def test_estimateTiledAcquisitionTime(self):
"""Test estimated acquisition time for overview imaging."""
# small area on center scintillator (~3x4 tiles)
scintillator5_area = (-0.002, -0.002, 0.002, 0.002) # l, b, r, t
self.stream.emitter.dwellTime.value = 1e-6 # s
est_time_1 = fastem.estimateTiledAcquisitionTime(self.stream, self.stage, scintillator5_area)
# increase dwell time
self.stream.emitter.dwellTime.value = 2e-6 # s
est_time_2 = fastem.estimateTiledAcquisitionTime(self.stream, self.stage, scintillator5_area)
# check that estimated time increases with dwell time
self.assertGreater(est_time_2, est_time_1)
def update_acquisition_time(self, _=None):
lvl = None # icon status shown
if not self._tab_data_model.is_calib_done.value:
lvl = logging.WARN
txt = "System is not calibrated."
elif not self._main_data_model.active_scintillators.value:
lvl = logging.WARN
txt = "No scintillator loaded (go to Chamber tab)."
elif not self._tab_data_model.selected_scintillators.value:
lvl = logging.WARN
txt = "No scintillator selected for overview acquisition."
else:
acq_time = 0
# Add up the acquisition time of all the selected scintillators
for num in self._tab_data_model.selected_scintillators.value:
center = self._tab_data_model.main.scintillator_positions[num]
sz = self._tab_data_model.main.scintillator_size
coords = (center[0] - sz[0] / 2, center[1] - sz[1] / 2,
center[0] + sz[0] / 2, center[1] + sz[1] / 2)
acq_time += fastem.estimateTiledAcquisitionTime(self._tab_data_model.streams.value[0],
self._main_data_model.stage, coords)
acq_time = math.ceil(acq_time) # round a bit pessimistic
txt = u"Estimated time is {}."
txt = txt.format(units.readable_time(acq_time))
logging.debug("Updating status message %s, with level %s", txt, lvl)
self._set_status_message(txt, lvl)
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 on_acquisition(self, evt):
"""
Start the acquisition (really)
"""
self.update_acquisition_time(
) # make sure we show the right label if the previous acquisition failed
self._main_data_model.is_acquiring.value = True
self.btn_acquire.Enable(False)
self.btn_cancel.Enable(True)
self.btn_cancel.Show()
self.gauge_acq.Show()
self.gauge_acq.Range = len(
self._tab_data_model.selected_scintillators.value)
self.gauge_acq.Value = 0
# Acquire ROAs for all projects
acq_futures = {}
for num in self._tab_data_model.selected_scintillators.value:
center = self._tab_data_model.main.scintillator_positions[num]
sz = self._tab_data_model.main.scintillator_size
coords = (center[0] - sz[0] / 2, center[1] - sz[1] / 2,
center[0] + sz[0] / 2, center[1] + sz[1] / 2)
try:
f = fastem.acquireTiledArea(
self._tab_data_model.streams.value[0],
self._main_data_model.stage, coords)
t = fastem.estimateTiledAcquisitionTime(
self._tab_data_model.streams.value[0],
self._main_data_model.stage, coords)
except Exception:
logging.exception("Failed to start overview acquisition")
# Try acquiring the other
continue
f.add_done_callback(partial(self.on_acquisition_done, num=num))
acq_futures[f] = t
if acq_futures:
self.acq_future = model.ProgressiveBatchFuture(acq_futures)
self.acq_future.add_done_callback(self.full_acquisition_done)
self._fs_connector = ProgressiveFutureConnector(
self.acq_future, self.gauge_acq, self.lbl_acqestimate)
else: # In case all acquisitions failed to start
self._main_data_model.is_acquiring.value = False
self._reset_acquisition_gui("Acquisition failed (see log panel).",
level=logging.WARNING)