PyROOT, numpy matrices and TSpectrum2::SearchHighRes

ROOT
1

Hello,

I’ve been trying to locate the peaks of a 2-d distribution using the TSpectrum2 class, but I just keep getting segfault errors (see attachment).

I guess the problem is the signature of the TSpectrum2::SearchHighRes function I am trying to use:

I am trying to use two numpy matrices as source and dest, as shown in the example attached.
May anybody suggest me a workaround, or a different array/vector/list/matrix data type compatible with this signature? I have also tried to use ROOT’s vector<vector> but I didn’t manage to get SearchHighRes working this way either.

The attached files provide:
[ul][li]a minimal (not) working example spectrum.py (380 Bytes)[/li]
[li]a rootfile containing the source histogram hh.root (65.3 KB)[/li]
[li]and the complete error stack trace spectrum-errors.txt (6.03 KB)[/li][/ul]

Cheers,

Elena

2

Elena,

you don’t want to use this …

Here’s what you’re up against: numpy does not support C-style 2D arrays particularly well, float in python is double in C, and in C there are float** and float[][] and they are not the same.

Now, if you insist, you can beat this into shape, but to make it even semi-usable, it would probably have to go something like this:[code]import array

binsx = 1800
binsy = 1000
source, c_source = {}, array.array( ‘L’, [0]*binsx )
dest, c_dest = {}, array.array( ‘L’, [0]*binsx )
def new_numpy1d_with_pointer(size):
np_a = np.zeros( size, dtype=np.float32 )
pointer, read_only_flag = np_a.array_interface[‘data’]
return np_a, pointer

for i in xrange(binsx):
source[i], c_source[i] = new_numpy1d_with_pointer( binsy )
dest[i], c_dest[i] = new_numpy1d_with_pointer( binsy )[/code]
This builds an array of pointers to arrays of C floats in c_source and c_dest, and that will work, as although PyROOT does not know about float**, it passes the array pointer as void*, which is fine. It also builds source and dest to a) keep the arrays alive from the reference counting, and b) still be usable in the expected way.

Cheers,
Wim

3

Dear Wim,

Ok, I understand the problem with pyroot and C arrays.
However, for my current purpose, your code efficiently solved my problem. Thank you very much!

Elena