def plot(self, num_pointsx=100, num_pointsy=100, num_contours=75,
logz=False, show=True):
"""Plot the spline.
Args
----
num_pointsx : int
The number of x sampling points to be used to draw the spline.
num_pointsy : int
The number of y sampling points to be used to draw the spline.
num_contours : int
The number of contours for the color plot.
show : bool, optional
If True, `plt.show()` is called at the end, interrupting the flow.
"""
from GRATools.utils.matplotlib_ import pyplot as plt
_x = numpy.logspace(self.xmin(), self.xmax(), num_pointsx)
_y = numpy.logspace(self.ymin(), self.ymax(), num_pointsy)
_x, _y = numpy.meshgrid(_x, _y)
_z = self(_x, _y, grid=False)
if logz:
from matplotlib.colors import LogNorm
_levels = numpy.logspace(-4, numpy.log10(_z.max()), num_contours)
contour = plt.contourf(_x, _y, _z, levels=_levels, norm = LogNorm())
else:
contour = plt.contourf(_x, _y, _z, num_contours)
bar = plt.colorbar()
if self.xname is not None:
plt.xlabel(self.xlabel())
if self.yname is not None:
plt.ylabel(self.ylabel())
if self.zname is not None:
bar.set_label(self.zlabel())
if show:
plt.show()
def plot(self, num_points=1000, overlay=False, logx=False, logy=False,
scale=1., offset=0., show=True, **kwargs):
"""Plot the spline.
Args
----
num_points : int, optional
The number of sampling points to be used to draw the spline.
overlay : bool, optional
If True, the original arrays passed to the spline are overlaid.
show : bool, optional
If True, `plt.show()` is called at the end, interrupting the flow.
"""
from GRATools.utils.matplotlib_ import pyplot as plt
if not logx:
_x = numpy.linspace(self.xmin(), self.xmax(), num_points)
else:
_x = numpy.logspace(numpy.log10(self.xmin()),
numpy.log10(self.xmax()), num_points)
_y = scale*self(_x) + offset
if overlay:
plt.plot(_x, _y, '-', self.x, self.y, 'o', **kwargs)
else:
plt.plot(_x, _y, '-', **kwargs)
if self.xname is not None:
plt.xlabel(self.xlabel())
if self.yname is not None:
plt.ylabel(self.ylabel())
if logx:
plt.gca().set_xscale('log')
if logy:
plt.gca().set_yscale('log')
if show:
plt.show()
def get_psf(psf_file, show=False):
"""Get the PSF from the fits file created by gtpsf
"""
hdu_list = pf.open(psf_file)
_th = np.radians(hdu_list['THETA'].data.field('Theta'))
_en = hdu_list['PSF'].data.field('ENERGY')
_psf = hdu_list['PSF'].data.field('PSF')
fmt = dict(yname='Theta', yunits='rad', xname='Energy',
xunits='MeV', zname='PSF')
psf_th_e = xInterpolatedBivariateSplineLinear(_en, _th, _psf, **fmt)
hdu_list.close()
if show == True:
for e in _en:
psf_th = psf_th_e.vslice(e)
fmt = dict(xname='cos(th)', xunits='', yname='psf[cos(th)]',\
yunits='')
_psfxsin = xInterpolatedUnivariateSplineLinear(psf_th.x, \
psf_th.y*np.sin(psf_th.x), **fmt)
plt.plot(np.degrees(psf_th.x), psf_th.y, label='%.2f'%e)
print 'INT(E=%.2f) ='%e, 2*np.pi*_psfxsin.integral(0, \
np.amax(psf_th.x[:-2]))
plt.yscale('log')
plt.legend()
plt.show()
return psf_th_e
def mkCl(**kwargs):
"""
"""
get_var_from_file(kwargs['config'])
logger.info('Starting Cl analysis...')
e_min = data.E_MIN
e_max = data.E_MAX
in_label = 'fore'
out_label = in_label
mask_file = data.MASK_FILE
cl_txt = open(os.path.join(GRATOOLS_OUT, '%s_polspicecls.txt' % out_label),
'w')
for i, (emin, emax) in enumerate(zip(e_min, e_max)):
logger.info('Considering bin %.2f - %.2f ...' % (emin, emax))
mask_f = mask_file
if type(mask_file) == list:
mask_f = mask_file[i]
cl_txt.write('ENERGY\t %.2f %.2f\n' % (emin, emax))
l_max = 1000
_l = np.arange(l_max)
flux_map_name = in_label + '_%i-%i.fits' % (emin, emax)
flux_map_f = os.path.join(GRATOOLS_OUT, 'output_fore/' + flux_map_name)
if kwargs['show'] == True:
hp.mollview(flux_map_masked.filled(),
title='fore map',
min=1e-7,
max=1e-4,
norm='log')
plt.show()
out_name = '%s_%i-%i' % (out_label, emin, emax)
out_folder = os.path.join(GRATOOLS_OUT, 'output_pol')
if not os.path.exists(out_folder):
os.makedirs(out_folder)
pol_dict = data.POLCEPICE_DICT
for key in pol_dict:
if key == 'clfile':
pol_dict[key] = os.path.join(out_folder,
'%s_cl.txt' % out_name)
if key == 'cl_outmap_file':
pol_dict[key] = os.path.join(out_folder,
'%s_clraw.txt' % out_name)
if key == 'covfileout':
pol_dict[key] = os.path.join(out_folder,
'%s_cov.fits' % out_name)
if key == 'mapfile':
pol_dict[key] = flux_map_f
if key == 'maskfile':
pol_dict[key] = mask_f
config_file_name = 'pol_%s' % (out_name)
_l, _cl, _cl_err = pol_cl_calculation(pol_dict, config_file_name)
cl_txt.write('Cl\t%s\n'%str(list(_cl)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.write('Cl_ERR\t%s\n\n'%str(list(_cl_err)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.close()
logger.info('Created %s' %
(os.path.join(GRATOOLS_OUT, '%s_polspicecls.txt' % out_label)))
def main():
"""Test module
"""
plt.figure()
leg, lab = ref_igrb_band()
igrb, lab2 = ref_igrb_noFGsub()
plt.xscale('log')
plt.yscale('log')
plt.legend([leg, igrb], [lab, lab2])
plt.show()
def main():
"""
"""
cl_f = 'output/output_pol/mask_check_cl.txt'
cov_f = 'output/output_pol/mask_check_cov.fits'
l, cl = pol_cl_parse(cl_f)
clerr = pol_cov_parse(cov_f)
#plt.errorbar(l, cl, fmt='o', markersize=3, elinewidth=1, yerr=clerr)
plt.plot(l, cl, 'o', markersize=3)
plt.xscale('log')
plt.yscale('log')
#plt.ylim(-1e-15, 1e-15)
plt.show()
def main():
"""
crbkg_PSF1_file = os.path.join(GRATOOLS_CONFIG,
'ascii/p8r2_bkg_flux_t8.txt')
crbkg_PSF1 = get_crbkg(crbkg_PSF1_file)
crbkg_PSF1.plot(show=False)
x = crbkg_PSF1.x
xx = x**2
print x
y1 = crbkg_PSF1.y
crbkg_PSF2_file = os.path.join(GRATOOLS_CONFIG,
'ascii/p8r2_bkg_flux_t16.txt')
crbkg_PSF2 = get_crbkg(crbkg_PSF2_file)
crbkg_PSF2.plot(show=False)
y2 = crbkg_PSF2(x)
crbkg_PSF3_file = os.path.join(GRATOOLS_CONFIG,
'ascii/p8r2_bkg_flux_t32.txt')
crbkg_PSF3 = get_crbkg(crbkg_PSF3_file)
crbkg_PSF3.plot(show=False)
y3 = crbkg_PSF2(x)
y = (y1/x+y2/x+y3/x)*x
print y
plt.yscale('log')
plt.xscale('log')
plt.show()
fore_files_list = [os.path.join(GRATOOLS_CONFIG, \
'fits/gll_iem_v06_hp512_146647.fits'),
os.path.join(GRATOOLS_CONFIG, \
'fits/gll_iem_v06_hp512_200561.fits'),
os.path.join(GRATOOLS_CONFIG, \
'fits/gll_iem_v06_hp512_274296.fits'),
os.path.join(GRATOOLS_CONFIG, \
'fits/gll_iem_v06_hp512_375138.fits'),
os.path.join(GRATOOLS_CONFIG, \
'fits/gll_iem_v06_hp512_513056.fits'),
]
e_min, e_max = 524807.00, 575439.00
get_foreground_integral_flux_map(fore_files_list, e_min, e_max)"""
from scipy.optimize import curve_fit
ClFORE_FILE = os.path.join(GRATOOLS_OUT, 'fore_polspicecls.txt')
min1, emax1, clsfore = clfore_parse(ClFORE_FILE)
l = np.arange(len(clsfore[0]))
clsfore_spline = xInterpolatedUnivariateSplineLinear(l, clsfore[0])
clsfore_spline.plot(show=False)
plt.xscale('log')
plt.yscale('log')
plt.show()
def mkForeCl(**kwargs):
"""
"""
get_var_from_file(kwargs['config'])
logger.info('Starting Cl analysis...')
in_label = data.IN_LABEL
out_label = data.OUT_LABEL
binning_label = data.BINNING_LABEL
from GRATools.utils.gFTools import get_cl_param
cl_param_file = os.path.join(
GRATOOLS_OUT, '%s_%s_parameters.txt' % (in_label, binning_label))
_emin, _emax, _emean, _f, _ferr, _cn, _fsky = get_cl_param(cl_param_file)
cl_txt = open(os.path.join(GRATOOLS_OUT, '%s_%s_forecls.txt' \
%(out_label, binning_label)), 'w')
for i, (emin, emax) in enumerate(zip(_emin, _emax)):
mask_file = data.MASK_FILE
if type(mask_file) == list:
mask_file = mask_file[i]
mask = hp.read_map(mask_file)
logger.info('Considering bin %.2f - %.2f ...' % (emin, emax))
cl_txt.write('ENERGY\t %.2f %.2f %.2f\n' % (emin, emax, _emean[i]))
l_max = 1000
_l = np.arange(l_max)
flux_map_name = in_label + '_fore_%i-%i.fits' % (emin, emax)
flux_map = hp.read_map(os.path.join(GRATOOLS_OUT_FORE, flux_map_name))
flux_map_masked = hp.ma(flux_map)
flux_map_masked.mask = np.logical_not(mask)
fsky = 1.-(len(np.where(flux_map_masked.filled() == hp.UNSEEN)[0])/\
float(len(flux_map)))
if kwargs['show'] == True:
hp.mollview(flux_map_masked.filled(),
title='f$_{sky}$ = %.3f' % fsky,
min=1e-7,
max=1e-4,
norm='log')
plt.show()
print 'fsky = ', fsky
nside = hp.npix2nside(len(flux_map))
wpix = hp.sphtfunc.pixwin(nside)[:l_max]
_cl = hp.sphtfunc.anafast(flux_map_masked.filled(), lmax=l_max-1, \
iter=5)
_cl_fit = hp.sphtfunc.anafast(flux_map_masked.filled(), iter=4)
cl_txt.write('Cl\t%s\n'%str(list(_cl)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.close()
logger.info('Created %s'%(os.path.join(GRATOOLS_OUT, '%s_%s_forecls.txt' \
%(out_label, binning_label))))
def main():
"""Test module
"""
leg, lab = ref_cp_band()
plt.legend()
plt.xscale('log')
plt.yscale('log')
plt.show()
plt.figure()
leg, lab = ref_igrb_band()
igrb, lab2 = ref_igrb_noFGsub()
plt.xscale('log')
plt.yscale('log')
plt.legend([leg, igrb], [lab, lab2])
plt.show()
def mkForeCl(**kwargs):
"""
"""
get_var_from_file(kwargs['config'])
logger.info('Starting Cl analysis...')
in_label = data.IN_LABEL
out_label = data.OUT_LABEL
binning_label = data.BINNING_LABEL
from GRATools.utils.gFTools import get_cl_param
cl_param_file = os.path.join(GRATOOLS_OUT, '%s_%s_parameters.txt'
%(in_label, binning_label))
_emin, _emax, _emean, _f, _ferr, _cn, _fsky = get_cl_param(cl_param_file)
cl_txt = open(os.path.join(GRATOOLS_OUT, '%s_%s_forecls.txt' \
%(out_label, binning_label)), 'w')
for i, (emin, emax) in enumerate(zip(_emin, _emax)):
mask_file = data.MASK_FILE
if type(mask_file) == list:
mask_file = mask_file[i]
mask = hp.read_map(mask_file)
logger.info('Considering bin %.2f - %.2f ...'%(emin, emax))
cl_txt.write('ENERGY\t %.2f %.2f %.2f\n'%(emin, emax, _emean[i]))
l_max= 1000
_l = np.arange(l_max)
flux_map_name = in_label+'_fore_%i-%i.fits'%(emin, emax)
flux_map = hp.read_map(os.path.join(GRATOOLS_OUT_FORE, flux_map_name))
flux_map_masked = hp.ma(flux_map)
flux_map_masked.mask = np.logical_not(mask)
fsky = 1.-(len(np.where(flux_map_masked.filled() == hp.UNSEEN)[0])/\
float(len(flux_map)))
if kwargs['show'] == True:
hp.mollview(flux_map_masked.filled(), title='f$_{sky}$ = %.3f'%fsky,
min=1e-7, max=1e-4, norm='log')
plt.show()
print 'fsky = ', fsky
nside = hp.npix2nside(len(flux_map))
wpix = hp.sphtfunc.pixwin(nside)[:l_max]
_cl = hp.sphtfunc.anafast(flux_map_masked.filled(), lmax=l_max-1, \
iter=5)
_cl_fit = hp.sphtfunc.anafast(flux_map_masked.filled(), iter=4)
cl_txt.write('Cl\t%s\n'%str(list(_cl)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.close()
logger.info('Created %s'%(os.path.join(GRATOOLS_OUT, '%s_%s_forecls.txt' \
%(out_label, binning_label))))
def remove_multipole(map_file_name, lmax=10):
"""Returns a map obtained from the one given and cleaned for monopole and
dipole.
map_file_name : str
path and name of the map you want to clean for monopole
and dipole.
lmax : int
maximum multiple number upto which perform the removal
"""
map_file_name_clean = map_file_name.replace('.fits', '_multiclean.fits')
flux_map = hp.read_map(map_file_name)
alm = hp.sphtfunc.map2alm(flux_map)
map_to_remove = hp.sphtfunc.alm2map(alm, hp.npix2nside(len(flux_map)))
hp.mollview(map_to_remove)
plt.show()
new_flux_map = flux_map - map_to_remove
hp.write_map(map_file_name_clean, new_flux_map)
return map_file_name_clean
def plot(self,
num_points=1000,
overlay=False,
logx=False,
logy=False,
scale=1.,
offset=0.,
show=True,
**kwargs):
"""Plot the spline.
Args
----
num_points : int, optional
The number of sampling points to be used to draw the spline.
overlay : bool, optional
If True, the original arrays passed to the spline are overlaid.
show : bool, optional
If True, `plt.show()` is called at the end, interrupting the flow.
"""
from GRATools.utils.matplotlib_ import pyplot as plt
if not logx:
_x = numpy.linspace(self.xmin(), self.xmax(), num_points)
else:
_x = numpy.logspace(numpy.log10(self.xmin()),
numpy.log10(self.xmax()), num_points)
_y = scale * self(_x) + offset
if overlay:
plt.plot(_x, _y, '-', self.x, self.y, 'o', **kwargs)
else:
plt.plot(_x, _y, '-', **kwargs)
if self.xname is not None:
plt.xlabel(self.xlabel())
if self.yname is not None:
plt.ylabel(self.ylabel())
if logx:
plt.gca().set_xscale('log')
if logy:
plt.gca().set_yscale('log')
if show:
plt.show()
def plot(self,
num_pointsx=100,
num_pointsy=100,
num_contours=75,
logz=False,
show=True):
"""Plot the spline.
Args
----
num_pointsx : int
The number of x sampling points to be used to draw the spline.
num_pointsy : int
The number of y sampling points to be used to draw the spline.
num_contours : int
The number of contours for the color plot.
show : bool, optional
If True, `plt.show()` is called at the end, interrupting the flow.
"""
from GRATools.utils.matplotlib_ import pyplot as plt
_x = numpy.linspace(self.xmin(), self.xmax(), num_pointsx)
_y = numpy.linspace(self.ymin(), self.ymax(), num_pointsy)
_x, _y = numpy.meshgrid(_x, _y)
_z = self(_x, _y, grid=False)
if logz:
from matplotlib.colors import LogNorm
_levels = numpy.logspace(-4, numpy.log10(_z.max()), num_contours)
contour = plt.contourf(_x, _y, _z, levels=_levels, norm=LogNorm())
else:
contour = plt.contourf(_x, _y, _z, num_contours)
bar = plt.colorbar()
if self.xname is not None:
plt.xlabel(self.xlabel())
if self.yname is not None:
plt.ylabel(self.ylabel())
if self.zname is not None:
bar.set_label(self.zlabel())
if show:
plt.show()
def main():
"""Simple test unit
"""
from GRATools.utils.gWindowFunc import get_psf_ref
psf_ref_file = os.path.join(GRATOOLS_CONFIG, 'ascii/PSF_UCV_PSF1.txt')
psf_ref = get_psf_ref(psf_ref_file)
energy = np.array([
743.73, 1340.69, 2208.67, 3692.56, 6416.93, 11151.34, 18370.95,
30713.33, 53373.66, 92752.78, 152802.88, 255462.38, 443942.75
])
psf_en = psf_ref(energy)
psf_min, psf_max = psf_ref.y[5], psf_ref.y[-1]
norm_min, norm_max = 1, 0.3
norm = norm_min + psf_en*((norm_max - norm_min)/(psf_max - psf_min)) -\
psf_min*((norm_max - norm_min)/(psf_max - psf_min))
plt.title('Normalization Factor')
plt.plot(energy, norm, 'ro--', ms=5, alpha=0.75)
#plt.plot((1e-12, 1e-5), (2, 2), '-', color='silver', linewidth=1.0)
plt.xlabel('Energy [MeV]')
plt.ylabel('Normalization factor')
plt.yscale('log')
plt.xscale('log')
plt.ylim(0.09, 2)
plt.show()
nside = 512
SRC_CATALOG_FILE = os.path.join(FT_DATA_FOLDER, 'catalogs/gll_psc_v16.fit')
bad_pix = mask_src_weighted(SRC_CATALOG_FILE, 10000, nside)
bad_pix += mask_gp(30, nside)
npix = hp.nside2npix(nside)
mask = np.ones(npix)
for bpix in np.unique(bad_pix):
mask[bpix] = 0
fsky = 1 - (len(np.unique(bad_pix)) / float(npix))
title = 'f$_{sky}$ = %.3f' % fsky
hp.mollview(mask, title=title, coord='G')
plt.show()
def main():
"""Test module
"""
"""
plt.figure(figsize=(10, 7), dpi=80)
_l = np.arange(0, 10, 2)
for l in _l:
pl_th = get_pl_vs_th(l, np.arange(-1, 1, 0.00001))
plt.plot(np.arange(-1, 1, 0.00001), pl_th, '.', label='l = %i'%l)
plt.legend()
#plt.show()
"""
#out_wbeam_txt = 'output/Wbeam_P8R2_ULTRACLEANVETO_V6_56.txt'
#wb = get_wbeam(out_wbeam_txt)
#wb.plot()
"""
NSIDE = 1
NPIX = hp.nside2npix(NSIDE)
iii = np.arange(NPIX)
dec, ra = IndexToDeclRa(NSIDE, iii)
index = np.where(abs(dec)>10)
ra = ra[index]
dec = dec[index]
#ra = ra
#dec = dec
plt.figure(figsize=(10, 7), dpi=80)
hp.mollview(iii, title="Mollview image RING")
plt.figure(figsize=(10, 7), dpi=80)
lab, plots = [], []
for i in range(0, len(ra)):
print ra[i], dec[i]
out_wbeam_txt = 'output/%i_prova.txt'%i
psf_file = 'output/%i_prova.fits'%i
dict_gtpsf = {'expcube':'/data1/data/FT-files/output/output_gtltcube'+\
'/Allyrs_filtered_gti_ltcube.fits',
'outfile': psf_file,
'irfs': 'P8R2_ULTRACLEANVETO_V6',
'evtype': 3,
'ra': ra[i],
'dec': dec[i],
'emin': 500,
'emax': 600000,
'nenergies': 10,
'thetamax': 30,
'ntheta': 300}
from GRATools.utils.ScienceTools_ import gtpsf
gtpsf(dict_gtpsf)
_l = np.arange(0, 1000, 4)
psf = get_psf(psf_file)
if not os.path.exists(out_wbeam_txt):
wb = build_wbeam(psf, _l, out_wbeam_txt)
else:
wb = get_wbeam(out_wbeam_txt)
wb_1GeV = wb.hslice(1000)
wl = wb_1GeV.plot(show=False, label='RA:%i, Dec:%i'%(ra[i],dec[i]))
#lab.append('%i-%i'%(ra[i],dec[i]))
#plots.append(wl)
"""
out_wbeam_txt = 'output/Wbeam_P8R2_ULTRACLEANVETO_V6_56.txt'
wb = get_wbeam(out_wbeam_txt)
plt.figure(figsize=(10, 7), dpi=80)
_l = np.arange(0, 1000, 4)
wb_500MeV = wb.hslice(500)
plt.plot(wb_500MeV.x, wb_500MeV.y**2, label='0.5 GeV')
wb_5GeV = wb.hslice(5000)
plt.plot(wb_5GeV.x, wb_5GeV.y**2, label='5 GeV')
wb_50GeV = wb.hslice(50000)
plt.plot(wb_50GeV.x, wb_50GeV.y**2, label='50 GeV')
wb_100GeV = wb.hslice(100000)
plt.plot(wb_100GeV.x, wb_100GeV.y**2, label='100 GeV')
wb_300GeV = wb.hslice(300000)
plt.plot(wb_300GeV.x, wb_300GeV.y**2, label='300 GeV')
plt.legend()
plt.xlabel('Energy [MeV]')
plt.ylabel('W$^{2}$$_{beam}$')
plt.show()
def main():
"""Simple test unit
"""
from scipy.interpolate import interp1d
cat_file = os.path.join(GRATOOLS_CONFIG,'catalogs/gll_psc_v16.fit')
src_cat = pf.open(cat_file)
CAT = src_cat['LAT_Point_Source_Catalog']
SOURCES = CAT.data
src_cat.close()
flux = np.sort(SOURCES.field('Flux1000'))
flux_min, flux_max = min(flux), max(flux)
"""
rad_min, rad_max = 0.5, 5.
RADdeg = rad_min + flux*((rad_max - rad_min)/(flux_max - flux_min)) -\
flux_min*((rad_max - rad_min)/(flux_max - flux_min))
plt.figure(facecolor='white')
plt.title('Disk Radius as a function of $\Phi_{src}$')
plt.plot(flux, RADdeg, '*-', color='cornflowerblue', linewidth=1,
ms=5, alpha=0.2)
plt.xlabel('Flux [photon/cm$^{2}$/s]')
plt.ylabel('mask disk Radius [$^{\circ}$]')
plt.yscale('log')
plt.xscale('log')
plt.ylim(1.5, 6)
plt.grid(which='both', linestyle='--', linewidth=1)
"""
"""
from GRATools.utils.gWindowFunc import get_psf_ref
psf_ref_file = os.path.join(GRATOOLS_CONFIG, 'ascii/PSF_UCV_custom.txt')
psf_ref = get_psf_ref(psf_ref_file)
energy = np.logspace(1, 6, 10)
energy = [301.99,524.81,1000.00,2754.23,
8317.64,22908.68,331131.12]
lab = ['PSF3','PSF3','PSF1+2+3', 'PSF1+2+3', 'PSF1+2+3','PSF1+2+3',
'PSF1+2+3']
plt.figure(facecolor='white')
for i, en in enumerate(energy):
r_min = 2*psf_ref(en)
r_max = 5*psf_ref(en)
print 'R min', r_min, 'R max', r_max
print 'F min', flux_min, 'F max', flux_max
RADdeg = r_min + np.log10(flux)*((r_max - r_min)/(np.log10(flux_max) - np.log10(flux_min))) -\
np.log10(flux_min)*((r_max - r_min)/(np.log10(flux_max) - np.log10(flux_min)))
#plt.figure(facecolor='white')
plt.title('Disk Radius as a function of $\Phi_{src}$')
plt.plot(np.log10(flux), RADdeg, 'o-', linewidth=1,
ms=3, alpha=0.4, label="%.1f GeV (%s)"%(en/1000., lab[i]))
plt.xlabel('Flux [photon/cm$^{2}$/s]')
plt.ylabel('Mask disk Radius [$^{\circ}$]')
#plt.yscale('log')
#plt.xscale('log')
#plt.ylim(1.5, 6)
plt.grid(which='both', linestyle='--', linewidth=1)
plt.legend(fontsize=11, loc=2)
"""
nside = 512
SRC_CATALOG_FILE = os.path.join(GRATOOLS_CONFIG,'catalogs/gll_psc_v16.fit')
bad_pix = mask_src_weighted(SRC_CATALOG_FILE, SRC_CATALOG_FILE,8317, nside)
bad_pix += mask_bat_gp(2.5e-7, nside)
npix = hp.nside2npix(nside)
mask = np.ones(npix)
for bpix in np.unique(bad_pix):
mask[bpix] = 0
fsky = 1-(len(np.unique(bad_pix))/float(npix))
#title = 'Energy = 100 GeV, F$_{sky}$ = %.3f'%(fsky)
title = 'F$_{sky}$ = %.3f'%(fsky)
hp.mollview(mask, title=title, coord='G', cmap='bone')
hp.graticule(color='silver')
plt.show()
def mkCl(**kwargs):
"""
"""
get_var_from_file(kwargs['config'])
logger.info('Calculating PSF with gtpsf...')
dict_gtpsf = data.DICT_GTPSF
logger.info('Calculating Wbeam Function...')
out_wb_label = data.OUT_W_LABEL
mask_label = data.MASK_LABEL
out_wb_txt = os.path.join(GRATOOLS_OUT, 'Wbeam_%s.txt' % out_wb_label)
if not os.path.exists(out_wb_txt):
from GRATools.utils.ScienceTools_ import gtpsf
gtpsf(dict_gtpsf)
from GRATools.utils.gWindowFunc import get_psf
psf_file = data.PSF_FILE
psf = get_psf(psf_file)
_l = np.arange(0, 1000)
from GRATools.utils.gWindowFunc import build_wbeam
wb = build_wbeam(psf, _l, out_wb_txt)
else:
from GRATools.utils.gWindowFunc import get_wbeam
wb = get_wbeam(out_wb_txt)
save_current_figure('Wbeam_%s.png' % out_wb_label, clear=True)
logger.info('Starting Cl analysis...')
in_label = data.IN_LABEL
in_label = in_label + '_' + mask_label
out_label = data.OUT_LABEL
binning_label = data.BINNING_LABEL
mask_file = data.MASK_FILE
mask = hp.read_map(mask_file)
cl_param_file = os.path.join(GRATOOLS_OUT, '%s_%s_parameters.txt' \
%(in_label, binning_label))
from GRATools.utils.gFTools import get_cl_param
_emin, _emax, _emean, _f, _ferr, _cn, _fsky = get_cl_param(cl_param_file)
cl_txt = open(os.path.join(GRATOOLS_OUT, '%s_%s_cls.txt' \
%(out_label, binning_label)), 'w')
for i, (emin, emax) in enumerate(zip(_emin, _emax)):
logger.info('Considering bin %.2f - %.2f ...' % (emin, emax))
gamma = data.WEIGHT_SPEC_INDEX
Im = (1 / (1 - gamma)) * (emax**(1 - gamma) -
emin**(1 - gamma)) / (emax - emin)
eweightedmean = np.power(1 / Im, 1 / gamma)
cl_txt.write('ENERGY\t %.2f %.2f %.2f\n' % (emin, emax, eweightedmean))
l_max = 1000
_l = np.arange(l_max)
wb_en = wb.hslice(eweightedmean)(_l)
flux_map_name = in_label + '_flux_%i-%i.fits' % (emin, emax)
flux_map = hp.read_map(os.path.join(GRATOOLS_OUT_FLUX, flux_map_name))
flux_map_masked = hp.ma(flux_map)
flux_map_masked.mask = np.logical_not(mask)
fsky = 1.-(len(np.where(flux_map_masked.filled() == hp.UNSEEN)[0])/\
float(len(flux_map)))
if kwargs['show'] == True:
hp.mollview(flux_map_masked.filled(),
title='f$_{sky}$ = %.3f' % fsky,
min=1e-7,
max=1e-4,
norm='log')
plt.show()
print 'fsky = ', fsky
nside = hp.npix2nside(len(flux_map))
wpix = hp.sphtfunc.pixwin(nside)[:l_max]
_cl = hp.sphtfunc.anafast(flux_map_masked.filled(), lmax=l_max-1, \
iter=5)
_cl_fit = hp.sphtfunc.anafast(flux_map_masked.filled(), iter=4)
cn_fit = np.average(_cl_fit[-500:-100] / fsky) / len(
_cl_fit[-500:-100])
print 'cn fit = ', cn_fit
print 'cn poisson = ', _cn[i]
cn = _cn[i]
wl = wb_en * wpix
_cl = (_cl / fsky - cn) / (wl**2)
cl_txt.write('Cl\t%s\n'%str(list(_cl)).replace('[',''). \
replace(']','').replace(', ', ' '))
_cl_err = np.sqrt(2. / ((2 * _l + 1) * fsky)) * (_cl + (cn / wl**2))
cl_txt.write('Cl_ERR\t%s\n\n'%str(list(_cl_err)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.close()
logger.info('Created %s'%(os.path.join(GRATOOLS_OUT, '%s_%s_cls.txt' \
%(out_label, binning_label))))
def fit_fore_src_poisson(fore_map, data_map, srctempl_map, mask_map=None,
n1_guess=1., c_guess=1, n2_guess=1., exp=None,
smooth=False, show=False):
"""Performs the poisonian fit, recursively computing the log likelihood
(using poisson_likelihood) for a grid of values of fit parameters around
the guess. Returns the values of parameters which minimize the log
likelihood, togather to the 1-sigma error
n1_guess : float
initial guess for normalization parameter
n2_guess : float
initial guess for normalization parameter
c_guess : float
initial guess for constant parameter
fore_map : numpy array
helapix map of foreground model
data_map : numpy array
helapix map of data. It could be either a count map or a flux map.
If a counts map is given, an exposure map should be given too. See
next parameter.
exp : numpy array or None
helapix map of the exposure. Should be given if the data map is in
counts (beacause foreground map is in flux units by default and it
needs to be turned to counts to be fitted). While, If data map is
in flux units, do not declare this parameter, which is None by
default.
smooth : bool
not implemented yet...
show : bool
if true it shows some usefull plot to check if the fit is functioning
"""
#show=True
logger.info('Performing poissonian fit...')
norm1_guess = n1_guess
norm2_guess = n2_guess
igrb_guess = c_guess
nside_out = 64
mask = 0.
if mask_map is None:
logger.info('fit outside default mask: 30deg gp, 2 deg srcs.')
mask_f = os.path.join(GRATOOLS_CONFIG, 'fits/Mask64_src2_gp30.fits')
mask = hp.read_map(mask_f)
else:
logger.info('fit outside mask given in config file.')
mask = mask_map
logger.info('down grade...')
fore_repix = np.array(hp.ud_grade(fore_map, nside_out=nside_out))
data_repix = np.array(hp.ud_grade(data_map, nside_out=nside_out,
power=-2))
srct_repix = np.array(hp.ud_grade(srctempl_map, nside_out=nside_out))
mask_repix = np.array(hp.ud_grade(mask, nside_out=nside_out,power=-2))
mask_repix[np.where(mask_repix!=np.amax(mask_repix))[0]] = 0
mask_repix[np.where(mask_repix==np.amax(mask_repix))[0]] = 1
_unmask = np.where(mask_repix > 1e-30)[0]
logger.info('initial guesses: n1=%.1e, n2=%.1e, c=%.1e'%(norm1_guess,
norm2_guess,
igrb_guess))
norm1_list = np.linspace(norm1_guess*0.3, norm1_guess*2, 21)
norm2_list = np.linspace(norm2_guess*0.1, norm2_guess*10, 21)
print norm2_list
print norm1_list
igrb_list = np.linspace(igrb_guess*0.01, igrb_guess*10., 101)
logger.info('Minimization likelihood run1...')
lh_list = []
combinations = list(product(norm1_list, norm2_list, igrb_list))
if exp is not None:
exposure = exp
exposure = np.array(hp.ud_grade(exposure, nside_out=nside_out))
areapix = 4*np.pi/(len(data_repix))
for i,j,k in combinations:
lh = poisson_likelihood_2(i, j, k, fore_repix[_unmask],
data_repix[_unmask],
srct_repix[_unmask],
exp=exposure[_unmask],
sr=areapix)
lh_list.append(lh)
else:
for i,j,k in combinations:
lh = poisson_likelihood_2(i, j, k, fore_repix[_unmask],
data_repix[_unmask], srct_repix[_unmask])
lh_list.append(lh)
lh_min = np.argmin(np.array(lh_list))
(norm1_min, norm2_min, igrb_min) = combinations[lh_min]
logger.info('Run1 results: n1=%.3f n2=%.2e c=%.2e'%(norm1_min, norm2_min,
igrb_min))
norm1_list = np.linspace(norm1_min*0.9, norm1_min*1.7, 21)
norm2_list = np.linspace(norm2_min*0.5, norm2_min*5, 21)
print norm2_list
print norm1_list
igrb_list = np.linspace(igrb_min*0.5, igrb_min*1.5, 101)
logger.info('Minimization likelihood run2...')
lh_list = []
combinations = np.array(list(product(norm1_list, norm2_list, igrb_list)))
if exp is not None:
exposure = exp
exposure = np.array(hp.ud_grade(exposure, nside_out=nside_out))
areapix = 4*np.pi/(len(data_repix))
for i,j,k in product(norm1_list, norm2_list, igrb_list):
lh = poisson_likelihood_2(i, j, k, fore_repix[_unmask],
data_repix[_unmask],
srct_repix[_unmask],
exp=exposure[_unmask],
sr=areapix)
lh_list.append(lh)
else:
for i,j,k in product(norm1_list, norm2_list, igrb_list):
lh = poisson_likelihood_2(i, j, k, fore_repix[_unmask],
data_repix[_unmask],srct_repix[_unmask])
lh_list.append(lh)
lh_list = np.array(lh_list)
lh_min = np.argmin(lh_list)
(norm1_min, norm2_min, igrb_min) = combinations[lh_min]
logger.info('Run2 results: n1=%.3f n2=%.2e c=%.2e'%(norm1_min, norm2_min,
igrb_min))
lh_delta = np.array(lh_list)[lh_min]+2.3
index = np.where(np.array(lh_list) < lh_delta)[0]
_norm1 = np.array([x[0] for x in combinations[index]])
logger.info('Norm1 err: %.4f - %.4f'%(_norm1[0], _norm1[-1]))
n1_err = (_norm1[0], _norm1[-1])
_norm2 = np.array([x[1] for x in combinations[index]])
logger.info('Norm2 err: %.2e - %.2e'%(_norm2[0], _norm2[-1]))
n2_err = (_norm2[0], _norm2[-1])
_igrb = np.array([x[2] for x in combinations[index]])
logger.info('Igrb err: %.2e - %.2e'%(np.amin(_igrb), np.amax(_igrb)))
igrb_err = (np.amin(_igrb), np.amax(_igrb))
if show == True:
n1 = np.array([x[0] for x in combinations])
n2 = np.array([x[1] for x in combinations])
c = np.array([x[2] for x in combinations])
plt.figure(facecolor='white')
plt.plot(n2, lh_list, 'o', color='coral', alpha=0.3)
plt.plot(norm2_min, lh_list[lh_min] , 'r*')
plt.plot([_norm2[0], _norm2[-1]], [lh_delta, lh_delta], 'r-')
plt.xlabel('Normalization')
plt.ylabel('-Log(Likelihood)')
plt.title('norm src')
plt.figure(facecolor='white')
plt.plot(n1, lh_list, 'o', color='coral', alpha=0.3)
plt.plot(norm1_min, lh_list[lh_min] , 'r*')
plt.plot([_norm1[0], _norm1[-1]], [lh_delta, lh_delta], 'r-')
plt.xlabel('Normalization')
plt.ylabel('-Log(Likelihood)')
plt.title('norm fore')
plt.figure(facecolor='white')
plt.plot(c, lh_list, 'o', color='coral', alpha=0.3)
plt.plot(igrb_min, lh_list[lh_min] , 'r*')
plt.xlabel('Normalization')
plt.ylabel('-Log(Likelihood)')
plt.show()
return norm1_min, norm2_min, igrb_min, n1_err, n2_err, igrb_err
def mkCross(**kwargs):
"""
"""
get_var_from_file(kwargs['config'])
logger.info('Calculating PSF with gtpsf...')
dict_gtpsf = data.DICT_GTPSF
logger.info('Calculating Wbeam Function...')
out_wb_label = data.OUT_W_LABEL
out_wb_txt = os.path.join(GRATOOLS_OUT, 'Wbeam_%s.txt'%out_wb_label)
if not os.path.exists(out_wb_txt):
from GRATools.utils.ScienceTools_ import gtpsf
gtpsf(dict_gtpsf)
from GRATools.utils.gWindowFunc import get_psf
psf_file = data.PSF_FILE
psf = get_psf(psf_file)
_l = np.arange(0, 1000)
from GRATools.utils.gWindowFunc import build_wbeam
wb = build_wbeam(psf, _l, out_wb_txt)
else:
from GRATools.utils.gWindowFunc import get_wbeam
wb = get_wbeam(out_wb_txt)
save_current_figure('Wbeam_%s.png'%out_wb_label, clear=True)
logger.info('Starting Cl analysis...')
in_label1 = data.IN_LABEL1
in_label2 = data.IN_LABEL2
out_label = data.OUT_LABEL
binning_label = data.BINNING_LABEL
mask_file = data.MASK_FILE
mask = hp.read_map(mask_file)
cl_param_file1 = os.path.join(GRATOOLS_OUT, '%s_%s_parameters.txt' \
%(in_label1, binning_label))
cl_param_file2 = os.path.join(GRATOOLS_OUT, '%s_%s_parameters.txt' \
%(in_label2, binning_label))
from GRATools.utils.gFTools import get_cl_param
_emin, _emax, _emean, _f, _ferr, _cn, _fsky = get_cl_param(cl_param_file1)
_emin2, _emax2, _emean2, _f2, _ferr2, _cn2, _fsky2 = get_cl_param(cl_param_file2)
cross_txt = open(os.path.join(GRATOOLS_OUT, '%s_%s_cross.txt' \
%(out_label, binning_label)), 'w')
for i, (emin, emax) in enumerate(zip(_emin, _emax)):
logger.info('Considering bin %.2f - %.2f ...'%(emin, emax))
gamma = data.WEIGHT_SPEC_INDEX
Im = (1/(1-gamma))*(emax**(1-gamma)-emin**(1-gamma))/(emax-emin)
eweightedmean = np.power(1/Im, 1/gamma)
cross_txt.write('ENERGY\t %.2f %.2f %.2f\n'%(emin, emax, eweightedmean))
l_max= 1000
_l = np.arange(l_max)
wb_en = wb.hslice(eweightedmean)(_l)
flux_map_name1 = in_label1+'_flux_%i-%i.fits'%(emin, emax)
flux_map_name2 = in_label2+'_flux_%i-%i.fits'%(emin, emax)
flux_map1 = hp.read_map(os.path.join(GRATOOLS_OUT_FLUX, flux_map_name1))
flux_map2 = hp.read_map(os.path.join(GRATOOLS_OUT_FLUX, flux_map_name2))
flux_map_masked1 = hp.ma(flux_map1)
flux_map_masked1.mask = np.logical_not(mask)
flux_map_masked2 = hp.ma(flux_map2)
flux_map_masked2.mask = np.logical_not(mask)
fsky1 = 1.-(len(np.where(flux_map_masked1.filled() == hp.UNSEEN)[0])/\
float(len(flux_map1)))
fsky2 = 1.-(len(np.where(flux_map_masked2.filled() == hp.UNSEEN)[0])/\
float(len(flux_map2)))
if kwargs['show'] == True:
hp.mollview(flux_map_masked1.filled(), title='f$_{sky}$ = %.3f'%fsky,
min=1e-7, max=1e-4, norm='log')
plt.show()
print 'fsky = ', fsky1, fsky2
fsky = np.sqrt(fsky1*fsky2)
nside1 = hp.npix2nside(len(flux_map1))
nside2 = hp.npix2nside(len(flux_map1))
wpix1 = hp.sphtfunc.pixwin(nside1)[:l_max]
wpix2 = hp.sphtfunc.pixwin(nside2)[:l_max]
_cl_cross = hp.sphtfunc.anafast(flux_map_masked1.filled(),
flux_map_masked2.filled(), lmax=l_max-1, \
iter=5)
wl2 = wb_en*wb_en*wpix1*wpix2
_cl_cross = (_cl_cross/fsky)/(wl2)
cross_txt.write('Cl\t%s\n'%str(list(_cl_cross)).replace('[',''). \
replace(']','').replace(', ', ' '))
_cl_cross_err = np.sqrt(2./((2*_l+1)*fsky))*(_cl_cross)
cross_txt.write('Cl_ERR\t%s\n\n'%str(list(_cl_cross_err)).replace('[',''). \
replace(']','').replace(', ', ' '))
cross_txt.close()
logger.info('Created %s'%(os.path.join(GRATOOLS_OUT, '%s_%s_cross.txt' \
%(out_label, binning_label))))
def fit_foreground_poisson(fore_map, data_map, mask_map=None, n_guess=1.,
c_guess=0.1,exp=None, smooth=False, show=False):
"""Performs the poisonian fit, recursively computing the log likelihood
(using poisson_likelihood) for a grid of values of fit parameters around
the guess. Returns the values of parameters which minimize the log
likelihood, togather to the 1-sigma error
n_guess : float
initial guess for normalization parameter
c_guess : float
initial guess for constant parameter
fore_map : numpy array
helapix map of foreground model
data_map : numpy array
helapix map of data. It could be either a count map or a flux map.
If a counts map is given, an exposure map should be given too. See
next parameter.
exp : numpy array or None
helapix map of the exposure. Should be given if the data map is in
counts (beacause foreground map is in flux units by default and it
needs to be turned to counts to be fitted). While, If data map is
in flux units, do not declare this parameter, which is None by
default.
smooth : bool
not implemented yet...
show : bool
if true it shows some usefull plot to check if the fit is functioning
"""
#show=True
logger.info('Performing poissonian fit...')
norm_guess = n_guess
igrb_guess = c_guess
nside_out = 64
mask = 0.
if mask_map is None:
logger.info('fit outside default mask: 30deg gp, 2 deg srcs.')
mask_f = os.path.join(GRATOOLS_CONFIG, 'fits/Mask64_src2_gp30.fits')
mask = hp.read_map(mask_f)
else:
logger.info('fit outside mask given in config file.')
mask = mask_map
logger.info('down grade...')
fore_repix = np.array(hp.ud_grade(fore_map, nside_out=nside_out))
data_repix = np.array(hp.ud_grade(data_map, nside_out=nside_out,
power=-2))
mask_repix = np.array(hp.ud_grade(mask, nside_out=nside_out,
power=-2))
mask_repix[np.where(mask_repix!=np.amax(mask_repix))[0]] = 0
mask_repix[np.where(mask_repix==np.amax(mask_repix))[0]] = 1
_unmask = np.where(mask_repix > 1e-30)[0]
norm_list = np.linspace(norm_guess*0.3, norm_guess*1.5, 50)
igrb_list = np.linspace(igrb_guess*0.01, igrb_guess*10., 200)
logger.info('Minimization likelihood run1...')
lh_list = []
combinations = list(product(norm_list, igrb_list))
if exp is not None:
exposure = exp
exposure = np.array(hp.ud_grade(exposure, nside_out=nside_out))
areapix = 4*np.pi/(len(data_repix))
for i,j in product(norm_list, igrb_list):
lh = poisson_likelihood(i, j, fore_repix[_unmask],
data_repix[_unmask],
exp=exposure[_unmask],
sr=areapix)
lh_list.append(lh)
else:
for i,j in product(norm_list, igrb_list):
lh = poisson_likelihood(i, j, fore_repix[_unmask],
data_repix[_unmask])
lh_list.append(lh)
lh_min = np.argmin(np.array(lh_list))
(norm_min, igrb_min) = combinations[lh_min]
logger.info('Run1 results: n=%.3f c=%.1e'%(norm_min, igrb_min))
norm_list = np.linspace(norm_min*0.7, norm_min*1.2, 51)
igrb_list = np.linspace(igrb_min*0.5, igrb_min*1.5, 101)
logger.info('Minimization likelihood run2...')
lh_list = []
combinations = np.array(list(product(norm_list, igrb_list)))
if exp is not None:
exposure = exp
exposure = np.array(hp.ud_grade(exposure, nside_out=nside_out))
areapix = 4*np.pi/(len(data_repix))
for i,j in product(norm_list, igrb_list):
lh = poisson_likelihood(i, j, fore_repix[_unmask],
data_repix[_unmask],
exp=exposure[_unmask],
sr=areapix)
lh_list.append(lh)
else:
for i,j in product(norm_list, igrb_list):
lh = poisson_likelihood(i, j, fore_repix[_unmask],
data_repix[_unmask])
lh_list.append(lh)
lh_list = np.array(lh_list)
lh_min = np.argmin(lh_list)
(norm_min, igrb_min) = combinations[lh_min]
logger.info('Run2 results: n=%.3f c=%e'%(norm_min, igrb_min))
lh_delta = np.array(lh_list)[lh_min]+2.3
index = np.where(np.array(lh_list) < lh_delta)[0]
_norm = np.array([x[0] for x in combinations[index]])
logger.info('Norm err: %.4f - %.4f'%(_norm[0], _norm[-1]))
_igrb = np.array([x[1] for x in combinations[index]])
logger.info('Igrb err: %.e - %.e'%(np.amin(_igrb), np.amax(_igrb)))
if show == True:
n = np.array([x[0] for x in combinations])
plt.figure(facecolor='white')
plt.plot(n, lh_list, 'o', color='coral', alpha=0.3)
plt.plot(norm_min, lh_list[lh_min] , 'r*')
plt.plot([_norm[0], _norm[-1]], [lh_delta, lh_delta], 'r-')
plt.xlabel('Normalization')
plt.ylabel('-Log(Likelihood)')
igrb = np.array([x[1] for x in combinations])
plt.figure(facecolor='white')
plt.plot(igrb, lh_list, 'o', color='coral', alpha=0.3)
plt.plot(igrb_min, lh_list[lh_min] , 'r*')
plt.plot([np.amin(_igrb), np.amax(_igrb)], [lh_delta, lh_delta], 'r-')
plt.xlabel('Constant')
plt.ylabel('-Log(Likelihood)')
fig = plt.figure(facecolor='white')
z = lh_list
zmin = lh_list[lh_min]
z.shape = (len(norm_list), len(igrb_list))
ax = fig.add_subplot(111)
cax = ax.matshow(z, origin='lower', cmap='Spectral',
aspect='auto')
plt.xlabel('$C$ $[cm^{-2}s^{-1}sr^{-1}]$')
plt.ylabel('$N$')
#plt.title('$\Phi_{data}=N\cdot\Phi_{model}+C$')
x_ticks = np.linspace(np.amin(igrb_list), np.amax(igrb_list), 6)
formatting_function = np.vectorize(lambda f: format(f, '6.1E'))
x_ticks = list(formatting_function(x_ticks))
y_ticks = list(np.around(np.linspace(np.amin(norm_list),
np.amax(norm_list), 6),
decimals=3))
ax.set_yticklabels(['']+y_ticks)
ax.set_xticklabels(['']+x_ticks)
ax.xaxis.set_ticks_position('bottom')
cb = plt.colorbar(cax, format='$%.1e$')
cb.set_label('-Log(Likelihood)', rotation=90)
norm_min_ind = list(norm_list).index(norm_min)
igrb_min_ind = list(igrb_list).index(igrb_min)
_norm_ind = []
_igrb_ind = []
for i in range(0, len(index)):
_norm_ind.append(list(norm_list).index(_norm[i]))
_igrb_ind.append(list(igrb_list).index(_igrb[i]))
_norm_ind = np.array(_norm_ind)
_igrb_ind = np.array(_igrb_ind)
plt.contourf(z, [zmin, zmin+2.3, zmin+4.61, zmin+5.99],
colors='w', origin='lower', alpha=0.3)
plt.scatter(igrb_min_ind, norm_min_ind, s=45, c='w', marker='+')
plt.show()
return norm_min, igrb_min, _norm[0], _norm[-1], np.amin(_igrb), \
np.amax(_igrb)
def mkCross(**kwargs):
"""
"""
get_var_from_file(kwargs['config'])
lmax = data.LMAX
_l = np.arange(0, lmax)
gamma = data.WEIGHT_SPEC_INDEX
out_label = data.OUT_LABEL
logger.info('Calculating energy spectrum...')
from GRATools.utils.gWindowFunc import get_powerlaw_spline
energy_spec = get_powerlaw_spline(gamma)
logger.info('Calculating PSF with gtpsf 1...')
dict_gtpsf1 = data.DICT_GTPSF1
logger.info('Calculating Wbeam Function1...')
out_wb_label1 = data.OUT_W_LABEL1
out_wb_txt1 = os.path.join(GRATOOLS_OUT, 'Wbeam_%s.txt'%out_wb_label1)
in_label1 = data.IN_LABEL1
if not os.path.exists(out_wb_txt1):
from GRATools.utils.ScienceTools_ import gtpsf
gtpsf(dict_gtpsf1)
from GRATools.utils.gWindowFunc import get_psf
psf_file1 = data.PSF_FILE1
psf1 = get_psf(psf_file1)
from GRATools.utils.gWindowFunc import build_wbeam
wb1 = build_wbeam(psf1, _l, out_wb_txt1)
else:
pass
logger.info('Calculating PSF with gtpsf 2...')
dict_gtpsf2 = data.DICT_GTPSF2
logger.info('Calculating Wbeam Function2...')
out_wb_label2 = data.OUT_W_LABEL2
out_wb_txt2 = os.path.join(GRATOOLS_OUT, 'Wbeam_%s.txt'%out_wb_label2)
in_label2 = data.IN_LABEL2
if not os.path.exists(out_wb_txt2):
from GRATools.utils.ScienceTools_ import gtpsf
gtpsf(dict_gtpsf2)
from GRATools.utils.gWindowFunc import get_psf
psf_file2 = data.PSF_FILE2
psf2 = get_psf(psf_file2)
from GRATools.utils.gWindowFunc import build_wbeam
wb2 = build_wbeam(psf2, _l, out_wb_txt2)
else:
pass
logger.info('Starting Cross analysis...')
mask_label1 = data.MASK_LABEL1
mask_label2 = data.MASK_LABEL2
in_label1 = in_label1 + '_' + mask_label1
in_label2 = in_label2 + '_' + mask_label2
binning_label1 = data.BINNING_LABEL1
binning_label2 = data.BINNING_LABEL2
mask_file1 = data.MASK_FILE1
mask_file2 = data.MASK_FILE2
cl_param_file1 = os.path.join(GRATOOLS_OUT, '%s_%s_parameters.txt' \
%(in_label1, binning_label1))
cl_param_file2 = os.path.join(GRATOOLS_OUT, '%s_%s_parameters.txt' \
%(in_label2, binning_label2))
from GRATools.utils.gFTools import get_cl_param
_emin, _emax, _emean, _f1, _ferr1, _cn1, _fsky1 = \
get_cl_param(cl_param_file1)
_emin, _emax, _emean, _f2, _ferr2, _cn2, _fsky2 = \
get_cl_param(cl_param_file2)
cl_txt = open(os.path.join(GRATOOLS_OUT, '%s_%s_polspicecross.txt' \
%(out_label, binning_label1)), 'w')
from GRATools.utils.gWindowFunc import get_integral_wbeam
for i, (emin, emax) in enumerate(zip(_emin, _emax)):
logger.info('Considering bin %.2f - %.2f ...'%(emin, emax))
mask_f1 = mask_file1
mask_f2 = mask_file2
if type(mask_file1) == list:
mask_f1 = mask_file1[i]
if type(mask_file2) == list:
mask_f2 = mask_file2[i]
mask1 = hp.read_map(mask_f1)
mask2 = hp.read_map(mask_f2)
wb1_en = get_integral_wbeam(out_wb_txt1, energy_spec, emin, emax)
wb2_en = get_integral_wbeam(out_wb_txt2, energy_spec, emin, emax)
cl_txt.write('ENERGY\t %.2f %.2f %.2f\n'%(emin, emax, _emean[i]))
l_max = lmax
_l = np.arange(l_max)
wb1_en = wb1_en(_l)
wb2_en = wb2_en(_l)
flux_map_name1 = in_label1+'_flux_%i-%i.fits'%(emin, emax)
flux_map_name2 = in_label2+'_flux_%i-%i.fits'%(emin, emax)
flux_map_f1 = os.path.join(GRATOOLS_OUT_FLUX, flux_map_name1)
flux_map_f2 = os.path.join(GRATOOLS_OUT_FLUX, flux_map_name2)
flux_map_f_mdclean1 = remove_monopole_dipole(flux_map_f1)
flux_map_f_mdclean2 = remove_monopole_dipole(flux_map_f2)
flux_map1 = hp.read_map(flux_map_f_mdclean1)
flux_map2 = hp.read_map(flux_map_f_mdclean2)
fsky1 = _fsky1[i]
fsky2 = _fsky2[i]
cn = 0.
if kwargs['show'] == True:
hp.mollview(flux_map1*mask1, title='f$_{sky}$ = %.3f'%fsky,
min=1e-7, max=1e-4, norm='log')
hp.mollview(flux_map2*mask2, title='f$_{sky}$ = %.3f'%fsky,
min=1e-7, max=1e-4, norm='log')
plt.show()
logger.info('fsky1 = %.3f'%fsky1)
logger.info('fsky2 = %.3f'%fsky2)
nside1 = hp.npix2nside(len(flux_map1))
nside2 = hp.npix2nside(len(flux_map2))
wpix1 = hp.sphtfunc.pixwin(nside1)[:l_max]
wpix2 = hp.sphtfunc.pixwin(nside2)[:l_max]
out_name = '%s_%i-%i' %(out_label, emin, emax)
out_folder = os.path.join(GRATOOLS_OUT, 'output_pol')
logger.info('cn poisson = %e'%cn)
wl = np.sqrt(wb1_en*wpix1*wb2_en*wpix2)
if not os.path.exists(out_folder):
os.makedirs(out_folder)
pol_dict = data.POLCEPICE_DICT
for key in pol_dict:
if key == 'clfile':
pol_dict[key] = os.path.join(out_folder,'%s_cl.txt'%out_name)
if key == 'cl_outmap_file':
pol_dict[key] = os.path.join(out_folder,'%s_clraw.txt'%out_name)
if key == 'covfileout':
pol_dict[key] = os.path.join(out_folder,'%s_cov.fits'%out_name)
if key == 'mapfile':
pol_dict[key] = flux_map_f_mdclean1
if key == 'maskfile':
pol_dict[key] = mask_f1
if key == 'mapfile2':
pol_dict[key] = flux_map_f_mdclean2
if key == 'maskfile2':
pol_dict[key] = mask_f2
config_file_name = 'pol_%s'%(out_name)
if os.path.exists(os.path.join(out_folder,'%s_cl.txt'%out_name)) and \
os.path.exists(os.path.join(out_folder,'%s_cov.fits'%out_name)):
logger.info('ATT: Retriving power spectrum...')
_l, _cl, _clerr = pol_cl_parse(os.path.join(out_folder,
'%s_cl.txt'%out_name),
os.path.join(out_folder,
'%s_cov.fits'%out_name),
raw_corr=(cn, wl),
rebin=True)
logger.info('... and covariance matrix.')
_cov = pol_cov_parse(os.path.join(out_folder,
'%s_cov.fits'%out_name),
wl_array=wl,
rebin=True, show=True)
else:
_l, _cl, _clerr, _cov = pol_cl_calculation(pol_dict,
config_file_name,
raw_corr=(cn, wl),
rebin=True,show=True)
cl_txt.write('multipole\t%s\n'%str(list(_l)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.write('Cl\t%s\n'%str(list(_cl)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.write('Cl_ERR\t%s\n\n'%str(list(_clerr)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.close()
logger.info('Created %s'%(os.path.join(GRATOOLS_OUT,'%s_%s_polspicecls.txt'
%(out_label, binning_label1))))
def mkCl(**kwargs):
"""
"""
get_var_from_file(kwargs['config'])
lmax = data.LMAX
_l = np.arange(0, lmax)
gamma = data.WEIGHT_SPEC_INDEX
out_label = data.OUT_LABEL
logger.info('Calculating energy spectrum...')
from GRATools.utils.gWindowFunc import get_powerlaw_spline
energy_spec = get_powerlaw_spline(gamma)
logger.info('Calculating PSF with gtpsf...')
dict_gtpsf = data.DICT_GTPSF
logger.info('Calculating Wbeam Function...')
out_wb_label = data.OUT_W_LABEL
out_wb_txt = os.path.join(GRATOOLS_OUT, 'Wbeam_%s.txt'%out_wb_label)
in_label = data.IN_LABEL
if not os.path.exists(out_wb_txt):
from GRATools.utils.ScienceTools_ import gtpsf
gtpsf(dict_gtpsf)
from GRATools.utils.gWindowFunc import get_psf
psf_file = data.PSF_FILE
psf = get_psf(psf_file)
#_l = np.arange(0, 1500)
from GRATools.utils.gWindowFunc import build_wbeam
wb = build_wbeam(psf, _l, out_wb_txt)
else:
pass
logger.info('Starting Cl analysis...')
mask_label = data.MASK_LABEL
in_label = in_label + '_' + mask_label
binning_label = data.BINNING_LABEL
mask_file = data.MASK_FILE
cl_param_file = os.path.join(GRATOOLS_OUT, '%s_%s_parameters.txt' \
%(in_label, binning_label))
from GRATools.utils.gFTools import get_cl_param
_emin, _emax, _emean, _f, _ferr, _cn, _fsky = get_cl_param(cl_param_file)
cl_txt = open(os.path.join(GRATOOLS_OUT, '%s_%s_polspicecls.txt' \
%(out_label, binning_label)), 'w')
monopoles, monopoles_err = [], []
dipol_vectors = []
from GRATools.utils.gWindowFunc import get_integral_wbeam
for i, (emin, emax) in enumerate(zip(_emin, _emax)):
logger.info('Considering bin %.2f - %.2f ...'%(emin, emax))
mask_f = mask_file
if type(mask_file) == list:
mask_f = mask_file[i]
#mask = hp.read_map(mask_f)
wb_en = get_integral_wbeam(out_wb_txt, energy_spec, emin, emax)
cl_txt.write('ENERGY\t %.2f %.2f %.2f\n'%(emin, emax, _emean[i]))
l_max= lmax
_l = np.arange(l_max)
wb_en = wb_en(_l)
# monopole and dipole cleaning from MASKED map, bad value = UNSEEN
flux_map_name = in_label+'_fluxmasked_%i-%i.fits'%(emin, emax)
flux_map_f = os.path.join(GRATOOLS_OUT_FLUX, flux_map_name)
flux_map_f_mdclean, mono, dipo = remove_monopole_dipole(flux_map_f)
monopoles.append(mono)
mono_err = np.sqrt(2/_fsky[i])*(mono+_cn[i])
monopoles_err.append(mono_err)
dipol_vectors.append(dipo)
logger.info('Monopole_term = %e +- %e'%(mono, mono_err))
logger.info('Dipole vector = %s' %(str(dipo)))
# Up to l=n cleaning from MASKED map (correction for fsky discarded)
if kwargs['multiclean'] is not None:
flux_map_f_multiclean = remove_multipole(flux_map_f_mdclean,
lmax=kwargs['multiclean'])
flux_map = hp.read_map(flux_map_f_multiclean)
else:
flux_map = hp.read_map(flux_map_f_mdclean)
fsky = _fsky[i]
cn = _cn[i]
if kwargs['show'] == True:
hp.mollview(flux_map, title='f$_{sky}$ = %.3f'%fsky)
plt.show()
logger.info('fsky = '%fsky)
nside = hp.npix2nside(len(flux_map))
wpix = hp.sphtfunc.pixwin(nside)[:l_max]
out_name = '%s_%i-%i' %(out_label, emin, emax)
out_folder = os.path.join(GRATOOLS_OUT, 'output_pol')
logger.info('cn poisson = %e'%cn)
wl = wb_en*wpix
if not os.path.exists(out_folder):
os.makedirs(out_folder)
pol_dict = data.POLCEPICE_DICT
for key in pol_dict:
if key == 'clfile':
pol_dict[key] = os.path.join(out_folder,'%s_cl.txt'%out_name)
if key == 'cl_outmap_file':
pol_dict[key] = os.path.join(out_folder,'%s_clraw.txt'%out_name)
if key == 'covfileout':
pol_dict[key] = os.path.join(out_folder,'%s_cov.fits'%out_name)
if key == 'mapfile':
pol_dict[key] = flux_map_f_mdclean
if key == 'maskfile':
pol_dict[key] = mask_f
config_file_name = 'pol_%s'%(out_name)
if os.path.exists(os.path.join(out_folder,'%s_cl.txt'%out_name)) and \
os.path.exists(os.path.join(out_folder,'%s_cov.fits'%out_name)):
logger.info('ATT: Retriving power spectrum...')
_l, _cl, _clerr = pol_cl_parse(os.path.join(out_folder,
'%s_cl.txt'%out_name),
os.path.join(out_folder,
'%s_cov.fits'%out_name),
raw_corr=(cn, wl),
rebin=True)
logger.info('... and covariance matrix.')
_cov = pol_cov_parse(os.path.join(out_folder,
'%s_cov.fits'%out_name),
wl_array=wl,
rebin=True, show=True)
else:
_l, _cl, _clerr, _cov = pol_cl_calculation(pol_dict,
config_file_name,
raw_corr=(cn, wl),
rebin=True,show=True)
cl_txt.write('multipole\t%s\n'%str(list(_l)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.write('Cl\t%s\n'%str(list(_cl)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.write('Cl_ERR\t%s\n\n'%str(list(_clerr)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.write('Monopoles\t%s\n\n'%str(monopoles).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.write('Monopoles_ERR\t%s\n\n'%str(monopoles_err).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.close()
logger.info('Created %s'%(os.path.join(GRATOOLS_OUT,'%s_%s_polspicecls.txt'
%(out_label, binning_label))))
def mkCl(**kwargs):
"""
"""
get_var_from_file(kwargs['config'])
logger.info('Calculating PSF with gtpsf...')
dict_gtpsf = data.DICT_GTPSF
logger.info('Calculating Wbeam Function...')
out_wb_label = data.OUT_W_LABEL
out_wb_txt = os.path.join(GRATOOLS_OUT, 'Wbeam_%s.txt' % out_wb_label)
if not os.path.exists(out_wb_txt):
from GRATools.utils.ScienceTools_ import gtpsf
gtpsf(dict_gtpsf)
from GRATools.utils.gWindowFunc import get_psf
psf_file = data.PSF_FILE
psf = get_psf(psf_file)
_l = np.arange(0, 1000)
from GRATools.utils.gWindowFunc import build_wbeam
wb = build_wbeam(psf, _l, out_wb_txt)
else:
from GRATools.utils.gWindowFunc import get_wbeam
wb = get_wbeam(out_wb_txt)
save_current_figure('Wbeam_%s.png' % out_wb_label, clear=True)
logger.info('Starting Cl analysis...')
in_label = data.IN_LABEL
mask_label = data.MASK_LABEL
in_label = in_label + '_' + mask_label
out_label = data.OUT_LABEL
binning_label = data.BINNING_LABEL
mask_file = data.MASK_FILE
cl_param_file = os.path.join(GRATOOLS_OUT, '%s_%s_parameters.txt' \
%(in_label, binning_label))
from GRATools.utils.gFTools import get_cl_param
_emin, _emax, _emean, _f, _ferr, _cn, _fsky = get_cl_param(cl_param_file)
cl_txt = open(os.path.join(GRATOOLS_OUT, '%s_%s_polspicecls.txt' \
%(out_label, binning_label)), 'w')
for i, (emin, emax) in enumerate(zip(_emin, _emax)):
logger.info('Considering bin %.2f - %.2f ...' % (emin, emax))
mask_f = mask_file
if type(mask_file) == list:
mask_f = mask_file[i]
gamma = data.WEIGHT_SPEC_INDEX
Im = (1 / (1 - gamma)) * (emax**(1 - gamma) -
emin**(1 - gamma)) / (emax - emin)
eweightedmean = np.power(1 / Im, 1 / gamma)
cl_txt.write('ENERGY\t %.2f %.2f %.2f\n' % (emin, emax, eweightedmean))
l_max = 1000
_l = np.arange(l_max)
wb_en = wb.hslice(eweightedmean)(_l)
flux_map_name = in_label + '_flux_%i-%i.fits' % (emin, emax)
flux_map_f = os.path.join(GRATOOLS_OUT_FLUX, flux_map_name)
flux_map = hp.read_map(flux_map_f)
fsky = _fsky[i]
if kwargs['show'] == True:
hp.mollview(flux_map_masked.filled(),
title='f$_{sky}$ = %.3f' % fsky,
min=1e-7,
max=1e-4,
norm='log')
plt.show()
logger.info('fsky = ' % fsky)
nside = hp.npix2nside(len(flux_map))
wpix = hp.sphtfunc.pixwin(nside)[:l_max]
out_name = '%s_%i-%i' % (out_label, emin, emax)
out_folder = os.path.join(GRATOOLS_OUT, 'output_pol')
if not os.path.exists(out_folder):
os.makedirs(out_folder)
pol_dict = data.POLCEPICE_DICT
for key in pol_dict:
if key == 'clfile':
pol_dict[key] = os.path.join(out_folder,
'%s_cl.txt' % out_name)
if key == 'cl_outmap_file':
pol_dict[key] = os.path.join(out_folder,
'%s_clraw.txt' % out_name)
if key == 'covfileout':
pol_dict[key] = os.path.join(out_folder,
'%s_cov.fits' % out_name)
if key == 'mapfile':
pol_dict[key] = flux_map_f
if key == 'maskfile':
pol_dict[key] = mask_f
config_file_name = 'pol_%s' % (out_name)
_l, _cl, _cl_err = pol_cl_calculation(pol_dict, config_file_name)
logger.info('cn poisson = %e' % _cn[i])
cn = _cn[i]
wl = wb_en * wpix
_cl = (_cl[:l_max] - cn) / (wl**2)
_cl_err = _cl_err[:l_max] / (wl**2)
cl_txt.write('Cl\t%s\n'%str(list(_cl)).replace('[',''). \
replace(']','').replace(', ', ' '))
#_cl_err = np.sqrt(2./((2*_l+1)*fsky))*(_cl+(cn/wl**2))
cl_txt.write('Cl_ERR\t%s\n\n'%str(list(_cl_err)).replace('[',''). \
replace(']','').replace(', ', ' '))
cl_txt.close()
logger.info(
'Created %s' %
(os.path.join(GRATOOLS_OUT, '%s_%s_polspicecls.txt' %
(out_label, binning_label))))
def maps_view(**kwargs):
"""Viewer interface for healpix maps
"""
input_file = kwargs['infile']
healpix_maps = hp.read_map(input_file, field=kwargs['field'])
if kwargs['smoothing'] is not None:
healpix_maps = hp.sphtfunc.smoothing(healpix_maps,
fwhm=np.radians(kwargs['smoothing']))
if not os.path.exists(input_file):
abort("Map %s not found!"%input_file)
t = os.path.basename(input_file)
nside_out = kwargs['udgrade']
logger.info('Returning a map with NSIDE=%i'%nside_out)
if kwargs['field'] == 0:
if kwargs['counts'] == True:
if kwargs['applymask'] is not None:
mask = hp.read_map(kwargs['applymask'])
healpix_maps = healpix_maps*mask
healpix_maps = hp.pixelfunc.ud_grade(healpix_maps, nside_out,
pess=True, power=-2)
else:
if kwargs['applymask'] is not None:
mask = hp.read_map(kwargs['applymask'])
healpix_maps = healpix_maps*mask
healpix_maps = hp.pixelfunc.ud_grade(healpix_maps, nside_out,
pess=True)
healpix_maps[np.where(healpix_maps==0)[0]] = hp.UNSEEN
if kwargs['zscale'] == 'optimized':
logger.info('Optimizing...')
hp.mollview(healpix_maps, title=t.replace('.fits',''), \
coord='G', min=-5e-7, max=1e-7, cmap=cool_cmap)
plt.show()
elif kwargs['zscale'] == 'log':
logger.info('Optimizinglog z scale...')
hp.mollview(healpix_maps, title=t.replace('.fits',''), \
coord='G', norm='log', cmap=cool_cmap)
plt.show()
elif kwargs['zscale'] == 'hist':
logger.info('Optimizinglog z scale...')
hp.mollview(healpix_maps, title=t.replace('.fits',''), \
coord='G', norm='hist', cmap=cool_cmap)
plt.show()
else:
hp.mollview(healpix_maps, title=t.replace('.fits',''), \
coord='G', cmap=cool_cmap)
plt.show()
else:
for i, maps in enumerate(healpix_maps):
healpix_maps = hp.pixelfunc.ud_grade(healpix_maps, nside_out, \
pess=True)
if kwargs['zscale'] == 'optimized':
logger.info('Optimizing...')
hp.mollview(healpix_maps, title=t.replace('.fits',''), \
coord='G', min=-5e-7, max=1e-7, cmap=cool_cmap)
plt.show()
elif kwargs['zscale'] == 'log':
logger.info('Optimizinglog z scale...')
hp.mollview(healpix_maps, title=t.replace('.fits',''), \
coord='G', norm='log', cmap=cool_cmap)
plt.show()
elif kwargs['zscale'] == 'hist':
logger.info('Optimizinglog z scale...')
hp.mollview(healpix_maps, title=t.replace('.fits',''), \
coord='G', norm='hist', cmap=cool_cmap)
plt.show()
else:
hp.mollview(healpix_maps, title=t.replace('.fits',''), \
coord='G', cmap=cool_cmap)
plt.show()
