update documentation to describe and consistently name all arguments

[hematthi]

EchelleCCFs.jl/src/convenience/ccf_chunklist.jl

Lines 7 to 34 in a639217

	""" `calc_ccf_chunklist ( chunklist, ccf_plans )`
	Convenience function to compute CCF based on a spectrum's chunklist.
	# Inputs:
	- chunklist
	- vector of ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	CCF summed over all chunks in a spectrum's chunklist, evaluated using the
	line list and mask_shape from the ccf plan for each chunk.
	"""
	function calc_ccf_chunklist(chunk_list::AbstractChunkList,
	plan_for_chunk::AbstractVector{PlanT};
	Δfwhm::Real = 0,
	assume_sorted::Bool = false ) where {
	PlanT<:AbstractCCFPlan }
	num_vels = calc_length_ccf_v_grid(first(plan_for_chunk))
	ccf_out = Array{Float64,1}(undef, num_vels)
	if Δfwhm > 0
	this_plan_for_chunk = copy(plan_for_chunk)
	#increase_mask_fwhm!(this_plan_for_chunk,Δfwhm)
	map(chid->increase_mask_fwhm!(this_plan_for_chunk[chid],Δfwhm), 1:num_chunks )
	else
	this_plan_for_chunk = plan_for_chunk
	end
	calc_ccf_chunklist!(ccf_out, chunk_list, this_plan_for_chunk, assume_sorted=assume_sorted )
	return ccf_out
	end

[hematthi]

Same for:

EchelleCCFs.jl/src/convenience/ccf_chunklist.jl

Lines 36 to 62 in a639217

	""" `calc_ccf_chunklist! ( ccfs_out, chunklist, ccf_plans )`
	Convenience function to compute CCF based on a spectrum's chunklist.
	# Inputs:
	- chunklist
	- vector of ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	CCF summed over all chunks in a spectrum's chunklist, evaluated using the
	line list and mask_shape from the ccf plan for each chunk.
	"""
	function calc_ccf_chunklist!(ccf_out::AbstractArray{T1,1}, chunk_list::AbstractChunkList,
	plan_for_chunk::AbstractVector{PlanT};
	assume_sorted::Bool = false ) where {
	T1<:Real, PlanT<:AbstractCCFPlan }
	num_chunks = length(chunk_list)
	@assert length(plan_for_chunk) == num_chunks
	num_vels = calc_length_ccf_v_grid(first(plan_for_chunk))
	@assert size(ccf_out,1) == num_vels
	@assert all(map(chid->calc_length_ccf_v_grid(plan_for_chunk[chid]), 1:num_chunks ) .== num_vels )
	@assert assume_sorted || all(map(chid->issorted( plan_for_chunk[chid].line_list.λ ), 1:num_chunks))
	num_lines = mapreduce(chid->length(plan_for_chunk[chid].line_list), +, 1:length(chunk_list.data) )
	ccf_out .= mapreduce(chid->calc_ccf_chunk(chunk_list.data[chid], plan_for_chunk[chid],
	assume_sorted=true ), +, 1:length(chunk_list.data) )
	ccf_out .*= num_lines
	end

[hematthi]

EchelleCCFs.jl/src/convenience/ccf_chunklist.jl

Lines 64 to 98 in a639217

	""" `calc_ccf_and_var_chunklist ( chunklist, ccf_plans )`
	Convenience function to compute CCF based on a spectrum's chunklist.
	# Inputs:
	- chunklist
	- vector of ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	CCF summed over all chunks in a spectrum's chunklist, evaluated using the
	line list and mask_shape from the ccf plan for each chunk.
	"""
	function calc_ccf_and_var_chunklist(chunk_list::AbstractChunkList,
	plan_for_chunk::AbstractVector{PlanT};
	ccf_var_scale::Real = 1.0, Δfwhm::Real = 0,
	assume_sorted::Bool = false ) where {
	PlanT<:AbstractCCFPlan }
	@assert length(chunk_list) == length(plan_for_chunk)
	num_chunks = length(chunk_list)
	num_vels = maximum(map(chid->calc_length_ccf_v_grid(plan_for_chunk[chid]), 1:num_chunks ))
	ccf_out = Array{Float64,1}(undef, num_vels)
	ccf_var_out = Array{Float64,1}(undef, num_vels)
	if Δfwhm > 0
	this_plan_for_chunk = copy(plan_for_chunk)
	map(chid->increase_mask_fwhm!(this_plan_for_chunk[chid],Δfwhm), 1:num_chunks )
	else
	this_plan_for_chunk = plan_for_chunk
	end
	#(ccf_out, ccf_var_out ) = mapreduce(chid->calc_ccf_and_var_chunk(chunk_list.data[chid], plan_for_chunk[chid],
	# assume_sorted=assume_sorted ), add_tuple_sum, 1:length(chunk_list.data) )
	calc_ccf_and_var_chunklist!(ccf_out, ccf_var_out, chunk_list,this_plan_for_chunk, ccf_var_scale=ccf_var_scale, assume_sorted=assume_sorted)
	return (ccf=ccf_out, ccf_var=ccf_var_out)
	end

[hematthi]

EchelleCCFs.jl/src/convenience/ccf_chunklist.jl

Lines 100 to 137 in a639217

	""" `calc_ccf_and_var_chunklist! ( ccf_out, ccf_var_out, chunklist, ccf_plans )`
	Convenience function to compute CCF based on a spectrum's chunklist.
	# Inputs:
	- chunklist
	- vector of ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	CCF summed over all chunks in a spectrum's chunklist, evaluated using the
	line list and mask_shape from the ccf plan for each chunk.
	"""
	function calc_ccf_and_var_chunklist!(ccfs_out::AbstractArray{T1,1}, ccf_vars_out::AbstractArray{T2,1},
	chunk_list::AbstractChunkList, plan_for_chunk::AbstractVector{PlanT};
	ccf_var_scale::Real = 1.0, assume_sorted::Bool = false ) where {
	T1<:Real, T2<:Real, PlanT<:AbstractCCFPlan }
	num_chunks = length(chunk_list)
	@assert length(plan_for_chunk) == num_chunks
	@assert assume_sorted || all(map(chid->issorted( plan_for_chunk[chid].line_list.λ ), 1:num_chunks))
	num_vels = maximum(map(chid->calc_length_ccf_v_grid(plan_for_chunk[chid]), 1:num_chunks ))
	@assert size(ccfs_out,1) == num_vels
	@assert size(ccf_vars_out,1) == num_vels
	#(ccf_out, ccf_var_out ) = mapreduce(chid->calc_ccf_and_var_chunk(chunk_list.data[chid], plan_for_chunk[chid],
	# assume_sorted=assume_sorted ), add_tuple_sum, 1:length(chunk_list.data) )
	ccfs_out .= 0
	ccf_vars_out .= 0
	ccfs_tmp = zeros(num_vels)
	ccf_vars_tmp = zeros(num_vels)
	for chid in 1:num_chunks
	calc_ccf_and_var_chunk!(ccfs_tmp, ccf_vars_tmp,
	chunk_list.data[chid], plan_for_chunk[chid], ccf_var_scale=ccf_var_scale, assume_sorted=true )
	ccfs_out .+= ccfs_tmp
	ccf_vars_out .+= ccf_vars_tmp
	end
	return (ccfs=ccfs_out, ccf_vars=ccf_vars_out)
	end

[hematthi]

EchelleCCFs.jl/src/convenience/ccf_chunklist.jl

Lines 139 to 176 in a639217

	""" `calc_ccf_and_covar_chunklist! ( ccf_out, ccf_cocovar_out, chunklist, ccf_plans )`
	Convenience function to compute CCF based on a spectrum's chunklist.
	# Inputs:
	- chunklist
	- vector of ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	CCF summed over all chunks in a spectrum's chunklist, evaluated using the
	line list and mask_shape from the ccf plan for each chunk.
	"""
	function calc_ccf_and_covar_chunklist!(ccfs_out::AbstractArray{T1,1}, ccf_covars_out::AbstractArray{T2,2},
	chunk_list::AbstractChunkList, plan_for_chunk::AbstractVector{PlanT};
	ccf_var_scale::Real = 1.0, assume_sorted::Bool = false ) where {
	T1<:Real, T2<:Real, PlanT<:AbstractCCFPlan }
	num_chunks = length(chunk_list)
	@assert length(plan_for_chunk) == num_chunks
	@assert assume_sorted || all(map(chid->issorted( plan_for_chunk[chid].line_list.λ ), 1:num_chunks))
	num_vels = maximum(map(chid->calc_length_ccf_v_grid(plan_for_chunk[chid]), 1:num_chunks ))
	@assert size(ccfs_out,1) == num_vels
	@assert size(ccf_covars_out,1) == size(ccf_covars_out,2) == num_vels
	#(ccf_out, ccf_covar_out ) = mapreduce(chid->calc_ccf_and_covar_chunk(chunk_list.data[chid], plan_for_chunk[chid],
	# assume_sorted=assume_sorted ), add_tuple_sum, 1:length(chunk_list.data) )
	ccfs_out .= 0
	ccf_covars_out .= 0
	ccfs_tmp = zeros(num_vels)
	ccf_covars_tmp = zeros(num_vels,num_vels)
	for chid in 1:num_chunks
	calc_ccf_and_covar_chunk!(ccfs_tmp, ccf_covars_tmp,
	chunk_list.data[chid], plan_for_chunk[chid], ccf_var_scale=ccf_var_scale, assume_sorted=true )
	ccfs_out .+= ccfs_tmp
	ccf_covars_out .+= ccf_covars_tmp
	end
	return (ccfs=ccfs_out, ccf_covars=ccf_covars_out)
	end

[hematthi]

EchelleCCFs.jl/src/convenience/ccf_chunklist.jl

Lines 178 to 214 in a639217

	""" `calc_ccf_and_covar_chunklist ( chunklist, ccf_plans )`
	Convenience function to compute CCF based on a spectrum's chunklist.
	# Inputs:
	- chunklist
	- vector of ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	CCF summed over all chunks in a spectrum's chunklist, evaluated using the
	line list and mask_shape from the ccf plan for each chunk.
	"""
	function calc_ccf_and_covar_chunklist(chunk_list::AbstractChunkList,
	plan_for_chunk::AbstractVector{PlanT};
	ccf_var_scale::Real = 1.0,
	Δfwhm::Real = 0,
	assume_sorted::Bool = false ) where {
	PlanT<:AbstractCCFPlan }
	@assert length(chunk_list) == length(plan_for_chunk)
	num_chunks = length(chunk_list)
	num_vels = maximum(map(chid->calc_length_ccf_v_grid(plan_for_chunk[chid]), 1:num_chunks ))
	ccf_out = Array{Float64,1}(undef, num_vels)
	ccf_covar_out = Array{Float64,2}(undef, num_vels, num_vels)
	if Δfwhm > 0
	this_plan_for_chunk = copy(plan_for_chunk)
	#increase_mask_fwhm!(this_plan_for_chunk,Δfwhm)
	map(chid->increase_mask_fwhm!(this_plan_for_chunk[chid],Δfwhm), 1:num_chunks )
	else
	this_plan_for_chunk = plan_for_chunk
	end
	#(ccf_out, ccf_covar_out ) = mapreduce(chid->calc_ccf_and_covar_chunk(chunk_list.data[chid], plan_for_chunk[chid],
	# assume_sorted=assume_sorted ), add_tuple_sum, 1:length(chunk_list.data) )
	calc_ccf_and_covar_chunklist!(ccf_out, ccf_covar_out, chunk_list,this_plan_for_chunk, ccf_var_scale=ccf_var_scale, assume_sorted=assume_sorted)
	return (ccf=ccf_out, ccf_covar=ccf_covar_out)
	end

[hematthi]

EchelleCCFs.jl/src/convenience/ccf_chunklist_timeseries.jl

Lines 7 to 23 in a639217

	""" `calc_ccf_chunklist_timeseries( chunklist_timeseries, line_list )`
	Convenience function to compute CCF for a timeseries of spectra, each with a chunklist.
	Uses multiple threads if avaliable.
	# Inputs:
	- chunklist_timeseries
	# Optional Arguments:
	- ccf_plan (BasicCCFPlan())
	- verbose (false)
	# Return:
	CCF summed over all chunks in a spectrum's chunklist, evaluated using the ccf_plan.
	Note that the ccf_plan provided is used as a template for creating a custom ccf_plan for each chunk that
	only includes lines that reliably appear in that order for all spectra in the chunklist_timeseries.
	"""
	function calc_ccf_chunklist_timeseries(clt::AbstractChunkListTimeseries,
	plan::PlanT = BasicCCFPlan(); verbose::Bool = false,
	ccf_var_scale::Real = 1.0, Δfwhm::AbstractVector{T} = zeros(0),
	calc_ccf_var::Bool = false, calc_ccf_covar::Bool = false ) where { PlanT<:AbstractCCFPlan, T<:Real }