def test_zero_zstep(self):
self.focus.moveAbsSync({"z": 1300e-6})
zMin = -500e-6
zMax = 500e-6
zrange = [zMin, zMax]
zStep = 0e-6
with self.assertRaises(ZeroDivisionError):
generate_zlevels(self.focus, zrange, zStep)
def test_zrange_not_in_proper_order(self):
self.focus.moveAbsSync({"z": 1300e-6})
zMin = -10e-6
zMax = 10e-6
zrange = [zMax, zMin]
zStep = 10e-6
with self.assertRaises(ValueError):
generate_zlevels(self.focus, zrange, zStep)
def test_zmax_and_zmin_both_zeros(self):
self.focus.moveAbsSync({"z": 1300e-6})
zMin = -0e-6
zMax = 0e-6
zrange = [zMin, zMax]
zStep = 10e-6
with self.assertRaises(ValueError):
generate_zlevels(self.focus, zrange, zStep)
def test_settings_observer_metadata_with_zstack(self):
settings_observer = SettingsObserver(model.getComponents())
vas = {"exposureTime"}
s1 = stream.FluoStream("FM",
self.ccd,
self.ccd.data,
self.light,
self.light_filter,
detvas=vas,
focuser=self.fm_focuser)
s1.detExposureTime.value = 0.023 # 23 ms
zlevels_list = generate_zlevels(self.fm_focuser, [-2e-6, 2e-6], 1e-6)
zlevels = {s1: list(zlevels_list)}
f = acquireZStack([s1], zlevels, settings_observer)
# get the data
data, exp = f.result()
self.assertIsNone(exp)
for d in data:
self.assertTrue(model.MD_EXTRA_SETTINGS in d.metadata)
# if zstack, so the center has 3 components
self.assertEqual(len(d.metadata[model.MD_POS]), 3)
# if zstack, so the pixel size has 3 components
self.assertEqual(len(d.metadata[model.MD_PIXEL_SIZE]), 3)
self.assertEqual(
data[0].metadata[model.MD_EXTRA_SETTINGS]["Camera"]
["exposureTime"], [0.023, "s"])
def test_large_number_of_levels(self):
self.focus.moveAbsSync({"z": 1000e-6})
zMax = 100e-6
zMin = -100e-6
zrange = [zMin, zMax]
zStep = 0.5e-6
output = generate_zlevels(self.focus, zrange, zStep)
self.assertEqual(len(output), 401)
def test_zmax_and_zmin_both_zeros(self):
self.focus.moveAbsSync({"z": 1300e-6})
zMin = -0e-6
zMax = 0e-6
zrange = [zMin, zMax]
zStep = 10e-6
actual = generate_zlevels(self.focus, zrange, zStep)
expected = self.focus.position.value
self.assertAlmostEqual(expected["z"], actual)
def test_clipping_zmax_on_actuator_upper_limit(self):
self.focus.moveAbsSync({"z": 2800e-6})
zMax = 300e-6
zMin = 0e-6
zrange = [zMin, zMax]
zStep = 100e-6
expected = numpy.asarray([0e-6, 100e-6, 200e-6]) + \
self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)
def test_normal_zlevels_output_with_rounding_up(self):
self.focus.moveAbsSync({"z": 1000e-6})
zMax = 24e-6
zMin = -24e-6
zrange = [zMin, zMax]
zStep = 17e-6
expected = numpy.asarray([-24e-6, -8e-6, 8e-6, 24e-6]) + \
self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)
def test_zstep_greater_than_zmax_and_zmin(self):
self.focus.moveAbsSync({"z": 1300e-6})
zMin = -10e-6
zMax = 10e-6
zrange = [zMin, zMax]
zStep = 70e-6
actual = generate_zlevels(self.focus, zrange, zStep)
expected = numpy.asarray([-10e-6, 10e-6
]) + self.focus.position.value["z"]
numpy.testing.assert_array_almost_equal(actual, expected)
def test_normal_zlevels_output_with_positive_zstep(self):
self.focus.moveAbsSync({"z": 1000e-6})
zMax = 100e-6
zMin = -250e-6
zrange = [zMin, zMax]
zStep = 50e-6
expected = numpy.asarray([
-250e-6, -200e-6, -150e-6, -100e-6, -50e-6, 0e-6, 50e-6, 100e-6
]) + self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)
def test_normal_zlevels_output_with_negative_zstep(self):
self.focus.moveAbsSync({"z": 1000e-6})
zMax = 100e-6
zMin = -250e-6
zrange = [zMin, zMax]
zStep = -50e-6
expected = numpy.asarray([
1.0e-04, 5.0e-05, 0.0, -5.0e-05, -1.0e-04, -1.5e-04, -2.0e-04,
-2.5e-04
]) + self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)
def test_FM_and_SEM_with_zstack(self):
s1 = stream.FluoStream("fluo1",
self.ccd,
self.ccd.data,
self.light,
self.light_filter,
focuser=self.fm_focuser)
s1.excitation.value = sorted(s1.excitation.choices)[0]
sems = stream.SEMStream("sem", self.sed, self.sed.data, self.ebeam)
self.streams = [s1, sems]
zlevels_list = generate_zlevels(self.fm_focuser, [-2e-6, 2e-6], 1e-6)
zlevels = {}
for s in self.streams:
if isinstance(s, stream.FluoStream):
zlevels[s] = list(zlevels_list)
est_time = acqmng.estimateZStackAcquisitionTime(self.streams, zlevels)
# about 5 seconds for fm streams, and 1 sec for sem stream, so should be
# greater than or equal 5 sec
self.assertGreaterEqual(est_time, 4)
# start the acquisition
f = acqmng.acquireZStack(self.streams, zlevels)
f.add_update_callback(self._on_progress_update)
data, exp = f.result()
self.assertIsNone(exp)
for i, d in enumerate(data):
self.assertIsInstance(d, model.DataArray)
if d.ndim > 2 and d.shape[-3] > 1: # 3D data (FM)
# if zstack, so the center has 3 components
self.assertEqual(len(d.metadata[model.MD_POS]), 3)
# if zstack, so the pixel size has 3 components
self.assertEqual(len(d.metadata[model.MD_PIXEL_SIZE]), 3)
else: # 2D data (SEM)
# even if zstack, it's SEM, so the center has 2 components
self.assertEqual(len(d.metadata[model.MD_POS]), 2)
# even if zstack, it's SEM, so the pixel size has 2 components
self.assertEqual(len(d.metadata[model.MD_PIXEL_SIZE]), 2)
# 2 streams, so 2 acquisitions
self.assertEqual(len(data), 2)
# 2 streams, 2 updates per stream, so >= 2 updates
self.assertGreaterEqual(self._nb_updates, 2)
def test_only_FM_streams_with_zstack(self):
# create streams
s1 = stream.FluoStream("fluo1",
self.ccd,
self.ccd.data,
self.light,
self.light_filter,
focuser=self.fm_focuser)
s1.excitation.value = sorted(s1.excitation.choices)[0]
s2 = stream.FluoStream("fluo2", self.ccd, self.ccd.data, self.light,
self.light_filter)
s2._focuser = self.fm_focuser
s2.excitation.value = sorted(s2.excitation.choices)[-1]
self.streams = [s1, s2]
zlevels_list = generate_zlevels(self.fm_focuser, [-2e-6, 2e-6], 1e-6)
zlevels = {}
for s in self.streams:
zlevels[s] = list(zlevels_list)
# there are about 5 zlevels, so should be greater than 2 seconds
est_time = acqmng.estimateZStackAcquisitionTime(self.streams, zlevels)
self.assertGreaterEqual(est_time, 2)
# start the acquisition
f = acqmng.acquireZStack(self.streams, zlevels)
f.add_update_callback(self._on_progress_update)
# get the data
data, exp = f.result()
self.assertIsNone(exp)
for d in data:
self.assertIsInstance(d, model.DataArray)
# since zstack, the center has 3 components
self.assertEqual(len(d.metadata[model.MD_POS]), 3)
# since zstack, the pixel size has 3 components
self.assertEqual(len(d.metadata[model.MD_PIXEL_SIZE]), 3)
# 2 streams, so 2 acquisitions
self.assertEqual(len(data), 2)
# 2 streams, 2 updates per stream, so 2 updates at least
self.assertGreaterEqual(self._nb_updates, 2)
