def compareW(PSF,sig,accd,cx,cy):
x1, y1 = centroid_com(PSF)
x2, y2 = centroid_1dg(PSF)
x3, y3 = centroid_2dg(PSF)
errx1=cx-1-x1
erry1=cy-1-y1
errx2=cx-1-x2
erry2=cy-1-y2
errx3=cx-1-x3
erry3=cy-1-y3
err1=((errx1)**2+(erry1)**2)**0.5
err2=((errx2)**2+(erry2)**2)**0.5
err3=((errx3)**2+(erry3)**2)**0.5
# print("%.2e,%.2e,%.2e,%.2e,%.2e,%.2e," % ( errx1,erry1,errx2,erry2,errx3,erry3))
# Weighted
Weight=GaussianFunc(sig,accd,cx,cy)
PSFW=PSF*Weight
x1, y1 = centroid_com(PSFW)
x2, y2 = centroid_1dg(PSFW)
x3, y3 = centroid_2dg(PSFW)
errx12=cx-1-x1
erry12=cy-1-y1
errx22=cx-1-x2
erry22=cy-1-y2
errx32=cx-1-x3
erry32=cy-1-y3
err12=((errx12)**2+(erry12)**2)**0.5
err22=((errx22)**2+(erry22)**2)**0.5
err32=((errx32)**2+(erry32)**2)**0.5
# print("%.2e,%.2e,%.2e,%.2e,%.2e,%.2e," % ( errx12,erry12,errx22,erry22,errx32,erry32))
return err1,err2,err3,err12,err22,err32
def Centroids(Stars, References, Trim=0, Plot=False):
"""
Calculate the centroid offsets for a set of reference stars.
"""
flags = np.zeros((Stars.shape[0]))
centroids = np.zeros((Stars.shape[0], Stars.shape[1], 2))
for i in range(len(Stars)):
star = Stars[i]
lc = np.nansum(star, axis=(1, 2))
lc[lc == 0] = np.nan
lc = lc / np.nanmedian(lc)
bads = np.nansum(lc > 1.2)
if bads >= 10:
flags[i] = 1
for j in range(len(star)):
if Trim == 0:
c = centroid_com(star[j])
ref = centroid_com(References[i])
else:
c = centroid_com(star[j, Trim:-Trim, Trim:-Trim])
ref = centroid_com(References[i, Trim:-Trim, Trim:-Trim])
c = c - ref
centroids[i, j] = c
if Plot:
Plot_centroids(centroids[i], star, i)
return centroids, flags
def get_centroids(fluxes, centroid_shift=None, method='abs_distance',
check_outliers=False, showfig=False):
'''
fluxes: array, 3D fluxes
method: str, (1) absolute distance (2) sklearn.ensemble
centroid_shift: int, maximum shift in pixels; if larger then mask is flagged
check_outliers: bool,
'''
xcen, ycen = [],[]
mask = np.zeros(len(fluxes))
if check_outliers:
stacked = np.nansum(fluxes, axis=0)
Xc, Yc = centroid_com(stacked)
for idx,img in enumerate(fluxes):
x,y = centroid_com(img)
if check_outliers:
if centroid_shift is not None:
#shift = int(round(centroid_shift))
shift = float(centroid_shift)
if abs(Xc-x) > shift or abs(Yc-y) > shift:
mask[idx] = 1
else:
raise ValueError('`centroid_shift` not defined')
else:
pass
xcen.append(x)
ycen.append(y)
#convert 0,1 into bool
mask = np.array(mask, dtype=bool)
if method == 'ensemble':
X = np.c_[xcen,ycen]
mask = IsolationForest(max_features=2, contamination=0.01).fit(X).predict(X)
#output is 1 or -1, convert to bool
mask = np.array([True if bool(i == 1.0) else False for i in mask])
xcen, ycen = np.array(xcen),np.array(ycen)
if showfig:
if method == 'ensemble':
pl.scatter(xcen, ycen, c=mask, cmap='RdBu')
else:
pl.plot(xcen,ycen,'bo',label='good data')
pl.plot(xcen[mask],ycen[mask],'ro',label='bad data')
pl.legend()
return (xcen,ycen), mask
def center(s_post, member_indices):
mem = gcat[member_indices]
""" Member Galaxy Locations """
mempix = convpix(mem, w)
x = mempix[:, 0]
y = mempix[:, 1]
""" Configuring Pixel Space"""
init_x, init_y = w.wcs_world2pix(s_post[0], s_post[1],
1) # initial estimate to draw box
wid_arcsec = 302 # 5'x 5' area around s-post
pix_scale = 0.8627 # "/pixel ---> 0.000239 deg/pixel
wid_pixels = int(wid_arcsec / pix_scale) # ~350x350 pixels
xmin = int(init_x - (wid_pixels / 2.0)) # boundaries
xmax = int(init_x + (wid_pixels / 2.0))
ymin = int(init_y - (wid_pixels / 2.0))
ymax = int(init_y + (wid_pixels / 2.0))
""" 2D-Histogram & Smoothing """
binstep = 10 # 10 pixel ~ 8.62 "
wght = np.asarray(
gcat[member_indices]['fch1']) # weights: irac ch1[3.6 um] flux
xedges = np.arange(xmin, xmax + binstep, binstep)
yedges = np.arange(ymin, ymax + binstep, binstep)
h, xedges, yedges = np.histogram2d(x,
y,
bins=(xedges, yedges),
weights=wght)
size = int(round(
(np.shape(h)[0]) / 4.0)) # kernel size : at least ~ 4 times smaller
stdev_ker = size / 3.0 # size = 3-sigma
gauss_kernel = Gaussian2DKernel(stddev=stdev_ker, x_size=size,
y_size=size) # kernel
smoothed_data_gauss = convolve_fft(h.T,
gauss_kernel) # convolution/smoothing
""" Finds Peak """
x_org, y_org = (xedges[0] + xedges[1]) / 2.0, (
yedges[0] + yedges[1]) / 2.0 # origin of bin-coordinate
fp_m = find_peaks(smoothed_data_gauss, 0,
npeaks=1) # 1 peak with max value
xbin_peak, ybin_peak = fp_m['x_peak'][0], fp_m['y_peak'][
0] # x, y positions of the peak
x_p, y_p = (x_org + xbin_peak * binstep), (
y_org + ybin_peak * binstep) # conversion to pixel coordinates
peak = (x_p, y_p)
ra_p, dec_p = w.wcs_pix2world(peak[0], peak[1], 1)
peak_fk5 = (ra_p, dec_p)
""" Centroid from Image Moments """
cen_pos = centroid_com(smoothed_data_gauss)
cenx, ceny = (x_org + cen_pos[0] * binstep), (y_org + cen_pos[1] * binstep)
ra_c, dec_c = w.wcs_pix2world(cenx, ceny, 1)
centre = (ra_c, dec_c)
return centre, peak_fk5
def plot_image():
std = np.std(stamp[stamp == stamp])
x1, y1 = centroid_com(stamp)
x2, y2 = centroid_1dg(stamp)
x3, y3 = centroid_2dg(stamp)
return [((x1 - dx + xcen), (x2 - dx + xcen), (x3 - dx + xcen)),
((y1 - dy + ycen), (y2 - dy + ycen), (y3 - dy + ycen))]
def plot_aper_mask(fluxes,rad,aper_shape,contrast=0.1,epic=None):
stacked = np.nansum(fluxes,axis=0)
mask = make_mask(fluxes, rad = rad, shape=aper_shape)
y,x = centroid_com(stacked)
fig, ax = pl.subplots(1,1)
interval = ZScaleInterval(contrast=contrast)
zmin,zmax = interval.get_limits(stacked)
cb = ax.imshow(stacked, origin='bottom', interpolation=None)
ax.imshow(mask, alpha=0.3)
if aper_shape == 'round':
circ = pl.Circle((x,y),rad,color='w',alpha=0.2,lw=5,label='r={}'.format(rad))
ax.add_artist(circ)
ax.plot(x,y,'r+',ms=20, lw=10,label='centroid')
pl.colorbar(cb, ax=ax)
pl.xlabel('X')
pl.ylabel('Y')
pl.legend()
if epic is not None:
pl.title('EPIC {}'.format(epic))
pl.show()
return fig
def psfpy(data):
x1, y1 = centroid_com(data)
x2, y2 = centroid_1dg(data)
x3, y3 = centroid_2dg(data)
# print(data)
# print(x1,y1,x2,y2,x3,y3)
# mean, median, std = sigma_clipped_stats(data, sigma=3.0, iters=5)
# data -= median # subtract background
cat = data_properties(data)
# print (cat)
#列输出
columns = [
'id', 'xcentroid', 'ycentroid', 'semimajor_axis_sigma',
'semiminor_axis_sigma', 'orientation', 'cxx', 'cyy', 'cxy',
'eccentricity'
]
tbl = cat.to_table(columns=columns)
tbl['cxy'].info.format = '.10f'
eccef = float(tbl['eccentricity'])
str1 = str(tbl['semimajor_axis_sigma'])
semimajorf = str1.split("[")[1].split("]")[0]
str1 = str(tbl['semiminor_axis_sigma'])
semiminorf = str1.split("[")[1].split("]")[0]
str1 = str(tbl['orientation'])
orientationf = str1.split("[")[1].split("]")[0]
str1 = str(tbl['cxx'])
cxxf = str1.split("[")[1].split("]")[0]
str1 = str(tbl['cxy'])
cxyf = str1.split("[")[1].split("]")[0]
str1 = str(tbl['cyy'])
cyyf = str1.split("[")[1].split("]")[0]
return (x1, y1, x2, y2, x3, y3, semimajorf, semiminorf, eccef,
orientationf, cxxf, cxyf, cyyf)
def plot_image(posx, posy, count, prevstds):
#We have to redefine the stamp every time, otherwise the program doesn't woek
stamp = data[i][int(round(posy - dy)):int(round(posy + dy)),
int(round(posx - dx)):int(round(posx + dx))]
#this is just to keep track of how much recursing we do
count = count + 1
std = np.std(stamp[stamp == stamp])
x1, y1 = centroid_com(stamp)
x2, y2 = centroid_1dg(stamp)
x3, y3 = centroid_2dg(stamp)
xavg = np.average([x2, x3])
yavg = np.average([y2, y3])
xstd = np.std([x2, x3])
ystd = np.std([y2, y3])
#xavg = np.average([x1,x2,x3])
#yavg = np.average([y1,y2,y3])
#xstd = np.std([x1,x2,x3])
#ystd = np.std([y1,y2,y3])
#print(count, posx-dx+xavg, posy-dy+yavg, xstd, ystd)
# RECURSION BITCH limit 100 times, while either std is higher than our 0.1 threshold
# and as long as the std is getting smaller
if (xstd + ystd > prevstds[0] + prevstds[1]):
return posx, posy, prevstds[0]**(-2), prevstds[1]**(-2), count - 1
if count < 100 and (xstd > 0.1 or ystd > 0.1) and (xstd <= prevstds[0] and
ystd <= prevstds[1]):
return plot_image(posx - dx + xavg, posy - dy + yavg, count,
[xstd, ystd])
else:
return posx - dx + xavg, posy - dy + yavg, 1 / (xstd**2), 1 / (
ystd**2), count
def Select_Target(self, image, x, y, box):
X = []
Y = []
#delete previous circles
for elem in self.redcircle:
self.canvas.delete(elem)
D = image[int(y) - box:int(y) + box, int(x) - box:int(x) + box]
xn, yn = centroid_com(D - numpy.median(D))
xn = xn + int(x) - box
yn = yn + int(y) - box
print('Center of the target: x = {} y = {}'.format(xn, yn))
X.append(xn)
Y.append(yn)
NX = X[0] - 22
NY = Y[0]
D = image[int(NY) - box:int(NY) + box, int(NX) - box:int(NX) + box]
xn, yn = centroid_com(D - numpy.median(D))
xn = xn + int(NX) - box
yn = yn + int(NY) - box
X.append(xn)
Y.append(yn)
for xe, ye in zip(X, Y):
self.redcircle.append(
self.canvas.create_oval(xe * self.zoom - 10,
ye * self.zoom - 10,
xe * self.zoom + 10,
ye * self.zoom + 10,
outline='blue',
width=2))
self.redcircle.append(
self.canvas.create_oval(xe * self.zoom - 1,
ye * self.zoom - 1,
xe * self.zoom + 1,
ye * self.zoom + 1,
outline='red',
width=2))
self.Tx[self.index] = X
self.Ty[self.index] = Y
def psf_norm_2d(array, fwhm, size, threshold, mask_core, full_output,
verbose):
""" 2d case """
if size is not None:
if size < array.shape[0]:
psfs = frame_crop(array, size, force=True, verbose=False)
else:
psfs = array.copy()
else:
psfs = array.copy()
# we check if the psf is centered and fix it if needed
cy, cx = frame_center(psfs, verbose=False)
xcom, ycom = photutils.centroid_com(psfs)
if not (np.allclose(cy, ycom, atol=1e-2) or
np.allclose(cx, xcom, atol=1e-2)):
# first we find the centroid and put it in the center of the array
centry, centrx = fit_2d(psfs)
shiftx, shifty = centrx - cx, centry - cy
psfs = frame_shift(array, -shifty, -shiftx, imlib=imlib,
interpolation=interpolation)
if size is not None:
psfs = frame_crop(psfs, size, force=True, verbose=False)
for _ in range(2):
centry, centrx = fit_2d(psfs)
cy, cx = frame_center(psfs, verbose=False)
shiftx, shifty = centrx - cx, centry - cy
psfs = frame_shift(psfs, -shifty, -shiftx, imlib=imlib,
interpolation=interpolation)
# we check whether the flux is normalized and fix it if needed
fwhm_aper = photutils.CircularAperture((frame_center(psfs)), fwhm/2)
fwhm_aper_phot = photutils.aperture_photometry(psfs, fwhm_aper,
method='exact')
fwhm_flux = np.array(fwhm_aper_phot['aperture_sum'])
if fwhm_flux > 1.1 or fwhm_flux < 0.9:
psf_norm_array = psfs / np.array(fwhm_aper_phot['aperture_sum'])
else:
psf_norm_array = psfs
if threshold is not None:
psf_norm_array[np.where(psf_norm_array < threshold)] = 0
if mask_core is not None:
psf_norm_array = get_circle(psf_norm_array, radius=mask_core)
if verbose:
print("Flux in 1xFWHM aperture: {:.3f}".format(fwhm_flux[0]))
if full_output:
return psf_norm_array, fwhm_flux, fwhm
else:
return psf_norm_array
def centroid(a):
top=19
bot=12
a = ma.masked_invalid(a)
#a=sigma_clip(a, sigma=7, iters=1)
a=a[bot:top+1, bot:top+1]
a2=np.multiply(a,a)
beta_np=np.sum(a)**2/np.sum(a2)
xcg, ycg = centroid_2dg(a)+bot
xc, yc = centroid_com(a)+bot
return xc,yc, xcg, ycg
def get_planicentre(img,
rad,
iterations=1,
croppix=400,
Debug=False,
endcrop=10):
croppedimg = img
for i in range(iterations):
imgcent = centroid_com(croppedimg)
if Debug:
print(imgcent)
plt.figure(figsize=(5, 5))
im5 = plt.imshow(croppedimg, cmap=col)
plt.axhline(imgcent[0], color=xcol)
plt.axvline(imgcent[1], color=xcol)
plt.title('Partial Image ' + str(i))
plt.colorbar(im5)
plt.show()
croppedimg = croppedimg[(int(imgcent[1] - croppix)):(int(imgcent[1] +
croppix)),
(int(imgcent[0] - croppix)):(int(imgcent[0] +
croppix))]
croppedimg = image.exp_despike(croppedimg, nsigma=1)
croppix = croppix / 3
planicentre1 = centroid_com(croppedimg)
DiscImg = croppedimg[(int(planicentre1[1]) -
(int(rad) + endcrop)):(int(planicentre1[1]) +
(int(rad) + endcrop)),
(int(planicentre1[0]) -
(int(rad) + endcrop)):int(planicentre1[0]) +
((int(rad) + endcrop))]
planicentre2 = get_disc(DiscImg, r0=rad)
return DiscImg, planicentre2
def plot_image():
std = np.std(stamp[stamp==stamp])
plt.imshow(stamp, interpolation='nearest', origin = 'lower', vmin = -1.*std, vmax = 3.*std, cmap='bone')
plt.tick_params(axis='both', which='major', labelsize=8)
circle0 = plt.Circle((dx,dy),0.1)
x1, y1 = centroid_com(stamp)
circle1 = plt.Circle((x1,y1),0.1,color='r')
ax.add_artist(circle1)
x2, y2 = centroid_1dg(stamp)
circle2 = plt.Circle((x2,y2),0.1,color='b')
ax.add_artist(circle2)
x3, y3 = centroid_2dg(stamp)
circle3 = plt.Circle((x3,y3),0.1,color='g')
ax.add_artist(circle3)
return ((x1, y1),(x2, y2),(x3, y3))
def get_centroid(image, method='com'):
'''
centroid_com(): Calculates the object 'center of mass' from 2D image moments.
centroid_1dg(): Calculates the centroid by fitting 1D Gaussians to the marginal x and y distributions of the data.
centroid_2dg(): Calculates the centroid by fitting a 2D Gaussian to the 2D distribution of the data.
Default is centroid_2dg.
'''
if method == 'com':
x, y = centroid_com(image)
elif method == '1d_gaussian':
x, y = centroid_1dg(image)
else: #default
x, y = centroid_2dg(image)
return (x, y)
def make_mask(fluxes, rad=None, cutoff_limit=1.0, shape='round', epic=None, showfig=False):
'''
create mask given 3D (t x h x w) fluxes
'''
#stack images
stacked = np.nansum(fluxes,axis=0)
#get centroid of stacked image
x,y = centroid_com(stacked)
xx,yy = int(round(x)), int(round(y))
mask = np.zeros_like(stacked)
if shape == 'square':
if rad is not None:
if stacked.size > (2*rad)**2:
assert ValueError('mask size bigger than tpf cutout')
for i in np.arange(-rad,rad,1):
for j in np.arange(-rad,rad,1):
mask[xx+i,yy+j] = 1
else:
raise ValueError('rad: aperture radius not defined')
elif shape == 'irregular':
mask = find_aperture(fluxes, cutoff_limit=1.0)
elif shape == 'round' or shape == 'cirle':
#default: round
if rad is not None:
if stacked.size > (2*rad)**2:
assert ValueError('mask size bigger than tpf cutout')
for i in range(stacked.shape[0]):
for j in range(stacked.shape[1]):
if np.sqrt((xx-i)**2+(yy-j)**2)<=rad:
mask[i,j] = 1
else:
raise ValueError('rad: aperture radius not defined')
else:
# no mask; use all pixels
mask = np.ones_like(stacked)
if showfig:
fig = plot_aper_mask(fluxes,rad,aper_shape=shape,contrast=0.1,epic=epic)
return np.array(mask,dtype=bool)
def plot_image(posx,posy, count, prevstds):
stamp = data[int(round(posy-dy)):int(round(posy+dy)), int(round(posx-dx)):int(round(posx+dx))]
count = count +1
std = np.std(stamp[stamp==stamp])
x1, y1 = centroid_com(stamp)
x2, y2 = centroid_1dg(stamp)
x3, y3 = centroid_2dg(stamp)
xavg = np.average([x1,x2,x3])
yavg = np.average([y1,y2,y3])
xstd = np.std([x1,x2,x3])
ystd = np.std([y1,y2,y3])
# RECURSION BITCH
if count < 100 and (xstd > 0.1 or ystd > 0.1) and (xstd <= prevstds[0] and ystd <= prevstds[1]):
print(count, posx-dx+xavg, posy-dy+yavg, xstd, ystd)
return plot_image(posx-dx+xavg, posy-dy+yavg, count, [xstd,ystd])
else:
return posx-dx+xavg, posy-dy+yavg, 1/(xstd**2), 1/(ystd**2), count
def get_centroid(image, method='com'):
'''
centroid_com(): Calculates the object “center of mass” from 2D image moments.
centroid_1dg(): Calculates the centroid by fitting 1D Gaussians to the marginal x and y distributions of the data.
centroid_2dg(): Calculates the centroid by fitting a 2D Gaussian to the 2D distribution of the data.
Default is com.
'''
if method == 'com':
x, y = centroid_com(image)
return (x, y)
elif method == '1d_gaussian':
x, y = centroid_1dg(image)
return (x, y)
elif method == '2d_gaussian':
#bug: takes too much time; fit may be unsuccessful
x, y = centroid_2dg(image)
return (x, y)
else:
print('invalid centroiding algorithm')
sys.exit()
def recenter(image, pos, window_size=5, method="1dg"):
"""
Recenter each star in each frame of the image cube before performing
aperture photometry to take care of slight misalignments between frames
because of atmospheric turbulence and tracking/pointing errors.
Parameters
----------
image : numpy array
2D image
pos : list
List of (x,y) tuples for star positions
window_size : int
Window size in which to fit the gaussian to the star to calculate
new center
method : string
Method used to find center of the star. Options are 1d Gaussian fit,
2d gaussian fit or com (center of mass)
Returns
-------
xcen, ycen : float
Source x and y centers
"""
pos = np.asarray(pos)
ny, nx = image.shape
window_size = int(window_size)
nstars = pos.shape[0]
star_pos = np.zeros([nstars, 2], dtype=np.float32)
for i in range(nstars):
x, y = pos[i][0], pos[i][1]
xmin, xmax = int(x) - int(window_size / 2), int(x) + int(
window_size / 2) + 1
ymin, ymax = int(y) - int(window_size / 2), int(y) + int(
window_size / 2) + 1
if xmin < 0:
xmin = 0
if ymin < 0:
ymin = 0
if xmax > nx:
xmax = nx
if ymax > ny:
ymax = ny
if method == "1dg":
xcen, ycen = centroid_1dg(image[ymin:ymax, xmin:xmax])
elif method == "2dg":
xcen, ycen = centroid_2dg(image[ymin:ymax, xmin:xmax])
elif method == "com":
xcen, ycen = centroid_com(image[ymin:ymax, xmin:xmax])
if (np.abs(xmin + xcen - x)) > 3. or (np.abs(ymin + ycen - y)) > 3.:
star_pos[i, 0] = x
star_pos[i, 1] = y
else:
star_pos[i, 0] = xmin + xcen
star_pos[i, 1] = ymin + ycen
return star_pos
def find_center(image, center_guess, cutout_size=30, max_iters=10):
"""
Find the centroid of a star from an initial guess of its position. Originally
written to find star from a mouse click.
Parameters
----------
image : numpy array or CCDData
Image containing the star.
center_guess : array or tuple
The position, in pixels, of the initial guess for the position of
the star. The coordinates should be horizontal first, then vertical,
i.e. opposite the usual Python convention for a numpy array.
cutout_size : int, optional
The default width of the cutout to use for finding the star.
max_iters : int, optional
Maximum number of iterations to go through in finding the center.
"""
pad = cutout_size // 2
x, y = center_guess
# Keep track of iterations
cnt = 0
# Grab the cutout...
sub_data = image[y - pad:y + pad, x - pad:x + pad] # - med
# ...do stats on it...
_, sub_med, _ = sigma_clipped_stats(sub_data)
# sub_med = 0
# ...and centroid.
x_cm, y_cm = centroid_com(sub_data - sub_med)
# Translate centroid back to original image (maybe use Cutout2D instead)
cen = np.array([x_cm + x - pad, y_cm + y - pad])
# ceno is the "original" center guess, set it to something nonsensical here
ceno = np.array([-100, -100])
while (cnt <= max_iters and (np.abs(np.array([x_cm, y_cm]) - pad).max() > 3
or np.abs(cen - ceno).max() > 0.1)):
# Update x, y positions for subsetting
x = int(np.floor(x_cm)) + x - pad
y = int(np.floor(y_cm)) + y - pad
sub_data = image[y - pad:y + pad, x - pad:x + pad] # - med
_, sub_med, _ = sigma_clipped_stats(sub_data)
# sub_med = 0
mask = (sub_data - sub_med) < 0
x_cm, y_cm = centroid_com(sub_data - sub_med, mask=mask)
ceno = cen
cen = np.array([x_cm + x - pad, y_cm + y - pad])
if not np.all(~np.isnan(cen)):
raise RuntimeError('Centroid finding failed, '
'previous was {}, current is {}'.format(
ceno, cen))
cnt += 1
return cen
def plot_image():
std = np.std(stamp[stamp == stamp])
x1, y1 = centroid_com(stamp)
x2, y2 = centroid_1dg(stamp)
x3, y3 = centroid_2dg(stamp)
return np.array([[x1, x2, x3], [y1, y2, y3]])
def center(iter_no, s_post, member_indices, apr, plotmap):
mem = gcat[
member_indices] # gcat = The galaxy catalog of which the overdensities are being computed.
""" Member Galaxy Locations in Pixel Space """
galpix = convpix(mem, w)
x = galpix[:, 0]
y = galpix[:, 1]
""" Configuring Pixel Space"""
init_x, init_y = w.wcs_world2pix(s_post[0], s_post[1],
0) # initial estimate to draw box
PIX_SCALE = imagefile[0].header[
'CDELT2'] * 3600.0 # "/pixel ---> 0.000239 deg/pixel, IRAC/bootes
if apr <= 2.0:
wid_arcsec = 302 # ~5'x5' region around the signpost
elif 2.0 < apr <= 5.0:
wid_arcsec = 716.5 # ~12'x12'
else:
wid_arcsec = 898 # ~15'x15'
wid_pixels = int(wid_arcsec /
PIX_SCALE) # ~350x350 pixels/ 830x830 /1040x1040
xmin, xmax = int(init_x - (wid_pixels / 2.0)), int(
init_x + (wid_pixels / 2.0)) # boundaries
ymin, ymax = int(init_y - (wid_pixels / 2.0)), int(init_y +
(wid_pixels / 2.0))
""" 2D-Histogram & Smoothing """
binstep = 5.0 # 10 pixel ~ 8.62 "
wght = np.asarray(
gcat[member_indices]['ch2_flux']) # weights: irac ch2[4.5 um] flux
xedges = np.arange(xmin, xmax + binstep, binstep)
yedges = np.arange(ymin, ymax + binstep, binstep)
h, xedges, yedges = np.histogram2d(x,
y,
bins=(xedges, yedges),
weights=wght)
xmid = [(xedges[ik] + xedges[ik + 1]) / 2.0
for ik in range(len(xedges) - 1)]
ymid = [(yedges[ij] + yedges[ij + 1]) / 2.0
for ij in range(len(yedges) - 1)]
size = int(round((np.shape(h)[0]) /
4.0)) # kernel size : at least ~ 4 times smaller
stdev_ker = size / 4.0 # size = 4-sigma
gauss_kernel = Gaussian2DKernel(x_stddev=stdev_ker,
y_stddev=stdev_ker,
x_size=size,
y_size=size) # kernel
smoothed_data_gauss = convolve_fft(
h.T, gauss_kernel) # convolution/smoothing
max_sm_val = max(smoothed_data_gauss.flatten())
""" Finds Peak """
x_org, y_org = (xedges[0] + xedges[1]) / 2.0, (
yedges[0] + yedges[1]) / 2.0 # origin of bin-coordinate
fp_m = find_peaks(smoothed_data_gauss, 0,
npeaks=1) # 1 peak with max value
xbin_peak, ybin_peak = fp_m['x_peak'][0], fp_m['y_peak'][
0] # x, y positions of the peak
x_p, y_p = (x_org + xbin_peak * binstep), (
y_org + ybin_peak * binstep) # conversion to pixel coordinates
peak_pix = (x_p, y_p)
ra_p, dec_p = w.wcs_pix2world(peak_pix[0], peak_pix[1], 0)
peak_fk5 = (ra_p, dec_p)
""" Centroid from Image Moments """
cen_pos = centroid_com(smoothed_data_gauss)
cenx, ceny = (x_org + cen_pos[0] * binstep), (y_org +
cen_pos[1] * binstep)
ra_c, dec_c = w.wcs_pix2world(cenx, ceny, 0)
centre = (ra_c, dec_c)
""" Plots """
if plotmap == 'ON':
fgm = plt.figure()
ax = fgm.add_subplot(111)
# ax_b.imshow(smoothed_data_gauss, extent=[xmin, xmax, ymin, ymax], cmap='jet')
cntf = ax.contourf(
xmid,
ymid,
smoothed_data_gauss,
cmap='Blues',
levels=[lt for lt in np.arange(0.10, max_sm_val + 0.02, 0.02)])
ax.scatter(x, y, marker='o', color='red', s=5)
ax.scatter(cenx, ceny, marker='s')
ax.scatter(x_p, y_p, marker='^')
ax.scatter(init_x, init_y, marker='o', color='lime')
fgm.colorbar(cntf)
fgm.savefig(catdir + 'clump_plots/' + str(iter_no) + '_map.png',
format='png',
dpi=100)
plt.close(fgm)
return centre, peak_fk5
def fit_2dmoffat(array,
crop=False,
cent=None,
cropsize=15,
fwhm=4,
threshold=False,
sigfactor=6,
full_output=True,
debug=True):
""" Fitting a 2D Moffat to the 2D distribution of the data.
Parameters
----------
array : numpy ndarray
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.
"""
check_array(array, dim=2, msg='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 Moffat model
init_amplitude = np.ptp(psf_subimage)
xcom, ycom = photutils.centroid_com(psf_subimage)
moffat = models.Moffat2D(amplitude=init_amplitude,
x_0=xcom,
y_0=ycom,
gamma=fwhm / 2.,
alpha=1)
# Levenberg-Marquardt algorithm
fitter = fitting.LevMarLSQFitter()
y, x = np.indices(psf_subimage.shape)
fit = fitter(moffat, 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
fwhm = fit.fwhm
amplitude = fit.amplitude.value
alpha = fit.alpha.value
gamma = fit.gamma.value
if debug:
if threshold:
label = ('Subimage thresholded', 'Model', 'Residuals')
else:
label = ('Subimage', 'Model', 'Residuals')
plot_frames((psf_subimage, fit(x, y), psf_subimage - fit(x, y)),
grid=True,
grid_spacing=1,
label=label)
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('alpha =', alpha)
print('gamma =', gamma)
# compute uncertainties
if fitter.fit_info['param_cov'] is not None:
perr = np.sqrt(np.diag(fitter.fit_info['param_cov']))
amplitude_err, mean_x_err, mean_y_err, gamma_err, alpha_err = perr
fwhm_err = 2 * gamma_err
else:
amplitude_err, mean_x_err, mean_y_err = None, None, None
gamma_err, alpha_err, fwhm_err = None, None, None
if full_output:
return pd.DataFrame(
{
'centroid_y': mean_y,
'centroid_x': mean_x,
'fwhm': fwhm,
'alpha': alpha,
'gamma': gamma,
'amplitude': amplitude,
'centroid_y_err': mean_y_err,
'centroid_x_err': mean_x_err,
'fwhm_err': fwhm_err,
'alpha_err': alpha_err,
'gamma_err': gamma_err,
'amplitude_err': amplitude_err
},
index=[0])
else:
return mean_y, mean_x
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 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 center(s_post, member_cat, image_wcs, apr, dog, itr_no):
mem = member_cat
mempix = convpix(mem, image_wcs) # member objects in pixel coordinates
x_pixels, y_pixels = mempix[:, 0], mempix[:, 1]
init_x, init_y = image_wcs.wcs_world2pix(s_post[0], s_post[1],
0) # initial estimate to draw box
dogx, dogy = image_wcs.wcs_world2pix(dog[0], dog[1],
0) # DOG location in pixel space
pix_scale = 0.000239631 * 3600. # "/pixel IRAC-Ch2/SDWFS survey
if apr <= 2.0:
wid_arcsec = 200.0 # ~6'x6' region around the DOG
elif 2.0 < apr <= 5.0:
wid_arcsec = 716.5 # ~12'x12'
else:
wid_arcsec = 898.0 # ~15'x15'
wid_pixels = int(
wid_arcsec / pix_scale
) # ~350x350 pixels/~830x830 /~1040x1040 depending on aperture.
xmin, xmax = int(dogx - (wid_pixels / 2.0)), int(
dogx + (wid_pixels / 2.0)) # boundaries
ymin, ymax = int(dogy - (wid_pixels / 2.0)), int(
dogy + (wid_pixels / 2.0)) # boundaries
# 2D-histogram
resol = 5 # (input in arcsec -- > degrees) resol is the grid resolution for histogram.
binstep = int(resol / pix_scale) # of image pixels in one bin
bnsx = list(np.arange(xmin, xmax + binstep,
binstep)) # bin-edges in X direction
bnsy = list(np.arange(ymin, ymax + binstep,
binstep)) # bin-edges in Y direction
nx_bins, ny_bins = len(bnsx), len(bnsy) # number of bins in the histogram
wght = np.asarray(mem['fch2']) # weights: irac ch2[4.5 um] flux
h, xedges, yedges = np.histogram2d(x_pixels,
y_pixels,
bins=[bnsx, bnsy],
weights=wght)
mesh_pixels = np.meshgrid(xedges, yedges)
mesh_wcs = image_wcs.wcs_pix2world(mesh_pixels[0], mesh_pixels[1], 0)
# Smoothing
size = int(round(
(np.shape(h)[0]) / 4.0)) # kernel size : at least ~ 4 times smaller
stdev_ker = size / 4.0 # size = 4-sigma
gauss_kernel = Gaussian2DKernel(x_stddev=stdev_ker,
y_stddev=stdev_ker,
x_size=size,
y_size=size) # kernel
smoothed_data_gauss = convolve_fft(h.T,
gauss_kernel) # convolution/smoothing
# Centroid of the image moments
x_org, y_org = (xedges[0] + xedges[1]) / 2.0, (
yedges[0] + yedges[1]) / 2.0 # origin of bin-coordinate
cen_pos = centroid_com(smoothed_data_gauss)
cenx, ceny = (x_org + cen_pos[0] * binstep), (y_org + cen_pos[1] * binstep)
centre = image_wcs.wcs_pix2world(cenx, ceny, 0)
dist_to_dog = sky_sep(s_post, dog)
print(round(dist_to_dog, 2))
""" Plotting """
fig = plt.figure(figsize=(5, 5), dpi=300, tight_layout=True)
ax = fig.add_subplot(111, projection=image_wcs)
max_sm_val = max(smoothed_data_gauss.flatten())
ax.contourf(
mesh_wcs[0][1:, :-1],
mesh_wcs[1][:-1, :-1],
smoothed_data_gauss,
interpolation="nearest",
origin='lower',
cmap='viridis',
extent=[xedges[0], xedges[-1], yedges[0], yedges[-1]],
levels=[lt for lt in np.arange(-0.10, max_sm_val + 0.30, 0.20)],
transform=ax.get_transform('icrs'))
ax.scatter(mem['ra'],
mem['dec'],
marker='o',
s=50,
transform=ax.get_transform('icrs'),
facecolor='red',
edgecolor='none',
alpha=1.,
zorder=4,
label='Member Galaxies')
circ = Circle((init_x, init_y), (apr * 60) / pix_scale,
edgecolor='w',
facecolor='none',
lw=2.0,
ls='--')
ax.add_patch(circ)
ax.plot(centre[0],
centre[1],
marker='x',
color='k',
fillstyle='none',
ls='',
ms=15,
label='Centroid',
mew=2.0,
transform=ax.get_transform('icrs'))
ax.plot(dog[0],
dog[1],
marker='o',
color='lime',
fillstyle='full',
ls='',
ms=8,
label='DOG',
mew=4.0,
transform=ax.get_transform('icrs'))
ax.text(dog[0] - 0.002,
dog[1] - 0.019,
r'$\mathrm{{Richness~={val}}}$'.format(val=len(mem)),
transform=ax.get_transform('icrs'),
fontsize=20,
color='w')
ax.text(dog[0] - 0.01,
dog[1] - 0.015,
r'$\mathrm{{Iteration~={val2}}}$'.format(val2=itr_no + 1),
transform=ax.get_transform('icrs'),
fontsize=15,
color='w')
# Accessories
ax.set_xlim(xmin, xmax - binstep)
ax.set_ylim(ymin, ymax - binstep)
ax.coords[0].set_ticks_position('b')
ax.coords[0].set_ticklabel_position('b')
ax.coords[0].set_axislabel_position('b')
ax.coords[1].set_ticks_position('l_dict')
ax.coords[1].set_ticklabel_position('l_dict')
ax.coords[1].set_axislabel_position('l_dict')
ax.coords[0].set_ticks(
np.arange(mesh_wcs[0][-1][-1], mesh_wcs[0][-1][0] + 0.02, 0.02) *
units.degree)
ax.coords[0].set_ticklabel(fontsize=10)
ax.coords[0].set_major_formatter('d.dd')
ax.coords[0].set_axislabel(r'$\mathrm{R.A.(J2000)}$', fontsize=13)
ax.coords[1].set_ticks(
np.arange(mesh_wcs[1][:, 0][0], mesh_wcs[1][:, 0][-1] + 0.02, 0.02) *
units.degree)
ax.coords[1].set_ticklabel(fontsize=10.0)
ax.coords[1].set_major_formatter('d.dd')
ax.coords[1].set_axislabel(r'$\mathrm{Dec.(J2000)}$', fontsize=13)
ax.legend(loc='best', fontsize=10)
plt.axis('off')
fig.show()
fig.savefig(anim_dir + 'itr' + str(itr_no + 1) + '.png', format='png')
plt.close(fig)
return centre
def get_centroid_cutout(self,
x,
y,
box_size=30,
method="howell",
dao_fwhm=10.,
dao_SNR=100.,
plot=False,
plot_full=False,
stretch=None):
"""
Perform centroiding on a cutout window.
INPUT:
x - a touple
y -
box_size - the total box size in pixels
method - the centroiding method to use for cutout. This can be
"centroid_2dg"
"centroid_com"
"daofind"
OUTPUT:
centroid positions
EXAMPLE:
PM = PhotoMetry(filenames[0])
PM.perform_photometry()
print(PM.get_centroid_cutout(234.227204448,25.6594515323,method="daofind",plot=True))
print(PM.get_centroid_cutout(234.227204448,25.6594515323,method="centroid_com",plot=True))
print(PM.get_centroid_cutout(234.227204448,25.6594515323,method="centroid_2dg",plot=True))
print(PM.get_centroid_cutout(234.227204448,25.6594515323,method="daofind",box_size=50,stretch="HistEqStretch"))
print(PM.get_centroid_cutout(234.227204448,25.6594515323,method="centroid_com",plot=True,box_size=50))
print(PM.get_centroid_cutout(234.227204448,25.6594515323,method="centroid_2dg",plot=True,box_size=50))
"""
int_x = int(round(x))
int_y = int(round(y))
postage_stamp = photutils.utils.cutouts.cutout_footprint(
self.data, (int_x, int_y), box_size)
# Only interested in the image data [1] is the mask
postage_stamp = np.array(postage_stamp[0])
#plt.imshow(postage_stamp)
#print(postage_stamp)
if method == "centroid_2dg":
x_stamp_centroid, y_stamp_centroid = photutils.centroid_com(
postage_stamp)
elif method == "centroid_com":
x_stamp_centroid, y_stamp_centroid = photutils.centroid_2dg(
postage_stamp)
elif method == "daofind":
daofind = DAOStarFinder(fwhm=dao_fwhm,
threshold=dao_SNR * self.bkg_sigma)
sources = daofind(postage_stamp)
positions = (sources['xcentroid'], sources['ycentroid'])
x_stamp_centroid, y_stamp_centroid = float(positions[0]), float(
positions[1])
elif method == "howell":
x_stamp_centroid, y_stamp_centroid = self.howell_center(
postage_stamp)
else:
print(
"Error: method must be 'daofind', centroid_2dg', 'centroid_com' or 'howell'"
)
pass
x_centroid = x_stamp_centroid + int_x - box_size / 2.
y_centroid = y_stamp_centroid + int_y - box_size / 2.
if plot:
fig, ax = plt.subplots()
if stretch:
norm = gkastro.stretch_data(postage_stamp, method=stretch)
else:
norm = None
ax.imshow(postage_stamp,
origin="lower",
extent=[
int_x - box_size / 2., int_x + box_size / 2.,
int_y - box_size / 2., int_y + box_size / 2.
],
interpolation="none",
norm=norm)
ax.set_xlim(int_x - box_size / 2., int_x + box_size / 2.)
ax.set_ylim(int_y - box_size / 2., int_y + box_size / 2.)
ax.set_xlabel("X pixel")
ax.set_ylabel("Y pixel")
ax.plot(x_centroid,
y_centroid,
color='#1f77b4',
marker="+",
ms=30,
mew=2)
if plot_full:
fig, ax = plt.subplots()
ax.imshow(self.data, origin="lower")
ax.plot(x_centroid,
y_centroid,
color='#1f77b4',
marker="+",
ms=30,
mew=2)
return x_centroid, y_centroid
def show_event(viewer, event, datax, datay):
i = iw._viewer.get_image()
data = i.get_data()
pad = 15
x = int(np.floor(event.data_x))
y = int(np.floor(event.data_y))
cnt = 0
sub_data = data[y - pad:y + pad, x - pad:x + pad] #- med
_, sub_med, _ = sigma_clipped_stats(sub_data)
#sub_med = 0
foo, moo = centroid_com(sub_data - sub_med)
cenx = foo + x - pad
ceny = moo + y - pad
cen = np.array([foo + x - pad, moo + y - pad])
ceno = np.array([-100, -100])
while cnt <= 10 and (np.abs(np.array([foo, moo]) - pad).max() >3 or np.abs(cen - ceno).max() > 0.1):
# print(cnt, foo, moo)
x = int(np.floor(foo)) + x - pad
y = int(np.floor(moo)) + y - pad
sub_data = data[y - pad:y + pad, x - pad:x + pad] #- med
_, sub_med, _ = sigma_clipped_stats(sub_data)
#sub_med = 0
mask = (sub_data - sub_med) < 0
foo, moo = centroid_com(sub_data - sub_med, mask=mask)
ceno = cen
cen = np.array([foo + x - pad, moo + y - pad])
# print(cen)
# print(cen - ceno)
cnt += 1
iw.add_markers(Table(data=[[cen[0]], [cen[1]]], names=['x', 'y']))
#print(foo, moo)
yd, xd = np.indices((sub_data.shape))
r = np.sqrt((xd - foo)**2 + (yd - moo)**2)
r_exact = r.copy()
r = r.astype(np.int)
tbin = np.bincount(r.ravel(), sub_data.ravel())
rbin = np.bincount(r.ravel(), r_exact.ravel())
nr = np.bincount(r.ravel())
radialprofile = tbin / nr
ravg = rbin / nr
adjust_max = radialprofile.max() - sub_med
scaled_profile = (radialprofile - sub_med) / adjust_max
scaled_exact_counts = (sub_data - sub_med) / adjust_max
out.clear_output(wait=True)
with out:
# print(dir(event))
#print(event.data_x, event.data_y)
plt.clf()
#sub_med += med
seeing_plot(r_exact, scaled_exact_counts, ravg, scaled_profile, 5,
'Some Image Name', file_name='some_name', gap=6, annulus_width=13)
plt.show()
out2.clear_output(wait=True)
with out2:
tbin2 = np.bincount(r.ravel(), (sub_data - sub_med).ravel())
counts = np.cumsum(tbin2)
mag_diff = -2.5 * np.log10(counts/counts.max())
plt.plot(range(len(radialprofile)), counts)
plt.xlim(0, 20)
#plt.ylim(0.2, 0)
plt.grid()
sub_blot = sub_data.copy()
sub_blot[10:30, 10:30] = np.nan
sub_std = np.nanstd(sub_blot)
plt.title('Net counts in aperture std {:.2f} med {:.2f}'.format(sub_std, sub_med))
sub_pois = (sub_data - sub_med)
e_sky = np.sqrt(sub_med)
rn = 10
sub_noise_sq = np.sqrt(sub_pois ** 2 + sub_std ** 2) ** 2
nbin = np.sqrt(np.bincount(r.ravel(), (sub_noise_sq).ravel()))
plt.xlabel('Aperture radius')
plt.show()
out3.clear_output(wait=True)
with out3:
poisson = np.sqrt(np.cumsum(tbin2))
error = np.sqrt(poisson ** 2 + np.cumsum(nr) * (e_sky ** 2 + rn ** 2))
snr = np.cumsum(tbin2) / error
snr_max = snr[:20].max()
plt.plot(range(len(radialprofile)), snr)
plt.title('Signal to noise ratio {}'.format(snr.max()))
plt.xlim(0, 20)
#plt.ylim(0, 2)
plt.xlabel('Aperture radius')
plt.grid()
plt.show()
# For the individual image cutouts
fig, ax = plt.subplots(nrows=1, ncols=3, figsize=(8, 4),
sharey=True)
# The actual work
for j, star in enumerate(stars):
crad = int(cutoutsize/2.)
scutout = tdata[star[1]-crad:star[1]+crad,
star[0]-crad:star[0]+crad]
im = ax[j].imshow(scutout, interpolation='none',
origin='lower', norm=norm,
vmin=0, vmax=200)
# Actually calculate the centroid
cen = centroid_com(scutout)
# cen = centroid_2dg(scutout)
cxseries[j, i] = cen[0]
cyseries[j, i] = cen[1]
# Plot the centroid on the image
ax[j].scatter(cen[0], cen[1], color='green')
print("\t\tStar%d: %f,%f" % (j, cen[0], cen[1]))
# cbar = fig.colorbar(im, pad=0.05, orientation='vertical')
if dnps is True:
units = "DN/sec"
else:
units = "DN"
def center(s_post, gal_cat, image_wcs, search_box_width):
# centroid of the gal_cat
# search box width = width of the search box around the signpost in arcmin. (5' x 5' BOX)
# image_wcs = WCS of the image where objects are detected.
# Search box
PIX_SCALE = 0.000239631 * 3600 # arcsec/pixel ; 0.000239631 degrees/pixel for IRAC-ch2 (SDWFS Survey)
wid_arcsec = search_box_width * 60 # arcsec
wid_pixels = int(wid_arcsec / PIX_SCALE) # in pixels
init_x, init_y = image_wcs.wcs_world2pix(
s_post[0], s_post[1], 0) # initial center estimate to draw box
xmin, xmax = int(init_x - (wid_pixels / 2.0)), int(
init_x + (wid_pixels / 2.0)) # boundaries
ymin, ymax = int(init_y - (wid_pixels / 2.0)), int(
init_y + (wid_pixels / 2.0)) # boundaries
# Galaxy catalog in image pixel coordinates
galpix = convpix(gal_cat, image_wcs) # objects in pixel coordinates
x_pixels, y_pixels = galpix[:, 0], galpix[:, 1]
# 2D-histogram on the grid in the search box
binstep = 5.0 # pixels, grid resolution
wght = np.asarray(gal_cat['ch2']) # weights: irac ch2[4.5 um] flux, uJy
xedges, yedges = np.arange(xmin, xmax + binstep,
binstep), np.arange(ymin, ymax + binstep,
binstep)
h, xedges, yedges = np.histogram2d(x_pixels,
y_pixels,
bins=(xedges, yedges),
weights=wght)
# Smoothing the 2D histogram of the galaxies in the search box
size = int(round(
(np.shape(h)[0]) / 4.0)) # kernel size : at least ~ 4 times smaller
stdev_ker = size / 4.0 # size = 4-sigma
gauss_kernel = Gaussian2DKernel(x_stddev=stdev_ker,
y_stddev=stdev_ker,
x_size=size,
y_size=size) # kernel
smoothed_data_gauss = convolve_fft(h.T,
gauss_kernel) # convolution/smoothing
# Peak of the histogram
x_org, y_org = (xedges[0] + xedges[1]) / 2.0, (
yedges[0] + yedges[1]) / 2.0 # origin of bin-coordinate
fp_m = find_peaks(smoothed_data_gauss, 0,
npeaks=1) # 1 peak with max value
xbin_peak, ybin_peak = fp_m['x_peak'][0], fp_m['y_peak'][
0] # x, y positions of the peak
x_p, y_p = (x_org + xbin_peak * binstep), (
y_org + ybin_peak * binstep) # conversion to pixel coordinates
peak_fk5 = image_wcs.wcs_pix2world(x_p, y_p, 0)
# Centroid of the image moments
cen_pos = centroid_com(smoothed_data_gauss)
cenx, ceny = (x_org + cen_pos[0] * binstep), (y_org + cen_pos[1] * binstep)
centre = image_wcs.wcs_pix2world(cenx, ceny, 0)
return centre, peak_fk5
# Set the approximate star coordinates of reference star chosen
estimated_star_x = [998,998,958]
estimated_star_y = [1161,1121,1121]
actual_star_x = [0,0,0] # dummy values
actual_star_y = [0,0,0]
for i in range(len(sciList)):
HDUList = fits.open(procList[i], ignore_missing_end=True)
procData = HDUList[0].data
HDUList.close()
(x0, x1) = (estimated_star_x[i]-20, estimated_star_x[i]+20) #create smaller area to cover the star
(y0, y1) = (estimated_star_y[i]-20, estimated_star_y[i]+20)
cutout = procData[y0:y1,x0:x1]
mean, median, std = sigma_clipped_stats(cutout)
cx, cy = photutils.centroid_com(cutout-median) #find the center position of the star
actual_star_x[i] = cx+x0 #fill in actual calculated locations of star center from above
actual_star_y[i] = cy+y0
print('Image %s unshifted ref location:' % (i+1), actual_star_x[i], actual_star_y[i], '\n')
#offset images to match centroid locations
#default crop region
xmin, xmax = 50, 2050
ymin, ymax = 150, 2150
alignedImages = np.zeros((ymax-ymin, xmax-xmin, len(sciList))) #create empty array the size of [y pix, x pix, # images]
#calcualte the offset for each image and apply it then add to 3D array
for i in range(len(sciList)):
xoffset = int(round(actual_star_x[i]-actual_star_x[0]))
yoffset = int(round(actual_star_y[i]-actual_star_y[0]))