From 06c310a5c1d2ba3c341f62060835ce866c951ab5 Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Mon, 16 Dec 2024 01:06:54 +0100
Subject: [PATCH 01/13] Fix bin_width + Bug Fixes

---
 src/sipm_simple_calibration.jl | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/sipm_simple_calibration.jl b/src/sipm_simple_calibration.jl
index 58590f7b..b8d6adf4 100644
--- a/src/sipm_simple_calibration.jl
+++ b/src/sipm_simple_calibration.jl
@@ -74,11 +74,11 @@ function find_peaks(
     min_amp = initial_min_amp
     max_quantile = initial_max_quantile
     max_amp = quantile(amps, max_quantile)
-    bin_width = get_friedman_diaconis_bin_width(filter(in(quantile(amps, 0.01)..quantile(amps, 0.9)), amps))
+    bin_width = get_friedman_diaconis_bin_width(filter(in(min_amp..quantile(amps, 0.9)), amps))
 
     # Initial peak search
     h_uncal = fit(Histogram, amps, min_amp:bin_width:max_amp)
-    h_decon, peakpos = peakfinder(h_uncal, σ=peakfinder_σ, backgroundRemove=true, threshold=peakfinder_threshold)
+    h_decon, peakpos = peakfinder(h_uncal, σ=peakfinder_σ, backgroundRemove=false, threshold=peakfinder_threshold)
 
     # Ensure at least 2 peaks
     num_peaks = length(peakpos)
@@ -98,18 +98,18 @@ function find_peaks(
     # while less than two peaks found, or second peakpos smaller than 1 pe peakpos, or gain smaller than 1 (peaks too close)
     while num_peaks < 2 || peakpos[2] <= first_pe_peak_pos || (peakpos[2] - peakpos[1]) <= 1.0
         # Adjust σ and recheck peaks
-        if peakfinder_σ < 10.0
-            println("Increasing peakfinder_σ: ", peakfinder_σ)
+        if peakfinder_σ < 25.0
+            @debug "Increasing peakfinder_σ: $peakfinder_σ"
             peakfinder_σ += 0.5
         else
             # If σ can't increase further, reduce threshold
-            println("Adjusting peakfinder_threshold: ", peakfinder_threshold)
+            @debug "Adjusting peakfinder_threshold: $peakfinder_threshold"
             peakfinder_threshold -= 1.0
             peakfinder_σ = 2.0  # Reset σ for new threshold
 
             # Safety check to avoid lowering threshold too much
             if peakfinder_threshold < 2.0
-                error("Unable to find two distinct peaks within reasonable quantile range.")
+                throw(ErrorException("Unable to find two peaks within reasonable quantile range."))
             end
         end
 
@@ -120,7 +120,7 @@ function find_peaks(
 
         # Safety check to avoid infinite loops
         if peakfinder_σ >= 10.0 && peakfinder_threshold < 2.0
-            error("Unable to find two peaks within reasonable quantile range.")
+            throw(ErrorException("Unable to find two peaks within reasonable quantile range."))
         end
     end
 

From 3c67043b3f1e61ccc6b3eee68eb91e351b6fc9ab Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Wed, 18 Dec 2024 23:23:07 +0100
Subject: [PATCH 02/13] Update binning

---
 src/sipm_simple_calibration.jl | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/src/sipm_simple_calibration.jl b/src/sipm_simple_calibration.jl
index b8d6adf4..a4bb87c6 100644
--- a/src/sipm_simple_calibration.jl
+++ b/src/sipm_simple_calibration.jl
@@ -67,17 +67,14 @@ end
 
 
 function find_peaks(
-    amps::Vector{<:Real}; initial_min_amp::Real=1.0, initial_max_quantile::Real=0.99, 
+    amps::Vector{<:Real}; initial_min_amp::Real=1.0, initial_max_amp::Real=100.0, initial_max_bin_width_quantile::Real=0.9, 
     peakfinder_σ::Real=2.0, peakfinder_threshold::Real=10.0
 )
     # Start with a big window where the noise peak is included
-    min_amp = initial_min_amp
-    max_quantile = initial_max_quantile
-    max_amp = quantile(amps, max_quantile)
-    bin_width = get_friedman_diaconis_bin_width(filter(in(min_amp..quantile(amps, 0.9)), amps))
+    bin_width = get_friedman_diaconis_bin_width(filter(in(initial_min_amp..quantile(amps, initial_max_bin_width_quantile)), amps))
 
     # Initial peak search
-    h_uncal = fit(Histogram, amps, min_amp:bin_width:max_amp)
+    h_uncal = fit(Histogram, amps, initial_min_amp:bin_width:initial_max_amp)
     h_decon, peakpos = peakfinder(h_uncal, σ=peakfinder_σ, backgroundRemove=false, threshold=peakfinder_threshold)
 
     # Ensure at least 2 peaks
@@ -114,12 +111,12 @@ function find_peaks(
         end
 
         # Find peaks with updated parameters
-        h_decon, peakpos = peakfinder(h_uncal, σ=peakfinder_σ, backgroundRemove=true, threshold=peakfinder_threshold)
+        h_decon, peakpos = peakfinder(h_uncal, σ=peakfinder_σ, backgroundRemove=false, threshold=peakfinder_threshold)
         filter!(x -> x >= first_pe_peak_pos, peakpos)
         num_peaks = length(peakpos)
 
         # Safety check to avoid infinite loops
-        if peakfinder_σ >= 10.0 && peakfinder_threshold < 2.0
+        if peakfinder_σ >= 10.0 && peakfinder_threshold < 0.1
             throw(ErrorException("Unable to find two peaks within reasonable quantile range."))
         end
     end

From 463d52681f1e4e22e25a476278a2936b1a0d1058 Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Mon, 30 Dec 2024 09:36:30 +0100
Subject: [PATCH 03/13] STASH

---
 src/sipm_simple_calibration.jl | 88 +++++++++++++---------------------
 1 file changed, 34 insertions(+), 54 deletions(-)

diff --git a/src/sipm_simple_calibration.jl b/src/sipm_simple_calibration.jl
index a4bb87c6..37c8392d 100644
--- a/src/sipm_simple_calibration.jl
+++ b/src/sipm_simple_calibration.jl
@@ -27,23 +27,39 @@ function sipm_simple_calibration end
 export sipm_simple_calibration
 
 function sipm_simple_calibration(pe_uncal::Vector{<:Real};
-                                kwargs...)
+    min_pe_peak::Int=2, max_pe_peak::Int=5, relative_cut_noise_cut::Real=0.5, n_fwhm_noise_cut::Real=5.0,
+    initial_min_amp::Real=1.0, initial_max_amp::Real=25.0, initial_max_bin_width_quantile::Real=0.9, 
+    peakfinder_σ::Real=2.0, peakfinder_threshold::Real=10.0, peakfinder_rtol::Real=0.1, peakfinder_α::Real=0.05
+)
     
-    h_uncal, peakpos = find_peaks(pe_uncal; kwargs...)
+    # Start with a big window where the noise peak is included
+    bin_width = get_friedman_diaconis_bin_width(filter(in(initial_min_amp..quantile(pe_uncal, initial_max_bin_width_quantile)), pe_uncal))
+
+    # Initial peak search
+    h_uncal = fit(Histogram, pe_uncal, initial_min_amp:bin_width:initial_max_amp)
+
+    cuts_1pe = cut_single_peak(pe_uncal, initial_min_amp, initial_max_amp, relative_cut=relative_cut_noise_cut)
+
+    h_uncal_cut = fit(Histogram, pe_uncal, cuts_1pe.max+n_fwhm_noise_cut*(cuts_1pe.high - cuts_1pe.max):bin_width:initial_max_amp)
+
+    c, h_deconv, peakpos, threshold = RadiationSpectra.determine_calibration_constant_through_peak_ratios(h_uncal_cut, collect(range(min_pe_peak, max_pe_peak, step=1)),
+        min_n_peaks = 2, max_n_peaks = 2*max_pe_peak, threshold=peakfinder_threshold, rtol=peakfinder_rtol, α=peakfinder_α, σ=peakfinder_σ)
+
 
     # simple calibration
     sort!(peakpos)
-    gain = peakpos[2] - peakpos[1]
+    gain = peakpos[min_pe_peak + 1] - peakpos[min_pe_peak]
     c = 1/gain
-    offset = - (peakpos[1] * c - 1) 
+    offset = - (peakpos[min_pe_peak] * c - min_pe_peak)
 
     f_simple_calib = x -> x .* c .+ offset
     f_simple_uncal = x -> (x .- offset) ./ c
-    pe_simple_cal = pe_uncal .* c .+ offset
-    peakpos_cal = peakpos .* c .+ offset
+
+    pe_simple_cal = f_simple_calib.(pe_uncal)
+    peakpos_cal = f_simple_calib.(peakpos)
 
     bin_width_cal = get_friedman_diaconis_bin_width(filter(in(0.5..1.5), pe_simple_cal))
-    bin_width_uncal = get_friedman_diaconis_bin_width(filter(in( (0.5 - offset) / c .. (1.5 - offset) / c), pe_simple_cal))
+    bin_width_uncal = f_simple_uncal(bin_width_cal) - f_simple_uncal(0.0)
 
     h_calsimple = fit(Histogram, pe_simple_cal, 0.0:bin_width_cal:6.0)
     h_uncal = fit(Histogram, pe_uncal, 0.0:bin_width_uncal:(6.0 - offset) / c)
@@ -67,59 +83,23 @@ end
 
 
 function find_peaks(
-    amps::Vector{<:Real}; initial_min_amp::Real=1.0, initial_max_amp::Real=100.0, initial_max_bin_width_quantile::Real=0.9, 
-    peakfinder_σ::Real=2.0, peakfinder_threshold::Real=10.0
+    amps::Vector{<:Real}; 
+    min_pe_peak::Real=1.0, max_pe_peak::Real=5.0, n_fwhm_noise_cut::Real=5.0,
+    initial_min_amp::Real=1.0, initial_max_amp::Real=100.0, initial_max_bin_width_quantile::Real=0.9, 
+    peakfinder_σ::Real=2.0, peakfinder_threshold::Real=10.0, peakfinder_rtol::Real=0.1, peakfinder_α::Real=0.05
 )
     # Start with a big window where the noise peak is included
     bin_width = get_friedman_diaconis_bin_width(filter(in(initial_min_amp..quantile(amps, initial_max_bin_width_quantile)), amps))
 
     # Initial peak search
     h_uncal = fit(Histogram, amps, initial_min_amp:bin_width:initial_max_amp)
-    h_decon, peakpos = peakfinder(h_uncal, σ=peakfinder_σ, backgroundRemove=false, threshold=peakfinder_threshold)
-
-    # Ensure at least 2 peaks
-    num_peaks = length(peakpos)
-    if num_peaks == 0
-        error("No peaks found.")
-    end
-
-    # Determine the 1 p.e. peak position based on the assumption that it is the highest
-    peakpos_idxs = StatsBase.binindex.(Ref(h_decon), peakpos)
-    cts_peakpos = h_decon.weights[peakpos_idxs]
-    first_pe_peak_pos = peakpos[argmax(cts_peakpos)]
-
-    # Remove all peaks with x vals < x pos of 1p.e. peak
-    filter!(x -> x >= first_pe_peak_pos, peakpos)
-    num_peaks = length(peakpos)
-
-    # while less than two peaks found, or second peakpos smaller than 1 pe peakpos, or gain smaller than 1 (peaks too close)
-    while num_peaks < 2 || peakpos[2] <= first_pe_peak_pos || (peakpos[2] - peakpos[1]) <= 1.0
-        # Adjust σ and recheck peaks
-        if peakfinder_σ < 25.0
-            @debug "Increasing peakfinder_σ: $peakfinder_σ"
-            peakfinder_σ += 0.5
-        else
-            # If σ can't increase further, reduce threshold
-            @debug "Adjusting peakfinder_threshold: $peakfinder_threshold"
-            peakfinder_threshold -= 1.0
-            peakfinder_σ = 2.0  # Reset σ for new threshold
-
-            # Safety check to avoid lowering threshold too much
-            if peakfinder_threshold < 2.0
-                throw(ErrorException("Unable to find two peaks within reasonable quantile range."))
-            end
-        end
-
-        # Find peaks with updated parameters
-        h_decon, peakpos = peakfinder(h_uncal, σ=peakfinder_σ, backgroundRemove=false, threshold=peakfinder_threshold)
-        filter!(x -> x >= first_pe_peak_pos, peakpos)
-        num_peaks = length(peakpos)
-
-        # Safety check to avoid infinite loops
-        if peakfinder_σ >= 10.0 && peakfinder_threshold < 0.1
-            throw(ErrorException("Unable to find two peaks within reasonable quantile range."))
-        end
-    end
+
+    cuts_1pe = cut_single_peak(amps, initial_min_amp, initial_max_amp, relative_cut=0.5)
+
+    h_uncal_cut = fit(Histogram, trig_max, cuts_1pe.max+n_fwhm_noise_cut*(cuts_1pe.high - cuts_1pe.max):bin_width:initial_max_amp)
+
+    c, h_deconv, peak_positions, threshold = RadiationSpectra.determine_calibration_constant_through_peak_ratios(h_uncal_cut, collect(range(min_pe_peak, max_pe_peak, step=1)),
+        min_n_peaks = 2, max_n_peaks = 2*max_pe_peak, threshold=peakfinder_threshold, rtol=peakfinder_rtol, α=peakfinder_α, σ=peakfinder_σ)
 
     return h_decon, peakpos
 end
\ No newline at end of file

From a980c53227a35231e1054d6abb142134f8d6d9c9 Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Wed, 22 Jan 2025 04:29:52 +0100
Subject: [PATCH 04/13] Add SiPM filter optimization based on window length
 sweep

---
 ext/LegendSpecFitsRecipesBaseExt.jl |  36 ++++++-
 src/LegendSpecFits.jl               |   1 +
 src/sipm_filter_optimization.jl     | 139 ++++++++++++++++++++++++++++
 3 files changed, 173 insertions(+), 3 deletions(-)
 create mode 100644 src/sipm_filter_optimization.jl

diff --git a/ext/LegendSpecFitsRecipesBaseExt.jl b/ext/LegendSpecFitsRecipesBaseExt.jl
index 8878a9fb..8a87e69f 100644
--- a/ext/LegendSpecFitsRecipesBaseExt.jl
+++ b/ext/LegendSpecFitsRecipesBaseExt.jl
@@ -154,6 +154,36 @@ end
     end
 end
 
+
+@recipe function f(report:: NamedTuple{(:wl, :min_obj, :gain, :res_1pe, :pos_1pe, :threshold, :a_grid_wl_sg, :obj, :report_simple, :report_fit)})
+    xlabel := "Window Length ($(unit(first(report.a_grid_wl_sg))))"
+    ylabel := "Objective \n σ  * √(threshold) \n ______________ \n gain * √(pos_1pe)"
+    grid := :true
+    gridcolor := :black
+    gridalpha := 0.2
+    gridlinewidth := 0.5
+    ylims := (0, 1.5 * maximum(Measurements.value.(report.obj)))
+    @series begin
+        seriestype := :scatter
+        label := "Obj"
+        ustrip.(report.a_grid_wl_sg), ustrip.(report.obj)
+    end
+    @series begin
+        seriestype := :hline
+        label := "Min. Obj $(report.min_obj) (WL: $(report.wl))"
+        color := :red
+        linewidth := 2.5
+        [ustrip(Measurements.value(report.min_obj))]
+    end
+    @series begin
+        seriestype := :hspan
+        label := ""
+        color := :red
+        alpha := 0.1
+        ustrip.([Measurements.value(report.min_obj)-Measurements.uncertainty(report.min_obj), Measurements.value(report.min_obj)+Measurements.uncertainty(report.min_obj)])
+    end
+end
+
 @recipe function f(report::NamedTuple{(:v, :h, :f_fit, :f_components, :gof)}; show_label=true, show_fit=true, show_components=true, show_residuals=true, f_fit_x_step_scaling=1/100, _subplot=1, x_label="Energy (keV)")
     f_fit_x_step = ustrip(value(report.v.σ)) * f_fit_x_step_scaling
     bin_centers = collect(report.h.edges[1])[1:end-1] .+ diff(collect(report.h.edges[1]))[1]/2 
@@ -509,14 +539,14 @@ end
         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)
+    min_y = minimum(h.weights) == 0.0 ? 1e1 : 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
+    y_vline = [min_y, maximum(h.weights)*1.1]
     for (i, p) in enumerate(pps)
         @series begin
             seriestype := :line
@@ -544,7 +574,7 @@ end
     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)
+    min_y = minimum(report_sipm.h_cal.weights) == 0.0 ? 1e1 : 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
diff --git a/src/LegendSpecFits.jl b/src/LegendSpecFits.jl
index 63a84aa8..6d4946b1 100644
--- a/src/LegendSpecFits.jl
+++ b/src/LegendSpecFits.jl
@@ -81,6 +81,7 @@ include("specfit_functions.jl")
 include("calfunc.jl")
 include("sipm_simple_calibration.jl")
 include("sipmfit.jl")
+include("sipm_filter_optimization.jl")
 abstract type UncertTag end
 ForwardDiff.:(≺)(::Type{<:ForwardDiff.Tag}, ::Type{UncertTag}) = true
 ForwardDiff.:(≺)(::Type{UncertTag}, ::Type{<:ForwardDiff.Tag}) = false
diff --git a/src/sipm_filter_optimization.jl b/src/sipm_filter_optimization.jl
new file mode 100644
index 00000000..3ecb51bb
--- /dev/null
+++ b/src/sipm_filter_optimization.jl
@@ -0,0 +1,139 @@
+
+"""
+    fit_sipm_wl(trig_max_grid::VectorOfVectors{<:Real}, e_grid_wl::StepRangeLen)
+
+Fit the SiPM spectrum for different window lengths and return the optimal window length.
+
+# Arguments
+- `trig_max_grid`: grid of trigger maxima for different window lengths
+- `e_grid_wl`: range of window lengths to sweep through
+
+# Returns
+- `result`: optimal window length and corresponding gain, resolution and position of 1pe peak
+- `report`: report with all window lengths and corresponding gains, resolutions and positions of 1pe peaks
+"""
+function fit_sipm_wl(trig_max_grid::VectorOfVectors{<:Real}, e_grid_wl::StepRangeLen, thresholds::Vector{<:Real}=zeros(length(e_grid_wl));
+    min_pe_peak::Int=1, max_pe_peak::Int=5, n_fwhm_noise_cut::Real=2.0, peakfinder_threshold::Real=5.0, initial_max_amp::Real = 50.0, initial_max_bin_width_quantile::Real=0.9999, 
+    peakfinder_rtol::Real=0.1, peakfinder_α::Real=0.1, peakfinder_σ::Real=-1.0, 
+    min_pe_fit::Real=0.6, max_pe_fit::Real=3.5, Δpe_peak_assignment::Real=0.3)
+    
+    gain_wl    = Vector{Measurement{Float64}}(undef, length(e_grid_wl))
+    res_1pe_wl = Vector{Measurement{Float64}}(undef, length(e_grid_wl))
+    pos_1pe_wl = Vector{Measurement{Float64}}(undef, length(e_grid_wl))
+    success    = Vector{Bool}(zeros(length(e_grid_wl)))
+    reports_simple     = Vector{NamedTuple}(undef, length(e_grid_wl))
+    reports_fit        = Vector{NamedTuple}(undef, length(e_grid_wl))
+
+    # for each window lenght, calculate gain, resolution and position of 1pe peak
+    Threads.@threads for w in eachindex(e_grid_wl)
+        wl = e_grid_wl[w]
+        trig_max = filter(isfinite, collect(trig_max_grid[w]))
+        threshold = thresholds[w]
+        try
+            result_simple, report_simple = sipm_simple_calibration(trig_max; initial_min_amp=threshold, initial_max_amp=initial_max_amp, initial_max_bin_width_quantile=initial_max_bin_width_quantile,
+                                            min_pe_peak=min_pe_peak, max_pe_peak=max_pe_peak, n_fwhm_noise_cut=n_fwhm_noise_cut, peakfinder_threshold=peakfinder_threshold, 
+                                            peakfinder_rtol=peakfinder_rtol, peakfinder_α=peakfinder_α, peakfinder_σ=peakfinder_σ)
+                                                # min_pe_peak=1, n_fwhm_noise_cut=2.0, peakfinder_threshold=5.0, initial_max_bin_width_quantile=0.9999, peakfinder_rtol=0.1, peakfinder_α=0.1, peakfinder_σ=-1.0)
+
+            result_fit, report_fit = fit_sipm_spectrum(result_simple.pe_simple_cal, min_pe_fit, max_pe_fit; f_uncal=result_simple.f_simple_uncal, Δpe_peak_assignment=Δpe_peak_assignment)
+
+            gain_wl[w] = minimum(result_simple.peakpos) - ifelse(threshold == 0.0, result_simple.noisepeakpos, threshold)
+            res_1pe_wl[w] = first(result_fit.resolutions)
+            pos_1pe_wl[w] = first(result_fit.positions)
+            reports_simple[w] = report_simple
+            reports_fit[w] = report_fit
+            success[w] = true
+        catch e
+            @warn "Failed to process wl: $wl: $e"
+        end
+    end
+
+    thrs = if all(thresholds .== 0.0) ones(length(e_grid_wl)) else thresholds end
+    obj = sqrt.(res_1pe_wl[success]) .* sqrt.(thrs[success]) ./ gain_wl[success] ./ sqrt.(pos_1pe_wl[success])
+    wls = collect(e_grid_wl)[success]
+
+    if isempty(obj)
+        @error "No valid gain found"
+        throw(ErrorException("No valid gain found, could not determine optimal window length"))
+    end
+    min_obj    = minimum(obj)
+    wl_min_obj = wls[findmin(obj)[2]]
+    min_res1pe = res_1pe_wl[success][findmin(obj)[2]]
+    min_gain   = gain_wl[success][findmin(obj)[2]]
+    min_pos1pe = pos_1pe_wl[success][findmin(obj)[2]]
+    min_threshold = thresholds[success][findmin(obj)[2]]
+    report_simple = reports_simple[success][findmin(obj)[2]]
+    report_fit = reports_fit[success][findmin(obj)[2]]
+
+    # generate result and report
+    result = (
+        wl = measurement(wl_min_obj, step(e_grid_wl)),
+        obj = min_obj,
+        res_1pe = min_res1pe,
+        gain = min_gain,
+        pos_1pe = min_pos1pe,
+        threshold = min_threshold
+    )
+    report = (
+        wl = result.wl,
+        min_obj = result.obj,
+        gain = result.gain,
+        res_1pe = result.res_1pe,
+        pos_1pe = result.pos_1pe,
+        threshold = result.threshold,
+        a_grid_wl_sg = wls,
+        obj = obj,
+        report_simple = report_simple,
+        report_fit = report_fit,
+    )
+    return result, report
+end
+export fit_sipm_wl
+
+
+
+"""
+    fit_sipm_threshold(thresholds::Vector{<:Real}, min_cut::Real=minimum(thresholds), max_cut::Real=maximum(thresholds); n_bins::Int=-1, relative_cut::Real=0.2, fit_thresholds::Bool=true, uncertainty::Bool=true)
+
+Fit the SiPM threshold spectrum and return the optimal threshold.
+
+# Arguments
+- `thresholds`: vector of thresholds
+- `min_cut`: minimum threshold
+- `max_cut`: maximum threshold
+- `n_bins`: number of bins for histogram
+- `relative_cut`: relative cut for threshold
+- `fit_thresholds`: fit thresholds
+- `uncertainty`: calculate uncertainty
+
+# Returns
+- `result`: optimal threshold and corresponding gain, resolution and position of 1pe peak
+- `report`: report with all thresholds and corresponding gains, resolutions and positions of 1pe peaks
+"""
+function fit_sipm_threshold(thresholds::Vector{<:Real}, min_cut::Real=minimum(thresholds), max_cut::Real=maximum(thresholds); n_bins::Int=-1, relative_cut::Real=0.2, fit_thresholds::Bool=true, uncertainty::Bool=true)
+    # cut out thresholds
+    filter!(in(min_cut .. max_cut), thresholds)
+
+    # get bin_width
+    h = if n_bins < 1
+        fit(Histogram, thresholds, min_cut:get_friedman_diaconis_bin_width(thresholds):max_cut)
+    else
+        fit(Histogram, thresholds, n_bins)
+    end
+    # get simple thresholds
+    result_simple = (μ_simple = mean(thresholds), σ_simple = std(thresholds))
+    
+    # fit histogram
+    result_trig, report_trig = if fit_thresholds
+        # generate cuts for thresholds
+        cuts_thres = cut_single_peak(thresholds, min_cut, max_cut; n_bins=n_bins, relative_cut=relative_cut)
+        # fit histogram
+        fit_binned_trunc_gauss(h, cuts_thres; uncertainty=uncertainty)
+    else
+        (μ = result_simple.μ_simple, σ = result_simple.σ_simple), h
+    end
+    # get simple std and mu values
+    result = merge(result_trig, result_simple)
+    return result, report_trig
+end
+export fit_sipm_threshold
\ No newline at end of file

From 221636bdfef91628886c710b8b2a246cafabb289 Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Wed, 22 Jan 2025 04:30:17 +0100
Subject: [PATCH 05/13] Decrease default nIter to 25

---
 src/sipmfit.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sipmfit.jl b/src/sipmfit.jl
index 5d4d76da..283d7f0a 100644
--- a/src/sipmfit.jl
+++ b/src/sipmfit.jl
@@ -24,7 +24,7 @@ Fit a Gaussian Mixture Model to the given pe calibration data and return the fit
 - `report`: a tuple with the fit report which can be plotted via a recipe
 """
 function fit_sipm_spectrum(pe_cal::Vector{<:Real}, min_pe::Real=0.5, max_pe::Real=3.5;
-    n_mixtures::Int=ceil(Int, (max_pe - min_pe) * 4), nIter::Int=50, nInit::Int=50, 
+    n_mixtures::Int=ceil(Int, (max_pe - min_pe) * 4), nIter::Int=25, nInit::Int=50, 
     method::Symbol=:kmeans, kind=:diag, Δpe_peak_assignment::Real=0.3, f_uncal::Function=identity, uncertainty::Bool=true)
     
     # first filter peak positions out of amplitude vector

From 1910588315d7ad3059bb4db61bcdde243afee5cd Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Wed, 22 Jan 2025 04:30:52 +0100
Subject: [PATCH 06/13] Refactor simple calibration based on cutting away noise
 peak and usage of peakfinder with peak ratios

---
 src/sipm_simple_calibration.jl | 90 +++++++++++++++++-----------------
 1 file changed, 46 insertions(+), 44 deletions(-)

diff --git a/src/sipm_simple_calibration.jl b/src/sipm_simple_calibration.jl
index 37c8392d..05c94af3 100644
--- a/src/sipm_simple_calibration.jl
+++ b/src/sipm_simple_calibration.jl
@@ -27,42 +27,65 @@ function sipm_simple_calibration end
 export sipm_simple_calibration
 
 function sipm_simple_calibration(pe_uncal::Vector{<:Real};
-    min_pe_peak::Int=2, max_pe_peak::Int=5, relative_cut_noise_cut::Real=0.5, n_fwhm_noise_cut::Real=5.0,
-    initial_min_amp::Real=1.0, initial_max_amp::Real=25.0, initial_max_bin_width_quantile::Real=0.9, 
-    peakfinder_σ::Real=2.0, peakfinder_threshold::Real=10.0, peakfinder_rtol::Real=0.1, peakfinder_α::Real=0.05
+    min_pe_peak::Int=1, max_pe_peak::Int=5, relative_cut_noise_cut::Real=0.5, n_fwhm_noise_cut::Real=5.0,
+    initial_min_amp::Real=0.0, initial_max_amp::Real=50.0, initial_max_bin_width_quantile::Real=0.9, 
+    peakfinder_σ::Real=-1.0, peakfinder_threshold::Real=10.0, peakfinder_rtol::Real=0.1, peakfinder_α::Real=0.05
 )
     
-    # Start with a big window where the noise peak is included
-    bin_width = get_friedman_diaconis_bin_width(filter(in(initial_min_amp..quantile(pe_uncal, initial_max_bin_width_quantile)), pe_uncal))
-
     # Initial peak search
-    h_uncal = fit(Histogram, pe_uncal, initial_min_amp:bin_width:initial_max_amp)
-
     cuts_1pe = cut_single_peak(pe_uncal, initial_min_amp, initial_max_amp, relative_cut=relative_cut_noise_cut)
-
-    h_uncal_cut = fit(Histogram, pe_uncal, cuts_1pe.max+n_fwhm_noise_cut*(cuts_1pe.high - cuts_1pe.max):bin_width:initial_max_amp)
-
-    c, h_deconv, peakpos, threshold = RadiationSpectra.determine_calibration_constant_through_peak_ratios(h_uncal_cut, collect(range(min_pe_peak, max_pe_peak, step=1)),
-        min_n_peaks = 2, max_n_peaks = 2*max_pe_peak, threshold=peakfinder_threshold, rtol=peakfinder_rtol, α=peakfinder_α, σ=peakfinder_σ)
-
+    
+    bin_width_cut_min = cuts_1pe.max+n_fwhm_noise_cut*(cuts_1pe.high - cuts_1pe.max)
+    bin_width_cut = get_friedman_diaconis_bin_width(filter(in(bin_width_cut_min..quantile(pe_uncal, initial_max_bin_width_quantile)), pe_uncal))
+    peakpos = []
+    for bin_width_scale in 10 .^ range(0, stop=-3, length=50)
+        @debug "Using bin width: $(bin_width_cut)"
+
+        bin_width_cut = bin_width_cut * bin_width_scale
+        h_uncal_cut = fit(Histogram, pe_uncal, bin_width_cut_min:bin_width_cut:initial_max_amp)
+        if peakfinder_σ <= 0.0
+            peakfinder_σ = round(Int, 2*(cuts_1pe.high - cuts_1pe.max) / bin_width_cut / 2.355)
+        end
+        @debug "Peakfinder σ: $(peakfinder_σ)"
+        try
+            c, h_deconv, peakpos, threshold = RadiationSpectra.determine_calibration_constant_through_peak_ratios(h_uncal_cut, collect(range(min_pe_peak, max_pe_peak, step=1)),
+                min_n_peaks = 2, max_n_peaks = 2*max_pe_peak, threshold=peakfinder_threshold, rtol=peakfinder_rtol, α=peakfinder_α, σ=peakfinder_σ)
+        catch e
+            @warn "Failed to find peaks with bin width scale $(bin_width_scale): $(e)"
+            continue
+        else
+            @debug "Found peaks with bin width scale $(bin_width_scale)"
+            if !isempty(peakpos)
+                break
+            end
+        end
+    end
+
+    if isempty(peakpos) || length(peakpos) < 2
+        throw(ErrorException("Failed to find peaks"))
+    end
 
     # simple calibration
     sort!(peakpos)
-    gain = peakpos[min_pe_peak + 1] - peakpos[min_pe_peak]
+    @debug "Found $(min_pe_peak) PE Peak positions: $(peakpos[1])"
+    @debug "Found $(min_pe_peak+1) PE Peak positions: $(peakpos[2])"
+    gain = peakpos[2] - peakpos[1]
+    @debug "Calculated gain: $(round(gain, digits=2))"
     c = 1/gain
-    offset = - (peakpos[min_pe_peak] * c - min_pe_peak)
+    offset = - (peakpos[1] * c - min_pe_peak)
+    @debug "Calculated offset: $(round(offset, digits=2))"
 
     f_simple_calib = x -> x .* c .+ offset
     f_simple_uncal = x -> (x .- offset) ./ c
 
     pe_simple_cal = f_simple_calib.(pe_uncal)
     peakpos_cal = f_simple_calib.(peakpos)
-
-    bin_width_cal = get_friedman_diaconis_bin_width(filter(in(0.5..1.5), pe_simple_cal))
+    
+    bin_width_cal = get_friedman_diaconis_bin_width(filter(in(0.5..min_pe_peak), pe_simple_cal))
     bin_width_uncal = f_simple_uncal(bin_width_cal) - f_simple_uncal(0.0)
 
-    h_calsimple = fit(Histogram, pe_simple_cal, 0.0:bin_width_cal:6.0)
-    h_uncal = fit(Histogram, pe_uncal, 0.0:bin_width_uncal:(6.0 - offset) / c)
+    h_calsimple = fit(Histogram, pe_simple_cal, 0.0:bin_width_cal:max_pe_peak + 1)
+    h_uncal = fit(Histogram, pe_uncal, 0.0:bin_width_uncal:f_simple_uncal(max_pe_peak + 1))
 
     result = (
         pe_simple_cal = pe_simple_cal,
@@ -70,7 +93,9 @@ function sipm_simple_calibration(pe_uncal::Vector{<:Real};
         f_simple_calib = f_simple_calib,
         f_simple_uncal = f_simple_uncal,
         c = c,
-        offset = offset
+        offset = offset,
+        noisepeakpos = cuts_1pe.max,
+        noisepeakwidth = cuts_1pe.high - cuts_1pe.low
     )
     report = (
         peakpos = peakpos,
@@ -79,27 +104,4 @@ function sipm_simple_calibration(pe_uncal::Vector{<:Real};
         h_calsimple = h_calsimple
     )
     return result, report
-end
-
-
-function find_peaks(
-    amps::Vector{<:Real}; 
-    min_pe_peak::Real=1.0, max_pe_peak::Real=5.0, n_fwhm_noise_cut::Real=5.0,
-    initial_min_amp::Real=1.0, initial_max_amp::Real=100.0, initial_max_bin_width_quantile::Real=0.9, 
-    peakfinder_σ::Real=2.0, peakfinder_threshold::Real=10.0, peakfinder_rtol::Real=0.1, peakfinder_α::Real=0.05
-)
-    # Start with a big window where the noise peak is included
-    bin_width = get_friedman_diaconis_bin_width(filter(in(initial_min_amp..quantile(amps, initial_max_bin_width_quantile)), amps))
-
-    # Initial peak search
-    h_uncal = fit(Histogram, amps, initial_min_amp:bin_width:initial_max_amp)
-
-    cuts_1pe = cut_single_peak(amps, initial_min_amp, initial_max_amp, relative_cut=0.5)
-
-    h_uncal_cut = fit(Histogram, trig_max, cuts_1pe.max+n_fwhm_noise_cut*(cuts_1pe.high - cuts_1pe.max):bin_width:initial_max_amp)
-
-    c, h_deconv, peak_positions, threshold = RadiationSpectra.determine_calibration_constant_through_peak_ratios(h_uncal_cut, collect(range(min_pe_peak, max_pe_peak, step=1)),
-        min_n_peaks = 2, max_n_peaks = 2*max_pe_peak, threshold=peakfinder_threshold, rtol=peakfinder_rtol, α=peakfinder_α, σ=peakfinder_σ)
-
-    return h_decon, peakpos
 end
\ No newline at end of file

From 434680ea61aa6f0fc2a0e69fe04c601ce8a80932 Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Fri, 31 Jan 2025 13:32:08 +0100
Subject: [PATCH 07/13] Bug Fix calibration constant

---
 src/sipm_simple_calibration.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sipm_simple_calibration.jl b/src/sipm_simple_calibration.jl
index 05c94af3..0598958e 100644
--- a/src/sipm_simple_calibration.jl
+++ b/src/sipm_simple_calibration.jl
@@ -49,7 +49,7 @@ function sipm_simple_calibration(pe_uncal::Vector{<:Real};
         @debug "Peakfinder σ: $(peakfinder_σ)"
         try
             c, h_deconv, peakpos, threshold = RadiationSpectra.determine_calibration_constant_through_peak_ratios(h_uncal_cut, collect(range(min_pe_peak, max_pe_peak, step=1)),
-                min_n_peaks = 2, max_n_peaks = 2*max_pe_peak, threshold=peakfinder_threshold, rtol=peakfinder_rtol, α=peakfinder_α, σ=peakfinder_σ)
+                min_n_peaks = 2, max_n_peaks = max_pe_peak, threshold=peakfinder_threshold, rtol=peakfinder_rtol, α=peakfinder_α, σ=peakfinder_σ)
         catch e
             @warn "Failed to find peaks with bin width scale $(bin_width_scale): $(e)"
             continue

From 3327a02e52022348cd8d2d3d01d73850ffce85d9 Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Fri, 31 Jan 2025 13:32:43 +0100
Subject: [PATCH 08/13] Bug Fix resolution calculation

---
 src/sipmfit.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/sipmfit.jl b/src/sipmfit.jl
index 283d7f0a..b2e109d6 100644
--- a/src/sipmfit.jl
+++ b/src/sipmfit.jl
@@ -104,10 +104,10 @@ function fit_sipm_spectrum(pe_cal::Vector{<:Real}, min_pe::Real=0.5, max_pe::Rea
 
     # get pe_pos
     get_pe_pos = pe -> let sel = in.(μ, (-Δpe_peak_assignment..Δpe_peak_assignment) .+ pe)
-        dot(view(μ,sel), view(w,sel)) / sum(view(w,sel))
+        dot(view(μ, sel), view(w, sel)) / sum(view(w, sel))
     end
     get_pe_res = pe -> let sel = in.(μ, (-Δpe_peak_assignment..Δpe_peak_assignment) .+ pe)
-        dot(view(σ,sel), view(w,sel)) / sum(view(w,sel))
+        sqrt(dot(view(σ, sel).^2, view(w, sel).^2))
     end 
     n_pos_mixtures = [count(in.(μ, (-Δpe_peak_assignment..Δpe_peak_assignment) .+ pe)) for pe in pes]
 

From e8f0a6ece77657f305aab0b2a6c99dc70cee95f1 Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Fri, 31 Jan 2025 13:33:12 +0100
Subject: [PATCH 09/13] Use kwargs for all fit parameters + return correct gain

---
 src/sipm_filter_optimization.jl | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/sipm_filter_optimization.jl b/src/sipm_filter_optimization.jl
index 3ecb51bb..5057dfd3 100644
--- a/src/sipm_filter_optimization.jl
+++ b/src/sipm_filter_optimization.jl
@@ -33,11 +33,11 @@ function fit_sipm_wl(trig_max_grid::VectorOfVectors{<:Real}, e_grid_wl::StepRang
             result_simple, report_simple = sipm_simple_calibration(trig_max; initial_min_amp=threshold, initial_max_amp=initial_max_amp, initial_max_bin_width_quantile=initial_max_bin_width_quantile,
                                             min_pe_peak=min_pe_peak, max_pe_peak=max_pe_peak, n_fwhm_noise_cut=n_fwhm_noise_cut, peakfinder_threshold=peakfinder_threshold, 
                                             peakfinder_rtol=peakfinder_rtol, peakfinder_α=peakfinder_α, peakfinder_σ=peakfinder_σ)
-                                                # min_pe_peak=1, n_fwhm_noise_cut=2.0, peakfinder_threshold=5.0, initial_max_bin_width_quantile=0.9999, peakfinder_rtol=0.1, peakfinder_α=0.1, peakfinder_σ=-1.0)
 
             result_fit, report_fit = fit_sipm_spectrum(result_simple.pe_simple_cal, min_pe_fit, max_pe_fit; f_uncal=result_simple.f_simple_uncal, Δpe_peak_assignment=Δpe_peak_assignment)
 
-            gain_wl[w] = minimum(result_simple.peakpos) - ifelse(threshold == 0.0, result_simple.noisepeakpos, threshold)
+            # gain_wl[w] = minimum(result_simple.peakpos) - ifelse(threshold == 0.0, result_simple.noisepeakpos, threshold)
+            gain_wl[w] = minimum(result_simple.peakpos) - result_simple.noisepeakpos
             res_1pe_wl[w] = first(result_fit.resolutions)
             pos_1pe_wl[w] = first(result_fit.positions)
             reports_simple[w] = report_simple
@@ -49,7 +49,7 @@ function fit_sipm_wl(trig_max_grid::VectorOfVectors{<:Real}, e_grid_wl::StepRang
     end
 
     thrs = if all(thresholds .== 0.0) ones(length(e_grid_wl)) else thresholds end
-    obj = sqrt.(res_1pe_wl[success]) .* sqrt.(thrs[success]) ./ gain_wl[success] ./ sqrt.(pos_1pe_wl[success])
+    obj = sqrt.(res_1pe_wl[success]) .* sqrt.(thrs[success]) ./ gain_wl[success]
     wls = collect(e_grid_wl)[success]
 
     if isempty(obj)
@@ -62,8 +62,8 @@ function fit_sipm_wl(trig_max_grid::VectorOfVectors{<:Real}, e_grid_wl::StepRang
     min_gain   = gain_wl[success][findmin(obj)[2]]
     min_pos1pe = pos_1pe_wl[success][findmin(obj)[2]]
     min_threshold = thresholds[success][findmin(obj)[2]]
-    report_simple = reports_simple[success][findmin(obj)[2]]
-    report_fit = reports_fit[success][findmin(obj)[2]]
+    min_report_simple = reports_simple[success][findmin(obj)[2]]
+    min_report_fit = reports_fit[success][findmin(obj)[2]]
 
     # generate result and report
     result = (
@@ -77,14 +77,14 @@ function fit_sipm_wl(trig_max_grid::VectorOfVectors{<:Real}, e_grid_wl::StepRang
     report = (
         wl = result.wl,
         min_obj = result.obj,
-        gain = result.gain,
-        res_1pe = result.res_1pe,
-        pos_1pe = result.pos_1pe,
-        threshold = result.threshold,
+        gain = gain_wl,
+        res_1pe = res_1pe_wl,
+        pos_1pe = pos_1pe_wl,
+        threshold = thresholds[success],
         a_grid_wl_sg = wls,
         obj = obj,
-        report_simple = report_simple,
-        report_fit = report_fit,
+        report_simple = min_report_simple,
+        report_fit = min_report_fit,
     )
     return result, report
 end

From b1c8fe1b5f14939acf73865e791f883ef204727b Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Mon, 3 Feb 2025 15:10:53 +0100
Subject: [PATCH 10/13] Resolved comments

---
 src/sipm_filter_optimization.jl | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/sipm_filter_optimization.jl b/src/sipm_filter_optimization.jl
index 5057dfd3..9ace64b9 100644
--- a/src/sipm_filter_optimization.jl
+++ b/src/sipm_filter_optimization.jl
@@ -20,7 +20,7 @@ function fit_sipm_wl(trig_max_grid::VectorOfVectors{<:Real}, e_grid_wl::StepRang
     gain_wl    = Vector{Measurement{Float64}}(undef, length(e_grid_wl))
     res_1pe_wl = Vector{Measurement{Float64}}(undef, length(e_grid_wl))
     pos_1pe_wl = Vector{Measurement{Float64}}(undef, length(e_grid_wl))
-    success    = Vector{Bool}(zeros(length(e_grid_wl)))
+    success    = falses(length(e_grid_wl))  
     reports_simple     = Vector{NamedTuple}(undef, length(e_grid_wl))
     reports_fit        = Vector{NamedTuple}(undef, length(e_grid_wl))
 
@@ -56,14 +56,14 @@ function fit_sipm_wl(trig_max_grid::VectorOfVectors{<:Real}, e_grid_wl::StepRang
         @error "No valid gain found"
         throw(ErrorException("No valid gain found, could not determine optimal window length"))
     end
-    min_obj    = minimum(obj)
-    wl_min_obj = wls[findmin(obj)[2]]
-    min_res1pe = res_1pe_wl[success][findmin(obj)[2]]
-    min_gain   = gain_wl[success][findmin(obj)[2]]
-    min_pos1pe = pos_1pe_wl[success][findmin(obj)[2]]
-    min_threshold = thresholds[success][findmin(obj)[2]]
-    min_report_simple = reports_simple[success][findmin(obj)[2]]
-    min_report_fit = reports_fit[success][findmin(obj)[2]]
+    min_obj, min_obj_idx = findmin(obj)  
+    wl_min_obj = wls[min_obj_idx]
+    min_res1pe = res_1pe_wl[success][min_obj_idx]
+    min_gain   = gain_wl[success][min_obj_idx]
+    min_pos1pe = pos_1pe_wl[success][min_obj_idx]
+    min_threshold = thresholds[success][min_obj_idx]
+    min_report_simple = reports_simple[success][min_obj_idx]
+    min_report_fit = reports_fit[success][min_obj_idx]
 
     # generate result and report
     result = (

From 32e6590ccd3a0ac939f6cd13faaed2501f148c6e Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Mon, 3 Feb 2025 15:19:22 +0100
Subject: [PATCH 11/13] Bug fix iterative bin_width_cut algorithm

---
 src/sipm_simple_calibration.jl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/sipm_simple_calibration.jl b/src/sipm_simple_calibration.jl
index 0598958e..607e9e15 100644
--- a/src/sipm_simple_calibration.jl
+++ b/src/sipm_simple_calibration.jl
@@ -38,13 +38,13 @@ function sipm_simple_calibration(pe_uncal::Vector{<:Real};
     bin_width_cut_min = cuts_1pe.max+n_fwhm_noise_cut*(cuts_1pe.high - cuts_1pe.max)
     bin_width_cut = get_friedman_diaconis_bin_width(filter(in(bin_width_cut_min..quantile(pe_uncal, initial_max_bin_width_quantile)), pe_uncal))
     peakpos = []
-    for bin_width_scale in 10 .^ range(0, stop=-3, length=50)
+    for bin_width_scale in exp10.(range(0, stop=-3, length=50))  # 1e-3 to 1
         @debug "Using bin width: $(bin_width_cut)"
 
-        bin_width_cut = bin_width_cut * bin_width_scale
-        h_uncal_cut = fit(Histogram, pe_uncal, bin_width_cut_min:bin_width_cut:initial_max_amp)
+        bin_width_cut_scaled = bin_width_cut * bin_width_scale
+        h_uncal_cut = fit(Histogram, pe_uncal, bin_width_cut_min:bin_width_cut_scaled:initial_max_amp)
         if peakfinder_σ <= 0.0
-            peakfinder_σ = round(Int, 2*(cuts_1pe.high - cuts_1pe.max) / bin_width_cut / 2.355)
+            peakfinder_σ = round(Int, 2*(cuts_1pe.high - cuts_1pe.max) / bin_width_cut_scaled / 2.355)
         end
         @debug "Peakfinder σ: $(peakfinder_σ)"
         try

From 5a14d82ff152d38d91f58ea16c73e8d35f00ac7e Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Mon, 3 Feb 2025 15:23:43 +0100
Subject: [PATCH 12/13] Bump GaussianMixtures to 0.3.12

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index 2e3185c5..80f771bd 100644
--- a/Project.toml
+++ b/Project.toml
@@ -61,7 +61,7 @@ Distributions = "0.25.87"
 FillArrays = "1.4.1"
 Format = "1.2, 1.3"
 ForwardDiff = "0.10.26"
-GaussianMixtures = "0.3.11"
+GaussianMixtures = "0.3.12"
 IntervalSets = "0.7"
 InverseFunctions = "0.1.8"
 IrrationalConstants = "0.1.1, 0.2"

From 2346c99cd3aae2248a7ba3c27abb8db856aeb2c9 Mon Sep 17 00:00:00 2001
From: Florian Henkes <florian.henkes@outlook.com>
Date: Mon, 3 Feb 2025 15:24:50 +0100
Subject: [PATCH 13/13] Remove range comment

---
 src/sipm_simple_calibration.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sipm_simple_calibration.jl b/src/sipm_simple_calibration.jl
index 607e9e15..85751b6e 100644
--- a/src/sipm_simple_calibration.jl
+++ b/src/sipm_simple_calibration.jl
@@ -38,7 +38,7 @@ function sipm_simple_calibration(pe_uncal::Vector{<:Real};
     bin_width_cut_min = cuts_1pe.max+n_fwhm_noise_cut*(cuts_1pe.high - cuts_1pe.max)
     bin_width_cut = get_friedman_diaconis_bin_width(filter(in(bin_width_cut_min..quantile(pe_uncal, initial_max_bin_width_quantile)), pe_uncal))
     peakpos = []
-    for bin_width_scale in exp10.(range(0, stop=-3, length=50))  # 1e-3 to 1
+    for bin_width_scale in exp10.(range(0, stop=-3, length=50))
         @debug "Using bin width: $(bin_width_cut)"
 
         bin_width_cut_scaled = bin_width_cut * bin_width_scale