# Problem reading ROOT branch containing Strings with UnROOT.jl

**URL:** <https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671>\
**Category:** High Energy Physics\
**Tags:** package, hep\
**Created:** [June 14, 2024, 7:18pm UTC](https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671 "2024-06-14T19:18:35Z")\
**Posts on this page:** 8\
**Page:** 1

<div class="post-metadata">

**Author:** ![GSavvidis](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/gsavvidis/32/207145_2.png) [@GSavvidis](https://discourse.julialang.org/u/GSavvidis)\
**Post date:** [June 14, 2024, 7:18pm UTC](https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671/1 "2024-06-14T19:18:35Z")

</div>

Hello,  
I’m using Geant4 to simulate some decays and I’m saving the result in a root file which I then read with UnROOT.jl. I have the following code:

```julia
using DrWatson
quickactivate(@ __DIR__ )

using UnROOT

f = UnROOT.ROOTFile(datadir("sims/root/ss", "ss_U238_p=10bar_Rmin=292mm_Rmax=300mm.root"))

```

with structure  
 ![tree](https://global.discourse-cdn.com/julialang/original/3X/6/0/6044d854082c3fbd35eea4749fafed43857f0d6d.png)

I can successfully access branches except those containing Strings, such as the one called “Particle”, shown in the picture above. When I do:

```julia
UnROOT.LazyBranch(f, "G4Sim/Particle")

```

I’m getting the following error:

```julia
 Failed to show value:

TaskFailedException

nested task error: DimensionMismatch: expected input array of length 16, got length 12

Stacktrace:

[1] dimension_mismatch_fail(::Type{StaticArraysCore.SVector{16, UInt8}}, a::SubArray{UInt8, 1, Vector{UInt8}, Tuple{UnitRange{Int64}}, true})

@ StaticArrays ~/.julia/packages/StaticArrays/85pEu/src/convert.jl:196

[2] convert

@ ~/.julia/packages/StaticArrays/85pEu/src/convert.jl:201 [inlined]

[3] StaticArray

@ ~/.julia/packages/StaticArrays/85pEu/src/convert.jl:174 [inlined]

[4] reinterpret(::Type{UnROOT.FixLenVector{16, UInt8}}, v::SubArray{UInt8, 1, Vector{UInt8}, Tuple{UnitRange{Int64}}, true})

@ UnROOT ~/.julia/packages/UnROOT/xaBnN/src/custom.jl:86

[5] #235

@ ./none:0 [inlined]

[6] iterate

@ ./generator.jl:47 [inlined]

[7] collect_to!(dest::Vector{UnROOT.FixLenVector{16, UInt8}}, itr::Base.Generator{Base.Iterators.PartitionIterator{Vector{UInt8}}, UnROOT.var"#235#236"{UnROOT.FixLenVector{16, UInt8}}}, offs::Int64, st::Int64)

@ Base ./array.jl:892

[8] collect_to_with_first!

@ ./array.jl:870 [inlined]

[9] collect(itr::Base.Generator{Base.Iterators.PartitionIterator{Vector{UInt8}}, UnROOT.var"#235#236"{UnROOT.FixLenVector{16, UInt8}}})

@ Base ./array.jl:844

[10] interped_data(rawdata::Vector{UInt8}, rawoffsets::Vector{Int32}, ::Type{UnROOT.FixLenVector{16, UInt8}}, ::Type{UnROOT.Nojagg})

@ UnROOT ~/.julia/packages/UnROOT/xaBnN/src/custom.jl:90

[11] basketarray(f::UnROOT.ROOTFile, branch::UnROOT.TBranch_13, ithbasket::Int64)

@ UnROOT ~/.julia/packages/UnROOT/xaBnN/src/iteration.jl:64

[12] basketarray(lb::UnROOT.LazyBranch{UnROOT.FixLenVector{16, UInt8}, UnROOT.Nojagg, Vector{UnROOT.FixLenVector{16, UInt8}}}, ithbasket::Int64)

@ UnROOT ~/.julia/packages/UnROOT/xaBnN/src/iteration.jl:135

[13] #214

@ ~/.julia/packages/UnROOT/xaBnN/src/iteration.jl:486 [inlined]

[14] iterate

@ ./generator.jl:47 [inlined]

[15] _collect(c::UnitRange{Int64}, itr::Base.Generator{UnitRange{Int64}, UnROOT.var"#214#217"{UnROOT.LazyBranch{UnROOT.FixLenVector{16, UInt8}, UnROOT.Nojagg, Vector{UnROOT.FixLenVector{16, UInt8}}}}}, ::Base.EltypeUnknown, isz::Base.HasShape{1})

@ Base ./array.jl:854

[16] collect_similar

@ ./array.jl:763 [inlined]

[17] map

@ ./abstractarray.jl:3285 [inlined]

[18] getindex(ba::UnROOT.LazyBranch{UnROOT.FixLenVector{16, UInt8}, UnROOT.Nojagg, Vector{UnROOT.FixLenVector{16, UInt8}}}, range::UnitRange{Int64})

@ UnROOT ~/.julia/packages/UnROOT/xaBnN/src/iteration.jl:486

[19] (::UnROOT.var"#244#246"{UnROOT.LazyBranch{UnROOT.FixLenVector{16, UInt8}, UnROOT.Nojagg, Vector{UnROOT.FixLenVector{16, UInt8}}}})()

@ UnROOT ~/.julia/packages/UnROOT/xaBnN/src/displays.jl:95

Stack trace

Here is what happened, the most recent locations are first:

1. <mark> **wait** </mark> @ *task.jl:352*

2. <mark> **show** (io::IOContext{IOBuffer}, ::MIME{Symbol("text/plain")}, br::UnROOT.LazyBranch{UnROOT.FixLenVector{16, UInt8}, UnROOT.Nojagg, Vector{UnROOT.FixLenVector{16, UInt8}}})</mark> @ *displays.jl:97*

```

I’m on Julia 1.10.2 working on Pluto and I’m using the v0.10.31 version of UnROOT.

---

<div class="post-metadata">

**Author:** ![tamasgal](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tamasgal/32/27946_2.png) [@tamasgal](https://discourse.julialang.org/u/tamasgal)\
**Post date:** [June 17, 2024, 9:27am UTC](https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671/2 "2024-06-17T09:27:21Z")

</div>

Can you upload the file somewhere?

---

<div class="post-metadata">

**Author:** ![GSavvidis](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/gsavvidis/32/207145_2.png) [@GSavvidis](https://discourse.julialang.org/u/GSavvidis)\
**Post date:** [June 17, 2024, 2:10pm UTC](https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671/3 "2024-06-17T14:10:32Z")

</div>

Sure! I uploaded it [here](https://drive.google.com/file/d/1fk8UCY8f6Y6JQgmR_4slT6Bc2W2dbGV0/view?usp=sharing) cos it’s a .root file and I couldn’t upload it here (apologies if I’m too ignorant).  
Also I kept digging trying to understand more. I will put some information here in case it could be useful:

From python’s uproot, after reading the tree and calling

```julia
tree.typenames()

```

I got

```julia
{'fEvent': 'int32_t', 'ParentID': 'int32_t', 'TrackID': 'int32_t', 
'Particle': 'char*', 'MeanLife': 'double', 'Charge': 'double', 
'Process': 'char*', 'Edep': 'double', 'preTime': 'double', 'postTime': 'double', 'localTime': 'double', 'preKE': 'double', 'postKE': 'double', 
'preX': 'double', 'preY': 'double', 'preZ': 'double', 
'postX': 'double', 'postY': 'double', 'postZ': 'double', 
'preVolume': 'char*', 'postVolume': 'char*'}

```

From inspection of the branch in Julia I got:

```julia
br = f["G4Sim/Process"]
println(br.fLeaves)

UnROOT.TObjArray("", 0, Any[UnROOT.TLeafC
  fName: String "Process"
  fTitle: String "Process"
  fLen: Int32 16
  fLenType: Int32 1
  fOffset: Int32 0
  fIsRange: Bool false
  fIsUnsigned: Bool false
  fLeafCount: UInt32 0x00000000
  fMinimum: Int32 0
  fMaximum: Int32 16
])

```

Hope this can be useful. Please let me know if more information is needed.

I also tried to convert my TTree into RNTuple using PyROOT but as I’m not using pyroot, I failed miserably.

Edit: Including also the part of Geant4 I implemented to save the data

```julia
    G4AnalysisManager* analysisManager2 = G4AnalysisManager::Instance();

    analysisManager2->FillNtupleIColumn(0, eventNumber);
    analysisManager2->FillNtupleIColumn(1, parentID);
    analysisManager2->FillNtupleIColumn(2, trackID);
    analysisManager2->FillNtupleSColumn(3, name);
    analysisManager2->FillNtupleDColumn(4, meanLife);
    analysisManager2->FillNtupleDColumn(5, fCharge);
    analysisManager2->FillNtupleSColumn(6, proc);
    analysisManager2->FillNtupleDColumn(7, edepStep);
    analysisManager2->FillNtupleDColumn(8, preTime);
    analysisManager2->FillNtupleDColumn(9, postTime);
    analysisManager2->FillNtupleDColumn(10, localTime);
    analysisManager2->FillNtupleDColumn(11, preKE);
    analysisManager2->FillNtupleDColumn(12, postKE);
    analysisManager2->FillNtupleDColumn(13, prePoint_x);
    analysisManager2->FillNtupleDColumn(14, prePoint_y);
    analysisManager2->FillNtupleDColumn(15, prePoint_z);
    analysisManager2->FillNtupleDColumn(16, postPoint_x);
    analysisManager2->FillNtupleDColumn(17, postPoint_y);
    analysisManager2->FillNtupleDColumn(18, postPoint_z);
    analysisManager2->FillNtupleSColumn(19, preVolume);
    analysisManager2->FillNtupleSColumn(20, postVolume);
    analysisManager2->AddNtupleRow(0);

```

---

<div class="post-metadata">

**Author:** ![jling](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jling/32/212909_2.png) [@jling](https://discourse.julialang.org/u/jling)\
**Post date:** [June 17, 2024, 6:59pm UTC](https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671/4 "2024-06-17T18:59:02Z")

</div>

> [@GSavvidis](#):
>
> `br = f["G4Sim/Process"]`

if I manually get the `rawdata` and `rawoffsets` out, I see:

```julia
julia> String.(VectorOfVectors(debug[].rawdata, debug[].rawoffsets .+ 1))
846-element Vector{String}:
 "\x0fRadioactivation"
 "\aionIoni"
 "\aionIoni"
 "\x0fRadioactivation"
 "\x05eIoni"
 "\x0eTransportation"
 "\x0eTransportation"
 "\x0fRadioactivation"
 "\x05eIoni"
 "\x0fRadioactivation"
 "\x05eIoni"
 "\aionIoni"
 "\x0fRadioactivation"
 "\x05eIoni"
 "\x05eIoni"
 "\x05eIoni"
 "\x05eIoni"
 "\x05eIoni"
 "\x05eIoni"

```

Which seems mildly reasonable.

The bug seems to be that we’re interpreting this branch as `FixLenVector` instead of the normal offset jagged vector.

---

<div class="post-metadata">

**Author:** ![jling](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jling/32/212909_2.png) [@jling](https://discourse.julialang.org/u/jling)\
**Post date:** [June 17, 2024, 7:01pm UTC](https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671/5 "2024-06-17T19:01:50Z")

</div>

> <https://github.com/JuliaHEP/UnROOT.jl/blob/01969242f7006350ba0f194e615be63fd448df48/src/root.jl#L480>

this is the root cause of the bug – in this case even though `leafLen` is \> 1, somehow it’s not really fixed length?

> <https://github.com/root-project/root/blob/86a5a713474e37d96735231da74c000056d86d0c/tree/tree/inc/TLeaf.h#L72>

according to ROOT, this should indeed be fixed length

---

<div class="post-metadata">

**Author:** ![jling](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jling/32/212909_2.png) [@jling](https://discourse.julialang.org/u/jling)\
**Post date:** [June 17, 2024, 8:38pm UTC](https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671/6 "2024-06-17T20:38:10Z")

</div>

> <https://github.com/JuliaHEP/UnROOT.jl/pull/342#issue-2358209471>
>
> fix: https://discourse.julialang.org/t/problem-reading-root-branch-containing-st…rings-with-unroot-jl/115671/5
> 
> 
> \`\`\`julia-repl
> julia\> a = LazyTree("./ss\_U238\_p=10bar\_Rmin=292mm\_Rmax=300mm.root", "G4Sim");
> 
> julia\> a
> Row │ postZ postTime preKE preX MeanLife localTime Edep Trac ⋯
> │ Float64 Float64 Float64 Float64 Float64 Float64 Float64 Int3 ⋯
> ─────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
> 1 │ -102.05345950608458 3.0685201317363455e26 0.0 49.73353991915856 2.034191e26 3.0685201317363455e26 0.0 1 ⋯
> 2 │ -102.04651578986307 3.0685201317363455e26 4.1979216899649145 49.73353991915856 -1.0 0.0005457291372516042 4.1979216899649145 3 ⋯
> 3 │ -102.05346001428659 3.0685201317363455e26 0.07182831002864987 49.73353991915856 3.004037e15 2.3330065525051903e-6 0.07182831002864987 2 ⋯
> 4 │ -102.05346001428659 3.0685201317567714e26 0.0 49.733540045379584 3.004037e15 2.0425886986503205e15 0.0 2 ⋯
> 5 │ -102.0539008556144 3.0685201317567714e26 0.025275776502425962 49.733540045379584 -1.0 5.298457306211964e-6 0.025275776502425962 6 ⋯
> 6 │ -106.84346294108786 3.0685201317567714e26 0.08209409297571678 49.733540045379584 -1.0 0.02146110939511165 0.0 5 ⋯
> 7 │ -2000.0 3.0685201317567714e26 0.08209409297571678 47.430551380285756 -1.0 8.503551864822667 0.0 5 ⋯
> 8 │ -102.05346001428659 3.0685201317567714e26 1.344596967101097e-7 49.733540045379584 0.0 7.878121781487446e-305 1.344596967101097e-7 4 ⋯
> 9 │ -102.05302086535103 3.0685201317567714e26 0.04298589500133121 49.733540045379584 -1.0 1.041804810150761e-5 0.04298589500133121 8 ⋯
> 10 │ -102.05346001428659 3.0685201317567714e26 1.050066202878952e-7 49.733540045379584 0.0 7.741051586449725e-306 1.050066202878952e-7 7 ⋯
> 11 │ -102.05337759223123 3.0685201317567714e26 0.012766969704394504 49.733540045379584 -1.0 2.2819678030339488e-6 0.012766969704394504 10 ⋯
> 12 │ -102.05346003677495 3.0685201317567714e26 3.0297087505459785e-8 49.733540045379584 1.00325e11 0.0002591365343473467 3.0297087505459785e-8 9 ⋯
> 13 │ -102.05346003677495 3.0685201317567714e26 0.0 49.73354002365522 1.00325e11 1.414757510502053e10 0.0 9 ⋯
> 14 │ -102.0850983567464 3.0685201317567714e26 0.6354402172300221 49.73354002365522 -1.0 0.0002512298153439289 0.09170627685882858 13 ⋯
> 15 │ -102.09325779364904 3.0685201317567714e26 0.5437339403711935 49.679954554654216 -1.0 0.00046216017918337645 0.11757367433007723 13 ⋯
> 16 │ -102.07580116793557 3.0685201317567714e26 0.42616026604111623 49.63375029065793 -1.0 0.000623815479346648 0.06776978396433882 13 ⋯
> 17 │ -102.08504063006555 3.0685201317567714e26 0.35839048207677743 49.59869675442205 -1.0 0.0007576498289719425 0.07490690583766167 13 ⋯
> 18 │ -102.07678505845898 3.0685201317567714e26 0.28348357623911574 49.62889262762954 -1.0 0.000861614254051986 0.042674996475252816 13 ⋯
> 19 │ -102.09451113711731 3.0685201317567714e26 0.24080857976386294 49.65041254089083 -1.0 0.000948895940544778 0.1282858215721039 13 ⋯
> 20 │ -102.09189861553278 3.0685201317567714e26 0.11252275819175905 49.6500709917623 -1.0 0.000985338653087699 0.03837228992128173 13 ⋯
> 21 │ -102.08989108494839 3.0685201317567714e26 0.07415046827047733 49.646863130739476 -1.0 0.0010065402178248463 0.047574254567196175 13 ⋯
> 22 │ -102.09023049871139 3.0685201317567714e26 0.026576213703281157 49.645250682518146 -1.0 0.0010121881336086595 0.026576213703281157 13 ⋯
> 23 │ -103.57478100532907 3.0685201317567714e26 1.6320048207520537 49.73354002365522 -1.0 0.01572578470351275 0.0 12 ⋯
> 24 │ -730.8722678518567 3.0685201317567714e26 1.6320048207520537 51.29807043849364 -1.0 6.500054487921658 0.0 12 ⋯
> 25 │ -102.0534596801017 3.0685201317567714e26 5.041423719376326e-6 49.73354002365522 1.117712e22 0.0002572019758040831 5.041423719376326e-6 11 ⋯
> 26 │ -102.0534596801017 3.0685363408853736e26 0.0 49.73354012060899 1.117712e22 1.6209128602251994e21 0.0 11 ⋯
> 27 │ -102.04642108042141 3.0685363408853736e26 4.7745444062238676 49.73354012060899 -1.0 0.000606515507465791 4.7745444062238676 15 ⋯
> 28 │ -102.05346024604968 3.0685363408853736e26 0.08312559378100559 49.73354012060899 3.432811e21 2.7993134822468136e-6 0.08312559378100559 14 ⋯
> 29 │ -102.05346024604968 3.0685467785417935e26 0.0 49.73354048515049 3.432811e21 1.0437656419799024e21 0.0 14 ⋯
> 30 │ -102.0578740887279 3.0685467785417935e26 4.686717724997379 49.73354048515049 -1.0 0.0005971372135061732 4.686717724997379 17 ⋯
> 31 │ -102.05345986634265 3.0685467785417935e26 0.08304227498592809 49.73354048515049 7.284479e19 2.8973621866059515e-6 0.08304227498592809 16 ⋯
> ⋮ │ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋱
> 14 columns and 117333 rows omitted
> 
> julia\> a.Process
> 117364-element LazyBranch{SubArray{Char, 1, Vector{Char}, Tuple{UnitRange{Int64}}, true}, UnROOT.Nooffsetjagg, ArraysOfArrays.VectorOfVectors{Char, Vector{Char}, Vector{Int32}, Vector{Tuple{}}}}:
> \['\\x0f', 'R', 'a', 'd', 'i', 'o', 'a', 'c', 't', 'i', 'v', 'a', 't', 'i', 'o', 'n'\]
> \['\\a', 'i', 'o', 'n', 'I', 'o', 'n', 'i'\]
> \['\\a', 'i', 'o', 'n', 'I', 'o', 'n', 'i'\]
> \['\\x0f', 'R', 'a', 'd', 'i', 'o', 'a', 'c', 't', 'i', 'v', 'a', 't', 'i', 'o', 'n'\]
> ...
> 
> julia\> a.Particle
> 117364-element LazyBranch{SubArray{Char, 1, Vector{Char}, Tuple{UnitRange{Int64}}, true}, UnROOT.Nooffsetjagg, ArraysOfArrays.VectorOfVectors{Char, Vector{Char}, Vector{Int32}, Vector{Tuple{}}}}:
> \['\\x04', 'U', '2', '3', '8'\]
> \['\\x05', 'a', 'l', 'p', 'h', 'a'\]
> \['\\x05', 'T', 'h', '2', '3', '4'\]
> \['\\x05', 'T', 'h', '2', '3', '4'\]
> \['\\x02', 'e', '-'\]
> \['\\t', 'a', 'n', 't', 'i', '\_', 'n', 'u', '\_', 'e'\]
> ...
> \`\`\`
> 
> I think somehow this is still wrong, but not sure how to fix without knowing what the data should be.

I have added a PR that fixes this now. Fundamentally we treat this as `Vector{Char}` since that’s what TLeafC seems to be. Let’s continue the discussion in the PR.

---

<div class="post-metadata">

**Author:** ![GSavvidis](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/gsavvidis/32/207145_2.png) [@GSavvidis](https://discourse.julialang.org/u/GSavvidis)\
**Post date:** [June 17, 2024, 10:12pm UTC](https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671/7 "2024-06-17T22:12:00Z")

</div>

Thank you!

---

<div class="post-metadata">

**Author:** ![tamasgal](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tamasgal/32/27946_2.png) [@tamasgal](https://discourse.julialang.org/u/tamasgal)\
**Post date:** [June 18, 2024, 7:19am UTC](https://discourse.julialang.org/t/problem-reading-root-branch-containing-strings-with-unroot-jl/115671/8 "2024-06-18T07:19:47Z")

</div>

That’s indeed a bummer. Thanks Jerry for the quick PR, looks good so far 🙂