update documentation to consistently describe and name all arguments

[hematthi]

EchelleCCFs.jl/src/convenience/order_ccf_chunklist.jl

Lines 7 to 34 in a639217

	""" `calc_order_ccfs_chunklist ( chunklist_timeseries, list_of_ccf_plans )`
	Convenience function to compute separate CCFs for each chunk (potentially an order or view around one or two lines) in a spectrum.
	CCF is evaluated using line list and mask_shape provided by the ccf plan for each chunk.
	# Inputs:
	- `chunklist_timeseries`:
	- `list_of_ccf_plans`: ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	A 2-d array containing the CCF at each (velocity, chunk)
	"""
	function calc_order_ccfs_chunklist!(chunk_ccfs_out::AbstractArray{T1,2}, chunk_list::AbstractChunkList,
	plan_for_chunk::AbstractVector{PlanT} = BasicCCFPlan(); assume_sorted::Bool = false ) where {
	T1<:Real, PlanT<:AbstractCCFPlan }
	num_chunks = length(chunk_list)
	@assert length(plan_for_chunk) == num_chunks
	@assert size(chunk_ccfs_out,2) == num_chunks
	@assert assume_sorted || issorted( first(plan_for_chunk).line_list.λ )
	num_vels = maximum(map(chid->calc_length_ccf_v_grid(plan_for_chunk[chid]), 1:num_chunks ))
	@assert size(chunk_ccfs_out,1) == num_vels
	#flush(stdout); println("num_vels = ",num_vels," num_chunks = ", num_chunks, " length(chunk_list.data)=", length(chunk_list.data)); flush(stdout);
	for chid in 1:num_chunks
	# chunk_ccfs_out[:,i] .=
	#flush(stdout); println("chid = ", chid); flush(stdout);
	calc_ccf_chunk!(view(chunk_ccfs_out, 1:num_vels, chid ), chunk_list.data[chid], plan_for_chunk[chid], assume_sorted=assume_sorted )
	end
	return chunk_ccfs_out
	end

[hematthi]

EchelleCCFs.jl/src/convenience/order_ccf_chunklist.jl

Lines 36 to 66 in a639217

	""" `calc_order_ccfs_chunklist ( chunklist_timeseries, list_of_ccf_plans )`
	Convenience function to compute separate CCFs for each chunk (potentially an order or view around one or two lines) in a spectrum.
	CCF is evaluated using line list and mask_shape provided by the ccf plan for each chunk.
	# Inputs:
	- `chunklist_timeseries`:
	- `list_of_ccf_plans`: ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	A 2-d array containing the CCF at each (velocity, chunk)
	"""
	function calc_order_ccfs_chunklist(chunk_list::AbstractChunkList,
	plan_for_chunk::AbstractVector{PlanT} = BasicCCFPlan();
	Δfwhm::Real = 0, assume_sorted::Bool = false ) where {
	PlanT<:AbstractCCFPlan }
	num_chunks = length(chunk_list)
	@assert length(plan_for_chunk) == num_chunks
	@assert assume_sorted || issorted( first(plan_for_chunk).line_list.λ )
	num_vels = maximum(map(chid->calc_length_ccf_v_grid(plan_for_chunk[chid]), 1:num_chunks ))
	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
	chunk_ccfs_out = zeros( num_vels, num_chunks )
	calc_order_ccfs_chunklist!(chunk_ccfs_out, chunk_list, this_plan_for_chunk, assume_sorted=assume_sorted )
	return chunk_ccfs_out
	end

[hematthi]

EchelleCCFs.jl/src/convenience/order_ccf_chunklist.jl

Lines 69 to 95 in a639217

	""" `calc_order_ccfs_chunklist ( chunklist_timeseries, list_of_ccf_plans )`
	Convenience function to compute separate CCFs for each chunk (potentially an order or view around one or two lines) in a spectrum.
	CCF is evaluated using line list and mask_shape provided by the ccf plan for each chunk.
	# Inputs:
	- `chunklist_timeseries`:
	- `list_of_ccf_plans`: ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	A 2-d array containing the CCF at each (velocity, chunk)
	"""
	function calc_order_ccf_and_vars_chunklist!(chunk_ccfs_out::AbstractArray{T1,2}, chunk_ccf_vars_out::AbstractArray{T1,2}, chunk_list::AbstractChunkList,
	plan_for_chunk::AbstractVector{PlanT} = BasicCCFPlan(); assume_sorted::Bool = false ) where {
	T1<:Real, PlanT<:AbstractCCFPlan }
	num_chunks = length(chunk_list)
	@assert length(plan_for_chunk) == num_chunks
	@assert size(chunk_ccfs_out,2) == num_chunks
	@assert assume_sorted || issorted( first(plan_for_chunk).line_list.λ )
	num_vels = maximum(map(chid->calc_length_ccf_v_grid(plan_for_chunk[chid]), 1:num_chunks ))
	@assert size(chunk_ccfs_out,1) == num_vels
	for chid in 1:num_chunks
	calc_ccf_and_var_chunk!(view(chunk_ccfs_out, 1:num_vels, chid ), view(chunk_ccf_vars_out, 1:num_vels, chid ),
	chunk_list.data[chid], plan_for_chunk[chid], assume_sorted=assume_sorted )
	end
	return (ccfs=chunk_ccfs_out, ccf_vars=chunk_ccf_vars_out)
	end

[hematthi]

EchelleCCFs.jl/src/convenience/order_ccf_chunklist.jl

Lines 97 to 130 in a639217

	""" `calc_order_ccfs_chunklist ( chunklist_timeseries, list_of_ccf_plans )`
	Convenience function to compute separate CCFs for each chunk (potentially an order or view around one or two lines) in a spectrum.
	CCF is evaluated using line list and mask_shape provided by the ccf plan for each chunk.
	# Inputs:
	- `chunklist_timeseries`:
	- `list_of_ccf_plans`: ccf plans (one for each chunk)
	# Optional Arguments:
	- `assume_sorted`: if true, skips checking the line_list is sorted by wavelength
	# Return:
	A 2-d array containing the CCF at each (velocity, chunk)
	"""
	function calc_order_ccf_and_vars_chunklist(chunk_list::AbstractChunkList,
	plan_for_chunk::AbstractVector{PlanT} = BasicCCFPlan();
	Δfwhm::Real = 0, assume_sorted::Bool = false ) where {
	PlanT<:AbstractCCFPlan }
	num_chunks = length(chunk_list)
	@assert length(plan_for_chunk) == num_chunks
	@assert assume_sorted || issorted( first(plan_for_chunk).line_list.λ )
	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
	num_vels = maximum(map(chid->calc_length_ccf_v_grid(plan_for_chunk[chid]), 1:num_chunks ))
	chunk_ccfs_out = zeros( num_vels, num_chunks )
	chunk_ccf_vars_out = zeros( num_vels, num_chunks )
	calc_order_ccf_and_vars_chunklist!(chunk_ccfs_out, chunk_ccf_vars_out, chunk_list, this_plan_for_chunk, assume_sorted=assume_sorted )
	return (ccfs=chunk_ccfs_out, ccf_vars=chunk_ccf_vars_out)
	end

[hematthi]

EchelleCCFs.jl/src/convenience/order_ccf_chunklist_timeseries.jl

Lines 8 to 24 in a639217

	""" `calc_order_ccf_chunklist_timeseries( chunklist_timeseries, ccf_plan )`
	Convenience function to compute separate CCFs for each chunk (potentially an order or view around one or two lines) of each spectrum in a timeseries.
	CCF is evaluated using line list and mask_shape provided by the ccf plan for each chunk.
	Uses multiple threads if avaliable.
	# Inputs:
	- chunklist_timeseries
	# Optional Arguments:
	- ccf_plan (BasicCCFPlan())
	# Return:
	A 3-d array containing the CCF at each (velocity, chunk, spectrum)
	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_order_ccf_chunklist_timeseries(clt::AbstractChunkListTimeseries,
	plan::PlanT = BasicCCFPlan(); verbose::Bool = false ,
	Δfwhm::AbstractVector{T} = zeros(0)
	) where { PlanT<:AbstractCCFPlan, T<:Real }

[hematthi]

EchelleCCFs.jl/src/convenience/order_ccf_chunklist_timeseries.jl

Lines 105 to 122 in a639217

	""" `calc_order_ccf_and_var_chunklist_timeseries( chunklist_timeseries, ccf_plan )`
	Convenience function to compute separate CCFs for each chunk (potentially an order or view around one or two lines) of each spectrum in a timeseries.
	CCF is evaluated using line list and mask_shape provided by the ccf plan for each chunk.
	Uses multiple threads if avaliable.
	# Inputs:
	- chunklist_timeseries
	# Optional Arguments:
	- ccf_plan (BasicCCFPlan())
	# Return:
	A 3-d array containing the CCF at each (velocity, chunk, spectrum)
	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_order_ccf_and_var_chunklist_timeseries(clt::AbstractChunkListTimeseries,
	plan::PlanT = BasicCCFPlan(); verbose::Bool = false,
	ccf_var_scale::Real = 1.0, Δfwhm::AbstractVector{T} = zeros(0)
	) where {
	PlanT<:AbstractCCFPlan, T<:Real }