def __init__(self, **kwargs):
Matter.__init__(self, **kwargs)
self.accepted_kwargs = {'world': None,
'coordinate_key': '0_0_0',
'impassible': True,
'layer': 1.2,
'float_offset': plist([0.5, 0.5]),
'controllable': False
}
for key in self.accepted_kwargs.keys():
if key in kwargs.keys():
self.__setattr__(key, kwargs[key])
else:
self.__setattr__(key, self.accepted_kwargs[key])
#Render related local variables..
self.width = sprite_manifest[self.image_key].frame_width
self.height = sprite_manifest[self.image_key].frame_height
self.tall = self.height
self.frame = 0 #the rendered last frame in a "strip" of frames
self.facing = 5
self.pixel_offsets = self.determine_pixel_offset()
#Thresholds for changes in milliseconds
#Thresholds for changes in milliseconds
self.move_threshold = 500
self.frame_threshold = self.move_threshold/5
self.tick_accumulator = 0
self.move_accumulator = 0
self.path = None
def set_universe(self, Om=0.3, OL=0.7, ns=0.96,
sig_8=0.81, h=1.0, T_cmb=2.725, h_transf=0.7,
k=None, k_min=1.e-3, k_max=2.e3, kbins=1000,
lnM_min=np.log(1e11), lnM_max=np.log(1e15),
transfer_fit="EH",
hmf_fit="Tinker",
bias_fit="Tinker"):
"""
Set the cosmological parameters and fitting functions used for the
power spectrum calculation. This attribute is an instance of the
Matter class defined in matter.py, which has functions for computing
the required dark matter statistics.
"""
self.universe = Matter(Om=Om, OL=OL, ns=ns,
sig_8=sig_8, h=h, T_cmb=T_cmb,
h_transf=h_transf,
k=k,
k_min=k_min, k_max=k_max, kbins=kbins,
lnM_min=lnM_min, lnM_max=lnM_max,
lnMbins=1000,
transfer_fit=transfer_fit,
hmf_fit=hmf_fit,
bias_fit=bias_fit)
self.lnm = self.universe.lnM
def __init__(self, **kwargs):
Matter.__init__(self, **kwargs)
self.accepted_kwargs = {'tall': 0, 'float_offset': plist([0.5, 0.5]), 'layer': 1.5,
'frame': (0, 0), 'weight' : 0.0, 'use_sound' : 'explosion.ogg'}
for key in self.accepted_kwargs.keys():
if key in kwargs.keys():
self.__setattr__(key, kwargs[key])
else:
self.__setattr__(key, self.accepted_kwargs[key])
def __init__(self, *args, **kwargs):
""" Initialization of object """
self.volume = '0 mL' # volume of solution
Matter.__init__(self, *args, **kwargs) # update with arguments
self.update(*args, **kwargs) # update object attributes
self.features += ['volume'] # add printed attributes
def __init__(self, **kwargs):
Matter.__init__(self, **kwargs)
self.accepted_kwargs = {'speedModifier': 1.0, 'layer': 0.1, 'pathable': True}
for key in self.accepted_kwargs.keys():
if key in kwargs.keys():
self.__setattr__(key, kwargs[key])
else:
self.__setattr__(key, self.accepted_kwargs[key])
#No Tiles offset. Would create gaps. Only here as placeholder values.
self.float_offset = plist([0.0,0.0])
self.pixel_offsets = plist([0, 0])
def __init__(self,*args,**kwargs):
""" Initialization of object """
self.species = '' # species of population
self.count = 0 # cell count
self.contents = [Sequence(name='gDNA',form='genomic')] # contents of cell
Matter.__init__(self) # update with arguments
self.update(*args,**kwargs) # update object attributes
self.features += ['species','count'] # add printed attributes
def __init__(self, *args, **kwargs):
""" Initialization of object """
self.contents = [] # list to fill with matter
self.instructions = '' # preparation instructions
self.reagents = {} # reagents log
Matter.__init__(self) # update with arguments
Mixture.__init__(self) # update with arguments
self.update(*args, **kwargs) # update object attributes
# list of features to print out on call
self.features += ['instructions']
def __init__(self, *args, **kwargs):
""" Initialization of object """
self.container = '' # container for sample
self.contents = [] # list to fill with matter
Matter.__init__(self) # update with arguments
Mixture.__init__(self) # update with arguments
self.update(*args, **kwargs) # update object attributes
self.volume = self.volume
# list of features to print out on call
self.features += ['container']
def __init__(self, *args, **kwargs):
""" Initialization of object """
self.sequence = '' # species of population
self.codon_set = 'standard' # codon set (only supported: standard)
self.elements = {} # elements to display in your sequence
self.material = 'dsDNA' # dsDNA,ssDNA,dsRNA,ssRNA
self.form = 'plasmid' # plasmid,genomic
self.shape = 'linear' # linear,circular
Matter.__init__(self) # add class features
Solute.__init__(self) # add class features
self.update(*args, **kwargs) # update object attributes
self.features += ['material', 'total_volume'] # add printed attributes
def __init__(self, **kwargs):
Matter.__init__(self, **kwargs)
self.accepted_kwargs = {'tall': 0,
'float_offset': plist([0.5, 0.5]),
'float_offset_ranges': plist(((0.25, 0.75),(0.25, 0.75))),
'speed_modifier': 1.0,
'layer': 1.0,
'impassible': False,
'blocksLOS': False
}
for key in self.accepted_kwargs.keys():
if key in kwargs.keys():
self.__setattr__(key, kwargs[key])
else:
self.__setattr__(key, self.accepted_kwargs[key])
self.pixel_offsets = self.determine_pixel_offset()
def __init__(self,*args,**kwargs):
""" Initialization of object """
self.molecular_weight = 0 # molecular weight
self._mass = 0 # mass of solute
self._moles = 0 # mols of solute
self._total_volume = 0 # hidden variable, for translating conc.
self._concentration = 0 # mass/volume of solute
self._molarity = 0 # mols/volume of solute
Matter.__init__(self) # update with arguments
self.update(*args,**kwargs) # update object attributes
# add printed attributes
self.features += ['molecular_weight','mass','moles','concentration','molarity']
import time
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import matplotlib.cm as cmx
from mpl_toolkits.mplot3d import Axes3D
from matter import Matter
testmat = Matter()
zs = np.arange(0, 2, 0.1)
cmap = plt.get_cmap("summer")
cNorm = colors.Normalize(vmin=np.min(zs), vmax=np.max(zs))
scalarMap = cmx.ScalarMappable(norm=cNorm, cmap=cmap)
# # test transfer function
# testmat.incl_baryons = False
# transfnc_nobaryons = testmat.T()
# testmat.incl_baryons = True
# transfnc = testmat.T()
# fig = plt.figure()
# ax = fig.add_subplot(111)
# ax.loglog(testmat.k, transfnc, 'b', testmat.k, transfnc_nobaryons, 'r')
# fig.savefig("transfncs.pdf")
#
# fig = plt.figure()
# ax = fig.add_subplot(111)
# ax.loglog(testmat.k, transfnc - transfnc_nobaryons)
# fig.savefig("transfnc_diff.pdf")
#
import time
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import matplotlib.cm as cmx
from mpl_toolkits.mplot3d import Axes3D
from matter import Matter
testmat = Matter()
zs = np.arange(0, 2, 0.1)
cmap = plt.get_cmap("summer")
cNorm = colors.Normalize(vmin=np.min(zs), vmax=np.max(zs))
scalarMap = cmx.ScalarMappable(norm=cNorm, cmap=cmap)
# # test transfer function
# testmat.incl_baryons = False
# transfnc_nobaryons = testmat.T()
# testmat.incl_baryons = True
# transfnc = testmat.T()
# fig = plt.figure()
# ax = fig.add_subplot(111)
# ax.loglog(testmat.k, transfnc, 'b', testmat.k, transfnc_nobaryons, 'r')
# fig.savefig("transfncs.pdf")
#
# fig = plt.figure()
# ax = fig.add_subplot(111)
# ax.loglog(testmat.k, transfnc - transfnc_nobaryons)
# fig.savefig("transfnc_diff.pdf")
class Pwspec:
"""
Object class for computing the analytic galaxy power spectrum as in the
appendix to Schneider et al, 2006 and Van der Bosch et al, 2013.
"""
def __init__(self, zvec, k=None, Mmin=1e11, Mmax=1e15):
"""
- k is a 1-d numpy array of wavenumbers. (unit = Mpc^-1)
- zvec is 1-d array of central values of the redshift bins
- Mmin (Mmax) is the minimum (maximum) halo mass. (unit = Msun/h)
"""
self.k = k
self.zvec = zvec
# self.lnm = np.logspace(np.log(Mmin), np.log(Mmax), base=np.exp(1))
self.set_universe()
self.precompute()
def set_universe(self, Om=0.3, OL=0.7, ns=0.96,
sig_8=0.81, h=1.0, T_cmb=2.725, h_transf=0.7,
k=None, k_min=1.e-3, k_max=2.e3, kbins=1000,
lnM_min=np.log(1e11), lnM_max=np.log(1e15),
transfer_fit="EH",
hmf_fit="Tinker",
bias_fit="Tinker"):
"""
Set the cosmological parameters and fitting functions used for the
power spectrum calculation. This attribute is an instance of the
Matter class defined in matter.py, which has functions for computing
the required dark matter statistics.
"""
self.universe = Matter(Om=Om, OL=OL, ns=ns,
sig_8=sig_8, h=h, T_cmb=T_cmb,
h_transf=h_transf,
k=k,
k_min=k_min, k_max=k_max, kbins=kbins,
lnM_min=lnM_min, lnM_max=lnM_max,
lnMbins=1000,
transfer_fit=transfer_fit,
hmf_fit=hmf_fit,
bias_fit=bias_fit)
self.lnm = self.universe.lnM
def precompute(self):
"""
Using the k-vector, redshift bins and mass range given to the Pwspec
object, this function precomputes a list for the redshift values of
halo mass functions, NFW fourier transforms and halo biases for use in
computing the galaxy power spectra for various HOD models. These are
computed using functions from the Matter class which the universe
attribute is an instance of.
"""
if not self.universe:
print "You must first set the universe parameters"
self.hmflist = []
self.uglist = []
self.biaslist = []
for z in self.zvec:
self.hmflist.append(self.universe.hmf(z))
self.uglist.append(self.universe.u_g(z))
self.biaslist.append(self.universe.bias(z))
def set_HOD(self, params):
"""
expects iterable of parameter values in the form
[Mmin, siglogm, alpha, M_1, Mcut]
where masses are in log10
"""
self.HOD = params
self.compute_nbarlist()
def compute_nbarlist(self):
"""
Use the halo mass function and HOD parameters to compute the galaxy
number density at a given redshift.
"""
self.nbarlist = []
for z in self.zvec:
self.nbarlist.append(nbar_g(self.universe.lnM, self.get_hmf(z), self.HOD))
def zind(self, z):
return np.where(self.zvec == z)[0]
def get_nbar(self, z):
return self.nbarlist[self.zind(z)]
def get_hmf(self, z):
return self.hmflist[self.zind(z)]
def get_ug(self, z):
return self.uglist[self.zind(z)]
def get_Plin(self, z1, z2):
"""
Compute variance per logarithmic interval in k as per Schneider et al
"""
g1 = self.universe.gf(z1)
g2 = self.universe.gf(z2)
psp = self.universe.normal_p0_lin()
return g1 * g2 * psp
def get_bias(self, z):
return self.biaslist[self.zind(z)]
def _1h_int(self, z, k_i):
"""
The integrand for the 1-halo term of the galaxy power spectrum.
"""
return self.get_hmf(z) * \
(N_sat(np.exp(self.lnm), self.HOD) ** 2 * \
self.get_ug(z)[k_i, :] ** 2 + \
2 * N_cen(np.exp(self.lnm), self.HOD) * \
N_sat(np.exp(self.lnm), self.HOD) * \
self.get_ug(z)[k_i, :])
def P_1h(self, z1, z2):
"""
1-halo term in the galaxy power spectrum
"""
if z1 != z2:
return 0.
else:
plist = []
for i in range(len(self.universe.k)):
plist.append((1. / self.get_nbar(z1) ** 2) * \
inty(self._1h_int(z1, i), self.lnm))
return np.array(plist)
def _I2inty(self, z, k_i):
"""
The integrand for the 2-halo term of the galaxy power spectrum.
"""
return self.get_hmf(z) * self.get_bias(z) * \
(N_cen(np.exp(self.lnm), self.HOD) + \
N_sat(np.exp(self.lnm), self.HOD) * self.get_ug(z)[k_i, :])
def I_2(self, z):
"""
Integral 2-halo term in the galaxy power spectrum
"""
ilist = []
for i in range(len(self.universe.k)):
ilist.append((1. / self.get_nbar(z)) * \
inty(self._I2inty(z, i), self.lnm))
return np.array(ilist)
def P_2h(self, z1, z2):
"""
2-halo term in the galaxy power spectrum
"""
# TODO : after finishing matter.py, modify this accordingly
return self.get_Plin(z1, z2) * self.I_2(z1) * self.I_2(z2)
def P_g(self, z1, z2):
"""
Galaxy power spectrum
Auto (Cross) power spectrum if z1=z2(z1!=z2)
"""
if not (z1 in self.zvec) * (z2 in self.zvec):
raise ValueError("These redshifts are not in the precomputed redshift values")
return self.P_1h(z1, z2) + self.P_2h(z1, z2)
