The km3io Python package¶
This software provides a set of Python classes to read KM3NeT ROOT files without having ROOT, Jpp or aanet installed. It only depends on Python 3.5+ and the amazing uproot package and gives you access to the data via numpy and awkward arrays.
It’s very easy to use and according to the uproot benchmarks, it is able to outperform the original ROOT I/O performance.
Installation¶
Install km3io using pip:
pip install km3io
or conda:
conda install km3io
To get the latest (stable) development release:
pip install git+https://git.km3net.de/km3py/km3io.git
Docker:
docker run -it docker.km3net.de/km3io
Singularity:
wget https://sftp.km3net.de/singularity/km3io_v0.27.2.sif # pick the version you like
singularity shell km3io_v0.27.2.sif
Reminder: km3io is not dependent on aanet, ROOT or Jpp!
Questions¶
If you have a question about km3io, please proceed as follows:
Read the documentation below.
Explore the examples in the documentation.
Haven’t you found an answer to your question in the documentation, post a git issue with your question showing us an example of what you have tried first, and what you would like to do.
Have you noticed a bug, please post it in a git issue, we appreciate your contribution.
Introduction¶
Most of km3net data is stored in root files. These root files are created using the KM3NeT Dataformat library A ROOT file created with Jpp is an “online” file and all other software usually produces “offline” files.
km3io is a Python package that provides a set of classes: OnlineReader, OfflineReader and a special class to read gSeaGen files. All of these ROOT files can be read installing any other software like Jpp, aanet or ROOT.
Data in km3io is returned as awkward.Array which is an advance Numpy-like container type to store
contiguous data for high performance computations.
Such an awkward.Array supports any level of nested arrays and records which can have different lengths, in contrast to Numpy where everything has to be rectangular.
The example is shown below shows the array which contains the dir_z values
of each track of the first 4 events. The type 4 * var * float64 means that
it has 4 subarrays with variable lengths of type float64:
>>> import km3io
>>> from km3net_testdata import data_path
>>> f = km3io.OfflineReader(data_path("offline/numucc.root"))
>>> f[:4].tracks.dir_z
<Array [[0.213, 0.213, ... 0.229, 0.323]] type='4 * var * float64'>
The same concept applies to all other branches, including hits, mc_hits,
mc_tracks, t_sec etc.
Architecture overview¶
km3io utilises uproot behind the scenes and creates a lazy and thin
wrapper which offers convenient slicing and iterations by delaying the access to
the actual ROOT data branches to the very last moment. When using the iteration
functionality, the data is loaded in chunks and the iteration is done over e.g.
events in each chunk or a bunch of frames in case of the summaryslice reader.
The base class for the event-based readout is the km3io.rootio.EventReader
class. When subclassing this class, the branches, aliases and nested branches
need to be defined in the static variables which are then used to mask unwanted
attributes. Especially in case of the Offline ROOT format, where the “one class
fits all” design was chosen, it is distracting that e.g. a Hit has many
attributes which make no sense depending on the context (MC hit, raw hit etc.).
By specifing the branches explicitely, the user API will only expose the
meaningful fields.
The online ROOT format support is partly still based on uproot3.
Many of the utility functions are using Numba to achieve the best possible
performance. km3io does not offer alternative implementations, so Numba is a
strict dependency and an integral part of the implementation.
Offline files reader¶
In general an offline file has two attributes to access data: the header and the events. Let’s start with the header.
Reading the file header¶
To read an offline file start with opening it with the OfflineReader:
>>> import km3io
>>> from km3net_testdata import data_path
>>> f = km3io.OfflineReader(data_path("offline/numucc.root"))
Accessing is as easy as typing:
>>> f.header
<km3io.offline.Header at 0x7fcd81025990>
Printing it will give an overview of the structure:
>>> print(f.header)
MC Header:
DAQ(livetime=394)
PDF(i1=4, i2=58)
can(zmin=0, zmax=1027, r=888.4)
can_user: can_user(field_0=0.0, field_1=1027.0, field_2=888.4)
coord_origin(x=0, y=0, z=0)
cut_in(Emin=0, Emax=0, cosTmin=0, cosTmax=0)
cut_nu(Emin=100, Emax=100000000.0, cosTmin=-1, cosTmax=1)
cut_primary(Emin=0, Emax=0, cosTmin=0, cosTmax=0)
cut_seamuon(Emin=0, Emax=0, cosTmin=0, cosTmax=0)
decay: decay(field_0='doesnt', field_1='happen')
detector: NOT
drawing: Volume
genhencut(gDir=2000, Emin=0)
genvol(zmin=0, zmax=1027, r=888.4, volume=2649000000.0, numberOfEvents=100000)
kcut: 2
livetime(numberOfSeconds=0, errorOfSeconds=0)
model(interaction=1, muon=2, scattering=0, numberOfEnergyBins=1, field_4=12)
ngen: 100000.0
norma(primaryFlux=0, numberOfPrimaries=0)
nuflux: nuflux(field_0=0, field_1=3, field_2=0, field_3=0.5, field_4=0.0, field_5=1.0, field_6=3.0)
physics(program='GENHEN', version='7.2-220514', date=181116, time=1138)
seed(program='GENHEN', level=3, iseed=305765867, field_3=0, field_4=0)
simul(program='JSirene', version=11012, date='11/17/18', time=7)
sourcemode: diffuse
spectrum(alpha=-1.4)
start_run(run_id=1)
target: isoscalar
usedetfile: false
xlat_user: 0.63297
xparam: OFF
zed_user: zed_user(field_0=0.0, field_1=3450.0)
To read the values in the header one can call them directly, as the structures
are simple namedtuple-like objects:
>>> f.header.DAQ.livetime
394
>>> f.header.cut_nu.Emin
100
>>> f.header.genvol.numberOfEvents
100000
Reading offline events¶
Events are at the top level of an offline file, so that each branch of an event
is directly accessible at the OfflineReader instance. The .keys() method
can be used to list the available attributes. Notice that some of them are aliases
for backwards compatibility (like mc_tracks and mc_trks). Another
backwards compatibility feature is the f.events attribute which is simply
mapping everything to f, so that f.events.mc_tracks is the same as
f.mc_tracks.
>>> f
OfflineReader (10 events)
>>> f.keys()
{'comment', 'det_id', 'flags', 'frame_index', 'hits', 'id', 'index',
'mc_hits', 'mc_id', 'mc_run_id', 'mc_t', 'mc_tracks', 'mc_trks',
'n_hits', 'n_mc_hits', 'n_mc_tracks', 'n_mc_trks', 'n_tracks',
'n_trks', 'overlays', 'run_id', 't_ns', 't_sec', 'tracks',
'trigger_counter', 'trigger_mask', 'trks', 'usr', 'usr_names',
'w', 'w2list', 'w3list'}
>>> f.tracks
<Branch [10] path='trks'>
>>> f.events.tracks
<Branch [10] path='trks'>
The [10] denotes that there are 10 events available, each containing a sub-array of tracks.
Using <TAB> completion gives an overview of available data. Alternatively the attribute fields can be used on event-branches and to see what is available for reading.
>>> f.tracks.fields
['id',
'pos_x',
'pos_y',
'pos_z',
'dir_x',
'dir_y',
'dir_z',
't',
'E',
'len',
'lik',
'rec_type',
'rec_stages',
'fitinf']
Reading the reconstructed values like energy and direction of an event can be done with:
>>> f.events.tracks.E
<Array [[117, 117, 0, 0, 0, ... 0, 0, 0, 0, 0]] type='10 * var * float64'>
The Array in this case is an awkward array with the data type
10 * var * float64 which means that there are 10 sub-arrays with var``iable lengths of type ``float64.
Awkward arrays allow high-performance access to arrays which are not rectangular (in contrast to numpy).
Read the documention of AwkwardArray to learn how to work with these structures efficiently. One example
to retrieve the energy of the very first reconstructed track for the first three events is:
>>> f.events.tracks.E[:3, 0]
<Array [117, 4.4e+03, 8.37] type='3 * float64'>
Online files reader¶
km3io is able to read events, summary slices and timeslices. Timeslices are
currently only supported with split level of 2 or more, which means that reading
L0 timeslices is not working at the moment (but is in progress).
Let’s have a look at some online data.
Reading online events¶
Now we use the OnlineReader to create our file object.
import km3io
f = km3io.OnlineReader(data_path("online/km3net_online.root"))
That’s it, we created an object which gives access to all the events, but the
relevant data is still not loaded into the memory (lazy access)!
The structure is different compared to the OfflineReader
because online files contain additional branches at the top level
(summaryslices and timeslices).
>>> f.events
Number of events: 3
>>> f.events.snapshot_hits[1].tot[:10]
array([27, 24, 21, 17, 22, 15, 24, 30, 19, 15], dtype=uint8)
>>> f.events.triggered_hits[1].channel_id[:10]
array([ 2, 3, 16, 22, 23, 0, 2, 3, 4, 5], dtype=uint8)
The resulting arrays are numpy arrays. The indexing convention is: the first indexing corresponds to the event, the second to the branch and consecutive ones to the optional dimensions of the arrays. In the last step we accessed the PMT channel IDs of the first 10 hits of the second event.
Reading SummarySlices¶
The following example shows how to access summary slices. The summary slices are returned in chunks to be more efficient with the I/O. The default chunk-size is 1000. In the example file we only have three summaryslices, so there is only a single chunk. The first index passed to the summaryslices reader is corresponding to the chunk and the second to the index of the summaryslice in that chunk.
>>> f.summaryslices
<SummarysliceReader 3 items, step_size=1000 (1 chunk)>
>>> f.summaryslices[0]
SummarysliceChunk(headers=<Array [{' cnt': 671088704, ... ] type='3 * {" cnt": uint32, " vers": uint16, " ...'>, slices=<Array [[{dom_id: 806451572, ... ch30: 48}]] type='3 * var * {"dom_id": int32, "...'>)
>>> f.summaryslices[0].headers
<Array [{' cnt': 671088704, ... ] type='3 * {" cnt": uint32, " vers": uint16, " ...'>
>>> f.summaryslices[0].slices[2]
<Array [{dom_id: 806451572, ... ch30: 48}] type='68 * {"dom_id": int32, "dq_stat...'>
>>> f.summaryslices[0].slices[2].dom_id
<Array [806451572, 806455814, ... 809544061] type='68 * int32'>
>>> f.summaryslices[0].slices[2].ch23
<Array [48, 43, 46, 54, 83, ... 51, 51, 52, 50] type='68 * uint8'>
Reading Timeslices¶
Timeslices are split into different streams since 2017 and km3io currently
supports everything except L0, i.e. L1, L2 and SN streams. The API is
work-in-progress and will be improved in future, however, all the data is
already accessible (although in ugly ways ;-)
To access the timeslice data, you need to specify which timeslice stream to read:
>>> f.timeslices
Available timeslice streams: SN, L1
>>> f.timeslices.stream("L1", 0).frames
{806451572: <Table [<Row 0> <Row 1> <Row 2> ... <Row 981> <Row 982> <Row 983>] at 0x00014c167340>,
806455814: <Table [<Row 984> <Row 985> <Row 986> ... <Row 1985> <Row 1986> <Row 1987>] at 0x00014c5f4760>,
806465101: <Table [<Row 1988> <Row 1989> <Row 1990> ... <Row 2236> <Row 2237> <Row 2238>] at 0x00014c5f45e0>,
806483369: <Table [<Row 2239> <Row 2240> <Row 2241> ... <Row 2965> <Row 2966> <Row 2967>] at 0x00014c12b910>,
...
809544061: <Table [<Row 48517> <Row 48518> <Row 48519> ... <Row 49240> <Row 49241> <Row 49242>] at 0x00014ca57100>}
The frames are represented by a dictionary where the key is the DOM ID and
the value an awkward array of hits, with the usual fields to access the PMT
channel, time and ToT:
>>> f.timeslices.stream("L1", 0).frames[809524432].dtype
dtype([('pmt', 'u1'), ('tdc', '<u4'), ('tot', 'u1')])
>>> f.timeslices.stream("L1", 0).frames[809524432].tot
array([25, 27, 28, ..., 29, 22, 28], dtype=uint8)