Merge pull request #120 from legend-exp/patch_sipm-simple-peakfinder

Patch `sipm_simple_calibration`

Project.toml

@@ -34,6 +34,7 @@ RadiationSpectra = "4f207c7e-01da-51d7-a1a0-c8c06dd1d883"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
+SavitzkyGolay = "c4bf5708-b6a6-4fbe-bcd0-6850ed671584"
 SnoopPrecompile = "66db9d55-30c0-4569-8b51-7e840670fc0c"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -67,9 +68,9 @@ InverseFunctions = "0.1.8"
 IrrationalConstants = "0.1.1, 0.2"
 KernelDensity = "0.6.4"
 LaTeXStrings = "1.3"
-LogExpFunctions = "0.3.16"
 LinearAlgebra = "<0.0.1, 1"
 LinearRegression = "0.2"
+LogExpFunctions = "0.3.16"
 LsqFit = "0.14, 0.15"
 Measurements = "2.5"
 Measures = "0.3"
@@ -85,6 +86,7 @@ Random = "<0.0.1, 1"
 RecipesBase = "1.3.4"
 Roots = "2"
 SnoopPrecompile = "1"
+SavitzkyGolay = "0.9"
 SpecialFunctions = "2.1.4"
 Statistics = "<0.0.1, 1"
 StatsBase = "0.33.7, 0.34"

src/LegendSpecFits.jl

@@ -37,6 +37,7 @@ using PropDicts
 using RadiationSpectra
 using RadiationSpectra: peakfinder
 using Roots
+using SavitzkyGolay
 using SpecialFunctions
 using StatsBase
 using StructArrays

src/sipm_simple_calibration.jl

@@ -35,33 +35,64 @@ function sipm_simple_calibration(pe_uncal::Vector{<:Real};
     # Initial peak search
     cuts_1pe = cut_single_peak(pe_uncal, initial_min_amp, initial_max_amp, relative_cut=relative_cut_noise_cut)
 
-    bin_width_cut_min = cuts_1pe.max+n_fwhm_noise_cut*(cuts_1pe.high - cuts_1pe.max)
+    bin_width_cut_min = if n_fwhm_noise_cut == 0.0
+        initial_min_amp
+    else
+        cuts_1pe.max+n_fwhm_noise_cut*(cuts_1pe.high - cuts_1pe.max)
+    end
     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))
-        @debug "Using bin width: $(bin_width_cut)"
-
         bin_width_cut_scaled = bin_width_cut * bin_width_scale
+        @debug "Using bin width: $(bin_width_cut_scaled)"
         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_scaled / 2.355)
+        peakfinder_σ_scaled = if peakfinder_σ <= 0.0
+            round(Int, 2*(cuts_1pe.high - cuts_1pe.max) / bin_width_cut_scaled / (2 * sqrt(2 * log(2))) )
+        else
+            rount(Int, peakfinder_σ)  
         end
-        @debug "Peakfinder σ: $(peakfinder_σ)"
+        @debug "Peakfinder σ: $(peakfinder_σ_scaled)"
         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 = max_pe_peak, threshold=peakfinder_threshold, rtol=peakfinder_rtol, α=peakfinder_α, σ=peakfinder_σ)
+            # use SavitzkyGolay filter to smooth the histogram
+            sg_uncal_cut = savitzky_golay(h_uncal_cut.weights, ifelse(isodd(peakfinder_σ_scaled), peakfinder_σ_scaled, peakfinder_σ_scaled + 1), 3)
+            h_uncal_cut_sg = Histogram(h_uncal_cut.edges[1], sg_uncal_cut.y)
+            _, _, peakpos, _ = RadiationSpectra.determine_calibration_constant_through_peak_ratios(h_uncal_cut_sg, collect(range(min_pe_peak, max_pe_peak, step=1)),
+                min_n_peaks = 2, max_n_peaks = max_pe_peak, threshold=peakfinder_threshold, rtol=peakfinder_rtol, α=peakfinder_α, σ=peakfinder_σ_scaled)
         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)
+            if !isempty(peakpos) && length(peakpos) >= 2
                 break
             end
         end
     end
 
-    if isempty(peakpos) || length(peakpos) < 2
+    if length(peakpos) < 2
+        @warn "Failed to find peaks with peakfinder method, use alternative"
+        bin_width_cut_scaled = bin_width_cut * 0.5
+        @debug "Using bin width: $(bin_width_cut_scaled)"
+
+        h_uncal_cut = fit(Histogram, pe_uncal, bin_width_cut_min:bin_width_cut_scaled:initial_max_amp)
+        peakfinder_σ_scaled = if peakfinder_σ <= 0.0
+            round(Int, 2*(cuts_1pe.high - cuts_1pe.max) / bin_width_cut_scaled / (2 * sqrt(2 * log(2))) )
+        else
+            rount(Int, peakfinder_σ)
+        end
+
+        # use SavitzkyGolay filter to smooth the histogram
+        sg_uncal_cut = savitzky_golay(h_uncal_cut.weights, ifelse(isodd(peakfinder_σ_scaled), peakfinder_σ_scaled, peakfinder_σ_scaled + 1), 3)
+        edges = StatsBase.midpoints(first(h_uncal_cut.edges))  # use midpoints as x values
+        counts_sg = sg_uncal_cut.y
+        # get local maxima
+        min_i_prominence = round(Int, peakfinder_σ_scaled / 2)
+        is_local_maximum(i, y) = i > min_i_prominence && i < length(y) - min_i_prominence && 
+                all(y[i] .> y[i-min_i_prominence:i-1]) && all(y[i] .> y[i+1:i+min_i_prominence])
+        peakpos = edges[findall(is_local_maximum.(eachindex(counts_sg), Ref(counts_sg)))]
+    end
+
+    if length(peakpos) < 2
         throw(ErrorException("Failed to find peaks"))
     end