def combine_flat(flatlist,outfilepath="flat.fits"):
"""Combines a series of flatfield exposures to create a single flatfield
image. Uses only the information contained inside the RSS aperture, which
is the only significant difference between this routine and the familiar
flat combination routines common to CCD astronomy.
Inputs:
flatlist -> A list of strings, each the path to a flatfield exposure
outfilepath -> A string, the path of the output file (default 'flat.fits')
"""
imagelist = []
for i in range(len(flatlist)):
imagelist.append(openfits(flatlist[i]))
xgrid, ygrid = np.meshgrid(np.arange(imagelist[i][0].data.shape[1]),np.arange(imagelist[i][0].data.shape[0]))
imagelist[i][0].data=imagelist[i][0].data/np.median(imagelist[i][0].data[np.power((xgrid-imagelist[i][0].header["fpaxcen"]),2)+np.power((ygrid-imagelist[i][0].header["fpaycen"]),2)<np.power(imagelist[i][0].header["fparad"],2)])
imagestack = np.empty((len(flatlist),imagelist[0][0].data.shape[0],imagelist[0][0].data.shape[1]))
for i in range(len(flatlist)):
imagestack[i,:,:] = imagelist[i][0].data
flatarray = np.median(imagestack,axis=0)
flatarray[flatarray<0.000001]=0
writefits(outfilepath,flatarray,clobber=True)
#Close images
for i in range(len(flatlist)): imagelist[i].close()
return
def fit_velmap_ha_n2_mode(wavelist, intylist, outdir, uncertlist=None, clobber=False):
"""
"""
#Create blank lists for filling with images
wavefilelist = []
intyfilelist = []
if not (uncertlist is None):
uncertfilelist = []
#Open images and populate the lists
for i in range(len(wavelist)):
wavefilelist.append(openfits(wavelist[i]))
intyfilelist.append(openfits(intylist[i]))
if not (uncertlist is None):
uncertfilelist.append(openfits(uncertlist[i]))
#Create blank arrays for filling with data
wavecube = np.zeros((intyfilelist[0][0].data.shape[0],intyfilelist[0][0].data.shape[1],len(wavelist)))
intycube = np.zeros((intyfilelist[0][0].data.shape[0],intyfilelist[0][0].data.shape[1],len(wavelist)))
if not (uncertlist is None):
uncertcube = np.zeros((intyfilelist[0][0].data.shape[0],intyfilelist[0][0].data.shape[1],len(wavelist)))
#Fill the cube arrays with data
for i in range(len(wavelist)):
wavecube[:,:,i] = wavefilelist[i][0].data
intycube[:,:,i] = intyfilelist[i][0].data
if not (uncertlist is None):
uncertcube[:,:,i] = uncertfilelist[i][0].data
#Create blank arrays for the velocity+etc fits
contarray = np.zeros_like(wavefilelist[0][0].data)
intyarray = np.zeros_like(wavefilelist[0][0].data)
intyratioarray = np.zeros_like(wavefilelist[0][0].data)
wavearray = np.zeros_like(wavefilelist[0][0].data)
two_line_success_array = np.zeros_like(wavefilelist[0][0].data,dtype="bool")
one_line_success_array = np.zeros_like(wavefilelist[0][0].data,dtype="bool")
#Create x and y arrays for the "progress bar"
numb_updates=20 #Number of progress updates
xgrid, ygrid = np.meshgrid(np.arange(contarray.shape[1]),np.arange(contarray.shape[0]))
xgrid = xgrid.flatten()
ygrid = ygrid.flatten()
progX = []
progY = []
progPerc = []
for i in range(1,numb_updates+1):
progX.append(xgrid[np.int(len(xgrid)*i/numb_updates)-1])
progY.append(ygrid[np.int(len(xgrid)*i/numb_updates)-1])
progPerc.append(i*100/numb_updates)
progX = np.array(progX)
progY = np.array(progY)
progPerc = np.array(progPerc)
#Loop over pixels
for y in range(wavearray.shape[0]):
for x in range(wavearray.shape[1]):
#Display the "progress bar" if appropriate
if np.any(np.logical_and(x==progX,y==progY)): print "Velocity map approximately "+repr(progPerc[np.logical_and(progX==x,progY==y)][0])+"% complete..."
#Get the spectrum to fit
waves = wavecube[y,x,:]
intys = intycube[y,x,:]
if not (uncertlist is None): uncerts = uncertcube[y,x,:]
else: uncerts = None
# #Attempt the two-lined fit (halpha and NII)
# if np.sum(waves!=0)>0.5*len(waves): fit, success = fit_ha_and_n2(waves[waves!=0], intys[intys!=0], uncerts[uncerts!=0])
# else: fit, success = np.zeros(8), False
# #Was the fit successful
# if success:
# contarray[y,x] = fit[0]
# intyarray[y,x] = fit[1]
# intyratioarray[y,x] = fit[2]/fit[1]
# wavearray[y,x] = fit[3]
# two_line_success_array[y,x] = True
# #If not, let's try only fitting the halpha line
# else:
# if np.sum(waves!=0)>0.5*len(waves): fit, success = fit_only_ha(waves[waves!=0], intys[intys!=0], uncerts[uncerts!=0])
# else: fit, success = np.zeros(5), False
# if success:
# contarray[y,x] = fit[0]
# intyarray[y,x] = fit[1]
# wavearray[y,x] = fit[2]
# one_line_success_array[y,x] = True
#Fit with voigtfit
if np.sum(waves!=0)>0.5*len(waves):
fit,_err,_chi2 = voigtfit.voigtfit(waves[waves!=0],intys[intys!=0],uncerts[uncerts!=0],voigtfit.voigtguess(waves[waves!=0],intys[intys!=0]),[True,True,True,True,True])
contarray[y,x] = fit[0]
intyarray[y,x] = fit[1]
wavearray[y,x] = fit[2]
#Convert wavelengths to velocities
velarray = np.zeros_like(wavearray)
velarray[wavearray!=0] = 299792.458*((wavearray[wavearray!=0]/6562.81)**2-1)/((wavearray[wavearray!=0]/6562.81)**2+1)
#Save the output images
writefits(join(outdir,"velocity.fits"), velarray, clobber=clobber)
writefits(join(outdir,"intensity.fits"), intyarray, clobber=clobber)
writefits(join(outdir,"intyratio.fits"), intyratioarray, clobber=clobber)
writefits(join(outdir,"continuum.fits"), contarray, clobber=clobber)
#writefits(join(outdir,"2linesuccess.fits"), two_line_success_array, clobber=clobber)
#writefits(join(outdir,"1linesuccess.fits"), one_line_success_array, clobber=clobber)
#Close input images
for i in range(len(wavelist)):
wavefilelist[i].close()
intyfilelist[i].close()
if not (uncertlist is None):
uncertfilelist[i].close()
return
def make_final_image(input_image, output_image, output_wave_image,
desired_fwhm,
input_uncert_image=None, output_uncert_image=None,
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.
output_wave_image -> Path to the output wavelength image.
desired_fwhm -> Desired FWHM for the resultant image to have.
Optional Inputs:
input_uncert_image -> Path to the input uncertainty image, if it exists.
output_uncert_image -> Path to the output uncertainty image, if it exists.
clobber -> Overwrite output images if they already exist. Default is False.
"""
print "Making final data cube images for image "+input_image
#Measure the sky background level in the input image
skyavg, skysig = fit_sky_level([input_image])
#Open the input image and get various header keywords, crash if necessary
intyimage = openfits(input_image)
intygrid = intyimage[0].data
fwhm = intyimage[0].header.get("fpfwhm")
wave0 = intyimage[0].header.get("fpwave0")
calf = intyimage[0].header.get("fpcalf")
xcen = intyimage[0].header.get("fpxcen")
ycen = intyimage[0].header.get("fpycen")
if fwhm == None: crash("Error! FWHM not measured for image "+input_image+".")
if wave0 == None or calf == None: crash("Error! Wavelength solution does "+
"not exist for image "+input_image+".")
if xcen == None or ycen == None: crash("Error! Center values not measured "+
"image "+input_image+".")
if fwhm>desired_fwhm: crash("Error! Desired FWHM too low for image "+
input_image+".")
#Subtract the sky background from the image
intygrid[intygrid!=0] -= skyavg[0]
#Calculate the necessary FWHM for convolution and make the gaussian kernel
fwhm_conv = np.sqrt(desired_fwhm**2-fwhm**2)
sig = fwhm_conv/2.3548+0.0001
ksize = np.ceil(4*sig) #Generate the kernel to 4-sigma
kxgrid, kygrid = np.meshgrid(np.linspace(-ksize,ksize,2*ksize+1),np.linspace(-ksize,ksize,2*ksize+1))
kern = np.exp(-(kxgrid**2+kygrid**2)/(2*sig**2)) #Gaussian (unnormalized because sig can be 0)
kern = kern/np.sum(kern) #Normalize the kernel
#Open and convolve the uncertainty image if one exists. Save the output.
if input_uncert_image != None:
uncertimage = openfits(input_uncert_image)
uncertgrid = uncertimage[0].data
#Add the sky background uncertainty to the uncertainty grid
uncertgrid[intygrid!=0] = np.sqrt(uncertgrid[intygrid!=0]**2+skysig[0]**2)
#Convolve the uncertainties appropriately
new_uncert_grid = convolve_uncert(uncertgrid, intygrid, kern)
#Write to output file
writefits(output_uncert_image,new_uncert_grid,header=uncertimage[0].header,clobber=clobber)
uncertimage.close()
#Create and convolve the wavelength image. Save the output.
xgrid, ygrid = np.meshgrid(np.arange(intyimage[0].data.shape[1]),
np.arange(intyimage[0].data.shape[0]))
r2grid = (xgrid-xcen)**2 + (ygrid-ycen)**2
wavegrid = wave0 / np.sqrt(1+r2grid/calf**2)
newwavegrid = convolve_wave(wavegrid, intygrid, kern)
writefits(output_wave_image,newwavegrid,header=intyimage[0].header,clobber=clobber)
#Convolve the intensity image. Save the output
newintygrid = convolve_inty(intygrid, kern)
intyimage[0].header["fpfwhm"] = desired_fwhm #Update header FWHM keyword
writefits(output_image,newintygrid,header=intyimage[0].header,clobber=clobber)
#Close images
intyimage.close()
return
