I originally posted this on the julia discourse <a href="https://discourse.julialang.o

UnROOT 0.10.26 will allow you <div class="highlight highlight-source-julia notrans

huh, I didn't realize but the test file is kinda of large: <div class="snippet-cli

<a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/us

Fix on the way in <a class="issue-link js-issue-link" data-error-text="Failed to load

Sure there you go: <a href="https://polybox.ethz.ch/index.php/s/PcYbFyA5WO2Txvt" r

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tamasgal commented on June 8, 2024 2

UnROOT 0.10.26 will allow you

julia> t = LazyTree(f, "sim", [r"ghost/ghost\.(.*)" => s"\1"])
 Row │ ypos             ghostID          time             stepID           fUniqueID        xmom             pd ⋯
     │ SubArray{Float3  SubArray{Int32,  SubArray{Float3  SubArray{Int32,  SubArray{UInt32  SubArray{Float3  Su ⋯
─────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────
 1   │ [982.0, 6.83]    [110000, 11000   [3230.0, 36.4]   [0, 0]           [0, 0]           [-25.6, -29.5]   [- ⋯
 2   │ [2590.0]         [110000]         [29.7]           [0]              [0]              [21.9]           [1 ⋯
 3   │ [258.0, -2230.   [110000, 11000   [774.0, 48.0]    [0, 0]           [0, 0]           [-44.3, 22.1]    [- ⋯
 4   │ [-1850.0]        [110000]         [60.6]           [0]              [0]              [14.1]           [1 ⋯
 5   │ []               []               []               []               []               []               [] ⋯
 6   │ [512.0]          [110000]         [587.0]          [0]              [0]              [-11.5]          [- ⋯
 7   │ [-11.0]          [110000]         [40.8]           [0]              [0]              [-2.61]          [2 ⋯
 8   │ [2890.0]         [110000]         [28.7]           [0]              [0]              [-8.56]          [1 ⋯
 9   │ []               []               []               []               []               []               [] ⋯
 10  │ [28.1]           [110000]         [41.0]           [0]              [0]              [-0.453]         [2 ⋯
 11  │ [2660.0]         [110000]         [799.0]          [0]              [0]              [-4.84]          [- ⋯
 12  │ [12.0]           [110000]         [41.0]           [0]              [0]              [2.28]           [2 ⋯
 13  │ [33.0]           [110000]         [41.8]           [0]              [0]              [-4.04]          [2 ⋯
 14  │ [-0.84]          [110000]         [40.5]           [0]              [0]              [-5.09]          [2 ⋯
 15  │ [664.0]          [110000]         [311.0]          [0]              [0]              [-3.08]          [1 ⋯
 16  │ []               []               []               []               []               []               [] ⋯
 17  │ [-1220.0]        [110000]         [640.0]          [0]              [0]              [7.4]            [1 ⋯
 18  │ [-2290.0, -269   [110000, 11000   [1410.0, 1410.   [0, 0, 0]        [0, 0, 0]        [0.0214, 0.01,   [2 ⋯
 19  │ [906.0]          [110000]         [8140.0]         [0]              [0]              [41.8]           [- ⋯
 20  │ [3430.0]         [110000]         [4960.0]         [0]              [0]              [-13.3]          [- ⋯
 21  │ []               []               []               []               []               []               [] ⋯
 22  │ [5.71]           [110000]         [41.0]           [0]              [0]              [6.6]            [2 ⋯
 23  │ []               []               []               []               []               []               [] ⋯
 24  │ [1330.0]         [110000]         [1250.0]         [0]              [0]              [-24.4]          [1 ⋯
 25  │ [-1050.0]        [110000]         [23.5]           [0]              [0]              [10.1]           [1 ⋯
 26  │ [-280.0, -2400   [110000, 11000   [1150.0, 39.1]   [0, 0]           [0, 0]           [0.412, -13.6]   [2 ⋯
 27  │ []               []               []               []               []               []               [] ⋯
 28  │ [-12.8]          [110000]         [1150.0]         [0]              [0]              [10.7]           [- ⋯
 29  │ [2770.0, 2080.   [110000, 11000   [1610.0, 20.5]   [0, 0]           [0, 0]           [20.8, -15.4]    [- ⋯
 30  │ [262.0, -866.0   [110000, 11000   [36.3, 35.7]     [0, 0]           [0, 0]           [-17.5, 5.21]    [1 ⋯
 31  │ []               []               []               []               []               []               [] ⋯
  ⋮  │        ⋮                ⋮                ⋮                ⋮                ⋮                ⋮            ⋱
                                                                                  7 columns and 1169 rows omitted

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TheFibonacciEffect commented on June 8, 2024 1

Thank you so much for the timely response! Even on a saturday, I appreciate that a lot.

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tamasgal commented on June 8, 2024 1

Science never sleeps ;)

Let me know if you have other issues. The next weeks will be very busy for me though 🙈

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Moelf commented on June 8, 2024 1

huh, I didn't realize but the test file is kinda of large:

 test/samples/issue323.root | Bin 0 -> 5890205 bytes

is it possible to reduce it

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TheFibonacciEffect commented on June 8, 2024 1

@Moelf
Sorry about that, this is also a way to solve large filesizes I guess 😅
Here this file should work: https://polybox.ethz.ch/index.php/s/i6KKEMt8A7UtVM0

julia> LazyTree("./issue323_small.root", "sim", [r"ghost/ghost\.(.*)"])
 Row │ ghost_ymom                   ghost_fBits                  ghost_pdgid                  ghost_trackID                ghost_ghostID                ghost_ ⋯
     │ SubArray{Float3              SubArray{UInt32              SubArray{Int32,              SubArray{Int32,              SubArray{Int32,              SubArr ⋯
─────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 1   │ [-3.08, -3.08, -3.08, -3.08  [50331648, 50331648, 503316  [-13, -13, -13, -13, -13, -  [3, 3, 3, 3, 3, 3, 3, 3, 3,  [110000, 110001, 110002, 11  [21.7, ⋯
 2   │ [-2.92, -2.92, -2.92, -2.92  [50331648, 50331648, 503316  [211, 211, 211, 211, 211, 2  [1, 1, 1, 1, 1, 1, 1, 1, 1,  [110000, 110001, 110002, 11  [22.8, ⋯
 3   │ [0.417, 0.417, 0.417, 0.417  [50331648, 50331648, 503316  [211, 211, 211, 211, 211, 2  [1, 1, 1, 1, 1, 1, 1, 1, 1,  [110000, 110001, 110002, 11  [21.8, ⋯
 4   │ [-10.8, -10.8, -10.8, -10.8  [50331648, 50331648, 503316  [-14, -14, -14, -14, -14, -  [4, 4, 4, 4, 4, 4, 4, 4, 4,  [110000, 110001, 110002, 11  [10100 ⋯
 5   │ [-21.3, -21.3, -21.3, -21.3  [50331648, 50331648, 503316  [14, 14, 14, 14, 14, 14, 14  [2, 2, 2, 2, 2, 2, 2, 2, 2,  [110000, 110001, 110002, 11  [13.2, ⋯
 6   │ [-15.2, -15.2, -15.2, -15.2  [50331648, 50331648, 503316  [211, 211, 211, 211, 211, 2  [1, 1, 1, 1, 1, 1, 1, 1, 1,  [110000, 110001, 110002, 11  [22.3, ⋯
 7   │ [2.34, 2.34, 2.34, 2.34, 2.  [50331648, 50331648, 503316  [-14, -14, -14, -14, -14, -  [4, 4, 4, 4, 4, 4, 4, 4, 4,  [110000, 110001, 110002, 11  [1140. ⋯
 8   │ [28.6, 28.6, 28.6, 28.6, 28  [50331648, 50331648, 503316  [14, 14, 14, 14, 14, 14, 14  [2, 2, 2, 2, 2, 2, 2, 2, 2,  [110000, 110001, 110002, 11  [20.3, ⋯
 9   │ [9.87, 9.87, 9.87, 9.87, 9.  [50331648, 50331648, 503316  [211, 211, 211, 211, 211, 2  [1, 1, 1, 1, 1, 1, 1, 1, 1,  [110000, 110001, 110002, 11  [22.1, ⋯
 10  │ [10.3, 10.3, 10.3, 10.3, 10  [50331648, 50331648, 503316  [14, 14, 14, 14, 14, 14, 14  [2, 2, 2, 2, 2, 2, 2, 2, 2,  [110000, 110001, 110002, 11  [10.3, ⋯
 11  │ [-24.1, -24.1, -24.1, -24.1  [50331648, 50331648, 503316  [14, 14, 14, 14, 14, 14, 14  [2, 2, 2, 2, 2, 2, 2, 2, 2,  [110000, 110001, 110002, 11  [15.0, ⋯
  ⋮  │              ⋮                            ⋮                            ⋮                            ⋮                            ⋮                      ⋱                                                                                                                               8 columns and 113 rows omitted

Thanks again for helping me out with the issue : )

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tamasgal commented on June 8, 2024

Just a very quick answer with a workaround, to allow you to proceed with your research. You can use the array() function to load the full data into memory. Since your file is small, laziness is not really needed, but your mileage may vary ;)

Anyways this is an example:

julia> f = ROOTFile("/Users/tamasgal/Downloads/pienu00002-02.root")
ROOTFile with 2 entries and 27 streamers.
/Users/tamasgal/Downloads/pienu00002-02.root
├─ sim (TTree)
│  ├─ "info"
│  ├─ "init"
│  ├─ "track"
│  ├─ "decay"
│  ├─ "ghost"
│  ├─ "ghostface"
│  └─ "upstream"
└─ PIMCRunHeader (PIMCRunHeader)


julia> UnROOT.array(f, "sim/ghost/ghost.pdgid")
1200-element ArraysOfArrays.VectorOfVectors{Int32, Vector{Int32}, Vector{Int32}, Vector{Tuple{}}}:
 Int32[-14, 14]
 Int32[14]
 Int32[-14, 14]
 Int32[14]
 0-element view(::Vector{Int32}, 7:6) with eltype Int32
 Int32[-14]
 Int32[211]

I will have a closer look at the file. LazyTree and LazyBranch are sometimes a bit hard to use with nested data.

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tamasgal commented on June 8, 2024

OK, the first problem is that you are using the wrong path to the subbranch. I don't blame you, this is just something which is probably (read obviously) not very well documented ;)

If the structure is the following:

julia> f["sim/ghost"]
ghost
├─ ghost.fUniqueID
├─ ghost.fBits
├─ ghost.ghostID
├─ ghost.trackID
├─ ghost.stepID
├─ ghost.pdgid
├─ ghost.xpos
├─ ghost.ypos
├─ ghost.zpos
├─ ghost.time
├─ ghost.xmom
├─ ghost.ymom
└─ ghost.zmom

the path to the subbranch is "sim/ghost/ghost.pdgid". A LazyTree would then be

LazyBranch(f, "sim", ["sim/ghost/ghost.pdgid"])

or using a regex:

julia> LazyTree(f, "sim", [r"ghost/ghost\.(.*)" => s"\1"])

However (now comes the real problem), you will face the following error:

ERROR: MethodError: no method matching UInt32()

Closest candidates are:
  UInt32(::HTTP.WebSockets.Mask)
   @ HTTP ~/.julia/packages/HTTP/1EWL3/src/WebSockets.jl:62
  UInt32(::Char)
   @ Base char.jl:127
  UInt32(::Float64)
   @ Base float.jl:884
  ...

Stacktrace:
 [1] LazyBranch(f::ROOTFile, b::UnROOT.TBranchElement_10)
   @ UnROOT ~/Dev/UnROOT.jl/src/iteration.jl:124)

which is there because we never had a flat array and we use VectorOfVectors and do not cover the case for a flat array 🙈

I'll try to provide a fix asap.

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tamasgal commented on June 8, 2024

Fix on the way in #324

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TheFibonacciEffect commented on June 8, 2024

Sure there you go:
https://polybox.ethz.ch/index.php/s/PcYbFyA5WO2Txvt

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Moelf commented on June 8, 2024

@TheFibonacciEffect that file seems to be empty:

julia> LazyTree("./test/samples/issue323_small.root", "sim", [r"ghost/ghost\.(.*)"])
 Row │ ghost_ymom       ghost_fBits      ghost_pdgid      ghost_trackID    ghost_ghostID    ghost_time       ghost_xmom       ghost_xpos       ghost_zmom      ⋯
     │ SubArray{Float3  SubArray{UInt32  SubArray{Int32,  SubArray{Int32,  SubArray{Int32,  SubArray{Float3  SubArray{Float3  SubArray{Float3  SubArray{Float3 ⋯
─────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
                                                                                                                                               4 columns omitted

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tamasgal commented on June 8, 2024

Oh shoot, that's my bad, I misread the file size for whatever reason (thought it's 500kB) 🙈

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