def simul(isodir):
params = parameters()
eps = 0.01
#feh
params.set("m0y", 0.9, -1, 1, True)
params.set("m0cphi", -0.001, -pi / 2 + eps, 0, True)
params.set("m0cr", 0.01, 0, 2, True)
params.set("m1y", -0.9, -1, 1, True)
params.set("m1cphi", 1.67, pi / 2 + eps, pi, True)
params.set("m1cr", 1.06, 0, 2, True)
params.set("sigma", 0.6, 0, 1, True)
#sfr
params.set("s0y", 1.11, 0.0, 2, True)
params.set("s0cphi", 0.0003, 0, pi / 2 - eps, True)
params.set("s0cr", 1, 0, 1, True)
params.set("s1x", 9.9, 8, 10, True)
params.set("s1y", 5.9, 1.5, 10, True)
params.set("s1cphi", 4.61, pi / 2 + eps, pi * 3 / 2 - eps, True)
params.set("s1cr", 0.49, 0, 0.5, True)
params.set("s2y", 0.89, 0, 2, True)
params.set("s2cphi", 3.04, pi / 2 + eps, pi - eps, True)
params.set("s2cr", 0.001, 0, 2, True)
if len(sys.argv) == 2: #run with a param to start from the beginning
params.save()
params.load()
data = iso.readfits(isodir + "/datarr.fits")
isos = iso.readisos(isodir)
t = utils.frange(8, 10.25, 0.001)
def f(par):
params.setvalues(par)
w = utils.calculateweights(t, sfr(t, params))
#isow=iso.getisosweights(w,10.**t,metallicity(t,params),isos)
isow = iso.getisosweights_gauss(w, 10.**t, metallicity(t, params),
isos, params.sigma)
m = iso.computeCMD(isow, isos)
m = utils.normalize(m, sum(data.flat))
return utils.loglikelihood(m, data)
d = numarray.maximum(data, 1e-20)
llhC = sum((d * numarray.log(d)).flat)
def b(par, value, iter):
params.setvalues(par)
params.save()
print "henry:", value, "tom:", 2.0 * (value + llhC), "iter:", iter
optimization.minmax(optimization.fmin_simplex, f, params.getvalues(),
params.min(), params.max(), b)
def simul(isodir):
params=parameters()
eps=0.01
#feh
params.set("m0y" ,0.9, -1,1,True)
params.set("m0cphi",-0.001, -pi/2+eps,0,True)
params.set("m0cr" ,0.01, 0,2,True)
params.set("m1y" ,-0.9, -1,1,True)
params.set("m1cphi",1.67, pi/2+eps,pi,True)
params.set("m1cr" ,1.06, 0,2,True)
params.set("sigma" ,0.6, 0,1, True)
#sfr
params.set("s0y" ,1.11, 0.0,2,True)
params.set("s0cphi",0.0003, 0,pi/2-eps,True)
params.set("s0cr" ,1, 0,1,True)
params.set("s1x" ,9.9, 8,10,True)
params.set("s1y" ,5.9, 1.5,10,True)
params.set("s1cphi",4.61, pi/2+eps,pi*3/2-eps,True)
params.set("s1cr" ,0.49, 0,0.5,True)
params.set("s2y" ,0.89, 0,2,True)
params.set("s2cphi",3.04, pi/2+eps,pi-eps,True)
params.set("s2cr" ,0.001, 0,2,True)
if len(sys.argv) == 2: #run with a param to start from the beginning
params.save()
params.load()
data=iso.readfits(isodir+"/datarr.fits")
isos = iso.readisos(isodir)
t=utils.frange(8,10.25,0.001)
def f(par):
params.setvalues(par)
w=utils.calculateweights(t,sfr(t,params))
#isow=iso.getisosweights(w,10.**t,metallicity(t,params),isos)
isow=iso.getisosweights_gauss(w,10.**t,metallicity(t,params),isos,
params.sigma)
m=iso.computeCMD(isow,isos)
m=utils.normalize(m,sum(data.flat))
return utils.loglikelihood(m,data)
d = numarray.maximum(data,1e-20)
llhC=sum( (d*numarray.log(d)).flat )
def b(par,value,iter):
params.setvalues(par)
params.save()
print "henry:",value,"tom:",2.0*(value+llhC),"iter:",iter
optimization.minmax(optimization.fmin_simplex,f,
params.getvalues(),params.min(),params.max(),b)
import numpy as numarray
from chemev import iso, utils, optimization
if not optimization.have_mcmc:
print "PyMC not installed correctly. Check the PYTHONPATH."
print "PYTHONPATH=", sys.path
sys.exit()
print "reading isochrones"
#isodir="m31iso"
#isodir="m117halo"
isodir = "../../isochrones/117/halo"
data = iso.readfits(isodir + "/datarr.fits")
isos = iso.readisos(isodir)
print "fitting"
pars = eval(file("bestfit117").readline())
ndata = sum(data.flat)
d = numarray.maximum(data, 1e-20)
llhC = sum((d * numarray.log(d)).flat)
iter = 0
out = file("mcmc.out", "w")
def f(params):
global iter
m = iso.computeCMD(params, isos)
C = ndata / sum(m.flat)
def simul(isodir):
params = parameters()
eps = 0.01
#feh
params.set("m0y", 0.9, -1, 1, True)
params.set("m0cphi", -0.001, -pi / 2 + eps, 0, True)
params.set("m0cr", 0.01, 0, 2, True)
params.set("m1y", -0.9, -1, 1, True)
params.set("m1cphi", 1.67, pi / 2 + eps, pi, True)
params.set("m1cr", 1.06, 0, 2, True)
# params.set("sigma" ,0.6, 0,1, True)
#sfr
params.set("s0y", 1.11, 0.0, 2, True)
params.set("s0cphi", 0.0003, 0, pi / 2 - eps, True)
params.set("s0cr", 1, 0, 1, True)
params.set("s1x", 9.9, 8, 10, True)
params.set("s1y", 5.9, 1.5, 10, True)
params.set("s1cphi", 4.61, pi / 2 + eps, pi * 3 / 2 - eps, True)
params.set("s1cr", 0.49, 0, 0.5, True)
params.set("s2y", 0.89, 0, 2, True)
params.set("s2cphi", 3.04, pi / 2 + eps, pi - eps, True)
params.set("s2cr", 0.001, 0, 2, True)
#if len(sys.argv) == 2: #run with a param to start from the beginning
params.save()
params.load()
data = iso.readfits(isodir + "/datarr.fits")
isos = iso.readisos(isodir)
t = utils.frange(8, 10.25, 0.001)
ndata = sum(data.flat)
def f(par):
params.setvalues(par)
w = utils.calculateweights(t, sfr(t, params))
isow = iso.getisosweights(w, 10.**t, metallicity(t, params), isos)
#isow=iso.getisosweights_gauss(w,10.**t,metallicity(t,params),isos,
# params.sigma)
m = iso.computeCMD(isow, isos)
m = utils.normalize(m, ndata)
return utils.loglikelihood(m, data)
d = maximum(data, 1e-20)
llhC = sum((d * log(d)).flat)
def b(par, value, iter):
params.setvalues(par)
params.save()
print "henry:", value, "tom:", 2.0 * (value + llhC), "iter:", iter
#always try a different initial guess:
params.randomize()
sfr_initial = sfr(t, params)
met_initial = metallicity(t, params)
print "start"
#pars=optimization.minmax(optimization.fmin_bfgs,
pars = optimization.minmax(
optimization.fmin_de,
#pars=optimization.minmax(optimization.fmin_anneal,
f,
params.getvalues(),
params.min(),
params.max(),
callback=b,
iter=100,
#logistics = optimization.ReflectLogistics)
logistics=optimization.ExpLogistics)
def simul(isodir):
params=parameters()
eps=0.01
#feh
params.set("m0y" ,0.9, -1,1,True)
params.set("m0cphi",-0.001, -pi/2+eps,0,True)
params.set("m0cr" ,0.01, 0,2,True)
params.set("m1y" ,-0.9, -1,1,True)
params.set("m1cphi",1.67, pi/2+eps,pi,True)
params.set("m1cr" ,1.06, 0,2,True)
# params.set("sigma" ,0.6, 0,1, True)
#sfr
params.set("s0y" ,1.11, 0.0,2,True)
params.set("s0cphi",0.0003, 0,pi/2-eps,True)
params.set("s0cr" ,1, 0,1,True)
params.set("s1x" ,9.9, 8,10,True)
params.set("s1y" ,5.9, 1.5,10,True)
params.set("s1cphi",4.61, pi/2+eps,pi*3/2-eps,True)
params.set("s1cr" ,0.49, 0,0.5,True)
params.set("s2y" ,0.89, 0,2,True)
params.set("s2cphi",3.04, pi/2+eps,pi-eps,True)
params.set("s2cr" ,0.001, 0,2,True)
#if len(sys.argv) == 2: #run with a param to start from the beginning
params.save()
params.load()
data=iso.readfits(isodir+"/datarr.fits")
isos = iso.readisos(isodir)
t=utils.frange(8,10.25,0.001)
ndata = sum(data.flat)
def f(par):
params.setvalues(par)
w=utils.calculateweights(t,sfr(t,params))
isow=iso.getisosweights(w,10.**t,metallicity(t,params),isos)
#isow=iso.getisosweights_gauss(w,10.**t,metallicity(t,params),isos,
# params.sigma)
m=iso.computeCMD(isow,isos)
m=utils.normalize(m,ndata)
return utils.loglikelihood(m,data)
d = maximum(data,1e-20)
llhC=sum( (d*log(d)).flat )
def b(par,value,iter):
params.setvalues(par)
params.save()
print "henry:",value,"tom:",2.0*(value+llhC),"iter:",iter
#always try a different initial guess:
params.randomize()
sfr_initial = sfr(t,params)
met_initial = metallicity(t,params)
print "start"
#todo:
#- the reflectlogistics randomizes the parameters once more, thus
#the sfr_initial and met_initial is nonsense then. fix it in
#ReflectLogistics.fracinv()
#- let the simplex method restart automatically
#pars=optimization.minmax(optimization.fmin_bfgs,
pars=optimization.minmax(optimization.fmin_simplex,
#pars=optimization.minmax(optimization.fmin_anneal,
f,params.getvalues(),params.min(),params.max(),
callback=b, iter=100,
#logistics = optimization.ReflectLogistics)
logistics = optimization.ExpLogistics)
m=utils.normalize(iso.computeCMD(params,isos),ndata)
return utils.loglikelihood(m,data)
d = maximum(data,1e-20)
llhC=sum( (d*log(d)).flat )
def b(params,value,iter):
"Print status everytime a best fit is found."
m=iso.computeCMD(params,isos)
C=sum(data.flat)/sum(m.flat)
x=array(params)
bestfit[0] = x*C
file("bestfit117","w").write(str(list(bestfit[0])))
print "henry:",value,"tom:",2.0*(value+llhC),"iter:",iter,"norm:",C
a= optimization.minc(optimization.fmin_bfgs,f,pars,callback=b,iter=iter)
b(a, f(a), -1)
return a
print "reading isochrones"
data=iso.readfits(chemev.isodir+"/117/stream/datarr.fits")
isos = iso.readisos(chemev.isodir+"/117/stream")
pars=[1.0]*117
print "fitting"
pars=fitting_iteration(pars,200)
print "done"
def b(params, value, iter):
"Print status everytime a best fit is found."
m = iso.computeCMD(params, isos)
C = sum(data.flat) / sum(m.flat)
x = array(params)
bestfit[0] = x * C
file("bestfit117", "w").write(str(list(bestfit[0])))
print "henry:", value, "tom:", 2.0 * (value +
llhC), "iter:", iter, "norm:", C
a = optimization.minc(optimization.fmin_bfgs,
f,
pars,
callback=b,
iter=iter)
b(a, f(a), -1)
return a
print "reading isochrones"
data = iso.readfits(chemev.isodir + "/117/disk/datarr.fits")
isos = iso.readisos(chemev.isodir + "/117/disk")
pars = [1.0] * 117
print "fitting"
pars = fitting_iteration(pars, 200)
print "done"
import numpy as numarray
from chemev import iso,utils,optimization
if not optimization.have_mcmc:
print "PyMC not installed correctly. Check the PYTHONPATH."
print "PYTHONPATH=",sys.path
sys.exit()
print "reading isochrones"
#isodir="m31iso"
#isodir="m117halo"
isodir="../../isochrones/117/halo"
data=iso.readfits(isodir+"/datarr.fits")
isos = iso.readisos(isodir)
print "fitting"
pars=eval(file("bestfit117").readline())
ndata=sum(data.flat)
d = numarray.maximum(data,1e-20)
llhC=sum( (d*numarray.log(d)).flat )
iter=0
out=file("mcmc.out","w")
def f(params):
global iter
m=iso.computeCMD(params,isos)
C=ndata/sum(m.flat)
x=numarray.array(params)
# out.write(str(list(x*C))+"\n")
def simul(isodir):
params = parameters()
eps = 0.01
#feh
params.set("m0y", 0.9, -1, 1, True)
params.set("m0cphi", -0.001, -pi / 2 + eps, 0, True)
params.set("m0cr", 0.01, 0, 2, True)
params.set("m1y", -0.9, -1, 1, True)
params.set("m1cphi", 1.67, pi / 2 + eps, pi, True)
params.set("m1cr", 1.06, 0, 2, True)
# params.set("sigma" ,0.6, 0,1, True)
#sfr
params.set("s0y", 1.11, 0.0, 2, True)
params.set("s0cphi", 0.0003, 0, pi / 2 - eps, True)
params.set("s0cr", 1, 0, 1, True)
params.set("s1x", 9.9, 8, 10, True)
params.set("s1y", 5.9, 1.5, 10, True)
params.set("s1cphi", 4.61, pi / 2 + eps, pi * 3 / 2 - eps, True)
params.set("s1cr", 0.49, 0, 0.5, True)
params.set("s2y", 0.89, 0, 2, True)
params.set("s2cphi", 3.04, pi / 2 + eps, pi - eps, True)
params.set("s2cr", 0.001, 0, 2, True)
#if len(sys.argv) == 2: #run with a param to start from the beginning
params.save()
params.load()
data = iso.readfits(isodir + "/datarr.fits")
isos = iso.readisos(isodir)
t = utils.frange(8, 10.25, 0.001)
ndata = sum(data.flat)
def f(params):
w = utils.calculateweights(t, sfr(t, params))
isow = iso.getisosweights(w, 10.**t, metallicity(t, params), isos)
#a3=time.time()
m = iso.computeCMD(isow, isos)
#a4=time.time()
m = utils.normalize(m, ndata)
l = utils.loglikelihood(m, data)
#print a4-a3
return l
d = maximum(data, 1e-20)
llhC = sum((d * log(d)).flat)
def b(par, value, iter):
params.setvalues(par)
params.save()
print "henry:", value, "tom:", 2.0 * (value + llhC), "iter:", iter
print "start"
bestfit = (0, 0)
it = 0
while 1:
it += 1
params.randomize()
#ti = time.time()
r = f(params)
#ti -= time.time()
#print "time:",ti
if r < bestfit[1]:
bestfit = (params.getvalues(), r)
print "%d:" % it, r
d = maximum(data,1e-20)
llhC=sum( (d*log(d)).flat )
def b(params,value,iter):
"Print status everytime a best fit is found."
m=iso.computeCMD(params,isos)
C=sum(data.flat)/sum(m.flat)
x=array(params)
bestfit[0] = x*C
file("bestfit117","w").write(str(list(bestfit[0])))
print "henry:",value,"tom:",2.0*(value+llhC),"iter:",iter,"norm:",C
optimization.minc(optimization.fmin_simplex,f,pars,callback=b,iter=iter)
return bestfit[0]
print "reading isochrones"
data=iso.readfits(chemev.isodir+"/117/halo/datarr.fits")
isos = iso.readisos(chemev.isodir+"/117/halo")
pars=[1.0]*117
print "fitting"
#this is the hardwired empirical key to achieve the best fit. :)
best_fit_path = [800, 1800, 1500, 2000]+ [2000]*100
print "we are going to do this amount of iterations:",best_fit_path
for iter in best_fit_path:
print "### doing %d iterations ###"%iter
pars=fitting_iteration(pars,iter)
print "done"
#! /usr/bin/env python
"""Writes all the information about the best fit to the file "protocol" """
import sys
from chemev import iso, isodir, utils
print "reading isochrones"
data = iso.readfits(isodir + "/117/halo/datarr.fits")
isos = iso.readisos(isodir + "/117/halo")
isow = eval(open("bestfit117").readline())
model = iso.computeCMD(isow, isos)
model = utils.normalize(model, sum(data.flat))
def plot_residuals(d, m, aspect=0.2):
"""
todo: the same color range for both data and model. the rediduals are ok
"""
import pylab
pylab.figure()
pylab.subplot(221)
pylab.imshow(d, origin='lower', interpolation="nearest", aspect=aspect)
pylab.title("data")
pylab.colorbar()
pylab.subplot(222)
pylab.imshow(m, origin='lower', interpolation="nearest", aspect=aspect)
pylab.title("model")
pylab.colorbar()
pylab.subplot(223)
residuals = d - m
m=utils.normalize(iso.computeCMD(params,isos),ndata)
return utils.loglikelihood(m,data)
d = maximum(data,1e-20)
llhC=sum( (d*log(d)).flat )
def b(params,value,iter):
"Print status everytime a best fit is found."
m=iso.computeCMD(params,isos)
C=sum(data.flat)/sum(m.flat)
x=array(params)
bestfit[0] = x*C
file("bestfit117","w").write(str(list(bestfit[0])))
print "henry:",value,"tom:",2.0*(value+llhC),"iter:",iter,"norm:",C
a= optimization.minc(optimization.fmin_bfgs,f,pars,callback=b,iter=iter)
b(a, f(a), -1)
return a
print "reading isochrones"
data=iso.readfits(chemev.isodir+"/117/disk/datarr.fits")
isos = iso.readisos(chemev.isodir+"/117/disk")
pars=[1.0]*117
print "fitting"
pars=fitting_iteration(pars,200)
print "done"
def b(params, value, iter):
"Print status everytime a best fit is found."
m = iso.computeCMD(params, isos)
C = sum(data.flat) / sum(m.flat)
x = array(params)
bestfit[0] = x * C
file("bestfit117", "w").write(str(list(bestfit[0])))
print "henry:", value, "tom:", 2.0 * (value +
llhC), "iter:", iter, "norm:", C
a = optimization.minc(optimization.fmin_bfgs,
f,
pars,
callback=b,
iter=iter)
b(a, f(a), -1)
return a
print "reading isochrones"
data = iso.readfits(chemev.isodir + "/696/halo/datarr.fits")
isos = iso.readisos(chemev.isodir + "/696/halo")
pars = [1.0] * 696
print "fitting"
pars = fitting_iteration(pars, 200)
print "done"
#! /usr/bin/env python
"""Writes all the information about the best fit to the file "protocol" """
import sys
from chemev import iso, isodir, utils
print "reading isochrones"
data = iso.readfits(isodir+"/117/halo/datarr.fits")
isos = iso.readisos(isodir+"/117/halo")
isow = eval(open("bestfit117").readline())
model = iso.computeCMD(isow,isos)
model = utils.normalize(model,sum(data.flat))
def plot_residuals(d,m,aspect=0.2):
"""
todo: the same color range for both data and model. the rediduals are ok
"""
import pylab
pylab.figure()
pylab.subplot(221)
pylab.imshow(d,origin='lower',interpolation="nearest",aspect=aspect)
pylab.title("data")
pylab.colorbar()
pylab.subplot(222)
pylab.imshow(m,origin='lower',interpolation="nearest",aspect=aspect)
pylab.title("model")
pylab.colorbar()
pylab.subplot(223)
residuals = d-m
pylab.imshow(residuals,origin='lower',interpolation="nearest",aspect=aspect)
def simul(isodir):
params=parameters()
eps=0.01
#feh
params.set("m0y" ,0.9, -1,1,True)
params.set("m0cphi",-0.001, -pi/2+eps,0,True)
params.set("m0cr" ,0.01, 0,2,True)
params.set("m1y" ,-0.9, -1,1,True)
params.set("m1cphi",1.67, pi/2+eps,pi,True)
params.set("m1cr" ,1.06, 0,2,True)
# params.set("sigma" ,0.6, 0,1, True)
#sfr
params.set("s0y" ,1.11, 0.0,2,True)
params.set("s0cphi",0.0003, 0,pi/2-eps,True)
params.set("s0cr" ,1, 0,1,True)
params.set("s1x" ,9.9, 8,10,True)
params.set("s1y" ,5.9, 1.5,10,True)
params.set("s1cphi",4.61, pi/2+eps,pi*3/2-eps,True)
params.set("s1cr" ,0.49, 0,0.5,True)
params.set("s2y" ,0.89, 0,2,True)
params.set("s2cphi",3.04, pi/2+eps,pi-eps,True)
params.set("s2cr" ,0.001, 0,2,True)
#if len(sys.argv) == 2: #run with a param to start from the beginning
params.save()
params.load()
data=iso.readfits(isodir+"/datarr.fits")
isos = iso.readisos(isodir)
t=utils.frange(8,10.25,0.001)
ndata = sum(data.flat)
def f(params):
w=utils.calculateweights(t,sfr(t,params))
isow=iso.getisosweights(w,10.**t,metallicity(t,params),isos)
#a3=time.time()
m=iso.computeCMD(isow,isos)
#a4=time.time()
m=utils.normalize(m,ndata)
l= utils.loglikelihood(m,data)
#print a4-a3
return l
d = maximum(data,1e-20)
llhC=sum( (d*log(d)).flat )
def b(par,value,iter):
params.setvalues(par)
params.save()
print "henry:",value,"tom:",2.0*(value+llhC),"iter:",iter
print "start"
bestfit = (0,0)
it = 0
while 1:
it += 1
params.randomize()
#ti = time.time()
r = f(params)
#ti -= time.time()
#print "time:",ti
if r < bestfit[1]:
bestfit = (params.getvalues(), r)
print "%d:"%it, r
def b(params, value, iter):
"Print status everytime a best fit is found."
m = iso.computeCMD(params, isos)
C = sum(data.flat) / sum(m.flat)
x = array(params)
bestfit[0] = x * C
file("bestfit117", "w").write(str(list(bestfit[0])))
print "henry:", value, "tom:", 2.0 * (value +
llhC), "iter:", iter, "norm:", C
a = optimization.minc(optimization.fmin_bfgs,
f,
pars,
callback=b,
iter=iter)
b(a, f(a), -1)
return a
print "reading isochrones"
data = iso.readfits(chemev.isodir + "/117/stream/datarr.fits")
isos = iso.readisos(chemev.isodir + "/117/stream")
pars = [1.0] * 117
print "fitting"
pars = fitting_iteration(pars, 200)
print "done"