def splreg(jds, mags, magerrs,knotstep=20.0, n=None, stab=True,stabext=300.0, stabgap=20.0, stabstep=5.0,
stabmagerr=-2.0, stabrampsize=0, stabrampfact=1.0, bokit=1, bokeps=2.0, boktests=5,
bokwindow=None, k=3, verbose=True):
"""
Give me datapoints x y, with errorbars on y
I return a function : you pass an array of new x, the func returns (newy, newyerr)
I return a spline as well, so I can use it for magshifts later
performed with a BOK spline fitting on the datas and the errors.
The errors on y take into account the seasons in y
"""
l = lc.factory(jds,mags,np.zeros(len(jds))+1e-5)
l_err = lc.factory(jds,magerrs,np.zeros(len(jds))+1e-5)
spl_mag = spl.fit([l],knotstep=knotstep, n=n, stab=stab, stabext=stabext, stabgap=stabgap, stabstep=stabstep,
stabmagerr=stabmagerr, stabrampsize=stabrampsize, stabrampfact=stabrampfact, bokit=bokit,
bokeps=bokeps,boktests=boktests,bokwindow=bokwindow, k=k, verbose=verbose)
spl_magerr = spl.fit([l_err],knotstep=knotstep, n=n, stab=stab, stabext=stabext, stabgap=stabgap, stabstep=stabstep,
stabmagerr=stabmagerr, stabrampsize=stabrampsize, stabrampfact=stabrampfact, bokit=bokit,
bokeps=bokeps,boktests=boktests,bokwindow=bokwindow, k=k, verbose=verbose)
interseasons = sea.autofactory(l,seasongap=30, tpe='interseasons')
def normaldistrib(x, mu, sig):
return np.exp(-np.power(x - mu, 2.) / (2 * np.power(sig, 2.)))
def errorinterseason(minintsea,maxintsea,rsjd):
# we modelise the error enveloppe as a gaussian curve, with sigma adapted to the length of interseason
normrsjd = (rsjd-minintsea+1e-5)/(maxintsea-minintsea)
return normaldistrib(normrsjd,0.5,0.2)**1.5
def outfct(rsjds):
newy = spl_mag.eval(rsjds)
newyerr = spl_magerr.eval(rsjds)
#let's modify the error enveloppe for the rsjds between seasons:
for interseason in interseasons:
for ind,rsjd in enumerate(rsjds):
#the height of the enveloppe will be related to the length of the interseason
ndays = interseason[1]-interseason[0]
multfact = ndays/8.0 #arbitrary factor, may be changed...
if rsjd < interseason[1] and rsjd > interseason[0]:
newyerr[ind] += newyerr[ind]*errorinterseason(interseason[0],interseason[1],rsjd)*multfact
return (newy, newyerr)
return outfct, spl_mag
def save(self):
"""
Save the data in a dictionnary of lightcurve define by the shifting part of the program
So we can directly take this pickle to test the main program
@todo: maybe give different name for archive
"""
dict = {}
for curve in self.curves:
dict[curve.name] = lc.factory(
curve.datatime, curve.datamag, magerrs=curve.dataerr, telescopename="simulation", object=curve.name
)
writepickle(dict, "lcs.pkl")
def save(self):
"""
Save the data in a dictionnary of lightcurve define by the shifting part of the program
So we can directly take this pickle to test the main program
@todo: maybe give different name for archive
"""
dict = {}
for curve in self.curves:
dict[curve.name] = lc.factory(curve.datatime,
curve.datamag,
magerrs=curve.dataerr,
telescopename="simulation",
object=curve.name)
writepickle(dict, 'lcs.pkl')
def flexibleimport(filepath, jdcol=1, magcol=2, errcol=3, startline=8,
flagcol=None, propertycols=None,
telescopename="Unknown", object="Unknown",
plotcolour="red", verbose = True, units='ABmags'):
"""
The general form of file reading. We read only one lightcurve
object. To comment a line in the input file, start the line with
'#'' like in python.
:param jdcol: The column number containing the MHJDs. First column is number 1, not 0 !
:param magcol: The column number containing the magnitudes.
:param errcol: The column number containing the magnitude errorbars.
:param flagcol: (default : None) The colum containing a mask (if available). This one should contain False (= will be masked) or True (not masked).
:param propertycols: (default : None) is a dict : ``propertycols = {"fwhm":7, "skylevel":8}`` means that col 7 should be read in as property "fwhm" and 8 as "skylevel".
:type propertycols: dictionary
"""
if verbose : print "Reading \"%s\"..." % (os.path.basename(filepath))
datafile = open(filepath, "r")
filelines = datafile.readlines()[startline-1:] # we directly "skip" the first lines of eventual headers ...
datafile.close()
jds = []
mags = []
magerrs = []
flags = []
properties = []
# Check all the lines for headers, empty lines, and consistent numbers of columns:
elsperline = None
for i, line in enumerate(filelines) :
# Check for header lines:
if line[0] == "#":
print "Skipping header line %i : %s" % (i+startline, repr(line))
continue
# Check for "empty" lines - this does not seem to work correctly...
if len(line.split()) < 5:
print "Skipping empty line %i : %s" % (i+startline, repr(line))
continue
# Check the consistency of the number of columns:
elements = line.split() # line is a string, elements is a list of strings
if elsperline is not None:
if len(elements) is not elsperline:
raise RuntimeError, "Parsing error in line %i, check columns : \n%s" % (i+startline, repr(line))
elsperline = len(elements)
# Now, extend data arrays using elements of this row:
jds.append(float(elements[jdcol-1]))
x,xerr = float(elements[magcol-1]), float(elements[errcol-1])
if units=='ABmags':
mags.append(x)
magerrs.append(xerr)
elif units=='nmgy':
m,merr = flux2magnitude(x,xerr)
mags.append(m)
magerrs.append(merr)
else:
raise RuntimeError, "Unknown units '%s'\n" % (units)
# Also append flag array, as required:
if flagcol is not None :
strflag = str(elements[flagcol-1])
if strflag == "True":
flags.append(True)
elif strflag == "False":
flags.append(False)
else:
print "Flag error in line %i : %s" % (i+startline, repr(line))
else:
flags.append(True)
propdict = {} # an empty dict for now
if propertycols is not None :
for (propname, propcol) in propertycols.items():
propdict[propname] = str(elements[propcol-1])
properties.append(propdict)
#Call the factory function from pycs
pycs.gen.lc.factory(jds, mags)
# Make a brand new lightcurve object:
newlc = factory(np.array(jds), np.array(mags), magerrs=np.array(magerrs), telescopename=telescopename, object=object)
newlc.properties = properties[:]
newlc.mask = np.array(flags[:])
newlc.plotcolour = plotcolour
nbmask = np.sum(newlc.mask==False)
commentcols = "(%i, %i, %i)" % (jdcol, magcol, errcol)
newlc.commentlist.insert(0, "Imported from %s, columns %s" % (os.path.basename(filepath), commentcols))
if verbose: print "%s with %i points imported (%i of them masked)." % (str(newlc), len(newlc.jds), nbmask)
return newlc
