Issues trying to open a bi-dimensional array leave contained in a ROOT Tree in Pyroot

[gyoice88]

Hi ROOT comunity,
I’m stuck with a problem using Pyroot. I’m not able to read a leaf on a tree which is a two dimensional array of float values. You can see the related Tree in the following:

root [1] TTree tr=(TTree)g->Get(“tevent_2nd_integral”)
root [2] tr.Print()
*Tree :tevent_2nd_integral: Event packet tree 2nd GTUs integral *
*Entries : 57344 : Total = 548967602 bytes File Size = 412690067 *

•    :          : Tree compression factor =   1.33                 *
  

*Br 7 :photon_count_data : photon_count_data[1][1][48][48]/F *
*Entries : 57344 : Total Size= 530758073 bytes File Size = 411860735 *
*Baskets : 19121 : Basket Size= 32000 bytes Compression= 1.29 *
…

The array (the bold one) is photon_count_data[1][1][48][48]. Actually i have several root files and I tried both to make a chain and to use hadd method like hadd file.root 'ls /path/.root’*.
I tried several ways as i will show soon. Anytime i found different problem: once the numpy array which should contain the 48x48 values per each event was not created at all, others just didn’t write anything or strange values (negative also which is not possible).
My code is the following:

# calling the root file after using hadd to merge all files
rootFile = path+"merge.root"
f = XROOT.TFile(rootFile,'read')
tree = f.Get('tevent_2nd_integral')

# making a chain
PDMchain=TChain("tevent_2nd_integral")
for filename in sorted(os.listdir(path)):
	if filename.endswith('.root') and("CPU_RUN_MAIN"  in filename) :
		PDMchain.Add(filename)

pdm_counts = []
#First method using python pyl class
leaves = tree.GetListOfLeaves()
# define dynamically a python class containing root Leaves objects
class PyListOfLeaves(dict) :
    pass

# create an istance
pyl = PyListOfLeaves()

for i in range(0,leaves.GetEntries() ) :
    leaf = leaves.At(i)
    name = leaf.GetName()
    # add dynamically attribute to my class 
    pyl.__setattr__(name,leaf)

for iev in range(0,nEntries_pixel) :
	tree.GetEntry(iev) 
	pdm_counts.append(pyl.photon_count_data.GetValue())

# the Draw method
count = tree.Draw("photon_count_data","","")
pdm_counts.append(np.array(np.frombuffer(tree.GetV1(), dtype=np.float64, count=count)))

#ROOT buffer method
for event in PDMchain:
	pdm_data_for_this_event = event.photon_count_data
	pdm_data_for_this_event.SetSize(2304)  #ROOT buffer
	pdm_couts.append(np.array(pdm_data_for_this_event,copy=True))

1. with the python class method the array pdm_counts is filled with just the first element contained in photon_count_data
2. with the Draw method I get a segmentation violation or a strange kernel issue
3. with the root buffer method I get right back a list containing all the 2304 (48x48) values but they are completely different from those in the photon_count_data, id est, negative values or orders of magnitude senseless

Could you tell me where I’m wrong or if there could be a more elegant and quick method to do so.
Thanks in advance

---

_ROOT Version: 5.34
Platform: Not Provided
_Compiler: gcc (crosstool-NG 1.23.0.450-d54ae) 7.3.0

---

[etejedor]

Hi,

Option #3 should be fine, what you get from PyROOT is just a flat buffer of floats, you can set the size for it as you did and even reshape it when you create the numpy array from it. What happens if you inspect pdm_data_for_this_event[0], you don’t get a good value?

On the other hand, I see you are using ROOT 5.34 which we don’t support anymore, please consider moving to a recent ROOT 6 release, where this issue should be gone.

[gyoice88]

Hi etejedor,
so, if I print pdm_data_for_this_event[0] it is correct. Actually all of them seem to be fine!
Also pdm_counts is correct after printing in the shell. The problem occurred when i try to open variables in Spyder environment…don’t know why but in Spyder the correct values are shifted by 4 positions. What i mean is that pdm_data_for_this_event[0] = pdm_counts[0] then pdm_data_for_this_event[1] = pdm_counts[4]…an so on (ok, i should have written pdm_counts[0][0] because is a list but i think you understood!). In positions 1, 2 and 3 there are incomprehensible values .
Anyway…today lesson: trust yourself and not to Spyder environment!

[etejedor]

Ok good to hear you could retrieve the correct values!