def Plot_Galaxy_Image(IMG, results, options):
"""
Plots an LSB image of the object without anything else drawn above it.
Useful for inspecting images for spurious features
"""
if 'center' in results:
center = results['center']
elif 'ap_set_center' in options:
center = options['ap_set_center']
elif 'ap_guess_center' in options:
center = options['ap_guess_center']
else:
center = {'x': IMG.shape[1]/2, 'y': IMG.shape[0]/2}
if 'prof data' in results:
edge = 1.2*results['prof data']['R'][-1]/options['pixscale']
elif 'init R' in results:
edge = 3*results['init R']
elif 'fit R' in results:
edge = 2*results['fit R']
else:
edge = max(IMG.shape)/2
edge = min([edge, abs(center['x'] - IMG.shape[1]), center['x'], abs(center['y'] - IMG.shape[0]), center['y']])
ranges = [[max(0,int(center['x']-edge)), min(IMG.shape[1],int(center['x']+edge))],
[max(0,int(center['y']-edge)), min(IMG.shape[0],int(center['y']+edge))]]
LSBImage(IMG[ranges[1][0]:ranges[1][1],ranges[0][0]:ranges[0][1]] - results['background'], results['background noise'])
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig('%sclean_image_%s.jpg' % (options['ap_plotpath'] if 'ap_plotpath' in options else '', options['ap_name']), dpi = options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
return IMG, {}
def Plot_PSF_Stars(
IMG, stars_x, stars_y, stars_fwhm, psf, results, options, flagstars=None
):
LSBImage(IMG - results["background"], results["background noise"])
AddScale(plt.gca(), IMG.shape[0]*options['ap_pixscale'])
for i in range(len(stars_fwhm)):
plt.gca().add_patch(
Ellipse(
(stars_x[i], stars_y[i]),
20 * psf,
20 * psf,
0,
fill=False,
linewidth=1.5,
color=autocolours["red1"]
if not flagstars is None and flagstars[i]
else autocolours["blue1"],
)
)
plt.tight_layout()
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
os.path.join(
options["ap_plotpath"] if "ap_plotpath" in options else "",
"PSF_Stars_%s.jpg" % options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
def Photutils_Fit(IMG, results, options):
"""
Function to run the photutils automated isophote analysis on an image.
"""
dat = IMG - results['background']
geo = EllipseGeometry(x0=results['center']['x'],
y0=results['center']['y'],
sma=results['init R'] / 2,
eps=results['init ellip'],
pa=results['init pa'])
ellipse = Photutils_Ellipse(dat, geometry=geo)
isolist = ellipse.fit_image(fix_center=True, linear=False)
res = {
'fit R': isolist.sma[1:],
'fit ellip': isolist.eps[1:],
'fit ellip_err': isolist.ellip_err[1:],
'fit pa': isolist.pa[1:],
'fit pa_err': isolist.pa_err[1:],
'auxfile fitlimit':
'fit limit semi-major axis: %.2f pix' % isolist.sma[-1]
}
if 'ap_doplot' in options and options['ap_doplot']:
ranges = [[
max(0, int(results['center']['y'] - res['fit R'][-1] * 1.2)),
min(dat.shape[1],
int(results['center']['y'] + res['fit R'][-1] * 1.2))
],
[
max(0,
int(results['center']['x'] -
res['fit R'][-1] * 1.2)),
min(dat.shape[0],
int(results['center']['x'] + res['fit R'][-1] * 1.2))
]]
LSBImage(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results['background noise'])
for i in range(len(res['fit R'])):
plt.gca().add_patch(
Ellipse(
(int(res['fit R'][-1] * 1.2), int(res['fit R'][-1] * 1.2)),
2 * res['fit R'][i],
2 * res['fit R'][i] * (1. - res['fit ellip'][i]),
res['fit pa'][i] * 180 / np.pi,
fill=False,
linewidth=0.5,
color='r'))
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sfit_ellipse_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=300)
plt.close()
return IMG, res
def Plot_Isophote_Init_Ellipse(dat, circ_ellipse_radii, ellip, phase, results, options):
ranges = [
[
max(0, int(results["center"]["x"] - circ_ellipse_radii[-1] * 1.5)),
min(
dat.shape[1], int(results["center"]["x"] + circ_ellipse_radii[-1] * 1.5)
),
],
[
max(0, int(results["center"]["y"] - circ_ellipse_radii[-1] * 1.5)),
min(
dat.shape[0], int(results["center"]["y"] + circ_ellipse_radii[-1] * 1.5)
),
],
]
LSBImage(
dat[ranges[1][0] : ranges[1][1], ranges[0][0] : ranges[0][1]],
results["background noise"],
)
AddScale(plt.gca(), (ranges[0][1] - ranges[0][0])*options['ap_pixscale'])
plt.gca().add_patch(
Ellipse(
(
results["center"]["x"] - ranges[0][0],
results["center"]["y"] - ranges[1][0],
),
2 * circ_ellipse_radii[-1],
2 * circ_ellipse_radii[-1] * (1.0 - ellip),
phase * 180 / np.pi,
fill=False,
linewidth=1,
color=autocolours["blue1"],
)
)
plt.plot(
[results["center"]["x"] - ranges[0][0]],
[results["center"]["y"] - ranges[1][0]],
marker="x",
markersize=3,
color=autocolours["red1"],
)
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
os.path.join(
options["ap_plotpath"] if "ap_plotpath" in options else "",
"initialize_ellipse_%s.jpg" % options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
def Mask_Segmentation_Map(IMG, results, options):
if 'ap_mask_file' not in options or options['ap_mask_file'] is None:
mask = np.zeros(IMG.shape, dtype=bool)
else:
mask = Read_Image(options['ap_mask_file'], options)
if 'center' in results:
if mask[int(results['center']['y']),
int(results['center']['x'])] > 1.1:
mask[mask == mask[int(results['center']['y']),
int(results['center']['x'])]] = 0
elif 'ap_set_center' in options:
if mask[int(options['ap_set_center']['y']),
int(options['ap_set_center']['x'])] > 1.1:
mask[mask == mask[int(options['ap_set_center']['y']),
int(options['ap_set_center']['x'])]] = 0
elif 'ap_guess_center' in options:
if mask[int(options['ap_guess_center']['y']),
int(options['ap_guess_center']['x'])] > 1.1:
mask[mask == mask[int(options['ap_guess_center']['y']),
int(options['ap_guess_center']['x'])]] = 0
elif mask[int(IMG.shape[0] / 2), int(IMG.shape[1] / 2)] > 1.1:
mask[mask == mask[int(IMG.shape[0] / 2), int(IMG.shape[1] / 2)]] = 0
# Plot star mask for diagnostic purposes
if 'ap_doplot' in options and options['ap_doplot']:
bkgrnd = results[
'background'] if 'background' in results else np.median(IMG)
noise = results[
'background noise'] if 'background noise' in results else iqr(
IMG, rng=[16, 84]) / 2
LSBImage(IMG - bkgrnd, noise)
showmask = np.copy(mask)
showmask[showmask > 1] = 1
showmask[showmask < 1] = np.nan
plt.imshow(showmask, origin='lower', cmap='Reds_r', alpha=0.5)
plt.tight_layout()
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%smask_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']))
plt.close()
return IMG, {'mask': mask.astype(bool)}
def Plot_Radial_Profiles(
dat, R, sb, sbE, pa, nwedges, wedgeangles, wedgewidth, results, options
):
zeropoint = options["ap_zeropoint"] if "ap_zeropoint" in options else 22.5
ranges = [
[
max(0, int(results["center"]["x"] - 1.5 * R[-1] - 2)),
min(dat.shape[1], int(results["center"]["x"] + 1.5 * R[-1] + 2)),
],
[
max(0, int(results["center"]["y"] - 1.5 * R[-1] - 2)),
min(dat.shape[0], int(results["center"]["y"] + 1.5 * R[-1] + 2)),
],
]
cmap = cm.get_cmap("hsv")
colorind = (np.linspace(0, 1 - 1 / nwedges, nwedges) + 0.1) % 1.0
for sa_i in range(len(wedgeangles)):
CHOOSE = np.logical_and(np.array(sb[sa_i]) < 99, np.array(sbE[sa_i]) < 1)
plt.errorbar(
np.array(R)[CHOOSE] * options["ap_pixscale"],
np.array(sb[sa_i])[CHOOSE],
yerr=np.array(sbE[sa_i])[CHOOSE],
elinewidth=1,
linewidth=0,
marker=".",
markersize=5,
color=cmap(colorind[sa_i]),
label="Wedge %.2f" % (wedgeangles[sa_i] * 180 / np.pi),
)
plt.xlabel("Radius [arcsec]", fontsize=16)
plt.ylabel("Surface Brightness [mag arcsec$^{-2}$]", fontsize=16)
bkgrdnoise = (
-2.5 * np.log10(results["background noise"])
+ zeropoint
+ 2.5 * np.log10(options["ap_pixscale"] ** 2)
)
plt.axhline(
bkgrdnoise,
color="purple",
linewidth=0.5,
linestyle="--",
label="1$\\sigma$ noise/pixel:\n%.1f mag arcsec$^{-2}$" % bkgrdnoise,
)
plt.gca().invert_yaxis()
plt.legend(fontsize=15)
plt.tick_params(labelsize=14)
plt.tight_layout()
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
os.path.join(
options["ap_plotpath"] if "ap_plotpath" in options else "",
"radial_profiles_%s.jpg" % options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
LSBImage(
dat[ranges[1][0] : ranges[1][1], ranges[0][0] : ranges[0][1]],
results["background noise"],
)
AddScale(plt.gca(), (ranges[0][1] - ranges[0][0])*options['ap_pixscale'])
cx, cy = (
results["center"]["x"] - ranges[0][0],
results["center"]["y"] - ranges[1][0],
)
for sa_i in range(len(wedgeangles)):
if np.all(pa == pa[0]):
plt.gca().add_patch(
Wedge(
(cx, cy),
R[-1],
(wedgeangles[sa_i] + pa[0] - wedgewidth[-1] / 2) * 180 / np.pi,
(wedgeangles[sa_i] + pa[0] + wedgewidth[-1] / 2) * 180 / np.pi,
facecolor=cmap(colorind[sa_i]),
linewidth=0,
alpha=0.3,
)
)
else:
endx, endy = (
R * np.cos(wedgeangles[sa_i] + pa),
R * np.sin(wedgeangles[sa_i] + pa),
)
plt.plot(endx + cx, endy + cy, color="w", linewidth=1.1)
plt.plot(endx + cx, endy + cy, color=cmap(colorind[sa_i]), linewidth=0.7)
endx, endy = (
R * np.cos(wedgeangles[sa_i] + pa + wedgewidth / 2),
R * np.sin(wedgeangles[sa_i] + pa + wedgewidth / 2),
)
plt.plot(endx + cx, endy + cy, color="w", linewidth=0.7)
plt.plot(
endx + cx,
endy + cy,
color=cmap(colorind[sa_i]),
linestyle="--",
linewidth=0.5,
)
endx, endy = (
R * np.cos(wedgeangles[sa_i] + pa - wedgewidth / 2),
R * np.sin(wedgeangles[sa_i] + pa - wedgewidth / 2),
)
plt.plot(endx + cx, endy + cy, color="w", linewidth=0.7)
plt.plot(
endx + cx,
endy + cy,
color=cmap(colorind[sa_i]),
linestyle="--",
linewidth=0.5,
)
plt.xlim([0, ranges[0][1] - ranges[0][0]])
plt.ylim([0, ranges[1][1] - ranges[1][0]])
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
os.path.join(
options["ap_plotpath"] if "ap_plotpath" in options else "",
"radial_profiles_wedges_%s.jpg" % options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
def Plot_Isophote_Fit(dat, sample_radii, parameters, results, options):
for i in range(len(parameters)):
if not "m" in parameters[i]:
parameters[i]["m"] = None
Rlim = sample_radii[-1] * (
1.0
if parameters[-1]["m"] is None
else np.exp(
sum(
np.abs(parameters[-1]["Am"][m]) for m in range(len(parameters[-1]["m"]))
)
)
)
ranges = [
[
max(0, int(results["center"]["x"] - Rlim * 1.2)),
min(dat.shape[1], int(results["center"]["x"] + Rlim * 1.2)),
],
[
max(0, int(results["center"]["y"] - Rlim * 1.2)),
min(dat.shape[0], int(results["center"]["y"] + Rlim * 1.2)),
],
]
LSBImage(
dat[ranges[1][0] : ranges[1][1], ranges[0][0] : ranges[0][1]],
results["background noise"],
)
AddScale(plt.gca(), (ranges[0][1] - ranges[0][0])*options['ap_pixscale'])
for i in range(len(sample_radii)):
N = max(15, int(0.9 * 2 * np.pi * sample_radii[i]))
theta = np.linspace(0, 2 * np.pi * (1.0 - 1.0 / N), N)
theta = np.arctan((1.0 - parameters[i]["ellip"]) * np.tan(theta)) + np.pi * (
np.cos(theta) < 0
)
R = sample_radii[i] * (
1.0
if parameters[i]["m"] is None
else np.exp(
sum(
parameters[i]["Am"][m]
* np.cos(parameters[i]["m"][m] * (theta + parameters[i]["Phim"][m]))
for m in range(len(parameters[i]["m"]))
)
)
)
X, Y = parametric_SuperEllipse(
theta,
parameters[i]["ellip"],
2 if parameters[i]["C"] is None else parameters[i]["C"],
)
X, Y = Rotate_Cartesian(parameters[i]["pa"], X, Y)
X, Y = (
R * X + results["center"]["x"] - ranges[0][0],
R * Y + results["center"]["y"] - ranges[1][0],
)
plt.plot(
list(X) + [X[0]],
list(Y) + [Y[0]],
linewidth=((i + 1) / len(sample_radii)) ** 2,
color=autocolours["red1"],
)
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
os.path.join(
options["ap_plotpath"] if "ap_plotpath" in options else "",
"fit_ellipse_%s.jpg" % options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
def _Plot_Isophotes(dat, R, parameters, results, options):
for i in range(len(parameters)):
if not "m" in parameters[i]:
parameters[i]["m"] = None
Rlim = R[-1] * (
1.0
if parameters[-1]["m"] is None
else np.exp(
sum(
np.abs(parameters[-1]["Am"][m]) for m in range(len(parameters[-1]["m"]))
)
)
)
ranges = [
[
max(0, int(results["center"]["x"] - Rlim * 1.2)),
min(dat.shape[1], int(results["center"]["x"] + Rlim * 1.2)),
],
[
max(0, int(results["center"]["y"] - Rlim * 1.2)),
min(dat.shape[0], int(results["center"]["y"] + Rlim * 1.2)),
],
]
LSBImage(
dat[ranges[1][0] : ranges[1][1], ranges[0][0] : ranges[0][1]],
results["background noise"],
)
AddScale(plt.gca(), (ranges[0][1] - ranges[0][0])*options['ap_pixscale'])
fitlim = results["fit R"][-1] if "fit R" in results else np.inf
for i in range(len(R)):
N = max(15, int(0.9 * 2 * np.pi * R[i]))
theta = np.linspace(0, 2 * np.pi * (1.0 - 1.0 / N), N)
theta = np.arctan((1.0 - parameters[i]["ellip"]) * np.tan(theta)) + np.pi * (
np.cos(theta) < 0
)
RR = R[i] * (
np.ones(N)
if parameters[i]["m"] is None
else np.exp(
sum(
parameters[i]["Am"][m]
* np.cos(parameters[i]["m"][m] * (theta + parameters[i]["Phim"][m]))
for m in range(len(parameters[i]["m"]))
)
)
)
X = RR * np.cos(theta)
Y = RR * (1 - parameters[i]["ellip"]) * np.sin(theta)
X, Y = (
X * np.cos(parameters[i]["pa"]) - Y * np.sin(parameters[i]["pa"]),
X * np.sin(parameters[i]["pa"]) + Y * np.cos(parameters[i]["pa"]),
)
X += results["center"]["x"] - ranges[0][0]
Y += results["center"]["y"] - ranges[1][0]
plt.plot(
list(X) + [X[0]],
list(Y) + [Y[0]],
linewidth=((i + 1) / len(R)) ** 2,
color=autocolours["blue1"] if (i % 4 == 0) else autocolours["red1"],
linestyle="-" if R[i] < fitlim else "--",
)
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
os.path.join(
options["ap_plotpath"] if "ap_plotpath" in options else "",
"photometry_ellipse_%s.jpg" % options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
def Axial_Profiles(IMG, results, options):
mask = results['mask'] if 'mask' in results else None
pa = results['init pa'] + ((options['ap_axialprof_pa'] * np.pi /
180) if 'ap_axialprof_pa' in options else 0.)
dat = IMG - results['background']
zeropoint = options['ap_zeropoint'] if 'ap_zeropoint' in options else 22.5
if 'prof data' in results:
Rproflim = results['prof data']['R'][-1] / options['ap_pixscale']
else:
Rproflim = min(IMG.shape) / 2
R = [0]
while R[-1] < Rproflim:
if 'ap_samplestyle' in options and options[
'ap_samplestyle'] == 'linear':
step = options[
'ap_samplelinearscale'] if 'ap_samplelinearscale' in options else 0.5 * results[
'psf fwhm']
else:
step = R[-1] * (options['ap_samplegeometricscale']
if 'ap_samplegeometricscale' in options else 0.1)
R.append(R[-1] + max(1, step))
sb = {}
sbE = {}
for rd in [1, -1]:
for ang in [1, -1]:
key = (rd, ang)
sb[key] = []
sbE[key] = []
branch_pa = (pa + ang * np.pi / 2) % (2 * np.pi)
for pi, pR in enumerate(R):
sb[key].append([])
sbE[key].append([])
width = (R[pi] - R[pi - 1]) if pi > 0 else 1.
flux, XX = _iso_line(
dat, R[-1], width, branch_pa, {
'x':
results['center']['x'] +
ang * rd * pR * np.cos(pa + (0 if ang > 0 else np.pi)),
'y':
results['center']['y'] +
ang * rd * pR * np.sin(pa + (0 if ang > 0 else np.pi))
})
for oi, oR in enumerate(R):
length = (R[oi] - R[oi - 1]) if oi > 0 else 1.
CHOOSE = np.logical_and(XX > (oR - length / 2), XX <
(oR + length / 2))
if np.sum(CHOOSE) == 0:
sb[key][-1].append(99.999)
sbE[key][-1].append(99.999)
continue
medflux = _average(
flux[CHOOSE], options['ap_isoaverage_method']
if 'ap_isoaverage_method' in options else 'median')
scatflux = _scatter(
flux[CHOOSE], options['ap_isoaverage_method']
if 'ap_isoaverage_method' in options else 'median')
sb[key][-1].append(
flux_to_sb(medflux, options['ap_pixscale'], zeropoint
) if medflux > 0 else 99.999)
sbE[key][-1].append((
2.5 * scatflux /
(np.sqrt(np.sum(CHOOSE)) * medflux *
np.log(10))) if medflux > 0 else 99.999)
with open(
'%s%s_axial_profile_AP.prof' %
((options['ap_saveto'] if 'ap_saveto' in options else ''),
options['ap_name']), 'w') as f:
f.write('R')
for rd in [1, -1]:
for ang in [1, -1]:
for pR in R:
f.write(',sb[%.3f:%s90],sbE[%.3f:%s90]' %
(rd * pR * options['ap_pixscale'],
'+' if ang > 0 else '-', rd * pR *
options['ap_pixscale'], '+' if ang > 0 else '-'))
f.write('\n')
f.write('arcsec')
for rd in [1, -1]:
for ang in [1, -1]:
for pR in R:
f.write(',mag*arcsec^-2,mag*arcsec^-2')
f.write('\n')
for oi, oR in enumerate(R):
f.write('%.4f' % (oR * options['ap_pixscale']))
for rd in [1, -1]:
for ang in [1, -1]:
key = (rd, ang)
for pi, pR in enumerate(R):
f.write(',%.4f,%.4f' %
(sb[key][pi][oi], sbE[key][pi][oi]))
f.write('\n')
if 'ap_doplot' in options and options['ap_doplot']:
#colours = {(1,1): 'cool', (1,-1): 'summer', (-1,1): 'autumn', (-1,-1): 'winter'}
count = 0
for rd in [1, -1]:
for ang in [1, -1]:
key = (rd, ang)
#cmap = matplotlib.cm.get_cmap('viridis_r')
norm = matplotlib.colors.Normalize(vmin=0,
vmax=R[-1] *
options['ap_pixscale'])
for pi, pR in enumerate(R):
if pi % 3 != 0:
continue
CHOOSE = np.logical_and(
np.array(sb[key][pi]) < 99,
np.array(sbE[key][pi]) < 1)
plt.errorbar(np.array(R)[CHOOSE] * options['ap_pixscale'],
np.array(sb[key][pi])[CHOOSE],
yerr=np.array(sbE[key][pi])[CHOOSE],
elinewidth=1,
linewidth=0,
marker='.',
markersize=3,
color=autocmap.reversed()(norm(
pR * options['ap_pixscale'])))
plt.xlabel('%s-axis position on line [arcsec]' %
('Major' if 'ap_axialprof_parallel' in options
and options['ap_axialprof_parallel'] else 'Minor'),
fontsize=16)
plt.ylabel('Surface Brightness [mag arcsec$^{-2}$]',
fontsize=16)
# cb1 = matplotlib.colorbar.ColorbarBase(plt.gca(), cmap=cmap,
# norm=norm)
cb1 = plt.colorbar(
matplotlib.cm.ScalarMappable(norm=norm,
cmap=autocmap.reversed()))
cb1.set_label(
'%s-axis position of line [arcsec]' %
('Minor' if 'ap_axialprof_parallel' in options
and options['ap_axialprof_parallel'] else 'Major'),
fontsize=16)
# plt.colorbar()
bkgrdnoise = -2.5 * np.log10(
results['background noise']) + zeropoint + 2.5 * np.log10(
options['ap_pixscale']**2)
plt.axhline(
bkgrdnoise,
color='purple',
linewidth=0.5,
linestyle='--',
label='1$\\sigma$ noise/pixel: %.1f mag arcsec$^{-2}$' %
bkgrdnoise)
plt.gca().invert_yaxis()
plt.legend(fontsize=15)
plt.tick_params(labelsize=14)
plt.title('%sR : pa%s90' %
('+' if rd > 0 else '-', '+' if ang > 0 else '-'),
fontsize=15)
plt.tight_layout()
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig('%saxial_profile_q%i_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options
else '', count, options['ap_name']),
dpi=options['ap_plotdpi']
if 'ap_plotdpi' in options else 300)
plt.close()
count += 1
CHOOSE = np.array(results['prof data']['SB_e']) < 0.2
firstbad = np.argmax(np.logical_not(CHOOSE))
if firstbad > 3:
CHOOSE[firstbad:] = False
outto = np.array(results['prof data']
['R'])[CHOOSE][-1] * 1.5 / options['ap_pixscale']
ranges = [[
max(0, int(results['center']['x'] - outto - 2)),
min(IMG.shape[1], int(results['center']['x'] + outto + 2))
],
[
max(0, int(results['center']['y'] - outto - 2)),
min(IMG.shape[0],
int(results['center']['y'] + outto + 2))
]]
LSBImage(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results['background noise'])
count = 0
cmap = matplotlib.cm.get_cmap('hsv')
colorind = (np.linspace(0, 1 - 1 / 4, 4) + 0.1) % 1
colours = list(cmap(c)
for c in colorind) #['b', 'r', 'orange', 'limegreen']
for rd in [1, -1]:
for ang in [1, -1]:
key = (rd, ang)
branch_pa = (pa + ang * np.pi / 2) % (2 * np.pi)
for pi, pR in enumerate(R):
if pi % 3 != 0:
continue
start = np.array([
results['center']['x'] +
ang * rd * pR * np.cos(pa + (0 if ang > 0 else np.pi)),
results['center']['y'] +
ang * rd * pR * np.sin(pa + (0 if ang > 0 else np.pi))
])
end = start + R[-1] * np.array(
[np.cos(branch_pa),
np.sin(branch_pa)])
start -= np.array([ranges[0][0], ranges[1][0]])
end -= np.array([ranges[0][0], ranges[1][0]])
plt.plot(
[start[0], end[0]], [start[1], end[1]],
linewidth=0.5,
color=colours[count],
label=('%sR : pa%s90' %
('+' if rd > 0 else '-',
'+' if ang > 0 else '-')) if pi == 0 else None)
count += 1
plt.legend()
plt.xlim([0, ranges[0][1] - ranges[0][0]])
plt.ylim([0, ranges[1][1] - ranges[1][0]])
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%saxial_profile_lines_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
return IMG, {}
def Isophote_Fit_FFT_mean(IMG, results, options):
"""Fit elliptical isophotes to a galaxy image using FFT coefficients and regularization.
Same as the standard isophote fitting routine, except uses less
robust mean/std measures. This is only intended for low S/N data
where pixels have low integer counts.
Parameters
-----------------
ap_scale : float, default 0.2
growth scale when fitting isophotes, not the same as
*ap_sample---scale*.
ap_fit_limit : float, default 2
noise level out to which to extend the fit in units of pixel
background noise level. Default is 2, smaller values will end
fitting further out in the galaxy image.
ap_regularize_scale : float, default 1
scale factor to apply to regularization coupling factor between
isophotes. Default of 1, larger values make smoother fits,
smaller values give more chaotic fits.
Notes
----------
:References:
- 'background'
- 'background noise'
- 'center'
- 'psf fwhm'
- 'init ellip'
- 'init pa'
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{'fit ellip': , # array of ellipticity values (ndarray)
'fit pa': , # array of PA values (ndarray)
'fit R': , # array of semi-major axis values (ndarray)
'fit ellip_err': , # optional, array of ellipticity error values (ndarray)
'fit pa_err': , # optional, array of PA error values (ndarray)
'auxfile fitlimit': # optional, auxfile message (string)
}
"""
if "ap_scale" in options:
scale = options["ap_scale"]
else:
scale = 0.2
# subtract background from image during processing
dat = IMG - results["background"]
mask = results["mask"] if "mask" in results else None
if not np.any(mask):
mask = None
# Determine sampling radii
######################################################################
shrink = 0
while shrink < 5:
sample_radii = [3 * results["psf fwhm"] / 2]
while sample_radii[-1] < (max(IMG.shape) / 2):
isovals = _iso_extract(
dat,
sample_radii[-1],
{
"ellip": results["init ellip"],
"pa": results["init pa"]
},
results["center"],
more=False,
mask=mask,
)
if (np.mean(isovals) <
(options["ap_fit_limit"] if "ap_fit_limit" in options else 1) *
results["background noise"]):
break
sample_radii.append(sample_radii[-1] * (1.0 + scale /
(1.0 + shrink)))
if len(sample_radii) < 15:
shrink += 1
else:
break
if shrink >= 5:
raise Exception(
"Unable to initialize ellipse fit, check diagnostic plots. Possible missed center."
)
ellip = np.ones(len(sample_radii)) * results["init ellip"]
pa = np.ones(len(sample_radii)) * results["init pa"]
logging.debug("%s: sample radii: %s" %
(options["ap_name"], str(sample_radii)))
# Fit isophotes
######################################################################
perturb_scale = np.array([0.03, 0.06])
regularize_scale = (options["ap_regularize_scale"]
if "ap_regularize_scale" in options else 1.0)
N_perturb = 5
count = 0
count_nochange = 0
use_center = copy(results["center"])
I = np.array(range(len(sample_radii)))
while count < 300 and count_nochange < (3 * len(sample_radii)):
# Periodically include logging message
if count % 10 == 0:
logging.debug("%s: count: %i" % (options["ap_name"], count))
count += 1
np.random.shuffle(I)
for i in I:
perturbations = []
perturbations.append({"ellip": copy(ellip), "pa": copy(pa)})
perturbations[-1]["loss"] = _FFT_mean_loss(
dat,
sample_radii,
perturbations[-1]["ellip"],
perturbations[-1]["pa"],
i,
use_center,
results["background noise"],
mask=mask,
reg_scale=regularize_scale if count > 4 else 0,
name=options["ap_name"],
)
for n in range(N_perturb):
perturbations.append({"ellip": copy(ellip), "pa": copy(pa)})
if count % 3 in [0, 1]:
perturbations[-1]["ellip"][i] = _x_to_eps(
_inv_x_to_eps(perturbations[-1]["ellip"][i]) +
np.random.normal(loc=0, scale=perturb_scale[0]))
if count % 3 in [1, 2]:
perturbations[-1]["pa"][i] = (
perturbations[-1]["pa"][i] + np.random.normal(
loc=0, scale=perturb_scale[1])) % np.pi
perturbations[-1]["loss"] = _FFT_mean_loss(
dat,
sample_radii,
perturbations[-1]["ellip"],
perturbations[-1]["pa"],
i,
use_center,
results["background noise"],
mask=mask,
reg_scale=regularize_scale if count > 4 else 0,
name=options["ap_name"],
)
best = np.argmin(list(p["loss"] for p in perturbations))
if best > 0:
ellip = copy(perturbations[best]["ellip"])
pa = copy(perturbations[best]["pa"])
count_nochange = 0
else:
count_nochange += 1
logging.info("%s: Completed isohpote fit in %i itterations" %
(options["ap_name"], count))
# detect collapsed center
######################################################################
for i in range(5):
if (_inv_x_to_eps(ellip[i]) - _inv_x_to_eps(ellip[i + 1])) > 0.5:
ellip[:i + 1] = ellip[i + 1]
pa[:i + 1] = pa[i + 1]
# Smooth ellip and pa profile
######################################################################
smooth_ellip = copy(ellip)
smooth_pa = copy(pa)
ellip[:3] = min(ellip[:3])
smooth_ellip = _ellip_smooth(sample_radii, smooth_ellip, 5)
smooth_pa = _pa_smooth(sample_radii, smooth_pa, 5)
if "ap_doplot" in options and options["ap_doplot"]:
ranges = [
[
max(0, int(use_center["x"] - sample_radii[-1] * 1.2)),
min(dat.shape[1],
int(use_center["x"] + sample_radii[-1] * 1.2)),
],
[
max(0, int(use_center["y"] - sample_radii[-1] * 1.2)),
min(dat.shape[0],
int(use_center["y"] + sample_radii[-1] * 1.2)),
],
]
LSBImage(
dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results["background noise"],
)
# plt.imshow(np.clip(dat[ranges[1][0]: ranges[1][1], ranges[0][0]: ranges[0][1]],
# a_min = 0,a_max = None), origin = 'lower', cmap = 'Greys', norm = ImageNormalize(stretch=LogStretch()))
for i in range(len(sample_radii)):
plt.gca().add_patch(
Ellipse(
(use_center["x"] - ranges[0][0],
use_center["y"] - ranges[1][0]),
2 * sample_radii[i],
2 * sample_radii[i] * (1.0 - ellip[i]),
pa[i] * 180 / np.pi,
fill=False,
linewidth=((i + 1) / len(sample_radii))**2,
color="r",
))
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
"%sfit_ellipse_%s.jpg" % (
options["ap_plotpath"] if "ap_plotpath" in options else "",
options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
plt.scatter(sample_radii, ellip, color="r", label="ellip")
plt.scatter(sample_radii, pa / np.pi, color="b", label="pa/$np.pi$")
show_ellip = _ellip_smooth(sample_radii, ellip, deg=5)
show_pa = _pa_smooth(sample_radii, pa, deg=5)
plt.plot(
sample_radii,
show_ellip,
color="orange",
linewidth=2,
linestyle="--",
label="smooth ellip",
)
plt.plot(
sample_radii,
show_pa / np.pi,
color="purple",
linewidth=2,
linestyle="--",
label="smooth pa/$np.pi$",
)
# plt.xscale('log')
plt.legend()
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
"%sphaseprofile_%s.jpg" % (
options["ap_plotpath"] if "ap_plotpath" in options else "",
options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
# Compute errors
######################################################################
ellip_err = np.zeros(len(ellip))
ellip_err[:2] = np.sqrt(np.sum((ellip[:4] - smooth_ellip[:4])**2) / 4)
ellip_err[-1] = np.sqrt(np.sum((ellip[-4:] - smooth_ellip[-4:])**2) / 4)
pa_err = np.zeros(len(pa))
pa_err[:2] = np.sqrt(np.sum((pa[:4] - smooth_pa[:4])**2) / 4)
pa_err[-1] = np.sqrt(np.sum((pa[-4:] - smooth_pa[-4:])**2) / 4)
for i in range(2, len(pa) - 1):
ellip_err[i] = np.sqrt(
np.sum((ellip[i - 2:i + 2] - smooth_ellip[i - 2:i + 2])**2) / 4)
pa_err[i] = np.sqrt(
np.sum((pa[i - 2:i + 2] - smooth_pa[i - 2:i + 2])**2) / 4)
res = {
"fit ellip":
ellip,
"fit pa":
pa,
"fit R":
sample_radii,
"fit ellip_err":
ellip_err,
"fit pa_err":
pa_err,
"auxfile fitlimit":
"fit limit semi-major axis: %.2f pix" % sample_radii[-1],
}
return IMG, res
def Radial_Profiles(IMG, results, options):
mask = results['mask'] if 'mask' in results else None
nwedges = options[
'ap_radialprofiles_nwedges'] if 'ap_radialprofiles_nwedges' in options else 4
wedgeangles = np.linspace(0, 2 * np.pi * (1 - 1. / nwedges), nwedges)
zeropoint = options['ap_zeropoint'] if 'ap_zeropoint' in options else 22.5
R = np.array(results['prof data']['R']) / options['ap_pixscale']
SBE = np.array(results['prof data']['SB_e'])
if 'ap_radialprofiles_variable_pa' in options and options[
'ap_radialprofiles_variable_pa']:
pa = np.array(results['prof data']['pa']) * np.pi / 180
else:
pa = np.ones(len(R)) * (
(options['ap_radialprofiles_pa'] * np.pi /
180) if 'ap_radialprofiles_pa' in options else results['init pa'])
dat = IMG - results['background']
maxwedgewidth = options[
'ap_radialprofiles_width'] if 'ap_radialprofiles_width' in options else 15.
maxwedgewidth *= np.pi / 180
if 'ap_radialprofiles_expwidth' in options and options[
'ap_radialprofiles_expwidth']:
wedgewidth = maxwedgewidth * np.exp(R / R[-1] - 1)
else:
wedgewidth = np.ones(len(R)) * maxwedgewidth
if wedgewidth[-1] * nwedges > 2 * np.pi:
logging.warning(
'%s: Radial sampling wedges are overlapping! %i wedges with a maximum width of %.3f rad'
% (nwedges, wedgewidth[-1]))
sb = list([] for i in wedgeangles)
sbE = list([] for i in wedgeangles)
for i in range(len(R)):
if R[i] < 100:
isovals = list(
_iso_extract(dat,
R[i],
0,
0,
results['center'],
more=True,
minN=int(5 * 2 * np.pi / wedgewidth[i]),
mask=mask))
else:
isobandwidth = R[i] * (options['ap_isoband_width']
if 'ap_isoband_width' in options else 0.025)
isovals = list(
_iso_between(dat,
R[i] - isobandwidth,
R[i] + isobandwidth,
0,
0,
results['center'],
more=True,
mask=mask))
isovals[1] -= pa[i]
for sa_i in range(len(wedgeangles)):
aselect = np.abs(Angle_TwoAngles(wedgeangles[sa_i],
isovals[1])) < (wedgewidth[i] / 2)
if np.sum(aselect) == 0:
sb[sa_i].append(99.999)
sbE[sa_i].append(99.999)
continue
medflux = _average(
isovals[0][aselect], options['ap_isoaverage_method']
if 'ap_isoaverage_method' in options else 'median')
scatflux = _scatter(
isovals[0][aselect], options['ap_isoaverage_method']
if 'ap_isoaverage_method' in options else 'median')
sb[sa_i].append(
flux_to_sb(medflux, options['ap_pixscale'], zeropoint
) if medflux > 0 else 99.999)
sbE[sa_i].append((2.5 * scatflux /
(np.sqrt(np.sum(aselect)) * medflux *
np.log(10))) if medflux > 0 else 99.999)
newprofheader = results['prof header']
newprofunits = results['prof units']
newprofformat = results['prof format']
newprofdata = results['prof data']
for sa_i in range(len(wedgeangles)):
p1, p2 = ('SB_rad[%.1f]' % (wedgeangles[sa_i] * 180 / np.pi),
'SB_rad_e[%.1f]' % (wedgeangles[sa_i] * 180 / np.pi))
newprofheader.append(p1)
newprofheader.append(p2)
newprofunits[p1] = 'mag*arcsec^-2'
newprofunits[p2] = 'mag*arcsec^-2'
newprofformat[p1] = '%.4f'
newprofformat[p2] = '%.4f'
newprofdata[p1] = sb[sa_i]
newprofdata[p2] = sbE[sa_i]
if 'ap_doplot' in options and options['ap_doplot']:
CHOOSE = SBE < 0.2
firstbad = np.argmax(np.logical_not(CHOOSE))
if firstbad > 3:
CHOOSE[firstbad:] = False
ranges = [
[
max(0, int(results['center']['x'] - 1.5 * R[CHOOSE][-1] - 2)),
min(IMG.shape[1],
int(results['center']['x'] + 1.5 * R[CHOOSE][-1] + 2))
],
[
max(0, int(results['center']['y'] - 1.5 * R[CHOOSE][-1] - 2)),
min(IMG.shape[0],
int(results['center']['y'] + 1.5 * R[CHOOSE][-1] + 2))
]
]
# cmap = matplotlib.cm.get_cmap('tab10' if nwedges <= 10 else 'viridis')
# colorind = np.arange(nwedges)/10
cmap = matplotlib.cm.get_cmap('hsv')
colorind = (np.linspace(0, 1 - 1 / nwedges, nwedges) + 0.1) % 1
for sa_i in range(len(wedgeangles)):
CHOOSE = np.logical_and(
np.array(sb[sa_i]) < 99,
np.array(sbE[sa_i]) < 1)
plt.errorbar(np.array(R)[CHOOSE] * options['ap_pixscale'],
np.array(sb[sa_i])[CHOOSE],
yerr=np.array(sbE[sa_i])[CHOOSE],
elinewidth=1,
linewidth=0,
marker='.',
markersize=5,
color=cmap(colorind[sa_i]),
label='Wedge %.2f' %
(wedgeangles[sa_i] * 180 / np.pi))
plt.xlabel('Radius [arcsec]', fontsize=16)
plt.ylabel('Surface Brightness [mag arcsec$^{-2}$]', fontsize=16)
bkgrdnoise = -2.5 * np.log10(
results['background noise']) + zeropoint + 2.5 * np.log10(
options['ap_pixscale']**2)
plt.axhline(bkgrdnoise,
color='purple',
linewidth=0.5,
linestyle='--',
label='1$\\sigma$ noise/pixel:\n%.1f mag arcsec$^{-2}$' %
bkgrdnoise)
plt.gca().invert_yaxis()
plt.legend(fontsize=15)
plt.tick_params(labelsize=14)
plt.tight_layout()
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sradial_profiles_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
LSBImage(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results['background noise'])
# plt.imshow(np.clip(dat[ranges[1][0]: ranges[1][1], ranges[0][0]: ranges[0][1]],
# a_min = 0,a_max = None), origin = 'lower', cmap = 'Greys_r', norm = ImageNormalize(stretch=LogStretch()))
cx, cy = (results['center']['x'] - ranges[0][0],
results['center']['y'] - ranges[1][0])
for sa_i in range(len(wedgeangles)):
endx, endy = (R * np.cos(wedgeangles[sa_i] + pa),
R * np.sin(wedgeangles[sa_i] + pa))
plt.plot(endx + cx, endy + cy, color='w', linewidth=1.1)
plt.plot(endx + cx,
endy + cy,
color=cmap(colorind[sa_i]),
linewidth=0.7)
endx, endy = (R * np.cos(wedgeangles[sa_i] + pa + wedgewidth / 2),
R * np.sin(wedgeangles[sa_i] + pa + wedgewidth / 2))
plt.plot(endx + cx, endy + cy, color='w', linewidth=0.7)
plt.plot(endx + cx,
endy + cy,
color=cmap(colorind[sa_i]),
linestyle='--',
linewidth=0.5)
endx, endy = (R * np.cos(wedgeangles[sa_i] + pa - wedgewidth / 2),
R * np.sin(wedgeangles[sa_i] + pa - wedgewidth / 2))
plt.plot(endx + cx, endy + cy, color='w', linewidth=0.7)
plt.plot(endx + cx,
endy + cy,
color=cmap(colorind[sa_i]),
linestyle='--',
linewidth=0.5)
plt.xlim([0, ranges[0][1] - ranges[0][0]])
plt.ylim([0, ranges[1][1] - ranges[1][0]])
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sradial_profiles_wedges_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
return IMG, {
'prof header': newprofheader,
'prof units': newprofunits,
'prof data': newprofdata,
'prof format': newprofformat
}
def Isophote_Initialize(IMG, results, options):
"""
Determine the global pa and ellipticity for a galaxy. First grow circular isophotes
until reaching near the noise floor, then evaluate the phase of the second FFT
coefficients and determine the average direction. Then fit an ellipticity for one
of the outer isophotes.
"""
######################################################################
# Initial attempt to find size of galaxy in image
# based on when isophotes SB values start to get
# close to the background noise level
circ_ellipse_radii = [results['psf fwhm']]
allphase = []
dat = IMG - results['background']
while circ_ellipse_radii[-1] < (len(IMG) / 2):
circ_ellipse_radii.append(circ_ellipse_radii[-1] * (1 + 0.2))
isovals = _iso_extract(dat,
circ_ellipse_radii[-1],
0.,
0.,
results['center'],
more=True,
sigmaclip=True,
sclip_nsigma=3,
interp_mask=True)
coefs = fft(isovals[0])
allphase.append(coefs[2])
# Stop when at 3 time background noise
if np.quantile(isovals[0], 0.8) < (3 * results['background noise']
) and len(circ_ellipse_radii) > 4:
break
logging.info('%s: init scale: %f pix' %
(options['ap_name'], circ_ellipse_radii[-1]))
# Find global position angle.
phase = (-Angle_Median(np.angle(allphase[-5:])) / 2) % np.pi
# Find global ellipticity
test_ellip = np.linspace(0.05, 0.95, 15)
test_f2 = []
for e in test_ellip:
test_f2.append(
sum(
list(
_fitEllip_loss(e, dat, circ_ellipse_radii[-2] *
m, phase, results['center'],
results['background noise'])
for m in np.linspace(0.8, 1.2, 5))))
ellip = test_ellip[np.argmin(test_f2)]
res = minimize(lambda e, d, r, p, c, n: sum(
list(
_fitEllip_loss(_x_to_eps(e[0]), d, r * m, p, c, n)
for m in np.linspace(0.8, 1.2, 5))),
x0=_inv_x_to_eps(ellip),
args=(dat, circ_ellipse_radii[-2], phase, results['center'],
results['background noise']),
method='Nelder-Mead',
options={
'initial_simplex': [[_inv_x_to_eps(ellip) - 1 / 15],
[_inv_x_to_eps(ellip) + 1 / 15]]
})
if res.success:
logging.debug(
'%s: using optimal ellipticity %.3f over grid ellipticity %.3f' %
(options['ap_name'], _x_to_eps(res.x[0]), ellip))
ellip = _x_to_eps(res.x[0])
# Compute the error on the parameters
######################################################################
RR = np.linspace(circ_ellipse_radii[-2] - results['psf fwhm'],
circ_ellipse_radii[-2] + results['psf fwhm'], 10)
errallphase = []
for rr in RR:
isovals = _iso_extract(dat,
rr,
0.,
0.,
results['center'],
more=True,
sigmaclip=True,
sclip_nsigma=3,
interp_mask=True)
coefs = fft(isovals[0])
errallphase.append(coefs[2])
sample_pas = (-np.angle(1j * np.array(errallphase) / np.mean(errallphase))
/ 2) % np.pi
pa_err = iqr(sample_pas, rng=[16, 84]) / 2
res_multi = map(
lambda rrp: minimize(lambda e, d, r, p, c, n: _fitEllip_loss(
_x_to_eps(e[0]), d, r, p, c, n),
x0=_inv_x_to_eps(ellip),
args=(dat, rrp[0], rrp[1], results['center'],
results['background noise']),
method='Nelder-Mead',
options={
'initial_simplex': [[
_inv_x_to_eps(ellip) - 1 / 15
], [_inv_x_to_eps(ellip) + 1 / 15]]
}), zip(RR, sample_pas))
ellip_err = iqr(list(_x_to_eps(rm.x[0])
for rm in res_multi), rng=[16, 84]) / 2
circ_ellipse_radii = np.array(circ_ellipse_radii)
if 'ap_doplot' in options and options['ap_doplot']:
ranges = [
[
max(0,
int(results['center']['x'] -
circ_ellipse_radii[-1] * 1.5)),
min(dat.shape[1],
int(results['center']['x'] + circ_ellipse_radii[-1] * 1.5))
],
[
max(0,
int(results['center']['y'] -
circ_ellipse_radii[-1] * 1.5)),
min(dat.shape[0],
int(results['center']['y'] + circ_ellipse_radii[-1] * 1.5))
]
]
LSBImage(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results['background noise'])
# plt.imshow(np.clip(dat[ranges[1][0]: ranges[1][1], ranges[0][0]: ranges[0][1]],a_min = 0, a_max = None),
# origin = 'lower', cmap = 'Greys_r', norm = ImageNormalize(stretch=LogStretch()))
plt.gca().add_patch(
Ellipse((results['center']['x'] - ranges[0][0],
results['center']['y'] - ranges[1][0]),
2 * circ_ellipse_radii[-1],
2 * circ_ellipse_radii[-1] * (1. - ellip),
phase * 180 / np.pi,
fill=False,
linewidth=1,
color='y'))
plt.plot([results['center']['x'] - ranges[0][0]],
[results['center']['y'] - ranges[1][0]],
marker='x',
markersize=3,
color='r')
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sinitialize_ellipse_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
fig, ax = plt.subplots(2, 1, figsize=(6, 6))
plt.subplots_adjust(hspace=0.01, wspace=0.01)
ax[0].plot(circ_ellipse_radii[:-1],
((-np.angle(allphase) / 2) % np.pi) * 180 / np.pi,
color='k')
ax[0].axhline(phase * 180 / np.pi, color='r')
ax[0].axhline((phase + pa_err) * 180 / np.pi,
color='r',
linestyle='--')
ax[0].axhline((phase - pa_err) * 180 / np.pi,
color='r',
linestyle='--')
#ax[0].axvline(circ_ellipse_radii[-2], color = 'orange', linestyle = '--')
ax[0].set_xlabel('Radius [pix]', fontsize=16)
ax[0].set_ylabel('FFT$_{1}$ phase [deg]', fontsize=16)
ax[0].tick_params(labelsize=12)
ax[1].plot(test_ellip, test_f2, color='k')
ax[1].axvline(ellip, color='r')
ax[1].axvline(ellip + ellip_err, color='r', linestyle='--')
ax[1].axvline(ellip - ellip_err, color='r', linestyle='--')
ax[1].set_xlabel('Ellipticity [1 - b/a]', fontsize=16)
ax[1].set_ylabel('Loss [FFT$_{2}$/med(flux)]', fontsize=16)
ax[1].tick_params(labelsize=14)
plt.tight_layout()
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sinitialize_ellipse_optimize_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
auxmessage = 'global ellipticity: %.3f +- %.3f, pa: %.3f +- %.3f deg, size: %f pix' % (
ellip, ellip_err, PA_shift_convention(phase) * 180 / np.pi,
pa_err * 180 / np.pi, circ_ellipse_radii[-2])
return IMG, {
'init ellip': ellip,
'init ellip_err': ellip_err,
'init pa': phase,
'init pa_err': pa_err,
'init R': circ_ellipse_radii[-2],
'auxfile initialize': auxmessage
}
def Slice_Profile(IMG, results, options):
dat = IMG - (results['background'] if 'background' in results else 0.)
zeropoint = options['ap_zeropoint'] if 'ap_zeropoint' in options else 22.5
use_anchor = results['center'] if 'center' in results else {'x': IMG.shape[1]/2, 'y': IMG.shape[0]/2}
if 'ap_slice_anchor' in options:
use_anchor = options['ap_slice_anchor']
else:
logging.warning('%s: ap_slice_anchor not specified by user, using: %s' % (options['ap_name'], str(use_anchor)))
use_pa = results['init pa'] if 'init pa' in results else 0.
if 'ap_slice_pa' in options:
use_pa = options['ap_slice_pa']*np.pi/180
else:
logging.warning('%s: ap_slice_pa not specified by user, using: %.2f' % (options['ap_name'], use_pa))
use_length = results['init R'] if 'init R' in results else min(IMG.shape)
if 'ap_slice_length' in options:
use_length = options['ap_slice_length']
else:
logging.warning('%s: ap_slice_length not specified by user, using: %.2f' % (options['ap_name'], use_length))
use_width = 10.
if 'ap_slice_width' in options:
use_width = options['ap_slice_width']
else:
logging.warning('%s: ap_slice_width not specified by user, using: %.2f' % (options['ap_name'], use_width))
use_step = results['psf fwhm'] if 'psf fwhm' in results else max(2., use_length/100)
if 'ap_slice_step' in options:
use_step = options['ap_slice_step']
else:
logging.warning('%s: ap_slice_step not specified by user, using: %.2f' % (options['ap_name'], use_step))
F, X = _iso_line(dat, use_length, use_width, use_pa, use_anchor, more = False)
windows = np.arange(0, use_length, use_step)
R = (windows[1:] + windows[:-1])/2
sb = []
sb_e = []
sb_sclip = []
sb_sclip_e = []
for i in range(len(windows)-1):
isovals = F[np.logical_and(X >= windows[i], X < windows[i+1])]
isovals_sclip = Sigma_Clip_Upper(isovals, iterations = 10, nsigma = 5)
medflux = _average(isovals, options['ap_isoaverage_method'] if 'ap_isoaverage_method' in options else 'median')
scatflux = _scatter(isovals, options['ap_isoaverage_method'] if 'ap_isoaverage_method' in options else 'median')
medflux_sclip = _average(isovals_sclip, options['ap_isoaverage_method'] if 'ap_isoaverage_method' in options else 'median')
scatflux_sclip = _scatter(isovals_sclip, options['ap_isoaverage_method'] if 'ap_isoaverage_method' in options else 'median')
sb.append(flux_to_sb(medflux, options['ap_pixscale'], zeropoint) if medflux > 0 else 99.999)
sb_e.append((2.5*scatflux / (np.sqrt(len(isovals))*medflux*np.log(10))) if medflux > 0 else 99.999)
sb_sclip.append(flux_to_sb(medflux_sclip, options['ap_pixscale'], zeropoint) if medflux_sclip > 0 else 99.999)
sb_sclip_e.append((2.5*scatflux_sclip / (np.sqrt(len(isovals))*medflux_sclip*np.log(10))) if medflux_sclip > 0 else 99.999)
with open('%s%s_slice_profile_AP.prof' % ((options['ap_saveto'] if 'ap_saveto' in options else ''), options['ap_name']), 'w') as f:
f.write('# flux sum: %f\n' % (np.sum(F[np.logical_and(X >= 0, X <= use_length)])))
f.write('# flux mean: %f\n' % (_average(F[np.logical_and(X >= 0, X <= use_length)], 'mean')))
f.write('# flux median: %f\n' % (_average(F[np.logical_and(X >= 0, X <= use_length)], 'median')))
f.write('# flux mode: %f\n' % (_average(F[np.logical_and(X >= 0, X <= use_length)], 'mode')))
f.write('# flux std: %f\n' % (np.std(F[np.logical_and(X >= 0, X <= use_length)])))
f.write('# flux 16-84%% range: %f\n' % (iqr(F[np.logical_and(X >= 0, X <= use_length)], rng = [16,84])))
f.write('R,sb,sb_e,sb_sclip,sb_sclip_e\n')
f.write('arcsec,mag*arcsec^-2,mag*arcsec^-2,mag*arcsec^-2,mag*arcsec^-2\n')
for i in range(len(R)):
f.write('%.4f,%.4f,%.4f,%.4f,%.4f\n' % (R[i]*options['ap_pixscale'], sb[i], sb_e[i], sb_sclip[i], sb_sclip_e[i]))
if 'ap_doplot' in options and options['ap_doplot']:
CHOOSE = np.array(sb_e) < 0.5
plt.errorbar(np.array(R)[CHOOSE]*options['ap_pixscale'], np.array(sb)[CHOOSE], yerr = np.array(sb_e)[CHOOSE],
elinewidth = 1, linewidth = 0, marker = '.', markersize = 3, color = 'r')
plt.xlabel('Position on line [arcsec]', fontsize = 16)
plt.ylabel('Surface Brightness [mag arcsec$^{-2}$]', fontsize = 16)
if 'background noise' in results:
bkgrdnoise = -2.5*np.log10(results['background noise']) + zeropoint + 2.5*np.log10(options['ap_pixscale']**2)
plt.axhline(bkgrdnoise, color = 'purple', linewidth = 0.5, linestyle = '--', label = '1$\\sigma$ noise/pixel: %.1f mag arcsec$^{-2}$' % bkgrdnoise)
plt.gca().invert_yaxis()
plt.legend(fontsize = 15)
plt.tick_params(labelsize = 14)
plt.tight_layout()
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig('%sslice_profile_%s.jpg' % (options['ap_plotpath'] if 'ap_plotpath' in options else '', options['ap_name']), dpi = options['ap_plotdpi'] if 'ap_plotdpi'in options else 300)
plt.close()
ranges = [[max(0,int(use_anchor['x']+0.5*use_length*np.cos(use_pa)-use_length*0.7)), min(IMG.shape[1],int(use_anchor['x']+0.5*use_length*np.cos(use_pa)+use_length*0.7))],
[max(0,int(use_anchor['y']+0.5*use_length*np.sin(use_pa)-use_length*0.7)), min(IMG.shape[0],int(use_anchor['y']+0.5*use_length*np.sin(use_pa)+use_length*0.7))]]
LSBImage(dat[ranges[1][0]: ranges[1][1], ranges[0][0]: ranges[0][1]], results['background noise'] if 'background noise' in results else iqr(dat, rng = (31.731/2, 100 - 31.731/2))/2)
XX, YY = np.meshgrid(np.arange(ranges[0][1] - ranges[0][0], dtype = float), np.arange(ranges[1][1] - ranges[1][0], dtype = float))
XX -= use_anchor['x'] - float(ranges[0][0])
YY -= use_anchor['y'] - float(ranges[1][0])
XX, YY = (XX*np.cos(-use_pa) - YY*np.sin(-use_pa), XX*np.sin(-use_pa) + YY*np.cos(-use_pa))
ZZ = np.ones(XX.shape)
ZZ[np.logical_not(np.logical_and(np.logical_and(YY <= use_width/2, YY >= -use_width/2),
np.logical_and(XX >= 0, XX <= use_length)))] = np.nan
plt.imshow(ZZ, origin = 'lower', cmap = 'Reds_r', alpha = 0.6)
plt.tight_layout()
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig('%sslice_profile_window_%s.jpg' % (options['ap_plotpath'] if 'ap_plotpath' in options else '', options['ap_name']), dpi = options['ap_plotdpi'] if 'ap_plotdpi'in options else 300)
plt.close()
return IMG, {}
def Isophote_Fit_Forced(IMG, results, options):
"""
Take isophotal fit from a given profile.
"""
with open(options['ap_forcing_profile'], 'r') as f:
raw = f.readlines()
for i, l in enumerate(raw):
if l[0] != '#':
readfrom = i
break
header = list(h.strip() for h in raw[readfrom].split(','))
force = dict((h, []) for h in header)
for l in raw[readfrom + 2:]:
for d, h in zip(l.split(','), header):
force[h].append(float(d.strip()))
force['pa'] = PA_shift_convention(np.array(force['pa']), deg=True)
if 'ap_doplot' in options and options['ap_doplot']:
dat = IMG - results['background']
ranges = [
[
max(
0,
int(results['center']['y'] -
(np.array(force['R'])[-1] / options['ap_pixscale']) *
1.2)),
min(
dat.shape[1],
int(results['center']['y'] +
(np.array(force['R'])[-1] / options['ap_pixscale']) *
1.2))
],
[
max(
0,
int(results['center']['x'] -
(np.array(force['R'])[-1] / options['ap_pixscale']) *
1.2)),
min(
dat.shape[0],
int(results['center']['x'] +
(np.array(force['R'])[-1] / options['ap_pixscale']) *
1.2))
]
]
LSBImage(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results['background noise'])
# plt.imshow(np.clip(dat[ranges[0][0]: ranges[0][1], ranges[1][0]: ranges[1][1]],
# a_min = 0,a_max = None), origin = 'lower', cmap = 'Greys_r', norm = ImageNormalize(stretch=LogStretch()))
for i in range(0, len(np.array(force['R'])), 2):
plt.gca().add_patch(
Ellipse(
(results['center']['x'] - ranges[0][0],
results['center']['y'] - ranges[1][0]),
2 * (np.array(force['R'])[i] / options['ap_pixscale']),
2 * (np.array(force['R'])[i] / options['ap_pixscale']) *
(1. - force['ellip'][i]),
force['pa'][i],
fill=False,
linewidth=0.5,
color='r'))
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sforcedfit_ellipse_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
res = {
'fit ellip': np.array(force['ellip']),
'fit pa': np.array(force['pa']) * np.pi / 180,
'fit R': list(np.array(force['R']) / options['ap_pixscale'])
}
if 'ellip_e' in force and 'pa_e' in force:
res['fit ellip_err'] = np.array(force['ellip_e'])
res['fit pa_err'] = np.array(force['pa_e']) * np.pi / 180
return IMG, res
def Isophote_Initialize_mean(IMG, results, options):
"""Fit global elliptical isophote to a galaxy image using FFT coefficients.
Same as the default isophote initialization routine, except uses
mean/std measures for low S/N applications.
Parameters
-----------------
ap_fit_limit : float, default 2
noise level out to which to extend the fit in units of pixel
background noise level. Default is 2, smaller values will end
fitting further out in the galaxy image.
Notes
----------
:References:
- 'background'
- 'background noise'
- 'psf fwhm'
- 'center'
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{'init ellip': , # Ellipticity of the global fit (float)
'init pa': ,# Position angle of the global fit (float)
'init R': ,# Semi-major axis length of global fit (float)
'auxfile initialize': # optional, message for aux file to record the global ellipticity and postition angle (string)
}
"""
######################################################################
# Initial attempt to find size of galaxy in image
# based on when isophotes SB values start to get
# close to the background noise level
circ_ellipse_radii = [results["psf fwhm"]]
allphase = []
dat = IMG - results["background"]
while circ_ellipse_radii[-1] < (len(IMG) / 2):
circ_ellipse_radii.append(circ_ellipse_radii[-1] * (1 + 0.2))
isovals = _iso_extract(
dat,
circ_ellipse_radii[-1],
{
"ellip": 0.0,
"pa": 0.0
},
results["center"],
more=True,
)
coefs = fft(isovals[0])
allphase.append(coefs[2])
# Stop when at 3 times background noise
if (np.mean(isovals[0]) < (3 * results["background noise"])
and len(circ_ellipse_radii) > 4):
break
logging.info("%s: init scale: %f pix" %
(options["ap_name"], circ_ellipse_radii[-1]))
# Find global position angle.
phase = (-Angle_Median(np.angle(allphase[-5:])) /
2) % np.pi # (-np.angle(np.mean(allphase[-5:]))/2) % np.pi
# Find global ellipticity
test_ellip = np.linspace(0.05, 0.95, 15)
test_f2 = []
for e in test_ellip:
test_f2.append(
sum(
list(
_fitEllip_mean_loss(
e,
dat,
circ_ellipse_radii[-2] * m,
phase,
results["center"],
results["background noise"],
) for m in np.linspace(0.8, 1.2, 5))))
ellip = test_ellip[np.argmin(test_f2)]
res = minimize(
lambda e, d, r, p, c, n: sum(
list(
_fitEllip_mean_loss(_x_to_eps(e[0]), d, r * m, p, c, n)
for m in np.linspace(0.8, 1.2, 5))),
x0=_inv_x_to_eps(ellip),
args=(
dat,
circ_ellipse_radii[-2],
phase,
results["center"],
results["background noise"],
),
method="Nelder-Mead",
options={
"initial_simplex": [
[_inv_x_to_eps(ellip) - 1 / 15],
[_inv_x_to_eps(ellip) + 1 / 15],
]
},
)
if res.success:
logging.debug(
"%s: using optimal ellipticity %.3f over grid ellipticity %.3f" %
(options["ap_name"], _x_to_eps(res.x[0]), ellip))
ellip = _x_to_eps(res.x[0])
# Compute the error on the parameters
######################################################################
RR = np.linspace(
circ_ellipse_radii[-2] - results["psf fwhm"],
circ_ellipse_radii[-2] + results["psf fwhm"],
10,
)
errallphase = []
for rr in RR:
isovals = _iso_extract(dat,
rr, {
"ellip": 0.0,
"pa": 0.0
},
results["center"],
more=True)
coefs = fft(isovals[0])
errallphase.append(coefs[2])
sample_pas = (-np.angle(1j * np.array(errallphase) / np.mean(errallphase))
/ 2) % np.pi
pa_err = np.std(sample_pas)
res_multi = map(
lambda rrp: minimize(
lambda e, d, r, p, c, n: _fitEllip_mean_loss(
_x_to_eps(e[0]), d, r, p, c, n),
x0=_inv_x_to_eps(ellip),
args=(dat, rrp[0], rrp[1], results["center"], results[
"background noise"]),
method="Nelder-Mead",
options={
"initial_simplex": [
[_inv_x_to_eps(ellip) - 1 / 15],
[_inv_x_to_eps(ellip) + 1 / 15],
]
},
),
zip(RR, sample_pas),
)
ellip_err = np.std(list(_x_to_eps(rm.x[0]) for rm in res_multi))
circ_ellipse_radii = np.array(circ_ellipse_radii)
if "ap_doplot" in options and options["ap_doplot"]:
ranges = [
[
max(0,
int(results["center"]["x"] -
circ_ellipse_radii[-1] * 1.5)),
min(
dat.shape[1],
int(results["center"]["x"] + circ_ellipse_radii[-1] * 1.5),
),
],
[
max(0,
int(results["center"]["y"] -
circ_ellipse_radii[-1] * 1.5)),
min(
dat.shape[0],
int(results["center"]["y"] + circ_ellipse_radii[-1] * 1.5),
),
],
]
LSBImage(
dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results["background noise"],
)
# plt.imshow(np.clip(dat[ranges[1][0]: ranges[1][1], ranges[0][0]: ranges[0][1]],a_min = 0, a_max = None),
# origin = 'lower', cmap = 'Greys_r', norm = ImageNormalize(stretch=LogStretch()))
plt.gca().add_patch(
Ellipse(
(
results["center"]["x"] - ranges[0][0],
results["center"]["y"] - ranges[1][0],
),
2 * circ_ellipse_radii[-1],
2 * circ_ellipse_radii[-1] * (1.0 - ellip),
phase * 180 / np.pi,
fill=False,
linewidth=1,
color="y",
))
plt.plot(
[results["center"]["x"] - ranges[0][0]],
[results["center"]["y"] - ranges[1][0]],
marker="x",
markersize=3,
color="r",
)
plt.tight_layout()
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
"%sinitialize_ellipse_%s.jpg" % (
options["ap_plotpath"] if "ap_plotpath" in options else "",
options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
fig, ax = plt.subplots(2, 1, figsize=(6, 6))
ax[0].plot(
circ_ellipse_radii[:-1],
((-np.angle(allphase) / 2) % np.pi) * 180 / np.pi,
color="k",
)
ax[0].axhline(phase * 180 / np.pi, color="r")
ax[0].axhline((phase + pa_err) * 180 / np.pi,
color="r",
linestyle="--")
ax[0].axhline((phase - pa_err) * 180 / np.pi,
color="r",
linestyle="--")
# ax[0].axvline(circ_ellipse_radii[-2], color = 'orange', linestyle = '--')
ax[0].set_xlabel("Radius [pix]")
ax[0].set_ylabel("FFT$_{1}$ phase [deg]")
ax[1].plot(test_ellip, test_f2, color="k")
ax[1].axvline(ellip, color="r")
ax[1].axvline(ellip + ellip_err, color="r", linestyle="--")
ax[1].axvline(ellip - ellip_err, color="r", linestyle="--")
ax[1].set_xlabel("Ellipticity [1 - b/a]")
ax[1].set_ylabel("Loss [FFT$_{2}$/med(flux)]")
plt.tight_layout()
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
"%sinitialize_ellipse_optimize_%s.jpg" % (
options["ap_plotpath"] if "ap_plotpath" in options else "",
options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
auxmessage = (
"global ellipticity: %.3f +- %.3f, pa: %.3f +- %.3f deg, size: %f pix"
% (
ellip,
ellip_err,
PA_shift_convention(phase) * 180 / np.pi,
pa_err * 180 / np.pi,
circ_ellipse_radii[-2],
))
return IMG, {
"init ellip": ellip,
"init ellip_err": ellip_err,
"init pa": phase,
"init pa_err": pa_err,
"init R": circ_ellipse_radii[-2],
"auxfile initialize": auxmessage,
}
def Slice_Profile(IMG, results, options):
"""Extract a very basic SB profile along a line.
A line of pixels can be identified by the user in image
coordinates to extract an SB profile. Primarily intended for
diagnostic purposes, this allows users to see very specific
pixels. While this tool can be used for examining the disk
structure (such as for edge on galaxies), users will likely prefer
the more powerful
:func:`~pipeline_steps.Axial_Profiles.Axial_Profiles` and
:func:`~pipeline_steps.Radial_Profiles.Radial_Profiles` methods
for such analysis.
Parameters
-----------------
ap_slice_anchor : dict, default None
Coordinates for the starting point of the slice as a dictionary
formatted "{'x': x-coord, 'y': y-coord}" in pixel units.
ap_slice_pa : float, default None
Position angle of the slice in degrees, counter-clockwise
relative to the x-axis.
ap_slice_length : float, default None
Length of the slice from anchor point in pixel units. By
default, use init ellipse semi-major axis length
ap_slice_width : float, default 10
Width of the slice in pixel units.
ap_slice_step : float, default None
Distance between samples for the profile along the
slice. By default use the PSF.
ap_isoaverage_method : string, default 'median'
Select the method used to compute the averafge flux along an
isophote. Choose from 'mean', 'median', and 'mode'. In general,
median is fast and robust to a few outliers. Mode is slow but
robust to more outliers. Mean is fast and accurate in low S/N
regimes where fluxes take on near integer values, but not robust
to outliers. The mean should be used along with a mask to remove
spurious objects such as foreground stars or galaxies, and
should always be used with caution.
ap_saveto : string, default None
Directory in which to save profile
ap_name : string, default None
Name of the current galaxy, used for making filenames.
ap_zeropoint : float, default 22.5
Photometric zero point. For converting flux to mag units.
Notes
----------
:References:
- 'background' (optional)
- 'background noise' (optional)
- 'center' (optional)
- 'init R' (optional)
- 'init pa' (optional)
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{}
"""
dat = IMG - (results["background"] if "background" in results else np.median(IMG))
zeropoint = options["ap_zeropoint"] if "ap_zeropoint" in options else 22.5
use_anchor = (
results["center"]
if "center" in results
else {"x": IMG.shape[1] / 2, "y": IMG.shape[0] / 2}
)
if "ap_slice_anchor" in options:
use_anchor = options["ap_slice_anchor"]
else:
logging.warning(
"%s: ap_slice_anchor not specified by user, using: %s"
% (options["ap_name"], str(use_anchor))
)
use_pa = results["init pa"] if "init pa" in results else 0.0
if "ap_slice_pa" in options:
use_pa = options["ap_slice_pa"] * np.pi / 180
else:
logging.warning(
"%s: ap_slice_pa not specified by user, using: %.2f"
% (options["ap_name"], use_pa)
)
use_length = results["init R"] if "init R" in results else min(IMG.shape)
if "ap_slice_length" in options:
use_length = options["ap_slice_length"]
else:
logging.warning(
"%s: ap_slice_length not specified by user, using: %.2f"
% (options["ap_name"], use_length)
)
use_width = 10.0
if "ap_slice_width" in options:
use_width = options["ap_slice_width"]
else:
logging.warning(
"%s: ap_slice_width not specified by user, using: %.2f"
% (options["ap_name"], use_width)
)
use_step = (
results["psf fwhm"] if "psf fwhm" in results else max(2.0, use_length / 100)
)
if "ap_slice_step" in options:
use_step = options["ap_slice_step"]
else:
logging.warning(
"%s: ap_slice_step not specified by user, using: %.2f"
% (options["ap_name"], use_step)
)
F, X = _iso_line(dat, use_length, use_width, use_pa, use_anchor, more=False)
windows = np.arange(0, use_length, use_step)
R = (windows[1:] + windows[:-1]) / 2
sb = []
sb_e = []
sb_sclip = []
sb_sclip_e = []
for i in range(len(windows) - 1):
isovals = F[np.logical_and(X >= windows[i], X < windows[i + 1])]
isovals_sclip = Sigma_Clip_Upper(isovals, iterations=10, nsigma=5)
medflux = _average(
isovals,
options["ap_isoaverage_method"]
if "ap_isoaverage_method" in options
else "median",
)
scatflux = _scatter(
isovals,
options["ap_isoaverage_method"]
if "ap_isoaverage_method" in options
else "median",
)
medflux_sclip = _average(
isovals_sclip,
options["ap_isoaverage_method"]
if "ap_isoaverage_method" in options
else "median",
)
scatflux_sclip = _scatter(
isovals_sclip,
options["ap_isoaverage_method"]
if "ap_isoaverage_method" in options
else "median",
)
sb.append(
flux_to_sb(medflux, options["ap_pixscale"], zeropoint)
if medflux > 0
else 99.999
)
sb_e.append(
(2.5 * scatflux / (np.sqrt(len(isovals)) * medflux * np.log(10)))
if medflux > 0
else 99.999
)
sb_sclip.append(
flux_to_sb(medflux_sclip, options["ap_pixscale"], zeropoint)
if medflux_sclip > 0
else 99.999
)
sb_sclip_e.append(
(
2.5
* scatflux_sclip
/ (np.sqrt(len(isovals)) * medflux_sclip * np.log(10))
)
if medflux_sclip > 0
else 99.999
)
with open(
"%s%s_slice_profile.prof"
% (
(options["ap_saveto"] if "ap_saveto" in options else ""),
options["ap_name"],
),
"w",
) as f:
f.write(
"# flux sum: %f\n" % (np.sum(F[np.logical_and(X >= 0, X <= use_length)]))
)
f.write(
"# flux mean: %f\n"
% (_average(F[np.logical_and(X >= 0, X <= use_length)], "mean"))
)
f.write(
"# flux median: %f\n"
% (_average(F[np.logical_and(X >= 0, X <= use_length)], "median"))
)
f.write(
"# flux mode: %f\n"
% (_average(F[np.logical_and(X >= 0, X <= use_length)], "mode"))
)
f.write(
"# flux std: %f\n" % (np.std(F[np.logical_and(X >= 0, X <= use_length)]))
)
f.write(
"# flux 16-84%% range: %f\n"
% (iqr(F[np.logical_and(X >= 0, X <= use_length)], rng=[16, 84]))
)
f.write("R,sb,sb_e,sb_sclip,sb_sclip_e\n")
f.write("arcsec,mag*arcsec^-2,mag*arcsec^-2,mag*arcsec^-2,mag*arcsec^-2\n")
for i in range(len(R)):
f.write(
"%.4f,%.4f,%.4f,%.4f,%.4f\n"
% (
R[i] * options["ap_pixscale"],
sb[i],
sb_e[i],
sb_sclip[i],
sb_sclip_e[i],
)
)
if "ap_doplot" in options and options["ap_doplot"]:
CHOOSE = np.array(sb_e) < 0.5
plt.errorbar(
np.array(R)[CHOOSE] * options["ap_pixscale"],
np.array(sb)[CHOOSE],
yerr=np.array(sb_e)[CHOOSE],
elinewidth=1,
linewidth=0,
marker=".",
markersize=3,
color="r",
)
plt.xlabel("Position on line [arcsec]", fontsize=16)
plt.ylabel("Surface Brightness [mag arcsec$^{-2}$]", fontsize=16)
if "background noise" in results:
bkgrdnoise = (
-2.5 * np.log10(results["background noise"])
+ zeropoint
+ 2.5 * np.log10(options["ap_pixscale"] ** 2)
)
plt.axhline(
bkgrdnoise,
color="purple",
linewidth=0.5,
linestyle="--",
label="1$\\sigma$ noise/pixel: %.1f mag arcsec$^{-2}$" % bkgrdnoise,
)
plt.gca().invert_yaxis()
plt.legend(fontsize=15)
plt.tick_params(labelsize=14)
plt.tight_layout()
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
"%sslice_profile_%s.jpg"
% (
options["ap_plotpath"] if "ap_plotpath" in options else "",
options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
ranges = [
[
max(
0,
int(
use_anchor["x"]
+ 0.5 * use_length * np.cos(use_pa)
- use_length * 0.7
),
),
min(
IMG.shape[1],
int(
use_anchor["x"]
+ 0.5 * use_length * np.cos(use_pa)
+ use_length * 0.7
),
),
],
[
max(
0,
int(
use_anchor["y"]
+ 0.5 * use_length * np.sin(use_pa)
- use_length * 0.7
),
),
min(
IMG.shape[0],
int(
use_anchor["y"]
+ 0.5 * use_length * np.sin(use_pa)
+ use_length * 0.7
),
),
],
]
LSBImage(
dat[ranges[1][0] : ranges[1][1], ranges[0][0] : ranges[0][1]],
results["background noise"]
if "background noise" in results
else iqr(dat, rng=(31.731 / 2, 100 - 31.731 / 2)) / 2,
)
XX, YY = np.meshgrid(
np.arange(ranges[0][1] - ranges[0][0], dtype=float),
np.arange(ranges[1][1] - ranges[1][0], dtype=float),
)
XX -= use_anchor["x"] - float(ranges[0][0])
YY -= use_anchor["y"] - float(ranges[1][0])
XX, YY = (
XX * np.cos(-use_pa) - YY * np.sin(-use_pa),
XX * np.sin(-use_pa) + YY * np.cos(-use_pa),
)
ZZ = np.ones(XX.shape)
ZZ[
np.logical_not(
np.logical_and(
np.logical_and(YY <= use_width / 2, YY >= -use_width / 2),
np.logical_and(XX >= 0, XX <= use_length),
)
)
] = np.nan
plt.imshow(ZZ, origin="lower", cmap="Reds_r", alpha=0.6)
plt.tight_layout()
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
"%sslice_profile_window_%s.jpg"
% (
options["ap_plotpath"] if "ap_plotpath" in options else "",
options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
return IMG, {}
def Plot_Galaxy_Image(IMG, results, options):
"""Generate a plain image of the galaxy
Plots an LSB image of the object without anything else drawn above
it. Useful for inspecting images for spurious features. This step
can be run at any point in the pipeline. It will take advantage of
whatever information has been determined so far. So if it is the
first pipeline step, it has little to work from and will simply
plot the whole image, if it is run after the isophote
initialization step then the plotted image will be cropped to
focus on the galaxy.
Parameters
-----------------
ap_guess_center : dict, default None
user provided starting point for center fitting. Center should
be formatted as:
.. code-block:: python
{'x':float, 'y': float}
, where the floats are the center coordinates in pixels. If not
given, Autoprof will default to a guess of the image center.
ap_set_center : dict, default None
user provided fixed center for rest of calculations. Center
should be formatted as:
.. code-block:: python
{'x':float, 'y': float}
, where the floats are the center coordinates in pixels. If not
given, Autoprof will default to a guess of the image center.
Notes
--------------
:References:
- 'background'
- 'background noise'
- 'center' (optional)
- 'init R' (optional)
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{}
"""
if "center" in results:
center = results["center"]
elif "ap_set_center" in options:
center = options["ap_set_center"]
elif "ap_guess_center" in options:
center = options["ap_guess_center"]
else:
center = {"x": IMG.shape[1] / 2, "y": IMG.shape[0] / 2}
if "prof data" in results:
edge = 1.2 * results["prof data"]["R"][-1] / options["ap_pixscale"]
elif "init R" in results:
edge = 3 * results["init R"]
elif "fit R" in results:
edge = 2 * results["fit R"]
else:
edge = max(IMG.shape) / 2
edge = min(
[
edge,
abs(center["x"] - IMG.shape[1]),
center["x"],
abs(center["y"] - IMG.shape[0]),
center["y"],
]
)
ranges = [
[max(0, int(center["x"] - edge)), min(IMG.shape[1], int(center["x"] + edge))],
[max(0, int(center["y"] - edge)), min(IMG.shape[0], int(center["y"] + edge))],
]
LSBImage(
IMG[ranges[1][0] : ranges[1][1], ranges[0][0] : ranges[0][1]]
- results["background"],
results["background noise"],
)
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
"%sclean_image_%s.jpg"
% (
options["ap_plotpath"] if "ap_plotpath" in options else "",
options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
return IMG, {}
def Mask_Segmentation_Map(IMG, results, options):
"""Reads the results from other masking routines into AutoProf.
Creates a mask from a supplied segmentation map. Such maps
typically number each source with an integer. In such a case,
AutoProf will check to see if the object center lands on one of
these segments, if so it will zero out that source-id before
converting the segmentation map into a mask. If the supplied image
is just a 0, 1 mask then AutoProf will take it as is.
Parameters
-----------------
ap_mask_file : string, default None
path to fits file which is a mask for the image. Must have the same dimensions as the main image.
See Also
--------
ap_savemask : bool, default False
indicates if the mask should be saved after fitting
Notes
----------
:References:
- 'background' (optional)
- 'background noise' (optional)
- 'center' (optional)
- 'mask' (optional)
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{'mask': # 2d mask image with boolean datatype (ndarray)
}
"""
if "ap_mask_file" not in options or options["ap_mask_file"] is None:
mask = np.zeros(IMG.shape, dtype=bool)
else:
mask = Read_Image(options["ap_mask_file"], options)
if "center" in results:
if mask[int(results["center"]["y"]),
int(results["center"]["x"])] > 1.1:
mask[mask == mask[int(results["center"]["y"]),
int(results["center"]["x"])]] = 0
elif "ap_set_center" in options:
if (mask[int(options["ap_set_center"]["y"]),
int(options["ap_set_center"]["x"])] > 1.1):
mask[mask == mask[int(options["ap_set_center"]["y"]),
int(options["ap_set_center"]["x"]), ]] = 0
elif "ap_guess_center" in options:
if (mask[int(options["ap_guess_center"]["y"]),
int(options["ap_guess_center"]["x"]), ] > 1.1):
mask[mask == mask[int(options["ap_guess_center"]["y"]),
int(options["ap_guess_center"]["x"]), ]] = 0
elif mask[int(IMG.shape[0] / 2), int(IMG.shape[1] / 2)] > 1.1:
mask[mask == mask[int(IMG.shape[0] / 2), int(IMG.shape[1] / 2)]] = 0
if "mask" in results:
mask = np.logical_or(mask, results["mask"])
# Plot star mask for diagnostic purposes
if "ap_doplot" in options and options["ap_doplot"]:
bkgrnd = results[
"background"] if "background" in results else np.median(IMG)
noise = (results["background noise"] if "background noise" in results
else iqr(IMG, rng=[16, 84]) / 2)
LSBImage(IMG - bkgrnd, noise)
showmask = np.copy(mask)
showmask[showmask > 1] = 1
showmask[showmask < 1] = np.nan
plt.imshow(showmask, origin="lower", cmap="Reds_r", alpha=0.5)
plt.tight_layout()
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
"%smask_%s.jpg" % (
options["ap_plotpath"] if "ap_plotpath" in options else "",
options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
return IMG, {"mask": mask.astype(bool)}
def Star_Mask(IMG, results, options):
"""Masking routine which identifies stars and masks a region around them.
Using an edge detecting convolutional filter, sources are
identified that are of similar scale as the PSF. These sources are
masked with a region roughly 2 times the FWHM of the source.
See Also
--------
ap_savemask : bool, default False
indicates if the mask should be saved after fitting
starfind
:func:`autoprofutils.SharedFunctions.StarFind`
Notes
----------
:References:
- 'background'
- 'background noise'
- 'psf fwhm'
- 'center'
- 'mask' (optional)
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{'mask': # 2d mask image with boolean datatype (ndarray)
}
"""
fwhm = results["psf fwhm"]
use_center = results["center"]
# Find scale of bounding box for galaxy. Stars will only be found within this box
smaj = results["fit R"][-1] if "fit R" in results else max(IMG.shape)
xbox = int(1.5 * smaj)
ybox = int(1.5 * smaj)
xbounds = [
max(0, int(use_center["x"] - xbox)),
min(int(use_center["x"] + xbox), IMG.shape[1]),
]
ybounds = [
max(0, int(use_center["y"] - ybox)),
min(int(use_center["y"] + ybox), IMG.shape[0]),
]
# Run photutils wrapper for IRAF star finder
dat = IMG - results["background"]
all_stars = StarFind(
dat[ybounds[0]:ybounds[1], xbounds[0]:xbounds[1]],
fwhm,
results["background noise"],
detect_threshold=10,
minsep=3,
reject_size=3,
)
mask = np.zeros(IMG.shape, dtype=bool)
# Mask star pixels and area around proportionate to their total flux
XX, YY = np.meshgrid(range(IMG.shape[0]),
range(IMG.shape[1]),
indexing="ij")
for x, y, f, d, p in zip(
all_stars["x"],
all_stars["y"],
all_stars["fwhm"],
all_stars["deformity"],
all_stars["peak"],
):
if (np.sqrt((x - (xbounds[1] - xbounds[0]) / 2)**2 +
(y - (ybounds[1] - ybounds[0]) / 2)**2) <
10 * results["psf fwhm"]):
continue
# compute distance of every pixel to the identified star
R = np.sqrt((YY - (x + xbounds[0]))**2 + (XX - (y + ybounds[0]))**2)
mask[R < (max(np.log10(p / results["background noise"]), 2) *
f)] = True
if "mask" in results:
mask = np.logical_or(mask, results["mask"])
# Plot star mask for diagnostic purposes
if "ap_doplot" in options and options["ap_doplot"]:
LSBImage(
dat[ybounds[0]:ybounds[1], xbounds[0]:xbounds[1]],
results["background noise"],
)
dat = mask.astype(float)[ybounds[0]:ybounds[1], xbounds[0]:xbounds[1]]
dat[dat == 0] = np.nan
plt.imshow(dat, origin="lower", cmap="Reds_r", alpha=0.7)
plt.tight_layout()
plt.savefig(
"%smask_%s.jpg" % (
options["ap_plotpath"] if "ap_plotpath" in options else "",
options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
return IMG, {"mask": mask}
def Plot_Axial_Profiles(dat, R, sb, sbE, pa, results, options):
zeropoint = options["ap_zeropoint"] if "ap_zeropoint" in options else 22.5
count = 0
for rd in [1, -1]:
for ang in [1, -1]:
key = (rd, ang)
# cmap = matplotlib.cm.get_cmap('viridis_r')
norm = matplotlib.colors.Normalize(
vmin=0, vmax=R[-1] * options["ap_pixscale"]
)
for pi, pR in enumerate(R):
if pi % 3 != 0:
continue
CHOOSE = np.logical_and(
np.array(sb[key][pi]) < 99, np.array(sbE[key][pi]) < 1
)
plt.errorbar(
np.array(R)[CHOOSE] * options["ap_pixscale"],
np.array(sb[key][pi])[CHOOSE],
yerr=np.array(sbE[key][pi])[CHOOSE],
elinewidth=1,
linewidth=0,
marker=".",
markersize=3,
color=autocmap.reversed()(norm(pR * options["ap_pixscale"])),
)
plt.xlabel(
"%s-axis position on line [arcsec]"
% (
"Major"
if "ap_axialprof_parallel" in options
and options["ap_axialprof_parallel"]
else "Minor"
),
fontsize=16,
)
plt.ylabel("Surface Brightness [mag arcsec$^{-2}$]", fontsize=16)
cb1 = plt.colorbar(
matplotlib.cm.ScalarMappable(norm=norm, cmap=autocmap.reversed())
)
cb1.set_label(
"%s-axis position of line [arcsec]"
% (
"Minor"
if "ap_axialprof_parallel" in options
and options["ap_axialprof_parallel"]
else "Major"
),
fontsize=16,
)
bkgrdnoise = (
-2.5 * np.log10(results["background noise"])
+ zeropoint
+ 2.5 * np.log10(options["ap_pixscale"] ** 2)
)
plt.axhline(
bkgrdnoise,
color="purple",
linewidth=0.5,
linestyle="--",
label="1$\\sigma$ noise/pixel: %.1f mag arcsec$^{-2}$" % bkgrdnoise,
)
plt.gca().invert_yaxis()
plt.legend(fontsize=15)
plt.tick_params(labelsize=14)
plt.title(
"%sR : pa%s90" % ("+" if rd > 0 else "-", "+" if ang > 0 else "-"),
fontsize=15,
)
plt.tight_layout()
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
os.path.join(
options["ap_plotpath"] if "ap_plotpath" in options else "",
"axial_profile_q%i_%s.jpg" % (count, options["ap_name"]),
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
count += 1
CHOOSE = np.array(results["prof data"]["SB_e"]) < 0.2
firstbad = np.argmax(np.logical_not(CHOOSE))
if firstbad > 3:
CHOOSE[firstbad:] = False
outto = (
np.array(results["prof data"]["R"])[CHOOSE][-1] * 1.5 / options["ap_pixscale"]
)
ranges = [
[
max(0, int(results["center"]["x"] - outto - 2)),
min(dat.shape[1], int(results["center"]["x"] + outto + 2)),
],
[
max(0, int(results["center"]["y"] - outto - 2)),
min(dat.shape[0], int(results["center"]["y"] + outto + 2)),
],
]
LSBImage(
dat[ranges[1][0] : ranges[1][1], ranges[0][0] : ranges[0][1]],
results["background noise"],
)
AddScale(plt.gca(), (ranges[0][1] - ranges[0][0])*options['ap_pixscale'])
count = 0
cmap = matplotlib.cm.get_cmap("hsv")
colorind = (np.linspace(0, 1 - 1 / 4, 4) + 0.1) % 1
colours = list(cmap(c) for c in colorind)
for rd in [1, -1]:
for ang in [1, -1]:
key = (rd, ang)
branch_pa = (pa + ang * np.pi / 2) % (2 * np.pi)
for pi, pR in enumerate(R):
if pi % 3 != 0:
continue
start = np.array(
[
results["center"]["x"]
+ ang * rd * pR * np.cos(pa + (0 if ang > 0 else np.pi)),
results["center"]["y"]
+ ang * rd * pR * np.sin(pa + (0 if ang > 0 else np.pi)),
]
)
end = start + R[-1] * np.array([np.cos(branch_pa), np.sin(branch_pa)])
start -= np.array([ranges[0][0], ranges[1][0]])
end -= np.array([ranges[0][0], ranges[1][0]])
plt.plot(
[start[0], end[0]],
[start[1], end[1]],
linewidth=0.5,
color=colours[count],
label=(
"%sR : pa%s90"
% ("+" if rd > 0 else "-", "+" if ang > 0 else "-")
)
if pi == 0
else None,
)
count += 1
plt.legend()
plt.xlim([0, ranges[0][1] - ranges[0][0]])
plt.ylim([0, ranges[1][1] - ranges[1][0]])
if not ("ap_nologo" in options and options["ap_nologo"]):
AddLogo(plt.gcf())
plt.savefig(
os.path.join(
options["ap_plotpath"] if "ap_plotpath" in options else "",
"axial_profile_lines_%s.jpg" % options["ap_name"],
),
dpi=options["ap_plotdpi"] if "ap_plotdpi" in options else 300,
)
plt.close()
def Isophote_Fit_FFT_mean(IMG, results, options):
"""
Fit isophotes by minimizing the amplitude of the second FFT coefficient, relative to the local median flux.
Included is a regularization term which penalizes isophotes for having large differences between parameters
of adjacent isophotes.
"""
if 'ap_scale' in options:
scale = options['ap_scale']
else:
scale = 0.2
# subtract background from image during processing
dat = IMG - results['background']
mask = results['mask'] if 'mask' in results else None
if not np.any(mask):
mask = None
# Determine sampling radii
######################################################################
shrink = 0
while shrink < 5:
sample_radii = [3 * results['psf fwhm'] / 2]
while sample_radii[-1] < (max(IMG.shape) / 2):
isovals = _iso_extract(dat,
sample_radii[-1],
results['init ellip'],
results['init pa'],
results['center'],
more=False,
mask=mask)
if np.mean(isovals) < (options['ap_fit_limit']
if 'ap_fit_limit' in options else
1) * results['background noise']:
break
sample_radii.append(sample_radii[-1] * (1. + scale /
(1. + shrink)))
if len(sample_radii) < 15:
shrink += 1
else:
break
if shrink >= 5:
raise Exception(
'Unable to initialize ellipse fit, check diagnostic plots. Possible missed center.'
)
ellip = np.ones(len(sample_radii)) * results['init ellip']
pa = np.ones(len(sample_radii)) * results['init pa']
logging.debug('%s: sample radii: %s' %
(options['ap_name'], str(sample_radii)))
# Fit isophotes
######################################################################
perturb_scale = np.array([0.03, 0.06])
regularize_scale = options[
'ap_regularize_scale'] if 'ap_regularize_scale' in options else 1.
N_perturb = 5
count = 0
count_nochange = 0
use_center = copy(results['center'])
I = np.array(range(len(sample_radii)))
while count < 300 and count_nochange < (3 * len(sample_radii)):
# Periodically include logging message
if count % 10 == 0:
logging.debug('%s: count: %i' % (options['ap_name'], count))
count += 1
np.random.shuffle(I)
for i in I:
perturbations = []
perturbations.append({'ellip': copy(ellip), 'pa': copy(pa)})
perturbations[-1]['loss'] = _FFT_mean_loss(
dat,
sample_radii,
perturbations[-1]['ellip'],
perturbations[-1]['pa'],
i,
use_center,
results['background noise'],
mask=mask,
reg_scale=regularize_scale if count > 4 else 0,
name=options['ap_name'])
for n in range(N_perturb):
perturbations.append({'ellip': copy(ellip), 'pa': copy(pa)})
if count % 3 in [0, 1]:
perturbations[-1]['ellip'][i] = _x_to_eps(
_inv_x_to_eps(perturbations[-1]['ellip'][i]) +
np.random.normal(loc=0, scale=perturb_scale[0]))
if count % 3 in [1, 2]:
perturbations[-1]['pa'][i] = (
perturbations[-1]['pa'][i] + np.random.normal(
loc=0, scale=perturb_scale[1])) % np.pi
perturbations[-1]['loss'] = _FFT_mean_loss(
dat,
sample_radii,
perturbations[-1]['ellip'],
perturbations[-1]['pa'],
i,
use_center,
results['background noise'],
mask=mask,
reg_scale=regularize_scale if count > 4 else 0,
name=options['ap_name'])
best = np.argmin(list(p['loss'] for p in perturbations))
if best > 0:
ellip = copy(perturbations[best]['ellip'])
pa = copy(perturbations[best]['pa'])
count_nochange = 0
else:
count_nochange += 1
logging.info('%s: Completed isohpote fit in %i itterations' %
(options['ap_name'], count))
# detect collapsed center
######################################################################
for i in range(5):
if (_inv_x_to_eps(ellip[i]) - _inv_x_to_eps(ellip[i + 1])) > 0.5:
ellip[:i + 1] = ellip[i + 1]
pa[:i + 1] = pa[i + 1]
# Smooth ellip and pa profile
######################################################################
smooth_ellip = copy(ellip)
smooth_pa = copy(pa)
ellip[:3] = min(ellip[:3])
smooth_ellip = _ellip_smooth(sample_radii, smooth_ellip, 5)
smooth_pa = _pa_smooth(sample_radii, smooth_pa, 5)
if 'ap_doplot' in options and options['ap_doplot']:
ranges = [[
max(0, int(use_center['x'] - sample_radii[-1] * 1.2)),
min(dat.shape[1], int(use_center['x'] + sample_radii[-1] * 1.2))
],
[
max(0, int(use_center['y'] - sample_radii[-1] * 1.2)),
min(dat.shape[0],
int(use_center['y'] + sample_radii[-1] * 1.2))
]]
LSBImage(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results['background noise'])
# plt.imshow(np.clip(dat[ranges[1][0]: ranges[1][1], ranges[0][0]: ranges[0][1]],
# a_min = 0,a_max = None), origin = 'lower', cmap = 'Greys', norm = ImageNormalize(stretch=LogStretch()))
for i in range(len(sample_radii)):
plt.gca().add_patch(
Ellipse((use_center['x'] - ranges[0][0],
use_center['y'] - ranges[1][0]),
2 * sample_radii[i],
2 * sample_radii[i] * (1. - ellip[i]),
pa[i] * 180 / np.pi,
fill=False,
linewidth=((i + 1) / len(sample_radii))**2,
color='r'))
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sfit_ellipse_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
plt.scatter(sample_radii, ellip, color='r', label='ellip')
plt.scatter(sample_radii, pa / np.pi, color='b', label='pa/$np.pi$')
show_ellip = _ellip_smooth(sample_radii, ellip, deg=5)
show_pa = _pa_smooth(sample_radii, pa, deg=5)
plt.plot(sample_radii,
show_ellip,
color='orange',
linewidth=2,
linestyle='--',
label='smooth ellip')
plt.plot(sample_radii,
show_pa / np.pi,
color='purple',
linewidth=2,
linestyle='--',
label='smooth pa/$np.pi$')
#plt.xscale('log')
plt.legend()
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sphaseprofile_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
# Compute errors
######################################################################
ellip_err = np.zeros(len(ellip))
ellip_err[:2] = np.sqrt(np.sum((ellip[:4] - smooth_ellip[:4])**2) / 4)
ellip_err[-1] = np.sqrt(np.sum((ellip[-4:] - smooth_ellip[-4:])**2) / 4)
pa_err = np.zeros(len(pa))
pa_err[:2] = np.sqrt(np.sum((pa[:4] - smooth_pa[:4])**2) / 4)
pa_err[-1] = np.sqrt(np.sum((pa[-4:] - smooth_pa[-4:])**2) / 4)
for i in range(2, len(pa) - 1):
ellip_err[i] = np.sqrt(
np.sum((ellip[i - 2:i + 2] - smooth_ellip[i - 2:i + 2])**2) / 4)
pa_err[i] = np.sqrt(
np.sum((pa[i - 2:i + 2] - smooth_pa[i - 2:i + 2])**2) / 4)
res = {
'fit ellip':
ellip,
'fit pa':
pa,
'fit R':
sample_radii,
'fit ellip_err':
ellip_err,
'fit pa_err':
pa_err,
'auxfile fitlimit':
'fit limit semi-major axis: %.2f pix' % sample_radii[-1]
}
return IMG, res
def _Generate_Profile(IMG, results, R, E, Ee, PA, PAe, options):
# Create image array with background and mask applied
try:
if np.any(results['mask']):
mask = results['mask']
else:
mask = None
except:
mask = None
dat = IMG - results['background']
zeropoint = options['ap_zeropoint'] if 'ap_zeropoint' in options else 22.5
sb = []
sbE = []
cogdirect = []
sbfix = []
sbfixE = []
count_neg = 0
medflux = np.inf
end_prof = None
for i in range(len(R)):
isobandwidth = R[i] * (options['ap_isoband_width']
if 'ap_isoband_width' in options else 0.025)
if medflux > (results['background noise'] *
(options['ap_isoband_start'] if 'ap_isoband_start'
in options else 2)) or isobandwidth < 0.5:
isovals = _iso_extract(
dat,
R[i],
E[i],
PA[i],
results['center'],
mask=mask,
rad_interp=(options['ap_iso_interpolate_start']
if 'ap_iso_interpolate_start' in options else 5) *
results['psf fwhm'],
sigmaclip=options['ap_isoclip']
if 'ap_isoclip' in options else False,
sclip_iterations=options['ap_isoclip_iterations']
if 'ap_isoclip_iterations' in options else 10,
sclip_nsigma=options['ap_isoclip_nsigma']
if 'ap_isoclip_nsigma' in options else 5)
isovalsfix = _iso_extract(
dat,
R[i],
results['init ellip'],
results['init pa'],
results['center'],
mask=mask,
rad_interp=(options['ap_iso_interpolate_start']
if 'ap_iso_interpolate_start' in options else 5) *
results['psf fwhm'],
sigmaclip=options['ap_isoclip']
if 'ap_isoclip' in options else False,
sclip_iterations=options['ap_isoclip_iterations']
if 'ap_isoclip_iterations' in options else 10,
sclip_nsigma=options['ap_isoclip_nsigma']
if 'ap_isoclip_nsigma' in options else 5)
else:
isovals = _iso_between(
dat,
R[i] - isobandwidth,
R[i] + isobandwidth,
E[i],
PA[i],
results['center'],
mask=mask,
sigmaclip=options['ap_isoclip']
if 'ap_isoclip' in options else False,
sclip_iterations=options['ap_isoclip_iterations']
if 'ap_isoclip_iterations' in options else 10,
sclip_nsigma=options['ap_isoclip_nsigma']
if 'ap_isoclip_nsigma' in options else 5)
isovalsfix = _iso_between(
dat,
R[i] - isobandwidth,
R[i] + isobandwidth,
results['init ellip'],
results['init pa'],
results['center'],
mask=mask,
sigmaclip=options['ap_isoclip']
if 'ap_isoclip' in options else False,
sclip_iterations=options['ap_isoclip_iterations']
if 'ap_isoclip_iterations' in options else 10,
sclip_nsigma=options['ap_isoclip_nsigma']
if 'ap_isoclip_nsigma' in options else 5)
isotot = np.sum(
_iso_between(dat,
0,
R[i],
E[i],
PA[i],
results['center'],
mask=mask))
medflux = _average(
isovals, options['ap_isoaverage_method']
if 'ap_isoaverage_method' in options else 'median')
scatflux = _scatter(
isovals, options['ap_isoaverage_method']
if 'ap_isoaverage_method' in options else 'median')
medfluxfix = _average(
isovalsfix, options['ap_isoaverage_method']
if 'ap_isoaverage_method' in options else 'median')
scatfluxfix = _scatter(
isovalsfix, options['ap_isoaverage_method']
if 'ap_isoaverage_method' in options else 'median')
sb.append(
flux_to_sb(medflux, options['ap_pixscale'], zeropoint
) if medflux > 0 else 99.999)
sbE.append((2.5 * scatflux / (np.sqrt(len(isovals)) * medflux *
np.log(10))) if medflux > 0 else 99.999)
sbfix.append(
flux_to_sb(medfluxfix, options['ap_pixscale'], zeropoint
) if medfluxfix > 0 else 99.999)
sbfixE.append((2.5 * scatfluxfix /
(np.sqrt(len(isovalsfix)) * np.median(isovalsfix) *
np.log(10))) if medfluxfix > 0 else 99.999)
cogdirect.append(
flux_to_mag(isotot, zeropoint) if isotot > 0 else 99.999)
if medflux <= 0:
count_neg += 1
if 'ap_truncate_evaluation' in options and options[
'ap_truncate_evaluation'] and count_neg >= 2:
end_prof = i + 1
break
# Compute Curve of Growth from SB profile
cog, cogE = SBprof_to_COG_errorprop(R[:end_prof] * options['ap_pixscale'],
np.array(sb),
np.array(sbE),
1. - E[:end_prof],
Ee[:end_prof],
N=100,
method=0,
symmetric_error=True)
cogE[cog > 99] = 99.999
cogfix, cogfixE = SBprof_to_COG_errorprop(R[:end_prof] *
options['ap_pixscale'],
np.array(sbfix),
np.array(sbfixE),
1. - E[:end_prof],
Ee[:end_prof],
N=100,
method=0,
symmetric_error=True)
cogfixE[cogfix > 99] = 99.999
# For each radius evaluation, write the profile parameters
params = [
'R', 'SB', 'SB_e', 'totmag', 'totmag_e', 'ellip', 'ellip_e', 'pa',
'pa_e', 'totmag_direct', 'SB_fix', 'SB_fix_e', 'totmag_fix',
'totmag_fix_e'
]
SBprof_data = dict((h, None) for h in params)
SBprof_units = {
'R': 'arcsec',
'SB': 'mag*arcsec^-2',
'SB_e': 'mag*arcsec^-2',
'totmag': 'mag',
'totmag_e': 'mag',
'ellip': 'unitless',
'ellip_e': 'unitless',
'pa': 'deg',
'pa_e': 'deg',
'totmag_direct': 'mag',
'SB_fix': 'mag*arcsec^-2',
'SB_fix_e': 'mag*arcsec^-2',
'totmag_fix': 'mag',
'totmag_fix_e': 'mag'
}
SBprof_format = {
'R': '%.4f',
'SB': '%.4f',
'SB_e': '%.4f',
'totmag': '%.4f',
'totmag_e': '%.4f',
'ellip': '%.3f',
'ellip_e': '%.3f',
'pa': '%.2f',
'pa_e': '%.2f',
'totmag_direct': '%.4f',
'SB_fix': '%.4f',
'SB_fix_e': '%.4f',
'totmag_fix': '%.4f',
'totmag_fix_e': '%.4f'
}
SBprof_data['R'] = list(R[:end_prof] * options['ap_pixscale'])
SBprof_data['SB'] = list(sb)
SBprof_data['SB_e'] = list(sbE)
SBprof_data['totmag'] = list(cog)
SBprof_data['totmag_e'] = list(cogE)
SBprof_data['ellip'] = list(E[:end_prof])
SBprof_data['ellip_e'] = list(Ee[:end_prof])
SBprof_data['pa'] = list(PA[:end_prof] * 180 / np.pi)
SBprof_data['pa_e'] = list(PAe[:end_prof] * 180 / np.pi)
SBprof_data['totmag_direct'] = list(cogdirect)
SBprof_data['SB_fix'] = list(sbfix)
SBprof_data['SB_fix_e'] = list(sbfixE)
SBprof_data['totmag_fix'] = list(cogfix)
SBprof_data['totmag_fix_e'] = list(cogfixE)
if 'ap_doplot' in options and options['ap_doplot']:
CHOOSE = np.logical_and(
np.array(SBprof_data['SB']) < 99,
np.array(SBprof_data['SB_e']) < 1)
errscale = 1.
if np.all(np.array(SBprof_data['SB_e'])[CHOOSE] < 0.5):
errscale = 1 / np.max(np.array(SBprof_data['SB_e'])[CHOOSE])
lnlist = []
lnlist.append(
plt.errorbar(np.array(SBprof_data['R'])[CHOOSE],
np.array(SBprof_data['SB'])[CHOOSE],
yerr=errscale * np.array(SBprof_data['SB_e'])[CHOOSE],
elinewidth=1,
linewidth=0,
marker='.',
markersize=5,
color='r',
label='Surface Brightness (err$\\cdot$%.1f)' %
errscale))
plt.errorbar(np.array(SBprof_data['R'])[np.logical_and(
CHOOSE,
np.arange(len(CHOOSE)) % 4 == 0)],
np.array(SBprof_data['SB'])[np.logical_and(
CHOOSE,
np.arange(len(CHOOSE)) % 4 == 0)],
yerr=np.array(SBprof_data['SB_e'])[np.logical_and(
CHOOSE,
np.arange(len(CHOOSE)) % 4 == 0)],
elinewidth=1,
linewidth=0,
marker='.',
markersize=5,
color='limegreen')
# plt.errorbar(np.array(SBprof_data['R'])[CHOOSE], np.array(SBprof_data['totmag'])[CHOOSE], yerr = np.array(SBprof_data['totmag_e'])[CHOOSE],
# elinewidth = 1, linewidth = 0, marker = '.', markersize = 5, color = 'orange', label = 'Curve of Growth')
plt.xlabel('Semi-Major-Axis [arcsec]', fontsize=16)
plt.ylabel('Surface Brightness [mag arcsec$^{-2}$]', fontsize=16)
bkgrdnoise = -2.5 * np.log10(
results['background noise']) + zeropoint + 2.5 * np.log10(
options['ap_pixscale']**2)
lnlist.append(
plt.axhline(
bkgrdnoise,
color='purple',
linewidth=0.5,
linestyle='--',
label='1$\\sigma$ noise/pixel: %.1f mag arcsec$^{-2}$' %
bkgrdnoise))
plt.gca().invert_yaxis()
plt.tick_params(labelsize=14)
# ax2 = plt.gca().twinx()
# lnlist += ax2.plot(np.array(SBprof_data['R'])[CHOOSE], np.array(SBprof_data['pa'])[CHOOSE]/180, color = 'b', label = 'PA/180')
# lnlist += ax2.plot(np.array(SBprof_data['R'])[CHOOSE], np.array(SBprof_data['ellip'])[CHOOSE], color = 'orange', linestyle = '--', label = 'ellipticity')
labs = [l.get_label() for l in lnlist]
plt.legend(lnlist, labs, fontsize=11)
# ax2.set_ylabel('Position Angle, Ellipticity', fontsize = 16)
# ax2.tick_params(labelsize = 14)
plt.tight_layout()
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sphotometry_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
useR = np.array(SBprof_data['R'])[CHOOSE] / options['ap_pixscale']
useE = np.array(SBprof_data['ellip'])[CHOOSE]
usePA = np.array(SBprof_data['pa'])[CHOOSE]
ranges = [[
max(0, int(results['center']['x'] - useR[-1] * 1.2)),
min(dat.shape[1], int(results['center']['x'] + useR[-1] * 1.2))
],
[
max(0, int(results['center']['y'] - useR[-1] * 1.2)),
min(dat.shape[0],
int(results['center']['y'] + useR[-1] * 1.2))
]]
LSBImage(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results['background noise'])
for i in range(len(useR)):
plt.gca().add_patch(
Ellipse(
(results['center']['x'] - ranges[0][0],
results['center']['y'] - ranges[1][0]),
2 * useR[i],
2 * useR[i] * (1. - useE[i]),
usePA[i],
fill=False,
linewidth=((i + 1) / len(useR))**2,
color='limegreen' if (i % 4 == 0) else 'r',
linestyle='-' if useR[i] < results['fit R'][-1] else '--'))
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sphotometry_ellipse_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
return {
'prof header': params,
'prof units': SBprof_units,
'prof data': SBprof_data,
'prof format': SBprof_format
}
def EllipseModel_General(IMG, results, options):
zeropoint = options['ap_zeropoint'] if 'ap_zeropoint' in options else 22.5
CHOOSE = np.array(results['prof data']['SB_e']) < 0.5
R = np.array(results['prof data']['R'])[CHOOSE] / options['ap_pixscale']
sb = UnivariateSpline(np.log10(R),
np.array(results['prof data']['SB'])[CHOOSE],
ext=3,
s=0)
pa = UnivariateSpline(np.log10(R),
np.array(results['prof data']['pa'])[CHOOSE] *
np.pi / 180,
ext=3,
s=0)
q = UnivariateSpline(np.log10(R),
1 - np.array(results['prof data']['ellip'])[CHOOSE],
ext=3,
s=0)
ranges = [[
max(0, int(results['center']['x'] - R[-1] - 2)),
min(IMG.shape[1], int(results['center']['x'] + R[-1] + 2))
],
[
max(0, int(results['center']['y'] - R[-1] - 2)),
min(IMG.shape[0], int(results['center']['y'] + R[-1] + 2))
]]
XX, YY = np.meshgrid(
np.arange(ranges[0][1] - ranges[0][0], dtype=float),
np.arange(ranges[1][1] - ranges[1][0], dtype=np.float32))
XX -= results['center']['x'] - float(ranges[0][0])
YY -= results['center']['y'] - float(ranges[1][0])
MM = np.zeros(XX.shape, dtype=np.float32)
Prox = np.zeros(XX.shape, dtype=np.float32) + np.inf
WINDOW = [[0, XX.shape[0]], [0, XX.shape[1]]]
for r in reversed(
np.logspace(
np.log10(R[0] / 2), np.log10(R[-1]),
int(
len(R) * 2 *
(option['ap_ellipsemodel_resolution']
if 'ap_ellipsemodel_resolution' in options else 1)))):
if r < (R[-1] / 2):
WINDOW = [[
max(
0,
int(results['center']['y'] - float(ranges[1][0]) -
r * 1.5)),
min(
XX.shape[0],
int(results['center']['y'] - float(ranges[1][0]) +
r * 1.5))
],
[
max(
0,
int(results['center']['x'] -
float(ranges[0][0]) - r * 1.5)),
min(
XX.shape[1],
int(results['center']['x'] -
float(ranges[0][0]) + r * 1.5))
]]
RR = np.sqrt((XX[WINDOW[0][0]:WINDOW[0][1],WINDOW[1][0]:WINDOW[1][1]]*np.cos(-pa(np.log10(r))) - YY[WINDOW[0][0]:WINDOW[0][1],WINDOW[1][0]:WINDOW[1][1]]*np.sin(-pa(np.log10(r))))**2 + \
((XX[WINDOW[0][0]:WINDOW[0][1],WINDOW[1][0]:WINDOW[1][1]]*np.sin(-pa(np.log10(r))) + YY[WINDOW[0][0]:WINDOW[0][1],WINDOW[1][0]:WINDOW[1][1]]*np.cos(-pa(np.log10(r))))/np.clip(q(np.log10(r)),a_min = 0.03,a_max = 1))**2)
D = np.abs(RR - r)
CLOSE = D < Prox[WINDOW[0][0]:WINDOW[0][1], WINDOW[1][0]:WINDOW[1][1]]
if np.any(CLOSE):
MM[WINDOW[0][0]:WINDOW[0][1],
WINDOW[1][0]:WINDOW[1][1]][CLOSE] = sb(np.log10(RR[CLOSE]))
Prox[WINDOW[0][0]:WINDOW[0][1],
WINDOW[1][0]:WINDOW[1][1]][CLOSE] = D[CLOSE]
MM = 10**(-(MM - zeropoint - 5 * np.log10(options['ap_pixscale'])) / 2.5)
RR = np.sqrt((XX * np.cos(-pa(np.log10(R[-1]))) -
YY * np.sin(-pa(np.log10(R[-1]))))**2 +
((XX * np.sin(-pa(np.log10(R[-1]))) +
YY * np.cos(-pa(np.log10(R[-1])))) /
np.clip(q(np.log10(R[-1])), a_min=0.03, a_max=1))**2)
MM[RR > R[-1]] = 0
Model = np.zeros(IMG.shape, dtype=np.float32)
Model[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]] = MM
header = fits.Header()
hdul = fits.HDUList([fits.PrimaryHDU(header=header), fits.ImageHDU(Model)])
hdul.writeto('%s%s_genmodel.fits' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
overwrite=True)
if 'ap_doplot' in options and options['ap_doplot']:
ranges = [[
max(0, int(results['center']['x'] - R[-1] * 1.2)),
min(IMG.shape[1], int(results['center']['x'] + R[-1] * 1.2))
],
[
max(0, int(results['center']['y'] - R[-1] * 1.2)),
min(IMG.shape[0],
int(results['center']['y'] + R[-1] * 1.2))
]]
plt.figure(figsize=(7, 7))
autocmap.set_under('k', alpha=0)
showmodel = Model[ranges[1][0]:ranges[1][1],
ranges[0][0]:ranges[0][1]].copy()
showmodel[showmodel > 0] += np.max(showmodel) / (10**3.5) - np.min(
showmodel[showmodel > 0])
plt.imshow(showmodel,
origin='lower',
cmap=autocmap,
norm=ImageNormalize(stretch=LogStretch(), clip=False))
plt.axis('off')
plt.subplots_adjust(left=0.03, right=0.97, top=0.97, bottom=0.05)
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sellipsemodel_gen_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
residual = IMG[ranges[1][0]:ranges[1][1],
ranges[0][0]:ranges[0][1]] - results[
'background'] - Model[ranges[1][0]:ranges[1][1],
ranges[0][0]:ranges[0][1]]
plt.figure(figsize=(7, 7))
plt.imshow(residual,
origin='lower',
cmap='PuBu',
vmin=np.quantile(residual, 0.0001),
vmax=0)
plt.imshow(np.clip(residual,
a_min=0,
a_max=np.quantile(residual, 0.9999)),
origin='lower',
cmap=autocmap,
norm=ImageNormalize(stretch=LogStretch(), clip=False),
interpolation='none',
clim=[1e-5, None])
plt.axis('off')
plt.subplots_adjust(left=0.03, right=0.97, top=0.97, bottom=0.05)
if not ('ap_nologo' in options and options['ap_nologo']):
AddLogo(plt.gcf())
plt.savefig(
'%sellipseresidual_gen_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
if 'ap_paperplots' in options and options['ap_paperplots']:
plt.figure(figsize=(7, 7))
LSBImage(
IMG[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]] -
results['background'], results['background noise'])
plt.axis('off')
plt.subplots_adjust(left=0.03, right=0.97, top=0.97, bottom=0.05)
plt.savefig(
'%sclearimage_%s.jpg' %
(options['ap_plotpath'] if 'ap_plotpath' in options else '',
options['ap_name']),
dpi=options['ap_plotdpi'] if 'ap_plotdpi' in options else 300)
plt.close()
return IMG, {'ellipse model': Model}