Esempio n. 1
0
def run(gp, pop):
    import gr_params
    gpr = gr_params.grParams(gp)
    xall,yall = np.loadtxt(gp.files.get_com_file(0), skiprows=1, \
                           usecols=(0,1), unpack=True)
    # 2*[Rscale0]
    R = np.sqrt(xall**2+yall**2) # [Rscale0]
    # set number and size of (linearly spaced) bins
    Rmin = 0. #[Rscale0]
    Rmax = max(R) if gp.maxR < 0 else 1.0*gp.maxR # [Rscale0]
    R = R[(R<Rmax)] # [Rscale0]
    Binmin, Binmax, Rbin = gh.determine_radius(R, Rmin, Rmax, gp) # [Rscale0]
    gp.xipol = Rbin
    minr = min(Rbin)                           # [pc]
    maxr = max(Rbin)                           # [pc]
    gp.xepol = np.hstack([minr/8., minr/4., minr/2., Rbin, 2*maxr, 4*maxr, 8*maxr]) # [pc]
    Vol = gh.volume_circular_ring(Binmin, Binmax, gp) # [Rscale0^2]
    Rscale0 = gf.read_Xscale(gp.files.get_scale_file(0)) # [pc]
    print('#######  working on component ',pop)
    print('input: ', gp.files.get_com_file(pop))
    # start from data centered on COM already:
    if gf.bufcount(gp.files.get_com_file(pop))<2:
        return
    # only read in data if needed: pops = 1: reuse data from pop=0 part
    x,y = np.loadtxt(gp.files.get_com_file(pop), skiprows=1, usecols=(0,1), unpack = True)
        # [Rscalei], [Rscalei]
    # calculate 2D radius on the skyplane
    R = np.sqrt(x**2+y**2) #[Rscalei]
    Rscalei = gf.read_Xscale(gp.files.get_scale_file(pop)) # [pc]
    # set maximum radius (if gp.maxR is set)
    Rmax = max(R) if gp.maxR<0 else 1.0*gp.maxR # [Rscale0]
    print('Rmax [Rscale0] = ', Rmax)
    sel = (R * Rscalei <= Rmax * Rscale0)
    x = x[sel] # [Rscalei]
    y = y[sel] # [Rscalei]
    R = R[sel] # [Rscalei]
    totmass_tracers = float(len(x)) # [Munit], Munit = 1/star
    Rs = R                   # + possible starting offset, [Rscalei]
    tr = open(gp.files.get_ntracer_file(pop),'w')
    print(totmass_tracers, file=tr)
    tr.close()
    f_Sig, f_nu, f_mass, f_sig, f_kap, f_zeta = gf.write_headers_2D(gp, pop)
    Sig_phot   = np.zeros((gp.nipol, gpr.n))
    # particle selections, shared by density, siglos, kappa and zeta calculations
    tpb       = np.zeros((gp.nipol,gpr.n))
    for k in range(gpr.n):
        Rsi   = gh.add_errors(Rs,   gpr.Rerr)   # [Rscalei]
        for i in range(gp.nipol):
            ind1 = np.argwhere(np.logical_and(Rsi * Rscalei >= Binmin[i] * Rscale0, \
                                          Rsi * Rscalei <  Binmax[i] * Rscale0)).flatten() # [1]
            tpb[i][k] = float(len(ind1)) #[1]
            Sig_phot[i][k] = float(len(ind1))*totmass_tracers/Vol[i] # [Munit/rscale^2]
    # do the following for all populations
    Sig0 = np.sum(Sig_phot[0])/float(gpr.n) # [Munit/Rscale^2]
    Sig0pc = Sig0/Rscale0**2              # [munis/pc^2]
    gf.write_Sig_scale(gp.files.get_scale_file(pop), Sig0pc, totmass_tracers)

    # calculate density and mass profile, store it
    # ----------------------------------------------------------------------
    P_dens  = np.zeros(gp.nipol)
    P_edens = np.zeros(gp.nipol)
    for b in range(gp.nipol):
        Sig = np.sum(Sig_phot[b])/(1.*gpr.n) # [Munit/Rscale^2]
        tpbb   = np.sum(tpb[b])/float(gpr.n)       # [1], mean number of tracers in bin
        Sigerr = Sig/np.sqrt(tpbb)       # [Munit/Rscale^2], Poissonian error
        # compare data and analytic profile <=> get stellar
        # density or mass ratio from Matt Walker
        if(np.isnan(Sigerr)):
            P_dens[b] = P_dens[b-1]  # [1]
            P_edens[b]= P_edens[b-1] # [1]
        else:
            P_dens[b] = Sig/Sig0   # [1]
            P_edens[b]= Sigerr/Sig0 # [1]
        print(Rbin[b], Binmin[b], Binmax[b], P_dens[b], P_edens[b], file=f_Sig)
        # 3*[rscale], [dens0], [dens0]
        indr = (R<Binmax[b])
        Menclosed = float(np.sum(indr))/totmass_tracers # for normalization to 1#[totmass_tracers]
        Merr = Menclosed/np.sqrt(tpbb) # or artificial Menclosed/10 #[totmass_tracers]
        print(Rbin[b], Binmin[b], Binmax[b], Menclosed, Merr, file=f_mass) # [Rscale0], 2* [totmass_tracers]
    f_Sig.close()
    f_mass.close()

    # deproject Sig to get nu
    numedi = gip.Sig_INT_rho(Rbin*Rscalei, Sig0pc*P_dens, gp)
    #numin  = gip.Sig_INT_rho(Rbin*Rscalei, Sig0pc*(P_dens-P_edens), gp)
    numax  = gip.Sig_INT_rho(Rbin*Rscalei, Sig0pc*(P_dens+P_edens), gp)
    nu0pc  = numedi[0]
    gf.write_nu_scale(gp.files.get_scale_file(pop), nu0pc)
    nuerr  = numax-numedi
    for b in range(gp.nipol):
        print(Rbin[b], Binmin[b], Binmax[b],\
              numedi[b]/nu0pc, nuerr[b]/nu0pc, \
              file = f_nu)
    f_nu.close()
    # write dummy sig scale, not to be used later on
    maxsiglos = -1. #[km/s]
    fpars = open(gp.files.get_scale_file(pop),'a')
    print(maxsiglos, file=fpars)          #[km/s]
    fpars.close()
Esempio n. 2
0
def run(gp):
    import gr_params
    gpr = gr_params.grParams(gp)
    xall,yall,zall = np.loadtxt(gp.files.get_com_file(0),skiprows=1,\
                                usecols=(0,1,2),unpack=True) # 2*[rscale0]
    rscale0 = gf.read_Xscale(gp.files.get_scale_file(0)+'_3D')
    xall *= rscale0
    yall *= rscale0
    zall *= rscale0

    # calculate 3D
    r = np.sqrt(xall**2+yall**2+zall**2) #[pc]

    # set number and size of (linearly spaced) bins
    rmin = 0. # [pc]
    rmax = max(r) if gp.maxR < 0 else 1.0*gp.maxR           # [pc]
    print('rmax [rscale] = ', rmax)
    r = r[(r<rmax)] # [pc]

    binmin, binmax, rbin = gh.determine_radius(r, rmin, rmax, gp) # [pc]
    vol = volume_spherical_shell(binmin, binmax, gp) # [pc^3]

    for pop in range(gp.pops+1):
        print('#######  working on component ',pop)
        print('input: ',gp.files.get_com_file(pop)+'_3D')
        # start from data centered on COM already:
        if gf.bufcount(gp.files.get_com_file(pop)+'_3D')<2: continue
        x,y,z,v = np.loadtxt(gp.files.get_com_file(pop)+'_3D',\
                           skiprows=1,usecols=(0,1,2,3),unpack=True)
        # 3*[rscale], [km/s]
        rscalei = gf.read_Xscale(gp.files.get_scale_file(pop)) # [pc]
        x *= rscalei
        y *= rscalei
        z *= rscalei
        # calculate 2D radius on the skyplane
        r = np.sqrt(x**2+y**2+z**2) # [pc]

        # set maximum radius (if gp.maxR is set)
        rmax = max(r) if gp.maxR<0 else 1.0*gp.maxR # [pc]
        print('rmax [pc] = ', rmax)
        sel = (r<=rmax)
        x = x[sel]; y = y[sel]; z = z[sel]; v = v[sel]; r = r[sel] # [rscale]
        totmass_tracers = 1.*len(x) # [Munit], Munit = 1/star

        rs = r                   # + possible starting offset, [rscale]
        vlos = v                 # + possible starting offset, [km/s]

        gf.write_tracer_file(gp.files.get_ntracer_file(pop)+'_3D', totmass_tracers)
        de, em = gf.write_headers_3D(gp, pop)

        # gpr.n=30 iterations for getting random picked radius values
        density = np.zeros((gp.nipol,gpr.n))
        a       = np.zeros((gp.nipol,gpr.n)) # shared by density, siglos, kappa calcs
        for k in range(gpr.n):
            rsi = gpr.Rerr * np.random.randn(len(rs)) + rs # [pc]
            vlosi = gpr.vrerr*np.random.randn(len(vlos)) + vlos # [km/s]
            for i in range(gp.nipol):
                ind1 = np.argwhere(np.logical_and(rsi>=binmin[i], rsi<binmax[i])).flatten() # [1]
                density[i][k] = (1.*len(ind1))/vol[i]*totmass_tracers # [Munit/rscale^2]
                vlos1 = vlosi[ind1]                           # [km/s]
                a[i][k] = 1.*len(ind1)                        # [1]


        dens0 = np.sum(density[0])/(1.*gpr.n) # [Munit/rscale^3]
        print('dens0 = ',dens0,' [Munit/rscale^3]')

        dens0pc = dens0/rscale0**3
        gf.write_Sig_scale(gp.files.get_scale_file(pop)+'_3D', dens0pc, totmass_tracers)

        tpb0   = np.sum(a[0])/float(gpr.n)     # [1] tracers per bin
        denserr0 = dens0/np.sqrt(tpb0)       # [Munit/rscale^3]
        p_dens  = np.zeros(gp.nipol)
        p_edens = np.zeros(gp.nipol)
        for b in range(gp.nipol):
            dens = np.sum(density[b])/float(gpr.n) # [Munit/rscale^3]
            tpb  = np.sum(a[b])/float(gpr.n)       # [1]
            denserr = dens/np.sqrt(tpb)            # [Munit/rscale^3]

            if(np.isnan(denserr)):
                p_dens[b] = p_dens[b-1]                          # [1]
                p_edens[b]= p_edens[b-1]                         # [1]
            else:
                p_dens[b] = dens/dens0                           # [1]
                p_edens[b]= denserr/dens0 # [1] #100/rbin would be artificial guess

            print(rbin[b], binmin[b], binmax[b], p_dens[b], p_edens[b], file=de)
            # [rscale], 2*[dens0]
            indr = (r<binmax[b])
            menclosed = float(np.sum(indr))/totmass_tracers # for normalization to 1
            # [totmass_tracers]
            merr = menclosed/np.sqrt(tpb) # artificial menclosed/10 # [totmass_tracers]
            print(rbin[b], binmin[b], binmax[b], menclosed, merr, file=em)
            # [rscale], 2*[totmass_tracers]
        de.close()
        em.close()

        if gpr.showplots:
            print('plotting for pop ', pop)
            #show_plots_dens(rbin, p_dens, p_edens, gp)
            mf1 = 0.02 #1/totmass_tracers
            mf2 = 0.02
            rho_dm, rho_star1, rho_star2 = ga.rho_walk(rbin*rscale0, gp, mf1, mf2)

            if pop == 0:
                loglog(rbin*rscale0, rho_star1+rho_star2, 'k.-', lw=0.5)
            elif pop == 1:
                loglog(rbin*rscale0, rho_star1, 'b.-', lw = 0.5)
            elif pop == 2:
                loglog(rbin*rscale0, rho_star2, 'g.-', lw = 0.5)

            loglog(rbin*rscale0, dens0pc*p_dens, 'r.-')
            pdb.set_trace()
            clf()
Esempio n. 3
0
def run(gp):
    import gr_params
    gpr = gr_params.grParams(gp)

    for pop in range(2):
        # get radius, used for all binning
        print('input: ', gp.files.get_com_file(pop))
        if gf.bufcount(gp.files.get_com_file(pop))<2:
            return
        x,y,vlos = np.loadtxt(gp.files.get_com_file(pop), skiprows=1, unpack=True) #2*[rscale], [km/s]
        # totmass_tracers = 1.*len(x)  # [Munit], [Munit], where each star is weighted with the same mass
        r = np.sqrt(x*x+y*y) # [rscale]

        #set binning
        #gp.nipol = (max - min)*N^(1/3)/(2*(Q3-Q1)) #(method of wand)
        rmin = 0.                                       # [rscale]
        rmax = max(r) if gp.maxR < 0 else 1.0*gp.maxR # [rscale]

        binmin, binmax, rbin = gh.determine_radius(r, rmin, rmax, gp) # [rscale0]

        # offset from the start!
        rs = gpr.Rerr*np.random.randn(len(r))+r #[rscale]
        vlos = gpr.vrerr*np.random.randn(len(vlos))+vlos #[km/s]
        vfil = open(gp.files.sigfiles[pop], 'w')
        print('r', 'sigma_r(r)', 'error', file=vfil)

        # 30 iterations for drawing a given radius in bin
        dispvelocity = np.zeros((gp.nipol,gpr.n))
        a = np.zeros((gp.nipol,gpr.n))
        p_dvlos = np.zeros(gp.nipol)
        p_edvlos = np.zeros(gp.nipol)

        for k in range(gpr.n):
            rsi = gpr.Rerr*np.random.randn(len(rs))+rs #[rscale]
            vlosi = gpr.vrerr*np.random.randn(len(vlos))+vlos #[km/s]
            for i in range(gp.nipol):
                ind1 = np.argwhere(np.logical_and(rsi>binmin[i],rsi<binmax[i])).flatten()
                a[i][k] = len(ind1) #[1]
                vlos1 = vlosi[ind1] #[km/s]
                if(len(ind1)<=1):
                    dispvelocity[i][k] = dispvelocity[i-1][k]
                    # attention! should be 0, uses last value
                else:
                    dispvelocity[i][k] = meanbiweight(vlos1,ci_perc=68.4,\
                                                      ci_mean=True,ci_std=True)[1]
                    # [km/s], see BiWeight.py

        for i in range(gp.nipol):
            dispvel = np.sum(dispvelocity[i])/gpr.n #[km/s]
            ab = np.sum(a[i])/(1.*gpr.n) #[1]
            if ab == 0:
                dispvelerr = p_edvlos[i-1] #[km/s]
                # attention! uses last error
            else:
                dispvelerr = dispvel/np.sqrt(ab) #[km/s]
            p_dvlos[i] = dispvel      #[km/s]
            p_edvlos[i]= dispvelerr #[km/s]

        maxsiglos = max(p_dvlos) #[km/s]
        print('maxsiglos = ',maxsiglos,'[km/s]')
        fpars = open(gp.files.get_scale_file(pop),'a')
        print(maxsiglos, file=fpars)          #[km/s]
        fpars.close()
        #import shutil
        #shutil.copy2(gp.files.get_scale_file(0), gp.files.get_scale_file(1))

        for i in range(gp.nipol):
            #             [rscale]  [maxsiglos]                  [maxsiglos]
            print(rbin[i], binmin[i], binmax[i], np.abs(p_dvlos[i]/maxsiglos),np.abs(p_edvlos[i]/maxsiglos), file=vfil) #/np.sqrt(n))
        vfil.close()
Esempio n. 4
0
def run(gp):
    pop = 0
    import gr_params
    gpr = gr_params.grParams(gp)
    xall, yall = np.loadtxt(gp.files.get_com_file(0),
                            skiprows=1,
                            usecols=(0, 1),
                            unpack=True)
    # 2*[Rscale0]
    R = np.sqrt(xall**2 + yall**2)  # [Rscale0]
    # set number and size of (linearly spaced) bins
    Rmin = 0.  # [Rscale0]
    Rmax = max(R) if gp.maxR < 0 else 1.0 * gp.maxR  # [Rscale0]
    R = R[(R < Rmax)]  # [Rscale0]
    Binmin, Binmax, Rbin = gh.determine_radius(R, Rmin, Rmax, gp)  # [Rscale0]
    gp.xipol = Rbin
    minr = min(Rbin)  # [pc]
    maxr = max(Rbin)  # [pc]
    gp.xepol = np.hstack(
        [minr / 8., minr / 4., minr / 2., Rbin, 2 * maxr, 4 * maxr,
         8 * maxr])  # [pc]
    Vol = gh.volume_circular_ring(Binmin, Binmax, gp)  # [Rscale0^2]
    Rscale0 = float(gf.read_Xscale(gp.files.get_scale_file(0)))  # [pc]
    print('#######  working on component ', pop)
    print('input: ', gp.files.get_com_file(pop))
    # start from data centered on COM already:
    if gf.bufcount(gp.files.get_com_file(pop)) < 2:
        return
    # only read in data if needed: pops = 1: reuse data from pop=0 part
    x, y = np.loadtxt(gp.files.get_com_file(pop),
                      skiprows=1,
                      usecols=(0, 1),
                      unpack=True)
    # [Rscalei], [Rscalei]
    # calculate 2D radius on the skyplane
    R = np.sqrt(x**2 + y**2)  #[Rscalei]
    Rscalei = gf.read_Xscale(gp.files.get_scale_file(pop))  # [pc]
    # set maximum radius (if gp.maxR is set)
    Rmax = max(R) if gp.maxR < 0 else 1.0 * gp.maxR  # [Rscale0]
    print('Rmax [Rscale0] = ', Rmax)
    sel = (R * Rscalei <= Rmax * Rscale0)
    x = x[sel]  # [Rscalei]
    y = y[sel]  # [Rscalei]
    R = R[sel]  # [Rscalei]
    totmass_tracers = float(len(x))  # [Munit], Munit = 1/star
    Rs = R  # + possible starting offset, [Rscalei]
    tr = open(gp.files.get_ntracer_file(pop), 'w')
    print(totmass_tracers, file=tr)
    tr.close()
    f_Sig, f_nu, f_mass, f_sig, f_kap, f_zeta = gf.write_headers_2D(gp, pop)
    Sig_phot = np.zeros((gp.nipol, gpr.n))
    # particle selections, shared by density, siglos, kappa and zeta calculations
    tpb = np.zeros((gp.nipol, gpr.n))
    for k in range(gpr.n):
        Rsi = gh.add_errors(Rs, gpr.Rerr)  # [Rscalei]
        for i in range(gp.nipol):
            ind1 = np.argwhere(np.logical_and(Rsi * Rscalei >= Binmin[i] * Rscale0, \
                                          Rsi * Rscalei <  Binmax[i] * Rscale0)).flatten() # [1]
            tpb[i][k] = float(len(ind1))  #[1]
            Sig_phot[i][k] = float(
                len(ind1)) * totmass_tracers / Vol[i]  # [Munit/rscale^2]
    # do the following for all populations
    Sig0 = np.sum(Sig_phot[0]) / float(gpr.n)  # [Munit/Rscale^2]
    Sig0pc = Sig0 / Rscale0**2  # [munis/pc^2]
    gf.write_Sig_scale(gp.files.get_scale_file(pop), Sig0pc, totmass_tracers)

    # calculate density and mass profile, store it
    # ----------------------------------------------------------------------
    P_dens = np.zeros(gp.nipol)
    P_edens = np.zeros(gp.nipol)
    for b in range(gp.nipol):
        Sig = np.sum(Sig_phot[b]) / (1. * gpr.n)  # [Munit/Rscale^2]
        tpbb = np.sum(tpb[b]) / float(
            gpr.n)  # [1], mean number of tracers in bin
        Sigerr = Sig / np.sqrt(tpbb)  # [Munit/Rscale^2], Poissonian error
        # compare data and analytic profile <=> get stellar
        # density or mass ratio from Matt Walker
        if (np.isnan(Sigerr)):
            P_dens[b] = P_dens[b - 1]  # [1]
            P_edens[b] = P_edens[b - 1]  # [1]
        else:
            P_dens[b] = Sig / Sig0  # [1]
            P_edens[b] = Sigerr / Sig0  # [1]
        print(Rbin[b], Binmin[b], Binmax[b], P_dens[b], P_edens[b], file=f_Sig)
        # 3*[rscale], [dens0], [dens0]
        indr = (R < Binmax[b])
        Menclosed = float(
            np.sum(indr)
        ) / totmass_tracers  # for normalization to 1#[totmass_tracers]
        Merr = Menclosed / np.sqrt(
            tpbb)  # or artificial Menclosed/10 #[totmass_tracers]
        print(Rbin[b], Binmin[b], Binmax[b], Menclosed, Merr,
              file=f_mass)  # [Rscale0], 2* [totmass_tracers]
    f_Sig.close()
    f_mass.close()

    # deproject Sig to get nu
    numedi = gip.Sig_INT_rho(Rbin * Rscalei, Sig0pc * P_dens, gp)
    #numin  = gip.Sig_INT_rho(Rbin*Rscalei, Sig0pc*(P_dens-P_edens), gp)
    numax = gip.Sig_INT_rho(Rbin * Rscalei, Sig0pc * (P_dens + P_edens), gp)
    nu0pc = numedi[0]
    gf.write_nu_scale(gp.files.get_scale_file(pop), nu0pc)
    nuerr = numax - numedi
    for b in range(gp.nipol):
        print(Rbin[b], Binmin[b], Binmax[b],\
              numedi[b]/nu0pc, nuerr[b]/nu0pc, \
              file = f_nu)
    f_nu.close()
    # write dummy sig scale, not to be used later on
    maxsiglos = -1.  #[km/s]
    fpars = open(gp.files.get_scale_file(pop), 'a')
    print(maxsiglos, file=fpars)  #[km/s]
    fpars.close()
Esempio n. 5
0
def run():
    Rscale = []
    Dens0Rscale = []
    Dens0pc = []
    Totmass_Tracers = []
    Maxvlos = []
    rscale = []
    dens0Rscale = []
    dens0pc = []
    totmass_tracers = []
    maxvlos = []

    for comp in range(3):
        A = np.loadtxt(gp.files.get_scale_file(comp), unpack=False, skiprows=1)
        Rscale.append(A[0])
        Dens0Rscale.append(A[1])
        Dens0pc.append(A[2])
        Totmass_Tracers.append(A[3])

        B = np.loadtxt(gp.files.get_scale_file(comp) + '_3D',
                       unpack=False,
                       skiprows=1)
        rscale.append(B[0])
        dens0Rscale.append(B[1])
        dens0pc.append(B[2])
        totmass_tracers.append(B[3])

        print('#######  working on component ', comp)
        print('input: ', gp.files.get_com_file(comp) + '_3D')
        # start from data centered on COM already:
        if gf.bufcount(gp.files.get_com_file(comp) + '_3D') < 2: continue



        Rbin,Binmin,Binmax,Dens,Denserr = np.loadtxt(gp.files.nufiles[comp],\
                                                     skiprows=1,usecols=(0,1,2,3,4),\
                                                     unpack=True) # 3*[Rscale], [km/s]
        Rbin *= Rscale[comp]
        Binmin *= Rscale[comp]
        Binmax *= Rscale[comp]
        Dens *= Dens0pc[comp]
        Denserr *= Dens0pc[comp]



        rbin,binmin,binmax,dens,denserr = np.loadtxt(gp.files.nufiles[comp]+'_3D',\
                                                     skiprows=1,usecols=(0,1,2,3,4),\
                                                     unpack=True) # 3*[Rscale], [km/s]
        rbin *= rscale[comp]
        binmin *= rscale[comp]
        binmax *= rscale[comp]
        dens *= dens0pc[comp]
        denserr *= dens0pc[comp]

        ion()
        f = figure(figsize=(6, 3))
        ax1 = f.add_subplot(121)  # Nu
        ax2 = f.add_subplot(122, sharex=ax1)  # nu

        ax1.plot(Rbin, Dens, 'b', lw=1)
        lbound = Dens - Denserr
        lbound[lbound < 1e-6] = 1e-6
        ubound = Dens + Denserr
        ax1.fill_between(Rbin, lbound, ubound, alpha=0.5, color='r')
        ax1.set_yscale('log')
        ax1.set_xlim([0, np.max(Binmax)])
        ax1.set_ylim([np.min(lbound), np.max(ubound)])
        ax1.set_xlabel(r'$R [R_c]$')
        ax1.set_ylabel(r'$\nu_{2D}(R)/\nu_{2D}(0)$')

        try:
            ax1.plot(Rbin, rho_INT_Rho(Rbin, dens, denserr))
            ax1.plot(
                Rbin,
                rho_INT_Rho(Rbin, Rho_INT_rho(Rbin, Dens, Denserr), denserr))
        except Exception as detail:
            print('rho_INT_Rho giving NaN in plotting')
        draw()

        ax2.plot(rbin, dens, 'b', lw=1)
        lbound = dens - denserr
        lbound[lbound < 1e-6] = 1e-6
        ubound = dens + denserr
        ax2.fill_between(rbin, lbound, ubound, alpha=0.5, color='r')

        ax2.set_yscale('log')
        ax2.set_xlim([0, np.max(binmax)])
        ax2.set_ylim([np.min(lbound), np.max(ubound)])
        ax2.set_xlabel(r'$r [R_c]$')
        ax2.set_ylabel(r'$\nu(r)/\nu(0)$')
        ax2.yaxis.tick_right()
        ax2.yaxis.set_label_position("right")
        draw()

        # projNu = rho_INT_Rho(rbin, dens)
        # projNu = test(rbin, binmin, binmax, dens)
        # ax1.plot(rbin, projNu)

        ax2.plot(rbin, Rho_INT_rho(Rbin, Dens, Denserr), color='green')
        draw()

        pdb.set_trace()
        ioff()
        show()
Esempio n. 6
0
def run(gp):
    import gr_params
    gpr = gr_params.grParams(gp)
    xall,yall = np.loadtxt(gp.files.get_com_file(0), skiprows=1, usecols=(0,1), unpack=True)
    # 2*[Rscale0]
    R = np.sqrt(xall**2+yall**2) # [Rscale0]
    # set number and size of (linearly spaced) bins
    Rmin = 0. #[Rscale0]
    Rmax = max(R) if gp.maxR < 0 else 1.0*gp.maxR # [Rscale0]
    R = R[(R<Rmax)] # [Rscale0]
    Binmin, Binmax, Rbin = gh.determine_radius(R, Rmin, Rmax, gp) # [Rscale0]
    gp.xipol = Rbin
    minr = min(Rbin) # [pc]
    maxr = max(Rbin) # [pc]
    gp.xepol = np.hstack([minr/8., minr/4., minr/2., Rbin, 2*maxr, 4*maxr, 8*maxr]) # [pc]
    Vol = gh.volume_circular_ring(Binmin, Binmax, gp) # [Rscale0^2]
    Rscale0 = gf.read_Xscale(gp.files.get_scale_file(0)) # [pc]
    for pop in range(gp.pops+1):
        print('#######  working on component ',pop)
        print('input: ', gp.files.get_com_file(pop))
        # exclude second condition if self-consistent approach wished
        if gp.investigate == "obs" and gp.case==1 and pop==0:
            # for Fornax, overwrite first Sigma with deBoer data
            import gr_MCMCbin_for
            gr_MCMCbin_for.run(gp)
            continue
        # start from data centered on COM already:
        if gf.bufcount(gp.files.get_com_file(pop))<2:
            continue
        # only read in data if needed: pops = 1: reuse data from pop=0 part
        if (gp.pops == 1 and pop < 1 or gp.pops == 2) or gp.investigate == 'obs':
            x,y,v = np.loadtxt(gp.files.get_com_file(pop), skiprows=1,usecols=(0,1,2),unpack=True)
            # [Rscalei], [Rscalei], [km/s]
            # calculate 2D radius on the skyplane
            R = np.sqrt(x**2+y**2) #[Rscalei]
            Rscalei = gf.read_Xscale(gp.files.get_scale_file(pop)) # [pc]
            # set maximum radius (if gp.maxR is set)
            Rmax = max(R) if gp.maxR<0 else 1.0*gp.maxR # [Rscale0]
            print('Rmax [Rscale0] = ', Rmax)
            #pdb.set_trace()
            #from pylab import clf, hist, axvline, xlim
            #clf()
            #hist(np.log10(R*Rscalei), 40)
            #for i in range(len(Rbin)):
            #    axvline(np.log10(Rbin[i]*Rscale0))
            #xlim([np.log10(min(gp.xepol*Rscale0)), np.log10(max(gp.xepol*Rscale0))])
            sel = (R * Rscalei <= Rmax * Rscale0)
            x = x[sel]
            y = y[sel]
            v = v[sel]
            R = R[sel] # [Rscalei]
            totmass_tracers = float(len(x)) # [Munit], Munit = 1/star
            Rs = R                   # + possible starting offset, [Rscalei]
            vlos = v                 # + possible starting offset, [km/s]
        tr = open(gp.files.get_ntracer_file(pop),'w')
        print(totmass_tracers, file=tr)
        tr.close()
        f_Sig, f_nu, f_mass, f_sig, f_kap, f_zeta = gf.write_headers_2D(gp, pop)
        if (gp.pops == 1 and pop < 1) or gp.pops == 2 or gp.investigate == 'obs':
            Sig_kin   = np.zeros((gp.nipol, gpr.n))
            siglos    = np.zeros((gp.nipol, gpr.n))
            if gp.usekappa:
                kappa     = np.zeros((gp.nipol, gpr.n))
            if gp.usezeta:
                v2        = np.zeros((gp.nipol, gpr.n))
                v4        = np.zeros((gp.nipol, gpr.n))
                Ntot      = np.zeros(gpr.n)
                zetaa     = np.zeros(gpr.n)
                zetab     = np.zeros(gpr.n)
            # particle selections, shared by density, siglos, kappa and zeta calculations
            tpb       = np.zeros((gp.nipol,gpr.n))
            for k in range(gpr.n):
                Rsi   = gh.add_errors(Rs,   gpr.Rerr)   # [Rscalei]
                vlosi = gh.add_errors(vlos, gpr.vrerr)   # [km/s]
                for i in range(gp.nipol):
                    ind1 = np.argwhere(np.logical_and(Rsi * Rscalei >= Binmin[i] * Rscale0, Rsi * Rscalei <  Binmax[i] * Rscale0)).flatten() # [1]
                    tpb[i][k] = float(len(ind1)) # [1]
                    Sig_kin[i][k] = float(len(ind1))*totmass_tracers/Vol[i] # [Munit/rscale**2]
                    if(len(ind1)<=1):
                        siglos[i][k] = siglos[i-1][k]
                        print('### using last value, missing data')
                        if gp.usekappa:
                            kappa[i][k] = kappa[i-1][k]
                            # attention! should be 0, uses last value
                        if gp.usezeta:
                            v2[i][k] = v2[i-1][k]
                            v4[i][k] = v4[i-1][k]
                    else:
                        siglos[i][k] = meanbiweight(vlosi[ind1], ci_perc=68.4, \
                                                    ci_mean=True, ci_std=True)[1]
                        # [km/s], see BiWeight.py
                        if gp.usekappa:
                            kappa[i][k] = kurtosis(vlosi[ind1], axis=0, \
                                                   fisher=False, bias=False) # [1]
                        if gp.usezeta:
                            ave, adev, sdev, var, skew, curt = gh.moments(vlosi[ind1])
                            v2[i][k] = var
                            v4[i][k] = (curt+3)*var**2
                Sigma = Sig_kin[:,k]
                if gp.usezeta:
                    pdb.set_trace()
                    Ntot[k] = gh.Ntot(Rbin, Sigma, gp)
                    zetaa[k] = gh.starred(Rbin, v4[:,k], Sigma, Ntot[k], gp)
                    v2denom = (gh.starred(Rbin, v2[:,k], Sigma, Ntot[k], gp))**2
                    zetaa[k] /= v2denom
                    zetab[k] = gh.starred(Rbin, v4[:,k]*Rbin**2, Sigma, Ntot[k], gp)
                    zetab[k] /= v2denom
                    zetab[k] /= (gh.starred(Rbin, Rbin, Sigma, Ntot[k], gp))**2
            if gp.investigate == 'obs' and gp.case < 5:
                Sig_phot = obs_Sig_phot(Binmin, Binmax, Rscale0, Sig_kin, gp, gpr)
            else:
                Sig_phot = Sig_kin
        # do the following for all populations
        Sig0 = np.sum(Sig_phot[0])/float(gpr.n) # [Munit/Rscale^2]
        Sig0pc = Sig0/Rscale0**2              # [munis/pc^2]
        gf.write_Sig_scale(gp.files.get_scale_file(pop), Sig0pc, totmass_tracers)

        # calculate density and mass profile, store it
        # ----------------------------------------------------------------------
        #tpb0   = np.sum(tpb[0])/float(gpr.n)     # [1]
        #Sigerr0 = Sig0/np.sqrt(tpb0)       # [Munit/Rscale^2]
        P_dens  = np.zeros(gp.nipol)
        P_edens = np.zeros(gp.nipol)
        for b in range(gp.nipol):
            Sig = np.sum(Sig_kin[b])/(1.*gpr.n) # [Munit/Rscale^2]
            tpbb   = np.sum(tpb[b])/float(gpr.n)       # [1], mean number of tracers in bin
            Sigerr = Sig/np.sqrt(tpbb)       # [Munit/Rscale^2], Poissonian error
            # compare data and analytic profile <=> get stellar
            # density or mass ratio from Matt Walker
            if(np.isnan(Sigerr)):
                P_dens[b] = P_dens[b-1]  # [1]
                P_edens[b]= P_edens[b-1] # [1]
            else:
                P_dens[b] = Sig/Sig0   # [1]
                P_edens[b]= Sigerr/Sig0 # [1]
            print(Rbin[b], Binmin[b], Binmax[b], P_dens[b], P_edens[b], file=f_Sig)
            # 3*[rscale], [dens0], [dens0]
            indr = (R<Binmax[b])
            Menclosed = float(np.sum(indr))/totmass_tracers # for normalization to 1#[totmass_tracers]
            Merr = Menclosed/np.sqrt(tpbb) # or artificial Menclosed/10 #[totmass_tracers]
            print(Rbin[b], Binmin[b], Binmax[b], Menclosed, Merr, file=f_mass) # [Rscale0], 2* [totmass_tracers]
        f_Sig.close()
        f_mass.close()
        # deproject Sig to get nu
        numedi = gip.Sig_INT_rho(Rbin*Rscalei, Sig0pc*P_dens, gp)
        #numin  = gip.Sig_INT_rho(Rbin*Rscalei, Sig0pc*(P_dens-P_edens), gp)
        numax  = gip.Sig_INT_rho(Rbin*Rscalei, Sig0pc*(P_dens+P_edens), gp)
        nu0pc  = numedi[0]
        gf.write_nu_scale(gp.files.get_scale_file(pop), nu0pc)
        nuerr  = numax-numedi
        for b in range(gp.nipol):
            print(Rbin[b], Binmin[b], Binmax[b], numedi[b]/nu0pc, nuerr[b]/nu0pc, file = f_nu)
        f_nu.close()
        # calculate and output siglos
        # --------------------------------------------
        p_dvlos = np.zeros(gp.nipol)
        p_edvlos = np.zeros(gp.nipol)
        for b in range(gp.nipol):
            sig = np.sum(siglos[b])/gpr.n #[km/s]
            tpbb = np.sum(tpb[b])/float(gpr.n) #[1]
            if tpbb == 0:
                sigerr = p_edvlos[b-1] #[km/s]
                # attention! uses last error
            else:
                # Poisson error with measurement errors
                #sigerr = sig/np.sqrt(tpbb)
                #sigerr = np.sqrt(sigerr**2+2**2) # 2km/s

                # standard deviation
                #sigerr = stddevbiweight(siglos[b])

                # Poisson error, first guess
                sigerr = sig/np.sqrt(tpbb) #[km/s]
            p_dvlos[b] = sig    #[km/s]
            p_edvlos[b]= sigerr #[km/s]
        maxsiglos = max(p_dvlos) #[km/s]
        print('maxsiglos = ', maxsiglos, '[km/s]')
        fpars = open(gp.files.get_scale_file(pop),'a')
        print(maxsiglos, file=fpars)          #[km/s]
        fpars.close()
        for b in range(gp.nipol):
            print(Rbin[b], Binmin[b], Binmax[b], np.abs(p_dvlos[b]/maxsiglos),\
                  np.abs(p_edvlos[b]/maxsiglos), file=f_sig)
            # 3*[rscale], 2*[maxsiglos]
        f_sig.close()
        # calculate and output kurtosis kappa
        # --------------------------------------------
        if gp.usekappa:
            p_kappa = np.zeros(gp.nipol) # needed for plotting later
            p_ekappa = np.zeros(gp.nipol)
            for b in range(gp.nipol):
                kappavel = np.sum(kappa[b])/gpr.n #[1]
                tpbb = np.sum(tpb[b])/float(gpr.n) #[1]
                if tpbb == 0:
                    kappavelerr = p_edvlos[b-1] #[1]
                    # attention! uses last error
                else:
                    kappavelerr = np.abs(kappavel/np.sqrt(tpbb)) #[1]
                p_kappa[b] = kappavel
                p_ekappa[b] = kappavelerr
                print(Rbin[b], Binmin[b], Binmax[b], \
                      kappavel, kappavelerr, file=f_kap)
                # [rscale], 2*[1]
            f_kap.close()
        # output zetas
        # -------------------------------------------------------------
        if gp.usezeta:
            print(np.median(zetaa), np.median(zetab), file=f_zeta)
            f_zeta.close()
        if gpr.showplots:
            gpr.show_plots_dens_2D(Rbin*Rscalei, P_dens, P_edens, Sig0pc)
            gpr.show_plots_sigma(Rbin*Rscalei, p_dvlos, p_edvlos)
            if gp.usekappa:
                gpr.show_plots_kappa(Rbin*Rscalei, p_kappa, p_ekappa)

        # overwrite Sig profile if photometric data is used
        if gp.investigate == 'obs' and gp.case==1 and pop==1 and not gp.selfconsistentnu:
            import os
            os.system('cp '+gp.files.get_scale_file(0)+' '+gp.files.get_scale_file(1))
            # replace last line with actual maxsiglos from tracer particles
            os.system("sed -i '$s/^.*/"+str(maxsiglos)+"/' "+gp.files.get_scale_file(1))
            os.system('cp '+gp.files.Sigfiles[0]+' '+gp.files.Sigfiles[1])
            continue
Esempio n. 7
0
def run():
    Rscale = []; Dens0Rscale = []; Dens0pc = []; Totmass_Tracers = []; Maxvlos = []
    rscale = []; dens0Rscale = []; dens0pc = []; totmass_tracers = []; maxvlos = []

    for comp in range(3):
        A = np.loadtxt(gp.files.get_scale_file(comp), unpack=False, skiprows=1)
        Rscale.append(A[0])
        Dens0Rscale.append(A[1])
        Dens0pc.append(A[2])
        Totmass_Tracers.append(A[3])

        B = np.loadtxt(gp.files.get_scale_file(comp)+'_3D', unpack=False, skiprows=1)
        rscale.append(B[0])
        dens0Rscale.append(B[1])
        dens0pc.append(B[2])
        totmass_tracers.append(B[3])

        print('#######  working on component ',comp)
        print('input: ',gp.files.get_com_file(comp)+'_3D')
        # start from data centered on COM already:
        if gf.bufcount(gp.files.get_com_file(comp)+'_3D')<2: continue



        Rbin,Binmin,Binmax,Dens,Denserr = np.loadtxt(gp.files.nufiles[comp],\
                                                     skiprows=1,usecols=(0,1,2,3,4),\
                                                     unpack=True) # 3*[Rscale], [km/s]
        Rbin*=Rscale[comp]; Binmin*=Rscale[comp]; Binmax*=Rscale[comp]; Dens*=Dens0pc[comp]; Denserr*=Dens0pc[comp]



        rbin,binmin,binmax,dens,denserr = np.loadtxt(gp.files.nufiles[comp]+'_3D',\
                                                     skiprows=1,usecols=(0,1,2,3,4),\
                                                     unpack=True) # 3*[Rscale], [km/s]
        rbin*=rscale[comp]; binmin*=rscale[comp]; binmax*=rscale[comp]; dens*=dens0pc[comp]; denserr*=dens0pc[comp]


        ion()
        f=figure(figsize=(6,3))
        ax1 = f.add_subplot(121)                         # Nu
        ax2 = f.add_subplot(122, sharex=ax1)             # nu

        ax1.plot(Rbin, Dens,'b',lw=1)
        lbound = Dens-Denserr; lbound[lbound<1e-6] = 1e-6
        ubound = Dens+Denserr;
        ax1.fill_between(Rbin,lbound,ubound,alpha=0.5,color='r')
        ax1.set_yscale('log')
        ax1.set_xlim([0,np.max(Binmax)])
        ax1.set_ylim([np.min(lbound),np.max(ubound)])
        ax1.set_xlabel(r'$R [R_c]$')
        ax1.set_ylabel(r'$\nu_{2D}(R)/\nu_{2D}(0)$')

        try:
            ax1.plot(Rbin,rho_INT_Rho(Rbin,dens,denserr))
            ax1.plot(Rbin,rho_INT_Rho(Rbin,Rho_INT_rho(Rbin,Dens,Denserr),denserr))
        except Exception as detail:
            print('rho_INT_Rho giving NaN in plotting')
        draw()


        ax2.plot(rbin, dens,'b',lw=1)
        lbound = dens-denserr; lbound[lbound<1e-6] = 1e-6
        ubound = dens+denserr;
        ax2.fill_between(rbin,lbound,ubound,alpha=0.5,color='r')

        ax2.set_yscale('log')
        ax2.set_xlim([0,np.max(binmax)])
        ax2.set_ylim([np.min(lbound),np.max(ubound)])
        ax2.set_xlabel(r'$r [R_c]$')
        ax2.set_ylabel(r'$\nu(r)/\nu(0)$')
        ax2.yaxis.tick_right()
        ax2.yaxis.set_label_position("right")
        draw()

        # projNu = rho_INT_Rho(rbin, dens)
        # projNu = test(rbin, binmin, binmax, dens)
        # ax1.plot(rbin, projNu)

        ax2.plot(rbin,Rho_INT_rho(Rbin,Dens,Denserr),color='green')
        draw()

        pdb.set_trace()
        ioff(); show()
Esempio n. 8
0
def run(gp):
    import gr_params
    gpr = gr_params.grParams(gp)
    xall,yall,zall = np.loadtxt(gp.files.get_com_file(0),skiprows=1,\
                                usecols=(0,1,2),unpack=True) # 2*[rscale0]
    rscale0 = gf.read_Xscale(gp.files.get_scale_file(0) + '_3D')
    xall *= rscale0
    yall *= rscale0
    zall *= rscale0

    # calculate 3D
    r = np.sqrt(xall**2 + yall**2 + zall**2)  #[pc]

    # set number and size of (linearly spaced) bins
    rmin = 0.  # [pc]
    rmax = max(r) if gp.maxR < 0 else 1.0 * gp.maxR  # [pc]
    print('rmax [rscale] = ', rmax)
    r = r[(r < rmax)]  # [pc]

    binmin, binmax, rbin = gh.determine_radius(r, rmin, rmax, gp)  # [pc]
    vol = volume_spherical_shell(binmin, binmax, gp)  # [pc^3]

    for pop in range(gp.pops + 1):
        print('#######  working on component ', pop)
        print('input: ', gp.files.get_com_file(pop) + '_3D')
        # start from data centered on COM already:
        if gf.bufcount(gp.files.get_com_file(pop) + '_3D') < 2: continue
        x,y,z,v = np.loadtxt(gp.files.get_com_file(pop)+'_3D',\
                           skiprows=1,usecols=(0,1,2,3),unpack=True)
        # 3*[rscale], [km/s]
        rscalei = gf.read_Xscale(gp.files.get_scale_file(pop))  # [pc]
        x *= rscalei
        y *= rscalei
        z *= rscalei
        # calculate 2D radius on the skyplane
        r = np.sqrt(x**2 + y**2 + z**2)  # [pc]

        # set maximum radius (if gp.maxR is set)
        rmax = max(r) if gp.maxR < 0 else 1.0 * gp.maxR  # [pc]
        print('rmax [pc] = ', rmax)
        sel = (r <= rmax)
        x = x[sel]
        y = y[sel]
        z = z[sel]
        v = v[sel]
        r = r[sel]  # [rscale]
        totmass_tracers = 1. * len(x)  # [Munit], Munit = 1/star

        rs = r  # + possible starting offset, [rscale]
        vlos = v  # + possible starting offset, [km/s]

        gf.write_tracer_file(
            gp.files.get_ntracer_file(pop) + '_3D', totmass_tracers)
        de, em = gf.write_headers_3D(gp, pop)

        # gpr.n=30 iterations for getting random picked radius values
        density = np.zeros((gp.nipol, gpr.n))
        a = np.zeros(
            (gp.nipol, gpr.n))  # shared by density, siglos, kappa calcs
        for k in range(gpr.n):
            rsi = gpr.Rerr * np.random.randn(len(rs)) + rs  # [pc]
            vlosi = gpr.vrerr * np.random.randn(len(vlos)) + vlos  # [km/s]
            for i in range(gp.nipol):
                ind1 = np.argwhere(
                    np.logical_and(rsi >= binmin[i],
                                   rsi < binmax[i])).flatten()  # [1]
                density[i][k] = (
                    1. *
                    len(ind1)) / vol[i] * totmass_tracers  # [Munit/rscale^2]
                vlos1 = vlosi[ind1]  # [km/s]
                a[i][k] = 1. * len(ind1)  # [1]

        dens0 = np.sum(density[0]) / (1. * gpr.n)  # [Munit/rscale^3]
        print('dens0 = ', dens0, ' [Munit/rscale^3]')

        dens0pc = dens0 / rscale0**3
        gf.write_Sig_scale(
            gp.files.get_scale_file(pop) + '_3D', dens0pc, totmass_tracers)

        tpb0 = np.sum(a[0]) / float(gpr.n)  # [1] tracers per bin
        denserr0 = dens0 / np.sqrt(tpb0)  # [Munit/rscale^3]
        p_dens = np.zeros(gp.nipol)
        p_edens = np.zeros(gp.nipol)
        for b in range(gp.nipol):
            dens = np.sum(density[b]) / float(gpr.n)  # [Munit/rscale^3]
            tpb = np.sum(a[b]) / float(gpr.n)  # [1]
            denserr = dens / np.sqrt(tpb)  # [Munit/rscale^3]

            if (np.isnan(denserr)):
                p_dens[b] = p_dens[b - 1]  # [1]
                p_edens[b] = p_edens[b - 1]  # [1]
            else:
                p_dens[b] = dens / dens0  # [1]
                p_edens[
                    b] = denserr / dens0  # [1] #100/rbin would be artificial guess

            print(rbin[b],
                  binmin[b],
                  binmax[b],
                  p_dens[b],
                  p_edens[b],
                  file=de)
            # [rscale], 2*[dens0]
            indr = (r < binmax[b])
            menclosed = float(
                np.sum(indr)) / totmass_tracers  # for normalization to 1
            # [totmass_tracers]
            merr = menclosed / np.sqrt(
                tpb)  # artificial menclosed/10 # [totmass_tracers]
            print(rbin[b], binmin[b], binmax[b], menclosed, merr, file=em)
            # [rscale], 2*[totmass_tracers]
        de.close()
        em.close()

        if gpr.showplots:
            print('plotting for pop ', pop)
            #show_plots_dens(rbin, p_dens, p_edens, gp)
            mf1 = 0.02  #1/totmass_tracers
            mf2 = 0.02
            rho_dm, rho_star1, rho_star2 = ga.rho_walk(rbin * rscale0, gp, mf1,
                                                       mf2)

            if pop == 0:
                loglog(rbin * rscale0, rho_star1 + rho_star2, 'k.-', lw=0.5)
            elif pop == 1:
                loglog(rbin * rscale0, rho_star1, 'b.-', lw=0.5)
            elif pop == 2:
                loglog(rbin * rscale0, rho_star2, 'g.-', lw=0.5)

            loglog(rbin * rscale0, dens0pc * p_dens, 'r.-')
            pdb.set_trace()
            clf()