add sth

docs/src/tutorial/index.md

@@ -4,4 +4,132 @@ To use **Jirachi**, we need to import...
 
 
 
-## Loading light curves
+## Loading light curves
+
+```julia
+# load light curves.
+i_lc = load_data("./data/montano_n1_i_4395.txt", [1, 2, 3]; band="i")
+z_lc = load_data("./data/montano_n1_z_4395.txt", [1, 2, 3]; band="z")
+
+# convert time to second, and start it from 0 second.
+i_lc.time = round.(i_lc.time * 24 * 3600, digits=2)
+i_lc.time = i_lc.time .- i_lc.time[1]
+z_lc.time = round.(z_lc.time * 24 * 3600, digits=2)
+z_lc.time = z_lc.time .- z_lc.time[1]
+```
+
+## Get the light curves binned
+
+```julia
+t_binsize = 103.68
+lc_edges = bin_lc_edges(t_binsize, 0, 25000)
+
+i_lc_bin = bin_light_curve(i_lc; lc_edges = lc_edges)
+z_lc_bin = bin_light_curve(z_lc; lc_edges = lc_edges)
+
+lc1_bin, lc2_bin = get_common_lc(i_lc_bin, z_lc_bin)
+```
+
+## check and plot it !
+
+```julia
+plotlc(i_lc, i_lc_bin, z_lc, z_lc_bin; 
+  		label=[i_lc.band, i_lc.band * "_bin", z_lc.band, z_lc.band * "_bin"], 
+  		lc_edges=lc_edges, 
+  		save_fig_path="./fig/lc_check_i_z.svg", 
+  		save_fig=true, 
+  		hwratio=0.3)
+```
+
+![lc](../assets/fig/lc_check_i_z.svg)
+
+### Begin calculating structure function!
+
+### input parameters
+
+```julia
+# structure function 
+sf_bin = 0.05
+sf_bin_edges = 0:sf_bin:5 # in log space
+mode = "both" # lc bootstrapped for structure function error
+nsim = 1000 # lc bootstrapped for structure function error
+lower_bounds = [0, 0, 0, 0.001]
+upper_bounds = [10, 2e4, 2, 0.1]
+p0 = [1, 1e3, 1, 0.005]
+
+t_fit = 10 .^ range(log10(1), log10(6e4), step=0.1)
+
+# color variation
+cv_bin = 0.1
+cv_bin_edges = 0:cv_bin:5 # in log space
+nsigma = 3
+erron=true
+
+# save all run results.
+fi_np::String="./data/run_i_z.h5"
+
+```
+
+
+
+### Structure function
+
+```julia
+fit_sf1 = fitsf_mcmc(lc1_bin; nsim=nsim, lb = lower_bounds , ub = upper_bounds, sf_bin_edges=sf_bin_edges, p0=p0, mode = mode)
+fit_sf2 = fitsf_mcmc(lc2_bin; nsim=nsim, lb = lower_bounds, ub = upper_bounds, sf_bin_edges=sf_bin_edges, p0=p0, mode = mode)
+
+binsf1, binsf2 = fit_sf1.binsf, fit_sf2.binsf
+
+par_1, par_1_err = fit_sf1.param, fit_sf1.param_err
+par_2, par_2_err = fit_sf2.param, fit_sf2.param_err
+
+
+t_break_1 = find_t_break(binsf1)
+t_break_2 = find_t_break(binsf2)
+
+itp1 = find_t_min(binsf1, par_1; t_fit=t_fit)
+itp2 = find_t_min(binsf2, par_2; t_fit=t_fit)
+
+t_min_1, sf_min_1 = itp1.t_min, itp1.sf_min
+t_min_2, sf_min_2 = itp2.t_min, itp2.sf_min
+
+t_fit_1, sf_fit_1 = itp1.t_fit, itp1.sf_fit
+t_fit_2, sf_fit_2 = itp2.t_fit, itp2.sf_fit
+
+
+proper_time = [maximum([t_min_1, t_min_2]), minimum([t_break_1, t_break_2])]
+```
+
+
+
+## and show it
+
+```julia
+plotsf(binsf1, binsf2; fitsf1=[t_fit_1, sf_fit_1], fitsf2=[t_fit_2, sf_fit_2], proper_time = proper_time)
+```
+
+![sf](../assets/fig/plot_sf.svg)
+
+### calculating color variation
+
+```julia
+nsigma = nsigma
+erron = erron
+
+# cv in flux-Flux
+cv_flux_res = color_variation(lc1_bin, lc2_bin, nsigma, erron, "flux")
+cv_flux = cv_flux_res
+
+bincv_flux = binned_color_variation(cv_flux, cv_bin_edges)
+
+# cv in mag-mag
+cv_mag_res = color_variation(lc1_bin, lc2_bin, nsigma, erron, "mag")
+cv_mag = cv_mag_res
+
+bincv_mag = binned_color_variation(cv_mag, cv_bin_edges)
+```
+
+and plot it
+
+![cv](../assets/fig/plot_cv.svg)
+

src/Jirachi.jl

@@ -46,7 +46,7 @@ export jmodel, model, fitsf, fitsf_mcmc, find_t_min, find_t_break
 
 export runall
 
-export IntegerTicks, theme_lc, theme_sf, plotlc, plotsf
+export IntegerTicks, theme_lc, theme_sf, plotlc, plotsf, plotcv
 
 
 end

src/plotting.jl

@@ -1,24 +1,24 @@
-export theme_sf, theme_hist, theme_lc, IntegerTicks, plotlc, plotsf
+export theme_sf, theme_hist, theme_lc, IntegerTicks, plotlc, plotsf, plotcv
 
 
 struct IntegerTicks end
 
 Makie.get_tickvalues(::IntegerTicks, vmin, vmax) = ceil(Int, vmin) : floor(Int, vmax)
 
 
-theme_lc = merge(theme_web(width=1000,
-                            colors=MakiePublication.tableau_10(),
-                            linestyles=[nothing, :dash, :dash],
-                            ishollowmarkers=[true, true, false],
-                            markers=[:circle, :diamond, :rtriangle],
-                            linecycle=Cycle([:color, :linestyle], covary=true),
-                            scattercycle=Cycle([:color=>:markercolor, :strokecolor=>:color, :marker], covary=true),
-                            markerstrokewidth=0.8, 
-                            heightwidthratio=0.3,
-                            ), theme_latexfonts())
+# theme_lc = merge(theme_web(width=1000,
+#                             colors=MakiePublication.tableau_10(),
+#                             linestyles=[nothing, :dash, :dash],
+#                             ishollowmarkers=[true, true, false],
+#                             markers=[:circle, :diamond, :rtriangle],
+#                             linecycle=Cycle([:color, :linestyle], covary=true),
+#                             scattercycle=Cycle([:color=>:markercolor, :strokecolor=>:color, :marker], covary=true),
+#                             markerstrokewidth=0.8, 
+#                             heightwidthratio=0.3,
+#                             ), theme_latexfonts())
 
 
-theme_hist = merge(theme_web(width=350, colors=MakiePublication.tableau_10(),linestyles=[nothing, :dash, :dash], ishollowmarkers=[true, true, false], markers=[:circle, :diamond, :rtriangle], linecycle=Cycle([:color, :linestyle], covary=true), scattercycle=Cycle([:color=>:markercolor, :strokecolor=>:color, :marker], covary=true), markerstrokewidth=0.8, heightwidthratio=0.9,), theme_latexfonts())
+# theme_hist = merge(theme_web(width=350, colors=MakiePublication.tableau_10(),linestyles=[nothing, :dash, :dash], ishollowmarkers=[true, true, false], markers=[:circle, :diamond, :rtriangle], linecycle=Cycle([:color, :linestyle], covary=true), scattercycle=Cycle([:color=>:markercolor, :strokecolor=>:color, :marker], covary=true), markerstrokewidth=0.8, heightwidthratio=0.9,), theme_latexfonts())
 
 # theme_llc = merge(theme_web(width=1000,
 #                             colors=MakiePublication.COLORS[5],
@@ -88,7 +88,7 @@ end
 
 
 
-function plotsf(binsf1::binned_result, binsf2::binned_result; fitsf1=[], fitsf2=[], proper_time=[])
+function plotsf(binsf1::binned_result, binsf2::binned_result; fitsf1=[], fitsf2=[], proper_time=[], save_fig_path::String="./fig/plot_sf.svg", save_fig::Bool=true)
     theme_sf = merge(theme_web(width=350, colors=MakiePublication.tableau_10(),linestyles=[nothing, :dash, :dash], ishollowmarkers=[true, true, false], markers=[:circle, :diamond, :rtriangle], linecycle=Cycle([:color, :linestyle], covary=true), scattercycle=Cycle([:color=>:markercolor, :strokecolor=>:color, :marker], covary=true), markerstrokewidth=0.8, heightwidthratio=0.9,), theme_latexfonts())
 
     fig_sf = with_theme(theme_sf) do 
@@ -101,6 +101,8 @@ function plotsf(binsf1::binned_result, binsf2::binned_result; fitsf1=[], fitsf2=
         yscale=log10, 
         xticks = LogTicks(IntegerTicks()),
         yticks = LogTicks(IntegerTicks()),
+        yminorticks=IntervalsBetween(9),
+        xminorticks=IntervalsBetween(9),
         xticksize=8,
         yticksize=8,
         xticksmirrored = true, yticksmirrored = true, 
@@ -125,7 +127,53 @@ function plotsf(binsf1::binned_result, binsf2::binned_result; fitsf1=[], fitsf2=
         fig
         # resize_to_layout!(fig)
     end
+    save_fig ? savefig(save_fig_path, fig_sf) : println(" ")
+
     return fig_sf
+end
+
+
+function plotcv(bincv::binned_result; mode="flux", proper_time=[],save_fig_path::String="./fig/plot_cv.svg", save_fig::Bool=true)
+
+    theme_cv = merge(theme_web(width=350, colors=MakiePublication.tableau_10(),linestyles=[nothing, :dash, :dash], ishollowmarkers=[true, true, false], markers=[:circle, :diamond, :rtriangle], linecycle=Cycle([:color, :linestyle], covary=true), scattercycle=Cycle([:color=>:markercolor, :strokecolor=>:color, :marker], covary=true), markerstrokewidth=0.8, heightwidthratio=0.9,), theme_latexfonts())
+
+    mode == "mag" && (ylabel = L"$C_m(\Delta t)$")
+    mode == "flux" && (ylabel = L"$C_f(\Delta t)$")
+
+    fig_cv = with_theme(theme_cv) do 
+        fig = Figure()  
+
+        ax = Axis(fig[1, 1],
+        xlabel=L"$\Delta t$ [sec]",
+        ylabel=ylabel,
+        xscale=log10, 
+        xticks = LogTicks(IntegerTicks()),
+        # yticks = 0.5:0.1:1.1,
+        yminorticks=IntervalsBetween(9),
+        xminorticks=IntervalsBetween(9),
+        xticksize=8,
+        yticksize=8,
+        xticksmirrored = true, yticksmirrored = true, 
+        )
+
+        s = scatter!(ax, 10 .^ bincv.x, bincv.y)
+
+
+        e = errorbars!(ax, 10 .^ bincv.x, bincv.y, bincv.yerr, bincv.yerr, linewidth=0.5, whiskerwidth = 0.2)
+
+        isempty(proper_time) ? print(" ") : band!(ax, 10 ^ proper_time[1]:10 ^ proper_time[2], 0.5, 1.1, color= (:red, 0.1))
+        # hspan!(-1.1, -0.9, color = (:blue, 0.5))
 
-    savefig("./fig/plot_sf.pdf", fig_sf)
+        ylims!(0.5, 1.1)
+        # ylims!(4e-3, 2e-1)
+        xlims!(80, 3e4)
+
+        fig
+        # resize_to_layout!(fig)
+    end
+
+    save_fig ? savefig(save_fig_path, fig_cv) : println(" ")
+
+    return fig_cv
+
 end