Merge pull request #82 from andrew-saydjari/main

merge back main

Project.toml

@@ -34,6 +34,7 @@ ThreadPinning = "811555cd-349b-4f26-b7bc-1f208b848042"
 [compat]
 AstroTime = "0.7"
 BLISBLAS = "0.1"
+BasisFunctions = "0.6"
 DataFrames = "1"
 EllipsisNotation = "1"
 FITSIO = "0.17"
@@ -46,6 +47,7 @@ PoissonRandom = "0.4"
 ProgressMeter = "1"
 ShiftedArrays = "2"
 SlurmClusterManager = "0.1"
+SortFilters = "0.1"
 StatsBase = "0.33, 0.34"
 Suppressor = "0.2"
 ThreadPinning = "0.7"

pipeline.jl

@@ -148,12 +148,12 @@ end
         starcache = cache_starname(tele,field,plate,mjd,fiberindx,cache_dir=cache_dir,inject_cache_dir=inject_cache_dir)
         if (isfile(starcache) & caching)
             fvec, fvarvec, cntvec, chipmidtimes, metaexport = deserialize(starcache)
-            starscale,framecnts,varoffset,varflux,a_relFlux,b_relFlux,c_relFlux = metaexport
+            starscale,framecnts,varoffset,varflux,a_relFlux,b_relFlux,c_relFlux,cartVisit = metaexport
         elseif tele[end]=='i'
             warn("Injections not found at injection cache dir!")
         else
             fvec, fvarvec, cntvec, chipmidtimes, metaexport = stack_out(release_dir,redux_ver,tele,field,plate,mjd,fiberindx,cache_dir=cache_dir)
-            starscale,framecnts,varoffset,varflux,a_relFlux,b_relFlux,c_relFlux = metaexport
+            starscale,framecnts,varoffset,varflux,a_relFlux,b_relFlux,c_relFlux,cartVisit = metaexport
             if caching
                 dirName = splitdir(starcache)[1]
                 if !ispath(dirName)
@@ -164,7 +164,7 @@ end
         end
         simplemsk = (cntvec.==framecnts) .& skymsk;
 
-        push!(out,(count(simplemsk), starscale, framecnts, chipmidtimes, varoffset, varflux, a_relFlux, b_relFlux, c_relFlux, nanify(fvec[simplemsk],simplemsk), nanify(fvarvec[simplemsk],simplemsk))) # 1
+        push!(out,(count(simplemsk), starscale, framecnts, chipmidtimes, varoffset, varflux, a_relFlux, b_relFlux, c_relFlux, cartVisit, nanify(fvec[simplemsk],simplemsk), nanify(fvarvec[simplemsk],simplemsk))) # 1
 
         if sky_off
             meanLocSky.=0
@@ -369,8 +369,9 @@ end
                 (x->x[metai][7],                        "a_relFlux"),
                 (x->x[metai][8],                        "b_relFlux"),
                 (x->x[metai][9],                        "c_relFlux"),
-                (x->x[metai][10],                       "flux"),
-                (x->x[metai][11],                       "fluxerr2"),
+                (x->x[metai][10],                       "cartVisit"),
+                (x->x[metai][11],                       "flux"),
+                (x->x[metai][12],                       "fluxerr2"),
                 (x->adjfibindx,                         "adjfiberindx"),
 
                 (x->Float64.(x[RVind][1][1]),           "RV_pixoff_final"),

src/fileNameHandling.jl

@@ -239,5 +239,5 @@ function build_apFluxPaths(release_dir,redux_ver,tele,field,plate,mjd)
         fluxFile = build_apFluxPath(release_dir,redux_ver,tele,mjd,chip,expectDome)
         push!(fluxFiles,fluxFile)
     end
-    return fluxFiles, expectDome
+    return fluxFiles, expectDome, cartVisit
 end

src/ingest.jl

@@ -3,11 +3,11 @@
 
 using AstroTime
 
-function getAndWrite_fluxing(release_dir,redux_ver,tele,field,plate,mjd; cache_dir="../local_cache")
-    flux_paths, domeflat_expid = build_apFluxPaths(release_dir,redux_ver,tele,field,plate,mjd)
+function getAndWrite_fluxing(release_dir,redux_ver,tele,field,plate,mjd; cache_dir="../local_cache",nattempts=5)
+    flux_paths, domeflat_expid, cartVisit = build_apFluxPaths(release_dir,redux_ver,tele,field,plate,mjd)
     fluxingcache = cache_fluxname(tele,field,plate,mjd; cache_dir=cache_dir)
 
-    hdr = FITSHeader(["pipeline","git_branch","git_commit","domeflat_expid"],["apMADGICS.jl",git_branch,git_commit,string(domeflat_expid)],["","","",""])
+    hdr = FITSHeader(["pipeline","git_branch","git_commit","domeflat_expid","CARTID"],["apMADGICS.jl",git_branch,git_commit,string(domeflat_expid),string(cartVisit)],["","","","",""])
 
     #should implement this everywhere to avoid race conditions
     tmpfname = tempname()*"fits"
@@ -21,7 +21,16 @@ function getAndWrite_fluxing(release_dir,redux_ver,tele,field,plate,mjd; cache_d
         write(h,thrpt,name=chip)
     end
     close(h)
-    if !isfile(fluxingcache)
+    try
+        for i=1:nattempts
+            if !isfile(fluxingcache)
+                mv(tmpfname,fluxingcache,force=true)
+                break
+            else
+                break
+            end
+        end
+    catch
         mv(tmpfname,fluxingcache,force=true)
     end
 end
@@ -122,6 +131,7 @@ function stack_out(release_dir,redux_ver,tele,field,plate,mjd,fiberindx; varoffs
         thrpt = read(f[chip],fiberindx)
         thrptDict[chip] = thrpt
     end
+    cartVisit = read_header(f[1])["CARTID"]
     close(f)
 
     fill!(outvec,0)
@@ -222,7 +232,7 @@ function stack_out(release_dir,redux_ver,tele,field,plate,mjd,fiberindx; varoffs
     chipmidtimes = zeros(3)
     chipmidtimes[goodframeIndx] .= mean.(time_lsts[goodframeIndx]) #consider making this flux weighted (need to worry about skyline variance driving it)
     chipmidtimes[.!goodframeIndx] .= NaN
-    metaexport = (starscale,framecnts,varoffset,(c^2*starscale^p),thrptDict["a"],thrptDict["b"],thrptDict["c"])
+    metaexport = (starscale,framecnts,varoffset,(c^2*starscale^p),thrptDict["a"],thrptDict["b"],thrptDict["c"],cartVisit)
     if telluric_div
         return outvec, outvar, cntvec, chipmidtimes, metaexport, telvec
     end

src/prior_build/get_sky_samples.jl

@@ -136,7 +136,7 @@ end
         skyLineCache = cache_skynameSpec(tele,field,plate,mjd,fiberindx,cache_dir=cache_dir)
         fvec, fvarvec, cntvec, chipmidtimes, metaexport = deserialize(skyLineCache)
         simplemsk = (cntvec.==maximum(cntvec));
-        return simplemsk
+        return simplemsk, fvarvec
     end
 
     function sky_smooth_fit(outvec,outvar,simplemsk,Vpoly_scaled)
@@ -169,7 +169,7 @@ end
     function get_sky_samples(adjfibindx;contscale=5e2,loc_parallel=false,seed=2023)
 
         # there is a race condition if loc_parallel is true... so added a shuffle... not a great solution, but fine for testing?
-        ntuplst = deserialize(prior_dir*"2024_01_20/dr17_dr17_sky_input_lst_plate_cleanManual_"*lpad(adjfibindx,3,"0")*".jdat")
+        ntuplst = deserialize(prior_dir*"2024_01_22/outlists/sky/dr17_dr17_sky_input_lst_plate_msked_"*lpad(adjfibindx,3,"0")*".jdat")
         # if loc_parallel
         #     rng = MersenneTwister(seed)
         #     shuffle!(rng,ntuplst)
@@ -234,19 +234,24 @@ end
         end
 
         savename = "sky_prior_disk/skymsk_"*lpad(adjfibindx,3,"0")*".jdat"
-        if !isfile(savename)
+        savename1 = "sky_prior_disk/skyvar_"*lpad(adjfibindx,3,"0")*".jdat"
+        if !(isfile(savename) & isfile(savename1))
             pout = if loc_parallel 
                 @showprogress pmap(sky_msk_wrapper,ntuplst);
             else
                 map(sky_msk_wrapper,ntuplst);
             end
             global skymsk = zeros(8700,size(pout,1));
+            global skyvar = zeros(8700,size(pout,1));
             for i=1:size(pout,1)
-                skymsk[:,i].=pout[i]
+                skymsk[:,i].=pout[i][1]
+                skyvar[:,i].=pout[i][2]
             end
             serialize(savename,skymsk)
+            serialize(savename1,skyvar)
         else
             global skymsk = deserialize(savename)
+            global skyvar = deserialize(savename1)
         end
 
         ### Save samples of tell-free sky decomposition for building Tfun/starCont prior
@@ -292,20 +297,26 @@ end
 
         # this is identical... just saving under a new name, but it is cheap
         savename = "sky_prior_disk/skymsk_tellDiv_"*lpad(adjfibindx,3,"0")*".jdat"
-        if !isfile(savename)
+        savename1 = "sky_prior_disk/skyvar_tellDiv_"*lpad(adjfibindx,3,"0")*".jdat"
+        if !(isfile(savename) & isfile(savename1))
             pout = if loc_parallel 
                 @showprogress pmap(sky_msk_wrapper,ntuplst);
             else
                 map(sky_msk_wrapper,ntuplst);
             end
             global skymsk = zeros(8700,size(pout,1));
+            global skyvar = zeros(8700,size(pout,1));
             for i=1:size(pout,1)
-                skymsk[:,i].=pout[i]
+                skymsk[:,i].=pout[i][1]
+                skyvar[:,i].=pout[i][2]
             end
             serialize(savename,skymsk)
+            serialize(savename1,skyvar)
         else
             global skymsk = deserialize(savename)
+            global skyvar = deserialize(savename1)
         end
+        serialize("sky_prior_disk/chebmsk_exp_"*lpad(adjfibindx,3,"0")*".jdat",chebmsk_exp)
     end
 end