def extract_class():
"""
Set up an Extract class and load
a particular shotid
"""
e = Extract()
e.load_shot("20190201012", survey="hdr2.1")
return e
def fit_ellipse_for_source(
friendid=None,
detectid=None,
coords=None,
shotid=None,
subcont=True,
convolve_image=False,
pixscale=pixscale,
imsize=imsize,
wave_range=None,
):
if detectid is not None:
global deth5
detectid_obj = detectid
if detectid_obj <= 2190000000:
det_info = deth5.root.Detections.read_where("detectid == detectid_obj")[0]
linewidth = det_info["linewidth"]
wave_obj = det_info["wave"]
redshift = wave_obj / (1216) - 1
else:
det_info = conth5.root.Detections.read_where("detectid == detectid_obj")[0]
redshift = 0
wave_obj = 4500
coords_obj = SkyCoord(det_info["ra"], det_info["dec"], unit="deg")
shotid_obj = det_info["shotid"]
fwhm = surveyh5.root.Survey.read_where("shotid == shotid_obj")["fwhm_virus"][0]
amp = det_info["multiframe"]
if wave_range is not None:
wave_range_obj = wave_range
else:
if detectid_obj <= 2190000000:
wave_range_obj = [wave_obj - 2 * linewidth, wave_obj + 2 * linewidth]
else:
wave_range_obj = [4100, 4200]
if coords is not None:
coords_obj = coords
if shotid is not None:
shotid_obj = shotid
fwhm = surveyh5.root.Survey.read_where("shotid == shotid_obj")[
"fwhm_virus"
][0]
try:
hdu = make_narrowband_image(
coords=coords_obj,
shotid=shotid_obj,
wave_range=wave_range_obj,
imsize=imsize * u.arcsec,
pixscale=pixscale * u.arcsec,
subcont=subcont,
convolve_image=convolve_image,
include_error=True,
)
except:
print("Could not make narrowband image for {}".format(detectid))
return np.nan, np.nan
elif friendid is not None:
global friend_cat
sel = friend_cat["friendid"] == friendid
group = friend_cat[sel]
coords_obj = SkyCoord(ra=group["icx"][0] * u.deg, dec=group["icy"][0] * u.deg)
wave_obj = group["icz"][0]
redshift = wave_obj / (1216) - 1
linewidth = group["linewidth"][0]
shotid_obj = group["shotid"][0]
fwhm = group["fwhm"][0]
amp = group["multiframe"][0]
if wave_range is not None:
wave_range_obj = wave_range
else:
wave_range_obj = [wave_obj - 2 * linewidth, wave_obj + 2 * linewidth]
if shotid is not None:
shotid_obj = shotid
fwhm = surveyh5.root.Survey.read_where("shotid == shotid_obj")[
"fwhm_virus"
][0]
try:
hdu = make_narrowband_image(
coords=coords_obj,
shotid=shotid_obj,
wave_range=wave_range_obj,
imsize=imsize * u.arcsec,
pixscale=pixscale * u.arcsec,
subcont=subcont,
convolve_image=convolve_image,
include_error=True,
)
except:
print("Could not make narrowband image for {}".format(friendid))
return None
elif coords is not None:
coords_obj = coords
if wave_range is not None:
wave_range_obj = wave_range
else:
print(
"You need to supply wave_range=[wave_start, wave_end] for collapsed image"
)
if shotid is not None:
shotid_obj = shotid
fwhm = surveyh5.root.Survey.read_where("shotid == shotid_obj")[
"fwhm_virus"
][0]
else:
print("Enter the shotid to use (eg. 20200123003)")
hdu = make_narrowband_image(
coords=coords_obj,
shotid=shotid_obj,
wave_range=wave_range_obj,
imsize=imsize * u.arcsec,
pixscale=pixscale * u.arcsec,
subcont=subcont,
convolve_image=convolve_image,
include_error=True,
)
else:
print("You must provide a detectid, friendid or coords/wave_range/shotid")
return np.nan, np.nan
w = wcs.WCS(hdu[0].header)
if friendid is not None:
sel_friend_group = friend_cat["friendid"] == friendid
group = friend_cat[sel_friend_group]
eps = 1 - group["a2"][0] / group["b2"][0]
pa = group["pa"][0] * np.pi / 180.0 - 90
sma = group["a"][0] * 3600 / pixscale
coords = SkyCoord(ra=group["icx"][0] * u.deg, dec=group["icy"][0] * u.deg)
wave_obj = group["icz"][0]
redshift = wave_obj / (1216) - 1
linewidth = np.nanmedian(group["linewidth"])
shotid_obj = group["shotid"][0]
fwhm = group["fwhm"][0]
geometry = EllipseGeometry(
x0=w.wcs.crpix[0], y0=w.wcs.crpix[0], sma=sma, eps=eps, pa=pa
)
else:
geometry = EllipseGeometry(
x0=w.wcs.crpix[0], y0=w.wcs.crpix[0], sma=20, eps=0.2, pa=20.0
)
geometry = EllipseGeometry(
x0=w.wcs.crpix[0], y0=w.wcs.crpix[0], sma=20, eps=0.2, pa=20.0
)
# geometry.find_center(hdu.data)
# aper = EllipticalAperture((geometry.x0, geometry.y0), geometry.sma,
# geometry.sma*(1 - geometry.eps), geometry.pa)
# plt.imshow(hdu.data, origin='lower')
# aper.plot(color='white')
ellipse = Ellipse(hdu[0].data)
isolist = ellipse.fit_image()
iso_tab = isolist.to_table()
if len(iso_tab) == 0:
geometry.find_center(hdu[0].data, verbose=False, threshold=0.5)
ellipse = Ellipse(hdu[0].data, geometry)
isolist = ellipse.fit_image()
iso_tab = isolist.to_table()
if len(iso_tab) == 0:
return np.nan, np.nan, np.nan
try:
# compute iso's manually in steps of 3 pixels
ellipse = Ellipse(hdu[0].data) # reset ellipse
iso_list = []
for sma in np.arange(1, 60, 2):
iso = ellipse.fit_isophote(sma)
if np.isnan(iso.intens):
# print('break at {}'.format(sma))
break
else:
iso_list.append(iso)
isolist = IsophoteList(iso_list)
iso_tab = isolist.to_table()
except:
return np.nan, np.nan, np.nan
try:
model_image = build_ellipse_model(hdu[0].data.shape, isolist)
residual = hdu[0].data - model_image
except:
return np.nan, np.nan, np.nan
sma = iso_tab["sma"] * pixscale
const_arcsec_to_kpc = cosmo.kpc_proper_per_arcmin(redshift).value / 60.0
def arcsec_to_kpc(sma):
dist = const_arcsec_to_kpc * sma
return dist
def kpc_to_arcsec(dist):
sma = dist / const_arcsec_to_kpc
return sma
dist_kpc = (
sma * u.arcsec.to(u.arcmin) * u.arcmin * cosmo.kpc_proper_per_arcmin(redshift)
)
dist_arcsec = kpc_to_arcsec(dist_kpc)
# print(shotid_obj, fwhm)
# s_exp1d = models.Exponential1D(amplitude=0.2, tau=-50)
alpha = 3.5
s_moffat = models.Moffat1D(
amplitude=1,
gamma=(0.5 * fwhm) / np.sqrt(2 ** (1.0 / alpha) - 1.0),
x_0=0.0,
alpha=alpha,
fixed={"amplitude": False, "x_0": True, "gamma": True, "alpha": True},
)
s_init = models.Exponential1D(amplitude=0.2, tau=-50)
fit = fitting.LevMarLSQFitter()
s_r = fit(s_init, dist_kpc, iso_tab["intens"])
# Fitting can be done using the uncertainties as weights.
# To get the standard weighting of 1/unc^2 for the case of
# Gaussian errors, the weights to pass to the fitting are 1/unc.
# fitted_line = fit(line_init, x, y, weights=1.0/yunc)
# s_r = fit(s_init, dist_kpc, iso_tab['intens'])#, weights=iso_tab['intens']/iso_tab['intens_err'] )
print(s_r)
try:
r_n = -1.0 * s_r.tau # _0 #* const_arcsec_to_kpc
except:
r_n = np.nan # r_n = -1. * s_r.tau_0
try:
sel_iso = np.where(dist_kpc >= 2 * r_n)[0][0]
except:
sel_iso = -1
aper = EllipticalAperture(
(isolist.x0[sel_iso], isolist.y0[sel_iso]),
isolist.sma[sel_iso],
isolist.sma[sel_iso] * (1 - isolist.eps[sel_iso]),
isolist.pa[sel_iso],
)
phottable = aperture_photometry(hdu[0].data, aper, error=hdu[1].data)
flux = phottable["aperture_sum"][0] * 10 ** -17 * u.erg / (u.cm ** 2 * u.s)
flux_err = phottable["aperture_sum_err"][0] * 10 ** -17 * u.erg / (u.cm ** 2 * u.s)
lum_dist = cosmo.luminosity_distance(redshift).to(u.cm)
lum = flux * 4.0 * np.pi * lum_dist ** 2
lum_err = flux_err * 4.0 * np.pi * lum_dist ** 2
if detectid:
name = detectid
elif friendid:
name = friendid
# Get Image data from Elixer
catlib = catalogs.CatalogLibrary()
try:
cutout = catlib.get_cutouts(
position=coords_obj,
side=imsize,
aperture=None,
dynamic=False,
filter=["r", "g", "f606W"],
first=True,
allow_bad_image=False,
allow_web=True,
)[0]
except:
print("Could not get imaging for " + str(name))
zscale = ZScaleInterval(contrast=0.5, krej=1.5)
vmin, vmax = zscale.get_limits(values=hdu[0].data)
fig = plt.figure(figsize=(20, 12))
fig.suptitle(
"{} ra={:3.2f}, dec={:3.2f}, wave={:5.2f}, z={:3.2f}, mf={}".format(
name, coords_obj.ra.value, coords_obj.dec.value, wave_obj, redshift, amp
),
fontsize=22,
)
ax1 = fig.add_subplot(231, projection=w)
plt.imshow(hdu[0].data, vmin=vmin, vmax=vmax)
plt.xlabel("RA")
plt.ylabel("Dec")
plt.colorbar()
plt.title("Image summed across 4*linewidth")
ax2 = fig.add_subplot(232, projection=w)
plt.imshow(model_image, vmin=vmin, vmax=vmax)
plt.xlabel("RA")
plt.ylabel("Dec")
plt.colorbar()
plt.title("model")
ax3 = fig.add_subplot(233, projection=w)
plt.imshow(residual, vmin=vmin, vmax=vmax)
plt.xlabel("RA")
plt.ylabel("Dec")
plt.colorbar()
plt.title("residuals (image-model)")
# fig = plt.figure(figsize=(10,5))
im_zscale = ZScaleInterval(contrast=0.5, krej=2.5)
im_vmin, im_vmax = im_zscale.get_limits(values=cutout["cutout"].data)
ax4 = fig.add_subplot(234, projection=cutout["cutout"].wcs)
plt.imshow(
cutout["cutout"].data,
vmin=im_vmin,
vmax=im_vmax,
origin="lower",
cmap=plt.get_cmap("gray"),
interpolation="none",
)
plt.text(
0.8,
0.9,
cutout["instrument"] + cutout["filter"],
transform=ax4.transAxes,
fontsize=20,
color="w",
)
plt.contour(hdu[0].data, transform=ax4.get_transform(w))
plt.xlabel("RA")
plt.ylabel("Dec")
aper.plot(
color="white", linestyle="dashed", linewidth=2, transform=ax4.get_transform(w)
)
ax5 = fig.add_subplot(235)
plt.errorbar(
dist_kpc.value,
iso_tab["intens"],
yerr=iso_tab["intens_err"] * iso_tab["intens"],
linestyle="none",
marker="o",
label="Lya SB profile",
)
plt.plot(dist_kpc, s_r(dist_kpc), color="r", label="Lya exp SB model", linewidth=2)
plt.xlabel("Semi-major axis (kpc)")
# plt.xlabel('Semi-major axis (arcsec)')
plt.ylabel("Flux ({})".format(10 ** -17 * (u.erg / (u.s * u.cm ** 2))))
plt.text(0.4, 0.7, "r_n={:3.2f}".format(r_n), transform=ax5.transAxes, fontsize=16)
plt.text(
0.4, 0.6, "L_lya={:3.2e}".format(lum), transform=ax5.transAxes, fontsize=16
)
secax = ax5.secondary_xaxis("top", functions=(kpc_to_arcsec, kpc_to_arcsec))
secax.set_xlabel("Semi-major axis (arcsec)")
# secax.set_xlabel('Semi-major axis (kpc)')
plt.xlim(0, 100)
# plt.plot(sma, s_r(sma), label='moffat psf')
# plt.plot(dist_kpc.value, s1(kpc_to_arcsec(dist_kpc.value)),
# linestyle='dashed', linewidth=2,
# color='green', label='PSF seeing:{:3.2f}'.format(fwhm))
# These two are the exact same
# s1 = models.Moffat1D()
# s1.amplitude = iso_tab['intens'][0]
# alpha=3.5
# s1.gamma = 0.5*(fwhm*const_arcsec_to_kpc)/ np.sqrt(2 ** (1.0 / alpha) - 1.0)
# s1.alpha = alpha
# plt.plot(r_1d, moffat_1d, color='orange')
# plt.plot(dist_kpc.value, (s1(dist_kpc.value)),
# linestyle='dashed', linewidth=2,
# color='blue', label='PSF seeing:{:3.2f}'.format(fwhm))
E = Extract()
E.load_shot(shotid_obj)
moffat_psf = E.moffat_psf(seeing=fwhm, boxsize=imsize, scale=pixscale)
moffat_shape = np.shape(moffat_psf)
xcen = int(moffat_shape[1] / 2)
ycen = int(moffat_shape[2] / 2)
moffat_1d = (
moffat_psf[0, xcen:-1, ycen] / moffat_psf[0, xcen, ycen] * iso_tab["intens"][0]
)
r_1d = moffat_psf[1, xcen:-1, ycen]
E.close()
plt.plot(
arcsec_to_kpc(pixscale * np.arange(80)),
iso_tab["intens"][0] * (moffat_psf[0, 80:-1, 80] / moffat_psf[0, 80, 80]),
linestyle="dashed",
color="green",
label="PSF seeing:{:3.2f}".format(fwhm),
)
plt.legend()
if friendid is not None:
ax6 = fig.add_subplot(236, projection=cutout["cutout"].wcs)
plot_friends(friendid, friend_cat, cutout, ax=ax6, label=False)
plt.savefig("fit2d_{}.png".format(name))
# filename = 'param_{}.txt'.format(name)
# np.savetxt(filename, (r_n.value, lum.value))
return r_n, lum, lum_err
def make_data_cube(
detectid=None,
coords=None,
shotid=None,
pixscale=0.25 * u.arcsec,
imsize=30.0 * u.arcsec,
wave_range=[3470, 5540],
dwave=2.0,
dcont=50.0,
convolve_image=True,
ffsky=True,
subcont=False,
):
"""
Function to make a datacube from either a detectid or from a
coordinate/shotid combination.
Paramaters
----------
detectid: int
detectid from the continuum or lines catalog. Default is
None. Provide a coords/shotid combo if this isn't given
coords: SkyCoords object
coordinates to define the centre of the data cube
pixscale: astropy angle quantity
plate scale
imsize: astropy angle quantity
spatial length of cube (equal dims is only option)
wave_range: list
start and stop value for the wavelength range in Angstrom
dwave
step in wavelength range in Angstrom
convolve_image: bool
option to convolve image with shotid seeing
ffsky: bool
option to use full frame calibrated fibers. Default is
True.
subcont: bool
option to subtract continuum. Default is False. This
will measure the continuum 50AA below and above the
input wave_range
dcont
width in angstrom to measure the continuum. Default is to
measure 50 AA wide regions on either side of the line
Returns
-------
hdu: PrimaryHDU object
the data cube 3D array and associated 3d header
Units are '10^-17 erg cm-2 s-1 per spaxel'
Examples
--------
Can either pass in a detectid:
>>> detectid_obj=2101602788
>>> hdu = make_data_cube( detectid=detectid_obj)
>>> hdu.writeto( str(detectid_obj) + '.fits', overwrite=True)
or can put in an SkyCoord object:
>>> star_coords = SkyCoord(9.625181, -0.043587, unit='deg')
>>> hdu = make_data_cube( coords=star_coords[0], shotid=20171016108, dwave=2.0)
>>> hdu.writeto( 'star.fits', overwrite=True)
"""
global config, detecth5, surveyh5
if detectid is not None:
detectid_obj = detectid
det_info = detecth5.root.Detections.read_where(
'detectid == detectid_obj')[0]
shotid = det_info["shotid"]
coords = SkyCoord(det_info["ra"], det_info["dec"], unit="deg")
if coords is None or shotid is None:
print("Provide a detectid or both a coords and shotid")
E = Extract()
E.load_shot(shotid, fibers=False)
# get spatial dims:
ndim = int(imsize / pixscale)
center = int(ndim / 2)
# get wave dims:
nwave = int((wave_range[1] - wave_range[0]) / dwave + 1)
w = wcs.WCS(naxis=3)
w.wcs.crval = [coords.ra.deg, coords.dec.deg, wave_range[0]]
w.wcs.crpix = [center, center, 1]
w.wcs.ctype = ["RA---TAN", "DEC--TAN", "WAVE"]
w.wcs.cdelt = [-pixscale.to(u.deg).value, pixscale.to(u.deg).value, dwave]
rad = imsize.to(u.arcsec).value
info_result = E.get_fiberinfo_for_coord(coords, radius=rad, ffsky=False)
ifux, ifuy, xc, yc, ra, dec, data, error, mask = info_result
# get ifu center:
ifux_cen, ifuy_cen = E.convert_radec_to_ifux_ifuy(ifux, ifuy, ra, dec,
coords.ra.deg,
coords.dec.deg)
# get FWHM and PA
surveyh5 = tb.open_file(config.surveyh5, "r")
shotid_obj = shotid
pa = surveyh5.root.Survey.read_where("shotid == shotid_obj")["pa"][0]
if convolve_image:
fwhm = surveyh5.root.Survey.read_where(
"shotid == shotid_obj")["fwhm_virus"][0]
else:
fwhm = 1.8 # just a dummy variable as convolve_image=False
surveyh5.close()
# add in rotation
sys_rot = 1.55
rot = 360. - (90. + pa + sys_rot)
w.wcs.crota = [0, rot, 0]
# rrot = np.deg2rad(rot)
# w.wcs.pc = [[np.cos(rrot),
# np.sin(rrot),0],
# [-1.0*np.sin(rrot),
# np.cos(rrot),0], [0,0,0]]
im_cube = np.zeros((nwave, ndim, ndim))
wave_i = wave_range[0]
i = 0
while wave_i <= wave_range[1]:
try:
im_src = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
scale=pixscale.to(u.arcsec).value,
wrange=[wave_i, wave_i + dwave],
nchunks=1,
seeing_fac=fwhm,
convolve_image=convolve_image,
boxsize=imsize.to(u.arcsec).value,
)
im_slice = im_src[0]
if subcont:
zarray_blue = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
nchunks=2,
wrange=[wave_i - dcont, wave_i],
convolve_image=convolve_image,
)
zarray_red = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
nchunks=2,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
wrange=[wave_i + dwave, wave_i + dwave + dcont],
convolve_image=convolve_image,
)
im_cont = (zarray_blue[0] + zarray_red[0]) / (2 * dcont)
im_slice = im_src[0] - dwave * im_cont
im_cube[i, :, :] = im_slice
except Exception:
im_cube[i, :, :] = np.zeros((ndim, ndim))
wave_i += dwave
i += 1
hdu = fits.PrimaryHDU(im_cube, header=w.to_header())
E.close()
return hdu
def make_narrowband_image(
detectid=None,
coords=None,
shotid=None,
pixscale=0.25 * u.arcsec,
imsize=30.0 * u.arcsec,
wave_range=None,
convolve_image=True,
ffsky=True,
subcont=False,
dcont=50.,
include_error=False,
):
"""
Function to make narrowband image from either a detectid or from a
coordinate/shotid combination.
Paramaters
----------
detectid: int
detectid from the continuum or lines catalog. Default is
None. Provide a coords/shotid combo if this isn't given
coords: SkyCoords object
coordinates to define the centre of the data cube
pixscale: astropy angle quantity
plate scale
imsize: astropy angle quantity
image size
wave_range: list or None
start and stop value for the wavelength range in Angstrom.
If not given, the detectid linewidth is used
convolve_image: bool
option to convolve image with shotid seeing
ffsky: bool
option to use full frame calibrated fibers. Default is
True.
subcont: bool
option to subtract continuum. Default is False. This
will measure the continuum 50AA below and above the
input wave_range
dcont
width in angstrom to measure the continuum. Default is to
measure 50 AA wide regions on either side of the line
include_error bool
option to include error array
Returns
-------
hdu: PrimaryHDU object
the 2D summed data array and associated 2d header
Units are '10^-17 erg cm-2 s-1'
If include_error=True will include addiional hdu
Examples
--------
For a specific detectid:
>>> hdu = make_narrowband_image(detectid=2101046271)
For a SkyCoords object. You must provide shotid and
wavelength range
>>> coords = SkyCoord(188.79312, 50.855747, unit='deg')
>>> wave_obj = 4235.84 #in Angstrom
>>> hdu = make_narrowband_image(coords=coords,
shotid=20190524021,
wave_range=[wave_obj-10, wave_obj+10])
"""
global config, detecth5, surveyh5
if detectid is not None:
detectid_obj = detectid
det_info = detecth5.root.Detections.read_where(
'detectid == detectid_obj')[0]
shotid_obj = det_info["shotid"]
wave_obj = det_info["wave"]
linewidth = det_info["linewidth"]
wave_range = [wave_obj - 2.0 * linewidth, wave_obj + 2.0 * linewidth]
coords = SkyCoord(det_info["ra"], det_info["dec"], unit="deg")
elif coords is not None:
if shotid is not None:
shotid_obj = shotid
else:
print("Provide a shotid")
if wave_range is None:
print("Provide a wavelength range to collapse. \
Example wave_range=[4500,4540]")
else:
print("Provide a detectid or both a coords and shotid")
fwhm = surveyh5.root.Survey.read_where(
"shotid == shotid_obj")["fwhm_virus"][0]
pa = surveyh5.root.Survey.read_where("shotid == shotid_obj")["pa"][0]
E = Extract()
E.load_shot(shotid_obj, fibers=False)
# get spatial dims:
ndim = int(imsize / pixscale)
center = int(ndim / 2)
rad = imsize.to(u.arcsec).value # convert to arcsec value, not quantity
info_result = E.get_fiberinfo_for_coord(coords, radius=rad, ffsky=ffsky)
ifux, ifuy, xc, yc, ra, dec, data, error, mask = info_result
# get ifu center:
ifux_cen, ifuy_cen = E.convert_radec_to_ifux_ifuy(ifux, ifuy, ra, dec,
coords.ra.deg,
coords.dec.deg)
if include_error:
zarray = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
error=error,
seeing_fac=fwhm,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
wrange=wave_range,
convolve_image=convolve_image,
)
imslice = zarray[0]
imerror = zarray[1]
else:
zarray = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
wrange=wave_range,
convolve_image=convolve_image,
)
imslice = zarray[0]
if subcont:
zarray_blue = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
wrange=[wave_range[0] - dcont - 10, wave_range[0] - 10],
convolve_image=convolve_image,
)
zarray_red = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
wrange=[wave_range[1] + 10, wave_range[1] + dcont + 10],
convolve_image=convolve_image,
)
dwave = wave_range[1] - wave_range[0]
im_cont = (zarray_blue[0] + zarray_red[0]) / (2 * dcont)
imslice = zarray[0] - dwave * im_cont
w = wcs.WCS(naxis=2)
imsize = imsize.to(u.arcsec).value
w.wcs.crval = [coords.ra.deg, coords.dec.deg]
w.wcs.crpix = [center, center]
w.wcs.ctype = ["RA---TAN", "DEC--TAN"]
w.wcs.cdelt = [-pixscale.to(u.deg).value, pixscale.to(u.deg).value]
# get rotation:
sys_rot = 1.55
rot = 360. - (90. + pa + sys_rot)
rrot = np.deg2rad(rot)
# w.wcs.crota = [ 0, rot]
w.wcs.pc = [[np.cos(rrot), np.sin(rrot)],
[-1.0 * np.sin(rrot), np.cos(rrot)]]
hdu = fits.PrimaryHDU(imslice, header=w.to_header())
E.close()
if include_error:
hdu_error = fits.ImageHDU(imerror, header=w.to_header())
hdu_x = fits.ImageHDU(zarray[2], header=w.to_header())
hdu_y = fits.ImageHDU(zarray[3], header=w.to_header())
return fits.HDUList([hdu, hdu_error, hdu_x, hdu_y])
else:
return hdu
def get_source_spectra_mp(source_dict, shotid, manager, args):
E = Extract()
FibIndex = FiberIndex(args.survey)
if args.survey == "hdr1":
source_num_switch = 20
else:
source_num_switch = 0
if len(args.matched_sources[shotid]) > 0:
args.log.info("Working on shot: %s" % shotid)
if args.survey == "hdr1":
fwhm = args.survey_class.fwhm_moffat[args.survey_class.shotid ==
shotid][0]
else:
fwhm = args.survey_class.fwhm_virus[args.survey_class.shotid ==
shotid][0]
moffat = E.moffat_psf(fwhm, 10.5, 0.25)
if len(args.matched_sources[shotid]) > source_num_switch:
E.load_shot(shotid, fibers=True, survey=args.survey)
else:
E.load_shot(shotid, fibers=False, survey=args.survey)
for ind in args.matched_sources[shotid]:
try:
info_result = E.get_fiberinfo_for_coord(
args.coords[ind],
radius=args.rad,
ffsky=args.ffsky,
return_fiber_info=True,
)
except TypeError:
info_result = E.get_fiberinfo_for_coord(
args.coords,
radius=args.rad,
ffsky=args.ffsky,
return_fiber_info=True,
)
if info_result is not None:
if np.size(args.ID) > 1:
args.log.info("Extracting %s" % args.ID[ind])
else:
args.log.info("Extracting %s" % args.ID)
ifux, ifuy, xc, yc, ra, dec, data, error, mask, fiberid, \
multiframe = info_result
weights = E.build_weights(xc, yc, ifux, ifuy, moffat)
# added by EMC 20210609
norm = np.sum(weights, axis=0)
weights = weights / norm[np.newaxis, :]
result = E.get_spectrum(data,
error,
mask,
weights,
remove_low_weights=False)
spectrum_aper, spectrum_aper_error = [res for res in result]
# apply aperture correction
spectrum_aper /= norm
spectrum_aper_error /= norm
weights *= norm[np.newaxis, :]
#add in the total weight of each fiber (as the sum of its weight per wavebin)
if args.fiberweights:
try:
fiber_weights = np.array([
x for x in zip(ra, dec,
np.sum(weights * mask, axis=1))
])
except:
fiber_weights = []
else:
fiber_weights = []
# get fiber info no matter what so we can flag
try:
fiber_info = np.array([
x for x in zip(fiberid, multiframe, ra, dec,
np.sum(weights * mask, axis=1))
])
except:
args.log.warning(
'Could not get fiber info, no flagging created')
fiber_info = []
if len(fiber_info) > 0:
try:
flags = FibIndex.get_fiber_flags(
coord=args.coords[ind], shotid=shotid)
except:
flags = FibIndex.get_fiber_flags(coord=args.coords,
shotid=shotid)
else:
flags = None
if np.size(args.ID) > 1:
if args.ID[ind] in source_dict:
source_dict[args.ID[ind]][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
else:
source_dict[args.ID[ind]] = manager.dict()
source_dict[args.ID[ind]][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
else:
if args.ID in source_dict:
source_dict[args.ID][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
else:
source_dict[args.ID] = manager.dict()
source_dict[args.ID][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
E.shoth5.close()
FibIndex.close()
return source_dict
def get_flim_sig_erin(detectid=None, coord=None, wave=None, datevobs=None, shotid=None):
"""
Script to grab flim_1sigma and sn_sig on demand from calibrated fiber extractions
Parameters
----------
detectid int
detectid for source
coord
astropy SkyCoord object
wave
central wavelength
shotid
observation ID
Returns
-------
flim_1sigma
the 1 sigma sensitivity calculated over 7 pixels of the PSF-weighted extracted spectra
"""
detectid_obj = detectid
det_info = source_table[source_table['detectid'] == detectid][0]
shotid = det_info['shotid']
wave = det_info['wave']
coord = SkyCoord(ra=det_info['ra'], dec=det_info['dec'], unit='deg')
fwhm = det_info['fwhm']
if datevobs is None:
datevobs = '{}v{}'.format( str(shotid)[0:8], str(shotid)[8:])
if shotid is None:
shotid_obj = int(datevobs[0:8] + datevobs[9:])
else:
shotid_obj = shotid
try:
E = Extract()
E.load_shot(datevobs, fibers=False)
info_result = E.get_fiberinfo_for_coord(coord, radius=3.5, fiber_lower_limit=2 )
ifux, ifuy, xc, yc, ra, dec, data, error, mask = info_result
#print(len(ifux))
moffat = E.moffat_psf(fwhm, 10.5, 0.25)
I = None
fac = None
weights, I, fac = E.build_weights(xc, yc, ifux, ifuy, moffat,
I=I, fac=fac, return_I_fac = True)
norm = np.sum(weights, axis=0)
weights = weights/norm
result = E.get_spectrum(data, error, mask, weights,
remove_low_weights=False)
spec, spec_err = [res for res in result]
w_index = np.where(E.wave >= wave)[0][0]
nfib = np.shape(weights)[0]
flim_1sigma = 2 * np.sqrt( np.nansum( (spec_err[w_index-3:w_index+4])**2))
sn_sig = 2 * np.sum( spec[w_index-3:w_index+4]) / flim_1sigma
npix = np.sum(np.isfinite(spec[w_index-3:w_index+4]))
apcor = np.sum( norm[w_index-3:w_index+4])/len( norm[w_index-3:w_index+4])
E.close()
# XXX divide by apcor ....
return flim_1sigma/apcor, apcor
except:
return 999
select.ygrid.grid_line_color = None
range_tool = RangeTool(x_range=plot.x_range)
range_tool.overlay.fill_color = "navy"
range_tool.overlay.fill_alpha = 0.2
select.add_tools(range_tool)
select.toolbar.active_multi = range_tool
imageplot.image(image=[image[0]], x=image[1].min(), y=image[2].min(),
dw=image[1].max()-image[1].min(),
dh=image[2].max()-image[2].min())
imageplot.scatter(sx, sy, marker='circle_x', size=15,
line_color="orange", fill_color="red", alpha=0.75)
output_file(name+".html", title=name)
save(row(column(plot, select), imageplot))
# Initiate class
E = Extract()
# Load a given shot
E.load_shot(sys.argv[1])
RA = E.fibers.hdfile.root.Shot.cols.ra[:][0]
Dec = E.fibers.hdfile.root.Shot.cols.dec[:][0]
# Get SDSS spectra in the field
# pip install --user astroquery
from astroquery.sdss import SDSS
from astropy import coordinates as coords
pos = coords.SkyCoord(RA * u.deg, Dec * u.deg, frame='fk5')
xid = SDSS.query_region(pos, radius=11*u.arcmin, spectro=True,
photoobj_fields=['ra', 'dec', 'u', 'g', 'r', 'i', 'z'],
specobj_fields=['plate', 'mjd', 'fiberID', 'z',
'specobjid', 'run2d', 'instrument'])
def get_source_spectra(shotid, args):
E = Extract()
source_dict = {}
if args.survey == "hdr1":
source_num_switch = 20
else:
source_num_switch = 0
if len(args.matched_sources[shotid]) > 0:
args.log.info("Working on shot: %s" % shotid)
if args.survey == "hdr1":
fwhm = args.survey_class.fwhm_moffat[args.survey_class.shotid == shotid][0]
else:
fwhm = args.survey_class.fwhm_virus[args.survey_class.shotid == shotid][0]
moffat = E.moffat_psf(fwhm, 10.5, 0.25)
if len(args.matched_sources[shotid]) > source_num_switch:
E.load_shot(shotid, fibers=True, survey=args.survey)
else:
E.load_shot(shotid, fibers=False, survey=args.survey)
for ind in args.matched_sources[shotid]:
try:
info_result = E.get_fiberinfo_for_coord(
args.coords[ind],
radius=args.rad,
ffsky=args.ffsky,
return_fiber_info=True,
)
except TypeError:
info_result = E.get_fiberinfo_for_coord(
args.coords,
radius=args.rad,
ffsky=args.ffsky,
return_fiber_info=True,
)
if info_result is not None:
try:
args.log.info("Extracting %s" % args.ID[ind])
except:
args.log.info("Extracting %s" % args.ID)
ifux, ifuy, xc, yc, ra, dec, data, error, mask, fiberid, \
multiframe = info_result
weights = E.build_weights(xc, yc, ifux, ifuy, moffat)
result = E.get_spectrum(data, error, mask, weights)
spectrum_aper, spectrum_aper_error = [res for res in result]
#add in the total weight of each fiber (as the sum of its weight per wavebin)
if args.fiberweights:
try:
fiber_weights = np.array( [x for x in zip(ra, dec, np.sum(weights*mask, axis=1))])
except:
fiber_weights = []
else:
fiber_weights = []
# get fiber info no matter what so we can flag
try:
fiber_info = np.array( [
x for x in zip(fiberid,
multiframe,
ra,
dec,
np.sum(weights*mask, axis=1))])
except:
fiber_info = []
if len(fiber_info) > 0:
flags = get_flags(fiber_info)
else:
flags = None
if np.size(args.ID) > 1:
if args.ID[ind] in source_dict:
source_dict[args.ID[ind]][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
else:
source_dict[args.ID[ind]] = dict()
source_dict[args.ID[ind]][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
else:
if args.ID in source_dict:
source_dict[args.ID][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
else:
source_dict[args.ID] = dict()
source_dict[args.ID][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
E.shoth5.close()
return source_dict
from hetdex_api.extract import Extract
import argparse
import sys
from astropy.io import fits
parser = argparse.ArgumentParser()
parser.add_argument("-s", "--shot", type=str, help="Shotid.")
args = parser.parse_args(sys.argv[1:])
shot = args.shot
E = Extract()
E.load_shot(shot, survey="hdr2")
gmag_limit = 22.
radius = 50.
psf = E.model_psf(gmag_limit=gmag_limit, radius=radius)
hdr = fits.Header()
hdr["SHOT"] = shot
hdr["GMAG_LIMIT"] = gmag_limit
hdr["RADIUS"] = radius
hdu = fits.PrimaryHDU(psf[0], header=hdr)
hdu_x, hdu_y = fits.ImageHDU(psf[1]), fits.ImageHDU(psf[2])
hdul = fits.HDUList([hdu, hdu_x, hdu_y])
hdul.writeto("/data/05865/maja_n/im2d/psf_hdr2/" + shot + ".fits",
overwrite=True)
print("Wrote to /data/05865/maja_n/im2d/psf_hdr2/" + shot + ".fits")
class ShotSensitivity(object):
"""
Generate completeness estimates for a shot
on the fly, using the Extract class. This
is written to be as backward compatible as
possible with the user interface of
hdf5_sensitivity_cubes:SensitivityCubeHDF5Container
A lot of this is adapted from
`hetdex_tools/get_spec.py` `hetdex_api/extract.py`
and scripts written by Erin Mentuch Cooper.
The aperture correction stuff was taken
from 'Remedy' by Greg Zeimann:
grzeimann Remedy
Parameters
----------
datevshot : str
the name of the shot in the form
YYYYMMDDvSSS
release : str (Optional)
The name of the release e.g. hdr2.1
defaults to latest
flim_model : str
The flux limit model to convert
the noise to completeness, defaults
to the latest (which might not be
compatible with the release, see README)
rad : float
A radius in arcseconds to grab fibers
from when computing the flux limit,
default 3.5
ffsky : boolean
Full frame sky subtraction (default: False)
wavenpix : int
Number of wave pixels either side of the
pixel the source is on to add in
quadrature, or sets the size of tophat
convolution when producing data cubes as
2*wavenpix + 1 (default 3)
d25scale : float
Sets the multiplier for the galaxy masks
applied (default 3.0)
sclean_bad : bool
Replace bad data using the sclean
tool (see hetdex_api.extract:Extract)
verbose : bool
Print information about the flux limit model
to the screen
"""
def __init__(self,
datevshot,
release=None,
flim_model=None,
rad=3.5,
ffsky=False,
wavenpix=3,
d25scale=3.0,
verbose=False,
sclean_bad=True,
log_level="WARNING"):
self.conf = HDRconfig()
self.extractor = Extract()
self.shotid = int(datevshot.replace("v", ""))
self.date = datevshot[:8]
self.rad = rad
self.ffsky = ffsky
self.wavenpix = wavenpix
self.sclean_bad = sclean_bad
logger = logging.getLogger(name="ShotSensitivity")
logger.setLevel(log_level)
if verbose:
raise DeprecationWarning(
"Using verbose is deprecated, set log_level instead")
logger.setLevel("DEBUG")
logger.info("shotid: {:d}".format(self.shotid))
if not release:
self.release = self.conf.LATEST_HDR_NAME
else:
self.release = release
logger.info("Data release: {:s}".format(self.release))
self.survey = Survey(survey=self.release)
# Set up flux limit model
self.f50_from_noise, self.sinterp, interp_sigmas \
= return_flux_limit_model(flim_model,
cache_sim_interp=False,
verbose=verbose)
# Generate astrometry for this shot
survey_sel = (self.survey.shotid == self.shotid)
self.shot_pa = self.survey.pa[survey_sel][0]
self.shot_ra = self.survey.ra[survey_sel][0]
self.shot_dec = self.survey.dec[survey_sel][0]
rot = 360.0 - (self.shot_pa + 90.)
self.tp = TangentPlane(self.shot_ra, self.shot_dec, rot)
#Set up masking
logger.info("Using d25scale {:f}".format(d25scale))
self.setup_mask(d25scale)
# Set up spectral extraction
if release == "hdr1":
fwhm = self.survey.fwhm_moffat[survey_sel][0]
else:
fwhm = self.survey.fwhm_virus[survey_sel][0]
logger.info("Using Moffat PSF with FWHM {:f}".format(fwhm))
self.moffat = self.extractor.moffat_psf(fwhm, 3. * rad, 0.25)
self.extractor.load_shot(self.shotid, fibers=True, survey=self.release)
# Set up the focal plane astrometry
fplane_table = self.extractor.shoth5.root.Astrometry.fplane
# Bit of a hack to avoid changing pyhetdex
with NamedTemporaryFile(mode='w') as tpf:
for row in fplane_table.iterrows():
tpf.write(
"{:03d} {:8.5f} {:8.5f} {:03d} {:03d} {:03d} {:8.5f} {:8.5f}\n"
.format(row['ifuslot'], row['fpx'], row['fpy'],
row['specid'], row['specslot'], row['ifuid'],
row['ifurot'], row['platesc']))
tpf.seek(0)
self.fplane = FPlane(tpf.name)
def setup_mask(self, d25scale):
"""
Setup the masking, to speed up checking
if sources are in the mask later. This
is run at initialisation, so you need
only run again to change `d25scale`
Parameters
----------
d25scale : float
Sets the multiplier for the galaxy masks
applied (default 3.5)
"""
logger = logging.getLogger(name="ShotSensitivity")
# see if this is a bad shot
#print("Bad shot from ", self.conf.badshot)
badshot = loadtxt(self.conf.badshot, dtype=int)
badtpshots = loadtxt(self.conf.lowtpshots, dtype=int)
if (self.shotid in badshot) or (self.shotid in badtpshots):
logger.warn("Shot is in bad. Making mask zero everywhere")
self.badshot = True
else:
self.badshot = False
# set up bad amps
logger.info("Bad amps from {:s}".format(self.conf.badamp))
self.bad_amps = Table.read(self.conf.badamp)
sel_shot = (self.bad_amps["shotid"] == self.shotid)
self.bad_amps = self.bad_amps[sel_shot]
# set up galaxy mask
logger.info("Galaxy mask from {:s}".format(self.conf.rc3cat))
galaxy_cat = Table.read(self.conf.rc3cat, format='ascii')
gal_coords = SkyCoord(galaxy_cat['Coords'], frame='icrs')
shot_coords = SkyCoord(ra=self.shot_ra, dec=self.shot_dec, unit="deg")
sel_reg = where(shot_coords.separation(gal_coords) < 1. * u.deg)[0]
self.gal_regions = []
if len(sel_reg) > 0:
for idx in sel_reg:
self.gal_regions.append(
create_gal_ellipse(galaxy_cat,
row_index=idx,
d25scale=d25scale))
# set up meteor mask
# check if there are any meteors in the shot:
logger.info("Meteors from {:s}".format(self.conf.meteor))
self.met_tab = Table.read(self.conf.meteor, format="ascii")
self.met_tab = self.met_tab[self.shotid == self.met_tab["shotid"]]
def extract_ifu_sensitivity_cube(self,
ifuslot,
nx=31,
ny=31,
ifusize=62,
generate_sigma_array=True,
cache_sim_interp=True):
"""
Extract the sensitivity cube
from IFU `ifuslot`
Parameters
----------
ifuslot : string
the IFU slot to extract
nx, ny : int
the dimensions in pixels
of the cube (default 31,31)
ifusize : float
the length of the side of
the cube in arcseconds,
default is 62 arcseconds
generate_sigma_array: bool
this fills the 3D array
of noise, this makes it quite
slow to run, so if you want
to just use the cube for
the astrometry do not use
this option (default: True)
cache_sim_interp : bool
cache the simulation interpolator
to speed up execution (default: True)
Returns
-------
scube : hetdex_api.flux_limits.sensitivity_cube:SensitivityCube
the sensitivity cube
"""
waves = self.extractor.get_wave()
wrange = [waves[0], waves[-1]]
nz = len(waves)
pa = self.shot_pa
ifu = self.fplane.difus_ifuslot[ifuslot.replace("ifuslot_", "")]
ra_ifu, dec_ifu = self.tp.xy2raDec(ifu.y, ifu.x)
scube = create_sensitivity_cube_from_astrom(
float(ra_ifu),
float(dec_ifu),
pa,
nx,
ny,
nz,
ifusize,
wrange=wrange,
cache_sim_interp=cache_sim_interp)
if generate_sigma_array:
ix, iy = meshgrid(arange(0, nx, 1.0), arange(0, ny, 1.0))
all_ra, all_dec, junk = scube.wcs.all_pix2world(
ix.ravel(), iy.ravel(), [500.], 0)
noises, norm, mask = self.get_f50(all_ra,
all_dec,
None,
1.0,
direct_sigmas=True)
sigmas = noises.ravel(order="F").reshape(nz, ny, nx)
mask = logical_not(mask.reshape(ny, nx))
mask3d = repeat(mask[newaxis, :, :], sigmas.shape[0], axis=0)
scube.sigmas = MaskedArray(sigmas, mask=mask3d, fill_value=999.0)
return scube
def get_f50(self,
ra,
dec,
wave,
sncut,
direct_sigmas=False,
nmax=5000,
return_amp=False,
linewidth=None):
"""
Return flux at 50% for the input positions
most of this is cut and paste from
`hetdex_tools/get_spec.py` and
the old sensitivity_cube:SensitivityCube
class.
This class splits the data up into sets of
up to `nmax` to save memory
Parameters
----------
ra, dec : array
right ascension and dec in degrees
wave : array
wavelength in Angstroms. If None,
then return flux limits for
all wave bins.
sncut : float
cut in detection significance
that defines this catalogue
direct_sigmas : bool
return the noise values directly
without passing them through
the noise to 50% completeness
flux (default = False)
nmax : int
maximum number of sources to
consider at once, otherwise split
up and loop.
return_amp : bool
if True return amplifier information
for the closest fiber to each source
(default = False)
linewidth : array
optionally pass the linewidth of
the source (in AA) to activate the linewidth
dependent part of the completeness
model (default = None).
Returns
-------
f50s : array
50% completeness. If outside
of cube return 999. If None
was passed for wave this is
a 2D array of ra, dec and
all wavelengths
mask : array
Only returned if `wave=None`. This
mask is True where the ra/dec
positions passed are in good
regions of data
amp : array
Only returned in `return_amp=True`,
it's an array of amplifier information
for the closest fiber to each source
"""
if type(wave) != type(None):
wave_passed = True
else:
wave_passed = False
try:
nsrc = len(ra)
if wave_passed:
# Trim stuff very far away
gal_coords = SkyCoord(ra=ra, dec=dec, unit="deg")
shot_coords = SkyCoord(ra=self.shot_ra,
dec=self.shot_dec,
unit="deg")
sel = array(shot_coords.separation(gal_coords) < 2.0 * u.deg)
ra_sel = array(ra)[sel]
dec_sel = array(dec)[sel]
wave_sel = array(wave)[sel]
nsel = len(ra_sel)
else:
# If not passing wave always loop
# over all ra/dec in range
ra_sel = ra
dec_sel = dec
wave_sel = None
nsel = len(ra)
nsplit = int(ceil(float(nsel) / float(nmax)))
except TypeError as e:
# If the user does not pass arrays
nsplit = 1
nsrc = 1
nsel = 1
sel = True
ra_sel = array([ra])
dec_sel = array([dec])
wave_sel = array([wave])
# Array to store output actually in the shot
f50s_sel = []
mask_sel = []
amp_sel = []
norm_sel = []
wave_rect = self.extractor.get_wave()
pixsize_aa = wave_rect[1] - wave_rect[0]
# This will give 999 once the noise is scaled suitably
badval = 999 * 1e17 / pixsize_aa
# Arrays to store full output
f50s = badval * ones(nsrc)
mask = ones(nsrc)
norm = ones(nsrc)
amp = array(["notinshot"] * nsrc)
if nsel > 0:
for i in range(nsplit):
tra = ra_sel[i * nmax:(i + 1) * nmax]
tdec = dec_sel[i * nmax:(i + 1) * nmax]
if wave_passed:
twave = wave_sel[i * nmax:(i + 1) * nmax]
if not self.badshot:
tf50s, tamp, tnorm = self._get_f50_worker(
tra,
tdec,
twave,
sncut,
direct_sigmas=direct_sigmas,
linewidth=linewidth)
else:
tamp = ["bad"] * len(tra)
tf50s = [badval] * len(tra)
tnorm = [1.0] * len(tra)
else:
# if bad shot then the mask is all set to zero
tf50s, tmask, tamp, tnorm = \
self._get_f50_worker(tra, tdec, None, sncut,
direct_sigmas = direct_sigmas,
linewidth = linewidth)
mask_sel.extend(tmask)
f50s_sel.extend(tf50s)
amp_sel.extend(tamp)
norm_sel.extend(tnorm)
if return_amp:
if wave_passed:
# copy to output
f50s[sel] = f50s_sel
amp[sel] = amp_sel
norm[sel] = norm_sel
return f50s, norm, amp
else:
return array(f50s_sel), array(norm_sel), array(
mask_sel), array(amp_sel)
else:
if wave_passed:
f50s[sel] = f50s_sel
norm[sel] = norm_sel
return f50s, norm
else:
return array(f50s_sel), array(norm_sel), array(mask_sel)
def _get_f50_worker(self,
ra,
dec,
wave,
sncut,
direct_sigmas=False,
linewidth=None):
"""
Return flux at 50% for the input positions
most of this is cut and paste from
`hetdex_tools/get_spec.py` and
the old sensitivity_cube:SensitivityCube
class.
Parameters
----------
ra, dec : array
right ascension and dec in degrees
wave : array
wavelength in Angstroms. If None,
then return flux limits for
all wave bins.
sncut : float
cut in detection significance
that defines this catalogue
direct_sigmas : bool
return the noise values directly
without passing them through
the noise to 50% completeness
flux
linewidth : array
optionally pass the linewidth of
the source (in AA) to activate the linewidth
dependent part of the completeness
model (default = None).
Returns
-------
f50s : array
50% completeness. If outside
of cube return 999. If None
was passed for wave this is
a 2D array of ra, dec and
all wavelengths
norm_all : array
the aperture corrections
mask : array
Only returned if `wave=None`. This
mask is True where the ra/dec
positions passed are in good
regions of data
amp : array
Only returned in `return_amp=True`,
it's an array of amplifier information
for the closest fiber to each source
"""
logger = logging.getLogger(name="ShotSensitivity")
try:
[x for x in ra]
except TypeError:
ra = array([ra])
dec = array([dec])
wave = array([wave])
coords = SkyCoord(ra=ra, dec=dec, unit="deg")
wave_rect = self.extractor.get_wave()
pixsize_aa = wave_rect[1] - wave_rect[0]
# This will give 999 once the noise is scaled suitably
badval = 999 * 1e17 / pixsize_aa
# Size of window in wave elements
filter_len = 2 * self.wavenpix + 1
if type(wave) != type(None):
wave_passed = True
else:
wave_passed = False
convolution_filter = ones(filter_len)
mask = True * ones(len(coords), dtype=int)
noise = []
info_results = self.extractor.get_fiberinfo_for_coords(
coords,
radius=self.rad,
ffsky=self.ffsky,
return_fiber_info=True,
fiber_lower_limit=2,
verbose=False)
id_, aseps, aifux, aifuy, axc, ayc, ara, adec, adata, aerror, afmask, afiberid, \
amultiframe = info_results
I = None
fac = None
norm_all = []
amp = []
nan_fib_mask = []
for i, c in enumerate(coords):
sel = (id_ == i)
if type(wave) != type(None):
logger.debug("Running on source {:f} {:f} {:f}".format(
ra[i], dec[i], wave[i]))
else:
logger.debug("Running on position {:f} {:f}".format(
ra[i], dec[i]))
logger.debug("Found {:d} fibers".format(sum(sel)))
if sum(sel) > 0:
# fiber properties
xc = axc[sel][0]
yc = ayc[sel][0]
ifux = aifux[sel]
ifuy = aifuy[sel]
data = adata[sel]
error = aerror[sel]
fmask = afmask[sel]
fiberid = afiberid[sel]
multiframe = amultiframe[sel]
seps = aseps[sel]
# Flag the zero elements as bad
fmask[(abs(data) < 1e-30) | (abs(error) < 1e-30)] = False
iclosest = argmin(seps)
amp.append(fiberid[iclosest])
if len(self.bad_amps) > 0:
amp_flag = amp_flag_from_fiberid(fiberid[iclosest],
self.bad_amps)
else:
amp_flag = True
# XXX Could be faster - reloads the file every run
meteor_flag = meteor_flag_from_coords(c, self.shotid)
if not (amp_flag and meteor_flag):
logger.debug("The data here are bad, position is masked")
if wave_passed:
noise.append(badval)
norm_all.append(1.0)
# value doesn't matter as in amp flag
nan_fib_mask.append(True)
continue
else:
mask[i] = False
weights, I, fac = self.extractor.build_weights(
xc,
yc,
ifux,
ifuy,
self.moffat,
I=I,
fac=fac,
return_I_fac=True)
# (See Greg Zeimann's Remedy code)
# normalized in the fiber direction
norm = sum(weights, axis=0)
weights = weights / norm
result = self.extractor.get_spectrum(
data,
error,
fmask,
weights,
remove_low_weights=False,
sclean_bad=self.sclean_bad,
return_scleaned_mask=True)
spectrum_aper, spectrum_aper_error, scleaned = [
res for res in result
]
if wave_passed:
index = where(wave_rect >= wave[i])[0][0]
ilo = index - self.wavenpix
ihi = index + self.wavenpix + 1
# If lower index less than zero, truncate
if ilo < 0:
ilo = 0
if ihi < 0:
ihi = 0
# Output lots of information for very detailed debugging
if logger.getEffectiveLevel() == logging.DEBUG:
logger.debug("Table of fibers:")
logger.debug(
"# fiberid wave_index ifux ifuy weight noise"
)
for fibidx, fid in enumerate(fiberid):
for wi, (tw, tnoise) in enumerate(
zip((weights * norm)[fibidx, ilo:ihi],
error[fibidx, ilo:ihi]), ilo):
logger.debug(
"{:s} {:d} {:f} {:f} {:f} {:f}".format(
fid, wi, ifux[fibidx], ifuy[fibidx],
tw, tnoise))
# Mask source if bad values within the central 3 wavebins
nan_fib = bad_central_mask(weights * norm,
logical_not(fmask), index)
nan_fib_mask.append(nan_fib)
# Account for NaN and masked spectral bins
bad = isnan(spectrum_aper_error[ilo:ihi])
goodfrac = 1.0 - sum(bad) / len(bad)
if all(isnan(spectrum_aper_error[ilo:ihi])):
sum_sq = badval
else:
sum_sq = \
sqrt(nansum(square(spectrum_aper_error[ilo:ihi])/goodfrac))
norm_all.append(mean(norm[ilo:ihi]))
noise.append(sum_sq)
else:
logger.debug(
"Convolving with window to get flux limits versus wave"
)
# Use astropy convolution so NaNs are ignored
convolved_variance = convolve(square(spectrum_aper_error),
convolution_filter,
normalize_kernel=False)
std = sqrt(convolved_variance)
# Also need to convolve aperture corrections to get
# a total apcor across the wavelength window
convolved_norm = convolve(norm,
convolution_filter,
normalize_kernel=True)
# To get mean account for the edges in
# the convolution
for iend in range(self.wavenpix):
fac = filter_len / (filter_len + iend - self.wavenpix)
convolved_norm[iend] *= fac
convolved_norm[-iend - 1] *= fac
# Mask wavelengths with too many bad pixels
# equivalent to nan_fib in the wave != None mode
wunorm = weights * norm
for index in range(len(convolved_variance)):
if not bad_central_mask(wunorm, logical_not(fmask),
index):
std[index] = badval
noise.append(std)
norm_all.append(convolved_norm)
else:
if wave_passed:
noise.append(badval)
norm_all.append(1.0)
amp.append("000")
nan_fib_mask.append(True)
else:
noise.append(badval * ones(len(wave_rect)))
norm_all.append(ones(len(wave_rect)))
amp.append("000")
mask[i] = False
# Apply the galaxy mask
gal_mask = ones(len(coords), dtype=int)
for gal_region in self.gal_regions:
dummy_wcs = create_dummy_wcs(gal_region.center,
imsize=2 * gal_region.height)
# zero if near galaxy
gal_mask = gal_mask & invert(gal_region.contains(
coords, dummy_wcs))
noise = array(noise)
snoise = pixsize_aa * 1e-17 * noise
if wave_passed:
bad = (gal_mask <
0.5) | (snoise > 998) | isnan(snoise) | invert(nan_fib_mask)
normnoise = snoise / norm_all
if not direct_sigmas:
normnoise = self.f50_from_noise(normnoise,
wave,
sncut,
linewidth=linewidth)
normnoise[bad] = 999.
return normnoise, amp, norm_all
else:
mask[gal_mask < 0.5] = False
if self.badshot:
mask[:] = False
bad = (snoise > 998) | logical_not(isfinite(snoise))
normnoise = snoise / norm_all
if not direct_sigmas:
normnoise = self.f50_from_noise(normnoise,
wave,
sncut,
linewidth=linewidth)
normnoise[bad] = 999
return normnoise, mask, amp, norm_all
def return_completeness(self,
flux,
ra,
dec,
lambda_,
sncut,
f50s=None,
linewidth=None):
"""
Return completeness at a 3D position as an array.
If for whatever reason the completeness is NaN, it's
replaced by 0.0. This is cut and paste from
sensitivity_cube:SensitivityCube
Parameters
----------
flux : array
fluxes of objects
ra, dec : array
right ascension and dec in degrees
lambda_ : array
wavelength in Angstrom
sncut : float
the detection significance (S/N) cut
applied to the data
f50s : array (optional)
optional array of precomputed
50% completeness fluxes. Otherwise
the method will compute them itself
from the ra/dec/linewidth (default:None)
linewidth : array (optional)
optionally pass the linewidth of
the source (in AA) to activate the linewidth
dependent part of the completeness
model (default = None). Only does
anything when you don't pass the f50s
(default: None)
Return
------
fracdet : array
fraction detected
Raises
------
WavelengthException :
Annoys user if they pass
wavelength outside of
VIRUS range
"""
logger = logging.getLogger(name="ShotSensitivity")
try:
if lambda_[0] < 3000.0 or lambda_[0] > 6000.0:
raise WavelengthException("""Odd wavelength value. Are you
sure it's in Angstrom?""")
except TypeError as e:
if lambda_ < 3000.0 or lambda_ > 6000.0:
raise WavelengthException("""Odd wavelength value. Are you
sure it's in Angstrom?""")
if type(f50s) == type(None):
f50s, norm = self.get_f50(ra,
dec,
lambda_,
sncut,
linewidth=linewidth)
try:
# to stop bad values breaking interpolation
bad = (f50s > 998)
f50s[bad] = 1e-16
fracdet = self.sinterp(flux, f50s, lambda_, sncut)
#print(min(flux), max(flux), min(f50s), max(f50s))
# check to see if we're passing multiple fluxes
# for one f50 value
if any(bad):
logger.debug("There are bad values here to mask")
if len(f50s) == 1:
logger.debug("Just one ra/dec/wave passed.")
fracdet[:] = 0.0
f50s[:] = 999.0
else:
fracdet[bad] = 0.0
f50s[bad] = 999.0
except IndexError as e:
print("Interpolation failed!")
print(min(flux), max(flux), min(f50s), max(f50s))
print(min(lambda_), max(lambda_))
raise e
try:
fracdet[isnan(fracdet)] = 0.0
except TypeError:
if isnan(fracdet):
fracdet = 0.0
return fracdet
def close(self):
"""
Close the Extractor object
(especially if it has a Shot HDF
file open)
"""
self.extractor.close()
def __enter__(self):
""" Added to support using the `with` statement """
return self
def __exit__(self, type_, value, traceback):
""" Support tidying up after using the `with` statement """
self.close()
def __init__(self,
datevshot,
release=None,
flim_model=None,
rad=3.5,
ffsky=False,
wavenpix=3,
d25scale=3.0,
verbose=False,
sclean_bad=True,
log_level="WARNING"):
self.conf = HDRconfig()
self.extractor = Extract()
self.shotid = int(datevshot.replace("v", ""))
self.date = datevshot[:8]
self.rad = rad
self.ffsky = ffsky
self.wavenpix = wavenpix
self.sclean_bad = sclean_bad
logger = logging.getLogger(name="ShotSensitivity")
logger.setLevel(log_level)
if verbose:
raise DeprecationWarning(
"Using verbose is deprecated, set log_level instead")
logger.setLevel("DEBUG")
logger.info("shotid: {:d}".format(self.shotid))
if not release:
self.release = self.conf.LATEST_HDR_NAME
else:
self.release = release
logger.info("Data release: {:s}".format(self.release))
self.survey = Survey(survey=self.release)
# Set up flux limit model
self.f50_from_noise, self.sinterp, interp_sigmas \
= return_flux_limit_model(flim_model,
cache_sim_interp=False,
verbose=verbose)
# Generate astrometry for this shot
survey_sel = (self.survey.shotid == self.shotid)
self.shot_pa = self.survey.pa[survey_sel][0]
self.shot_ra = self.survey.ra[survey_sel][0]
self.shot_dec = self.survey.dec[survey_sel][0]
rot = 360.0 - (self.shot_pa + 90.)
self.tp = TangentPlane(self.shot_ra, self.shot_dec, rot)
#Set up masking
logger.info("Using d25scale {:f}".format(d25scale))
self.setup_mask(d25scale)
# Set up spectral extraction
if release == "hdr1":
fwhm = self.survey.fwhm_moffat[survey_sel][0]
else:
fwhm = self.survey.fwhm_virus[survey_sel][0]
logger.info("Using Moffat PSF with FWHM {:f}".format(fwhm))
self.moffat = self.extractor.moffat_psf(fwhm, 3. * rad, 0.25)
self.extractor.load_shot(self.shotid, fibers=True, survey=self.release)
# Set up the focal plane astrometry
fplane_table = self.extractor.shoth5.root.Astrometry.fplane
# Bit of a hack to avoid changing pyhetdex
with NamedTemporaryFile(mode='w') as tpf:
for row in fplane_table.iterrows():
tpf.write(
"{:03d} {:8.5f} {:8.5f} {:03d} {:03d} {:03d} {:8.5f} {:8.5f}\n"
.format(row['ifuslot'], row['fpx'], row['fpy'],
row['specid'], row['specslot'], row['ifuid'],
row['ifurot'], row['platesc']))
tpf.seek(0)
self.fplane = FPlane(tpf.name)