Merge branch 'main' of github.com:RvSpectML/RvSpectMLBase.jl into main

Author: eford

Project.toml

@@ -16,7 +16,7 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
 CSV = "0.7, 0.8"
-DataFrames = "0.21, 0.22"
+DataFrames = "0.21, 0.22, 1.0, 1.1"
 Interpolations = "0.12, 0.13"
 NaNMath = "0.3"
 Query = "1.0"

src/types/spectra.jl

@@ -67,7 +67,9 @@ function Spectra2DBasic(λ::A1, flux::A2, var::A3, inst::InstT;
      InstT<:AbstractInstrument  }
     @assert size(λ) == size(flux)
     @assert size(λ) == size(var)
-    @assert 1 <= min_pixel_in_order(inst) <= max_pixel_in_order(inst) <= size(λ,1)
-    @assert 1 <= min_order(inst) <= max_order(inst) <= size(λ,2)
+    @assert 1 <= size(λ,1) <= max_pixel_in_order(inst)
+    @assert 1 <= size(λ,2) <= max_order(inst)
+    @assert 1 <= min_order(inst) <= max_order(inst)
+    @assert 1 <= min_pixel_in_order(inst) <= max_pixel_in_order(inst)
     Spectra2DBasic{eltype(λ),eltype(flux),eltype(var),typeof(λ),typeof(flux),typeof(var),typeof(inst)}(λ,flux,var,inst,metadata)
 end

src/util/physics.jl

@@ -43,6 +43,8 @@ calc_doppler_factor(rv::Real, v_perp::Real) = (one(rv) + rv/speed_of_light_mps)/
 
 calc_doppler_factor(;z::Real) = one(z) + z
 
+calc_doppler_factor(;rv_kmps::Real) = one(rv_kmps) + rv_kmps*1000.0/speed_of_light_mps
+
 
 """
    `absorption_line(x; mid, width, depth)`

src/util/spectra.jl

@@ -42,7 +42,7 @@ global have_issued_ssb_warning = false
 global have_issued_drift_warning = false
 global have_issued_diffext_warning = false
 function apply_doppler_boost!(spectra::AS, dict::AbstractDict ) where { AS<:AbstractSpectra }
-    global have_issued_ssb_warning, have_issued_drift_warning, have_issued_diffext_warning
+    global have_issued_ssb_warning, have_issued_drift_warning, have_issued_diffext_warning, have_issued_multiple_ssb_warning
     local doppler_factor = one(eltype(spectra.λ))
     #= NEID drift model is now included in wavelengths provided
     if !haskey(dict,:drift_rv) && !haskey(dict,:drift_z ) && !have_issued_drift_warning
@@ -55,14 +55,24 @@ function apply_doppler_boost!(spectra::AS, dict::AbstractDict ) where { AS<:Abst
         doppler_factor *= calc_doppler_factor(dict[:drift_rv])
     end
     =#
-    if !haskey(dict,:ssb_rv) && !haskey(dict,:ssbz) && !have_issued_ssb_warning
-         @info "apply_doppler_boost! didn't find :ssb_rv or :ssbz to apply."
+    if !haskey(dict,:ssb_rv) && !haskey(dict,:ssbz) && !haskey(dict,:ssb_rv_kmps) && !have_issued_ssb_warning
+         @info "apply_doppler_boost! didn't find :ssbz, :ssb_rv or :ssb_rv_kmps to apply."
          have_issued_ssb_warning = true
     end
     if  haskey(dict,:ssbz)
         doppler_factor   *= calc_doppler_factor(z=dict[:ssbz])
+        if  haskey(dict,:ssb_rv) || haskey(dict,:ssb_rv_kmps)
+            @info "apply_doppler_boost! found ssbz and either ssb_rv or ssb_rv_kmps. Defaulting to only use ssbz."
+            have_issued_multiple_ssb_warning = true
+        end
     elseif  haskey(dict,:ssb_rv)
         doppler_factor   *= calc_doppler_factor(dict[:ssb_rv])
+        if  haskey(dict,:ssb_rv_kmps)
+            @info "apply_doppler_boost! found ssb_rv (in m/s) and ssb_rv_kmps (in km/s). Defaulting to only use ssb_rv."
+            have_issued_multiple_ssb_warning = true
+        end
+    elseif  haskey(dict,:ssb_rv_kmps)
+        doppler_factor   *= calc_doppler_factor(rv_kmps=dict[:ssb_rv_kmps])
     end
     #=
     # Now plan to apply correction at end, rather than to wavelength  
@@ -71,6 +81,7 @@ function apply_doppler_boost!(spectra::AS, dict::AbstractDict ) where { AS<:Abst
         have_issued_diffext_warning = true
     end
     if  haskey(dict,:diff_ext_rv)  doppler_factor   *= calc_doppler_factor.(dict[:diff_ext_rv])  end
+    if  haskey(dict,:binaryRV)  doppler_factor   *= calc_doppler_factor.(dict[:binaryRV])  end
     apply_doppler_boost!(spectra,doppler_factor)
     =#
     return spectra
@@ -122,11 +133,11 @@ function calc_snr end
 
 function calc_snr(flux::AbstractArray{T1},var::AbstractArray{T2}) where {T1<:Real, T2<:Real}
     @assert size(flux) == size(var)
-    sqrt(NaNMath.sum( flux.^2 ./ var))
+    sqrt(NaNMath.sum( max.(0.0,flux.^2 ./ var)))
 end
 
 function calc_snr(flux::Real,var::Real)
-    flux / sqrt(var)
+    flux / sqrt(max(0.0,var))
 end
 
 function calc_snr(spectrum::ST, pixels::AR, order::Integer) where { ST<:AbstractSpectra2D, AR<:AbstractRange{Int64}, AA1<:AbstractArray{Int64,1} } #, AAR<:AbstractArray{AR,1} }