Reading bare variables from a tree

ROOT
1

Hi,
I have a tree filled with an event class: the class is complicated and contains subclasses in vectors. The tree works pretty fine when read with the event itself.

For a macro* I would like to read some variable in a ntuple way, like: Int_t evnum, n_clusters; tree->SetBranchAddress ("evnum", &evnum); tree->SetBranchAddress ("v.npmt", &npmt); tree->GetEntry (100); Unfortunately when doing this way, it does not work: every variable remains empty.

Moreover, as a general comment: immagine that v (in the previous code) is a vector of classes; (if reading this way is possible), will npmt point always to variable in the first element of v? like v[0].npmt?

Thanks,
Alessandro

*I have to modify the current long macro and keeping the ntuple reading style would simplify the porting.

2

try the following:

Int_t evnum, n_clusters; tree->SetMakeClass(1); //<========== tree->SetBranchAddress ("evnum", &evnum); tree->SetBranchAddress ("v.npmt", &npmt); tree->GetEntry (100);

Rene

3

Now it crashes :slight_smile:
Have root 5.26.00 (but the same happen for 5.25)

Hints?

4

Hi,

Most likely the variable you use for SetBranchAddress is no longer in scope.
You can pinpoint what the problem really is by using valgrind.

[quote]Moreover, as a general comment: immagine that v (in the previous code) is a vector of classes; (if reading this way is possible), will npmt point always to variable in the first element of v? like v[0].npmt? [/quote]No,
you actually MUST pass the address of an array (of the right fundamental type) large enough to hold the largest number of element in the vector. So
something likeInt_t evnum, npmt[1000]; tree->SetBranchAddress ("evnum", &evnum); tree->SetBranchAddress ("v.npmt", &npmt); tree->GetEntry (100);

Cheers,
Philippe.

5

Not a variable out of scope problem:

[quote]$ root -l /bxstorage/rootfiles/cycle_12/2009/Aug_30/Run011002_c12.root
Attaching file /bxstorage/rootfiles/cycle_12/2009/Aug_30/Run011002_c12.root as _file0…
Warning in TClass::TClass: no dictionary for class BxEvent is available
[…]
Warning in TClass::TClass: no dictionary for class BxPhysTags is available
root [1] TTree bxtree = (TTree)_file0->Get (“bxtree”);
root [2] Int_t evnum, n_clusters, npmts;
root [3] bxtree->SetMakeClass(1);
root [4] bxtree->SetBranchAddress (“evnum”, &evnum);
root [5] bxtree->GetEntry (200);

*** Break *** segmentation violation
Using host libthread_db library “/lib/tls/i686/cmov/libthread_db.so.1”.
Attaching to program: /proc/20132/exe, process 20132
[Thread debugging using libthread_db enabled]
[New Thread -1226904672 (LWP 20132)]
0xffffe410 in __kernel_vsyscall ()
[…]
[/quote]
(same with other versions of root)

6

Hi,

What type is ‘evnum’ in the TTree (you may cross-check using bxtree->MakeSelector(“bxsel”) and look at the content of bxsel.h)?

What does

valgrind root.exe -b -l /bxstorage/rootfiles/cycle_12/2009/Aug_30/Run011002_c12.root outputs for the same example?

Cheers,
Philippe.

7

Hi,
it’s a Int_t.

Here the valgring output for the GetEntry command with the old root:[quote][…]
root [5] bxtree->GetEntry (200)
==13210==
==13210== Invalid write of size 4
==13210== at 0x6177AA6: TBufferFile::ReadInt(int&) (in /home/cern_etch/root_v5.20.00-1/lib/libRIO.so.5.20)
==13210== by 0x6F34D8A: TBranchElement::ReadLeaves(TBuffer&) (in /home/cern_etch/root_v5.20.00-1/lib/libTree.so.5.20)
==13210== by 0x6F2B51D: TBranch::GetEntry(long long, int) (in /home/cern_etch/root_v5.20.00-1/lib/libTree.so.5.20)
==13210== by 0x6F318B3: TBranchElement::GetEntry(long long, int) (in /home/cern_etch/root_v5.20.00-1/lib/libTree.so.5.20)
==13210== by 0x6F31765: TBranchElement::GetEntry(long long, int) (in /home/cern_etch/root_v5.20.00-1/lib/libTree.so.5.20)
==13210== by 0x6F31765: TBranchElement::GetEntry(long long, int) (in /home/cern_etch/root_v5.20.00-1/lib/libTree.so.5.20)
==13210== by 0x6F7FAE2: TTree::GetEntry(long long, int) (in /home/cern_etch/root_v5.20.00-1/lib/libTree.so.5.20)
==13210== by 0x6FFD32B: G__G__Tree_103_0_66(G__value*, char const*, G__param*, int) (in /home/cern_etch/root_v5.20.00-1/lib/libTree.so.5.20)
==13210== by 0x4710379: Cint::G__ExceptionWrapper(int ()(G__value, char const*, G__param*, int), G__value*, char*, G__param*, int) (in /home/cern_etch/root_v5.20.00-1/lib/libCint.so.5.20)
==13210== by 0x47B10E7: G__execute_call (in /home/cern_etch/root_v5.20.00-1/lib/libCint.so.5.20)
==13210== by 0x47B2148: G__call_cppfunc (in /home/cern_etch/root_v5.20.00-1/lib/libCint.so.5.20)
==13210== by 0x4788AB8: G__interpret_func (in /home/cern_etch/root_v5.20.00-1/lib/libCint.so.5.20)
==13210== Address 0x0 is not stack’d, malloc’d or (recently) free’d
[/quote]

And here the full output of valgrind for root 5.26:[quote]
[2069:0]~$ valgrind root.exe -b -l
==19842== Memcheck, a memory error detector
==19842== Copyright © 2002-2009, and GNU GPL’d, by Julian Seward et al.
==19842== Using Valgrind-3.5.0-Debian and LibVEX; rerun with -h for copyright info
==19842== Command: root.exe -b -l
==19842==
root [0] TFile f(“Run011002_c12.root”);
==19842== Conditional jump or move depends on uninitialised value(s)
==19842== at 0x5260A2E: inflateReset2 (in /usr/lib/libz.so.1.2.3.4)
==19842== by 0x5260B0C: inflateInit2_ (in /usr/lib/libz.so.1.2.3.4)
==19842== by 0x5260B82: inflateInit_ (in /usr/lib/libz.so.1.2.3.4)
==19842== by 0x425C6CC: R__unzip (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libCore.so.5.26)
==19842== by 0x6B9F55B: TKey::ReadObjWithBuffer(char*) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libRIO.so.5.26)
==19842== by 0x6B8B2DF: TFile::GetStreamerInfoList() (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libRIO.so.5.26)
==19842== by 0x6B88761: TFile::ReadStreamerInfo() (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libRIO.so.5.26)
==19842== by 0x6B8A855: TFile::Init(bool) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libRIO.so.5.26)
==19842== by 0x6B8B9C6: TFile::TFile(char const*, char const*, char const*, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libRIO.so.5.26)
==19842== by 0x6C4E11A: G__G__IO_107_0_22(G__value*, char const*, G__param*, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libRIO.so.5.26)
==19842== by 0x47EEBE6: Cint::G__ExceptionWrapper(int ()(G__value, char const*, G__param*, int), G__value*, char*, G__param*, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libCint.so.5.26)
==19842== by 0x4899B3E: G__execute_call (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libCint.so.5.26)
==19842==
Warning in TClass::TClass: no dictionary for class BxEvent is available
[…]
root [1] Int_t evnum, n_clusters, npmts;
root [2] bxtree->SetMakeClass(1);
root [3] bxtree->SetBranchAddress (“evnum”, &evnum);
root [4] bxtree->GetEntry (200)
==19842== Invalid write of size 4
==19842== at 0x6B769D4: TBufferFile::ReadInt(int&) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libRIO.so.5.26)
==19842== by 0x89D289F: TBranchElement::ReadLeaves(TBuffer&) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libTree.so.5.26)
==19842== by 0x89C3381: TBranch::GetEntry(long long, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libTree.so.5.26)
==19842== by 0x89C9C04: TBranchElement::GetEntry(long long, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libTree.so.5.26)
==19842== by 0x89C9A94: TBranchElement::GetEntry(long long, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libTree.so.5.26)
==19842== by 0x89C9A94: TBranchElement::GetEntry(long long, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libTree.so.5.26)
==19842== by 0x8A128D3: TTree::GetEntry(long long, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libTree.so.5.26)
==19842== by 0x8A41DC1: G__G__Tree_109_0_69(G__value*, char const*, G__param*, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libTree.so.5.26)
==19842== by 0x47EEBE6: Cint::G__ExceptionWrapper(int ()(G__value, char const*, G__param*, int), G__value*, char*, G__param*, int) (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libCint.so.5.26)
==19842== by 0x4899B3E: G__execute_call (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libCint.so.5.26)
==19842== by 0x489B569: G__call_cppfunc (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libCint.so.5.26)
==19842== by 0x4876262: G__interpret_func (in /mnt/scratch/Software/Cern/root_v5.26.00/lib/libCint.so.5.26)
==19842== Address 0x0 is not stack’d, malloc’d or (recently) free’d
==19842==
[/quote]

The first log came from a production machine with debian old-stable, the second from my laptop with debian sid.

Thanks

8

And what is the result of bxtree->Print()? I suspect that evnum is kept in a vector of object rather than an object … in which case you need to pass the address of an array of int rather than the address of a single int …

Cheers,
Philippe.

9

[quote]root [1] bxtree->Print()

*Tree :bxtree : Borexino Events Tree (generated by echidna) *
*Entries : 51799 : Total = 505035351 bytes File Size = 141053219 *

  •    :          : Tree compression factor =   3.58                       *

*Branch :events *
*Entries : 51799 : BranchElement (see below) *
…
*Br 0 :fUniqueID : *
*Entries : 51799 : Total Size= 208002 bytes File Size = 1344 *
*Baskets : 4 : Basket Size= 64000 bytes Compression= 154.40 *
…
*Br 1 :fBits : *
*Entries : 51799 : Total Size= 415710 bytes File Size = 64829 *
*Baskets : 10 : Basket Size= 64000 bytes Compression= 6.40 *
…
*Br 2 :run : *
*Entries : 51799 : Total Size= 207954 bytes File Size = 1444 *
*Baskets : 4 : Basket Size= 64000 bytes Compression= 143.69 *
…
*Br 3 :evnum : *
*Entries : 51799 : Total Size= 207970 bytes File Size = 72662 *
*Baskets : 4 : Basket Size= 64000 bytes Compression= 2.86 *
[/quote]

10

Hi,

Quite odd ! Can you send your data file so that I can reproduce this issue?

Thanks,
Philippe.

11

Sure, where can i send to you? I have several root files for my data but none very small (>100MB).

Else you can download them by http, just tell me a source IP.

Thanks

12

Hi,

In your file there is 2 set of branches that tickles a deficiency in the SetMakeClass support when the address are not set. To work-around the problem simply disable those branches:TFile f("Run011002_c12.root"); bxtree->SetMakeClass(1); bxtree->SetBranchStatus("laben.*",0) bxtree->SetBranchStatus("muon.*",0) Int_t evnum, n_clusters, npmts; bxtree->SetBranchAddress ("evnum", &evnum); bxtree->GetEntry(200)

Cheers,
Philippe.

13

I have 2 branches but I did not create them on my own, they happen to be created. Do you know why? I thought it was a root stuff :neutral_face:

This is the code I use to create the file:file = TFile::Open (file_name().c_str (), "recreate"); tree = new TTree ("bxtree", "Borexino Events Tree (generated by bx_phys)"); tree->SetMaxTreeSize(Long64_t(0x2000000000ULL)); internal_ptr = new BxEvent; tree->Branch ("events", "BxEvent", &internal_ptr, 64000, 99); ... tree->Fill ()

I will try how to manage disabling the branches i do not need.

Thanks

14

[quote] Do you know why? I thought it was a root stuff [/quote]They are acutally sub-branches of you ‘events’ branch. They contains some of the data member of the class BxEvent.

Cheers,
Philippe.

15

Ok, so I can not avoid that.

If I create the following code:[code]TFile f = TFile::Open (“M4_merger/Run011002_c12.root”);
Int_t evnum, n_clusters, npmts[20];
TTree bxtree = (TTree)f->Get (“bxtree”);
bxtree->SetBranchStatus("",0)
bxtree->SetMakeClass(1);
bxtree->SetBranchStatus(“evnum”,1)
bxtree->SetBranchAddress (“evnum”, &evnum);
bxtree->SetBranchStatus(“laben.n_clusters”,1)
bxtree->SetBranchAddress (“laben.n_clusters”, &n_clusters);
//bxtree->SetBranchStatus(“laben.clusters.npmts”,1);
//bxtree->SetBranchAddress (“laben.clusters.npmts”, &npmts);

for (int i = 2033; i < 2050; i++) { bxtree->GetEntry (i); cout << evnum << " " << n_clusters << " " << npmts[0] << endl; }
[/code]
It works untill I try uncomment the lines of npmts…

16

Could you post a small data file in a public space and also a small analysis script?

Rene

17

Hi,

If you are going to use anything in the laben data member you must set of the data members. At this point I strongly recommend that you simply set all the variables address. The simpliest way to do so is to use the result of MakeSelector (or MakeClass) … or better yet MakeProxy.

TFile *f = TFile::Open ("M4_merger/Run011002_c12.root"); bxtree->MakeSelector("bxsel"); // edit the Process member function in bxsel.C bxtree->Process("bxsel.C");

Cheers,
Philippe.