def cubestack(cubefile, rangespec='', clobber=False):
ranges = []
for rangestr in rangespec.split(','):
a, b = rangestr.split('-')
ranges.append((int(a), int(b)))
debug("stacking range pairs:", ranges)
path, filename = os.path.split(cubefile)
filebase = cubefile.rsplit('.', 1)[0]
target_dir = os.path.join(path, '{0}_stacks'.format(filebase))
debug("target:", target_dir)
tmp_target_dir = tempfile.mkdtemp()
outimgs = combine_cube_frames(cubefile, ranges, tmp_target_dir)
if os.path.isdir(target_dir):
debug("target dir exists, removing", target_dir)
shutil.rmtree(target_dir)
shutil.copytree(tmp_target_dir, target_dir)
def aoavgcube(cubefile, outfile, newexposure, fromidx=1, toidx=None):
"""
Combine (without rejection) many short exposures in a data cube
to approximate a "seeing disk" from a longer integration time.
cubefile - input data cube path
outfile - output data cube path
fromidx - 1-based index of start of combining range (default: 1)
toidx - 1-based index of end of range (default: None, end of cube)
"""
newexposure = float(newexposure)
ffile = pyfits.open(cubefile)
header = ffile[0].header
data = ffile[0].data
if 'EXPOSURE' in header.keys():
oldexposure = float(header['EXPOSURE'])
elif 'EXPTIME' in header.keys():
oldexposure = float(header['EXPTIME'])
else:
raise Exception("No exposure time value found in the datacube header!")
assert newexposure > oldexposure, ("Can't get a shorter exposure time by combining frames! "
"oldexposure {0} > newexposure {1}".format(oldexposure, newexposure))
frames_per_combined = int(newexposure / oldexposure)
epsilon = (newexposure / oldexposure) - int(newexposure / oldexposure)
if epsilon > 0.01:
warn("New exposure is not an integer multiple of old exposure, rounding to", frames_per_combined)
assert frames_per_combined > 1, "Only one old frame per combined frame; this is probably not what you want"
if toidx <= fromidx:
# use entire cube
toidx = data.shape[0]
else:
assert toidx <= data.shape[0], "toidx ({0}) > number of frames ({1})".format(toidx, data.shape[0])
assert data.shape[0] > 1, "Only one frame found! Is this a data cube?"
total_frames = toidx - fromidx
debug("toidx=",toidx,"fromidx=",fromidx)
if total_frames % frames_per_combined != 0:
warn("Total frames in range (toidx - fromidx =", toidx - fromidx, ") is not an integer multiple "
"of the number of frames per combined exposure (", frames_per_combined,
") so", total_frames % frames_per_combined, "frames from the end of "
"the range will be left off.")
toidx = toidx - (total_frames % frames_per_combined)
total_frames = toidx - fromidx
total_combined_frames = int(total_frames / frames_per_combined)
info("Output data cube will have", total_combined_frames, "total frames of", newexposure, "sec exposure")
info("Processing input data cube frames", fromidx, "to", toidx)
target_dir = tempfile.mkdtemp()
info("Created working directory {0} for intermediate data".format(target_dir))
try:
range_pairs = list((
fromidx + n * frames_per_combined,
fromidx + (n+1) * frames_per_combined - 1
) for n in range(0, total_combined_frames))
frame_paths = combine_cube_frames(cubefile, range_pairs, target_dir)
# frames_to_cube(frame_paths, outfile)
finally:
# Don't leave clutter if the task fails
# shutil.rmtree(target_dir)
info("Removed working directory {0}".format(target_dir))