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Merged
tbaudier merged 2 commits into from
Apr 16, 2026
Merged

Try with a version of uproot <5.7.0 to avoid error #98

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b96cf7f
Try with a version of uproot <5.7.0 to avoid error
tbaudier Apr 16, 2026
a6dac79
Use mktree now for uproot
tbaudier Apr 16, 2026
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172 changes: 100 additions & 72 deletions gatetools/merge_root.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,16 @@
# -----------------------------------------------------------------------------


import gatetools as gt
import logging

import numpy as np
import tqdm
import logging
logger=logging.getLogger(__name__)
import uproot

import gatetools as gt

logger = logging.getLogger(__name__)


def unicity(root_keys):
"""
Expand All @@ -38,34 +43,30 @@ def unicity(root_keys):
name = name[0]
if not name in root_array:
root_array.append(name)
return(root_array)
return root_array


def merge_root(rootfiles, outputfile, incrementRunId=False):
"""
Merge root files in output files
"""
try:
import uproot
except:
print("uproot4 is mandatory to merge root file. Please, do:")
print("pip install uproot")

uproot.default_library = "np"

out = uproot.recreate(outputfile)

#Previous ID values to be able to increment runIn or EventId
# Previous ID values to be able to increment runIn or EventId
previousId = {}

#create the dict reading all input root files
trees = {} #TTree with TBranch
hists = {} #Directory with THist
pbar = tqdm.tqdm(total = len(rootfiles))
# create the dict reading all input root files
trees = {} # TTree with TBranch
hists = {} # Directory with THist
pbar = tqdm.tqdm(total=len(rootfiles))
for file in rootfiles:
root = uproot.open(file)
root_keys = unicity(root.keys())
for tree in root_keys:
if hasattr(root[tree], 'keys'):
if hasattr(root[tree], "keys"):
if not tree in trees:
trees[tree] = {}
trees[tree]["rootDictType"] = {}
Expand All @@ -75,67 +76,95 @@ def merge_root(rootfiles, outputfile, incrementRunId=False):
hists[tree]["rootDictValue"] = {}
previousId[tree] = {}
for branch in root[tree].keys():
if isinstance(root[tree],uproot.reading.ReadOnlyDirectory):
if isinstance(root[tree], uproot.reading.ReadOnlyDirectory):
array = root[tree][branch].values()
if len(array) > 0:
branchName = tree + "/" + branch
if type(array[0]) is type('c'):
if type(array[0]) is type("c"):
array = np.array([0 for xi in array])
if not branchName in hists[tree]["rootDictType"]:
hists[tree]["rootDictType"][branchName] = root[tree][branch].to_numpy()
hists[tree]["rootDictValue"][branchName] = np.zeros(array.shape)
hists[tree]["rootDictType"][branchName] = root[tree][
branch
].to_numpy()
hists[tree]["rootDictValue"][branchName] = np.zeros(
array.shape
)
hists[tree]["rootDictValue"][branchName] += array
else:
array = root[tree][branch].array(library="np")
if len(array) > 0 and not (type(array[0]) is type(np.ndarray(2,))):
if type(array[0]) is type('c'):
if len(array) > 0 and (
type(array[0])
is not type(
np.ndarray(
2,
)
)
):
if type(array[0]) is type("c"):
array = np.array([0 for xi in array])
if not branch in trees[tree]["rootDictType"]:
if branch not in trees[tree]["rootDictType"]:
trees[tree]["rootDictType"][branch] = type(array[0])
trees[tree]["rootDictValue"][branch] = np.array([])
if (not incrementRunId and branch.startswith('eventID')) or (incrementRunId and branch.startswith('runID')):
if not branch in previousId[tree]:
if (
not incrementRunId and branch.startswith("eventID")
) or (incrementRunId and branch.startswith("runID")):
if branch not in previousId[tree]:
previousId[tree][branch] = 0
array += previousId[tree][branch]
previousId[tree][branch] = max(array) +1
trees[tree]["rootDictValue"][branch] = np.append(trees[tree]["rootDictValue"][branch], array)
previousId[tree][branch] = max(array) + 1
trees[tree]["rootDictValue"][branch] = np.append(
trees[tree]["rootDictValue"][branch], array
)
pbar.update(1)
pbar.close()

#Set the dict in the output root file
# Set the dict in the output root file
for tree in trees:
if not trees[tree]["rootDictValue"] == {} or not trees[tree]["rootDictType"] == {}:
#out.mktree(tree, trees[tree]["rootDictType"])
out[tree] = trees[tree]["rootDictValue"]
if (
not trees[tree]["rootDictValue"] == {}
or not trees[tree]["rootDictType"] == {}
):
out.mktree(tree, trees[tree]["rootDictType"])
out[tree].extend(trees[tree]["rootDictValue"])
for hist in hists:
if not hists[hist]["rootDictValue"] == {} or not hists[hist]["rootDictType"] == {}:
if (
not hists[hist]["rootDictValue"] == {}
or not hists[hist]["rootDictType"] == {}
):
for branch in hists[hist]["rootDictValue"]:
for i in range(len(hists[hist]["rootDictValue"][branch])):
hists[hist]["rootDictType"][branch][0][i] = hists[hist]["rootDictValue"][branch][i]
out[branch[:-2]] = hists[hist]["rootDictType"][branch]
hists[hist]["rootDictType"][branch][0][i] = hists[hist][
"rootDictValue"
][branch][i]
out.mktree(branch[:-2], hists[hist]["rootDictType"][branch])
out[branch[:-2]].extend(hists[hist]["rootDictType"][branch])


#####################################################################################
import unittest
import tempfile
import wget
import os
import shutil
import tempfile
import unittest

import numpy as np
import uproot
import wget

from .logging_conf import LoggedTestCase


class Test_MergeRoot(LoggedTestCase):
def test_merge_root_phsp(self):
try:
import uproot
except:
print("uproot4 is mandatory to merge root file. Please, do:")
print("pip install uproot")

logger.info('Test_MergeRoot test_merge_root_phsp')
logger.info("Test_MergeRoot test_merge_root_phsp")
tmpdirpath = tempfile.mkdtemp()
filenameRoot = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/phsp.root?inline=false", out=tmpdirpath, bar=None)
gt.merge_root([filenameRoot, filenameRoot], os.path.join(tmpdirpath, "output.root"))
filenameRoot = wget.download(
"https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/phsp.root?inline=false",
out=tmpdirpath,
bar=None,
)
gt.merge_root(
[filenameRoot, filenameRoot], os.path.join(tmpdirpath, "output.root")
)
input = uproot.open(filenameRoot)
output = uproot.open(os.path.join(tmpdirpath, "output.root"))
self.assertTrue(output.keys() == input.keys())
Expand All @@ -144,57 +173,56 @@ def test_merge_root_phsp(self):
self.assertTrue(outputTree.keys() == inputTree.keys())
inputBranch = inputTree[inputTree.keys()[1]].array(library="np")
outputBranch = outputTree[outputTree.keys()[1]].array(library="np")
self.assertTrue(2*len(inputBranch) == len(outputBranch))
self.assertTrue(2 * len(inputBranch) == len(outputBranch))
shutil.rmtree(tmpdirpath)

def test_merge_root_pet_incrementEvent(self):
try:
import uproot
except:
print("uproot4 is mandatory to merge root file. Please, do:")
print("pip install uproot")

logger.info('Test_MergeRoot test_merge_root_pet')
logger.info("Test_MergeRoot test_merge_root_pet")
tmpdirpath = tempfile.mkdtemp()
filenameRoot = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/pet.root?inline=false", out=tmpdirpath, bar=None)
gt.merge_root([filenameRoot, filenameRoot], os.path.join(tmpdirpath, "output.root"))
filenameRoot = wget.download(
"https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/pet.root?inline=false",
out=tmpdirpath,
bar=None,
)
gt.merge_root(
[filenameRoot, filenameRoot], os.path.join(tmpdirpath, "output.root")
)
input = uproot.open(filenameRoot)
output = uproot.open(os.path.join(tmpdirpath, "output.root"))
inputTree = input[input.keys()[0]]
outputTree = output[output.keys()[0]]
inputRunBranch = inputTree[inputTree.keys()[0]].array(library="np")
outputRunBranch = outputTree[outputTree.keys()[0]].array(library="np")
self.assertTrue(max(inputRunBranch) == max(outputRunBranch))
self.assertTrue(2*len(inputRunBranch) == len(outputRunBranch))
self.assertTrue(2 * len(inputRunBranch) == len(outputRunBranch))
inputEventBranch = inputTree[inputTree.keys()[1]].array(library="np")
outputEventBranch = outputTree[outputTree.keys()[1]].array(library="np")
self.assertTrue(2*max(inputEventBranch)+1 == max(outputEventBranch))
self.assertTrue(2*len(inputEventBranch) == len(outputEventBranch))
self.assertTrue(2 * max(inputEventBranch) + 1 == max(outputEventBranch))
self.assertTrue(2 * len(inputEventBranch) == len(outputEventBranch))
shutil.rmtree(tmpdirpath)

def test_merge_root_pet_incrementRun(self):
try:
import uproot
except:
print("uproot4 is mandatory to merge root file. Please, do:")
print("pip install uproot")

logger.info('Test_MergeRoot test_merge_root_pet')
logger.info("Test_MergeRoot test_merge_root_pet")
tmpdirpath = tempfile.mkdtemp()
print(tmpdirpath)
filenameRoot = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/pet.root?inline=false", out=tmpdirpath, bar=None)
gt.merge_root([filenameRoot, filenameRoot], os.path.join(tmpdirpath, "output.root"), True)
filenameRoot = wget.download(
"https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/pet.root?inline=false",
out=tmpdirpath,
bar=None,
)
gt.merge_root(
[filenameRoot, filenameRoot], os.path.join(tmpdirpath, "output.root"), True
)
input = uproot.open(filenameRoot)
output = uproot.open(os.path.join(tmpdirpath, "output.root"))
inputTree = input[input.keys()[0]]
outputTree = output[output.keys()[0]]
inputRunBranch = inputTree[inputTree.keys()[0]].array(library="np")
outputRunBranch = outputTree[outputTree.keys()[0]].array(library="np")
self.assertTrue(2*max(inputRunBranch)+1 == max(outputRunBranch))
self.assertTrue(2*len(inputRunBranch) == len(outputRunBranch))
self.assertTrue(2 * max(inputRunBranch) + 1 == max(outputRunBranch))
self.assertTrue(2 * len(inputRunBranch) == len(outputRunBranch))
inputEventBranch = inputTree[inputTree.keys()[1]].array(library="np")
outputEventBranch = outputTree[outputTree.keys()[1]].array(library="np")
self.assertTrue(max(inputEventBranch) == max(outputEventBranch))
self.assertTrue(2*len(inputEventBranch) == len(outputEventBranch))
#shutil.rmtree(tmpdirpath)

self.assertTrue(2 * len(inputEventBranch) == len(outputEventBranch))
# shutil.rmtree(tmpdirpath)
1 change: 0 additions & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -85,4 +85,3 @@ gt_digi_mac_converter = "gatetools.bin.gt_digi_mac_converter:convert_macro"
gate_split_and_run = "gatetools.clustertools.gate_split_and_run:runJobs"
opengate_run = "gatetools.clustertools.opengate_run:runJobs_click"
computeElapsedTime = "gatetools.clustertools.computeElapsedTime:computeElapsedTime"

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