def fname(tmpdir, fname_template):
"""Copy the Fe file into a temporary directory and return the file name"""
fe_name = py.path.local(prefix_filename(fname_template, "Fe"))
fe_name.copy(tmpdir)
fe_name = tmpdir.join(fe_name.basename)
return str(fe_name)
def reffiles(fname_template):
"""Subtracted and sky reference file name"""
skysub_ref = prefix_filename(fname_template, 'FeS')
sky_ref = prefix_filename(fname_template, 'FeSky')
return skysub_ref, sky_ref
def outfiles(fname):
"""Subtracted and sky output file name"""
skysub_fname = prefix_filename(fname, 'S')
sky_fname = prefix_filename(fname, 'Sky')
return skysub_fname, sky_fname
def get_image(ra, dec, pa, size, ifu_centers, yflip, outdir):
"""Create the SDSS image around the given coordinates
.. todo::
``filename``: is hard coded. Instead of the output directory pass the
full output name in the function arguments
Rename the function: probably ``plot_image`` would be more appropriate
``box``, ``size_cut_out``: they should not be hard coded
html size should not be hard code
Parameters
----------
ra, dec : float
coordinates of the plot
pa : ?
??
size : float
??
ifu_centers : list
list of ifu coordinates?
yflip : bool
flip the image around the y axis
outdir : string
output directory
Returns
-------
outfile : string
full name of the saved plot
"""
filename = "quicklook_sky_%f_%f_%f.jpeg" % (ra, dec, pa)
filename = os.path.join(outdir, filename)
# Size in degrees
imarray, CD, url, img_src = retrieve_image(ra, dec, size, yflip)
size_pix = len(imarray)
scale = pyhwcs.deg2pix(size, scale=size_pix)
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1], frameon=False)
coll = plotFocalPlaneQuicklook(0,
0,
pa,
scale,
ifu_centers,
ra,
dec,
CD,
size_pix,
color='green')
ax.add_collection(coll)
ax.imshow(imarray, origin='lower', cmap='gray', interpolation="nearest")
ax.axis('off')
tempfile = ft.prefix_filename(filename, "temp_")
fig.savefig(tempfile, bbox_inches='tight')
plt.close(fig)
# Convert array to Image object
img = Image.open(tempfile)
# Cut out the 600x600 image part of the plot
box = (42, 8, 642, 608)
imgCrop = img.crop(box)
size_cut_out = 600.0
# Set size to get 25 arcseconds per pixel - hardcoded scale of the HTML
# interface
rescale = int(size_cut_out * 25.0 / scale)
imgCrop.resize((rescale, rescale))
# Match position angle
rotImg = imgCrop.rotate(-1.0 * pa)
# Finally trim the image to be the correct dimensions for the 478 width by
# 586 height html div
xsize, ysize = rotImg.size
left = (xsize - 478) / 2
right = xsize - (xsize - 478) / 2
top = (ysize - 586) / 2
bottom = ysize - (ysize - 586) / 2
rotImgCrop = rotImg.crop((left, top, right, bottom))
finalImg = rotImgCrop.filter(ImageFilter.SMOOTH)
finalImg.save(filename, "JPEG")
os.remove(tempfile)
return filename
def fe_sky_subtraction(fname,
sig=2.5,
iters=None,
wmin=None,
wmax=None,
width=20,
prefix='S',
skyprefix='Sky',
output_both=True):
"""Perform the sky subtraction from a fiber extracted frame
Parameters
----------
fname : string
name of the fits file to process
sig : float, optional
number of standard deviations to use for the clipping limit
iters : int or `None`, optional
number of iterations to perform clipping for, or `None` to clip
until convergence is achieved (i.e. continue until the last
iteration clips nothing).
wmin, wmax : floats, optional
maximum and minimum wavelength in Armstrong to use for the sigma
clipping. Converted to indices using the 'CRVAL1' and 'CDELT1' keyword
in the header of the fits file. If None the minimum and/or maximum of
the range used
width : int, optional
width of the moving window used to estimate the sky background
prefix : string, optional
prefix of the sky subtracted file
skyprefix : string, optional
prefix of the sky file
output_both : bool, optional
save both sky and sky subtracted frames, instead of the latter alone
"""
with fits.open(fname) as hdulist:
header = hdulist[0].header
data = hdulist[0].data
# get the index of the input wavelengths
imin = wavelength_to_index(header, wmin)
imax = wavelength_to_index(header, wmax)
# take the median along the fibers within the give wavelength range
median_data = np.median(data[:, imin:imax], axis=1)
# and get the inverse of the mask from the sigma clipping
clip_mask = np.logical_not(
sigma_clip(median_data,
sigma=sig,
iters=iters,
cenfunc=np.ma.median).mask)
# construct the sky frame
sky = np.empty_like(data)
for i, _ in enumerate(clip_mask):
win_mask = moving_window(clip_mask, i, width=width)
sky[i, :] = np.median(data[win_mask, :], axis=0)
if parse_version(astropy.__version__) < parse_version('1.3'):
writeto_kwars = {'clobber': True}
else:
writeto_kwars = {'overwrite': True}
# save the sky subtracted file
hdulist[0].data = data - sky
hdulist.writeto(prefix_filename(fname, prefix), **writeto_kwars)
if output_both: # save the sky file
hdulist[0].data = sky
hdulist.writeto(prefix_filename(fname, skyprefix), **writeto_kwars)
def test_prefix_filename(infname, prefix, outfname):
"test the insertion of a prefix in front of the file name"
fout = ft.prefix_filename(infname, prefix)
assert fout == outfname