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_compressed_stack(self):
"""
Test the whole procedure (acquire compressed zstack + stitch) of acquireTiledArea function
"""
# With fm streams
settings_obs = SettingsObserver([self.stage])
fm_fov = compute_camera_fov(self.ccd)
# Using "songbird-sim-ccd.h5" in simcam with tile max_res: (260, 348)
area = (0, 0, fm_fov[0] * 2, fm_fov[1] * 2) # left, top, right, bottom
overlap = 0.2
focus_value = self.focus.position.value['z']
zsteps = 3
# Create focus zlevels from the given zsteps number
zlevels = numpy.linspace(focus_value - (zsteps / 2 * 1e-6),
focus_value + (zsteps / 2 * 1e-6),
zsteps).tolist()
future = acquireTiledArea(self.fm_streams,
self.stage,
area=area,
overlap=overlap,
settings_obs=settings_obs,
zlevels=zlevels)
data = future.result()
self.assertTrue(future.done())
self.assertEqual(len(data), 2)
self.assertIsInstance(data[0], model.DataArray)
self.assertEqual(len(data[0].shape), 2)
def test_metadata(self):
"""
Check if extra metadata are saved
"""
settings_obs = SettingsObserver(model.getComponents())
self.ccd.binning.value = (
1, 1) # make sure we don't save the right metadata by accident
detvas = {'exposureTime', 'binning', 'gain'}
s1 = stream.FluoStream("fluo2",
self.ccd,
self.ccd.data,
self.light,
self.light_filter,
detvas=detvas)
s2 = stream.BrightfieldStream("bf",
self.ccd,
self.ccd.data,
self.light,
detvas=detvas)
# Set different binning values for each stream
s1.detBinning.value = (2, 2)
s2.detBinning.value = (4, 4)
st = stream.StreamTree(streams=[s1, s2])
f = acqmng.acquire(st.getProjections(), settings_obs=settings_obs)
data, e = f.result()
for s in data:
self.assertTrue(model.MD_EXTRA_SETTINGS in s.metadata,
"Stream %s didn't save extra metadata." % s)
self.assertEqual(
data[0].metadata[model.MD_EXTRA_SETTINGS][self.ccd.name]
['binning'], [(2, 2), 'px'])
self.assertEqual(
data[1].metadata[model.MD_EXTRA_SETTINGS][self.ccd.name]
['binning'], [(4, 4), 'px'])
def test_whole_procedure(self):
"""
Test the whole procedure (acquire + stitch) of acquireTiledArea function
"""
# With fm streams
settings_obs = SettingsObserver([self.stage])
fm_fov = compute_camera_fov(self.ccd)
# Using "songbird-sim-ccd.h5" in simcam with tile max_res: (260, 348)
area = (0, 0, fm_fov[0] * 4, fm_fov[1] * 4) # left, top, right, bottom
overlap = 0.2
self.stage.moveAbs({'x': 0, 'y': 0}).result()
future = acquireTiledArea(self.fm_streams,
self.stage,
area=area,
overlap=overlap,
settings_obs=settings_obs)
data = future.result()
self.assertEqual(future._state, FINISHED)
self.assertEqual(len(data), 2)
self.assertIsInstance(data[0], odemis.model.DataArray)
self.assertEqual(len(data[0].shape), 2)
# With sem stream
area = (0, 0, 0.00001, 0.00001)
self.stage.moveAbs({'x': 0, 'y': 0}).result()
future = acquireTiledArea(self.sem_streams,
self.stage,
area=area,
overlap=overlap)
data = future.result()
self.assertEqual(future._state, FINISHED)
self.assertEqual(len(data), 1)
self.assertIsInstance(data[0], model.DataArray)
self.assertEqual(len(data[0].shape), 2)
def test_metadata(self):
"""
Check if extra metadata are saved
"""
settings_obs = SettingsObserver(model.getComponents())
detvas = {"binning", "exposureTime"}
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
specs = stream.SpectrumSettingsStream("test spec",
self.spec,
self.spec.data,
self.ebeam,
detvas=detvas)
sps = stream.SEMSpectrumMDStream("test sem-spec", [sems, specs])
specs.roi.value = (0, 0, 1, 1)
specs.repetition.value = (2, 3)
specs.detBinning.value = (2, specs.detBinning.value[1])
specs.detExposureTime.value = 0.1
specs2 = stream.SpectrumSettingsStream("test spec2",
self.spec,
self.spec.data,
self.ebeam,
detvas=detvas)
sps2 = stream.SEMSpectrumMDStream("test sem-spec2", [sems, specs2])
specs2.roi.value = (0, 0, 1, 1)
specs2.repetition.value = (2, 3)
specs2.detBinning.value = (4, specs2.detBinning.value[1])
specs2.detExposureTime.value = 0.05
f = acqmng.acquire([sps, sps2], settings_obs)
data = f.result()
spec1_data = data[0][1]
spec2_data = data[0][3]
self.assertEqual(
spec1_data.metadata[model.MD_EXTRA_SETTINGS][self.spec.name]
['binning'], [(2, specs.detBinning.value[1]), 'px'])
self.assertEqual(
spec2_data.metadata[model.MD_EXTRA_SETTINGS][self.spec.name]
['binning'], [(4, specs2.detBinning.value[1]), 'px'])
self.assertEqual(
spec1_data.metadata[model.MD_EXTRA_SETTINGS][self.spec.name]
['exposureTime'], [0.1, 's'])
self.assertEqual(
spec2_data.metadata[model.MD_EXTRA_SETTINGS][self.spec.name]
['exposureTime'], [0.05, 's'])