def caustic_stack(self,Rdata,Vdata,HaloID,HaloData,stack_num,
ens_shiftgap=True,edge_int_remove=True,gal_reduce=True,stack_raw=False,est_v_center=False,
feed_mags=True,G_Mags=None,R_Mags=None,I_Mags=None,clus_z=0):
"""
-- Takes an array of individual phase spaces and stacks them, then runs
a caustic technique over the ensemble and/or individual phase spaces.
-- Returns a dictionary
-- Relies on a few parameters to be defined outside of the function:
self.gal_num - Equivalent to Ngal: number of galaxies to take per cluster to then be stacked
self.line_num - Equivalent to Nclus: number of clusters to stack into one ensemble cluster
self.scale_data - Scale r data by R200 while stacking, then un-scale by BinR200
self.run_los - run caustic technique over individual cluster (aka line-of-sight)
self.avg_meth - method by which averaging of Bin Properties should be, 'mean' or 'median' or 'biweight' etc..
self.mirror - mirror phase space before solving for caustic?
Including others... see RunningTheCode.pdf for a list
* These parameters should be fed to initialization of Stack() class as a dictionary, for ex:
variables = {'run_los':False, ...... }
S = Stack(variables)
"rdata" - should be a 2 dimensional array with individual phase spaces as rows
"vdata" - should be a 2 dimensional array with individual phase spaces as rows
ex. rdata[0] => 0th phase space data
'HaloID' : 1 dimensional array containing Halo Identification Numbers, len(HaloID) == len(rdata)
'HaloData' : 2 dimensional array containing M200, R200, HVD, Z of Halos, with unique halos as columns
'stack_num' : number of individual clusters to stack into the one ensemble
'ens_shiftgap' - do a shiftgapper over final ensemble phase space?
'gal_reduce' - before caustic run, reduce ensemble phase space to Ngal gals within R200?
'stack_raw' - don't worry about limiting or building the phase space, just stack the Rdata and Vdata together as is
'est_v_center' - take median of Vdata for new velocity center
'feed_gal_mags' - feed magnitudes for individual galaxies, must feed all three mags if True
-- 'ens' stands for ensemble cluster
-- 'ind' stands for individual cluster
-- Uppercase arrays contain data for multiple clusters,
lowercase arrays contain data for 1 cluster
"""
# Define a container for holding stacked data, D
D = Data()
# Assign some parameters to Class scope
self.__dict__.update(ez.create(['stack_raw','feed_mags','gal_reduce','ens_shiftgap','edge_int_remove'],locals()))
# New Velocity Center
if est_v_center == True:
v_offset = astats.biweight_location(vdata[np.where(rdata < 1.0)])
vdata -= v_offset
# Unpack HaloData
if HaloData == None:
self.fed_halo_data = False
# Estimate R200
R200 = []
HVD = []
Z = []
for i in range(stack_num):
R200.append(np.exp(-1.86)*len(np.where((R_Mags[i] < -19.55) & (Rdata[i] < 1.0) & (np.abs(Vdata[i]) < 3500))[0])**0.51)
HVD.append(astats.biweight_midvariance(Vdata[i][np.where((Rdata[i] < 1.0)&(np.abs(Vdata[i])<4000))]))
R200 = np.array(R200)
HVD = np.array(HVD)
Z = np.array([0.05]*len(R200))
if self.avg_meth == 'mean': BinR200 = np.mean(R200); BinHVD = np.mean(HVD); BinZ = np.mean(Z)
elif self.avg_meth == 'median': BinR200 = np.median(R200); BinHVD = np.median(HVD); BinZ = np.median(Z)
D.add({'BinR200':BinR200,'BinHVD':BinHVD,'BinZ':BinZ,'R200':R200,'HVD':HVD,'Z':Z})
else:
self.fed_halo_data = True
M200,R200,HVD,Z = HaloData
if self.avg_meth == 'mean':
BinM200 = np.mean(M200)
BinR200 = np.mean(R200)
BinHVD = np.mean(HVD)
BinZ = np.mean(Z)
elif self.avg_meth == 'median':
BinM200 = np.median(M200)
BinR200 = np.median(R200)
BinHVD = np.median(HVD)
BinZ = np.median(Z)
# Append to Data
D.add({'BinM200':BinM200,'BinR200':BinR200,'BinHVD':BinHVD,'BinZ':BinZ})
# Create Dummy Variables for Magnitudes if necessary
if self.feed_mags == False:
G_Mags,R_Mags,I_Mags = [],[],[]
for i in range(stack_num):
G_Mags.append([None]*len(Rdata[i]))
R_Mags.append([None]*len(Rdata[i]))
I_Mags.append([None]*len(Rdata[i]))
G_Mags,R_Mags,I_Mags = np.array(G_Mags),np.array(R_Mags),np.array(I_Mags)
# Create galaxy identification arrays
ENS_gal_id,ENS_clus_id,IND_gal_id = [],[],[]
gal_count = 0
for i in range(stack_num):
ENS_gal_id.append(np.arange(gal_count,gal_count+len(Rdata[i])))
ENS_clus_id.append(np.array([HaloID[i]]*len(Rdata[i]),int))
IND_gal_id.append(np.arange(len(Rdata[i])))
ENS_gal_id,ENS_clus_id,ENS_gal_id = np.array(ENS_gal_id),np.array(ENS_clus_id),np.array(IND_gal_id)
# Iterate through phase spaces
for self.l in range(stack_num):
# Limit Phase Space
if self.stack_raw == False:
r,v,ens_gal_id,ens_clus_id,ind_gal_id,gmags,rmags,imags,samp_size = self.U.limit_gals(Rdata[self.l],Vdata[self.l],ENS_gal_id[self.l],ENS_clus_id[self.l],IND_gal_id[self.l],G_Mags[self.l],R_Mags[self.l],I_Mags[self.l],R200[self.l])
# Build Ensemble and LOS Phase Spaces
if self.stack_raw == False:
ens_r,ens_v,ens_gal_id,ens_clus_id,ens_gmags,ens_rmags,ens_imags,ind_r,ind_v,ind_gal_id,ind_gmags,ind_rmags,ind_imags = self.U.build(r,v,ens_gal_id,ens_clus_id,ind_gal_id,gmags,rmags,imags,R200[self.l])
# If Scale data before stack is desired
if self.scale_data == True:
ens_r /= R200[self.l]
# Stack Ensemble Data by extending to Data() container
names = ['ens_r','ens_v','ens_gmags','ens_rmags','ens_imags','ens_gal_id','ens_clus_id']
D.extend(ez.create(names,locals()))
if self.run_los == True:
# Create Data Block
ind_data = np.vstack([ind_r,ind_v,ind_gal_id,ind_gmags,ind_rmags,ind_imags])
# Sort by Rmag
bright = np.argsort(ind_rmags)
ind_data = ind_data.T[bright].T
ind_r,ind_v,ind_gal_id,ind_gmags,ind_rmags,ind_imags = ind_data
# Reduce phase space
if self.stack_raw == False and self.gal_reduce == True:
within = np.where(ind_r <= R200[self.l])[0]
end = within[:self.gal_num + 1][-1]
ind_data = ind_data.T[:end].T
ind_r,ind_v,ind_gal_id,ind_gmags,ind_rmags,ind_imags = ind_data
# Calculate individual HVD
# Pick out gals within r200
within = np.where(ind_r <= R200[self.l])[0]
gal_count = len(within)
if gal_count <= 3:
'''biweightScale can't take less than 4 elements'''
# Calculate hvd with numpy std of galaxies within r200 (b/c this is quoted richness)
ind_hvd = np.std(np.copy(ind_v)[within])
else:
# Calculate hvd with astStats biweightScale (see Beers 1990)
try:
ind_hvd = astats.biweight_midvariance(np.copy(ind_v)[within])
# Sometimes divide by zero error in biweight function for low gal_num
except ZeroDivisionError:
print 'ZeroDivisionError in biweightfunction'
print 'ind_v[within]=',ind_v[within]
ind_hvd = np.std(np.copy(ind_v)[within])
# If run_los == True, run Caustic Technique on individual cluster
self.U.print_separation('# Running Caustic for LOS '+str(self.l),type=2)
self.run_caustic(ind_r,ind_v,R200[self.l],ind_hvd,clus_z=Z[self.l],mirror=self.mirror)
ind_caumass = np.array([self.C.M200_fbeta])
ind_caumass_est = np.array([self.C.Mass2.M200_est])
ind_edgemass = np.array([self.C.M200_edge])
ind_edgemass_est = np.array([self.C.MassE.M200_est])
ind_causurf = np.array(self.C.caustic_profile)
ind_nfwsurf = np.array(self.C.caustic_fit)
ind_edgesurf = np.array(self.C.caustic_edge)
# Append Individual Cluster Data
names = ['ind_r','ind_v','ind_gal_id','ind_gmags','ind_rmags','ind_imags',
'ind_hvd','ind_caumass','ind_caumass_est','ind_edgemass','ind_edgemass_est',
'ind_causurf','ind_nfwsurf']
D.append(ez.create(names,locals()))
# Turn Ensemble into Arrays
names = ['ens_r','ens_v','ens_gal_id','ens_clus_id','ens_gmags','ens_rmags','ens_imags','ens_caumass','ens_caumass_est','ens_edgemass','ens_edgemass_est','ens_causurf','ens_nfwsurf','ens_edgesurf']
D.to_array(names,ravel=True)
# Re-scale data if scale_data == True:
if self.scale_data == True:
D.ens_r *= BinR200
# Create Ensemble Data Block
D.ens_data = np.vstack([D.ens_r,D.ens_v,D.ens_gal_id,D.ens_clus_id,D.ens_gmags,D.ens_rmags,D.ens_imags])
# Shiftgapper for Interloper Treatment
if self.stack_raw == False and self.ens_shiftgap == True:
self.D = D
try:
D.ens_data = self.C.shiftgapper(D.ens_data.T).T
D.ens_r,D.ens_v,D.ens_gal_id,D.ens_clus_id,D.ens_gmags,D.ens_rmags,D.ens_imags = D.ens_data
except UnboundLocalError: # A couple or no galaxies within RVIR
print '-'*40
print 'UnboundLocalError raised on Ensemble Shiftgapper'
print '-'*40
D.ens_r,D.ens_v,D.ens_gal_id,D.ens_clus_id,D.ens_gmags,D.ens_rmags,D.ens_imags = D.ens_data
# Sort by R_Mag
bright = np.argsort(D.ens_rmags)
D.ens_data = D.ens_data.T[bright].T
D.ens_r,D.ens_v,D.ens_gal_id,D.ens_clus_id,D.ens_gmags,D.ens_rmags,D.ens_imags = D.ens_data
# Reduce System Down to gal_num richness within BinR200
if self.stack_raw and self.gal_reduce == True:
within = np.where(D.ens_r <= BinR200)[0]
print 'len(within)',len(within)
print 'gal_num,line_num',self.gal_num,self.line_num
end = within[:self.gal_num*self.line_num + 1][-1]
D.ens_data = D.ens_data.T[:end].T
D.ens_r,D.ens_v,D.ens_gal_id,D.ens_clus_id,D.ens_gmags,D.ens_rmags,D.ens_imags = D.ens_data
# Calculate Ensemble Velocity Dispersion for galaxies within R200
ens_hvd = astats.biweight_midvariance(np.copy(D.ens_v)[np.where(D.ens_r<=BinR200)])
# Run Caustic Technique!
try: self.U.print_separation('# Running Caustic on Ensemble '+str(self.j),type=2)
except: pass
try:
self.run_caustic(D.ens_r,D.ens_v,BinR200,ens_hvd,clus_z=BinZ,mirror=self.mirror,shiftgap=self.ens_shiftgap,edge_int_remove=self.edge_int_remove)
ens_caumass = np.array([self.C.M200_fbeta])
ens_caumass_est = np.array([self.C.Mass2.M200_est])
ens_edgemass = np.array([self.C.M200_edge])
ens_edgemass_est = np.array([self.C.MassE.M200_est])
ens_causurf = np.array(self.C.caustic_profile)
ens_nfwsurf = np.array(self.C.caustic_fit)
ens_edgesurf = np.array(self.C.caustic_edge)
ens_caumass500_est = np.array(self.C.Mass2.M500_est)
ens_edgemass500_est = np.array(self.C.MassE.M500_est)
ens_r200_est = np.array(self.C.r200_est_fbeta)
ens_r500_est = np.array(self.C.r500_est_fbeta)
ens_r200_est_edge = np.array(self.C.r200_est_edge)
except:
print ''
print '-'*45
print 'CAUSTIC TECHNIQUE FAILED ON THIS CLUSTER'
print '-'*45
print ''
ens_caumass = np.array([0])
ens_caumass_est = np.array([0])
ens_edgemass = np.array([0])
ens_edgemass_est = np.array([0])
ens_causurf = np.array([0]*len(self.C.x_range))
ens_nfwsurf = np.array([0]*len(self.C.x_range))
ens_edgesurf = np.array([0]*len(self.C.x_range))
ens_caumass500_est = np.array([0])
ens_edgemass500_est = np.array([0])
ens_r200_est = np.array([0])
ens_r500_est = np.array([0])
ens_r200_est_edge = np.array([0])
# Other Arrays
x_range = self.C.x_range
# Append Data
names = ['ens_caumass','ens_hvd','ens_caumass_est','ens_edgemass','ens_edgemass_est','ens_causurf','ens_nfwsurf','ens_edgesurf','x_range','ens_caumass500_est','ens_edgemass500_est','ens_r200_est','ens_r500_est','ens_r200_est_edge']
D.add(ez.create(names,locals()))
# Turn Individual Data into Arrays
if self.run_los == True:
names = ['ind_caumass','ind_caumass_est','ind_edgemass','ind_edgemass_est','ind_hvd']
D.to_array(names,ravel=True)
names = ['ind_r','ind_v','ind_gal_id','ind_gmags','ind_rmags','ind_imags','ind_causurf','ind_nfwsurf','ind_edgesurf']
D.to_array(names)
# Output Data
return D.__dict__
def stat_calc(self,
MASS_EST,
MASS_TRUE,
HVD_EST,
HVD_TRUE,
data_set='full',
ens=True):
''' Does bias and scatter calculations '''
# Cut data set if necessary
if data_set == 'cut_low_mass':
'''Cutting all 'true' mass estimates below 1e14 off'''
cut = np.where(MASS_TRUE > 1e14)[0]
MASS_EST = MASS_EST[cut]
MASS_TRUE = MASS_TRUE[cut]
HVD_EST = HVD_EST[cut]
HVD_TRUE = HVD_TRUE[cut]
# Define a Masked array for sometimes zero terms
epsilon = 10.0
use_est = False # Use MassCalc estimated r200 mass values if true
maMASS_EST = ma.masked_array(
MASS_EST, mask=MASS_EST < epsilon) # Mask essentially zero values
maHVD_EST = ma.masked_array(HVD_EST, mask=HVD_EST < epsilon)
# Mass / HVD Fractions
if ens == True:
# Ensemble Arrays
MFRAC = np.log(maMASS_EST / MASS_TRUE)
VFRAC = np.log(maHVD_EST / HVD_TRUE)
else:
# LOS Mass Fraction Arrays: 0th axis is halo number, 1st axis is line of sight number
MFRAC, VFRAC = [], []
for a in range(len(MASS_EST)):
MFRAC.append(ma.log(maMASS_EST[a] / MASS_TRUE[a]))
VFRAC.append(ma.log(maHVD_EST[a] / HVD_TRUE[a]))
MFRAC, VFRAC = np.array(MFRAC), np.array(VFRAC)
if ens == True:
mbias, mscat = astrostats.biweight_location(
MFRAC, 6.0), astrostats.biweight_midvariance(MFRAC, 9.0)
vbias, vscat = astrostats.biweight_location(
VFRAC, 6.0), astrostats.biweight_midvariance(VFRAC, 9.0)
return MFRAC, mbias, mscat, VFRAC, vbias, vscat
else:
if self.ss:
# Create vertically averaged (by halo averaged) arrays, with line_num elements
# biweightLocation takes only arrays with 4 or more elements
HORZ_MFRAC, HORZ_VFRAC = [], []
VERT_MFRAC, VERT_VFRAC = [], []
for a in range(self.line_num):
if len(ma.compressed(MFRAC[:, a])) > 4:
VERT_MFRAC.append(
astrostats.biweight_location(
ma.compressed(MFRAC[:, a]), 6.0))
VERT_VFRAC.append(
astrostats.biweight_location(
ma.compressed(VFRAC[:, a]), 6.0))
else:
VERT_MFRAC.append(np.median(ma.compressed(MFRAC[:,
a])))
VERT_VFRAC.append(np.median(ma.compressed(VFRAC[:,
a])))
VERT_MFRAC, VERT_VFRAC = np.array(VERT_MFRAC), np.array(
VERT_VFRAC)
# Create horizontally averaged (by line of sight) arrays, with halo_num elements
for a in self.halo_range:
if len(ma.compressed(MFRAC[a])) > 4:
HORZ_MFRAC.append(
astrostats.biweight_location(
ma.compressed(MFRAC[a]), 6.0))
HORZ_VFRAC.append(
astrostats.biweight_location(
ma.compressed(VFRAC[a]), 6.0))
else:
HORZ_MFRAC.append(np.median(ma.compressed(MFRAC[a])))
HORZ_VFRAC.append(np.median(ma.compressed(VFRAC[a])))
HORZ_MFRAC, HORZ_VFRAC = np.array(HORZ_MFRAC), np.array(
HORZ_VFRAC)
# Bias and Scatter Calculations
mbias, mscat = astrostats.biweight_location(
VERT_MFRAC,
6.0), astrostats.biweight_midvariance(VERT_MFRAC, 9.0)
vbias, vscat = astrostats.biweight_location(
VERT_VFRAC,
6.0), astrostats.biweight_midvariance(VERT_VFRAC, 9.0)
else:
# Bin stack LOS systems need only one average
mbias, mscat = astrostats.biweight_location(
MFRAC, 6.0), astrostats.biweight_midvariance(MFRAC, 9.0)
vbias, vscat = astrostats.biweight_location(
VFRAC, 6.0), astrostats.biweight_midvariance(VFRAC, 9.0)
return MFRAC, mbias, mscat, VFRAC, vbias, vscat
def stat_calc(self,MASS_EST,MASS_TRUE,HVD_EST,HVD_TRUE,data_set='full',ens=True):
''' Does bias and scatter calculations '''
# Cut data set if necessary
if data_set == 'cut_low_mass':
'''Cutting all 'true' mass estimates below 1e14 off'''
cut = np.where(MASS_TRUE>1e14)[0]
MASS_EST = MASS_EST[cut]
MASS_TRUE = MASS_TRUE[cut]
HVD_EST = HVD_EST[cut]
HVD_TRUE = HVD_TRUE[cut]
# Define a Masked array for sometimes zero terms
epsilon = 10.0
use_est = False # Use MassCalc estimated r200 mass values if true
maMASS_EST = ma.masked_array(MASS_EST,mask=MASS_EST<epsilon) # Mask essentially zero values
maHVD_EST = ma.masked_array(HVD_EST,mask=HVD_EST<epsilon)
# Mass / HVD Fractions
if ens == True:
# Ensemble Arrays
MFRAC = np.log(maMASS_EST/MASS_TRUE)
VFRAC = np.log(maHVD_EST/HVD_TRUE)
else:
# LOS Mass Fraction Arrays: 0th axis is halo number, 1st axis is line of sight number
MFRAC,VFRAC = [],[]
for a in range(len(MASS_EST)):
MFRAC.append( ma.log( maMASS_EST[a]/MASS_TRUE[a] ) )
VFRAC.append( ma.log( maHVD_EST[a]/HVD_TRUE[a] ) )
MFRAC,VFRAC = np.array(MFRAC),np.array(VFRAC)
if ens == True:
mbias,mscat = astrostats.biweight_location(MFRAC,6.0),astrostats.biweight_midvariance(MFRAC,9.0)
vbias,vscat = astrostats.biweight_location(VFRAC,6.0),astrostats.biweight_midvariance(VFRAC,9.0)
return MFRAC,mbias,mscat,VFRAC,vbias,vscat
else:
if self.ss:
# Create vertically averaged (by halo averaged) arrays, with line_num elements
# biweightLocation takes only arrays with 4 or more elements
HORZ_MFRAC,HORZ_VFRAC = [],[]
VERT_MFRAC,VERT_VFRAC = [],[]
for a in range(self.line_num):
if len(ma.compressed(MFRAC[:,a])) > 4:
VERT_MFRAC.append( astrostats.biweight_location( ma.compressed( MFRAC[:,a] ), 6.0 ) )
VERT_VFRAC.append( astrostats.biweight_location( ma.compressed( VFRAC[:,a] ), 6.0 ) )
else:
VERT_MFRAC.append( np.median( ma.compressed( MFRAC[:,a] ) ) )
VERT_VFRAC.append( np.median( ma.compressed( VFRAC[:,a] ) ) )
VERT_MFRAC,VERT_VFRAC = np.array(VERT_MFRAC),np.array(VERT_VFRAC)
# Create horizontally averaged (by line of sight) arrays, with halo_num elements
for a in self.halo_range:
if len(ma.compressed(MFRAC[a])) > 4:
HORZ_MFRAC.append( astrostats.biweight_location( ma.compressed( MFRAC[a] ), 6.0 ) )
HORZ_VFRAC.append( astrostats.biweight_location( ma.compressed( VFRAC[a] ), 6.0 ) )
else:
HORZ_MFRAC.append( np.median( ma.compressed( MFRAC[a] ) ) )
HORZ_VFRAC.append( np.median( ma.compressed( VFRAC[a] ) ) )
HORZ_MFRAC,HORZ_VFRAC = np.array(HORZ_MFRAC),np.array(HORZ_VFRAC)
# Bias and Scatter Calculations
mbias,mscat = astrostats.biweight_location(VERT_MFRAC,6.0),astrostats.biweight_midvariance(VERT_MFRAC,9.0)
vbias,vscat = astrostats.biweight_location(VERT_VFRAC,6.0),astrostats.biweight_midvariance(VERT_VFRAC,9.0)
else:
# Bin stack LOS systems need only one average
mbias,mscat = astrostats.biweight_location(MFRAC,6.0),astrostats.biweight_midvariance(MFRAC,9.0)
vbias,vscat = astrostats.biweight_location(VFRAC,6.0),astrostats.biweight_midvariance(VFRAC,9.0)
return MFRAC,mbias,mscat,VFRAC,vbias,vscat
def richness_est(self,
ra,
dec,
z,
pz,
gmags,
rmags,
imags,
abs_rmags,
haloid,
clus_ra,
clus_dec,
clus_z,
clus_rvir=None,
gr_slope=None,
gr_width=None,
gr_inter=None,
shiftgap=True,
use_specs=False,
use_bcg=False,
fit_rs=False,
spec_list=None,
fixed_aperture=False,
fixed_vdisp=False,
plot_gr=False,
plot_sky=False,
plot_phase=False,
find_pairs=True):
''' Richness estimator, magnitudes should be apparent mags except for abs_rmag
z : spectroscopic redshift
pz : photometric redshift
gr_slope : if fed color-mag (g-r vs. r) slope of fit to red sequence
gr_width : if fed color-mag (g-r vs. r) width of fit to red sequence
gr_inter : if red color-mag (g-r vs. r) intercept of fit to red sequence
spec_list : indexing array specifying gals w/ spectroscopic redshifts, preferably fed as boolean numpy array
fixed_aperture : clus_rvir = 1 Mpc
fixed_vdisp : clus_vdisp = 1000 km/s (members < clus_vdisp*2)
use_specs : includes all spectro members in richness regardless of their color, subject to counting twice
use_bcg : use bcg RS_color as cluster RS_color
fit_rs : fit a line to the member galaxy RS relationship, as of now this does not work and we take a flat RS relationship
plot_gr : plot r vs g-r color diagram with RS fits
plot_sky : plot RA and DEC of gals with signal and background annuli
plot_phase : plot rdata and vdata phase space
find_pairs : run c4 cluster pair identifier on phase spaces
- If at least one quarter of the outer annuli doesn't have any galaxies (perhaps because it has run over the observation edge),
it will return -99 as a richness
'''
# Put Into Class Namespace
keys = [
'ra', 'dec', 'z', 'pz', 'gmags', 'rmags', 'imags', 'clus_ra',
'clus_dec', 'clus_z', 'clus_rvir', 'vel_disp', 'color_data',
'color_cut', 'RS_color', 'RS_sigma', 'clus_color_cut', 'signal',
'background', 'richness', 'mems', 'phot', 'spec', 'spec_mems',
'deg_per_rvir', 'SA_outer', 'SA_inner', 'outer_red_dense',
'inner_background', 'Nphot_inner', 'Nphot_outer', 'red_inner',
'red_outer', 'all', 'outer_edge', 'inner_edge', 'shift_cut', 'set',
'pair', 'Nspec', 'gr_slope', 'gr_inter', 'gr_width', 'obs_tot',
'obs_back_scaled'
]
self.__dict__.update(ez.create(keys, locals()))
# Take rough virial radius measurement, this method is BAD...
if clus_rvir == None:
clus_rvir = np.exp(-1.86) * len(
np.where((rmags < -19.55) & (rdata < 1.0)
& (np.abs(vdata) < 3500))[0])**0.51
self.clus_rvir = clus_rvir
# Set clus_rvir = 1.0 Mpc if fixed aperture == True
if fixed_aperture == True:
clus_rvir = 1.0
# Magnitue Cut at 19.1 Apparent R Mag, then at -19 Absolute R Mag and sort by them
bright = np.where(rmags < 19.1)[0]
data = np.vstack([ra, dec, z, pz, gmags, rmags, imags, abs_rmags])
data = data.T[bright].T
ra, dec, z, pz, gmags, rmags, imags, abs_rmags = data
bright = np.where(abs_rmags < -19.5)[0]
data = np.vstack([ra, dec, z, pz, gmags, rmags, imags, abs_rmags])
data = data.T[bright].T
ra, dec, z, pz, gmags, rmags, imags, abs_rmags = data
sorts = np.argsort(abs_rmags)
data = np.vstack([ra, dec, z, pz, gmags, rmags, imags, abs_rmags])
data = data.T[sorts].T
ra, dec, z, pz, gmags, rmags, imags, abs_rmags = data
self.__dict__.update(ez.create(keys, locals()))
# Separate Into Spectro Z and Photo Z DataSets
# Define the Spectro Z catalogue
if spec_list == None:
spec_cut = np.abs(z) > 1e-4
else:
if type(spec_list) == list: spec_list = np.array(spec_list)
if spec_list.dtype != 'bool':
spec_cut = np.array([False] * len(ra))
spec_cut[spec_list] = True
all = {
'ra': ra,
'dec': dec,
'z': z,
'pz': pz,
'gmags': gmags,
'rmags': rmags,
'imags': imags,
'abs_rmags': abs_rmags
}
spec = {
'ra': ra[spec_cut],
'dec': dec[spec_cut],
'z': z[spec_cut],
'pz': pz[spec_cut],
'gmags': gmags[spec_cut],
'rmags': rmags[spec_cut],
'imags': imags[spec_cut],
'abs_rmags': abs_rmags[spec_cut]
}
phot = {
'ra': ra[~spec_cut],
'dec': dec[~spec_cut],
'z': z[~spec_cut],
'pz': pz[~spec_cut],
'gmags': gmags[~spec_cut],
'rmags': rmags[~spec_cut],
'imags': imags[~spec_cut],
'abs_rmags': abs_rmags[~spec_cut]
}
# Project Spectra into radius and velocity
ang_d, lum_d = C.zdistance(clus_z, self.H0)
angles = C.findangle(spec['ra'], spec['dec'], clus_ra, clus_dec)
rdata = angles * ang_d
vdata = self.c * (spec['z'] - clus_z) / (1 + clus_z)
spec.update({'rdata': rdata, 'vdata': vdata})
self.__dict__.update(ez.create(keys, locals()))
# Take Hard Phasespace Limits
limit = np.where((rdata < 5) & (np.abs(vdata) < 5000))[0]
clus_data = np.vstack([
rdata, vdata, spec['ra'], spec['dec'], spec['z'], spec['pz'],
spec['gmags'], spec['rmags'], spec['imags'], spec['abs_rmags']
])
clus_data = clus_data.T[limit].T
rdata, vdata, spec['ra'], spec['dec'], spec['z'], spec['pz'], spec[
'gmags'], spec['rmags'], spec['imags'], spec[
'abs_rmags'] = clus_data
spec.update({'rdata': rdata, 'vdata': vdata})
self.__dict__.update(ez.create(keys, locals()))
# Shiftgapper for Interlopers
if shiftgap == True:
len_before = np.where((rdata < clus_rvir * 1.5)
& (np.abs(vdata) < 4000))[0].size
clus_data = np.vstack([
rdata, vdata, spec['ra'], spec['dec'], spec['z'], spec['pz'],
spec['gmags'], spec['rmags'], spec['imags'], spec['abs_rmags']
])
clus_data = C.shiftgapper(clus_data.T).T
sorts = np.argsort(clus_data[-1])
clus_data = clus_data.T[sorts].T
rdata, vdata, spec['ra'], spec['dec'], spec['z'], spec['pz'], spec[
'gmags'], spec['rmags'], spec['imags'], spec[
'abs_rmags'] = clus_data
shift_cut = len_before - np.where((rdata < clus_rvir)
& (np.abs(vdata) < 4000))[0].size
# Measure Velocity Dispersion of all galaxies within 1 * r_vir and np.abs(vdata) < 4000 km/s
spec.update({'rdata': rdata, 'vdata': vdata})
self.__dict__.update(ez.create(keys, locals()))
vel_disp = astats.biweight_midvariance(
vdata[np.where((rdata < clus_rvir * 1) & (np.abs(vdata) < 4000))])
if fixed_vdisp == True: vel_disp = 1000
# Run Cluster Pair Finder
if find_pairs == True:
pair, d1_chi, d2_chi, d3_chi, s_chi, double1, double2, double3, single, v_range, bins = pair_find(
rdata, vdata)
# Calculate Nspec, Nspec = # of galaxies within RVIR
try:
Nspec = np.where(rdata < clus_rvir)[0].size
except:
Nspec = 0
self.__dict__.update(ez.create(keys, locals()))
# Get Members from Specta, get their red sequence color
mems = np.where((spec['rdata'] < clus_rvir)
& (np.abs(spec['vdata']) < 2 * vel_disp))[0]
color_data = spec['gmags'] - spec['rmags']
color_cut = np.where((color_data[mems] < 1.2)
& (color_data[mems] > 0.65))[0]
RS_color = astats.biweight_location(color_data[mems][color_cut])
RS_shift = color_data[mems][color_cut] - RS_color
RS_sigma = astats.biweight_midvariance(
RS_shift[np.where(np.abs(RS_shift) < .15)])
if fit_rs == True:
clf = linear_model.LinearRegression()
set = np.where(
np.abs(color_data[mems] - RS_color) < 3 * RS_sigma)[0]
clf.fit(spec['rmags'][mems][set].reshape(set.size, 1),
color_data[mems][set])
if use_bcg == True:
bright = np.argsort(all['abs_rmags'][mems])[0]
RS_color = color_data[mems][bright]
RS_shift = color_data[mems][color_cut] - RS_color
RS_sigma = astats.biweight_midvariance(
RS_shift[np.where(np.abs(RS_shift) < .15)])
# spec_mems is # of members that are within 2 sigma of cluster color
clus_color_cut = np.where(
np.abs(color_data[mems] - RS_color) < RS_sigma * 2)[0]
spec_mems = len(clus_color_cut)
self.__dict__.update(ez.create(keys, locals()))
# If fed gr fit
if gr_slope != None:
def RS_color(r_mag):
return r_mag * gr_slope + gr_inter
RS_sigma = gr_width / 2
clus_color_cut = np.where(
np.abs(color_data[mems] -
RS_color(spec['rmags'])[mems]) < RS_sigma * 2)[0]
spec_mems = len(clus_color_cut)
self.__dict__.update(ez.create(keys, locals()))
# Get Rdata from PhotoZ & SpecZ Data Set
angles = C.findangle(all['ra'], all['dec'], clus_ra, clus_dec)
all['rdata'] = angles * ang_d
# Get deg per RVIR proper
deg_per_rvir = R.Cosmo.arcsec_per_kpc_proper(
clus_z).value * 1e3 * clus_rvir / 3600
# Get Area of Virial Circle out to 1 rvir, and Area of outer annuli, which is annuli from 4rvir < R < 6rvir, or dependent on rvir
if clus_rvir < 2.5:
outer_edge = 6.0
inner_edge = 4.0
elif clus_rvir >= 2.5 and clus_rvir < 3:
outer_edge = 5.0
inner_edge = 3.5
else:
outer_edge = 3.0
inner_edge = 2.0
SA_inner = np.pi * deg_per_rvir**2
SA_outer = np.pi * ((outer_edge * deg_per_rvir)**2 -
(inner_edge * deg_per_rvir)**2)
# Get Number of Cluster Color Galaxies from Photo Data Set in Inner Circle and Outer Annuli
RS_color_sig = 2.0
if gr_slope == None:
red_inner = np.where(((all['gmags'] - all['rmags']) < RS_color +
RS_color_sig * RS_sigma)
& ((all['gmags'] - all['rmags']) > RS_color -
RS_color_sig * RS_sigma)
& (all['rdata'] < clus_rvir))[0]
red_outer = np.where((
(all['gmags'] - all['rmags']) < RS_color + 1.5 * RS_sigma) & (
(all['gmags'] - all['rmags']) > RS_color - 1.5 * RS_sigma)
& (all['rdata'] < outer_edge * clus_rvir)
& (all['rdata'] > inner_edge * clus_rvir))[0]
else:
red_inner = np.where((
(all['gmags'] - all['rmags']) < RS_color(all['rmags']) +
RS_color_sig * RS_sigma) & (
(all['gmags'] - all['rmags']) > RS_color(all['rmags']) -
RS_color_sig * RS_sigma) & (all['rdata'] < clus_rvir))[0]
red_outer = np.where((
(all['gmags'] -
all['rmags']) < RS_color(all['rmags']) + 1.5 * RS_sigma) & (
(all['gmags'] - all['rmags']) > RS_color(all['rmags']) -
1.5 * RS_sigma) & (all['rdata'] < outer_edge * clus_rvir)
& (all['rdata'] > inner_edge * clus_rvir))[0]
Nphot_inner = len(red_inner)
Nphot_outer = len(red_outer)
self.__dict__.update(ez.create(keys, locals()))
# Get Solid Angle Density of Outer Red Galaxies
outer_red_dense = Nphot_outer / SA_outer
inner_background = int(np.ceil(outer_red_dense * SA_inner))
# Define obs_tot and obs_back_scaled, where obs_back_scaled is obs_back already scaled to inner aperture (aka. inner_background)
obs_tot = np.copy(Nphot_inner)
obs_back_scaled = np.copy(inner_background)
# If inner_background is less than Nphot_inner, then Nphot_inner -= inner_background, otherwise Nphot_inner = 0
if inner_background < Nphot_inner:
Nphot_inner -= inner_background
else:
Nphot_inner = 0
# Richness = spec_mems + Nphot_inner or just Nphot_inner
if use_specs == True:
richness = spec_mems + Nphot_inner
else:
richness = Nphot_inner
self.__dict__.update(ez.create(keys, locals()))
# Plot
if plot_gr == True:
fig, ax = mp.subplots()
ax.plot(rmags, gmags - rmags, 'ko', alpha=.8)
ax.plot(spec['rmags'][mems], color_data[mems], 'co')
if gr_slope == None:
ax.axhline(RS_color, color='r')
ax.axhline(RS_color + RS_sigma, color='b')
ax.axhline(RS_color - RS_sigma, color='b')
else:
xdata = np.arange(spec['rmags'][mems].min(),
spec['rmags'][mems].max(), .1)
ax.plot(xdata, RS_color(xdata), color='r')
ax.plot(xdata, RS_color(xdata) + RS_sigma, color='b')
ax.plot(xdata, RS_color(xdata) - RS_sigma, color='b')
ax.set_xlim(13, 19)
ax.set_ylim(0, 1.3)
ax.set_xlabel('Apparent R Mag', fontsize=16)
ax.set_ylabel('App G Mag - App R Mag', fontsize=16)
ax.set_title('Color-Mag Diagram, Cluster ' + str(haloid))
fig.savefig('colormag_' + str(haloid) + '.png',
bbox_inches='tight')
mp.close(fig)
if plot_sky == True:
fig, ax = mp.subplots()
ax.plot(all['ra'], all['dec'], 'ko')
ax.plot(all['ra'][red_inner], all['dec'][red_inner], 'ro')
ax.plot(all['ra'][red_outer], all['dec'][red_outer], 'yo')
ax.plot(clus_ra, clus_dec, 'co', markersize=9)
ax.set_xlabel('RA', fontsize=15)
ax.set_ylabel('Dec.', fontsize=15)
ax.set_title('Richness Annuli for Halo ' + str(haloid))
fig.savefig('skyplot_' + str(haloid) + '.png', bbox_inches='tight')
mp.close(fig)
if plot_phase == True:
fig, ax = mp.subplots()
ax.plot(spec['rdata'], spec['vdata'], 'ko')
ax.plot(spec['rdata'][mems], spec['vdata'][mems], 'co')
bcg = np.where(
spec['abs_rmags'] == spec['abs_rmags'][mems].min())[0][0]
ax.plot(spec['rdata'][bcg], spec['vdata'][bcg], 'ro')
ax.set_xlim(0, 5)
ax.set_ylim(-5000, 5000)
ax.set_xlabel('Radius (Mpc)', fontsize=15)
ax.set_ylabel('Velocity (km/s)', fontsize=15)
ax.set_title('phasespace haloid ' + str(haloid))
fig.savefig('phasespace_' + str(haloid) + '.png',
bbox_inches='tight')
mp.close(fig)
# Check to make sure galaxies exist (somewhat) uniformely in outer annuli (aka. cluster isn't on edge of observation strip)
# First, project all galaxies into polar coordinates centered on cluster center
x = (all['ra'] - clus_ra) / np.cos(
clus_dec * np.pi /
180) # x coordinate in arcsec (of dec) centered on cluster center
y = (all['dec'] - clus_dec)
all['radius'] = np.sqrt(x**2 +
y**2) / deg_per_rvir #radius scaled by RVIR
all['theta'] = np.arctan(y / x)
# Add corrections to arctan function
all['theta'][np.where((x < 0) & (y > 0))] += np.pi # Quadrant II
all['theta'][np.where((x < 0) & (y < 0))] += np.pi # Quadrant III
all['theta'][np.where((x > 0) & (y < 0))] += 2 * np.pi # Quadrant IV
# Then break outer annuli into 4 sections and check if at least 1 galaxy exists in each section
sizes1 = np.array([
np.where((np.abs(all['theta'] - i) <= np.pi / 2)
& (all['radius'] > inner_edge)
& (all['radius'] < 15))[0].size
for i in np.linspace(0, 2 * np.pi, 4)
])
# Do it again but shift theta by np.pi/8 this time
sizes2 = np.array([
np.where((np.abs(all['theta'] - i) <= np.pi / 2)
& (all['radius'] > inner_edge)
& (all['radius'] < 15))[0].size
for i in np.linspace(np.pi / 8, 17 * np.pi / 8, 4)
])
if 0 in sizes1 or 0 in sizes2:
p = False
if p == True:
mp.plot(all['radius'], all['theta'], 'ko')
mp.xlabel('radius')
mp.ylabel('theta')
mp.savefig('rth_' + str(haloid) + '.png')
mp.close()
print 'sizes1=', sizes1
print 'sizes2=', sizes2
return -99
return richness