def test_measure_alignment():
"align on 1 phase or another as needed"
track = randtrack(driftargs=None, baselineargs=(.1, .05, 'rand'), seed=0)
for i in range(3):
ini = track.cycles.withphases(PHASE.initial)[0, i]
ini += (track.cycles.withphases(PHASE.pull)[0, i].mean() -
ini.mean()) * .5
for i in range(5):
ini = track.cycles.withphases(PHASE.measure)[0, i]
ini += (track.cycles.withphases(PHASE.pull)[0, i].mean() -
ini.mean()) * .5
bead = ExtremumAlignmentProcessor.apply(track.beads,
phase=AlignmentTactic.measure)
inipos = [
i.mean() for i in # type: ignore
track.beads[0, ...].withphases(PHASE.pull).values()
]
corrpos = [
i.mean() for i in # type: ignore
bead[0, ...].withphases(PHASE.pull).values()
]
assert np.std(inipos[3:]) > 10 * np.std(corrpos[3:])
assert all(i > .95 for i in corrpos[:3])
def test_pull_alignment():
"align on 1 phase or another as needed"
track = randtrack(driftargs=None, baselineargs=(.1, .05, 'rand'))
for i in range(3):
ini = track.cycles.withphases(PHASE.initial)[0, i]
ini -= ini.mean()
pull = track.cycles.withphases(PHASE.pull)[0, i]
pull += .2 - pull.mean()
meas = track.cycles.withphases(PHASE.measure)[0, i]
meas[:] = 0.
pull = track.cycles.withphases(PHASE.pull)[0, 3].mean()
meas = track.cycles.withphases(PHASE.measure)[0, 3]
meas[:] = pull.mean() - .2
pull = track.cycles.withphases(PHASE.pull)[0, 4].mean()
meas = track.cycles.withphases(PHASE.initial)[0, 4]
meas[:] = pull.mean() - .2
bead = ExtremumAlignmentProcessor.apply(track.beads,
phase=AlignmentTactic.pull)
inipos = [
i.mean() for i in track.beads[0, ...].withphases(PHASE.pull).values()
]
corrpos = [i.mean() for i in bead[0, ...].withphases(PHASE.pull).values()]
assert np.std(inipos[3:]) > 20 * np.std(corrpos[3:])
assert all(i < .6 for i in corrpos[:3])
def _create(phase):
track = randtrack(driftargs=None, baselineargs=(.1, .05, 'rand'))
ini = track.cycles.withphases(PHASE.initial)[0, 0]
ini += (track.cycles.withphases(PHASE.pull)[0, 0].mean() -
ini.mean()) * .5
bead = ExtremumAlignmentProcessor.apply(track.beads, phase=phase)
return [
i.mean() for i in bead[0, ...].withphases(PHASE.initial).values()
]
def test_processor():
"test processor"
# pylint: disable=expression-not-assigned
cache = {} # type: ignore
trk = randtrack().beads
DataCleaningProcessor.apply(trk, cache=cache, maxsaturation=100)[0]
assert list(cache) == [0]
tmp = cache[0]
DataCleaningProcessor.apply(trk, cache=cache, maxsaturation=100)[0]
assert tmp is cache[0]
def test_edgeminmaxprocessor():
"align on min/max value"
track = randtrack(driftargs=None, baselineargs=(.1, None, 'rand'))
inipos = [
i.mean() for i in track.cycles.withphases(PHASE.initial).values()
]
bead = ExtremumAlignmentProcessor.apply(track.beads,
phase=AlignmentTactic.onlyinitial,
edge='right')
corrpos = [
i.mean() for i in bead[0, ...].withphases(PHASE.initial).values()
]
assert np.std(inipos) > .015
assert np.std(corrpos) < .001
def test_precision():
"tests that peaks can be found with a given precision"
track = randtrack(durations=[15, 30, 15, 60, 60, 200, 15, 100],
drift=None,
baseline=None,
poisson=dict(rates=[.05, .05, .1, .1, .2, .2],
sizes=[20, 10, 20, 10, 20, 10],
peaks=[0.1, 0.2, 0.3, 0.4, 0.5, 0.6],
store=['sizes']),
seed=0,
nbeads=1,
ncycles=100)
data = track.beads.new(Events)
found = np.array([len(i) for _, i in data[0, ...]], dtype='i4')
sizes = getattr(track, 'simulator')[0]['sizes']
sim = np.sum(sizes >= data.events.select.minduration, 1)
assert list(np.nonzero(found - sim - 1)[0]) == []