def test_guess_mode(self):
# test guess mode for ar
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARSettingsStream("test ar", self.ccd, self.ccd.data,
self.ebeam)
sas = stream.SEMARMDStream("test sem-ar", sems, ars)
guess = self.optmngr.guessMode(ars)
self.assertEqual(guess, "ar")
guess = self.optmngr.guessMode(sas)
self.assertEqual(guess, "ar")
# test guess mode for spectral-dedicated
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
specs = stream.SpectrumSettingsStream("test spec", self.spec,
self.spec.data, self.ebeam)
sps = stream.SEMSpectrumMDStream("test sem-spec", sems, specs)
guess = self.optmngr.guessMode(specs)
self.assertIn(guess, ("spectral", "spectral-dedicated"))
guess = self.optmngr.guessMode(sps)
self.assertIn(guess, ("spectral", "spectral-dedicated"))
def test_sync_sem_ccd(self):
"""
try acquisition with fairly complex SEM/CCD stream
"""
# Create the streams and streamTree
semsur = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
sems = stream.SEMStream("test sem cl", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARSettingsStream("test ar", self.ccd, self.ccd.data,
self.ebeam)
semars = stream.SEMARMDStream("test SEM/AR", [sems, ars])
st = stream.StreamTree(streams=[semsur, semars])
# SEM survey settings are via the current hardware settings
self.ebeam.dwellTime.value = self.ebeam.dwellTime.range[0]
# SEM/AR settings are via the AR stream
ars.roi.value = (0.1, 0.1, 0.8, 0.8)
mx_brng = self.ccd.binning.range[1]
binning = tuple(min(4, mx) for mx in mx_brng) # try binning 4x4
self.ccd.binning.value = binning
self.ccd.exposureTime.value = 1 # s
ars.repetition.value = (2, 3)
num_ar = numpy.prod(ars.repetition.value)
est_time = acq.estimateTime(st.getProjections())
# prepare callbacks
self.start = None
self.end = None
self.updates = 0
self.done = 0
# Run acquisition
start = time.time()
f = acq.acquire(st.getProjections())
f.add_update_callback(self.on_progress_update)
f.add_done_callback(self.on_done)
data, e = f.result()
dur = time.time() - start
self.assertGreaterEqual(dur, est_time /
2) # Estimated time shouldn't be too small
self.assertIsInstance(data[0], model.DataArray)
self.assertIsNone(e)
self.assertEqual(len(data), num_ar + 2)
thumb = acq.computeThumbnail(st, f)
self.assertIsInstance(thumb, model.DataArray)
self.assertGreaterEqual(self.updates, 1) # at least one update at end
self.assertLessEqual(self.end, time.time())
self.assertTrue(not f.cancelled())
time.sleep(0.1)
self.assertEqual(self.done, 1)
def test_only_SEM_streams_with_zstack(self):
sems = stream.SEMStream("sem", self.sed, self.sed.data, self.ebeam)
self.streams = [sems]
zlevels = {}
est_time = acqmng.estimateZStackAcquisitionTime(self.streams, zlevels)
# only one sem stream, so should be greater than or equal to 1 sec
self.assertGreaterEqual(est_time, 1)
# 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 d in data:
self.assertIsInstance(d, model.DataArray)
# even if zstack, it's only 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)
# 1 streams, so 1 acquisitions
self.assertEqual(len(data), 1)
# 1 streams, 1 updates per stream, so 1 updates
self.assertGreaterEqual(self._nb_updates, 1)
def test_acq_fine_align(self):
"""
try acquisition with SEM + Optical + overlay streams
"""
# Create the streams
sems = stream.SEMStream("test sem", self.sed, self.sed.data, self.ebeam)
# SEM settings are via the current hardware settings
self.ebeam.dwellTime.value = self.ebeam.dwellTime.range[0]
fs1 = stream.FluoStream("test orange", self.ccd, self.ccd.data,
self.light, self.light_filter)
fs1.excitation.value = fs1.excitation.range[0] + 5e-9
fs1.emission.value = fs1.emission.range[0] + 5e-9
fs2 = stream.FluoStream("test blue", self.ccd, self.ccd.data,
self.light, self.light_filter)
fs2.excitation.value = fs2.excitation.range[1] - 5e-9
fs2.emission.value = fs2.emission.range[1] - 5e-9
self.ccd.exposureTime.value = 0.1 # s
ovrl = stream.OverlayStream("overlay", self.ccd, self.ebeam, self.sed)
ovrl.dwellTime.value = 0.3
ovrl.repetition.value = (7, 7)
streams = [sems, fs1, fs2, ovrl]
est_time = acq.estimateTime(streams)
sum_est_time = sum(s.estimateAcquisitionTime() for s in streams)
self.assertGreaterEqual(est_time, sum_est_time)
# prepare callbacks
self.past = None
self.left = None
self.updates = 0
self.done = 0
# Run acquisition
start = time.time()
f = acq.acquire(streams)
f.add_update_callback(self.on_progress_update)
f.add_done_callback(self.on_done)
data = f.result()
dur = time.time() - start
self.assertGreater(dur, est_time / 2) # Estimated time shouldn't be too small
self.assertIsInstance(data[0], model.DataArray)
self.assertEqual(len(data), len(streams) - 1)
# No overlay correction metadata anywhere (it has all been merged)
for d in data:
for k in [model.MD_ROTATION_COR, model.MD_PIXEL_SIZE_COR, model.MD_POS_COR]:
self.assertNotIn(k, d.metadata)
# thumb = acq.computeThumbnail(st, f)
# self.assertIsInstance(thumb, model.DataArray)
self.assertGreaterEqual(self.updates, 1) # at least one update at end
self.assertEqual(self.left, 0)
self.assertEqual(self.done, 1)
self.assertTrue(not f.cancelled())
def test_drift_stream(self):
escan = self.ebeam
detector = self.sed
ccd = self.ccd
# Create the stream
sems = stream.SEMStream("test sem", detector, detector.data, escan)
ars = stream.ARSettingsStream("test ar", ccd, ccd.data, escan)
sas = stream.SEMARMDStream("test sem-ar", [sems, ars])
# Long acquisition
ccd.exposureTime.value = 1e-02 # s
dc = leech.AnchorDriftCorrector(escan, detector)
dc.period.value = 5
dc.roi.value = (0.525, 0.525, 0.6, 0.6)
dc.dwellTime.value = 1e-04
sems.leeches.append(dc)
escan.dwellTime.value = 1e-02
ars.roi.value = (0.4, 0.4, 0.6, 0.6)
ars.repetition.value = (5, 5)
start = time.time()
for l in sas.leeches:
l.series_start()
f = sas.acquire()
x = f.result()
for l in sas.leeches:
l.series_complete(x)
dur = time.time() - start
logging.debug("Acquisition took %g s", dur)
self.assertTrue(f.done())
def test_drift_stream(self):
escan = self.ebeam
detector = self.sed
ccd = self.ccd
# Create the stream
sems = stream.SEMStream("test sem", detector, detector.data, escan)
ars = stream.ARStream("test ar", ccd, ccd.data, escan)
sas = stream.SEMARMDStream("test sem-ar", sems, ars)
# Long acquisition
ccd.exposureTime.value = 1e-02 # s
sems.dcPeriod.value = 5
sems.dcRegion.value = (0.525, 0.525, 0.6, 0.6)
sems.dcDwellTime.value = 1e-04
escan.dwellTime.value = 1e-02
ars.roi.value = (0.4, 0.4, 0.6, 0.6)
ars.repetition.value = (5, 5)
start = time.time()
f = sas.acquire()
x = f.result()
dur = time.time() - start
logging.debug("Acquisition took %g s", dur)
self.assertTrue(f.done())
def test_set_path_stream(self):
# test guess mode for ar
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARSettingsStream("test ar", self.ccd, self.ccd.data,
self.ebeam)
sas = stream.SEMARMDStream("test sem-ar", sems, ars)
self.optmngr.setPath(ars).result()
# Assert that actuator was moved according to mode given
self.assert_pos_as_in_mode(self.lenswitch, "ar")
self.assert_pos_as_in_mode(self.slit, "ar")
self.assert_pos_as_in_mode(self.specgraph, "ar")
self.assertEqual(self.spec_det_sel.position.value, {'rx': 0})
self.assertAlmostEqual(self.spec_sel.position.value["x"], 0.022)
# Change positions back
self.optmngr.setPath("mirror-align").result()
self.optmngr.setPath(sas).result()
# Assert that actuator was moved according to mode given
self.assert_pos_as_in_mode(self.lenswitch, "ar")
self.assert_pos_as_in_mode(self.slit, "ar")
self.assert_pos_as_in_mode(self.specgraph, "ar")
self.assertEqual(self.spec_det_sel.position.value, {'rx': 0})
self.assertAlmostEqual(self.spec_sel.position.value["x"], 0.022)
# test guess mode for spectral-dedicated
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
specs = stream.SpectrumSettingsStream("test spec", self.spec,
self.spec.data, self.ebeam)
sps = stream.SEMSpectrumMDStream("test sem-spec", sems, specs)
self.optmngr.setPath(specs).result()
# Assert that actuator was moved according to mode given
self.assert_pos_as_in_mode(self.lenswitch, "spectral")
# No slit/spectrograph as they are not affecting the detector
self.assertAlmostEqual(self.spec_sel.position.value["x"], 0.026112848)
# Change positions back
self.optmngr.setPath("chamber-view").result()
self.optmngr.setPath(sps).result()
# Assert that actuator was moved according to mode given
self.assert_pos_as_in_mode(self.lenswitch, "spectral")
self.assertAlmostEqual(self.spec_sel.position.value["x"], 0.026112848)
def test_progressive_future(self):
"""
Test .acquire interface (should return a progressive future with updates)
"""
self.image = None
self.done = False
self.updates = 0
# Create the stream
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARStream("test ar", self.ccd, self.ccd.data, self.ebeam)
sas = stream.SEMARMDStream("test sem-ar", sems, ars)
ars.roi.value = (0.1, 0.1, 0.8, 0.8)
self.ccd.binning.value = (4, 4) # hopefully always supported
# Long acquisition
self.ccd.exposureTime.value = 0.2 # s
ars.repetition.value = (2, 3)
exp_shape = ars.repetition.value[::-1]
num_ar = numpy.prod(ars.repetition.value)
# Start acquisition
timeout = 1 + 1.5 * sas.estimateAcquisitionTime()
f = sas.acquire()
f.add_update_callback(self.on_progress_update)
f.add_done_callback(self.on_done)
data = f.result(timeout)
self.assertEqual(len(data), num_ar + 1)
self.assertEqual(data[0].shape, exp_shape)
self.assertGreaterEqual(self.updates,
4) # at least a couple of updates
self.assertEqual(self.left, 0)
self.assertTrue(self.done)
self.assertTrue(not f.cancelled())
# short acquisition
self.done = False
self.updates = 0
self.ccd.exposureTime.value = 0.02 # s
ars.repetition.value = (5, 4)
exp_shape = ars.repetition.value[::-1]
num_ar = numpy.prod(ars.repetition.value)
# Start acquisition
timeout = 1 + 1.5 * sas.estimateAcquisitionTime()
f = sas.acquire()
f.add_update_callback(self.on_progress_update)
f.add_done_callback(self.on_done)
data = f.result(timeout)
self.assertEqual(len(data), num_ar + 1)
self.assertEqual(data[0].shape, exp_shape)
self.assertGreaterEqual(self.updates, 5) # at least a few updates
self.assertEqual(self.left, 0)
self.assertTrue(self.done)
self.assertTrue(not f.cancelled())
def __init__(self, microscope, main_app):
"""
:param microscope: (Microscope or None) The main back-end component.
:param main_app: (wx.App) The main GUI component.
"""
super(CLAcqPlugin, self).__init__(microscope, main_app)
# Can only be used with a microscope
if not microscope:
return
else:
# Check which stream the microscope supports
self.main_data = self.main_app.main_data
if not (self.main_data.ccd and self.main_data.ebeam):
return
self.exposureTime = self.main_data.ccd.exposureTime
self.binning = self.main_data.ccd.binning
# Trick to pass the component (ccd to binning_1d_from_2d())
self.vaconf["binning"]["choices"] = (
lambda cp, va, cf: cutil.binning_1d_from_2d(
self.main_data.ccd, va, cf))
self._survey_stream = None
self._optical_stream = acqstream.BrightfieldStream(
"Optical",
self.main_data.ccd,
self.main_data.ccd.data,
emitter=None,
focuser=self.main_data.focus)
self._secom_cl_stream = SECOMCLSettingsStream("Secom-CL",
self.main_data.ccd,
self.main_data.ccd.data,
self.main_data.ebeam)
self._sem_stream = acqstream.SEMStream(
"Secondary electrons concurrent", self.main_data.sed,
self.main_data.sed.data, self.main_data.ebeam)
self._secom_sem_cl_stream = SECOMCLSEMMDStream(
"SECOM SEM CL", [self._sem_stream, self._secom_cl_stream])
self._driftCorrector = leech.AnchorDriftCorrector(
self.main_data.ebeam, self.main_data.sed)
self.conf = get_acqui_conf()
self.expectedDuration = model.VigilantAttribute(1,
unit="s",
readonly=True)
self.exposureTime.subscribe(self._update_exp_dur)
self.filename = self._secom_sem_cl_stream.filename # duplicate VA
self.filename.subscribe(self._on_filename)
self.addMenu("Acquisition/CL acquisition...", self.start)
def start_sem(self):
main_data = self.main_app.main_data
sem_stream = stream.SEMStream(
"Secondary electrons survey",
main_data.sed,
main_data.sed.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
emtvas=get_local_vas(main_data.ebeam),
detvas=get_local_vas(main_data.sed),
)
self.start(sem_stream)
def test_guess_mode(self):
# test guess mode for ar
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARSettingsStream("test ar", self.ccd, self.ccd.data,
self.ebeam)
sas = stream.SEMARMDStream("test sem-ar", sems, ars)
guess = self.optmngr.guessMode(ars)
self.assertEqual(guess, "ar")
guess = self.optmngr.guessMode(sas)
self.assertEqual(guess, "ar")
# test guess mode for spectral
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
specs = stream.SpectrumSettingsStream("test spec", self.spec,
self.spec.data, self.ebeam)
sps = stream.SEMSpectrumMDStream("test sem-spec", sems, specs)
guess = self.optmngr.guessMode(specs)
self.assertEqual(guess, "spectral")
guess = self.optmngr.guessMode(sps)
self.assertEqual(guess, "spectral")
# test guess mode for cli
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
cls = stream.SpectrumSettingsStream("test cl", self.cld, self.cld.data,
self.ebeam)
sls = stream.SEMSpectrumMDStream("test sem-cl", sems, cls)
guess = self.optmngr.guessMode(cls)
self.assertEqual(guess, "cli")
guess = self.optmngr.guessMode(sls)
self.assertEqual(guess, "cli")
def setUpClass(cls):
try:
test.start_backend(ENZEL_CONFIG)
except LookupError:
logging.info("A running backend is already found, skipping tests")
cls.backend_was_running = True
return
except IOError as exp:
logging.error(str(exp))
raise
# create some streams connected to the backend
cls.microscope = model.getMicroscope()
cls.ccd = model.getComponent(role="ccd")
cls.ebeam = model.getComponent(role="e-beam")
cls.sed = model.getComponent(role="se-detector")
cls.light = model.getComponent(role="light")
cls.focus = model.getComponent(role="focus")
cls.light_filter = model.getComponent(role="filter")
cls.stage = model.getComponent(role="stage")
# Make sure the lens is referenced
cls.focus.reference({'z'}).result()
# The 5DoF stage is not referenced automatically, so let's do it now
stage_axes = set(cls.stage.axes.keys())
cls.stage.reference(stage_axes).result()
# Create 1 sem stream and 2 fm streams to be used in testing
ss1 = stream.SEMStream(
"sem1",
cls.sed,
cls.sed.data,
cls.ebeam,
emtvas={"dwellTime", "scale", "magnification", "pixelSize"})
cls.ccd.exposureTime.value = cls.ccd.exposureTime.range[0] # go fast
fs1 = stream.FluoStream("fluo1",
cls.ccd,
cls.ccd.data,
cls.light,
cls.light_filter,
focuser=cls.focus)
fs1.excitation.value = sorted(fs1.excitation.choices)[0]
fs2 = stream.FluoStream("fluo2",
cls.ccd,
cls.ccd.data,
cls.light,
cls.light_filter,
focuser=cls.focus)
fs2.excitation.value = sorted(fs2.excitation.choices)[-1]
cls.sem_streams = [ss1]
cls.fm_streams = [fs1, fs2]
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'])
def test_overview_acquisition(self):
s = stream.SEMStream(
"Single beam",
self.sed,
self.sed.data,
self.ebeam,
focuser=self.
efocuser, # Not used during acquisition, but done by the GUI
hwemtvas={"scale", "dwellTime", "horizontalFoV"})
# This should be used by the acquisition
s.dwellTime.value = 1e-6 # s
# Use random settings and check they are overridden by the overview acquisition
s.scale.value = (2, 2)
s.horizontalFoV.value = 20e-6 # m
# Known position of the center scintillator
scintillator5_area = (-0.007, -0.007, 0.007, 0.007) # l, b, r, t
# Small area for DEBUG (3x3)
# scintillator5_area = (-0.002, -0.002, 0.002, 0.002) # l, b, r, t
est_time = fastem.estimateTiledAcquisitionTime(s, self.stage,
scintillator5_area)
# don't use for DEBUG example
self.assertGreater(est_time,
10) # It should take more than 10s! (expect ~5 min)
before_start_t = time.time()
f = fastem.acquireTiledArea(s, self.stage, scintillator5_area)
time.sleep(1)
start_t, end_t = f.get_progress()
self.assertGreater(start_t, before_start_t)
# don't use for DEBUG example
self.assertGreater(end_t,
time.time() +
10) # Should report still more than 10s
overview_da = f.result()
self.assertGreater(overview_da.shape[0], 2000)
self.assertGreater(overview_da.shape[1], 2000)
# Check the final area fits the requested area, with possibly a little bit of margin
bbox = img.getBoundingBox(overview_da)
fov = bbox[2] - bbox[0], bbox[3] - bbox[1]
logging.debug("Got image of size %s, with FoV %s = %s",
overview_da.shape, fov, bbox)
self.assertLessEqual(bbox[0], scintillator5_area[0]) # Left
self.assertLessEqual(bbox[1], scintillator5_area[1]) # Bottom
self.assertGreaterEqual(bbox[2], scintillator5_area[2]) # Right
self.assertGreaterEqual(bbox[3], scintillator5_area[3]) # Top
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_guess_mode(self):
# test guess mode for spectral
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
specs = stream.SpectrumSettingsStream("test spec", self.spec,
self.spec.data, self.ebeam)
sps = stream.SEMSpectrumMDStream("test sem-spec", sems, specs)
guess = self.optmngr.guessMode(specs)
self.assertEqual(guess, "spectral")
guess = self.optmngr.guessMode(sps)
self.assertEqual(guess, "spectral")
with self.assertRaises(LookupError):
guess = self.optmngr.guessMode(sems)
def test_sync_future_cancel(self):
self.image = None
# Create the stream
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARStream("test ar", self.ccd, self.ccd.data, self.ebeam)
sas = stream.SEMARMDStream("test sem-ar", sems, ars)
ars.roi.value = (0.1, 0.1, 0.8, 0.8)
self.ccd.binning.value = (4, 4) # hopefully always supported
# Long acquisition
self.updates = 0
self.ccd.exposureTime.value = 0.2 # s
ars.repetition.value = (2, 3)
# Start acquisition
f = sas.acquire()
f.add_update_callback(self.on_progress_update)
f.add_done_callback(self.on_done)
time.sleep(self.ccd.exposureTime.value) # wait a bit
f.cancel()
self.assertGreaterEqual(self.updates, 1) # at least at the end
self.assertEqual(self.left, 0)
self.assertTrue(f.cancelled())
# short acquisition
self.updates = 0
self.ccd.exposureTime.value = 0.02 # s
ars.repetition.value = (5, 4)
# Start acquisition
f = sas.acquire()
f.add_update_callback(self.on_progress_update)
f.add_done_callback(self.on_done)
time.sleep(self.ccd.exposureTime.value) # wait a bit
f.cancel()
self.assertGreaterEqual(self.updates, 1) # at least at the end
self.assertEqual(self.left, 0)
self.assertTrue(f.cancelled())
def setUpClass(cls):
try:
test.start_backend(CRYOSECOM_CONFIG)
except LookupError:
logging.info("A running backend is already found, skipping tests")
cls.backend_was_running = True
return
except IOError as exp:
logging.error(str(exp))
raise
# create some streams connected to the backend
cls.microscope = model.getMicroscope()
cls.ccd = model.getComponent(role="ccd")
cls.ebeam = model.getComponent(role="e-beam")
cls.sed = model.getComponent(role="se-detector")
cls.light = model.getComponent(role="light")
cls.focus = model.getComponent(role="focus")
cls.light_filter = model.getComponent(role="filter")
cls.stage = model.getComponent(role="stage")
# Create 1 sem stream and 2 fm streams to be used in testing
ss1 = stream.SEMStream(
"sem1",
cls.sed,
cls.sed.data,
cls.ebeam,
emtvas={"dwellTime", "scale", "magnification", "pixelSize"})
fs1 = stream.FluoStream("fluo1",
cls.ccd,
cls.ccd.data,
cls.light,
cls.light_filter,
focuser=cls.focus)
fs1.excitation.value = sorted(fs1.excitation.choices)[0]
fs2 = stream.FluoStream("fluo2", cls.ccd, cls.ccd.data, cls.light,
cls.light_filter)
fs2.excitation.value = sorted(fs2.excitation.choices)[-1]
cls.sem_streams = [ss1]
cls.fm_streams = [fs1, fs2]
def addSEMBSD(self, **kwargs):
"""
Creates a new backscattered electron stream and panel in the stream bar
returns (StreamPanel): the panel created
"""
if self._main_data_model.role == "delphi":
# For the Delphi, the SEM stream needs to be more "clever" because
# it needs to run a simple spot alignment every time the stage has
# moved before starting to acquire.
s = acqstream.AlignedSEMStream("Backscattered electrons",
self._main_data_model.bsd,
self._main_data_model.bsd.data,
self._main_data_model.ebeam,
self._main_data_model.ccd,
self._main_data_model.stage,
shiftebeam="Ebeam shift")
# Select between "Metadata update" and "Stage move"
# TODO: use shiftebeam once the phenom driver supports it
else:
s = acqstream.SEMStream("Backscattered electrons",
self._main_data_model.bsd,
self._main_data_model.bsd.data,
self._main_data_model.ebeam)
return self._addStream(s, **kwargs)
def test_set_path_stream(self):
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARSettingsStream("test ar", self.ccd, self.ccd.data,
self.ebeam)
sas = stream.SEMARMDStream("test sem-ar", sems, ars)
self.optmngr.setPath(ars).result()
# Assert that actuator was moved according to mode given
self.assert_pos_as_in_mode(self.lenswitch, "ar")
self.assert_pos_as_in_mode(self.slit, "ar")
self.assert_pos_as_in_mode(self.specgraph, "ar")
self.assertEqual(self.spec_det_sel.position.value, {'rx': 0})
# Change positions back
self.optmngr.setPath("mirror-align").result()
self.optmngr.setPath(sas).result()
# Assert that actuator was moved according to mode given
self.assert_pos_as_in_mode(self.lenswitch, "ar")
self.assert_pos_as_in_mode(self.slit, "ar")
self.assert_pos_as_in_mode(self.specgraph, "ar")
self.assertEqual(self.spec_det_sel.position.value, {'rx': 0})
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
specs = stream.SpectrumSettingsStream("test spec", self.spec,
self.spec.data, self.ebeam)
sps = stream.SEMSpectrumMDStream("test sem-spec", sems, specs)
self.optmngr.setPath(specs).result()
# Assert that actuator was moved according to mode given
self.assertEqual(self.spec_det_sel.position.value,
{'rx': 1.5707963267948966})
self.assertEqual(self.cl_det_sel.position.value, {'x': 0.01})
# Change positions back
self.optmngr.setPath("chamber-view").result()
self.optmngr.setPath(sps).result()
# Assert that actuator was moved according to mode given
self.assert_pos_as_in_mode(self.lenswitch, "spectral")
self.assert_pos_as_in_mode(self.slit, "spectral")
self.assert_pos_as_in_mode(self.specgraph, "spectral")
self.assertEqual(self.spec_det_sel.position.value,
{'rx': 1.5707963267948966})
self.assertEqual(self.cl_det_sel.position.value, {'x': 0.01})
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
specs = stream.SpectrumSettingsStream("test spec",
self.spec_integrated,
self.spec_integrated.data,
self.ebeam)
sps = stream.SEMSpectrumMDStream("test sem-spec", sems, specs)
# Change positions back
self.optmngr.setPath("chamber-view").result()
self.optmngr.setPath(specs).result()
# Assert that actuator was moved according to mode given
self.assert_pos_as_in_mode(self.lenswitch, "spectral-integrated")
self.assert_pos_as_in_mode(self.slit, "spectral-integrated")
self.assert_pos_as_in_mode(self.specgraph, "spectral-integrated")
self.assertEqual(self.spec_det_sel.position.value, {'rx': 0})
self.assertEqual(self.cl_det_sel.position.value, {'x': 0.01})
# Check the focus is remembered before going to chamber-view
orig_focus = self.focus.position.value
# Change positions back
self.optmngr.setPath("chamber-view").result()
self.focus.moveRel({"z": 1e-3}).result()
self.optmngr.setPath(sps).result()
# Assert that actuator was moved according to mode given
self.assert_pos_as_in_mode(self.lenswitch, "spectral")
self.assert_pos_as_in_mode(self.slit, "spectral")
self.assert_pos_as_in_mode(self.specgraph, "spectral")
self.assertEqual(self.spec_det_sel.position.value, {'rx': 0})
self.assertEqual(self.cl_det_sel.position.value, {'x': 0.01})
self.assertEqual(self.focus.position.value, orig_focus)
def acquire_timelapse(num, period, filename):
"""
num (int or None): if None, will never stop, unless interrupted
"""
# Find components by their role
ccd = model.getComponent(role="ccd")
ebeam = model.getComponent(role="e-beam")
sed = model.getComponent(role="se-detector")
light = model.getComponent(role="light")
light_filter = model.getComponent(role="filter")
stage = model.getComponent(role="stage")
focus = model.getComponent(role="focus")
# Prepare the streams and acquisition manager
# The settings of the emissions and excitation are based on the current
# hardware settings.
stfm = stream.FluoStream("Fluorescence image", ccd, ccd.data, light, light_filter)
# Force the excitation light using that command:
# stfm.excitation.value = (4.72e-07, 4.79e-07, 4.85e-07, 4.91e-07, 4.97e-07)
stem = stream.SEMStream("Secondary electrons", sed, sed.data, ebeam)
# Special stream that will run the overlay and update the metadata based on this
# Note: if more complex overlay is needed (eg, with background subtraction,
# or with saving the CCD image), we'd need to directly call FindOverlay())
stovl = stream.OverlayStream("Overlay", ccd, ebeam, sed)
stovl.dwellTime.value = OVERLAY_DT
acq_streams = [stem, stfm, stovl]
# Prepare to save each acquisition in a separate file
exporter = dataio.find_fittest_converter(filename)
basename, ext = os.path.splitext(filename)
fn_pattern = basename + "%04d" + ext
fn_pos = basename + "pos.csv"
fpos = open(fn_pos, "a")
fpos.write("time\tX\tY\tZ\n")
# Run acquisition every period
try:
i = 1
while True:
logging.info("Acquiring image %d", i)
start = time.time()
# Acquire all the images
f = acq.acquire(acq_streams)
data, e = f.result()
if e:
logging.error("Acquisition failed with %s", e)
# It can partially fail, so still allow to save the data successfully acquired
# Note: the actual time of the position is the one when the position was read
# by the pigcs driver.
spos = stage.position.value
fpos.write("%.20g\t%g\t%g\t%g\n" %
(time.time(), spos["x"], spos["y"], focus.position.value["z"]))
# Save the file
if data:
exporter.export(fn_pattern % (i,), data)
# TODO: run autofocus from time to time?
left = period - (time.time() - start)
if left < 0:
logging.warning("Acquisition took longer than the period (%g s overdue)", -left)
else:
logging.info("Sleeping for another %g s", left)
time.sleep(left)
if i == num: # will never be True if num is None
break
i += 1
except KeyboardInterrupt:
logging.info("Closing after only %d images acquired", i)
except Exception:
logging.exception("Failed to acquire all the images.")
raise
fpos.close()
def test_leech(self):
"""
try acquisition with leech
"""
# Create the streams and streamTree
semsur = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
sems = stream.SEMStream("test sem cl", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARSettingsStream("test ar", self.ccd, self.ccd.data,
self.ebeam)
semars = stream.SEMARMDStream("test SEM/AR", [sems, ars])
st = stream.StreamTree(streams=[semsur, semars])
pcd = Fake0DDetector("test")
pca = ProbeCurrentAcquirer(pcd)
sems.leeches.append(pca)
semsur.leeches.append(pca)
# SEM survey settings are via the current hardware settings
self.ebeam.dwellTime.value = self.ebeam.dwellTime.range[0]
# SEM/AR settings are via the AR stream
ars.roi.value = (0.1, 0.1, 0.8, 0.8)
mx_brng = self.ccd.binning.range[1]
binning = tuple(min(4, mx) for mx in mx_brng) # try binning 4x4
self.ccd.binning.value = binning
self.ccd.exposureTime.value = 1 # s
ars.repetition.value = (2, 3)
num_ar = numpy.prod(ars.repetition.value)
pca.period.value = 10 # Only at beginning and end
est_time = acq.estimateTime(st.getProjections())
# prepare callbacks
self.start = None
self.end = None
self.updates = 0
self.done = 0
# Run acquisition
start = time.time()
f = acq.acquire(st.getProjections())
f.add_update_callback(self.on_progress_update)
f.add_done_callback(self.on_done)
data, e = f.result()
dur = time.time() - start
self.assertGreaterEqual(dur, est_time /
2) # Estimated time shouldn't be too small
self.assertIsInstance(data[0], model.DataArray)
self.assertIsNone(e)
self.assertEqual(len(data), num_ar + 2)
thumb = acq.computeThumbnail(st, f)
self.assertIsInstance(thumb, model.DataArray)
self.assertGreaterEqual(self.updates, 1) # at least one update at end
self.assertLessEqual(self.end, time.time())
self.assertTrue(not f.cancelled())
time.sleep(0.1)
self.assertEqual(self.done, 1)
for da in data:
pcmd = da.metadata[model.MD_EBEAM_CURRENT_TIME]
self.assertEqual(len(pcmd), 2)
def test_sync_path_guess(self):
"""
try synchronized acquisition using the Optical Path Manager
"""
# Create the streams and streamTree
opmngr = path.OpticalPathManager(self.microscope)
semsur = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
sems = stream.SEMStream("test sem cl", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARSettingsStream("test ar",
self.ccd,
self.ccd.data,
self.ebeam,
opm=opmngr)
semars = stream.SEMARMDStream("test SEM/AR", [sems, ars])
specs = stream.SpectrumSettingsStream("test spec",
self.spec,
self.spec.data,
self.ebeam,
opm=opmngr)
sps = stream.SEMSpectrumMDStream("test sem-spec", [sems, specs])
st = stream.StreamTree(streams=[semsur, semars, sps])
# SEM survey settings are via the current hardware settings
self.ebeam.dwellTime.value = self.ebeam.dwellTime.range[0]
# SEM/AR/SPEC settings are via the AR stream
ars.roi.value = (0.1, 0.1, 0.8, 0.8)
specs.roi.value = (0.2, 0.2, 0.7, 0.7)
mx_brng = self.ccd.binning.range[1]
binning = tuple(min(4, mx) for mx in mx_brng) # try binning 4x4
self.ccd.binning.value = binning
self.ccd.exposureTime.value = 1 # s
ars.repetition.value = (2, 3)
specs.repetition.value = (3, 2)
num_ar = numpy.prod(ars.repetition.value)
est_time = acq.estimateTime(st.getProjections())
# prepare callbacks
self.start = None
self.end = None
self.updates = 0
self.done = 0
# Run acquisition
start = time.time()
f = acq.acquire(st.getProjections())
f.add_update_callback(self.on_progress_update)
f.add_done_callback(self.on_done)
data, e = f.result()
dur = time.time() - start
self.assertGreaterEqual(dur, est_time /
2) # Estimated time shouldn't be too small
self.assertIsInstance(data[0], model.DataArray)
self.assertIsNone(e)
self.assertEqual(len(data), num_ar + 4)
thumb = acq.computeThumbnail(st, f)
self.assertIsInstance(thumb, model.DataArray)
self.assertGreaterEqual(self.updates, 1) # at least one update at end
self.assertLessEqual(self.end, time.time())
self.assertTrue(not f.cancelled())
# assert optical path configuration
exp_pos = path.SPARC_MODES["spectral"][1]
self.assertEqual(self.lenswitch.position.value, exp_pos["lens-switch"])
self.assertEqual(self.spec_det_sel.position.value,
exp_pos["spec-det-selector"])
self.assertEqual(self.ar_spec_sel.position.value,
exp_pos["ar-spec-selector"])
time.sleep(0.1)
self.assertEqual(self.done, 1)
def test_histogram(self):
"""
Check the histogram updates correctly, including if the BPP changes
"""
ebeam = FakeEBeam("ebeam")
se = FakeDetector("se")
ss = stream.SEMStream("test", se, se.data, ebeam)
# without data, the histogram should be empty, and the intensity range
# based on the depth of the detector
h = ss.histogram.value
ir = ss.intensityRange.range
self.assertEqual(len(h), 0)
self.assertEqual((ir[0][0], ir[1][1]), (0, se.shape[0] - 1))
# "start" the stream, so it expects data
ss.should_update.value = True
ss.is_active.value = True
# send a simple 8 bit image (with correct metadata) =>
# * The intensity range should update to 8-bit
# * The histogram should be 256 long
d = numpy.zeros(ebeam.shape[::-1], "uint8")
md = {
model.MD_BPP: 8,
model.MD_PIXEL_SIZE: (1e-6, 2e-5), # m/px
model.MD_POS: (1e-3, -30e-3), # m
}
da = model.DataArray(d, md)
se.data.notify(da)
time.sleep(0.5) # make sure all the delayed code is executed
self.assertIsInstance(ss.image.value, model.DataArray)
h = ss.histogram.value
ir = ss.intensityRange.range
self.assertEqual(len(h), 256)
self.assertEqual((ir[0][0], ir[1][1]), (0, (2**8) - 1))
# Send a 16 bit image with 16 BPP =>
# * The intensity range should update to 16-bit
# * The histogram should stay not too long (<=1024 values)
d = numpy.zeros(ebeam.shape[::-1], "uint16")
md = {
model.MD_BPP: 16,
model.MD_PIXEL_SIZE: (1e-6, 2e-5), # m/px
model.MD_POS: (1e-3, -30e-3), # m
}
da = model.DataArray(d, md)
se.data.notify(da)
time.sleep(0.5) # make sure all the delayed code is executed
self.assertIsInstance(ss.image.value, model.DataArray)
h = ss.histogram.value
ir = ss.intensityRange.range
self.assertLessEqual(len(h), 1024)
self.assertEqual((ir[0][0], ir[1][1]), (0, (2**16) - 1))
# Send a 16 bit image with 12 BPP =>
# * The intensity range should update to 12-bit
# * The histogram should stay not too long (<=1024 values)
d = numpy.zeros(ebeam.shape[::-1], "uint16")
md = {
model.MD_BPP: 12,
model.MD_PIXEL_SIZE: (1e-6, 2e-5), # m/px
model.MD_POS: (1e-3, -30e-3), # m
}
da = model.DataArray(d, md)
se.data.notify(da)
time.sleep(0.5) # make sure all the delayed code is executed
self.assertIsInstance(ss.image.value, model.DataArray)
h = ss.histogram.value
ir = ss.intensityRange.range
self.assertLessEqual(len(h), 1024)
self.assertEqual((ir[0][0], ir[1][1]), (0, (2**12) - 1))
def test_acq_ar(self):
"""
Test short & long acquisition for AR
"""
# Create the stream
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
ars = stream.ARStream("test ar", self.ccd, self.ccd.data, self.ebeam)
sas = stream.SEMARMDStream("test sem-ar", sems, ars)
ars.roi.value = (0.1, 0.1, 0.8, 0.8)
self.ccd.binning.value = (4, 4) # hopefully always supported
# Long acquisition (small rep to avoid being too long)
# The acquisition method is different for time > 0.1 s, but we had bugs
# with dwell time > 4s, so let's directly test both.
self.ccd.exposureTime.value = 5 # s
ars.repetition.value = (2, 3)
exp_shape = ars.repetition.value[::-1]
num_ar = numpy.prod(ars.repetition.value)
# Start acquisition
timeout = 1 + 1.5 * sas.estimateAcquisitionTime()
start = time.time()
f = sas.acquire()
# wait until it's over
data = f.result(timeout)
dur = time.time() - start
logging.debug("Acquisition took %g s", dur)
self.assertTrue(f.done())
self.assertEqual(len(data), len(sems.raw) + len(ars.raw))
self.assertEqual(len(sems.raw), 1)
self.assertEqual(sems.raw[0].shape, exp_shape)
self.assertEqual(len(ars.raw), num_ar)
md = ars.raw[0].metadata
self.assertIn(model.MD_POS, md)
self.assertIn(model.MD_AR_POLE, md)
# Short acquisition (< 0.1s)
self.ccd.exposureTime.value = 0.03 # s
ars.repetition.value = (30, 20)
exp_shape = ars.repetition.value[::-1]
num_ar = numpy.prod(ars.repetition.value)
# Start acquisition
timeout = 1 + 1.5 * sas.estimateAcquisitionTime()
start = time.time()
f = sas.acquire()
# wait until it's over
data = f.result(timeout)
dur = time.time() - start
logging.debug("Acquisition took %g s", dur)
self.assertTrue(f.done())
self.assertEqual(len(data), len(sems.raw) + len(ars.raw))
self.assertEqual(len(sems.raw), 1)
self.assertEqual(sems.raw[0].shape, exp_shape)
self.assertEqual(len(ars.raw), num_ar)
md = ars.raw[0].metadata
self.assertIn(model.MD_POS, md)
self.assertIn(model.MD_AR_POLE, md)
def acquire_spec(wls, wle, res, dt, filename):
"""
wls (float): start wavelength in m
wle (float): end wavelength in m
res (int): number of points to acquire
dt (float): dwell time in seconds
filename (str): filename to save to
"""
# TODO: take a progressive future to update and know if it's the end
ebeam = model.getComponent(role="e-beam")
sed = model.getComponent(role="se-detector")
mchr = model.getComponent(role="monochromator")
try:
sgrh = model.getComponent(role="spectrograph")
except LookupError:
sgrh = model.getComponent(role="spectrograph-dedicated")
opm = acq.path.OpticalPathManager(model.getMicroscope())
prev_dt = ebeam.dwellTime.value
prev_res = ebeam.resolution.value
prev_scale = ebeam.scale.value
prev_trans = ebeam.translation.value
prev_wl = sgrh.position.value["wavelength"]
# Create a stream for monochromator scan
mchr_s = MonochromatorScanStream("Spectrum", mchr, ebeam, sgrh, opm=opm)
mchr_s.startWavelength.value = wls
mchr_s.endWavelength.value = wle
mchr_s.numberOfPixels.value = res
mchr_s.dwellTime.value = dt
mchr_s.emtTranslation.value = ebeam.translation.value
# Create SEM survey stream
survey_s = stream.SEMStream(
"Secondary electrons survey",
sed,
sed.data,
ebeam,
emtvas={"translation", "scale", "resolution", "dwellTime"},
)
# max FoV, with scale 4
survey_s.emtTranslation.value = (0, 0)
survey_s.emtScale.value = (4, 4)
survey_s.emtResolution.value = (v / 4 for v in ebeam.resolution.range[1])
survey_s.emtDwellTime.value = 10e-6 # 10µs is hopefully enough
# Acquire using the acquisition manager
# Note: the monochromator scan stream is unknown to the acquisition manager,
# so it'll be done last
expt = acq.estimateTime([survey_s, mchr_s])
f = acq.acquire([survey_s, mchr_s])
try:
# Note: the timeout is important, as it allows to catch KeyboardInterrupt
das, e = f.result(2 * expt + 1)
except KeyboardInterrupt:
logging.info("Stopping before end of acquisition")
f.cancel()
return
finally:
logging.debug("Restoring hardware settings")
if prev_res != (1, 1):
ebeam.resolution.value = prev_res
ebeam.dwellTime.value = prev_dt
sgrh.moveAbs({"wavelength": prev_wl})
ebeam.scale.value = prev_scale
ebeam.translation.value = prev_trans
if prev_res != (1, 1):
ebeam.resolution.value = prev_res
ebeam.dwellTime.value = prev_dt
if e:
logging.error("Acquisition failed: %s", e)
if das:
# Save the file
exporter = dataio.find_fittest_converter(filename)
exporter.export(filename, das)
logging.info("Spectrum successfully saved to %s", filename)
input("Press Enter to close.")
def setUp(self):
self.stream = stream.SEMStream("Single beam", self.sed, self.sed.data, self.ebeam,
focuser=self.efocuser, # Not used during acquisition, but done by the GUI
hwemtvas={"scale", "dwellTime", "horizontalFoV"})
def __init__(self, microscope, main_app):
super(QuickCLPlugin, self).__init__(microscope, main_app)
# Can only be used with a SPARC with CL detector (or monochromator)
if not microscope:
return
main_data = self.main_app.main_data
if not main_data.ebeam or not (main_data.cld
or main_data.monochromator):
return
self.conf = get_acqui_conf()
self.filename = model.StringVA("")
self.filename.subscribe(self._on_filename)
self.expectedDuration = model.VigilantAttribute(1,
unit="s",
readonly=True)
self.hasDatabar = model.BooleanVA(False)
# Only put the VAs that do directly define the image as local, everything
# else should be global. The advantage is double: the global VAs will
# set the hardware even if another stream (also using the e-beam) is
# currently playing, and if the VAs are changed externally, the settings
# will be displayed correctly (and not reset the values on next play).
emtvas = set()
hwemtvas = set()
for vaname in get_local_vas(main_data.ebeam,
main_data.hw_settings_config):
if vaname in ("resolution", "dwellTime", "scale"):
emtvas.add(vaname)
else:
hwemtvas.add(vaname)
self._sem_stream = stream.SEMStream(
"Secondary electrons",
main_data.sed,
main_data.sed.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
hwemtvas=hwemtvas,
hwdetvas=None,
emtvas=emtvas,
detvas=get_local_vas(main_data.sed, main_data.hw_settings_config),
)
# This stream is used both for rendering and acquisition.
# LiveCLStream is more or less like a SEMStream, but ensures the icon in
# the merge slider is correct, and provide a few extra.
if main_data.cld:
self._cl_stream = LiveCLStream(
"CL intensity",
main_data.cld,
main_data.cld.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
emtvas=emtvas,
detvas=get_local_vas(main_data.cld,
main_data.hw_settings_config),
opm=main_data.opm,
)
# TODO: allow to type in the resolution of the CL?
# TODO: add the cl-filter axis (or reset it to pass-through?)
self.logScale = self._cl_stream.logScale
if hasattr(self._cl_stream, "detGain"):
self._cl_stream.detGain.subscribe(self._on_cl_gain)
# Update the acquisition time when it might change (ie, the scan settings
# change)
self._cl_stream.emtDwellTime.subscribe(self._update_exp_dur)
self._cl_stream.emtResolution.subscribe(self._update_exp_dur)
# Note: for now we don't really support SPARC with BOTH CL-detector and
# monochromator.
if main_data.monochromator:
self._mn_stream = LiveCLStream(
"Monochromator",
main_data.monochromator,
main_data.monochromator.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
emtvas=emtvas,
detvas=get_local_vas(main_data.monochromator,
main_data.hw_settings_config),
opm=main_data.opm,
)
self._mn_stream.emtDwellTime.subscribe(self._update_exp_dur)
self._mn_stream.emtResolution.subscribe(self._update_exp_dur)
# spg = self._getAffectingSpectrograph(main_data.spectrometer)
# TODO: show axes
self._dlg = None
self.addMenu("Acquisition/Quick CL...\tF2", self.start)
def test_acq_spec(self):
"""
Test short & long acquisition for Spectrometer
"""
# Create the stream
sems = stream.SEMStream("test sem", self.sed, self.sed.data,
self.ebeam)
specs = stream.SpectrumStream("test spec", self.spec, self.spec.data,
self.ebeam)
sps = stream.SEMSpectrumMDStream("test sem-spec", sems, specs)
specs.roi.value = (0.15, 0.6, 0.8, 0.8)
# Long acquisition (small rep to avoid being too long) > 0.1s
self.spec.exposureTime.value = 0.3 # s
specs.repetition.value = (5, 6)
exp_shape = specs.repetition.value[::-1]
# Start acquisition
timeout = 1 + 1.5 * sps.estimateAcquisitionTime()
start = time.time()
f = sps.acquire()
# wait until it's over
data = f.result(timeout)
dur = time.time() - start
logging.debug("Acquisition took %g s", dur)
self.assertTrue(f.done())
self.assertEqual(len(data), len(sems.raw) + len(specs.raw))
self.assertEqual(len(sems.raw), 1)
self.assertEqual(sems.raw[0].shape, exp_shape)
self.assertEqual(len(specs.raw), 1)
sshape = specs.raw[0].shape
self.assertEqual(len(sshape), 5)
self.assertGreater(sshape[0], 1) # should have at least 2 wavelengths
sem_md = sems.raw[0].metadata
spec_md = specs.raw[0].metadata
self.assertAlmostEqual(sem_md[model.MD_POS], spec_md[model.MD_POS])
self.assertAlmostEqual(sem_md[model.MD_PIXEL_SIZE],
spec_md[model.MD_PIXEL_SIZE])
# Short acquisition (< 0.1s)
self.spec.exposureTime.value = 0.01 # s
specs.repetition.value = (25, 60)
exp_shape = specs.repetition.value[::-1]
# Start acquisition
timeout = 1 + 1.5 * sps.estimateAcquisitionTime()
start = time.time()
f = sps.acquire()
# wait until it's over
data = f.result(timeout)
dur = time.time() - start
logging.debug("Acquisition took %g s", dur)
self.assertTrue(f.done())
self.assertEqual(len(data), len(sems.raw) + len(specs.raw))
self.assertEqual(len(sems.raw), 1)
self.assertEqual(sems.raw[0].shape, exp_shape)
self.assertEqual(len(specs.raw), 1)
sshape = specs.raw[0].shape
self.assertEqual(len(sshape), 5)
self.assertGreater(sshape[0], 1) # should have at least 2 wavelengths
sem_md = sems.raw[0].metadata
spec_md = specs.raw[0].metadata
self.assertAlmostEqual(sem_md[model.MD_POS], spec_md[model.MD_POS])
self.assertAlmostEqual(sem_md[model.MD_PIXEL_SIZE],
spec_md[model.MD_PIXEL_SIZE])