From 1ce019b6c61124bddbd3cdb96778ccb9a822d81f Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Wed, 15 Sep 2021 13:15:44 -0700 Subject: [PATCH 01/59] factorize interpretation --- src/root.jl | 116 ++++++++++++++++++++++++++-------------------------- 1 file changed, 59 insertions(+), 57 deletions(-) diff --git a/src/root.jl b/src/root.jl index a20a6c52..1335e04a 100644 --- a/src/root.jl +++ b/src/root.jl @@ -197,66 +197,68 @@ function interped_data(rawdata, rawoffsets, ::Type{Bool}, ::Type{Nojagg}) # specialized case to get Vector{Bool} instead of BitVector return map(ntoh,reinterpret(Bool, rawdata)) end -function interped_data(rawdata, rawoffsets, ::Type{T}, ::Type{J}) where {T, J<:JaggType} - # there are two possibility, one is the leaf is just normal leaf but the title has "[...]" in it - # magic offsets, seems to be common for a lot of types, see auto.py in uproot3 - # only needs when the jaggedness comes from TLeafElements, not needed when - # the jaggedness comes from having "[]" in TLeaf's title - # the other is where we need to auto detector T bsaed on class name - # we want the fundamental type as `reinterpret` will create vector - if J === Nojagg - return ntoh.(reinterpret(T, rawdata)) - elseif J === Offsetjaggjagg # the branch is doubly jagged - jagg_offset = 10 - subT = eltype(eltype(T)) - out = VectorOfVectors(T(), Int32[1]) - @views for i in 1:(length(rawoffsets)-1) - flat = rawdata[(rawoffsets[i]+1+jagg_offset:rawoffsets[i+1])] - row = VectorOfVectors{subT}() - cursor = 1 - while cursor < length(flat) - n = ntoh(reinterpret(Int32, flat[cursor:cursor+sizeof(Int32)-1])[1]) - cursor += sizeof(Int32) - b = ntoh.(reinterpret(subT, flat[cursor:cursor+n*sizeof(subT)-1])) - cursor += n*sizeof(subT) - push!(row, b) - end - push!(out, row) - end - return out - else # the branch is singly jagged - # for each "event", the index range is `offsets[i] + jagg_offset + 1` to `offsets[i+1]` - # this is why we need to append `rawoffsets` in the `readbranchraw()` call - # when you use this range to index `rawdata`, you will get raw bytes belong to each event - # Say your real data is Int32 and you see 8 bytes after indexing, then this event has [num1, num2] as real data - _size = sizeof(eltype(T)) - if J === Offsetjagg - jagg_offset = 10 - dp = 0 # book keeping for copy_to! - lr = length(rawoffsets) - offset = Vector{Int32}(undef, lr) - offset[1] = 0 - @views @inbounds for i in 1:lr-1 - start = rawoffsets[i]+jagg_offset+1 - stop = rawoffsets[i+1] - l = stop-start+1 - if l > 0 - unsafe_copyto!(rawdata, dp+1, rawdata, start, l) - dp += l - offset[i+1] = offset[i] + l - else - # when we have an empty [] in jagged basket - offset[i+1] = offset[i] - end - end - resize!(rawdata, dp) +function interped_data(rawdata, rawoffsets, ::Type{T}, ::Type{Nojagg}) where T + return ntoh.(reinterpret(T, rawdata)) +end +# there are two possibility, one is the leaf is just normal leaf but the title has "[...]" in it +# magic offsets, seems to be common for a lot of types, see auto.py in uproot3 +# only needs when the jaggedness comes from TLeafElements, not needed when +# the jaggedness comes from having "[]" in TLeaf's title +# the other is where we need to auto detector T bsaed on class name +# we want the fundamental type as `reinterpret` will create vector +function interped_data(rawdata, rawoffsets, ::Type{T}, ::Type{Nooffsetjagg}) where T + _size = sizeof(eltype(T)) + real_data = ntoh.(reinterpret(T, rawdata)) + rawoffsets .= (rawoffsets .÷ _size) .+ 1 + return VectorOfVectors(real_data, rawoffsets, ArraysOfArrays.no_consistency_checks) +end +function interped_data(rawdata, rawoffsets, ::Type{T}, ::Type{Offsetjagg}) where T + # for each "event", the index range is `offsets[i] + jagg_offset + 1` to `offsets[i+1]` + # this is why we need to append `rawoffsets` in the `readbranchraw()` call + # when you use this range to index `rawdata`, you will get raw bytes belong to each event + # Say your real data is Int32 and you see 8 bytes after indexing, then this event has [num1, num2] as real data + _size = sizeof(eltype(T)) + jagg_offset = 10 + dp = 0 # book keeping for copy_to! + lr = length(rawoffsets) + offset = Vector{Int32}(undef, lr) + offset[1] = 0 + @views @inbounds for i in 1:lr-1 + start = rawoffsets[i]+jagg_offset+1 + stop = rawoffsets[i+1] + l = stop-start+1 + if l > 0 + unsafe_copyto!(rawdata, dp+1, rawdata, start, l) + dp += l + offset[i+1] = offset[i] + l else - offset = rawoffsets + # when we have an empty [] in jagged basket + offset[i+1] = offset[i] + end + end + resize!(rawdata, dp) + real_data = ntoh.(reinterpret(T, rawdata)) + offset .= (offset .÷ _size) .+ 1 + return VectorOfVectors(real_data, offset, ArraysOfArrays.no_consistency_checks) +end +function interped_data(rawdata, rawoffsets, ::Type{T}, ::Type{Offsetjaggjagg}) where T + jagg_offset = 10 + subT = eltype(eltype(T)) + out = VectorOfVectors(T(), Int32[1]) + @views for i in 1:(length(rawoffsets)-1) + flat = rawdata[(rawoffsets[i]+1+jagg_offset:rawoffsets[i+1])] + row = VectorOfVectors{subT}() + cursor = 1 + while cursor < length(flat) + n = ntoh(reinterpret(Int32, flat[cursor:cursor+sizeof(Int32)-1])[1]) + cursor += sizeof(Int32) + b = ntoh.(reinterpret(subT, flat[cursor:cursor+n*sizeof(subT)-1])) + cursor += n*sizeof(subT) + push!(row, b) end - real_data = ntoh.(reinterpret(T, rawdata)) - offset .= (offset .÷ _size) .+ 1 - return VectorOfVectors(real_data, offset, ArraysOfArrays.no_consistency_checks) + push!(out, row) end + return out end function _normalize_ftype(fType) From fadd2aa456a114df68f313c9566c17cdcb1dcc27 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Wed, 15 Sep 2021 13:15:55 -0700 Subject: [PATCH 02/59] make methods more specific --- src/custom.jl | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/src/custom.jl b/src/custom.jl index 1425bcd0..7d1c6490 100644 --- a/src/custom.jl +++ b/src/custom.jl @@ -73,7 +73,7 @@ function interped_data(rawdata, rawoffsets, ::Type{Vector{LVF64}}, ::Type{Offset offset .+= 1 VectorOfVectors(real_data, offset) end -function interped_data(rawdata, rawoffsets, ::Type{LVF64}, ::Type{J}) where {T, J <: JaggType} +function interped_data(rawdata, rawoffsets, ::Type{LVF64}, ::Type{Nojagg}) # even with rawoffsets, we know each TLV is destinied to be 64 bytes [ reinterpret(LVF64, x) for x in Base.Iterators.partition(rawdata, 64) @@ -91,7 +91,10 @@ end function readtype(io::IO, T::Type{_KM3NETDAQHit}) T(readtype(io, Int32), read(io, UInt8), read(io, Int32), read(io, UInt8)) end -function interped_data(rawdata, rawoffsets, ::Type{Vector{_KM3NETDAQHit}}, ::Type{J}) where {T, J <: UnROOT.JaggType} +function interped_data(rawdata, rawoffsets, ::Type{Vector{_KM3NETDAQHit}}, ::Type{Nojagg}) + UnROOT.splitup(rawdata, rawoffsets, _KM3NETDAQHit, skipbytes=10) +end +function interped_data(rawdata, rawoffsets, ::Type{Vector{_KM3NETDAQHit}}, ::Type{Offsetjagg}) UnROOT.splitup(rawdata, rawoffsets, _KM3NETDAQHit, skipbytes=10) end @@ -114,7 +117,10 @@ function readtype(io::IO, T::Type{_KM3NETDAQTriggeredHit}) T(dom_id, channel_id, tdc, tot, trigger_mask) end -function UnROOT.interped_data(rawdata, rawoffsets, ::Type{Vector{_KM3NETDAQTriggeredHit}}, ::Type{J}) where {T, J <: UnROOT.JaggType} +function UnROOT.interped_data(rawdata, rawoffsets, ::Type{Vector{_KM3NETDAQTriggeredHit}}, ::Type{Nojagg}) + UnROOT.splitup(rawdata, rawoffsets, _KM3NETDAQTriggeredHit, skipbytes=10) +end +function UnROOT.interped_data(rawdata, rawoffsets, ::Type{Vector{_KM3NETDAQTriggeredHit}}, ::Type{Offsetjagg}) UnROOT.splitup(rawdata, rawoffsets, _KM3NETDAQTriggeredHit, skipbytes=10) end @@ -146,6 +152,6 @@ function readtype(io::IO, T::Type{_KM3NETDAQEventHeader}) T(detector_id, run, frame_index, UTC_seconds, UTC_16nanosecondcycles, trigger_counter, trigger_mask, overlays) end -function UnROOT.interped_data(rawdata, rawoffsets, ::Type{_KM3NETDAQEventHeader}, ::Type{J}) where {T, J <: UnROOT.JaggType} +function UnROOT.interped_data(rawdata, rawoffsets, ::Type{_KM3NETDAQEventHeader}, ::Type{Nojagg}) UnROOT.splitup(rawdata, rawoffsets, _KM3NETDAQEventHeader, jagged=false) end From e608734e00bc00f09e53d806e1de04a5fc417e7c Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Wed, 15 Sep 2021 13:24:03 -0700 Subject: [PATCH 03/59] for ci --- test/runtests.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/runtests.jl b/test/runtests.jl index a7438143..5527f521 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -329,7 +329,7 @@ end @testset "Branch filtering" begin # Branch selection behavior: if not regex, require exact name match treebranches = ["Muon_pt", "Muon_eta", "Muon_phi", "Muon_charge", "Muon_ptErr", - "Muon_", "_pt", "Muon.pt"] + "Muon_", "_pt", "Muon.pt"] _m(s::AbstractString) = isequal(s) _m(r::Regex) = Base.Fix1(occursin, r) filter_branches(selected) = Set(mapreduce(b->filter(_m(b), treebranches), ∪, selected)) From e17bd8314556cf2b235c33c15c225379812deb0c Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Thu, 16 Sep 2021 01:08:15 -0700 Subject: [PATCH 04/59] TDirectory support (#107) * try1 * recursive and unit tests * add files * actually add tests --- src/bootstrap.jl | 14 +++++++++ src/displays.jl | 18 +++++++---- src/root.jl | 18 ++++++++++- test/runtests.jl | 12 ++++++++ test/samples/issue11_tdirectory.c | 43 ++++++++++++++++++++++++++ test/samples/issue11_tdirectory.root | Bin 0 -> 15274 bytes test/samples/tdir_complicated.py | 44 +++++++++++++++++++++++++++ test/samples/tdir_complicated.root | Bin 0 -> 9850 bytes 8 files changed, 142 insertions(+), 7 deletions(-) create mode 100644 test/samples/issue11_tdirectory.c create mode 100644 test/samples/issue11_tdirectory.root create mode 100644 test/samples/tdir_complicated.py create mode 100644 test/samples/tdir_complicated.root diff --git a/src/bootstrap.jl b/src/bootstrap.jl index 2cfaa6b8..4afbda67 100644 --- a/src/bootstrap.jl +++ b/src/bootstrap.jl @@ -827,6 +827,20 @@ function TH(io, tkey::TKey, refs) fields end +function TDirectory(io, tkey::TKey, refs) + fobj = io + seekstart(fobj, tkey) + + # almost verbatim from L95 to L101 of root.jl + dir_header = unpack(fobj, ROOTDirectoryHeader) + seek(fobj, dir_header.fSeekKeys) + header_key = unpack(fobj, TKey) + n_keys = readtype(fobj, Int32) + keys = [unpack(fobj, TKey) for _ in 1:n_keys] + + directory = ROOTDirectory(header_key.fName, dir_header, keys, fobj, refs) + return directory +end # FIXME idk what is going on but this just looks like a TTree..... function TNtuple(io, tkey::TKey, refs) diff --git a/src/displays.jl b/src/displays.jl index e410cbe7..f8f42228 100644 --- a/src/displays.jl +++ b/src/displays.jl @@ -7,14 +7,14 @@ struct TKeyNode name::AbstractString classname::AbstractString end -function children(f::ROOTFile) +function children(f::T) where T <: Union{ROOTFile,ROOTDirectory} # display TTrees recursively # subsequent TTrees with duplicate fName will be skipped # since TKey cycle number is guaranteed to be decreasing # then all TKeys in the file which are not for a TTree seen = Set{String}() - ch = Vector{Union{TTree,TKeyNode}}() - lock(f) + ch = Vector{Union{TTree,TKeyNode,ROOTDirectory}}() + T === ROOTFile ? lock(f) : nothing for k in keys(f) try obj = f[k] @@ -25,12 +25,17 @@ function children(f::ROOTFile) catch end end - for tkey in f.directory.keys + tkeys = T === ROOTFile ? f.directory.keys : f.keys + for tkey in tkeys kn = TKeyNode(tkey.fName, tkey.fClassName) kn.classname == "TTree" && continue - push!(ch, kn) + if kn.classname == "TDirectory" + push!(ch, f[tkey.fName]) + else + push!(ch, kn) + end end - unlock(f) + T === ROOTFile ? unlock(f) : nothing ch end function children(t::TTree) @@ -45,6 +50,7 @@ function children(t::TTree) end printnode(io::IO, t::TTree) = print(io, "$(t.fName) (TTree)") printnode(io::IO, f::ROOTFile) = print(io, f.filename) +printnode(io::IO, f::ROOTDirectory) = print(io, "$(f.name) (TDirectory)") printnode(io::IO, k::TKeyNode) = print(io, "$(k.name) ($(k.classname))") function Base.show(io::IO, tree::LazyTree) diff --git a/src/root.jl b/src/root.jl index 1335e04a..a7518673 100644 --- a/src/root.jl +++ b/src/root.jl @@ -2,6 +2,8 @@ struct ROOTDirectory name::AbstractString header::ROOTDirectoryHeader keys::Vector{TKey} + fobj::IOStream + refs::Dict{Int32, Any} end struct ROOTFile @@ -92,7 +94,7 @@ function ROOTFile(filename::AbstractString; customstructs = Dict("TLorentzVector n_keys = readtype(fobj, Int32) keys = [unpack(fobj, TKey) for _ in 1:n_keys] - directory = ROOTDirectory(tkey.fName, dir_header, keys) + directory = ROOTDirectory(tkey.fName, dir_header, keys, fobj, streamers.refs) ROOTFile(filename, format_version, header, fobj, tkey, streamers, directory, customstructs, ReentrantLock()) end @@ -154,6 +156,20 @@ end end end +# FIXME unify with above? +@memoize LRU(maxsize = 2000) function getindex(d::ROOTDirectory, s) +# function getindex(d::ROOTDirectory, s) + if '/' ∈ s + @debug "Splitting path '$s' and getting items recursively" + paths = split(s, '/') + return d[first(paths)][join(paths[2:end], "/")] + end + tkey = d.keys[findfirst(isequal(s), keys(d))] + streamer = getfield(@__MODULE__, Symbol(tkey.fClassName)) + S = streamer(d.fobj, tkey, d.refs) + return S +end + function Base.keys(f::ROOTFile) keys(f.directory) end diff --git a/test/runtests.jl b/test/runtests.jl index 5527f521..43faac90 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -656,3 +656,15 @@ end end end end + +@testset "TDirectory" begin + f = UnROOT.samplefile("tdir_complicated.root") + @test length(keys(f["mydir"])) == 4 + @test sort(keys(f["mydir"])) == ["Events", "c", "d", "mysubdir"] + @test sort(keys(f["mydir/mysubdir"])) == ["e", "f"] + @test sum(length.(LazyTree(f, "mydir/Events").Jet_pt)) == 4 + @test sum(length.(f["mydir/Events/Jet_pt"])) == 4 + + f = UnROOT.samplefile("issue11_tdirectory.root") + @test sum(f["Data/mytree/Particle0_E"]) ≈ 1012.0 +end diff --git a/test/samples/issue11_tdirectory.c b/test/samples/issue11_tdirectory.c new file mode 100644 index 00000000..4d5d2566 --- /dev/null +++ b/test/samples/issue11_tdirectory.c @@ -0,0 +1,43 @@ +#include "TString.h" +#include "TFile.h" +#include "TTree.h" + +#include +#include "stdlib.h" + +int issue11_tdirectory() { + + TFile *f = new TFile("issue11_tdirectory.root", "recreate"); + f->mkdir("Data"); + f->cd("Data"); + TTree *t = new TTree("mytree", "mytree"); + + auto app = "EXYZ"; + const uint Np = 10; + + // + double v[Np][4]; + for (uint n=0; nBranch(TString::Format("Particle%d_%c", n, app[i]), &v[n][i]); + } + } + + const int Nev = 23; + double inc = 0.0; + + for (uint i=0; iFill(); + } + + t->Write(); + f->Close(); + + return 0; +} diff --git a/test/samples/issue11_tdirectory.root b/test/samples/issue11_tdirectory.root new file mode 100644 index 0000000000000000000000000000000000000000..963133add7dfb9da544a023773d75da34d8d0a7e GIT binary patch literal 15274 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00:00:00 2001 From: Tamas Gal Date: Thu, 16 Sep 2021 10:11:49 +0200 Subject: [PATCH 05/59] Bump version number --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 531b8232..1ea2ab5b 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.6.0" +version = "0.6.1" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From 0939b2762fc62e7b0b5dafc80e1719f304469607 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Thu, 16 Sep 2021 16:06:29 -0700 Subject: [PATCH 06/59] fix --- src/root.jl | 4 ++++ test/runtests.jl | 8 ++++++++ test/samples/issue108_small.root | Bin 0 -> 169905 bytes 3 files changed, 12 insertions(+) create mode 100644 test/samples/issue108_small.root diff --git a/src/root.jl b/src/root.jl index a7518673..3d38ded2 100644 --- a/src/root.jl +++ b/src/root.jl @@ -367,6 +367,10 @@ function auto_T_JaggT(f::ROOTFile, branch; customstructs::Dict{String, Type}) UInt32 elseif elname == "unsigned char" Char + elseif elname == "unsigned short" + UInt16 + elseif elname == "ulong64" + UInt64 else _type = getfield(Base, Symbol(:C, elname)) end diff --git a/test/runtests.jl b/test/runtests.jl index 43faac90..36e682fb 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -536,6 +536,14 @@ end _ = length.(arr); @test length.(arr.buffer) == length.(arr.buffer_range) close(rootfile) + + # issue 108 + # unsigned short -> Int16, ulong64 -> UInt64 + # file minified with `rooteventselector --recreate -l 2 "trackntuple.root:trackingNtuple/tree" issue108_small.root` + rootfile = ROOTFile(joinpath(SAMPLES_DIR, "issue108_small.root")) + @test rootfile["tree/trk_algoMask"][2] == [0x0000000000004000, 0x0000000000004000, 0x0000000000004000, 0x0000000000004000] + @test rootfile["tree/pix_ladder"][3][1:5] == UInt16[0x0001, 0x0001, 0x0001, 0x0001, 0x0003] + close(rootfile) end @testset "jagged subbranch type by leaf" begin diff --git a/test/samples/issue108_small.root b/test/samples/issue108_small.root new file mode 100644 index 0000000000000000000000000000000000000000..b8f704801bb2e45569b0de391d228cfa9f594dac GIT binary patch literal 169905 zcmcG%2|QH)_xL}HeH}a521SuI`!aLK8p)a{*|(H^7s(p3WJ##VRw*h`DOm=SC0UZU zB_$+URH#r{{`U?|5`EsE@Bj0AJ>EC-m^*Xt^PJatopWC2^}6%+@$~eA!KU(HFqk6@ zk$DR|e8AUO@PLDd9vS$L6ATfa1cR|h!r%)ukpUby>B$?Yp6y+idESF(|5ZB)gDzxz z#16IxCP%!oBlJD;ecG;WPAsmzzWz?qQi?Xd?sjf&5qhHt{ip(_xt0)sh#7tjL_ z;*~&d#{YErLQ@fA&oUx2=}dXx~aXitRHUA+zr{%Q3U36jFk=ctWW z&~F!or+}Y=Ff(BQ48{PX245m@32jC7$tVQ)4m8svxF5Twp|)MNhwwe}jXdi|?N5NK7aIO{>T`a=$f@pmE_f!i!wz%#3;>K%3A z4L#THHH@7KZV10ApdK!HQGF~z1HAdaN1Xyc4YhR!@cS^>&;ZnNSIN{hd#(e&P)p(;0BKI;QF4N1<$Oa;;h28aSpvNaD%0b>O4Y+)w$ydxWW5(!5eRcdTWiX8iJo8 zHnQ`pFG#3#kgd9UcsTiNYOy(MEjE#2q&}%T4j=*7U%N<#EAIG=>yN3f?|u9NJVUbB zgDNv-@motGmAUx zV=B7=l1bEGb=1RM70JR4kX6?Ilk)>S^V5d+Yv{jRYqQwoi4uiMf$RtYF_~D=F42(ty{4~@^ 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z(NF{5(xd#17MhtZ;#c9~HRUhr3(eC!6%Mz?y$<^oNp;Zz;BP|9Sn( z#5UxD*J}QpghEv6Kxmmu_o(7rCDx7tTu$kAuvJ0)Ri@cNd0OvM<+b7QATh4)z^JL` zCf7OmaaU5BBMu(RA#MbENh41RUz zCz=sd41u)^ajzkA4a@e3_bK~a{0x+%?P0f3u>oIWGm#W3-2q+Ygb$^zjj+sais4Od zeE7YS=}5?f`m?emXin#i{=4TrPWFd;T|*q(f+w7sEjg2){I*83XF(E7pdbxaRR~SU zI{x7sq#J#s_=949Yt*ucmCP-E$mI{Q$r{?I=ek}~C4~!K*k-HI|(6)^nX~uarBvxl3BPbdCtOw;MdW|Fo{^=tz z=5+1WjS+w3+5y&*)512i_I_+A0SX`$m#&yHhmOCccHkJ8IAkOUJs2p&?w~;Z>x*wB5-o?Fdwpjk8p^6|U>3?9fjb>L+F4y&}VhHG@LS%0^oni4D zt+&^Jl%#qSZ+>UqC)nGNt0?q$VflhvcCI7=B%i7vo5!t%Ad06pq3z@h%nAzKNx;iL1Pk literal 0 HcmV?d00001 From a90904f8cedda0aca8dcd9b5e4880b9f5e4d2e1e Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Thu, 16 Sep 2021 16:11:31 -0700 Subject: [PATCH 07/59] [skip ci] bump version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 1ea2ab5b..cd813eba 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.6.1" +version = "0.6.2" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From 2a9e4ca20a0fd41873a18737f6a429b28c7acb2c Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Thu, 16 Sep 2021 18:34:01 -0700 Subject: [PATCH 08/59] add more basic types (#110) --- src/iteration.jl | 1 + src/root.jl | 14 +++++--- test/runtests.jl | 6 ++++ test/samples/tree_basictypes.py | 57 ++++++++++++++++++++++++++++++ test/samples/tree_basictypes.root | Bin 0 -> 9106 bytes 5 files changed, 73 insertions(+), 5 deletions(-) create mode 100644 test/samples/tree_basictypes.py create mode 100644 test/samples/tree_basictypes.root diff --git a/src/iteration.jl b/src/iteration.jl index 1cfee31b..776c51a8 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -97,6 +97,7 @@ mutable struct LazyBranch{T,J,B} <: AbstractVector{T} function LazyBranch(f::ROOTFile, b::Union{TBranch,TBranchElement}) T, J = auto_T_JaggT(f, b; customstructs=f.customstructs) + T = (T === Vector{Bool} ? BitVector : T) _buffer = J === Nojagg ? T[] : VectorOfVectors(T(), Int32[1]) return new{T,J,typeof(_buffer)}(f, b, length(b), b.fBasketEntry, diff --git a/src/root.jl b/src/root.jl index 3d38ded2..0969072a 100644 --- a/src/root.jl +++ b/src/root.jl @@ -127,11 +127,11 @@ end function Base.getindex(f::ROOTFile, s::AbstractString) S = _getindex(f, s) if S isa Union{TBranch, TBranchElement} - try # if we can't construct LazyBranch, just give up (maybe due to custom class) + # try # if we can't construct LazyBranch, just give up (maybe due to custom class) return LazyBranch(f, S) - catch - @warn "Can't automatically create LazyBranch for branch $s. Returning a branch object" - end + # catch + # @warn "Can't automatically create LazyBranch for branch $s. Returning a branch object" + # end end S end @@ -366,9 +366,13 @@ function auto_T_JaggT(f::ROOTFile, branch; customstructs::Dict{String, Type}) elseif elname == "unsigned int" UInt32 elseif elname == "unsigned char" - Char + UInt8 elseif elname == "unsigned short" UInt16 + elseif elname == "unsigned long" + UInt64 + elseif elname == "long64" + Int64 elseif elname == "ulong64" UInt64 else diff --git a/test/runtests.jl b/test/runtests.jl index 36e682fb..b5ffb36b 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -676,3 +676,9 @@ end f = UnROOT.samplefile("issue11_tdirectory.root") @test sum(f["Data/mytree/Particle0_E"]) ≈ 1012.0 end + +@testset "Basic C++ types" begin + f = UnROOT.samplefile("tree_basictypes.root") + onesrow = LazyTree(f,"t")[2] |> values .|> first .|> Int + @test all(onesrow .== 1) +end diff --git a/test/samples/tree_basictypes.py b/test/samples/tree_basictypes.py new file mode 100644 index 00000000..5340be9b --- /dev/null +++ b/test/samples/tree_basictypes.py @@ -0,0 +1,57 @@ +import ROOT as r + +# from https://en.cppreference.com/w/cpp/language/types +typenames = [ + # char + "char", "unsigned char", + # bool + "bool", + # short + "short", "short int", "signed short", "signed short int", "unsigned short", "unsigned short int", + # int + "int", "signed", "signed int", "unsigned", "unsigned int", + # long + "long", "long int", "long int", "signed long", "signed long int", "unsigned long", "unsigned long int", + # long long + "long long", "long long int", "signed long long", "signed long long int", "unsigned long long", "unsigned long long int", + # float/double + "float", "double", + ] + +print(len(typenames), typenames) + +roottypestrs = set() +for typename in typenames: + obj = r.vector(typename) + # print(typename, obj, obj()) + roottypestr = str(obj).split("'")[1].split("<")[1].split(">")[0] + roottypestrs.add(roottypestr) + +# since many of the above map to the same "root type", `roottypestrs` ends up being + +# {'long', 'Long64_t', 'unsigned char', 'short', 'unsigned long', 'long double', +# 'char', 'unsigned short', 'ULong64_t', 'float', 'bool', 'double', +# 'int', 'unsigned int'} + +print(len(roottypestrs), roottypestrs) + +import ROOT as r +f = r.TFile("tree_basictypes.root", "recreate") +t = r.TTree("t", "") + +d_objs = dict() +for typename in roottypestrs: + nicename = typename.lower().replace("_t","").replace(" ","") + obj = r.vector(typename)() + t.Branch(nicename, obj) + d_objs[typename] = obj + +for ievt in range(3): + for typename, obj in d_objs.items(): + obj.clear() + for _ in range(ievt): + obj.push_back(1) + t.Fill() + +t.Write() +f.Close() diff --git a/test/samples/tree_basictypes.root b/test/samples/tree_basictypes.root new file mode 100644 index 0000000000000000000000000000000000000000..ba0da600c5be4461bc48a48dc0cbd21b30ea7ce8 GIT binary patch literal 9106 zcmbVS1yo$wvTfXP0gr~%>`ZZa0K89@A!q;qoQAZmgC&le ztEHu}nJL)T+|B!?C78|ik7 zRA{Kjpgp?!Xj};*x)6CBul@!2k@C}kf<*Rd`~i&W?gX~AcCxhi8v>61HGxMEEr^)@ 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z^F{p8L4pK$RBOjsAvvYfLXD{eV@UHAuBlkmPJS7+E~Sn7&J4SHBwr>2WzSf=nm;b_ z;`H7@(ZkuI@jQ7r_q4N9#cuz8LJUt0$UWGbE&Lo;IflL>OmaI_QnW1e3~G*&f8^Jc zLMv70X`(v<@hMY+_(63v9^iAp;du$0fu*w@o(JCw32!+|ngo|pwIVD_t({zvQX2`Y zTn@2WPDQlf$OlA%@(sN+d}YLw&14esg9=M(uaGm3Lb#svTB9E|Oi)Z|LJZ278VMeJDBYn-} zN%BotxT{{y1MTWFPM<2dkicN9@XJ_6zAPk^n%!bbMpi@}g(zIb9St&C0wrb^Qp`ca z%-U7m)GG0pqhwj*`fF%vSlrn1#~SW<<%F4=+x^{*1M#>PBA3?`Sz0kcRb{`|kr>?B}4s&071jYOT zd0khwTOv2gxzlFa3>KNpmxNrr+uXVWH(Mi=|5PEX49Zt-y|tIj-I~=I@I%>(+L(y3 zC3Q1?pw23?wg&s%pw6}13%f?f{p6*7@K{dRr{bYzeI94~QIS+I||u z%1|=5pfEkCA$+AT-z2HSz^^l)BSrwgC%dH?%Bm0EuOrNm{&67CvE3;0>({%Z>ze4asv94?`zuupRKy`D!sm(l@=Z#N0O(Qk2Fw;llU>fmh18nEHh zE)DvpmEoriDUi)0Pb Date: Fri, 17 Sep 2021 14:16:22 -0700 Subject: [PATCH 09/59] iterate on baskets + an optimization (#111) * iterate on baskets * 10-50% speedup for simple benchmarks * simplify --- src/bootstrap.jl | 1 + src/iteration.jl | 41 ++++++++++++++++++++++++++++++----------- test/runtests.jl | 8 ++++++++ 3 files changed, 39 insertions(+), 11 deletions(-) diff --git a/src/bootstrap.jl b/src/bootstrap.jl index 4afbda67..8768bb34 100644 --- a/src/bootstrap.jl +++ b/src/bootstrap.jl @@ -418,6 +418,7 @@ function Base.hash(b::Union{TBranch, TBranchElement}, h::UInt) end Base.length(b::Union{TBranch, TBranchElement}) = b.fEntries Base.eachindex(b::Union{TBranch, TBranchElement}) = Base.OneTo(b.fEntries) +numbaskets(b::Union{TBranch, TBranchElement}) = findfirst(x->x>(b.fEntries-1),b.fBasketEntry)-1 function Base.eltype(b::Union{TBranch, TBranchElement}) T, jagT = interp_jaggT(b) jagT === Nojagg ? T : Vector{T} diff --git a/src/iteration.jl b/src/iteration.jl index 776c51a8..0ff09b13 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -38,6 +38,7 @@ end """ basketarray(f::ROOTFile, path::AbstractString, ith) basketarray(f::ROOTFile, branch::Union{TBranch, TBranchElement}, ith) + basketarray(lb::LazyBranch, ith) Reads actual data from ith basket of a branch. This function first calls [`readbasket`](@ref) to obtain raw bytes and offsets of a basket, then calls [`auto_T_JaggT`](@ref) followed @@ -57,6 +58,16 @@ function basketarray(f::ROOTFile, branch, ithbasket) return interped_data(rawdata, rawoffsets, T, J) end +""" + basketarray_iter(f::ROOTFile, branch::Union{TBranch, TBranchElement}) + basketarray_iter(lb::LazyBranch) + +Returns a `Base.Generator` yielding the output of `basketarray()` for all baskets. +""" +function basketarray_iter(f::ROOTFile, branch) + return (basketarray(f, branch, i) for i in 1:numbaskets(branch)) +end + # function barrior to make getting individual index faster # TODO upstream some types into parametric types for Branch/BranchElement """ @@ -121,6 +132,9 @@ Base.firstindex(ba::LazyBranch) = 1 Base.lastindex(ba::LazyBranch) = ba.L Base.eltype(ba::LazyBranch{T,J,B}) where {T,J,B} = T +basketarray(lb::LazyBranch, ithbasket) = basketarray(lb.f, lb.b, ithbasket) +basketarray_iter(lb::LazyBranch) = basketarray_iter(lb.f, lb.b) + function Base.show(io::IO, lb::LazyBranch) summary(io, lb) println(io, ":") @@ -145,23 +159,28 @@ and update buffer and buffer range accordingly. moment, access a `LazyBranch` from different threads at the same time can cause performance issue and incorrect event result. """ + function Base.getindex(ba::LazyBranch{T,J,B}, idx::Integer) where {T,J,B} tid = Threads.threadid() - br = ba.buffer_range[tid] - if idx ∉ br - seek_idx = findfirst(x -> x > (idx - 1), ba.fEntry) - 1 #support 1.0 syntax - bb = basketarray(ba.f, ba.b, seek_idx) - if typeof(bb) !== B - error("Expected type of interpreted data: $(B), got: $(typeof(bb))") - end - ba.buffer[tid] = bb - br = (ba.fEntry[seek_idx] + 1):(ba.fEntry[seek_idx + 1]) - ba.buffer_range[tid] = br + br = @inbounds ba.buffer_range[tid] + localidx = if idx ∉ br + _localindex_newbasket!(ba, idx, tid) + else + idx - br.start + 1 end - localidx = idx - br.start + 1 return @inbounds ba.buffer[tid][localidx] end +function _localindex_newbasket!(ba::LazyBranch{T,J,B}, idx::Integer, tid::Int) where {T,J,B} + seek_idx = findfirst(x -> x > (idx - 1), ba.fEntry) - 1 #support 1.0 syntax + ba.buffer[tid] = basketarray(ba.f, ba.b, seek_idx) + br = (ba.fEntry[seek_idx] + 1):(ba.fEntry[seek_idx + 1]) + ba.buffer_range[tid] = br + return idx - br.start + 1 +end + +Base.IndexStyle(::Type{<:LazyBranch}) = IndexCartesian() + function Base.iterate(ba::LazyBranch{T,J,B}, idx=1) where {T,J,B} idx > ba.L && return nothing return (ba[idx], idx + 1) diff --git a/test/runtests.jl b/test/runtests.jl index b5ffb36b..510d36ab 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -682,3 +682,11 @@ end onesrow = LazyTree(f,"t")[2] |> values .|> first .|> Int @test all(onesrow .== 1) end + +@testset "basketarray_iter()" begin + f = UnROOT.samplefile("tree_with_vector_multiple_baskets.root") + t = LazyTree(f,"t1") + @test (UnROOT.basketarray_iter(f, f["t1"]["b1"]) .|> length) == [1228, 1228, 44] + @test (UnROOT.basketarray_iter(t.b1) .|> length) == [1228, 1228, 44] + @test length(UnROOT.basketarray(t.b1, 1)) == 1228 +end From 1d06a984e180aaadc9f83c9b62419e6d47a0f3df Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Sun, 26 Sep 2021 17:04:22 -0700 Subject: [PATCH 10/59] optimize TBasketKey unpacking (#115) * avoid slow merging * faster than in the try block * faster without dict * single read for rest of tkey bytes --- src/types.jl | 68 ++++++++++++++++++++++++++++++++++------------------ src/utils.jl | 1 + 2 files changed, 46 insertions(+), 23 deletions(-) diff --git a/src/types.jl b/src/types.jl index e7e29da6..613fa5f8 100644 --- a/src/types.jl +++ b/src/types.jl @@ -59,31 +59,53 @@ end function unpack(io, T::Type{TBasketKey}) start = position(io) - fields = Dict{Symbol, Union{Integer, String}}() - fields[:fNbytes] = readtype(io, Int32) - fields[:fVersion] = readtype(io, Int16) # FIXME if "complete" it's UInt16 (acc. uproot) - - inttype = fields[:fVersion] <= 1000 ? Int32 : Int64 - - fields[:fObjlen] = readtype(io, Int32) - fields[:fDatime] = readtype(io, UInt32) - fields[:fKeylen] = readtype(io, Int16) - fields[:fCycle] = readtype(io, Int16) - fields[:fSeekKey] = readtype(io, inttype) - fields[:fSeekPdir] = readtype(io, inttype) - fields[:fClassName] = readtype(io, String) - fields[:fName] = readtype(io, String) - fields[:fTitle] = readtype(io, String) + + fNbytes = readtype(io, Int32) + fVersion = readtype(io, Int16) # FIXME if "complete" it's UInt16 (acc. uproot) + + inttype = fVersion <= 1000 ? Int32 : Int64 + + fObjlen = readtype(io, Int32) + fDatime = readtype(io, UInt32) + fKeylen = readtype(io, Int16) + + # do a single read to get rest of bytes into memory + # and offset by the 16 bytes we already read + io = IOBuffer(read(io, fKeylen - 16)) + start = -16 + + fCycle = readtype(io, Int16) + fSeekKey = readtype(io, inttype) + fSeekPdir = readtype(io, inttype) + fClassName = readtype(io, String) + fName = readtype(io, String) + fTitle = readtype(io, String) # if complete (which is true for compressed, it seems?) - seek(io, start + fields[:fKeylen] - 18 - 1) - fields[:fVersion] = readtype(io, Int16) # FIXME if "complete" it's UInt16 (acc. uproot) - fields[:fBufferSize] = readtype(io, Int32) - fields[:fNevBufSize] = readtype(io, Int32) - fields[:fNevBuf] = readtype(io, Int32) - fields[:fLast] = readtype(io, Int32) - - T(; fields...) + seek(io, start + fKeylen - 18 - 1) + fVersion = readtype(io, Int16) # FIXME if "complete" it's UInt16 (acc. uproot) + fBufferSize = readtype(io, Int32) + fNevBufSize = readtype(io, Int32) + fNevBuf = readtype(io, Int32) + fLast = readtype(io, Int32) + + T( + fNbytes, + fVersion, + fObjlen, + fDatime, + fKeylen, + fCycle, + fSeekKey, + fSeekPdir, + fClassName, + fName, + fTitle, + fBufferSize, + fNevBufSize, + fNevBuf, + fLast, + ) end iscompressed(t::T) where T<:Union{TKey, TBasketKey} = t.fObjlen != t.fNbytes - t.fKeylen diff --git a/src/utils.jl b/src/utils.jl index 8c63d395..8aeb1e39 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -60,6 +60,7 @@ function JaggType(f, branch, leaf) # https://github.com/scikit-hep/uproot3/blob/54f5151fb7c686c3a161fbe44b9f299e482f346b/uproot3/interp/auto.py#L144 (match(r"\[.*\]", leaf.fTitle) !== nothing) && return Nooffsetjagg leaf isa TLeafElement && leaf.fLenType==0 && return Offsetjagg + !hasproperty(branch, :fClassName) && return Nojagg try streamer = streamerfor(f, branch.fClassName).streamer.fElements.elements[1] From d2f639cefa221806d7401cc4f3695f8d2782e015 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Mon, 27 Sep 2021 10:27:30 -0700 Subject: [PATCH 11/59] default byte for fIOFeatures (#117) --- src/bootstrap.jl | 2 +- test/runtests.jl | 5 +++++ test/samples/issue116.root | Bin 0 -> 26048 bytes 3 files changed, 6 insertions(+), 1 deletion(-) create mode 100644 test/samples/issue116.root diff --git a/src/bootstrap.jl b/src/bootstrap.jl index 8768bb34..dbe24b66 100644 --- a/src/bootstrap.jl +++ b/src/bootstrap.jl @@ -639,7 +639,7 @@ end fWriteBasket fEntryNumber - fIOFeatures + fIOFeatures=0x00 fOffset fMaxBaskets diff --git a/test/runtests.jl b/test/runtests.jl index 510d36ab..4c8eed05 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -544,6 +544,11 @@ end @test rootfile["tree/trk_algoMask"][2] == [0x0000000000004000, 0x0000000000004000, 0x0000000000004000, 0x0000000000004000] @test rootfile["tree/pix_ladder"][3][1:5] == UInt16[0x0001, 0x0001, 0x0001, 0x0001, 0x0003] close(rootfile) + + # issue 116 + rootfile = ROOTFile(joinpath(SAMPLES_DIR, "issue116.root")) + 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z590+Q?;{50#TpU!Zyxmks6K%a^DovEjL}ZC_6UnFkJUL?QzY|?knd%1lXTb4!ozk1 z^*CB6{^aaR@|JwN2@|u6L6t0XNIn!(Cy Date: Mon, 27 Sep 2021 13:27:49 -0400 Subject: [PATCH 12/59] bump --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index cd813eba..f7325c2d 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.6.2" +version = "0.6.3" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From 514187dd4ca882e431b58710509ae8cafc05deba Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Tue, 28 Sep 2021 00:34:18 -0700 Subject: [PATCH 13/59] basket cluster iteration utilities (#118) * add some functions * add tests * fix --- Project.toml | 1 + src/UnROOT.jl | 1 + src/iteration.jl | 26 ++++++++++++++++++++++++++ test/runtests.jl | 12 ++++++++++++ test/samples/tree_with_clusters.py | 19 +++++++++++++++++++ test/samples/tree_with_clusters.root | Bin 0 -> 64439 bytes 6 files changed, 59 insertions(+) create mode 100644 test/samples/tree_with_clusters.py create mode 100644 test/samples/tree_with_clusters.root diff --git a/Project.toml b/Project.toml index f7325c2d..9396b1a9 100644 --- a/Project.toml +++ b/Project.toml @@ -10,6 +10,7 @@ CodecLz4 = "5ba52731-8f18-5e0d-9241-30f10d1ec561" CodecXz = "ba30903b-d9e8-5048-a5ec-d1f5b0d4b47b" CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193" CodecZstd = "6b39b394-51ab-5f42-8807-6242bab2b4c2" +IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e" LRUCache = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637" LorentzVectors = "3f54b04b-17fc-5cd4-9758-90c048d965e3" Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" diff --git a/src/UnROOT.jl b/src/UnROOT.jl index 2e58975c..9c08e5cb 100644 --- a/src/UnROOT.jl +++ b/src/UnROOT.jl @@ -10,6 +10,7 @@ import AbstractTrees: children, printnode, print_tree using CodecZlib, CodecLz4, CodecXz, CodecZstd, StaticArrays, LorentzVectors, ArraysOfArrays using Mixers, Parameters, Memoization, LRUCache +import IterTools: groupby import Tables, TypedTables, PrettyTables diff --git a/src/iteration.jl b/src/iteration.jl index 0ff09b13..67766c78 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -307,3 +307,29 @@ end function Base.getindex(ba::LazyBranch{T,J,B}, rang::UnitRange) where {T,J,B} return [ba[i] for i in rang] end + +_clusterranges(t::LazyTree) = _clusterranges([getproperty(t,p) for p in propertynames(t)]) +function _clusterranges(lbs::AbstractVector{<:LazyBranch}) + basketentries = [lb.b.fBasketEntry[1:numbaskets(lb.b)+1] for lb in lbs] + common = mapreduce(Set, ∩, basketentries) |> collect |> sort + return [common[i]+1:common[i+1] for i in 1:length(common)-1] +end +_clusterbytes(t::LazyTree; kw...) = _clusterbytes([getproperty(t,p) for p in propertynames(t)]; kw...) +function _clusterbytes(lbs::AbstractVector{<:LazyBranch}; compressed=false) + basketentries = [lb.b.fBasketEntry[1:numbaskets(lb.b)+1] for lb in lbs] + common = mapreduce(Set, ∩, basketentries) |> collect |> sort + bytes = zeros(Float64, length(common)-1) + for lb in lbs + b = lb.b + finflate = compressed ? 1.0 : b.fTotBytes/b.fZipBytes + entries = b.fBasketEntry[1:numbaskets(b)+1] + basketbytes = b.fBasketBytes[1:numbaskets(b)+1] * finflate + iclusters = searchsortedlast.(Ref(common), entries[1:end-1]) + pairs = zip(iclusters, basketbytes) + sumbytes = [sum(last.(g)) for g in groupby(first, pairs)] + bytes .+= sumbytes + end + return bytes +end + +Tables.partitions(t::LazyTree) = (t[r] for r in _clusterranges(t)) diff --git a/test/runtests.jl b/test/runtests.jl index 4c8eed05..2990c11d 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -695,3 +695,15 @@ end @test (UnROOT.basketarray_iter(t.b1) .|> length) == [1228, 1228, 44] @test length(UnROOT.basketarray(t.b1, 1)) == 1228 end + +@testset "Cluster ranges" begin + t = LazyTree(UnROOT.samplefile("tree_with_clusters.root"),"t1"); + @test all(UnROOT._clusterbytes(t; compressed=true) .< 10000) + @test all(UnROOT._clusterbytes(t; compressed=false) .< 10000) + @test UnROOT._clusterbytes([t.b1,t.b2]) == UnROOT._clusterbytes(t) + @test length(UnROOT._clusterranges([t.b1])) == 157 + @test length(UnROOT._clusterranges([t.b2])) == 70 + @test length(UnROOT._clusterranges(t)) == 18 # same as uproot4 + @test sum(UnROOT._clusterbytes([t.b1]; compressed=true)) == 33493.0 # same as uproot4 + @test sum(UnROOT._clusterbytes([t.b2]; compressed=true)) == 23710.0 # same as uproot4 +end diff --git a/test/samples/tree_with_clusters.py b/test/samples/tree_with_clusters.py new file mode 100644 index 00000000..8b83fd2c --- /dev/null +++ b/test/samples/tree_with_clusters.py @@ -0,0 +1,19 @@ +#!/usr/bin/env python +import ROOT as r + +f = r.TFile("tree_with_clusters.root", "recreate") +t = r.TTree("t1","t1") +v1 = r.vector("int")() +v2 = r.vector("int")() +t.Branch("b1", v1, 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zA$0v%_gwwiYn7qcZ@4CH=Y_Hnt%HS9E974Yq(87P zFnBamMS(vs`Yx6vVY7|X6@{PIZxZ#bmISDi&8Ik1|T%zj18IZU5LV@Fy&wGQfm%uWZ9 z1SEl;&yfqyEJBK(;91pc)!8e}tkTC;W>!yIqv5Y~HANlp(G<0pjhk3ERFf&rSv`qa zD!Rr&cB^oT(RweRXqxW9=d`cN-AsD4vo|gbkCsxZb6p?l?y*y=lDJrUEwDrti?BQU zo`6DR?IwLxt?DifeTt_1`p`XPs;H<8!KD$Z_Q;gQy5g`N$Ec{H{f%tZvq`b%$bH0% z_Vps0QLxE`Ht+Aw-KS3X%BLg~y!l0!x1!3$bdAg)eW-;zmRW#nLp+mGd6x~DO%s|I zxeQh5;2009bWBi{ZinTlN+)A&XO3!OXKcmldq4n_x}JDqAaKY literal 0 HcmV?d00001 From 4a9c9b3a8a0dca6dc1b56edbf9cca5b878b11a50 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Fri, 1 Oct 2021 10:50:37 -0700 Subject: [PATCH 14/59] match DataFrames behavior for `show` (#121) --- src/displays.jl | 6 +++++- test/runtests.jl | 5 +++++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/src/displays.jl b/src/displays.jl index f8f42228..b7572750 100644 --- a/src/displays.jl +++ b/src/displays.jl @@ -53,7 +53,9 @@ printnode(io::IO, f::ROOTFile) = print(io, f.filename) printnode(io::IO, f::ROOTDirectory) = print(io, "$(f.name) (TDirectory)") printnode(io::IO, k::TKeyNode) = print(io, "$(k.name) ($(k.classname))") -function Base.show(io::IO, tree::LazyTree) +Base.show(tree::LazyTree; kwargs...) = _show(stdout, tree; crop=:both, kwargs...) +Base.show(io::IO, tree::LazyTree; kwargs...) = _show(io, tree; kwargs...) +function _show(io::IO, tree::LazyTree; kwargs...) _hs = _make_header(tree) _ds = displaysize(io) PrettyTables.pretty_table( @@ -70,7 +72,9 @@ function Base.show(io::IO, tree::LazyTree) compact_printing=false, formatters=(v, i, j) -> _treeformat(v, _ds[2] ÷ min(8, length(_hs[1]))), display_size=(min(_ds[1], 40), min(_ds[2], 160)), + kwargs... ) + nothing end _symtup2str(symtup, trunc=15) = collect(first.(string.(symtup), trunc)) function _make_header(t) diff --git a/test/runtests.jl b/test/runtests.jl index 2990c11d..005ab4a7 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -366,6 +366,11 @@ end show(_io, t.Muon_pt[1:10]) s = repr(t[1:10]) @test length(collect(eachmatch(r"Float32\[", s))) == 0 + _io = IOBuffer() + show(_io, t) + @test length(split(String(take!(_io)),'\n')) > length(t) + show(_io, t; crop=:both) + @test length(split(String(take!(_io)),'\n')) <= Base.displaysize()[1] close(f) end From fe7edd969264d3b5fbb45064ea430bb768ce3574 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Fri, 1 Oct 2021 19:46:18 -0700 Subject: [PATCH 15/59] add interface function (#124) --- src/iteration.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/iteration.jl b/src/iteration.jl index 67766c78..99248be7 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -332,4 +332,5 @@ function _clusterbytes(lbs::AbstractVector{<:LazyBranch}; compressed=false) return bytes end +Tables.columns(t::LazyTree) = NamedTuple((p, getproperty(t, p)) for p in propertynames(t)) Tables.partitions(t::LazyTree) = (t[r] for r in _clusterranges(t)) From 6c481389aab9067e6d6192d3f3b90d6aa20843fa Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Sat, 2 Oct 2021 17:16:06 -0700 Subject: [PATCH 16/59] lower bound for PrettyTables (#125) --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 9396b1a9..4691a2d3 100644 --- a/Project.toml +++ b/Project.toml @@ -35,7 +35,7 @@ Memoization = "^0.1.10" Mixers = "^0.1.0" Parameters = "^0.12.0" Polyester = "^0.4.2" -PrettyTables = "^1.0.0" +PrettyTables = "^1.2.0" Requires = "^1" StaticArrays = "^0.12.0, ^1" Tables = "^1.0.0" From 4f6e62d97bdce7a6445d3e56d7f61d265cafea27 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Sun, 3 Oct 2021 23:56:48 -0700 Subject: [PATCH 17/59] optimize and return VoV (#122) --- src/iteration.jl | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/iteration.jl b/src/iteration.jl index 99248be7..9029fa15 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -303,9 +303,12 @@ function Base.iterate(tree::T, idx=1) where {T<:LazyTree} return LazyEvent(innertable(tree), idx), idx + 1 end -# TODO this is not terribly slow, but we can get faster implementation still ;) -function Base.getindex(ba::LazyBranch{T,J,B}, rang::UnitRange) where {T,J,B} - return [ba[i] for i in rang] +function Base.getindex(ba::LazyBranch{T,J,B}, range::UnitRange) where {T,J,B} + ib1 = findfirst(x -> x > (first(range) - 1), ba.fEntry) - 1 + ib2 = findfirst(x -> x > (last(range) - 1), ba.fEntry) - 1 + offset = ba.fEntry[ib1] + range = (first(range)-offset):(last(range)-offset) + return vcat([basketarray(ba, i) for i in ib1:ib2]...)[range] end _clusterranges(t::LazyTree) = _clusterranges([getproperty(t,p) for p in propertynames(t)]) From 2334368116a34ee7d55ac9cbf9978ae0daee8376 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Mon, 4 Oct 2021 16:40:34 -0400 Subject: [PATCH 18/59] add broadcasting fusion (#126) * add broadcasting fusion * fix allocation and let getindex be lazy * better lazyevent display * fix CI * add tree displaying tests --- Project.toml | 2 +- src/displays.jl | 1 + src/iteration.jl | 31 +++++++++++++++++++------------ test/runtests.jl | 25 +++++++++++++++++++++++-- 4 files changed, 44 insertions(+), 15 deletions(-) diff --git a/Project.toml b/Project.toml index 4691a2d3..cd0ac60b 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.6.3" +version = "0.7.0" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" diff --git a/src/displays.jl b/src/displays.jl index b7572750..941b3b6d 100644 --- a/src/displays.jl +++ b/src/displays.jl @@ -55,6 +55,7 @@ printnode(io::IO, k::TKeyNode) = print(io, "$(k.name) ($(k.classname))") Base.show(tree::LazyTree; kwargs...) = _show(stdout, tree; crop=:both, kwargs...) Base.show(io::IO, tree::LazyTree; kwargs...) = _show(io, tree; kwargs...) +Base.show(io::IO, ::MIME"text/plain", tree::LazyTree) = _show(io, tree) function _show(io::IO, tree::LazyTree; kwargs...) _hs = _make_header(tree) _ds = displaysize(io) diff --git a/src/iteration.jl b/src/iteration.jl index 9029fa15..d009c93b 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -179,14 +179,18 @@ function _localindex_newbasket!(ba::LazyBranch{T,J,B}, idx::Integer, tid::Int) w return idx - br.start + 1 end -Base.IndexStyle(::Type{<:LazyBranch}) = IndexCartesian() +Base.IndexStyle(::Type{<:LazyBranch}) = IndexLinear() function Base.iterate(ba::LazyBranch{T,J,B}, idx=1) where {T,J,B} idx > ba.L && return nothing return (ba[idx], idx + 1) end -struct LazyTree{T} +struct LazyEvent{T<:TypedTables.Table} + tree::T + idx::Int64 +end +struct LazyTree{T} <: AbstractVector{LazyEvent{T}} treetable::T end @@ -195,15 +199,18 @@ end Base.propertynames(lt::LazyTree) = propertynames(innertable(lt)) Base.getproperty(lt::LazyTree, s::Symbol) = getproperty(innertable(lt), s) -# a specific branch -Base.getindex(lt::LazyTree, row::Int) = innertable(lt)[row] +Base.broadcastable(lt::LazyTree) = lt +Base.IndexStyle(::Type{<:LazyTree}) = IndexLinear() +Base.getindex(lt::LazyTree, row::Int) = LazyEvent(innertable(lt), row) +# kept lazy for broadcasting purpose +Base.getindex(lt::LazyTree, row::CartesianIndex{1}) = LazyEvent(innertable(lt), row[1]) function Base.getindex(lt::LazyTree, rang::UnitRange) return LazyTree(innertable(lt)[rang]) end -Base.getindex(lt::LazyTree, ::typeof(!), s::Symbol) = lt[:, s] -Base.getindex(lt::LazyTree, ::Colon, s::Symbol) = getproperty(innertable(lt), s) # the real deal # a specific event +Base.getindex(lt::LazyTree, ::typeof(!), s::Symbol) = lt[:, s] +Base.getindex(lt::LazyTree, ::Colon, s::Symbol) = getproperty(innertable(lt), s) # the real deal Base.getindex(lt::LazyTree, row::Int, col::Symbol) = lt[:, col][row] Base.getindex(lt::LazyTree, rows::UnitRange, col::Symbol) = lt[:, col][rows] Base.getindex(lt::LazyTree, ::Colon) = lt[1:end] @@ -220,6 +227,8 @@ Base.getindex(e::Iterators.Enumerate{LazyTree{T}}, row::Int) where T = (row, fir # interfacing Table Base.names(lt::LazyTree) = collect(String.(propertynames(innertable(lt)))) Base.length(lt::LazyTree) = length(innertable(lt)) +Base.ndims(::Type{<:LazyTree}) = 1 +Base.size(lt::LazyTree) = size(innertable(lt)) function getbranchnamesrecursive(obj) out = Vector{String}() @@ -282,17 +291,15 @@ function LazyTree(f::ROOTFile, s::AbstractString, branch::Union{AbstractString,R return LazyTree(f, s, [branch]) end -struct LazyEvent{T<:TypedTables.Table} - tree::T - idx::Int64 -end function Base.show(io::IO, evt::LazyEvent) idx = Core.getfield(evt, :idx) fields = propertynames(Core.getfield(evt, :tree)) nfields = length(fields) sfields = nfields < 20 ? ": $(fields)" : "" - show(io, "LazyEvent $(idx) with $(nfields) fields$(sfields)") + println(io, "UnROOT.LazyEvent at index $(idx) with $(nfields) columns:") + show(io, collect(evt)) end + function Base.getproperty(evt::LazyEvent, s::Symbol) @inbounds getproperty(Core.getfield(evt, :tree), s)[Core.getfield(evt, :idx)] end @@ -335,5 +342,5 @@ function _clusterbytes(lbs::AbstractVector{<:LazyBranch}; compressed=false) return bytes end -Tables.columns(t::LazyTree) = NamedTuple((p, getproperty(t, p)) for p in propertynames(t)) +Tables.columns(t::LazyTree) = Tables.columns(innertable(t)) Tables.partitions(t::LazyTree) = (t[r] for r in _clusterranges(t)) diff --git a/test/runtests.jl b/test/runtests.jl index 005ab4a7..b97c216c 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -368,7 +368,10 @@ end @test length(collect(eachmatch(r"Float32\[", s))) == 0 _io = IOBuffer() show(_io, t) - @test length(split(String(take!(_io)),'\n')) > length(t) + _iostring = String(take!(_io)) + @test length(split(_iostring,'\n')) > length(t) + @test occursin("───────", _iostring) + @test !occursin("NamedTuple", _iostring) show(_io, t; crop=:both) @test length(split(String(take!(_io)),'\n')) <= Base.displaysize()[1] close(f) @@ -689,7 +692,7 @@ end @testset "Basic C++ types" begin f = UnROOT.samplefile("tree_basictypes.root") - onesrow = LazyTree(f,"t")[2] |> values .|> first .|> Int + onesrow = LazyTree(f,"t")[2] |> collect |> values .|> first .|> Int @test all(onesrow .== 1) end @@ -712,3 +715,21 @@ end @test sum(UnROOT._clusterbytes([t.b1]; compressed=true)) == 33493.0 # same as uproot4 @test sum(UnROOT._clusterbytes([t.b2]; compressed=true)) == 23710.0 # same as uproot4 end + + +@static if VERSION > v"1.5.0" + @testset "Broadcast fusion" begin + rootfile = ROOTFile(joinpath(SAMPLES_DIR, "NanoAODv5_sample.root")) + t = LazyTree(rootfile, "Events", "nMuon") + testf(evt) = evt.nMuon == 4 + testf2(evt) = evt.nMuon == 4 + alloc1 = @allocated a1 = testf.(t) + alloc1 += @allocated a2 = testf2.(t) + alloc1 += @allocated idx1 = findall(a1 .& a2) + alloc2 = @allocated idx2 = findall(@. testf(t) & testf2(t)) + @assert !isempty(idx1) + @test idx1 == idx2 + # compiler optimization is good on 1.8 + @test alloc1 > 1.4*alloc2 + end +end From 20ddaa7bbed594df9e5985edd4f3e27f94756189 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Mon, 4 Oct 2021 18:27:22 -0400 Subject: [PATCH 19/59] Update Project.toml --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index cd0ac60b..e9dc09b4 100644 --- a/Project.toml +++ b/Project.toml @@ -29,6 +29,7 @@ CodecLz4 = "^0.3.0, ^0.4.0" CodecXz = "^0.6.0, ^0.7.0" CodecZlib = "^0.6.0, ^0.7.0" CodecZstd = "^0.6.0, ^0.7.0" +IterTools = "^1" LRUCache = "^1.3.0" LorentzVectors = "^0.4.0" Memoization = "^0.1.10" From 776eee714f3c96606e2e166e6e7943ae4275c221 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Mon, 4 Oct 2021 19:48:24 -0700 Subject: [PATCH 20/59] avoid intermediate array for lz4/zlib (#128) --- src/types.jl | 52 ++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 44 insertions(+), 8 deletions(-) diff --git a/src/types.jl b/src/types.jl index 613fa5f8..1526d179 100644 --- a/src/types.jl +++ b/src/types.jl @@ -127,6 +127,31 @@ function compressed_datastream(io, tkey) return read(io, tkey.fNbytes - tkey.fKeylen) end +function _decompress_zlib!(input_ptr, input_size, output_ptr, output_size) + # References: + # https://github.com/JuliaIO/CodecZlib.jl/blob/a777d8f53aebd223fe7c7399436a5050784d210f/src/libz.jl + # https://github.com/root-project/root/blob/87a998d48803bc207288d90038e60ff148827664/core/zip/src/RZip.cxx#L392 + zstream = CodecZlib.ZStream() + zstream.next_in = input_ptr + zstream.avail_in = input_size + zstream.next_out = output_ptr + zstream.avail_out = output_size + CodecZlib.inflate_init!(zstream, CodecZlib.Z_DEFAULT_WINDOWBITS) + while (err = CodecZlib.inflate!(zstream, CodecZlib.Z_FINISH) != CodecZlib.Z_STREAM_END) + if (err != CodecZlib.Z_OK) + CodecZlib.inflate_end!(zstream) + error(CodecZlib.zlib_error_message(zstream, err)) + end + end + CodecZlib.inflate_end!(zstream) + nothing +end + +function _decompress_lz4!(input_ptr, input_size, output_ptr, output_size) + CodecLz4.LZ4_decompress_safe(input_ptr, output_ptr, input_size, output_size) + nothing +end + """ decompress_datastreambytes(compbytes, tkey) @@ -147,19 +172,30 @@ function decompress_datastreambytes(compbytes, tkey) cname, _, compbytes, uncompbytes = unpack(compression_header) rawbytes = read(io, compbytes) - # indexing `0+1 to 0+2` are two bytes, no need to +1 in the second term - @view(uncomp_data[fufilled+1:fufilled+uncompbytes]) .= if cname == "ZL" - transcode(ZlibDecompressor, rawbytes) + if cname == "L4" + # skip checksum which is 8 bytes + # original: lz4_decompress(rawbytes[9:end], uncompbytes) + input = @view rawbytes[9:end] + input_ptr = pointer(input) + input_size = length(input) + output_ptr = pointer(uncomp_data) + fufilled + output_size = uncompbytes + _decompress_lz4!(input_ptr, input_size, output_ptr, output_size) + elseif cname == "ZL" + # original: @view(uncomp_data[fufilled+1:fufilled+uncompbytes]) .= transcode(ZlibDecompressor, rawbytes) + input_ptr = pointer(rawbytes) + input_size = length(rawbytes) + output_ptr = pointer(uncomp_data) + fufilled + output_size = uncompbytes + _decompress_zlib!(input_ptr, input_size, output_ptr, output_size) elseif cname == "XZ" - transcode(XzDecompressor, rawbytes) + @view(uncomp_data[fufilled+1:fufilled+uncompbytes]) .= transcode(XzDecompressor, rawbytes) elseif cname == "ZS" - transcode(ZstdDecompressor, rawbytes) - elseif cname == "L4" - # skip checksum which is 8 bytes - lz4_decompress(rawbytes[9:end], uncompbytes) + @view(uncomp_data[fufilled+1:fufilled+uncompbytes]) .= transcode(ZstdDecompressor, rawbytes) else error("Unsupported compression type '$(String(compression_header.algo))'") end + fufilled += uncompbytes end return uncomp_data From 961b1d1319e2c4a0534c10fe360465b1d6148b91 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Tue, 5 Oct 2021 05:06:39 -0700 Subject: [PATCH 21/59] test zstd compression (#129) * add zstd compression tests --- src/streamers.jl | 2 +- test/runtests.jl | 5 +++++ test/samples/tree_with_int_array_zstd.root | Bin 0 -> 4929 bytes test/samples/zstd_tree.py | 18 ++++++++++++++++++ 4 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 test/samples/tree_with_int_array_zstd.root create mode 100755 test/samples/zstd_tree.py diff --git a/src/streamers.jl b/src/streamers.jl index 4b14ffb3..e0f869f9 100644 --- a/src/streamers.jl +++ b/src/streamers.jl @@ -87,7 +87,7 @@ function Streamers(io) elseif cname == "XZ" IOBuffer(transcode(XzDecompressor, compressedbytes)) elseif cname == "ZS" - IOBuffer(transcode(ZstdDecompressor, io)) + IOBuffer(transcode(ZstdDecompressor, compressedbytes)) elseif cname == "L4" IOBuffer(lz4_decompress(compressedbytes[9:end], tkey.fObjlen)) else diff --git a/test/runtests.jl b/test/runtests.jl index b97c216c..2a922a83 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -183,6 +183,11 @@ end @test 100000 == length(arr) @test [0.0, 1.0588236, 2.1176472, 3.1764705, 4.2352943] ≈ arr[1:5] atol=1e-7 close(rootfile) + + rootfile = ROOTFile(joinpath(SAMPLES_DIR, "tree_with_int_array_zstd.root")) + arr = collect(rootfile["t1/a"]) + @test arr == 0:99 + close(rootfile) end @testset "ROOTDirectoryHeader" begin diff --git a/test/samples/tree_with_int_array_zstd.root b/test/samples/tree_with_int_array_zstd.root new file mode 100644 index 0000000000000000000000000000000000000000..82cbfcaa4edc45b006a505ba933d26c1fcf0fb86 GIT binary patch literal 4929 zcmb7IWmJ@1*S?3L2I&Urk`zf{5UHU%1w>$w7(!YJ=`JbhmKGQqRHOuk4ndHRp`}3( z9+CbAo*&=O_kH(Td!2i&`270V;brfMu&{Ubw1B(2!+k7#Jv^=NyJMomx5aF6hQIi4w*fdeD7Q!e;DP~h z#`rB7hK9y}q;Lt|#ZXSXJuiO~Shog-r2#)0`1b_j+|K`sPISd47 z0x;DF)dN5x2;goKytGUN6mfuNT5fXEj|)T>*VosJnT9upO2c9SSOIq6^G=@B{)Zpt zQhNn3@nNJ?>oTFm$1aNagV4LJOW4dGJHf;U zi~hfIPa6Dw@@h*CYCHcEsTt$6S3YdDi 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a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.7.0" +version = "0.7.1" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From 4a284bf032c46a92f497e38c7d3a8971087fa2e4 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Thu, 7 Oct 2021 12:41:59 -0700 Subject: [PATCH 23/59] custom html repr (#132) * custom html repr * limit columns too * consolidate text * reduce clutter Co-authored-by: Jerry Ling * Update src/displays.jl --- src/displays.jl | 36 +++++++++++++++++++++++++++++++++++- test/runtests.jl | 4 ++++ 2 files changed, 39 insertions(+), 1 deletion(-) diff --git a/src/displays.jl b/src/displays.jl index 941b3b6d..6c82e270 100644 --- a/src/displays.jl +++ b/src/displays.jl @@ -77,6 +77,39 @@ function _show(io::IO, tree::LazyTree; kwargs...) ) nothing end +function Base.show(io::IO, ::MIME"text/html", tree::LazyTree) + _hs = _make_header(tree) + maxrows = 10 + maxcols = 30 + nrow = length(tree) + t = @view innertable(tree)[1:min(maxrows,nrow)] + ncol = length(Tables.columns(t)) + withcommas(value) = reverse(join(join.(Iterators.partition(reverse(string(value)),3)),",")) + write(io, "

") + write(io, "$(withcommas(nrow)) rows × $(ncol) columns") + if (nrow > maxrows) && (ncol > maxcols) + write(io, " (omitted printing of $(withcommas(nrow-maxrows)) rows and $(ncol-maxcols) columns)") + elseif (nrow > maxrows) + write(io, " (omitted printing of $(withcommas(nrow-maxrows)) rows)") + elseif (ncol > maxcols) + write(io, " (omitted printing of $(ncol-maxcols) columns)") + end + write(io, "

") + PrettyTables.pretty_table( + io, + t; + header=_hs, + alignment=:l, + row_number_column_title="", + show_row_number=true, + compact_printing=false, + filters_col = ((_,i) -> i <= maxcols,), + formatters=(v, i, j) -> _treeformat(v, 100), + tf = PrettyTables.HTMLTableFormat(css = """th { color: #000; background-color: #fff; }"""), + backend=Val(:html), + ) + nothing +end _symtup2str(symtup, trunc=15) = collect(first.(string.(symtup), trunc)) function _make_header(t) pn = propertynames(t) @@ -86,7 +119,8 @@ function _make_header(t) end function _treeformat(val, trunc) s = if val isa AbstractArray{T} where T<:Integer - string(Int.(val)) + T = Int + replace(string(T.(val)), string(T)=>"") elseif val isa AbstractArray{T} where T<:AbstractFloat T = eltype(val) replace(string(round.(T.(val); sigdigits=3)), string(T)=>"") diff --git a/test/runtests.jl b/test/runtests.jl index 2a922a83..406d9bc0 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -379,6 +379,10 @@ end @test !occursin("NamedTuple", _iostring) show(_io, t; crop=:both) @test length(split(String(take!(_io)),'\n')) <= Base.displaysize()[1] + _io = IOBuffer() + show(_io, MIME"text/html"(), t) + _iostring = String(take!(_io)) + @test occursin("", _iostring) close(f) end From 0d1ed21d42ce64e7dfaf6836585bc57d205f312b Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Thu, 7 Oct 2021 21:02:45 -0400 Subject: [PATCH 24/59] add lazy Chain/Vcat for Tree (#131) --- Project.toml | 5 ++++- src/UnROOT.jl | 2 +- src/iteration.jl | 19 +++++++++++++++++-- test/runtests.jl | 29 ++++++++++++++++++++++++++--- 4 files changed, 48 insertions(+), 7 deletions(-) diff --git a/Project.toml b/Project.toml index 2ffff512..2e644fc2 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.7.1" +version = "0.7.2" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" @@ -12,12 +12,14 @@ CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193" CodecZstd = "6b39b394-51ab-5f42-8807-6242bab2b4c2" IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e" LRUCache = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637" +LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" LorentzVectors = "3f54b04b-17fc-5cd4-9758-90c048d965e3" Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" Mixers = "2a8e4939-dab8-5edc-8f64-72a8776f13de" Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a" PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" Requires = "ae029012-a4dd-5104-9daa-d747884805df" +SentinelArrays = "91c51154-3ec4-41a3-a24f-3f23e20d615c" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" @@ -31,6 +33,7 @@ CodecZlib = "^0.6.0, ^0.7.0" CodecZstd = "^0.6.0, ^0.7.0" IterTools = "^1" LRUCache = "^1.3.0" +LazyArrays = "^0.22, ^1" LorentzVectors = "^0.4.0" Memoization = "^0.1.10" Mixers = "^0.1.0" diff --git a/src/UnROOT.jl b/src/UnROOT.jl index 9c08e5cb..18b40412 100644 --- a/src/UnROOT.jl +++ b/src/UnROOT.jl @@ -1,6 +1,6 @@ module UnROOT -using Requires +using Requires, LazyArrays export ROOTFile, LazyBranch, LazyTree, @batch import Base: close, keys, get, getindex, getproperty, show, length, iterate, position, ntoh, lock, unlock, reinterpret diff --git a/src/iteration.jl b/src/iteration.jl index d009c93b..ff2b83a3 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -109,7 +109,13 @@ mutable struct LazyBranch{T,J,B} <: AbstractVector{T} function LazyBranch(f::ROOTFile, b::Union{TBranch,TBranchElement}) T, J = auto_T_JaggT(f, b; customstructs=f.customstructs) T = (T === Vector{Bool} ? BitVector : T) - _buffer = J === Nojagg ? T[] : VectorOfVectors(T(), Int32[1]) + _buffer = T[] + if J != Nojagg + # if branch is jagged, fix the buffer and eltype according to what + # VectorOfVectors would return in `getindex` + _buffer = VectorOfVectors(T(), Int32[1]) + T = SubArray{eltype(T), 1, T, Tuple{UnitRange{Int64}}, true} + end return new{T,J,typeof(_buffer)}(f, b, length(b), b.fBasketEntry, [_buffer for _ in 1:Threads.nthreads()], @@ -230,6 +236,15 @@ Base.length(lt::LazyTree) = length(innertable(lt)) Base.ndims(::Type{<:LazyTree}) = 1 Base.size(lt::LazyTree) = size(innertable(lt)) +function LazyArrays.Vcat(ts::LazyTree...) + cs = Tables.columns.(innertable.(ts)) + LazyTree(TypedTables.Table(map(Vcat, cs...))) +end +Base.vcat(ts::LazyTree...) = Vcat(ts...) +Base.reduce(::typeof(vcat), ts::AbstractVector{<:LazyTree}) = Vcat((ts)...) +Base.mapreduce(f::Function, ::typeof(vcat), ts::AbstractVector{<:LazyTree}) = Vcat(f.(ts)...) +Base.mapreduce(f::Function, ::typeof(Vcat), ts::AbstractVector{<:LazyTree}) = Vcat(f.(ts)...) + function getbranchnamesrecursive(obj) out = Vector{String}() for b in obj.fBranches.elements @@ -300,7 +315,7 @@ function Base.show(io::IO, evt::LazyEvent) show(io, collect(evt)) end -function Base.getproperty(evt::LazyEvent, s::Symbol) +@inline function Base.getproperty(evt::LazyEvent, s::Symbol) @inbounds getproperty(Core.getfield(evt, :tree), s)[Core.getfield(evt, :idx)] end Base.collect(evt::LazyEvent) = @inbounds Core.getfield(evt, :tree)[Core.getfield(evt, :idx)] diff --git a/test/runtests.jl b/test/runtests.jl index 406d9bc0..4a9c33dd 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -263,7 +263,8 @@ end branch = rootfile["t1/LVs"] tree = LazyTree(rootfile, "t1") - @test eltype(branch) === Vector{LorentzVectors.LorentzVector{Float64}} + @test eltype(branch) <: AbstractVector{LorentzVectors.LorentzVector{Float64}} + @test eltype(branch) <: SubArray @test length.(branch[1:10]) == 0:9 close(rootfile) end @@ -292,7 +293,7 @@ end rootfile = ROOTFile(joinpath(SAMPLES_DIR, "tree_with_jagged_array_double.root")) data = rootfile["t1/double_array"] @test data isa AbstractVector - @test eltype(data) === Vector{T} + @test eltype(data) <: AbstractVector{T} @test data[1] == T[] @test data[1:2] == [T[], T[0]] @test data[end] == T[90, 91, 92, 93, 94, 95, 96, 97, 98] @@ -317,7 +318,7 @@ end event = UnROOT.array(rootfile, "Events/event") @test event[1:3] == UInt64[12423832, 12423821, 12423834] Electron_dxy = rootfile["Events/Electron_dxy"] - @test eltype(Electron_dxy) == Vector{Float32} + @test eltype(Electron_dxy) == SubArray{Float32, 1, Vector{Float32}, Tuple{UnitRange{Int64}}, true} @test Electron_dxy[1:3] ≈ [Float32[0.0003705], Float32[-0.00981903], Float32[]] HLT_Mu3_PFJet40 = UnROOT.array(rootfile, "Events/HLT_Mu3_PFJet40") @test eltype(HLT_Mu3_PFJet40) == Bool @@ -677,6 +678,14 @@ end end @test count(>(0), nmus) > 1 # test @batch is actually threading @test sum(nmus) == 878 + + nmus .= 0 + t_dummy = LazyTree(ROOTFile(joinpath(SAMPLES_DIR, "NanoAODv5_sample.root")), "Events", ["Muon_pt"]) + @batch for evt in vcat(t,t_dummy) # avoid using the same underlying file handler + nmus[Threads.threadid()] += length(evt.Muon_pt) + end + @test sum(nmus) == 2*878 + for j in 1:3 inds = [Vector{Int}() for _ in 1:Threads.nthreads()] @batch for (i, evt) in enumerate(t) @@ -725,6 +734,20 @@ end @test sum(UnROOT._clusterbytes([t.b2]; compressed=true)) == 23710.0 # same as uproot4 end +@testset "Vcat/chaining" begin + rootfile = ROOTFile(joinpath(SAMPLES_DIR, "NanoAODv5_sample.root")) + t = LazyTree(rootfile, "Events", ["nMuon", "Muon_pt"]) + tt = vcat(t,t) + @test (@allocated vcat(t,t)) < 1000 + @test length(tt) == 2*length(t) + s1 = sum(t.nMuon) + s2 = sum(tt.nMuon) + @test s2 == 2*s1 + alloc1 = @allocated sum(length, t.Muon_pt) + alloc2 = @allocated sum(evt->length(evt.nMuon), tt) + @test alloc2 < 2.1 * alloc1 + close(rootfile) +end @static if VERSION > v"1.5.0" @testset "Broadcast fusion" begin From 0409b7c9560d34b20553b98834d128ce725a3be6 Mon Sep 17 00:00:00 2001 From: Moelf Date: Thu, 7 Oct 2021 21:03:42 -0400 Subject: [PATCH 25/59] remove unused --- Project.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/Project.toml b/Project.toml index 2e644fc2..1db6d673 100644 --- a/Project.toml +++ b/Project.toml @@ -19,7 +19,6 @@ Mixers = "2a8e4939-dab8-5edc-8f64-72a8776f13de" Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a" PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" Requires = "ae029012-a4dd-5104-9daa-d747884805df" -SentinelArrays = "91c51154-3ec4-41a3-a24f-3f23e20d615c" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" From 8c2c452ec7017559b00ff6789a7b338f3a553bd7 Mon Sep 17 00:00:00 2001 From: Moelf Date: Thu, 7 Oct 2021 21:07:49 -0400 Subject: [PATCH 26/59] fix compat --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 1db6d673..f94db293 100644 --- a/Project.toml +++ b/Project.toml @@ -32,7 +32,7 @@ CodecZlib = "^0.6.0, ^0.7.0" CodecZstd = "^0.6.0, ^0.7.0" IterTools = "^1" LRUCache = "^1.3.0" -LazyArrays = "^0.22, ^1" +LazyArrays = "^0.15, ^0.21, ^0.22, ^1" LorentzVectors = "^0.4.0" Memoization = "^0.1.10" Mixers = "^0.1.0" From 4d526eec11ed44fa4bbe4582bd0199a8f616b826 Mon Sep 17 00:00:00 2001 From: Moelf Date: Thu, 7 Oct 2021 22:46:56 -0400 Subject: [PATCH 27/59] remove ill-defined method --- src/bootstrap.jl | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/bootstrap.jl b/src/bootstrap.jl index dbe24b66..92ef2ea8 100644 --- a/src/bootstrap.jl +++ b/src/bootstrap.jl @@ -419,10 +419,6 @@ end Base.length(b::Union{TBranch, TBranchElement}) = b.fEntries Base.eachindex(b::Union{TBranch, TBranchElement}) = Base.OneTo(b.fEntries) numbaskets(b::Union{TBranch, TBranchElement}) = findfirst(x->x>(b.fEntries-1),b.fBasketEntry)-1 -function Base.eltype(b::Union{TBranch, TBranchElement}) - T, jagT = interp_jaggT(b) - jagT === Nojagg ? T : Vector{T} -end @with_kw struct TBranch_12 <: TBranch cursor::Cursor From ef0bae839ffe8cb7747f36cf5b727a6278cef5ab Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Thu, 7 Oct 2021 23:52:02 -0400 Subject: [PATCH 28/59] performance bug fix from Polyester --- Project.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index f94db293..822be732 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.7.2" +version = "0.7.3" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" @@ -37,7 +37,7 @@ LorentzVectors = "^0.4.0" Memoization = "^0.1.10" Mixers = "^0.1.0" Parameters = "^0.12.0" -Polyester = "^0.4.2" +Polyester = "^0.5.3" PrettyTables = "^1.2.0" Requires = "^1" StaticArrays = "^0.12.0, ^1" From 934b8dcaa02eb78a0a4670476c7ad2fb12518507 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Mon, 11 Oct 2021 21:36:06 -0400 Subject: [PATCH 29/59] remove Polyester (#134) --- Project.toml | 4 +--- README.md | 4 +--- docs/src/index.md | 19 +++++++------------ docs/src/performancetips.md | 24 ------------------------ src/UnROOT.jl | 8 ++------ src/iteration.jl | 4 ++-- src/polyester.jl | 8 -------- test/runtests.jl | 15 +-------------- 8 files changed, 14 insertions(+), 72 deletions(-) delete mode 100644 src/polyester.jl diff --git a/Project.toml b/Project.toml index 822be732..e6524dbd 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.7.3" +version = "0.8.0" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" @@ -18,7 +18,6 @@ Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" Mixers = "2a8e4939-dab8-5edc-8f64-72a8776f13de" Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a" PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" @@ -39,7 +38,6 @@ Mixers = "^0.1.0" Parameters = "^0.12.0" Polyester = "^0.5.3" PrettyTables = "^1.2.0" -Requires = "^1" StaticArrays = "^0.12.0, ^1" Tables = "^1.0.0" TypedTables = "^1.0.0" diff --git a/README.md b/README.md index cb662c03..b81f02c3 100644 --- a/README.md +++ b/README.md @@ -45,9 +45,7 @@ julia> for event in mytree end event.Electron_dxy = Float32[0.00037050247] -julia> using Polyester #optional dependency - -julia> @batch for event in mytree # multi-threading +julia> Threads.@threads for event in mytree # multi-threading ... end ``` diff --git a/docs/src/index.md b/docs/src/index.md index 2623912f..3d57fb4b 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -33,23 +33,18 @@ julia> for (i, event) in enumerate(mytree) end ``` -Both of which are compostable with `@batch` from `Polyester.jl` for multi-threading: +Both of which are compostable with `@threads` for multi-threading: ```julia -julia> using Polyester # need to install it first as it's an optional dependency - -julia> @batch for event in mytree +julia> Threads.@threads for event in mytree ... end -julia> @batch for (i, event) in enumerate(mytree) +julia> Threads.@threads for (i, event) in enumerate(mytree) ... end ``` -On finer control over `@batch`, such as batch size or per-core/thread, see [Polyester](https://github.com/JuliaSIMD/Polyester.jl)'s page. - Only one basket per branch will be cached so you don't have to worry about running out of RAM. -At the same time, `event` inside the for-loop is not materialized until a field is accessed. If your event -is fairly small or you need all of them anyway, you can `collect(event)` first inside the loop. +At the same time, `event` inside the for-loop is not materialized until a field is accessed. ## Laziness in Indexing, Slicing, and Looping Laziness (or eagerness) in UnROOT generally refers to if an "event" has read each branches of the tree or not. @@ -84,6 +79,6 @@ The laziness of the main interfaces are summarized below: | | `mytree` | `enumerate(mytree)` | | ---------------------- |:-----------:|:-------------------:| | `for X in ...` | 💤 | 💤 | -| `@threads for X in ...`| 🚨 | 💤 | -| `@batch for X in ...` | 💤 | 💤 | -| `getindex()` | 🚨 | 💤 | +| `@threads for X in ...`| 💤 | 💤 | +| `getindex(tree, row::Int)`| 💤 | N/A | +| `getindex(tree, row::Range)`| 🚨 | N/A | diff --git a/docs/src/performancetips.md b/docs/src/performancetips.md index 59ca1f95..555c3edb 100644 --- a/docs/src/performancetips.md +++ b/docs/src/performancetips.md @@ -15,27 +15,3 @@ for evt in mytree calculation(nmu) end ``` - -## `Threads.@threads` should go with `enumerate()` -tl;dr: just use `@batch` provided by [Polyester.jl](https://github.com/JuliaSIMD/Polyester.jl) since UnROOT -can customize behavior. - -Unlike `@batch`, there's not much we can do to customize behavior of `@threads`. It is essentially -calling `getindex()`, which we want to keep eager for regular use (e.v `mytree[120]` is eager). Thus, if for some -reason you want to use `@threads` instead of `@batch`, you should use it with `enumerate`: -```julia -julia> for evt in mytree - @show evt - break - end -evt = "LazyEvent with: (:tree, :idx)" - -julia> Threads.@threads for evt in mytree - @show evt - break - end -evt = (nMuon = 0x00000000, Muon_pt = Float32[]) -evt = (nMuon = 0x00000001, Muon_pt = Float32[3.4505641]) -evt = (nMuon = 0x00000000, Muon_pt = Float32[]) -evt = (nMuon = 0x00000002, Muon_pt = Float32[21.279676, 7.6710315]) -``` diff --git a/src/UnROOT.jl b/src/UnROOT.jl index 18b40412..04b1de76 100644 --- a/src/UnROOT.jl +++ b/src/UnROOT.jl @@ -1,7 +1,7 @@ module UnROOT -using Requires, LazyArrays -export ROOTFile, LazyBranch, LazyTree, @batch +using LazyArrays +export ROOTFile, LazyBranch, LazyTree import Base: close, keys, get, getindex, getproperty, show, length, iterate, position, ntoh, lock, unlock, reinterpret ntoh(b::Bool) = b @@ -30,8 +30,4 @@ include("iteration.jl") include("custom.jl") include("displays.jl") -function __init__() - @require Polyester="f517fe37-dbe3-4b94-8317-1923a5111588" include("polyester.jl") -end - end # module diff --git a/src/iteration.jl b/src/iteration.jl index ff2b83a3..f70eccb7 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -225,11 +225,11 @@ Base.lastindex(lt::LazyTree) = length(lt) Base.eachindex(lt::LazyTree) = 1:lastindex(lt) # allow enumerate() to be chunkable (eg with Threads.@threads) +Base.step(e::Iterators.Enumerate{LazyTree{T}}) where T = 1 Base.firstindex(e::Iterators.Enumerate{LazyTree{T}}) where T = firstindex(e.itr) Base.lastindex(e::Iterators.Enumerate{LazyTree{T}}) where T = lastindex(e.itr) Base.eachindex(e::Iterators.Enumerate{LazyTree{T}}) where T = eachindex(e.itr) -Base.getindex(e::Iterators.Enumerate{LazyTree{T}}, row::Int) where T = (row, first(iterate(e.itr, row))) - +Base.getindex(e::Iterators.Enumerate{LazyTree{T}}, row::Int) where T = (row, LazyEvent(innertable(e.itr), row)) # interfacing Table Base.names(lt::LazyTree) = collect(String.(propertynames(innertable(lt)))) Base.length(lt::LazyTree) = length(innertable(lt)) diff --git a/src/polyester.jl b/src/polyester.jl deleted file mode 100644 index 3f4b0b07..00000000 --- a/src/polyester.jl +++ /dev/null @@ -1,8 +0,0 @@ -# special Requires.jl syntax -import .Polyester: splitloop, combine, NoLoop - -splitloop(t::LazyTree) = NoLoop(), eachindex(t), t -combine(t::LazyTree, ::NoLoop, j) = LazyEvent(innertable(t), j) - -splitloop(e::Base.Iterators.Enumerate{LazyTree{T}}) where T = NoLoop(), eachindex(e.itr), e -combine(e::Iterators.Enumerate{LazyTree{T}}, ::NoLoop, j) where T = @inbounds e[j] diff --git a/test/runtests.jl b/test/runtests.jl index 4a9c33dd..6854bab4 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -658,19 +658,6 @@ end @test count(>(0), nmus) > 1 # test @threads is actually threading @test sum(nmus) == 878 - nmus .= 0 - @batch for (i, evt) in enumerate(t) - nmus[Threads.threadid()] += length(evt.Muon_pt) - end - @test count(>(0), nmus) > 1 # test @batch is actually threading - @test sum(nmus) == 878 - - event_nums = zeros(Int, Threads.nthreads()) - @batch for (i, evt) in enumerate(t) - event_nums[Threads.threadid()] += 1 - end - @test count(>(0), event_nums) > 1 # test @batch is actually threading - @test sum(event_nums) == length(t) nmus .= 0 @batch for evt in t @@ -688,7 +675,7 @@ end for j in 1:3 inds = [Vector{Int}() for _ in 1:Threads.nthreads()] - @batch for (i, evt) in enumerate(t) + Threads.@threads for (i, evt) in enumerate(t) push!(inds[Threads.threadid()], i) end @test sum([length(inds[i] ∩ inds[j]) for i=1:length(inds), j=1:length(inds) if j>i]) == 0 From 3cf9cd59e72f4b94f84f69a84f801d5722504b66 Mon Sep 17 00:00:00 2001 From: Moelf Date: Wed, 20 Oct 2021 23:05:36 -0400 Subject: [PATCH 30/59] add LazyTree(path) methods --- src/iteration.jl | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/iteration.jl b/src/iteration.jl index f70eccb7..e5fb5267 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -199,6 +199,9 @@ end struct LazyTree{T} <: AbstractVector{LazyEvent{T}} treetable::T end +function LazyTree(path::String, x...) + LazyTree(ROOTFile(path), x...) +end @inline innertable(t::LazyTree) = Core.getfield(t, :treetable) From 972e71da810ad0018d387a67292ff72a88de1b32 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Sat, 27 Nov 2021 10:38:13 -0600 Subject: [PATCH 31/59] use LibDeflate for zlib (#137) --- Project.toml | 4 ++-- src/UnROOT.jl | 4 +++- src/streamers.jl | 4 +++- src/types.jl | 41 +++++++++++++++++------------------------ 4 files changed, 25 insertions(+), 28 deletions(-) diff --git a/Project.toml b/Project.toml index e6524dbd..250cb20b 100644 --- a/Project.toml +++ b/Project.toml @@ -8,11 +8,11 @@ AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" ArraysOfArrays = "65a8f2f4-9b39-5baf-92e2-a9cc46fdf018" CodecLz4 = "5ba52731-8f18-5e0d-9241-30f10d1ec561" CodecXz = "ba30903b-d9e8-5048-a5ec-d1f5b0d4b47b" -CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193" CodecZstd = "6b39b394-51ab-5f42-8807-6242bab2b4c2" IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e" LRUCache = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637" LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" +LibDeflate = "9255714d-24a7-4b30-8ea3-d46a97f7e13b" LorentzVectors = "3f54b04b-17fc-5cd4-9758-90c048d965e3" Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" Mixers = "2a8e4939-dab8-5edc-8f64-72a8776f13de" @@ -27,11 +27,11 @@ AbstractTrees = "^0.3.0" ArraysOfArrays = "^0.5.3" CodecLz4 = "^0.3.0, ^0.4.0" CodecXz = "^0.6.0, ^0.7.0" -CodecZlib = "^0.6.0, ^0.7.0" CodecZstd = "^0.6.0, ^0.7.0" IterTools = "^1" LRUCache = "^1.3.0" LazyArrays = "^0.15, ^0.21, ^0.22, ^1" +LibDeflate = "^0.4.0" LorentzVectors = "^0.4.0" Memoization = "^0.1.10" Mixers = "^0.1.0" diff --git a/src/UnROOT.jl b/src/UnROOT.jl index 04b1de76..dc2cf173 100644 --- a/src/UnROOT.jl +++ b/src/UnROOT.jl @@ -8,10 +8,12 @@ ntoh(b::Bool) = b import AbstractTrees: children, printnode, print_tree -using CodecZlib, CodecLz4, CodecXz, CodecZstd, StaticArrays, LorentzVectors, ArraysOfArrays +using CodecLz4, CodecXz, CodecZstd, StaticArrays, LorentzVectors, ArraysOfArrays using Mixers, Parameters, Memoization, LRUCache import IterTools: groupby +import LibDeflate: unsafe_zlib_decompress!, Decompressor + import Tables, TypedTables, PrettyTables @static if VERSION < v"1.6" diff --git a/src/streamers.jl b/src/streamers.jl index e0f869f9..5a1e30a9 100644 --- a/src/streamers.jl +++ b/src/streamers.jl @@ -83,7 +83,9 @@ function Streamers(io) cname = String(compression_header.algo) if cname == "ZL" - IOBuffer(transcode(ZlibDecompressor, compressedbytes)) + output = Vector{UInt8}(undef, tkey.fObjlen) + _decompress_zlib!(output, compressedbytes, length(output)) + IOBuffer(output) elseif cname == "XZ" IOBuffer(transcode(XzDecompressor, compressedbytes)) elseif cname == "ZS" diff --git a/src/types.jl b/src/types.jl index 1526d179..cc41add8 100644 --- a/src/types.jl +++ b/src/types.jl @@ -127,24 +127,21 @@ function compressed_datastream(io, tkey) return read(io, tkey.fNbytes - tkey.fKeylen) end -function _decompress_zlib!(input_ptr, input_size, output_ptr, output_size) - # References: - # https://github.com/JuliaIO/CodecZlib.jl/blob/a777d8f53aebd223fe7c7399436a5050784d210f/src/libz.jl - # https://github.com/root-project/root/blob/87a998d48803bc207288d90038e60ff148827664/core/zip/src/RZip.cxx#L392 - zstream = CodecZlib.ZStream() - zstream.next_in = input_ptr - zstream.avail_in = input_size - zstream.next_out = output_ptr - zstream.avail_out = output_size - CodecZlib.inflate_init!(zstream, CodecZlib.Z_DEFAULT_WINDOWBITS) - while (err = CodecZlib.inflate!(zstream, CodecZlib.Z_FINISH) != CodecZlib.Z_STREAM_END) - if (err != CodecZlib.Z_OK) - CodecZlib.inflate_end!(zstream) - error(CodecZlib.zlib_error_message(zstream, err)) - end - end - CodecZlib.inflate_end!(zstream) - nothing +# Based on +# https://github.com/jakobnissen/LibDeflate.jl/blob/d172c4429404a6ce73b3d44541e80d6f69a0f38a/src/zlib.jl#L38 +function _decompress_zlib!( + output::AbstractArray{UInt8}, + input, + n_out::Integer +) + GC.@preserve output input unsafe_zlib_decompress!( + Base.HasLength(), + Decompressor(), + pointer(output), + n_out, + pointer(input), + sizeof(input) + ) end function _decompress_lz4!(input_ptr, input_size, output_ptr, output_size) @@ -182,12 +179,8 @@ function decompress_datastreambytes(compbytes, tkey) output_size = uncompbytes _decompress_lz4!(input_ptr, input_size, output_ptr, output_size) elseif cname == "ZL" - # original: @view(uncomp_data[fufilled+1:fufilled+uncompbytes]) .= transcode(ZlibDecompressor, rawbytes) - input_ptr = pointer(rawbytes) - input_size = length(rawbytes) - output_ptr = pointer(uncomp_data) + fufilled - output_size = uncompbytes - _decompress_zlib!(input_ptr, input_size, output_ptr, output_size) + output = @view(uncomp_data[fufilled+1:fufilled+uncompbytes]) + _decompress_zlib!(output, rawbytes, uncompbytes) elseif cname == "XZ" @view(uncomp_data[fufilled+1:fufilled+uncompbytes]) .= transcode(XzDecompressor, rawbytes) elseif cname == "ZS" From 29e206fdd9d5d72a956033767f4539919316e86f Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Sat, 27 Nov 2021 11:38:35 -0500 Subject: [PATCH 32/59] Update Project.toml LibDeflate fast! --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 250cb20b..02cf07eb 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.8.0" +version = "0.8.1" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From fe44d2b46fb5fc91b0e52a0a988df8e23df636a0 Mon Sep 17 00:00:00 2001 From: Nick Amin Date: Sat, 27 Nov 2021 18:19:31 -0600 Subject: [PATCH 33/59] use safe api for LibDeflate (#138) --- Project.toml | 2 +- src/UnROOT.jl | 2 +- src/streamers.jl | 2 +- src/types.jl | 19 +------------------ 4 files changed, 4 insertions(+), 21 deletions(-) diff --git a/Project.toml b/Project.toml index 02cf07eb..b2c4e8b6 100644 --- a/Project.toml +++ b/Project.toml @@ -31,7 +31,7 @@ CodecZstd = "^0.6.0, ^0.7.0" IterTools = "^1" LRUCache = "^1.3.0" LazyArrays = "^0.15, ^0.21, ^0.22, ^1" -LibDeflate = "^0.4.0" +LibDeflate = "^0.4.1" LorentzVectors = "^0.4.0" Memoization = "^0.1.10" Mixers = "^0.1.0" diff --git a/src/UnROOT.jl b/src/UnROOT.jl index dc2cf173..17c966b8 100644 --- a/src/UnROOT.jl +++ b/src/UnROOT.jl @@ -12,7 +12,7 @@ using CodecLz4, CodecXz, CodecZstd, StaticArrays, LorentzVectors, ArraysOfArrays using Mixers, Parameters, Memoization, LRUCache import IterTools: groupby -import LibDeflate: unsafe_zlib_decompress!, Decompressor +import LibDeflate: zlib_decompress!, Decompressor import Tables, TypedTables, PrettyTables diff --git a/src/streamers.jl b/src/streamers.jl index 5a1e30a9..3449acbf 100644 --- a/src/streamers.jl +++ b/src/streamers.jl @@ -84,7 +84,7 @@ function Streamers(io) if cname == "ZL" output = Vector{UInt8}(undef, tkey.fObjlen) - _decompress_zlib!(output, compressedbytes, length(output)) + zlib_decompress!(Decompressor(), output, compressedbytes, length(output)) IOBuffer(output) elseif cname == "XZ" IOBuffer(transcode(XzDecompressor, compressedbytes)) diff --git a/src/types.jl b/src/types.jl index cc41add8..ce0ac1ff 100644 --- a/src/types.jl +++ b/src/types.jl @@ -127,23 +127,6 @@ function compressed_datastream(io, tkey) return read(io, tkey.fNbytes - tkey.fKeylen) end -# Based on -# https://github.com/jakobnissen/LibDeflate.jl/blob/d172c4429404a6ce73b3d44541e80d6f69a0f38a/src/zlib.jl#L38 -function _decompress_zlib!( - output::AbstractArray{UInt8}, - input, - n_out::Integer -) - GC.@preserve output input unsafe_zlib_decompress!( - Base.HasLength(), - Decompressor(), - pointer(output), - n_out, - pointer(input), - sizeof(input) - ) -end - function _decompress_lz4!(input_ptr, input_size, output_ptr, output_size) CodecLz4.LZ4_decompress_safe(input_ptr, output_ptr, input_size, output_size) nothing @@ -180,7 +163,7 @@ function decompress_datastreambytes(compbytes, tkey) _decompress_lz4!(input_ptr, input_size, output_ptr, output_size) elseif cname == "ZL" output = @view(uncomp_data[fufilled+1:fufilled+uncompbytes]) - _decompress_zlib!(output, rawbytes, uncompbytes) + zlib_decompress!(Decompressor(), output, rawbytes, uncompbytes) elseif cname == "XZ" @view(uncomp_data[fufilled+1:fufilled+uncompbytes]) .= transcode(XzDecompressor, rawbytes) elseif cname == "ZS" From 47ba3bf694de9e05d68a336116df77e69250388d Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Wed, 1 Dec 2021 09:33:14 -0500 Subject: [PATCH 34/59] Update ci.yml --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 22f7efcc..85b03cc3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,6 +15,7 @@ jobs: fail-fast: false matrix: version: + - '1.6' - '1.5' - '1.4' - '1.3' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'. From 2d028ce0ef0bb1318ede775eabdc4620b7fcdf37 Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Thu, 20 Jan 2022 19:53:14 +0100 Subject: [PATCH 35/59] Fix gitlab ci (#141) * Use two threads * Remove Julia 1.3 * Oh, we still support Julia 1.3, readding * Simplify CI and fix threading in Julia 1.3 --- .gitlab-ci.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 0d753315..d9542168 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -4,9 +4,8 @@ stages: .test_template: &test_definiton | export JULIA_PROJECT=@. export JL_PKG=ROOTIO - julia --color=yes -e "if VERSION < v\"0.7.0-DEV.5183\"; Pkg.clone(pwd()); Pkg.build(\"${JL_PKG}\"); else using Pkg; if VERSION >= v\"1.1.0-rc1\"; Pkg.build(verbose=true); else Pkg.build(); end; end" - julia --check-bounds=yes --color=yes -e "if VERSION < v\"0.7.0-DEV.5183\"; Pkg.test(\"${JL_PKG}\", coverage=true); else using Pkg; Pkg.test(coverage=true); end" - + export JULIA_NUM_THREADS=3 + julia --check-bounds=yes --color=yes -e "using Pkg; Pkg.test(coverage=true)" test-julia-1.3: image: julia:1.3 From d41491dad62d81e26ca65d3936cd722a5a1304e9 Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Tue, 8 Feb 2022 00:48:54 +0100 Subject: [PATCH 36/59] Improve thread handling in tests (#144) * Improve thread handling in tests * Test threading --- test/runtests.jl | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/test/runtests.jl b/test/runtests.jl index 6854bab4..3e9b4272 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -625,6 +625,7 @@ end if get(ENV, "CI", "false") == "true" + # Make sure CI runs with more than 1 thread @test Threads.nthreads() > 1 end nmus = zeros(Int, Threads.nthreads()) @@ -645,7 +646,9 @@ end @static if VERSION > v"1.5.1" t = LazyTree(ROOTFile(joinpath(SAMPLES_DIR, "NanoAODv5_sample.root")), "Events", ["Muon_pt"]) @testset "Multi threading" begin - nmus = zeros(Int, Threads.nthreads()) + nthreads = Threads.nthreads() + nthreads == 1 && @warn "Running on a single thread. Please re-run the test suite with at least two threads (`julia --threads 2 ...`)" + nmus = zeros(Int, nthreads) Threads.@threads for (i, evt) in enumerate(t) nmus[Threads.threadid()] += length(t.Muon_pt[i]) end @@ -655,7 +658,7 @@ end Threads.@threads for evt in t nmus[Threads.threadid()] += length(evt.Muon_pt) end - @test count(>(0), nmus) > 1 # test @threads is actually threading + nthreads > 1 && @test count(>(0), nmus) > 1 # test @threads is actually threading @test sum(nmus) == 878 @@ -663,7 +666,7 @@ end @batch for evt in t nmus[Threads.threadid()] += length(evt.Muon_pt) end - @test count(>(0), nmus) > 1 # test @batch is actually threading + nthreads > 1 && @test count(>(0), nmus) > 1 # test @threads is actually threading @test sum(nmus) == 878 nmus .= 0 @@ -674,7 +677,7 @@ end @test sum(nmus) == 2*878 for j in 1:3 - inds = [Vector{Int}() for _ in 1:Threads.nthreads()] + inds = [Vector{Int}() for _ in 1:nthreads] Threads.@threads for (i, evt) in enumerate(t) push!(inds[Threads.threadid()], i) end From c309eb7c143fdfb5b88138c5270c8e3f186094a0 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Wed, 23 Feb 2022 18:28:04 -0500 Subject: [PATCH 37/59] faster vcat (#152) --- src/iteration.jl | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/iteration.jl b/src/iteration.jl index e5fb5267..f644a7ef 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -240,8 +240,11 @@ Base.ndims(::Type{<:LazyTree}) = 1 Base.size(lt::LazyTree) = size(innertable(lt)) function LazyArrays.Vcat(ts::LazyTree...) - cs = Tables.columns.(innertable.(ts)) - LazyTree(TypedTables.Table(map(Vcat, cs...))) + branch_names = propertynames(first(ts)) + res_branches = map(branch_names) do bname + LazyArrays.Vcat(getproperty.(ts, bname)...) + end + LazyTree(TypedTables.Table(NamedTuple{branch_names}(res_branches))) end Base.vcat(ts::LazyTree...) = Vcat(ts...) Base.reduce(::typeof(vcat), ts::AbstractVector{<:LazyTree}) = Vcat((ts)...) From 39eb35bc655d8ea375351005681e927dd4a60116 Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Thu, 24 Feb 2022 10:41:57 +0100 Subject: [PATCH 38/59] Bump version number --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index b2c4e8b6..dbbe0cfa 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.8.1" +version = "0.8.2" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From cc39f3eb81bf09cad2e796f4f0f905b97effac79 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Fri, 25 Feb 2022 16:10:53 -0500 Subject: [PATCH 39/59] fix stacktrace too long (#149) * fix stacktrace too long * fix stacktrace too long try 2 * fix stacktrace too long try 3 * fix before 1.6 --- src/UnROOT.jl | 1 + src/displays.jl | 9 +++++++++ 2 files changed, 10 insertions(+) diff --git a/src/UnROOT.jl b/src/UnROOT.jl index 17c966b8..aea5830f 100644 --- a/src/UnROOT.jl +++ b/src/UnROOT.jl @@ -17,6 +17,7 @@ import LibDeflate: zlib_decompress!, Decompressor import Tables, TypedTables, PrettyTables @static if VERSION < v"1.6" + Base.first(itr, n::Integer) = collect(Iterators.take(itr, n)) Base.first(a::AbstractVector{S}, n::Integer) where S<: AbstractString = a[1:(length(a) > n ? n : end)] Base.first(a::S, n::Integer) where S<: AbstractString = a[1:(length(a) > n ? n : end)] end diff --git a/src/displays.jl b/src/displays.jl index 6c82e270..6335a85b 100644 --- a/src/displays.jl +++ b/src/displays.jl @@ -77,6 +77,15 @@ function _show(io::IO, tree::LazyTree; kwargs...) ) nothing end + +# stop crazy stracktrace +function Base.show(io::IO, + ::Type{<:LazyTree{<:UnROOT.TypedTables.Table{NamedTuple{Ns, Vs}}}}) where {T, Ns, Vs} + elip = length(Ns) > 5 ? "..." : "" + println(io, "LazyTree with $(length(Ns)) branches:") + println(io, join(first(Ns, 5), ", "), elip) +end + function Base.show(io::IO, ::MIME"text/html", tree::LazyTree) _hs = _make_header(tree) maxrows = 10 From d35aa9ce872d7a66de961cec5103d61ecc9c6f24 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Wed, 2 Mar 2022 01:18:49 -0500 Subject: [PATCH 40/59] reduce number of read during `ROOTFile` and basket unpacking, use more async, add remote (HTTP) source, (#154) * reduce basket reading io from 4 -> 1 * use more OffsetBuffer when appropriate * bump compatibility * add HTTP source support * Mmap based local file * async chunking * better error * 100% lock-free * scitoken ready * faster display branch * backport upgrade --- .github/workflows/ci.yml | 6 +- Project.toml | 3 + README.md | 12 ++++ docs/make.jl | 1 + docs/src/exampleusage.md | 19 +++++++ src/UnROOT.jl | 26 ++++++++- src/bootstrap.jl | 2 + src/displays.jl | 18 +++++- src/iteration.jl | 16 +++--- src/root.jl | 101 ++++++++++++++++----------------- src/streamsource.jl | 119 +++++++++++++++++++++++++++++++++++++++ src/types.jl | 2 +- test/runtests.jl | 25 +++++--- 13 files changed, 273 insertions(+), 77 deletions(-) create mode 100644 docs/src/exampleusage.md create mode 100644 src/streamsource.jl diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 85b03cc3..5dcc9416 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,10 +15,10 @@ jobs: fail-fast: false matrix: version: - - '1.6' - - '1.5' + - '1.3' - '1.4' - - '1.3' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'. + - '1.5' + - '1.6' - '1' # Leave this line unchanged. '1' will automatically expand to the latest stable 1.x release of Julia. - 'nightly' os: diff --git a/Project.toml b/Project.toml index dbbe0cfa..7dce77d5 100644 --- a/Project.toml +++ b/Project.toml @@ -9,6 +9,7 @@ ArraysOfArrays = "65a8f2f4-9b39-5baf-92e2-a9cc46fdf018" CodecLz4 = "5ba52731-8f18-5e0d-9241-30f10d1ec561" CodecXz = "ba30903b-d9e8-5048-a5ec-d1f5b0d4b47b" CodecZstd = "6b39b394-51ab-5f42-8807-6242bab2b4c2" +HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3" IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e" LRUCache = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637" LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" @@ -16,6 +17,7 @@ LibDeflate = "9255714d-24a7-4b30-8ea3-d46a97f7e13b" LorentzVectors = "3f54b04b-17fc-5cd4-9758-90c048d965e3" Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" Mixers = "2a8e4939-dab8-5edc-8f64-72a8776f13de" +Mmap = "a63ad114-7e13-5084-954f-fe012c677804" Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a" PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" @@ -28,6 +30,7 @@ ArraysOfArrays = "^0.5.3" CodecLz4 = "^0.3.0, ^0.4.0" CodecXz = "^0.6.0, ^0.7.0" CodecZstd = "^0.6.0, ^0.7.0" +HTTP = "^0.9.7" IterTools = "^1" LRUCache = "^1.3.0" LazyArrays = "^0.15, ^0.21, ^0.22, ^1" diff --git a/README.md b/README.md index b81f02c3..2fcdba16 100644 --- a/README.md +++ b/README.md @@ -54,6 +54,18 @@ Only one basket per branch will be cached so you don't have to worry about runni At the same time, `event` inside the for-loop is not materialized until a field is accessed. If your event is fairly small or you need all of them anyway, you can `collect(event)` first inside the loop. +XRootD is also supported, depending on the protocol: +- the "url" has to start with `http://` or `https://`: +- (1.6+ only) or the "url" has to start with `root://` and have another `//` to separate server and file path +```julia +julia> r = @time ROOTFile("https://scikit-hep.org/uproot3/examples/Zmumu.root") + 0.034877 seconds (5.13 k allocations: 533.125 KiB) +ROOTFile with 1 entry and 18 streamers. + +julia> r = ROOTFile("root://eospublic.cern.ch//eos/root-eos/cms_opendata_2012_nanoaod/Run2012B_DoubleMuParked.root") +ROOTFile with 1 entry and 19 streamers. +``` + ## Branch of custom struct We provide an experimental interface for hooking up UnROOT with your custom types diff --git a/docs/make.jl b/docs/make.jl index 97c7fbaa..03fc2f89 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -8,6 +8,7 @@ makedocs(; ), pages=[ "Introduction" => "index.md", + "Example Usage" => "exampleusage.md", "Performance Tips" => "performancetips.md", "Advanced Usage" => [ "Parse Custom Branch" => "advanced/custom_branch.md", diff --git a/docs/src/exampleusage.md b/docs/src/exampleusage.md new file mode 100644 index 00000000..05a87b3f --- /dev/null +++ b/docs/src/exampleusage.md @@ -0,0 +1,19 @@ +## Chunk Iteration +```julia +t = LazyTree(...) +res = 0.0 +for rang in Iterators.partition(1:lastindex(t), 10^6) + res += sum(t[rang].nMuon) # +end +res +``` +Note, `t[rang]` is eager, if you don't need all branches, it's much better to use `t.nMuon[rang]`, or limit which +branches are selected during `LazyTree()` creation time. + +This pattern works the best over network, for local files, stick with: +``` +for evt in t + ... +end +``` +usually is the best approach. diff --git a/src/UnROOT.jl b/src/UnROOT.jl index aea5830f..1097951f 100644 --- a/src/UnROOT.jl +++ b/src/UnROOT.jl @@ -1,9 +1,10 @@ module UnROOT using LazyArrays +import Mmap: mmap export ROOTFile, LazyBranch, LazyTree -import Base: close, keys, get, getindex, getproperty, show, length, iterate, position, ntoh, lock, unlock, reinterpret +import Base: close, keys, get, getindex, getproperty, show, length, iterate, position, ntoh, reinterpret ntoh(b::Bool) = b import AbstractTrees: children, printnode, print_tree @@ -22,7 +23,23 @@ import Tables, TypedTables, PrettyTables Base.first(a::S, n::Integer) where S<: AbstractString = a[1:(length(a) > n ? n : end)] end +""" + OffsetBuffer + +Works with seek, position of the original file. Think of it as a view of IOStream that can be +indexed with original positions. +""" +struct OffsetBuffer{T} + io::T + offset::Int +end +Base.read(io::OffsetBuffer, nb) = Base.read(io.io, nb) +Base.seek(io::OffsetBuffer, i) = Base.seek(io.io, i - io.offset) +Base.skip(io::OffsetBuffer, i) = Base.skip(io.io, i) +Base.position(io::OffsetBuffer) = position(io.io) + io.offset + include("constants.jl") +include("streamsource.jl") include("io.jl") include("types.jl") include("utils.jl") @@ -33,4 +50,11 @@ include("iteration.jl") include("custom.jl") include("displays.jl") +if ccall(:jl_generating_output, Cint, ()) == 1 # if we're precompiling the package + let + r = ROOTFile("https://scikit-hep.org/uproot3/examples/Zmumu.root") + show(devnull, r) + end +end + end # module diff --git a/src/bootstrap.jl b/src/bootstrap.jl index 92ef2ea8..ea1b3feb 100644 --- a/src/bootstrap.jl +++ b/src/bootstrap.jl @@ -395,6 +395,8 @@ primitivetype(l::TLeafD) = Float64 fMaximum end +primitivetype(l::TLeafC) = UInt8 + function parsefields!(io, fields, ::Type{T}) where {T<:TLeafC} preamble = Preamble(io, T) parsefields!(io, fields, TLeaf) diff --git a/src/displays.jl b/src/displays.jl index 6335a85b..ce1335fa 100644 --- a/src/displays.jl +++ b/src/displays.jl @@ -14,7 +14,6 @@ function children(f::T) where T <: Union{ROOTFile,ROOTDirectory} # then all TKeys in the file which are not for a TTree seen = Set{String}() ch = Vector{Union{TTree,TKeyNode,ROOTDirectory}}() - T === ROOTFile ? lock(f) : nothing for k in keys(f) try obj = f[k] @@ -35,7 +34,6 @@ function children(f::T) where T <: Union{ROOTFile,ROOTDirectory} push!(ch, kn) end end - T === ROOTFile ? unlock(f) : nothing ch end function children(t::TTree) @@ -78,6 +76,22 @@ function _show(io::IO, tree::LazyTree; kwargs...) nothing end + +function Base.show(io::IO, ::MIME"text/plain", br::LazyBranch) + print(io, summary(br)) + println(": ") + if length(br) < 200 + Base.print_array(IOContext(io, :limit => true), br[:]) + else + head = @async br[1:100] + tail = @async br[end-99:end] + wait(head) + wait(tail) + Base.print_array(IOContext(io, :limit => true), Vcat(head.result, tail.result)) + end + nothing +end + # stop crazy stracktrace function Base.show(io::IO, ::Type{<:LazyTree{<:UnROOT.TypedTables.Table{NamedTuple{Ns, Vs}}}}) where {T, Ns, Vs} diff --git a/src/iteration.jl b/src/iteration.jl index f644a7ef..815930ed 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -122,6 +122,8 @@ mutable struct LazyBranch{T,J,B} <: AbstractVector{T} [0:-1 for _ in 1:Threads.nthreads()]) end end +basketarray(lb::LazyBranch, ithbasket) = basketarray(lb.f, lb.b, ithbasket) +basketarray_iter(lb::LazyBranch) = basketarray_iter(lb.f, lb.b) function Base.hash(lb::LazyBranch, h::UInt) h = hash(lb.f, h) @@ -138,8 +140,6 @@ Base.firstindex(ba::LazyBranch) = 1 Base.lastindex(ba::LazyBranch) = ba.L Base.eltype(ba::LazyBranch{T,J,B}) where {T,J,B} = T -basketarray(lb::LazyBranch, ithbasket) = basketarray(lb.f, lb.b, ithbasket) -basketarray_iter(lb::LazyBranch) = basketarray_iter(lb.f, lb.b) function Base.show(io::IO, lb::LazyBranch) summary(io, lb) @@ -213,14 +213,17 @@ Base.IndexStyle(::Type{<:LazyTree}) = IndexLinear() Base.getindex(lt::LazyTree, row::Int) = LazyEvent(innertable(lt), row) # kept lazy for broadcasting purpose Base.getindex(lt::LazyTree, row::CartesianIndex{1}) = LazyEvent(innertable(lt), row[1]) -function Base.getindex(lt::LazyTree, rang::UnitRange) - return LazyTree(innertable(lt)[rang]) +function Base.getindex(lt::LazyTree, rang) + bnames = propertynames(lt) + branches = asyncmap(b->getproperty(lt, b)[rang], bnames) + return LazyTree(TypedTables.Table(NamedTuple{bnames}(branches))) end # a specific event Base.getindex(lt::LazyTree, ::typeof(!), s::Symbol) = lt[:, s] Base.getindex(lt::LazyTree, ::Colon, s::Symbol) = getproperty(innertable(lt), s) # the real deal Base.getindex(lt::LazyTree, row::Int, col::Symbol) = lt[:, col][row] +Base.getindex(lt::LazyTree, row, ::Colon) = lt[row] Base.getindex(lt::LazyTree, rows::UnitRange, col::Symbol) = lt[:, col][rows] Base.getindex(lt::LazyTree, ::Colon) = lt[1:end] Base.firstindex(lt::LazyTree) = 1 @@ -290,9 +293,6 @@ julia> mytree = LazyTree(f, "Events", ["Electron_dxy", "nMuon", r"Muon_(pt|eta)\ function LazyTree(f::ROOTFile, s::AbstractString, branches) tree = f[s] tree isa TTree || error("$s is not a tree name.") - if length(branches) > 30 - @warn "Your tree is quite wide, with $(length(branches)) branches, this will take compiler a moment." - end d = Dict{Symbol,LazyBranch}() _m(s::AbstractString) = isequal(s) _m(r::Regex) = Base.Fix1(occursin, r) @@ -336,7 +336,7 @@ function Base.getindex(ba::LazyBranch{T,J,B}, range::UnitRange) where {T,J,B} ib2 = findfirst(x -> x > (last(range) - 1), ba.fEntry) - 1 offset = ba.fEntry[ib1] range = (first(range)-offset):(last(range)-offset) - return vcat([basketarray(ba, i) for i in ib1:ib2]...)[range] + return Vcat(asyncmap(i->basketarray(ba, i), ib1:ib2)...)[range] end _clusterranges(t::LazyTree) = _clusterranges([getproperty(t,p) for p in propertynames(t)]) diff --git a/src/root.jl b/src/root.jl index 0969072a..1c9ba5ce 100644 --- a/src/root.jl +++ b/src/root.jl @@ -2,23 +2,21 @@ struct ROOTDirectory name::AbstractString header::ROOTDirectoryHeader keys::Vector{TKey} - fobj::IOStream + fobj::SourceStream refs::Dict{Int32, Any} end struct ROOTFile - filename::AbstractString + filename::String format_version::Int32 header::FileHeader - fobj::IOStream + fobj::SourceStream tkey::TKey streamers::Streamers directory::ROOTDirectory customstructs::Dict{String, Type} - lk::ReentrantLock end function close(f::ROOTFile) - # TODO: should we take care of the lock? close(f.fobj) end function ROOTFile(f::Function, args...; pv...) @@ -29,8 +27,7 @@ function ROOTFile(f::Function, args...; pv...) close(rootfile) end end -lock(f::ROOTFile) = lock(f.lk) -unlock(f::ROOTFile) = unlock(f.lk) + function Base.hash(rf::ROOTFile, h::UInt) hash(rf.fobj, h) end @@ -58,45 +55,51 @@ test/samples/NanoAODv5_sample.root └─ "⋮" ``` """ +const HEAD_BUFFER_SIZE = 1024 function ROOTFile(filename::AbstractString; customstructs = Dict("TLorentzVector" => LorentzVector{Float64})) - fobj = Base.open(filename) - preamble = unpack(fobj, FilePreamble) - String(preamble.identifier) == "root" || error("Not a ROOT file!") + fobj = if startswith(filename, r"https?://") + HTTPStream(filename) + else + !isfile(filename) && "$filename is not a file" + MmapStream(filename) + end + header_bytes = read(fobj, HEAD_BUFFER_SIZE) + @assert header_bytes[1:4] == [0x72, 0x6f, 0x6f, 0x74] "$filename is not a ROOT file." + head_buffer = IOBuffer(header_bytes) + preamble = unpack(head_buffer, FilePreamble) format_version = preamble.fVersion - if format_version < 1000000 + header = if format_version < 1000000 @debug "32bit ROOT file" - header = unpack(fobj, FileHeader32) + unpack(head_buffer, FileHeader32) else @debug "64bit ROOT file" - header = unpack(fobj, FileHeader64) + unpack(head_buffer, FileHeader64) end # Streamers - if header.fSeekInfo != 0 - @debug "Reading streamer info." - seek(fobj, header.fSeekInfo) - streamers = Streamers(fobj) - else - @debug "No streamer info present, skipping." - end + seek(fobj, header.fSeekInfo) + stream_buffer = OffsetBuffer(IOBuffer(read(fobj, 10^5)), Int(header.fSeekInfo)) + streamers = Streamers(stream_buffer) - seek(fobj, header.fBEGIN) - tkey = unpack(fobj, TKey) + seek(head_buffer, header.fBEGIN + header.fNbytesName) + dir_header = unpack(head_buffer, ROOTDirectoryHeader) + dirkey = dir_header.fSeekKeys + seek(fobj, dirkey) + tail_buffer = @async IOBuffer(read(fobj, 10^6)) - # Reading the header key for the top ROOT directory - seek(fobj, header.fBEGIN + header.fNbytesName) - dir_header = unpack(fobj, ROOTDirectoryHeader) + seek(head_buffer, header.fBEGIN) + tkey = unpack(head_buffer, TKey) - seek(fobj, dir_header.fSeekKeys) - header_key = unpack(fobj, TKey) + wait(tail_buffer) + unpack(tail_buffer.result, TKey) - n_keys = readtype(fobj, Int32) - keys = [unpack(fobj, TKey) for _ in 1:n_keys] + n_keys = readtype(tail_buffer.result, Int32) + keys = [unpack(tail_buffer.result, TKey) for _ in 1:n_keys] directory = ROOTDirectory(tkey.fName, dir_header, keys, fobj, streamers.refs) - ROOTFile(filename, format_version, header, fobj, tkey, streamers, directory, customstructs, ReentrantLock()) + ROOTFile(filename, format_version, header, fobj, tkey, streamers, directory, customstructs) end function Base.show(io::IO, f::ROOTFile) @@ -146,14 +149,8 @@ end tkey = f.directory.keys[findfirst(isequal(s), keys(f))] @debug "Retrieving $s ('$(tkey.fClassName)')" streamer = getfield(@__MODULE__, Symbol(tkey.fClassName)) - lock(f) - try - S = streamer(f.fobj, tkey, f.streamers.refs) - return S - catch - finally - unlock(f) - end + S = streamer(f.fobj, tkey, f.streamers.refs) + return S end # FIXME unify with above? @@ -409,9 +406,9 @@ function readbranchraw(f::ROOTFile, branch) datas = sizehint!(Vector{UInt8}(), sum(nbytes)) # maximum length if all data are UInt8 offsets = sizehint!(zeros(Int32, 1), branch.fEntries+1) # this is always Int32 position = 0 - foreach(branch.fBasketSeek) do seek - seek==0 && return - data, offset = readbasketseek(f, branch, seek) + for (seek, nb) in zip(branch.fBasketSeek, nbytes) + seek==0 && break + data, offset = readbasketseek(f, branch, seek, nb) append!(datas, data) # FIXME: assuming offset has always 0 or at least 2 elements ;) append!(offsets, (@view offset[2:end]) .+ position) @@ -435,7 +432,7 @@ end # 3GB cache for baskets """ readbasket(f::ROOTFile, branch, ith) - readbasketseek(f::ROOTFile, branch::Union{TBranch, TBranchElement}, seek_pos::Int) + readbasketseek(f::ROOTFile, branch::Union{TBranch, TBranchElement}, seek_pos::Int, nbytes) The fundamental building block of reading read data from a .root file. Read read one basket's raw bytes and offsets at a time. These raw bytes and offsets then (potentially) get @@ -443,19 +440,15 @@ processed by [`interped_data`](@ref). See also: [`auto_T_JaggT`](@ref), [`basketarray`](@ref) """ -readbasket(f::ROOTFile, branch, ith) = readbasketseek(f, branch, branch.fBasketSeek[ith]) +function readbasket(f::ROOTFile, branch, ith) + readbasketseek(f, branch, branch.fBasketSeek[ith], branch.fBasketBytes[ith]) +end -function readbasketseek(f::ROOTFile, branch::Union{TBranch, TBranchElement}, seek_pos::Int) - lock(f) - local basketkey, compressedbytes - try - seek(f.fobj, seek_pos) - basketkey = unpack(f.fobj, TBasketKey) - compressedbytes = compressed_datastream(f.fobj, basketkey) - catch - finally - unlock(f) - end +function readbasketseek(f::ROOTFile, branch::Union{TBranch, TBranchElement}, seek_pos::Int, nb) + local rawbuffer + rawbuffer = OffsetBuffer(IOBuffer(read_seek_nb(f.fobj, seek_pos, nb)), seek_pos) + basketkey = unpack(rawbuffer, TBasketKey) + compressedbytes = compressed_datastream(rawbuffer, basketkey) basketrawbytes = decompress_datastreambytes(compressedbytes, basketkey) diff --git a/src/streamsource.jl b/src/streamsource.jl new file mode 100644 index 00000000..9ff4b005 --- /dev/null +++ b/src/streamsource.jl @@ -0,0 +1,119 @@ +import HTTP + +mutable struct MmapStream # Mmap based + mmap_ary::Vector{UInt8} + seekloc::Int + size::Int + function MmapStream(filepath::AbstractString) + size = filesize(filepath) + new(mmap(filepath), 0, size) + end +end + +read_seek_nb(fobj::MmapStream, seek, nb) = fobj.mmap_ary[seek+1:seek+nb] + +function Base.read(fobj::MmapStream, nb::Integer) + stop = min(fobj.seekloc + nb, fobj.size) + b = fobj.mmap_ary[fobj.seekloc+1 : stop] + fobj.seekloc += nb + return b +end + +function Base.close(fobj::MmapStream) # no-op + nothing +end + +# SciToken discovery https://zenodo.org/record/3937438 +function _find_scitoken() + op1 = get(ENV, "BEARER_TOKEN", "") + op2 = get(ENV, "BEARER_TOKEN_FILE", "") + op3 = get(ENV, "XDG_RUNTIME_DIR", "") + uid = strip(read(`id -u`, String)) + op3_file = joinpath(op3, "bt_u$uid") + op4_file = "/tmp/bt_u$uid" + token = if !isempty(op1) + op1 + elseif !isempty(op2) + read(op2, String) + elseif !isempty(op3) && isfile(op3_file) + read(op3_file, String) + elseif isfile(op4_file) + read(op4_file, String) + else + "" + end + return strip(token) +end + +mutable struct HTTPStream + uri::HTTP.URI + seekloc::Int + size::Int + multipart::Bool + scitoken::String + function HTTPStream(uri::AbstractString; scitoken = _find_scitoken()) + #TODO: determin multipart support + test = HTTP.request("GET", uri, + ("Range" => "bytes=0-3", "User-Agent" => "UnROOTjl", "Authorization" => "Bearer $scitoken") + ) + @assert test.status==206 "bad network or wrong server" + @assert String(test.body)=="root" "not a root file" + multipart = false + local v + for pair in test.headers + if lowercase(pair[1]) == "content-range" + v = pair[2] + break + end + end + size = parse(Int, match(r"/(\d+)", v).captures[1]) + new(HTTP.URI(uri), 0, size, multipart, scitoken) + end +end + +const SourceStream = Union{MmapStream, HTTPStream} + +function Base.read(fobj::SourceStream, ::Type{T}) where T + return reinterpret(T, read(fobj, sizeof(T)))[1] # TODO: use `only` +end + +function Base.position(fobj::SourceStream) + fobj.seekloc +end + +function Base.seek(fobj::SourceStream, loc) + fobj.seekloc = loc + return fobj +end + +function Base.skip(fobj::SourceStream, stride) + fobj.seekloc += stride + return fobj +end + +function Base.seekstart(fobj::SourceStream) + fobj.seekloc = 0 + return fobj +end + +function Base.close(fobj::HTTPStream) # no-op + nothing +end + +function Base.read(fobj::HTTPStream, nb::Integer) + @debug nb + b = read_seek_nb(fobj, fobj.seekloc, nb) + fobj.seekloc += nb + return b +end + +function read_seek_nb(fobj::HTTPStream, seek, nb) + stop = seek+nb-1 + hd = ("Range" => "bytes=$(seek)-$stop", "Authorization" => "Bearer $(fobj.scitoken)") + b = HTTP.request(HTTP.stack(), "GET", fobj.uri, hd, UInt8[]).body + return b +end + +function Base.read(fobj::SourceStream) + read(fobj, fobj.size - fobj.seekloc + 1) +end diff --git a/src/types.jl b/src/types.jl index ce0ac1ff..bf7af636 100644 --- a/src/types.jl +++ b/src/types.jl @@ -238,7 +238,7 @@ end const ROOTDirectoryHeader = Union{ROOTDirectoryHeader32, ROOTDirectoryHeader64} -function unpack(io::IOStream, ::Type{ROOTDirectoryHeader}) +function unpack(io, ::Type{ROOTDirectoryHeader}) fVersion = readtype(io, Int16) skip(io, -2) diff --git a/test/runtests.jl b/test/runtests.jl index 3e9b4272..490ddabf 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -583,16 +583,18 @@ end end @testset "Type stability" begin - function isfullystable(func) - io = IOBuffer() - print(io, (@code_typed func()).first); - typed = String(take!(io)) - return !occursin("::Any", typed) - end + # function isfullystable(func) + # io = IOBuffer() + # print(io, (@code_typed func()).first); + # typed = String(take!(io)) + # println(typed) + # return !occursin("::Any", typed) + # end rootfile = ROOTFile(joinpath(SAMPLES_DIR, "NanoAODv5_sample.root")) t = LazyTree(rootfile, "Events", ["MET_pt"])[1:10] + # LazyArray has a BoundsArray that is ::Any but is "fine" function f1() s = 0.0f0 for evt in t @@ -602,8 +604,8 @@ end end f2() = sum(t.MET_pt) - @test isfullystable(f1) - @test isfullystable(f2) + @inferred f1() + @inferred f2() close(rootfile) end @@ -712,6 +714,13 @@ end @test length(UnROOT.basketarray(t.b1, 1)) == 1228 end +@testset "SourceStream remote" begin + t = LazyTree("https://scikit-hep.org/uproot3/examples/Zmumu.root", "events") + @test t.eta1[1] ≈ -1.21769 + @test t.eta1[end] ≈ -1.57044 + show(devnull, t) # test display +end + @testset "Cluster ranges" begin t = LazyTree(UnROOT.samplefile("tree_with_clusters.root"),"t1"); @test all(UnROOT._clusterbytes(t; compressed=true) .< 10000) From e60d17fa3477ded4da7b354dc5bc28ffd330832d Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Wed, 2 Mar 2022 01:19:12 -0500 Subject: [PATCH 41/59] bump version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 7dce77d5..e5dce610 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.8.2" +version = "0.8.3" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From f6a0d4afdc6164cb8716b58bb91b9d9eb3341f25 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Fri, 11 Mar 2022 10:53:26 -0500 Subject: [PATCH 42/59] improve LV and add a debug for compression type --- src/custom.jl | 3 ++- src/types.jl | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/custom.jl b/src/custom.jl index 7d1c6490..e69da402 100644 --- a/src/custom.jl +++ b/src/custom.jl @@ -38,7 +38,8 @@ Base.show(io::IO, lv::LorentzVector) = print(io, "LV(x=$(lv.x), y=$(lv.y), z=$(l function Base.reinterpret(::Type{LVF64}, v::AbstractVector{UInt8}) where T # first 32 bytes are TObject header we don't care # x,y,z,t in ROOT - v4 = ntoh.(reinterpret(Float64, @view v[1+32:end])) + v4 = (reinterpret(Float64, @view v[1+32:end])) + v4 .= ntoh.(v4) # t,x,y,z in LorentzVectors.jl LVF64(v4[4], v4[1], v4[2], v4[3]) end diff --git a/src/types.jl b/src/types.jl index bf7af636..124a026d 100644 --- a/src/types.jl +++ b/src/types.jl @@ -151,6 +151,7 @@ function decompress_datastreambytes(compbytes, tkey) compression_header = unpack(io, CompressionHeader) cname, _, compbytes, uncompbytes = unpack(compression_header) rawbytes = read(io, compbytes) + @debug cname if cname == "L4" # skip checksum which is 8 bytes From 00e7815c3892027d1ee221a0e3ea1627ea405e09 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Tue, 15 Mar 2022 14:54:05 -0400 Subject: [PATCH 43/59] fix split branches (#155) * fix split branches --- src/iteration.jl | 22 ++++++++++++++++------ src/root.jl | 2 ++ 2 files changed, 18 insertions(+), 6 deletions(-) diff --git a/src/iteration.jl b/src/iteration.jl index 815930ed..e6437aeb 100644 --- a/src/iteration.jl +++ b/src/iteration.jl @@ -258,7 +258,9 @@ function getbranchnamesrecursive(obj) out = Vector{String}() for b in obj.fBranches.elements push!(out, b.fName) - for subname in getbranchnamesrecursive(b) + subs = getbranchnamesrecursive(b) + !isempty(subs) && pop!(out) + for subname in subs push!(out, "$(b.fName)/$(subname)") end end @@ -294,12 +296,20 @@ function LazyTree(f::ROOTFile, s::AbstractString, branches) tree = f[s] tree isa TTree || error("$s is not a tree name.") d = Dict{Symbol,LazyBranch}() - _m(s::AbstractString) = isequal(s) _m(r::Regex) = Base.Fix1(occursin, r) - branches = mapreduce(b -> filter(_m(b), getbranchnamesrecursive(tree)), ∪, branches) - SB = Symbol.(branches) - for b in SB - d[b] = f["$s/$b"] + all_bnames = getbranchnamesrecursive(tree) + res_bnames = mapreduce(∪, branches) do b + if b isa Regex + filter(_m(b), all_bnames) + elseif b isa String + expand = filter(n->startswith(n, "$b/$b"), all_bnames) + isempty(expand) ? filter(isequal(b), all_bnames) : expand + else + error("branch selection must be string or regex") + end + end + for b in res_bnames + d[Symbol(b)] = f["$s/$b"] end return LazyTree(TypedTables.Table(d)) end diff --git a/src/root.jl b/src/root.jl index 1c9ba5ce..bbeff6e4 100644 --- a/src/root.jl +++ b/src/root.jl @@ -362,6 +362,8 @@ function auto_T_JaggT(f::ROOTFile, branch; customstructs::Dict{String, Type}) Bool elseif elname == "unsigned int" UInt32 + elseif elname == "signed char" + Int8 elseif elname == "unsigned char" UInt8 elseif elname == "unsigned short" From f6339ccd89866a8233c62fc58609be7da5b7cf5d Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Tue, 15 Mar 2022 14:54:28 -0400 Subject: [PATCH 44/59] bump version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index e5dce610..7b1eb3e1 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.8.3" +version = "0.8.4" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From e822e5d65a4220105221f97210090c5af2ce7df6 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Tue, 5 Apr 2022 13:34:15 -0400 Subject: [PATCH 45/59] fix windows `id -u` (#158) * fix windows `id -u` * remove hacky precompile * fix CI --- src/UnROOT.jl | 7 ------- src/streamsource.jl | 6 +++++- test/runtests.jl | 2 +- 3 files changed, 6 insertions(+), 9 deletions(-) diff --git a/src/UnROOT.jl b/src/UnROOT.jl index 1097951f..d4e74334 100644 --- a/src/UnROOT.jl +++ b/src/UnROOT.jl @@ -50,11 +50,4 @@ include("iteration.jl") include("custom.jl") include("displays.jl") -if ccall(:jl_generating_output, Cint, ()) == 1 # if we're precompiling the package - let - r = ROOTFile("https://scikit-hep.org/uproot3/examples/Zmumu.root") - show(devnull, r) - end -end - end # module diff --git a/src/streamsource.jl b/src/streamsource.jl index 9ff4b005..78935cf6 100644 --- a/src/streamsource.jl +++ b/src/streamsource.jl @@ -28,7 +28,11 @@ function _find_scitoken() op1 = get(ENV, "BEARER_TOKEN", "") op2 = get(ENV, "BEARER_TOKEN_FILE", "") op3 = get(ENV, "XDG_RUNTIME_DIR", "") - uid = strip(read(`id -u`, String)) + uid = @static if Sys.iswindows() + "julia" + else + strip(read(`id -u`, String)) + end op3_file = joinpath(op3, "bt_u$uid") op4_file = "/tmp/bt_u$uid" token = if !isempty(op1) diff --git a/test/runtests.jl b/test/runtests.jl index 490ddabf..d10663eb 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -665,7 +665,7 @@ end nmus .= 0 - @batch for evt in t + Threads.@threads for evt in t nmus[Threads.threadid()] += length(evt.Muon_pt) end nthreads > 1 && @test count(>(0), nmus) > 1 # test @threads is actually threading From 03614f4fa8f8ea77a1934af67901cb0f5f1e1206 Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Tue, 5 Apr 2022 13:34:34 -0400 Subject: [PATCH 46/59] Update Project.toml bump version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 7b1eb3e1..5e156837 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.8.4" +version = "0.8.5" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From 4df552ea130b01af8850407dc172790849c48ba5 Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Tue, 5 Apr 2022 21:01:39 +0200 Subject: [PATCH 47/59] Fix URLs (#159) --- README.md | 18 +++++++++--------- docs/make.jl | 2 +- docs/src/advanced/custom_branch.md | 10 +++++----- test/samples/issue61.py | 2 +- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 2fcdba16..4b32be80 100644 --- a/README.md +++ b/README.md @@ -3,14 +3,14 @@ [![All Contributors](https://img.shields.io/badge/all_contributors-7-orange.svg?style=flat-square)](#contributors-) -[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://tamasgal.github.io/UnROOT.jl/dev) -[![Build Status](https://github.com/tamasgal/UnROOT.jl/workflows/CI/badge.svg)](https://github.com/tamasgal/UnROOT.jl/actions) -[![Codecov](https://codecov.io/gh/tamasgal/UnROOT.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/tamasgal/UnROOT.jl) +[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliahep.github.io/UnROOT.jl/dev) +[![Build Status](https://github.com/JuliaHEP/UnROOT.jl/workflows/CI/badge.svg)](https://github.com/JuliaHEP/UnROOT.jl/actions) +[![Codecov](https://codecov.io/gh/JuliaHEP/UnROOT.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaHEP/UnROOT.jl) UnROOT.jl is a reader for the [CERN ROOT](https://root.cern) file format written entirely in Julia, without any dependence on ROOT or Python. -## Quick Start (see [docs](https://tamasgal.github.io/UnROOT.jl/dev/) for more) +## Quick Start (see [docs](https://JuliaHEP.github.io/UnROOT.jl/dev/) for more) ```julia julia> using UnROOT @@ -69,7 +69,7 @@ ROOTFile with 1 entry and 19 streamers. ## Branch of custom struct We provide an experimental interface for hooking up UnROOT with your custom types -that only takes 2 steps, as explained [in the docs](https://tamasgal.github.io/UnROOT.jl/dev/advanced/custom_branch/). +that only takes 2 steps, as explained [in the docs](https://JuliaHEP.github.io/UnROOT.jl/dev/advanced/custom_branch/). As a show case for this functionality, the `TLorentzVector` support in UnROOT is implemented with the said plug-in system. @@ -202,10 +202,10 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d - - - - + + + + diff --git a/docs/make.jl b/docs/make.jl index 03fc2f89..bb4837a7 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -17,7 +17,7 @@ makedocs(; "For Contributors" => "devdocs.md", "APIs" => "internalapis.md", ], - repo="https://github.com/tamasgal/UnROOT.jl/blob/{commit}{path}#L{line}", + repo="https://github.com/JuliaHEP/UnROOT.jl/blob/{commit}{path}#L{line}", sitename="UnROOT.jl", authors="Tamas Gal and contributors", ) diff --git a/docs/src/advanced/custom_branch.md b/docs/src/advanced/custom_branch.md index 5f71367c..bcc1f003 100644 --- a/docs/src/advanced/custom_branch.md +++ b/docs/src/advanced/custom_branch.md @@ -3,17 +3,17 @@ It is possible to parse Branches with custom structure as long as you know how t As an example, the `TLorentzVector` is added using this mechanism and we will walk through the steps needed: ### 1. Provide a map between `fClassName` of your struct (as seen in .root) to a Julia type. -Pass a `Dict{String, Type}` to `ROOTFile(filepath; customstructs)`. The `TLorentzVector` is shipped [by default](https://github.com/tamasgal/UnROOT.jl/blob/06b692523bbff3f467f6b7fe3544e411a719bc9e/src/root.jl#L21): +Pass a `Dict{String, Type}` to `ROOTFile(filepath; customstructs)`. The `TLorentzVector` is shipped [by default](https://github.com/JuliaHEP/UnROOT.jl/blob/06b692523bbff3f467f6b7fe3544e411a719bc9e/src/root.jl#L21): ```julia ROOTFile(filepath; customstructs = Dict("TLorentzVector" => LorentzVector{Float64})) ``` -This `Dict` will subsequently be used by the `auto_T_JaggT` function [at here](https://github.com/tamasgal/UnROOT.jl/blob/06b692523bbff3f467f6b7fe3544e411a719bc9e/src/root.jl#L213-L222) such that when we encounter a branch with this `fClassName`, we will return your `Type` as the detected element type of this branch. +This `Dict` will subsequently be used by the `auto_T_JaggT` function [at here](https://github.com/JuliaHEP/UnROOT.jl/blob/06b692523bbff3f467f6b7fe3544e411a719bc9e/src/root.jl#L213-L222) such that when we encounter a branch with this `fClassName`, we will return your `Type` as the detected element type of this branch. ### 2. Extend the raw bytes interpreting function `UnROOT.interped_data` -By default, given a branch element type and a "jaggness" type, a general function [is defined](https://github.com/tamasgal/UnROOT.jl/blob/06b692523bbff3f467f6b7fe3544e411a719bc9e/src/root.jl#L149) which will try to parse the raw bytes into Julia data structure. The `::Type{T}` will match what you have provided in the `Dict` in the previous step. +By default, given a branch element type and a "jaggness" type, a general function [is defined](https://github.com/JuliaHEP/UnROOT.jl/blob/06b692523bbff3f467f6b7fe3544e411a719bc9e/src/root.jl#L149) which will try to parse the raw bytes into Julia data structure. The `::Type{T}` will match what you have provided in the `Dict` in the previous step. -Thus, to "teach" UnROOT how to interpret bytes for your type `T`, you would want to defined a more specific `UnROOT.interped_data` than the default one. Taking the `TLorentzVector` [as example](https://github.com/tamasgal/UnROOT.jl/blob/06b692523bbff3f467f6b7fe3544e411a719bc9e/src/custom.jl#L23) again, we define a function: +Thus, to "teach" UnROOT how to interpret bytes for your type `T`, you would want to defined a more specific `UnROOT.interped_data` than the default one. Taking the `TLorentzVector` [as example](https://github.com/JuliaHEP/UnROOT.jl/blob/06b692523bbff3f467f6b7fe3544e411a719bc9e/src/custom.jl#L23) again, we define a function: ```julia using LorentzVector const LVF64 = LorentzVector{Float64} @@ -32,7 +32,7 @@ function Base.reinterpret(::Type{LVF64}, v::AbstractVector{UInt8}) where T end ``` -The `Base.reinterpret` function is just a helper function, you could instead write everything inside `UnROOT.interped_data`. We then builds on these, to interpret Jagged TLV branch: https://github.com/tamasgal/UnROOT.jl/blob/4747f6f5fd97ed1a872765485b4eb9e99ec5a650/src/custom.jl#L47 +The `Base.reinterpret` function is just a helper function, you could instead write everything inside `UnROOT.interped_data`. We then builds on these, to interpret Jagged TLV branch: https://github.com/JuliaHEP/UnROOT.jl/blob/4747f6f5fd97ed1a872765485b4eb9e99ec5a650/src/custom.jl#L47 ### More details To expand a bit what we're doing here, the `rawdata` for a single `TLV` is always `64 bytes` long and the first `32 bytes` are TObject header which we don't care (which is why we don't care about `rawoffsets` here). The last `32 bytes` make up 4 `Float64` and we simply parse them and return a collection of (julia) `LorentzVector{Float64}`. diff --git a/test/samples/issue61.py b/test/samples/issue61.py index a19d5147..e26d4ca7 100644 --- a/test/samples/issue61.py +++ b/test/samples/issue61.py @@ -1,6 +1,6 @@ import ROOT as r -# https://github.com/tamasgal/UnROOT.jl/issues/61 +# https://github.com/JuliaHEP/UnROOT.jl/issues/61 # needs to be run in a specific environment to trigger the issue # in the first place From b05997fb259a06733541833c171a8484f9133d9b Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Thu, 7 Apr 2022 11:46:32 -0400 Subject: [PATCH 48/59] add TLeafS (#161) --- src/bootstrap.jl | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/src/bootstrap.jl b/src/bootstrap.jl index ea1b3feb..3c2e72a6 100644 --- a/src/bootstrap.jl +++ b/src/bootstrap.jl @@ -202,6 +202,41 @@ end primitivetype(l::TLeafI) = l.fIsUnsigned ? UInt32 : Int32 +# FIXME this should be generated and inherited from TLeaf +@with_kw struct TLeafS + # from TNamed + fName + fTitle + + # from TLeaf + fLen + fLenType + fOffset + fIsRange + fIsUnsigned + fLeafCount + + # own fields + fMinimum + fMaximum +end + +function parsefields!(io, fields, T::Type{TLeafS}) + preamble = Preamble(io, T) + parsefields!(io, fields, TLeaf) + fields[:fMinimum] = readtype(io, Int16) + fields[:fMaximum] = readtype(io, Int16) + endcheck(io, preamble) +end + +function unpack(io, tkey::TKey, refs::Dict{Int32, Any}, T::Type{TLeafS}) + @initparse + parsefields!(io, fields, T) + T(;fields...) +end + +primitivetype(l::TLeafS) = l.fIsUnsigned ? UInt16 : Int16 + # FIXME this should be generated and inherited from TLeaf @with_kw struct TLeafL # from TNamed From e5746a002b52f9ff6e3793dd37b595851b4f8e6a Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Fri, 8 Apr 2022 11:02:53 +0200 Subject: [PATCH 49/59] Change the URL of deploydocs to the new one --- docs/make.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/make.jl b/docs/make.jl index bb4837a7..c863d999 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -23,5 +23,5 @@ makedocs(; ) deploydocs(; - repo="github.com/tamasgal/UnROOT.jl", + repo="github.com/JulieHEP/UnROOT.jl", ) From 494f19186a09559e426ab7af55c58837b5e2e5d4 Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Mon, 25 Apr 2022 09:51:23 +0100 Subject: [PATCH 50/59] Fix error when file is not existent (#164) * Fix error when file is not existent * Use SystemError instead of general error * Add test for non-existent-file opening --- src/root.jl | 2 +- test/runtests.jl | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/root.jl b/src/root.jl index bbeff6e4..2f107d51 100644 --- a/src/root.jl +++ b/src/root.jl @@ -60,7 +60,7 @@ function ROOTFile(filename::AbstractString; customstructs = Dict("TLorentzVector fobj = if startswith(filename, r"https?://") HTTPStream(filename) else - !isfile(filename) && "$filename is not a file" + !isfile(filename) && throw(SystemError("opening file $filename", 2)) MmapStream(filename) end header_bytes = read(fobj, HEAD_BUFFER_SIZE) diff --git a/test/runtests.jl b/test/runtests.jl index d10663eb..93ca152a 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -91,6 +91,8 @@ end @testset "ROOTFile" begin + @test_throws SystemError ROOTFile("non_existent_fname.root") + ROOTFile(joinpath(SAMPLES_DIR, "tree_with_histos.root")) do rootfile @test 100 == rootfile.header.fBEGIN @test 1 == length(rootfile.directory.keys) From 353b5b0410926b6cd06748deccd4cd2e568c8a32 Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Mon, 25 Apr 2022 10:52:06 +0200 Subject: [PATCH 51/59] Bump version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 5e156837..9ecbb10a 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "UnROOT" uuid = "3cd96dde-e98d-4713-81e9-a4a1b0235ce9" authors = ["Tamas Gal", "Jerry Ling", "Johannes Schumann", "Nick Amin"] -version = "0.8.5" +version = "0.8.6" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" From 9b42eb886447f1f3f1a045127cd53ab5f57e2033 Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Fri, 29 Apr 2022 16:46:17 +0200 Subject: [PATCH 52/59] C-style arrays (#166) * Add samples for issue 165 * fix C-stype array * fix io Co-authored-by: Jerry Ling --- src/custom.jl | 22 ++++++++++++++++++++ src/displays.jl | 2 +- src/root.jl | 5 ++++- test/runtests.jl | 14 +++++++++++++ test/samples/issue165.root | Bin 0 -> 5758 bytes test/samples/issue165_multiple_baskets.root | Bin 0 -> 7068 bytes 6 files changed, 41 insertions(+), 2 deletions(-) create mode 100644 test/samples/issue165.root create mode 100644 test/samples/issue165_multiple_baskets.root diff --git a/src/custom.jl b/src/custom.jl index e69da402..6668d05d 100644 --- a/src/custom.jl +++ b/src/custom.jl @@ -31,6 +31,28 @@ end # Custom struct interpretation abstract type CustomROOTStruct end +struct FixLenVector{N, T} <: AbstractVector{T} + vec::SVector{N, T} +end +(::Type{FixLenVector{N, T}})() where {N, T} = FixLenVector(zero(SVector{N, T})) +Base.length(x::FixLenVector) = length(x.vec) +Base.length(::Type{FixLenVector{N, T}}) where {N, T} = N +Base.size(x::FixLenVector) = size(x.vec) +Base.eltype(x::FixLenVector) = eltype(x.vec) +Base.iterate(x::FixLenVector) = iterate(x.vec) +Base.iterate(x::FixLenVector, n) = iterate(x.vec, n) +Base.getindex(x::FixLenVector, n) = getindex(x.vec, n) +function Base.reinterpret(::Type{FixLenVector{N, T}}, v::AbstractVector{UInt8}) where {N, T} + vs = reinterpret(T, v) + @. vs = ntoh(vs) + FixLenVector(SVector{N, T}(vs)) +end +function interped_data(rawdata, rawoffsets, ::Type{T}, ::Type{Nojagg}) where {T <: FixLenVector} + n = sizeof(T) + [ + reinterpret(T, x) for x in Base.Iterators.partition(rawdata, n) + ] +end # TLorentzVector const LVF64 = LorentzVector{Float64} diff --git a/src/displays.jl b/src/displays.jl index ce1335fa..ae143a38 100644 --- a/src/displays.jl +++ b/src/displays.jl @@ -79,7 +79,7 @@ end function Base.show(io::IO, ::MIME"text/plain", br::LazyBranch) print(io, summary(br)) - println(": ") + println(io, ": ") if length(br) < 200 Base.print_array(IOContext(io, :limit => true), br[:]) else diff --git a/src/root.jl b/src/root.jl index 2f107d51..b5a11293 100644 --- a/src/root.jl +++ b/src/root.jl @@ -395,9 +395,12 @@ function auto_T_JaggT(f::ROOTFile, branch; customstructs::Dict{String, Type}) end else _type = primitivetype(leaf) + if leaf.fLen > 1 # treat NTuple as Nojagg since size is static + _type = FixLenVector{Int(leaf.fLen), _type} + return _type, Nojagg + end _type = _jaggtype === Nojagg ? _type : Vector{_type} end - return _type, _jaggtype end diff --git a/test/runtests.jl b/test/runtests.jl index 93ca152a..9b27eb4e 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -708,6 +708,20 @@ end @test all(onesrow .== 1) end +@testset "C-array types" begin + tree = LazyTree(UnROOT.samplefile("issue165_multiple_baskets.root"), "arrays") + ele = tree.carr[3] + @test length(tree.carr) == 3 + @test length(ele) == 9 + @test eltype(ele) == Float64 + @test length(typeof(ele)) == 9 + @test all(ele .≈ + [0.7775048011809144, 0.8664217530127716, 0.4918492038230641, + 0.24464299401484568, 0.38991686533667, 0.15690925771226608, + 0.3850047958013624, 0.9268160513261408, 0.9298329730191421]) + @test all(ele .== [ele...]) +end + @testset "basketarray_iter()" begin f = UnROOT.samplefile("tree_with_vector_multiple_baskets.root") t = LazyTree(f,"t1") diff --git a/test/samples/issue165.root b/test/samples/issue165.root new file mode 100644 index 0000000000000000000000000000000000000000..298fc3ba1bef300d6acfa35874586ffcf8d3d3d4 GIT binary patch literal 5758 zcmbtY2T&A2mtJy|MKXxEfPiF>9Ardt4iW^3!Xi2BuH@i?1O>@Cg9OPL7L<&Dx=&aum|3{>-}I1=qZ=_C}idX zv_+UFvoN#+lP=vY<;&4PNn;yC!s{KdFjXL)RizCqQ~u3m<@^i$lp+pp@}>ngNt5Cp zGYSAp_S)qules|KWnU=EpClj#+q{JpzXNFAxH1HWFMx>$4bD8k8(^<_?dcQ0exUvn zMWlc{JMfb?x3|eu6&QKs8J?qg0_^2_Z8R$X2KIK#CK_kVfJ(t5s)sgfz&ew%L#b@s z&E)>O0AYsy*8ss0|5Je0Y@;%Ze=q|}qd#(>`9;8rhLE>)x*hOEbl6$gF2&!y8kOMy~38*-_$$+WDKdu6+N5ERk&y+AwyfCZBfkSH5=E-kZu-Eg8e{%evJ4Q(iJ=M6 z!vcPWS3U&pTLP;_>3Cc9lIQ^K-;fIr_m)Ax4X?0@(ZR9A(b0iHq5q%^wIURT-aAl; 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See + [Issue 156](https://github.com/JuliaHEP/UnROOT.jl/pull/156) for context. + # Example ```julia julia> mytree = LazyTree(f, "Events", ["Electron_dxy", "nMuon", r"Muon_(pt|eta)\$"]) @@ -309,7 +313,19 @@ function LazyTree(f::ROOTFile, s::AbstractString, branches) end end for b in res_bnames - d[Symbol(b)] = f["$s/$b"] + # split by `.` or `/` + norm_name = b + v = split(b, r"\.|\/") + if length(v) >= 2 # only normalize name when branches are split + head = v[1] + tail = v[2:end] + # remove duplicated info + replace!(tail, head => "") + # remove known split branch information + replace!(tail, "fCoordinates" => "") + norm_name = join([head; join(tail)], "_") + end + d[Symbol(norm_name)] = f["$s/$b"] end return LazyTree(TypedTables.Table(d)) end diff --git a/test/runtests.jl b/test/runtests.jl index 9b27eb4e..82eb6b1e 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -528,16 +528,16 @@ end # Issues @testset "issues" begin - rootfile = ROOTFile(joinpath(SAMPLES_DIR, "issue7.root")) + rootfile = UnROOT.samplefile("issue7.root") @test 2 == length(keys(rootfile)) @test [1.0, 2.0, 3.0] == UnROOT.array(rootfile, "TreeD/nums") @test [1.0, 2.0, 3.0] == UnROOT.array(rootfile, "TreeF/nums") close(rootfile) - # issue 55 - rootfile = ROOTFile(joinpath(SAMPLES_DIR, "cms_ntuple_wjet.root")) + # issue #55 and #156 + rootfile = UnROOT.samplefile("cms_ntuple_wjet.root") pts1 = UnROOT.array(rootfile, "variable/met_p4/fCoordinates/fCoordinates.fPt"; raw=false) - pts2 = LazyTree(rootfile, "variable", [r"met_p4/fCoordinates/.*", "mll"])[!, Symbol("met_p4/fCoordinates/fCoordinates.fPt")] + pts2 = LazyTree(rootfile, "variable", [r"met_p4/fCoordinates/.*", "mll"])[!, Symbol("met_p4_fPt")] pts3 = rootfile["variable/good_jets_p4/good_jets_p4.fCoordinates.fPt"] @test 24 == length(pts1) @test Float32[69.96958, 25.149912, 131.66693, 150.56802] == pts1[1:4] @@ -546,7 +546,7 @@ end close(rootfile) # issue 61 - rootfile = ROOTFile(joinpath(SAMPLES_DIR, "issue61.root")) + rootfile = UnROOT.samplefile("issue61.root") @test rootfile["Events/Jet_pt"][:] == Vector{Float32}[[], [27.324587, 24.889547, 20.853024], [], [20.33066], [], []] close(rootfile) From 23d87edc7cb984a4dfc94d1733bccaead1a0770b Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Wed, 1 Jun 2022 11:28:14 -0500 Subject: [PATCH 55/59] xrootd read support (#150) * xrootd * bump Julia requirement to >=1.6 --- .github/workflows/ci.yml | 3 --- Project.toml | 4 ++- src/root.jl | 5 ++++ src/streamsource.jl | 57 ++++++++++++++++++++++++++++++++++++++-- test/runtests.jl | 4 +++ 5 files changed, 67 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5dcc9416..f6686aa3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,9 +15,6 @@ jobs: fail-fast: false matrix: version: - - '1.3' - - '1.4' - - '1.5' - '1.6' - '1' # Leave this line unchanged. '1' will automatically expand to the latest stable 1.x release of Julia. - 'nightly' diff --git a/Project.toml b/Project.toml index bace3bf8..490ab880 100644 --- a/Project.toml +++ b/Project.toml @@ -23,6 +23,7 @@ PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" +xrootdgo_jll = "9d84c17e-11f2-50ef-8cc9-e9701362097f" [compat] AbstractTrees = "^0.3.0" @@ -44,7 +45,8 @@ PrettyTables = "^1.2.0" StaticArrays = "^0.12.0, ^1" Tables = "^1.0.0" TypedTables = "^1.0.0" -julia = "^1.3" +julia = "^1.6" +xrootdgo_jll = "^0.31.1" [extras] InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240" diff --git a/src/root.jl b/src/root.jl index b5a11293..765c9160 100644 --- a/src/root.jl +++ b/src/root.jl @@ -59,6 +59,11 @@ const HEAD_BUFFER_SIZE = 1024 function ROOTFile(filename::AbstractString; customstructs = Dict("TLorentzVector" => LorentzVector{Float64})) fobj = if startswith(filename, r"https?://") HTTPStream(filename) + elseif startswith(filename, "root://") + sep_idx = findlast("//", filename) + baseurl = filename[8:first(sep_idx)-1] + filepath = filename[last(sep_idx):end] + XRDStream(baseurl, filepath, "go") else !isfile(filename) && throw(SystemError("opening file $filename", 2)) MmapStream(filename) diff --git a/src/streamsource.jl b/src/streamsource.jl index 78935cf6..8ac211b7 100644 --- a/src/streamsource.jl +++ b/src/streamsource.jl @@ -1,5 +1,12 @@ +using xrootdgo_jll import HTTP +mutable struct XRDStream + gofile_id::Cstring # used as key to a global `map` on the Go side + seekloc::Int + size::Int +end + mutable struct MmapStream # Mmap based mmap_ary::Vector{UInt8} seekloc::Int @@ -75,10 +82,10 @@ mutable struct HTTPStream end end -const SourceStream = Union{MmapStream, HTTPStream} +const SourceStream = Union{MmapStream, HTTPStream, XRDStream} function Base.read(fobj::SourceStream, ::Type{T}) where T - return reinterpret(T, read(fobj, sizeof(T)))[1] # TODO: use `only` + return only(reinterpret(T, read(fobj, sizeof(T)))) end function Base.position(fobj::SourceStream) @@ -121,3 +128,49 @@ end function Base.read(fobj::SourceStream) read(fobj, fobj.size - fobj.seekloc + 1) end + +function XRDStream(urlbase::AbstractString, filepath::AbstractString, username::AbstractString) + file_id = @ccall xrootdgo.Open(urlbase::Cstring, filepath::Cstring, username::Cstring)::Cstring + # file_id = @threadcall((:Open, xrootdgo), Cstring, (Cstring, Cstring, Cstring), urlbase, filepath, username) + size = @ccall xrootdgo.Size(file_id::Cstring)::Int + XRDStream(file_id, 0, size) +end + +function Base.close(fobj::XRDStream) + xrootdgo.Close(fobj.gofile_id) +end + +function read_seek_nb(fobj::XRDStream, seek, nb) + buffer = Vector{UInt8}(undef, nb) + @threadcall((:ReadAt, xrootdgo), Cvoid, (Ptr{UInt8}, Cstring, Clong, Clong), buffer, fobj.gofile_id, nb, seek) + # @ccall xrootdgo.ReadAt(buffer::Ptr{UInt8}, + # fobj.gofile_id::Cstring, nb::Clong, seek::Clong)::Cvoid + return buffer +end +function _read!(ptr, fobj, nb, seekloc) + @ccall xrootdgo.ReadAt(ptr::Ptr{UInt8}, + fobj.gofile_id::Cstring, nb::Clong, seekloc::Clong)::Cvoid +end + +function _read!(ptr, fobj, nb) + _read!(ptr, fobj, nb, fobj.seekloc) +end + +function Base.read(fobj::XRDStream, ::Type{T}) where T + @debug @show T, sizeof(T) + nb = sizeof(T) + output = Ref{T}() + tko = Base.@_gc_preserve_begin output + po = Ptr{UInt8}(pointer_from_objref(output)) + _read!(po, fobj, nb, fobj.seekloc) + Base.@_gc_preserve_end tko + fobj.seekloc += nb + return output[] +end + +function Base.read(fobj::XRDStream, nb::Integer) + buffer = Vector{UInt8}(undef, nb) + GC.@preserve buffer _read!(buffer, fobj, nb, fobj.seekloc) + fobj.seekloc += nb + return buffer +end diff --git a/test/runtests.jl b/test/runtests.jl index 82eb6b1e..5a29c749 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -731,6 +731,10 @@ end end @testset "SourceStream remote" begin + r = ROOTFile("root://eospublic.cern.ch//eos/root-eos/cms_opendata_2012_nanoaod/Run2012B_DoubleMuParked.root") + @test r["Events"].fEntries == 29308627 + show(devnull, r) # test display + t = LazyTree("https://scikit-hep.org/uproot3/examples/Zmumu.root", "events") @test t.eta1[1] ≈ -1.21769 @test t.eta1[end] ≈ -1.57044 From 247f65e2a4f926e6532715a66adda85d0345d3a8 Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Fri, 3 Jun 2022 19:06:23 +0200 Subject: [PATCH 56/59] JOSS Paper (#135) * Add skeleton * Add open journal PDF generator GHA * Fix path to source file * Set output path * summary and statement of need * Minor cosmetics * Add comparison intro and uproot * Add uproot reference * add functionality * add performance citation * small additions * for ci * Cite pandas and numpy * Add ROOT citation * Cleanup and some additions * Minor updates and additions * Update references * Cleanup and additions * Update conclusions with Jerry's comments * Fix typo * Add NanoAOD refernce * Add reference to CMS/NanoAOD * Fix pandas reference * Add spaces between words and references * Fix typo Co-authored-by: Jerry Ling Co-authored-by: Nick Amin --- .github/workflows/draft-pdf.yml | 23 +++++ paper/LICENSE | 21 ++++ paper/paper.bib | 143 ++++++++++++++++++++++++++ paper/paper.md | 174 ++++++++++++++++++++++++++++++++ 4 files changed, 361 insertions(+) create mode 100644 .github/workflows/draft-pdf.yml create mode 100644 paper/LICENSE create mode 100644 paper/paper.bib create mode 100644 paper/paper.md diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml new file mode 100644 index 00000000..76310246 --- /dev/null +++ b/.github/workflows/draft-pdf.yml @@ -0,0 +1,23 @@ +on: [push] + +jobs: + paper: + runs-on: ubuntu-latest + name: Paper Draft + steps: + - name: Checkout + uses: actions/checkout@v2 + - name: Build draft PDF + uses: openjournals/openjournals-draft-action@master + with: + journal: joss + # This should be the path to the paper within your repo. + paper-path: paper/paper.md + - name: Upload + uses: actions/upload-artifact@v1 + with: + name: paper + # This is the output path where Pandoc will write the compiled + # PDF. Note, this should be the same directory as the input + # paper.md + path: paper/paper.pdf diff --git a/paper/LICENSE b/paper/LICENSE new file mode 100644 index 00000000..ffd0f5e8 --- /dev/null +++ b/paper/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2020 Tamas Gal, Jerry Ling and Nick Amin + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 00000000..b9eb5265 --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1,143 @@ +@article{Julia, + author = {Bezanson, Jeff. and Edelman, Alan. and Karpinski, Stefan. and Shah, Viral B.}, + title = {Julia: A Fresh Approach to Numerical Computing}, + journal = {SIAM Review}, + volume = {59}, + number = {1}, + pages = {65-98}, + year = {2017}, + doi = {10.1137/141000671}, + URL = { https://doi.org/10.1137/141000671}, + eprint = {https://doi.org/10.1137/141000671} +} + +@article{JuliaPerformance, + title={Performance of julia for high energy physics analyses}, + author={Stanitzki, Marcel and Strube, Jan}, + journal={Computing and Software for Big Science}, + volume={5}, + number={1}, + pages={1--11}, + year={2021}, + publisher={Springer} +} + +@software{jim_pivarski_2021_5539722, + author = {Jim Pivarski and + Henry Schreiner and + Nicholas Smith and + Chris Burr and + Dmitry Kalinkin and + Giordon Stark and + Nikolai Hartmann and + Doug Davis and + Ryunosuke O'Neil and + Andrzej Novak and + Ben Greiner and + Beojan Stanislaus and + ChristopheRappold and + Cosmin Deaconu and + Daniel Cervenkov and + Jonas Rübenach and + Josh Bendavid and + Kilian Lieret and + Michele Peresano and + Raymond Ehlers and + Ruggero Turra and + Tamas Gal and + Alexander Held}, + title = {scikit-hep/uproot4: 4.1.3}, + month = sep, + year = 2021, + publisher = {Zenodo}, + version = {4.1.3}, + doi = {10.5281/zenodo.5539722}, + url = {https://doi.org/10.5281/zenodo.5539722} +} +@software{pivarski_jim_2018_6522027, + author = {Pivarski, Jim and + Osborne, Ianna and + Ifrim, Ioana and + Schreiner, Henry and + Hollands, Angus and + Biswas, Anish and + Das, Pratyush and + Roy Choudhury, Santam and + Smith, Nicholas}, + title = {Awkward Array}, + month = oct, + year = 2018, + note = {If you use this software, please cite it as below.}, + publisher = {Zenodo}, + version = {1.9.0rc4}, + doi = {10.5281/zenodo.6522027}, + url = {https://doi.org/10.5281/zenodo.6522027} +} +@Article{harris2020array, + title = {Array programming with {NumPy}}, + author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J. + van der Walt and Ralf Gommers and Pauli Virtanen and David + Cournapeau and Eric Wieser and Julian Taylor and Sebastian + Berg and Nathaniel J. Smith and Robert Kern and Matti Picus + and Stephan Hoyer and Marten H. van Kerkwijk and Matthew + Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del + R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre + G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and + Warren Weckesser and Hameer Abbasi and Christoph Gohlke and + Travis E. Oliphant}, + year = {2020}, + month = sep, + journal = {Nature}, + volume = {585}, + number = {7825}, + pages = {357--362}, + doi = {10.1038/s41586-020-2649-2}, + publisher = {Springer Science and Business Media {LLC}}, + url = {https://doi.org/10.1038/s41586-020-2649-2} +} +@software{reback2020pandas, + author = {{The pandas development team}}, + title = {Pandas}, + month = feb, + year = 2020, + publisher = {Zenodo}, + version = {latest}, + doi = {10.5281/zenodo.3509134}, + url = {https://doi.org/10.5281/zenodo.3509134} +} +@article{Brun:1997pa, + author = "Brun, R. and Rademakers, F.", + editor = "Werlen, M. and Perret-Gallix, D.", + title = "{ROOT: An object oriented data analysis framework}", + doi = "10.1016/S0168-9002(97)00048-X", + journal = "Nucl. Instrum. Meth. A", + volume = "389", + pages = "81--86", + year = "1997" +} + +@article{Adri_n_Mart_nez_2016, + doi = {10.1088/0954-3899/43/8/084001}, + url = {https://doi.org/10.1088%2F0954-3899%2F43%2F8%2F084001}, + year = 2016, + month = {jun}, + publisher = {{IOP} Publishing}, + volume = {43}, + number = {8}, + pages = {084001}, + author = {S Adri{\'{a} +}n-Mart{\'{\i}}nez and M Ageron and F Aharonian and S Aiello and A Albert and F Ameli and E Anassontzis and M Andre and G Androulakis and M Anghinolfi and G Anton and M Ardid and T Avgitas and G Barbarino and E Barbarito and B Baret and J Barrios-Mart{\'{\i}} and B Belhorma and A Belias and E Berbee and A van den Berg and V Bertin and S Beurthey and V van Beveren and N Beverini and S Biagi and A Biagioni and M Billault and M Bond{\`{\i}} and R Bormuth and B Bouhadef and G Bourlis and S Bourret and C Boutonnet and M Bouwhuis and C Bozza and R Bruijn and J Brunner and E Buis and J Busto and G Cacopardo and L Caillat and M Calamai and D Calvo and A Capone and L Caramete and S Cecchini and S Celli and C Champion and R Cherkaoui El Moursli and S Cherubini and T Chiarusi and M Circella and L Classen and R Cocimano and J A B Coelho and A Coleiro and S Colonges and R Coniglione and M Cordelli and A Cosquer and P Coyle and A Creusot and G Cuttone and A D'Amico and G De Bonis and G De Rosa and C De Sio and F Di Capua and I Di Palma and A F D{\'{\i}}az Garc{\'{\i}}a and C Distefano and C Donzaud and D Dornic and Q Dorosti-Hasankiadeh and E Drakopoulou and D Drouhin and L Drury and M Durocher and T Eberl and S Eichie and D van Eijk and I El Bojaddaini and N El Khayati and D Elsaesser and A Enzenhöfer and F Fassi and P Favali and P Fermani and G Ferrara and C Filippidis and G Frascadore and L A Fusco and T Gal and S Galat{\`{a}} and F Garufi and P Gay and M Gebyehu and V Giordano and N Gizani and R Gracia and K Graf and T Gr{\'{e}}goire and G Grella and R Habel and S Hallmann and H van Haren and S Harissopulos and T Heid and A Heijboer and E Heine and S Henry and J J Hern{\'{a}}ndez-Rey and M Hevinga and J Hofestädt and C M F Hugon and G Illuminati and C W James and P Jansweijer and M Jongen and M de Jong and M Kadler and O Kalekin and A Kappes and U F Katz and P Keller and G Kieft and D Kie{\ss}ling and E N Koffeman and P Kooijman and A Kouchner and V Kulikovskiy and R Lahmann and P Lamare and A Leisos and E Leonora and M Lindsey Clark and A Liolios and C D Llorens Alvarez and D Lo Presti and H Löhner and A Lonardo and M Lotze and S Loucatos and E Maccioni and K Mannheim and A Margiotta and A Marinelli and O Mari{\c{s}} and C Markou and J A Mart{\'{\i}}nez-Mora and A Martini and R Mele and K W Melis and T Michael and P Migliozzi and E Migneco and P Mijakowski and A Miraglia and C M Mollo and M Mongelli and M Morganti and A Moussa and P Musico and M Musumeci and S Navas and C A Nicolau and I Olcina and C Olivetto and A Orlando and A Papaikonomou and R Papaleo and G E P{\u{a}}v{\u{a}}la{\c{s}} and H Peek and C Pellegrino and C Perrina and M Pfutzner and P Piattelli and K Pikounis and G E Poma and V Popa and T Pradier and F Pratolongo and G Pühlhofer and S Pulvirenti and L Quinn and C Racca and F Raffaelli and N Randazzo and P Rapidis and P Razis and D Real and L Resvanis and J Reubelt and G Riccobene and C Rossi and A Rovelli and M Salda{\~{n}}a and I Salvadori and D F E Samtleben and A S{\'{a}}nchez Garc{\'{\i}}a and A S{\'{a}}nchez Losa and M Sanguineti and A Santangelo and D Santonocito and P Sapienza and F Schimmel and J Schmelling and V Sciacca and M Sedita and T Seitz and I Sgura and F Simeone and I Siotis and V Sipala and B Spisso and M Spurio and G Stavropoulos and J Steijger and S M Stellacci and D Stransky and M Taiuti and Y Tayalati and D T{\'{e}}zier and S Theraube and L Thompson and P Timmer and C Tönnis and L Trasatti and A Trovato and A Tsirigotis and S Tzamarias and E Tzamariudaki and B Vallage and V Van Elewyck and J Vermeulen and P Vicini and S Viola and D Vivolo and M Volkert and G Voulgaris and L Wiggers and J Wilms and E de Wolf and K Zachariadou and J D Zornoza and J Z{\'{u}}{\~{n}}iga}, + title = {Letter of intent for {KM}3NeT 2.0}, + journal = {Journal of Physics G: Nuclear and Particle Physics} +} +@article{Ehataht:2020ebp, + author = {Ehat\"aht, Karl}, + editor = "Doglioni, C. and Kim, D. and Stewart, G. A. and Silvestris, L. and Jackson, P. and Kamleh, W.", + collaboration = "CMS", + title = "{NANOAOD: a new compact event data format in CMS}", + doi = "10.1051/epjconf/202024506002", + journal = "EPJ Web Conf.", + volume = "245", + pages = "06002", + year = "2020" +} diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 00000000..d9b5ede5 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,174 @@ +--- +title: 'UnROOT: an I/O library for the CERN ROOT file format written in Julia' +tags: + - Julia + - HEP +authors: + - name: Tamás Gál + orcid: 0000-0001-7821-8673 + affiliation: "1, 2" + - name: Jerry (Jiahong) Ling + orcid: 0000-0002-3359-0380 + affiliation: "3" + - name: Nick Amin + orcid: 0000-0003-2560-0013 + affiliation: "4" +affiliations: + - name: Erlangen Centre for Astroparticle Physics + index: 1 + - name: Friedrich-Alexander-Universität Erlangen-Nürnberg + index: 2 + - name: Harvard University + index: 3 + - name: University of California, Santa Barbara + index: 4 +date: 08 October 2021 +bibliography: paper.bib +--- +# Summary +`UnROOT.jl` is a pure Julia implementation of CERN ROOT [@Brun:1997pa] files I/O +(`.root`) that is fast, memory-efficient, and composes well with Julia's +high-performance iteration, array, and multi-threading interfaces. + +# Statement of need +The High-Energy Physics (HEP) community has been troubled by the two-language +problem for a long time. Often, physicists would start prototyping with a +`Python` front-end which glues to a `C/C++/Fortran` back-end. Soon they will hit +a task which is extremely hard to express in columnar (i.e. "vectorized") style, +a type of problems which are normally tackled with libraries like +`numpy` [@harris2020array] or `pandas` [@reback2020pandas]. This usually leads to +either writing `C++` kernels and interface them with `Python`, or porting the +prototype to `C++` and start to maintain two code bases including the wrapper +code. Both options are engineering challenges for physicists who usually have no +or little background in software engineering. Many steps of this process are +critical, like identifying bottlenecks, creating an architecture which is both +performant and maintainable at the same time while still being user-friendly and +logically structured. Using a `Python` front-end and dancing across language +barriers also hinders the ability to parallelize tasks that are conceptually +trivial most of the time. + +`UnROOT.jl` attempts to solve all of the above by choosing Julia, a +high-performance language with simple and expressive syntax [@Julia]. Julia is +designed to solve the two-language problem in general. This has been studied for +HEP specifically as well [@JuliaPerformance]. Analysis software written in Julia +can freely escape to a `for-loop` whenever vectorized-style processing is not +flexible enough, without any performance degradation. At the same time, +`UnROOT.jl` transparently supports multi-threading and multi-processing by +simply providing data structures which are a subtype of `AbstractArray`, the +built-in abstract type for array-like objects, which allows to interface with +array-routines from other packages easily, thanks to multiple dispatch, one of +the main features of Julia. + +# Features and Functionality + +The `ROOT` dataformat is flexible and mostly self-descriptive. Users can define +their own data structures (C++ classes) which derive from `ROOT` classes and +serialise them into directories, trees and branches. The information about the +deserialisation is written to the output file (therefore: self-descriptive) but +there are some basic structures and constants needed to bootstrap the parsing +process. One of the biggest advantages of the `ROOT` data format is the ability +to store jagged structures like nested arrays of structs with different +sub-array lengths. In high-energy physics, such structures are preferred to +resemble e.g. particle interactions and detector responses as signals from +different hardware components, combined into a tree of events. + +`UnROOT.jl` understands the core structure of `ROOT` files, and is able to +decompress and deserialize instances of the commonly used `TH1`, `TH2`, +`TDirectory`, `TTree` etc. ROOT classes. All basic C++ types for `TTree` +branches are supported as well, including their nested variants. Additionally, +`UnROOT.jl` provides a way to hook into the deserialisation process of custom +types where the automatic parsing fails. By the time of writing, `UnROOT` is +already used successfully in the data analysis of the KM3NeT neutrino +telescope [@Adri_n_Mart_nez_2016] and the CMS detector [@Ehataht:2020ebp]. + +Opening and loading a `TTree` lazily -- i.e. without reading the whole data into +memory -- is simple: + +```julia +julia> using UnROOT + +julia> f = ROOTFile("test/samples/NanoAODv5_sample.root") +ROOTFile with 2 entries and 21 streamers. +test/samples/NanoAODv5_sample.root + Events + "run" + "luminosityBlock" + "event" + "HTXS_Higgs_pt" + "HTXS_Higgs_y" + ... + +julia> mytree = LazyTree(f, "Events", ["Electron_dxy", "nMuon", r"Muon_(pt|eta)$"]) + Row Electron_dxy nMuon Muon_eta Muon_pt + Vector{Float32} UInt32 Vector{Float32} Vector{Float32} + + 1 [0.000371] 0 [] [] + 2 [-0.00982] 2 [0.53, 0.229] [19.9, 15.3] + 3 [] 0 [] [] + 4 [-0.00157] 0 [] [] + ... +``` + +As seen in the above example, the entries in the columns are multi-dimensional +and jagged. The `LazyTree` object acts as a table which suports sequential +or parallel iteration, selections and filtering based on ranges or masks, and +operations on whole columns: + +```julia +for event in mytree + # ... Operate on event +end + +Threads.@threads for event in mytree # multi-threading + # ... Operate on event +end + +mytree.Muon_pt # a column as a lazy vector of vectors +``` + +The `LazyTree` is designed as `<: AbstractArray` which makes it compose well +with the rest of the Julia ecosystem. For example, syntactic loop fusion [^1] or +Query-style tabular manipulations provided by packages like `Query.jl` [^2] without +any additional code support just work out-of-the-box. + +# Comparison with existing software + +This section focusses on the comparison with other existing ROOT I/O solutions +in the Julia universe, however, one honorable mention is `uproot` +[@jim_pivarski_2021_5539722], which is a purely Python-based ROOT I/O library +and played (still plays) an important role for the development of `UnROOT.jl` as +it is by the time of writing the most complete and best documented ROOT I/O +implementation. + +- `UpROOT.jl` is a wrapper for the aforementioned `uproot` Python package and + uses `PyCall.jl` [^3] as a bridge, which means that it relies on `Python` as a + glue language. In addition to that, `uproot` itself utilises the C++ library + `AwkwardArray` [@pivarski_jim_2018_6522027] to efficiently deal with jagged + data in `ROOT` files. Most of the features of `uproot` are available in the + Julia context, but there are intrinsic performance and usability drawbacks due + to the three language architecture. + +- `ROOT.jl` [^4] is one of the oldest Julia `ROOT` packages. It uses C++ bindings to + directly wrap the `ROOT` framework and therefore is not limited ot I/O. + Unfortunately, the `Cxx.jl` [^5] package which is used to generate the C++ glue + code does not support Julia 1.4 or later. The multi-threaded features are also + limited. + +# Conclusion + +`UnROOT.jl` is an important package in high-energy physics and related +scientific fields where the `ROOT` dataformat is established, since the ability +to read and parse scientific data is certainly the first mandatory step to open +the window to a programming language and its package ecosystem. `UnROOT.jl` has +demonstrated tree processing speeds at the same level as the `C++` `ROOT` +framework in per-event iteration as well as the Python-based `uproot` library in +chunked iteration. + +# References + + +[^1]: https://julialang.org/blog/2017/01/moredots/ +[^2]: https://github.com/queryverse/Query.jl +[^3]: https://github.com/JuliaPy/PyCall.jl +[^4]: https://github.com/JuliaHEP/ROOT.jl +[^5]: https://github.com/JuliaInterop/Cxx.jl From 54aea8b04ab1040ba93c3373d8e9a8c8f2493f40 Mon Sep 17 00:00:00 2001 From: Moelf Date: Fri, 3 Jun 2022 14:39:03 -0400 Subject: [PATCH 57/59] add DOI --- paper/paper.bib | 1 + 1 file changed, 1 insertion(+) diff --git a/paper/paper.bib b/paper/paper.bib index b9eb5265..4485c99b 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -17,6 +17,7 @@ @article{JuliaPerformance journal={Computing and Software for Big Science}, volume={5}, number={1}, + doi = {10.1007/s41781-021-00053-3}, pages={1--11}, year={2021}, publisher={Springer} From 9358bd596b2f3673a0324172b90870f8348902ca Mon Sep 17 00:00:00 2001 From: Jerry Ling Date: Fri, 3 Jun 2022 16:26:51 -0400 Subject: [PATCH 58/59] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 4b32be80..ab538115 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,7 @@ [![All Contributors](https://img.shields.io/badge/all_contributors-7-orange.svg?style=flat-square)](#contributors-) +[![status](https://joss.theoj.org/papers/bab42b0c60f9dc7ef3b8d6460bc7229c/status.svg)](https://joss.theoj.org/papers/bab42b0c60f9dc7ef3b8d6460bc7229c) [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliahep.github.io/UnROOT.jl/dev) [![Build Status](https://github.com/JuliaHEP/UnROOT.jl/workflows/CI/badge.svg)](https://github.com/JuliaHEP/UnROOT.jl/actions) [![Codecov](https://codecov.io/gh/JuliaHEP/UnROOT.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaHEP/UnROOT.jl) From fe28a4483236ea58cc43fefdad620e356c4bb674 Mon Sep 17 00:00:00 2001 From: Tamas Gal Date: Fri, 3 Jun 2022 23:23:01 +0200 Subject: [PATCH 59/59] Add JOSS badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index ab538115..77475c30 100644 --- a/README.md +++ b/README.md @@ -7,6 +7,7 @@ [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliahep.github.io/UnROOT.jl/dev) [![Build Status](https://github.com/JuliaHEP/UnROOT.jl/workflows/CI/badge.svg)](https://github.com/JuliaHEP/UnROOT.jl/actions) [![Codecov](https://codecov.io/gh/JuliaHEP/UnROOT.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaHEP/UnROOT.jl) +[![status](https://joss.theoj.org/papers/bab42b0c60f9dc7ef3b8d6460bc7229c/status.svg)](https://joss.theoj.org/papers/bab42b0c60f9dc7ef3b8d6460bc7229c) UnROOT.jl is a reader for the [CERN ROOT](https://root.cern) file format written entirely in Julia, without any dependence on ROOT or Python.

Tamas Gal
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Jerry Ling
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Tamas Gal
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