.where((Wave_R > 119.42) & (Wave_R < 119.46))]
g_init_OH_1, g_init_OH_2 = fit_lines_gauss(
Wave_R, Flux_R, OH_1,
'Abs')[1], fit_lines_gauss(Wave_R, Flux_R, OH_2, 'Abs')[1]
l_init_continuum = models.Polynomial1D(degree=2)
g_line_OH = g_init_OH_1 + g_init_OH_2 + l_init_continuum
fit_line = fit_g(g_line_OH, Wave_R, Flux_R)
if line == 'OI_63':
OI_63 = Flux_B[np.where((Wave_B > 62) & (Wave_B < 64))]
fit_line = fit_lines_gauss(Wave_B, Flux_B, OI_63, 'Em')[2]
if line == 'OI_145':
OI_145 = Flux_R[np.where((Wave_R > 144.8) & (Wave_R < 145.8))]
fit_line = fit_lines_gauss(Wave_R, Flux_R, OI_145, 'Em')[2]
amplitude, std = abs(fit_line.amplitude_0[0]), fit_line.stddev_0[
0] #On retrouve les paramètres A et sigma pour le calcul du flux des lines
Line_flux = amplitude * std * np.sqrt(2 * np.pi)
else:
Line_flux = 0
if instru == 'SPIRE_Map':
Wave_red, Flux_red = plot_image_flux_SPIRE_Map(
source_name, 'HR',
'SSW')[2], plot_image_flux_SPIRE_Map(source_name, 'HR', 'SSW')[4]
Wave_blue, Flux_blue = plot_image_flux_SPIRE_Map(
source_name, 'HR',
'SLW')[2], plot_image_flux_SPIRE_Map(source_name, 'HR', 'SLW')[4]
fit_g = fitting.LevMarLSQFitter()
if line == 'NII_1461' or line == 'OH_971' or line == 'OH_1033' or line == 'H2O_1113' or line == 'H2O_1115':
cond = np.where(np.isfinite(Flux_red[:, row, column]))
Wave_R, Flux_R = Wave_red[cond], Flux_red[:, row, column][cond]
if line == 'CI_10' or line == 'CI_21' or line == 'CO_43' or line == 'CO_54' or line == 'CO_65' or line == 'CO_76' or line == 'CO_87' or line == 'CH_835' or line == 'OH_909':
cond = np.where(np.isfinite(Flux_blue[:, row, column]))
Wave_B, Flux_B = Wave_blue[cond], Flux_blue[:, row, column][cond]
if np.shape(cond)[1] != 0:
#High frequencies
if line == 'NII_1461':
NII = Flux_R[np.where((Wave_R > 1450) & (Wave_R < 1466))]
fit_line = fit_lines_sinc(Wave_R, Flux_R, NII, 'Em')[2]
if line == 'HF_10':
HF_10 = Flux_R[np.where((Wave_R > 1230) & (Wave_R < 1234))]
fit_line = fit_lines_sinc(Wave_R, Flux_R, HF_10, 'Abs')[2]
if line == 'H2O_1113':
H2O_1113 = Flux_R[np.where((Wave_R > 1112) & (Wave_R < 1114))]
fit_line = fit_lines_sinc(Wave_R, Flux_R, H2O_1113, 'Abs')[2]
if line == 'H2O_1115':
H2O_1115 = Flux_R[np.where((Wave_R > 1114) & (Wave_R < 1116))]
fit_line = fit_lines_sinc(Wave_R, Flux_R, H2O_1115, 'Abs')[2]
if line == 'OH_971':
OH_971 = Flux_R[np.where((Wave_R > 970) & (Wave_R < 974))]
fit_line = fit_lines_sinc(Wave_R, Flux_R, OH_971, 'Abs')[2]
if line == 'OH_1033':
OH_1033 = Flux_R[np.where((Wave_R > 1031) & (Wave_R < 1034))]
fit_line = fit_lines_sinc(Wave_R, Flux_R, OH_1033, 'Abs')[2]
#Low Frequencies
if line == 'CI_10':
CI_10 = Flux_B[np.where((Wave_B > 490) & (Wave_B < 493.8))]
fit_line = fit_lines_sinc(Wave_B, Flux_B, CI_10, 'Em')[2]
if line == 'CI_21':
#if source_name=='MGE_4121':
CI_21 = Flux_B[np.where((Wave_B > 807) & (Wave_B < 812))]
fit_line = fit_lines_sinc(Wave_B, Flux_B, CI_21, 'Em')[2]
if line == 'CO_43':
CO_43 = Flux_B[np.where((Wave_B > 459) & (Wave_B < 463))]
fit_line = fit_lines_sinc(Wave_B, Flux_B, CO_43, 'Em')[2]
if line == 'CO_54':
CO_54 = Flux_B[np.where((Wave_B > 573.5) & (Wave_B < 580))]
fit_line = fit_lines_sinc(Wave_B, Flux_B, CO_54, 'Em')[2]
if line == 'CO_65':
CO_65 = Flux_B[np.where((Wave_B > 689) & (Wave_B < 693))]
fit_line = fit_lines_sinc(Wave_B, Flux_B, CO_65, 'Em')[2]
if line == 'CO_76':
CO_65 = Flux_B[np.where((Wave_B > 804) & (Wave_B < 807))]
fit_line = fit_lines_sinc(Wave_B, Flux_B, CO_76, 'Em')[2]
if line == 'CO_87':
CO_65 = Flux_B[np.where((Wave_B > 920) & (Wave_B < 922))]
fit_line = fit_lines_sinc(Wave_B, Flux_B, CO_87, 'Em')[2]
if line == 'CH_835':
CH_835 = Flux_B[np.where((Wave_B > 834) & (Wave_B < 837))]
fit_line = fit_lines_sinc(Wave_B, Flux_B, CH_835, 'Abs')[2]
if line == 'OH_909':
OH_909 = Flux_B[np.where((Wave_B > 907) & (Wave_B < 911))]
fit_line = fit_lines_sinc(Wave_B, Flux_B, OH_909, 'Abs')[2]
amplitude, std = abs(fit_line.amplitude_0[0]), abs(
fit_line.sigma_0[0]
) #On retrouve les paramètres A et sigma pour le calcul du flux des lines
Line_flux = amplitude * std * np.pi
else:
Line_flux = 0
return Line_flux
def test_deriv_2D(self, model_class, test_parameters):
"""
Test the derivative of a model by fitting with an estimated and
analytical derivative.
"""
x_lim = test_parameters['x_lim']
y_lim = test_parameters['y_lim']
if model_class.fit_deriv is None:
pytest.skip("Derivative function is not defined for model.")
if issubclass(model_class, PolynomialBase):
pytest.skip("Skip testing derivative of polynomials.")
if "log_fit" in test_parameters:
if test_parameters['log_fit']:
x = np.logspace(x_lim[0], x_lim[1], self.N)
y = np.logspace(y_lim[0], y_lim[1], self.M)
else:
x = np.linspace(x_lim[0], x_lim[1], self.N)
y = np.linspace(y_lim[0], y_lim[1], self.M)
xv, yv = np.meshgrid(x, y)
try:
model_with_deriv = create_model(model_class,
test_parameters,
use_constraints=False,
parameter_key='deriv_initial')
model_no_deriv = create_model(model_class,
test_parameters,
use_constraints=False,
parameter_key='deriv_initial')
model = create_model(model_class,
test_parameters,
use_constraints=False,
parameter_key='deriv_initial')
except KeyError:
model_with_deriv = create_model(model_class,
test_parameters,
use_constraints=False)
model_no_deriv = create_model(model_class,
test_parameters,
use_constraints=False)
model = create_model(model_class,
test_parameters,
use_constraints=False)
# add 10% noise to the amplitude
rsn = np.random.RandomState(1234567890)
amplitude = test_parameters['parameters'][0]
n = 0.1 * amplitude * (rsn.rand(self.M, self.N) - 0.5)
data = model(xv, yv) + n
fitter_with_deriv = fitting.LevMarLSQFitter()
new_model_with_deriv = fitter_with_deriv(model_with_deriv, xv, yv,
data)
fitter_no_deriv = fitting.LevMarLSQFitter()
new_model_no_deriv = fitter_no_deriv(model_no_deriv,
xv,
yv,
data,
estimate_jacobian=True)
assert_allclose(new_model_with_deriv.parameters,
new_model_no_deriv.parameters,
rtol=0.1)
def test_nircam_coron_wfe_offset(fov_pix=15, oversample=2, fit_gaussian=True):
"""
Test offset of LW coronagraphic PSF w.r.t. wavelength due to optical wedge dispersion.
Option to fit a Gaussian to PSF core in order to better determine peak position.
Difference from 2.5 to 3.3 um should be ~0.015mm.
Difference from 3.3 to 5.0 um should be ~0.030mm.
"""
# Disable Gaussian fit if astropy not installed
if fit_gaussian:
try:
from astropy.modeling import models, fitting
except ImportError:
fit_gaussian = False
# Ensure oversample to >1 no Gaussian fitting
if fit_gaussian == False:
oversample = 2 if oversample < 2 else oversample
rtol = 0.2
else:
rtol = 0.1
# Set up an off-axis coronagraphic PSF
inst = webbpsf_core.NIRCam()
inst.filter = 'F335M'
inst.pupil_mask = 'CIRCLYOT'
inst.image_mask = None
inst.include_si_wfe = True
inst.options['jitter'] = None
# size of an oversampled pixel in mm (detector pixels are 18um)
mm_per_pix = 18e-3 / oversample
# Investigate the differences between three wavelengths
warr = np.array([2.5, 3.3, 5.0])
# Find PSF position for each wavelength
yloc = []
for w in warr:
hdul = inst.calc_psf(monochromatic=w * 1e-6,
oversample=oversample,
add_distortion=False,
fov_pixels=fov_pix)
# Vertical image cross section of oversampled PSF
im = hdul[0].data
sh = im.shape
xvals = mm_per_pix * (np.arange(sh[0]) - sh[0] / 2)
yvals = im[:, int(sh[1] / 2)]
# Fit 1D Gaussian to vertical cross section of PSF
if fit_gaussian:
# Create Gaussian model fit of PSF core to determine y offset
g_init = models.Gaussian1D(amplitude=yvals.max(),
mean=0,
stddev=0.01)
fit_g = fitting.LevMarLSQFitter()
g = fit_g(g_init, xvals, yvals)
yloc.append(g.mean.value)
else:
# Just use PSF max location
yloc.append(xvals[yvals == yvals.max()][0])
yloc = np.array(yloc)
# Difference from 2.5 to 3.3 um should be ~0.015mm
diff_25_33 = np.abs(yloc[0] - yloc[1])
assert np.allclose(
diff_25_33, 0.016, rtol=rtol
), "PSF shift between {:.2f} and {:.2f} um of {:.3f} mm does not match expected value (~0.016 mm).".format(
warr[1], warr[0], diff_25_33)
# Difference from 3.3 to 5.0 um should be ~0.030mm
diff_50_33 = np.abs(yloc[2] - yloc[1])
assert np.allclose(
diff_50_33, 0.032, rtol=rtol
), "PSF shift between {:.2f} and {:.2f} um of {:.3f} mm does not match expected value (~0.032 mm).".format(
warr[1], warr[2], diff_50_33)
def test_gaussian2d_positive_stddev():
# This is 2D Gaussian with noise to be fitted, as provided by @ysBach
test = [
[
-54.33, 13.81, -34.55, 8.95, -143.71, -0.81, 59.25, -14.78, -204.9,
-30.87, -124.39, 123.53, 70.81, -109.48, -106.77, 35.64, 18.29
],
[
-126.19, -89.13, 63.13, 50.74, 61.83, 19.06, 65.7, 77.94, 117.14,
139.37, 52.57, 236.04, 100.56, 242.28, -180.62, 154.02, -8.03
],
[
91.43, 96.45, -118.59, -174.58, -116.49, 80.11, -86.81, 14.62,
79.26, 7.56, 54.99, 260.13, -136.42, -20.77, -77.55, 174.52, 134.41
],
[
33.88, 7.63, 43.54, 70.99, 69.87, 33.97, 273.75, 176.66, 201.94,
336.34, 340.54, 163.77, -156.22, 21.49, -148.41, 94.88, 42.55
],
[
82.28, 177.67, 26.81, 17.66, 47.81, -31.18, 353.23, 589.11, 553.27,
242.35, 444.12, 186.02, 140.73, 75.2, -87.98, -18.23, 166.74
],
[
113.09, -37.01, 134.23, 71.89, 107.88, 198.69, 273.88, 626.63,
551.8, 547.61, 580.35, 337.8, 139.8, 157.64, -1.67, -26.99, 37.35
],
[
106.47, 31.97, 84.99, -125.79, 195.0, 493.65, 861.89, 908.31,
803.9, 781.01, 532.59, 404.67, 115.18, 111.11, 28.08, 122.05,
-58.36
],
[
183.62, 45.22, 40.89, 111.58, 425.81, 321.53, 545.09, 866.02,
784.78, 731.35, 609.01, 405.41, -19.65, 71.2, -140.5, 144.07, 25.24
],
[
137.13, -86.95, 15.39, 180.14, 353.23, 699.01, 1033.8, 1014.49,
814.11, 647.68, 461.03, 249.76, 94.8, 41.17, -1.16, 183.76, 188.19
],
[
35.39, 26.92, 198.53, -37.78, 638.93, 624.41, 816.04, 867.28,
697.0, 491.56, 378.21, -18.46, -65.76, 98.1, 12.41, -102.18, 119.05
],
[
190.73, 125.82, 311.45, 369.34, 554.39, 454.37, 755.7, 736.61,
542.43, 188.24, 214.86, 217.91, 7.91, 27.46, -172.14, -82.36,
-80.31
],
[
-55.39, 80.18, 267.19, 274.2, 169.53, 327.04, 488.15, 437.53,
225.38, 220.94, 4.01, -92.07, 39.68, 57.22, 144.66, 100.06, 34.96
],
[
130.47, -4.23, 46.3, 101.49, 115.01, 217.38, 249.83, 115.9, 87.36,
105.81, -47.86, -9.94, -82.28, 144.45, 83.44, 23.49, 183.9
],
[
-110.38, -115.98, 245.46, 103.51, 255.43, 163.47, 56.52, 33.82,
-33.26, -111.29, 88.08, 193.2, -100.68, 15.44, 86.32, -26.44,
-194.1
],
[
109.36, 96.01, -124.89, -16.4, 84.37, 114.87, -65.65, -58.52,
-23.22, 42.61, 144.91, -209.84, 110.29, 66.37, -117.85, -147.73,
-122.51
],
[
10.94, 45.98, 118.12, -46.53, -72.14, -74.22, 21.22, 0.39, 86.03,
23.97, -45.42, 12.05, -168.61, 27.79, 61.81, 84.07, 28.79
],
[
46.61, -104.11, 56.71, -90.85, -16.51, -66.45, -141.34, 0.96,
58.08, 285.29, -61.41, -9.01, -323.38, 58.35, 80.14, -101.22,
145.65
]
]
g_init = models.Gaussian2D(x_mean=8, y_mean=8)
fitter = fitting.LevMarLSQFitter()
y, x = np.mgrid[:17, :17]
g_fit = fitter(g_init, x, y, test)
# Compare with @ysBach original result:
# - x_stddev was negative, so its abs value is used for comparison here.
# - theta is beyond (-90, 90) deg, which doesn't make sense, so ignored.
assert_allclose([g_fit.amplitude.value, g_fit.y_stddev.value],
[984.7694929790363, 3.1840618351417307],
rtol=1.5e-6)
assert_allclose(g_fit.x_mean.value, 7.198391516587464)
assert_allclose(g_fit.y_mean.value, 7.49720660088511, rtol=5e-7)
assert_allclose(g_fit.x_stddev.value, 1.9840185107597297, rtol=2e-6)
def fitting(wave_range, flux_range, z, plot=0):
set_params = set_parameters(z)
elines = set_params[0]
redshift = set_params[1]
z = redshift[0]
z_min, z_max = redshift[1], redshift[2]
disp = set_params[2]
fit_sigma, sigma, sigma_min, sigma_max = disp[0], disp[1], disp[2], disp[3]
link = np.asarray(set_params[3])
eline_link = set_params[4]
type = set_params[5]
n_elines = np.count_nonzero(~np.isnan(elines))
if n_elines == 1:
def G_model(x, A0=1, sigma0=2, z00=z):
l_0 = elines[0] * (1 + z00)
model0 = A0 * np.exp(-0.5 * (x - l_0)**2 / (sigma0**2))
return model0 + model1
def G_deriv(x, A0=1, sigma0=2, z00=z):
# Jacobian of G_model
l_0 = elines[0] * (1 + z00)
y0 = (x - l_0) / (sigma0)
model0 = A0 * np.exp(-0.5 * y0**2)
d_A0 = np.exp(-0.5 * y0**2)
d_sigma0 = A0 * d_A0 * (x - l_0)**2 / sigma0**3
d_z00 = elines[0] * A0 * d_A0 * (x - l_0) / sigma0**2
return [d_A0, d_sigma0, d_z00]
# initialize fitters
from astropy.modeling import models, fitting
fit = fitting.LevMarLSQFitter()
or_fit = fitting.FittingWithOutlierRemoval(fit,
sigma_clip,
niter=3,
sigma=3.0)
GaussModel = custom_model(G_model, fit_deriv=G_deriv)
model = GaussModel()
or_fitted_model, mask = or_fit(model, wave_range, flux_range)
A0_best, sigma_best, z_best = mask.A0, mask.sigma0, mask.z00
if plot == 1:
plt.plot(wave_range, flux_range, 'k+')
plt.plot(wave_range,
G_model(wave_range, A0_best, sigma_best, z_best), "k-")
return [sigma_best, [A0_best], z_best, or_fitted_model] #best_vals
if n_elines == 2:
def G_model(x, A0=1, A1=1, sigma0=2, z00=z):
l_0 = elines[0] * (1 + z00)
l_1 = elines[1] * (1 + z00)
model0 = A0 * np.exp(-0.5 * (x - l_0)**2 / (sigma0**2))
model1 = A1 * np.exp(-0.5 * (x - l_1)**2 / (sigma0**2))
return model0 + model1
def G_deriv(x, A0=1, A1=1, sigma0=2, z00=z):
# Jacobian of G_model
l_0 = elines[0] * (1 + z00)
l_1 = elines[1] * (1 + z00)
y0 = (x - l_0) / (sigma0)
y1 = (x - l_1) / (sigma0)
model0 = A0 * np.exp(-0.5 * y0**2)
model1 = A1 * np.exp(-0.5 * y1**2)
d_A0 = np.exp(-0.5 * y0**2)
d_A1 = np.exp(-0.5 * y1**2)
d_sigma0 = A0 * d_A0 * (x - l_0)**2 / sigma0**3 + A1 * d_A1 * (
x - l_1)**2 / sigma0**3
d_z00 = elines[0] * A0 * d_A0 * (x - l_0) / sigma0**2 + elines[
1] * A1 * d_A1 * (x - l_1) / sigma0**2
return [d_A0, d_A1, d_sigma0, d_z00]
if 0 in link:
#Amplitud que no se va a ajustar
link_index_0 = np.where(link == 0)[0][0]
#Las que si se van a ajustar
link_index_1 = np.where(link == 1)[0][0]
#A que linea se va a linkear.
eline_to_link = eline_link[link_index_0]
if link_index_0 == 0 and eline_to_link == 1:
A0_best = A1_best / 3.
if link_index_0 == 1 and eline_to_link == 0:
A1_best = A0_best / 3.
# initialize fitters
from astropy.modeling import models, fitting
fit = fitting.LevMarLSQFitter()
or_fit = fitting.FittingWithOutlierRemoval(fit,
sigma_clip,
niter=3,
sigma=3.0)
GaussModel = custom_model(G_model, fit_deriv=G_deriv)
model = GaussModel()
or_fitted_model, mask = or_fit(model, wave_range, flux_range)
A0_best, A1_best, sigma_best, z_best = mask.A0, mask.A1, mask.sigma0, mask.z00
if plot == 1:
plt.plot(wave_range, flux_range, 'k+')
plt.plot(wave_range,
G_model(wave_range, A0_best, A1_best, sigma_best, z_best),
"k-")
return [sigma_best, [A0_best, A1_best], z_best,
or_fitted_model] #best_vals
if n_elines == 3:
################################################################################
def G_model(x, A0=1, A1=1, A2=1, sigma0=2, z00=z):
l_0 = elines[0] * (1 + z00)
l_1 = elines[1] * (1 + z00)
l_2 = elines[2] * (1 + z00)
model0 = A0 * np.exp(-0.5 * (x - l_0)**2 / (sigma0**2))
model1 = A1 * np.exp(-0.5 * (x - l_1)**2 / (sigma0**2))
model2 = A2 * np.exp(-0.5 * (x - l_2)**2 / (sigma0**2))
#A0=A2/3.
return model0 + model1 + model2
def G_deriv(x, A0=1, A1=1, A2=1, sigma0=2, z00=z):
# Jacobian of G_model
l_0 = elines[0] * (1 + z00)
l_1 = elines[1] * (1 + z00)
l_2 = elines[2] * (1 + z00)
y0 = (x - l_0) / (sigma0)
y1 = (x - l_1) / (sigma0)
y2 = (x - l_2) / (sigma0)
#A0=A2/3.
model0 = A0 * np.exp(-0.5 * y0**2)
model1 = A1 * np.exp(-0.5 * y1**2)
model2 = A2 * np.exp(-0.5 * y2**2)
d_A0 = np.exp(-0.5 * y0**2)
d_A1 = np.exp(-0.5 * y1**2)
d_A2 = np.exp(-0.5 * y2**2)
d_sigma0 = A0 * d_A0 * (x - l_0)**2 / sigma0**3 + A1 * d_A1 * (
x - l_1)**2 / sigma0**3 + A2 * d_A2 * (x - l_2)**2 / sigma0**3
d_z00 = elines[0] * A0 * d_A0 * (
x - l_0) / sigma0**2 + elines[1] * A1 * d_A1 * (
x - l_1) / sigma0**2 + elines[2] * A2 * d_A2 * (
x - l_2) / sigma0**2
return [d_A0, d_A1, d_A2, d_sigma0, d_z00]
# initialize fitters
from astropy.modeling import models, fitting
fit = fitting.LevMarLSQFitter()
#or_fit = fitting.FittingWithOutlierRemoval(fit, sigma_clip,niter=1, sigma=3)
GaussModel = custom_model(G_model, fit_deriv=G_deriv)
model = GaussModel(
bounds={
"sigma0": (1., 10.),
"z00": (z - 400. / 3e5, z + 400. / 3e5),
"A1": (0.2, 1.5)
})
#or_fitted_model, mask = or_fit(model, wave_range,flux_range)
fitted_model = fit(model, wave_range, flux_range)
#A0_best,A1_best,A2_best,sigma_best,z_best=mask.A2,mask.A1,mask.A2,mask.sigma0,mask.z00
A0_best, A1_best, A2_best, sigma_best, z_best = fitted_model.A2.value, fitted_model.A1.value, fitted_model.A2.value, fitted_model.sigma0.value, fitted_model.z00.value
if 0 in link:
#Amplitud que no se va a ajustar
link_index_0 = np.where(link == 0)[0][0]
#Las que si se van a ajustar
link_index_1 = np.where(link == 1)[0][0]
#A que linea se va a linkear.
eline_to_link = eline_link[link_index_0]
if link_index_0 == 0 and eline_to_link == 2:
A0_best = A2_best / 3.
if link_index_0 == 0 and eline_to_link == 1:
A0_best = A1_best / 3.
if link_index_0 == 1 and eline_to_link == 0:
A1_best = A0_best / 3.
if link_index_0 == 1 and eline_to_link == 2:
A1_best = A2_best / 3.
if link_index_0 == 2 and eline_to_link == 0:
A2_best = A0_best / 3.
if link_index_0 == 2 and eline_to_link == 1:
A2_best = A1_best / 3.
################################################################################
if plot == 1:
plt.plot(wave_range, flux_range, 'k+')
plt.plot(
wave_range,
G_model(wave_range, A0_best, A1_best, A2_best, sigma_best,
z_best), "k-")
plt.plot(wave_range, or_fitted_model, "ro")
return [sigma_best, [A0_best, A1_best, A2_best], z_best] #best_vals
def poly_fit(xp, yp, grado_pol):
t_init = polynomial.Polynomial1D(degree=int(grado_pol))
fit_t = fitting.LevMarLSQFitter()
t = fit_t(t_init, xp, yp)
return t
def fit_2dgaussian(array, crop=False, cent=None, cropsize=15, fwhmx=4, fwhmy=4,
theta=0, threshold=False, sigfactor=6, full_output=False,
debug=False):
""" Fitting a 2D Gaussian to the 2D distribution of the data.
Parameters
----------
array : array_like
Input frame with a single PSF.
crop : bool, optional
If True an square sub image will be cropped.
cent : tuple of int, optional
X,Y integer position of source in the array for extracting the subimage.
If None the center of the frame is used for cropping the subframe (the
PSF is assumed to be ~ at the center of the frame).
cropsize : int, optional
Size of the subimage.
fwhmx, fwhmy : float, optional
Initial values for the standard deviation of the fitted Gaussian, in px.
theta : float, optional
Angle of inclination of the 2d Gaussian counting from the positive X
axis.
threshold : bool, optional
If True the background pixels (estimated using sigma clipped statistics)
will be replaced by small random Gaussian noise.
sigfactor : int, optional
The background pixels will be thresholded before fitting a 2d Gaussian
to the data using sigma clipped statistics. All values smaller than
(MEDIAN + sigfactor*STDDEV) will be replaced by small random Gaussian
noise.
full_output : bool, optional
If False it returns just the centroid, if True also returns the
FWHM in X and Y (in pixels), the amplitude and the rotation angle.
debug : bool, optional
If True, the function prints out parameters of the fit and plots the
data, model and residuals.
Returns
-------
mean_y : float
Source centroid y position on input array from fitting.
mean_x : float
Source centroid x position on input array from fitting.
If ``full_output`` is True it returns a Pandas dataframe containing the
following columns:
'amplitude' : Float value. Amplitude of the Gaussian.
'centroid_x' : Float value. X coordinate of the centroid.
'centroid_y' : Float value. Y coordinate of the centroid.
'fwhm_x' : Float value. FHWM in X [px].
'fwhm_y' : Float value. FHWM in Y [px].
'theta' : Float value. Rotation angle.
"""
if array.ndim != 2:
raise TypeError('Input array is not a frame or 2d array')
if crop:
if cent is None:
ceny, cenx = frame_center(array)
else:
cenx, ceny = cent
imside = array.shape[0]
psf_subimage, suby, subx = get_square(array, min(cropsize, imside),
ceny, cenx, position=True)
else:
psf_subimage = array.copy()
if threshold:
_, clipmed, clipstd = sigma_clipped_stats(psf_subimage, sigma=2)
indi = np.where(psf_subimage <= clipmed + sigfactor * clipstd)
subimnoise = np.random.randn(psf_subimage.shape[0],
psf_subimage.shape[1]) * clipstd
psf_subimage[indi] = subimnoise[indi]
# Creating the 2D Gaussian model
init_amplitude = np.ptp(psf_subimage)
xcom, ycom = photutils.centroid_com(psf_subimage)
gauss = models.Gaussian2D(amplitude=init_amplitude, theta=theta,
x_mean=xcom, y_mean=ycom,
x_stddev=fwhmx * gaussian_fwhm_to_sigma,
y_stddev=fwhmy * gaussian_fwhm_to_sigma)
# Levenberg-Marquardt algorithm
fitter = fitting.LevMarLSQFitter()
y, x = np.indices(psf_subimage.shape)
fit = fitter(gauss, x, y, psf_subimage)
if crop:
mean_y = fit.y_mean.value + suby
mean_x = fit.x_mean.value + subx
else:
mean_y = fit.y_mean.value
mean_x = fit.x_mean.value
fwhm_y = fit.y_stddev.value*gaussian_sigma_to_fwhm
fwhm_x = fit.x_stddev.value*gaussian_sigma_to_fwhm
amplitude = fit.amplitude.value
theta = np.rad2deg(fit.theta.value)
if debug:
if threshold:
msg = ['Subimage thresholded', 'Model', 'Residuals']
else:
msg = ['Subimage', 'Model', 'Residuals']
pp_subplots(psf_subimage, fit(x, y), psf_subimage-fit(x, y),
grid=True, gridspacing=1, label=msg)
print('FWHM_y =', fwhm_y)
print('FWHM_x =', fwhm_x, '\n')
print('centroid y =', mean_y)
print('centroid x =', mean_x)
print('centroid y subim =', fit.y_mean.value)
print('centroid x subim =', fit.x_mean.value, '\n')
print('amplitude =', amplitude)
print('theta =', theta)
if full_output:
return pd.DataFrame({'centroid_y': mean_y, 'centroid_x': mean_x,
'fwhm_y': fwhm_y, 'fwhm_x': fwhm_x,
'amplitude': amplitude, 'theta': theta}, index=[0])
else:
return mean_y, mean_x
def run(self) -> None:
"""
Run method of the module. Locates the position of the calibration spots in the center
frame. From the four spots, the position of the star behind the coronagraph is fitted,
and the images are shifted and cropped.
Returns
-------
NoneType
None
"""
@typechecked
def _get_center(
image_number: int, center: Optional[Tuple[int, int]]
) -> Tuple[np.ndarray, Tuple[int, int]]:
if center_shape[-3] > 1:
warnings.warn(
'Multiple center images found. Using the first image of the stack.'
)
if ndim == 3:
center_frame = self.m_center_in_port[0, ]
elif ndim == 4:
center_frame = self.m_center_in_port[image_number, 0, ]
if center is None:
center = center_pixel(center_frame)
else:
center = (int(np.floor(center[0])), int(np.floor(center[1])))
return center_frame, center
center_shape = self.m_center_in_port.get_shape()
im_shape = self.m_image_in_port.get_shape()
ndim = self.m_image_in_port.get_ndim()
center_frame, self.m_center = _get_center(0, self.m_center)
# Read in wavelength information or set it to default values
if ndim == 4:
wavelength = self.m_image_in_port.get_attribute('WAVELENGTH')
if wavelength is None:
raise ValueError(
'The wavelength information is required to centre IFS data. '
'Please add it via the WavelengthReadingModule before using '
'the WaffleCenteringModule.')
if im_shape[0] != center_shape[0]:
raise ValueError(
f'Number of science wavelength channels: {im_shape[0]}. '
f'Number of center wavelength channels: {center_shape[0]}. '
'Exactly one center image per wavelength is required.')
wavelength_min = np.min(wavelength)
elif ndim == 3:
# for none ifs data, use default value
wavelength = [1.]
wavelength_min = 1.
# check if science and center images have the same shape
if im_shape[-2:] != center_shape[-2:]:
raise ValueError(
'Science and center images should have the same shape.')
# Setting angle via pattern (used for backwards compability)
if self.m_pattern is not None:
if self.m_pattern == 'x':
self.m_angle = 45.
elif self.m_pattern == '+':
self.m_angle = 0.
else:
raise ValueError(
f'The pattern {self.m_pattern} is not valid. Please select '
f'either \'x\' or \'+\'.')
warnings.warn(
f'The \'pattern\' parameter will be deprecated in a future release. '
f'Please Use the \'angle\' parameter instead and set it to '
f'{self.m_angle} degrees.', DeprecationWarning)
pixscale = self.m_image_in_port.get_attribute('PIXSCALE')
self.m_sigma /= pixscale
if self.m_size is not None:
self.m_size = int(math.ceil(self.m_size / pixscale))
if self.m_dither:
dither_x = self.m_image_in_port.get_attribute('DITHER_X')
dither_y = self.m_image_in_port.get_attribute('DITHER_Y')
nframes = self.m_image_in_port.get_attribute('NFRAMES')
nframes = np.cumsum(nframes)
nframes = np.insert(nframes, 0, 0)
# size of center image, only works with odd value
ref_image_size = 21
# Arrays for the positions
x_pos = np.zeros(4)
y_pos = np.zeros(4)
# Arrays for the center position for each wavelength
x_center = np.zeros((len(wavelength)))
y_center = np.zeros((len(wavelength)))
# Loop for 4 waffle spots
for w, wave_nr in enumerate(wavelength):
# Prapre centering frame
center_frame, _ = _get_center(w, self.m_center)
center_frame_unsharp = center_frame - gaussian_filter(
input=center_frame, sigma=self.m_sigma)
for i in range(4):
# Approximate positions of waffle spots
radius = self.m_radius * wave_nr / wavelength_min
x_0 = np.floor(self.m_center[0] + radius *
np.cos(self.m_angle * np.pi / 180 + np.pi / 4. *
(2 * i)))
y_0 = np.floor(self.m_center[1] + radius *
np.sin(self.m_angle * np.pi / 180 + np.pi / 4. *
(2 * i)))
tmp_center_frame = crop_image(image=center_frame_unsharp,
center=(int(y_0), int(x_0)),
size=ref_image_size)
# find maximum in tmp image
coords = np.unravel_index(indices=np.argmax(tmp_center_frame),
shape=tmp_center_frame.shape)
y_max, x_max = coords[0], coords[1]
pixmax = tmp_center_frame[y_max, x_max]
max_pos = np.array([x_max, y_max]).reshape(1, 2)
# Check whether it is the correct maximum: second brightest pixel should be nearby
tmp_center_frame[y_max, x_max] = 0.
# introduce distance parameter
dist = np.inf
while dist > 2:
coords = np.unravel_index(
indices=np.argmax(tmp_center_frame),
shape=tmp_center_frame.shape)
y_max_new, x_max_new = coords[0], coords[1]
pixmax_new = tmp_center_frame[y_max_new, x_max_new]
# Caculate minimal distance to previous points
tmp_center_frame[y_max_new, x_max_new] = 0.
dist = np.amin(
np.linalg.norm(np.vstack((max_pos[:, 0] - x_max_new,
max_pos[:, 1] - y_max_new)),
axis=0))
if dist <= 2 and pixmax_new < pixmax:
break
max_pos = np.vstack((max_pos, [x_max_new, y_max_new]))
x_max = x_max_new
y_max = y_max_new
pixmax = pixmax_new
x_0 = x_0 - (ref_image_size - 1) / 2 + x_max
y_0 = y_0 - (ref_image_size - 1) / 2 + y_max
# create reference image around determined maximum
ref_center_frame = crop_image(image=center_frame_unsharp,
center=(int(y_0), int(x_0)),
size=ref_image_size)
# Fit the data using astropy.modeling
gauss_init = models.Gaussian2D(
amplitude=np.amax(ref_center_frame),
x_mean=x_0,
y_mean=y_0,
x_stddev=1.,
y_stddev=1.,
theta=0.)
fit_gauss = fitting.LevMarLSQFitter()
y_grid, x_grid = np.mgrid[y_0 - (ref_image_size - 1) / 2:y_0 +
(ref_image_size - 1) / 2 + 1,
x_0 - (ref_image_size - 1) / 2:x_0 +
(ref_image_size - 1) / 2 + 1]
gauss = fit_gauss(gauss_init, x_grid, y_grid, ref_center_frame)
x_pos[i] = gauss.x_mean.value
y_pos[i] = gauss.y_mean.value
# Find star position as intersection of two lines
x_center[w] = ((y_pos[0]-x_pos[0]*(y_pos[2]-y_pos[0])/(x_pos[2]-float(x_pos[0]))) -
(y_pos[1]-x_pos[1]*(y_pos[1]-y_pos[3])/(x_pos[1]-float(x_pos[3])))) / \
((y_pos[1]-y_pos[3])/(x_pos[1]-float(x_pos[3])) -
(y_pos[2]-y_pos[0])/(x_pos[2]-float(x_pos[0])))
y_center[w] = x_center[w]*(y_pos[1]-y_pos[3])/(x_pos[1]-float(x_pos[3])) + \
(y_pos[1]-x_pos[1]*(y_pos[1]-y_pos[3])/(x_pos[1]-float(x_pos[3])))
# Adjust science images
nimages = self.m_image_in_port.get_shape()[-3]
npix = self.m_image_in_port.get_shape()[-2]
nwavelengths = len(wavelength)
start_time = time.time()
for i in range(nimages):
im_storage = []
for j in range(nwavelengths):
im_index = i * nwavelengths + j
progress(im_index, nimages * nwavelengths,
'Centering the images...', start_time)
if ndim == 3:
image = self.m_image_in_port[i, ]
elif ndim == 4:
image = self.m_image_in_port[j, i, ]
shift_yx = np.array([
(float(im_shape[-2]) - 1.) / 2. - y_center[j],
(float(im_shape[-1]) - 1.) / 2. - x_center[j]
])
if self.m_dither:
index = np.digitize(i, nframes, right=False) - 1
shift_yx[0] -= dither_y[index]
shift_yx[1] -= dither_x[index]
if npix % 2 == 0 and self.m_size is not None:
im_tmp = np.zeros((image.shape[0] + 1, image.shape[1] + 1))
im_tmp[:-1, :-1] = image
image = im_tmp
shift_yx[0] += 0.5
shift_yx[1] += 0.5
im_shift = shift_image(image, shift_yx, 'spline')
if self.m_size is not None:
im_crop = crop_image(im_shift, None, self.m_size)
im_storage.append(im_crop)
else:
im_storage.append(im_shift)
if ndim == 3:
self.m_image_out_port.append(im_storage[0], data_dim=3)
elif ndim == 4:
self.m_image_out_port.append(np.asarray(im_storage),
data_dim=4)
print(f'Center [x, y] = [{x_center}, {y_center}]')
history = f'[x, y] = [{round(x_center[j], 2)}, {round(y_center[j], 2)}]'
self.m_image_out_port.copy_attributes(self.m_image_in_port)
self.m_image_out_port.add_history('WaffleCenteringModule', history)
self.m_image_out_port.close_port()
def fit_2dairydisk(array, crop=False, cent=None, cropsize=15, fwhm=4,
threshold=False, sigfactor=6, full_output=False, debug=False):
""" Fitting a 2D Moffat to the 2D distribution of the data.
Parameters
----------
array : array_like
Input frame with a single PSF.
crop : bool, optional
If True an square sub image will be cropped.
cent : tuple of int, optional
X,Y integer position of source in the array for extracting the subimage.
If None the center of the frame is used for cropping the subframe (the
PSF is assumed to be ~ at the center of the frame).
cropsize : int, optional
Size of the subimage.
fwhm : float, optional
Initial values for the FWHM of the fitted 2d Moffat, in px.
threshold : bool, optional
If True the background pixels (estimated using sigma clipped statistics)
will be replaced by small random Gaussian noise.
sigfactor : int, optional
The background pixels will be thresholded before fitting a 2d Moffat
to the data using sigma clipped statistics. All values smaller than
(MEDIAN + sigfactor*STDDEV) will be replaced by small random Gaussian
noise.
full_output : bool, optional
If False it returns just the centroid, if True also returns the
FWHM in X and Y (in pixels), the amplitude and the rotation angle.
debug : bool, optional
If True, the function prints out parameters of the fit and plots the
data, model and residuals.
Returns
-------
mean_y : float
Source centroid y position on input array from fitting.
mean_x : float
Source centroid x position on input array from fitting.
If ``full_output`` is True it returns a Pandas dataframe containing the
following columns:
'alpha': Float value. Alpha parameter.
'amplitude' : Float value. Moffat Amplitude.
'centroid_x' : Float value. X coordinate of the centroid.
'centroid_y' : Float value. Y coordinate of the centroid.
'fwhm' : Float value. FHWM [px].
'gamma' : Float value. Gamma parameter.
"""
if array.ndim != 2:
raise TypeError('Input array is not a frame or 2d array')
if crop:
if cent is None:
ceny, cenx = frame_center(array)
else:
cenx, ceny = cent
imside = array.shape[0]
psf_subimage, suby, subx = get_square(array, min(cropsize, imside),
ceny, cenx, position=True)
else:
psf_subimage = array.copy()
if threshold:
_, clipmed, clipstd = sigma_clipped_stats(psf_subimage, sigma=2)
indi = np.where(psf_subimage <= clipmed + sigfactor * clipstd)
subimnoise = np.random.randn(psf_subimage.shape[0],
psf_subimage.shape[1]) * clipstd
psf_subimage[indi] = subimnoise[indi]
# Creating the 2d Airy disk model
init_amplitude = np.ptp(psf_subimage)
xcom, ycom = photutils.centroid_com(psf_subimage)
diam_1st_zero = (fwhm * 2.44) / 1.028
airy = models.AiryDisk2D(amplitude=init_amplitude, x_0=xcom, y_0=ycom,
radius=diam_1st_zero/2.)
# Levenberg-Marquardt algorithm
fitter = fitting.LevMarLSQFitter()
y, x = np.indices(psf_subimage.shape)
fit = fitter(airy, x, y, psf_subimage)
if crop:
mean_y = fit.y_0.value + suby
mean_x = fit.x_0.value + subx
else:
mean_y = fit.y_0.value
mean_x = fit.x_0.value
amplitude = fit.amplitude.value
radius = fit.radius.value
fwhm = ((radius * 1.028) / 2.44) * 2
if debug:
if threshold:
msg = ['Subimage thresholded', 'Model', 'Residuals']
else:
msg = ['Subimage', 'Model', 'Residuals']
pp_subplots(psf_subimage, fit(x, y), psf_subimage - fit(x, y),
grid=True, gridspacing=1, label=msg)
print('FWHM =', fwhm)
print('centroid y =', mean_y)
print('centroid x =', mean_x)
print('centroid y subim =', fit.y_0.value)
print('centroid x subim =', fit.x_0.value, '\n')
print('amplitude =', amplitude)
print('radius =', radius)
if full_output:
return pd.DataFrame({'centroid_y': mean_y, 'centroid_x': mean_x,
'fwhm': fwhm, 'radius': radius,
'amplitude': amplitude}, index=[0])
else:
return mean_y, mean_x
def find_stars_single(img_file, fwhm, threshold, N_passes, plot_psf_compare,
mask_file, sharp_lim, peak_max):
pid = mp.current_process().pid
print(f' p{pid} - Working on image: {img_file}')
img, hdr = fits.getdata(img_file, header=True, ignore_missing_end=True)
mask = fits.getdata(mask_file).astype('bool')
img = np.ma.masked_array(img, mask=mask)
fwhm_curr = fwhm
# Calculate the bacgkround and noise (iteratively)
print(f' p{pid} - Calculating background')
bkg_threshold_above = 1
bkg_threshold_below = 3
good_pix = np.where(np.isfinite(img))
for nn in range(5):
bkg_mean = img[good_pix].mean()
bkg_std = img[good_pix].std()
bad_hi = bkg_mean + (bkg_threshold_above * bkg_std)
bad_lo = bkg_mean - (bkg_threshold_below * bkg_std)
good_pix = np.where((img > bad_lo) & (img < bad_hi))
bkg_mean = img[good_pix].mean()
bkg_std = img[good_pix].std()
img_threshold = threshold * bkg_std
print(f' p{pid} - Bkg = {bkg_mean:.2f} +/- {bkg_std:.2f}')
print(f' p{pid} - Bkg Threshold = {img_threshold:.2f}')
# Detect stars
print(f' p{pid} - Detecting Stars')
# Each pass will have an updated fwhm for the PSF.
for nn in range(N_passes):
print(f' p{pid} - Pass {nn:d} assuming FWHM = {fwhm_curr:.1f}')
daofind = DAOStarFinder(fwhm=fwhm_curr,
threshold=img_threshold,
exclude_border=True,
sharplo=-sharp_lim,
sharphi=sharp_lim,
peakmax=peak_max)
sources = daofind(img - bkg_mean, mask=mask)
print(
f' p{pid} - {len(sources)} sources found, now fitting for FWHM.'
)
# Calculate FWHM for each detected star.
x_fwhm = np.zeros(len(sources), dtype=float)
y_fwhm = np.zeros(len(sources), dtype=float)
theta = np.zeros(len(sources), dtype=float)
# Calculate measure of fits
fvu = np.zeros(len(sources), dtype=float)
lss = np.zeros(len(sources), dtype=float)
mfr = np.zeros(len(sources), dtype=float)
# We will actually be resampling the images for the Gaussian fits.
resamp = 1 #2 #BUG - changed this value for testing bin1 open loop
cutout_half_size = int(round(fwhm_curr * 3.5))
cutout_size = 2 * cutout_half_size + 1
# Define variables to hold final averages PSFs
final_psf_obs = np.zeros((cutout_size * resamp, cutout_size * resamp),
dtype=float)
final_psf_mod = np.zeros((cutout_size * resamp, cutout_size * resamp),
dtype=float)
final_psf_count = 0
# Setup our gaussian fitter with some good initial guesses.
sigma_init_guess = fwhm_curr * gaussian_fwhm_to_sigma
g2d_model = models.Gaussian2D(1.0,
cutout_half_size * resamp,
cutout_half_size * resamp,
sigma_init_guess * resamp,
sigma_init_guess * resamp,
theta=0,
bounds={
'x_stddev': [0, fwhm * 2 * resamp],
'y_stddev': [0, fwhm * 2 * resamp],
'amplitude': [0, 2]
})
c2d_model = models.Const2D(0.0)
the_model = g2d_model + c2d_model
the_fitter = fitting.LevMarLSQFitter()
cut_y, cut_x = np.mgrid[:cutout_size, :cutout_size]
for ss in range(len(sources)):
x_lo = int(round(sources[ss]['xcentroid'] - cutout_half_size))
x_hi = x_lo + cutout_size
y_lo = int(round(sources[ss]['ycentroid'] - cutout_half_size))
y_hi = y_lo + cutout_size
cutout_tmp = img[y_lo:y_hi, x_lo:x_hi].astype(float)
if ((cutout_tmp.shape[0] != cutout_size) |
(cutout_tmp.shape[1] != cutout_size)):
# Edge source... fitting is no good
continue
# Oversample the image
cutout_resamp = scipy.ndimage.zoom(cutout_tmp, resamp, order=1)
#cutout_resamp /= cutout_resamp.sum() #normed sum to 1
cutout_resamp /= cutout_resamp.max(
) #normed peak to 1 # BUG: what if bright outlier?
cut_y_resamp, cut_x_resamp = np.mgrid[:cutout_size *
resamp, :cutout_size *
resamp]
# Fit a 2D gaussian + constant
with warnings.catch_warnings():
# Suppress warnings... too many.
warnings.simplefilter("ignore", category=UserWarning)
warnings.simplefilter("ignore", category=AstropyWarning)
g2d_params = the_fitter(
the_model,
cut_x_resamp,
cut_y_resamp,
cutout_resamp,
epsilon=1e-12,
acc=1e-12,
maxiter=300,
weights=None) #added values for better fit
g2d_image = g2d_params(cut_x_resamp, cut_y_resamp)
# Catch bad fits and ignore.
if (np.isnan(g2d_params.x_mean_0.value)
or (np.abs(g2d_params.x_mean_0.value) >
(cutout_size * resamp))
or (np.abs(g2d_params.y_mean_0.value) >
(cutout_size * resamp))):
print(f' p{pid} - Bad fit for {ss}')
continue
# Add to our average observed/model PSFs
if sources['flux'][ss] > 1.9:
final_psf_count += 1
final_psf_obs += cutout_resamp
final_psf_mod += g2d_image
# Save the FWHM and angle.
x_fwhm[
ss] = g2d_params.x_stddev_0.value / gaussian_fwhm_to_sigma / resamp
y_fwhm[
ss] = g2d_params.y_stddev_0.value / gaussian_fwhm_to_sigma / resamp
theta[ss] = g2d_params.theta_0.value
# calc residuals - based on FWHM
# relevant part of cutout
mid_ss = cutout_resamp.shape[0] / 2
x_hi_ss = int(round(mid_ss + x_fwhm[ss]))
x_lo_ss = int(round(mid_ss - x_fwhm[ss]))
y_hi_ss = int(round(mid_ss + y_fwhm[ss]))
y_lo_ss = int(round(mid_ss - y_fwhm[ss]))
cutout_resamp_cut = cutout_resamp[y_lo_ss:y_hi_ss, x_lo_ss:x_hi_ss]
# fit metrics
diff_img_ss = cutout_resamp_cut - g2d_image[y_lo_ss:y_hi_ss,
x_lo_ss:x_hi_ss]
PSF_mean_ss = np.mean(cutout_resamp_cut)
residual_ss = np.sum(diff_img_ss**2) # Least Squares Sum (LSS)
med_fr_ss = np.median(
np.abs(diff_img_ss /
cutout_resamp_cut)) # median fractional residual (MFR)
fvu_ss = residual_ss / np.sum(
(cutout_resamp_cut - PSF_mean_ss)**
2) # fraction of variance unexplained (FVU)
# Save the fit
lss[ss] = residual_ss
fvu[ss] = fvu_ss
mfr[ss] = med_fr_ss
if (plot_psf_compare == True) and (x_lo > 200) and (y_lo > 200):
#plt.figure(4, figsize=(6, 4))
vmin = cutout_resamp.min()
vmax = cutout_resamp.max()
plt.figure(4, figsize=(12, 3))
plt.clf()
# 1. Cut out Source
plt.subplot(1, 4, 1)
plt.imshow(cutout_resamp, origin='lower', vmin=vmin, vmax=vmax)
plt.gca().add_patch(
Rectangle((x_lo_ss, y_lo_ss),
x_hi_ss - x_lo_ss,
y_hi_ss - y_lo_ss,
edgecolor='red',
facecolor='none',
lw=2))
plt.colorbar(fraction=0.046, pad=0.05)
plt.title(f'Image (resamp={resamp:d})')
# 2. Model of source
plt.subplot(1, 4, 2)
plt.imshow(g2d_image, origin='lower', vmin=vmin, vmax=vmax)
plt.gca().add_patch(
Rectangle((x_lo_ss, y_lo_ss),
x_hi_ss - x_lo_ss,
y_hi_ss - y_lo_ss,
edgecolor='red',
facecolor='none',
lw=2))
plt.colorbar(fraction=0.046, pad=0.05)
plt.title(f'Model (resamp={resamp:d})')
# 3. Residual - Subtraction
plt.subplot(1, 4, 3)
plt.imshow(cutout_resamp - g2d_image,
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(f"Data-Model (resamp={resamp:d})")
# 4. Residual - Fraction
plt.subplot(1, 4, 4)
plt.subplots_adjust(left=0.08)
plt.imshow((cutout_resamp - g2d_image) / cutout_resamp,
vmin=-1,
vmax=1) # take out outliers?
plt.colorbar(fraction=0.046, pad=0.05)
plt.title('Residual fraction')
plt.suptitle(
f"Source {ss} fit, FWHM x: {x_fwhm[ss]:.2f} y: {y_fwhm[ss]:.2f} | LSS {residual_ss:.2e} | FVU {fvu_ss:.2e} | MFR {med_fr_ss:.2e}"
)
plt.tight_layout()
plt.pause(0.05)
pdb.set_trace()
# Some occasional display
if (plot_psf_compare == True) and (ss % 250 == 0):
plt.figure(2, figsize=(8, 3))
plt.clf()
plt.subplot(1, 2, 1)
plt.subplots_adjust(left=0.08)
plt.imshow(final_psf_obs)
plt.colorbar(fraction=0.25)
plt.title(f'Obs PSF (resamp = {resamp:d})')
plt.subplot(1, 2, 2)
plt.subplots_adjust(left=0.08)
plt.imshow(final_psf_mod)
plt.colorbar(fraction=0.25)
#plt.axis('equal')
plt.title(f'Mod PSF (resamp = {resamp:d})')
plt.suptitle(f"Observed vs. Model PSF average fit")
plt.pause(0.05)
print(
f' p{pid} - ss={ss} fwhm_x={x_fwhm[ss]:.1f} fwhm_y={y_fwhm[ss]:.1f}'
)
sources['x_fwhm'] = x_fwhm
sources['y_fwhm'] = y_fwhm
sources['theta'] = theta
sources['LSS'] = lss
sources['FVU'] = fvu
sources['MFR'] = mfr
# Save the average PSF (flux-weighted). Note we are making a slight mistake
# here since each PSF has a different sub-pixel position... still same for both
# obs and model
final_psf_obs /= final_psf_count
final_psf_mod /= final_psf_count
final_psf_obs /= final_psf_obs.sum()
final_psf_mod /= final_psf_mod.sum()
# saving psf
img_dir_name, img_file_name = os.path.split(img_file)
psf_dir = img_dir_name + '/psf/'
util.mkdir(psf_dir)
fits.writeto(psf_dir + img_file_name.replace('.fits', '_psf_obs.fits'),
final_psf_obs,
hdr,
overwrite=True)
fits.writeto(psf_dir + img_file_name.replace('.fits', '_psf_mod.fits'),
final_psf_mod,
hdr,
overwrite=True)
#TODO: make starlist specific
# Drop sources with flux (signifiance) that isn't good enough.
# Empirically this is <1.2
# Also drop sources that couldn't be fit.
good = np.where((sources['flux'] > 1.9) & (sources['x_fwhm'] > 0)
& (sources['y_fwhm'] > 0))[0]
sources = sources[good]
# Only use the brightest sources for calculating the mean. This is just for printing.
idx = np.where(sources['flux'] > 5)[0]
x_fwhm_med = np.median(sources['x_fwhm'][idx])
y_fwhm_med = np.median(sources['y_fwhm'][idx])
print(f' p{pid} - Number of sources = {len(sources)}')
print(
f' p{pid} - Median x_fwhm = {x_fwhm_med:.1f} +/- {sources["x_fwhm"].std():.1f}'
)
print(
f' p{pid} - Median y_fwhm = {y_fwhm_med:.1f} +/- {sources["y_fwhm"].std():.1f}'
)
fwhm_curr = np.mean([x_fwhm_med, y_fwhm_med])
formats = {
'xcentroid': '%8.3f',
'ycentroid': '%8.3f',
'sharpness': '%.2f',
'roundness1': '%.2f',
'roundness2': '%.2f',
'peak': '%10.1f',
'flux': '%10.6f',
'mag': '%6.2f',
'x_fwhm': '%5.2f',
'y_fwhm': '%5.2f',
'theta': '%6.3f',
'LSS': '%5.2f',
'FVU': '%5.2f',
'MFR': '%5.2f',
}
sources.write(img_file.replace('.fits', '_stars.txt'),
format='ascii.fixed_width',
delimiter=None,
bookend=False,
formats=formats,
overwrite=True)
return
def run(self) -> None:
"""
Run method of the module. Locates the position of the calibration spots in the center
frame. From the four spots, the position of the star behind the coronagraph is fitted,
and the images are shifted and cropped.
Returns
-------
NoneType
None
"""
def _get_center(center):
center_frame = self.m_center_in_port[0, ]
if center_shape[0] > 1:
warnings.warn(
'Multiple center images found. Using the first image of the stack.'
)
if center is None:
center = center_pixel(center_frame)
else:
center = (np.floor(center[0]), np.floor(center[1]))
return center_frame, center
self.m_image_out_port.del_all_data()
self.m_image_out_port.del_all_attributes()
center_shape = self.m_center_in_port.get_shape()
im_shape = self.m_image_in_port.get_shape()
center_frame, self.m_center = _get_center(self.m_center)
if im_shape[-2:] != center_shape[-2:]:
raise ValueError(
'Science and center images should have the same shape.')
pixscale = self.m_image_in_port.get_attribute('PIXSCALE')
self.m_sigma /= pixscale
if self.m_size is not None:
self.m_size = int(math.ceil(self.m_size / pixscale))
if self.m_dither:
dither_x = self.m_image_in_port.get_attribute('DITHER_X')
dither_y = self.m_image_in_port.get_attribute('DITHER_Y')
nframes = self.m_image_in_port.get_attribute('NFRAMES')
nframes = np.cumsum(nframes)
nframes = np.insert(nframes, 0, 0)
center_frame_unsharp = center_frame - gaussian_filter(
input=center_frame, sigma=self.m_sigma)
# size of center image, only works with odd value
ref_image_size = 21
# Arrays for the positions
x_pos = np.zeros(4)
y_pos = np.zeros(4)
# Loop for 4 waffle spots
for i in range(4):
# Approximate positions of waffle spots
if self.m_pattern == 'x':
x_0 = np.floor(self.m_center[0] +
self.m_radius * np.cos(np.pi / 4. *
(2 * i + 1)))
y_0 = np.floor(self.m_center[1] +
self.m_radius * np.sin(np.pi / 4. *
(2 * i + 1)))
elif self.m_pattern == '+':
x_0 = np.floor(self.m_center[0] +
self.m_radius * np.cos(np.pi / 4. * (2 * i)))
y_0 = np.floor(self.m_center[1] +
self.m_radius * np.sin(np.pi / 4. * (2 * i)))
tmp_center_frame = crop_image(image=center_frame_unsharp,
center=(int(y_0), int(x_0)),
size=ref_image_size)
# find maximum in tmp image
coords = np.unravel_index(indices=np.argmax(tmp_center_frame),
shape=tmp_center_frame.shape)
y_max, x_max = coords[0], coords[1]
pixmax = tmp_center_frame[y_max, x_max]
max_pos = np.array([x_max, y_max]).reshape(1, 2)
# Check whether it is the correct maximum: second brightest pixel should be nearby
tmp_center_frame[y_max, x_max] = 0.
# introduce distance parameter
dist = np.inf
while dist > 2:
coords = np.unravel_index(indices=np.argmax(tmp_center_frame),
shape=tmp_center_frame.shape)
y_max_new, x_max_new = coords[0], coords[1]
pixmax_new = tmp_center_frame[y_max_new, x_max_new]
# Caculate minimal distance to previous points
tmp_center_frame[y_max_new, x_max_new] = 0.
dist = np.amin(
np.linalg.norm(np.vstack((max_pos[:, 0] - x_max_new,
max_pos[:, 1] - y_max_new)),
axis=0))
if dist <= 2 and pixmax_new < pixmax:
break
max_pos = np.vstack((max_pos, [x_max_new, y_max_new]))
x_max = x_max_new
y_max = y_max_new
pixmax = pixmax_new
x_0 = x_0 - (ref_image_size - 1) / 2 + x_max
y_0 = y_0 - (ref_image_size - 1) / 2 + y_max
# create reference image around determined maximum
ref_center_frame = crop_image(image=center_frame_unsharp,
center=(int(y_0), int(x_0)),
size=ref_image_size)
# Fit the data using astropy.modeling
gauss_init = models.Gaussian2D(amplitude=np.amax(ref_center_frame),
x_mean=x_0,
y_mean=y_0,
x_stddev=1.,
y_stddev=1.,
theta=0.)
fit_gauss = fitting.LevMarLSQFitter()
y_grid, x_grid = np.mgrid[y_0 - (ref_image_size - 1) / 2:y_0 +
(ref_image_size - 1) / 2 + 1,
x_0 - (ref_image_size - 1) / 2:x_0 +
(ref_image_size - 1) / 2 + 1]
gauss = fit_gauss(gauss_init, x_grid, y_grid, ref_center_frame)
x_pos[i] = gauss.x_mean.value
y_pos[i] = gauss.y_mean.value
# Find star position as intersection of two lines
x_center = ((y_pos[0]-x_pos[0]*(y_pos[2]-y_pos[0])/(x_pos[2]-float(x_pos[0]))) -
(y_pos[1]-x_pos[1]*(y_pos[1]-y_pos[3])/(x_pos[1]-float(x_pos[3])))) / \
((y_pos[1]-y_pos[3])/(x_pos[1]-float(x_pos[3])) -
(y_pos[2]-y_pos[0])/(x_pos[2]-float(x_pos[0])))
y_center = x_center*(y_pos[1]-y_pos[3])/(x_pos[1]-float(x_pos[3])) + \
(y_pos[1]-x_pos[1]*(y_pos[1]-y_pos[3])/(x_pos[1]-float(x_pos[3])))
nimages = self.m_image_in_port.get_shape()[0]
npix = self.m_image_in_port.get_shape()[1]
start_time = time.time()
for i in range(nimages):
progress(i, nimages, 'Running WaffleCenteringModule...',
start_time)
image = self.m_image_in_port[i, ]
shift_yx = np.array([(float(im_shape[-2]) - 1.) / 2. - y_center,
(float(im_shape[-1]) - 1.) / 2. - x_center])
if self.m_dither:
index = np.digitize(i, nframes, right=False) - 1
shift_yx[0] -= dither_y[index]
shift_yx[1] -= dither_x[index]
if npix % 2 == 0 and self.m_size is not None:
im_tmp = np.zeros((image.shape[0] + 1, image.shape[1] + 1))
im_tmp[:-1, :-1] = image
image = im_tmp
shift_yx[0] += 0.5
shift_yx[1] += 0.5
im_shift = shift_image(image, shift_yx, 'spline')
if self.m_size is not None:
im_crop = crop_image(im_shift, None, self.m_size)
self.m_image_out_port.append(im_crop, data_dim=3)
else:
self.m_image_out_port.append(im_shift, data_dim=3)
sys.stdout.write('Running WaffleCenteringModule... [DONE]\n')
sys.stdout.write('Center [x, y] = [' + str(x_center) + ', ' +
str(y_center) + ']\n')
sys.stdout.flush()
history = f'[x, y] = [{round(x_center, 2)}, {round(y_center, 2)}]'
self.m_image_out_port.copy_attributes(self.m_image_in_port)
self.m_image_out_port.add_history('WaffleCenteringModule', history)
self.m_image_out_port.close_port()
def getFWHM(psf,
pixelScale,
rebin=1,
method='contour',
nargout=2,
center=None,
std_guess=2):
# Gaussian and Moffat fitting are not really efficient on
# anisoplanatic PSF. Prefer the coutour function in such a
# case. The cutting method is not compliant to PSF not oriented
#along x or y-axis.
#Interpolation
Ny, Nx = psf.shape
if rebin > 1:
im_hr = interpolateSupport(psf, rebin * np.array([Nx, Ny]))
else:
im_hr = psf
if method == 'cutting':
# Brutal approach when the PSF is centered and aligned x-axis FWHM
imy = im_hr[:, int(Ny * rebin / 2)]
w = np.where(imy >= imy.max() / 2)[0]
FWHMy = pixelScale * (w.max() - w.min()) / rebin
#y-axis FWHM
imx = im_hr[int(Nx * rebin / 2), :]
w = np.where(imx >= imx.max() / 2)[0]
FWHMx = (w.max() - w.min()) / rebin * pixelScale
theta = 0
elif method == 'contour':
# Contour approach~: something wrong about the ellipse orientation
mpl.interactive(False)
fig = plt.figure()
C = plt.contour(im_hr, levels=[im_hr.max() / 2])
plt.close(fig)
C = C.collections[0].get_paths()[0]
C = C.vertices
xC = C[:, 0]
yC = C[:, 1]
# centering the ellispe
mx = np.array([xC.max(), yC.max()])
mn = np.array([xC.min(), yC.min()])
cent = (mx + mn) / 2
wx = xC - cent[0]
wy = yC - cent[1]
# Get the module
wr = np.hypot(wx, wy) / rebin * pixelScale
# Getting the FWHM
FWHMx = 2 * wr.max()
FWHMy = 2 * wr.min()
#Getting the ellipse orientation
xm = wx[wr.argmax()]
ym = wy[wr.argmax()]
theta = np.mean(180 * np.arctan2(ym, xm) / np.pi)
mpl.interactive(True)
elif method == 'gaussian':
# Prepare array r with radius in arcseconds
y, x = np.indices(psf.shape, dtype=float)
if center is None:
# Normalize
psf = psf / psf.max()
# get exact center of image
center = tuple((a - 1) / 2.0 for a in psf.shape[::-1])
x -= center[0]
y -= center[1]
Y, X = np.mgrid[:Ny, :Nx] * pixelScale
std_guess = std_guess * pixelScale
# Define the model
g_init = models.Gaussian2D(amplitude=1.,
x_mean=0,
y_mean=0,
x_stddev=std_guess,
y_stddev=std_guess)
g_init.x_mean.fixed = True
g_init.y_mean.fixed = True
fit_g = fitting.LevMarLSQFitter()
# fit x axis
g = fit_g(g_init, X - center[0], Y - center[1], psf)
FWHMx = 2 * np.sqrt(2 * np.log(2)) * np.abs(g.x_stddev)
FWHMy = 2 * np.sqrt(2 * np.log(2)) * np.abs(g.y_stddev)
# Get Ellipticity
aRatio = np.max([FWHMx / FWHMy, FWHMy / FWHMx])
if nargout == 1:
return 0.5 * (FWHMx + FWHMy)
elif nargout == 2:
return FWHMx, FWHMy
elif nargout == 3:
return FWHMx, FWHMy, aRatio
elif nargout == 4:
return FWHMx, FWHMy, aRatio, theta
def find_best_fit(yeldax,
yelday,
plot_look=False,
pos_txt='sig_trimapril_pos.txt',
errtype=1,
fitter=None):
'''
go throigh order of legendre polynomial
look at residuals / errors
Fit with gaussian with sigma of 1
measure chi squared
print those number on a plot, call it a day
'''
if fitter == None:
fitter = high_order.LegTransform
orders = range(3, 10)
tab = Table.read(pos_txt, format='ascii.fixed_width')
if errtype == 1:
tot_err = np.sqrt(tab['xerr']**2 + tab['yerr']**2 +
(tab['xrerr'] * 5)**2 + (tab['yrerr'] * 5)**2)
elif errtype == 2:
tot_err = np.sqrt(tab['xerr']**2 + tab['yerr']**2)
for i in orders:
tapr, dx, dy, gbool, sbool = fit_dist(pos_txt=pos_txt,
order=i,
n_iter_fit=1,
lookup=False)
dxn = dx[sbool] / tot_err[gbool][sbool]
dyn = dy[sbool] / tot_err[gbool][sbool]
xN, xbin_edge = np.histogram(dxn, bins=100, range=(-5, 5))
yN, ybin_edge = np.histogram(dyn, bins=100, range=(-5, 5))
#import pdb; pdb.set_trace()
bcenx = np.zeros(len(xbin_edge) - 1)
bceny = np.zeros(len(xbin_edge) - 1)
for dd in range(len(xbin_edge) - 1):
bcenx[dd] = np.mean(xbin_edge[dd] + xbin_edge[dd + 1]) / 2.0
bceny[dd] = np.mean(ybin_edge[dd] + ybin_edge[dd + 1]) / 2.0
#import pdb; pdb.set_trace()
fit_p = fitting.LevMarLSQFitter()
gy = models.Gaussian1D(mean=0, stddev=1.0)
gy.mean.fixed = True
#gy.stddev.fixed = True
gx = models.Gaussian1D(mean=0, stddev=1.0)
gx.mean.fixed = True
#gx.stddev.fixed = True
mx = fit_p(gx, bcenx, xN)
my = fit_p(gy, bceny, yN)
#import pdb; pdb.set_trace()
chix = np.sum((mx(bcenx) - xN)**2 / mx(bcenx))
chiy = np.sum((my(bceny) - yN)**2 / my(bceny))
plt.figure(1)
plt.clf()
plt.scatter(bcenx, xN)
plt.plot(bcenx, mx(bcenx))
plt.text(
np.min(bcenx) + 1,
np.max(xN) / 2.0, r'$\chi^{2}$: ' + str(chix)[:5])
plt.text(
np.min(bcenx) + 1,
np.max(xN) / 2.0 - 20, r'$\sigma$:' + str(mx.stddev.value)[:6])
#plt.text(np.min(bcenx)+2, np.max(xN)/2.0-30,'smooth factor: '+str(i))
plt.title('X residual Leg order' + str(i))
plt.xlabel('residual / error')
plt.ylabel('N')
plt.savefig('Leg_x_resid_ord' + str(i) + '.png')
plt.figure(2)
plt.clf()
#plt.hist(dyn, bins=100)
plt.scatter(bceny, yN)
plt.plot(bceny, my(bceny))
plt.text(
np.min(bceny) + 1,
np.max(yN) / 2.0, r'$\chi^{2}$: ' + str(chiy)[:5])
plt.text(
np.min(bceny) + 1,
np.max(yN) / 2.0 - 20, r'$\sigma$:' + str(my.stddev.value)[:6])
#plt.text(np.min(bceny)+2, np.max(yN)/2.0-30,'smooth factor: '+str(i))
plt.title('Y residual Leg order' + str(i))
plt.xlabel('residual / error')
plt.ylabel('N')
plt.savefig('Leg_y_resid_ord' + str(i) + '.png')
plt.figure(3)
plt.clf()
lx, ly = leg2lookup(tapr)
plot_lookup_diff(lx, ly, yeldax, yelday)
plt.title('Difference Legendre and Yelda')
plt.savefig('Leg' + str(i) + '_resid_yelda.png')
def test_deriv_1D(self, model_class, test_parameters):
"""
Test the derivative of a model by comparing results with an estimated
derivative.
"""
x_lim = test_parameters['x_lim']
if model_class.fit_deriv is None or issubclass(model_class,
PolynomialBase):
return
if "log_fit" in test_parameters:
if test_parameters['log_fit']:
x = np.logspace(x_lim[0], x_lim[1], self.N)
else:
x = np.linspace(x_lim[0], x_lim[1], self.N)
parameters = test_parameters['parameters']
model_with_deriv = create_model(model_class,
test_parameters,
use_constraints=False)
model_no_deriv = create_model(model_class,
test_parameters,
use_constraints=False)
# NOTE: PR 10644 replaced deprecated usage of RandomState but could not
# find a new seed that did not cause test failure, resorted to hardcoding.
# add 10% noise to the amplitude
rsn_rand_1234567890 = np.array([
0.61879477, 0.59162363, 0.88868359, 0.89165480, 0.45756748,
0.77818808, 0.26706377, 0.99610621, 0.54009489, 0.53752161,
0.40099938, 0.70540579, 0.40518559, 0.94999075, 0.03075388,
0.13602495, 0.08297726, 0.42352224, 0.23449723, 0.74743526,
0.65177865, 0.68998682, 0.16413419, 0.87642114, 0.44733314,
0.57871104, 0.52377835, 0.62689056, 0.34869427, 0.26209748,
0.07498055, 0.17940570, 0.82999425, 0.98759822, 0.11326099,
0.63846415, 0.73056694, 0.88321124, 0.52721004, 0.66487673,
0.74209309, 0.94083846, 0.70123128, 0.29534353, 0.76134369,
0.77593881, 0.36985514, 0.89519067, 0.33082813, 0.86108824,
0.76897859, 0.61343376, 0.43870907, 0.91913538, 0.76958966,
0.51063556, 0.04443249, 0.57463611, 0.31382006, 0.41221713,
0.21531811, 0.03237521, 0.04166386, 0.73109303, 0.74556052,
0.64716325, 0.77575353, 0.64599254, 0.16885816, 0.48485480,
0.53844248, 0.99690349, 0.23657074, 0.04119088, 0.46501519,
0.35739006, 0.23002665, 0.53420791, 0.71639475, 0.81857486,
0.73994342, 0.07948837, 0.75688276, 0.13240193, 0.48465576,
0.20624753, 0.02298276, 0.54257873, 0.68123230, 0.35887468,
0.36296147, 0.67368397, 0.29505730, 0.66558885, 0.93652252,
0.36755130, 0.91787687, 0.75922703, 0.48668067, 0.45967890
])
n = 0.1 * parameters[0] * (rsn_rand_1234567890 - 0.5)
data = model_with_deriv(x) + n
fitter_with_deriv = fitting.LevMarLSQFitter()
new_model_with_deriv = fitter_with_deriv(model_with_deriv, x, data)
fitter_no_deriv = fitting.LevMarLSQFitter()
new_model_no_deriv = fitter_no_deriv(model_no_deriv,
x,
data,
estimate_jacobian=True)
assert_allclose(new_model_with_deriv.parameters,
new_model_no_deriv.parameters,
atol=0.15)
def comp_yelda(yeldax, yelday, yelda_pos='yelda_pos.txt'):
'''
goes through successive orders of legendre polynomial and compare the results for fitting the yelda data to the final Yelada distortion map
'''
for i in range(3, 8):
t, outx, outy, dx, dy, sbooln = fit_dist(pos_txt=yelda_pos,
order=i,
n_iter_fit=1,
wtype=2)
plot_dist(yeldax,
outx,
title2='Leg:' + str(i),
title1='Yelda',
title3='Difference',
title4='Difference',
vmind=-.5,
vmaxd=.5,
outfile='yelda_plots/Dist_sol_X_' + str(i) + '.png')
plot_dist(yelday,
outy,
title2='Leg:' + str(i),
title1='Yelda',
title3='Difference',
title4='Difference',
vmind=-.5,
vmaxd=.5,
outfile='yelda_plots/Dist_sol_Y_' + str(i) + '.png')
plt.figure(1)
plt.clf()
plt.hist((yeldax - outx).flatten(), bins=100, alpha=.5, label='x')
plt.hist((yelday - outy).flatten(), bins=100, alpha=.5, label='y')
plt.xlabel('difference (pixels)')
plt.ylabel('N')
plt.title('Difference L' + str(i) + ' and Yelda')
plt.savefig('yelda_plots/residual_' + str(i) + '.png')
ref = Table.read(yelda_pos, format='ascii.fixed_width')
tot_err = np.sqrt(ref['xerr']**2 + ref['yerr']**2)
dxn = dx / tot_err[sbooln]
dyn = dy / tot_err[sbooln]
xN, xbin_edge = np.histogram(dxn, bins=100, range=(-10, 10))
yN, ybin_edge = np.histogram(dyn, bins=100, range=(-10, 10))
#import pdb; pdb.set_trace()
bcenx = np.zeros(len(xbin_edge) - 1)
bceny = np.zeros(len(xbin_edge) - 1)
for dd in range(len(xbin_edge) - 1):
bcenx[dd] = np.mean(xbin_edge[dd] + xbin_edge[dd + 1]) / 2.0
bceny[dd] = np.mean(ybin_edge[dd] + ybin_edge[dd + 1]) / 2.0
#import pdb; pdb.set_trace()
fit_p = fitting.LevMarLSQFitter()
gy = models.Gaussian1D(mean=0, stddev=1.0)
gy.mean.fixed = True
#gy.stddev.fixed = True
gx = models.Gaussian1D(mean=0, stddev=1.0)
gx.mean.fixed = True
#gx.stddev.fixed = True
mx = fit_p(gx, bcenx, xN)
my = fit_p(gy, bceny, yN)
#import pdb; pdb.set_trace()
chix = np.sum((mx(bcenx) - xN)**2 / mx(bcenx))
chiy = np.sum((my(bceny) - yN)**2 / my(bceny))
plt.figure(1)
plt.clf()
plt.scatter(bcenx, xN)
plt.plot(bcenx, mx(bcenx))
plt.text(
np.min(bcenx) + 1,
np.max(xN) / 2.0, r'$\chi^{2}$: ' + str(chix)[:5])
plt.text(
np.min(bcenx) + 1,
np.max(xN) / 2.0 + 10, r'$\sigma$:' + str(mx.stddev.value)[:6])
#plt.text(np.min(bcenx)+2, np.max(xN)/2.0-30,'smooth factor: '+str(i))
plt.title('X residual Leg order' + str(i))
plt.xlabel('residual / error')
plt.ylabel('N')
plt.savefig('yelda_plots/Leg_x_resid_ord' + str(i) + '.png')
plt.figure(2)
plt.clf()
#plt.hist(dyn, bins=100)
plt.scatter(bceny, yN)
plt.plot(bceny, my(bceny))
plt.text(
np.min(bceny) + 1,
np.max(yN) / 2.0, r'$\chi^{2}$: ' + str(chiy)[:5])
plt.text(
np.min(bceny) + 1,
np.max(yN) / 2.0 - +10, r'$\sigma$:' + str(my.stddev.value)[:6])
#plt.text(np.min(bceny)+2, np.max(yN)/2.0-30,'smooth factor: '+str(i))
plt.title('Y residual Leg order' + str(i))
plt.xlabel('residual / error')
plt.ylabel('N')
plt.savefig('yelda_plots/Leg_y_resid_ord' + str(i) + '.png')
def fit_lines(spectrum, model, fitter=fitting.LevMarLSQFitter(),
exclude_regions=None, weights=None, window=None,
**kwargs):
"""
Fit the input models to the spectrum. The parameter values of the
input models will be used as the initial conditions for the fit.
Parameters
----------
spectrum : Spectrum1D
The spectrum object over which the equivalent width will be calculated.
model: `~astropy.modeling.Model` or list of `~astropy.modeling.Model`
The model or list of models that contain the initial guess.
fitter : `~astropy.modeling.fitting.Fitter`, optional
Fitter instance to be used when fitting model to spectrum.
exclude_regions : list of `~specutils.SpectralRegion`
List of regions to exclude in the fitting.
weights : list or 'unc', optional
If 'unc', the unceratinties from the spectrum object are used to
to calculate the weights. If list/ndarray, represents the weights to
use in the fitting.
window : `~specutils.SpectralRegion` or list of `~specutils.SpectralRegion`
Regions of the spectrum to use in the fitting. If None, then the
whole spectrum will be used in the fitting.
Additional keyword arguments are passed directly into the call to the
``fitter``.
Returns
-------
models : Compound model of `~astropy.modeling.Model`
A compound model of models with fitted parameters.
Notes
-----
* Could add functionality to set the bounds in
``model`` if they are not set.
* The models in the list of ``model`` are added
together and passed as a compound model to the
`~astropy.modeling.fitting.Fitter` class instance.
"""
#
# If we are to exclude certain regions, then remove them.
#
if exclude_regions is not None:
spectrum = excise_regions(spectrum, exclude_regions)
#
# Make the model a list if not already
#
single_model_in = not isinstance(model, list)
if single_model_in:
model = [model]
#
# If a single model is passed in then just do that.
#
fitted_models = []
for modeli, model_guess in enumerate(model):
#
# Determine the window if it is not None. There
# are several options here:
# window = 4 * u.Angstrom -> Quantity
# window = (4*u.Angstrom, 6*u.Angstrom) -> tuple
# window = (4, 6)*u.Angstrom -> Quantity
#
#
# Determine the window if there is one
#
if window is not None and isinstance(window, list):
model_window = window[modeli]
elif window is not None:
model_window = window
else:
model_window = None
#
# Check to see if the model has units. If it does not
# have units then we are going to ignore them.
#
ignore_units = getattr(model_guess, model_guess.param_names[0]).unit is None
fit_model = _fit_lines(spectrum, model_guess, fitter,
exclude_regions, weights, model_window,
ignore_units, **kwargs)
fitted_models.append(fit_model)
if single_model_in:
fitted_models = fitted_models[0]
return fitted_models
Image_Data_All = fits1.data[:,:]
Image_Data_All2 = Image_Data_All[300:400]
#Define a running median calculator
def RunMedian(x,N):
idx = np.arange(N) + np.arange(len(x)-N+1)[:,None]
b = [row[row>0] for row in x[idx]]
return np.array(map(np.median,b))
#Create the Gaussian and Moffat fits and creates Fit_Data and Fit_Data2
#which contains the parameters for the two models (Moffat still does not work correct)
x = np.linspace(-50,50,100)
Gauss_Model = models.Gaussian1D(amplitude = 1000., mean = 0, stddev = 1.)
Moffat_Model = models.Moffat1D(amplitude = 1000, x_0 = 0, gamma = 1, alpha = 2)
Fitting_Model = fitting.LevMarLSQFitter()
Fit_Data = []
Fit_Data_2 = []
for i in range(0, Image_Data_All2.shape[1]):
Fit_Data_2.append(Fitting_Model(Gauss_Model, x, Image_Data_All2[:,i]))
#for i in range(0, Image_Data_All2.shape[1]):
# Fit_Data_2.append(Fitting_Model(Moffat_Model, x, Image_Data_All2[:,i]))
for i in range(0, Image_Data_All2.shape[1]):
if Fit_Data: # true if not an empty list
Gauss_Model = models.Gaussian1D(amplitude=Fit_Data[-1].amplitude,
mean=Fit_Data[-1].mean,
stddev=Fit_Data[-1].stddev)
fwhm = 2.355
import numpy as np, pyfits, cPickle
from matplotlib.patches import Ellipse
from astropy.modeling import models, fitting
fit_p = fitting.LevMarLSQFitter()
from scipy.optimize import curve_fit
from scipy.special import erf
def beam_factor(xpix, ypix, freqGHz, ratios, noise_list):
nSamples = 10000
factor = freqGHz / 60 * 0.5
pctrs = pctrs = [(750, 750), (917.42261089116289, 452.48369657494271),
(806.96861768041856, 452.42720948105159),
(917.27641014690346, 643.54361577204429),
(806.91944976081186, 643.48717830145449),
(972.55227473819843, 548.05291404475804),
(862.1467847912545, 547.96840887824237),
(751.74125821542486, 547.93998944819577),
(1027.8765912332021, 452.59629406062078),
(1027.6333576756713, 643.65611434189077),
(696.56242900649295, 643.48680190600885),
(1082.9577056577434, 548.19350494100092),
(972.35753377858964, 739.11284658633997),
(862.04908851816867, 739.02841569859129),
(751.7406066611278, 739.00002124865318),
(696.5145640484626, 452.42683275461894),
(1027.3900902000746, 834.6959976649191),
(917.13018901551754, 834.58359802467032),
(806.87027498486566, 834.52721018446596),
(696.61030063911267, 834.52683411992791),
def _fit_lines(spectrum,
model,
fitter=fitting.LevMarLSQFitter(calc_uncertainties=True),
exclude_regions=None,
weights=None,
window=None,
get_fit_info=False,
ignore_units=False,
**kwargs):
"""
Fit the input model (initial conditions) to the spectrum. Output will be
the same model with the parameters set based on the fitting.
spectrum, model -> model
"""
#
# If we are to exclude certain regions, then remove them.
#
if exclude_regions is not None:
spectrum = excise_regions(spectrum, exclude_regions)
if isinstance(weights, str):
if weights == 'unc':
uncerts = spectrum.uncertainty
# Astropy fitters expect weights in 1/sigma
if uncerts is not None:
weights = uncerts.array**-1
else:
warnings.warn("Uncertainty values are not defined, but are "
"trying to be used in model fitting.")
else:
raise ValueError("Unrecognized value `%s` in keyword argument.",
weights)
elif weights is not None:
# Assume that the weights argument is list-like
weights = np.array(weights)
mask = spectrum.mask
dispersion = spectrum.spectral_axis
flux = spectrum.flux
flux_unit = spectrum.flux.unit
#
# Determine the window if it is not None. There
# are several options here:
# window = 4 * u.Angstrom -> Quantity
# window = (4*u.Angstrom, 6*u.Angstrom) -> tuple
# window = (4, 6)*u.Angstrom -> Quantity
#
#
# Determine the window if there is one
#
# In this case the window defines the area around the center of each model
window_indices = None
if window is not None and isinstance(window, (float, int)):
center = model.mean
window_indices = np.nonzero((dispersion >= center - window)
& (dispersion < center + window))
# In this case the window is the start and end points of where we
# should fit
elif window is not None and isinstance(window, tuple):
window_indices = np.nonzero((dispersion >= window[0])
& (dispersion <= window[1]))
# in this case the window is spectral regions that determine where
# to fit.
elif window is not None and isinstance(window, SpectralRegion):
idx1, idx2 = window.bounds
if idx1 == idx2:
raise IndexError("Tried to fit a region containing no pixels.")
# HACK WARNING! This uses the extract machinery to create a set of
# indices by making an "index spectrum"
# note that any unit will do but Jy is at least flux-y
# TODO: really the spectral region machinery should have the power
# to create a mask, and we'd just use that...
idxarr = np.arange(spectrum.flux.size).reshape(spectrum.flux.shape)
index_spectrum = Spectrum1D(spectral_axis=dispersion,
flux=u.Quantity(idxarr, u.Jy, dtype=int))
extracted_regions = extract_region(index_spectrum, window)
if isinstance(extracted_regions, list):
if len(extracted_regions) == 0:
raise ValueError('The whole spectrum is windowed out!')
window_indices = np.concatenate(
[s.flux.value.astype(int) for s in extracted_regions])
else:
if len(extracted_regions.flux) == 0:
raise ValueError('The whole spectrum is windowed out!')
window_indices = extracted_regions.flux.value.astype(int)
if window_indices is not None:
dispersion = dispersion[window_indices]
flux = flux[window_indices]
if mask is not None:
mask = mask[window_indices]
if weights is not None:
weights = weights[window_indices]
if flux is None or len(flux) == 0:
raise Exception("Spectrum flux is empty or None.")
input_spectrum = spectrum
spectrum = Spectrum1D(
flux=flux.value * flux_unit,
spectral_axis=dispersion,
wcs=input_spectrum.wcs,
velocity_convention=input_spectrum.velocity_convention,
rest_value=input_spectrum.rest_value)
if not model._supports_unit_fitting:
# Not all astropy models support units. For those that don't
# we will strip the units and then re-add them before returning
# the model.
model, dispersion, flux = _strip_units_from_model(
model, spectrum, convert=not ignore_units)
#
# Do the fitting of spectrum to the model.
#
if mask is not None:
nmask = ~mask
dispersion = dispersion[nmask]
flux = flux[nmask]
if weights is not None:
weights = weights[nmask]
fit_model = fitter(model, dispersion, flux, weights=weights, **kwargs)
if hasattr(fitter, 'fit_info') and get_fit_info:
fit_model.meta['fit_info'] = fitter.fit_info
if not model._supports_unit_fitting:
fit_model = QuantityModel(fit_model, spectrum.spectral_axis.unit,
spectrum.flux.unit)
return fit_model
