########## Setup
##########
################################################################################
logger.setLevel(-1)
args = parse_args()
pdf = plot_setup(args.plotFile)
logger.info('Loading data from: %s' % args.db)
db = openFile(args.db)
try:
logger.info('Galaxy: %s' % args.galaxyName)
g = db.getNode('/%s' % args.galaxyName)
except:
logger.error('Unknown galaxy: %s' % args.galaxyName)
sys.exit()
masked = (g.flag_ifs[...] > 0) | (g.full_ifs[...] < 0.0)
masked2d = masked.sum(axis=0) > masked.shape[0] / 2
bulge_image = g.bulge_image[...]
disk_image = g.disk_image[...]
full_image = np.ma.array(bulge_image + disk_image, mask=masked2d)
bulge_ifs = g.bulge_ifs[...]
bulge_ifs_nopsf = g.bulge_ifs_nopsf[...]
disk_ifs = g.disk_ifs[...]
disk_ifs_nopsf = g.disk_ifs_nopsf[...]
full_ifs = np.ma.array(g.full_ifs[...], mask=masked)
help='PSF beta parameter for Moffat profile. If not set, use Gaussian.')
parser.add_argument('--psf-size', dest='psfSize', type=int, default=15,
help='PSF size, in pixels. Must be an odd number.')
parser.add_argument('--overwrite', dest='overwrite', action='store_true',
help='Overwrite data.')
parser.add_argument('--nproc', dest='nproc', type=int, default=None,
help='Number of processors to use.')
return parser.parse_args()
################################################################################
################################################################################
if __name__ =='__main__':
args = parse_args()
if args.verbose:
logger.setLevel(-1)
logger.debug('Verbose output enabled.')
sample = load_sample(args.sample)
sampleId = path.basename(args.sample)
for gal in sample:
cube = gal['cube']
try:
c = decomp(cube, sampleId, args)
except Exception as e:
logger.error('Error decomposing cube %s' % cube)
logger.error('Exception: %s.' % str(e))
logger.warn('Skipping to next galaxy.')
def decomp(cube, sampleId, args):
galaxyId = califa_id_from_cube(cube)
c = DecompContainer()
if not args.overwrite:
logger.info('Checking if the decomposition is already done for %s ...' % galaxyId)
try:
c.loadHDF5(args.db, sampleId, galaxyId)
logger.warn('Previous data found, skipping decomposition.')
return c
except Exception as e:
print e
logger.info('No previous data found, continuing decomposition.')
logger.info('Starting fit for %s...' % galaxyId)
dec = CALIFADecomposer(cube, grating=args.grating, nproc=args.nproc)
npix = dec.K.qMask.sum()
dec.minNPix = npix / 2
logger.info('Minimum number of pixels for fitting: %d' % dec.minNPix)
dec.useEstimatedVariance = args.estVar
dec.setSynthPSF(FWHM=args.psfFWHM, beta=args.psfBeta, size=args.psfSize)
logger.warn('Computing initial model using DE algorithm (takes a LOT of time).')
t1 = time.time()
if not path.exists(args.maskFile):
logger.error('Mask file %s not found.' % args.maskFile)
exit(1)
logger.info('Using mask file %s.' % args.maskFile)
masked_wl = load_line_mask(args.maskFile, dec.wl)
l1 = find_nearest_index(dec.wl, 4500.0)
l2 = dec.Nl_obs
cache_file = cube + '.initmodel'
if not path.exists(cache_file):
logger.info('Creating gray image for initial model.')
gray_image, gray_noise, _ = dec.getSpectraSlice(l1, l2, masked_wl)
else:
gray_image = None
gray_noise = None
initial_model = bd_initial_model(gray_image, gray_noise, dec.PSF, quiet=False, nproc=args.nproc,
cache_model_file=cache_file)
logger.debug('Refined initial model:\n%s\n' % initial_model)
logger.warn('Initial model time: %.2f\n' % (time.time() - t1))
t1 = time.time()
c.zones = np.ma.array(dec.K.qZones, mask=dec.K.qZones < 0)
c.initialParams = initial_model.getParams()
c.attrs = dict(PSF_FWHM=args.psfFWHM,
PSF_beta=args.psfBeta,
PSF_size=args.psfSize,
box_step=args.boxStep,
box_radius=args.boxRadius,
orig_file=cube,
mask_file=args.maskFile,
object_name=dec.K.galaxyName,
flux_unit=dec.flux_unit,
distance_Mpc=dec.K.distance_Mpc,
x0=dec.K.x0,
y0=dec.K.y0,
target_vd=dec.targetVd,
wl_FWHM=dec.wlFWHM)
models = dec.fitSpectra(step=50*args.boxStep, box_radius=25*args.boxStep,
initial_model=initial_model, mode=args.fitAlgorithm, masked_wl=masked_wl)
c.firstPassParams = np.array([m.getParams() for m in models], dtype=models[0].dtype)
logger.info('Done first pass modeling, time: %.2f' % (time.time() - t1))
t1 = time.time()
logger.info('Smoothing parameters.')
models = smooth_models(models, dec.wl, degree=1)
logger.info('Starting second pass modeling...')
models = dec.fitSpectra(step=args.boxStep, box_radius=args.boxRadius,
initial_model=models, mode=args.fitAlgorithm, insist=False, masked_wl=masked_wl)
logger.info('Done second pass modeling, time: %.2f' % (time.time() - t1))
t1 = time.time()
logger.info('Computing model spectra...')
c.total.f_obs = dec.flux[::args.boxStep]
c.total.f_err = dec.error[::args.boxStep]
c.total.f_flag = dec.flags[::args.boxStep]
c.total.mask = dec.K.qMask
c.total.wl = dec.wl[::args.boxStep]
c.bulge.f_obs, c.disk.f_obs = dec.getModelSpectra(models, args.nproc)
c.bulge.mask = dec.K.qMask
c.bulge.wl = dec.wl[::args.boxStep]
c.disk.mask = dec.K.qMask
c.disk.wl = dec.wl[::args.boxStep]
# TODO: better array and dtype handling.
c.fitParams = np.array([m.getParams() for m in models], dtype=models[0].dtype)
flag_bad_fit = c.fitParams['flag'][:, np.newaxis, np.newaxis] > 0.0
c.updateErrorsFlags(flag_bad_fit)
c.updateIntegratedSpec()
logger.info('Saving qbick planes...')
fname = path.join(args.zoneFileDir, '%s_%s-planes.fits' % (galaxyId, sampleId))
save_qbick_images(c.total, dec, fname, overwrite=args.overwrite)
fname = path.join(args.zoneFileDir, '%s_%s-bulge-planes.fits' % (galaxyId, sampleId))
save_qbick_images(c.bulge, dec, fname, overwrite=args.overwrite)
fname = path.join(args.zoneFileDir, '%s_%s-disk-planes.fits' % (galaxyId, sampleId))
save_qbick_images(c.disk, dec, fname, overwrite=args.overwrite)
logger.info('Saving to storage...')
c.writeHDF5(args.db, sampleId, galaxyId, args.overwrite)
logger.info('Storage complete, time: %.2f' % (time.time() - t1))
return c
flag_ifs[badpix] |= flags.bad_pixel
# TODO: add other flags
logger.info("Took %.2f seconds to create the IFS." % (time.clock() - t1))
################################################################################
##########
########## Write IFS
##########
################################################################################
logger.info("Saving to storage...")
db = openFile(args.dbOutput, "a")
if not args.overwrite and args.galaxyName in db.root:
logger.error("Galaxy %s already exists. Use --overwrite.")
sys.exit()
try:
grp = db.getNode("/%s" % args.galaxyName)
except:
grp = db.createGroup("/", args.galaxyName)
save_array(db, grp, "bulge_image", bulge_image_pad[Ny_psf:-Ny_psf, Nx_psf:-Nx_psf], args.overwrite)
save_array(db, grp, "disk_image", disk_image_pad[Ny_psf:-Ny_psf, Nx_psf:-Nx_psf], args.overwrite)
save_array(db, grp, "wl", l_ssp, args.overwrite)
save_array(db, grp, "bulge_ifs_nopsf", bulge_ifs_pad[:, Ny_psf:-Ny_psf, Nx_psf:-Nx_psf], args.overwrite)
save_array(db, grp, "bulge_ifs", bulge_ifs, args.overwrite)
save_array(db, grp, "disk_ifs_nopsf", disk_ifs_pad[:, Ny_psf:-Ny_psf, Nx_psf:-Nx_psf], args.overwrite)
save_array(db, grp, "disk_ifs", disk_ifs, args.overwrite)
save_array(db, grp, "full_ifs", full_ifs, args.overwrite)
save_array(db, grp, "full_ifs_noise", full_ifs_noise, args.overwrite)
