def list_mesa_data(filename='profiles.index'):
"""
Return a chronological list of *.data files in a MESA LOG directory
"""
number,priority,lognr = ascii.read2array(filename,skip_lines=1).T
logfiles = [os.path.join(os.path.dirname(filename),'profile%d.data'%(nr)) for nr in lognr]
return number,logfiles
def list_mesa_data(filename='profiles.index'):
"""
Return a chronological list of *.data files in a MESA LOG directory
"""
number, priority, lognr = ascii.read2array(filename, skip_lines=1).T
logfiles = [
os.path.join(os.path.dirname(filename), 'profile%d.data' % (nr))
for nr in lognr
]
return number, logfiles
def get_response(photband):
"""
Retrieve the response curve of a photometric system 'SYSTEM.FILTER'
OPEN.BOL represents a bolometric open filter.
Example usage:
>>> p = pl.figure()
>>> for band in ['J','H','KS']:
... p = pl.plot(*get_response('2MASS.%s'%(band)))
If you defined a custom filter with the same name as an existing one and
you want to use that one in the future, set C{prefer_file=False} in the
C{custom_filters} module dictionary.
@param photband: photometric passband
@type photband: str ('SYSTEM.FILTER')
@return: (wavelength [A], response)
@rtype: (array, array)
"""
photband = photband.upper()
prefer_file = custom_filters["_prefer_file"]
if photband == "OPEN.BOL":
return np.array([1, 1e10]), np.array([1 / (1e10 - 1), 1 / (1e10 - 1)])
# -- either get from file or get from dictionary
photfile = os.path.join(basedir, "filters", photband)
photfile_is_file = os.path.isfile(photfile)
# -- if the file exists and files have preference
if photfile_is_file and prefer_file:
wave, response = ascii.read2array(photfile).T[:2]
# -- if the custom_filter exist
elif photband in custom_filters:
wave, response = custom_filters[photband]["response"]
# -- if the file exists but custom filters have preference
elif photfile_is_file:
wave, response = ascii.read2array(photfile).T[:2]
else:
raise IOError, ("{0} does not exist {1}".format(photband, custom_filters.keys()))
sa = np.argsort(wave)
return wave[sa], response[sa]
def csv2recarray(filename):
"""
Read a MAST csv (comma-sep) file into a record array.
@param filename: name of the TCSV file
@type filename: str
@return: catalog data columns, units, comments
@rtype: record array, dict, list of str
"""
data, comms = ascii.read2array(filename,
dtype=np.str,
splitchar=',',
return_comments=True)
results = None
units = {}
#-- retrieve the data and put it into a record array
if len(data) > 1:
#-- now convert this thing into a nice dictionary
data = np.array(data)
#-- retrieve the format of the columns. They are given in the
# Fortran format. In rare cases, columns contain multiple values
# themselves (so called vectors). In those cases, we interpret
# the contents as a long string
formats = np.zeros_like(data[0])
for i, fmt in enumerate(data[1]):
if 'string' in fmt or fmt == 'datetime': formats[i] = 'a100'
if fmt == 'integer': formats[i] = 'f8'
if fmt == 'ra': formats[i] = 'f8'
if fmt == 'dec': formats[i] = 'f8'
if fmt == 'float': formats[i] = 'f8'
#-- define dtypes for record array
dtypes = np.dtype([(i, j) for i, j in zip(data[0], formats)])
#-- remove spaces or empty values
cols = []
for i, key in enumerate(data[0]):
col = data[2:, i]
#-- fill empty values with nan
cols.append([(row.isspace() or not row) and np.nan or row
for row in col])
#-- fix unit name
for source in cat_info.sections():
if cat_info.has_option(source, data[0, i] + '_unit'):
units[key] = cat_info.get(source, data[0, i] + '_unit')
break
else:
units[key] = 'nan'
#-- define columns for record array and construct record array
cols = [np.cast[dtypes[i]](cols[i]) for i in range(len(cols))]
results = np.rec.array(cols, dtype=dtypes)
else:
results = None
units = {}
return results, units, comms
def csv2recarray(filename):
"""
Read a MAST csv (comma-sep) file into a record array.
@param filename: name of the TCSV file
@type filename: str
@return: catalog data columns, units, comments
@rtype: record array, dict, list of str
"""
data,comms = ascii.read2array(filename,dtype=np.str,splitchar=',',return_comments=True)
results = None
units = {}
#-- retrieve the data and put it into a record array
if len(data)>1:
#-- now convert this thing into a nice dictionary
data = np.array(data)
#-- retrieve the format of the columns. They are given in the
# Fortran format. In rare cases, columns contain multiple values
# themselves (so called vectors). In those cases, we interpret
# the contents as a long string
formats = np.zeros_like(data[0])
for i,fmt in enumerate(data[1]):
if 'string' in fmt or fmt=='datetime': formats[i] = 'a100'
if fmt=='integer': formats[i] = 'f8'
if fmt=='ra': formats[i] = 'f8'
if fmt=='dec': formats[i] = 'f8'
if fmt=='float': formats[i] = 'f8'
#-- define dtypes for record array
dtypes = np.dtype([(i,j) for i,j in zip(data[0],formats)])
#-- remove spaces or empty values
cols = []
for i,key in enumerate(data[0]):
col = data[2:,i]
#-- fill empty values with nan
cols.append([(row.isspace() or not row) and np.nan or row for row in col])
#-- fix unit name
for source in cat_info.sections():
if cat_info.has_option(source,data[0,i]+'_unit'):
units[key] = cat_info.get(source,data[0,i]+'_unit')
break
else:
units[key] = 'nan'
#-- define columns for record array and construct record array
cols = [np.cast[dtypes[i]](cols[i]) for i in range(len(cols))]
results = np.rec.array(cols, dtype=dtypes)
else:
results = None
units = {}
return results,units,comms
def fitz2004chiar2006(Rv=3.1,curve='ism',**kwargs):
"""
Combined and extrapolated extinction curve Fitzpatrick 2004 and
from Chiar and Tielens (2006).
We return A(lambda)/E(B-V), by multiplying A(lambda)/Av with Rv.
This is only defined for Rv=3.1. If it is different, this will raise an
AssertionError
Extra kwags are to catch unwanted keyword arguments.
@param Rv: Rv
@type Rv: float
@param curve: extinction curve
@type curve: string (one of 'gc' or 'ism', galactic centre or local ISM)
@return: wavelengths (A), A(lambda)/Av
@rtype: (ndarray,ndarray)
"""
if curve.lower() not in ['ism','gc']:
raise ValueError,'No Fitzpatrick2004/Chiar2006 curve available for %s.'\
%(curve)
fn = 'fitzpatrick2004_chiar2006%s_extrapol.dat'%curve
source = os.path.join(basename,fn)
#-- check Rv
assert(Rv==3.1)
wavelengths,alam_ak = ascii.read2array(source).T
#-- Convert to AA
wavelengths *= 1e4
#-- Convert from Ak normalization to Av normalization.
norm_reddening = model.synthetic_flux(wavelengths,alam_ak,\
['JOHNSON.V','JOHNSON.K'])
ak_to_av = norm_reddening[1]/norm_reddening[0]
alam_aV = alam_ak * ak_to_av
return wavelengths,alam_aV
def read_cles_sum(sumfile):
"""
Read the input from a CLES '-sum.txt' file.
Keys: C{logTeff}, C{logg}, C{M}, C{R}, C{logL}, C{age}(, C{num}, C{Xc})
@param sumfile: filename of the '-sum.txt' file.
@type param:str
@return: model track
@rtype: recarray
"""
c = {'summary':{'logTeff':7,'logg':11,'M':2,'R':10,'logL':8,'age':6},
'sum': {'logTeff':2,'logg': 8,'M':6,'R': 7,'logL':3,'age':1,'num':0,'Xc':4}}
data = ascii.read2array(sumfile)
if 'summary' in sumfile:
t = 'summary'
else:
t = 'sum'
#-- not all info readily available, build it
data_ = np.zeros((len(data[:,0]),3))
mass = float(os.path.basename(sumfile).split('_')[0][1:])
data_[:,0] = mass
radi = conversions.derive_radius((data[:,c[t]['logL']],'[Lsol]'),\
(data[:,c[t]['logTeff']],'[K]'),units='Rsol')[0]
data_[:,1] = radi
logg_ = conversions.derive_logg((float(mass),'Msol'),(data_[:,1],'Rsol'))
data_[:,2] = logg_
data = np.hstack([data,data_])
keys = np.array(c[t].keys())
cols = np.array([c[t][key] for key in keys])
sa = np.argsort(cols)
keys = keys[sa]
cols = cols[sa]
mydata = np.rec.fromarrays([data[:,col] for col in cols],names=list(keys))
logger.debug('CLES summary %s read'%(sumfile))
return mydata
def fitzpatrick2004(Rv=3.1,**kwargs):
"""
From Fitzpatrick 2004 (downloaded from FTP)
This function returns A(lambda)/A(V).
To get A(lambda)/E(B-V), multiply the return value with Rv (A(V)=Rv*E(B-V))
Extra kwags are to catch unwanted keyword arguments.
@param Rv: Rv (2.1, 3.1 or 5.0)
@type Rv: float
@return: wavelengths (A), A(lambda)/Av
@rtype: (ndarray,ndarray)
"""
filename = 'Fitzpatrick2004_Rv_%.1f.red'%(Rv)
myfile = os.path.join(basename,filename)
wave_inv,elamv_ebv = ascii.read2array(myfile,skip_lines=15).T
logger.info('Fitzpatrick2004 curve with Rv=%.2f'%(Rv))
return 1e4/wave_inv[::-1],((elamv_ebv+Rv)/Rv)[::-1]
def fitzpatrick2004(Rv=3.1, **kwargs):
"""
From Fitzpatrick 2004 (downloaded from FTP)
This function returns A(lambda)/A(V).
To get A(lambda)/E(B-V), multiply the return value with Rv (A(V)=Rv*E(B-V))
Extra kwags are to catch unwanted keyword arguments.
@param Rv: Rv (2.1, 3.1 or 5.0)
@type Rv: float
@return: wavelengths (A), A(lambda)/Av
@rtype: (ndarray,ndarray)
"""
filename = 'Fitzpatrick2004_Rv_%.1f.red' % (Rv)
myfile = os.path.join(basename, filename)
wave_inv, elamv_ebv = ascii.read2array(myfile, skip_lines=15).T
logger.info('Fitzpatrick2004 curve with Rv=%.2f' % (Rv))
return 1e4 / wave_inv[::-1], ((elamv_ebv + Rv) / Rv)[::-1]
def chiar2006(Rv=3.1,curve='ism',**kwargs):
"""
Extinction curve at infrared wavelengths from Chiar and Tielens (2006)
We return A(lambda)/Av, by multiplying A(lambda)/Ak Ak/Av=0.09 (see Chiar
and Tielens (2006).
This is only defined for Rv=3.1. If it is different, this will raise an
AssertionError
Extra kwags are to catch unwanted keyword arguments.
UNCERTAIN NORMALISATION
@param Rv: Rv
@type Rv: float
@param curve: extinction curve
@type curve: string (one of 'gc' or 'ism', galactic centre or local ISM)
@return: wavelengths (A), A(lambda)/Av
@rtype: (ndarray,ndarray)
"""
source = os.path.join(basename,'Chiar2006.red')
#-- check Rv
assert(Rv==3.1)
wavelengths,gc,ism = ascii.read2array(source).T
if curve=='gc':
alam_ak = gc
elif curve=='ism':
keep = ism>0
alam_ak = ism[keep]
wavelengths = wavelengths[keep]
else:
raise ValueError,'no curve %s'%(curve)
alam_aV = alam_ak * 0.09
#plot(1/wavelengths,alam_aV,'o-')
return wavelengths*1e4,alam_aV
def fitzpatrick1999(Rv=3.1, **kwargs):
"""
From Fitzpatrick 1999 (downloaded from ASAGIO database)
This function returns A(lambda)/A(V).
To get A(lambda)/E(B-V), multiply the return value with Rv (A(V)=Rv*E(B-V))
Extra kwags are to catch unwanted keyword arguments.
@param Rv: Rv (2.1, 3.1 or 5.0)
@type Rv: float
@return: wavelengths (A), A(lambda)/Av
@rtype: (ndarray,ndarray)
"""
filename = 'Fitzpatrick1999_Rv_%.1f' % (Rv)
filename = filename.replace('.', '_') + '.red'
myfile = os.path.join(basename, filename)
wave, alam_ebv = ascii.read2array(myfile).T
alam_av = alam_ebv / Rv
logger.info('Fitzpatrick1999 curve with Rv=%.2f' % (Rv))
return wave, alam_av
def fitzpatrick1999(Rv=3.1,**kwargs):
"""
From Fitzpatrick 1999 (downloaded from ASAGIO database)
This function returns A(lambda)/A(V).
To get A(lambda)/E(B-V), multiply the return value with Rv (A(V)=Rv*E(B-V))
Extra kwags are to catch unwanted keyword arguments.
@param Rv: Rv (2.1, 3.1 or 5.0)
@type Rv: float
@return: wavelengths (A), A(lambda)/Av
@rtype: (ndarray,ndarray)
"""
filename = 'Fitzpatrick1999_Rv_%.1f'%(Rv)
filename = filename.replace('.','_') + '.red'
myfile = os.path.join(basename,filename)
wave,alam_ebv = ascii.read2array(myfile).T
alam_av = alam_ebv/Rv
logger.info('Fitzpatrick1999 curve with Rv=%.2f'%(Rv))
return wave,alam_av
def chiar2006(Rv=3.1, curve='ism', **kwargs):
"""
Extinction curve at infrared wavelengths from Chiar and Tielens (2006)
We return A(lambda)/E(B-V), by multiplying A(lambda)/Av with Rv.
This is only defined for Rv=3.1. If it is different, this will raise an
AssertionError
Extra kwags are to catch unwanted keyword arguments.
UNCERTAIN NORMALISATION
@param Rv: Rv
@type Rv: float
@param curve: extinction curve
@type curve: string (one of 'gc' or 'ism', galactic centre or local ISM)
@return: wavelengths (A), A(lambda)/Av
@rtype: (ndarray,ndarray)
"""
source = os.path.join(basename, 'Chiar2006.red')
#-- check Rv
assert (Rv == 3.1)
wavelengths, gc, ism = ascii.read2array(source).T
if curve == 'gc':
alam_ak = gc
elif curve == 'ism':
keep = ism > 0
alam_ak = ism[keep]
wavelengths = wavelengths[keep]
else:
raise ValueError, 'no curve %s' % (curve)
alam_aV = alam_ak * 0.09
#plot(1/wavelengths,alam_aV,'o-')
return wavelengths * 1e4, alam_aV
def plot_logRho_logT(starl):
"""
Plot Density -Temperature diagram for one given profile.
"""
#-- list all burning regions
pl.xlabel('log (Density [g cm$^{-1}$]) [dex]')
pl.ylabel('log (Temperature [K]) [dex]')
for species in ['hydrogen','helium','carbon','oxygen']:
logRho,logT = ascii.read2array(os.path.join(os.path.dirname(__file__),'plot_info','%s_burn.data'%(species))).T
pl.plot(logRho,logT,'k--',lw=2)
pl.annotate(species,(logRho[-1],logT[-1]),ha='right')
bounds = ['elect','gamma_4_thirds','kap_rad_cond_eq','opal_clip','psi4','scvh_clip']
bounds = ['gamma_4_thirds','opal_clip','scvh_clip']
names = ['$\Gamma$<4/3','OPAL','SCVH']
for limits,name in zip(bounds,names):
logRho,logT = ascii.read2array(os.path.join(os.path.dirname(__file__),'plot_info','%s.data'%(limits))).T
pl.plot(logRho,logT,'--',lw=2,color='0.5')
xann,yann = logRho.mean(),logT.mean()
pl.annotate(name,(xann,yann),color='0.5')
#-- plot stellar profile
color_radiative = 'g'
color_convective = (0.33,0.33,1.00)
x = np.log10(starl['Rho'])
y = np.log10(starl['temperature'])
# first convective regions and radiative regions
stab_type = starl['stability_type']
# Create a colormap for convective and radiative regions
cmap = ListedColormap([color_radiative,color_convective])
norm = BoundaryNorm([0, 1, 5], cmap.N)
# Create a set of line segments so that we can color them individually
# This creates the points as a N x 1 x 2 array so that we can stack points
# together easily to get the segments. The segments array for line collection
# needs to be numlines x points per line x 2 (x and y)
points = np.array([x, y]).T.reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
# Create the line collection object, setting the colormapping parameters.
# Have to set the actual values used for colormapping separately.
lc = LineCollection(segments, cmap=cmap, norm=norm)
lc.set_array(stab_type)
lc.set_linewidth(10)
pl.gca().add_collection(lc)
# burning regions
limits = [0,1,1e3,1e7,np.inf]
burn = starl['eps_nuc'][:-1]
colors = np.zeros((len(segments),4))
colors[:,0] = 1
colors[:,-1] = 1
colors[(burn<=1e0),-1] = 0
colors[(1e0<burn)&(burn<=1e3),1] = 1
colors[(1e3<burn)&(burn<=1e7),1] = 0.5
# Create the line collection object, setting the colormapping parameters.
# Have to set the actual values used for colormapping separately.
lc = LineCollection(segments,colors=colors)
lc.set_linewidth(4)
pl.gca().add_collection(lc)
p1 = pl.Line2D([0,0],[1,1], color=(1,1.0,0),lw=3)
p2 = pl.Line2D([0,0],[1,1], color=(1,0.5,0),lw=3)
p3 = pl.Line2D([0,0],[1,1], color=(1,0,0),lw=3)
p4 = pl.Line2D([0,0],[1,1], color='g',lw=3)
p5 = pl.Line2D([0,0],[1,1], color=(0.33,0.33,1.0),lw=3)
leg = pl.legend([p1,p2,p3,p4,p5], [">1 erg/s/g",">10$^3$ erg/s/g",">10$^7$ erg/s/g",'Radiative','Convective'],loc='best',fancybox=True)
leg.get_frame().set_alpha(0.5)
pl.xlim(-10,11)
pl.ylim(4.0,9.4)
def plot_logRho_logT(starl):
"""
Plot Density -Temperature diagram for one given profile.
"""
#-- list all burning regions
pl.xlabel('log (Density [g cm$^{-1}$]) [dex]')
pl.ylabel('log (Temperature [K]) [dex]')
for species in ['hydrogen', 'helium', 'carbon', 'oxygen']:
logRho, logT = ascii.read2array(
os.path.join(os.path.dirname(__file__), 'plot_info',
'%s_burn.data' % (species))).T
pl.plot(logRho, logT, 'k--', lw=2)
pl.annotate(species, (logRho[-1], logT[-1]), ha='right')
bounds = [
'elect', 'gamma_4_thirds', 'kap_rad_cond_eq', 'opal_clip', 'psi4',
'scvh_clip'
]
bounds = ['gamma_4_thirds', 'opal_clip', 'scvh_clip']
names = ['$\Gamma$<4/3', 'OPAL', 'SCVH']
for limits, name in zip(bounds, names):
logRho, logT = ascii.read2array(
os.path.join(os.path.dirname(__file__), 'plot_info',
'%s.data' % (limits))).T
pl.plot(logRho, logT, '--', lw=2, color='0.5')
xann, yann = logRho.mean(), logT.mean()
pl.annotate(name, (xann, yann), color='0.5')
#-- plot stellar profile
color_radiative = 'g'
color_convective = (0.33, 0.33, 1.00)
x = np.log10(starl['Rho'])
y = np.log10(starl['temperature'])
# first convective regions and radiative regions
stab_type = starl['stability_type']
# Create a colormap for convective and radiative regions
cmap = ListedColormap([color_radiative, color_convective])
norm = BoundaryNorm([0, 1, 5], cmap.N)
# Create a set of line segments so that we can color them individually
# This creates the points as a N x 1 x 2 array so that we can stack points
# together easily to get the segments. The segments array for line collection
# needs to be numlines x points per line x 2 (x and y)
points = np.array([x, y]).T.reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
# Create the line collection object, setting the colormapping parameters.
# Have to set the actual values used for colormapping separately.
lc = LineCollection(segments, cmap=cmap, norm=norm)
lc.set_array(stab_type)
lc.set_linewidth(10)
pl.gca().add_collection(lc)
# burning regions
limits = [0, 1, 1e3, 1e7, np.inf]
burn = starl['eps_nuc'][:-1]
colors = np.zeros((len(segments), 4))
colors[:, 0] = 1
colors[:, -1] = 1
colors[(burn <= 1e0), -1] = 0
colors[(1e0 < burn) & (burn <= 1e3), 1] = 1
colors[(1e3 < burn) & (burn <= 1e7), 1] = 0.5
# Create the line collection object, setting the colormapping parameters.
# Have to set the actual values used for colormapping separately.
lc = LineCollection(segments, colors=colors)
lc.set_linewidth(4)
pl.gca().add_collection(lc)
p1 = pl.Line2D([0, 0], [1, 1], color=(1, 1.0, 0), lw=3)
p2 = pl.Line2D([0, 0], [1, 1], color=(1, 0.5, 0), lw=3)
p3 = pl.Line2D([0, 0], [1, 1], color=(1, 0, 0), lw=3)
p4 = pl.Line2D([0, 0], [1, 1], color='g', lw=3)
p5 = pl.Line2D([0, 0], [1, 1], color=(0.33, 0.33, 1.0), lw=3)
leg = pl.legend([p1, p2, p3, p4, p5], [
">1 erg/s/g", ">10$^3$ erg/s/g", ">10$^7$ erg/s/g", 'Radiative',
'Convective'
],
loc='best',
fancybox=True)
leg.get_frame().set_alpha(0.5)
pl.xlim(-10, 11)
pl.ylim(4.0, 9.4)
def read_cles_sum(sumfile):
"""
Read the input from a CLES '-sum.txt' file.
Keys: C{logTeff}, C{logg}, C{M}, C{R}, C{logL}, C{age}(, C{num}, C{Xc})
@param sumfile: filename of the '-sum.txt' file.
@type param:str
@return: model track
@rtype: recarray
"""
c = {
'summary': {
'logTeff': 7,
'logg': 11,
'M': 2,
'R': 10,
'logL': 8,
'age': 6
},
'sum': {
'logTeff': 2,
'logg': 8,
'M': 6,
'R': 7,
'logL': 3,
'age': 1,
'num': 0,
'Xc': 4
}
}
data = ascii.read2array(sumfile)
if 'summary' in sumfile:
t = 'summary'
else:
t = 'sum'
#-- not all info readily available, build it
data_ = np.zeros((len(data[:, 0]), 3))
mass = float(os.path.basename(sumfile).split('_')[0][1:])
data_[:, 0] = mass
radi = conversions.derive_radius((data[:,c[t]['logL']],'[Lsol]'),\
(data[:,c[t]['logTeff']],'[K]'),units='Rsol')[0]
data_[:, 1] = radi
logg_ = conversions.derive_logg((float(mass), 'Msol'),
(data_[:, 1], 'Rsol'))
data_[:, 2] = logg_
data = np.hstack([data, data_])
keys = np.array(c[t].keys())
cols = np.array([c[t][key] for key in keys])
sa = np.argsort(cols)
keys = keys[sa]
cols = cols[sa]
mydata = np.rec.fromarrays([data[:, col] for col in cols],
names=list(keys))
logger.debug('CLES summary %s read' % (sumfile))
return mydata
pi1 = ((2.*en+1.)*amu*pi- (en+1.)*pi0)/ en
pi0 = 0+pipi # 0+pi because we want a hard copy of the values
#*** Have summed sufficient terms.
# Now compute QSCA,QEXT,QBACK,and GSCA
# we have to reverse the order of the elements of the second part of s1 and s2
s1=np.concatenate((s1_1,s1_2[:,-2::-1]), axis=1)
s2=np.concatenate((s2_1,s2_2[:,-2::-1]), axis=1)
gsca = 2.*gsca/qsca
qsca = (2./(x*x))*qsca
qext = (4./(x*x))*np.real(s1[:,0])
# more common definition of the backscattering efficiency,
# so that the backscattering cross section really
# has dimension of length squared
qback = 4*(abs(s1[:,2*nang-2])/x)**2
return np.array(qext, dtype=float), np.array(qsca, dtype=float), np.array(qback, dtype=float), np.array(gsca, dtype=float)
if __name__ == '__main__':
from ivs.io.ascii import read2array
lnk = read2array("/home/kristofs/python/IVSdata/optical_constants/alumino-silicates/A/ca2al2sio7_02.91_0000_001.lnk")
wavelength = lnk[:,0]
refrel = lnk[:,1] + lnk[:,2]*complex(0,1)
radius = .01
nang = 5.
qext1, qsca1, qback1, gsca1 = bhmie(wavelength, refrel, nang, radius)
qext2, qsca2, qback2, gsca2 = bhmie_slow(wavelength, refrel, nang, radius)
pl.show()
sys.exit()
#-- if arguments are given, we assume the user wants to run one of the
# functions with arguments given in the command line
# EXAMPLES:
# $:> python freqanalyse.py find_frequency infile=test.dat full_output=True
# $:> python freqanalyse.py time_frequency infile=test.dat full_output=True
else:
method, args, kwargs = argkwargparser.parse()
print "Running method %s with arguments %s and keyword arguments %s" % (
method, args, kwargs)
if '--help' in args or 'help' in args or 'help' in kwargs:
sys.exit()
full_output = kwargs.get('full_output', False)
times, signal = ascii.read2array(kwargs.pop('infile')).T[:2]
out = globals()[method](times, signal, **kwargs)
#-- when find_frequency is called
if method == 'find_frequency' and full_output:
print pl.mlab.rec2txt(out[0], precision=8)
pl.figure()
pl.subplot(211)
pl.plot(out[1][0], out[1][1], 'k-')
pl.subplot(212)
pl.plot(times, signal, 'ko', ms=2)
pl.plot(times, out[2], 'r-', lw=2)
pl.show()
elif method == 'find_frequency':
print pl.mlab.rec2txt(out)
doctest.testmod()
pl.show()
sys.exit()
#-- if arguments are given, we assume the user wants to run one of the
# functions with arguments given in the command line
# EXAMPLES:
# $:> python freqanalyse.py find_frequency infile=test.dat full_output=True
# $:> python freqanalyse.py time_frequency infile=test.dat full_output=True
else:
method,args,kwargs = argkwargparser.parse()
print "Running method %s with arguments %s and keyword arguments %s"%(method,args,kwargs)
if '--help' in args or 'help' in args or 'help' in kwargs:
sys.exit()
full_output = kwargs.get('full_output',False)
times,signal = ascii.read2array(kwargs.pop('infile')).T[:2]
out = globals()[method](times,signal, **kwargs)
#-- when find_frequency is called
if method=='find_frequency' and full_output:
print pl.mlab.rec2txt(out[0],precision=8)
pl.figure()
pl.subplot(211)
pl.plot(out[1][0],out[1][1],'k-')
pl.subplot(212)
pl.plot(times,signal,'ko',ms=2)
pl.plot(times,out[2],'r-',lw=2)
pl.show()
elif method=='find_frequency':
print pl.mlab.rec2txt(out)
if reference == 'VEGA':
#-- calculate Flam based on the Vega spectrum
hdu = pyfits.open('alpha_lyr_stis_008.fits')
wave, flux = hdu[1].data['wavelength'], hdu[1].data['flux']
hdu.close()
else:
#-- calculate Flam for the AB system
wave = np.arange(3000, 9000, step=0.5)
flux = cv.convert(cc.cc_units, 'AA/s', cc.cc) / wave**2 * 3631e-23
Flam_0 = model.synthetic_flux(wave, flux, photbands=photbands)
#-- load the calibrators
calibrators = ascii.read2array(basedir + 'calspec.ident',
splitchar=',',
dtype=str)
def get_synthetic_photometry(calibrator):
"""
Integrate the spectrum belonging to this calibrator and return the synthetic magnitudes
"""
hdu = pyfits.open(basedir + calibrator[1])
wave, flux = hdu[1].data['wavelength'], hdu[1].data['flux']
hdu.close()
#-- integrate the flux over the 5 pass bands.
flam = model.synthetic_flux(wave, flux, photbands=photbands)