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icweavericweaver
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cleanup
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‎src/Spectra.jl‎

Lines changed: 12 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -2,16 +2,18 @@ module Spectra
22

33
# Uniform API
44
export AbstractSpectrum, Spectrum, spectrum, spectral_axis, flux_axis
5-
# spectra_single.jl, spectra_ifu.jl, spectra_echelle.jl, spectra_binned.jl
6-
export SingleSpectrum, IFUSpectrum, EchelleSpectrum, spectral_axis, flux_axis
7-
# utils.jl
5+
6+
# AbstractSpectrum types
7+
export SingleSpectrum, IFUSpectrum, EchelleSpectrum
8+
9+
# Transforms
10+
export SpectrumResampler, redden, redden!, deredden, deredden!
11+
12+
# Utilities
813
export blackbody #, line_flux, equivalent_width
9-
# fitting/fitting.jl
14+
15+
# Fitting
1016
#export continuum, continuum!
11-
# transforms/redden.jl
12-
export redden, redden!, deredden, deredden!
13-
# transforms/resampler
14-
export SpectrumResampler
1517

1618
using RecipesBase: @recipe
1719
using Measurements: Measurements, Measurement
@@ -208,15 +210,6 @@ include("spectrum_echelle.jl")
208210
include("spectrum_ifu.jl")
209211
#include("spectrum_binned.jl")
210212

211-
# Resampler type
212-
include("transforms/resampler.jl")
213-
214-
# tools
215-
include("utils.jl")
216-
include("transforms/transforms.jl")
217-
include("plotting.jl")
218-
include("fitting/fitting.jl")
219-
220213
"""
221214
spectrum(spectral_axis, flux_axis, [meta])
222215
@@ -305,10 +298,10 @@ function spectrum(spectral_axis::AbstractMatrix{<:Quantity}, flux_axis::Abstract
305298
Spectrum(spectral_axis, flux_axis, Dict{Symbol,Any}(kwds))
306299
end
307300

308-
# tools
309301
include("utils.jl")
302+
include("transforms/resampler.jl")
310303
include("transforms/transforms.jl")
311304
include("plotting.jl")
312305
#include("fitting/fitting.jl")
313306

314-
end # module
307+
end # module

‎src/transforms/resampler.jl‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -72,16 +72,17 @@ struct SpectrumResampler{A <: Spectrum, B}
7272
end
7373

7474
spectrum(s::SpectrumResampler) = s.spectrum
75-
wave(s::SpectrumResampler) = wave(spectrum(s))
76-
flux(s::SpectrumResampler) = flux(spectrum(s))
75+
spectral_axis(s::SpectrumResampler) = (spectral_axis ∘ spectrum)(s)
76+
flux_axis(s::SpectrumResampler) = (flux_axis ∘ spectrum)(s)
77+
meta(s::SpectrumResampler) = (meta ∘ spectrum)(s)
7778

7879
function (s::SpectrumResampler)(wave_sampled)
7980
flux_resampled = (s.interp)(wave_sampled)
80-
return Spectrum(wave_sampled, flux_resampled, spectrum(s).meta)
81+
return Spectrum(wave_sampled, flux_resampled, meta(s))
8182
end
8283

8384
function Base.show(io::IO, s::SpectrumResampler)
84-
println(io, "SpectrumResampler($(eltype(wave(s))), $(eltype(flux(s))))")
85-
println(io, " spec: ", spectrum(s))
85+
println(io, "SpectrumResampler(", (eltype ∘ spectral_axis)(s), ", ", (eltype ∘ flux_axis)(s), ")")
86+
println(io, " spec: ", (typeof ∘ spectrum)(s))
8687
print(io, " interpolator: ", typeof(s.interp))
8788
end

‎test/transforms/resample.jl‎

Lines changed: 30 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
using Spectra: Spectra, AbstractSpectrum, SpectrumResampler, spectrum, wave, flux
1+
using Spectra: Spectra, AbstractSpectrum, SpectrumResampler, spectrum, spectral_axis, flux_axis
22
using DataInterpolations: LinearInterpolation, ExtrapolationType
33
using Unitful: @u_str, uconvert
44
using UnitfulAstro
@@ -7,28 +7,16 @@ using Measurements: ±
77
# TODO: See if it makes sense to have an exported API for resample/resample! even though we are using external interpolators.
88

99
function resample(spec, new_wave)
10-
interp = LinearInterpolation(flux(spec), wave(spec); extrapolation = ExtrapolationType.Constant)
10+
interp = LinearInterpolation(flux_axis(spec), spectral_axis(spec); extrapolation = ExtrapolationType.Constant)
1111
resampler = SpectrumResampler(spec, interp)
1212
return resampler(new_wave)
1313
end
1414

1515
function resample(spec1::AbstractSpectrum, spec2::AbstractSpectrum)
16-
new_wave = wave(spec2)
16+
new_wave = spectral_axis(spec2)
1717
return resample(spec1, new_wave)
1818
end
1919

20-
#function resample!(spec::AbstractSpectrum, new_wave)
21-
# spec_new = resample(spec, new_wave)
22-
# spec.flux = flux(spec_new)
23-
# spec.wave = wave(spec_new)
24-
# return spec
25-
#end
26-
27-
#function resample!(spec1::AbstractSpectrum, spec2::AbstractSpectrum)
28-
# new_wave = wave(spec2)
29-
# resample!(spec1, new_wave)
30-
#end
31-
3220
function mock_spectrum(n::Int = Int(1e3); use_units::Bool = false)
3321
wave = range(1e4, 3e4, length = n)
3422
sigma = 0.1 .* sin.(wave)
@@ -43,77 +31,69 @@ end
4331

4432
@testset "Resampler" begin
4533
spec = mock_spectrum()
46-
interp = LinearInterpolation(flux(spec), wave(spec); extrapolation = ExtrapolationType.Constant)
34+
s, f = spectral_axis(spec), flux_axis(spec)
35+
interp = LinearInterpolation(f, s; extrapolation = ExtrapolationType.Constant)
4736
resampler = SpectrumResampler(spec, interp)
4837
expected = """
4938
SpectrumResampler(Float64, Measurements.Measurement{Float64})
50-
spec: Spectrum(Float64, Measurements.Measurement{Float64})
51-
name: Test Spectrum
52-
interpolator: DataInterpolations.LinearInterpolation{Vector{Measurements.Measurement{Float64}}, Vector{Float64}, Vector{Measurements.Measurement{Float64}}, Vector{Measurements.Measurement{Float64}}, Measurements.Measurement{Float64}}"""
39+
spec: Spectra.SingleSpectrum{Float64, Measurements.Measurement{Float64}}
40+
interpolator: DataInterpolations.LinearInterpolation{Vector{Measurements.Measurement{Float64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, Vector{Measurements.Measurement{Float64}}, Vector{Measurements.Measurement{Float64}}, Measurements.Measurement{Float64}}"""
5341

5442
@test sprint(show, resampler) == expected
55-
@test wave(resampler) == wave(spec)
56-
@test flux(resampler) == flux(spec)
43+
@test spectral_axis(resampler) == s
44+
@test flux_axis(resampler) == f
5745
end
5846

5947
@testset "Resampling" begin
6048
spec = mock_spectrum()
61-
new_wave = range(minimum(spec.wave), maximum(spec.wave); length = Integer(length(spec.wave) ÷ 2.4))
49+
s, f = spectral_axis(spec), flux_axis(spec)
50+
new_wave = range(minimum(s), maximum(s); length = Integer(length(s) ÷ 2.4))
6251
res_spec = resample(spec, new_wave)
6352
expected = """
64-
Spectrum(Float64, Measurements.Measurement{Float64})
65-
name: Test Spectrum"""
53+
SingleSpectrum(Float64, Measurements.Measurement{Float64})
54+
spectral axis (416,): 10000.0 .. 30000.0
55+
flux axis (416,): 67.0 ± 0.031 .. 0.827 ± 0.08
56+
meta: Dict{Symbol, Any}(:name => "Test Spectrum")"""
6657

6758
@test sprint(show, res_spec) == expected
68-
@test wave(res_spec) == new_wave
69-
@test length(flux(res_spec)) == length(new_wave)
70-
71-
#resample!(spec, new_wave)
72-
#@test wave(res_spec) == spec.wave
73-
#@test flux(res_spec) == spec.flux
59+
@test spectral_axis(res_spec) == new_wave
60+
@test length(flux_axis(res_spec)) == length(new_wave)
7461

7562
# Unitful
76-
spec = mock_spectrum(use_units=true)
77-
new_wave = range(minimum(spec.wave), maximum(spec.wave), length=Integer(length(spec.wave) ÷ 2.4))
78-
@assert unit(eltype(new_wave)) == unit(eltype(spec.wave))
63+
spec = mock_spectrum(; use_units = true)
64+
s, f = spectral_axis(spec), flux_axis(spec)
65+
new_wave = range(minimum(s), maximum(s); length = Integer(length(s) ÷ 2.4))
66+
@assert unit(eltype(new_wave)) == unit(eltype(s))
7967
res_spec = resample(spec, new_wave)
8068

81-
@test wave(res_spec) == new_wave
82-
@test length(flux(res_spec)) == length(new_wave)
83-
84-
#resample!(spec, new_wave)
85-
#@test wave(res_spec) == spec.wave
86-
#@test flux(res_spec) == spec.flux
69+
@test spectral_axis(res_spec) == new_wave
70+
@test length(flux_axis(res_spec)) == length(new_wave)
8771

8872
# Test resampling to another Spectrum
8973
spec1 = mock_spectrum(Integer(1e4))
9074
spec2 = mock_spectrum(Integer(1e3))
9175
res_spec = resample(spec1, spec2)
92-
@test wave(res_spec) == wave(spec2)
93-
94-
#resample!(spec1, spec2)
95-
#@test wave(spec1) == spec2.wave
96-
#@test flux(spec1) == flux(res_spec)
76+
@test spectral_axis(res_spec) == spectral_axis(spec2)
9777

9878
# Unitful
99-
spec1 = mock_spectrum(Integer(1e4), use_units=true)
100-
spec2 = mock_spectrum(Integer(1e3), use_units=true)
79+
spec1 = mock_spectrum(Integer(1e4); use_units = true)
80+
spec2 = mock_spectrum(Integer(1e3); use_units = true)
10181
res_spec = resample(spec1, spec2)
10282

103-
@test wave(res_spec) == spec2.wave
104-
@test unit(eltype(flux(spec1))) == unit(eltype(flux(spec2))) == unit(eltype(flux(res_spec)))
83+
@test spectral_axis(res_spec) == spectral_axis(spec2)
84+
@test unit(eltype(flux_axis(spec1))) == unit(eltype(flux_axis(spec2))) == unit(eltype(flux_axis(res_spec)))
10585

10686
# Test when spectra2 has different units
10787
#spec1 = mock_spectrum(Integer(1e4), use_units=true)
10888
#spec2 = mock_spectrum(Integer(1e3), use_units=true)
10989
#spec1.wave = uconvert.(u"cm", spec1.wave)
11090
#resample!(spec1, spec2)
111-
#@test ustrip.(wave(spec1)) ≈ ustrip.(unit(eltype(wave(spec1))), wave(spec2))
91+
#@test ustrip.(spectral_axis(spec1)) ≈ ustrip.(unit(eltype(spectral_axis(spec1))), spectral_axis(spec2))
11292

11393
# address bug when doing the same thing but affecting spec2
11494
#spec1 = mock_spectrum(Integer(1e4), use_units=true)
11595
#spec2 = mock_spectrum(Integer(1e3), use_units=true)
11696
#spec2.wave = uconvert.(u"cm", spec2.wave)
11797
#resample!(spec1, spec2)
118-
#@test ustrip.(wave(spec1)) ≈ ustrip.(unit(eltype(wave(spec1))), wave(spec2))
98+
#@test ustrip.(spectral_axis(spec1)) ≈ ustrip.(unit(eltype(spectral_axis(spec1))), spectral_axis(spec2))
11999
end

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