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Deprecate functions: surrival --> survival #100

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Dec 11, 2024
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Deprecate functions: surrival --> survival #100

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2 changes: 1 addition & 1 deletion ext/LegendSpecFitsRecipesBaseExt.jl
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Expand Up @@ -127,7 +127,7 @@

@recipe function f(report:: NamedTuple{(:wl, :min_sf, :a_grid_wl_sg, :sfs)})
xlabel := "Window Length ($(unit(first(report.a_grid_wl_sg))))"
ylabel := "SEP Surrival Fraction ($(unit(first(report.sfs))))"
ylabel := "SEP Survival Fraction ($(unit(first(report.sfs))))"

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grid := :true
gridcolor := :black
gridalpha := 0.2
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41 changes: 23 additions & 18 deletions src/aoe_cut.jl
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Expand Up @@ -88,14 +88,14 @@


"""
get_peaks_surrival_fractions(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, peaks::Vector{<:T}, peak_names::Vector{Symbol}, windows::Vector{<:Tuple{T, T}}, aoe_cut::Unitful.RealOrRealQuantity,; uncertainty::Bool=true, inverted_mode::Bool=false, bin_width_window::T=2.0u"keV", sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe)), fit_funcs::Vector{Symbol}=fill(:gamma_def, length(peaks))) where T<:Unitful.Energy{<:Real}
get_peaks_survival_fractions(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, peaks::Vector{<:T}, peak_names::Vector{Symbol}, windows::Vector{<:Tuple{T, T}}, aoe_cut::Unitful.RealOrRealQuantity,; uncertainty::Bool=true, inverted_mode::Bool=false, bin_width_window::T=2.0u"keV", sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe)), fit_funcs::Vector{Symbol}=fill(:gamma_def, length(peaks))) where T<:Unitful.Energy{<:Real}

Get the surrival fraction of a peak after a AoE cut value `aoe_cut` for a given `peak` and `window` size while performing a peak fit with fixed position.
Get the survival fraction of a peak after a AoE cut value `aoe_cut` for a given `peak` and `window` size while performing a peak fit with fixed position.
# Return
- `result`: Dict of results for each peak
- `report`: Dict of reports for each peak
"""
function get_peaks_surrival_fractions(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, peaks::Vector{<:T}, peak_names::Vector{Symbol}, windows::Vector{<:Tuple{T, T}}, aoe_cut::Unitful.RealOrRealQuantity,; uncertainty::Bool=true, inverted_mode::Bool=false, bin_width_window::T=2.0u"keV", sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe)), fit_funcs::Vector{Symbol}=fill(:gamma_def, length(peaks))) where T<:Unitful.Energy{<:Real}
function get_peaks_survival_fractions(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, peaks::Vector{<:T}, peak_names::Vector{Symbol}, windows::Vector{<:Tuple{T, T}}, aoe_cut::Unitful.RealOrRealQuantity,; uncertainty::Bool=true, inverted_mode::Bool=false, bin_width_window::T=2.0u"keV", sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe)), fit_funcs::Vector{Symbol}=fill(:gamma_def, length(peaks))) where T<:Unitful.Energy{<:Real}

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@assert length(peaks) == length(peak_names) == length(windows) "Length of peaks, peak_names and windows must be equal"
# create return and result vectors
v_result = Vector{NamedTuple}(undef, length(peak_names))
Expand All @@ -106,7 +106,7 @@
# extract peak, name and window
peak, name, window, fit_func = peaks[i], peak_names[i], windows[i], fit_funcs[i]
# fit peak
result_peak, report_peak = get_peak_surrival_fraction(aoe, e, peak, collect(window), aoe_cut; uncertainty=uncertainty, inverted_mode=inverted_mode, bin_width_window=bin_width_window, sigma_high_sided=sigma_high_sided, fit_func=fit_func)
result_peak, report_peak = get_peak_survival_fraction(aoe, e, peak, collect(window), aoe_cut; uncertainty=uncertainty, inverted_mode=inverted_mode, bin_width_window=bin_width_window, sigma_high_sided=sigma_high_sided, fit_func=fit_func)

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# save results
v_result[i] = result_peak
v_report[i] = report_peak
Expand All @@ -118,24 +118,25 @@

return result, report
end
export get_peaks_surrival_fractions
get_peaks_surrival_fractions(aoe, e, peaks, peak_names, left_window_sizes::Vector{<:Unitful.Energy{<:Real}}, right_window_sizes::Vector{<:Unitful.Energy{<:Real}}, aoe_cut; kwargs...) = get_peaks_surrival_fractions(aoe, e, peaks, peak_names, [(l,r) for (l,r) in zip(left_window_sizes, right_window_sizes)], aoe_cut; kwargs...)
get_peaks_survival_fractions(aoe, e, peaks, peak_names, left_window_sizes::Vector{<:Unitful.Energy{<:Real}}, right_window_sizes::Vector{<:Unitful.Energy{<:Real}}, aoe_cut; kwargs...) = get_peaks_survival_fractions(aoe, e, peaks, peak_names, [(l,r) for (l,r) in zip(left_window_sizes, right_window_sizes)], aoe_cut; kwargs...)

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Base.@deprecate get_peaks_surrival_fractions(args...; kwargs...) get_peaks_survival_fractions(args...; kwargs...)
export get_peaks_survival_fractions, get_peaks_surrival_fractions

"""
get_peak_surrival_fraction(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, peak::T, window::Vector{T}, aoe_cut::Unitful.RealOrRealQuantity,;
get_peak_survival_fraction(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, peak::T, window::Vector{T}, aoe_cut::Unitful.RealOrRealQuantity,;
uncertainty::Bool=true, inverted_mode::Bool=false, bin_width_window::T=2.0u"keV", sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe)), fit_func::Symbol=:gamma_def) where T<:Unitful.Energy{<:Real}

Get the surrival fraction of a peak after a AoE cut value `aoe_cut` for a given `peak` and `window` size while performing a peak fit with fixed position.
Get the survival fraction of a peak after a AoE cut value `aoe_cut` for a given `peak` and `window` size while performing a peak fit with fixed position.

# Returns
- `peak`: Peak position
- `n_before`: Number of counts before the cut
- `n_after`: Number of counts after the cut
- `sf`: Surrival fraction
- `sf`: Survival fraction
- `err`: Uncertainties
"""
function get_peak_surrival_fraction(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, peak::T, window::Vector{T}, aoe_cut::Unitful.RealOrRealQuantity,;
function get_peak_survival_fraction(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, peak::T, window::Vector{T}, aoe_cut::Unitful.RealOrRealQuantity,;

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uncertainty::Bool=true, inverted_mode::Bool=false, bin_width_window::T=2.0u"keV", sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe)), fit_func::Symbol=:gamma_def) where T<:Unitful.Energy{<:Real}
# estimate bin width
bin_width = get_friedman_diaconis_bin_width(e[e .> peak - bin_width_window .&& e .< peak + bin_width_window])
Expand All @@ -162,7 +163,7 @@
cut = fit(Histogram, ustrip(e_cut), ustrip(peak-first(window):bin_width:peak+last(window)))
# fit peak and return number of signal counts
result_after, report_after = fit_subpeaks_th228(survived, cut, result_before; uncertainty=uncertainty, fit_func=fit_func)
# calculate surrival fraction
# calculate survival fraction
sf = result_after.sf * 100u"percent"
result = (
peak = peak,
Expand All @@ -182,21 +183,23 @@
)
return result, report
end
export get_peak_surrival_fraction

Base.@deprecate get_peak_surrival_fraction(args...; kwargs...) get_peak_survival_fraction(args...; kwargs...)
export get_peak_survival_fraction, get_peak_surrival_fraction


"""
get_continuum_surrival_fraction(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, center::T, window::T, aoe_cut::Unitful.RealOrRealQuantity,; inverted_mode::Bool=false, sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe))) where T<:Unitful.Energy{<:Real}
Get the surrival fraction of a continuum after a AoE cut value `aoe_cut` for a given `center` and `window` size.
get_continuum_survival_fraction(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, center::T, window::T, aoe_cut::Unitful.RealOrRealQuantity,; inverted_mode::Bool=false, sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe))) where T<:Unitful.Energy{<:Real}
Get the survival fraction of a continuum after a AoE cut value `aoe_cut` for a given `center` and `window` size.

# Returns
- `center`: Center of the continuum
- `window`: Window size
- `n_before`: Number of counts before the cut
- `n_after`: Number of counts after the cut
- `sf`: Surrival fraction
- `sf`: Survival fraction
"""
function get_continuum_surrival_fraction(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, center::T, window::T, aoe_cut::Unitful.RealOrRealQuantity,; inverted_mode::Bool=false, sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe))) where T<:Unitful.Energy{<:Real}
function get_continuum_survival_fraction(aoe::Vector{<:Unitful.RealOrRealQuantity}, e::Vector{<:T}, center::T, window::T, aoe_cut::Unitful.RealOrRealQuantity,; inverted_mode::Bool=false, sigma_high_sided::Unitful.RealOrRealQuantity=Inf*unit(first(aoe))) where T<:Unitful.Energy{<:Real}

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# scale unit
e_unit = u"keV"
# get energy around center
Expand All @@ -216,7 +219,7 @@
end
n_after = length(e_survived)

# calculate surrival fraction
# calculate survival fraction
sf = n_after / n_before
result = (
window = measurement(center, window),
Expand All @@ -238,4 +241,6 @@
)
return result, report
end
export get_continuum_surrival_fraction

Base.@deprecate get_continuum_surrival_fraction(args...; kwargs...) get_continuum_survival_fraction(args...; kwargs...)
export get_continuum_survival_fraction, get_continuum_surrival_fraction
4 changes: 2 additions & 2 deletions src/aoe_filter_optimization.jl
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Expand Up @@ -83,7 +83,7 @@
aoe_sep_i = flatview(aoe_sep)[i_aoe, :][isfinite.(flatview(aoe_sep)[i_aoe, :])] ./ result_sep.m_calib
e_sep_i = e_sep_calib[isfinite.(flatview(aoe_sep)[i_aoe, :])]

result_sep_sf, _ = get_peak_surrival_fraction(aoe_sep_i, e_sep_i, sep, sep_window, psd_cut.lowcut; uncertainty=uncertainty, fit_func=sep_cut_search_fit_func)
result_sep_sf, _ = get_peak_survival_fraction(aoe_sep_i, e_sep_i, sep, sep_window, psd_cut.lowcut; uncertainty=uncertainty, fit_func=sep_cut_search_fit_func)

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sep_sfs[i_aoe] = result_sep_sf.sf
wls[i_aoe] = wl
Expand All @@ -98,7 +98,7 @@
sep_sfs = sep_sfs[fts_success]
wls = wls[fts_success]

# get minimal surrival fraction and window length
# get minimal survival fraction and window length
sep_sfs_cut = 1.0u"percent" .< sep_sfs .< 100u"percent"
if isempty(sep_sfs[sep_sfs_cut])
@error "No valid SEP SF found"
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6 changes: 3 additions & 3 deletions src/qc.jl
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Expand Up @@ -10,15 +10,15 @@
# get bl mean cut
result_blmean, report_blmean = get_centered_gaussian_window_cut(data.blmean, qc_config.blmean.min, qc_config.blmean.max, qc_config.blmean.sigma, ; n_bins_cut=convert(Int64, round(length(data) * qc_config.blmean.n_bins_fraction)), relative_cut=qc_config.blmean.relative_cut, fixed_center=false, left=true)
blmean_qc = result_blmean.low_cut .< data.blmean .< result_blmean.high_cut
@debug format("Baseline Mean cut surrival fraction {:.2f}%", count(blmean_qc) / length(data) * 100)
@debug format("Baseline Mean cut survival fraction {:.2f}%", count(blmean_qc) / length(data) * 100)

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# get bl slope cut
result_blslope, report_blslope = get_centered_gaussian_window_cut(data.blslope, qc_config.blslope.min, qc_config.blslope.max, qc_config.blslope.sigma, ; n_bins_cut=convert(Int64, round(length(data) * qc_config.blslope.n_bins_fraction)), relative_cut=qc_config.blslope.relative_cut, fixed_center=true, left=false, center=zero(data.blslope[1]))
blslope_qc = result_blslope.low_cut .< data.blslope .< result_blslope.high_cut
@debug format("Baseline Slope cut surrival fraction {:.2f}%", count(blslope_qc) / length(data) * 100)
@debug format("Baseline Slope cut survival fraction {:.2f}%", count(blslope_qc) / length(data) * 100)

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# get blsigma cut
result_blsigma, report_blsigma = get_centered_gaussian_window_cut(data.blsigma, qc_config.blsigma.min, qc_config.blsigma.max, qc_config.blsigma.sigma, ; n_bins_cut=convert(Int64, round(length(data) * qc_config.blsigma.n_bins_fraction)), relative_cut=qc_config.blsigma.relative_cut, fixed_center=false, left=true)
blsigma_qc = result_blsigma.low_cut .< data.blsigma .< result_blsigma.high_cut
@debug format("Baseline Sigma cut surrival fraction {:.2f}%", count(blsigma_qc) / length(data) * 100)
@debug format("Baseline Sigma cut survival fraction {:.2f}%", count(blsigma_qc) / length(data) * 100)

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result = (blmean = result_blmean, blslope = result_blslope, blsigma = result_blsigma)
report = (blmean = report_blmean, blslope = report_blslope, blsigma = report_blsigma)
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