test5 failure

[tbaudier]

Describe the bug The test5 (pet) failed for all tests on Github Actions.

Desktop (please complete the following information):

• Github actions

Additional context The error was introduced after the merging of that commit: https://github.com/OpenGATE/Gate/pull/534

See https://github.com/OpenGATE/Gate/runs/6832531413?check_suite_focus=true

The error is :

Traceback (most recent call last):
  File "/usr/local/bin/gt_merge_root", line 6, in <module>
    exec(compile(open(__file__).read(), __file__, 'exec'))
  File "/software/gatetools/bin/gt_merge_root", line 54, in <module>
    gt_merge_root_main()
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/software/gatetools/bin/gt_merge_root", line 49, in gt_merge_root_main
    gt.merge_root(inputs, output, incrementrunid)
  File "/software/gatetools/gatetools/merge_root.py", line 87, in merge_root
    out[tree] = uproot.newtree(trees[tree]["rootDictType"])
  File "/usr/local/lib/python3.6/site-packages/uproot3/write/TFile.py", line 90, in __setitem__
    what = TTree(where, what, self)
  File "/usr/local/lib/python3.6/site-packages/uproot3/write/objects/TTree.py", line 86, in __init__
    self._branches[name] = TBranch(name, branch, compression, self, file)
  File "/usr/local/lib/python3.6/site-packages/uproot3/write/objects/TTree.py", line 253, in __init__
    self._branch = TBranchImpl(name, branchobj, compression, file)
  File "/usr/local/lib/python3.6/site-packages/uproot3/write/objects/TTree.py", line 819, in __init__
    raise NotImplementedError
NotImplementedError
Traceback (most recent call last):
  File "runBenchmark.py", line 98, in <module>
    runTests_click()
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "runBenchmark.py", line 31, in runTests_click
    returnedTest = runTests(test)
  File "runBenchmark.py", line 89, in runTests
    analyseOutput = runAnalysis.analyse_all_folders(outputFolders)
  File "./runAnalysis.py", line 297, in analyse_all_folders
    r = plot_all(outputFolders, ax)
  File "./runAnalysis.py", line 255, in plot_all
    dictTest = analyse_pet(o, ax, 3*i)
  File "./runAnalysis.py", line 54, in analyse_pet
    singles = f['Singles']
  File "/usr/local/lib/python3.6/site-packages/uproot/reading.py", line 2096, in __getitem__
    return self.key(where).get()
  File "/usr/local/lib/python3.6/site-packages/uproot/reading.py", line 2047, in key
    item, cycle="any", keys=self.keys(), file_path=self._file.file_path
uproot.exceptions.KeyInFileError: not found: 'Singles' (with any cycle number)
    Available keys: 'pet_data;1'
in file output/pet.root
+ OutputTest='/software/gate/bin/Gate
Found Gate in folder: /software/gate/bin/Gate
WARNING: The output folder already exist: /home/t5_pet/output
Evereything will be overwritten
Run Id is: output
No qsub, run Gate on multiple cores.
2 jobs running
Run folder is: /home/t5_pet/output
!!!! this is /software/gatetools/clustertools/gate_power_merge.sh v0.3k !!!!
Usage: gate_power_merge.sh run.dir [--force]
   where --force allows to merge files even if the file is missing in some output directories
found 2 partial output dirs
output dir is results
files pet.root stat.txt
merging pet.root
  ** testing file type on output/output.local_1/pet.root
  ** this is a root file
    ** entering root merger
    ** merger is gt_merge_root
    ** creating results/pet.root
ERROR: error while calling gt_merge_root

[tbaudier]

The test is due to gt_merge_root. The new key "volumeID" in Singles tree leads to the error.

The types in Singles tree is:

{b'runID': <class 'numpy.int32'>, 
b'eventID': <class 'numpy.int32'>, 
b'sourceID': <class 'numpy.int32'>, 
b'sourcePosX': <class 'numpy.float32'>, 
b'sourcePosY': <class 'numpy.float32'>, 
b'sourcePosZ': <class 'numpy.float32'>, 
b'time': <class 'numpy.float64'>, 
b'energy': <class 'numpy.float32'>, 
b'globalPosX': <class 'numpy.float32'>, 
b'globalPosY': <class 'numpy.float32'>, 
b'globalPosZ': <class 'numpy.float32'>, 
b'gantryID': <class 'numpy.int32'>, 
b'rsectorID': <class 'numpy.int32'>, 
b'moduleID': <class 'numpy.int32'>, 
b'submoduleID': <class 'numpy.int32'>, 
b'crystalID': <class 'numpy.int32'>, 
b'layerID': <class 'numpy.int32'>, 
b'comptonPhantom': <class 'numpy.int32'>, 
b'comptonCrystal': <class 'numpy.int32'>, 
b'RayleighPhantom': <class 'numpy.int32'>, 
b'RayleighCrystal': <class 'numpy.int32'>, 
b'axialPos': <class 'numpy.float32'>, 
b'rotationAngle': <class 'numpy.float32'>, 
b'comptVolName': <class 'numpy.int64'>, 
b'RayleighVolName': <class 'numpy.int64'>, 
b'volumeID': <class 'numpy.ndarray'>}

So it seems that volumeID type is ndArray instead of number.

Is it normal to store a vector? In the gatetools, maybe we can try to detect the type and merge the vector differently if needed.

[dsarrut]

corrected with updated gatetools