def main():
"""
Script to loop though bursts and normalise arms
"""
data_dir = "../data/"
bursts = glob(data_dir + "*")
# Loop through burst names
for ii, kk in enumerate(bursts):
# List of extractions in burst dir
extractions = [
ll for ll in glob(kk + "/*") if ".dat" in ll or ".spec" in ll
]
# print(extractions)
# Loop through extractions and normalize
for ll in extractions:
if "GRB11" in ll:
print("Normalizing file:")
print(ll)
burst_name = ll.split("/")[2]
if "spec" in ll:
outname = (ll.split("/")[-1]).replace("skysub", "")[:-5]
else:
outname = (ll.split("/")[-1]).replace("skysub", "")[:-4]
print(kk + "/" + outname + "_norm.npy")
if not os.path.exists(kk + "/" + outname + "_norm.npy"):
wl, flux, error, bpmap = stitch_arms.load_array(
np.genfromtxt(ll))
mask = ~bpmap.astype("bool")
normalise = xsh_norm.automatic.xsh_norm(
wl[mask], flux[mask], error[mask], bpmap, wl, flux,
error, kk + "/" + outname)
# if burst_name == "GRB090809A":
# normalise.leg_order = 4
# normalise.endpoint_order = 4
# elif burst_name == "GRB091018A":
# normalise.leg_order = 4
# normalise.lover_mask = -5e-17
# normalise.exclude_width = 2
# normalise.sigma_mask = 10
# normalise.leg_order = 5 #float(raw_input('Filtering Chebyshev Order (default = 3) = '))
# normalise.endpoint_order = 5#float(raw_input('Order of polynomial used for placing endpoints (default = 3) = '))
normalise.exclude_width = 5 #float(raw_input('Exclude_width (default = 5) = '))
normalise.sigma_mask = 5 #float(raw_input('Sigma_mask (default = 5) = '))
normalise.lover_mask = -1e-17 #float(raw_input('Lover bound mask (default = -1e-17) = '))
# normalise.tolerance = 0.5#float(raw_input('Filtering tolerance (default = 0.25) = '))
# normalise.leg_order = #float(raw_input('Filtering Chebyshev Order (default = 3) = '))
normalise.spacing = 400 #float(raw_input('Spacing in pixels between spline points (default = 150) = '))
normalise.division = 30 #float(raw_input('Maximum number of allowed points (default = 300) = '))
normalise.endpoint_order = 2 #float(raw_input('Order of polynomial used for placing endpoints (default = 3) = '))
normalise.endpoint = "t" #str(raw_input('Insert endpoint before interpolation(y/n)? '))
try:
normalise.run()
except:
pass
def main():
"""
Script to loop though bursts and normalise arms
"""
data_dir = "../data/"
bursts = glob(data_dir+"*")
# Loop through burst names
for ii, kk in enumerate(bursts):
# List of extractions in burst dir
extractions = [ll for ll in glob(kk+"/*") if ".dat" in ll or ".spec" in ll]
# print(extractions)
# Loop through extractions and normalize
for ll in extractions:
if "GRB" in ll:
print("Normalizing file:")
print(ll)
burst_name = ll.split("/")[2]
if "spec" in ll:
outname = (ll.split("/")[-1]).replace("skysub", "")[:-5]
else:
outname = (ll.split("/")[-1]).replace("skysub", "")[:-4]
print(kk+"/"+outname+"_norm.npy")
if not os.path.exists(kk+"/"+outname+"_norm.npy"):
wl, flux, error, bpmap = stitch_arms.load_array(np.genfromtxt(ll))
mask = ~bpmap.astype("bool")
normalise = xsh_norm.interactive.xsh_norm(wl[mask], flux[mask], error[mask], bpmap, wl, flux, error, kk+"/"+outname)
# change = raw_input('Change default maskparameters(y/n)? ')
# if change == 'y':
if burst_name == "GRB090809A":
normalise.leg_order = 4
normalise.endpoint_order = 4
elif burst_name == "GRB091018A":
normalise.leg_order = 4
normalise.lover_mask = -5e-17
normalise.exclude_width = 2
normalise.sigma_mask = 10
elif burst_name == "GRB100205A":
normalise.lover_mask = -1e-16
elif burst_name == "GRB100219A":
normalise.leg_order = 1
normalise.endpoint_order = 1
normalise.exclude_width = 5
normalise.lover_mask = 0
elif burst_name == "GRB100316B":
normalise.fluxerror[normalise.wave > 10000] *= 2
elif burst_name == "GRB100418A1":
normalise.fluxerror[normalise.wave > 10000] *= 2
elif burst_name == "GRB100724A":
normalise.leg_order = 6
normalise.endpoint_order = 6
elif burst_name == "GRB110715A":
normalise.leg_order = 2
normalise.endpoint_order = 2
elif burst_name == "GRB100814A2":
normalise.fluxerror[normalise.wave > 10000] *= 2
normalise.leg_order = 5
normalise.endpoint_order = 5
elif burst_name == "GRB110818A":
normalise.leg_order = 2
normalise.endpoint_order = 2
normalise.lover_mask = -4e-17
elif burst_name == "GRB111008A1":
normalise.leg_order = 1
normalise.endpoint_order = 1
elif burst_name == "GRB111008A2":
normalise.leg_order = 1
normalise.endpoint_order = 1
elif burst_name == "GRB111211A":
normalise.tolerance = 0.50
elif burst_name == "GRB111211A":
normalise.tolerance = 0.50
elif burst_name == "GRB111228A":
normalise.leg_order = 2
normalise.endpoint_order = 2
# normalise.endpoint = "n"
normalise.lover_mask = 0
elif burst_name == "GRB120119A1":
normalise.leg_order = 3
normalise.endpoint_order = 3
normalise.endpoint = "t"
normalise.sigma_mask = 10
elif burst_name == "GRB120327A1":
normalise.leg_order = 7
normalise.endpoint_order = 7
normalise.tolerance = 1.0
normalise.endpoint = "n"
elif burst_name == "GRB120404A":
normalise.lover_mask = -0.5e-17
elif burst_name == "GRB130427A":
normalise.endpoint = "n"
elif burst_name == "GRB130606A0":
normalise.leg_order = 1
normalise.endpoint_order = 1
elif burst_name == "GRB130606A1":
normalise.leg_order = 1
normalise.endpoint_order = 1
elif burst_name == "GRB131030A":
normalise.endpoint = "n"
# normalise.leg_order = 5 #float(raw_input('Filtering Chebyshev Order (default = 3) = '))
# normalise.endpoint_order = 5#float(raw_input('Order of polynomial used for placing endpoints (default = 3) = '))
normalise.exclude_width = 1#float(raw_input('Exclude_width (default = 5) = '))
normalise.sigma_mask = 10#float(raw_input('Sigma_mask (default = 5) = '))
normalise.lover_mask = -1e-17#float(raw_input('Lover bound mask (default = -1e-17) = '))
# normalise.tolerance = 0.5#float(raw_input('Filtering tolerance (default = 0.25) = '))
# normalise.leg_order = #float(raw_input('Filtering Chebyshev Order (default = 3) = '))
normalise.spacing = 500#float(raw_input('Spacing in pixels between spline points (default = 150) = '))
normalise.division = 20#float(raw_input('Maximum number of allowed points (default = 300) = '))
normalise.endpoint_order = 1#float(raw_input('Order of polynomial used for placing endpoints (default = 3) = '))
normalise.endpoint = "n"#str(raw_input('Insert endpoint before interpolation(y/n)? '))
try:
normalise.run()
except:
pass
pl.title(burst_name)
pl.xlabel(r'Observed Wavelength [$\mathrm{\AA}$]')
pl.ylabel(r'Flux [erg/cm$^2$/s/$\mathrm{\AA}$]')
# print(np.median(flux_arr[~np.isnan(flux_arr)]))
# sn = np.median(flux_arr[~np.isnan(flux_arr)]) / np.median(error_arr[~np.isnan(error_arr)])
l, h = np.percentile(flux[mask], (1, 99))
pl.ylim(l, h)
pl.show()