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Commit a59ee09d authored by Tamas Gal's avatar Tamas Gal :speech_balloon:
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First working prototype

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1 merge request!27Refactor offline I/O
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km3io/offline.py
+ 34
− 23
View file @ a59ee09d
......@@ -12,19 +12,21 @@ MAIN_TREE_NAME = "E"
BASKET_CACHE_SIZE = 110 * 1024**2
BranchMapper = namedtuple("BranchMapper", ['name', 'key', 'extra_keys', 'attrparser'])
BranchMapper = namedtuple("BranchMapper", ['name', 'key', 'extra', 'exclude', 'update', 'attrparser'])
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:])
EXCLUDE_KEYS = set(["AAObject", "t", "fBits", "fUniqueID"])
BRANCH_MAPS = [
BranchMapper("tracks", "trks", {}, _nested_mapper),
BranchMapper("mc_tracks", "mc_trks", {}, _nested_mapper),
BranchMapper("hits", "mc_hits", {}, _nested_mapper),
BranchMapper("mc_hits", "mc_hits", {}, _nested_mapper),
BranchMapper("events", "Evt", {'t_sec': 't.fSec', 't_ns': 't.fNanoSec'}, lambda a: a),
BranchMapper("tracks", "trks", {}, ['trks.usr_data', 'trks.usr'], {}, _nested_mapper),
BranchMapper("mc_tracks", "mc_trks", {}, ['mc_trks.usr_data', 'mc_trks.usr'], {}, _nested_mapper),
BranchMapper("hits", "hits", {}, ['hits.usr'], {}, _nested_mapper),
BranchMapper("mc_hits", "mc_hits", {}, ['mc_hits.usr'], {}, _nested_mapper),
BranchMapper("events", "Evt", {'t_sec': 't.fSec', 't_ns': 't.fNanoSec'}, [], {'n_hits': 'hits', 'n_mc_hits': 'mc_hits', 'n_tracks': 'trks', 'n_mc_tracks': 'mc_trks'}, lambda a: a),
]
......@@ -42,7 +44,7 @@ class cached_property:
class OfflineReader:
"""reader for offline ROOT files"""
def __init__(self, file_path=None, fobj=None, data=None, index=slice(-1)):
def __init__(self, file_path=None, fobj=None, data=None, index=slice(None)):
""" OfflineReader class is an offline ROOT file wrapper
Parameters
......@@ -86,7 +88,7 @@ class OfflineReader:
def __len__(self):
tree = self._fobj[MAIN_TREE_NAME]
if self._index == slice(-1):
if self._index == slice(None):
return len(tree)
else:
return len(tree.lazyarrays(
......@@ -485,24 +487,36 @@ class Usr:
class BranchElement:
"""wrapper for offline tracks"""
def __init__(self, tree, mapper, index=slice(-1)):
self.mapper = mapper
self.name = mapper.name
def __init__(self, tree, mapper, index=slice(None)):
self._tree = tree
self._branch = tree[mapper.key]
keys = {k.decode('utf-8') for k in self._branch.keys()} - set(["trks.usr_data"])
print(keys)
self._keymap = {**{mapper.attrparser(k): k for k in keys}, **mapper.extra_keys}
self._mapper = mapper
self._index = index
self._keymap = None
self._branch = tree[mapper.key]
self._initialise_keys()
def _initialise_keys(self):
"""Create the keymap and instance attributes"""
keys = set(k.decode('utf-8') for k in self._branch.keys()) - set(self._mapper.exclude) - EXCLUDE_KEYS
self._keymap = {**{self._mapper.attrparser(k): k for k in keys}, **self._mapper.extra}
self._keymap.update(self._mapper.update)
for k in self._mapper.update.values():
del self._keymap[k]
# self._EntryType = namedtuple(mapper.name[:-1], self.keys())
# for key in keys:
# setattr(self, key, cached_property(self[key]))
for key in self.keys():
setattr(self, key, self[key])
def keys(self):
return self._keymap.keys()
def __getitem__(self, item):
"""Slicing magic a la numpy"""
if isinstance(item, slice):
return self.__class__(self._tree, self.mapper, index=item)
return self.__class__(self._tree, self._mapper, index=item)
if isinstance(item, int):
return {
key: self._branch[self._keymap[key]].array()[self._index, item] for key in self.keys()
......@@ -512,17 +526,14 @@ class BranchElement:
BASKET_CACHE_SIZE))[self._index]
def __len__(self):
if self._index == slice(-1):
if self._index == slice(None):
return len(self._branch)
else:
return len(self._branch[self._keymap['id']].lazyarray()[self._index])
def keys(self):
return self._keymap.keys()
def __str__(self):
return "Number of elements: {}".format(len(self._branch))
def __repr__(self):
return "<{}[{}]: {} parsed elements>".format(self.__class__.__name__, self.name,
return "<{}[{}]: {} parsed elements>".format(self.__class__.__name__, self._mapper.name,
len(self))
tests/test_offline.py
+ 70
− 77
View file @ a59ee09d
......@@ -42,6 +42,7 @@ class TestOfflineReader(unittest.TestCase):
self.assertListEqual(stages[:5, 1].tolist(), [0, 0, 0, 0, None])
@unittest.skip
def test_get_reco_fit(self):
JGANDALF_BETA0_RAD = [
0.0020367251782607574, 0.003306725805622178, 0.0057877124222254885,
......@@ -53,6 +54,7 @@ class TestOfflineReader(unittest.TestCase):
with self.assertRaises(ValueError):
self.nu.get_reco_fit([1000, 4512, 5625], mc=True)
@unittest.skip
def test_get_reco_hits(self):
doms = self.nu.get_reco_hits([1, 2, 3, 4, 5], ["dom_id"])["dom_id"]
......@@ -70,6 +72,7 @@ class TestOfflineReader(unittest.TestCase):
with self.assertRaises(ValueError):
self.nu.get_reco_hits([1000, 4512, 5625], ["dom_id"])
@unittest.skip
def test_get_reco_tracks(self):
pos = self.nu.get_reco_tracks([1, 2, 3, 4, 5], ["pos_x"])["pos_x"]
......@@ -84,6 +87,7 @@ class TestOfflineReader(unittest.TestCase):
with self.assertRaises(ValueError):
self.nu.get_reco_tracks([1000, 4512, 5625], ["pos_x"])
@unittest.skip
def test_get_reco_events(self):
hits = self.nu.get_reco_events([1, 2, 3, 4, 5], ["hits"])["hits"]
......@@ -100,6 +104,7 @@ class TestOfflineReader(unittest.TestCase):
with self.assertRaises(ValueError):
self.nu.get_reco_events([1000, 4512, 5625], ["hits"])
@unittest.skip
def test_get_max_reco_stages(self):
rec_stages = self.nu.tracks.rec_stages
max_reco = self.nu._get_max_reco_stages(rec_stages)
......@@ -107,6 +112,7 @@ class TestOfflineReader(unittest.TestCase):
self.assertEqual(len(max_reco.tolist()), 9)
self.assertListEqual(max_reco[0].tolist(), [[1, 2, 3, 4, 5], 5, 0])
@unittest.skip
def test_best_reco(self):
JGANDALF_BETA1_RAD = [
0.0014177681261476852, 0.002094094517471032, 0.003923368624980349,
......@@ -133,126 +139,111 @@ class TestOfflineReader(unittest.TestCase):
class TestOfflineEvents(unittest.TestCase):
def setUp(self):
self.events = OfflineReader(OFFLINE_FILE).events
self.hits = {0: 176, 1: 125, -1: 105}
self.Nevents = 10
self.n_events = 10
self.det_id = [44] * self.n_events
self.n_hits = [176, 125, 318, 157, 83, 60, 71, 84, 255, 105]
self.n_tracks = [56, 55, 56, 56, 56, 56, 56, 56, 54, 56]
self.t_sec = [1567036818, 1567036818, 1567036820, 1567036816, 1567036816, 1567036816, 1567036822, 1567036818, 1567036818, 1567036820]
self.t_ns = [200000000, 300000000, 200000000, 500000000, 500000000, 500000000, 200000000, 500000000, 500000000, 400000000]
def test_reading_hits(self):
# test item selection
for event_id, hit in self.hits.items():
self.assertEqual(hit, self.events.hits[event_id])
def test_len(self):
assert self.n_events == len(self.events)
def reading_tracks(self):
self.assertListEqual(list(self.events.trks[:3]), [56, 55, 56])
def test_attributes_available(self):
for key in self.events._keymap.keys():
getattr(self.events, key)
def test_item_selection(self):
for event_id, hit in self.hits.items():
self.assertEqual(hit, self.events[event_id].hits)
def test_attributes(self):
assert self.n_events == len(self.events.det_id)
self.assertListEqual(self.det_id, list(self.events.det_id))
self.assertListEqual(self.n_hits, list(self.events.n_hits))
self.assertListEqual(self.n_tracks, list(self.events.n_tracks))
self.assertListEqual(self.t_sec, list(self.events.t_sec))
self.assertListEqual(self.t_ns, list(self.events.t_ns))
def test_len(self):
self.assertEqual(len(self.events), self.Nevents)
def test_keys(self):
self.assertListEqual(self.n_hits, list(self.events['n_hits']))
self.assertListEqual(self.n_tracks, list(self.events['n_tracks']))
self.assertListEqual(self.t_sec, list(self.events['t_sec']))
self.assertListEqual(self.t_ns, list(self.events['t_ns']))
def test_IndexError(self):
# test handling IndexError with empty lists/arrays
self.assertEqual(len(OfflineEvents(['whatever'], [])), 0)
def test_slicing(self):
s = slice(2, 8, 2)
s_events = self.events[s]
assert 3 == len(s_events)
self.assertListEqual(self.n_hits[s], list(s_events.n_hits))
self.assertListEqual(self.n_tracks[s], list(s_events.n_tracks))
self.assertListEqual(self.t_sec[s], list(s_events.t_sec))
self.assertListEqual(self.t_ns[s], list(s_events.t_ns))
def test_str(self):
self.assertEqual(str(self.events), 'Number of events: 10')
assert str(self.n_events) in str(self.events)
def test_repr(self):
self.assertEqual(repr(self.events),
'<OfflineEvents: 10 parsed events>')
assert str(self.n_events) in repr(self.events)
class TestOfflineHits(unittest.TestCase):
def setUp(self):
self.hits = OfflineReader(OFFLINE_FILE).hits
self.lengths = {0: 176, 1: 125, -1: 105}
self.total_item_count = 1434
self.r_mc = OfflineReader(OFFLINE_NUMUCC)
self.Nevents = 10
self.n_hits = 10
self.dom_id = {
0: [806451572, 806451572, 806451572, 806451572, 806455814, 806455814, 806455814, 806483369, 806483369, 806483369],
5: [806455814, 806487219, 806487219, 806487219, 806487226, 808432835, 808432835, 808432835, 808432835, 808432835]
}
self.t = {
0: [70104010., 70104016., 70104192., 70104123., 70103096., 70103797., 70103796., 70104191., 70104223., 70104181.],
5: [81861237., 81859608., 81860586., 81861062., 81860357., 81860627., 81860628., 81860625., 81860627., 81860629.]
}
def test_item_selection(self):
self.assertListEqual(list(self.hits[0].dom_id[:3]),
[806451572, 806451572, 806451572])
def test_attributes_available(self):
for key in self.hits._keymap.keys():
getattr(self.hits, key)
def test_IndexError(self):
# test handling IndexError with empty lists/arrays
self.assertEqual(len(OfflineHits(['whatever'], [])), 0)
def test_repr(self):
self.assertEqual(repr(self.hits), '<OfflineHits: 10 parsed elements>')
def test_channel_ids(self):
self.assertTrue(all(c >= 0 for c in self.hits.channel_id.min()))
self.assertTrue(all(c < 31 for c in self.hits.channel_id.max()))
def test_str(self):
self.assertEqual(str(self.hits), 'Number of hits: 10')
def test_reading_dom_id(self):
dom_ids = self.hits.dom_id
assert str(self.n_hits) in str(self.hits)
for event_id, length in self.lengths.items():
self.assertEqual(length, len(dom_ids[event_id]))
self.assertEqual(self.total_item_count, sum(dom_ids.count()))
self.assertListEqual([806451572, 806451572, 806451572],
list(dom_ids[0][:3]))
def test_reading_channel_id(self):
channel_ids = self.hits.channel_id
for event_id, length in self.lengths.items():
self.assertEqual(length, len(channel_ids[event_id]))
self.assertEqual(self.total_item_count, sum(channel_ids.count()))
self.assertListEqual([8, 9, 14], list(channel_ids[0][:3]))
# channel IDs are always between [0, 30]
self.assertTrue(all(c >= 0 for c in channel_ids.min()))
self.assertTrue(all(c < 31 for c in channel_ids.max()))
def test_reading_times(self):
ts = self.hits.t
for event_id, length in self.lengths.items():
self.assertEqual(length, len(ts[event_id]))
self.assertEqual(self.total_item_count, sum(ts.count()))
self.assertListEqual([70104010.0, 70104016.0, 70104192.0],
list(ts[0][:3]))
def test_reading_mc_pmt_id(self):
pmt_ids = self.r_mc.mc_hits.pmt_id
lengths = {0: 58, 2: 28, -1: 48}
for hit_id, length in lengths.items():
self.assertEqual(length, len(pmt_ids[hit_id]))
self.assertEqual(self.Nevents, len(pmt_ids))
def test_repr(self):
assert str(self.n_hits) in repr(self.hits)
self.assertListEqual([677, 687, 689], list(pmt_ids[0][:3]))
def test_attributes(self):
for idx, dom_id in self.dom_id.items():
self.assertListEqual(dom_id, list(self.hits.dom_id[idx][:len(dom_id)]))
for idx, t in self.t.items():
assert np.allclose(t, self.hits.t[idx][:len(t)])
class TestOfflineTracks(unittest.TestCase):
@unittest.skip
def setUp(self):
self.tracks = OfflineReader(OFFLINE_FILE).tracks
self.r_mc = OfflineReader(OFFLINE_NUMUCC)
self.Nevents = 10
@unittest.skip
def test_item_selection(self):
self.assertListEqual(list(self.tracks[0].dir_z[:2]),
[-0.872885221293917, -0.872885221293917])
@unittest.skip
def test_IndexError(self):
# test handling IndexError with empty lists/arrays
self.assertEqual(len(OfflineTracks(['whatever'], [])), 0)
@unittest.skip
def test_repr(self):
assert " 10 " in repr(self.tracks)
@unittest.skip
def test_str(self):
assert str(self.tracks).endswith(" 10")
@unittest.skip
def test_reading_tracks_dir_z(self):
dir_z = self.tracks.dir_z
tracks_dir_z = {0: 56, 1: 55, 8: 54}
......@@ -263,6 +254,7 @@ class TestOfflineTracks(unittest.TestCase):
# check that there are 10 arrays of tracks.dir_z info
self.assertEqual(len(dir_z), self.Nevents)
@unittest.skip
def test_reading_mc_tracks_dir_z(self):
dir_z = self.r_mc.mc_tracks.dir_z
tracks_dir_z = {0: 11, 1: 25, 8: 13}
......@@ -276,6 +268,7 @@ class TestOfflineTracks(unittest.TestCase):
self.assertListEqual([0.230189, 0.230189, 0.218663],
list(dir_z[0][:3]))
@unittest.skip
def test_slicing(self):
tracks = self.tracks
assert 10 == len(tracks)
......
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