resolving merging conflicts

src/juobs.jl

@@ -11,12 +11,7 @@ include("juobs_obs.jl")
 
 export read_mesons, read_mesons_correction, read_ms1, read_ms, read_md, truncate_data!, concat_data!
 export get_matrix, energies, uwdot, uweigvals, uweigvecs, uweigen, invert, getall_eigvals, getall_eigvecs, hess_reduce, uwcholesky, transpose, tridiag_reduction, make_positive_def, invert_covar_matrix
-<<<<<<< HEAD
-export corr_obs, corr_obs_TSM, corr_sym, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine, global_fit_routine, bayesian_av
-export meff, mpcac, dec_const, dec_const_w, dec_const_pcvc, comp_t0
-=======
 export corr_obs, corr_obs_TSM, corr_sym, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine, global_fit_routine, bayesian_av, pvalue
-export meff, mpcac, dec_const, dec_const_pcvc, comp_t0
->>>>>>> alejandro
+export meff, mpcac, dec_const, dec_const_w, dec_const_pcvc, comp_t0
 
 end # module

src/juobs_obs.jl

@@ -217,12 +217,8 @@ function dec_const(a0p::Vector{uwreal}, pp::Vector{uwreal}, plat::Vector{Int64},
         T = length(corr_a0p)
         aux = exp.((collect(1:T) .- (T)/2) .* [m for k = 1:T])
     else
-<<<<<<< HEAD
         T = length(corr_a0p)
-        aux = exp.((collect(1:T) .- T/2) .* [m for k = 1:T])
-=======
         aux = exp.((collect(0:T-1) .- (T-1)/2) .* [m for k = 1:T])
->>>>>>> alejandro
     end
 
     R = corr_a0p .* aux ./ [((corr_pp[T-y0])^2)^(1/4) for k = 1:length(corr_a0p)]

src/juobs_reader.jl

@@ -684,7 +684,6 @@ function concat_data!(data1::Vector{Vector{CData}}, data2::Vector{Vector{CData}}
             data1[k][r].vcfg = vcat(data1[k][r].vcfg, data2[k][r].vcfg)
             data1[k][r].re_data = vcat(data1[k][r].re_data, data2[k][r].re_data)
             data1[k][r].im_data = vcat(data1[k][r].im_data, data2[k][r].im_data)
-<<<<<<< HEAD
             idx = sortperm(data1[k][r].vcfg)
             data1[k][r].vcfg = data1[k][r].vcfg[idx]
             data1[k][r].re_data = data1[k][r].re_data[idx, :] 
@@ -693,9 +692,3 @@ function concat_data!(data1::Vector{Vector{CData}}, data2::Vector{Vector{CData}}
     end
     return nothing
 end
-=======
-        end
-    end
-    return nothing
-end
->>>>>>> alejandro

src/juobs_tools.jl

 #TODO: apply_rw with gaps
-<<<<<<< HEAD
-function apply_rw(data::Array{Float64}, W::Matrix{Float64}; vcfg::Union{Nothing, Vector{Int32}}=nothing)
+function apply_rw(data::Array{Float64}, W::Matrix{Float64}, id::Union{String, Nothing}=nothing; vcfg::Union{Nothing, Vector{Int32}}=nothing)
     nc =  isnothing(vcfg) ? collect(1:size(data, 1)) : vcfg
     W1 = W[1, nc]
     W2 = W[2, nc]
-=======
-function apply_rw(data::Array{Float64}, W::Matrix{Float64}, id::Union{String, Nothing}=nothing)
-    nc = size(data, 1)
-    W1 = W[1, 1:nc]
-    W2 = W[2, 1:nc]
->>>>>>> alejandro
 
     if id == "J303" || id == "J303r003"
         W_J303 = [1 for i in 1:length(data)]
@@ -167,11 +160,7 @@ corr_pp = corr_obs.(data)
 corr_pp_r = corr_obs.(data, rw=[rw1, rw2])
 ```
 """
-<<<<<<< HEAD
-function corr_obs(cdata::CData; real::Bool=true, rw::Union{Array{Float64, 2}, Nothing}=nothing, L::Int64=1, info::Bool=false, idm::Union{Vector{Int64},Nothing}=nothing, nms::Int64=Int64(maximum(cdata.vcfg)))
-=======
-function corr_obs(cdata::CData; real::Bool=true, rw::Union{Array{Float64, 2}, Nothing}=nothing, L::Int64=1, info::Bool=false, flag_strange::Bool=false)
->>>>>>> alejandro
+function corr_obs(cdata::CData; real::Bool=true, rw::Union{Array{Float64, 2}, Nothing}=nothing, L::Int64=1, info::Bool=false, idm::Union{Vector{Int64},Nothing}=nothing, nms::Int64=Int64(maximum(cdata.vcfg)), flag_strange::Bool=false)
 
     real ? data = cdata.re_data ./ L^3 : data = cdata.im_data ./ L^3
     nt = size(data)[2]
@@ -185,20 +174,10 @@ function corr_obs(cdata::CData; real::Bool=true, rw::Union{Array{Float64, 2}, No
         # idm = isnothing(idm) ? collect(1:nms) : idm
         obs = [uwreal(data[:, x0], cdata.id, idm, nms) for x0 = 1:nt]
     else
-<<<<<<< HEAD
         # idm = isnothing(idm) ? collect(1:nms) : idm
-        data_r, W = apply_rw(data, rw)
+        data_r, W = apply_rw(data, rw, cdata.id)
         ow = [uwreal(data_r[:, x0], cdata.id, idm, nms) for x0 = 1:nt]
         W_obs = uwreal(W, cdata.id, idm, nms)
-=======
-        if flag_strange == true
-            data_r, W = apply_rw(data, rw, cdata.id)
-        else
-            data_r, W = apply_rw(data, rw)
-        end
-        ow = [uwreal(data_r[:, x0], cdata.id) for x0 = 1:nt]
-        W_obs = uwreal(W, cdata.id)
->>>>>>> alejandro
         obs = [ow[x0] / W_obs for x0 = 1:nt]
     end
 
@@ -212,11 +191,7 @@ function corr_obs(cdata::CData; real::Bool=true, rw::Union{Array{Float64, 2}, No
 end
 #function corr_obs for R != 1
 #TODO: vcfg with gaps
-<<<<<<< HEAD
-function corr_obs(cdata::Array{CData, 1}; real::Bool=true, rw::Union{Array{Array{Float64, 2}, 1}, Nothing}=nothing, L::Int64=1, info::Bool=false, idm::Union{Vector{Int64},Nothing}=nothing, nms::Union{Int64, Nothing}=nothing)
-=======
-function corr_obs(cdata::Array{CData, 1}; real::Bool=true, rw::Union{Array{Array{Float64, 2}, 1}, Nothing}=nothing, L::Int64=1, info::Bool=false, flag_strange::Bool=false)
->>>>>>> alejandro
+function corr_obs(cdata::Array{CData, 1}; real::Bool=true, rw::Union{Array{Array{Float64, 2}, 1}, Nothing}=nothing, L::Int64=1, info::Bool=false, idm::Union{Vector{Int64},Nothing}=nothing, nms::Union{Int64, Nothing}=nothing, flag_strange::Bool=false)
     nr = length(cdata)
     id = getfield.(cdata, :id)
     vcfg = getfield.(cdata, :vcfg)
@@ -246,11 +221,8 @@ function corr_obs(cdata::Array{CData, 1}; real::Bool=true, rw::Union{Array{Array
         [tmp = cat(tmp, data[k], dims=1) for k = 2:nr]
         obs = [uwreal(tmp[:, x0], id[1], replica, idm, nms) for x0 = 1:nt]
     else
-        if flag_strange == true
-            data_r, W = apply_rw(data, rw, id[1])
-        else
-            data_r, W = apply_rw(data, rw)
-        end
+
+        data_r, W = apply_rw(data, rw, id[1])
         tmp = data_r[1]
         tmp_W = W[1]
         [tmp = cat(tmp, data_r[k], dims=1) for k = 2:nr]
@@ -1551,7 +1523,6 @@ function get_chi2_cov(f::Function, data, C, par, Nalpha) # full + cov
     return chi2
 end
 
-<<<<<<< HEAD
 function get_covar(obs::Vector{uwreal}; wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
     isnothing(wpm) ? uwerr.(obs) :  [uwerr(yaux, wpm) for yaux in obs]
     ens = vcat(ensembles.(obs)...)
@@ -1588,8 +1559,6 @@ function inv_covar_multi_id(obs::Vector{uwreal}; wpm::Union{Dict{Int64,Vector{Fl
     return (cov_inv' + cov_inv) / 2.
 end
 
-=======
->>>>>>> alejandro
 @doc raw"""
     pvalue(chisq::Function,
     chi2::Float64,
@@ -1625,13 +1594,8 @@ Q = pvalue(chisq, chi2, value.(up), y, wpm; W = 1.0 ./ err.(y) .^ 2, nmc=10000)
 function pvalue(chisq::Function,
     chi2::Float64,
     xp::Vector{Float64}, 
-<<<<<<< HEAD
     data::Vector{uwreal};
     wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing} =  Dict{Int64,Vector{Float64}}(),
-=======
-    data::Vector{uwreal},
-    wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing} = Dict{Int64,Vector{Float64}}();
->>>>>>> alejandro
     W::Union{Vector{Float64},Array{Float64,2}} = Vector{Float64}(),
     nmc::Int64 = 5000)
 
@@ -1662,10 +1626,7 @@ function pvalue(chisq::Function,
             Ww = zeros(Float64, m)
             for i in 1:m
                 if (data[i].err == 0.0)
-<<<<<<< HEAD
                     #isnothing(wpm) ? wuerr(data[i]) : uwerr(data[i], wpm)
-=======
->>>>>>> alejandro
                     uwerr(data[i], wpm)
                     if (data[i].err == 0.0)
                         error("Zero error in fit data")
@@ -1715,9 +1676,4 @@ function pvalue(chisq::Function,
     end
 
     return Q #uwreal([Q,dQ],"")
-<<<<<<< HEAD
 end
-=======
-end
-
->>>>>>> alejandro