From 134ea3e1ae350f8fbd578c3f31617d42b9888164 Mon Sep 17 00:00:00 2001 From: Rayne Liu <rl746@cornell.edu> Date: Tue, 6 Oct 2020 03:02:15 +0000 Subject: [PATCH] As in the title. Ad atlas per aspera --- code/NR_Interpolate-0001_t_10M_wandt.py | 290 ++++++++++++++++++++++++ 1 file changed, 290 insertions(+) create mode 100644 code/NR_Interpolate-0001_t_10M_wandt.py diff --git a/code/NR_Interpolate-0001_t_10M_wandt.py b/code/NR_Interpolate-0001_t_10M_wandt.py new file mode 100644 index 0000000..1979eba --- /dev/null +++ b/code/NR_Interpolate-0001_t_10M_wandt.py @@ -0,0 +1,290 @@ +#!/usr/bin/env python +# coding: utf-8 + +# ### Let's try the NR_Interpolate for the 0.0001 stepsize. + +# In[99]: + + +#Import relevant modules, import data and all that +import numpy as np +from scipy import interpolate +import corner +import os +os.environ['MPLCONFIGDIR'] = '/home/rayne.liu/.config/matplotlib' +import matplotlib.pyplot as plt +from matplotlib.ticker import MaxNLocator +from matplotlib import rc +#plt.rcParams['font.family'] = 'DejaVu Sans' +#rc('text', usetex=True) +plt.rcParams.update({'font.size': 16.5}) + +import ptemcee +#from pycbc.pool import choose_pool +from multiprocessing import Pool +import h5py +import inspect +import pandas as pd +import json +import qnm +import random + +#Remember to change the following global variables +#rootpath: root path to nr data +#npoints: number of points you re using for your sampling +#nmax: tone index --> nmax = 0 if fitting the fundamental tone +#tshift: time shift after the strain peak +#vary_fund: whether you vary the fundamental frequency. Works in the model_dv function. + +rootpath= "/work/rayne.liu/git/rdstackingproject"#"/Users/RayneLiu/git/rdstackingproject" +nmax=1 +tshift=10 +vary_fund = True + +#sampler parameters +npoints = 10 +nwalkers = 20 +ntemps=12 +dim = nmax+1 +ndim = 4*dim +burnin = 5 #How many points do you burn before doing the corner plot. You need to watch the convergence of the chain plot a bit. + #This is trivial but often forgotten: this cannot be more than npoints! I usually use half the points. +numbins = 42 #corner plot parameter - how many bins you want +datacolor = '#105670' #'#4fa3a7' +pkcolor = '#f2c977' #'#ffb45f' +mediancolor = '#f7695c' #'#9b2814' + +#Import data and necessary functions + +#TimeOfMaximum +def FindTmaximum(y): + #Determines the maximum absolute value of the complex waveform + absval = y[:,1]*y[:,1]+y[:,2]*y[:,2] + vmax=np.max(absval) + index = np.argmax(absval == vmax) + timemax=gw_sxs_bbh_0305[index,0] + return timemax + + + + +#This loads the 22 mode data +gw = {} +gw["SXS:BBH:0305"] = h5py.File(rootpath+"/SXS/BBH_SKS_d14.3_q1.22_sA_0_0_0.330_sB_0_0_-0.440/Lev6/rhOverM_Asymptotic_GeometricUnits_CoM.h5", 'r') +gw_sxs_bbh_0305 = gw["SXS:BBH:0305"]["Extrapolated_N2.dir"]["Y_l2_m2.dat"] + +# Remember to download metadata.json from the simulation with number: 0305. Download Lev6/metadata.json +# This postprocesses the metadata file to find the final mass and final spin +metadata = {} +with open(rootpath+"/SXS/BBH_SKS_d14.3_q1.22_sA_0_0_0.330_sB_0_0_-0.440/Lev6/metadata.json") as file: + metadata["SXS:BBH:0305"] = json.load(file) + +af = metadata["SXS:BBH:0305"]['remnant_dimensionless_spin'][-1] +mf = metadata["SXS:BBH:0305"]['remnant_mass'] + + + +#times --> x axis of your data +times = gw_sxs_bbh_0305[:,0] +tmax=FindTmaximum(gw_sxs_bbh_0305) +t0=tmax +tshift + +#Select the data from t0 onwards +position = np.argmax(times >= (t0)) +gw_sxs_bbh_0305rd=gw_sxs_bbh_0305[position:-1] +timesrd=gw_sxs_bbh_0305[position:-1][:,0][:920] +#print(timesrd[0]) +#print(t0) #(This checks that timesrd[0] is indeed t0 - acturally this is a bit off due to stepsize issues, + #but nvm, we'll fix it right away) +t0 = timesrd[0] +#print(t0) +timespan = timesrd - t0 +gwdata_re = gw_sxs_bbh_0305rd[:,1][:920] +gwdata_im = gw_sxs_bbh_0305rd[:,2][:920] + +# Depending on nmax, you load nmax number of freqs. and damping times from the qnm package +omegas = [qnm.modes_cache(s=-2,l=2,m=2,n=i)(a=af)[0] for i in range (0,dim)] +w = (np.real(omegas))/mf +tau=-1/(np.imag(omegas))*mf + + +# In[84]: + +gwnew_re = interpolate.interp1d(timespan, gwdata_re, kind = 'cubic') +gwnew_im = interpolate.interp1d(timespan, gwdata_im, kind = 'cubic') + + +# In[87]: + + +timespan_new = np.linspace(0, timespan[-1], len(timespan)*1000) +gwdatanew_re = gwnew_re(timespan_new) +gwdatanew_im = gwnew_im(timespan_new) + + + +# In[92]: + + +#Test the new interpolated data +figtest = plt.figure(figsize = (12, 8)) +plt.plot(timespan, gwdata_re, "r", alpha=0.3, lw=2, label='Before_re') +plt.plot(timespan_new, gwdatanew_re, "b", alpha=0.3, lw=2, label='After_re') +plt.plot(timespan, gwdata_im, alpha=0.3, lw=2, label='Before_im') +plt.plot(timespan_new, gwdatanew_im, alpha=0.3, lw=2, label='After_im') +plt.legend() +figtest.savefig(rootpath + '/plotsmc/0001_interpolated_datatest_wandt.png', format='png', bbox_inches='tight', dpi=300) + + +# ### Now the interpolation seems nice according to what we have above...let's start sampling! + +# In[100]: + + +#Fitting +#RD model for nmax tones. Amplitudes are in (xn*Exp[i yn]) version. Used here. +def model_dv(theta): + #x0, y0= theta + #Your nmax might not align with the dim of theta. Better check it here. + assert int(len(theta)/4) == dim, 'Please recheck your n and parameters' + + wvars = theta[ : (dim)] + tvars = theta[(dim) : 2*(dim)] + xvars = theta[2*(dim) : 3*(dim)] + yvars = theta[3*(dim) : ] + + #if vary_fund == False: + # avars[0]=0 + # bvars[0]=0 + + ansatz = 0 + for i in range (0,dim): + #bvars[1]=0 + #avars[1]=0 + ansatz += (xvars[i]*np.exp(1j*yvars[i]))*np.exp(-timespan_new/tvars[i]) * (np.cos(wvars[i]*timespan_new)-1j*np.sin(wvars[i]*timespan_new)) + # -1j to agree with SXS convention + return ansatz + +# Logprior distribution. It defines the allowed range my variables can vary over. +#It works for the (xn*Exp[iyn]) version. +def log_prior(theta): + #Warning: we are specifically working with nmax=1 so here individual prior to the parameters are manually adjusted. This does not apply to all other nmax's. + #avars = theta[ : (dim)] + #bvars = theta[(dim) : 2*(dim)] + #xvars = theta[2*(dim) : 3*(dim)] + #yvars = theta[3*(dim) : ] + omega0, omega1, tau0, tau1, xvar0, xvar1, yvar0, yvar1 = theta + if tshift == 0: + if all([0.45 <= omega0 <= 0.63, 0.27 <= omega1 <= 0.6, 0. <= tau0 <= 30., 0. <= tau1 <= 20., \ + 0 <= xvar0 <= 6, 0 <= xvar1 <= 6, -np.pi <= yvar0 <= np.pi, 0. <= yvar1 <= 2*np.pi]): + return 0.0 + + elif tshift == 10: + if all([0.56 <= omega0 <= 0.64, 0.4 <= omega1 <= 0.56, 6.45 <= tau0 <= 13.6, 1.94 <= tau1 <= 10., \ + 0. <= xvar0 <= 1.5, 0. <= xvar1 <= 1.2, 0 <= yvar0 <= 2*np.pi, 0. <= yvar1 <= 2*np.pi]): + return 0.0 + + return -np.inf + + +# LogLikelihood function. It is just a Gaussian loglikelihood based on computing the residuals^2 +def log_likelihood(theta): + modelev = model_dv(theta) + result = -np.sum((gwdatanew_re - (modelev.real))**2+(gwdatanew_im - (modelev.imag))**2) + if np.isnan(result): + return -np.inf + return result + + +# Logposterior distribution for the residuals case. +# The evidence is just a normalization factor +def log_probability(theta): + lp = log_prior(theta) + if not np.isfinite(lp): + return -np.inf + return lp + log_likelihood(theta) + + +# In[101]: + + +#This cell uses the tshift=10 results +#Set the number of cores of your processors +#pool = choose_pool(1) +#pool.size = 1 +np.random.seed(42) +pos = np.array([random.uniform(0.58,0.62), random.uniform(0.42,0.54), random.uniform(7., 12.), random.uniform(2.,4.), random.uniform(0.5,1.), random.uniform(0.5, 1.), random.uniform(1., 2.), random.uniform(1., 2.)]) +pos = list(pos) +pos += 1e-5 * np.random.randn(ntemps, nwalkers, ndim) +with Pool() as pool: + sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps, pool=pool) + sampler.run_mcmc(pos,npoints) + +dim = 2 +paramlabels_w = [r'$\omega_'+str(i)+'$' for i in range (dim)] +paramlabels_t = [r'$\tau_'+str(i)+'$' for i in range (dim)] +paramlabels_x = [r'$x_'+str(i)+'$' for i in range (dim)] +paramlabels_y = [r'$y_'+str(i)+'$' for i in range (dim)] + +paramlabels = paramlabels_w + paramlabels_t + paramlabels_x + paramlabels_y + +print('The chain plot:') +#Chain plot +figchain, axes = plt.subplots(ndim, 1, sharex=True, figsize=(12, 4*(4))) +for i in range(ndim): + axes[i].plot(sampler.chain[0,:, :, i].T, color="k", alpha=0.4, rasterized=True) + axes[i].yaxis.set_major_locator(MaxNLocator(5)) + axes[i].set_ylabel(paramlabels[i]) +axes[-1].set_xlabel('Iterations') +figchain.savefig(rootpath + '/plotsmc/0001_10M_interpolated_chainplot_wandt_'+str(nwalkers)+'walkers_'+str(npoints)+'pts.png', format='png', bbox_inches='tight', dpi=300) + +for temp in range(ntemps): + dftemp = pd.DataFrame(sampler.chain[temp,:, :, :].reshape((-1, ndim)), columns=paramlabels) + dftemp.to_csv(rootpath+'/plotsmc/0001_10M_interpolated'+'_nmax'+str(nmax)+'_tshift'+str(tshift)+'_'+str(npoints)+'pt_temp'+str(temp)+'_chain.csv', index = False) + +print('We\'re using ptemcee. Our constraints:') +#Burn samples, calculate peak likelihood value (not necessarily so in atlas) and make corner plot +samples = sampler.chain[0,:, burnin:, :].reshape((-1, ndim)) +#samples for corner plot +samples_corn = samples #if vary_fund == True else np.delete(samples, np.s_[0,2], 1) + +#print('Values with peak likelihood:') +lglk = np.array([log_likelihood(samples[i]) for i in range(len(samples))]) +pk = samples[np.argmax(lglk)] +#print('pk:') +#print(pk) +pk_corn = pk #if vary_fund == True else np.delete(pk, [0,2]) +#y_0 range needs some messaging to make the plot. But in order to make the whole picture consistent, better change the range of y_1 too. +#if vary_fund == False: +# samples_corn.T[-dim:] -= np.pi #This indeed changes samples_corn itself +# pk[-dim:] -= np.pi + +#print('pkFalse:') +#print(pk) + +#print(pk) +#Now calculate median (50-percentile) value +median = np.median(samples_corn, axis=0) +#print(samples) +#print(samples_corn) + +figcorn = corner.corner(samples_corn, bins = numbins, hist_bin_factor = 5, color = datacolor, truths=pk_corn, truth_color = pkcolor, plot_contours = True, labels = paramlabels, quantiles=(0.05, 0.16, 0.5, 0.84, 0.95), levels=[1-np.exp(-0.5), 1-np.exp(-1.64 ** 2/2)], show_titles=True) + + +#Extract the axes in order to add more important line plots +naxes = len(pk_corn) +axes = np.array(figcorn.axes).reshape((naxes, naxes)) + +# Loop over the diagonal +for i in range(naxes): + ax = axes[i, i] + ax.axvline(median[i], color=mediancolor) + +# Loop over the histograms +for yi in range(naxes): + for xi in range(yi): + ax = axes[yi, xi] + ax.axvline(median[xi], color=mediancolor) + ax.axhline(median[yi], color=mediancolor) + ax.plot(median[xi], median[yi], color = mediancolor, marker = 's') +figcorn.savefig(rootpath + '/plotsmc/0001_10M_interpolated_cornerplot_wandt_'+'nmax'+str(nmax)+'_tshift'+str(tshift)+'_'+str(nwalkers)+'walkers_'+str(npoints)+'pts.png', format='png', bbox_inches='tight', dpi=300) -- GitLab