repetitive large blocks of code can be made into separate function

[hematthi]

The following large blocks of code are identical and can be made into a separate function to reduce repetitive code:

EchelleCCFs.jl/src/convenience/order_ccf_chunklist_timeseries.jl

Lines 34 to 92 in a639217

	for chid in 1:num_chunks(clt)
	order = clt[1].order[chid]
	if typeof(plan.line_list) <: BasicLineList2D
	start_order_idx = searchsortedfirst(plan.line_list.order,order)
	stop_order_idx = searchsortedlast(view(plan.line_list.order,start_order_idx:num_lines),order) + start_order_idx-1
	else
	start_order_idx = 1
	stop_order_idx = num_lines
	end
	if (1<=start_order_idx<=stop_order_idx<=num_lines)
	# find the maximum lower wavelength for the chunk, and the minumum upper wavelength, over all observations
	λmin = maximum(map(obsid->first(clt.chunk_list[obsid].data[chid].λ), 1:length(clt) ))
	λmax = minimum(map(obsid->last( clt.chunk_list[obsid].data[chid].λ), 1:length(clt) ))
	# extend λmin/λmax by the velocity range over which we don't want the mask to change
	λmin = λmin / (calc_doppler_factor(plan.v_center)*calc_doppler_factor(-plan.v_range_no_mask_change))
	λmax = λmax / (calc_doppler_factor(plan.v_center)*calc_doppler_factor(plan.v_range_no_mask_change))
	# extend λmin/λmax by the mask width
	upper_edge_of_mask_for_line_at_λmin = λ_max(plan.mask_shape,λmin)
	lower_edge_of_mask_for_line_at_λmax = λ_min(plan.mask_shape,λmax)
	# find the first and last mask entries to use in each chunk
	start_line_idx = searchsortedfirst(view(plan.line_list.λ,start_order_idx:stop_order_idx),upper_edge_of_mask_for_line_at_λmin) + start_order_idx-1
	#stop_line_idx = num_lines+1 - searchsortedfirst(view(plan.line_list.λ,num_lines:-1:1),lower_edge_of_mask_for_line_at_λmax,rev=true)
	stop_line_idx = start_order_idx-1 + searchsortedlast(view(plan.line_list.λ,start_order_idx:stop_order_idx),lower_edge_of_mask_for_line_at_λmax)
	if verbose
	flush(stdout)
	println("extrema(plan.line_list.λ) = ",extrema(plan.line_list.λ) )
	if (1 <= start_line_idx <= length(plan.line_list.λ)) && (1 <= stop_line_idx <= length(plan.line_list.λ))
	println("start_order_idx = ", start_order_idx, " stop_order_idx = ", stop_order_idx)
	println("start_line_idx = ", start_line_idx, " λ= ", plan.line_list.λ[start_line_idx]) #, " order= ", plan.line_list.order[start_line_idx])
	println("stop_line_idx = ", stop_line_idx, " λ= ", plan.line_list.λ[stop_line_idx]) #, " order= ", plan.line_list.order[stop_line_idx])
	end
	println("upper_edge_of_mask_for_line_at_λmin = ", upper_edge_of_mask_for_line_at_λmin, " Lower_edge_of_mask_for_line_at_λmax = ", lower_edge_of_mask_for_line_at_λmax)
	end
	if (1 <= start_line_idx <= length(plan.line_list.λ)) && (1 <= stop_line_idx <= length(plan.line_list.λ))
	if verbose && typeof(plan.line_list) <: BasicLineList2D
	println("start_line_idx = ", start_line_idx, " λ= ", plan.line_list.λ[start_line_idx], " order= ", plan.line_list.order[start_line_idx])
	println("stop_line_idx = ", stop_line_idx, " λ= ", plan.line_list.λ[stop_line_idx], " order= ", plan.line_list.order[stop_line_idx])
	println(" Using ", length(start_line_idx:stop_line_idx), " lines for chunk ", chid, " order ", order)
	end
	if ! issorted( view(plan.line_list.λ, start_line_idx:stop_line_idx ) )
	println("# View is not sorted. Why?")
	for i in start_line_idx:stop_line_idx
	println("i= ", i, " λ= ", plan.line_list.λ[i], " order= ", plan.line_list.order[i])
	end
	end
	@assert issorted( view(plan.line_list.λ, start_line_idx:stop_line_idx ) )
	# line_list_for_chunk = BasicLineList2D(view(plan.line_list.λ,start_line_idx:stop_line_idx), view(plan.line_list.weight,start_line_idx:stop_line_idx), fill(order,length(start_line_idx:stop_line_idx)) )
	line_list_for_chunk = BasicLineList(view(plan.line_list.λ,start_line_idx:stop_line_idx), view(plan.line_list.weight,start_line_idx:stop_line_idx) )
	else # No lines in this chunk!
	line_list_for_chunk = EmptyBasicLineList()
	end
	else
	line_list_for_chunk = EmptyBasicLineList()
	end
	#create a plan for this chunk that only includes the mask entries we want for this chunk
	plan_for_chunk[chid] = BasicCCFPlan( line_list=line_list_for_chunk, midpoint=plan.v_center, step=plan.v_step, max=plan.v_max, mask_shape=plan.mask_shape )
	end

EchelleCCFs.jl/src/convenience/order_ccf_chunklist_timeseries.jl

Lines 132 to 188 in a639217

	for chid in 1:num_chunks(clt)
	order = clt[1].order[chid]
	if typeof(plan.line_list) <: BasicLineList2D
	start_order_idx = searchsortedfirst(plan.line_list.order,order)
	stop_order_idx = searchsortedlast(view(plan.line_list.order,start_order_idx:num_lines),order) + start_order_idx-1
	else
	start_order_idx = 1
	stop_order_idx = num_lines
	end
	if (1<=start_order_idx<=stop_order_idx<=num_lines)
	# find the maximum lower wavelength for the chunk, and the minumum upper wavelength, over all observations
	λmin = maximum(map(obsid->first(clt.chunk_list[obsid].data[chid].λ), 1:length(clt) ))
	λmax = minimum(map(obsid->last( clt.chunk_list[obsid].data[chid].λ), 1:length(clt) ))
	# extend λmin/λmax by the velocity range over which we don't want the mask to change
	λmin = λmin / (calc_doppler_factor(plan.v_center)*calc_doppler_factor(-plan.v_range_no_mask_change))
	λmax = λmax / (calc_doppler_factor(plan.v_center)*calc_doppler_factor(plan.v_range_no_mask_change))
	# extend λmin/λmax by the mask width
	upper_edge_of_mask_for_line_at_λmin = λ_max(plan.mask_shape,λmin)
	lower_edge_of_mask_for_line_at_λmax = λ_min(plan.mask_shape,λmax)
	# find the first and last mask entries to use in each chunk
	start_line_idx = searchsortedfirst(view(plan.line_list.λ,start_order_idx:stop_order_idx),upper_edge_of_mask_for_line_at_λmin) + start_order_idx-1
	stop_line_idx = start_order_idx-1 + searchsortedlast(view(plan.line_list.λ,start_order_idx:stop_order_idx),lower_edge_of_mask_for_line_at_λmax)
	if verbose
	flush(stdout)
	println("extrema(plan.line_list.λ) = ",extrema(plan.line_list.λ) )
	if (1 <= start_line_idx <= length(plan.line_list.λ)) && (1 <= stop_line_idx <= length(plan.line_list.λ))
	println("start_order_idx = ", start_order_idx, " stop_order_idx = ", stop_order_idx)
	println("start_line_idx = ", start_line_idx, " λ= ", plan.line_list.λ[start_line_idx]) #, " order= ", plan.line_list.order[start_line_idx])
	println("stop_line_idx = ", stop_line_idx, " λ= ", plan.line_list.λ[stop_line_idx]) #, " order= ", plan.line_list.order[stop_line_idx])
	end
	println("upper_edge_of_mask_for_line_at_λmin = ", upper_edge_of_mask_for_line_at_λmin, " Lower_edge_of_mask_for_line_at_λmax = ", lower_edge_of_mask_for_line_at_λmax)
	end
	if (1 <= start_line_idx <= length(plan.line_list.λ)) && (1 <= stop_line_idx <= length(plan.line_list.λ))
	if verbose && typeof(plan.line_list) <: BasicLineList2D
	println("start_line_idx = ", start_line_idx, " λ= ", plan.line_list.λ[start_line_idx], " order= ", plan.line_list.order[start_line_idx])
	println("stop_line_idx = ", stop_line_idx, " λ= ", plan.line_list.λ[stop_line_idx], " order= ", plan.line_list.order[stop_line_idx])
	println(" Using ", length(start_line_idx:stop_line_idx), " lines for chunk ", chid, " order ", order)
	end
	if ! issorted( view(plan.line_list.λ, start_line_idx:stop_line_idx ) )
	println("# View is not sorted. Why?")
	for i in start_line_idx:stop_line_idx
	println("i= ", i, " λ= ", plan.line_list.λ[i], " order= ", plan.line_list.order[i])
	end
	end
	@assert issorted( view(plan.line_list.λ, start_line_idx:stop_line_idx ) )
	# line_list_for_chunk = BasicLineList(view(plan.line_list.λ,start_line_idx:stop_line_idx), view(plan.line_list.weight,start_line_idx:stop_line_idx) )
	line_list_for_chunk = BasicLineList(view(plan.line_list.λ,start_line_idx:stop_line_idx), view(plan.line_list.weight,start_line_idx:stop_line_idx) )
	else # No lines in this chunk!
	line_list_for_chunk = EmptyBasicLineList()
	end
	else
	line_list_for_chunk = EmptyBasicLineList()
	end
	#create a plan for this chunk that only includes the mask entries we want for this chunk
	plan_for_chunk[chid] = BasicCCFPlan( line_list=line_list_for_chunk, midpoint=plan.v_center, step=plan.v_step, max=plan.v_max, mask_shape=plan.mask_shape )
	end

This would also help improve readability and bug-fixing.

[hematthi]

The same block of code exists here too (other than lines 40-46):

EchelleCCFs.jl/src/convenience/ccf_chunklist_timeseries.jl

Lines 30 to 96 in a639217

	for chid in 1:num_chunks(clt)
	order = clt[1].order[chid]
	if typeof(plan.line_list) <: BasicLineList2D
	start_order_idx = searchsortedfirst(plan.line_list.order,order)
	stop_order_idx = searchsortedlast(view(plan.line_list.order,start_order_idx:num_lines),order) + start_order_idx-1
	else
	start_order_idx = 1
	stop_order_idx = num_lines
	end
	if verbose
	println("# Chunk ", chid, " order= ", order)
	println("# start_order_idx = ", start_order_idx, " stop_order_idx = ", stop_order_idx)
	if (1<=start_order_idx<=stop_order_idx<=num_lines) && typeof(plan.line_list) <: BasicLineList2D
	println(" order = ", plan.line_list.order[start_order_idx], " - ", plan.line_list.order[stop_order_idx])
	end
	end
	if (1<=start_order_idx<=stop_order_idx<=num_lines)
	# find the maximum lower wavelength for the chunk, and the minumum upper wavelength, over all observations
	λmin = maximum(map(obsid->first(clt.chunk_list[obsid].data[chid].λ), 1:length(clt) ))
	λmax = minimum(map(obsid->last( clt.chunk_list[obsid].data[chid].λ), 1:length(clt) ))
	# extend λmin/λmax by the velocity range over which we don't want the mask to change
	λmin = λmin / (calc_doppler_factor(plan.v_center)*calc_doppler_factor(-plan.v_range_no_mask_change))
	λmax = λmax / (calc_doppler_factor(plan.v_center)*calc_doppler_factor(plan.v_range_no_mask_change))
	# extend λmin/λmax by the mask width
	upper_edge_of_mask_for_line_at_λmin = λ_max(plan.mask_shape,λmin)
	lower_edge_of_mask_for_line_at_λmax = λ_min(plan.mask_shape,λmax)
	# find the first and last mask entries to use in each chunk
	start_line_idx = searchsortedfirst(view(plan.line_list.λ,start_order_idx:stop_order_idx),upper_edge_of_mask_for_line_at_λmin) + start_order_idx-1
	stop_line_idx = start_order_idx-1 + searchsortedlast(view(plan.line_list.λ,start_order_idx:stop_order_idx),lower_edge_of_mask_for_line_at_λmax)
	if verbose
	flush(stdout)
	println("extrema(plan.line_list.λ) = ",extrema(plan.line_list.λ) )
	if (1 <= start_line_idx <= length(plan.line_list.λ)) && (1 <= stop_line_idx <= length(plan.line_list.λ))
	println("start_order_idx = ", start_order_idx, " stop_order_idx = ", stop_order_idx)
	println("start_line_idx = ", start_line_idx, " λ= ", plan.line_list.λ[start_line_idx]) #, " order= ", plan.line_list.order[start_line_idx])
	println("stop_line_idx = ", stop_line_idx, " λ= ", plan.line_list.λ[stop_line_idx]) #, " order= ", plan.line_list.order[stop_line_idx])
	end
	println("upper_edge_of_mask_for_line_at_λmin = ", upper_edge_of_mask_for_line_at_λmin, " Lower_edge_of_mask_for_line_at_λmax = ", lower_edge_of_mask_for_line_at_λmax)
	end
	if (1 <= start_line_idx <= length(plan.line_list.λ)) && (1 <= stop_line_idx <= length(plan.line_list.λ))
	if verbose && typeof(plan.line_list) <: BasicLineList2D
	println("start_line_idx = ", start_line_idx, " λ= ", plan.line_list.λ[start_line_idx], " order= ", plan.line_list.order[start_line_idx])
	println("stop_line_idx = ", stop_line_idx, " λ= ", plan.line_list.λ[stop_line_idx], " order= ", plan.line_list.order[stop_line_idx])
	println(" Using ", length(start_line_idx:stop_line_idx), " lines for chunk ", chid, " order ", order)
	end
	if ! issorted( view(plan.line_list.λ, start_line_idx:stop_line_idx ) )
	println("# View is not sorted. Why?")
	for i in start_line_idx:stop_line_idx
	println("i= ", i, " λ= ", plan.line_list.λ[i], " order= ", plan.line_list.order[i])
	end
	end
	@assert issorted( view(plan.line_list.λ, start_line_idx:stop_line_idx ) )
	# line_list_for_chunk = BasicLineList2D(view(plan.line_list.λ,start_line_idx:stop_line_idx), view(plan.line_list.weight,start_line_idx:stop_line_idx), fill(order,length(start_line_idx:stop_line_idx)) )
	line_list_for_chunk = BasicLineList(view(plan.line_list.λ,start_line_idx:stop_line_idx), view(plan.line_list.weight,start_line_idx:stop_line_idx) )
	else # No lines in this chunk!
	line_list_for_chunk = EmptyBasicLineList()
	end
	else
	line_list_for_chunk = EmptyBasicLineList()
	end
	#create a plan for this chunk that only includes the mask entries we want for this chunk
	plan_for_chunk[chid] = BasicCCFPlan( line_list=line_list_for_chunk, midpoint=plan.v_center, step=plan.v_step, max=plan.v_max, mask_shape=plan.mask_shape )
	end