ccf_orders can take Δfwhm

Author: eford

Project.toml

@@ -1,7 +1,7 @@
 name = "RvSpectML"
 uuid = "1f61ac2c-3a1c-440a-925a-2707197041c8"
 authors = ["Eric B. Ford, Christian Gilbertson, Joe Ninan, Michael L. Palumbo III, Alex Wise, and contributors"]
-version = "0.2.1"
+version = "0.2.2"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -58,7 +58,7 @@ Query = "1"
 RvSpectMLBase = "0.2"
 Scalpels = "0.1"
 SpecialFunctions = "1.0, 1.1"
-StaticArrays = "1" 
+StaticArrays = "1"
 StatsBase = "0.33"
 Stheno = "0.6"
 TemporalGPs = "0.3, 0.4, 0.5"

src/pipeline/ccf_orders.jl

@@ -1,7 +1,9 @@
 function ccf_orders(order_list_timeseries::AbstractChunkListTimeseries,  line_list_df::DataFrame, pipeline::PipelinePlan; verbose::Bool = false, calc_ccf_var::Bool = false, recalc::Bool = false,
    orders_to_use = RvSpectMLBase.orders_to_use_default(order_list_timeseries.inst),
    range_no_mask_change::Real=RvSpectMLBase.max_bc, ccf_mid_velocity::Real=0.0,
-    v_step::Real=250.0, v_max=RvSpectMLBase.max_bc, mask_scale_factor::Real=1, mask_type::Symbol = :tophat, allow_nans::Bool = false )
+    v_step::Real=250.0, v_max=RvSpectMLBase.max_bc, mask_scale_factor::Real=1,
+    mask_type::Symbol = :tophat, Δfwhm::AbstractVector{T} = zeros(0),
+    allow_nans::Bool = false ) where { T<:Real }
 
    if need_to(pipeline, :ccf_orders)  || recalc # Compute order CCF's & measure RVs
       if mask_type == :tophat
@@ -23,10 +25,10 @@ function ccf_orders(order_list_timeseries::AbstractChunkListTimeseries,  line_li
       tstart = now()    # Compute CCFs for each order
 
       if calc_ccf_var
-         (order_ccfs, order_ccf_vars ) = EchelleCCFs.calc_order_ccf_and_var_chunklist_timeseries(order_list_timeseries, ccf_plan)
+         (order_ccfs, order_ccf_vars ) = EchelleCCFs.calc_order_ccf_and_var_chunklist_timeseries(order_list_timeseries, ccf_plan, Δfwhm=Δfwhm)
          set_cache!(pipeline,:ccf_orders, (order_ccfs = order_ccfs, order_ccf_vars = order_ccf_vars, v_grid=v_grid) )
       else
-         order_ccfs = EchelleCCFs.calc_order_ccf_chunklist_timeseries(order_list_timeseries, ccf_plan)
+         order_ccfs = EchelleCCFs.calc_order_ccf_chunklist_timeseries(order_list_timeseries, ccf_plan, Δfwhm=Δfwhm)
          set_cache!(pipeline,:ccf_orders, (order_ccfs = order_ccfs, v_grid=v_grid) )
       end
       if verbose   println("# Order CCFs runtime: ", now()-tstart)  end

src/pipeline/ccf_total.jl

@@ -1,6 +1,8 @@
 function ccf_total(order_list_timeseries::AbstractChunkListTimeseries, line_list_df::DataFrame, pipeline::PipelinePlan; recalc::Bool = false,
-                  output_fn_suffix::String = "", range_no_mask_change::Real=RvSpectMLBase.max_bc, ccf_mid_velocity::Real=0.0, v_step::Real=250.0,
-                  v_max=RvSpectMLBase.max_bc, mask_scale_factor::Real=1, ccf_var_scale::Real=1.0, mask_type::Symbol = :tophat, Δfwhm::AbstractVector{T} = zeros(0),
+                  output_fn_suffix::String = "",
+                  range_no_mask_change::Real=RvSpectMLBase.max_bc, ccf_mid_velocity::Real=0.0,
+                  v_step::Real=250.0, v_max=RvSpectMLBase.max_bc, mask_scale_factor::Real=1,
+                  ccf_var_scale::Real=1.0, mask_type::Symbol = :tophat, Δfwhm::AbstractVector{T} = zeros(0),
                   calc_ccf_var::Bool = false, calc_ccf_covar::Bool = false, allow_nans::Bool = false, verbose::Bool = false ) where { T<:Real }
     if need_to(pipeline,:ccf_total) || recalc
       if verbose println("# Computing CCF.")  end