def test_get_timepoint(self, timepoints):
colony = Colony(1, timepoints)
# Get timepoint
assert colony.get_timepoint(
timepoints[0].date_time) == timepoints[0]
with pytest.raises(ValueError):
colony.get_timepoint(None)
def test_remove_timepoint(
self,
timepoints,
):
colony = Colony(1, timepoints)
colony.remove_timepoint(timepoints[0].date_time)
assert timepoints[0].date_time not in colony.timepoints
def test_growth_rate_average(self, timepoints, timepoint_empty):
colony = Colony(id, timepoints)
colony_empty = Colony(1, [timepoint_empty])
assert colony.growth_rate_average == (
(timepoints[-1].area - timepoints[0].area)
**(1 / len(timepoints))) - 1
assert colony_empty.growth_rate_average == 0
def test_center(self, timepoints):
from statistics import mean
colony = Colony(1, timepoints)
for i, coord in enumerate(colony.center):
assert round(coord, 4) == round(mean([t.center[i] for t in timepoints]), 4)
def test_append_timepoint(self, timepoints, timepoint_empty):
colony = Colony(1, timepoints)
colony.append_timepoint(timepoint_empty)
assert timepoint_empty in colony.timepoints
with pytest.raises(ValueError):
colony.append_timepoint(timepoints[0])
def timepoints(request):
timepoints = list()
for i, center in enumerate(centers, start=1):
timepoints.append(
Colony.Timepoint(timestamp=timedelta(seconds=i),
area=i,
center=center,
diameter=i * 1.0,
perimeter=i * 1.0,
color_average=(0, 0, 0)))
yield timepoints
def timepoints(request):
timepoints = list()
date_time = datetime.now()
for i, center in enumerate(centers, start=1):
timepoints.append(
Colony.Timepoint(date_time=date_time + timedelta(seconds=i),
elapsed_minutes=i,
area=i,
center=center,
diameter=i * 1.0,
perimeter=i * 1.0))
yield timepoints
def test_doubling_time(self, timepoints_iter, timepoint_empty, window,
elapsed_minutes, expected, expected_minutes):
colony = Colony(1, timepoints_iter)
colony_empty = Colony(1, [timepoint_empty])
if timepoints_iter is not None:
doubling_times = colony.get_doubling_times(
window=window, elapsed_minutes=elapsed_minutes)
if elapsed_minutes:
doubling_times = [round(t, 2) for t in doubling_times]
expected = expected_minutes
assert max(doubling_times) == expected
assert colony_empty.get_doubling_times() == list()
else:
with pytest.raises(ValueError):
colony.get_doubling_times(window=window,
elapsed_minutes=elapsed_minutes)
def test_doubling_time_average(self, timepoints_iter, timepoint_empty,
window, elapsed_minutes, expected,
expected_minutes):
colony = Colony(1, timepoints_iter)
colony_empty = Colony(1, [timepoint_empty])
if timepoints_iter is not None:
doubling_time_average = colony.get_doubling_time_average(
window=window, elapsed_minutes=elapsed_minutes)
if elapsed_minutes:
doubling_time_average = round(doubling_time_average, 2)
expected = expected_minutes
assert doubling_time_average == expected
assert colony_empty.get_doubling_time_average() == 0
else:
with pytest.raises(ValueError):
colony.get_doubling_time_average(
window=window, elapsed_minutes=elapsed_minutes)
def test_local_doubling_time(self, timepoint_empty):
colony = Colony(1, [timepoint_empty])
assert colony._Colony__local_doubling_time(0, [0], [0],
window=0) == 0
def test_empty(self):
colony = Colony(1)
assert colony.id == 1
with pytest.raises(ValueError):
colony.timepoints
def test_iterable(self, timepoints_iter):
with pytest.raises(ValueError):
Colony(1, timepoints_iter)
def test_init(self, timepoints_iter):
colony = Colony(1, timepoints_iter)
assert isinstance(colony.timepoints, list)
assert len(colony.timepoints) == len(timepoints_iter)
def timepoint_empty(self):
yield Colony.Timepoint(timedelta.min, 0, (0, 0), 0, 0, (0, 0, 0))
def test_filter(self, timepoints):
# It is very difficult to rigorously and exhaustively test the filtering
# The results are also somewhat subjective and outside the scope of a unit test
colonies = [Colony(1, timepoints)]
assert colonies_filtered(colonies) == colonies
def test_update_timepoint(self, timepoints, timepoint_empty):
colony = Colony(1, timepoints)
colony.update_timepoint(timepoints[0], timepoint_empty)
assert colony.timepoint_first == timepoint_empty
def test_remove_timepoint(self, timepoints):
colony = Colony(1, timepoints)
colony.remove_timepoint(timepoints[0].timestamp)
assert timepoints[0] not in colony.timepoints
def test_get_timepoint(self, timepoints):
colony = Colony(1, timepoints)
assert colony.get_timepoint(
timepoints[0].timestamp) == timepoints[0]
assert colony.get_timepoint(timedelta(seconds=-1)) is None
def test_circularity(self, timepoints, timepoint_index, expected):
colony = Colony(1, timepoints)
circularity = colony.circularity_at_timepoint(
timepoints[timepoint_index].date_time)
assert round(circularity, 2) == expected
def timepoint_empty(self):
yield Colony.Timepoint(datetime.now(), 0, 0, (0, 0), 0, 0)
def test_id(self, timepoints_iter, id):
colony = Colony(id, timepoints_iter)
assert colony.id == id
def colony(self, timepoints):
yield Colony(1, timepoints)
def test_growth_rate(self, timepoints, timepoint_empty):
colony = Colony(1, timepoints)
colony_empty = Colony(1, [timepoint_empty])
assert colony.growth_rate == len(timepoints) - 1
assert colony_empty.growth_rate == 0