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Resolve "uproot4 integration"

Merged Resolve "uproot4 integration"
58-uproot4-integration-2 into master
Merged Tamas Gal requested to merge 58-uproot4-integration-2 into master
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km3io/offline.py
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import binascii
from collections import namedtuple
import uproot3
import logging
import warnings
import numba as nb
import uproot
import numpy as np
import awkward as ak
from .definitions import mc_header, fitparameters, reconstruction
from .definitions import mc_header
from .tools import cached_property, to_num, unfold_indices
from .rootio import Branch, BranchMapper
from .rootio import EventReader
MAIN_TREE_NAME = "E"
EXCLUDE_KEYS = ["AAObject", "t", "fBits", "fUniqueID"]
log = logging.getLogger("offline")
# 110 MB based on the size of the largest basket found so far in km3net
BASKET_CACHE_SIZE = 110 * 1024 ** 2
BASKET_CACHE = uproot3.cache.ThreadSafeArrayCache(BASKET_CACHE_SIZE)
def _nested_mapper(key):
"""Maps a key in the ROOT file to another key (e.g. trks.pos.x -> pos_x)"""
return "_".join(key.split(".")[1:])
EVENTS_MAP = BranchMapper(
name="events",
key="Evt",
extra={"t_sec": "t.fSec", "t_ns": "t.fNanoSec"},
exclude=EXCLUDE_KEYS,
update={
"n_hits": "hits",
"n_mc_hits": "mc_hits",
"n_tracks": "trks",
"n_mc_tracks": "mc_trks",
},
)
SUBBRANCH_MAPS = [
BranchMapper(
name="tracks",
key="trks",
extra={},
exclude=EXCLUDE_KEYS
+ ["trks.usr_data", "trks.usr", "trks.fUniqueID", "trks.fBits"],
attrparser=_nested_mapper,
flat=False,
toawkward=["fitinf", "rec_stages"],
),
BranchMapper(
name="mc_tracks",
key="mc_trks",
exclude=EXCLUDE_KEYS
+ [
"mc_trks.rec_stages",
"mc_trks.fitinf",
"mc_trks.fUniqueID",
"mc_trks.fBits",
],
attrparser=_nested_mapper,
toawkward=["usr", "usr_names"],
flat=False,
),
BranchMapper(
name="hits",
key="hits",
exclude=EXCLUDE_KEYS
+ [
"hits.usr",
"hits.pmt_id",
"hits.origin",
"hits.a",
"hits.pure_a",
"hits.fUniqueID",
"hits.fBits",
],
attrparser=_nested_mapper,
flat=False,
),
BranchMapper(
name="mc_hits",
key="mc_hits",
exclude=EXCLUDE_KEYS
+ [
"mc_hits.usr",
"mc_hits.dom_id",
"mc_hits.channel_id",
"mc_hits.tdc",
"mc_hits.tot",
"mc_hits.trig",
"mc_hits.fUniqueID",
"mc_hits.fBits",
],
attrparser=_nested_mapper,
flat=False,
),
]
class OfflineBranch(Branch):
@cached_property
def usr(self):
return Usr(self._mapper, self._branch, index_chain=self._index_chain)
class Usr:
"""Helper class to access AAObject `usr` stuff (only for events.usr)"""
def __init__(self, mapper, branch, index_chain=None):
self._mapper = mapper
self._name = mapper.name
self._index_chain = [] if index_chain is None else index_chain
self._branch = branch
self._usr_names = []
self._usr_idx_lookup = {}
self._usr_key = "usr" if mapper.flat else mapper.key + ".usr"
self._initialise()
def _initialise(self):
try:
self._branch[self._usr_key]
# This will raise a KeyError in old aanet files
# which has a different strucuter and key (usr_data)
# We do not support those (yet)
except (KeyError, IndexError):
print(
"The `usr` fields could not be parsed for the '{}' branch.".format(
self._name
)
)
return
self._usr_names = [
n.decode("utf-8")
for n in self._branch[self._usr_key + "_names"].lazyarray()[0]
]
self._usr_idx_lookup = {
name: index for index, name in enumerate(self._usr_names)
}
data = self._branch[self._usr_key].lazyarray()
if self._index_chain:
data = unfold_indices(data, self._index_chain)
self._usr_data = data
for name in self._usr_names:
setattr(self, name, self[name])
def __getitem__(self, item):
if self._index_chain:
return unfold_indices(self._usr_data, self._index_chain)[
:, self._usr_idx_lookup[item]
]
else:
return self._usr_data[:, self._usr_idx_lookup[item]]
def keys(self):
return self._usr_names
def __str__(self):
entries = []
for name in self.keys():
entries.append("{}: {}".format(name, self[name]))
return "\n".join(entries)
def __repr__(self):
return "<{}[{}]>".format(self.__class__.__name__, self._name)
class OfflineReader:
class OfflineReader(EventReader):
"""reader for offline ROOT files"""
def __init__(self, file_path=None):
"""OfflineReader class is an offline ROOT file wrapper
Parameters
----------
file_path : path-like object
Path to the file of interest. It can be a str or any python
path-like object that points to the file.
"""
self._fobj = uproot3.open(file_path)
self._filename = file_path
self._tree = self._fobj[MAIN_TREE_NAME]
self._uuid = binascii.hexlify(self._fobj._context.uuid).decode("ascii")
@property
def uuid(self):
return self._uuid
def close(self):
self._fobj.close()
def __enter__(self):
return self
def __exit__(self, *args):
self.close()
@cached_property
def events(self):
"""The `E` branch, containing all offline events."""
return OfflineBranch(
self._tree, mapper=EVENTS_MAP, subbranchmaps=SUBBRANCH_MAPS
)
event_path = "E/Evt"
item_name = "OfflineEvent"
skip_keys = ["t", "AAObject"]
aliases = {
"t_sec": "t/t.fSec",
"t_ns": "t/t.fNanoSec",
"usr": "AAObject/usr",
"usr_names": "AAObject/usr_names",
}
nested_branches = {
"hits": {
"id": "hits.id",
"channel_id": "hits.channel_id",
"dom_id": "hits.dom_id",
"t": "hits.t",
"tot": "hits.tot",
"trig": "hits.trig", # non-zero if the hit is a triggered hit
},
"mc_hits": {
"id": "mc_hits.id",
"pmt_id": "mc_hits.pmt_id",
"t": "mc_hits.t", # hit time (MC truth)
"a": "mc_hits.a", # hit amplitude (in p.e.)
"origin": "mc_hits.origin", # track id of the track that created this hit
"pure_t": "mc_hits.pure_t", # photon time before pmt simultion
"pure_a": "mc_hits.pure_a", # amplitude before pmt simution,
"type": "mc_hits.type", # particle type or parametrisation used for hit
},
"trks": {
"id": "trks.id",
"pos_x": "trks.pos.x",
"pos_y": "trks.pos.y",
"pos_z": "trks.pos.z",
"dir_x": "trks.dir.x",
"dir_y": "trks.dir.y",
"dir_z": "trks.dir.z",
"t": "trks.t",
"E": "trks.E",
"len": "trks.len",
"lik": "trks.lik",
"rec_type": "trks.rec_type",
"rec_stages": "trks.rec_stages",
"fitinf": "trks.fitinf",
},
"mc_trks": {
"id": "mc_trks.id",
"pos_x": "mc_trks.pos.x",
"pos_y": "mc_trks.pos.y",
"pos_z": "mc_trks.pos.z",
"dir_x": "mc_trks.dir.x",
"dir_y": "mc_trks.dir.y",
"dir_z": "mc_trks.dir.z",
"E": "mc_trks.E",
"t": "mc_trks.t",
"len": "mc_trks.len",
# "status": "mc_trks.status", # TODO: check this
# "mother_id": "mc_trks.mother_id", # TODO: check this
"pdgid": "mc_trks.type",
"hit_ids": "mc_trks.hit_ids",
"usr": "mc_trks.usr", # TODO: trouble with uproot4
"usr_names": "mc_trks.usr_names", # TODO: trouble with uproot4
},
}
nested_aliases = {
"tracks": "trks",
"mc_tracks": "mc_trks",
}
@cached_property
def header(self):
"""The file header"""
if "Head" in self._fobj:
header = {}
for n, x in self._fobj["Head"]._map_3c_string_2c_string_3e_.items():
header[n.decode("utf-8")] = x.decode("utf-8").strip()
return Header(header)
return Header(self._fobj["Head"].tojson()["map<string,string>"])
else:
warnings.warn("Your file header has an unsupported format")