def Trms2_vs_umag(uvs, bms, umag_px, uv_bm_area=2., umin=4., umax=200., logstep=.1):
ubins = 10**n.arange(n.log10(umin), n.log10(umax), logstep)
errs, Trms2, wgts = [], [], []
ratio = n.abs(uvs)**2 / n.abs(bms)**2
for u in ubins:
r_px_inner = u * 10**(-logstep/2) / umag_px
r_px_outer = u * 10**(logstep/2) / umag_px
rng = ring(uvs.shape[0], r_px_inner, r_px_outer)
uvs2_r = n.abs(uvs)**2 * rng
bms2_r = n.abs(bms)**2 * rng
wgts.append(bms2_r.sum())
uvs2_r_avg = uvs2_r.sum() / wgts[-1]
print '-'*20
print u / umag_px, uvs2_r_avg,
print n.sum(ratio*rng) / n.sum(rng)
Trms2.append(uvs2_r_avg)
# Estimate average variance of samples around the ring
sig2_r = n.abs(uvs2_r - uvs2_r_avg * bms2_r)**2
sig = n.sqrt(sig2_r.sum() / bms2_r.sum())
# Estimate number of independent samples around ring
#nsamples = rng.sum() * umag_px**2 / uv_bm_area / 2
#err = n.sqrt(var) / n.sqrt(nsamples)
errs.append(sig)
print u, Trms2[-1], errs[-1]
Trms2 = n.array(Trms2); errs = n.array(errs); wgts = n.array(wgts)
#Cls = Cl_from_Trms(Trms, ells)
#errs = Cl_from_Trms(errs, ells)
return ubins, Trms2, errs, wgts
def remlplen_ichige(fp, fs, dp, ds):
"""Determine the length of the low pass filter with passband frequency
fp, stopband frequency fs, passband ripple dp, and stopband ripple ds.
fp and fs must be normalized with respect to the sampling frequency.
Note that the filter order is one less than the filter length.
References
----------
K. Ichige, M. Iwaki, and R. Ishii, Accurate Estimation of Minimum
Filter Length for Optimum FIR Digital Filters, IEEE Transactions on
Circuits and Systems, 47(10):1008-1017, October 2000.
"""
dF = fs-fp
v = lambda dF,dp:2.325*((-log10(dp))**-0.445)*dF**(-1.39)
g = lambda fp,dF,d:(2.0/pi)*arctan(v(dF,dp)*(1.0/fp-1.0/(0.5-dF)))
h = lambda fp,dF,c:(2.0/pi)*arctan((c/dF)*(1.0/fp-1.0/(0.5-dF)))
Nc = ceil(1.0+(1.101/dF)*(-log10(2.0*dp))**1.1)
Nm = (0.52/dF)*log10(dp/ds)*(-log10(dp))**0.17
N3 = ceil(Nc*(g(fp,dF,dp)+g(0.5-dF-fp,dF,dp)+1.0)/3.0)
DN = ceil(Nm*(h(fp,dF,1.1)-(h(0.5-dF-fp,dF,0.29)-1.0)/2.0))
N4 = N3+DN
return int(N4)
def cd_sphere_vector_bool(Re):
from numpy import log10,array,polyval
condition1 = Re < 0
condition2 = logical_and(0 < Re, Re <= 0.5)
condition3 = logical_and(0.5 < Re, Re <= 100.0)
condition4 = logical_and(100.0 < Re, Re <= 1.0e4)
condition5 = logical_and(1.0e4 < Re, Re <= 3.35e5)
condition6 = logical_and(3.35e5< Re, Re <= 5.0e5)
condition7 = logical_and(5.0e5 < Re, Re <= 8.0e6)
condition8 = Re > 8.0e6
cd = zeros_like(Re)
cd[condition1] = 0.0
cd[condition2] = 24/Re[condition2]
p = array([4.22,-14.05,34.87,0.658])
cd[condition3] = polyval(p,1.0/Re[condition3])
p = array([-30.41,43.72,-17.08,2.41])
cd[condition4] = polyval(p,1.0/log10(Re[condition4]))
p = array([-0.1584,2.031,-8.472,11.932])
cd[condition5] = polyval(p,log10(Re[condition5]))
cd[condition6] = 91.08*(log10(Re[condition6]/4.5e5))**4 + 0.0764
p = array([-0.06338,1.1905,-7.332,14.93])
cd[condition7] = polyval(p,log10(Re[condition7]))
cd[condition8] = 0.2
return cd
def get_mean_and_stddevs(self, sites, rup, dists, imt, stddev_types):
"""
See :meth:`superclass method
<.base.GroundShakingIntensityModel.get_mean_and_stddevs>`
for spec of input and result values.
"""
# Distance term
R = np.sqrt(dists.rjb ** 2 + 11.29 ** 2)
# Magnitude term
M = rup.mag - 6
# Site term only distinguishes between lava and ash;
# since ash sites have Vs30 in the range 60-200m/s,
# we use this upper value as class separator
S = np.zeros(R.shape)
S[sites.vs30 <= 200] = 1
# Mean ground motion (log10)
mean = (0.518 + 0.387*M - np.log10(R) - 0.00256*R + 0.335*S)
# Converting to natural log
mean /= np.log10(np.e)
# Check for standard deviation type
assert all(stddev_type in self.DEFINED_FOR_STANDARD_DEVIATION_TYPES
for stddev_type in stddev_types)
# Constant (total) standard deviation
stddevs = [0.237/np.log10(np.e) + np.zeros(R.shape)]
return mean, stddevs
def compute_angular_momentum_transfer(snapshot, Rmin, Rmax, NR = None, Nphi = None, alpha=0.1, h0=0.1):
"""
Compute the angular momentum transfer as a function of
radius from a simulation snapshot and a prescribed grid
data structure containing the coordinates of grid points
where the torque balance should be evaluated.
"""
if (NR is None):
NR = 512
if (Nphi is None):
Nphi = int(2 * np.pi / (10**((np.log10(Rmax) - np.log10(Rmin))/NR) - 1))
# Create a polar grid
grid = grid_polar(NR = NR, Nphi = Nphi, Rmin= Rmin,Rmax = Rmax,scale='log')
mdot = mass_advection(snapshot,grid)
torque_adv = angular_momentum_advection(snapshot,grid)
torque_visc = angular_momentum_viscosity(snapshot,grid, alpha = alpha, h0 = h0)
torque_grav = angular_momentum_gravity(snapshot,grid)
return grid.R.mean(axis=0),mdot, torque_adv,torque_visc,torque_grav
def cd_sphere(Re):
"Computes the drag coefficient of a sphere as a function of the Reynolds number Re."
# Curve fitted after fig . A -56 in Evett & Liu :% " Fluid Mechanics & Hydraulics ",
# Schaum ' s Solved Problems McGraw - Hill 1989.
from numpy import log10,array,polyval
if Re <= 0.0:
CD = 0.0
elif Re > 8.0e6:
CD = 0.2
elif Re > 0.0 and Re <= 0.5:
CD = 24.0/Re
elif Re > 0.5 and Re <= 100.0:
p = array([4.22,-14.05,34.87,0.658])
CD = polyval(p,1.0/Re)
elif Re > 100.0 and Re <= 1.0e4:
p = array([-30.41,43.72,-17.08,2.41])
CD = polyval(p,1.0/log10(Re))
elif Re > 1.0e4 and Re <= 3.35e5:
p = array([-0.1584,2.031,-8.472,11.932])
CD = polyval(p,log10(Re))
elif Re > 3.35e5 and Re <= 5.0e5:
x1 = log10(Re/4.5e5)
CD = 91.08*x1**4 + 0.0764
else:
p = array([-0.06338,1.1905,-7.332,14.93])
CD = polyval(p,log10(Re))
return CD
def cd_sphere_vector(Re):
"Computes the drag coefficient of a sphere as a function of the Reynolds number Re."
# Curve fitted after fig . A -56 in Evett & Liu :% " Fluid Mechanics & Hydraulics ",
# Schaum ' s Solved Problems McGraw - Hill 1989.
from numpy import log10,array,polyval
CD = zeros_like(Re)
CD = where(Re<0,0.0,0.0) # condition 1
CD = where((Re > 0.0) & (Re <=0.5),24/Re,CD) # condition 2
p = array([4.22,-14.05,34.87,0.658])
CD = where((Re > 0.5) & (Re <=100.0),polyval(p,1.0/Re),CD) #condition 3
p = array([-30.41,43.72,-17.08,2.41])
CD = where((Re >100.0) & (Re <=1.0e4) ,polyval(p,1.0/log10(Re)),CD) #condition 4
p = array([-0.1584,2.031,-8.472,11.932])
CD = where((Re > 1.0e4) & (Re <=3.35e5),polyval(p,log10(Re)),CD) #condition 5
CD = where((Re > 3.35e5) & (Re <=5.0e5),91.08*(log10(Re/4.5e5))**4 + 0.0764,CD) #condition 6
p = array([-0.06338,1.1905,-7.332,14.93])
CD = where((Re > 5.05e5) & (Re <=8.0e6),polyval(p,log10(Re)),CD) #condition 7
CD = where(Re>8.0e6,0.2,CD) # condition 8
return CD
def srcdiff_plot(env, model, **kwargs):
obj_index = kwargs.pop('obj_index', 0)
src_index = kwargs.pop('src_index', 0)
with_colorbar = kwargs.pop('with_colorbar', False)
xlabel = kwargs.pop('xlabel', r'arcsec')
ylabel = kwargs.pop('ylabel', r'arcsec')
obj, data = model['obj,data'][obj_index]
S = obj.basis.subdivision
R = obj.basis.mapextent
g = obj.basis.srcdiff_grid(data)[src_index]
vmin = np.log10(np.amin(g[g>0]))
g = g.copy() + 1e-10
kw = default_kw(R, kwargs) #, vmin=vmin, vmax=vmin+2)
#loglev = logspace(1, log(amax(g)-amin(g)), 20, base=math.e) + amin(g)
pl.matshow(np.log10(g), **kw)
matplotlib.rcParams['contour.negative_linestyle'] = 'solid'
if with_colorbar: glspl.colorbar()
# pl.over(contour, g, 50, colors='w', linewidths=1,
# extent=[-R,R,-R,R], origin='upper', extend='both')
#pl.grid()
pl.xlabel(xlabel)
pl.ylabel(ylabel)
def get_cs(e_0=100, z=74):
"""
Returns a function representing the scaled bremsstrahlung cross_section.
Args:
e_0 (float): The electron kinetic energy, used to scale u=e_e/e_0.
z (int): Atomic number of the material.
Returns:
A function representing cross_section(e_g,u) in mb/keV, with e_g in keV.
"""
# NOTE: Data is given for E0>1keV. CS values below this level should be used with caution.
# The default behaviour is to keep it constant
with open(os.path.join(data_path, "cs/grid.csv"), 'r') as csvfile:
r = csv.reader(csvfile, delimiter=' ', quotechar='|',
quoting=csv.QUOTE_MINIMAL)
t = next(r)
e_e = np.array([float(a) for a in t[0].split(",")])
log_e_e = np.log10(e_e)
t = next(r)
k = np.array([float(a) for a in t[0].split(",")])
t = []
with open(os.path.join(data_path, "cs/%d.csv" % z), 'r') as csvfile:
r = csv.reader(csvfile, delimiter=' ', quotechar='|',
quoting=csv.QUOTE_MINIMAL)
for row in r:
t.append([float(a) for a in row[0].split(",")])
t = np.array(t)
scaled = interpolate.RectBivariateSpline(log_e_e, k, t, kx=3, ky=1)
m_electron = 511
z2 = z * z
return lambda e_g, u: (u * e_0 + m_electron) ** 2 * z2 / (u * e_0 * e_g * (u * e_0 + 2 * m_electron)) * (
scaled(np.log10(u * e_0), e_g / (u * e_0)))
def test_Moster13SmHm_behavior(): """ """ default_model = Moster13SmHm() mstar1 = default_model.mean_stellar_mass(prim_haloprop = 1.e12) ratio1 = mstar1/3.4275e10 np.testing.assert_array_almost_equal(ratio1, 1.0, decimal=3) default_model.param_dict['n10'] *= 1.1 mstar2 = default_model.mean_stellar_mass(prim_haloprop = 1.e12) assert mstar2 > mstar1 default_model.param_dict['n11'] *= 1.1 mstar3 = default_model.mean_stellar_mass(prim_haloprop = 1.e12) assert mstar3 == mstar2 mstar4_z1 = default_model.mean_stellar_mass(prim_haloprop = 1.e12, redshift=1) default_model.param_dict['n11'] *= 1.1 mstar5_z1 = default_model.mean_stellar_mass(prim_haloprop = 1.e12, redshift=1) assert mstar5_z1 != mstar4_z1 mstar_realization1 = default_model.mc_stellar_mass(prim_haloprop = np.ones(1e4)*1e12, seed=43) mstar_realization2 = default_model.mc_stellar_mass(prim_haloprop = np.ones(1e4)*1e12, seed=43) mstar_realization3 = default_model.mc_stellar_mass(prim_haloprop = np.ones(1e4)*1e12, seed=44) assert np.array_equal(mstar_realization1, mstar_realization2) assert not np.array_equal(mstar_realization1, mstar_realization3) measured_scatter1 = np.std(np.log10(mstar_realization1)) model_scatter = default_model.param_dict['scatter_model_param1'] np.testing.assert_allclose(measured_scatter1, model_scatter, rtol=1e-3) default_model.param_dict['scatter_model_param1'] = 0.3 mstar_realization4 = default_model.mc_stellar_mass(prim_haloprop = np.ones(1e4)*1e12, seed=43) measured_scatter4 = np.std(np.log10(mstar_realization4)) np.testing.assert_allclose(measured_scatter4, 0.3, rtol=1e-3)
def __init__(self,fname=None,mindx=None,mlist=[],logopt = 0, Lbox=2750., massfxnfname=None):
"""
Read in a list of masses. If logopt==1, then input masses are understood to be logarithmic.
"""
self.Lbox = Lbox
if mlist != []:
if logopt == 0:
self.m = np.array(mlist)
self.lg10m = np.log10(self.m)
else:
self.lg10m = np.array(mlist)
self.m = 10**(self.log10m)
self.lg10mcen, self.Nofm = None, None ## set these later with massfxn.
elif massfxnfname is not None:
self.lg10mcen, self.Nofm = np.loadtxt(massfxnfname,unpack=True,usecols=[0,1])
else:
if 0==0:
# try:
if logopt == 0:
self.m = np.loadtxt(fname,usecols=[mindx],unpack=True)
self.lg10m = np.log10(self.m)
else:
self.lg10m = np.loadtxt(fname,usecols=[mindx],unpack=True)
self.m = 10**(self.lg10m)
self.lg10mcen, self.Nofm = None, None ## set these later with massfxn.
else:
# except:
print 'file read did not work.'
self.m = None
self.lg10m = None
def display_fluxes(fluxes, id_convert=None, mnx_path=None, log=False, abstol=1e-6, **kwargs):
if id_convert is not None:
if mnx_path is None:
print('Please specify local path of MetaNetX database.')
return
mnx = MetaNetX(mnx_path, version=3)
# TODO: still need to find how to deal with ambiguous conversions
fluxes = {
kegg_id: abs(value)
for r_id, value in fluxes.items()
for kegg_id in mnx.translate_reaction_id(r_id[2:], id_convert, 'kegg')
}
else:
fluxes = {key: abs(val) for key, val in fluxes.items()}
if log:
lb = np.log10(min([x for x in fluxes.values() if x > abstol]))
fluxes = {key: np.log10(val) - lb for key, val in fluxes.items() if val > abstol}
return iPATH_display(fluxes, **kwargs)
def plotPSD(self, chan, time_interval):
Npackets = np.int(time_interval * self.accum_freq)
plot_range = (Npackets / 2) + 1
figure = plt.figure(num= None, figsize=(12,12), dpi=80, facecolor='w', edgecolor='w')
# I
plt.suptitle('Channel ' + str(chan) + ' , Freq = ' + str((self.freqs[chan] + self.LO_freq)/1.0e6) + ' MHz')
plot1 = figure.add_subplot(311)
plot1.set_xscale('log')
plot1.set_autoscale_on(True)
plt.ylim((-160,-80))
plt.title('I')
line1, = plot1.plot(np.linspace(0, self.accum_freq/2., (Npackets/2) + 1), np.zeros(plot_range), label = 'I', color = 'green', linewidth = 1)
plt.grid()
# Q
plot2 = figure.add_subplot(312)
plot2.set_xscale('log')
plot2.set_autoscale_on(True)
plt.ylim((-160,-80))
plt.title('Q')
line2, = plot2.plot(np.linspace(0, self.accum_freq/2., (Npackets/2) + 1), np.zeros(plot_range), label = 'Q', color = 'red', linewidth = 1)
plt.grid()
# Phase
plot3 = figure.add_subplot(313)
plot3.set_xscale('log')
plot3.set_autoscale_on(True)
plt.ylim((-120,-70))
#plt.xlim((0.0001, self.accum_freq/2.))
plt.title('Phase')
plt.ylabel('dBc rad^2/Hz')
plt.xlabel('log Hz')
line3, = plot3.plot(np.linspace(0, self.accum_freq/2., (Npackets/2) + 1), np.zeros(plot_range), label = 'Phase', color = 'black', linewidth = 1)
plt.grid()
plt.show(block = False)
count = 0
stop = 1.0e10
while count < stop:
Is, Qs, phases = self.get_stream(chan, time_interval)
I_mags = np.fft.rfft(Is, Npackets)
Q_mags = np.fft.rfft(Is, Npackets)
phase_mags = np.fft.rfft(phases, Npackets)
I_vals = (np.abs(I_mags)**2 * ((1./self.accum_freq)**2 / (1.0*time_interval)))
Q_vals = (np.abs(Q_mags)**2 * ((1./self.accum_freq)**2 / (1.0*time_interval)))
phase_vals = (np.abs(phase_mags)**2 * ((1./self.accum_freq)**2 / (1.0*time_interval)))
phase_vals = 10*np.log10(phase_vals)
phase_vals -= phase_vals[0]
#line1.set_ydata(Is)
#line2.set_ydata(Qs)
#line3.set_ydata(phases)
line1.set_ydata(10*np.log10(I_vals))
line2.set_ydata(10*np.log10(Q_vals))
line3.set_ydata(phase_vals)
plot1.relim()
plot1.autoscale_view(True,True,False)
plot2.relim()
plot2.autoscale_view(True,True,False)
#plot3.relim()
plot3.autoscale_view(True,True,False)
plt.draw()
count +=1
return
def test_behroozi10_smhm_z1():
""" The arrays ``logmh_z01`` and ``logmratio_z01`` were provided by Peter Behroozi
via private communication. These quantities are in the h=0.7 units adopted in
Behroozi+10. This test function treats these arrays as truth,
and enforces that the result computed by Halotools agrees with them.
"""
model = Behroozi10SmHm()
logmh_z1 = np.array(
[11.368958, 11.493958, 11.618958, 11.743958,
11.868958, 11.993958, 12.118958, 12.243958,
12.368958, 12.493958, 12.618958, 12.743958,
12.868958, 12.993958, 13.118958, 13.243958,
13.368958, 13.493958, 13.618958, 13.743958,
13.868958, 13.993958, 14.118958, 14.243958]
)
logmratio_z1 = np.array(
[-2.145909, -2.020974, -1.924020, -1.852937,
-1.804730, -1.776231, -1.764455, -1.766820,
-1.781140, -1.805604, -1.838727, -1.879292,
-1.926290, -1.978890, -2.036405, -2.098245,
-2.163930, -2.233045, -2.305230, -2.380185,
-2.457643, -2.537377, -2.619191, -2.702901]
)
halo_mass_z1 = (10.**logmh_z1)*model.littleh
logmratio_z1 = np.log10((10.**logmratio_z1)*model.littleh)
z1_sm = model.mean_stellar_mass(prim_haloprop=halo_mass_z1, redshift=1.0)
z1_ratio = z1_sm / halo_mass_z1
z1_result = np.log10(z1_ratio)
assert np.allclose(z1_result, logmratio_z1, rtol=0.02)
def plot_hist(axis, data_list, label_list, logx, logy, overlaid):
"""
"""
if logx:
# Setup the logarithmic scale on the X axis
data_array = np.array(data_list)
vmin = np.log10(data_array.min())
vmax = np.log10(data_array.max())
bins = np.logspace(vmin, vmax, 50) # Make a range from 10**vmin to 10**vmax
else:
bins = 50
if overlaid:
for data_array, label in zip(data_list, label_list):
res_tuple = axis.hist(data_array,
bins=bins,
log=logy, # Set log scale on the Y axis
histtype=HIST_TYPE,
alpha=ALPHA,
label=label)
else:
res_tuple = axis.hist(data_list,
bins=bins,
log=logy, # Set log scale on the Y axis
histtype=HIST_TYPE,
alpha=ALPHA,
label=label_list)
def plot_sphere_x( s, fname ):
""" put plot of ionization fractions from sphere `s` into fname """
plt.figure()
s.Edges.units = 'kpc'
s.r_c.units = 'kpc'
xx = s.r_c
L = s.Edges[-1]
plt.plot( xx, np.log10( s.xHe1 ),
color='green', ls='-', label = r'$x_{\rm HeI}$' )
plt.plot( xx, np.log10( s.xHe2 ),
color='green', ls='--', label = r'$x_{\rm HeII}$' )
plt.plot( xx, np.log10( s.xHe3 ),
color='green', ls=':', label = r'$x_{\rm HeIII}$' )
plt.plot( xx, np.log10( s.xH1 ),
color='red', ls='-', label = r'$x_{\rm HI}$' )
plt.plot( xx, np.log10( s.xH2 ),
color='red', ls='--', label = r'$x_{\rm HII}$' )
plt.xlim( -L/20, L+L/20 )
plt.xlabel( 'r_c [kpc]' )
plt.ylim( -4.5, 0.2 )
plt.ylabel( 'log 10 ( x )' )
plt.grid()
plt.legend(loc='best', ncol=2)
plt.tight_layout()
plt.savefig( 'doc/img/x_' + fname )
def pltytfield():
fig=plt.figure()
ppy=yt.ProjectionPlot(ds, "x", "Bxy", weight_field="density") #Project X-component of B-field from z-direction
By=ppy._frb["Bxy"]
ax=fig.add_subplot(111)
plt.xticks(tick_locs,tick_lbls)
plt.yticks(tick_locs,tick_lbls)
Bymag=ax.pcolormesh(np.log10(By))
cbar_m=plt.colorbar(Bymag)
cbar_m.set_label("Bxy")
plt.title("Bxy in yz plane")
fig=plt.figure()
ppy=yt.ProjectionPlot(ds, "y", "Bxy", weight_field="density") #Project X-component of B-field from z-direction
By=ppy._frb["Bxy"]
ax=fig.add_subplot(111)
plt.xticks(tick_locs,tick_lbls)
plt.yticks(tick_locs,tick_lbls)
Bymag=ax.pcolormesh(np.log10(By))
cbar_m=plt.colorbar(Bymag)
cbar_m.set_label("Bxy")
plt.title("Bxy in xz plane")
fig=plt.figure()
ppy=yt.ProjectionPlot(ds, "z", "Bxy", weight_field="density") #Project X-component of B-field from z-direction
By=ppy._frb["Bxy"]
ax=fig.add_subplot(111)
plt.xticks(tick_locs,tick_lbls)
plt.yticks(tick_locs,tick_lbls)
Bymag=ax.pcolormesh(np.log10(By))
cbar_m=plt.colorbar(Bymag)
cbar_m.set_label("Bxy")
plt.title("Bxy in xy plane")
def plot_kappa_vs_n(show=False):
import biggles
np = 1000
nmin = 0.25
nmax = 8.0
nvals = numpy.logspace(numpy.log10(nmin), numpy.log10(nmax), np)
kappas = numpy.zeros(np)
kfinder = KappaFinder()
for i in xrange(np):
kappas[i] = kfinder(nvals[i])
plt = biggles.FramedPlot()
plt.xlabel = "sersic n"
plt.ylabel = r"$\kappa$"
plt.xlog = True
plt.ylog = True
pts = biggles.Points(nvals, kappas, type="filled circle", size=0.5, color="blue")
plt.add(pts)
if show:
plt.show()
f = os.path.expanduser("~/tmp/kappa-vs-n.eps")
print f
plt.write_eps(f)
def correlation_test(self, x, y, tol): # Find scaling / correlation between Menv and intensity # Return fit parameters and flag indicating which fit is best # Always first try linear fit with y = a + b*x: fit_m = ofit.lin_test(x, y) if (fit_m[3] < tol) & (fit_m[2] > tol): print "A proportionality I = %4.2f * Menv is acceptable at 1 sigma" %(fit_m[1]) print "Fit probabilities are %6.4f and %6.4f respectively" %(fit_m[2], fit_m[3]) return [0, fit_m[1]], 'lin' elif (fit_m[3] < tol) & (fit_m[2] < tol): print "A linear fit with I = %4.2f + %4.2f * Menv is acceptable at 1 sigma" %(fit_m[0], fit_m[1]) print "Fit probabilities are %6.4f and %6.4f respectively" %(fit_m[2], fit_m[3]) return [fit_m[0], fit_m[1]], 'lin' # If a linear fit is not good enough, try power-law: else: fit_m = ofit.lin_test(np.log10(x), np.log10(y)) if (fit_m[3] < tol) & (fit_m[2] > tol): print "A power-law fit with log(I) = %4.2f * log(Menv) is acceptable at 1 sigma" %(fit_m[0], fit_m[1]) print "Fit probabilities are %6.4f and %6.4f respectively" %(fit_m[2], fit_m[3]) return [0, fit_m[1]], 'pow' elif (fit_m[3] < tol) & (fit_m[2] < tol): print "A power-law fit with log(I) = %4.2f + %4.2f * log(Menv) is acceptable at 1 sigma" %(fit_m[0], fit_m[1]) print "Fit probabilities are %6.4f and %6.4f respectively" %(fit_m[2], fit_m[3]) return [fit_m[0], fit_m[1]], 'pow' else: print 'I and Menv are not correlated, neither linearly nor by power-law' print 'Model is terminated, please try again' sys.exit()
def sutherland_gaunt_factor(self, wavelength):
"""
Calculates the free-free gaunt factor calculations of [1]_.
The Gaunt factors of [1]_ are read in using `ChiantiPy.tools.io.gffRead`
as a function of :math:`u` and :math:`\gamma^2`. The data are interpolated
to the appropriate wavelength and temperature values using
`~scipy.ndimage.map_coordinates`.
References
----------
.. [1] Sutherland, R. S., 1998, MNRAS, `300, 321 <http://adsabs.harvard.edu/abs/1998MNRAS.300..321S>`_
"""
# calculate scaled quantities
lower_u = ch_const.planck*(1.e8*ch_const.light)/ch_const.boltzmann/np.outer(self.Temperature,wavelength)
gamma_squared = (self.Z**2)*ch_const.ryd2erg/ch_const.boltzmann/self.Temperature[:,np.newaxis]*np.ones(lower_u.shape)
# convert to index coordinates
i_lower_u = (np.log10(lower_u) + 4.)*10.
i_gamma_squared = (np.log10(gamma_squared) + 4.)*5.
# read in sutherland data
gf_sutherland_data = ch_io.gffRead()
# interpolate data to scaled quantities
gf_sutherland = map_coordinates(gf_sutherland_data['gff'],
[i_gamma_squared.flatten(), i_lower_u.flatten()]).reshape(lower_u.shape)
return np.where(gf_sutherland < 0., 0., gf_sutherland)
def _calculate_histogram(self):
"""Recalculate the histogram, creating new patches"""
self.clear()
try:
data = self.layer[self.att].ravel()
if not np.isfinite(data).any():
return False
except IncompatibleAttribute as exc:
self.disable_invalid_attributes(*exc.args)
return False
if data.size == 0:
return
if self.lo > np.nanmax(data) or self.hi < np.nanmin(data):
return
if self.xlog:
data = np.log10(data)
rng = [np.log10(self.lo), np.log10(self.hi)]
else:
rng = self.lo, self.hi
nbinpatch = self._axes.hist(data,
bins=self.nbins,
range=rng)
self._y, self.x, self.artists = nbinpatch
return True
def update_all_baseline_plots(i, fig, crawler, lines, norm_cross=False, forward=True):
if forward:
try:
crawler.forward()
except EOFError as err:
print err
raw_input("End of File. Press enter to quit.")
sys.exit()
burst = crawler
for k in range(len(BASELINES)):
if k < 4:
#autos
lines[k].set_data(FREQS, 10*np.log10(burst.autos[BASELINES[k]]))
#overlays
lines[-(k+1)].set_data(FREQS,10*np.log10(burst.autos[BASELINES[k]]))
elif norm_cross:
norm_val = np.array(burst.cross[BASELINES[k]])/np.sqrt(np.array(burst.autos[BASELINES[k][0]*2])*np.array(burst.autos[BASELINES[k][1]*2]))
lines[k]['real'].set_data(FREQS, np.real(norm_val))
lines[k]['imag'].set_data(FREQS, np.imag(norm_val))
else:
lines[k].set_data(FREQS, 10*np.log10(np.abs(np.real(burst.cross[BASELINES[k]]))))
return lines
def __repr__(self):
pars = ""
if not isinstance(self.parameters, OrderedDict):
keys = sorted(self.parameters.keys()) # to ensure the order is always the same
else:
keys = self.parameters.keys()
for k in keys:
v = self.parameters[k].value
par_fmt = "{}"
post = ""
if hasattr(v, 'unit'):
post = " {}".format(v.unit)
v = v.value
if isinstance(v, float):
if v == 0:
par_fmt = "{:.0f}"
elif np.log10(v) < -2 or np.log10(v) > 5:
par_fmt = "{:.2e}"
else:
par_fmt = "{:.2f}"
elif isinstance(v, int) and np.log10(v) > 5:
par_fmt = "{:.2e}"
pars += ("{}=" + par_fmt + post).format(k, v) + ", "
if isinstance(self.units, DimensionlessUnitSystem):
return "<{}: {} (dimensionless)>".format(self.__class__.__name__, pars.rstrip(", "))
else:
return "<{}: {} ({})>".format(self.__class__.__name__, pars.rstrip(", "), ",".join(map(str, self.units._core_units)))
def _default_response_frequencies(A, n):
"""Compute a reasonable set of frequency points for bode plot.
This function is used by `bode` to compute the frequency points (in rad/s)
when the `w` argument to the function is None.
Parameters
----------
A : ndarray
The system matrix, which is square.
n : int
The number of time samples to generate.
Returns
-------
w : ndarray
The 1-D array of length `n` of frequency samples (in rad/s) at which
the response is to be computed.
"""
vals = linalg.eigvals(A)
# Remove poles at 0 because they don't help us determine an interesting
# frequency range. (And if we pass a 0 to log10() below we will crash.)
poles = [pole for pole in vals if pole != 0]
# If there are no non-zero poles, just hardcode something.
if len(poles) == 0:
minpole = 1
maxpole = 1
else:
minpole = min(abs(real(poles)))
maxpole = max(abs(real(poles)))
# A reasonable frequency range is two orders of magnitude before the
# minimum pole (slowest) and two orders of magnitude after the maximum pole
# (fastest).
w = numpy.logspace(numpy.log10(minpole) - 2, numpy.log10(maxpole) + 2, n)
return w
def error_vs_updates(self, output_dir=None):
fig = plt.figure()
ax = fig.add_subplot(111)
ax.scatter(log10(centered(self.w_truth)) - log10(centered(self.medians)), self.updates, c=self.stds, cmap=plt.jet(), s=25, clip_on=False, lw=0.5)
ax.set_xlabel('log10(w_truth)-log10(median w)')
ax.set_ylabel('num updates')
show(fig, output_dir, 'error_vs_updates.png')
def fluence_dist(self):
""" Plots the fluence distribution and gives the mean and median fluence
values of the sample """
fluences = []
for i in range(0,len(self.fluences),1):
try:
fluences.append(float(self.fluences[i]))
except ValueError:
continue
fluences = np.array(fluences)
mean_fluence = np.mean(fluences)
median_fluence = np.median(fluences)
print('Mean Fluence =',mean_fluence,'(15-150 keV) [10^-7 erg cm^-2]')
print('Median Fluence =',median_fluence,'(15-150 keV) [10^-7 erg cm^-2]')
plt.figure()
plt.xlabel('Fluence (15-150 keV) [$10^{-7}$ erg cm$^{-2}$]')
plt.ylabel('Number of GRBs')
plt.xscale('log')
minimum, maximum = min(fluences), max(fluences)
plt.axvline(mean_fluence,color='red',linestyle='-')
plt.axvline(median_fluence,color='blue',linestyle='-')
plt.hist(fluences,bins= 10**np.linspace(np.log10(minimum),np.log10(maximum),20),color='grey',alpha=0.5)
plt.show()
def create_center_frequencies(stt=180, stp=7000, n_bands=32, kind='log'):
'''
Define center frequencies for spectrograms.
Generally this is for auditory spectrogram extraction. Most auditory
analysis uses 180 - 7000 Hz, so for now those
are the defaults.
Parameters
----------
stt : float | int
The starting frequency
stp : float | int
The end frequency
n_bands : int
The number of bands to calculate
kind : 'log' | 'erb'
Whether to use log or erb spacing
Returns
-------
freqs : array, shape (n_frequencies,)
An array of center frequencies.
'''
if kind == 'log':
freqs = np.logspace(np.log10(stt), np.log10(stp), n_bands).astype(int)
elif kind == 'erb':
freqs = hears.erbspace(stt * Hz, stp * Hz, n_bands)
else:
print("I don't know what kind of spacing that is")
return freqs
def compatibility(par_low, par_high):
"""Quantify spectral compatibility of power-law
measurements in two energy bands.
Reference: 2008ApJ...679.1299F Equation (2)
Compute spectral compatibility parameters for the
situation where two power laws were measured in a low
and a high spectral energy band.
par_low and par_high are the measured parameters,
which must be lists in the following order:
e, f, f_err, g, g_err
where e is the pivot energy, f is the flux density
and g the spectral index
"""
# Unpack power-law paramters
e_high, f_high, f_err_high, g_high, g_err_high = par_high
e_low, f_low, f_err_low, g_low, g_err_low = par_low
log_delta_e = np.log10(e_high) - np.log10(e_low)
log_delta_f = np.log10(f_high) - np.log10(f_low)
# g_match is the index obtained by connecting the two points
# with a power law, i.e. a straight line in the log_e, log_f plot
g_match = -log_delta_f / log_delta_e
# sigma is the number of standar deviations the match index
# is different from the measured index in one band.
# (see Funk et al. (2008ApJ...679.1299F) eqn. 2)
sigma_low = (g_match - g_low) / g_err_low
sigma_high = (g_match - g_high) / g_err_high
sigma_comb = np.sqrt(sigma_low ** 2 + sigma_high ** 2)
return g_match, sigma_low, sigma_high, sigma_comb
def t90_dist(self):
""" Plots T90 distribution, gives the mean and median T90 values of the
sample and calculates the number of short, long bursts in the sample """
t90s = []
for i in range(0,len(self.t90s),1):
try:
t90s.append(float(self.t90s[i]))
except ValueError:
continue
t90s = np.array(t90s)
mean_t90 = np.mean(t90s)
median_t90 = np.median(t90s)
print('Mean T90 time =',mean_t90,'s')
print('Median T90 time=',median_t90,'s')
mask = np.ma.masked_where(t90s < 2, t90s)
short_t90s = t90s[mask == False]
long_t90s = t90s[mask != False]
print('Number of Short/Long GRBs =',len(short_t90s),'/',len(long_t90s))
plt.figure()
plt.xlabel('T$_{90}$ (s)')
plt.ylabel('Number of GRBs')
plt.xscale('log')
minimum, maximum, = min(short_t90s), max(long_t90s)
plt.axvline(mean_t90,color='red',linestyle='-')
plt.axvline(median_t90,color='blue',linestyle='-')
plt.hist(t90s,bins= 10**np.linspace(np.log10(minimum),np.log10(maximum),20),color='grey',alpha=0.5)
plt.show()
def get_log_fluxes(self):
# Initialize arrays
log_flux = np.zeros(self.flux.shape, dtype=np.float64)
log_error = np.zeros(self.error.shape, dtype=np.float64)
weight = np.zeros(self.valid.shape, dtype=np.float64)
# Fluxes
r = self.valid == 1
log_flux[r] = np.log10(self.flux[r]) - 0.5 * (self.error[r] / self.flux[r]) ** 2. / np.log(10.)
log_error[r] = np.abs(self.error[r] / self.flux[r]) / np.log(10.)
weight[r] = 1. / log_error[r] ** 2.
# Lower and upper limits
r = (self.valid == 2) | (self.valid == 3)
log_flux[r] = np.log10(self.flux[r])
log_error[r] = self.error[r]
# Log10[Fluxes]
r = self.valid == 4
log_flux[r] = self.flux[r]
log_error[r] = self.error[r]
weight[r] = 1. / log_error[r] ** 2.
# Ignored points
r = self.valid == 9
log_flux[r] = np.log10(self.flux[r]) - 0.5 * (self.error[r] / self.flux[r]) ** 2. / np.log(10.)
log_error[r] = np.abs(self.error[r] / self.flux[r]) / np.log(10.)
return weight, log_flux, log_error
h = 0.6777 L_box = 1000.0 / h cosmo = cosmoMD if env == "UNIT_fA1_DIR" or env == "UNIT_fA1i_DIR" or env == "UNIT_fA2_DIR": cosmoUNIT = FlatLambdaCDM(H0=67.74 * u.km / u.s / u.Mpc, Om0=0.308900) h = 0.6774 L_box = 1000.0 / h cosmo = cosmoUNIT area = 27143./2. # deg2 sel_area = (abs(data['g_lat'])>20) # &(data['dec']<0) Mvir = data['HALO_Mvir'] M500c = data['HALO_M500c'].data logM500c = n.log10(M500c ) log_vmax = n.log10(data['HALO_vmax']) b_2_a = data['HALO_b_to_a_500c'] HALO_rs = data['HALO_rs'] HALO_rvir = data['HALO_rvir'] zzs = data['redshift_S'] N_clu = len(Mvir) path_2_cbp = os.path.join(os.environ['GIT_CBP']) Mpc=3.0856776e+24 msun=1.98892e33 nsim = 1000000
#Find minimum MSE and its index
min_MSE = np.amin(Kfold_MSE_Lasso)
min_index = np.where(Kfold_MSE_Lasso == np.amin(Kfold_MSE_Lasso))
print("Minimum MSE value for Lasso", min_MSE)
#Plot the MSEs and the corresponding polynomial degree and lambda value
f, ax = plt.subplots(figsize=(9, 6))
polymincrop = 5
ax.add_patch(Rectangle((min_index[1][0], min_index[0][0]-polymincrop), 1, 1, fill=False, edgecolor='pink', lw=3))
lambdas_labels = np.array_str(np.log10(lambdas))
Kfold_MSE_Lasso_scaled = 100 * Kfold_MSE_Lasso
Poly_lables = ["2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13"]
sns.set(font_scale=1.2)
ax = sns.heatmap(Kfold_MSE_Lasso_scaled[polymincrop:, :10],
cbar=False,
annot=True,
square=True,
yticklabels=Poly_lables[polymincrop-1:],
fmt='.2f')
plt.xlabel(r"$\lambda$ values enumerated low->high")
plt.ylabel("Polynomial order")
plt.title(r'MSE of Lasso, scaled $10^2$')
plt.tight_layout()
plt.show()
from photutils import detect_sources threshold = 2.5 npixels = 5 segm = detect_sources(sig, threshold, npixels) # --- now measure the flux in every source # fluxes = np.zeros(segm.nlabels) # for i in range(segm.nlabels): # masked_sci = np.ma.masked_where(segm.data != i+1, sci) # flux = np.sum(masked_sci) # fluxes[i] = flux fluxes = np.array([np.sum(sci[np.where(segm.data == i+1)]) for i in range(segm.nlabels)]) from photutils import deblend_sources segm_deblend = deblend_sources(sig, segm, npixels=npixels, nlevels=32, contrast=0.001) fluxes_deblended = np.array([np.sum(sci[np.where(segm_deblend.data == i+1)]) for i in range(segm_deblend.nlabels)]) plt.hist(np.log10(fluxes), bins=10, alpha = 0.5, label = 'simple') plt.hist(np.log10(fluxes_deblended), bins=10, alpha = 0.5, label = 'deblended') plt.legend() plt.show()
def __init__(self):
# communication parameters
self.roach_ip = "192.168.1.13"
# model parameters
self.bandwidth = 140
# calibration model parameters
self.cal_acclen_reg = "cal_acc_len"
self.cal_cntrst_reg = "cal_cnt_rst"
self.cal_phase_regs = ['cal_phase_re', 'cal_phase_im']
self.cal_addr_regs = ['cal_phase_addr']
self.cal_nbits = 18
self.cal_binpt = 17
self.cal_we_reg = 'cal_phase_we'
self.cal_awidth = 8 # bits
self.cal_dwidth = 128 # bits
self.cal_pow_dtype = '>u8'
self.cal_xab_dtype = '>i8'
self.cal_pow_brams = ["cal_probe0_xpow_pow0", "cal_probe0_xpow_pow1",
"cal_probe1_xpow_pow0", "cal_probe1_xpow_pow1",
"cal_probe2_xpow_pow0", "cal_probe2_xpow_pow1",
"cal_probe3_xpow_pow0", "cal_probe3_xpow_pow1"]
self.cal_xab_brams = ["cal_probe0_xab_ab0", "cal_probe0_xab_ab1",
"cal_probe0_xab_ab2", "cal_probe0_xab_ab3",
"cal_probe1_xab_ab0", "cal_probe1_xab_ab1",
"cal_probe1_xab_ab2", "cal_probe1_xab_ab3",
"cal_probe2_xab_ab0", "cal_probe2_xab_ab1",
"cal_probe2_xab_ab2", "cal_probe2_xab_ab3",
"cal_probe3_xab_ab0", "cal_probe3_xab_ab1",
"cal_probe3_xab_ab2", "cal_probe3_xab_ab3"]
# beamforming model parameters
self.bf_acclen_reg = "bf_acc_len"
self.bf_cntrst_reg = "bf_cnt_rst"
self.bf_phase_regs = ['bf_phase_re', 'bf_phase_im']
self.bf_addr_regs = ['bf_addr_x', 'bf_addr_y',
'bf_addr_t', 'bf_addr_sub']
self.bf_we_reg = 'bf_phase_we'
self.bf_nbits = 18
self.bf_binpt = 17
self.bf_awidth = 10 # bits
self.bf_dwidth = 64 # bits
self.bf_dtype = '>u8'
self.bf_brams = ["bf_probe0_xpow_s0", "bf_probe0_xpow_s1",
"bf_probe0_xpow_s2", "bf_probe0_xpow_s3",
"bf_probe0_xpow_s4", "bf_probe0_xpow_s5",
"bf_probe0_xpow_s6", "bf_probe0_xpow_s7",
"bf_probe0_xpow_s8", "bf_probe0_xpow_s9",
"bf_probe0_xpow_s10", "bf_probe0_xpow_s11",
"bf_probe0_xpow_s12", "bf_probe0_xpow_s13",
"bf_probe0_xpow_s14", "bf_probe0_xpow_s15"]
# front-end parameters
self.ninputs = 16
# element positions: a 2D array with the XYZ position of each element
# in the array. The position is given in wavelength units. The
# coordinate system origin of the center of the array.
self.elpos = [[(0.75, 0, 0.75), (0.25, 0, 0.75), (-0.25, 0, 0.75), (-0.75, 0, 0.75)],
[(0.75, 0, 0.25), (0.25, 0, 0.25), (-0.25, 0, 0.25), (-0.75, 0, 0.25)],
[(0.75, 0, -0.25), (0.25, 0, -0.25), (-0.25, 0, -0.25), (-0.75, 0, -0.25)],
[(0.75, 0, -0.75), (0.25, 0, -0.75), (-0.25, 0, -0.75), (-0.75, 0, -0.75)]]
# derivative parameters
self.nchannels = 2**self.cal_awidth
self.freqs = np.linspace(0, self.bandwidth, self.nchannels, endpoint=False)
self.dBFS = 6.02*8 + 1.76 + 10*np.log10(self.nchannels/2) # Hard-coded 8-bits ADC
ppchd = pchd[pDchd >= .1] ppspd = pspd[pDspd >= .1] ppusd = pusd[pDusd >= .1] ppDfrd = pDfrd[pDfrd >= .1] ppDitd = pDitd[pDitd >= .1] ppDbrd = pDbrd[pDbrd >= .1] ppDchd = pDchd[pDchd >= .1] ppDspd = pDspd[pDspd >= .1] ppDusd = pDusd[pDusd >= .1] N = 40 points = np.arange(40) / 40 * 3.8 t = 10 ** points tt = t / 10. plt.plot(np.log10(t), np.log10(tt),':', color ='gray') tt = t / 100. plt.plot(np.log10(t), np.log10(tt),':', color ='gray') tt = t / 100. * 6.3 plt.plot(np.log10(t), np.log10(tt),'--', color ='gray') plt.text(1.2,.7, r'10%' , fontsize=18, color = 'gray') plt.text(3.4,2, r'6.3%', fontsize=18, color = 'gray') plt.text(3,.7, r'1%' , fontsize=18, color = 'gray') plt.scatter(np.log10(ppfrd), np.log10(ppDfrd), label = 'Francia', color ='C9') plt.scatter(np.log10(ppusd), np.log10(ppDusd), label = 'US', color ='green') plt.scatter(np.log10(ppspd), np.log10(ppDspd), label = r'España', color ='orange') plt.scatter(np.log10(ppbrd), np.log10(ppDbrd), label = 'Brasil', color ='blue') plt.scatter(np.log10(ppchd), np.log10(ppDchd), label = 'Chile', color ='k')
def IntegrateWell(CommunityInstance,
well_info,
T0=0,
T=1,
ns=2,
return_all=False,
log_time=False,
compress_resources=False,
compress_species=True):
"""
Integrator for Propagate and TestWell methods of the Community class
"""
#MAKE LOGARITHMIC TIME AXIS FOR LONG SINGLE RUNS
if log_time:
t = 10**(np.linspace(np.log10(T0), np.log10(T0 + T), ns))
else:
t = np.linspace(T0, T0 + T, ns)
#UNPACK INPUT
y0 = well_info['y0']
#COMPRESS STATE AND PARAMETERS TO GET RID OF EXTINCT SPECIES
S = well_info['params']['S']
M = len(y0) - S
not_extinct = y0 > 0
if not compress_species:
not_extinct[:S] = True
if not compress_resources: #only compress resources if we're running non-renewable dynamics
not_extinct[S:] = True
S_comp = np.sum(
not_extinct[:S]) #record the new point dividing species from resources
not_extinct_idx = np.where(not_extinct)[0]
y0_comp = y0[not_extinct]
not_extinct_consumers = not_extinct[:S]
not_extinct_resources = not_extinct[S:]
#Compress parameters
params_comp = CompressParams(not_extinct_consumers, not_extinct_resources,
well_info['params'],
CommunityInstance.dimensions, S, M)
#INTEGRATE AND RESTORE STATE VECTOR TO ORIGINAL SIZE
if return_all:
out = integrate.odeint(CommunityInstance.dydt,
y0_comp,
t,
args=(params_comp, S_comp),
mxstep=10000,
atol=1e-4)
traj = np.zeros((np.shape(out)[0], S + M))
traj[:, not_extinct_idx] = out
return t, traj
else:
out = integrate.odeint(CommunityInstance.dydt,
y0_comp,
t,
args=(params_comp, S_comp),
mxstep=10000,
atol=1e-4)[-1]
yf = np.zeros(len(y0))
yf[not_extinct_idx] = out
return yf
def m500_to_qty(logM500, z, slope_efunc, slope_m500, normalization): return n.e**normalization * \
(cosmoMD.efunc(z) / E035)**(slope_efunc) * (10**(logM500 - n.log10(6) - 14))**(slope_m500)
def logM500_to_logMgas(
def Plot_Topology_Robustness(R_T, runs):
data_points = np.zeros((9, len(COLOURS), runs), dtype=np.float64)
N_runs = -1
N_mut = -1
Colours = []
for run in range(runs):
#lines=[line.rstrip('\n') for line in open('/rscratch/asl47/Topology_Robustness_{}_R{}.txt'.format(R_T,run+1))]
#lines=[line.rstrip('\n') for line in open('/rscratch/asl47/Topology_Robustness_R{}_2.txt'.format(run+1))]
lines = [
line.rstrip('\n')
for line in open('/rscratch/asl47/Topology_Robustness_{}_R{}.txt'.
format(R_T, run + 1))
]
for line in lines:
if 'runs' in line:
N_runs = int(line.split()[-2])
elif 'N_mutations:' in line:
N_mut = int(line.split()[-1])
else:
for C, R in enumerate(line.split(' ')[3::4]):
data_points[N_mut][int(C)][run] = float(R) / N_runs
pcs = [cm.inferno(x) for x in np.linspace(0, 0.9, len(COLOURS))]
mean_data = np.mean(data_points, axis=2, dtype=np.float64)
MuLs_local = np.logspace(-2, np.log10(8), 1000)
binom_Set = binom(8, MuLs / 8.)
binom_local = binom(8, MuLs_local / 8.)
c_r = {}
#for C,colour_data in enumerate(mean_data.T):
# plt.plot(range(9),colour_data,color=pcs[C],ls='-')
#plt.plot(MuLs_local,np.sum(binom_local.pmf(T)*(1-mean_data[T][C]) for T in xrange(9)),color=pcs[C],ls=':')
f, (ax, ax2) = plt.subplots(2, 1)
for C, colour_data in enumerate(mean_data.T):
ax.plot(list(range(9)), colour_data, color=pcs[C])
ax2.plot(MuLs_local,
np.sum(
binom_local.pmf(T) * (1 - mean_data[T][C])
for T in range(9)),
color=pcs[C])
c_r[C] = np.sum(
binom_Set.pmf(T) * (1 - mean_data[T][C]) for T in range(9))
sm = plt.cm.ScalarMappable(cmap=cm.inferno,
norm=plt.Normalize(vmin=0, vmax=0.9))
sm._A = []
cax = f.add_axes([0.1, 0.625, 0.5, 0.05])
cbar = f.colorbar(sm, cax=cax, orientation='horizontal')
cbar.set_ticks(np.arange(0, 0.9, 1. / (1 + len(COLOURS))))
cbar.set_ticklabels(COLOURS)
cbar.ax.set_title('Colours')
ax.set_yscale('log', nonposy='mask')
ax.set_ylim((10**-8, 1))
ax.set_xlabel(r'$N_{\textrm{mutations}}$', fontsize=18)
ax.set_ylabel(r'$\chi_{\mathrm{robust}}$', fontsize=18)
ax.set_title(r'\textbf{{{}}}'.format('Thick Cross' if R_T ==
'TC' else 'Small Cross'),
fontsize=24)
ax2.set_xlabel(r'$\langle \mu L\rangle$', fontsize=18)
ax2.set_ylabel(r'$\chi_{\mathrm{del}}$', fontsize=18)
ax2.set_xscale('log')
ax2.set_yscale('log')
plt.show(block=False)
return c_r
def figure(
self,
title="Manhattan Plot",
showgrid=True,
xlabel=None,
ylabel='-log10(p)',
point_size=5,
showlegend=True,
col=None,
suggestiveline_value=-np.log10(1e-8),
suggestiveline_color='blue',
suggestiveline_width=1,
genomewideline_value=-np.log10(5e-8),
genomewideline_color='red',
genomewideline_width=1,
highlight=True,
highlight_color="red",
):
"""
Keyword arguments:
- title (string; optional) The title of the graph. (Default:
"Manhattan Plot")
- showgrid (bool; optional): Boolean indicating whether gridlines should be
shown. (Default: True)
- xlabel (string; optional): Label of the x axis. (Default: None)
- ylabel: (string; optional): Label of the y axis. (Default:
"-log10(p)")
- point_size (number; optional): Size of the points of the Scatter
plot. (Default: 5)
- showlegend (bool; optional): Boolean indicating whether legends should be
shown. (Default: True)
- col (string; optional): A string representing the color of the
points of the Scatter plot. Can be in any color format accepted by
plotly_js graph_objs. (Default: None) Default = None
- suggestiveline_value (bool/float; optional): A value which must
be False to deactivate the option, or a numerical value
corresponding to the p-value at which the line should be drawn.
The line has no influence on the data points. (Default:
-np.log10(1e-8))
- suggestiveline_color (string; optional): Color of the suggestive
line. (Default: "grey")
- suggestiveline_width (number): Width of the suggestive
line. (Default: 2)
- genomewideline_value (bool/float; optional): A boolean which must be
False to deactivate the option, or a numerical value corresponding
to the p-value above which the data points are considered
significant. (Default: -np.log10(5e-8))
- genomewideline_color (string; optional): Color of the genome wide
line. Can be in any color format accepted by plotly_js
graph_objs. (Default: "red")
- genomewideline_width (number; optional): Width of the genome wide
line. (Default: 1)
- highlight (bool; optional): turning on/off the highlighting of
data points considered significant. (Default: True)
- highlight_color (string; optional): Color of the data points
highlighted because they are significant Can be in any color
format accepted by plotly_js graph_objs. (Default: "red")
Returns:
- A figure formatted for plotly.graph_objs."""
xmin = min(self.data[self.pos].values)
xmax = max(self.data[self.pos].values)
horizontallines = []
if suggestiveline_value:
suggestiveline = go.layout.Shape(name=SUGGESTIVE_LINE_LABEL,
type="line",
fillcolor=suggestiveline_color,
line=dict(
color=suggestiveline_color,
width=suggestiveline_width),
x0=xmin,
x1=xmax,
xref="x",
y0=suggestiveline_value,
y1=suggestiveline_value,
yref="y")
horizontallines.append(suggestiveline)
if genomewideline_value:
genomewideline = go.layout.Shape(name=GENOMEWIDE_LINE_LABEL,
type="line",
fillcolor=genomewideline_color,
line=dict(
color=genomewideline_color,
width=genomewideline_width),
x0=xmin,
x1=xmax,
xref="x",
y0=genomewideline_value,
y1=genomewideline_value,
yref="y")
horizontallines.append(genomewideline)
data_to_plot = [] # To contain the data traces
tmp = pd.DataFrame() # Empty DataFrame to contain the highlighted data
if highlight:
if not isinstance(highlight, bool):
if self.snpName not in self.data.columns.values:
raise KeyError(
"snp argument specified for highlight as %s but "
"column not found in the data.frame" % self.snpName)
else:
if not genomewideline_value:
raise Warning(
"The genomewideline_value you entered is not a "
"positive value, or False, you cannot set highlight "
"to True in that case.")
tmp = self.data
# Sort the p-values (or -log10(p-values) above the line
if genomewideline_value:
if self.logp:
tmp = tmp.loc[
-np.log10(tmp[self.pName]) > genomewideline_value]
else:
tmp = tmp.loc[tmp[self.pName] > genomewideline_value]
highlight_hover_text = _get_hover_text(
tmp,
snpname=self.snpName,
genename=self.geneName,
annotationname=self.annotationName)
if not tmp.empty:
data_to_plot.append(
go.Scattergl(x=tmp[self.pos].values,
y=-np.log10(tmp[self.pName].values)
if self.logp else tmp[self.pName].values,
mode="markers",
text=highlight_hover_text,
marker=dict(color=highlight_color,
size=point_size),
name="Point(s) of interest"))
# Remove the highlighted data from the DataFrame if not empty
if tmp.empty:
data = self.data
else:
data = self.data.drop(self.data.index[tmp.index])
if self.nChr == 1:
if col is None:
col = ['black']
# If single chromosome, ticks and labels automatic.
layout = go.Layout(title=title,
xaxis={
'title':
self.xlabel if xlabel is None else xlabel,
'showgrid': showgrid,
'range': [xmin, xmax],
},
yaxis={'title': ylabel},
hovermode='closest')
hover_text = _get_hover_text(data,
snpname=self.snpName,
genename=self.geneName,
annotationname=self.annotationName)
data_to_plot.append(
go.Scattergl(x=data[self.pos].values,
y=-np.log10(data[self.pName].values)
if self.logp else data[self.pName].values,
mode="markers",
showlegend=showlegend,
marker={
'color': col[0],
'size': point_size,
'name': "chr%i" % data[self.chrName].unique()
},
text=hover_text))
else:
# if multiple chrms, use the ticks and labels you created above.
layout = go.Layout(title=title,
xaxis={
'title':
self.xlabel if xlabel is None else xlabel,
'showgrid': showgrid,
'range': [xmin, xmax],
'tickmode': "array",
'tickvals': self.ticks,
'ticktext': self.ticksLabels,
'ticks': "outside"
},
yaxis={'title': ylabel},
hovermode='closest')
icol = 0
if col is None:
col = [
'black' if np.mod(i, 2) else 'grey'
for i in range(self.nChr)
]
for i in data[self.index].unique():
tmp = data[data[self.index] == i]
chromo = tmp[self.chrName].unique() # Get chromosome name
hover_text = _get_hover_text(
data,
snpname=self.snpName,
genename=self.geneName,
annotationname=self.annotationName)
data_to_plot.append(
go.Scattergl(x=tmp[self.pos].values,
y=-np.log10(tmp[self.pName].values)
if self.logp else tmp[self.pName].values,
mode="markers",
showlegend=showlegend,
name="Chr%i" % chromo,
marker={
'color': col[icol],
'size': point_size
},
text=hover_text))
icol = icol + 1
layout.shapes = horizontallines
return go.Figure(data=data_to_plot, layout=layout)
degreeCount = collections.Counter(degree_sequence)
deg, cnt = zip(*degreeCount.items())
plt.bar(deg, cnt, width=0.80, color="b")
plt.title("Degree Histogram")
plt.ylabel("Count")
plt.xlabel("Degree")
plt.show()
plt.clf()
print("The network is a power-law")
print("G is a directed graph with unweighted links")
print("The network is weakly connected")
print("The network is highly clustered")
bin_edges = np.logspace(np.log10(kmin), np.log10(kmax), num=20)
density, _ = np.histogram(degrees, bins=bin_edges, density=True)
fig = plt.figure(figsize=(6, 4))
log_be = np.log10(bin_edges)
x = 10**((log_be[1:] + log_be[:-1]) / 2)
plt.loglog(x, density, marker='o', linestyle='none')
plt.xlabel(r"degree $k$", fontsize=16)
plt.ylabel(r"$P(k)$", fontsize=16)
plt.show()
plt.clf()
fig = plt.figure(figsize=(10, 10))
nx.draw_spring(G, node_size=20, node_color="purple")
plt.show()
plt.clf()
def comm_profile(logdir, cfg, df_gpu):
total_traffic = 0.0
total_h2d_traffic = 0.0
total_d2h_traffic = 0.0
total_p2p_traffic = 0.0
total_memcopy_time = 0.0
# sofa_fieldnames = [
# 'timestamp',
# "event",
# "duration",
# "deviceId",
# "copyKind",
# "payload",
# "bandwidth",
# "pkt_src",
# "pkt_dst",
# "pid",
# "tid",
# "name",
# "category"]
n_gpus = 0
for i in range(len(df_gpu)):
if df_gpu.iat[i, 3] > n_gpus:
n_gpus = int(df_gpu.iat[i, 3])
if n_gpus == 0:
print_warning("No GPU communication traces are collected.")
return
print_title("Data Traffic for each CopyKind (MB)")
data_copyKind = grouped_df = df_gpu.groupby("copyKind")["payload"]
for key, item in grouped_df:
print((
"[%s]: %lf" %
(cktable[key], grouped_df.get_group(key).sum() / 1000000.0)))
if int(key) == 1:
total_h2d_traffic = grouped_df.get_group(key).sum() / 1000000.0
if int(key) == 2:
total_d2h_traffic = grouped_df.get_group(key).sum() / 1000000.0
if int(key) == 10:
total_p2p_traffic = grouped_df.get_group(key).sum() / 1000000.0
if int(key) != 8:
total_traffic = total_traffic + \
grouped_df.get_group(key).sum() / 1000000.0
print(("Total traffic: %.2lf" % total_traffic))
print_title("Data Communication Time for each CopyKind (s)")
durations_copyKind = grouped_df = df_gpu.groupby("copyKind")["duration"]
for key, item in grouped_df:
print(("[%s]: %lf" % (cktable[key], grouped_df.get_group(key).sum())))
if key == 0:
total_kernel_time = grouped_df.get_group(key).sum()
else:
total_memcopy_time = total_memcopy_time + \
grouped_df.get_group(key).sum()
bw = (data_copyKind.sum() / 1000000) / durations_copyKind.sum() / 1000
bw_h2d = bw_d2h = bw_p2p = avg_bw = 1e-10
for i in range(len(bw)):
key = list(bw.keys())[i]
if cktable[key] == 'H2D' or cktable[key] == 'D2H' or cktable[key] == 'D2D' or cktable[key] == 'P2P':
print(("Averaged Achieved %s Unidirectional Bandwidth: %.1f (GB/s)" % (cktable[key], bw.iloc[i])))
else:
continue
print_title("Summary of Comm.")
print(("MeasuredTotalTraffic : %lf (MB)" % total_traffic))
print(("MeasuredTotalH2DTraffic : %lf (MB)" % total_h2d_traffic))
print(("MeasuredTotalD2HTraffic : %lf (MB)" % total_d2h_traffic))
print(("MeasuredTotalP2PTraffic : %lf (MB)" % total_p2p_traffic))
accum = np.zeros((1 + n_gpus, 1 + n_gpus))
accum_count = np.zeros((1 + n_gpus, 1 + n_gpus))
# TODO: Parallelize payload accumulatoin
#print("df length: %d" % len(df_gpu))
#cpu_count = mp.cpu_count()
#pool = mp.Pool(processes=cpu_count)
#res_accum = pool.map( partial(payload_sum), df_gpu)
for i in range(len(df_gpu)):
if df_gpu.iat[i, 4] == 0 or df_gpu.iat[i, 4] == 8:
continue
src = df_gpu.iat[i, 7]
dst = df_gpu.iat[i, 8]
payload = df_gpu.iat[i, 5]
accum[src][dst] = float(accum[src][dst] + payload)
accum_count[src][dst] = int(accum_count[src][dst] + 1)
print("Traffic Matrix (log10(B)):")
row_str = "\tHOST\t"
for i in range(1, accum.shape[1]):
row_str = row_str + "GPU%d" % i + "\t"
print(row_str)
for i in range(accum.shape[0]):
if i == 0:
row_str = "HOST\t"
else:
row_str = "GPU%d\t" % i
for j in range(accum.shape[1]):
row_str = row_str + "%d" % (int(np.log10(1 + accum[i][j]))) + "\t"
print(row_str)
print("Traffic Matrix (MB):")
row_str = "\tHOST\t"
for i in range(1, accum.shape[1]):
row_str = row_str + "GPU%d" % i + "\t"
print(row_str)
for i in range(accum.shape[0]):
if i == 0:
row_str = "HOST\t"
else:
row_str = "GPU%d\t" % i
for j in range(accum.shape[1]):
row_str = row_str + "%d" % (accum[i][j] / (1024 * 1024)) + "\t"
print(row_str)
df_gpu.to_csv(
logdir + '/' + 'comm.csv',
columns=[
"timestamp",
"pkt_src",
"pkt_dst",
"payload",
"bandwidth"])
def temperature_guess(self,
T_in,
p_in,
T_out,
tube_diameters_in,
tube_diameters_out,
tube_conductivity,
emissions_guess,
coating_thickness,
coating_conductivity,
tube_roughness,
uconvloss,
passive=None,
tube_material=None):
'''
Makes a first guess on temperature profiles approximating the enthalpy gain of the water/steam mixture to be equal to flux input on the tubes external walls. The tube walls are coated with a selective coating. Default arguments are for Pyromark2500(R).
Arguments:
- T_in: Inlet temperature of the water in (K).
- p_in: Inlet pressure of the water in (pa).
- T_out: Outlet temeprature of the water in (K).
- tube_diameters_in: inner diameter of the tubes in (m).
- tube_diameters_out: outer diameter of the tubesin (m).
- tube_conductivity: thermal conductivity of teh tubes in (W/mK).
- emissions_guess: emissive losses guess to account for thermal emissions in (W).
- passive: array of the indices of the adiabatic surfaces in the cavity.
- coating_thickness: thickness of the coating layer on the tubes in (m).
- coating_conductivity: coating thermal conductivity in (W/mK).
Returns:
- strings 'good_geom' or 'bad_geom' depending on the mass flow guess to meet the input/output arguments and amount of actually going in the receiver. This is a quick hack to prevent issues with receivers forcing in the required inpu/output by lowering the mass flow too much/putting it negative, thus impacting the enthalpy guess... and basically screwing-up the convergence process for non-performing geometries.
'''
# Get active surfaces net radiative power
active = N.ones(len(self.areas), dtype=N.bool)
active[0] = 0. # aperture
if passive != None:
active[passive] = 0.
# Check the tube_diameters arrays or make one:
tube_diameters_in = N.hstack([tube_diameters_in])
tube_diameters_out = N.hstack([tube_diameters_out])
if len(tube_diameters_in) != (N.sum(active) + 1):
if len(tube_diameters_in) == 1:
tube_diameters_in = N.ones(N.sum(active) +
1) * tube_diameters_in[0]
else:
stop
if len(tube_diameters_out) == 1:
tube_diameters_out = N.ones(N.sum(active) +
1) * tube_diameters_out[0]
else:
stop
# Equivalent tube sections radii:
R_in = (tube_diameters_in[:-1] + tube_diameters_in[1:]) / 4.
R_out = (tube_diameters_out[:-1] + tube_diameters_out[1:]) / 4.
self.R_in = R_in
self.R_out = R_out
# Get tubes lengths and positions:
tube_lengths = N.array(self.areas[active] / (2. * R_out))
self.tube_lengths = tube_lengths + 2. * N.pi * (R_out - R_in)
tube_positions = N.add.accumulate(N.hstack([0, self.tube_lengths]))
# Initialise pressures and steam quality at each position along the flow path:
self.p = N.ones(len(tube_positions)) * p_in
self.qual = N.zeros(len(tube_positions) - 1)
self.v = N.zeros(len(tube_positions))
# Correlation single phase:
def single_phase_u(Re, Pr, f_F, k, tube_D):
if Re < 1e4:
#if Re<1e5: # STG code error
# Gnielinski:
return ((Re - 1000.) * Pr * (f_F * k / (2. * tube_D))) / (
1. + 12.7 * (Pr**(2. / 3.) - 1.) * N.sqrt(f_F / 2.))
else:
# Petukhov
return (Re * Pr * (f_F * k / (2. * tube_D)) /
(1.07 + 12.7 *
(Pr**(2. / 3.) - 1.) * N.sqrt(f_F / 2.)))
# Evaluate convective losses and qnets:
Qconvloss = uconvloss * self.areas[1:] * (self.T[1:] - self.T[0])
qnets = self.bin_abs[active[1:]] - emissions_guess[
active[1:]] - Qconvloss[active[1:]]
# Get starting enthalpy via Freesteam and initialise enthalpy array:
h_in = steam_pT(p_in, T_in).h
h_out = steam_pT(self.p[-1], T_out).h
hs_p = h_in + N.add.accumulate(
N.hstack([0, qnets]) / N.sum(qnets)) * (h_out - h_in)
self.h = N.ones(len(qnets) + 1) * h_in
# Enthalpy convergence loop:
conv_h = N.ones(len(hs_p)) * N.inf
iterh = 0
while (conv_h > 1e-9).any():
# Evaluate the mass-flow:
self.m = N.sum(qnets) / (h_out - h_in)
# Evaluate convective losses and qnets:
Qconvloss = uconvloss * self.areas[1:] * (self.T[1:] - self.T[0])
qnets = self.bin_abs[active[1:]] - emissions_guess[
active[1:]] - Qconvloss[active[1:]]
# Initialise internal convective heat trasnfer coefficient:
uconv = N.zeros(len(tube_diameters_in) - 1)
# Go through the flow-path, actualise the pressures and evaluate the heat transfer coefficients.
for i in xrange(len(tube_positions) - 1):
# Evaluate the steam properties:
steam_state = steam_ph(self.p[i], hs_p[i])
rho = steam_state.rho
Cp = steam_state.cp
x = steam_state.x
Tsat = Tsat_p(self.p[i])
steam_L = steam_Tx(Tsat, 0.)
steam_G = steam_Tx(Tsat, 1.)
h_LG = steam_G.h - steam_L.h
qual = (hs_p[i] - steam_L.h) / h_LG
v = self.m / (rho * N.pi * (tube_diameters_in[i] / 2.)**2.)
if qual <= 0.:
mu = steam_state.mu
k = steam_state.k
# Calculate Reynolds, Prandtl, Darcy and Fanning friction factors
Re = rho * v * tube_diameters_in[i] / mu
Pr = mu / (k / Cp)
S = N.log(Re / (1.816 * N.log(1.1 * Re /
(N.log(1. + 1.1 * Re)))))
f_D = (
-2. *
N.log10(tube_roughness /
(3.71 * tube_diameters_in[i]) + 2.18 * S / Re)
)**(
-2.
) # Brkic using Lambert W-function approximation to solve Colebrook's implicit equation.
f_F = 0.25 * f_D
# Calculate heat transfer coefficient:
uconv[i] = single_phase_u(Re, Pr, f_F, k, tube_diameters_in[i])
rho_L = steam_L.rho
rho_G = steam_G.rho
mult = 1. # Carey Friction factor multiplier
if ((qual > 0.) and (qual < 1.)):
mu_L = steam_L.mu
mu_G = steam_G.mu
#v_L = self.m/(rho_L*N.pi*(tube_diameters_in[i]/2.)**2.)
#Re_L = rho_L*v_L*tube_diameters_in[i]/mu_L
#mult = (1.+(mu_L/mu_G-1.)*qual)**(-0.25) # Carey Friction factor multiplier
#f_D = 4.*mult*(1.58*N.log(Re_L)-3.28)**(-2) # Correlation in Kandlikar (less precise presumably) which gives significantly lower heat transfer coefficients in the pre-dryout region
if (qual < 0.8):
k_L = steam_L.k
Cp_L = steam_L.cp
v_L = self.m / (rho_L * N.pi *
(tube_diameters_in[i] / 2.)**2.)
h_LG = steam_G.h - steam_L.h
Re_L = rho_L * v_L * tube_diameters_in[i] / mu_L
#Re_L = rho_L*v_L*(1.-qual)*tube_diameters_in[i]/mu_L # from Notes from Jose. My interpretation is all liquid in the tube (saturated then).
Pr_L = mu_L / (k_L / Cp_L)
S_L = N.log(Re_L /
(1.816 * N.log(1.1 * Re_L /
(N.log(1. + 1.1 * Re_L)))))
f_F_L = 0.25 * (
(-2. * N.log10(tube_roughness /
(3.71 * tube_diameters_in[i]) +
2.18 * S_L / Re_L))**(-2.))
#f_F_L = (1.58*N.log(Re_L)-3.28)**(-2) # Correlation in Kandlikar (less precise presumably) which gives significantly lower heat transfer coefficients in the pre-dryout region
# Kandlikar
Co = (rho_G / rho_L)**0.5 * ((1. - qual) / qual)**0.8
if i == 0:
Bo = 0.
else:
Bo = qnets[i] / (N.pi * R_in[i] * tube_lengths[i]
) / (rho * v * h_LG)
#Bo = qnets[i]/(N.pi*R_out[i]*tube_lengths[i])/(rho*v*h_LG) # Changed to the outer flux to compare with the STG version
uconv_L = single_phase_u(Re_L, Pr_L, f_F_L, k_L,
tube_diameters_in[i])
uconvNB = uconv_L * (0.6683 * Co**(-0.2) + 1058. *
Bo**0.7) * (1. - qual)**0.8
uconvCB = uconv_L * (1.136 * Co**(-0.9) + 667.2 *
Bo**0.7) * (1. - qual)**0.8
uconv[i] = N.amax([uconvNB, uconvCB])
elif qual < 0.9: # Here the validity of the correlation is changed from the STG version.
# Groeneveld
a = 1.09e-3
b = 0.989
c = 1.41
d = -1.15
Y = 1. - 0.1 * ((rho_L / rho_G - 1.) *
(1. - qual))**0.4
k_G = steam_G.k
Cp_G = steam_G.cp
v_G = self.m / (rho_G * N.pi *
(tube_diameters_in[i] / 2.)**2.)
Re_G = rho_G * v_G * tube_diameters_in[i] / mu_G
Pr_G = mu_G / (k_G / Cp_G)
uconv[i] = a * (
Re_G * (qual + rho_G / rho_L * (1. - qual))
)**b * Pr_G**c * Y**d * k_G / tube_diameters_in[i]
# Calculate pressure drop for the next element:
#f_D = 4.*f_F # For using the friction factor formula advised by Kandlikar
dp = f_D * self.tube_lengths[i] / (2. *
R_in[i]) * rho * v**2. / 2.
steam_next = steam_ph(self.p[i + 1], self.h[i + 1])
rho_next = steam_next.rho
v_next = self.m / (rho_next * N.pi *
(tube_diameters_in[i + 1] / 2.)**2.)
self.p[i + 1] = self.p[
i] + rho * v**2. / 2. - rho_next * v_next**2. / 2. - dp
self.v[i] = v
# Store dryness fractions;
self.qual[i] = qual
# Re-evaluate enthalpies:
hs_p[i + 1] = hs_p[i] + qnets[i] / self.m
# Final velocity storage:
self.v[i + 1] = v_next
# Evaluate the enthalpy at the outlet:
#h_out = steam_pT(self.p[-1], T_out).h
h_out = hs_p[-1]
#FIXME: need a more reliable convergence insurance
if self.m < 0.01:
print 'bad_geom'
return 'bad_geom'
# Evaluate convergence:
conv_h = N.abs((self.h - hs_p) / self.h)
self.h = (self.h + hs_p) / 2.
iterh += 1
if iterh > 100:
print conv_h
print self.h
stop
# Get the tube elements properties:
self.uconv = uconv
# Get temperatures from enthalpies via Freesteam
T_guess_fluid = N.zeros(len(self.h))
T_guess_fluid[0] = T_in
for i in xrange(1, len(self.h)):
T_guess_fluid[i] = steam_ph(self.p[i], self.h[i]).T
# Central differences scheme:
self.T_guess_fluid = (T_guess_fluid[:-1] + T_guess_fluid[1:]) / 2.
T_guess_wall = N.zeros(len(self.areas) - 1)
Rconv = 1. / (N.pi * tube_lengths * R_in * self.uconv)
Rcond = 1. / (N.pi * tube_lengths) * (
N.log(R_out / R_in) / tube_conductivity + N.log(
(R_out + coating_thickness) / R_out) / coating_conductivity)
T_guess_wall[active[1:]] = self.T_guess_fluid + qnets * (Rconv + Rcond)
self.T_wall_in = self.T_guess_fluid + qnets * (Rconv)
self.T_guess = T_guess_wall
self.tube_positions = tube_positions
self.Q_conv_loss = Qconvloss
assert (self.T_guess == float('inf')).any() == False, str(
self.T_guess) + str(T_guess_wall) + str(emissions_guess) + str(
self.m) + str([
self.apertureRadius, self.frustaRadii, self.frustaDepths,
self.coneDepth
])
return 'good_geom'
import matplotlib.pyplot as plt
from astropy.io import fits
import numpy as np
hdu = fits.open('The Hipparcos Main Catalogue.fit')
hdu.info()
hdu[0].header
#1pc~100pc
Plx1 = (hdu[1].data['Plx']>10)
Plx2 = (hdu[1].data['Plx']<1000)
Plxs = Plx1*Plx2
dat = hdu[1].data[Plxs]
S = dat['Plx']/1000
Mv = 5+dat['Vmag']+5*np.log10(S)
n = plt.hist(Mv,14,range=(-2,12),ls='--',histtype='step')
plt.close()
plt.figure(figsize=(10,7))
V = 4/3*np.pi*(100**3-1**3)
x = n[1][0:len(n[1])-1]+0.5
y = np.log10(n[0][0:]/V)+10
plt.plot(x, y,'k')
plt.xlabel('Mv')
plt.ylabel('log $\phi$(M)+10')
plt.savefig('IMF.png')
plt.show()
def ManhattanPlot(
dataframe,
chrm="CHR",
bp="BP",
p="P",
snp="SNP",
gene="GENE",
annotation=None,
logp=True,
title="Manhattan Plot",
showgrid=True,
xlabel=None,
ylabel='-log10(p)',
point_size=5,
showlegend=True,
col=None,
suggestiveline_value=-np.log10(1e-8),
suggestiveline_color='#636efa',
suggestiveline_width=1,
genomewideline_value=-np.log10(5e-8),
genomewideline_color='#EF553B',
genomewideline_width=1,
highlight=True,
highlight_color="red",
):
"""Returns a figure for a manhattan plot.
Keyword arguments:
- dataframe (dataframe; required): A pandas dataframe which must contain at
least the following three columns:
- the chromosome number
- genomic base-pair position
- a numeric quantity to plot such as a p-value or zscore
- chrm (string; optional): A string denoting the column name for the
chromosome. This column must be float or integer. Minimum number
of chromosomes required is 1. If you have X, Y, or MT chromosomes,
be sure to renumber these 23, 24, 25, etc. (Default: "CHR")
- bp (string; optional): A string denoting the column name for the
chromosomal position. (Default: "BP")
- p (string; optional): A string denoting the column name for the
float quantity to be plotted on the y-axis. This column must be
numeric. This does not have to be a p-value. It can be any
numeric quantity such as peak heights, bayes factors, test
statistics. If it is not a p-value, make sure to set logp = FALSE.
(Default: "P")
- snp (string; optional): A string denoting the column name for the
SNP names (e.g. rs number). More generally, this column could be
anything that identifies each point being plotted. For example, in
an Epigenomewide association study (EWAS) this could be the probe
name or cg number. This column should be a character. This
argument is optional, however it is necessary to specify if you
want to highlight points on the plot using the highlight argument
in the figure method. (Default: "SNP")
- gene (string; optional): A string denoting the column name for the
GENE names. This column could be a string or a float. More
generally this could be any annotation information that you want
to include in the plot. (Default: "GENE")
- annotation (string; optional): A string denoting the column name for
an annotation. This column could be a string or a float. This
could be any annotation information that you want to include in
the plot (e.g. zscore, effect size, minor allele frequency).
(Default: None)
- logp (bool; optional): If True, the -log10 of the p-value is
plotted. It isn't very useful to plot raw p-values; however,
plotting the raw value could be useful for other genome-wide plots
(e.g., peak heights, bayes factors, test statistics, other
"scores", etc.) (Default: True)
- title (string; optional) The title of the graph. (Default: "Manhattan Plot")
- showgrid (bool; optional): Boolean indicating whether gridlines should be
shown. (Default: True)
- xlabel (string; optional): Label of the x axis. (Default: None)
- ylabel: (string; optional): Label of the y axis. (Default:
"-log10(p)")
- point_size (number; optional): Size of the points of the Scatter
plot. (Default: 5)
- showlegend (bool; optional): Boolean indicating whether legends should be
shown. (Default: True)
- col (string; optional): A string representing the color of the
points of the Scatter plot. Can be in any color format accepted by
plotly_js graph_objs. (Default: None) Default = None
- suggestiveline_value (bool/float; optional): A value which must
be False to deactivate the option, or a numerical value
corresponding to the p-value at which the line should be drawn.
The line has no influence on the data points. (Default:
-np.log10(1e-8))
- suggestiveline_color (string; optional): Color of the suggestive
line. (Default: "grey")
- suggestiveline_width (number): Width of the suggestive
line. (Default: 2)
- genomewideline_value (bool/float; optional): A boolean which must be
False to deactivate the option, or a numerical value corresponding
to the p-value above which the data points are considered
significant. (Default: -np.log10(5e-8))
- genomewideline_color (string; optional): Color of the genome wide
line. Can be in any color format accepted by plotly_js
graph_objs. (Default: "red")
- genomewideline_width (number; optional): Width of the genome wide
line. (Default: 1)
- highlight (bool; optional): turning on/off the highlighting of data points
considered significant. (Default: True)
- highlight_color (string; optional): Color of the data points
highlighted because they are significant Can be in any color
format accepted by plotly_js graph_objs. (Default: "red")
# ...
Example 1: Random Manhattan Plot
'''
dataframe = pd.DataFrame(
np.random.randint(0,100,size=(100, 3)),
columns=['P', 'CHR', 'BP'])
fig = create_manhattan(dataframe, title='XYZ Manhattan plot')
plotly.offline.plot(fig, image='png')
'''
"""
mh = _ManhattanPlot(dataframe,
chrm=chrm,
bp=bp,
p=p,
snp=snp,
gene=gene,
annotation=annotation,
logp=logp)
return mh.figure(title=title,
showgrid=showgrid,
xlabel=xlabel,
ylabel=ylabel,
point_size=point_size,
showlegend=showlegend,
col=col,
suggestiveline_value=suggestiveline_value,
suggestiveline_color=suggestiveline_color,
suggestiveline_width=suggestiveline_width,
genomewideline_value=genomewideline_value,
genomewideline_color=genomewideline_color,
genomewideline_width=genomewideline_width,
highlight=highlight,
highlight_color=highlight_color)
def on_batch_end(self, batch, logs=None):
if self.current_epoch_ > 1:
return
if self.use_validation_set:
X, Y = self.validation_data[0], self.validation_data[1]
# use 5 random batches from test set for fast approximate of loss
num_samples = self.batch_size * self.validation_sample_rate
if num_samples > X.shape[0]:
num_samples = X.shape[0]
idx = np.random.choice(X.shape[0], num_samples, replace=False)
x = X[idx]
y = Y[idx]
values = self.model.evaluate(x,
y,
batch_size=self.batch_size,
verbose=False)
loss = values[0]
else:
loss = logs['loss']
# smooth the loss value and bias correct
running_loss = self.loss_smoothing_beta * loss + (
1. - self.loss_smoothing_beta) * loss
running_loss = running_loss / (
1. - self.loss_smoothing_beta**self.current_batch_)
# stop logging if loss is too large
if self.current_batch_ > 1 and self.stopping_criterion_factor is not None and (
running_loss >
self.stopping_criterion_factor * self.best_loss_):
if self.verbose:
print(
" - LRFinder: Skipping iteration since loss is %d times as large as best loss (%0.4f)"
% (self.stopping_criterion_factor, self.best_loss_))
return
if running_loss < self.best_loss_ or self.current_batch_ == 1:
self.best_loss_ = running_loss
current_lr = K.get_value(self.model.optimizer.lr)
self.history.setdefault('running_loss_', []).append(running_loss)
if self.lr_scale == 'exp':
self.history.setdefault('log_lrs', []).append(np.log10(current_lr))
else:
self.history.setdefault('log_lrs', []).append(current_lr)
# compute the lr for the next batch and update the optimizer lr
if self.lr_scale == 'exp':
current_lr *= self.lr_multiplier_
else:
current_lr = self.lr_multiplier_[self.current_batch_ - 1]
K.set_value(self.model.optimizer.lr, current_lr)
# save the other metrics as well
for k, v in logs.items():
self.history.setdefault(k, []).append(v)
if self.verbose:
if self.use_validation_set:
print(" - LRFinder: val_loss: %1.4f - lr = %1.8f " %
(values[0], current_lr))
else:
print(" - LRFinder: lr = %1.8f " % current_lr)
def bitbertober(bitber_exp):
ber = sum([10**i for i in bitber_exp])
ber_exp = np.log10(ber)
return ber_exp
def run(self, dataSlice, slicePoint=None):
return 1.25 * np.log10(np.sum(10.**(.8*dataSlice[self.colname])))
print('velocity variance: %10.4f\n' % (np.sum(wvel*wvel)/totsize))
fig,theAx=plt.subplots(1,1,figsize=(8,8))
frequencies[0]=np.NaN
Power[0]=np.NaN
Power_half=Power[:halfpoint:]
theAx.loglog(frequencies,Power_half)
theAx.set_title('raw wvel spectrum with $f^{-5/3}$')
theAx.set(xlabel='frequency (HZ)',ylabel='Power (m^2/s^2)')
#
# pick one point the line should pass through (by eye)
# note that y intercept will be at log10(freq)=0
# or freq=1 Hz
#
leftspec=np.log10(Power[1]*1.e-3)
logy=leftspec - 5./3.*np.log10(frequencies)
yvals=10.**logy
theAx.loglog(frequencies,yvals,'r-')
thePoint=theAx.plot(1.,Power[1]*1.e-3,'g+')
thePoint[0].set_markersize(15)
thePoint[0].set_marker('h')
thePoint[0].set_markerfacecolor('g')
# %% [markdown]
# ## power spectrum layout
# %% [markdown]
# Here is what the entire power spectrum looks like, showing positive and negative frequencies
'N', 'OR', 'STAT', 'P'])
add2 = add2.set_index('Position')
to_condition['P value 1st'] = add1.P
to_condition['P value 2nd'] = add2.P
to_condition['Region'] = (range(1, 1 + len(to_condition)))
to_condition['Region'] = 'r' + to_condition.Region.astype(str) + ' lead'
to_condition
frames = [g, to_condition]
result = pd.concat(frames)
result = result.sort_values('P value').loc[~result.index.duplicated(
keep='last')]
result.to_csv('table_for_paper.csv')
add1['-logP'] = -(np.log10(add1.P))
add2['-logP'] = -(np.log10(add2.P))
fig, ax = plt.subplots(3, 1, sharey=True, sharex=True)
ax[0].scatter(fisher['BP'], fisher['-logP'])
ax[1].scatter(add1['BP'], add1['-logP'])
ax[2].scatter(add2['BP'], add2['-logP'])
plt.show()
plt.savefig('regresions.tiff')
errors_a,
markers[markerIndex],
label=legend,
markersize=3)
pressurePlot.loglog(timeStepList,
errors_p,
markers[markerIndex],
label=legend,
markersize=3)
markerIndex += 1
try:
print '\n' + legend
for i in np.arange(nbComputations - 1):
print(np.log10(errors_u[i + 1]) - np.log10(errors_u[i])) / (
np.log10(timeStepList[i + 1]) - np.log10(timeStepList[i]))
except:
pass
velocityPlot.set_xlabel('Time step [s]')
velocityPlot.set_ylabel('Error in velocity [-]')
velocityPlot.grid('on')
lgd = velocityPlot.legend(loc='upper center',
bbox_to_anchor=(0.5, 1.45),
ncol=3,
fancybox=True,
shadow=False)
velocityFig.savefig('tubeflow_velocity.pdf',
bbox_extra_artists=(lgd, ),
transparent=True,
## dist_sat[i,j,k]:
## i --> the node i
## j --> 0 for x-position, 1 for y-position, 2 for z-position
## k --> the step time in sat pass
#### FOR COMPUTE DISTANCE MAGNITUDE (ABS) FROM END-DEVICE TO SAT PASSING BY ####
distance = np.zeros((sites_pos.shape[0],leo_pos.shape[0]))
distance[:,:] = (dist_sat[:,0,:]**2 + dist_sat[:,1,:]**2 + dist_sat[:,2,:]**2)**(1/2)
## WHERE:
## distance[i,j]:
## i --> the node i
## j --> the step time in sat pass
##MATRIX FOR LINK BUDGET Lpl ###
Lpl = np.zeros((sites_pos.shape[0],leo_pos.shape[0]))
Lpl = 20*np.log10(distance*1000) + 20*np.log10(freq) - 147.55 #DISTANCE MUST BE IN METERS
## WHERE:
## Lpl[i,j]:
## i --> the node i
## j --> the step time in sat pass
##MATRIX FOR LINK BUDGET, USING Prx ###
Prx = np.zeros((sites_pos.shape[0],leo_pos.shape[0]))
Prx = Ptx + G_sat + G_device - Lpl #DISTANCE IS CONVERTED TO METERS
## WHERE:
## Prx[i,j]:
## i --> the node i
## j --> the step time in sat pass
from scipy.optimize import curve_fit
from scipy.misc import factorial
from scipy.stats import ks_2samp
from scipy import stats
import sys
import pdb
filename = sys.argv[1]
datain = np.genfromtxt(filename, delimiter=",")
data = datain[:, 1] * 1e9
min = np.min(data)
max = np.max(data)
bins = 10 * np.size(data)
time = np.logspace(np.log10(min), np.log10(max), num=bins)
mu = np.mean(data)
time_centers = np.r_[0.5 * (time[:-1] + time[1:])]
def analyticalCDF(times, tau):
return 1 - np.exp(-times / tau)
#print np.std(data)
#print stats.sem(data)
hist, bins2 = np.histogram(data, bins=time, density=False)
cdf = np.cumsum(hist) * 1.0 / data.size
#combine total subsector basis
basis = np.hstack((cube_basisL, basis))
basis = np.hstack((basis, cube_basisR))
# project Hamiltonian + dynamics
basis = np.unique(basis, axis=1)
basis, temp = np.linalg.qr(basis)
from Diagnostics import print_wf
for n in range(0, np.size(basis, axis=1)):
print("\n")
print_wf(basis[:, n], pxp, 1e-2)
H_rot = np.dot(np.conj(np.transpose(basis)), np.dot(H.sector.matrix(), basis))
e, u = np.linalg.eigh(H_rot)
overlap = np.log10(np.abs(u[1, :])**2)
H.sector.find_eig()
z = zm_state(2, 1, pxp)
eig_overlap(z, H).plot()
plt.scatter(e,
overlap,
marker="s",
s=200,
alpha=0.6,
color="red",
label="subcube")
#perm approx for comp, FSA
perm_basis = np.zeros(pxp.dim)
for n in range(0, len(sector_refs)):
return helper_func(θ)
# #######################################
# PYCCL PARAMETERS
#########################################
nz = 1000 #redshift resolution
zmin = 0.
zmax = 2.
z = np.linspace(zmin,zmax,nz)
# number of tomographic bins
nbins = 1
# number of cross/auto angular power spectra
ncombinations = int(nbins*(nbins+1)/2)
# 100 log equal spaced ell samples should be fine according to https://arxiv.org/pdf/0705.0163.pdf
ells = np.logspace(np.log10(100),np.log10(6000),100)
# I think this is 1
delta_l = 1
"""
Assume a redshift distribution given by
z^alpha * exp(z/z0)^beta
with alpha=1.3, beta = 1.5 and z0 = 0.65
"""
dNdz_true = ccl.dNdzSmail(alpha = 1.3, beta = 1.5, z0=0.65)
# Assumes photo-z error is Gaussian with a bias is 0.05(1+z)
pz = ccl.PhotoZGaussian(sigma_z0=0.05)
fsky = 15000/41252.96 # fraction of the sky observed by Euclid
# sampled ells
sn = 0.26
# TODO: inspect this num_dens and nzs
from sklearn.preprocessing import PolynomialFeatures# 导入多项式
from sklearn.model_selection import cross_val_score # 交叉检验
from sklearn.metrics import explained_variance_score, mean_absolute_error, mean_squared_error, r2_score # 批量导入指标算法
import pandas as pd # 导入pandas
import matplotlib.pyplot as plt # 导入图形展示库
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
import random
import math
###todo : 导入数据 开始###
data = np.loadtxt(r'D:\Course Plus\华中数模\第十二届华中地区数学建模大赛B题\回归数据\train_data.txt',
encoding='utf-8',skiprows=1,delimiter=',') # 读取数据文件
data = np.log10(data+1)
X = data[:, :-1] # 分割自变量
Y = data[:, -1] # 分割因变量
###todo : 导入数据 结束###
# model_br = BayesianRidge(n_iter=2, tol=0.01, param_1=0.1, param_2=0.00001, lambda_1=0.00001,
# lambda_2=50) # 建立贝叶斯岭回归模型对象
# model_lr = LinearRegression(fit_intercept=True, normalize=True) # 建立普通线性回归模型对
#
# model_svr = SVR(kernel='rbf', C=3400, param=0.0016, tol=0.001,
# epsilon=0.14)
# model_svr = SVR(kernel='linear', C=10, tol=0.000001,
# epsilon=0.000001)
param = [0.00001,0.0001,0.001,0.01,0.1,1,10,100]
# param = [1,10,100,1000]
def eval(self,nu=None,fill_SED=True,get_model=False,loglog=False,label=None,phys_output=False):
"""
evaluates the SED for the current parameters and fills the :class:`.SED` member
"""
if nu is None:
#print ("--->", self.nu_min,self.nu_max,self.nu_size)
x1=np.log10(self.nu_min)
x2=np.log10(self.nu_max)
lin_nu=np.logspace(x1,x2,self.nu_size)
log_nu=np.log10(lin_nu)
model=np.zeros(lin_nu.size)
else:
if np.shape(nu)==():
nu=np.array([nu])
if loglog==True:
lin_nu=np.power(10.,nu)
log_nu=nu
else:
log_nu=np.log10(nu)
lin_nu=nu
#print lin_nu
model=np.zeros(lin_nu.size)
for model_comp in self.components_list:
#print "model",model_comp.name
if loglog==False:
model+= model_comp.eval(nu=lin_nu,fill_SED=fill_SED,get_model=True,loglog=loglog)
else:
model+= np.power(10.,model_comp.eval(nu=log_nu,fill_SED=fill_SED,get_model=True,loglog=loglog))
if fill_SED==True:
self.SED.fill(nu=lin_nu,nuFnu=model)
#TODO ADD cosmo properly to all components
#self.SED.fill_nuLnu(z=self.jet_obj.get_par_by_type('redshift').val, dl=self.jet_obj.get_DL_cm())
if get_model==True:
if loglog==True:
model=np.log10(model)
return model
else:
return None
def dist_mod(z, cosmo):
ld = cosmology.funcs.luminosity_distance(z, cosmo=cosmo).value
dist_mod = 5.0 * (np.log10(ld * 1000.0 * 1000.0) - 1.0)
return dist_mod
0.15671181
] #, 0.03627285 -0.05957562 -0.13237366 -0.17996786 -0.21153889 -0.23183063]
nhi = [
14.06075461, 13.56412484, 13.03211818, 12.44580853, 11.79029004,
11.080321, 10.33237421, 9.55585859, 8.75205882, 7.95434865, 7.16719688,
6.40544992, 5.67945472, 5.01192144, 4.39851996, 3.83386894, 3.33763753,
2.89468833, 2.50068819
] #, 2.15612715, 1.85457562, 1.59877366, 1.38206786, 1.18913889, 1.02633063]
mstars = [
1.00000000e+03, 1.46779927e+03, 2.15443469e+03, 3.16227766e+03,
4.64158883e+03, 6.81292069e+03, 1.00000000e+04, 1.46779927e+04,
2.15443469e+04, 3.16227766e+04, 4.64158883e+04, 6.81292069e+04,
1.00000000e+05, 1.46779927e+05, 2.15443469e+05, 3.16227766e+05,
4.64158883e+05, 6.81292069e+05, 1.00000000e+06
] #, 1.46779927e+06, 2.15443469e+06, 3.16227766e+06, 4.64158883e+06, 6.81292069e+06, 1.00000000e+07] #[1e3, 1e4, 1e5, 1e6]
Mvs = [np.log10(m / 3.2e9) * -2.5 + -18.8 for m in mstars]
print len(mstars), len(Mvs), len(nlums)
#shortened lists
Mvs2 = [
np.log10(1e3 / 3.2e9) * -2.5 + -18.8,
np.log10(1e4 / 3.2e9) * -2.5 + -18.8,
np.log10(1e5 / 3.2e9) * -2.5 + -18.8,
np.log10(1e6 / 3.2e9) * -2.5 + -18.8
]
nlums2 = np.array([nlums[0], nlums[6], nlums[12], nlums[18]])
print Mvs2, nlums2
nlos2 = np.array([nlo[0], nlo[6], nlo[12], nlo[18]])
nhis2 = np.array([nhi[0], nhi[6], nhi[12], nhi[18]])
print nhis2 - nlums2
print nlums2 - nlos2
def main():
savepath = '/scratch/dac29/output/processed_data/berlind_groupcat/mock_runs/4th_run/custom_catalogues/'
#############################################################################################
catalogue = sys.argv[1]
#open the mock group cat
filepath = cu.get_output_path(
) + 'processed_data/berlind_groupcat/mock_runs/4th_run/'
catalogue_1 = catalogue + '_radec_mock'
f = h5py.File(filepath + catalogue_1 + '.hdf5', 'r')
GC = f.get(catalogue_1)
GC = np.array(GC)
print 'length:', len(GC)
for name in GC.dtype.names:
print '\t', name
#open the true groups
filepath = cu.get_output_path(
) + 'processed_data/hearin_mocks/custom_catalogues/'
catalogue_2 = catalogue
f = h5py.File(filepath + catalogue_2 + '.hdf5', 'r')
mock = f.get(catalogue_2)
mock = np.array(mock)
print 'length:', len(mock)
for name in mock.dtype.names:
print '\t', name
#open the ra,dec mock fed into the group finder
filepath = cu.get_output_path(
) + 'processed_data/hearin_mocks/custom_catalogues/'
filename = catalogue + '_radec_mock.dat'
mock_radec = ascii.read(filepath + filename,
delimiter='\s',
Reader=ascii.Basic,
data_start=1)
print 'length:', len(mock_radec)
print mock_radec
mock_radec = np.array(mock_radec)
#############################################################################################
#define some things....
c = 299792.458 #km/s
cosmo = cosmology.FlatLambdaCDM(H0=100, Om0=0.27) #h=1
Omega_m = 0.27
z_upper_lim = 0.068
z_lower_lim = 0.020
#create a new catalogue to store results
dtype=[('ID','>i8'),('k_1','>i8'),('k_2','>i8'),('RA','>f8'),('DEC','>f8'),('Z','>f8'),('red','>i8'),\
('M_u,0.1','>f8'),('M_g,0.1','>f8'),('M_r,0.1','>f8'),('M_i,0.1','>f8'),('M_z,0.1','>f8'),('MSTAR','>f8'),\
('GROUP_ID','>i8'),('MGROUP','>f8'),('ZGROUP','>f8'),('R200','>f8'),\
('CEN_IND','>i8'),('RANK','>i8'),('RPROJ','>f8'),('N_sat','>i8'),('N_sat_red','>i8'),('N_sat_blue','>i8'),\
('HALO_M','>f8'),('HALO_RANK','>i8')]
dtype = np.dtype(dtype)
data = np.recarray((len(GC), ), dtype=dtype)
data.fill(-99.9) #empty value indicator
#catalgues matched by row index
data['GROUP_ID'] = GC['IDgroup']
#caclulate index into ra-dec mock file
index = np.argsort(mock_radec['ID'])
sorted_x = mock_radec['ID'][index]
ind = np.searchsorted(sorted_x, GC['IDgal'])
ind = index[ind]
#grab data from ra-dec mock
data['k_1'] = ind
data['ID'] = mock_radec['ID'][ind]
data['RA'] = mock_radec['ra'][ind]
data['DEC'] = mock_radec['dec'][ind]
data['Z'] = mock_radec['z'][ind]
#calculate index into xyz mock
ind = mock_radec['k'][ind]
#grab values from xyz mock
data['k_2'] = ind
data['M_g,0.1'] = mock['M_r,0.1'][ind] + mock['g-r'][ind]
data['M_r,0.1'] = mock['M_r,0.1'][ind]
data['HALO_M'] = mock['M200b_host'][ind]
#determine cen/sat designation in xyz mock
result = np.where(mock['ID_host'][ind] == -1)[0]
data['HALO_RANK'][result] = 1 #central
result = np.where(mock['ID_host'][ind] != -1)[0]
data['HALO_RANK'][result] = 0 #satellite
#calculate galaxy colors
color = data['M_g,0.1'] - data['M_r,0.1']
LHS = 0.7 - 0.032 * (data['M_r,0.1'] + 16.5) #Weinmann 2006
blue = np.where(color < LHS)[0] #indices of blue galaxies
red = np.where(color > LHS)[0] #indicies of red galaxies
#record color designation
data['red'][red] = 1
data['red'][blue] = 0
for i in range(0, len(data)):
group_id = data['GROUP_ID'][i]
members = np.where(data['GROUP_ID'] == group_id)[0]
central = np.where(
data['M_r,0.1'][members] == min(data['M_r,0.1'][members]))[0][0]
central = members[central]
satellites = np.where(members != central)[0]
satellites = members[satellites]
#record rank
data['RANK'][central] = 1
data['RANK'][satellites] = 0
#record number of satellites in the group
data['N_sat'][members] = len(satellites)
sat_red = np.where(np.in1d(satellites, red) == True)[0]
data['N_sat_red'][members] = len(sat_red)
sat_blue = np.where(np.in1d(satellites, blue) == True)[0]
data['N_sat_blue'][members] = len(sat_blue)
#record other group information
data['CEN_IND'][members] = central
data['ZGROUP'][members] = data['Z'][central]
#calculate projected distance from central
da = cu.spheredist(data['RA'][central], data['DEC'][central],
data['RA'][members], data['DEC'][members])
da = np.radians(da) #convert to radians
chi = cosmology.funcs.comoving_distance(
data['ZGROUP'][central], cosmo=cosmo).value * 1000.0 #in kpc
data['RPROJ'][members] = chi / (
1.0 + data['ZGROUP'][members]) * da #caclulate physical seperation
data['RPROJ'][central] = 0.0 #==0 if it is the central
for i in range(0, len(data)):
group_id = data['GROUP_ID'][i]
members = np.where(data['GROUP_ID'] == group_id)[0]
central = np.where(
data['M_r,0.1'][members] == min(data['M_r,0.1'][members]))[0][0]
central = members[central]
data['CEN_IND'][members] = central
#read in mass halo function
filepath = '/scratch/dac29/fortran_code/mass_functions/'
filename = 'Bolshoi_Massfunc.dat'
names = ['dM', 'dn', 'nsum']
dndM = ascii.read(filepath + filename,
delimiter='\s',
names=names,
data_start=0)
dndM = np.array(dndM)
#idenditify centrals and satellites
centrals = np.where(data['RPROJ'] == 0)[0]
satellites = np.where(data['RPROJ'] > 0)[0]
#calculate group total r-band luminosities
S_r = 4.64
group_L = np.zeros((len(data), ), dtype=np.float)
for i in range(0, len(centrals)):
gal = np.where(data['GROUP_ID'] == data['GROUP_ID'][centrals[i]])[0]
group_L[gal] = np.log10(
np.sum(10.0**(solar_lum(data['M_r,0.1'][gal], S_r))))
tot_lum = group_L[centrals]
#calculate abundance matched masses for groups
geo_f = 1.0 / 8.0 #gemoetric factor: spherical octant
r_max = cosmology.funcs.comoving_distance(z_upper_lim,
cosmo=cosmo).value #in Mpc
r_min = cosmology.funcs.comoving_distance(z_lower_lim,
cosmo=cosmo).value #in Mpc
mock_volume = (4.0 / 3.0) * math.pi * (r_max**3.0 - r_min**3) * geo_f
#caclulate the group luminosity function
N_gal = np.cumsum(np.zeros(len(centrals)) +
1) #cumulative number of groups
n_gal = N_gal / mock_volume #number density
L_gal = np.sort(tot_lum)[::-1] #group luminosity
ind = np.argsort(tot_lum)[::-1]
#integrate halo mass function
n_halo = dndM['nsum'][::-1] #cumulative number desnity
M_halo = dndM['dM'][::-1] #halo mass
#interpolate the halo mass function
x = np.log10(n_halo)
y = M_halo
f = interpolate.interp1d(x,
y,
kind='cubic',
bounds_error='False',
fill_value=0.0)
data['MGROUP'][centrals[ind]] = f(np.log10(n_gal))
for i in range(0, len(centrals)):
gal = np.where(data['GROUP_ID'] == data['GROUP_ID'][centrals[i]])[0]
data['MGROUP'][gal] = data['MGROUP'][centrals[i]]
R_200 = 258.1 * (10.0**data['MGROUP'] / (10.0**12.0))**(1.0 / 3.0) * (
Omega_m / 0.25)**(1.0 / 3.0) * (1.0 + data['ZGROUP'])**(-1.0)
data['R200'] = R_200
print 'saving hdf5 version of the catalogue...'
filename = catalogue + '_groups'
f = h5py.File(savepath + filename + '.hdf5', 'w')
dset = f.create_dataset(filename, data=data)
f.close()
print 'saving ascii version of the catalogue...'
data_table = table.table.Table(data=data)
ascii.write(data_table, savepath + filename + '.dat')
print data_table
cosmology.Dinterp[auxcut] / params.boxsize)
# Check which replications are compressed by the lens
replicationsinside = geometry[(geometry['nearestpoint'] < dlsup *
(1 + params.beta_buffer))
& (geometry['farthestpoint'] >= dlinf *
(1 - params.beta_buffer))]
if not rank:
print(" Replications inside:")
# Loop on the replications
for ii, repi in enumerate(replicationsinside):
if not rank:
print(" * Replication [{}/{}] of snap [{}/{}] {} {} {} "\
.format( str(ii + 1).zfill(int(np.log10(replicationsinside.size) + 1)), replicationsinside.size,
str(snapnum + 1).zfill(int(np.log10(params.numfiles) + 1)), params.numfiles,
repi['x'], repi['y'], repi['z']))
# Set the 1st guess for plc-crossing to a-collapse
aplcslicei = np.copy(aplcslice)
aplcslicei[Zaccslice != -1] = 1.0 / (Zaccslice[Zaccslice != -1] +
1)
aplcslicei[Zaccslice == -1] = 1.0
# Position shift of the replication
shift = (np.array(repi[['x', 'y', 'z']].tolist()).dot(
params.change_of_basis)).astype(np.float32)
# Get the scale parameter of the moment that the particle crossed the PLC
if not rank:
t0 = time()
