Python array of strings in a ROOT TTree

Question

I'm doing some work with CERN's pyROOT module, and I'm trying to store an array of strings as a leaf in a binary tree. In order to do so, I have to pass it an array, obviously, using not lists or dictionaries, but the array module. The module supports standard C arrays, of characters, integers, and so forth, but does anyone know of a way I can nest them in order to have an array of strings, or, effectively, an array of character arrays? Or have I gone too far and I need to take a step back from the keyboard for a while :)?

Code:

import ROOT

rowtree = ROOT.TTree("rowstor", "rowtree")

ROOT.gROOT.ProcessLine(
    "struct runLine {\
    Char_t test[20];\
    Char_t test2[20];\
    };" );
from ROOT import runLine
newline = runLine()
rowtree.Branch("test1", newline, "test/C:test2")

newline.test = ["AbcDefgHijkLmnOp","aaaaaaaaaaaaaaaaaaa"]

rowtree.Fill()

Error:

python branchtest
Traceback (most recent call last):
  File "branchtest", line 14, in <module>
    newline.test = ["AbcDefgHijkLmnOp","aaaaaaaaaaaaaaaaaaa"]
TypeError: expected string or Unicode object, list found

I'm wondering if it's possible to turn the list shown in this example into an array of strings.

Answer 1

A char array and a Python list of Python strings are two very different things.

If you want a branch containing a char array (one string) then I suggest using Python's built-in bytearray type:

import ROOT
# create an array of bytes (chars) and reserve the last byte for null
# termination (last byte remains zero)
char_array = bytearray(21)
# all bytes of char_array are zeroed by default here (all b'\x00')

# create the tree
tree = ROOT.TTree('tree', 'tree')
# add a branch for char_array
tree.Branch('char_array', char_array, 'char_array[21]/C')
# set the first 20 bytes to characters of a string of length 20
char_array[:21] = 'a' * 20
# important to keep the last byte zeroed for null termination!
tree.Fill()
tree.Scan('', '', 'colsize=21')

The output of tree.Scan('', '', 'colsize=21') is:

************************************
*    Row   *            char_array *
************************************
*        0 *  aaaaaaaaaaaaaaaaaaaa *
************************************

So we know the tree is accepting the bytes correctly.

If you want to store a list of strings, then I suggest using a std::vector<std::string>:

import ROOT

strings = ROOT.vector('string')()

tree = ROOT.TTree('tree', 'tree')
tree.Branch('strings', strings)
strings.push_back('Hello')
strings.push_back('world!')
tree.Fill()
tree.Scan()

The output of tree.Scan() is:

***********************************
*    Row   * Instance *   strings *
***********************************
*        0 *        0 *     Hello *
*        0 *        1 *    world! *
***********************************

In a loop you would want to strings.clear() before filling with a new list of strings in the next entry.

Now, the rootpy package (also see the repository on github) provides a better way of creating trees in Python. Here is an example of how you can use char arrays in a "friendlier" way with rootpy:

from rootpy import stl
from rootpy.io import TemporaryFile
from rootpy.tree import Tree, TreeModel, CharArrayCol

class Model(TreeModel):
    # define the branches you want here
    # with branchname = branchvalue
    char_array = CharArrayCol(21)
    # the dictionary is compiled and cached for later
    # if not already available
    strings = stl.vector('string')

# create the tree inside a temporary file
with TemporaryFile():
    # all branches are created automatically according to your model above
    tree = Tree('tree', model=Model)

    tree.char_array = 'a' * 20
    # attemping to set char_array with a string of length 21 or longer will
    # result in a ValueError being raised.
    tree.strings.push_back('Hello')
    tree.strings.push_back('world!')
    tree.Fill()
    tree.Scan('', '', 'colsize=21')

The output of tree.Scan('', '', 'colsize=21') is:

***********************************************************************
*    Row   * Instance *            char_array *               strings *
***********************************************************************
*        0 *        0 *  aaaaaaaaaaaaaaaaaaaa *                 Hello *
*        0 *        1 *  aaaaaaaaaaaaaaaaaaaa *                world! *
***********************************************************************

See another example of using TreeModels with rootpy here:

https://github.com/rootpy/rootpy/blob/master/examples/tree/model_simple.py