add documentation and warnings for default values (address TODO)

[hematthi]

EchelleCCFs.jl/src/io/write_ccf_fits.jl

Lines 5 to 12 in a639217

	function make_ccf_fits_header(metadata::AbstractDict; line_list_filename::Union{Nothing,String} = "unknown",
	v::Union{Nothing,Float64} = nothing, e_v::Union{Nothing,Float64} = nothing,
	blue_ord::Union{Nothing,Int64} = 118, red_ord::Union{Nothing,Int64} = 89, # TODO: WARNING: Hardwired
	mask_shape::Union{Nothing,String} = "tophat", barycor::Union{Nothing,String} = "chromatic", # TODO: WARNING: Hardwired
	ccord::Union{Nothing,Bool} = false, blazenorm::Union{Nothing,Bool} = false, contnorm::Union{Nothing,Bool} = true,
	div_tell::Union{Nothing,Bool} = false, rawnorm::Union{Nothing,Bool} = nothing, plate_scale::Union{Nothing,Float64} = nothing,
	)
	# TODO: WARNING: several parameters, e.g., BLUE_ORD, RED_ORD, WINDOW, BARYCOR, PLATESCL, given default value above instead of defaulting to outputing nothing

rawnorm argument is also not used in this function

[hematthi]

Also add documentation for:

EchelleCCFs.jl/src/io/write_ccf_fits.jl

Lines 106 to 130 in a639217

	function write_ccf_fits(filename::String, v_grid::AbstractArray{T1,1}, ccf_total::AbstractArray{T2,1}, ccf_total_var::AbstractArray{T3,1};
	orders::AbstractArray{T4,1}=zeros(Int64,0), ccf_orders::AbstractArray{T5,2}=zeros(T2,0,0), ccf_orders_var::AbstractArray{T6,2}=zeros(T3,0,0),
	fits_hdr::FITSHeader,
	#total_vel::Union{Nothing,Real} = nothing, sigma_total_vel::Union{Nothing,Real} = nothing,
	order_vels::Union{Nothing,AbstractArray{T7,1}} = nothing, sigma_order_vels::Union{Nothing,AbstractArray{T8,1}} = nothing ) where {
	T1<:Real, T2<:Real, T3<:Real, T4<:Real, T5<:Real, T6<:Real, T7<:Real, T8<:Real }
	f = FITS(filename, "w")
	#if isnothing(total_vel) || isnothing(sigma_total_vel)
	write(f,UInt8[],header=fits_hdr,name="metadata")
	#else
	# write(f,UInt8[],header=fits_hdr,name="metadata",v=total_vel,e_V=sigma_total_vel)
	#end
	t2 = OrderedDict("V_grid"=>collect(v_grid),"ccf"=>ccf_total,"e_ccf"=>sqrt.(ccf_total_var) )
	write(f,collect(keys(t2)),collect(values(t2)),name="ccf_total")
	if length(orders) > 0 && length(ccf_orders) > 0 && length(ccf_orders_var) > 0
	if isnothing(order_vels) || isnothing(sigma_order_vels)
	t3 = OrderedDict("orders"=>convert.(Int64,orders),"ccfs"=>ccf_orders,"errs"=>sqrt.(ccf_orders_var) )
	else
	t3 = OrderedDict("orders"=>convert.(Int64,orders),"ccfs"=>ccf_orders,"errs"=>sqrt.(ccf_orders_var),
	"v" => order_vels,"e_v" => sigma_order_vels)
	end
	write(f,collect(keys(t3)),collect(values(t3)),name="ccf_order")
	end
	close(f)
	end

and clean up unused types

[hematthi]

And for:

EchelleCCFs.jl/src/io/write_ccf_fits.jl

Lines 132 to 163 in a639217

	function write_each_ccf_fits(metadata::AbstractArray{Dict{Symbol,Any},1}, v_grid::AbstractArray{T1,1}, ccf_total::AbstractArray{T2,2}, ccf_total_var::AbstractArray{T3,2};
	orders::AbstractArray{T4,1}=zeros(Int64,0), ccf_orders::AbstractArray{T5,3}=zeros(T2,0,0,size(ccf_total,2)), ccf_orders_var::AbstractArray{T6,3}=zeros(T3,0,0,size(ccf_total,2)),
	fits_hdr::FITSHeader, line_list_filename::Union{Nothing,String} = "unknown", # )
	total_vel::Union{Nothing,AbstractArray{T7,1}} = nothing, sigma_total_vel::Union{Nothing,AbstractArray{T7,1}} = nothing,
	order_vels::Union{Nothing,AbstractArray{T8,2}} = nothing, sigma_order_vels::Union{Nothing,AbstractArray{T8,2}} = nothing ) where {
	T1<:Real, T2<:Real, T3<:Real, T4<:Real, T5<:Real, T6<:Real, T7<:Real, T8<:Real }
	@assert length(metadata) == size(ccf_total,2) == size(ccf_total_var,2)
	num_files = length(metadata)
	for i in 1:num_files
	fits_fn = last(splitpath(metadata[i][:Filename]))
	ccf_fn = replace(fits_fn, ".fits" => "_ccf.fits")
	if isnothing(total_vel) || isnothing(sigma_total_vel)
	fits_hdr = make_ccf_fits_header(metadata[i], line_list_filename=line_list_filename)
	else
	fits_hdr = make_ccf_fits_header(metadata[i],v=total_vel[i],e_v=sigma_total_vel[i], line_list_filename=line_list_filename)
	end
	if isnothing(order_vels) || isnothing(sigma_order_vels)
	write_ccf_fits(ccf_fn, v_grid, ccf_total[:,i], ccf_total_var[:,i],
	orders=orders, ccf_orders=ccf_orders[:,:,i], ccf_orders_var=ccf_orders_var[:,:,i],
	fits_hdr=fits_hdr)
	else
	@assert size(order_vels) == size(sigma_order_vels)
	@assert size(order_vels,1) == num_files
	@assert size(order_vels,2) == length(orders)
	write_ccf_fits(ccf_fn, v_grid, ccf_total[:,i], ccf_total_var[:,i],
	orders=orders, ccf_orders=ccf_orders[:,:,i], ccf_orders_var=ccf_orders_var[:,:,i],
	fits_hdr=fits_hdr,
	order_vels=order_vels[i,:], sigma_order_vels=sigma_order_vels[i,:] )
	end
	# break # WARNING: Aborts after one file for testing purposes
	end
	end