Sipm calibration routines

Project.toml

@@ -12,13 +12,15 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 Format = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+GaussianMixtures = "cc18c42c-b769-54ff-9e2a-b28141a64aae"
 IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
 InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
 IrrationalConstants = "92d709cd-6900-40b7-9082-c6be49f344b6"
 KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearRegression = "92481ed7-9fb7-40fd-80f2-46fd0f076581"
+LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
 LsqFit = "2fda8390-95c7-5789-9bda-21331edee243"
 Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
 Measures = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
@@ -43,8 +45,8 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 ValueShapes = "136a8f8c-c49b-4edb-8b98-f3d64d48be8f"
 
 [weakdeps]
-RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 
 [extensions]
 LegendSpecFitsRecipesBaseExt = ["RecipesBase", "Plots"]
@@ -59,11 +61,13 @@ Distributions = "0.24, 0.25"
 FillArrays = "0.7, 0.8, 0.9, 0.10, 0.11, 0.12, 0.13, 1"
 Format = "1.2, 1.3"
 ForwardDiff = "0.10"
+GaussianMixtures = "0.3"
 IntervalSets = "0.7"
 InverseFunctions = "0.1"
 IrrationalConstants = "0.1, 0.2"
 KernelDensity = "0.5, 0.6"
 LaTeXStrings = "1.3"
+LogExpFunctions = "0.3"
 LinearAlgebra = "1"
 LinearRegression = "0.2"
 LsqFit = "0.14, 0.15"

ext/LegendSpecFitsRecipesBaseExt.jl

@@ -490,6 +490,198 @@
     end
 end
 
+@recipe function f(report::NamedTuple{(:peakpos, :peakpos_cal, :h_uncal, :h_calsimple)}; cal=true)
+    legend := :topright
+    size := (1000, 600)
+    thickness_scaling := 1.5
+    framestyle := :box
+    yformatter := :plain
+    if cal
+        h = LinearAlgebra.normalize(report.h_calsimple, mode = :density)
+        xlabel := "Peak Amplitudes (P.E.)"
+        ylabel := "Counts / $(round_wo_units(step(first(h.edges)), digits=2)) P.E."
+        xticks := (0:0.5:last(first(h.edges)))
+        pps = report.peakpos_cal
+    else
+        h = LinearAlgebra.normalize(report.h_uncal, mode = :density)
+        xlabel := "Peak Amplitudes (ADC)"
+        ylabel := "Counts / $(round_wo_units(step(first(h.edges)), digits=2)) ADC"
+        pps = report.peakpos
+    end
+    xlims := (0, last(first(h.edges)))
+    min_y = minimum(h.weights) == 0.0 ? 1e-3*maximum(h.weights) : 0.8*minimum(h.weights)
+    ylims --> (min_y, maximum(h.weights)*1.1)
+    @series begin
+        seriestype := :stepbins
+        label := "amps"
+        h
+    end
+    y_vline = min_y:1:maximum(h.weights)*1.1
+    for (i, p) in enumerate(pps)
+        @series begin
+            seriestype := :line
+            if i == 1
+                label := "Peak Pos. Guess"
+            else
+                label := ""
+            end
+            color := :red
+            linewidth := 1.5
+            fill(p, length(y_vline)), y_vline
+        end
+    end
+end
+
+@recipe function f(report_sipm::NamedTuple{(:h_cal, :f_fit, :f_fit_components, :min_pe, :max_pe, :bin_width, :n_mixtures, :n_pos_mixtures, :peaks, :positions, :μ , :gof)}; xerrscaling=1, show_residuals=true, show_peaks=true, show_components=false)
+    legend := :topright
+    size := (1000, 600)
+    margins := (4, :mm)
+    thickness_scaling := 1.5
+    framestyle := :box
+    yformatter := :plain
+    foreground_color_legend := :silver
+    background_color_legend := :white
+    ylabel := "Counts / $(round_wo_units(report_sipm.bin_width * 1e3, digits=2))E-3 P.E."
+    xlims := (first(first(report_sipm.h_cal.edges)), last(first(report_sipm.h_cal.edges)))
+    xticks := (ceil(first(first(report_sipm.h_cal.edges)))-0.5:0.5:last(first(report_sipm.h_cal.edges)))
+    min_y = minimum(report_sipm.h_cal.weights) == 0.0 ? 1e-3*maximum(report_sipm.h_cal.weights) : 0.8*minimum(report_sipm.h_cal.weights)
+    ylims := (min_y, maximum(report_sipm.h_cal.weights)*1.1)
+    bin_centers = collect(report_sipm.h_cal.edges[1])[1:end-1] .+ diff(collect(report_sipm.h_cal.edges[1]))[1]/2 
+    @series begin
+        yscale --> :log10
+        label := "Amplitudes"
+        subplot --> 1
+        seriestype := :bar
+        alpha --> 1.0
+        fillalpha --> 0.85
+        fillcolor --> :lightgrey
+        linecolor --> :lightgrey
+        fillrange := 1e-1
+        bins --> :sqrt
+        bar_width := diff(report_sipm.h_cal.edges[1])[1]
+        bin_centers, report_sipm.h_cal.weights
+    end
+    @series begin
+        seriestype := :line
+        if !isempty(report_sipm.gof)
+            label := "Best Fit (p = $(round(report_sipm.gof.pvalue, digits=2)))"
+        else
+            label := "Best Fit"
+        end
+        if show_residuals && !isempty(report_sipm.gof)
+            xlabel := ""
+            xticks := []
+        else
+            xlabel := "Peak Amplitudes (P.E.)"
+        end
+        subplot --> 1
+        color := :black
+        linewidth := 1.5
+        report_sipm.min_pe:report_sipm.bin_width/100:report_sipm.max_pe, report_sipm.f_fit
+    end
+    if show_components
+        for (i, μ) in enumerate(report_sipm.μ)
+            @series begin
+                seriestype := :line
+                if i == 1
+                    label := "Mixture Components"
+                else
+                    label := ""
+                end
+                if show_residuals && !isempty(report_sipm.gof)
+                    xlabel := ""
+                    xticks := []
+                else
+                    xlabel := "Peak Amplitudes (P.E.)"
+                end
+                subplot --> 1
+                color := i + 1 + length(report_sipm.positions)
+                linestyle := :dash
+                linewidth := 1.3
+                # fillalpha := 1
+                alpha := 0.4
+                xi = report_sipm.min_pe:report_sipm.bin_width/100:report_sipm.max_pe
+                yi = Base.Fix2(report_sipm.f_fit_components, i).(xi)
+                # ribbon := (yi .- 1, zeros(length(xi)))
+                xi, yi
+            end
+        end
+    end
+    if show_peaks
+        y_vline = [min_y, maximum(report_sipm.h_cal.weights)*1.1]
+        for (i, p) in enumerate(report_sipm.positions)
+            @series begin
+                seriestype := :line
+                if xerrscaling == 1
+                    label := "$(report_sipm.peaks[i]) P.E. [$(report_sipm.n_pos_mixtures[i]) Mix.]"
+                else
+                    label := "$(report_sipm.peaks[i]) P.E. [$(report_sipm.n_pos_mixtures[i]) Mix.] (error x$xerrscaling)"
+                end
+                subplot --> 1
+                color := i + 1
+                linewidth := 1.5
+                fill(value(p), length(y_vline)), y_vline
+            end
+            @series begin
+                seriestype := :vspan
+                label := ""
+                fillalpha := 0.1
+                subplot --> 1
+                if show_residuals && !isempty(report_sipm.gof)
+                    xlabel := ""
+                    xticks := []
+                else
+                    xlabel := "Peak Amplitudes (P.E.)"
+                end
+                color := i + 1
+                [value(p) - xerrscaling * uncertainty(p), value(p) + xerrscaling * uncertainty(p)]
+            end
+        end
+    end
+    if show_residuals && !isempty(report_sipm.gof)
+        link --> :x
+        layout --> @layout([a{0.7h}; b{0.3h}])
+        @series begin
+            seriestype := :hline
+            ribbon := 3
+            subplot --> 2
+            fillalpha := 0.5
+            label := ""
+            fillcolor := :lightgrey
+            linecolor := :darkgrey
+            [0.0]
+        end
+        @series begin
+            seriestype := :hline
+            ribbon := 1
+            subplot --> 2
+            fillalpha := 0.5
+            label := ""
+            fillcolor := :grey
+            linecolor := :darkgrey
+            [0.0]
+        end
+        @series begin
+            seriestype := :scatter
+            subplot --> 2
+            label := ""
+            title := ""
+            markercolor --> :darkgrey
+            markersize --> 3.0
+            markerstrokewidth := 0.1
+            ylabel := "Residuals (σ)"
+            xlabel := "Peak Amplitudes (P.E.)"
+            link --> :x
+            top_margin --> (-8, :mm)
+            ylims := (-6, 6)
+            xlims := (first(first(report_sipm.h_cal.edges)), last(first(report_sipm.h_cal.edges)))
+            yscale --> :identity
+            yticks := ([-3, 0, 3])
+            report_sipm.gof.bin_centers, [ifelse(abs(r) < 1e-6, 0.0, r) for r in report_sipm.gof.residuals_norm]
+        end        
+    end
+end
+
 @recipe function f(report_ctc::NamedTuple{(:peak, :window, :fct, :bin_width, :bin_width_qdrift, :e_peak, :e_ctc, :qdrift_peak, :h_before, :h_after, :fwhm_before, :fwhm_after, :report_before, :report_after)})
     if !("StatsPlots" in string.(Base.loaded_modules_array()))
         throw(ErrorException("StatsPlots not loaded. Please load StatsPlots before using this recipe."))
@@ -608,9 +800,9 @@
     framestyle := :box
     xformatter := :plain
     yformatter := :plain
+    margins := (0, :mm)
     if !isempty(report.gof)
         layout --> @layout([a{0.8h}; b{0.2h}])
-        margins --> (-11.5, :mm)
         link --> :x
     end
     @series begin
@@ -643,6 +835,10 @@
             label := "Data (x-Error x$(xerrscaling), y-Error x$(yerrscaling))"
         end
         markercolor --> :black
+        if !isempty(report.gof)
+            xguide := ""
+            xticks := []
+        end
         xerror := uncertainty.(report.x) .* xerrscaling
         yerror := uncertainty.(report.y) .* yerrscaling
         value.(report.x), value.(report.y)
@@ -663,6 +859,10 @@
             ms --> 3
             markershape --> :circle
             markerstrokecolor --> :black
+            if !isempty(report.gof)
+                xguide := ""
+                xticks := []
+            end
             linewidth --> 0.5
             markercolor --> :silver
             xerror := uncertainty.(additional_pts.x) .* xerrscaling
@@ -709,7 +909,8 @@
             subplot --> 2
             label --> ""
             markercolor --> :black
-            ylabel --> "Residuals (σ)"
+            yguide := "Residuals (σ)"
+            top_margin --> (-4, :mm)
             ylims --> (-5, 5)
             yticks --> ([-3, 0, 3])
             value.(report.x), report.gof.residuals_norm
@@ -729,14 +930,14 @@
         else
             NamedTuple()
         end
-        xlabel := "Energy (keV)"
         legend := :topleft
         framestyle := :box
         xlims := (0, 3000)
         xticks := (0:500:3000, ["$i" for i in 0:500:3000])
         @series begin
             grid --> :all
             xerrscaling --> xerrscaling
+            xlabel := "Energy (keV)"
             yerrscaling --> yerrscaling
             additional_pts --> additional_pts
             (par = report.par, f_fit = report.f_fit, x = report.x, y = report.y, gof = get(report, :gof, NamedTuple()))
@@ -762,36 +963,22 @@
     if report.type == :cal
         additional_pts = if !isempty(additional_pts)
             μ_cal = report.f_fit.(additional_pts.μ) .* report.e_unit
-            (x = additional_pts.μ, y = additional_pts.peaks, 
-                residuals_norm = (value.(μ_cal) .- additional_pts.peaks)./ uncertainty.(μ_cal))
+            (x = additional_pts.μ, y = ustrip.(report.e_unit, additional_pts.peaks),
+                residuals_norm = (value.(μ_cal) .- additional_pts.peaks) ./ uncertainty.(μ_cal))
         else
             NamedTuple()
         end
-        xlabel := "Energy (ADC)"
-        legend := :bottomright
         framestyle := :box
-        xlims := (0, 168000)
-        xticks := (0:16000:176000)
+        xlims := (0, 1.1*maximum(value.(report.x)))
         @series begin
+            xlabel := "Energy (ADC)"
+            ylabel := "Energy ($(report.e_unit))"
             grid --> :all
             xerrscaling --> xerrscaling
             yerrscaling --> yerrscaling
             additional_pts := additional_pts
             (par = report.par, f_fit = report.f_fit, x = report.x, y = report.y, gof = report.gof)
         end
-        @series begin
-            seriestype := :hline
-            label := L"Q_{\beta \beta}"
-            color := :green
-            fillalpha := 0.2
-            linewidth := 2.5
-            xticks := :none
-            ylabel := "Energy ($(report.e_unit))"
-            ylims := (0, 1.2*value(maximum(report.y)))
-            yticks := (500:500:3000)
-            subplot := 1
-            [2039]
-        end
     end
 end
 

src/LegendSpecFits.jl

@@ -14,13 +14,16 @@ using Random
 using ArgCheck
 using ArraysOfArrays
 using BAT
+using DensityInterface
 using Distributions
 using FillArrays
 using Format
 using ForwardDiff
+using GaussianMixtures
 using IntervalSets
 using InverseFunctions
 using IrrationalConstants
+using LogExpFunctions
 using LsqFit
 using Measurements
 using Measurements: value
@@ -31,6 +34,7 @@ using OptimizationNLopt
 using OptimizationOptimJL
 using PropDicts
 using RadiationSpectra
+using RadiationSpectra: peakfinder
 using Roots
 using SpecialFunctions
 using StatsBase
@@ -74,6 +78,7 @@ include("pseudo_prior.jl")
 include("specfit_functions.jl")
 include("calfunc.jl")
 include("sipm_simple_calibration.jl")
+include("sipmfit.jl")
 abstract type UncertTag end
 ForwardDiff.:(≺)(::Type{<:ForwardDiff.Tag}, ::Type{UncertTag}) = true
 ForwardDiff.:(≺)(::Type{UncertTag}, ::Type{<:ForwardDiff.Tag}) = false

src/fit_calibration.jl

@@ -13,7 +13,7 @@
     @assert length(peaks) == length(μ) "Number of calibration points does not match the number of energies"
     @assert pol_order >= 1 "The polynomial order must be greater than 0"
 
-    e_unit = u"keV"
+    e_unit = unit(first(peaks))
     # make all inputs unitless with the dimension e_unit
     μ_nounit = if !Unitful.isunitless(unit(first(μ)))
         @warn "µ has a unit, it will be converted to $(e_unit) and stripped."