def main(argv=None):
''' Main Function '''
# Call initial parser from init_utils
parser = ap.ArgumentParser(description="""Create HDF5 file.""",
add_help=True)
parser.add_argument("-d",
"--date",
help='''Date, e.g., 20170321, YYYYMMDD''',
type=str,
default=None)
parser.add_argument("-o",
"--observation",
help='''Observation number, "00000007" or "7"''',
type=str,
default=None)
parser.add_argument("-r",
"--rootdir",
help='''Root Directory for Reductions''',
type=str,
default='/work/03946/hetdex/maverick')
parser.add_argument('-of',
'--outfilename',
type=str,
help='''Relative or absolute path for output HDF5
file.''',
default=None)
parser.add_argument('-a',
'--append',
help='''Appending to existing file.''',
action="count",
default=0)
args = parser.parse_args(argv)
args.log = setup_logging()
# Get the daterange over which reduced files will be collected
files = get_files(args)
# Creates a new file if the "--append" option is not set or the file
# does not already exist.
if op.exists(args.outfilename) and args.append:
fileh = tb.open_file(args.outfilename, 'a')
else:
fileh = tb.open_file(args.outfilename, 'w')
imagetable = fileh.create_table(fileh.root, 'Cals', VIRUSImage,
'Cal Info')
for fn in files:
args.log.info('Working on %s' % fn)
im = imagetable.row
success = append_fibers_to_table(im, fn, args)
if success:
imagetable.flush()
fileh.close()
def main(argv=None):
''' Main Function '''
# Call initial parser from init_utils
parser = ap.ArgumentParser(description="""Create HDF5 file.""",
add_help=True)
parser.add_argument("hdf5_file", type=str, help='''Name of h5/hdf5 file''')
parser.add_argument("-e",
"--extension",
help='''Extension or extensions''',
type=str,
default=None)
parser.add_argument("-q",
"--query",
help='''Query to be applied''',
type=str,
default=None)
parser.add_argument('-s',
'--show',
help='''Show tables/extensions within file''',
action="count",
default=0)
args = parser.parse_args(argv)
args.log = setup_logging()
try:
h5file = open_file(args.hdf5_file, mode='r')
except:
if not op.exists(args.hdf5_file):
args.log.error('%s does not exist' % args.hdf5_file)
return None
else:
args.log.error('File exists but could not open %s' %
args.hdf5_file)
return None
if args.show:
table_names = ['Shot', 'Fibers', 'Images']
for kind in table_names:
print('%s column names:' % kind)
b = getattr(h5file.root.Info, kind)
for name in b.colnames:
base = getattr(b.cols, name)
shape = str(base.shape)
print('\t%s: %s %s' % (name, base.type, shape))
return None
if args.extension is None:
args.log.error('No extension provided to display in ds9')
return None
table = h5file.root.Info.Fibers
spec = np.array(table.cols.spectrum[:])
ds9 = pyds9.DS9()
ds9.set_np2arr(spec)
h5file.close()
def __init__(self, wave=None):
'''
Initialize Extract class
Parameters
----------
wave: numpy 1d array
wavelength of calfib extension for hdf5 files, does not need to be
set unless needed by development team
'''
if wave is not None:
self.wave = wave
else:
self.wave = self.get_wave()
self.get_ADR()
self.log = setup_logging('Extract')
self.set_dither_pattern()
# Mask additionally spectra whose average weight is less than 5%
if np.nanmedian(weigh) < 0.05:
mask = True
return mask
DIRNAME = get_script_path()
T = Table.read(op.join(DIRNAME, 'filters/ps1g.dat'), format='ascii')
filtg = np.interp(def_wave, T['col1'], T['col2'], left=0.0, right=0.0)
filtg /= filtg.sum()
T = Table.read(op.join(DIRNAME, 'calibration', 'normalization.txt'),
format='ascii.fixed_width_two_line')
flux_normalization = np.array(T['normalization'])
log = setup_logging('extractions')
parser = ap.ArgumentParser(add_help=True)
parser.add_argument("folder",
help='''Folder with h5 files''',
type=str)
parser.add_argument("extraction_file",
help='''list of RA and Decs to extract''',
type=str)
parser.add_argument("outputname",
help='''Name of fits file output''',
type=str)
parser.add_argument('outfolder', type=str, help='''name of the output file''')
parser.add_argument("-lr",
"--lowres",
help='''low resolution''',
action="count",
default=0)
folder = '/Users/gregz/cure/Remedy/virusw/VIRUS-W_Jan21'
outfolder = '/Users/gregz/cure/Remedy/virusw/reductions'
argv = [folder, outfolder, "-lr"]
argv = None
args = parser.parse_args(args=argv)
folder = args.folder
outfolder = args.outfolder
log = setup_logging('virusw_reductions')
gain = 0.62
rdnoise = 2.55
# =============================================================================
# LowRes Mode
# =============================================================================
if args.lowres:
lines = [
4046.563, 4077.831, 4348.063, 4358.327, 4916.068, 5037.75, 5330.778,
5400.562, 5719.23, 5820.16, 5852.488, 5881.895, 5944.834, 5975.534
]
fiberref = 130
xref = np.array([
462.4524, 514.266, 990.160, 1009.781, 2042.973, 2275.308, 2843.932,
2980.563, 3607.36, 3806.076, 3870.173, 3928.036, 4050.715, 4109.934
def main(argv=None):
''' Main Function '''
# Call initial parser from init_utils
parser = ap.ArgumentParser(description="""Create rsp tmpXXX.datfiles.""",
add_help=True)
parser.add_argument("-s", "--datevobs",
help='''ShotID, e.g., 20170321v009, YYYYMMDDvOBS''',
type=str, default=None)
parser.add_argument("-ra", "--ra",
help='''ra, e.g., right ascension in degrees''',
type=float, default=None)
parser.add_argument("-dec", "--dec",
help='''ra, e.g., right ascension in degrees''',
type=float, default=None)
parser.add_argument("-rad", "--rad",
help='''radius, e.g., aperture radius in arcsec''',
type=float, default=3.0)
parser.add_argument("-w", "--wave",
help='''wavelength in AA''',
type=float, default=None)
parser.add_argument("-dw", "--dwave",
help='''delta wavelength in AA''',
type=float, default=50.0)
args = parser.parse_args(argv)
args.log = setup_logging()
# initiate Fibers and Survey Classes
print(args)
fibers = Fibers(args.datevobs)
survey = Survey('hdr1')
fwhm = survey.fwhm_moffat[survey.datevobs == args.datevobs]
structaz = survey.structaz[survey.datevobs == args.datevobs]
ascii.write([fwhm, structaz], 'shot.info',
names=['fwhm_moffat', 'structaz'], overwrite=True)
obj_coords = SkyCoord(args.ra * u.deg, args.dec * u.deg, frame='icrs')
idx = fibers.query_region_idx(obj_coords, radius=(args.rad/3600.))
output = Table()
output['ra'] = fibers.coords.ra[idx]*u.deg
output['dec'] = fibers.coords.dec[idx]*u.deg
filenames = []
fileidx = 101
for i in idx:
filename = 'tmp' + str(fileidx) + '.dat'
filenames.append(filename)
save_rsp_spectrum(fibers, i, file=filename, )
fileidx += 1
output['filename'] = np.array(filenames)
ascii.write(output, 'fib_coords.dat', overwrite=True)
y[j] = evalf(x[j], n, avg=y[j])
for nsi in ns:
y[nsi] = savgol_filter(y[nsi], 11, 1)
ftf[:, k] = y / n
for i in np.arange(len(scispectra)):
I = interp1d(W, ftf[i, :], kind='quadratic', fill_value='extrapolate')
scispectra[i] /= I(def_wave)
log.info('Getting average sky')
sky = np.nanmedian(scispectra, axis=0)
return scispectra - sky, sky
# GET DIRECTORY NAME FOR PATH BUILDING
DIRNAME = get_script_path()
instrument = 'virus'
log = setup_logging()
if args.hdf5file is None:
args.hdf5file = op.join(DIRNAME, 'cals', 'default_cals.h5')
# OPEN HDF5 FILE
h5file = open_file(args.hdf5file, mode='r')
h5table = h5file.root.Cals
# Collect indices for ifuslot
ifuslots = h5table.cols.ifuslot[:]
ifuloop = np.arange(len(ifuslots))
# Reducing IFUSLOT
log.info('Reducing all ifus in CAL HDF5')
pos, twispectra, scispectra, errspectra, fn = reduce_ifuslot(ifuloop, h5table)
average_twi = np.percentile(twispectra, 95, axis=0)
type=str,
help='''name of the output file''')
parser.add_argument("-f",
"--folder",
help='''Output folder''',
type=str,
default='output')
parser.add_argument("-i",
"--ifuslot",
help='''IFUSLOT''',
type=str,
default='047')
args = parser.parse_args(args=None)
args.log = setup_logging(logname='build_master_bias')
args = set_daterange(args)
kinds = ['twi', 'cmp']
mkpath(args.folder)
dirname = get_script_path()
filename_dict = {}
tarname_dict = {}
for kind in kinds:
args.log.info('Getting file names for %s' % kind)
if kind == 'drk':
daterange = expand_date_range(args.daterange, 7)
else:
daterange = list(args.daterange)
filename_dict[kind] = get_filenames(args, daterange, kind)
tarname_dict[kind] = get_tarfiles(filename_dict[kind])
trajcra = float(b.split(' ')[5]) * 15.
trajcdec = float(b.split(' ')[6])
mjd = float(b.split(' ')[4])
except:
exptime = 180.
trajcra = 180.
trajcdec = 50.
mjd = -999.
return [trajcra, trajcdec, mjd, exptime]
outname = sys.argv[1]
def_wave = np.linspace(3470, 5540, 1036)
log = setup_logging('catalog')
loc = EarthLocation.of_site('McDonald Observatory')
basedir = '/work/00115/gebhardt/maverick/gettar'
folder = '/work/03946/hetdex/virus_parallels/data'
DIRNAME = get_script_path()
T = Table.read(op.join(DIRNAME, 'filters/ps1g.dat'), format='ascii')
filtg = np.interp(def_wave, T['col1'], T['col2'], left=0.0, right=0.0)
filtg /= filtg.sum()
h5names = sorted(glob.glob(op.join(folder, '*.h5')))
totN = 0
Nshots = 0
cnt = 0
C = 0
(indy < N) or (indy >= (len(yg) - N))):
continue
ly = indy - N
hy = indy + N + 1
lx = indx - N
hx = indx + N + 1
d = np.sqrt((xgrid[ly:hy,lx:hx]-p[0])**2 + (ygrid[ly:hy,lx:hx]-p[1])**2)
G = np.exp(-0.5 * d**2 / sigma**2)
G[:] /= G.sum()
image[ly:hy,lx:hx] += yi*G
weight[ly:hy,lx:hx] += G
image[weight < 0.8 * np.max(weight)] = 0.
return image
args = parser.parse_args(args=None)
args.log = setup_logging('make_image_from_h5')
def_wave = np.linspace(3470., 5540., 1036)
wave_extract = [float(i.replace(' ', '')) for i in args.wave_extract.split(',')]
back_wave = [float(i.replace(' ', '')) for i in args.back_wave.split(',')]
bsel = (def_wave >= back_wave[0]) * (def_wave <= back_wave[1])
wsel = np.abs(def_wave - wave_extract[0]) < (2.5 * wave_extract[1])
bsel = bsel * (~wsel)
Gmodel = np.exp(-0.5 * (def_wave - wave_extract[0])**2 / wave_extract[1]**2)
Gmodel[:] = Gmodel / Gmodel[wsel].sum()
t = tables.open_file(args.h5file)
ra = t.root.Info.cols.ra[:]
dec = t.root.Info.cols.dec[:]
RA = t.root.Survey.cols.ra[0]
Dec = t.root.Survey.cols.dec[0]