How to access and plot a histogram from an std::vector

[TerKim]

Hi, I'm new to Uproot, and ROOT in general, with a very lacking foundation of the data structures of ROOT. I originally used ROOT directly to access and plot for example ev.pmt.charge, with no issue. I wanted to use Uproot due to its ease of use compared to the conventional ROOT. Anyway, I wanted to ask how to access the ev.pmt in the TTree, and plot something like ev.pmt.charge (or time ,dTime, dCharge).

I did the following to plot the data, but I get an empty plot (most likely due to me missing or misusing something):
`file = uproot.open("output.root")
tree = file["T"]

ev_pmt = uproot.containers.STLVector(tree["ds/ev/ev.pmt"])

charge_data = np.array([x.charge for x in ev_pmt])
charge_df = pd.DataFrame(charge_data, columns=["charge"])

Create a histogram of the charge data

charge_df.plot(kind='hist', y='charge', bins = 100)
plt.xlabel("Charge")
plt.ylabel("Frequency")
plt.title("Histogram of Charge")
plt.show()

Summary of charge data:

print(charge_df.describe())`

I hope to have some updated code to help me with this as I've been stuck on this for quite a while now, and I have a deadline coming up for thesis work. Any help would be much appreciated.
Also, if possible, could you show how to apply cuts aswell? I posted the root file as a zip file for anyone to help. Thanks in advance to everybody who helps.
output.zip

P.S. Forgive me if someone asked a similar question, I could not find one if there was.

[agoose77]

The proper way to read from a single branch in uproot is to invoke the .array() method, e.g.

import uproot
with uproot.open("output.root:T") as tree:
    ev_pmt = tree["ds/ev/ev.pmt"].array()

In uproot==5.*, this will use Awkward Array to represent the result. For your data, this does not succeed on my machine:

---------------------------------------------------------------------------
NotImplementedError                       Traceback (most recent call last)
Cell In [7], line 2
      1 with uproot.open("/home/angus/Downloads/output.root:T") as tree:
----> 2     ev_pmt = tree["ds/ev/ev.pmt"].array()

File ~/Git/uproot5/src/uproot/behaviors/TBranch.py:1818, in TBranch.array(self, interpretation, entry_start, entry_stop, decompression_executor, interpretation_executor, array_cache, library, ak_add_doc)
   1815                 ranges_or_baskets.append((branch, basket_num, range_or_basket))
   1817 interp_options = {"ak_add_doc": ak_add_doc}
-> 1818 _ranges_or_baskets_to_arrays(
   1819     self,
   1820     ranges_or_baskets,
   1821     branchid_interpretation,
   1822     entry_start,
   1823     entry_stop,
   1824     decompression_executor,
   1825     interpretation_executor,
   1826     library,
   1827     arrays,
   1828     False,
   1829     interp_options,
   1830 )
   1832 _fix_asgrouped(
   1833     arrays,
   1834     expression_context,
   (...)
   1838     ak_add_doc,
   1839 )
   1841 if array_cache is not None:

File ~/Git/uproot5/src/uproot/behaviors/TBranch.py:3124, in _ranges_or_baskets_to_arrays(hasbranches, ranges_or_baskets, branchid_interpretation, entry_start, entry_stop, decompression_executor, interpretation_executor, library, arrays, update_ranges_or_baskets, interp_options)
   3121     pass
   3123 elif isinstance(obj, tuple) and len(obj) == 3:
-> 3124     uproot.source.futures.delayed_raise(*obj)
   3126 else:
   3127     raise AssertionError(obj)

File ~/Git/uproot5/src/uproot/source/futures.py:36, in delayed_raise(exception_class, exception_value, traceback)
     32 def delayed_raise(exception_class, exception_value, traceback):
     33     """
     34     Raise an exception from a background thread on the main thread.
     35     """
---> 36     raise exception_value.with_traceback(traceback)

File ~/Git/uproot5/src/uproot/behaviors/TBranch.py:3066, in _ranges_or_baskets_to_arrays.<locals>.basket_to_array(basket)
   3063 context = dict(branch.context)
   3064 context["forth"] = forth_context[branch.cache_key]
-> 3066 basket_arrays[basket.basket_num] = interpretation.basket_array(
   3067     basket.data,
   3068     basket.byte_offsets,
   3069     basket,
   3070     branch,
   3071     context,
   3072     basket.member("fKeylen"),
   3073     library,
   3074     interp_options,
   3075 )
   3076 if basket.num_entries != len(basket_arrays[basket.basket_num]):
   3077     raise ValueError(
   3078         """basket {} in tree/branch {} has the wrong number of entries """
   3079         """(expected {}, obtained {}) when interpreted as {}
   (...)
   3087         )
   3088     )

File ~/Git/uproot5/src/uproot/interpretation/objects.py:139, in AsObjects.basket_array(self, data, byte_offsets, basket, branch, context, cursor_offset, library, options)
    136 assert basket.byte_offsets is not None
    138 if self._forth and isinstance(library, uproot.interpretation.library.Awkward):
--> 139     output = self.basket_array_forth(
    140         data,
    141         byte_offsets,
    142         basket,
    143         branch,
    144         context,
    145         cursor_offset,
    146         library,
    147         options,
    148     )
    149 else:
    150     output = ObjectArray(
    151         self._model, branch, context, byte_offsets, data, cursor_offset
    152     ).to_numpy()

File ~/Git/uproot5/src/uproot/interpretation/objects.py:206, in AsObjects.basket_array_forth(self, data, byte_offsets, basket, branch, context, cursor_offset, library, options)
    200 with self._forth_lock:
    201     # all threads have to wait until complete_forth_code is ready
    203     if self._complete_forth_code is None:
    204         # another thread didn't make it while this thread waited
    205         # this thread tries to make it now
--> 206         output = self._discover_forth(
    207             data, byte_offsets, branch, context, cursor_offset
    208         )
    210         if output is not None:
    211             # Forth discovery was unsuccessful; return Python-derived
    212             # output and maybe another basket will be more fruitful
    213             self.hook_after_basket_array(
    214                 data=data,
    215                 byte_offsets=byte_offsets,
   (...)
    222                 options=options,
    223             )

File ~/Git/uproot5/src/uproot/interpretation/objects.py:286, in AsObjects._discover_forth(self, data, byte_offsets, branch, context, cursor_offset)
    284 if "forth" in context.keys():
    285     context["forth"].gen.var_set = False
--> 286 output[i] = self._model.read(
    287     chunk,
    288     cursor,
    289     context,
    290     branch.file,
    291     branch.file.detached,
    292     branch,
    293 )
    294 if context["cancel_forth"] and "forth" in context.keys():
    295     del context["forth"]

File ~/Git/uproot5/src/uproot/containers.py:716, in AsArray.read(self, chunk, cursor, context, file, selffile, parent, header)
    714                     forth_stash.add_to_pre(f"{temp_jump} stream skip\n")
    715             if is_memberwise:
--> 716                 raise NotImplementedError(
    717                     """memberwise serialization of {}
    718 in file {}""".format(
    719                         type(self).__name__, selffile.file_path
    720                     )
    721                 )
    723             if isinstance(self._values, numpy.dtype):
    724                 remainder = chunk.get(
    725                     cursor.index, cursor.index + num_bytes, cursor, context
    726                 )

NotImplementedError: memberwise serialization of AsArray
in file /home/angus/Downloads/output.root

If we inspect the interpretation of the data, we see

>>> with uproot.open("output.root:T") as tree:
>>>     ev_pmt = tree["ds/ev/ev.pmt"]
>>>     print(ev_pmt.interpretation)
AsObjects(AsArray(True, False, AsVector(False, Model_RAT_3a3a_DS_3a3a_PMT), ()))

It looks like you're reading a structure, and uproot needs to deserialise it memberwise. We don't support all of the various peculiar ways that ROOT can serialise an object, though @ioanaif and @jpivarski can pick this up and tell you more, such as where to go next.

[TerKim]

I see, I look forward to more guidance. Thanks for letting me know.