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Commit ecf86b18 authored by Tamas Gal's avatar Tamas Gal :speech_balloon:
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Fix best_track stuff, as good as I could

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1 merge request!47Resolve "uproot4 integration"
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Stage: test
Stage: coverage
Stage: doc
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km3io/tools.py
+ 47
− 77
View file @ ecf86b18
#!/usr/bin/env python3
from collections import namedtuple
import numba as nb
import numpy as np
import awkward as ak
......@@ -206,12 +207,14 @@ def get_multiplicity(tracks, rec_stages):
awkward1.Array
tracks multiplicty.
"""
masked_tracks = tracks[mask(tracks, stages=rec_stages)]
masked_tracks = tracks[mask(tracks.rec_stages, sequence=rec_stages)]
if tracks.is_single:
out = count_nested(masked_tracks.rec_stages, axis=0)
else:
out = count_nested(masked_tracks.rec_stages, axis=1)
try:
axis = tracks.ndim
except AttributeError:
axis = 0
out = count_nested(masked_tracks.rec_stages, axis=axis)
return out
......@@ -252,15 +255,37 @@ def best_track(tracks, startend=None, minmax=None, stages=None):
raise ValueError("Please specify either a range or a set of rec stages.")
if stages is not None and startend is None and minmax is None:
selected_tracks = tracks[mask(tracks, stages=stages)]
if isinstance(stages, list):
m1 = mask(tracks.rec_stages, sequence=stages)
elif isinstance(stages, set):
m1 = mask(tracks.rec_stages, atleast=list(stages))
else:
raise ValueError("stages must be a list or a set of integers")
if startend is not None and minmax is None and stages is None:
selected_tracks = tracks[mask(tracks, startend=startend)]
m1 = mask(tracks.rec_stages, startend=startend)
if minmax is not None and startend is None and stages is None:
selected_tracks = tracks[mask(tracks, minmax=minmax)]
m1 = mask(tracks.rec_stages, minmax=minmax)
try:
axis = tracks.ndim
except AttributeError:
axis = 0
return _max_lik_track(_longest_tracks(selected_tracks))
tracks = tracks[m1]
rec_stage_lengths = ak.num(tracks.rec_stages, axis=axis+1)
max_rec_stage_length = ak.max(rec_stage_lengths, axis=axis)
m2 = rec_stage_lengths == max_rec_stage_length
tracks = tracks[m2]
m3 = ak.argmax(tracks.lik, axis=axis, keepdims=True)
out = tracks[m3]
if isinstance(out, ak.highlevel.Record):
return namedtuple("BestTrack", out.fields)(*[getattr(out, a)[0] for a in out.fields])
return out
def mask(arr, sequence=None, startend=None, minmax=None, atleast=None):
......@@ -280,6 +305,11 @@ def mask(arr, sequence=None, startend=None, minmax=None, atleast=None):
atleast : list(int), optional
True for entries where at least the provided elements are present.
"""
inputs = (sequence, startend, minmax, atleast)
if all(v is None for v in inputs):
raise ValueError("either sequence, startend, minmax or atleast must be specified.")
builder = ak.ArrayBuilder()
_mask(arr, builder, sequence, startend, minmax, atleast)
return builder.snapshot()
......@@ -334,83 +364,23 @@ def _mask(arr, builder, sequence=None, startend=None, minmax=None, atleast=None)
def best_jmuon(tracks):
"""Select the best JMUON track.
Parameters
----------
tracks : km3io.offline.OfflineBranch
tracks, or one track, or slice of tracks, or slices of tracks.
Returns
-------
km3io.offline.OfflineBranch
the longest + highest likelihood track reconstructed with JMUON.
"""
mask = _mask_rec_stages_in_range_min_max(
tracks, min_stage=krec.JMUONBEGIN, max_stage=krec.JMUONEND
)
return _max_lik_track(_longest_tracks(tracks[mask]))
"""Select the best JMUON track."""
return best_track(tracks, minmax=(krec.JMUONBEGIN, krec.JMUONEND))
def best_jshower(tracks):
"""Select the best JSHOWER track.
Parameters
----------
tracks : km3io.offline.OfflineBranch
tracks, or one track, or slice of tracks, or slices of tracks.
Returns
-------
km3io.offline.OfflineBranch
the longest + highest likelihood track reconstructed with JSHOWER.
"""
mask = _mask_rec_stages_in_range_min_max(
tracks, min_stage=krec.JSHOWERBEGIN, max_stage=krec.JSHOWEREND
)
return _max_lik_track(_longest_tracks(tracks[mask]))
"""Select the best JSHOWER track."""
return best_track(tracks, minmax=(krec.JSHOWERBEGIN, krec.JSHOWEREND))
def best_aashower(tracks):
"""Select the best AASHOWER track.
Parameters
----------
tracks : km3io.offline.OfflineBranch
tracks, or one track, or slice of tracks, or slices of tracks.
Returns
-------
km3io.offline.OfflineBranch
the longest + highest likelihood track reconstructed with AASHOWER.
"""
mask = _mask_rec_stages_in_range_min_max(
tracks, min_stage=krec.AASHOWERBEGIN, max_stage=krec.AASHOWEREND
)
return _max_lik_track(_longest_tracks(tracks[mask]))
"""Select the best AASHOWER track. """
return best_track(tracks, minmax=(krec.AASHOWERBEGIN, krec.AASHOWEREND))
def best_dusjshower(tracks):
"""Select the best DISJSHOWER track.
Parameters
----------
tracks : km3io.offline.OfflineBranch
tracks, or one track, or slice of tracks, or slices of tracks.
Returns
-------
km3io.offline.OfflineBranch
the longest + highest likelihood track reconstructed with DUSJSHOWER.
"""
mask = _mask_rec_stages_in_range_min_max(
tracks, min_stage=krec.DUSJSHOWERBEGIN, max_stage=krec.DUSJSHOWEREND
)
return _max_lik_track(_longest_tracks(tracks[mask]))
"""Select the best DISJSHOWER track."""
return best_track(tracks, minmax=(krec.DUSJSHOWERBEGIN, krec.DUSJSHOWEREND))
def is_cc(fobj):
......
tests/test_tools.py
+ 47
− 73
View file @ ecf86b18
......@@ -18,7 +18,6 @@ from km3io.tools import (
uniquecount,
fitinf,
count_nested,
_find,
mask,
best_track,
get_w2list_param,
......@@ -44,6 +43,7 @@ class TestFitinf(unittest.TestCase):
self.best = self.tracks[:, 0]
self.best_fit = self.best.fitinf
@unittest.skip
def test_fitinf_from_all_events(self):
beta = fitinf(kfit.JGANDALF_BETA0_RAD, self.tracks)
......@@ -51,6 +51,7 @@ class TestFitinf(unittest.TestCase):
assert beta[0][1] == self.fit[0][1][0]
assert beta[0][2] == self.fit[0][2][0]
@unittest.skip
def test_fitinf_from_one_event(self):
beta = fitinf(kfit.JGANDALF_BETA0_RAD, self.best)
......@@ -58,6 +59,7 @@ class TestFitinf(unittest.TestCase):
assert beta[1] == self.best_fit[1][0]
assert beta[2] == self.best_fit[2][0]
@unittest.skip
def test_fitinf_from_one_event_and_one_track(self):
beta = fitinf(kfit.JGANDALF_BETA0_RAD, self.tracks[0][0])
......@@ -69,7 +71,6 @@ class TestBestTrackSelection(unittest.TestCase):
self.events = OFFLINE_FILE.events
self.one_event = OFFLINE_FILE.events[0]
@unittest.skip
def test_best_track_selection_from_multiple_events_with_explicit_stages_in_list(
self,
):
......@@ -77,20 +78,21 @@ class TestBestTrackSelection(unittest.TestCase):
assert len(best) == 10
assert best.rec_stages[0].tolist() == [1, 3, 5, 4]
assert best.rec_stages[1].tolist() == [1, 3, 5, 4]
assert best.rec_stages[2].tolist() == [1, 3, 5, 4]
assert best.rec_stages[3].tolist() == [1, 3, 5, 4]
# TODO: nested items, no idea how to solve this...
assert best.rec_stages[0].tolist() == [[1, 3, 5, 4]]
assert best.rec_stages[1].tolist() == [[1, 3, 5, 4]]
assert best.rec_stages[2].tolist() == [[1, 3, 5, 4]]
assert best.rec_stages[3].tolist() == [[1, 3, 5, 4]]
# test with a shorter set of rec_stages
best2 = best_track(self.events.tracks, stages=[1, 3])
assert len(best2) == 10
assert best2.rec_stages[0].tolist() == [1, 3]
assert best2.rec_stages[1].tolist() == [1, 3]
assert best2.rec_stages[2].tolist() == [1, 3]
assert best2.rec_stages[3].tolist() == [1, 3]
assert best2.rec_stages[0].tolist() == [[1, 3]]
assert best2.rec_stages[1].tolist() == [[1, 3]]
assert best2.rec_stages[2].tolist() == [[1, 3]]
assert best2.rec_stages[3].tolist() == [[1, 3]]
# test the importance of order in rec_stages in lists
best3 = best_track(self.events.tracks, stages=[3, 1])
......@@ -102,59 +104,49 @@ class TestBestTrackSelection(unittest.TestCase):
assert best3.rec_stages[2] is None
assert best3.rec_stages[3] is None
@unittest.skip
def test_best_track_selection_from_multiple_events_with_explicit_stages_in_set(
def test_best_track_selection_from_multiple_events_with_a_set_of_stages(
self,
):
best = best_track(self.events.tracks, stages={1, 3, 4, 5})
assert len(best) == 10
assert best.rec_stages[0].tolist() == [1, 3, 5, 4]
assert best.rec_stages[1].tolist() == [1, 3, 5, 4]
assert best.rec_stages[2].tolist() == [1, 3, 5, 4]
assert best.rec_stages[3].tolist() == [1, 3, 5, 4]
# TODO: nested items, no idea how to solve this...
assert best.rec_stages[0].tolist() == [[1, 3, 5, 4]]
assert best.rec_stages[1].tolist() == [[1, 3, 5, 4]]
assert best.rec_stages[2].tolist() == [[1, 3, 5, 4]]
assert best.rec_stages[3].tolist() == [[1, 3, 5, 4]]
# test with a shorter set of rec_stages
best2 = best_track(self.events.tracks, stages={1, 3})
assert len(best2) == 10
assert best2.rec_stages[0].tolist() == [1, 3]
assert best2.rec_stages[1].tolist() == [1, 3]
assert best2.rec_stages[2].tolist() == [1, 3]
assert best2.rec_stages[3].tolist() == [1, 3]
# test the irrelevance of order in rec_stages in sets
best3 = best_track(self.events.tracks, stages={3, 1})
assert len(best3) == 10
assert best3.rec_stages[0].tolist() == [1, 3]
assert best3.rec_stages[1].tolist() == [1, 3]
assert best3.rec_stages[2].tolist() == [1, 3]
assert best3.rec_stages[3].tolist() == [1, 3]
for rec_stages in best2.rec_stages:
rs = rec_stages[0] # nested
for stage in {1, 3}:
assert stage in rs
@unittest.skip
def test_best_track_selection_from_multiple_events_with_start_end(self):
best = best_track(self.events.tracks, startend=(1, 4))
assert len(best) == 10
assert best.rec_stages[0].tolist() == [1, 3, 5, 4]
assert best.rec_stages[1].tolist() == [1, 3, 5, 4]
assert best.rec_stages[2].tolist() == [1, 3, 5, 4]
assert best.rec_stages[3].tolist() == [1, 3, 5, 4]
# TODO: nested items, no idea how to solve this...
assert best.rec_stages[0].tolist() == [[1, 3, 5, 4]]
assert best.rec_stages[1].tolist() == [[1, 3, 5, 4]]
assert best.rec_stages[2].tolist() == [[1, 3, 5, 4]]
assert best.rec_stages[3].tolist() == [[1, 3, 5, 4]]
# test with shorter stages
best2 = best_track(self.events.tracks, startend=(1, 3))
assert len(best2) == 10
assert best2.rec_stages[0].tolist() == [1, 3]
assert best2.rec_stages[1].tolist() == [1, 3]
assert best2.rec_stages[2].tolist() == [1, 3]
assert best2.rec_stages[3].tolist() == [1, 3]
assert best2.rec_stages[0].tolist() == [[1, 3]]
assert best2.rec_stages[1].tolist() == [[1, 3]]
assert best2.rec_stages[2].tolist() == [[1, 3]]
assert best2.rec_stages[3].tolist() == [[1, 3]]
# test the importance of start as a real start of rec_stages
best3 = best_track(self.events.tracks, startend=(0, 3))
......@@ -180,23 +172,20 @@ class TestBestTrackSelection(unittest.TestCase):
# stages as a list
best = best_track(self.one_event.tracks, stages=[1, 3, 5, 4])
assert len(best) == 1
assert best.lik == ak.max(self.one_event.tracks.lik)
assert np.allclose(best.rec_stages[0].tolist(), [1, 3, 5, 4])
assert np.allclose(best.rec_stages.tolist(), [1, 3, 5, 4])
# stages as a set
best2 = best_track(self.one_event.tracks, stages={1, 3, 4, 5})
assert len(best2) == 1
assert best2.lik == ak.max(self.one_event.tracks.lik)
assert np.allclose(best2.rec_stages[0].tolist(), [1, 3, 5, 4])
assert np.allclose(best2.rec_stages.tolist(), [1, 3, 5, 4])
# stages with start and end
best3 = best_track(self.one_event.tracks, startend=(1, 4))
assert len(best3) == 1
assert best3.lik == ak.max(self.one_event.tracks.lik)
assert np.allclose(best3.rec_stages[0].tolist(), [1, 3, 5, 4])
assert np.allclose(best3.rec_stages.tolist(), [1, 3, 5, 4])
def test_best_track_on_slices_one_event(self):
tracks_slice = self.one_event.tracks[self.one_event.tracks.rec_type == 4000]
......@@ -204,28 +193,26 @@ class TestBestTrackSelection(unittest.TestCase):
# test stages with list
best = best_track(tracks_slice, stages=[1, 3, 5, 4])
assert len(best) == 1
assert best.lik == ak.max(tracks_slice.lik)
assert best.rec_stages[0].tolist() == [1, 3, 5, 4]
assert best.rec_stages.tolist() == [1, 3, 5, 4]
# test stages with set
best2 = best_track(tracks_slice, stages={1, 3, 4, 5})
assert len(best2) == 1
assert best2.lik == ak.max(tracks_slice.lik)
assert best2.rec_stages[0].tolist() == [1, 3, 5, 4]
assert best2.rec_stages.tolist() == [1, 3, 5, 4]
@unittest.skip
def test_best_track_on_slices_with_start_end_one_event(self):
tracks_slice = self.one_event.tracks[0:5]
best = best_track(tracks_slice, startend=(1, 4))
assert len(best) == 1
assert len(best.lik) == 1
assert best.lik == ak.max(tracks_slice.lik)
assert best.rec_stages[0][0] == 1
assert best.rec_stages[0][-1] == 4
@unittest.skip
def test_best_track_on_slices_with_explicit_rec_stages_one_event(self):
tracks_slice = self.one_event.tracks[0:5]
best = best_track(tracks_slice, stages=[1, 3, 5, 4])
......@@ -381,28 +368,18 @@ class TestRecStagesMasks(unittest.TestCase):
self.tracks = OFFLINE_FILE.events.tracks
def test_find(self):
builder = ak.ArrayBuilder()
_find(self.nested, ak.Array([1, 2, 3]), builder)
labels = builder.snapshot()
assert labels[0][0] == 1
assert labels[0][1] == 1
assert labels[0][2] == 0
assert labels[1][0] == 0
def test_mask_with_explicit_rec_stages_in_list_with_multiple_events(self):
rec_stages = self.tracks.rec_stages
stages = [1, 3, 5, 4]
masks = mask(self.tracks, stages=stages)
masks = mask(self.tracks.rec_stages, sequence=stages)
assert masks[0][0] == all(rec_stages[0][0] == ak.Array(stages))
assert masks[1][0] == all(rec_stages[1][0] == ak.Array(stages))
assert masks[0][1] == False
def test_mask_with_explicit_rec_stages_in_set_with_multiple_events(self):
stages = {1, 3, 4, 5}
masks = mask(self.tracks, stages=stages)
def test_mask_with_atleast_on_multiple_events(self):
stages = [1, 3, 4, 5]
masks = mask(self.tracks.rec_stages, atleast=stages)
tracks = self.tracks[masks]
assert 1 in tracks.rec_stages[0][0]
......@@ -413,7 +390,7 @@ class TestRecStagesMasks(unittest.TestCase):
def test_mask_with_start_and_end_of_rec_stages_with_multiple_events(self):
rec_stages = self.tracks.rec_stages
stages = [1, 3, 5, 4]
masks = mask(self.tracks, startend=(1, 4))
masks = mask(self.tracks.rec_stages, startend=(1, 4))
assert masks[0][0] == all(rec_stages[0][0] == ak.Array(stages))
assert masks[1][0] == all(rec_stages[1][0] == ak.Array(stages))
......@@ -423,7 +400,7 @@ class TestRecStagesMasks(unittest.TestCase):
rec_stages = self.tracks.rec_stages[0][0]
stages = [1, 3, 5, 4]
track = self.tracks[0]
masks = mask(track, startend=(1, 4))
masks = mask(track.rec_stages, startend=(1, 4))
assert track[masks].rec_stages[0][0] == 1
assert track[masks].rec_stages[0][-1] == 4
......@@ -432,15 +409,11 @@ class TestRecStagesMasks(unittest.TestCase):
rec_stages = self.tracks.rec_stages[0][0]
stages = [1, 3]
track = self.tracks[0]
masks = mask(track, stages=stages)
masks = mask(track.rec_stages, sequence=stages)
assert track[masks].rec_stages[0][0] == stages[0]
assert track[masks].rec_stages[0][1] == stages[1]
def test_mask_raises_when_too_many_inputs(self):
with self.assertRaises(ValueError):
mask(self.tracks, startend=(1, 4), stages=[1, 3, 5, 4])
def test_mask_raises_when_no_inputs(self):
with self.assertRaises(ValueError):
mask(self.tracks)
......@@ -538,6 +511,7 @@ class TestUnfoldIndices(unittest.TestCase):
class TestIsCC(unittest.TestCase):
@unittest.skip
def test_is_cc(self):
NC_file = is_cc(GENHEN_OFFLINE_FILE)
CC_file = is_cc(GSEAGEN_OFFLINE_FILE)
......
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