run.jl

using Pkg
Pkg.activate(".")

Z = 0.019422
EBV = 0.077

using Revise, Statistics, Dierckx, DataFrames
using QSFit, GFit, Gnuplot, GFitViewer, MyAstroUtils
using CL_1ES_1927p654
using Dates
using TextParse
import StatsBase, JLD2

path = "output-" * readlines(`git branch --show-current`)[1]
mkdir("$(path)")
epoch_filenames = Vector{String}()
for (root, dirs, files) in walkdir("AT2018zf")
    for file in files
        if file[end-3:end] == ".dat"
            push!(epoch_filenames, root * "/" * file)
        end
    end
end

function read_spec(epoch_id; kw...)
    if epoch_id == "B03"
        file = "boller2003.txt"
    else
        file = epoch_filenames[epoch_id]
    end
    println(file)
	spec = Spectrum(Val(:ASCII), file, columns=[1,2]; label="$epoch_id: $file", kw...);
    if isa(epoch_id, Number)
        spec.flux ./= all_scale[epoch_id]
        spec.err  ./= all_scale[epoch_id]
    end
    return spec
end


source = QSO{q1927p654}("1ES 1927+654 (Boller03)", Z, ebv=EBV);
source.options[:min_spectral_coverage][:OIII_5007] = 0.35
# source.options[:host_template] = "/home/gcalderone/Mbi1.30Zm1.49T00.0700_iTp0.00_baseFe_linear_FWHM_2.51"
#=
Resolution: from  Sect 3 it is  6 / 5007 * 3e5 ~ 360 km/s
however with this value the [OIII] FWHM is 100 km/s (limit)
I tried 180, 200 and 250, and the [OIII] luminosity do not change
=#
spec = read_spec("B03", resolution=200.)
add_spec!(source, spec);
res = qsfit(source);
viewer(res, showcomps=[:qso_cont, :galaxy, :balmer],
       filename="$(path)/results_boller.html")
println(res.model[:OIII_5007].norm.val )
# 0.0002913095378291511
println(res.model[:OIII_5007].norm.val / res.model[:galaxy].norm.val )
# 61.34678931179987



if !isfile("$(path)/scale_fwhm.dat")
    all_scale = fill(1., length(epoch_filenames))
    all_fwhm  = fill(NaN,length(epoch_filenames))
    for id in 1:length(epoch_filenames)
        spec = read_spec(id)
        all_scale[id] *= median(spec.flux) / 25000

        try
            source = QSO{q1927p654}("1ES 1927+654 ($id)", Z, ebv=EBV);
            source.options[:min_spectral_coverage][:OIII_5007] = 0.5
            # source.options[:host_template] = "/home/gcalderone/Mbi1.30Zm1.49T00.0700_iTp0.00_baseFe_linear_FWHM_2.51"
            spec = read_spec(id)
            add_spec!(source, spec);
            res = qsfit(source);
            viewer(res, showcomps=[:qso_cont, :galaxy, :balmer],
                   filename="$(path)/results_$(id).html")

            # Update all_scale and store FWHM
            @info res.model[:OIII_5007].norm.val
            all_scale[id] *= res.model[:OIII_5007].norm.val
            all_fwhm[ id]  = res.model[:OIII_5007].fwhm.val
        catch
        end
    end
    all_scale[.!isfinite.(all_fwhm)] .= NaN
    JLD2.save_object("$(path)/scale_fwhm.dat", (all_scale, all_fwhm))
else
    (all_scale, all_fwhm) = JLD2.load_object("$(path)/scale_fwhm.dat")
end

@gp :prenorm "set key bottom right" "set grid" xlab="Epoch" ylab="Value" :-
@gp :- :prenorm all_scale./1e-18 "w lp t '[OIII] norm.'" :-
@gp :- :prenorm  all_fwhm./1000 "w lp t '[OIII] FWHM (x1000 km/s)"
save(:prenorm, term="png size 800,600", output="$(path)/oiii_norm_fwhm.png")

w = 10 .^(2:0.01:log10(400));
r = sqrt.(400^2 .- w.^2) ./ 2.355;
@gp w r "w l t '400 km/s'"

w = 10 .^(2:0.01:log10(900));
r = sqrt.(900^2 .- w.^2) ./ 2.355;
@gp :- w r "w l t '900 km/s'"
@gp :- "set grid" xlab="Actual FWHM" ylab="Instr. resolution"


# Ensure no sample is negative
@gp :allepochs "set grid" xr=[3e3,1e4] cbr=[1,29] :-
@gp :- :allepochs cblabel="Epoch" xlab="Rest frame wavelength[A]" ylab="Flux density [arb.units]"
for id in 1:length(epoch_filenames)
	s = read_spec(id)
	x = s.λ;
	y = s.flux;
    y .-= median(y)
    y ./= maximum(y)
    @gp :- :allepochs x./(1+Z) y "u 1:(\$2+$id):($id) w l notit lc pal" :-
end
@gp :- :allepochs yr=[1, 29]
save(:allepochs, term="png size 800,600", output="$(path)/all_epochs.png")
@gp :- :allepochs xr=[4900, 5100]
save(:allepochs, term="png size 800,2000", output="$(path)/all_epochs_zoom.png")



dict_chosen_epochs = Dict(
    :vecchi   => [17, 10, 21, 23],
    :lowres   => [8,9,10,11,12,14,15,16,18,21,22,23,24,25],
    :highres  => [5, 7, 13, 17, 20],
    :limited  => [1,2,3,13],
    :all      => collect(5:26))
# deleteat!(dict_chosen_epochs[:all], 4)  #insufficient coverage in na_Hg

# Can't use resolution smaller than 150 km / s otherwise some line
# will be neglected because of spectral coverage
resolution = Dict()
#    :lowres  => 350.,
#    :highres => 150.)

job = :all
chosen_epochs = dict_chosen_epochs[job]
Nloop = 6
(all_scale, all_fwhm) = JLD2.load_object("$(path)/scale_fwhm.dat")
for loop in 1:Nloop
    file = "$(path)/results_$(job)_$(loop).dat"
    if !isfile(file)
        source = QSO{q1927p654}("1ES 1927+654", Z, ebv=EBV);
        source.options[:min_spectral_coverage][:OIII_5007] = 0.5
        source.options[:wavelength_range] = [3500, 6900]
        @gp :zoom "set grid" :-
        for id in chosen_epochs
            spec = read_spec(id, resolution=get(resolution, job, NaN))
            add_spec!(source, spec);
            @gp :- :zoom xr=[4750,5150] spec.λ ./ (1 + source.z) spec.flux "w l t '$(id)'"
        end
        res = qsfit_multi(source);
        JLD2.jldsave(file; res)
        viewer(res, showcomps=[:qso_cont, :galaxy, :balmer], filename="$(path)/results_$(job)_$(loop).html")
        viewer(res, showcomps=[:qso_cont, :galaxy, :balmer], filename="$(path)/results_$(job)_$(loop)_rebin4.html", rebin=4)

        # Find best normalization for [OIII]
        multi2 = deepcopy(res.multi);
        for id in 1:length(chosen_epochs)
            for cname in collect(keys(multi2[id]))
                if cname == :OIII_5007
                    multi2[id][cname].norm.fixed = false
                    multi2[id][cname].fwhm.fixed = true  # degenerate with norm
                else
                    freeze(multi2[id], cname)
                end
            end
        end
        bestfit2 = fit!(res.source, multi2, res.pspecs)
        
        OIII_norm = fill(0., length(chosen_epochs))
        for id in 1:length(chosen_epochs)
            OIII_norm[id] = multi2[id][:OIII_5007].norm.val
            all_scale[chosen_epochs[id]] *= ((1 + multi2[id][:OIII_5007].norm.val) / 2)
        end
        JLD2.jldsave(file; res, all_scale, OIII_norm)
    else
        # res       = JLD2.load(file, "res")
        # all_scale = JLD2.load(file, "all_scale")
        # OIII_norm = JLD2.load(file, "OIII_norm")
        res, all_scale, OIII_norm = values(JLD2.load(file));
    end
end


OIII_norm_evol = fill(NaN, length(chosen_epochs))
for loop in 1:Nloop
    file = "$(path)/results_$(job)_$(loop).dat"
    res, all_scale, OIII_norm = values(JLD2.load(file))
    OIII_norm_evol = hcat(OIII_norm_evol, OIII_norm)
    println(res.fitres.fitstat / res.fitres.dof)
end
OIII_norm_evol = OIII_norm_evol[:,2:end]
@gp "set grid" :-
for id in 1:length(chosen_epochs)
    @gp :- 1:Nloop OIII_norm_evol[id, :] "w lp t '$(chosen_epochs[id])'"
end




function cont_at(bestfit, λ)
    A1 = bestfit[:qso_cont].norm.val - bestfit[:qso_cont].norm.unc
    A  = bestfit[:qso_cont].norm.val
    A2 = bestfit[:qso_cont].norm.val + bestfit[:qso_cont].norm.unc
    if A1 > A2
        A1, A2 = A2, A1
    end
    @assert A1 <= A2

    B1 = (λ / bestfit[:qso_cont].x0.val)^(bestfit[:qso_cont].alpha.val - bestfit[:qso_cont].alpha.unc)
    B  = (λ / bestfit[:qso_cont].x0.val)^(bestfit[:qso_cont].alpha.val)
    B2 = (λ / bestfit[:qso_cont].x0.val)^(bestfit[:qso_cont].alpha.val + bestfit[:qso_cont].alpha.unc)
    if B1 > B2
        B1, B2 = B2, B1
    end
    @assert B1 <= B2

    dd = extrema([A1*B1, A1*B2, A2*B1, A2*B2])

    return λ * A * B, λ * (dd[2]-dd[1])
end


tab = DataFrame(epoch=Int[], date=String[], instr=String[], galaxy=Float64[],
                contslope=Float64[],
                c3500=Float64[], c5100=Float64[],
                bb_Ha_norm=Float64[], bb_Ha_fwhm=Float64[], bb_Ha_voff=Float64[],
                br_Ha_norm=Float64[], br_Ha_fwhm=Float64[], br_Ha_voff=Float64[],
                na_Ha_norm=Float64[], na_Ha_fwhm=Float64[], na_Ha_voff=Float64[],
                bb_Hb_norm=Float64[], bb_Hb_fwhm=Float64[], bb_Hb_voff=Float64[],
                br_Hb_norm=Float64[], br_Hb_fwhm=Float64[], br_Hb_voff=Float64[],
                na_Hb_norm=Float64[], na_Hb_fwhm=Float64[], na_Hb_voff=Float64[],
                oiii_fwhm=Float64[],  oiii_voff=Float64[])

for id in 1:length(res.bestfit.models)
    push!(tab,
          (id, epoch_filenames[chosen_epochs[id]][27:end-4], "",
           res.bestfit[id][:galaxy].norm.val,
           res.bestfit[id][:qso_cont].alpha.val,
           cont_at(res.bestfit[id], 3500)[1],
           cont_at(res.bestfit[id], 5100)[1],
           res.bestfit[id][:bb_Ha].norm.patched, res.bestfit[id][:bb_Ha].fwhm.patched, res.bestfit[id][:bb_Ha].voff.patched,
           res.bestfit[id][:br_Ha].norm.patched, res.bestfit[id][:br_Ha].fwhm.patched, res.bestfit[id][:br_Ha].voff.patched,
           res.bestfit[id][:na_Ha].norm.patched, res.bestfit[id][:na_Ha].fwhm.patched, res.bestfit[id][:na_Ha].voff.patched,
           res.bestfit[id][:bb_Hb].norm.patched, res.bestfit[id][:bb_Hb].fwhm.patched, res.bestfit[id][:bb_Hb].voff.patched,
           res.bestfit[id][:br_Hb].norm.patched, res.bestfit[id][:br_Hb].fwhm.patched, res.bestfit[id][:br_Hb].voff.patched,
           res.bestfit[id][:na_Hb].norm.patched, res.bestfit[id][:na_Hb].fwhm.patched, res.bestfit[id][:na_Hb].voff.patched,
           res.bestfit[id][:OIII_5007].fwhm.patched, res.bestfit[id][:OIII_5007].voff.patched))
end

tab[!, :l3500] .= [3500 .* Spline1D(domain(res.multi[id])[:], res.multi[id]())(3500.) for id in 1:length(chosen_epochs)]
tab[!, :l5100] .= [5100 .* Spline1D(domain(res.multi[id])[:], res.multi[id]())(5100.) for id in 1:length(chosen_epochs)]
tab[!, :Ha] .= tab.br_Ha_norm .+ tab.bb_Ha_norm .+ tab.na_Ha_norm
tab[!, :Hb] .= tab.br_Hb_norm .+ tab.bb_Hb_norm .+ tab.na_Hb_norm

dd = Date.(tab.date, Ref("yyyymmdd"))
tab[!, :day] .= getproperty.(dd - Date("2018-03-06") .+ Day(72), :value)


(d, c) = csvread("misc/tabula-2019-Trakhtenbrot-mod.csv", ',', header_exists=true)
tmp = DataFrame(collect(d), Symbol.(c))
tmp[!, :Date] .= string.(tmp.Date)

tab[!, :instr] .= ""
for i in 1:nrow(tab)
    j = findfirst(tmp.Date .== tab[i, :date])
    isnothing(j)  &&  continue
    tab[i, :instr] = tmp[j, :Inst]
end

f = FITS("$(path)/1ES_1927p654_results_$(job).fits", "w")
write(f, tab)
close(f)


tab[!, :pt] .= 0
for i in 1:nrow(tab)
    j = findfirst(sort(unique(tab.instr)) .== tab[i, :instr])
    isnothing(j)  &&  continue
    tab[i, :pt] = j
end
cm = StatsBase.countmap(tab.instr)
setindex!.(Ref(cm), 1:length(cm), collect(keys(cm))[sortperm(collect(values(cm)), rev=true)])
tab.pt .= getindex.(Ref(cm), tab.instr)


@gp    tab.contslope tab.Ha    tab.pt "w lp t 'Ha'    pt var ps 2"  ylog=true
@gp :- tab.contslope tab.Hb    tab.pt "w lp t 'Hb'    pt var ps 2"
@gp :- tab.contslope tab.c5100 tab.pt "w lp t 'c5100' pt var ps 2"
@gp :- tab.contslope tab.l5100 tab.pt "w lp t 'l5100' pt var ps 2"
@gp :- tab.contslope tab.c3500 tab.pt "w lp t 'c3500' pt var ps 2"
@gp :- tab.contslope tab.l3500 tab.pt "w lp t 'l3500' pt var ps 2"


@gp    xlog=true ylog=true
@gp :- tab.c5100 tab.Ha tab.pt "w lp t 'c5100' pt var ps 2"
@gp :- tab.l5100 tab.Ha tab.pt "w lp t 'l5100' pt var ps 2"


@gp    tab.day tab.c5100 tab.pt "w lp t 'c5100' pt var ps 2" ylog=true
@gp :- tab.day tab.l5100 tab.pt "w lp t 'l5100' pt var ps 2"
@gp :- tab.day tab.Ha    tab.pt "w lp t 'Ha'    pt var ps 2"
@gp :- tab.day tab.Hb    tab.pt "w lp t 'Hb'    pt var ps 2"

@gp  tab.day tab.contslope tab.pt "w lp t 'SLope' pt var ps 2"


@gp "set grid"
for i in 1:nrow(tab)
    ss = "w l t '$(tab[i, :date])' dt $(tab[i, :pt]) lw 2"
    @gp :- domain(res.model[i])[:] res.model[i](:qso_cont) ss
end
save(:prenorm, term="png size 800,600", output="$(path)/evolution.png")


@gp "set grid"
for i in 1:length(chosen_epochs)
    println(res.bestfit[i][:OIII_5007])
    x  = domain(res.multi[i])[:]
    y  = res.multi[i]()
    y0 = y .- res.multi[i](:OIII_5007)
    ss = "w l t '$(tab[i, :date])' dt $(tab[i, :pt]) lw 2"
    @gp :- x y  .- Spline1D(x, y0)(5007.) ss
end
save(:prenorm, term="png size 800,600", output="$(path)/evolution_oiii_norm.png")