Updated meff to use plot_data and plot_func. Now the function output also...

Updated meff to use plot_data and plot_func. Now the function output also fig,ax if pl is true. Updated documentation

src/juobs_obs.jl

-@doc raw"""
-    meff(corr::Vector{uwreal}, plat::Vector{Int64}; pl::Bool=true, data::Bool=false, wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)     
+@doc raw""" 
+    meff(corr::Vector{uwreal}, plat::Vector{Int64}; pl::Bool=false, data::Bool=false, 
+    mu::Union{Vector{Float64}, Nothing}=nothing, kappa::Union{Vector{Float64}, Nothing}=nothing,
+    wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing, savepl::Bool=false,
+    filename::String="",plot_kw...) 
+    
+    meff(corr::Corr, plat::Vector{Int64}; kwargs..)
 
-    meff(corr::Corr, plat::Vector{Int64}; pl::Bool=true, data::Bool=false, wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
+    meff(corr::Vector{Corr},plat::Vector{Vector{Int64}}; kwargs...)
 
-Computes effective mass for a given correlator corr at a given plateau `plat`.
+Computes the mass associated to given correlator `corr` at a given plateau `plat`.
 Correlator can be passed as an `Corr` struct or `Vector{uwreal}`.
+In case of Vector{Corr} it is better to not broadcast, especially in case of `data=true` or `pl=true`, since the the overloaded function for Vector{Corr} takes care of the extra outputs and organize them into a `Tuple` of Vector
+
+# Arguments
+- `pl::Bool=false` and `savepl::Bool=false`: show and save the plots. The plots are made through the functions `plot_data` and `plot_func`. It is possible to pass keyword arguments for these two functions. 
+     When `savepl = true`, the plots are saved and closed. When `pl = true` the plot are generated, displayed and the last two returns are always `fig,ax` object to allow more costumability.
+     If both are `true`, `pl` is ignored.
     
-The flags `pl` and `data` allow to show the plots and return data as an extra result.
+     See also: [`plot_data`](@ref), [`plot_funct`](@ref).
+  - `data::Bool=false`: if set to `true`, the second return is a vector with the effective mass.
+  - `filename::String=""`: if given, overrides the automatically generated filename. `mkpath(dirname(filename))` is called before saving. If not given, a folder "meff/" is made and the correlator `μ` or `κ` are used to name the figure 
 
+# Examples
+- with one correlator
 ```@example
-data = read_mesons(path, "G5", "G5")
-corr_pp = corr_obs.(data)
-m = meff(corr_pp[1], [50, 60], pl=false)
+    data = read_mesons(path, "G5", "G5")[1]
+    corr_pp = corr_obs(data)
+    m = meff(corr_pp, [50, 60]) # return only meff
+```
+
+- with more correlator, making plots and returning data vector too 
+```@example
+    data = read_mesons(path, "G5", "G5")
+    corr_pp = corr_obs.(data)
+    m,fig,ax = meff(corr_pp, [[50, 60] for eachindex(corr_pp), pl=true)
+    # return meff, a vector of fig obj and a vector of ax obj
+    m,data = meff(corr_pp[1], [50, 60], pl=true,data=true, savepl=true)
+    # since pl and savepl are both true, pl is ignored, the plot is generated and saved 
+    # the second arguments is given by the data vector
+```
+- with more correlator, making plots and returning effective PCAC masses 
+```@example
+    data_pp = read_mesons(path, "G5", "G5")
+    corr_pp = corr_obs.(data_pp)
+    m, data,fig,ax = meff(corr_a0p, corr_pp, [[50, 60] for eachindex(corr_pp), pl=true,data=true)
+    #the return is a Vector{uwreal} with the pseudoscalar masses, a Vector{Vector{uwreal}} with the effective , 
+    #a Vector{Figure} with the figure objects and a Vector{PyPlot.PyCall.PyObject} with the axes objects  
 ```
 """
-function meff(corr::Vector{uwreal}, plat::Vector{Int64}; pl::Bool=true, data::Bool=false, 
-    mu::Union{Vector{Float64}, Nothing}=nothing, kappa::Union{Vector{Float64}, Nothing}=nothing,
-    wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing, savepl::Bool=false,
-    label::Union{String, Nothing}=nothing,)     
-    dim = length(corr)                                                                                    
-    aux = 0.5 .* log.((corr[2:dim-2] ./ corr[3:dim-1]).^2)     
-    mass = plat_av(aux, plat, wpm)                                                                            
-    if pl || savepl
-        isnothing(wpm) ? uwerr(mass) : uwerr(mass, wpm)                       
-        x = 1:length(aux)
-        y = abs.(value.(aux))
-        dy = err.(aux)
-        v = abs(value(mass))
-        e = err(mass)
-        
-        filename = "meff/";
-        fig,ax = subplots(1)
-        ax.fill_between(plat[1]:plat[2], v-e, v+e, color="green", alpha=0.75)
-        l,=ax.errorbar(x, y, dy, fmt="x", color="black")
-        if !isnothing(label)
-            l.set_label(label)
-            ax.legend()
-            filename*=label*"_"
-        end
-        ax.set_ylabel(L"$m_\mathrm{eff}$")
-        ax.set_xlabel(L"$x_0$")
-        _, max_idx = findmax(value.(corr))
-        ax.set_ylim(v-20*e, v+20*e)
-        ax.set_xlim(left=max_idx)
-        
+function meff(corr::Vector{uwreal}, plat::Vector{Int64}; pl::Bool=false, data::Bool=false, 
+  mu::Union{Vector{Float64}, Nothing}=nothing, kappa::Union{Vector{Float64}, Nothing}=nothing,
+  wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing, savepl::Bool=false,
+  filename::String="",plot_kw...)     
+  dim = length(corr)                                                                                    
+  aux = 0.5 .* log.((corr[2:dim-2] ./ corr[3:dim-1]).^2)     
+  mass = plat_av(aux, plat, wpm)                                                                            
+  if pl || savepl
+    abs_mass = abs2(mass);
+    isnothing(wpm) ? uwerr(abs_mass) : uwerr(abs_mass, wpm)
+    v,e = value(abs_mass), err(abs_mass);                       
+    x = [_ for _ in eachindex(aux)]
+    fig,ax = plot_data(abs2.(aux),x;plot_kw...)
+    fig,ax = plot_func(x->abs_mass,x[plat[1]:plat[2]],figs=(fig,ax) ;plot_kw...)
     
-        if !isnothing(kappa)
-            title(string(L"$\kappa_1 = $", kappa[1], L" $\kappa_2 = $", kappa[2]))
-            filename*="kappa_1_$(kappa[1])_kappa_2_$(kappa[2]).png"
-        end
-        if !isnothing(mu)
-            title(string(L"$\mu_1 = $", mu[1], L" $\mu_2 = $", mu[2]))
-            filename*="mu_1_$(mu[1])_mu_2_$(mu[2]).png"
-        end
-        if savepl
-            fig.tight_layout()
-            fig.set_size_inches(10,5)
-            mkpath(dirname(filename));
-            fig.savefig(filename)
-            close(fig)
-        else
-            display(gcf())
-        end
-        # close("all")
-    end   
-    if pl && !savepl
-      return data ? (mass,aux,fig,ax) : (mass,fig,ax)
-    else                 
-      return data ? (mass,aux) : mass                                        
-    end                    
+    if !haskey(plot_kw,:title)
+      temp = isnothing(kappa) ? L"$\mu_1 = %$(mu[1])$ $\mu_2 = %$(mu[2])$" : L"$\kappa_1 = %$(kappa[1])$ $\kappa_2 = %$(kappa[2])$"
+      fig.suptitle(temp);
+    end
+
+    if !haskey(plot_kw,:ylabel)
+      ax.set_ylabel(L"$m_\mathrm{eff}$")
+    end
+    if !haskey(plot_kw,:xlabel) 
+      ax.set_xlabel(L"$x_0$")
+    end
+
+    _, max_idx = findmax(value.(corr))
+    ax.set_xlim(left=max_idx)
+    ax.set_ylim(v-20*e,v+20*e)
+    
+    if savepl
+      fig.tight_layout();  
+      if filename ==""
+        filename = "meff/"
+        filename *= isnothing(kappa) ? "" : "kappa_1_$(kappa[1])_kappa_2_$(kappa[2]).png"
+        filename *= isnothing(mu) ? "" : "mu_1_$(mu[1])_mu_2_$(mu[2]).png"
+      end
+      mkpath(dirname(filename))
+      fig.savefig(filename)
+      close(fig)
+    elseif pl
+      display(fig);
+    end
+  end   
+  if pl && !savepl
+    return data ? (mass,aux,fig,ax) : (mass,fig,ax)
+  else                 
+    return data ? (mass,aux) : mass                                        
+  end                    
 end   
 function meff(corr::Corr, plat::Vector{Int64}; kwargs...)
     
@@ -79,8 +108,8 @@ function meff(corr::Corr, plat::Vector{Int64}; kwargs...)
     end
 end
 
-function meff(pp::Vector{Corr},plat::Vector{Vector{Int64}}; kwargs...)
-  a = meff.(pp,plat; kwargs...)
+function meff(corr::Vector{Corr},plat::Vector{Vector{Int64}}; kwargs...)
+  a = meff.(corr,plat; kwargs...)
   if length(a[1])==1
     return a
   end
@@ -114,7 +143,7 @@ end
 
 Computes the bare PCAC mass for a given correlator `a0p` and `pp` at a given plateau `plat`.
 Correlator can be passed as an `Corr` struct or `Vector{uwreal}`. 
-In case of Vector{Corr} it is better to not broadcast, espectially in case of `data=true` or `pl=true`, since the the overloaded function for Vector{Corr} takes care of the extra outputs and organize them into a `Tuple` of Vector
+In case of Vector{Corr} it is better to not broadcast, especially in case of `data=true` or `pl=true`, since the the overloaded function for Vector{Corr} takes care of the extra outputs and organize them into a `Tuple` of Vector
 
 The return structure is: mpcac[,data][,figs,axs]
 
@@ -183,10 +212,11 @@ function mpcac(a0p::Vector{uwreal}, pp::Vector{uwreal}, plat::Vector{Int64}; ca:
 
   aux = der_a0p ./ ( 2. .* corr_pp[3:end-2])
   mass = plat_av(aux, plat, wpm)                                                                            
-
+  
   if pl|| savepl
     x = [_ for _ in eachindex(aux)] 
     fig,ax = plot_data(aux,x,wpm=wpm,ylabel =L"$m_\mathrm{PCAC}$",xlabel=L"$x_0$";plot_kw...)
+    isnothing(wpm) ? uwerr(mass) : uwerr(mass,wpm)
     fig,ax = plot_func(x->mass,[plat[1]:plat[2]...],figs=(fig,ax);plot_kw...)
     if !isnothing(kappa)
       fig.suptitle(string(L"$\kappa_1 = $", kappa[1], L" $\kappa_2 = $", kappa[2]))
@@ -195,9 +225,6 @@ function mpcac(a0p::Vector{uwreal}, pp::Vector{uwreal}, plat::Vector{Int64}; ca:
       fig.suptitle(string(L"$\mu_1 = $", mu[1], L" $\mu_2 = $", mu[2]))
     end   
     _, max_idx = findmax(value.(pp))
-    isnothing(wpm) ? uwerr(mass) : uwerr(mass,wpm)
-    v,e = value(mass), err(mass)
-    ax.set_ylim(v-20*e, v+20*e)
     ax.set_xlim(left=max_idx)
       
     if savepl

src/juobs_plots.jl

@@ -32,7 +32,7 @@ It return a tuple `fig,ax` to easily allow any modification to the plot.
   xdata2 = [uwreal([x,0.1], "xdata") for x in xdata];
   fig,ax = data_plot(ydata2,xdata2,label=L"$\cos(\frac{x*\pi}{10}$",figs = (fig,ax))
 ```
-See also [`plot_func`](@ref)
+See also: [`plot_func`](@ref)
 """
 function plot_data(data::Vector{uwreal},xdata::Vector{T} where T <: Real; 
   wpm::Union{Dict{String, Vector{Float64}},Nothing} = nothing,
@@ -108,7 +108,7 @@ It returns a tuple with `fig,ax` to easiy edit the plot
   f(x) = uwreal([sin(x*0.1*π),0.1],"sin")
   fig,ax = plot_func(f,xdata,label=L"\sin(\frac{x*\pi}{10})")
 ```
-See also [`plot_data`](@ref)
+See also: [`plot_data`](@ref)
 """
 function plot_func(f::Function, xdata::Vector{T} where T<:Real; 
   wpm::Union{Dict{String,Vector{Float64}},Nothing} = nothing,