def main(argv):
if len(sys.argv) != 2:
print("usage : %s lkl_file")
sys.exit(1)
lkls = hpy.File(sys.argv[1])["clik"]
print("found %d likelihoods" % lkls.attrs["n_lkl_object"])
f0 = sys.argv[1]
f_tmpl = f0.split(".")
f_tmpl = ".".join(f_tmpl[:-1] + ["%s"] + [f_tmpl[-1]])
for lkln in ("lkl_%d" % v for v in range(lkls.attrs["n_lkl_object"])):
fname = f_tmpl % lkln
lkl = lkls[lkln]
print(" " + fname)
hf = hpy.File(fname, "w", lkls)
if "lmax" in lkl.attrs:
lmax = lkl.attrs["lmax"]
else:
ell = lkl.attrs["ell"]
lmax = nm.max(ell)
lmaxs = nm.where(lkl.attrs["has_cl"], lmax, -nm.ones(6, dtype=nm.int))
chf = hf.create_group("clik")
chf.attrs["lmax"] = lmaxs
chf.attrs["n_lkl_object"] = 1
lkl.copy(lkl, chf, "lkl_0")
hf.close()
def main_lensing(argv):
lkl = clik.clik_lensing(sys.argv[1])
print("clik lensing file = %s"%sys.argv[1])
if hpy.cldf.is_cldf(argv[1]):
ff = hpy.File(argv[1])
ty = ff["clik_lensing/itype"]
if ty==0:
renorm = 1
ren1 = 0
else:
renorm = ff["clik_lensing/renorm"]
ren1 = 0
if ty in [3,4]:
ren1 = ff["clik_lensing/ren1"]
else:
rr = file(argv[1]).read()
if ("# format: mono") in rr:
renorm = 1
ren1 = 0
elif ("# format: qecl") in rr:
renorm = 1
ren1 = 0
else:
renorm = 1
ren1 = 1
print(" Renormalization: %s\n N1 computation: %s"%(["Off","On"][renorm],["Off","On"][ren1]))
print(" lmax = %s (PP TT EE BB TE TB EB)"%lkl.lmax)
print(" number of extra parameters %d"%len(lkl.extra_parameter_names))
for nn in lkl.extra_parameter_names:
print(" %s"%nn)
def change_plik_cmbonly(inhf, lklfile, outfile, lmin, lmax):
olmin = 30
olmax = 2508
if lmin == -1 or lmin > lmax or lmin < olmin:
lmin = olmin
if lmax == -1 or lmax > olmax:
lmax = olmax
nb = 215
blmin = nm.loadtxt(inhf._name + "/clik/lkl_0/_external/blmin.dat")
blmax = nm.loadtxt(inhf._name + "/clik/lkl_0/_external/blmax.dat")
bmin = nm.argmin((blmin + olmin - lmin)**2)
bmax = nm.argmin((blmax + olmin - lmax)**2)
lmin = blmin[bmin] + olmin
lmax = blmax[bmax] + olmin
print("restrict to %d %d [%d %d]" % (lmin, lmax, bmin, bmax))
hpy.copyfile(lklfile, outfile)
outhf = hpy.File(outfile, "r+")
outhf["clik/lkl_0/bin_min_tt"] = bmin + 1
outhf["clik/lkl_0/bin_max_tt"] = bmax + 1
outhf["clik/lkl_0/bin_min_te"] = 1
outhf["clik/lkl_0/bin_max_te"] = 199
outhf["clik/lkl_0/bin_min_ee"] = 1
outhf["clik/lkl_0/bin_max_ee"] = 199
php.remove_selfcheck(root_grp=outhf["clik"])
outhf.close()
def main(argv):
if len(sys.argv)!=2:
print "usage : %s parfile\n copy input_clik to output_clik, change lmin and lmax of output_clik.\n lmin and lmax can be set to -1 to keep the input_clik values.\n input_clik, must be a plik or commander file.\n if input_clik is a binned plik file, the effective lmin and lmax will be the set to the closest bins.\n Here is an example parfile\n #input and output clik files\n input_clik = plik_dx11dr2_HM_v18_TT.clik\n\n output_clik = plik_dx11dr2_HM_v18_TT_no143x143.clik\n\n #set to -1 to use default value\n #set to anything else to change lmin\n lmin = -1 -1 -1 &\n -1 -1 -1 &\n -1 -1 -1 \n\n \n #set to -1 to use default value\n #set to anything else to change lmax\n #set any non negative value inferior than lmin (0 is a good example) ro remove a cross spectra\n lmax = -1 -1 -1 &\n -1 0 -1 &\n -1 -1 -1 \n\n "%osp.basename(sys.argv[0])
sys.exit(0)
pars = clik.miniparse(argv[1])
lklfile = pars.str.input_clik
lmin = pars.int_array.lmin
lmax = pars.int_array.lmax
if "beg_notch" in pars:
beg = pars.int_array.beg_notch
nd = pars.int_array.end_notch
else:
beg = [-1]*len(lmin)
nd = [-1]*len(lmin)
outfile = pars.str.output_clik
inhf = hpy.File(lklfile)
ty = inhf["clik/lkl_0/lkl_type"]
if ty not in ("smica"):
print "can only change lmin and lmax for plik likelihoods"
sys.exit(-1)
assert ty in ["smica"],"Cannot change lrange for likelihood type %s"%ty
fnc = globals()["change_%s"%ty]
fnc(inhf,lklfile,outfile,lmin,lmax,beg,nd)
def change_simlow(inhf, lklfile, outfile, lmin, lmax):
hpy.copyfile(lklfile, outfile)
outhf = hpy.File(outfile, "r+")
outhf["clik/lmax"] = [-1, lmax, -1, -1, -1, -1]
outhf["clik/lkl_0/lmin"] = lmin
outhf["clik/lkl_0/lmax"] = lmax
php.remove_selfcheck(root_grp=outhf["clik"])
outhf.close()
def main(argv):
lkl = hpy.File(sys.argv[1], "r")
cls = lkl["clik/check_param"][:]
if len(argv) == 2:
clfile = argv[1] + ".cls"
else:
clfile = argv[2]
cls.tofile(clfile, sep=" ")
def main(argv):
pars = clik.miniparse(argv[1])
inhf = hpy.File(pars.input_object)
if "external_dir" in inhf["clik/lkl_%d" % pars.int(
default=0).lkl_id].attrs and inhf["clik/lkl_%d" % pars.int(
default=0).lkl_id].attrs["external_dir"] == ".":
import shutil
shutil.copytree(
pars.input_object +
"/clik/lkl_%d/_external" % pars.int(default=0).lkl_id,
pars.install_path)
else:
dts = inhf["clik/lkl_%d/external_data" % pars.int(default=0).lkl_id][:]
inhf.close()
if not osp.exists(pars.install_path):
os.mkdir(pars.install_path)
f = open(osp.join(pars.install_path, "data.tar"), "w")
f.write(dts.tostring())
f.close()
assert os.system("cd %s;tar xvf data.tar" % pars.install_path) == 0
assert os.system("cd %s;rm -f data.tar" % pars.install_path) == 0
if "res_object" in pars:
hpy.copyfile(pars.input_object, pars.res_object)
outhf = hpy.File(pars.res_object, "r+")
try:
del outhf["clik/lkl_%d/external_data" % pars.int(default=0).lkl_id]
except Exception as e:
pass
try:
rmtree(pars.input_object +
"/clik/lkl_%d/_external" % pars.int(default=0).lkl_id)
except Exception as e:
pass
outhf["clik/lkl_%d" % pars.int(
default=0).lkl_id].attrs["external_dir"] = pars.install_path
outhf.close()
def main(argv):
if clik.lkl_lensing.try_lensing(argv[1]):
return main_lensing(argv)
lkl = hpy.File(sys.argv[1], "r")
cls = lkl["clik/check_param"][:]
if len(argv) == 2:
clfile = argv[1] + ".cls"
else:
clfile = argv[2]
cls.tofile(clfile, sep=" ")
def change_gibbs_gauss(inhf, lklfile, outfile, lmin, lmax):
olmin = inhf["clik/lkl_0/lmin"]
if lmin == -1 or lmin > lmax:
lmin = inhf["clik/lkl_0/lmin"]
if lmax == -1:
lmax = inhf["clik/lkl_0/lmax"]
if lmax > 249:
print("not possible")
sys.exit(-1)
hpy.copyfile(lklfile, outfile)
outhf = hpy.File(outfile, "r+")
outhf["clik/lmax"] = [lmax, -1, -1, -1, -1, -1]
outhf["clik/lkl_0/lmin"] = lmin
outhf["clik/lkl_0/lmax"] = lmax
outhf["clik/lkl_0/delta_l"] = lmax
php.remove_selfcheck(root_grp=outhf["clik"])
outhf.close()
def main(argv):
if len(sys.argv) != 5:
print("usage : %s input_clik lmin lmax output_clik\n copy input_clik to output_clik, change lmin and lmax of output_clik.\n lmin and lmax can be set to -1 to keep the input_clik values.\n input_clik, must be a plik or commander file.\n if input_clik is a binned plik file, the effective lmin and lmax will be the set to the closest bins." % osp.basename(sys.argv[0]))
sys.exit(0)
lklfile = sys.argv[1]
lmin = int(sys.argv[2])
lmax = int(sys.argv[3])
outfile = sys.argv[4]
inhf = hpy.File(lklfile)
ty = inhf["clik/lkl_0/lkl_type"]
if ty not in ("smica", "gibbs_gauss"):
print("can only change lmin and lmax for plik and commander TT likelihoods")
sys.exit(-1)
assert ty in [
"smica", "gibbs_gauss"], "Cannot change lrange for likelihood type %s" % ty
fnc = globals()["change_%s" % ty]
fnc(inhf, lklfile, outfile, lmin, lmax)
def main_CMB(argv):
clikl = clik.clik(sys.argv[1])
extn = clikl.extra_parameter_names
lkl = hpy.File(sys.argv[1],"r")["clik"]
print("clik lkl file = %s"%sys.argv[1])
print(" number of likelihoods = %d"%lkl.attrs["n_lkl_object"])
print(" lmax ( "+ " ".join([nl+" = %d"%ll for nl,ll in zip(("TT","EE","BB","TE","TB","EB"),lkl.attrs["lmax"]) if ll >-1])+" )")
print(" number of varying extra parameters %d"%(len(extn)))
for n in extn:
print(" %s"%n)
if "prior" in lkl:
names = lkl["prior"].attrs["name"]
names = [names[i*256:(i+1)*256].strip() for i in range(len(names)/256)]
print(" gaussian priors on %s"%", ".join(names))
loc = lkl["prior/loc"][:]
print(" at \n %s"%" ".join([str(l) for l in loc]))
var = lkl["prior/var"][:]
if len(var)==len(loc):
var = nm.diag(var)
var.shape=(len(loc),-1)
print(" with variance")
print("\n".join([" "+" ".join([str(v) for v in vl]) for vl in var]))
if "default" in lkl:
loc = lkl["default/loc"][:]
print(" number of fixed parameters = %d"%len(loc))
nms = lkl["default"].attrs["name"]
nms = [nms[i*256:i*256+256].strip() for i in range(len(loc))]
for n,l in zip(nms,loc):
print(" %s = %g"%(n,l))
ilkl = 0
for lkli_n in ("lkl_%d"%v for v in range(lkl.attrs["n_lkl_object"])):
lkli = lkl[lkli_n]
print("\n %s"%lkli_n)
print(" lkl_type = %s"%lkli.attrs["lkl_type"])
print(" unit = %g"%lkli.attrs["unit"])
if "lmax" in lkli.attrs:
lmax = lkli.attrs["lmax"]
lmin = 0
if "lmin" in lkli.attrs:
lmin = lkli.attrs["lmin"]
ellh = False
else:
ell = lkli.attrs["ell"]
lmax = nm.max(ell)
lmin = nm.min(ell)
ellh = not nm.alltrue((ell[1:]-ell[:-1]) == 1)
print(" "+" ".join([nl+" = [%d , %d]"%(lmin,lmax) for nl,hl in zip(("TT","EE","BB","TE","TB","EB"),lkli.attrs["has_cl"]) if hl ])+" (discontinous)"*ellh)
if "wl" in lkli.attrs:
print(" has window function")
if "nbins" in lkli.attrs:
print(" nbins = %d"%lkli.attrs["nbins"])
if lkli.attrs["lkl_type"]=="smica":
print(" component 0 : CMB")
for nc in range(1,lkli.attrs["n_component"]):
if "component_name" in lkli["component_%d"%nc]:
print(" component %d : %s"%(nc,lkli["component_%d"%nc].attrs["component_name"]))
else:
print(" component %d : %s"%(nc,lkli["component_%d"%nc].attrs["component_type"]))
extn = clikl.get_extra_parameter_names_by_lkl(ilkl)
print(" number of extra parameters = %d %s"%(len(extn),extn))
ilkl +=1
def change_smica(inhf, lklfile, outfile, lmin, lmax):
olmin = inhf["clik/lkl_0/lmin"]
olmax = inhf["clik/lkl_0/lmax"]
if lmin == -1 or lmin > lmax or lmin < olmin:
lmin = olmin
if lmax == -1 or lmax > olmax:
lmax = olmax
nb = inhf["clik/lkl_0/nbins"]
blmin = inhf["clik/lkl_0/bin_lmin"]
blmax = inhf["clik/lkl_0/bin_lmax"]
bmin = nm.argmin((blmin + olmin - lmin)**2)
bmax = nm.argmin((blmax + olmin - lmax)**2)
lmin = blmin[bmin] + olmin
lmax = blmax[bmax] + olmin
print("restrict to %d %d" % (lmin, lmax))
hascl = inhf["clik/lkl_0/has_cl"]
assert hascl[1:].sum() == 0, "do not work yet on polar data"
mT = inhf["clik/lkl_0/m_channel_T"]
ord = inhf["clik/lkl_0/criterion_gauss_ordering"]
ord.shape = (-1, 2)
nmsk = inhf["clik/lkl_0/criterion_gauss_mask"]
nmsk.shape = (nb, mT, mT)
kp = []
mx = 0
for i, j in ord:
cur = nm.arange(nb)[nmsk[:, i, j] == 1]
kp += [nm.where((cur < bmax + 1) * (cur > bmin - 1))[0] + mx]
mx += len(cur)
kp = nm.concatenate(kp)
siginv = inhf["clik/lkl_0/criterion_gauss_mat"]
siginv.shape = (siginv.shape[0]**.5, -1)
sig = nm.linalg.inv(siginv)
del(siginv)
nsig = ((sig[kp])[:, kp]) * 1.
del(sig)
nsiginv = nm.linalg.inv(nsig)
del(nsig)
hpy.copyfile(lklfile, outfile)
outhf = hpy.File(outfile, "r+")
outhf["clik/lmax"] = [lmax, -1, -1, -1, -1, -1]
outhf["clik/lkl_0/lmin"] = lmin
outhf["clik/lkl_0/lmax"] = lmax
outhf["clik/lkl_0/nbins"] = bmax + 1 - bmin
cutarr(inhf, outhf, 0, nb - 1, bmin, bmax, "clik/lkl_0/bin_lmin")
outhf["clik/lkl_0/bin_lmin"] = outhf["clik/lkl_0/bin_lmin"] - \
(lmin - olmin)
cutarr(inhf, outhf, 0, nb - 1, bmin, bmax, "clik/lkl_0/bin_lmax")
outhf["clik/lkl_0/bin_lmax"] = outhf["clik/lkl_0/bin_lmax"] - \
(lmin - olmin)
cutarr(inhf, outhf, olmin, olmax, lmin, lmax, "clik/lkl_0/bin_ws")
cutarr(inhf, outhf, 0, nb - 1, bmin, bmax, "clik/lkl_0/Rq_hat")
cutarr(inhf, outhf, 0, nb - 1, bmin, bmax, "clik/lkl_0/wq")
cutarr(inhf, outhf, 0, nb - 1, bmin, bmax,
"clik/lkl_0/criterion_gauss_mask")
outhf["clik/lkl_0/criterion_gauss_mat"] = nsiginv.flat[:]
for i in range(1, inhf["clik/lkl_0/n_component"]):
if "lmin" not in inhf["clik/lkl_0/component_%d" % i]:
continue
outhf["clik/lkl_0/component_%d/lmin" % i] = lmin
outhf["clik/lkl_0/component_%d/lmax" % i] = lmax
php.remove_selfcheck(root_grp=outhf["clik"])
outhf.close()
def main(argv):
if len(sys.argv) < 4:
print(
"usage : %s lkl_file_1 lkl_file_2 [lkl_file_3 ...] result_lkl_file"
)
sys.exit(1)
for fl in sys.argv[1:-1]:
if clik.try_lensing(fl):
print("clik_join doesn't work yet with lensing likelihood, sorry")
sys.exit(1)
lkls = [hpy.File(ll)["clik"] for ll in sys.argv[1:-1]]
reslkl = hpy.File(sys.argv[-1], "w", ty=lkls[0])
nlkl = 0
lmax = -nm.ones(6, dtype=nm.int)
resclik = reslkl.create_group("clik")
name = []
loc = []
defn = []
defloc = []
var = nm.zeros((0, 0))
for lklin in lkls:
if "prior" in lklin:
prid = lklin["prior"]
pname = [n.strip() for n in prid.attrs["name"].split('\0') if n]
for n in name:
if n in pname:
raise Exception("already got a prior on %s" % n)
ploc = prid["loc"][:]
pvar = prid["var"][:]
if len(pvar) == len(ploc):
pvar = nm.diag(pvar)
pvar.shape = (len(ploc), -1)
nvar = nm.zeros((len(loc) + len(ploc), len(loc) + len(ploc)))
nvar[:len(loc), :len(loc)] = var
nvar[len(loc):, len(loc):] = pvar
var = nvar
name = list(name) + list(pname)
loc = nm.concatenate((loc, ploc))
lmaxin = lklin.attrs["lmax"]
lmax = nm.max((lmax, lmaxin), 0)
nlklin = lklin.attrs["n_lkl_object"]
for i in range(nlklin):
grpin = "lkl_%d" % i
grpout = "lkl_%d" % nlkl
nlkl += 1
lklin.copy(lklin[grpin], resclik, grpout)
if "default" in lklin:
prid = lklin["default"]
pname = [n.strip() for n in prid.attrs["name"].split('\0') if n]
ploc = prid["loc"][:]
for i, n in enumerate(pname):
l = ploc[i]
add = True
for ii, nn in enumerate(defn):
if n == nn:
if l != defloc[ii]:
raise Exception(
"cannot fix the same parameter with different values"
)
add = False
break
if add:
defn += [n]
defloc += [l]
if len(name):
prid = resclik.create_group("prior")
prid.attrs["name"] = php.pack256(*name)
prid.create_dataset("loc", data=loc.flat[:])
prid.create_dataset("var", data=var.flat[:])
if len(defn):
prid = resclik.create_group("default")
prid.attrs["name"] = php.pack256(*defn)
prid.create_dataset("loc", data=nm.array(defloc).flat[:])
resclik.attrs["lmax"] = lmax.astype(nm.int)
resclik.attrs["n_lkl_object"] = nlkl
reslkl.close()
def __init__(self, clikfile, paramnames=None):
# paramnames will be used to do the mapping to the extra parameters
self.dffile = clikfile
self.name = os.path.splitext(os.path.basename(clikfile))[0]
if isinstance(paramnames, (list, tuple)):
self.parnames = paramnames
else:
if paramnames is None:
# match versions to the baseline .paramnames file
for rem in ['_', 'a_', 'b_', 'c_', 'd_']:
name = self.name.replace(rem, '_').replace('_bin1', '')
paramnames = os.path.join(
os.path.dirname(__file__),
'../../data/' + name + '.paramnames')
if os.path.exists(paramnames):
break
self.paramnamefile = paramnames
self.paramnames = ParamNames(paramnames)
self.parnames = self.paramnames.list()
self.clik = clik.clik(clikfile)
self._translate_parname(self.parnames)
self.fi = hpy.File(self.dffile)
# some metadata
self.hascl = self.fi["clik/lkl_0/has_cl"]
self.lmin = self.fi["clik/lkl_0/lmin"]
self.lmax = self.fi["clik/lkl_0/lmax"]
self.mt = self.fi["clik/lkl_0/m_channel_T"] * self.hascl[0]
self.me = self.fi["clik/lkl_0/m_channel_P"] * self.hascl[1]
self.mb = self.fi["clik/lkl_0/m_channel_P"] * self.hascl[2]
self.m = self.mt + self.me + self.mb
self.nb = self.fi["clik/lkl_0/nbins"] / self.hascl.sum()
self.rq_shape = (self.nb, self.m, self.m)
# binning details
self.blmin = self.fi["clik/lkl_0/bin_lmin"]
self.blmax = self.fi["clik/lkl_0/bin_lmax"]
self.b_ws = self.fi["clik/lkl_0/bin_ws"]
# the binning matrix is also simply obtained this way (but using it is slower than using the binning details, 'cause it's full of zeros)
self.bns = php.read_bins(self.fi["clik/lkl_0"])
# compute the binned ells
self.lm = np.dot(self.bns[:self.nb, :self.lmax - self.lmin + 1],
np.arange(self.lmin, self.lmax + 1))
# get the calibration part (and beam for plik 2015)
# cal and bal are functions that expect a vector of parameters whose name and ordering are given by cal.varpar and bal.varpar
# overal calibration is given by cal(pars)*vec(pars)*outer(acmb,acmb)[nm.newaxis,:,:]
self.cal = smh.calTP_from_smica(self.dffile)
self.bal = smh.beamTP_from_smica(self.dffile)
self.acmb = self.fi["clik/lkl_0/A_cmb"]
# get the binned Cl data array
self.rqh = self.fi["clik/lkl_0/Rq_hat"]
self.rqh.shape = self.rq_shape
# get the additive nuisance components
self.prms = smh.parametric_from_smica(self.dffile)
self.prms_name = [p.get_name() for p in self.prms]
# get the selection vector
self.oo, self.Jt = smh.ordering_from_smica(self.dffile)
# get the inverse covariance
self.siginv = self.fi["clik/lkl_0/criterion_gauss_mat"]
self.siginv.shape = (len(self.oo), len(self.oo))
ls = np.arange(self.lmax + 1)
self.llp1 = ls * (ls + 1) / (2 * np.pi)
self.llp1[0] = 1
self.indices = [(0, 0), (1, 1), (2, 2), (0, 1), (0, 2), (1, 2)]
self.spectra = ["tt", "ee", "bb", "te", "tb", "eb"]
def change_smica(inhf,lklfile,outfile,lmins,lmaxs,beg,nd):
olmin = inhf["clik/lkl_0/lmin"]
olmax = inhf["clik/lkl_0/lmax"]
lmaxs = nm.array([olmax if (lm == -1 or lm>olmax) else lm for lm in lmaxs])
lmins = nm.array([olmin if (lm == -1 or lm<olmin) else lm for lm in lmins])
beg_notch = nm.array([lmx if (lm == -1 or lm>lmx) else lm for lm,lmx in zip(beg,lmaxs)])
end_notch = nm.array([lmx if (lm == -1 or lm<lmx) else lm for lm,lmx in zip(nd,lmins)])
kpp = lmaxs>lmins
nb = inhf["clik/lkl_0/nbins"]
hascl = inhf["clik/lkl_0/has_cl"]
mT = inhf["clik/lkl_0/m_channel_T"]
mP = inhf["clik/lkl_0/m_channel_P"]
mE = mT*hascl[0]
mB = mE + mP*hascl[1]
m = mB + mP*hascl[2]
blmin = inhf["clik/lkl_0/bin_lmin"][:nb/nm.sum(hascl)]
blmax = inhf["clik/lkl_0/bin_lmax"][:nb/nm.sum(hascl)]
bmins = nm.array([nm.argmin((blmin+olmin-lm)**2) for lm in lmins])
bmaxs = nm.array([nm.argmin((blmax+olmin-lm)**2) for lm in lmaxs])
bbeg_notch = nm.array([nm.argmin((blmin+olmin-lm)**2) for lm in beg_notch])
bend_notch = nm.array([nm.argmin((blmin+olmin-lm)**2) for lm in end_notch])
lmins = nm.array([blmin[bm]+olmin for bm in bmins])
lmaxs = nm.array([blmax[bm]+olmin for bm in bmaxs])
beg_notch = nm.array([blmin[bm]+olmin for bm in bbeg_notch])
end_notch = nm.array([blmax[bm]+olmin for bm in bend_notch])
dnames = inhf["clik/lkl_0/dnames"]
dnames = [dnames[i*256:(i+1)*256].strip("\0") for i in range(len(dnames)/256)]
print "restrict to"
cc = 0
for a in range(3):
aT = "TEB"[a]
for ii in range(mT if a==0 else mP*hascl[a]):
for b in range(3):
bT = "TEB"[b]
for jj in range(mT if b==0 else mP*hascl[b]):
print " %s%s %s%s lmin = %d, lmax = %d"%(aT,dnames[mT*(a!=0)+ii][:-1],bT,dnames[mT*(b!=0)+jj][:-1],lmins[cc]*kpp[cc],lmaxs[cc]*kpp[cc]),
if beg_notch[cc]*kpp[cc]<end_notch[cc]*kpp[cc]:
print "[notch %d -> %d]"%(beg_notch[cc]*kpp[cc],end_notch[cc]*kpp[cc],),
print ""
cc+=1
lmin = min(lmins[kpp])
lmax = max(lmaxs[kpp])
bmin = min(bmins[kpp])
bmax = max(bmaxs[kpp])
#sys.exit(-1)
ord = inhf["clik/lkl_0/criterion_gauss_ordering"]
ord.shape=(-1,2)
nmsk = inhf["clik/lkl_0/criterion_gauss_mask"]
nmsk.shape=(nb/nm.sum(hascl),m,m)
kp = []
mx = 0
bmins.shape=(m,m)
bmaxs.shape=(m,m)
bbeg_notch.shape=(m,m)
bend_notch.shape=(m,m)
kpp.shape=(m,m)
nnmsk = nmsk*1
for i,j in ord:
cur = nm.arange(nb/nm.sum(hascl))[nmsk[:,i,j]==1]
nnmsk[:bmins[i,j],i,j] = 0
nnmsk[bmaxs[i,j]+1:,i,j] = 0
nnmsk[bbeg_notch[i,j]:bend_notch[i,j]+1,i,j]=0
if kpp[i,j]:
kp += [nm.where((cur<bmaxs[i,j]+1) * (cur>bmins[i,j]-1) * (((cur>bbeg_notch[i,j]-1) * (cur<bend_notch[i,j]+1))==False))[0]+mx]
#print "cur",cur+mx
#print "kp",kp[-1]
#print i,j,len(cur),len(kp[-1])
#print (cur<bmaxs[i,j]+1)
#print (cur>bmins[i,j]-1)
#print (cur<bbeg_notch[i,j]+1),bbeg_notch[i,j]
#print (cur>bend_notch[i,j]-1),bend_notch[i,j]
else:
nnmsk[:,i,j] = 0
mx += len(cur)
kp = nm.concatenate(kp)
siginv = inhf["clik/lkl_0/criterion_gauss_mat"]
siginv.shape=(siginv.shape[0]**.5,-1)
sig = nm.linalg.inv(siginv)
del(siginv)
nsig = ((sig[kp])[:,kp])*1.
del(sig)
nsiginv = nm.linalg.inv(nsig)
del(nsig)
hpy.copyfile(lklfile,outfile)
outhf = hpy.File(outfile,"r+")
#outhf["clik/lmax"] = [lmax,-1,-1,-1,-1,-1]
#outhf["clik/lkl_0/lmin"] = lmin
#outhf["clik/lkl_0/lmax"] = lmax
#outhf["clik/lkl_0/nbins"] = bmax + 1 - bmin
#cutarr(inhf,outhf,0,nb-1,bmin,bmax,"clik/lkl_0/bin_lmin")
#outhf["clik/lkl_0/bin_lmin"] = outhf["clik/lkl_0/bin_lmin"]-(lmin-olmin)
#cutarr(inhf,outhf,0,nb-1,bmin,bmax,"clik/lkl_0/bin_lmax")
#outhf["clik/lkl_0/bin_lmax"] = outhf["clik/lkl_0/bin_lmax"]-(lmin-olmin)
#cutarr(inhf,outhf,olmin,olmax,lmin,lmax,"clik/lkl_0/bin_ws")
#cutarr(inhf,outhf,0,nb-1,bmin,bmax,"clik/lkl_0/Rq_hat")
#cutarr(inhf,outhf,0,nb-1,bmin,bmax,"clik/lkl_0/wq")
#cutarr(inhf,outhf,0,nb-1,bmin,bmax,"clik/lkl_0/criterion_gauss_mask",nnmsk)
outhf["clik/lkl_0/criterion_gauss_mask"] = nnmsk.flat[:]
outhf["clik/lkl_0/criterion_gauss_mat"] = nsiginv.flat[:]
#for i in range(1,inhf["clik/lkl_0/n_component"]):
# if "lmin" not in inhf["clik/lkl_0/component_%d"%i]:
# continue
# outhf["clik/lkl_0/component_%d/lmin"%i]=lmin
# outhf["clik/lkl_0/component_%d/lmax"%i]=lmax
php.remove_selfcheck(root_grp=outhf["clik"])
outhf.close()
