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 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 Center_Peak(IMG, results, options):
current_center = {"x": IMG.shape[1] / 2, "y": IMG.shape[0] / 2}
dat = IMG - results["background"]
if "ap_guess_center" in options:
current_center = deepcopy(options["ap_guess_center"])
logging.info("%s: Center initialized by user: %s" %
(options["ap_name"], str(current_center)))
if "ap_set_center" in options:
logging.info("%s: Center set by user: %s" %
(options["ap_name"], str(options["ap_set_center"])))
sb0 = flux_to_sb(
_iso_extract(dat, 0.0, {
"ellip": 0.0,
"pa": 0.0
}, options["ap_set_center"])[0],
options["ap_pixscale"],
options["ap_zeropoint"] if "zeropoint" in options else 22.5,
)
return IMG, {
"center":
deepcopy(options["ap_set_center"]),
"auxfile central sb":
"central surface brightness: %.4f mag arcsec^-2" % sb0,
}
searchring = int(
(options["ap_centeringring"] if "ap_centeringring" in options else 10)
* results["psf fwhm"])
xx, yy = np.meshgrid(np.arange(searchring), np.arange(searchring))
xx = xx.flatten()
yy = yy.flatten()
A = np.array([
np.ones(xx.shape),
xx,
yy,
xx**2,
yy**2,
xx * yy,
xx * yy**2,
yy * xx**2,
xx**2 * yy**2,
]).T
ranges = [
[
max(0, int(current_center["x"] - searchring / 2)),
min(IMG.shape[1], int(current_center["x"] + searchring / 2)),
],
[
max(0, int(current_center["y"] - searchring / 2)),
min(IMG.shape[0], int(current_center["y"] + searchring / 2)),
],
]
chunk = np.clip(
dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]].T,
a_min=results["background noise"] / 5,
a_max=None,
)
poly2dfit = np.linalg.lstsq(A, np.log10(chunk.flatten()), rcond=None)
current_center = {
"x": -poly2dfit[0][2] / (2 * poly2dfit[0][4]) + ranges[0][0],
"y": -poly2dfit[0][1] / (2 * poly2dfit[0][3]) + ranges[1][0],
}
sb0 = flux_to_sb(
_iso_extract(dat, 0.0, {
"ellip": 0.0,
"pa": 0.0
}, current_center)[0],
options["ap_pixscale"],
options["ap_zeropoint"] if "zeropoint" in options else 22.5,
)
return IMG, {
"center":
current_center,
"auxfile center":
"center x: %.2f pix, y: %.2f pix" %
(current_center["x"], current_center["y"]),
"auxfile central sb":
"central surface brightness: %.4f mag arcsec^-2" % sb0,
}
def Center_HillClimb(IMG, results, options):
"""Follow locally increasing brightness (robust to PSF size objects) to find peak.
Using 10 circular isophotes out to 10 times the PSF length, the first FFT coefficient
phases are averaged to find the direction of increasing flux. Flux values are sampled
along this direction and a quadratic fit gives the maximum. This is iteratively
repeated until the step size becomes very small.
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.
ap_centeringring : int, default 10
Size of ring to use when finding galaxy center, in units of
PSF. Larger rings will be robust to features (i.e., foreground
stars), while smaller rings may be needed for small galaxies.
Notes
----------
:References:
- 'background'
- 'background noise'
- 'psf fwhm'
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{'center': {'x': , # x coordinate of the center (pix)
'y': }, # y coordinate of the center (pix)
'auxfile center': # optional, message for aux file to record galaxy center (string)
'auxfile centeral sb': # optional, central surface brightness value (float)
}
"""
current_center = {"x": IMG.shape[1] / 2, "y": IMG.shape[0] / 2}
dat = IMG - results["background"]
if "ap_guess_center" in options:
current_center = deepcopy(options["ap_guess_center"])
logging.info("%s: Center initialized by user: %s" %
(options["ap_name"], str(current_center)))
if "ap_set_center" in options:
logging.info("%s: Center set by user: %s" %
(options["ap_name"], str(options["ap_set_center"])))
sb0 = flux_to_sb(
_iso_extract(dat, 0.0, {
"ellip": 0.0,
"pa": 0.0
}, options["ap_set_center"])[0],
options["ap_pixscale"],
options["ap_zeropoint"] if "zeropoint" in options else 22.5,
)
return IMG, {
"center":
deepcopy(options["ap_set_center"]),
"auxfile central sb":
"central surface brightness: %.4f mag arcsec^-2" % sb0,
}
searchring = (int(options["ap_centeringring"])
if "ap_centeringring" in options else 10)
sampleradii = np.linspace(1, searchring, searchring) * results["psf fwhm"]
track_centers = []
small_update_count = 0
total_count = 0
while small_update_count <= 5 and total_count <= 100:
total_count += 1
phases = []
isovals = []
coefs = []
for r in sampleradii:
isovals.append(
_iso_extract(dat,
r, {
"ellip": 0.0,
"pa": 0.0
},
current_center,
more=True))
coefs.append(
fft(
np.clip(
isovals[-1][0],
a_max=np.quantile(isovals[-1][0], 0.85),
a_min=None,
)))
phases.append((-np.angle(coefs[-1][1])) % (2 * np.pi))
direction = Angle_Median(phases) % (2 * np.pi)
levels = []
level_locs = []
for i, r in enumerate(sampleradii):
floc = np.argmin(np.abs((isovals[i][1] % (2 * np.pi)) - direction))
rloc = np.argmin(
np.abs((isovals[i][1] % (2 * np.pi)) - ((direction + np.pi) %
(2 * np.pi))))
smooth = np.abs(
ifft(coefs[i][:min(10, len(coefs[i]))], n=len(coefs[i])))
levels.append(smooth[floc])
level_locs.append(r)
levels.insert(0, smooth[rloc])
level_locs.insert(0, -r)
try:
p = np.polyfit(level_locs, levels, deg=2)
if p[0] < 0 and len(levels) > 3:
dist = np.clip(-p[1] / (2 * p[0]),
a_min=min(level_locs),
a_max=max(level_locs))
else:
dist = level_locs[np.argmax(levels)]
except:
dist = results["psf fwhm"]
current_center["x"] += dist * np.cos(direction)
current_center["y"] += dist * np.sin(direction)
if abs(dist) < (0.5 * results["psf fwhm"]):
small_update_count += 1
else:
small_update_count = 0
track_centers.append([current_center["x"], current_center["y"]])
# refine center
ranges = [
[
max(0, int(current_center["x"] - results["psf fwhm"] * 5)),
min(dat.shape[1],
int(current_center["x"] + results["psf fwhm"] * 5)),
],
[
max(0, int(current_center["y"] - results["psf fwhm"] * 5)),
min(dat.shape[0],
int(current_center["y"] + results["psf fwhm"] * 5)),
],
]
res = minimize(
_hillclimb_loss,
x0=[
current_center["x"] - ranges[0][0],
current_center["y"] - ranges[1][0]
],
args=(
dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]],
results["psf fwhm"],
results["background noise"],
),
method="Nelder-Mead",
)
if res.success:
current_center["x"] = res.x[0] + ranges[0][0]
current_center["y"] = res.x[1] + ranges[1][0]
track_centers.append([current_center["x"], current_center["y"]])
sb0 = flux_to_sb(
_iso_extract(dat, 0.0, {
"ellip": 0.0,
"pa": 0.0
}, current_center)[0],
options["ap_pixscale"],
options["ap_zeropoint"] if "zeropoint" in options else 22.5,
)
return IMG, {
"center":
current_center,
"auxfile center":
"center x: %.2f pix, y: %.2f pix" %
(current_center["x"], current_center["y"]),
"auxfile central sb":
"central surface brightness: %.4f mag arcsec^-2" % sb0,
}
def Center_Forced(IMG, results, options):
"""Extracts previously fit center coordinates.
Extracts the center coordinates from an aux file for a previous
AutoProf fit. Can instead simply be given a set center value, just
like other centering methods. A given center will override teh
fitted aux file center.
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.
ap_forcing_profile : string, default None
(required for forced photometry) file path to .prof file
providing forced photometry PA and ellip values to apply to
*ap_image_file*.
Notes
----------
:References:
- 'background'
- 'background noise'
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{'center': {'x': , # x coordinate of the center (pix)
'y': }, # y coordinate of the center (pix)
'auxfile center': # optional, message for aux file to record galaxy center (string)
'auxfile centeral sb': # optional, central surface brightness value (float)
}
"""
current_center = {"x": IMG.shape[1] / 2, "y": IMG.shape[0] / 2}
if "ap_guess_center" in options:
current_center = deepcopy(options["ap_guess_center"])
logging.info("%s: Center initialized by user: %s" %
(options["ap_name"], str(current_center)))
if "ap_set_center" in options:
logging.info("%s: Center set by user: %s" %
(options["ap_name"], str(options["ap_set_center"])))
sb0 = flux_to_sb(
_iso_extract(
IMG - results["background"],
0.0,
{
"ellip": 0.0,
"pa": 0.0
},
options["ap_set_center"],
)[0],
options["ap_pixscale"],
options["ap_zeropoint"] if "zeropoint" in options else 22.5,
)
return IMG, {
"center":
deepcopy(options["ap_set_center"]),
"auxfile central sb":
"central surface brightness: %.4f mag arcsec^-2" % sb0,
}
try:
with open(options["ap_forcing_profile"][:-4] + "aux", "r") as f:
for line in f.readlines():
if line[:6] == "center":
x_loc = line.find("x:")
y_loc = line.find("y:")
current_center = {
"x": float(line[x_loc + 3:line.find("pix")]),
"y": float(line[y_loc + 3:line.rfind("pix")]),
}
break
else:
logging.warning(
"%s: Forced center failed! Using image center (or guess)."
% options["ap_name"])
except:
logging.warning(
"%s: Forced center failed! Using image center (or guess)." %
options["ap_name"])
sb0 = flux_to_sb(
_iso_extract(IMG - results["background"], 0.0, {
"ellip": 0.0,
"pa": 0.0
}, current_center)[0],
options["ap_pixscale"],
options["ap_zeropoint"] if "zeropoint" in options else 22.5,
)
return IMG, {
"center":
current_center,
"auxfile center":
"center x: %.2f pix, y: %.2f pix" %
(current_center["x"], current_center["y"]),
"auxfile central sb":
"central surface brightness: %.4f mag arcsec^-2" % sb0,
}
def Center_OfMass(IMG, results, options):
"""Find the light weighted galaxy center.
Iteratively computes the light weighted centroid within a window,
moves to the new center and computes the light weighted centroid
again. The size of the search area is 10PSF by default. The
iterative process will continue until the center is updated by
less than 1/10th of the PSF size or when too mny iterations have
been reached.
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.
ap_centeringring : int, default 10
Size of ring to use when finding galaxy center, in units of
PSF. Larger rings will allow for the starting position to be
further from the true galaxy center. Smaller rings will include
fewer spurious objects, and can stop the centroid from being
distracted by larger nearby objects/galaxies.
Notes
----------
:References:
- 'background'
- 'psf fwhm'
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{'center': {'x': , # x coordinate of the center (pix)
'y': }, # y coordinate of the center (pix)
'auxfile center': # optional, message for aux file to record galaxy center (string)
'auxfile centeral sb': # optional, central surface brightness value (float)
}
"""
current_center = {"x": IMG.shape[1] / 2, "y": IMG.shape[0] / 2}
dat = IMG - results["background"]
if "ap_guess_center" in options:
current_center = deepcopy(options["ap_guess_center"])
logging.info("%s: Center initialized by user: %s" %
(options["ap_name"], str(current_center)))
if "ap_set_center" in options:
logging.info("%s: Center set by user: %s" %
(options["ap_name"], str(options["ap_set_center"])))
sb0 = flux_to_sb(
_iso_extract(dat, 0.0, {
"ellip": 0.0,
"pa": 0.0
}, options["ap_set_center"])[0],
options["ap_pixscale"],
options["ap_zeropoint"] if "zeropoint" in options else 22.5,
)
return IMG, {
"center":
deepcopy(options["ap_set_center"]),
"auxfile central sb":
"central surface brightness: %.4f mag arcsec^-2" % sb0,
}
searchring = int(
(options["ap_centeringring"] if "ap_centeringring" in options else 10)
* results["psf fwhm"])
xx, yy = np.meshgrid(np.arange(searchring), np.arange(searchring))
N_updates = 0
while N_updates < 100:
N_updates += 1
old_center = deepcopy(current_center)
ranges = [
[
max(0, int(current_center["x"] - searchring / 2)),
min(IMG.shape[1], int(current_center["x"] + searchring / 2)),
],
[
max(0, int(current_center["y"] - searchring / 2)),
min(IMG.shape[0], int(current_center["y"] + searchring / 2)),
],
]
current_center = {
"x":
ranges[0][0] + np.sum(
(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]] *
xx)) /
np.sum(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]]),
"y":
ranges[1][0] + np.sum(
(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]] *
yy)) /
np.sum(dat[ranges[1][0]:ranges[1][1], ranges[0][0]:ranges[0][1]]),
}
if (abs(current_center["x"] - old_center["x"]) <
0.1 * results["psf fwhm"]
and abs(current_center["y"] - old_center["y"]) <
0.1 * results["psf fwhm"]):
break
sb0 = flux_to_sb(
_iso_extract(dat, 0.0, {
"ellip": 0.0,
"pa": 0.0
}, current_center)[0],
options["ap_pixscale"],
options["ap_zeropoint"] if "zeropoint" in options else 22.5,
)
return IMG, {
"center":
current_center,
"auxfile center":
"center x: %.2f pix, y: %.2f pix" %
(current_center["x"], current_center["y"]),
"auxfile central sb":
"central surface brightness: %.4f mag arcsec^-2" % sb0,
}
def Isophote_Extract_Photutils(IMG, results, options):
"""Wrapper of photutils method for extracting SB profiles.
This simply gives users access to the photutils isophote
extraction methods. The one exception is that SB values are taken
as the median instead of the mean, as recomended in the photutils
documentation. See: `photutils
<https://photutils.readthedocs.io/en/stable/isophote.html>`_ for
more information.
Parameters
----------
ap_zeropoint : float, default 22.5
Photometric zero point. For converting flux to mag units.
ap_fluxunits : str, default "mag"
units for outputted photometry. Can either be "mag" for log
units, or "intensity" for linear units.
ap_plot_sbprof_ylim : tuple, default None
Tuple with axes limits for the y-axis in the SB profile
diagnostic plot. Be careful when using intensity units
since this will change the ideal axis limits.
ap_plot_sbprof_xlim : tuple, default None
Tuple with axes limits for the x-axis in the SB profile
diagnostic plot.
ap_plot_sbprof_set_errscale : float, default None
Float value by which to scale errorbars on the SB profile
this makes them more visible in cases where the statistical
errors are very small.
Notes
----------
:References:
- 'background'
- 'background noise'
- 'psf fwhm'
- 'center'
- 'init R' (optional)
- 'init ellip' (optional)
- 'init pa' (optional)
- 'fit R' (optional)
- 'fit ellip' (optional)
- 'fit pa' (optional)
- 'fit photutils isolist' (optional)
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
.. code-block:: python
{'prof header': , # List object with strings giving the items in the header of the final SB profile (list)
'prof units': , # dict object that links header strings to units (given as strings) for each variable (dict)
'prof data': # dict object linking header strings to list objects containing the rows for a given variable (dict)
}
"""
zeropoint = options["ap_zeropoint"] if "ap_zeropoint" in options else 22.5
fluxunits = options["ap_fluxunits"] if "ap_fluxunits" in options else "mag"
if fluxunits == "intensity":
params = [
"R",
"I",
"I_e",
"totflux",
"totflux_e",
"ellip",
"ellip_e",
"pa",
"pa_e",
"a3",
"a3_e",
"b3",
"b3_e",
"a4",
"a4_e",
"b4",
"b4_e",
]
SBprof_units = {
"R": "arcsec",
"I": "flux*arcsec^-2",
"I_e": "flux*arcsec^-2",
"totflux": "flux",
"totflux_e": "flux",
"ellip": "unitless",
"ellip_e": "unitless",
"pa": "deg",
"pa_e": "deg",
"a3": "unitless",
"a3_e": "unitless",
"b3": "unitless",
"b3_e": "unitless",
"a4": "unitless",
"a4_e": "unitless",
"b4": "unitless",
"b4_e": "unitless",
}
else:
params = [
"R",
"SB",
"SB_e",
"totmag",
"totmag_e",
"ellip",
"ellip_e",
"pa",
"pa_e",
"a3",
"a3_e",
"b3",
"b3_e",
"a4",
"a4_e",
"b4",
"b4_e",
]
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",
"a3": "unitless",
"a3_e": "unitless",
"b3": "unitless",
"b3_e": "unitless",
"a4": "unitless",
"a4_e": "unitless",
"b4": "unitless",
"b4_e": "unitless",
}
SBprof_data = dict((h, []) for h in params)
res = {}
dat = IMG - results["background"]
if not "fit R" in results and not "fit photutils isolist" in results:
logging.info(
"%s: photutils fitting and extracting image data" % options["ap_name"]
)
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.update(
{
"fit photutils isolist": isolist,
"auxfile fitlimit": "fit limit semi-major axis: %.2f pix"
% isolist.sma[-1],
}
)
elif not "fit photutils isolist" in results:
logging.info("%s: photutils extracting image data" % options["ap_name"])
list_iso = []
for i in range(len(results["fit R"])):
if results["fit R"][i] <= 0:
continue
# Container for ellipse geometry
geo = EllipseGeometry(
sma=results["fit R"][i],
x0=results["center"]["x"],
y0=results["center"]["y"],
eps=results["fit ellip"][i],
pa=results["fit pa"][i],
)
# Extract the isophote information
ES = EllipseSample(dat, sma=results["fit R"][i], geometry=geo)
ES.update(fixed_parameters=None)
list_iso.append(Isophote(ES, niter=30, valid=True, stop_code=0))
isolist = IsophoteList(list_iso)
res.update(
{
"fit photutils isolist": isolist,
"auxfile fitlimit": "fit limit semi-major axis: %.2f pix"
% isolist.sma[-1],
}
)
else:
isolist = results["fit photutils isolist"]
for i in range(len(isolist.sma)):
SBprof_data["R"].append(isolist.sma[i] * options["ap_pixscale"])
if fluxunits == "intensity":
SBprof_data["I"].append(
np.median(isolist.sample[i].values[2]) / options["ap_pixscale"] ** 2
)
SBprof_data["I_e"].append(isolist.int_err[i])
SBprof_data["totflux"].append(isolist.tflux_e[i])
SBprof_data["totflux_e"].append(isolist.rms[i] / np.sqrt(isolist.npix_e[i]))
else:
SBprof_data["SB"].append(
flux_to_sb(
np.median(isolist.sample[i].values[2]),
options["ap_pixscale"],
zeropoint,
)
)
SBprof_data["SB_e"].append(
2.5 * isolist.int_err[i] / (isolist.intens[i] * np.log(10))
)
SBprof_data["totmag"].append(flux_to_mag(isolist.tflux_e[i], zeropoint))
SBprof_data["totmag_e"].append(
2.5
* isolist.rms[i]
/ (np.sqrt(isolist.npix_e[i]) * isolist.tflux_e[i] * np.log(10))
)
SBprof_data["ellip"].append(isolist.eps[i])
SBprof_data["ellip_e"].append(isolist.ellip_err[i])
SBprof_data["pa"].append(isolist.pa[i] * 180 / np.pi)
SBprof_data["pa_e"].append(isolist.pa_err[i] * 180 / np.pi)
SBprof_data["a3"].append(isolist.a3[i])
SBprof_data["a3_e"].append(isolist.a3_err[i])
SBprof_data["b3"].append(isolist.b3[i])
SBprof_data["b3_e"].append(isolist.b3_err[i])
SBprof_data["a4"].append(isolist.a4[i])
SBprof_data["a4_e"].append(isolist.a4_err[i])
SBprof_data["b4"].append(isolist.b4[i])
SBprof_data["b4_e"].append(isolist.b4_err[i])
for k in SBprof_data.keys():
if not np.isfinite(SBprof_data[k][-1]):
SBprof_data[k][-1] = 99.999
res.update(
{"prof header": params, "prof units": SBprof_units, "prof data": SBprof_data}
)
if "ap_doplot" in options and options["ap_doplot"]:
if fluxunits == "intensity":
Plot_I_Profile(
dat,
np.array(SBprof_data["R"]),
np.array(SBprof_data["I"]),
np.array(SBprof_data["I_e"]),
np.array(SBprof_data["ellip"]),
np.array(SBprof_data["pa"]),
results,
options,
)
else:
Plot_SB_Profile(
dat,
np.array(SBprof_data["R"]),
np.array(SBprof_data["SB"]),
np.array(SBprof_data["SB_e"]),
np.array(SBprof_data["ellip"]),
np.array(SBprof_data["pa"]),
results,
options,
)
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 _Generate_Profile(IMG, results, R, parameters, 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
fluxunits = options["ap_fluxunits"] if "ap_fluxunits" in options else "mag"
for p in range(len(parameters)):
# Indicate no Fourier modes if supplied parameters does not include it
if not "m" in parameters[p]:
parameters[p]["m"] = None
if not "C" in parameters[p]:
parameters[p]["C"] = None
# If no ellipticity error supplied, assume zero
if not "ellip err" in parameters[p]:
parameters[p]["ellip err"] = 0.0
# If no position angle error supplied, assume zero
if not "pa err" in parameters[p]:
parameters[p]["pa err"] = 0.0
sb = []
sbE = []
pixels = []
maskedpixels = []
cogdirect = []
sbfix = []
sbfixE = []
measFmodes = []
count_neg = 0
medflux = np.inf
end_prof = len(R)
compare_interp = []
for i in range(len(R)):
if "ap_isoband_fixed" in options and options["ap_isoband_fixed"]:
isobandwidth = (
options["ap_isoband_width"] if "ap_isoband_width" in options else 0.5
)
else:
isobandwidth = R[i] * (
options["ap_isoband_width"] if "ap_isoband_width" in options else 0.025
)
isisophoteband = False
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],
parameters[i],
results["center"],
mask=mask,
more=True,
rad_interp=(
options["ap_iso_interpolate_start"]
if "ap_iso_interpolate_start" in options
else 5
)
* results["psf fwhm"],
interp_method=(
options["ap_iso_interpolate_method"]
if "ap_iso_interpolate_method" in options
else "lanczos"
),
interp_window=(
int(options["ap_iso_interpolate_window"])
if "ap_iso_interpolate_window" in options
else 5
),
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:
isisophoteband = True
isovals = _iso_between(
dat,
R[i] - isobandwidth,
R[i] + isobandwidth,
parameters[i],
results["center"],
mask=mask,
more=True,
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], parameters[i], results["center"], mask=mask)
)
medflux = _average(
isovals[0],
options["ap_isoaverage_method"]
if "ap_isoaverage_method" in options
else "median",
)
scatflux = _scatter(
isovals[0],
options["ap_isoaverage_method"]
if "ap_isoaverage_method" in options
else "median",
)
if (
"ap_iso_measurecoefs" in options
and not options["ap_iso_measurecoefs"] is None
):
if (
mask is None
and (not "ap_isoclip" in options or not options["ap_isoclip"])
and not isisophoteband
):
coefs = fft(isovals[0])
else:
N = max(15, int(0.9 * 2 * np.pi * R[i]))
theta = np.linspace(0, 2 * np.pi * (1.0 - 1.0 / N), N)
coefs = fft(np.interp(theta, isovals[1], isovals[0], period=2 * np.pi))
measFmodes.append(
{
"a": [np.imag(coefs[0]) / len(coefs)]
+ list(
np.imag(coefs[np.array(options["ap_iso_measurecoefs"])])
/ (np.abs(coefs[0]))
),
"b": [np.real(coefs[0]) / len(coefs)]
+ list(
np.real(coefs[np.array(options["ap_iso_measurecoefs"])])
/ (np.abs(coefs[0]))
),
}
)
pixels.append(len(isovals[0]))
maskedpixels.append(isovals[2])
if fluxunits == "intensity":
sb.append(medflux / options["ap_pixscale"] ** 2)
sbE.append(scatflux / np.sqrt(len(isovals[0])))
cogdirect.append(isotot)
else:
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[0])) * medflux * np.log(10)))
if medflux > 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
if fluxunits == "intensity":
cog, cogE = Fmode_fluxdens_to_fluxsum_errorprop(
R[:end_prof] * options["ap_pixscale"],
np.array(sb),
np.array(sbE),
parameters[:end_prof],
N=100,
symmetric_error=True,
)
if cog is None:
cog = -99.999 * np.ones(len(R))
cogE = -99.999 * np.ones(len(R))
else:
cog[np.logical_not(np.isfinite(cog))] = -99.999
cogE[cog < 0] = -99.999
else:
cog, cogE = SBprof_to_COG_errorprop(
R[:end_prof] * options["ap_pixscale"],
np.array(sb),
np.array(sbE),
parameters[:end_prof],
N=100,
symmetric_error=True,
)
if cog is None:
cog = 99.999 * np.ones(len(R))
cogE = 99.999 * np.ones(len(R))
else:
cog[np.logical_not(np.isfinite(cog))] = 99.999
cogE[cog > 99] = 99.999
# For each radius evaluation, write the profile parameters
if fluxunits == "intensity":
params = [
"R",
"I",
"I_e",
"totflux",
"totflux_e",
"ellip",
"ellip_e",
"pa",
"pa_e",
"pixels",
"maskedpixels",
"totflux_direct",
]
SBprof_units = {
"R": "arcsec",
"I": "flux*arcsec^-2",
"I_e": "flux*arcsec^-2",
"totflux": "flux",
"totflux_e": "flux",
"ellip": "unitless",
"ellip_e": "unitless",
"pa": "deg",
"pa_e": "deg",
"pixels": "count",
"maskedpixels": "count",
"totflux_direct": "flux",
}
else:
params = [
"R",
"SB",
"SB_e",
"totmag",
"totmag_e",
"ellip",
"ellip_e",
"pa",
"pa_e",
"pixels",
"maskedpixels",
"totmag_direct",
]
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",
"pixels": "count",
"maskedpixels": "count",
"totmag_direct": "mag",
}
SBprof_data = dict((h, None) for h in params)
SBprof_data["R"] = list(R[:end_prof] * options["ap_pixscale"])
SBprof_data["I" if fluxunits == "intensity" else "SB"] = list(sb)
SBprof_data["I_e" if fluxunits == "intensity" else "SB_e"] = list(sbE)
SBprof_data["totflux" if fluxunits == "intensity" else "totmag"] = list(cog)
SBprof_data["totflux_e" if fluxunits == "intensity" else "totmag_e"] = list(cogE)
SBprof_data["ellip"] = list(parameters[p]["ellip"] for p in range(end_prof))
SBprof_data["ellip_e"] = list(parameters[p]["ellip err"] for p in range(end_prof))
SBprof_data["pa"] = list(parameters[p]["pa"] * 180 / np.pi for p in range(end_prof))
SBprof_data["pa_e"] = list(
parameters[p]["pa err"] * 180 / np.pi for p in range(end_prof)
)
SBprof_data["pixels"] = list(pixels)
SBprof_data["maskedpixels"] = list(maskedpixels)
SBprof_data[
"totflux_direct" if fluxunits == "intensity" else "totmag_direct"
] = list(cogdirect)
if "ap_iso_measurecoefs" in options and not options["ap_iso_measurecoefs"] is None:
whichcoefs = [0] + list(options["ap_iso_measurecoefs"])
for i in list(range(len(whichcoefs))):
aa, bb = "a%i" % whichcoefs[i], "b%i" % whichcoefs[i]
params += [aa, bb]
SBprof_units.update(
{
aa: "flux" if whichcoefs[i] == 0 else "a%i/F0" % whichcoefs[i],
bb: "flux" if whichcoefs[i] == 0 else "b%i/F0" % whichcoefs[i],
}
)
SBprof_data[aa] = list(F["a"][i] for F in measFmodes)
SBprof_data[bb] = list(F["b"][i] for F in measFmodes)
if any(not p["m"] is None for p in parameters):
for m in range(len(parameters[0]["m"])):
AA, PP = "A%i" % parameters[0]["m"][m], "Phi%i" % parameters[0]["m"][m]
params += [AA, PP]
SBprof_units.update({AA: "unitless", PP: "deg"})
SBprof_data[AA] = list(p["Am"][m] for p in parameters[:end_prof])
SBprof_data[PP] = list(p["Phim"][m] for p in parameters[:end_prof])
if any(not p["C"] is None for p in parameters):
params += ["C"]
SBprof_units["C"] = "unitless"
SBprof_data["C"] = list(p["C"] for p in parameters[:end_prof])
if "ap_doplot" in options and options["ap_doplot"]:
Plot_Phase_Profile(
np.array(SBprof_data["R"]), parameters[:end_prof], results, options
)
if fluxunits == "intensity":
Plot_I_Profile(
dat,
np.array(SBprof_data["R"]),
np.array(SBprof_data["I"]),
np.array(SBprof_data["I_e"]),
parameters[:end_prof],
results,
options,
)
else:
Plot_SB_Profile(
dat,
np.array(SBprof_data["R"]),
np.array(SBprof_data["SB"]),
np.array(SBprof_data["SB_e"]),
parameters[:end_prof],
results,
options,
)
return {"prof header": params, "prof units": SBprof_units, "prof data": SBprof_data}
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 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 Axial_Profiles(IMG, results, options):
"""Extracts SB profiles perpendicular to the major (or minor) axis.
For some applications, such as examining edge on galaxies, it is
beneficial to observe the vertical structure in a disk. This can
be achieved with the Axial Profiles method. It will construct a
series of lines, each one with a starting point on the major axis
of the galaxy and radiating perpendicular from it. The location of
these lines are, by default, geometrically spaced so that they can
gather more light in the fainter outskirts. Along a given line,
and SB profile is extracted, with the distance between points on
the profile also increasing geometrically, allowing more light
collection. The outputted profile is formatted similar to a
regular SB profile, except that there are many SB profiles with
each one having a corresponding distance from the center and
quadrant of the image. A diagnostic image is generated to aid in
identifying where each profile is extracted.
Parameters
-----------------
ap_axialprof_pa : float, default 0
user set position angle at which to align the axial profiles
relative to the global position angle+90, in degrees. A common
choice would be "90" which would then sample along the
semi-major axis instead of the semi-minor axis.
ap_zeropoint : float, default 22.5
Photometric zero point
ap_samplestyle : string, default 'geometric'
indicate if isophote sampling radii should grow linearly or
geometrically. Can also do geometric sampling at the center and
linear sampling once geometric step size equals linear. Options
are: 'linear', 'geometric', and 'geometric-linear'.
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.
Notes
----------
:References:
- 'mask' (optional)
- 'background'
- 'psf fwhm'
- 'center'
- 'prof data' (optional)
- 'init pa'
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
No results provided as this method writes its own profile
.. code-block:: python
{}
"""
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 0.0
)
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 1.0
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 1.0
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.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"]:
Plot_Axial_Profiles(dat, R, sb, sbE, pa, results, options)
return IMG, {}
def Radial_Profiles(IMG, results, options):
"""Extracts SB profiles along lines radiating from the galaxy center.
For some applications, such as examining edge on galaxies, it is
beneficial to observe the structure in a disk as well as (or
instead of) the average isophotal profile. This can done with
radial profiles which sample along lines radiating form the galaxy
center. These lines are by default placed on the 4 semi-axes of
the galaxy. The lines are actually wedges with increasing width as
a function of radius. This helps keep roughly constant S/N in the
bins, allowing the profile to extend far into the outskirts of a
galaxy. The user may increase the number of wedgest to extract
more stucture from the galaxy, however at some point the wedges
will begin to cross each other. AutoProf will warn the user when
this happens, but will carry on anyway.
Parameters
-----------------
ap_radialprofiles_nwedges : int, default 4
number of radial wedges to sample. Recommended choosing a power
of 2.
ap_radialprofiles_width : float, default 15
User set width of radial sampling wedges in degrees.
ap_radialprofiles_pa : float, default 0
user set position angle at which to measure radial wedges
relative to the global position angle, in degrees.
ap_radialprofiles_expwidth : bool, default False
Tell AutoProf to use exponentially increasing widths for radial
samples. In this case *ap_radialprofiles_width* corresponds to
the final width of the radial sampling.
ap_radialprofiles_variable_pa : bool, default False
Tell AutoProf to rotate radial sampling wedges with the position
angle profile of the galaxy.
Notes
----------
:References:
- 'prof header' (optional)
- 'prof units' (optional)
- 'prof data' (optional)
- 'mask' (optional)
- 'background'
- 'center'
- 'init pa' (optional)
Returns
-------
IMG : ndarray
Unaltered galaxy image
results : dict
No results provided as this method writes its own profile
.. code-block:: python
{'prof header': , # Previously extracted SB profile, with extra columns appended for radial profiles (list)
'prof units': , # Previously extracted SB profile, with extra units appended for radial profiles (dict)
'prof data': # Previously extracted SB profile, with extra columns appended for radial profiles (dict)
}
"""
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 - 1.0 / nwedges), nwedges)
zeropoint = options["ap_zeropoint"] if "ap_zeropoint" in options else 22.5
if "prof data" in results:
R = np.array(results["prof data"]["R"]) / options["ap_pixscale"]
else:
startR = (options["ap_sampleinitR"] if "ap_sampleinitR" in options else
min(1.0, results["psf fwhm"] / 2))
endR = (options["ap_sampleendR"] if "ap_sampleendR" in options else
min(max(IMG.shape) / np.sqrt(2), 3 * results["init R"]))
R = np.logspace(
np.log10(startR),
np.log10(endR),
int(
np.log10(endR / startR) /
np.log10(1 + (options["ap_samplegeometricscale"] if
"ap_samplegeometricscale" in options else 0.1))),
)
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 15.0)
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)
avgmedflux = np.inf
for i in range(len(R)):
isobandwidth = R[i] * (options["ap_isoband_width"]
if "ap_isoband_width" in options else 0.025)
if (avgmedflux > (results["background noise"] *
(options["ap_isoband_start"] if "ap_isoband_start"
in options else 2)) or isobandwidth < 0.5):
isovals = list(
_iso_extract(
dat,
R[i],
{
"ellip": 0,
"pa": 0
},
results["center"],
more=True,
minN=int(5 * 2 * np.pi / wedgewidth[i]),
mask=mask,
))
else:
isovals = list(
_iso_between(
dat,
R[i] - isobandwidth,
R[i] + isobandwidth,
{
"ellip": 0,
"pa": 0
},
results["center"],
more=True,
mask=mask,
))
isovals[1] -= pa[i]
avgmedflux = []
for sa_i in range(len(wedgeangles)):
aselect = np.abs(Angle_TwoAngles_cos(
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",
)
avgmedflux.append(medflux)
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)
avgmedflux = np.mean(avgmedflux)
if "prof header" in results:
newprofheader = results["prof header"]
newprofunits = results["prof units"]
newprofdata = results["prof data"]
else:
newprofheader = ["R"]
newprofunits = {"R": "arcsec"}
newprofdata = {"R": R * options["ap_pixscale"]}
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"
newprofdata[p1] = sb[sa_i]
newprofdata[p2] = sbE[sa_i]
if "ap_doplot" in options and options["ap_doplot"]:
Plot_Radial_Profiles(dat, R, sb, sbE, pa, nwedges, wedgeangles,
wedgewidth, results, options)
return IMG, {
"prof header": newprofheader,
"prof units": newprofunits,
"prof data": newprofdata,
}