def mask_regions(imagepath, regionpath):
"""Adds the ds9 regions from a specified region file to the bad pixel mask
of an image.
The region file should be of the kind output by ds9 (region->save regions)
with the following modes selected:
format: Anything other than 'XML' or 'X Y'
coordinate system: 'image'
Currently this code only supports the following region types:
box, ellipse, circle
Inputs:
imagepath -> String, path to an image
regionpath -> String, path to a region file
"""
shapes, par = parse_region_file(regionpath)
# Open the input image and run it through the various region masks
im = FPImage(imagepath, update=True)
for i in range(len(shapes)):
if shapes[i] == "circle":
im.badp[mask_circle(im.badp, par[i])] = 1
im.badp = mask_circle(im.badp, par[i])
elif shapes[i] == "box":
im.badp[mask_box(im.badp, par[i])] = 1
elif shapes[i] == "ellipse":
im.badp[mask_ellipse(im.badp, par[i])] = 1
# Close files
im.close()
return
def flatten(fnlist, flatfile):
"""Flattens a series of images by dividing them by a flatfield image.
This differs from traditional flatfielding only in that in maintains the
RSS aperture mask.
Inputs:
fnlist -> A list of strings, each the path to an image to flatten
flatfile -> The location of a master flat image
"""
flatimage = fits.open(flatfile)
for i in range(len(fnlist)):
print("Flattening image " + str(i + 1) + " of " + str(len(fnlist)) + ": " + fnlist[i])
image = FPImage(fnlist[i], update=True)
image.flattog = "True"
image.inty /= flatimage[0].data # Flatten data
image.vari /= flatimage[0].data ** 2 # Flatten variance
image.badp[np.isnan(image.inty)] = 1 # Fix bad pixels:
image.inty[np.isnan(image.inty)] = 0
image.badp[np.isinf(image.inty)] = 1
image.inty[np.isinf(image.inty)] = 0
image.close()
flatimage.close()
return
def aperture_mask(fnlist, axcen, aycen, arad):
"""Opens a series of images and masks pixels outside a circular aperture.
The images are overwritten with the new masked image. The values of axcen,
aycen, and arad are added to the FITS headers as keywords 'fpaxcen',
'fpaycen', and 'fparad' respectively.
Inputs:
fnlist -> A list containing strings, each the path to a fits image.
axcen -> The aperture x center
aycen -> The aperture y center
arad -> The aperture radius
"""
for i in range(len(fnlist)):
print ("Masking pixels outside aperture for image " +
str(i+1)+" of "+str(len(fnlist))+": "+fnlist[i])
image = FPImage(fnlist[i], update=True)
rgrid = image.rarray(axcen, aycen)
image.inty[rgrid > arad] = 0
image.badp[rgrid > arad] = 1
image.axcen = axcen
image.aycen = aycen
image.arad = arad
image.close()
def solar_velocity_shift(imagelist, restwave):
"""Opens the images of a data cube and shifts the wavelength planes
so they are shifted to the solar frame. This is accomplished using the
IRAF task 'rvcorrect'.
It does it in a really really stupid way, which is to temporarily redirect
IRAF's output to a string, because IRAF doesn't actually save the output
anywhere (that I know of), it only prints it to the terminal. Then this
routine searches through that string for the necessary value. It's a bit
backwards, but it works!
Note that the boost here is a Lorentz boost, not a Galilean boost, though
values for either will be similar (i.e. the relativistic formula is used)
Inputs:
imagelist -> List of strings, the paths to wavelength images to be
updated.
restwave -> The rest wavelength of the line you're interested in.
"""
c = 299792.458 # in km/s
for i in range(len(imagelist)):
sys.stdout = iraf_output = StringIO()
image = FPImage(imagelist[i], update=True)
iraf.rvcorrect(header="N",
input="N",
imupdate="N",
observatory="SAAO",
year=float(image.datestring.split("-")[0]),
month=float(image.datestring.split("-")[1]),
day=float(image.datestring.split("-")[2]),
ut=image.ut,
ra=image.ra,
dec=image.dec,
vobs=0,
mode="a")
image.solarvel = float(iraf_output.getvalue().split()[-6])
iraf_output.close()
beta_earth = (((image.wave/restwave)**2-1) /
((image.wave/restwave)**2+1))
beta_shift = image.solarvel/c
beta_helio = (beta_earth+beta_shift)/(1+beta_earth*beta_shift)
image.wave = restwave*(1+beta_helio)/np.sqrt(1-beta_helio**2)
image.wave[np.isnan(image.wave)] = 0
image.close()
sys.stdout = sys.__stdout__
return
def get_aperture(path):
"""Opens a fits image and has the user click on points near the image
aperture to fit a circle to those points. Once at least three points
on the aperture boundary have been clicked, begins displaying a best-fit
circle to those points overlayed on the image.
Inputs:
path -> Path to the fits file to open
Outputs:
axcen -> The aperture x center
aycen -> The aperture y center
arad -> The aperture radius
"""
image = FPImage(path)
xs, ys = [], []
axcen, aycen, arad = image.xsize / 2, image.ysize / 2, 0
apguess = np.array([image.xsize / 2, image.ysize / 2, min(image.xsize, image.ysize) / 2], dtype="float64")
while True:
click = Click_Near_Aperture_Plot(image.inty, xs, ys, axcen, aycen, arad)
if (
click.xcoo is not None
and click.xcoo > 26
and click.ycoo > 26
and click.xcoo < image.xsize - 26
and click.ycoo < image.ysize - 26
):
# If the click was in a not-stupid place
zoomdata = image.inty[click.ycoo - 25 : click.ycoo + 25, click.xcoo - 25 : click.xcoo + 25]
newclick = Zoom_Aperture_Plot(zoomdata)
if not (newclick.xcoo is None):
xs.append(newclick.xcoo + click.xcoo - 25)
ys.append(newclick.ycoo + click.ycoo - 25)
if len(xs) > 2:
# Fit a circle to the points
def fun(x):
return np.sum(((np.array(xs) - x[0]) ** 2 + (np.array(ys) - x[1]) ** 2 - x[2] ** 2) ** 2)
apparams = minimize(fun, apguess).x
axcen, aycen, arad = apparams[0], apparams[1], apparams[2]
elif len(xs) > 2 and click.xcoo is None:
break
image.close()
return axcen, aycen, arad
def fit_wave_soln(fnlist, doprint=False):
"""Fits a wavelength solution to rings in a set of images. Appends this
wavelength solution to the image headers as the keywords:
'fpwave0' and 'fpcalf'
Each object in fnlist must have a corresponding "median.fits" in its
image directory, or this routine will not work.
ARC ring images are fitted by adjusting the center, while the center is
held fixed for night sky rings. A combination of fits to both sets of
rings is used to determine a wavelength solution for the whole set of
images.
If the ARC rings disagree substantially with the night sky rings, it is
recommended that users delete the ARC rings from the fit and use only the
night sky rings.
It is also known that the wavelength solution can sometimes be piecewise in
time when a large jump in 'z' happens between two images; i.e. different
wavelength solutions exist before and after the jump. The routine allows
the user to make a piecewise solution for this reason, but this ability
should be used sparingly.
This routine contains one of the few hard-coded numbers in the pipeline,
Fguess=5600. Currently F values are not written to the fits image headers,
and this is a reasonable guess.
Inputs:
fnlist -> List of strings, each the path to a fits image. These images
should all have been taken with the same order filter. If not, the routine
will crash.
"""
# This bit takes care of the 's' to save shortcut in matplotlib.
oldsavekey = plt.rcParams["keymap.save"]
plt.rcParams["keymap.save"] = ""
# Open all of the images
arclist = []
objlist = []
images = [FPImage(fn) for fn in fnlist]
# Separate ARCs and Object images and median-subtract Object images
isarclist = [image.object == "ARC" for image in images]
for i in range(len(isarclist)):
if isarclist[i]:
arclist.append(images[i])
else:
if not isfile(join(split(fnlist[i])[0], "median.fits")):
exit("Error! No 'median.fits' file found.")
medimage = fits.open(join(split(fnlist[i])[0], "median.fits"))
images[i].inty -= medimage[0].data
images[i].inty -= np.median(images[i].inty[images[i].badp != 1])
medimage.close()
objlist.append(images[i])
filts = [image.filter for image in images]
arclibs = []
nightlibs = []
for i in range(len(fnlist)):
if isarclist[i]:
arclibs.append(get_libraries(filts[i])[0])
else:
nightlibs.append(get_libraries(filts[i])[1])
if get_libraries(filts[i])[0] is None:
exit("Error! Filter "+filts[i]+" not in the wavelength library!")
# This next bit fits all of the rings that the user marks
# Fit rings in the object images
radlists = []
for i in range(len(objlist)):
radlists.append([])
i = 0
while True:
xcen = objlist[i].xcen
ycen = objlist[i].ycen
axcen = objlist[i].axcen
aycen = objlist[i].aycen
arad = objlist[i].arad
rgrid = objlist[i].rarray(axcen, aycen)
# Create radius bins
rbins = np.arange(arad-np.int(max(abs(axcen-xcen), abs(aycen-ycen))))+1
intbins = np.empty_like(rbins)
# Get the median intensity within each radius bin
for j in range(len(rbins)):
binmask = np.logical_and(rgrid > rbins[j]-1,
rgrid < rbins[j])
goodbinmask = np.logical_and(binmask,
objlist[i].badp == 0)
if np.sum(goodbinmask) != 0:
intbins[j] = np.median(objlist[i].inty[goodbinmask])
else:
intbins[j] = 0
# Shift/scale the radius and intensity for the purposes of plotting
plotxcen = xcen-axcen+arad
plotycen = ycen-aycen+arad
plotrbins = rbins+plotxcen
plotintbins = intbins*arad/np.percentile(np.abs(intbins), 98)+plotycen
# Plot the data interactively
ringplot = PlotRingProfile(objlist[i].inty[aycen-arad:aycen+arad,
axcen-arad:axcen+arad],
plotrbins, plotintbins,
plotxcen, plotycen,
radlists[i],
repr(i+1)+"/"+repr(len(objlist)))
# Changing images and loop breakout conditions
if ringplot.key == "d":
i += 1
if ringplot.key == "a":
i += -1
if i == -1 or i == len(objlist):
while True:
yn = raw_input("Finished marking sky rings? (y/n) ")
if "n" in yn or "N" in yn:
if i == -1:
i = 0
if i == len(objlist):
i = len(objlist)-1
break
elif "y" in yn or "Y" in yn:
break
if i == -1 or i == len(objlist):
break
# Force-marking a ring
if ringplot.key == "e" and ringplot.xcoo is not None:
radlists[i].append(ringplot.xcoo-arad-(xcen-axcen))
# Deleting a ring
if (ringplot.key == "s" and ringplot.xcoo is not None and
len(radlists[i]) > 0):
distarray = np.abs((np.array(radlists[i]) -
np.sqrt((ringplot.xcoo-arad-(xcen-axcen))**2 +
(ringplot.ycoo-arad-(ycen-aycen))**2)))
radlists[i].pop(np.argmin(distarray))
# Fitting a ring profile
if ringplot.key == "w" and ringplot.xcoo is not None:
lower_index = max(ringplot.xcoo-plotxcen-50, 0)
upper_index = min(ringplot.xcoo-plotxcen+50, len(rbins))
x = rbins[lower_index:upper_index]**2
y = intbins[lower_index:upper_index]
fit = GaussFit(x, y)
fitplot = PlotRingFit(x, y, fit)
if fitplot.key == "w":
radlists[i].append(np.sqrt(fit[2]))
zo = []
to = []
ro = []
lib_o = []
for i in range(len(objlist)):
for j in range(len(radlists[i])):
zo.append(objlist[i].z)
to.append(objlist[i].jd)
ro.append(radlists[i][j])
lib_o.append(nightlibs[i])
if doprint:
print objlist[i].z, objlist[i].jd, radlists[i][j]
# Fit rings in the ARC images if there are any
xcen = objlist[0].xcen
ycen = objlist[0].ycen
radlists = []
for i in range(len(arclist)):
radlists.append([])
i = 0
while len(arclist) > 0:
axcen = arclist[i].axcen
aycen = arclist[i].aycen
arad = arclist[i].arad
rgrid = arclist[i].rarray(axcen, aycen)
# Create radius bins
rbins = np.arange(arad-np.int(max(abs(axcen-xcen), abs(aycen-ycen))))+1
intbins = np.empty_like(rbins)
# Get the median intensity in each radius bin
for j in range(len(rbins)):
binmask = np.logical_and(rgrid > rbins[j]-1,
rgrid < rbins[j])
goodbinmask = np.logical_and(binmask,
arclist[i].badp == 0)
intbins[j] = np.median(arclist[i].inty[goodbinmask])
# Shift/scale the radius and intensity for the purposes of plotting
plotxcen = xcen-axcen+arad
plotycen = ycen-aycen+arad
plotrbins = rbins+plotxcen
plotintbins = intbins*arad/np.percentile(np.abs(intbins), 98)+plotycen
# Plot the data interactively
ringplot = PlotRingProfile(arclist[i].inty[aycen-arad:aycen+arad,
axcen-arad:axcen+arad],
plotrbins, plotintbins,
plotxcen, plotycen,
radlists[i],
repr(i+1)+"/"+repr(len(arclist)))
# Changing images and loop breakout conditions
if ringplot.key == "d":
i += 1
if ringplot.key == "a":
i += -1
if i == -1 or i == len(arclist):
while True:
yn = raw_input("Finished marking ARC rings? (y/n) ")
if "n" in yn or "N" in yn:
if i == -1:
i = 0
if i == len(arclist):
i = len(arclist)-1
break
elif "y" in yn or "Y" in yn:
break
if i == -1 or i == len(arclist):
break
# Force-marking a ring
if ringplot.key == "e" and ringplot.xcoo is not None:
radlists[i].append(ringplot.xcoo-arad-(xcen-axcen))
# Deleting a ring
if (ringplot.key == "s" and ringplot.xcoo is not None and
len(radlists[i]) > 0):
distarray = np.abs((np.array(radlists[i]) -
np.sqrt((ringplot.xcoo-arad-(xcen-axcen))**2 +
(ringplot.ycoo-arad-(ycen-aycen))**2)))
radlists[i].pop(np.argmin(distarray))
# Fitting a ring profile
if ringplot.key == "w" and ringplot.xcoo is not None:
lower_index = max(ringplot.xcoo-plotxcen-50, 0)
upper_index = min(ringplot.xcoo-plotxcen+50, len(rbins))
x = rbins[lower_index:upper_index]**2
y = intbins[lower_index:upper_index]
fit = GaussFit(x, y)
fitplot = PlotRingFit(x, y, fit)
if fitplot.key == "w":
radlists[i].append(np.sqrt(fit[2]))
za = []
ta = []
ra = []
lib_a = []
for i in range(len(arclist)):
for j in range(len(radlists[i])):
za.append(arclist[i].z)
ta.append(arclist[i].jd)
ra.append(radlists[i][j])
lib_a.append(arclibs[i])
if doprint:
print arclist[i].z, arclist[i].jd, radlists[i][j]
# Now we try to get a good guess at the wavelengths
# Get a good guess at which wavelengths are which
Bguess = objlist[0].b
Fguess = objlist[0].f
if Fguess is None:
Fguess = 5600
# Figure out A by matching rings to the wavelength libraries
master_r = np.array(ro+ra)
master_z = np.array(zo+za)
wavematch = np.zeros_like(master_r)
oldrms = 10000 # Really high initial RMS for comparisons
master_lib = lib_o+lib_a
for i in range(len(master_r)):
lib = master_lib[i]
for j in range(len(lib)):
# Assume the i'th ring is the j'th line
Aguess = (lib[j]*np.sqrt(1+master_r[i]**2/Fguess**2) -
Bguess*master_z[i])
# What are all of the other rings, given this A?
waveguess = ((Aguess+Bguess*master_z) /
np.sqrt(1+master_r**2/Fguess**2))
for k in range(len(master_r)):
wherematch = np.argmin(np.abs(master_lib[k]-waveguess[k]))
wavematch[k] = master_lib[k][wherematch]
rms = np.sqrt(np.average((waveguess-wavematch)**2))
if rms < oldrms:
# This is the new best solution. Keep it!
oldrms = rms
bestA = Aguess
master_wave = wavematch.copy()
# Make more master arrays for the plotting
master_t = np.array(to+ta)
t0 = np.min(master_t)
master_t += -t0
master_t *= 24*60 # Convert to minutes
master_color = np.array(len(ro)*["blue"]+len(ra)*["red"])
toggle = np.ones(len(master_r), dtype="bool")
dotime = False
time_dividers = []
# Do the interactive plotting
while True:
rplot = master_r[toggle]
zplot = master_z[toggle]
tplot = master_t[toggle]
colorplot = master_color[toggle]
wplot = master_wave[toggle]
fitplot = np.zeros(len(wplot))
xs = np.zeros((3, len(rplot)))
xs[0] = rplot
xs[1] = zplot
xs[2] = tplot
fit = [0]*(len(time_dividers)+1)
time_dividers = sorted(time_dividers)
if len(time_dividers) > 1:
print ("Warning: Too many time divisions is likely unphysical." +
"Be careful!")
for i in range(len(time_dividers)+1):
# Create a slice for all of the wavelengths before this time
# divider but after the one before it
if len(time_dividers) == 0:
tslice = tplot == tplot
elif i == 0:
tslice = tplot < time_dividers[i]
elif i == len(time_dividers):
tslice = tplot > time_dividers[i-1]
else:
tslice = np.logical_and(tplot < time_dividers[i],
tplot > time_dividers[i-1])
# Case for fitting time dependence
if dotime:
fit[i] = curve_fit(fpfunc_for_curve_fit_with_t,
xs[:, tslice], wplot[tslice],
p0=(bestA, Bguess, 0, Fguess))[0]
fitplot[tslice] = fpfunc_for_curve_fit_with_t(xs[:, tslice],
fit[i][0],
fit[i][1],
fit[i][2],
fit[i][3])
# Case without time dependence
else:
fit[i] = curve_fit(fpfunc_for_curve_fit,
xs[:, tslice], wplot[tslice],
p0=(bestA, Bguess, Fguess))[0]
fitplot[tslice] = fpfunc_for_curve_fit(xs[:, tslice],
fit[i][0],
fit[i][1],
fit[i][2])
# Calculate residuals to the fit
resid = wplot - fitplot
# Interactively plot the residuals
solnplot = WaveSolnPlot(rplot, zplot, tplot, wplot,
resid, colorplot, time_dividers)
# Breakout case
if solnplot.key == "a":
while True:
for i in range(len(time_dividers)+1):
if dotime:
solnstring = ("Solution "+repr(i+1) +
": A = "+str(fit[i][0]) +
", B = "+str(fit[i][1]) +
", E = "+str(fit[i][2]) +
", F = "+str(fit[i][3]))
else:
solnstring = ("Solution "+repr(i+1) +
": A = "+str(fit[i][0]) +
", B = "+str(fit[i][1]) +
", F = "+str(fit[i][2]))
print solnstring
rms = np.sqrt(np.average(resid**2))
print ("Residual rms="+str(rms) +
" for "+repr(len(time_dividers)+1) +
" independent "+repr(3+dotime) +
"-parameter fits to "+repr(len(rplot))+" rings.")
yn = raw_input("Accept wavelength solution? (y/n) ")
if "n" in yn or "N" in yn:
break
elif "y" in yn or "Y" in yn:
solnplot.key = "QUIT"
break
if solnplot.key == "QUIT":
break
# Restore all points case
if solnplot.key == "r":
toggle = np.ones(len(master_r), dtype="bool")
# Delete nearest point case
if solnplot.key == "d" and solnplot.axis is not None:
# Figure out which plot was clicked in
if solnplot.axis == 1:
# Resid vs. z plot
z_loc = solnplot.xcoo
resid_loc = solnplot.ycoo
dist2 = (((zplot-z_loc)/(np.max(zplot)-np.min(zplot)))**2 +
((resid-resid_loc)/(np.max(resid)-np.min(resid)))**2)
elif solnplot.axis == 2:
# Resid vs. R plot
r_loc = solnplot.xcoo
resid_loc = solnplot.ycoo
dist2 = (((rplot-r_loc)/(np.max(rplot)-np.min(rplot)))**2 +
((resid-resid_loc)/(np.max(resid)-np.min(resid)))**2)
elif solnplot.axis == 3:
# Resit vs. T plot
t_loc = solnplot.xcoo
resid_loc = solnplot.ycoo
dist2 = (((tplot-t_loc)/(np.max(tplot)-np.min(tplot)))**2 +
((resid-resid_loc)/(np.max(resid)-np.min(resid)))**2)
elif solnplot.axis == 4:
# Resid vs. Wave plot
wave_loc = solnplot.xcoo
resid_loc = solnplot.ycoo
dist2 = (((wplot-wave_loc)/(np.max(wplot)-np.min(wplot)))**2 +
((resid-resid_loc)/(np.max(resid)-np.min(resid)))**2)
# Get the radius and time of the worst ring
r_mask = rplot[dist2 == np.min(dist2)][0]
t_mask = tplot[dist2 == np.min(dist2)][0]
toggle[np.logical_and(master_r == r_mask,
master_t == t_mask)] = False
# Toggle time fit case
if solnplot.key == "t":
dotime = not dotime
# Add time break case
if solnplot.key == "w":
timeplot = TimePlot(tplot, resid, colorplot, time_dividers)
if timeplot.xcoo is not None:
time_dividers.append(timeplot.xcoo)
# Remove time breaks case
if solnplot.key == "q":
time_dividers = []
# Close all images
for image in images:
image.close()
# For each image, write the central wavelength and F to the image header
for i in range(len(fnlist)):
image = FPImage(fnlist[i], update=True)
image_t = (image.jd-t0)*24*60
# Figure out which time division it's in
div_index = np.where(np.array(time_dividers) > image_t)[0]
if len(div_index > 0):
div_index = div_index[0]
else:
div_index = len(time_dividers)
image_fit = fit[div_index]
if dotime:
image_wave0 = (image_fit[0] +
image_fit[1]*image.z +
image_fit[2]*image_t)
image_F = image_fit[3]
else:
image_wave0 = (image_fit[0] +
image_fit[1]*image.z)
image_F = image_fit[2]
image.wave0 = image_wave0
image.calf = image_F
image.calrms = rms
image.calnring = repr(len(rplot))
image.calnfits = repr(len(time_dividers)+1)
image.calnpars = repr(3+dotime)
image.close()
# Restore the old keyword shortcut
plt.rcParams["keymap.save"] = oldsavekey
return
def make_final_image(input_image, output_image,
desired_fwhm, clobber=False):
"""This routine makes the 'final' images for a data cube. At least the
paths to the input image, output image, and output wavelength image are
necessary for this. Beyond that, the user may also have the routine create
uncertainty images as well.
Images are convolved to the resolution 'desired_fwhm'. If the current fwhm
is already higher than that, the routine will throw an error.
A number of fits header keywords are necessary for this program to function
properly. Any of these missing will throw an error.
The output images are intensity-weighted, i.e. the wavelength image will be
created such that the wavelengths at each pixel are the 'most likely'
wavelength for the intensity at that pixel, etc.
Inputs:
input_image -> Path to the input image.
output_image -> Path to the output image.
desired_fwhm -> Desired FWHM for the resultant image to have.
Optional Inputs:
clobber -> Overwrite output images if they already exist. Default is False.
"""
print "Making final data cube images for image "+input_image
# Open the image
image = FPImage(input_image)
# Measure the sky background level in the input image
skyavg, _truesig, skysig = image.skybackground()
# Get various header keywords, crash if necessary
intygrid = image.inty
fwhm = image.fwhm
wave0 = image.wave0
calf = image.calf
xcen = image.xcen
ycen = image.ycen
if fwhm is None:
exit("Error! FWHM not measured for image "+input_image+".")
if wave0 is None or calf is None:
exit("Error! Wavelength solution does " +
"not exist for image "+input_image+".")
if xcen is None or ycen is None:
exit("Error! Center values not measured " +
"image "+input_image+".")
if fwhm > desired_fwhm:
exit("Error! Desired FWHM too low for image " +
input_image+".")
# Calculate the necessary FWHM for convolution
fwhm_conv = np.sqrt(desired_fwhm**2-fwhm**2)
# Magic number converts sigma to fwhm
sig = fwhm_conv/2.3548
# Extremely conservative "safe" kernel size
ksize = np.ceil(4*sig)
# Generate the gaussian kernel, shifted to shift the image
kxgrid, kygrid = np.meshgrid(np.linspace(-ksize, ksize, 2*ksize+1),
np.linspace(-ksize, ksize, 2*ksize+1))
xshift, yshift = image.xshift, image.yshift
rad2grid = (kxgrid + xshift)**2 + (kygrid + yshift)**2
kern = np.exp(-rad2grid/(2*sig**2))
# Normalize the kernel
kern = kern/np.sum(kern)
# Extract relevant arrays
vargrid = image.vari
badpixgrid = image.badp
# Convolve the variances appropriately
new_vargrid = convolve_variance(vargrid, badpixgrid, kern)
# Add the sky background uncertainty to the uncertainty grid
vargrid = vargrid+skysig**2
# Create and convolve the wavelength array
if image.wave is None:
rgrid = image.rarray(xcen, ycen)
wavegrid = wave0 / np.sqrt(1+rgrid**2/calf**2)
else:
wavegrid = image.wave
new_wavegrid = convolve_wave(wavegrid, intygrid, badpixgrid, kern)
# Convolve the intensity image
new_intygrid = convolve_inty(intygrid, badpixgrid, kern)
new_intygrid[new_intygrid == 0] = intygrid[new_intygrid == 0]
new_intygrid[np.isnan(new_intygrid)] = intygrid[np.isnan(new_intygrid)]
image.fwhm = desired_fwhm # Update header FWHM keyword
# Subtract the sky background from the image
new_intygrid[new_intygrid != 0] -= skyavg
# Create a new fits extension for the wavelength array
if image.wave is None:
waveheader = image.openimage[2].header.copy()
waveheader['EXTVER'] = 4
wavehdu = ImageHDU(data=new_wavegrid,
header=waveheader,
name="WAVE")
image.openimage[1].header.set('WAVEEXT', 4,
comment='Extension for Wavelength Frame')
image.openimage.append(wavehdu)
# Put all of the convolved images in the right extensions
image.inty = new_intygrid
image.vari = new_vargrid
image.wave = new_wavegrid
# Adjust header keywords (even though they're kinda irrelevant now)
image.xcen += image.xshift
image.ycen += image.yshift
image.axcen += image.xshift
image.aycen += image.yshift
# Write the output file
image.writeto(output_image, clobber=clobber)
# Close images
image.close()
return
def pipeline(rawdir="raw", mode="halpha"):
"""Runs successive steps of the saltfp data reduction, checking along the
way to see if each step was successful. This is the main driver program of
the SALT Fabry-Perot pipeline.
Inputs:
rawdir -> String, containing the path to the 'raw' directory. By
default, this is 'raw'
mode -> Mode for velocity fitting. Currently the only option is H-Alpha
line fitting.
"""
# Set rest wave based on the mode called
if mode == "halpha":
rest_wave = 6562.81
# Create product directory
if isdir("product"):
while True:
yn = raw_input("Product directory already exists. " + "Recreate it? (y/n) ")
if "n" in yn or "N" in yn:
break
elif "y" in yn or "Y" in yn:
# Confirmation
yn = raw_input("Are you sure? This takes a while. (y/n) ")
if ("y" in yn or "Y" in yn) and not ("n" in yn or "N" in yn):
rmtree("product")
break
if not isdir("product"):
# Acquire the list of filenames from the raw directory
fnlist = sorted(listdir(rawdir))
for i in range(len(fnlist)):
fnlist[i] = join(rawdir, fnlist[i])
# Run the first two steps of imred on the first image
iraf.pysalt(_doprint=0)
iraf.saltred(_doprint=0)
iraf.saltprepare(
fnlist[0],
"temp.fits",
"",
createvar=False,
badpixelimage="",
clobber=True,
logfile="temp.log",
verbose=True,
)
iraf.saltbias(
"temp.fits",
"temp.fits",
"",
subover=True,
trim=True,
subbias=False,
masterbias="",
median=False,
function="polynomial",
order=5,
rej_lo=3.0,
rej_hi=5.0,
niter=10,
plotover=False,
turbo=False,
clobber=True,
logfile="temp.log",
verbose=True,
)
# Create the bad pixel mask
image = fits.open("temp.fits")
for i in range(1, len(image)):
mask = image[i].data != image[i].data
image[i].data = 1 * mask
image.writeto("badpixmask.fits", clobber="True")
image.close()
# Remove temporary files
remove("temp.fits")
remove("temp.log")
# Run the raw images through the first few data reduction pipeline
# steps
imred(fnlist, "product", bpmfile="badpixmask.fits")
# Delete the temporary bad pixel mask
remove("badpixmask.fits")
# Move these raw images into the product directory
mkdir("product")
fnlist = sorted(listdir("."))
for i in range(len(fnlist)):
if "mfxgbpP" in fnlist[i] and ".fits" in fnlist[i]:
move(fnlist[i], join("product", fnlist[i]))
# List of files in the product directory
fnlist = sorted(listdir("product"))
for i in range(len(fnlist)):
fnlist[i] = join("product", fnlist[i])
# Manual verification of fits images and headers
firstimage = FPImage(fnlist[0])
verify = firstimage.verifytog
firstimage.close()
if verify is None:
while True:
prompt = "Manually verify image contents? (Recommended) (y/n) "
yn = raw_input(prompt)
if "n" in yn or "N" in yn:
print ("Skipping manual verification of image contents " + "(Not recommended)")
break
if "y" in yn or "Y" in yn:
fnlist = verify_images(fnlist)
break
# Make separate lists of the different fits files
(flatlist, list_of_objs, objlists, list_of_filts, filtlists) = separate_lists(fnlist)
# Masking of pixels outside the aperture
firstimage = FPImage(objlists[0][0])
axcen = firstimage.axcen
firstimage.close()
if axcen is None:
print "Masking pixels outside the RSS aperture..."
axcen, aycen, arad = get_aperture(objlists[0][0])
aperture_mask(fnlist, axcen, aycen, arad)
else:
print "Images have already been aperture-masked."
# Masking bad pixels from external region file
for objlist in objlists:
for i in range(len(objlist)):
if isfile(splitext(split(objlist[i])[1])[0] + ".reg"):
print ("Adding regions from file " + splitext(split(objlist[i])[1])[0] + ".reg to the bad pixel mask.")
mask_regions(objlist[i], splitext(split(objlist[i])[1])[0] + ".reg")
# Measure stellar FWHMs
firstimage = FPImage(objlists[0][0])
fwhm = firstimage.fwhm
firstimage.close()
if fwhm is None:
dofwhm = True
else:
while True:
yn = raw_input("Seeing FWHM has already been measured. " + "Redo this? (y/n) ")
if "n" in yn or "N" in yn:
dofwhm = False
break
elif "y" in yn or "Y" in yn:
dofwhm = True
break
if dofwhm:
print "Measuring seeing FWHMs..."
for objlist in objlists:
measure_fwhm(objlist)
# Find image centers using ghost pairs
for i in range(len(objlists)):
firstimage = FPImage(objlists[i][0])
xcen = firstimage.xcen
deghosted = firstimage.ghosttog
firstimage.close()
if deghosted is None:
if xcen is None:
ghosttog = True
else:
while True:
yn = raw_input(
"Optical centers already measured for " + "object " + list_of_objs[i] + ". Redo this? (y/n) "
)
if "n" in yn or "N" in yn:
ghosttog = False
break
elif "y" in yn or "Y" in yn:
ghosttog = True
break
if ghosttog:
print (
"Identifying optical centers for object "
+ list_of_objs[i]
+ ". This may take a while for crowded fields..."
)
find_ghost_centers(objlists[i])
# Deghost images
for i in range(len(objlists)):
firstimage = FPImage(objlists[i][0])
deghosted = firstimage.ghosttog
firstimage.close()
if deghosted is None:
print "Deghosting images for object " + list_of_objs[i] + "..."
for j in range(len(objlists[i])):
deghost(objlists[i][j])
else:
print ("Images for object " + list_of_objs[i] + " have already been deghosted.")
# Image Flattening
firstimage = FPImage(objlists[0][0])
flattog = firstimage.flattog
firstimage.close()
if flattog is None:
print "Flattening images..."
if len(flatlist) == 0:
while True:
print "Uh oh! No flatfield exposure found!"
flatpath = raw_input("Enter path to external flat image: " + "(leave blank to skip flattening) ")
if flatpath == "" or isfile(flatpath):
break
else:
combine_flat(flatlist, "flat.fits")
flatpath = "flat.fits"
if flatpath != "":
notflatlist = []
for objlist in objlists:
notflatlist += objlist
flatten(notflatlist, flatpath)
else:
print "Skipping image flattening. (Not recommended!)"
else:
print "Images have already been flattened."
# Make separate directories for each object.
# This is the first bit since 'singext' to create a new directory, because
# this is the first point where it's really necessary to start treating the
# images from different tracks very differently.
for i in range(len(objlists)):
if isdir(list_of_objs[i].replace(" ", "")):
while True:
yn = raw_input("A directory for object " + list_of_objs[i] + " already exists. Recreate? (y/n) ")
if "n" in yn or "N" in yn:
do_copy = False
break
elif "y" in yn or "Y" in yn:
do_copy = True
rmtree(list_of_objs[i].replace(" ", ""))
break
else:
do_copy = True
if do_copy:
mkdir(list_of_objs[i].replace(" ", ""))
for j in range(len(objlists[i])):
copyfile(objlists[i][j], join(list_of_objs[i].replace(" ", ""), split(objlists[i][j])[1]))
for j in range(len(objlists[i])):
objlists[i][j] = join(list_of_objs[i].replace(" ", ""), split(objlists[i][j])[1])
# Update the filter lists
for i in range(len(filtlists)):
for j in range(len(filtlists[i])):
for k in range(len(objlists)):
for l in range(len(objlists[k])):
if split(filtlists[i][j])[1] == split(objlists[k][l])[1]:
filtlists[i][j] = objlists[k][l]
# Image alignment and normalization
for i in range(len(objlists)):
firstimage = FPImage(objlists[i][0])
aligned = firstimage.phottog
firstimage.close()
if aligned is None:
print ("Aligning and normalizing images for object " + list_of_objs[i] + "...")
align_norm(objlists[i])
else:
print ("Images for object " + list_of_objs[i] + " have already been aligned and normalized.")
# Make a median image for each object
for i in range(len(objlists)):
if isfile(join(list_of_objs[i].replace(" ", ""), "median.fits")):
while True:
yn = raw_input("Median image for object " + list_of_objs[i] + " already exists. Replace it? (y/n) ")
if "n" in yn or "N" in yn:
break
elif "y" in yn or "Y" in yn:
make_median(objlists[i], join(list_of_objs[i].replace(" ", ""), "median.fits"))
break
else:
make_median(objlists[i], join(list_of_objs[i].replace(" ", ""), "median.fits"))
# Wavelength calibrations
all_rings_list = []
for i in range(len(list_of_filts)):
all_rings_list = all_rings_list + filtlists[i]
firstimage = FPImage(all_rings_list[0])
calf = firstimage.calf
firstimage.close()
if not (calf is None):
while True:
yn = raw_input("Wavelength solution already found. " + "Redo it? (y/n) ")
if "n" in yn or "N" in yn:
break
elif "y" in yn or "Y" in yn:
fit_wave_soln(all_rings_list)
break
else:
fit_wave_soln(all_rings_list)
# Sky ring removal
for i in range(len(objlists)):
for j in range(len(objlists[i])):
# Check to see if sky rings have already been removed
image = FPImage(objlists[i][j])
deringed = image.ringtog
image.close()
if deringed is None:
print "Subtracting sky rings for image " + objlists[i][j]
sub_sky_rings([objlists[i][j]], [join(list_of_objs[i].replace(" ", ""), "median.fits")])
else:
print ("Sky ring subtraction already done for image " + objlists[i][j])
# Creation of data cube and convolution to uniform PSF
for i in range(len(objlists)):
if isdir(list_of_objs[i].replace(" ", "") + "_cube"):
while True:
yn = raw_input("A data cube for object " + list_of_objs[i] + " already exists. Recreate? (y/n) ")
if "n" in yn or "N" in yn:
do_create = False
break
elif "y" in yn or "Y" in yn:
# Confirmation
yn = raw_input("Are you sure? This takes a while. (y/n) ")
if ("y" in yn or "Y" in yn) and not ("n" in yn or "N" in yn):
do_create = True
rmtree(list_of_objs[i].replace(" ", "") + "_cube")
break
else:
do_create = True
if do_create:
mkdir(list_of_objs[i].replace(" ", "") + "_cube")
for j in range(len(objlists[i])):
image = FPImage(objlists[i][j])
fwhm = image.fwhm
if j == 0:
largestfwhm = fwhm
if fwhm > largestfwhm:
largestfwhm = fwhm
image.close()
while True:
prompt = "Enter desired final fwhm or leave blank to use" + " default (" + str(largestfwhm) + " pix) "
user_fwhm = raw_input(prompt)
if user_fwhm == "":
user_fwhm = largestfwhm
break
else:
try:
user_fwhm = float(user_fwhm)
except ValueError:
print "That wasn't a valid number..."
else:
if user_fwhm < largestfwhm:
print ("Final fwhm must exceed " + str(largestfwhm) + " pixels.")
else:
break
desired_fwhm = user_fwhm * 1.01
for j in range(len(objlists[i])):
make_final_image(
objlists[i][j],
join(list_of_objs[i].replace(" ", "") + "_cube", split(objlists[i][j])[1]),
desired_fwhm,
clobber=True,
)
# Get final lists for the velocity map fitting for each object
final_lists = []
for i in range(len(list_of_objs)):
final_lists.append([])
for j in range(len(objlists[i])):
final_lists[i].append(join(list_of_objs[i].replace(" ", "") + "_cube", split(objlists[i][j])[1]))
# Shift to solar velocity frame
for i in range(len(list_of_objs)):
firstimage = FPImage(final_lists[i][0])
velshift = firstimage.solarvel
firstimage.close()
if velshift is None:
print ("Performing solar velocity shift for object " + list_of_objs[i] + "...")
solar_velocity_shift(final_lists[i], rest_wave)
else:
print ("Solar velocity shift for object " + list_of_objs[i] + " already done.")
if not do_velmap:
sys.exit("Velocity map not made - Voigt-fitting software not found.")
# Velocity map fitting
for i in range(len(list_of_objs)):
if isfile(join(list_of_objs[i].replace(" ", "") + "_cube", "velocity.fits")):
while True:
yn = raw_input("Velocity map already fitted for object " + list_of_objs[i] + ". Redo this? (y/n) ")
if "n" in yn or "N" in yn:
domap = False
break
elif "y" in yn or "Y" in yn:
# Confirmation
yn = raw_input("Are you sure? This takes a while. (y/n) ")
if ("y" in yn or "Y" in yn) and not ("n" in yn or "N" in yn):
domap = True
break
else:
domap = True
if domap:
print "Fitting velocity map for object " + list_of_objs[i] + "..."
if mode == "halpha":
fit_velmap_ha_n2_mode(final_lists[i], list_of_objs[i].replace(" ", "") + "_cube", clobber=True)
# Clean velocity map
for i in range(len(list_of_objs)):
make_clean_map(list_of_objs[i].replace(" ", "") + "_cube", clobber=True)
def separate_lists(fnlist):
"""Separates a list of images into separate lists based on their header
keywords 'OBJECT' and 'FILTER'
Inputs:
fnlist -> A list containing strings, each the location of a fits image
Outputs:
flatlist -> List of paths to flatfield images
list_of_objects -> List of distinct objects
objectlists -> List of lists, each one all of the files for an object
list_of_filters -> List of distinct filters
filterlists -> List of lists, each one all the files for a filter
"""
# Open each file and look for flats and new filters/objects
list_of_objects = []
list_of_filters = []
flatlist = []
for i in range(len(fnlist)):
image = FPImage(fnlist[i])
# Skip the rest if image was previously flagged as bad
if image.goodtog is None:
# Case for flats
if image.object == "FLAT":
flatlist.append(fnlist[i])
# Case for ARCs
elif image.object == "ARC":
if not (image.filter in list_of_filters):
list_of_filters.append(image.filter)
# Case for Objects
else:
if not (image.filter in list_of_filters):
list_of_filters.append(image.filter)
if not (image.object in list_of_objects):
list_of_objects.append(image.object)
image.close()
list_of_filters = np.array(list_of_filters)
list_of_objects = np.array(list_of_objects)
# Reopen the files and populate the object lists
objectlists = []
filterlists = []
for i in range(len(list_of_objects)):
objectlists.append([])
for i in range(len(list_of_filters)):
filterlists.append([])
for i in range(len(fnlist)):
image = FPImage(fnlist[i])
# Skip the rest if image was previously flagged as bad
if image.goodtog is None:
if image.object != "FLAT":
if image.object != "ARC":
object_index = np.where(image.object == list_of_objects)[0][0]
objectlists[object_index].append(fnlist[i])
filter_index = np.where(image.filter == list_of_filters)[0][0]
filterlists[filter_index].append(fnlist[i])
image.close()
return flatlist, list_of_objects, objectlists, list_of_filters, filterlists
def verify_images(fnlist):
"""Interactively plots all of the images in 'fnlist' to verify their
contents are correct. Allows user to mark bad images and change image
header keywords to correct issues.
Inputs:
fnlist -> List of filenames to be plotted
Outputs:
newfnlist -> New list of filenames with bad files removed from the list
"""
# Change pyplot shortcut keys
oldsavekey = plt.rcParams["keymap.save"]
plt.rcParams["keymap.save"] = ""
# How many total images are there?
num_images = len(fnlist)
flagged = np.zeros(len(fnlist), dtype="bool")
# Interactively look at the images
current_num = 0
while True:
image = FPImage(fnlist[current_num], update=True)
image.header["fpverify"] = "True"
verify = Verify_Images_Plot(image.inty, image.object, flagged[current_num], current_num + 1, num_images)
image.close()
if verify.key == "a":
current_num = current_num - 1
if verify.key == "d":
current_num = current_num + 1
if verify.key == "w":
flagged[current_num] = True
if verify.key == "s":
flagged[current_num] = False
# Breakout condition
if current_num == -1:
while True:
yn = raw_input("Finished flagging images? (y/n) ")
if "n" in yn or "N" in yn:
current_num = 0
break
elif "y" in yn or "Y" in yn:
break
elif current_num == num_images:
while True:
yn = raw_input("Finished flagging images? (y/n) ")
if "n" in yn or "N" in yn:
current_num = current_num - 1
break
elif "y" in yn or "Y" in yn:
break
if current_num == -1 or current_num == num_images or verify.key == "q":
break
# Review flagged images
print "Reviewing " + str(np.sum(flagged)) + " flagged images..."
newfnlist = []
for i in range(len(fnlist)):
if flagged[i]:
image = FPImage(fnlist[i], update=True)
review = Review_Images_Plot(image.inty, image.object, fnlist[i])
if review.key == "h":
# Correct header
while True:
prompt = "New object type for header (ARC, FLAT, etc.): "
newhead = raw_input(prompt)
prompt = "New object header: '" + newhead + "'. Is this okay? (y/n) "
yn = raw_input(prompt)
if ("y" in yn or "Y" in yn) and not ("n" in yn or "N" in yn):
image.object = newhead
break
newfnlist.append(fnlist[i])
if review.key == "a":
newfnlist.append(fnlist[i])
if review.key == "d":
print fnlist[i] + " removed from file list."
image.goodtog = "False"
image.close()
else:
newfnlist.append(fnlist[i])
plt.rcParams["keymap.save"] = oldsavekey
return newfnlist
def deghost(fn):
"""Routine to deghost an image by rotating it about a central point and
subtracting a constant multiple of this rotated image from the original.
My experience has shown that about 0.04 is the right value, but your
mileage may vary.
The fits header must contain values in "fpxcen" and "fpycen" for the center
about which to be rotated.
Optionally also modifies an uncertainty image to account for the effects
of deghosting on the error propagation.
Creates the fits header keyword "fpghost" = "True".
Inputs:
fn -> String, the path to the fits image to be deghosted.
"""
# Open the image and check for center coordinates
image = FPImage(fn, update=True)
if image.xcen is None:
exit("Error! Image "+fn+" doesn't have center coordinates in header!")
xcen = image.xcen+1
ycen = image.ycen+1
bins = int(image.bins.split()[0])
reflection_xcen = image.xcen + reflection_center_x_shift/bins
reflection_ycen = image.ycen + reflection_center_y_shift/bins
r_array = image.rarray(reflection_xcen, reflection_ycen)
g_array = reflection_intercept + reflection_slope*bins*r_array
# Deghost the intensity image
print "Deghosting image "+fn
# Determine image size
xsize, ysize = image.xsize, image.ysize
# Make a mask for the chip gaps and outside-aperture stuff
mask = image.inty == 0
# Make an array of the flipped data
flipinty = image.inty[::-1, ::-1].copy()*1.0
flipvari = image.vari[::-1, ::-1].copy()*1.0
flip_g = g_array[::-1, ::-1].copy()*1.0
# Calculate the difference between the image's geometric center (midpoint)
# and the axis of rotation
xshift = 2*xcen-xsize-1
yshift = 2*ycen-ysize-1
# A given pixel's position, when rotated, will overlap its four
# neighboring pixels. All pixels will have the same four overlapping
# regions because the rotation is 180 degrees. Here we take a weighted
# sum of these four pixels, where the weights are equal to the areas
# of overlap. This weighted sum is subtracted from the original pixel.
for i in range(4):
# This branching is for the four overlapping pixel regions
if i == 0:
miny = max(np.floor(yshift), 0)
maxy = min(ysize+np.floor(yshift), ysize)
minx = max(np.floor(xshift), 0)
maxx = min(xsize+np.floor(xshift), xsize)
flipminy = max(-np.floor(yshift), 0)
flipmaxy = min(ysize, ysize-np.floor(yshift))
flipminx = max(-np.floor(xshift), 0)
flipmaxx = min(xsize, xsize-np.floor(xshift))
frac = abs((np.ceil(yshift)-yshift)*(np.ceil(xshift)-xshift))
if i == 1:
miny = max(np.ceil(yshift), 0)
maxy = min(ysize+np.ceil(yshift), ysize)
minx = max(np.floor(xshift), 0)
maxx = min(xsize+np.floor(xshift), xsize)
flipminy = max(-np.ceil(yshift), 0)
flipmaxy = min(ysize, ysize-np.ceil(yshift))
flipminx = max(-np.floor(xshift), 0)
flipmaxx = min(xsize, xsize-np.floor(xshift))
frac = abs((np.floor(yshift)-yshift)*(np.ceil(xshift)-xshift))
if i == 2:
miny = max(np.floor(yshift), 0)
maxy = min(ysize+np.floor(yshift), ysize)
minx = max(np.ceil(xshift), 0)
maxx = min(xsize+np.ceil(xshift), xsize)
flipminy = max(-np.floor(yshift), 0)
flipmaxy = min(ysize, ysize-np.floor(yshift))
flipminx = max(-np.ceil(xshift), 0)
flipmaxx = min(xsize, xsize-np.ceil(xshift))
frac = abs((np.ceil(yshift)-yshift)*(np.floor(xshift)-xshift))
if i == 3:
miny = max(np.ceil(yshift), 0)
maxy = min(ysize+np.ceil(yshift), ysize)
minx = max(np.ceil(xshift), 0)
maxx = min(xsize+np.ceil(xshift), xsize)
flipminy = max(-np.ceil(yshift), 0)
flipmaxy = min(ysize, ysize-np.ceil(yshift))
flipminx = max(-np.ceil(xshift), 0)
flipmaxx = min(xsize, xsize-np.ceil(xshift))
frac = abs((np.floor(yshift)-yshift)*(np.floor(xshift)-xshift))
g = flip_g[flipminy:flipmaxy,
flipminx:flipmaxx]
# Rotate and subtract the intensity array
image.inty[miny:maxy,
minx:maxx] -= g*frac*flipinty[flipminy:flipmaxy,
flipminx:flipmaxx]
image.vari[miny:maxy,
minx:maxx] += (g*frac)**2*flipvari[flipminy:flipmaxy,
flipminx:flipmaxx]
# Remask the intensity data using the mask we created
image.inty[mask] = 0
# Update the header
image.ghosttog = "True"
# Close the image
image.close()
return
def sub_sky_rings(fnlist, medfilelist):
"""Fits for night sky rings in a series of images, then subtracts them off.
If uncertainty images exist, updates them with better uncertainties.
The rings are fitted in an interactive way by the user.
After the ring subtraction, the header keyword "fpdering" is created and
set to "True."
Note: A 'median.fits' image must exist for the object or this routine will
not work.
Inputs:
fnlist -> List of strings, each the path to a fits image.
medfilelist -> List of paths to median images for each image to subtract
off (probably all the same, but could be different)
"""
# This bit takes care of the 's' to save shortcut in matplotlib.
oldsavekey = plt.rcParams["keymap.save"]
plt.rcParams["keymap.save"] = ""
oldfullscreenkey = plt.rcParams['keymap.fullscreen']
plt.rcParams['keymap.fullscreen'] = ""
# Open all of the images, median-subtract them, make wavelength arrays
# make skywavelibs for each, make spectra for each, trim images
images = [FPImage(fn) for fn in fnlist]
wavearraylist = []
skywavelibs = []
skywavelibs_extended = []
spectrum_wave = []
spectrum_inty = []
minwavelist = []
maxwavelist = []
xcenlist = []
ycenlist = []
Flist = []
wave0list = []
has_been_saved = np.zeros(len(fnlist), dtype="bool")
for i in range(len(fnlist)):
# Get a bunch of relevant header values
medimage = fits.open(medfilelist[i])
Flist.append(images[i].calf)
wave0list.append(images[i].wave0)
xcen = images[i].xcen
ycen = images[i].ycen
arad = images[i].arad
axcen = images[i].axcen
aycen = images[i].aycen
# Median subtract it
images[i].inty -= medimage[0].data
images[i].inty -= np.median(images[i].inty[images[i].badp != 1])
# Make wavelength array
r2grid = images[i].rarray(xcen, ycen)**2
wavearraylist.append(wave0list[i]/np.sqrt(1+r2grid/Flist[i]**2))
# Get the sky wave library
minwavelist.append(np.min(wavearraylist[i][r2grid < arad**2]))
maxwavelist.append(np.max(wavearraylist[i][r2grid < arad**2]))
skywaves = get_libraries(images[i].filter)[1]
skywavelibs.append(skywaves[np.logical_and(skywaves > minwavelist[i],
skywaves < maxwavelist[i])])
# Make an "extended" sky wave library
lowermask = np.logical_and(skywaves < minwavelist[i],
skywaves > minwavelist[i]-5)
uppermask = np.logical_and(skywaves > maxwavelist[i],
skywaves < maxwavelist[i]+5)
skywavelibs_extended.append(skywaves[np.logical_or(uppermask,
lowermask)])
# Make the spectrum
minwav = np.min(wavearraylist[i][r2grid < arad**2])
maxwav = np.max(wavearraylist[i][r2grid < arad**2])
wavstep = 0.25 # Quarter-angstrom spacing
spectrum_wave.append(np.linspace(minwav, maxwav,
np.int(((maxwav-minwav)/wavstep))))
spectrum_inty.append(np.zeros_like(spectrum_wave[i][1:]))
for j in range(len(spectrum_wave[i])-1):
uppermask = wavearraylist[i] < spectrum_wave[i][j+1]
lowermask = wavearraylist[i] > spectrum_wave[i][j]
mask = np.logical_and(uppermask, lowermask)
goodmask = np.logical_and(mask, images[i].badp == 0)
spectrum_inty[i][j] = np.median(images[i].inty[goodmask])
spectrum_wave[i] = 0.5*(spectrum_wave[i][:-1]+spectrum_wave[i][1:])
# Trim the images and arrays to the aperture size
images[i].inty = images[i].inty[aycen-arad:aycen+arad,
axcen-arad:axcen+arad]
wavearraylist[i] = wavearraylist[i][aycen-arad:aycen+arad,
axcen-arad:axcen+arad]
xcenlist.append(arad+xcen-axcen)
ycenlist.append(arad+ycen-aycen)
# Convert skywavelibs to lists
skywavelibs[i] = list(skywavelibs[i])
skywavelibs_extended[i] = list(skywavelibs_extended[i])
# Close median image
medimage.close()
# Try to fix the NaNs
mask = np.logical_not(np.isnan(spectrum_inty[i]))
spectrum_wave[i] = spectrum_wave[i][mask]
spectrum_inty[i] = spectrum_inty[i][mask]
# Interactive plotting of ring profiles
addedwaves = []
final_fitted_waves = []
final_fitted_intys = []
final_fitted_sigs = []
for i in range(len(fnlist)):
addedwaves.append([])
final_fitted_waves.append([])
final_fitted_intys.append([])
final_fitted_sigs.append([])
i = 0
while True:
# Determine which wavelengths we want to fit
waves_to_fit = skywavelibs[i]+addedwaves[i]
# Generate a fitting function from those wavelengths
func_to_fit = make_sum_gaussians(waves_to_fit)
# Come up with reasonable guesses for the fitting function parameters
contguess = [0]
intyguesses = []
sigguesses = []
for j in range(len(waves_to_fit)):
uppermask = spectrum_wave[i] < waves_to_fit[j]+4
lowermask = spectrum_wave[i] > waves_to_fit[j]-4
mask = np.logical_and(uppermask, lowermask)
# Guess at line intensity via integral
intyguesses.append(np.sum(spectrum_inty[i][mask] *
(spectrum_wave[i][1] -
spectrum_wave[i][0])))
# Guess sigma is 2 angstroms
sigguesses.append(2)
guess = contguess+intyguesses+sigguesses
# Fit the spectrum
fitsuccess = True
try:
fit = curve_fit(func_to_fit, spectrum_wave[i],
spectrum_inty[i], p0=guess)[0]
except RuntimeError:
print ("Warning: Fit did not converge. " +
"Maybe remove some erroneous lines from the fit?")
fit = guess
fitsuccess = False
fitcont = fit[0]
fitintys = np.array(fit[1:len(waves_to_fit)+1])
fitsigs = np.array(fit[len(waves_to_fit)+1:2*len(waves_to_fit)+1])
# Flip signs of negative sigma fits (sign degeneracy)
fitintys[fitsigs < 0] = -1*fitintys[fitsigs < 0]
fitsigs[fitsigs < 0] = -1*fitsigs[fitsigs < 0]
# Make the subtracted plot array
subarray = images[i].inty.copy()
for j in range(len(waves_to_fit)):
subarray -= fitintys[j]*nGauss(wavearraylist[i]-waves_to_fit[j],
fitsigs[j])
# Figure out which radius each wavelength is at
radiilist = []
for j in range(len(waves_to_fit)):
radiilist.append(Flist[i] *
np.sqrt((wave0list[i]/waves_to_fit[j])**2-1))
# Create the subtracted spectrum
sub_spec_inty = spectrum_inty[i] - fitcont
for j in range(len(waves_to_fit)):
sub_spec_inty -= (fitintys[j] *
nGauss(spectrum_wave[i]-waves_to_fit[j],
fitsigs[j]))
# Create the spectrum fit plot
fit_X = np.linspace(minwavelist[i], maxwavelist[i], 500)
fit_Y = np.ones_like(fit_X)*fitcont
for j in range(len(waves_to_fit)):
fit_Y += fitintys[j]*nGauss(fit_X-waves_to_fit[j], fitsigs[j])
# Plot the image, spectrum, and fit
profile_plot = SkyRingPlot(images[i].inty, subarray,
xcenlist[i], ycenlist[i], radiilist,
spectrum_wave[i], spectrum_inty[i],
sub_spec_inty, fit_X, fit_Y,
skywavelibs[i], addedwaves[i],
skywavelibs_extended[i],
repr(i+1)+"/"+repr(len(fnlist)),
has_been_saved[i], fitsuccess)
# Shifting images and breakout condition
if profile_plot.key == "a":
i += -1
if profile_plot.key == "d":
i += 1
quitloop = False
if (i == -1 or i == len(fnlist) or profile_plot.key == "q"):
if (np.sum(np.logical_not(has_been_saved)) == 0):
# while True:
# yn = raw_input("Finished fitting ring profiles? (y/n) ")
# if "n" in yn or "N" in yn:
# break
# if "y" in yn or "Y" in yn:
# quitloop = True
# break
quitloop = True
else:
print ("Error: Ring fits have not yet been " +
"saved for the following images:")
imagenumbers = np.arange(len(fnlist))+1
print imagenumbers[np.logical_not(has_been_saved)]
if quitloop:
break
if i == -1:
i = 0
if i == len(fnlist):
i = len(fnlist)-1
# Delete ring option
if profile_plot.key == "s":
nearest_wave = None
if profile_plot.axis in [1, 3] and len(waves_to_fit) != 0:
# The keypress was made in an image plot
clicked_radius = np.sqrt((profile_plot.xcoo - xcenlist[i])**2 +
(profile_plot.ycoo - ycenlist[i])**2)
near_index = np.argmin(np.abs((np.array(radiilist) -
clicked_radius)))
nearest_wave = waves_to_fit[near_index]
elif profile_plot.axis in [2, 4] and len(waves_to_fit) != 0:
# The keypress was in a spectrum plot
clicked_wave = profile_plot.xcoo
near_index = np.argmin(np.abs(np.array(waves_to_fit) -
clicked_wave))
nearest_wave = waves_to_fit[near_index]
if nearest_wave is not None:
# Remove the nearest wavelength from the sky_wave_lib or
# added waves, add it to extra waves
if nearest_wave in skywavelibs[i]:
skywavelibs[i].remove(nearest_wave)
skywavelibs_extended[i].append(nearest_wave)
if nearest_wave in addedwaves[i]:
addedwaves[i].remove(nearest_wave)
# Add ring option
if profile_plot.key == "w":
clicked_wave = None
if profile_plot.axis in [1, 3]:
# The keypress was made in an image plot
clicked_radius = np.sqrt((profile_plot.xcoo - xcenlist[i])**2 +
(profile_plot.ycoo - ycenlist[i])**2)
# Convert radius to wavelength
clicked_wave = (wave0list[i] /
(1+clicked_radius**2/Flist[i]**2)**0.5)
elif profile_plot.axis in [2, 4]:
# The keypress was in a spectrum plot
clicked_wave = profile_plot.xcoo
if clicked_wave is not None:
# Find the nearest wavelength in the extended list
if len(np.array(skywavelibs_extended[i])-clicked_wave) > 0:
near = np.argmin(np.abs(np.array(skywavelibs_extended[i]) -
clicked_wave))
wave_to_add = skywavelibs_extended[i][near]
# Add that wave to skywavelibs, remove it from extended
skywavelibs[i].append(wave_to_add)
skywavelibs_extended[i].remove(wave_to_add)
# Force add ring option
if profile_plot.key == "e":
clicked_wave = None
if profile_plot.axis in [1, 3]:
# The click was made in an image plot
clicked_radius = np.sqrt((profile_plot.xcoo - xcenlist[i])**2 +
(profile_plot.ycoo - ycenlist[i])**2)
# Convert radius to wavelength
clicked_wave = (wave0list[i] /
(1+clicked_radius**2/Flist[i]**2)**0.5)
elif profile_plot.axis in [2, 4]:
# The click was in a spectrum plot
clicked_wave = profile_plot.xcoo
if clicked_wave is not None:
# Add this wavelength to the added array
addedwaves[i].append(clicked_wave)
# Save option
if profile_plot.key == "r":
final_fitted_waves[i] = waves_to_fit[:]
final_fitted_intys[i] = fitintys[:]
final_fitted_sigs[i] = fitsigs[:]
has_been_saved[i] = True
# Manual Mode Option
if profile_plot.key == "x":
# Initialize the manual mode lists
man_waves = list(waves_to_fit)
man_intys = list(fitintys)
man_sigs = list(fitsigs)
man_cont = fitcont
man_real = []
for wave in man_waves:
if wave in skywavelibs[i] or wave in skywavelibs_extended[i]:
man_real.append(True)
else:
man_real.append(False)
# Initialize refinement level and selected line
selected_line = 0
refine = 1
inty_refine = 0.25*(np.max(spectrum_inty[i]) -
np.min(spectrum_inty[i]))
sig_refine = 0.5
cont_refine = inty_refine
# Loop until completion
while True:
# Make the subtracted plot array
subarray = images[i].inty.copy()
for j in range(len(man_waves)):
subarray -= man_intys[j]*nGauss((wavearraylist[i] -
man_waves[j]),
man_sigs[j])
# Figure out which radius each wavelength is at
radiilist = []
for j in range(len(man_waves)):
radiilist.append(Flist[i] *
np.sqrt((wave0list[i]/man_waves[j])**2-1))
for skywav in skywavelibs_extended[i]:
radiilist.append(Flist[i] *
np.sqrt((wave0list[i] / skywav)**2-1))
# Create the subtracted spectrum
sub_spec_inty = spectrum_inty[i] - man_cont
for j in range(len(man_waves)):
sub_spec_inty -= (man_intys[j] *
nGauss(spectrum_wave[i]-man_waves[j],
man_sigs[j]))
# Create the spectrum fit plot
fit_X = np.linspace(minwavelist[i], maxwavelist[i], 500)
fit_Y = np.ones_like(fit_X)*man_cont
for j in range(len(man_waves)):
fit_Y += man_intys[j]*nGauss(fit_X-man_waves[j],
man_sigs[j])
# What colors are we using?
colors = []
for k in range(len(man_waves)):
if selected_line == k:
colors.append('purple')
elif not man_real[k]:
colors.append('green')
elif man_real[k]:
colors.append('blue')
for _w in skywavelibs_extended[i]:
colors.append('red')
# Plot the spectrum and fit, get user input
man_plot = ManualPlot(images[i].inty, subarray,
xcenlist[i], ycenlist[i],
spectrum_wave[i], spectrum_inty[i],
sub_spec_inty,
fit_X, fit_Y,
has_been_saved[i], (repr(i+1)+"/" +
repr(len(fnlist))),
radiilist,
man_waves+skywavelibs_extended[i],
colors)
# Cycle selected line
if man_plot.key == "z":
selected_line += 1
if selected_line >= len(man_waves):
selected_line = 0
refine = 1
# Save fit
if man_plot.key == "r":
final_fitted_waves[i] = man_waves[:]
final_fitted_intys[i] = man_intys[:]
final_fitted_sigs[i] = man_sigs[:]
has_been_saved[i] = True
break
# Refinement levels
if man_plot.key == "c":
refine *= 0.5
if man_plot.key == "v":
refine *= 2
# Increase/decrease inty
if len(man_waves) != 0:
if man_plot.key == "w":
man_intys[selected_line] += refine*inty_refine
if man_plot.key == "s":
man_intys[selected_line] -= refine*inty_refine
# Increase/decrease line width
if len(man_waves) != 0:
if man_plot.key == "q":
man_sigs[selected_line] += refine*sig_refine
if man_plot.key == "a":
man_sigs[selected_line] -= refine*sig_refine
# Increase/decrease continuum
if man_plot.key == "t":
man_cont += refine*cont_refine
if man_plot.key == "g":
man_cont -= refine*cont_refine
# Add the known line nearest the keypress
if man_plot.key == "e":
clicked_wave = None
if man_plot.axis in [1, 3]:
# The keypress was made in an image plot
clicked_radius = np.sqrt((man_plot.xcoo -
xcenlist[i])**2 +
(man_plot.ycoo -
ycenlist[i])**2)
# Convert radius to wavelength
clicked_wave = (wave0list[i] /
(1+clicked_radius**2/Flist[i]**2)**0.5)
elif man_plot.axis in [2, 4]:
# The keypress was in a spectrum plot
clicked_wave = man_plot.xcoo
if clicked_wave is not None:
# Find the nearest wavelength in the extended list
if len(np.array(skywavelibs_extended[i]) -
clicked_wave) > 0:
sky = np.array(skywavelibs_extended[i])
near = np.argmin(np.abs(sky-clicked_wave))
wave_to_add = skywavelibs_extended[i][near]
# Add that wave to manwaves,
# remove from extended list
man_waves.append(wave_to_add)
man_intys.append(0)
man_sigs.append(1)
man_real.append(True)
skywavelibs_extended[i].remove(wave_to_add)
selected_line = len(man_waves)-1
# Remove line nearest the keypress
if man_plot.key == "d":
nearest_wave = None
if man_plot.axis in [1, 3] and len(man_waves) != 0:
# The keypress was made in an image plot
clicked_radius = np.sqrt((man_plot.xcoo -
xcenlist[i])**2 +
(man_plot.ycoo -
ycenlist[i])**2)
near_index = np.argmin(np.abs((np.array(radiilist) -
clicked_radius)))
nearest_wave = man_waves[near_index]
elif man_plot.axis in [2, 4] and len(man_waves) != 0:
# The keypress was in a spectrum plot
clicked_wave = man_plot.xcoo
near_index = np.argmin(np.abs(np.array(man_waves) -
clicked_wave))
nearest_wave = man_waves[near_index]
if nearest_wave is not None:
# Remove the nearest wavelength
# re-add to extended list
# if it was real
wave_index = np.where(np.array(man_waves) ==
nearest_wave)[0][0]
man_waves.pop(wave_index)
man_intys.pop(wave_index)
man_sigs.pop(wave_index)
if man_real[wave_index]:
skywavelibs_extended[i].append(nearest_wave)
man_real.pop(wave_index)
if wave_index == selected_line:
selected_line = 0
# Force-add
if man_plot.key == "f":
clicked_wave = None
if profile_plot.axis in [1, 3]:
# The click was made in an image plot
clicked_radius = np.sqrt((man_plot.xcoo -
xcenlist[i])**2 +
(man_plot.ycoo -
ycenlist[i])**2)
# Convert radius to wavelength
clicked_wave = (wave0list[i] /
(1+clicked_radius**2 /
Flist[i]**2)**0.5)
elif profile_plot.axis in [2, 4]:
# The click was in a spectrum plot
clicked_wave = man_plot.xcoo
if clicked_wave is not None:
# Add this wavelength to the added array
man_waves.append(clicked_wave)
man_intys.append(0)
man_sigs.append(1)
man_real.append(False)
selected_line = len(man_waves)-1
# Switch back to automatic
if man_plot.key == "x":
break
# Close all of the images
for image in images:
image.close()
# Subtract the ring profiles and update headers
for i in range(len(fnlist)):
image = FPImage(fnlist[i], update=True)
arad = image.arad
axcen = image.axcen
aycen = image.aycen
mask = image.inty == 0 # For re-correcting chip gaps
for j in range(len(final_fitted_waves[i])):
image.header['subwave'+repr(j)] = final_fitted_waves[i][j]
image.header['subinty'+repr(j)] = final_fitted_intys[i][j]
image.header['subsig'+repr(j)] = final_fitted_sigs[i][j]
ringimg = (final_fitted_intys[i][j] *
nGauss(wavearraylist[i]-final_fitted_waves[i][j],
final_fitted_sigs[i][j]))
image.inty[aycen-arad:aycen+arad, axcen-arad:axcen+arad] -= ringimg
image.ringtog = "True"
image.inty[mask] = 0 # For re-correcting chip gaps
image.close()
# Restore the old keyword shortcut
plt.rcParams["keymap.save"] = oldsavekey
plt.rcParams['keymap.fullscreen'] = oldfullscreenkey
return
def find_ghost_centers(fnlist, tolerance=3, thresh=4, guess=None):
"""This routine finds the most likely optical center for a series of images
by attempting to match ghost reflections of stars with their stellar
counterparts. It can be rather slow if the fields are very dense with
stars, but is also much more likely to succeed in locating the correct
center in dense fields.
Images should have already been aperture masked at this point. If they
haven't, run 'aperture_mask' on them first.
It is useful if the images have had their seeing FWHMs measured. If they
have, these values (in pixels) should be in the fits headers as "FPFWHM".
If not, the FWHM is assumed to be 5 pixels (and this is not ideal).
The routine creates a number of temporary files while running, which are
deleted at the end of the routine. Interrupting the routine while running
is probably not a great idea.
The routine returns a list of image centers as well as appending these to
the fits headers as "fpxcen" and "fpycen"
Inputs:
fnlist -> List of strings, each one containing the path to a fits image.
The images should be roughly aligned to one another or the
routine will not work.
tolerance -> Optional. How close two pixels can be and be "close enough"
Default is 3 pixels.
thresh -> Optional. Level above sky background variation to look for objs.
Default is 4.5 (times SkySigma). Decrease if center positions
aren't being found accurately. Increase for crowded fields to
decrease computation time.
guess -> Optional. If you already have an idea of where the center should
be, you'd put it here. Should be a 2-long iterable, with guess[0]
being the X center guess, and guess[1] being the y center guess.
Outputs:
xcenlist -> List of image center X coordinates
ycenlist -> List of image center Y coordinates
"""
# Get image FWHMs
fwhm = np.empty(len(fnlist))
firstimage = FPImage(fnlist[0])
toggle = firstimage.fwhm
axcen = firstimage.axcen
aycen = firstimage.aycen
arad = firstimage.arad
firstimage.close()
if axcen is None:
exit("Error! Images have not yet been aperture-masked! Do this first!")
if toggle is None:
print "Warning: FWHMs have not been measured!"
print "Assuming 5 pixel FWHM for all images."
fwhm = 5.*np.ones(len(fnlist))
else:
for i in range(len(fnlist)):
image = FPImage(fnlist[i])
fwhm[i] = image.fwhm
image.close()
# Get sky background levels
skyavg = np.empty(len(fnlist))
skysig = np.empty(len(fnlist))
for i in range(len(fnlist)):
image = FPImage(fnlist[i])
skyavg[i], skysig[i], _skyvar = image.skybackground()
image.close()
# Identify the stars in each image
xlists = []
ylists = []
maglists = []
print "Identifying stars and ghosts in each image..."
for i in range(len(fnlist)):
xlists.append([])
ylists.append([])
maglists.append([])
image = FPImage(fnlist[i])
axcen = image.axcen
aycen = image.aycen
arad = image.arad
sources = daofind(image.inty-skyavg[i],
fwhm=fwhm[i],
threshold=thresh*skysig[i]).as_array()
for j in range(len(sources)):
# Masks for center and edge of image
cenmask = ((sources[j][1]-axcen)**2 +
(sources[j][2]-aycen)**2 > (0.05*arad)**2)
edgemask = ((sources[j][1]-axcen)**2 +
(sources[j][2]-aycen)**2 < (0.95*arad)**2)
if np.logical_and(cenmask, edgemask):
xlists[i].append(sources[j][1])
ylists[i].append(sources[j][2])
maglists[i].append(sources[j][-1])
image.close()
if guess is None:
# Use the found stars to come up with a center guess for each image
xcen = np.zeros(len(fnlist))
ycen = np.zeros(len(fnlist))
goodcen = np.zeros(len(fnlist))
for i in range(len(fnlist)):
N = len(xlists[i])
xcenarray = np.zeros(((N*N-N)/2))
ycenarray = np.zeros(((N*N-N)/2))
dist2array = np.zeros(((N*N-N)/2))
sub1array = np.zeros(((N*N-N)/2))
index = 0
# All "possible" centers for all possible pairs of stars
for j in range(N):
for k in range(j+1, N):
xcenarray[index] = xlists[i][j]+xlists[i][k]
ycenarray[index] = ylists[i][j]+ylists[i][k]
index = index+1
xcenarray, ycenarray = 0.5*xcenarray, 0.5*ycenarray
# Cross check the various possible centers against each other
for j in range(len(xcenarray)):
dist2array = ((xcenarray-xcenarray[j])**2 +
(ycenarray-ycenarray[j])**2)
sub1array[j] = np.sum(dist2array < tolerance**2)
# Determine the locations of the "best" centers.
bestcenloc = np.where(sub1array == max(sub1array))[0]
# Now cross check JUST the best ones against each other
sub1array = np.zeros(len(bestcenloc))
xcenarray = xcenarray[bestcenloc]
ycenarray = ycenarray[bestcenloc]
for j in range(len(bestcenloc)):
dist2array = ((xcenarray-xcenarray[j])**2 +
(ycenarray-ycenarray[j])**2)
sub1array[j] = np.sum(dist2array < tolerance**2)
# Again, determine the locations of the "best" centers.
bestcenloc = np.where(sub1array == max(sub1array))[0]
xcen[i] = np.average(xcenarray[bestcenloc])
ycen[i] = np.average(ycenarray[bestcenloc])
# Cross-check the various image's centers against each other
for i in range(len(fnlist)):
dist2array = (xcen-xcen[i])**2 + (ycen-ycen[i])**2
goodcen[i] = np.sum(dist2array < tolerance**2)
# Determine where in the arrays the best fitting centers are
bestcenloc = np.where(goodcen == max(goodcen))[0]
bestxcen = np.average(xcen[bestcenloc])
bestycen = np.average(ycen[bestcenloc])
else:
# Forced guess:
bestxcen, bestycen = guess[0], guess[1]
# Now we want to improve the center for each image using the best guesses
xcenlist = np.zeros(len(fnlist))
ycenlist = np.zeros(len(fnlist))
objxs = []
objys = []
ghoxs = []
ghoys = []
for i in range(len(fnlist)):
# Where would the reflected objects be if they exist
refxlist = 2.*bestxcen - np.array(xlists[i])
refylist = 2.*bestycen - np.array(ylists[i])
# Populate lists of objects and ghosts based on this
objxs.append([])
objys.append([])
ghoxs.append([])
ghoys.append([])
for j in range(len(xlists[i])):
dist2list = ((xlists[i] - refxlist[j])**2 +
(ylists[i] - refylist[j])**2)
matchlist = dist2list < tolerance**2
if np.sum(matchlist) >= 1:
# We found a match! Now we need to know where the match is
matchloc = np.where(matchlist == 1)[0][0]
# Cool, now, is this thing brighter than the ghost?
if maglists[i][matchloc] < maglists[i][j]:
# It is! Record it:
objxs[i].append(xlists[i][matchloc])
objys[i].append(ylists[i][matchloc])
ghoxs[i].append(xlists[i][j])
ghoys[i].append(ylists[i][j])
# Calculate the centers based on the object / ghost coords
if len(objxs[i]) == 0:
xcenlist[i] = 0
ycenlist[i] = 0
else:
xcenlist[i] = 0.5*(np.average(objxs[i])+np.average(ghoxs[i]))
ycenlist[i] = 0.5*(np.average(objys[i])+np.average(ghoys[i]))
# Fill in the blanks with a "best guess"
xcenlist[xcenlist == 0] = np.average(xcenlist[xcenlist != 0])
ycenlist[ycenlist == 0] = np.average(ycenlist[ycenlist != 0])
xcenlist[np.isnan(xcenlist)] = bestxcen
ycenlist[np.isnan(ycenlist)] = bestycen
# Append the values to the image headers
for i in range(len(fnlist)):
image = FPImage(fnlist[i], update=True)
image.xcen = xcenlist[i]
image.ycen = ycenlist[i]
image.close()
# Manually verify ghost centers
while True:
yn = raw_input("Manually verify ghost centers? (Recommended) (y/n) ")
if "n" in yn or "N" in yn:
break
elif "y" in yn or "Y" in yn:
goodtog = verify_center(fnlist,
objxs, objys,
ghoxs, ghoys,
xcenlist, ycenlist)
if goodtog:
break
else:
exit("Centers not approved!")
return xcenlist, ycenlist
def align_norm(fnlist, tolerance=5, thresh=3.5):
"""Aligns a set of images to each other, as well as normalizing the images
to the same average brightness.
Both the alignment and normalization are accomplished through stellar
photometry using the IRAF routine 'daophot'. The centroids of a handful
of stars are found and used to run the IRAF routine 'imalign'. The
instrumental magnitudes of the stars are used to determine by how much
each image must be scaled for the photometry to match across images.
The images are simply updated with their rescaled, shifted selves. This
overwrites the previous images and adds the header keyword 'fpphot' to
the images.
A handful of temporary files are created during this process, which should
all be deleted by the routine at the end. But if it is interrupted, they
might not be.
If the uncertainty images exist, this routine also shifts them by the same
amounts as the intensity images, as well as updating the uncertainty values
for both the new normalization and the uncertainties in normalizing the
images.
Inputs:
fnlist -> List of strings, each the path to a fits image.
tolerance -> How close two objects can be and still be considered the same
object. Default is 3 pixels.
thresh -> Optional. Level above sky background variation to look for objs.
Default is 3.5 (times SkySigma). Decrease if center positions
aren't being found accurately. Increase for crowded fields to
decrease computation time.
"""
# Get image FWHMs
fwhm = np.empty(len(fnlist))
firstimage = FPImage(fnlist[0])
toggle = firstimage.fwhm
axcen = firstimage.axcen
aycen = firstimage.aycen
arad = firstimage.arad
firstimage.close()
if axcen is None:
print "Error! Images have not yet been aperture-masked! Do this first!"
crash()
if toggle is None:
print "Warning! FWHMs have not been measured!"
print "Assuming 5 pixel FWHM for all images."
for i in range(len(fnlist)):
fwhm[i] = 5
else:
for i in range(len(fnlist)):
image = FPImage(fnlist[i])
fwhm[i] = image.fwhm
image.close()
# Get sky background levels
skyavg = np.empty(len(fnlist))
skysig = np.empty(len(fnlist))
for i in range(len(fnlist)):
image = FPImage(fnlist[i])
skyavg[i], skysig[i], _skyvar = image.skybackground()
image.close()
# Identify the stars in each image
xlists = []
ylists = []
print "Identifying stars in each image..."
for i in range(len(fnlist)):
xlists.append([])
ylists.append([])
image = FPImage(fnlist[i])
axcen = image.axcen
aycen = image.aycen
arad = image.arad
sources = daofind(image.inty-skyavg[i],
fwhm=fwhm[i],
threshold=thresh*skysig[i]).as_array()
for j in range(len(sources)):
# If the source is not near the center or edge
centermask = ((sources[j][1]-axcen)**2 +
(sources[j][2]-aycen)**2 > (0.05*arad)**2)
edgemask = ((sources[j][1]-axcen)**2 +
(sources[j][2]-aycen)**2 < (0.95*arad)**2)
if np.logical_and(centermask, edgemask):
xlists[i].append(sources[j][1])
ylists[i].append(sources[j][2])
image.close()
# Match objects between fields
print "Matching objects between images..."
xcoo = []
ycoo = []
for i in range(len(xlists[0])):
# For each object in the first image
accept = True
for j in range(1, len(fnlist)):
# For each other image
dist2 = ((np.array(xlists[j])-xlists[0][i])**2 +
(np.array(ylists[j])-ylists[0][i])**2)
if (min(dist2) > tolerance**2):
accept = False
break
if accept:
# We found an object at that position in every image
xcoo.append(xlists[0][i])
ycoo.append(ylists[0][i])
# Create coordinate arrays for the photometry and shifting
x = np.zeros((len(fnlist), len(xcoo)))
y = np.zeros_like(x)
for i in range(len(xcoo)):
# For every object found in the first image
for j in range(len(fnlist)):
# Find that object in every image
dist2 = ((np.array(xlists[j])-xcoo[i])**2 +
(np.array(ylists[j])-ycoo[i])**2)
index = np.argmin(dist2)
x[j, i] = xlists[j][index]
y[j, i] = ylists[j][index]
# Do aperture photometry on the matched objects
print "Performing photometry on matched stars..."
counts = np.zeros_like(x)
dcounts = np.zeros_like(x)
for i in range(len(fnlist)):
image = FPImage(fnlist[i])
apertures = CircularAperture((x[i], y[i]), r=2*fwhm[i])
annuli = CircularAnnulus((x[i], y[i]), r_in=3*fwhm[i], r_out=4*fwhm[i])
phot_table = aperture_photometry(image.inty,
apertures, error=np.sqrt(image.vari))
sky_phot_table = aperture_photometry(image.inty, annuli,
error=np.sqrt(image.vari))
counts[i] = phot_table["aperture_sum"] / apertures.area()
counts[i] -= sky_phot_table["aperture_sum"] / annuli.area()
counts[i] *= apertures.area()
dcounts[i] = phot_table["aperture_sum_err"] / apertures.area()
image.close()
# Calculate the shifts and normalizations
norm, dnorm = calc_norm(counts, dcounts)
for i in range(x.shape[1]):
x[:, i] = -(x[:, i] - x[0, i])
y[:, i] = -(y[:, i] - y[0, i])
xshifts = np.average(x, axis=1)
yshifts = np.average(y, axis=1)
# Normalize the images and put shifts in the image headers
for i in range(len(fnlist)):
image = FPImage(fnlist[i], update=True)
image.phottog = "True"
image.dnorm = dnorm[i]
image.inty /= norm[i]
image.vari = image.vari/norm[i]**2
image.xshift = xshifts[i]
image.yshift = yshifts[i]
image.close()
return
