update documentation to describe and consistently name all arguments (`plan` instead of `ccf_plan`; `var`)

[hematthi]

EchelleCCFs.jl/src/convenience/ccf_chunk.jl

Lines 7 to 26 in a639217

	""" `calc_ccf_chunk!( cccf_out, chunk, ccf_plan )`
	Convenience function to compute CCF for one chunk of spectrum, evaluated using mask_shape and line list from ccf plan
	# Inputs:
	- `ccf_out`: `AbstractArray` to store output
	- `chunk`: ChunkOfSpectrum to compute CCF for
	- `ccf_plan`: for now, just a BasicCCFPlan that provides line_list, mask_shape and other parameters for calculating CCF
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Returns:
	- `ccf_out`
	"""
	function calc_ccf_chunk!(ccf_out::AbstractArray{T1,1}, chunk::AbstractChunkOfSpectrum, plan::PlanT = BasicCCFPlan()
	; var::AbstractVector{T2} = chunk.var,
	assume_sorted::Bool = false ) where { T1<:Real, T2<:Real, PlanT<:AbstractCCFPlan }
	@assert assume_sorted || issorted( plan.line_list.λ )
	@assert length(ccf_out) == calc_length_ccf_v_grid(plan)
	ccf_1D!(ccf_out, chunk.λ, chunk.flux, plan; assume_sorted=true)
	return ccf_out
	end

[hematthi]

Same for:

EchelleCCFs.jl/src/convenience/ccf_chunk.jl

Lines 28 to 50 in a639217

	""" `calc_ccf_and_var_chunk!( chunk, ccf_plan )`
	Convenience function to compute CCF and variance of each "CCF pixel" for one chunk of spectrum, evaluated using mask_shape and line list from `ccf_plan`.
	# Inputs:
	- `ccf_out`: `AbstractArray` to store output
	- `ccf_var_out`: `AbstractArray` to store output
	- `chunk`: ChunkOfSpectrum to compute CCF for
	- `ccf_plan`: for now, just a BasicCCFPlan that provides line_list, mask_shape and other parameters for calculating CCF
	# Optional Arguments:
	- `var`: `AbstractArray` with variance to use for each pixel (overides value in chunk)
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Returns Named Tuple with:
	- `ccf_out`:
	- `ccf_var_out`:
	"""
	function calc_ccf_and_var_chunk!(ccf_out::AbstractArray{T1,1}, ccf_var_out::AbstractArray{T2,1},
	chunk::AbstractChunkOfSpectrum, plan::PlanT = BasicCCFPlan()
	; var::AbstractVector{T3} = chunk.var, ccf_var_scale::Real = 1.0,
	assume_sorted::Bool = false ) where { T1<:Real, T2<:Real, T3<:Real, PlanT<:AbstractCCFPlan }
	@assert assume_sorted || issorted( plan.line_list.λ )
	@assert length(ccf_out) == calc_length_ccf_v_grid(plan)
	ccf_1D!(ccf_out, ccf_var_out, chunk.λ, chunk.flux, var, plan; ccf_var_scale=ccf_var_scale, assume_sorted=true)
	return (ccf=ccf_out, ccf_var=ccf_var_out)
	end

[hematthi]

Same for:

EchelleCCFs.jl/src/convenience/ccf_chunk.jl

Lines 52 to 74 in a639217

	""" `calc_ccf_and_covar_chunk!( chunk, ccf_plan )`
	Convenience function to compute CCF and covariance of each pair of "CCF pixels" for one chunk of spectrum, evaluated using mask_shape and line list from `ccf_plan`.
	# Inputs:
	- `ccf_out`: `AbstractArray` to store output
	- `ccf_covar_out`: `AbstractArray` to store output
	- `chunk`: ChunkOfSpectrum to compute CCF for
	- `ccf_plan`: for now, just a BasicCCFPlan that provides line_list, mask_shape and other parameters for calculating CCF
	# Optional Arguments:
	- `var`: `AbstractArray` with variance to use for each pixel (overides value in chunk)
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Returns Named Tuple with:
	- `ccf_out`:
	- `ccf_covar_out`:
	"""
	function calc_ccf_and_covar_chunk!(ccf_out::AbstractArray{T1,1}, ccf_covar_out::AbstractArray{T2,2},
	chunk::AbstractChunkOfSpectrum, plan::PlanT = BasicCCFPlan()
	; var::AbstractVector{T3} = chunk.var, ccf_var_scale::Real = 1.0,
	assume_sorted::Bool = false ) where { T1<:Real, T2<:Real, T3<:Real, PlanT<:AbstractCCFPlan }
	@assert assume_sorted || issorted( plan.line_list.λ )
	@assert length(ccf_out) == calc_length_ccf_v_grid(plan)
	ccf_1D!(ccf_out, ccf_covar_out, chunk.λ, chunk.flux, var, plan; ccf_var_scale=ccf_var_scale, assume_sorted=true)
	return (ccf=ccf_out, ccf_covar=ccf_covar_out)
	end

[hematthi]

EchelleCCFs.jl/src/convenience/ccf_chunk.jl

Lines 77 to 168 in a639217

	""" `calc_ccf_chunk( chunk, ccf_plan )`
	Convenience function to compute CCF for one chunk of spectrum.
	# Inputs:
	- `ccf_out`: `AbstractArray` to store output
	- `chunk`: ChunkOfSpectrum to compute CCF for
	- `ccf_plan`: for now, just a BasicCCFPlan that provides line_list, mask_shape and other parameters for calculating CCF
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	- `calc_ccf_var`: if true also computes estimate of variance for each value of ccf
	# Returns:
	- CCF for one chunk of spectrum, evaluated using mask_shape and line list from ccf plan
	"""
	function calc_ccf_chunk(chunk::AbstractChunkOfSpectrum, plan::PlanT = BasicCCFPlan()
	; var::AbstractVector{T} = chunk.var, ccf_var_scale::Real = 1.0, Δfwhm::Real = 0,
	assume_sorted::Bool = false, calc_ccf_var::Bool = false ) where { T<:Real, PlanT<:AbstractCCFPlan }
	if Δfwhm > 0
	this_plan_for_chunk = copy(plan)
	increase_mask_fwhm!(this_plan_for_chunk,Δfwhm)
	else
	this_plan_for_chunk = plan
	end
	len_v_grid = calc_length_ccf_v_grid(plan)
	ccf_out = zeros(len_v_grid)
	if calc_ccf_var
	ccf_var_out = zeros(len_v_grid)
	return calc_ccf_and_var_chunk!(ccf_out, ccf_var_out, chunk, this_plan_for_chunk, var=var, ccf_var_scale=ccf_var_scale, assume_sorted=assume_sorted )
	else
	return calc_ccf_chunk!(ccf_out, chunk, this_plan_for_chunk, var=var, assume_sorted=assume_sorted )
	end
	end
	""" `calc_ccf_and_var_chunk( chunk, ccf_plan )`
	Convenience function to compute CCF and variance of each "CCF pixel" for one chunk of spectrum, evaluated using mask_shape and line list from `ccf_plan`.
	# Inputs:
	- `ccf_out`: `AbstractArray` to store output
	- `ccf_var_out`: `AbstractArray` to store output
	- `chunk`: ChunkOfSpectrum to compute CCF for
	- `ccf_plan`: for now, just a BasicCCFPlan that provides line_list, mask_shape and other parameters for calculating CCF
	# Optional Arguments:
	- `var`: `AbstractArray` with variance to use for each pixel (overides value in chunk)
	`- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Returns Named Tuple with:
	- `ccf_out`:
	- `ccf_var_out`:
	"""
	function calc_ccf_and_var_chunk(chunk::AbstractChunkOfSpectrum, plan::PlanT = BasicCCFPlan()
	; var::AbstractVector{T} = chunk.var, ccf_var_scale::Real = 1.0, Δfwhm::Real = 0,
	assume_sorted::Bool = false ) where { T<:Real, PlanT<:AbstractCCFPlan }
	@assert assume_sorted || issorted( plan.line_list.λ )
	if Δfwhm > 0
	this_plan_for_chunk = copy(plan)
	increase_mask_fwhm!(this_plan_for_chunk,Δfwhm)
	else
	this_plan_for_chunk = plan
	end
	len_v_grid = calc_length_ccf_v_grid(plan)
	ccf_out = zeros(len_v_grid)
	ccf_var_out = zeros(len_v_grid)
	calc_ccf_and_var_chunk!(ccf_out, ccf_var_out, chunk, this_plan_for_chunk, var=var, ccf_var_scale=ccf_var_scale, assume_sorted=true )
	return (ccf=ccf_out, ccf_var=ccf_var_out)
	end
	""" `calc_ccf_and_covar_chunk( chunk, ccf_plan )`
	Convenience function to compute CCF and covariance of each pair of "CCF pixels" for one chunk of spectrum, evaluated using mask_shape and line list from `ccf_plan`.
	# Inputs:
	- `ccf_out`: `AbstractArray` to store output
	- `ccf_covar_out`: `AbstractArray` to store output
	- `chunk`: ChunkOfSpectrum to compute CCF for
	- `ccf_plan`: for now, just a BasicCCFPlan that provides line_list, mask_shape and other parameters for calculating CCF
	# Optional Arguments:
	- `var`: `AbstractArray` with variance to use for each pixel (overides value in chunk)
	`- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Returns Named Tuple with:
	- `ccf_out`:
	- `ccf_covar_out`:
	"""
	function calc_ccf_and_covar_chunk(chunk::AbstractChunkOfSpectrum, plan::PlanT = BasicCCFPlan()
	; var::AbstractVector{T} = chunk.var, ccf_var_scale::Real = 1.0, Δfwhm::Real = 0,
	assume_sorted::Bool = false ) where { T<:Real, PlanT<:AbstractCCFPlan }
	@assert assume_sorted || issorted( plan.line_list.λ )
	if Δfwhm > 0
	this_plan_for_chunk = copy(plan)
	increase_mask_fwhm!(this_plan_for_chunk,Δfwhm)
	else
	this_plan_for_chunk = plan
	end
	len_v_grid = calc_length_ccf_v_grid(plan)
	ccf_out = zeros(len_v_grid)
	ccf_covar_out = zeros(len_v_grid,len_v_grid)
	calc_ccf_and_covar_chunk!(ccf_out, ccf_covar_out, chunk, this_plan_for_chunk, var=var, ccf_var_scale=ccf_var_scale, assume_sorted=true )
	return (ccf=ccf_out, ccf_covar=ccf_covar_out)
	end