def test_get_progress(self):
"""
Test getMovementProgress function behaves as expected
"""
start_point = {'x': 0, 'y': 0, 'z': 0}
end_point = {'x': 2, 'y': 2, 'z': 2}
current_point = {'x': 1, 'y': 1, 'z': 1}
progress = getMovementProgress(current_point, start_point, end_point)
self.assertTrue(util.almost_equal(progress, 0.5, rtol=RTOL_PROGRESS))
current_point = {
'x': .998,
'y': .999,
'z': .999
} # slightly off the line
progress = getMovementProgress(current_point, start_point, end_point)
self.assertTrue(util.almost_equal(progress, 0.5, rtol=RTOL_PROGRESS))
current_point = {'x': 3, 'y': 3, 'z': 3} # away from the line
progress = getMovementProgress(current_point, start_point, end_point)
self.assertIsNone(progress)
current_point = {'x': 1, 'y': 1, 'z': 3} # away from the line
progress = getMovementProgress(current_point, start_point, end_point)
self.assertIsNone(progress)
current_point = {'x': -1, 'y': 0, 'z': 0} # away from the line
progress = getMovementProgress(current_point, start_point, end_point)
self.assertIsNone(progress)
def getMovementProgress(current_pos, start_pos, end_pos):
"""
Compute the position on the path between start and end positions of a stage movement (such as LOADING to IMAGING)
If it’s too far from the line between the start and end positions, then it’s considered out of the path.
:param current_pos: (dict str->float) Current position of the stage
:param start_pos: (dict str->float) A position to start the movement from
:param end_pos: (dict str->float) A position to end the movement to
:return:(0<=float<=1, or None) Ratio of the progress, None if it's far away from of the path
"""
def get_distance(start, end):
# Calculate the euclidean distance between two 3D points
axes = start.keys() & end.keys() # only the axes found on both points
sp = numpy.array([start[a] for a in axes])
ep = numpy.array([end[a] for a in axes])
return scipy.spatial.distance.euclidean(ep, sp)
# Get distance for current point in respect to start and end
from_start = get_distance(start_pos, current_pos)
to_end = get_distance(current_pos, end_pos)
total_length = get_distance(start_pos, end_pos)
if total_length == 0: # same value
return 1
# Check if current position is on the line from start to end position
# That would happen if start_to_current + current_to_start = total_distance from start to end
if util.almost_equal((from_start + to_end),
total_length,
rtol=RTOL_PROGRESS):
return min(from_start / total_length,
1.0) # Clip in case from_start slightly > total_length
else:
return None
def _onUpdateTriggerDelayMD(self, evt):
"""
Callback method for trigger delay ctrl GUI element.
Overwrites the triggerDelay value in the MD after a new value was requested via the GUI.
"""
evt.Skip()
cur_timeRange = self.streak_unit.timeRange.value
requested_triggerDelay = self.ctrl_triggerDelay.GetValue()
# get a copy of MD
trigger2delay_MD = self.streak_delay.getMetadata()[model.MD_TIME_RANGE_TO_DELAY]
# check if key already exists (prevent creating new key due to floating point issues)
key = util.find_closest(cur_timeRange, trigger2delay_MD.keys())
if util.almost_equal(key, cur_timeRange):
# Replace the current delay value with the requested for an already existing timeRange in the dict.
# This avoid duplication of keys, which are only different because of floating point issues.
trigger2delay_MD[key] = requested_triggerDelay
else:
trigger2delay_MD[cur_timeRange] = requested_triggerDelay
logging.warning("A new entry %s was added to MD_TIME_RANGE_TO_DELAY, "
"which is not in the device .timeRange choices.", cur_timeRange)
# check the number of keys in the dict is same as choices for VA
if len(trigger2delay_MD.keys()) != len(self.streak_unit.timeRange.choices):
logging.warning("MD_TIME_RANGE_TO_DELAY has %d entries, while the device .timeRange has %d choices.",
len(trigger2delay_MD.keys()), len(self.streak_unit.timeRange.choices))
self.streak_delay.updateMetadata({model.MD_TIME_RANGE_TO_DELAY: trigger2delay_MD})
# Note: updateMetadata should here never raise an exception as the UnitFloatCtrl already
# catches errors regarding type and out-of-range inputs
# update txt displayed in GUI
self._onUpdateTriggerDelayGUI("Calibration not saved yet", odemis.gui.FG_COLOUR_WARNING)
def assert_pos_almost_equal(actual, expected, *args, **kwargs):
"""
Asserts that two stage positions have almost equal coordinates.
"""
if set(expected.keys()) != set(actual.keys()):
raise AssertionError("Dimensions of position do not match: %s != %s" % (actual.keys(), expected.keys()))
for k in expected.keys():
if not util.almost_equal(actual[k], expected[k], *args, **kwargs):
raise AssertionError("Position %s != %s" % (actual, expected))
def assert_pos_almost_equal(actual, expected, *args, **kwargs):
"""
Asserts that two stage positions have almost equal coordinates.
"""
if set(expected.keys()) != set(actual.keys()):
raise AssertionError("Dimensions of position do not match: %s != %s" %
(actual.keys(), expected.keys()))
for k in expected.keys():
if not util.almost_equal(actual[k], expected[k], *args, **kwargs):
raise AssertionError("Position %s != %s" % (actual, expected))
def test_simple(self):
in_exp = {(0., 0): True,
(-5, -5.): True,
(1., 1. - 1e-9): True,
(1., 1. - 1e-3): False,
(1., 1. + 1e-3): False,
(-5e-8, -5e-8 + 1e-19): True,
(5e18, 5e18 + 1): True,
}
for i, eo in in_exp.items():
o = util.almost_equal(*i)
self.assertEqual(o, eo, "Failed to get correct output for %s" % (i,))
def cb_set(value, ctrl=value_ctrl, unit=unit):
for i in range(ctrl.GetCount()):
if ((isinstance(value, float) and util.almost_equal(ctrl.GetClientData(i), value)) or
ctrl.GetClientData(i) == value):
logging.debug("Setting ComboBox value to %s", ctrl.Items[i])
ctrl.SetSelection(i)
break
else:
logging.warning("No existing label found for value %s", value)
# entering value as free text
txt = value_to_str(value, unit)
ctrl.SetValue(txt)
def cb_set(value, ctrl=value_ctrl, unit=unit):
for i in range(ctrl.GetCount()):
if ((isinstance(value, float) and util.almost_equal(ctrl.GetClientData(i), value)) or
ctrl.GetClientData(i) == value):
logging.debug("Setting ComboBox value to %s", ctrl.Items[i])
ctrl.SetSelection(i)
break
else:
logging.warning("No existing label found for value %s", value)
# entering value as free text
txt = value_to_str(value, unit)
ctrl.SetValue(txt)
def acquire_volts(volts, detector):
"""
vots (list of floats > 0): voltage in kV
detector (str): role of the spectrometer to use
returns (list of DataArray): all the spectra, in order
"""
ebeam = model.getComponent(role="e-beam")
sed = model.getComponent(role="se-detector")
spmt = model.getComponent(role=detector)
hw_settings = save_hw_settings(ebeam)
# Go to spot mode (ie, res = 1x1)
if ebeam.resolution.value != (1, 1):
ebeam.resolution.value = (1, 1)
ebeam.translation.value = (0, 0) # at the center of the FoV
else:
logging.info("Leaving the e-beam in spot mode at %s",
ebeam.translation.value)
ebeam.dwellTime.value = 0.1
try:
# Activate the e-beam
sed.data.subscribe(discard_data)
das = []
for vstr in volts:
v = float(vstr) * 1000
ebeam.accelVoltage.value = v
if not util.almost_equal(ebeam.accelVoltage.value, v):
logging.warning(
"Voltage requested at %g kV, but e-beam set at %g kV",
v / 1000, ebeam.accelVoltage.value / 1000)
else:
logging.info("Acquiring at %g kV", v / 1000)
# Acquire one spectrum
spec = spmt.data.get()
# Add dimensions to make it a spectrum (X, first dim -> C, 5th dim)
spec.shape = (spec.shape[-1], 1, 1, 1, 1)
# Add some useful metadata
spec.metadata[model.MD_DESCRIPTION] = "Spectrum at %g kV" % (v /
1000)
spec.metadata[model.MD_EBEAM_VOLTAGE] = v
# TODO: store the spot position in MD_POS
das.append(spec)
finally:
sed.data.unsubscribe(discard_data) # Just to be sure
resume_hw_settings(ebeam, hw_settings)
return das
def assert_pos_almost_equal(actual, expected, match_all=True, *args, **kwargs):
"""
Asserts that two stage positions have almost equal coordinates.
:param match_all: (bool) if False, only the expected keys are checked, and actual can have more keys
"""
if match_all and set(expected.keys()) != set(actual.keys()):
raise AssertionError("Dimensions of position do not match: %s != %s" %
(list(actual.keys()), list(expected.keys())))
for k in expected.keys():
if not util.almost_equal(actual[k], expected[k], *args, **kwargs):
raise AssertionError("Position %s != %s" % (actual, expected))
def _updatePosition(self):
"""
update the position VA
"""
# if it is an unsupported position report the nearest supported one
real_pos = self._position[self._axis]
nearest = util.find_closest(real_pos, self._positions.keys())
if not util.almost_equal(real_pos, nearest):
logging.warning("Reporting axis %s @ %s (known position), while physical axis %s @ %s",
self._axis, nearest, self._caxis, real_pos)
pos = {self._axis: nearest}
logging.debug("reporting position %s", pos)
self.position._set_value(pos, force_write=True)
def _updatePosition(self):
"""
update the position VA
"""
# if it is an unsupported position report the nearest supported one
real_pos = self._position[self._axis]
nearest = util.find_closest(real_pos, self._positions.keys())
if not util.almost_equal(real_pos, nearest):
logging.warning("Reporting axis %s @ %s (known position), while physical axis %s @ %s",
self._axis, nearest, self._caxis, real_pos)
pos = {self._axis: nearest}
logging.debug("reporting position %s", pos)
self.position._set_value(pos, force_write=True)
def _check_fov(self, das, sfov):
"""
Checks the fov based on the data arrays.
das: list of DataArryas
sfov: previous estimate for the fov
"""
afovs = [self._get_fov(d) for d in das]
asfov = (min(f[1] for f in afovs), min(f[0] for f in afovs))
if not all(util.almost_equal(e, a) for e, a in zip(sfov, asfov)):
logging.warning("Unexpected min FoV = %s, instead of %s", asfov,
sfov)
sfov = asfov
return sfov
def _check_fov(self, das, sfov):
"""
Checks the fov based on the data arrays.
das: list of DataArryas
sfov: previous estimate for the fov
"""
afovs = [self._get_fov(d) for d in das]
asfov = (min(f[1] for f in afovs),
min(f[0] for f in afovs))
if not all(util.almost_equal(e, a) for e, a in zip(sfov, asfov)):
logging.warning("Unexpected min FoV = %s, instead of %s", asfov, sfov)
sfov = asfov
return sfov
def get_time_range_to_trigger_delay(data, timeRange_choices,
triggerDelay_range):
"""
Reads the time range and trigger delay values from a csv object.
Checks values for validity.
:parameter data: (csv.reader object) calibration file
:parameter timeRange_choices: (frozenset) choices possible for timeRange VA
:parameter triggerDelay_range: (tuple) range possible for trigger delay values
:return: (dict) new dictionary containing the loaded time range to trigger delay info
"""
new_dict = {}
for timeRange, delay in data:
try:
timeRange = float(timeRange)
delay = float(delay)
except ValueError:
raise ValueError(
"Trigger delay %s and/or time range %s is not of type float. "
"Please check calibration file for trigger delay." %
(delay, timeRange))
# check delay in range allowed
if not triggerDelay_range[0] <= delay <= triggerDelay_range[1]:
raise ValueError(
"Trigger delay %s corresponding to time range %s is not in range %s. "
"Please check the calibration file for the trigger delay." %
(delay, timeRange, triggerDelay_range))
# check timeRange is in possible choices for timeRange on HW
choice = find_closest(timeRange, timeRange_choices)
if not almost_equal(timeRange, choice):
raise ValueError(
"Time range % s found in calibration file is not a possible choice "
"for the time range of the streak unit. "
"Please modify csv file so it fits the possible choices for the "
"time range of the streak unit. "
"Values in file must be of format timeRange:triggerDelay (per line)."
% timeRange)
new_dict[timeRange] = delay
# check all time ranges are there
if len(new_dict) == len(timeRange_choices):
return new_dict
else:
raise ValueError(
"The total number of %s time ranges in the loaded calibration file does not "
"match the requested number of %s time ranges." %
(len(new_dict), len(timeRange_choices)))
def acquire_volts(volts, detector):
"""
vots (list of floats > 0): voltage in kV
detector (str): role of the spectrometer to use
returns (list of DataArray): all the spectra, in order
"""
ebeam = model.getComponent(role="e-beam")
sed = model.getComponent(role="se-detector")
spmt = model.getComponent(role=detector)
hw_settings = save_hw_settings(ebeam)
# Go to spot mode (ie, res = 1x1)
if ebeam.resolution.value != (1, 1):
ebeam.resolution.value = (1, 1)
ebeam.translation.value = (0, 0) # at the center of the FoV
else:
logging.info("Leaving the e-beam in spot mode at %s", ebeam.translation.value)
ebeam.dwellTime.value = 0.1
try:
# Activate the e-beam
sed.data.subscribe(discard_data)
das = []
for vstr in volts:
v = float(vstr) * 1000
ebeam.accelVoltage.value = v
if not util.almost_equal(ebeam.accelVoltage.value, v):
logging.warning("Voltage requested at %g kV, but e-beam set at %g kV",
v / 1000, ebeam.accelVoltage.value / 1000)
else:
logging.info("Acquiring at %g kV", v / 1000)
# Acquire one spectrum
spec = spmt.data.get()
# Add dimensions to make it a spectrum (X, first dim -> C, 5th dim)
spec.shape = (spec.shape[-1], 1, 1, 1, 1)
# Add some useful metadata
spec.metadata[model.MD_DESCRIPTION] = "Spectrum at %g kV" % (v / 1000)
spec.metadata[model.MD_EBEAM_VOLTAGE] = v
# TODO: store the spot position in MD_POS
das.append(spec)
finally:
sed.data.unsubscribe(discard_data) # Just to be sure
resume_hw_settings(ebeam, hw_settings)
return das
def test_simple(self):
in_exp = {
(0., 0): True,
(-5, -5.): True,
(1., 1. - 1e-9): True,
(1., 1. - 1e-3): False,
(1., 1. + 1e-3): False,
(-5e-8, -5e-8 + 1e-19): True,
(5e18, 5e18 + 1): True,
}
for i, eo in in_exp.items():
o = util.almost_equal(*i)
self.assertEqual(o, eo,
"Failed to get correct output for %s" % (i, ))
def read_trigger_delay_csv(filename, time_choices, trigger_delay_range):
"""
Read the MD_TIME_RANGE_TO_DELAY from a CSV file, and check its validity based on the hardware
filename (str): the path to file
time_choices (set): choices possible for timeRange VA
trigger_delay_range (float, float): min/max value of the trigger delay
return (dict float -> float): new dictionary containing the loaded time range to trigger delay info
raise ValueError: if the data of the CSV file cannot be parsed or doesn't fit the hardware
raise IOError: if the file doesn't exist
"""
tr2d = {}
with open(filename, 'r', newline='') as csvfile:
calibFile = csv.reader(csvfile, delimiter=':')
for time_range, delay in calibFile:
try:
time_range = float(time_range)
delay = float(delay)
except ValueError:
raise ValueError(
"Trigger delay %s and/or time range %s is not of type float. "
"Please check calibration file for trigger delay." %
(delay, time_range))
# check delay in range allowed
if not trigger_delay_range[0] <= delay <= trigger_delay_range[1]:
raise ValueError(
"Trigger delay %s corresponding to time range %s is not in range %s. "
"Please check the calibration file for the trigger delay."
% (delay, time_range, trigger_delay_range))
# check timeRange is in possible choices for timeRange on HW
time_range_hw = find_closest(time_range, time_choices)
if not almost_equal(time_range, time_range_hw):
raise ValueError(
"Time range % s found in calibration file is not a possible choice "
"for the time range of the streak unit. "
"Please modify CSV file so it fits the possible choices for the "
"time range of the streak unit. "
"Values in file must be of format timeRange:triggerDelay (per line)."
% time_range)
tr2d[time_range_hw] = delay
# check all time ranges are there
if len(tr2d) != len(time_choices):
raise ValueError(
"The total number of %s time ranges in the loaded calibration file does not "
"match the requested number of %s time ranges." %
(len(tr2d), len(time_choices)))
return tr2d
def cb_set(value, ctrl=value_ctrl, u=unit, acc=accuracy):
for i in range(ctrl.Count):
d = ctrl.GetClientData(i)
if (d == value or
(all(isinstance(v, float) for v in (value, d)) and
util.almost_equal(d, value))
):
logging.debug("Setting combobox value to %s", ctrl.Items[i])
ctrl.SetSelection(i)
break
else:
logging.debug("No existing label found for value %s in combobox ctrl %d",
value, id(ctrl))
# entering value as free text
txt = readable_str(value, u, sig=acc)
ctrl.SetValue(txt)
def get_time_range_to_trigger_delay(data, timeRange_choices, triggerDelay_range):
"""
Reads the time range and trigger delay values from a csv object.
Checks values for validity.
:parameter data: (csv.reader object) calibration file
:parameter timeRange_choices: (frozenset) choices possible for timeRange VA
:parameter triggerDelay_range: (tuple) range possible for trigger delay values
:return: (dict) new dictionary containing the loaded time range to trigger delay info
"""
new_dict = {}
for timeRange, delay in data:
try:
timeRange = float(timeRange)
delay = float(delay)
except ValueError:
raise ValueError("Trigger delay %s and/or time range %s is not of type float. "
"Please check calibration file for trigger delay." % (delay, timeRange))
# check delay in range allowed
if not triggerDelay_range[0] <= delay <= triggerDelay_range[1]:
raise ValueError("Trigger delay %s corresponding to time range %s is not in range (0, 1). "
"Please check the calibration file for the trigger delay." % (delay, timeRange))
# check timeRange is in possible choices for timeRange on HW
choice = find_closest(timeRange, timeRange_choices)
if not almost_equal(timeRange, choice):
raise ValueError("Time range % s found in calibration file is not a possible choice "
"for the time range of the streak unit. "
"Please modify csv file so it fits the possible choices for the "
"time range of the streak unit. "
"Values in file must be of format timeRange:triggerDelay (per line)."
% timeRange)
new_dict[timeRange] = delay
# check all time ranges are there
if len(new_dict) == len(timeRange_choices):
return new_dict
else:
raise ValueError("The total number of %s time ranges in the loaded calibration file does not "
"match the requested number of %s time ranges."
% (len(new_dict), len(timeRange_choices)))
def cb_set(value, va=va, ctrl=value_ctrl, u=unit, acc=accuracy):
# Re-read the value from the VA because it'll be called via
# CallAfter(), and if the value is changed multiple times, it might
# not be in chronological order.
value = va.value
for i in range(ctrl.GetCount()):
d = ctrl.GetClientData(i)
if (d == value or
(all(isinstance(v, float) for v in (value, d)) and
util.almost_equal(d, value))
):
logging.debug("Setting combobox value to %s", ctrl.Items[i])
ctrl.SetSelection(i)
break
else:
logging.debug("No existing label found for value %s in combobox ctrl %d",
value, id(ctrl))
# entering value as free text
txt = value_to_str(value, u, acc)
ctrl.SetValue(txt)
def cb_set(value, va=va, ctrl=value_ctrl, u=unit, acc=accuracy):
# Re-read the value from the VA because it'll be called via
# CallAfter(), and if the value is changed multiple times, it might
# not be in chronological order.
value = va.value
for i in range(ctrl.GetCount()):
d = ctrl.GetClientData(i)
if (d == value or
(all(isinstance(v, float) for v in (value, d)) and
util.almost_equal(d, value))
):
logging.debug("Setting combobox value to %s", ctrl.Items[i])
ctrl.SetSelection(i)
break
else:
logging.debug("No existing label found for value %s in combobox ctrl %d",
value, id(ctrl))
# entering value as free text
txt = value_to_str(value, u, acc)
ctrl.SetValue(txt)
def assert_pos_not_almost_equal(actual,
expected,
match_all=True,
*args,
**kwargs):
"""
Asserts that two stage positions do not have almost equal coordinates. This means at least one of the axes has a
different value.
:param match_all: (bool) if False, only the expected keys are checked, and actual can have more keys
"""
if match_all and set(expected.keys()) != set(actual.keys()):
raise AssertionError("Dimensions of position do not match: %s != %s" %
(list(actual.keys()), list(expected.keys())))
# Check that at least one of the axes not equal
for k in expected.keys():
if not util.almost_equal(actual[k], expected[k], *args, **kwargs):
return
# Otherwise coordinates are almost equal
raise AssertionError("Position %s == %s" % (actual, expected))
def _setTimeRange(self, value):
"""
Updates the timeRange VA.
:parameter value: (float) value to be set
:return: (float) current time range
"""
logging.debug("Reporting time range %s for streak unit.", value)
self._metadata[model.MD_STREAK_TIMERANGE] = value
# set corresponding trigger delay
tr2d = self.parent._delaybox._metadata.get(model.MD_TIME_RANGE_TO_DELAY)
if tr2d:
key = util.find_closest(value, tr2d.keys())
if util.almost_equal(key, value):
self.parent._delaybox.triggerDelay.value = tr2d[key]
else:
logging.warning("Time range %s is not a key in MD for time range to "
"trigger delay calibration" % value)
return value
def _setTimeRange(self, value):
"""
Updates the timeRange VA.
:parameter value: (float) value to be set
:return: (float) current time range
"""
logging.debug("Reporting time range %s for streak unit.", value)
self._metadata[model.MD_STREAK_TIMERANGE] = value
# set corresponding trigger delay
tr2d = self.parent._delaybox._metadata.get(model.MD_TIME_RANGE_TO_DELAY)
if tr2d:
key = util.find_closest(value, tr2d.keys())
if util.almost_equal(key, value):
self.parent._delaybox.triggerDelay.value = tr2d[key]
else:
logging.warning("Time range %s is not a key in MD for time range to "
"trigger delay calibration" % value)
return value
def hfw_choices(comp, va, conf):
""" Return a set of HFW choices
If the VA has predefined choices, return those. Otherwise calculate the choices using the range
of the VA.
"""
try:
choices = va.choices
except (NotApplicableError, AttributeError):
# Pick every x2, x5, x10, starting from the min value
factors = (2, 5, 10)
mn, mx = va.range
choices = {mn}
cur_val = va.value
# starting point (might be even less than mn)
base = 10 ** int(math.log10(mn) - 1)
while base < mx and max(choices) < mx:
for f in factors:
v = base * f
if mn < v < mx:
if util.almost_equal(v, cur_val):
# To avoid having twice (almost) the same value shown in
# the choices when the current value is among them, but
# slightly modified due to rounding.
choices.add(cur_val)
else:
choices.add(v)
elif v >= mx:
break
base *= 10
choices.add(mx)
# We don't add the current value, as it's a range, so anyway any other
# value can also happen so the GUI must be able to handle well any other
# value.
return choices
def hfw_choices(comp, va, conf):
""" Return a set of HFW choices
If the VA has predefined choices, return those. Otherwise calculate the choices using the range
of the VA.
"""
try:
choices = va.choices
except AttributeError:
# Pick every x2, x5, x10, starting from the min value
factors = (2, 5, 10)
mn, mx = va.range
choices = {mn}
cur_val = va.value
# starting point (might be even less than mn)
base = 10 ** int(math.log10(mn) - 1)
while base < mx and max(choices) < mx:
for f in factors:
v = base * f
if mn < v < mx:
if util.almost_equal(v, cur_val):
# To avoid having twice (almost) the same value shown in
# the choices when the current value is among them, but
# slightly modified due to rounding.
choices.add(cur_val)
else:
choices.add(v)
elif v >= mx:
break
base *= 10
choices.add(mx)
# We don't add the current value, as it's a range, so anyway any other
# value can also happen so the GUI must be able to handle well any other
# value.
return choices
def getMovementProgress(current_pos, start_pos, end_pos):
"""
Compute the position on the path between start and end positions of a stage movement (such as LOADING to IMAGING)
If it’s too far from the line between the start and end positions, then it’s considered out of the path.
:param current_pos: (dict str->float) Current position of the stage
:param start_pos: (dict str->float) A position to start the movement from
:param end_pos: (dict str->float) A position to end the movement to
:return:(0<=float<=1, or None) Ratio of the progress, None if it's far away from of the path
"""
# Get distance for current point in respect to start and end
from_start = _getDistance(start_pos, current_pos)
to_end = _getDistance(current_pos, end_pos)
total_length = _getDistance(start_pos, end_pos)
if total_length == 0: # same value
return 1
# Check if current position is on the line from start to end position
# That would happen if start_to_current + current_to_start = total_distance from start to end
if util.almost_equal((from_start + to_end), total_length, rtol=RTOL_PROGRESS):
return min(from_start / total_length, 1.0) # Clip in case from_start slightly > total_length
else:
return None
def getMovementProgress(current_pos, start_pos, end_pos):
"""
Compute the position on the path between start and end positions of a stage movement (such as LOADING to IMAGING)
If it’s too far from the line between the start and end positions, then it’s considered out of the path.
:param current_pos: (dict str->float) Current position of the stage
:param start_pos: (dict str->float) A position to start the movement from
:param end_pos: (dict str->float) A position to end the movement to
:return:(0<=float<=1, or None) Ratio of the progress, None if it's far away from of the path
"""
def get_distance(start, end):
# Calculate the euclidean distance between two 3D points
sp = numpy.array([start['x'], start['y'], start['z']])
ep = numpy.array([end['x'], end['y'], end['z']])
return scipy.spatial.distance.euclidean(ep, sp)
def check_axes(pos):
if not {'x', 'y', 'z'}.issubset(set(pos.keys())):
raise ValueError(
"Missing x,y,z axes in {} for correct distance measurement.".
format(pos))
# Check we have the x,y,z axes in all points
check_axes(current_pos)
check_axes(start_pos)
check_axes(end_pos)
# Get distance for current point in respect to start and end
from_start = get_distance(start_pos, current_pos)
to_end = get_distance(current_pos, end_pos)
total_length = get_distance(start_pos, end_pos)
# Check if current position is on the line from start to end position
# That would happen if start_to_current + current_to_start = total_distance from start to end
if util.almost_equal((from_start + to_end),
total_length,
rtol=RTOL_PROGRESS):
return min(from_start / total_length,
1.0) # Clip in case from_start slightly > total_length
else:
return None
def _get_center_pxs(self, rep, sub_shape, datatl, pxs):
"""
Computes the center and pixel size of the entire data based on the
top-left data acquired.
rep (int, int): number of pixels (tiles) in X, Y
sub_shape (int, int): number of sub-pixels in a pixel
datatl (DataArray): first data array acquired
pxs (float, float): the pixel in m of a pixel
return:
center (tuple of floats): position in m of the whole data
pxs (tuple of floats): pixel size in m of the sub-pixels
"""
# Compute center of area, based on the position of the first point (the
# position of the other points can be wrong due to drift correction)
center_tl = datatl.metadata[model.MD_POS]
dpxs = datatl.metadata[model.MD_PIXEL_SIZE]
tl = (center_tl[0] - (dpxs[0] * (datatl.shape[-1] - 1)) / 2,
center_tl[1] + (dpxs[1] * (datatl.shape[-2] - 1)) / 2)
logging.debug("Computed center of top-left pixel at at %s", tl)
# Note: we don't rely on the MD_PIXEL_SIZE, because if the e-beam was in
# spot mode (res 1x1), the scale is not always correct, which gives an
# incorrect metadata.
sub_pxs = pxs[0] / sub_shape[0], pxs[1] / sub_shape[1]
trep = rep[0] * sub_shape[0], rep[1] * sub_shape[1]
center = (tl[0] + (sub_pxs[0] * (trep[0] - 1)) / 2,
tl[1] - (sub_pxs[1] * (trep[1] - 1)) / 2)
logging.debug("Computed data width to be %s x %s, with center at %s",
pxs[0] * rep[0], pxs[1] * rep[1], center)
if numpy.prod(datatl.shape) > 1:
# pxs and dpxs ought to be identical
if not util.almost_equal(sub_pxs[0], dpxs[0]):
logging.warning("Expected pixel size of %s, but data has %s",
sub_pxs, dpxs)
return center, sub_pxs
def _get_center_pxs(self, rep, sub_shape, datatl, pxs):
"""
Computes the center and pixel size of the entire data based on the
top-left data acquired.
rep (int, int): number of pixels (tiles) in X, Y
sub_shape (int, int): number of sub-pixels in a pixel
datatl (DataArray): first data array acquired
pxs (float, float): the pixel in m of a pixel
return:
center (tuple of floats): position in m of the whole data
pxs (tuple of floats): pixel size in m of the sub-pixels
"""
# Compute center of area, based on the position of the first point (the
# position of the other points can be wrong due to drift correction)
center_tl = datatl.metadata[model.MD_POS]
dpxs = datatl.metadata[model.MD_PIXEL_SIZE]
tl = (center_tl[0] - (dpxs[0] * (datatl.shape[-1] - 1)) / 2,
center_tl[1] + (dpxs[1] * (datatl.shape[-2] - 1)) / 2)
logging.debug("Computed center of top-left pixel at at %s", tl)
# Note: we don't rely on the MD_PIXEL_SIZE, because if the e-beam was in
# spot mode (res 1x1), the scale is not always correct, which gives an
# incorrect metadata.
sub_pxs = pxs[0] / sub_shape[0], pxs[1] / sub_shape[1]
trep = rep[0] * sub_shape[0], rep[1] * sub_shape[1]
center = (tl[0] + (sub_pxs[0] * (trep[0] - 1)) / 2,
tl[1] - (sub_pxs[1] * (trep[1] - 1)) / 2)
logging.debug("Computed data width to be %s x %s, with center at %s",
pxs[0] * rep[0], pxs[1] * rep[1], center)
if numpy.prod(datatl.shape) > 1:
# pxs and dpxs ought to be identical
if not util.almost_equal(sub_pxs[0], dpxs[0]):
logging.warning("Expected pixel size of %s, but data has %s",
sub_pxs, dpxs)
return center, sub_pxs
def __init__(self, name, data, *args, **kwargs):
"""
name (string)
data (model.DataArray(Shadow) of shape (YX) or list of such DataArray(Shadow)).
The metadata MD_POS, MD_AR_POLE and MD_POL_MODE should be provided
"""
if not isinstance(data, collections.Iterable):
data = [data] # from now it's just a list of DataArray
# TODO: support DAS, as a "delayed loading" by only calling .getData()
# when the projection for the particular data needs to be computed (or
# .raw needs to be accessed?)
# Ensure all the data is a DataArray, as we don't handle (yet) DAS
data = [d.getData() if isinstance(d, model.DataArrayShadow) else d for d in data]
# find positions of each acquisition
# (float, float, str or None)) -> DataArray: position on SEM + polarization -> data
self._pos = {}
sempositions = set()
polpositions = set()
for d in data:
try:
sempos_cur = d.metadata[MD_POS]
# When reading data: floating point error (slightly different keys for same ebeam pos)
# -> check if there is already a position specified, which is very close by
# (and therefore the same ebeam pos) and replace with that ebeam position
# (e.g. all polarization positions for the same ebeam positions will have exactly the same ebeam pos)
for sempos in sempositions:
if almost_equal(sempos_cur[0], sempos[0]) and almost_equal(sempos_cur[1], sempos[1]):
sempos_cur = sempos
break
self._pos[sempos_cur + (d.metadata.get(MD_POL_MODE, None),)] = img.ensure2DImage(d)
sempositions.add(sempos_cur)
if MD_POL_MODE in d.metadata:
polpositions.add(d.metadata.get(MD_POL_MODE))
except KeyError:
logging.info("Skipping DataArray without known position")
# Cached conversion of the CCD image to polar representation
# TODO: automatically fill it in a background thread
self._polar = {} # dict tuple (float, float, str or None) -> DataArray
# SEM position VA
# SEM position displayed, (None, None) == no point selected (x, y)
self.point = model.VAEnumerated((None, None),
choices=frozenset([(None, None)] + list(sempositions)))
if self._pos:
# Pick one point, e.g., top-left
bbtl = (min(x for x, y in sempositions if x is not None),
min(y for x, y in sempositions if y is not None))
# top-left point is the closest from the bounding-box top-left
def dis_bbtl(v):
try:
return math.hypot(bbtl[0] - v[0], bbtl[1] - v[1])
except TypeError:
return float("inf") # for None, None
self.point.value = min(sempositions, key=dis_bbtl)
# no need for init=True, as Stream.__init__ will update the image
self.point.subscribe(self._onPoint)
# polarization VA
# check if any polarization analyzer data, (None) == no analyzer data (pol)
if self._pos.keys()[0][-1]:
# use first entry in acquisition to populate VA (acq could have 1 or 6 pol pos)
self.polarization = model.VAEnumerated(self._pos.keys()[0][-1],
choices=polpositions)
if self._pos.keys()[0][-1]:
self.polarization.subscribe(self._onPolarization)
if "acq_type" not in kwargs:
kwargs["acq_type"] = model.MD_AT_AR
super(StaticARStream, self).__init__(name, list(self._pos.values()), *args, **kwargs)
def getFullImage(self):
"""
return (2D DataArray): same dtype as the tiles, with shape corresponding to the bounding box.
"""
tiles = self.tiles
# Compute the bounding box of each tile and the global bounding box
# Get a fixed pixel size by using the first one
# TODO: use the mean, in case they are all slightly different due to
# correction?
pxs = tiles[0].metadata[model.MD_PIXEL_SIZE]
tbbx_phy = [] # tuples of ltrb in physical coordinates
for t in tiles:
c = t.metadata[model.MD_POS]
w = t.shape[-1], t.shape[-2]
if not util.almost_equal(pxs[0], t.metadata[model.MD_PIXEL_SIZE][0], rtol=0.01):
logging.warning("Tile @ %s has a unexpected pixel size (%g vs %g)",
c, t.metadata[model.MD_PIXEL_SIZE][0], pxs[0])
bbx = (c[0] - (w[0] * pxs[0] / 2), c[1] - (w[1] * pxs[1] / 2),
c[0] + (w[0] * pxs[0] / 2), c[1] + (w[1] * pxs[1] / 2))
tbbx_phy.append(bbx)
gbbx_phy = (min(b[0] for b in tbbx_phy), min(b[1] for b in tbbx_phy),
max(b[2] for b in tbbx_phy), max(b[3] for b in tbbx_phy))
# Compute the bounding-boxes in pixel coordinates
tbbx_px = []
# that's the origin (Y is max as Y is inverted)
glt = gbbx_phy[0], gbbx_phy[3]
for bp, t in zip(tbbx_phy, tiles):
lt = (int(round((bp[0] - glt[0]) / pxs[0])),
int(round(-(bp[3] - glt[1]) / pxs[1])))
w = t.shape[-1], t.shape[-2]
bbx = (lt[0], lt[1],
lt[0] + w[0], lt[1] + w[1])
tbbx_px.append(bbx)
gbbx_px = (min(b[0] for b in tbbx_px), min(b[1] for b in tbbx_px),
max(b[2] for b in tbbx_px), max(b[3] for b in tbbx_px))
assert gbbx_px[0] == gbbx_px[1] == 0
if numpy.greater(gbbx_px[-2:], 4 * numpy.sum(tbbx_px[-2:])).any():
# Overlap > 50% or missing tiles
logging.warning("Global area much bigger than sum of tile areas")
# Paste each tile
logging.debug("Generating global image of size %dx%d px",
gbbx_px[-2], gbbx_px[-1])
im = numpy.empty((gbbx_px[-1], gbbx_px[-2]), dtype=tiles[0].dtype)
# Use minimum of the values in the tiles for background
im[:] = numpy.amin(tiles)
for b, t in zip(tbbx_px, tiles):
im[b[1]:b[1] + t.shape[0], b[0]:b[0] + t.shape[1]] = t
# TODO: border
# Update metadata
# TODO: check this is also correct based on lt + half shape * pxs
c_phy = ((gbbx_phy[0] + gbbx_phy[2]) / 2,
(gbbx_phy[1] + gbbx_phy[3]) / 2)
md = tiles[0].metadata.copy()
md[model.MD_POS] = c_phy
return model.DataArray(im, md)
def getFullImage(self):
"""
return (2D DataArray): same dtype as the tiles, with shape corresponding to the bounding box.
"""
tiles = self.tiles
# Compute the bounding box of each tile and the global bounding box
# Get a fixed pixel size by using the first one
# TODO: use the mean, in case they are all slightly different due to
# correction?
pxs = tiles[0].metadata[model.MD_PIXEL_SIZE]
tbbx_phy = [] # tuples of ltrb in physical coordinates
for t in tiles:
c = t.metadata[model.MD_POS]
w = t.shape[-1], t.shape[-2]
if not util.almost_equal(pxs[0], t.metadata[model.MD_PIXEL_SIZE][0], rtol=0.01):
logging.warning("Tile @ %s has a unexpected pixel size (%g vs %g)",
c, t.metadata[model.MD_PIXEL_SIZE][0], pxs[0])
bbx = (c[0] - (w[0] * pxs[0] / 2), c[1] - (w[1] * pxs[1] / 2),
c[0] + (w[0] * pxs[0] / 2), c[1] + (w[1] * pxs[1] / 2))
tbbx_phy.append(bbx)
gbbx_phy = (min(b[0] for b in tbbx_phy), min(b[1] for b in tbbx_phy),
max(b[2] for b in tbbx_phy), max(b[3] for b in tbbx_phy))
# Compute the bounding-boxes in pixel coordinates
tbbx_px = []
# that's the origin (Y is max as Y is inverted)
glt = gbbx_phy[0], gbbx_phy[3]
for bp, t in zip(tbbx_phy, tiles):
lt = (int(round((bp[0] - glt[0]) / pxs[0])),
int(round(-(bp[3] - glt[1]) / pxs[1])))
w = t.shape[-1], t.shape[-2]
bbx = (lt[0], lt[1],
lt[0] + w[0], lt[1] + w[1])
tbbx_px.append(bbx)
gbbx_px = (min(b[0] for b in tbbx_px), min(b[1] for b in tbbx_px),
max(b[2] for b in tbbx_px), max(b[3] for b in tbbx_px))
assert gbbx_px[0] == gbbx_px[1] == 0
if numpy.greater(gbbx_px[-2:], 4 * numpy.sum(tbbx_px[-2:])).any():
# Overlap > 50% or missing tiles
logging.warning("Global area much bigger than sum of tile areas")
# Weave tiles by using a smooth gradient. The part of the tile that does not overlap
# with any previous tiles is inserted into the part of the
# ovv image that is still empty. This part is determined by a mask, which indicates
# the parts of the image that already contain image data (True) and the ones that are still
# empty (False). For the overlapping parts, the tile is multiplied with weights corresponding
# to a gradient that has its maximum at the center of the tile and
# smoothly decreases toward the edges. The function for creating the weights is
# a distance measure resembling the maximum-norm, i.e. equidistant points lie
# on a rectangle (instead of a circle like for the euclidean norm). Additionally,
# the x and y values generating this norm are raised to the power of 6 to
# create a steeper gradient. The value 6 is quite arbitrary and was found to give
# good results during experimentation.
# The part of the overview image that overlaps with the new tile is multiplied with the
# complementary weights (1 - weights) and the weighted overlapping parts of the new tile and
# the ovv image are added, so the resulting image contains a gradient in the overlapping regions
# between all the tiles that have been inserted before and the newly inserted tile.
# Paste each tile
logging.debug("Generating global image of size %dx%d px",
gbbx_px[-2], gbbx_px[-1])
im = numpy.empty((gbbx_px[-1], gbbx_px[-2]), dtype=tiles[0].dtype)
# Use minimum of the values in the tiles for background
im[:] = numpy.amin(tiles)
# The mask is multiplied with the tile, thereby creating a tile with a gradient
mask = numpy.zeros((gbbx_px[-1], gbbx_px[-2]), dtype=numpy.bool)
for b, t in zip(tbbx_px, tiles):
# Part of image overlapping with tile
roi = im[b[1]:b[1] + t.shape[0], b[0]:b[0] + t.shape[1]]
moi = mask[b[1]:b[1] + t.shape[0], b[0]:b[0] + t.shape[1]]
# Insert image at positions that are still empty
roi[~moi] = t[~moi]
# Create gradient in overlapping region. Ratio between old image and new tile values determined by
# distance to the center of the tile
# Create weight matrix with decreasing values from its center that
# has the same size as the tile.
hh, hw = numpy.divide(roi.shape, 2) # half-height, half-width
# Deal with even/odd tile sizes
sz = roi.shape
if sz[1] % 2 == 0:
x = numpy.arange(-hw, hw, 1)
else:
x = numpy.arange(-hw, hw + 1, 1)
if sz[0] % 2 == 0:
y = numpy.arange(-hh, hh, 1)
else:
y = numpy.arange(-hh, hh + 1, 1)
xx, yy = numpy.meshgrid((x / hw) ** 6, (y / hh) ** 6)
w = numpy.maximum(xx, yy)
# Hardcoding a weight function is quite arbitrary and might result in
# suboptimal solutions in some cases.
# Alternatively, different weights might be used. One option would be to select
# a fixed region on the sides of the image, e.g. 20% (expected overlap), and
# only apply a (linear) gradient to these parts, while keeping the new tile for the
# rest of the region. However, this approach does not solve the hardcoding problem
# since the overlap region is still arbitrary. Future solutions might adaptively
# select the this region.
# Use weights to create gradient in overlapping region
roi[moi] = (t * (1 - w))[moi] + (roi * w)[moi]
# Update mask
mask[b[1]:b[1] + t.shape[0], b[0]:b[0] + t.shape[1]] = True
# Update metadata
# TODO: check this is also correct based on lt + half shape * pxs
c_phy = ((gbbx_phy[0] + gbbx_phy[2]) / 2,
(gbbx_phy[1] + gbbx_phy[3]) / 2)
md = tiles[0].metadata.copy()
md[model.MD_POS] = c_phy
return model.DataArray(im, md)
def man_calib(logpath, keep_loaded=False):
escan = None
detector = None
ccd = None
# find components by their role
for c in model.getComponents():
if c.role == "e-beam":
escan = c
elif c.role == "bs-detector":
detector = c
elif c.role == "ccd":
ccd = c
elif c.role == "sem-stage":
sem_stage = c
elif c.role == "align":
opt_stage = c
elif c.role == "ebeam-focus":
ebeam_focus = c
elif c.role == "overview-focus":
navcam_focus = c
elif c.role == "focus":
focus = c
elif c.role == "overview-ccd":
overview_ccd = c
elif c.role == "chamber":
chamber = c
if not all([escan, detector, ccd]):
logging.error("Failed to find all the components")
raise KeyError("Not all components found")
hw_settings = aligndelphi.list_hw_settings(escan, ccd)
try:
# Get pressure values
pressures = chamber.axes["pressure"].choices
vacuum_pressure = min(pressures.keys())
vented_pressure = max(pressures.keys())
if overview_ccd:
for p, pn in pressures.items():
if pn == "overview":
overview_pressure = p
break
else:
raise IOError("Failed to find the overview pressure in %s" %
(pressures, ))
calibconf = get_calib_conf()
shid, sht = chamber.sampleHolder.value
calib_values = calibconf.get_sh_calib(shid)
if calib_values is None:
first_hole = second_hole = offset = resa = resb = hfwa = scaleshift = (
0, 0)
scaling = iscale = iscale_xy = (1, 1)
rotation = irot = ishear = 0
hole_focus = aligndelphi.SEM_KNOWN_FOCUS
opt_focus = aligndelphi.OPTICAL_KNOWN_FOCUS
print_col(
ANSI_RED,
"Calibration values missing! All the steps will be performed anyway..."
)
force_calib = True
else:
first_hole, second_hole, hole_focus, opt_focus, offset, scaling, rotation, iscale, irot, iscale_xy, ishear, resa, resb, hfwa, scaleshift = calib_values
force_calib = False
print_col(
ANSI_CYAN, "**Delphi Manual Calibration steps**\n"
"1.Sample holder hole detection\n"
" Current values: 1st hole: " + str(first_hole) + "\n"
" 2st hole: " + str(second_hole) + "\n"
" hole focus: " + str(hole_focus) + "\n"
"2.SEM image calibration\n"
" Current values: resolution-a: " + str(resa) + "\n"
" resolution-b: " + str(resb) + "\n"
" hfw-a: " + str(hfwa) + "\n"
" spot shift: " + str(scaleshift) + "\n"
"3.Twin stage calibration\n"
" Current values: offset: " + str(offset) + "\n"
" scaling: " + str(scaling) + "\n"
" rotation: " + str(rotation) + "\n"
" optical focus: " + str(opt_focus) + "\n"
"4.Fine alignment\n"
" Current values: scale: " + str(iscale) + "\n"
" rotation: " + str(irot) + "\n"
" scale-xy: " + str(iscale_xy) + "\n"
" shear: " + str(ishear))
print_col(
ANSI_YELLOW,
"Note that you should not perform any stage move during the process.\n"
"Instead, you may zoom in/out while focusing.")
print_col(ANSI_BLACK, "Now initializing, please wait...")
# Default value for the stage offset
position = (offset[0] * scaling[0], offset[1] * scaling[1])
if keep_loaded and chamber.position.value[
"pressure"] == vacuum_pressure:
logging.info(
"Skipped optical lens detection, will use previous value %s",
position)
else:
# Move to the overview position first
f = chamber.moveAbs({"pressure": overview_pressure})
f.result()
# Reference the (optical) stage
f = opt_stage.reference({"x", "y"})
f.result()
f = focus.reference({"z"})
f.result()
# SEM stage to (0,0)
f = sem_stage.moveAbs({"x": 0, "y": 0})
f.result()
# Calculate offset approximation
try:
f = aligndelphi.LensAlignment(overview_ccd, sem_stage, logpath)
position = f.result()
except IOError as ex:
logging.warning(
"Failed to locate the optical lens (%s), will use previous value %s",
ex, position)
# Just to check if move makes sense
f = sem_stage.moveAbs({"x": position[0], "y": position[1]})
f.result()
# Move to SEM
f = chamber.moveAbs({"pressure": vacuum_pressure})
f.result()
# Set basic e-beam settings
escan.spotSize.value = 2.7
escan.accelVoltage.value = 5300 # V
# Without automatic blanker, the background subtraction doesn't work
if (model.hasVA(escan, "blanker") and # For simulator
None in escan.blanker.choices and escan.blanker.value
is not None):
logging.warning("Blanker set back to automatic")
escan.blanker.value = None
# Detect the holes/markers of the sample holder
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(
ANSI_MAGENTA,
"Do you want to execute the sample holder hole detection? [Y/n]"
)
if ans in YES_CHARS:
# Move Phenom sample stage next to expected hole position
sem_stage.moveAbsSync(aligndelphi.SHIFT_DETECTION)
ebeam_focus.moveAbsSync({"z": hole_focus})
# Set the FoV to almost 2mm
escan.horizontalFoV.value = escan.horizontalFoV.range[1]
input_col(
ANSI_BLUE,
"Please turn on the SEM stream and focus the SEM image. Then turn off the stream and press Enter..."
)
print_col(
ANSI_BLACK,
"Trying to detect the holes/markers, please wait...")
try:
hole_detectionf = aligndelphi.HoleDetection(
detector,
escan,
sem_stage,
ebeam_focus,
manual=True,
logpath=logpath)
new_first_hole, new_second_hole, new_hole_focus = hole_detectionf.result(
)
print_col(
ANSI_CYAN, "Values computed: 1st hole: " +
str(new_first_hole) + "\n"
" 2st hole: " + str(new_second_hole) +
"\n"
" hole focus: " + str(new_hole_focus))
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(
ANSI_MAGENTA,
"Do you want to update the calibration file with these values? [Y/n]"
)
if ans in YES_CHARS:
first_hole, second_hole, hole_focus = new_first_hole, new_second_hole, new_hole_focus
calibconf.set_sh_calib(shid, first_hole, second_hole,
hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot,
iscale_xy, ishear, resa, resb,
hfwa, scaleshift)
print_col(ANSI_BLACK, "Calibration file is updated.")
break
except IOError:
print_col(ANSI_RED, "Sample holder hole detection failed.")
else:
break
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(
ANSI_MAGENTA,
"Do you want to execute the SEM image calibration? [Y/n]")
if ans in YES_CHARS:
# Resetting shift parameters, to not take them into account during calib
blank_md = dict.fromkeys(aligndelphi.MD_CALIB_SEM, (0, 0))
escan.updateMetadata(blank_md)
# We measure the shift in the area just behind the hole where there
# are always some features plus the edge of the sample carrier. For
# that reason we use the focus measured in the hole detection step
sem_stage.moveAbsSync(aligndelphi.SHIFT_DETECTION)
ebeam_focus.moveAbsSync({"z": hole_focus})
try:
# Compute spot shift percentage
print_col(
ANSI_BLACK,
"Spot shift measurement in progress, please wait...")
f = aligndelphi.ScaleShiftFactor(detector, escan, logpath)
new_scaleshift = f.result()
# Compute resolution-related values.
print_col(ANSI_BLACK,
"Calculating resolution shift, please wait...")
resolution_shiftf = aligndelphi.ResolutionShiftFactor(
detector, escan, logpath)
new_resa, new_resb = resolution_shiftf.result()
# Compute HFW-related values
print_col(ANSI_BLACK,
"Calculating HFW shift, please wait...")
hfw_shiftf = aligndelphi.HFWShiftFactor(
detector, escan, logpath)
new_hfwa = hfw_shiftf.result()
print_col(
ANSI_CYAN, "Values computed: resolution-a: " +
str(new_resa) + "\n"
" resolution-b: " + str(new_resb) +
"\n"
" hfw-a: " + str(new_hfwa) + "\n"
" spot shift: " + str(new_scaleshift))
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(
ANSI_MAGENTA,
"Do you want to update the calibration file with these values? [Y/n]"
)
if ans in YES_CHARS:
resa, resb, hfwa, scaleshift = new_resa, new_resb, new_hfwa, new_scaleshift
calibconf.set_sh_calib(shid, first_hole, second_hole,
hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot,
iscale_xy, ishear, resa, resb,
hfwa, scaleshift)
print_col(ANSI_BLACK, "Calibration file is updated.")
break
except IOError:
print_col(ANSI_RED, "SEM image calibration failed.")
else:
break
# Update the SEM metadata to have the spots already at corrected place
escan.updateMetadata({
model.MD_RESOLUTION_SLOPE: resa,
model.MD_RESOLUTION_INTERCEPT: resb,
model.MD_HFW_SLOPE: hfwa,
model.MD_SPOT_SHIFT: scaleshift
})
f = sem_stage.moveAbs({"x": position[0], "y": position[1]})
f.result()
f = opt_stage.moveAbs({"x": 0, "y": 0})
f.result()
if hole_focus is not None:
good_focus = hole_focus - aligndelphi.GOOD_FOCUS_OFFSET
else:
good_focus = aligndelphi.SEM_KNOWN_FOCUS - aligndelphi.GOOD_FOCUS_OFFSET
f = ebeam_focus.moveAbs({"z": good_focus})
f.result()
# Set min fov
# We want to be as close as possible to the center when we are zoomed in
escan.horizontalFoV.value = escan.horizontalFoV.range[0]
pure_offset = None
# Start with the best optical focus known so far
f = focus.moveAbs({"z": opt_focus})
f.result()
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(
ANSI_MAGENTA,
"Do you want to execute the twin stage calibration? [Y/n]")
if ans in YES_CHARS:
# Configure CCD and e-beam to write CL spots
ccd.binning.value = ccd.binning.clip((4, 4))
ccd.resolution.value = ccd.resolution.range[1]
ccd.exposureTime.value = 900e-03
escan.scale.value = (1, 1)
escan.resolution.value = (1, 1)
escan.translation.value = (0, 0)
if not escan.rotation.readonly:
escan.rotation.value = 0
escan.shift.value = (0, 0)
escan.dwellTime.value = 5e-06
detector.data.subscribe(_discard_data)
print_col(
ANSI_BLUE,
"Please turn on the Optical stream, set Power to 0 Watt "
"and focus the image so you have a clearly visible spot.\n"
"Use the up and down arrows or the mouse to move the "
"optical focus and right and left arrows to move the SEM focus. "
"Then turn off the stream and press Enter...")
if not force_calib:
print_col(
ANSI_YELLOW,
"If you cannot see the whole source background (bright circle) "
"you may try to move to the already known offset position. \n"
"To do this press the R key at any moment and use I to go back "
"to the initial position.")
rollback_pos = (offset[0] * scaling[0],
offset[1] * scaling[1])
else:
rollback_pos = None
ar = ArrowFocus(sem_stage, focus, ebeam_focus,
ccd.depthOfField.value, 10e-6)
ar.focusByArrow(rollback_pos)
# Did the user adjust the ebeam-focus? If so, let's use this,
# as it's probably better than the focus for the hole.
new_ebeam_focus = ebeam_focus.position.value.get('z')
new_hole_focus = new_ebeam_focus + aligndelphi.GOOD_FOCUS_OFFSET
if not util.almost_equal(
new_hole_focus, hole_focus, atol=10e-6):
print_col(
ANSI_CYAN,
"Updating e-beam focus: %s (ie, hole focus: %s)" %
(new_ebeam_focus, new_hole_focus))
good_focus = new_ebeam_focus
hole_focus = new_hole_focus
detector.data.unsubscribe(_discard_data)
print_col(ANSI_BLACK,
"Twin stage calibration starting, please wait...")
try:
# TODO: the first point (at 0,0) isn't different from the next 4 points,
# excepted it might be a little harder to focus.
# => use the same code for all of them
align_offsetf = aligndelphi.AlignAndOffset(
ccd, detector, escan, sem_stage, opt_stage, focus,
logpath)
align_offset = align_offsetf.result()
new_opt_focus = focus.position.value.get('z')
# If the offset is large, it can prevent the SEM stage to follow
# the optical stage. If it's really large (eg > 1mm) it will
# even prevent from going to the calibration locations.
# So warn about this, as soon as we detect it. It could be
# caused either due to a mistake in the offset detection, or
# because the reference switch of the optical axis is not
# centered (enough) on the axis. In such case, a technician
# should open the sample holder and move the reference switch.
# Alternatively, we could try to be more clever and support
# the range of the tmcm axes to be defined per sample
# holder, and set some asymmetric range (to reflect the fact
# that 0 is not at the center).
for a, trans in zip(("x", "y"), align_offset):
# SEM pos = Opt pos + offset
rng_sem = sem_stage.axes[a].range
rng_opt = opt_stage.axes[a].range
if (rng_opt[0] + trans < rng_sem[0]
or rng_opt[1] + trans > rng_sem[1]):
logging.info(
"Stage align offset = %s, which could cause "
"moves on the SEM stage out of range (on axis %s)",
align_offset, a)
input_col(
ANSI_RED,
"Twin stage offset on axis %s is %g mm, which could cause moves out of range.\n"
"Check that the reference switch in the sample holder is properly at the center."
% (a, trans * 1e3))
def ask_user_to_focus(n):
detector.data.subscribe(_discard_data)
input_col(
ANSI_BLUE,
"About to calculate rotation and scaling (%d/4). "
% (n + 1, ) + "Please turn on the Optical stream, "
"set Power to 0 Watt and focus the image using the mouse "
"so you have a clearly visible spot. \n"
"If you do not see a spot nor the source background, "
"move the sem-stage from the command line by steps of 200um "
"in x and y until you can see the source background at the center. \n"
"Then turn off the stream and press Enter...")
# TODO: use ArrowFocus() too?
print_col(
ANSI_BLACK,
"Calculating rotation and scaling (%d/4), please wait..."
% (n + 1, ))
detector.data.unsubscribe(_discard_data)
f = aligndelphi.RotationAndScaling(
ccd,
detector,
escan,
sem_stage,
opt_stage,
focus,
align_offset,
manual=ask_user_to_focus,
logpath=logpath)
acc_offset, new_rotation, new_scaling = f.result()
# Offset is divided by scaling, since Convert Stage applies scaling
# also in the given offset
pure_offset = acc_offset
new_offset = ((acc_offset[0] / new_scaling[0]),
(acc_offset[1] / new_scaling[1]))
print_col(
ANSI_CYAN,
"Values computed: offset: " + str(new_offset) + "\n"
" scaling: " + str(new_scaling) + "\n"
" rotation: " + str(new_rotation) +
"\n"
" optical focus: " +
str(new_opt_focus))
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(
ANSI_MAGENTA,
"Do you want to update the calibration file with these values? [Y/n]"
)
if ans in YES_CHARS:
offset, scaling, rotation, opt_focus = new_offset, new_scaling, new_rotation, new_opt_focus
calibconf.set_sh_calib(shid, first_hole, second_hole,
hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot,
iscale_xy, ishear, resa, resb,
hfwa, scaleshift)
print_col(ANSI_BLACK, "Calibration file is updated.")
break
except IOError:
print_col(ANSI_RED, "Twin stage calibration failed.")
else:
break
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(
ANSI_MAGENTA,
"Do you want to execute the fine alignment? [Y/n]")
if ans in YES_CHARS:
# Return to the center so fine alignment can be executed just after calibration
f = opt_stage.moveAbs({"x": 0, "y": 0})
f.result()
if pure_offset is not None:
f = sem_stage.moveAbs({
"x": pure_offset[0],
"y": pure_offset[1]
})
elif offset is not None:
f = sem_stage.moveAbs({
"x": offset[0] * scaling[0],
"y": offset[1] * scaling[1]
})
else:
f = sem_stage.moveAbs({"x": position[0], "y": position[1]})
fof = focus.moveAbs({"z": opt_focus})
fef = ebeam_focus.moveAbs({"z": good_focus})
f.result()
fof.result()
fef.result()
# Run the optical fine alignment
# TODO: reuse the exposure time
# Configure e-beam to write CL spots
escan.horizontalFoV.value = escan.horizontalFoV.range[0]
escan.scale.value = (1, 1)
escan.resolution.value = (1, 1)
escan.translation.value = (0, 0)
if not escan.rotation.readonly:
escan.rotation.value = 0
escan.shift.value = (0, 0)
escan.dwellTime.value = 5e-06
detector.data.subscribe(_discard_data)
print_col(
ANSI_BLUE,
"Please turn on the Optical stream, set Power to 0 Watt "
"and focus the image so you have a clearly visible spot.\n"
"Use the up and down arrows or the mouse to move the "
"optical focus and right and left arrows to move the SEM focus. "
"Then turn off the stream and press Enter...")
ar = ArrowFocus(sem_stage, focus, ebeam_focus,
ccd.depthOfField.value, 10e-6)
ar.focusByArrow()
detector.data.unsubscribe(_discard_data)
print_col(ANSI_BLACK,
"Fine alignment in progress, please wait...")
# restore CCD settings (as the GUI/user might have changed them)
ccd.binning.value = (1, 1)
ccd.resolution.value = ccd.resolution.range[1]
ccd.exposureTime.value = 900e-03
# Center (roughly) the spot on the CCD
f = spot.CenterSpot(ccd, sem_stage, escan, spot.ROUGH_MOVE,
spot.STAGE_MOVE, detector.data)
dist, vect = f.result()
if dist is None:
logging.warning(
"Failed to find a spot, twin stage calibration might have failed"
)
try:
escan.horizontalFoV.value = 80e-06
f = align.FindOverlay(
(4, 4),
0.5, # s, dwell time
10e-06, # m, maximum difference allowed
escan,
ccd,
detector,
skew=True,
bgsub=True)
trans_val, cor_md = f.result()
trans_md, skew_md = cor_md
new_iscale = trans_md[model.MD_PIXEL_SIZE_COR]
new_irot = -trans_md[model.MD_ROTATION_COR] % (2 * math.pi)
new_ishear = skew_md[model.MD_SHEAR_COR]
new_iscale_xy = skew_md[model.MD_PIXEL_SIZE_COR]
print_col(
ANSI_CYAN,
"Values computed: scale: " + str(new_iscale) + "\n"
" rotation: " + str(new_irot) + "\n"
" scale-xy: " + str(new_iscale_xy) +
"\n"
" shear: " + str(new_ishear))
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(
ANSI_MAGENTA,
"Do you want to update the calibration file with these values? [Y/n]"
)
if ans in YES_CHARS:
iscale, irot, iscale_xy, ishear = new_iscale, new_irot, new_iscale_xy, new_ishear
calibconf.set_sh_calib(shid, first_hole, second_hole,
hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot,
iscale_xy, ishear, resa, resb,
hfwa, scaleshift)
print_col(ANSI_BLACK, "Calibration file is updated.")
break
except ValueError:
print_col(ANSI_RED, "Fine alignment failed.")
else:
break
except Exception:
logging.exception("Unexpected failure during calibration")
finally:
aligndelphi.restore_hw_settings(escan, ccd, hw_settings)
# Store the final version of the calibration file in the log folder
try:
shutil.copy(calibconf.file_path, logpath)
except Exception:
logging.info("Failed to log calibration file", exc_info=True)
if not keep_loaded:
# Eject the sample holder
print_col(
ANSI_BLACK,
"Calibration ended, now ejecting sample, please wait...")
f = chamber.moveAbs({"pressure": vented_pressure})
f.result()
ans = input_col(ANSI_MAGENTA, "Press Enter to close")
def __init__(self, name, data, *args, **kwargs):
"""
name (string)
data (model.DataArray(Shadow) of shape (YX) or list of such DataArray(Shadow)).
The metadata MD_POS, MD_AR_POLE and MD_POL_MODE should be provided
"""
if not isinstance(data, collections.Iterable):
data = [data] # from now it's just a list of DataArray
# TODO: support DAS, as a "delayed loading" by only calling .getData()
# when the projection for the particular data needs to be computed (or
# .raw needs to be accessed?)
# Ensure all the data is a DataArray, as we don't handle (yet) DAS
data = [
d.getData() if isinstance(d, model.DataArrayShadow) else d
for d in data
]
# find positions of each acquisition
# (float, float, str or None)) -> DataArray: position on SEM + polarization -> data
self._pos = {}
sempositions = set()
polpositions = set()
for d in data:
try:
sempos_cur = d.metadata[MD_POS]
# When reading data: floating point error (slightly different keys for same ebeam pos)
# -> check if there is already a position specified, which is very close by
# (and therefore the same ebeam pos) and replace with that ebeam position
# (e.g. all polarization positions for the same ebeam positions will have exactly the same ebeam pos)
for sempos in sempositions:
if almost_equal(sempos_cur[0], sempos[0]) and almost_equal(
sempos_cur[1], sempos[1]):
sempos_cur = sempos
break
self._pos[sempos_cur + (d.metadata.get(MD_POL_MODE, None),
)] = img.ensure2DImage(d)
sempositions.add(sempos_cur)
if MD_POL_MODE in d.metadata:
polpositions.add(d.metadata.get(MD_POL_MODE))
except KeyError:
logging.info("Skipping DataArray without known position")
# Cached conversion of the CCD image to polar representation
# TODO: automatically fill it in a background thread
self._polar = {} # dict tuple (float, float, str or None) -> DataArray
# SEM position VA
# SEM position displayed, (None, None) == no point selected (x, y)
self.point = model.VAEnumerated(
(None, None),
choices=frozenset([(None, None)] + list(sempositions)))
if self._pos:
# Pick one point, e.g., top-left
bbtl = (min(x for x, y in sempositions if x is not None),
min(y for x, y in sempositions if y is not None))
# top-left point is the closest from the bounding-box top-left
def dis_bbtl(v):
try:
return math.hypot(bbtl[0] - v[0], bbtl[1] - v[1])
except TypeError:
return float("inf") # for None, None
self.point.value = min(sempositions, key=dis_bbtl)
# no need for init=True, as Stream.__init__ will update the image
self.point.subscribe(self._onPoint)
# polarization VA
# check if any polarization analyzer data, set([]) == no analyzer data (pol)
if polpositions:
# use first entry in acquisition to populate VA (acq could have 1 or 6 pol pos)
self.polarization = model.VAEnumerated(list(polpositions)[0],
choices=polpositions)
self.polarization.subscribe(self._onPolarization)
if "acq_type" not in kwargs:
kwargs["acq_type"] = model.MD_AT_AR
super(StaticARStream, self).__init__(name, list(self._pos.values()),
*args, **kwargs)
def __init__(self, name, data, *args, **kwargs):
"""
:param name: (string)
:param data: (model.DataArray(Shadow) of shape (YX) or list of such DataArray(Shadow)).
The metadata MD_POS, MD_AR_POLE and MD_POL_MODE should be provided
"""
if not isinstance(data, collections.Iterable):
data = [data] # from now it's just a list of DataArray
# TODO: support DAS, as a "delayed loading" by only calling .getData()
# when the projection for the particular data needs to be computed (or
# .raw needs to be accessed?)
# Ensure all the data is a DataArray, as we don't handle (yet) DAS
data = [d.getData() if isinstance(d, model.DataArrayShadow) else d for d in data]
# find positions of each acquisition
# (float, float, str or None)) -> DataArray: position on SEM + polarization -> data
self._pos = {}
sempositions = set()
polpositions = set()
for d in data:
try:
sempos_cur = d.metadata[MD_POS]
# When reading data: floating point error (slightly different keys for same ebeam pos)
# -> check if there is already a position specified, which is very close by
# (and therefore the same ebeam pos) and replace with that ebeam position
# (e.g. all polarization positions for the same ebeam positions will have exactly the same ebeam pos)
for sempos in sempositions:
if almost_equal(sempos_cur[0], sempos[0]) and almost_equal(sempos_cur[1], sempos[1]):
sempos_cur = sempos
break
self._pos[sempos_cur + (d.metadata.get(MD_POL_MODE, None),)] = img.ensure2DImage(d)
sempositions.add(sempos_cur)
if MD_POL_MODE in d.metadata:
polpositions.add(d.metadata[MD_POL_MODE])
except KeyError:
logging.info("Skipping DataArray without known position")
# SEM position VA
# SEM position displayed, (None, None) == no point selected (x, y)
self.point = model.VAEnumerated((None, None),
choices=frozenset([(None, None)] + list(sempositions)))
if self._pos:
# Pick one point, e.g., top-left
bbtl = (min(x for x, y in sempositions if x is not None),
min(y for x, y in sempositions if y is not None))
# top-left point is the closest from the bounding-box top-left
def dis_bbtl(v):
try:
return math.hypot(bbtl[0] - v[0], bbtl[1] - v[1])
except TypeError:
return float("inf") # for None, None
self.point.value = min(sempositions, key=dis_bbtl)
# check if any polarization analyzer data, (None) == no analyzer data (pol)
if polpositions:
# Check that for every position, all the polarizations are available,
# as the GUI expects all the combinations possible, and weird errors
# will happen when one is missing.
for pos in sempositions:
for pol in polpositions:
if pos + (pol,) not in self._pos:
logging.warning("Polarization data is not complete: missing %s,%s/%s",
pos[0], pos[1], pol)
# use first entry in acquisition to populate VA (acq could have 1 or 6 pol pos)
current_pol = util.sorted_according_to(polpositions, POL_POSITIONS)[0]
self.polarization = model.VAEnumerated(current_pol, choices=polpositions)
# Add a polarimetry VA containing the polarimetry image results.
# Note: Polarimetry analysis are only possible if all 6 images per ebeam pos exist.
# Also check if arpolarimetry package can be imported as might not be installed.
if polpositions >= set(POL_POSITIONS) and arpolarimetry:
self.polarimetry = model.VAEnumerated(MD_POL_S0, choices=set(POL_POSITIONS_RESULTS))
if "acq_type" not in kwargs:
kwargs["acq_type"] = model.MD_AT_AR
super(StaticARStream, self).__init__(name, list(self._pos.values()), *args, **kwargs)
def _DoBinaryFocus(future, detector, emt, focus, dfbkg, good_focus, rng_focus):
"""
Iteratively acquires an optical image, measures its focus level and adjusts
the optical focus with respect to the focus level.
future (model.ProgressiveFuture): Progressive future provided by the wrapper
detector: model.DigitalCamera or model.Detector
emt (None or model.Emitter): In case of a SED this is the scanner used
focus (model.Actuator): The focus actuator (with a "z" axis)
dfbkg (model.DataFlow): dataflow of se- or bs- detector
good_focus (float): if provided, an already known good focus position to be
taken into consideration while autofocusing
rng_focus (tuple of floats): if provided, the search of the best focus position is limited
within this range
returns:
(float): Focus position (m)
(float): Focus level
raises:
CancelledError if cancelled
IOError if procedure failed
"""
# TODO: dfbkg is mis-named, as it's the dataflow to use to _activate_ the
# emitter. It's necessary to acquire the background, as otherwise we assume
# the emitter is always active, but during background acquisition, that
# emitter is explicitly _disabled_.
# => change emt to "scanner", and "dfbkg" to "emitter". Or pass a stream?
# Note: the emt is almost not used, only to estimate completion time,
# and read the depthOfField.
# It does a dichotomy search on the focus level. In practice, it means it
# will start going into the direction that increase the focus with big steps
# until the focus decreases again. Then it'll bounce back and forth with
# smaller and smaller steps.
# The tricky parts are:
# * it's hard to estimate the focus level (on an arbitrary image)
# * two acquisitions at the same focus position can have (slightly) different
# focus levels (due to noise and sample degradation)
# * if the focus actuator is not precise (eg, open loop), it's hard to
# even go back to the same focus position when wanted
logging.debug("Starting binary autofocus on detector %s...", detector.name)
try:
# Big timeout, most important being that it's shorter than eternity
timeout = 3 + 2 * estimateAcquisitionTime(detector, emt)
# use the .depthOfField on detector or emitter as maximum stepsize
avail_depths = (detector, emt)
if model.hasVA(emt, "dwellTime"):
# Hack in case of using the e-beam with a DigitalCamera detector.
# All the digital cameras have a depthOfField, which is updated based
# on the optical lens properties... but the depthOfField in this
# case depends on the e-beam lens.
# TODO: or better rely on which component the focuser affects? If it
# affects (also) the emitter, use this one first? (but in the
# current models the focusers affects nothing)
avail_depths = (emt, detector)
for c in avail_depths:
if model.hasVA(c, "depthOfField"):
dof = c.depthOfField.value
break
else:
logging.debug("No depth of field info found")
dof = 1e-6 # m, not too bad value
logging.debug("Depth of field is %f", dof)
min_step = dof / 2
# adjust to rng_focus if provided
rng = focus.axes["z"].range
if rng_focus:
rng = (max(rng[0], rng_focus[0]), min(rng[1], rng_focus[1]))
max_step = (rng[1] - rng[0]) / 2
if max_step <= 0:
raise ValueError("Unexpected focus range %s" % (rng,))
max_reached = False # True once we've passed the maximum level (ie, start bouncing)
# It's used to cache the focus level, to avoid reacquiring at the same
# position. We do it only for the 'rough' max search because for the fine
# search, the actuator and acquisition delta are likely to play a role
focus_levels = {} # focus pos (float) -> focus level (float)
best_pos = focus.position.value['z']
best_fm = 0
last_pos = None
# Pick measurement method based on the heuristics that SEM detectors
# are typically just a point (ie, shape == data depth).
# TODO: is this working as expected? Alternatively, we could check
# MD_DET_TYPE.
if len(detector.shape) > 1:
logging.debug("Using Optical method to estimate focus")
Measure = MeasureOpticalFocus
else:
logging.debug("Using SEM method to estimate focus")
Measure = MeasureSEMFocus
step_factor = 2 ** 7
if good_focus is not None:
current_pos = focus.position.value['z']
image = AcquireNoBackground(detector, dfbkg, timeout)
fm_current = Measure(image)
logging.debug("Focus level at %f is %f", current_pos, fm_current)
focus_levels[current_pos] = fm_current
focus.moveAbsSync({"z": good_focus})
good_focus = focus.position.value["z"]
image = AcquireNoBackground(detector, dfbkg, timeout)
fm_good = Measure(image)
logging.debug("Focus level at %f is %f", good_focus, fm_good)
focus_levels[good_focus] = fm_good
last_pos = good_focus
if fm_good < fm_current:
# Move back to current position if good_pos is not that good
# after all
focus.moveAbsSync({"z": current_pos})
# it also means we are pretty close
step_factor = 2 ** 4
if step_factor * min_step > max_step:
# Large steps would be too big. We can reduce step_factor and/or
# min_step. => let's take our time, and maybe find finer focus
min_step = max_step / step_factor
logging.debug("Reducing min step to %g", min_step)
# TODO: to go a bit faster, we could use synchronised acquisition on
# the detector (if it supports it)
# TODO: we could estimate the quality of the autofocus by looking at the
# standard deviation of the the focus levels (and the standard deviation
# of the focus levels measured for the same focus position)
logging.debug("Step factor used for autofocus: %g", step_factor)
step_cntr = 1
while step_factor >= 1 and step_cntr <= MAX_STEPS_NUMBER:
# TODO: update the estimated time (based on how long it takes to
# move + acquire, and how many steps are approximately left)
# Start at the current focus position
center = focus.position.value['z']
# Don't redo the acquisition either if we've just done it, or if it
# was already done and we are still doing a rough search
if (not max_reached or last_pos == center) and center in focus_levels:
fm_center = focus_levels[center]
else:
image = AcquireNoBackground(detector, dfbkg, timeout)
fm_center = Measure(image)
logging.debug("Focus level (center) at %f is %f", center, fm_center)
focus_levels[center] = fm_center
last_pos = center
# Move to right position
right = center + step_factor * min_step
right = max(rng[0], min(right, rng[1])) # clip
if not max_reached and right in focus_levels:
fm_right = focus_levels[right]
else:
focus.moveAbsSync({"z": right})
right = focus.position.value["z"]
last_pos = right
image = AcquireNoBackground(detector, dfbkg, timeout)
fm_right = Measure(image)
logging.debug("Focus level (right) at %f is %f", right, fm_right)
focus_levels[right] = fm_right
# Move to left position
left = center - step_factor * min_step
left = max(rng[0], min(left, rng[1])) # clip
if not max_reached and left in focus_levels:
fm_left = focus_levels[left]
else:
focus.moveAbsSync({"z": left})
left = focus.position.value["z"]
last_pos = left
image = AcquireNoBackground(detector, dfbkg, timeout)
fm_left = Measure(image)
logging.debug("Focus level (left) at %f is %f", left, fm_left)
focus_levels[left] = fm_left
fm_range = (fm_left, fm_center, fm_right)
if all(almost_equal(fm_left, fm, rtol=1e-6) for fm in fm_range[1:]):
logging.debug("All focus levels identical, picking the middle one")
# Most probably the images are all noise, or they are not affected
# by the focus. In any case, the best is to not move the focus,
# so let's "center" on it. That's better than the default behaviour
# which would tend to pick "left" because that's the first one.
i_max = 1
best_pos, best_fm = center, fm_center
else:
pos_range = (left, center, right)
best_fm = max(fm_range)
i_max = fm_range.index(best_fm)
best_pos = pos_range[i_max]
if future._autofocus_state == CANCELLED:
raise CancelledError()
if left == right:
logging.info("Seems to have reached minimum step size (at %g m)", 2 * step_factor * min_step)
break
# if best focus was found at the center
if i_max == 1:
step_factor /= 2
if not max_reached:
logging.debug("Now zooming in on improved focus")
max_reached = True
elif (rng[0] > best_pos - step_factor * min_step or
rng[1] < best_pos + step_factor * min_step):
step_factor /= 1.5
logging.debug("Reducing step factor to %g because the focus (%g) is near range limit %s",
step_factor, best_pos, rng)
if step_factor <= 8:
max_reached = True # Force re-checking data
focus.moveAbsSync({"z": best_pos})
step_cntr += 1
worst_fm = min(focus_levels.values())
if step_cntr == MAX_STEPS_NUMBER:
logging.info("Auto focus gave up after %d steps @ %g m", step_cntr, best_pos)
elif (best_fm - worst_fm) < best_fm * 0.5:
# We can be confident of the data if there is a "big" (50%) difference
# between the focus levels.
logging.info("Auto focus indecisive but picking level %g @ %g m (lowest = %g)",
best_fm, best_pos, worst_fm)
else:
logging.info("Auto focus found best level %g @ %g m", best_fm, best_pos)
return best_pos, best_fm
except CancelledError:
# Go to the best position known so far
focus.moveAbsSync({"z": best_pos})
finally:
with future._autofocus_lock:
if future._autofocus_state == CANCELLED:
raise CancelledError()
future._autofocus_state = FINISHED
def getFullImage(self):
"""
return (2D DataArray): same dtype as the tiles, with shape corresponding to the bounding box.
"""
tiles = self.tiles
# Compute the bounding box of each tile and the global bounding box
# Get a fixed pixel size by using the first one
# TODO: use the mean, in case they are all slightly different due to
# correction?
pxs = tiles[0].metadata[model.MD_PIXEL_SIZE]
tbbx_phy = [] # tuples of ltrb in physical coordinates
for t in tiles:
c = t.metadata[model.MD_POS]
w = t.shape[-1], t.shape[-2]
if not util.almost_equal(pxs[0], t.metadata[model.MD_PIXEL_SIZE][0], rtol=0.01):
logging.warning("Tile @ %s has a unexpected pixel size (%g vs %g)",
c, t.metadata[model.MD_PIXEL_SIZE][0], pxs[0])
bbx = (c[0] - (w[0] * pxs[0] / 2), c[1] - (w[1] * pxs[1] / 2),
c[0] + (w[0] * pxs[0] / 2), c[1] + (w[1] * pxs[1] / 2))
tbbx_phy.append(bbx)
gbbx_phy = (min(b[0] for b in tbbx_phy), min(b[1] for b in tbbx_phy),
max(b[2] for b in tbbx_phy), max(b[3] for b in tbbx_phy))
# Compute the bounding-boxes in pixel coordinates
tbbx_px = []
# that's the origin (Y is max as Y is inverted)
glt = gbbx_phy[0], gbbx_phy[3]
for bp, t in zip(tbbx_phy, tiles):
lt = (int(round((bp[0] - glt[0]) / pxs[0])),
int(round(-(bp[3] - glt[1]) / pxs[1])))
w = t.shape[-1], t.shape[-2]
bbx = (lt[0], lt[1],
lt[0] + w[0], lt[1] + w[1])
tbbx_px.append(bbx)
gbbx_px = (min(b[0] for b in tbbx_px), min(b[1] for b in tbbx_px),
max(b[2] for b in tbbx_px), max(b[3] for b in tbbx_px))
assert gbbx_px[0] == gbbx_px[1] == 0
if numpy.greater(gbbx_px[-2:], 4 * numpy.sum(tbbx_px[-2:])).any():
# Overlap > 50% or missing tiles
logging.warning("Global area much bigger than sum of tile areas")
# Paste each tile
logging.debug("Generating global image of size %dx%d px",
gbbx_px[-2], gbbx_px[-1])
im = numpy.empty((gbbx_px[-1], gbbx_px[-2]), dtype=tiles[0].dtype)
# Use minimum of the values in the tiles for background
im[:] = numpy.amin(tiles)
for b, t in zip(tbbx_px, tiles):
im[b[1]:b[1] + t.shape[0], b[0]:b[0] + t.shape[1]] = t
# TODO: border
# Update metadata
# TODO: check this is also correct based on lt + half shape * pxs
c_phy = ((gbbx_phy[0] + gbbx_phy[2]) / 2,
(gbbx_phy[1] + gbbx_phy[3]) / 2)
md = tiles[0].metadata.copy()
md[model.MD_POS] = c_phy
md[model.MD_DIMS] = "YX"
return model.DataArray(im, md)
def getFullImage(self):
"""
return (2D DataArray): same dtype as the tiles, with shape corresponding to the bounding box.
"""
tiles = self.tiles
# Compute the bounding box of each tile and the global bounding box
# Get a fixed pixel size by using the first one
# TODO: use the mean, in case they are all slightly different due to
# correction?
pxs = tiles[0].metadata[model.MD_PIXEL_SIZE]
tbbx_phy = [] # tuples of ltrb in physical coordinates
for t in tiles:
c = t.metadata[model.MD_POS]
w = t.shape[-1], t.shape[-2]
if not util.almost_equal(pxs[0], t.metadata[model.MD_PIXEL_SIZE][0], rtol=0.01):
logging.warning("Tile @ %s has a unexpected pixel size (%g vs %g)",
c, t.metadata[model.MD_PIXEL_SIZE][0], pxs[0])
bbx = (c[0] - (w[0] * pxs[0] / 2), c[1] - (w[1] * pxs[1] / 2),
c[0] + (w[0] * pxs[0] / 2), c[1] + (w[1] * pxs[1] / 2))
tbbx_phy.append(bbx)
gbbx_phy = (min(b[0] for b in tbbx_phy), min(b[1] for b in tbbx_phy),
max(b[2] for b in tbbx_phy), max(b[3] for b in tbbx_phy))
# Compute the bounding-boxes in pixel coordinates
tbbx_px = []
# that's the origin (Y is max as Y is inverted)
glt = gbbx_phy[0], gbbx_phy[3]
for bp, t in zip(tbbx_phy, tiles):
lt = (int(round((bp[0] - glt[0]) / pxs[0])),
int(round(-(bp[3] - glt[1]) / pxs[1])))
w = t.shape[-1], t.shape[-2]
bbx = (lt[0], lt[1],
lt[0] + w[0], lt[1] + w[1])
tbbx_px.append(bbx)
gbbx_px = (min(b[0] for b in tbbx_px), min(b[1] for b in tbbx_px),
max(b[2] for b in tbbx_px), max(b[3] for b in tbbx_px))
assert gbbx_px[0] == gbbx_px[1] == 0
if numpy.greater(gbbx_px[-2:], 4 * numpy.sum(tbbx_px[-2:])).any():
# Overlap > 50% or missing tiles
logging.warning("Global area much bigger than sum of tile areas")
# Weave tiles by using a smooth gradient. The part of the tile that does not overlap
# with any previous tiles is inserted into the part of the
# ovv image that is still empty. This part is determined by a mask, which indicates
# the parts of the image that already contain image data (True) and the ones that are still
# empty (False). For the overlapping parts, the tile is multiplied with weights corresponding
# to a gradient that has its maximum at the center of the tile and
# smoothly decreases toward the edges. The function for creating the weights is
# a distance measure resembling the maximum-norm, i.e. equidistant points lie
# on a rectangle (instead of a circle like for the euclidean norm). Additionally,
# the x and y values generating this norm are raised to the power of 6 to
# create a steeper gradient. The value 6 is quite arbitrary and was found to give
# good results during experimentation.
# The part of the overview image that overlaps with the new tile is multiplied with the
# complementary weights (1 - weights) and the weighted overlapping parts of the new tile and
# the ovv image are added, so the resulting image contains a gradient in the overlapping regions
# between all the tiles that have been inserted before and the newly inserted tile.
# Paste each tile
logging.debug("Generating global image of size %dx%d px",
gbbx_px[-2], gbbx_px[-1])
im = numpy.empty((gbbx_px[-1], gbbx_px[-2]), dtype=tiles[0].dtype)
# Use minimum of the values in the tiles for background
im[:] = numpy.amin(tiles)
# The mask is multiplied with the tile, thereby creating a tile with a gradient
mask = numpy.zeros((gbbx_px[-1], gbbx_px[-2]), dtype=numpy.bool)
for b, t in zip(tbbx_px, tiles):
# Part of image overlapping with tile
roi = im[b[1]:b[1] + t.shape[0], b[0]:b[0] + t.shape[1]]
moi = mask[b[1]:b[1] + t.shape[0], b[0]:b[0] + t.shape[1]]
# Insert image at positions that are still empty
roi[~moi] = t[~moi]
# Create gradient in overlapping region. Ratio between old image and new tile values determined by
# distance to the center of the tile
# Create weight matrix with decreasing values from its center that
# has the same size as the tile.
sz = numpy.array(roi.shape)
hh, hw = sz / 2 # half-height, half-width
x = numpy.linspace(-hw, hw, sz[1])
y = numpy.linspace(-hh, hh, sz[0])
xx, yy = numpy.meshgrid((x / hw) ** 6, (y / hh) ** 6)
w = numpy.maximum(xx, yy)
# Hardcoding a weight function is quite arbitrary and might result in
# suboptimal solutions in some cases.
# Alternatively, different weights might be used. One option would be to select
# a fixed region on the sides of the image, e.g. 20% (expected overlap), and
# only apply a (linear) gradient to these parts, while keeping the new tile for the
# rest of the region. However, this approach does not solve the hardcoding problem
# since the overlap region is still arbitrary. Future solutions might adaptively
# select the this region.
# Use weights to create gradient in overlapping region
roi[moi] = (t * (1 - w))[moi] + (roi * w)[moi]
# Update mask
mask[b[1]:b[1] + t.shape[0], b[0]:b[0] + t.shape[1]] = True
# Update metadata
# TODO: check this is also correct based on lt + half shape * pxs
c_phy = ((gbbx_phy[0] + gbbx_phy[2]) / 2,
(gbbx_phy[1] + gbbx_phy[3]) / 2)
md = tiles[0].metadata.copy()
md[model.MD_POS] = c_phy
md[model.MD_DIMS] = "YX"
return model.DataArray(im, md)
def move_abs(comp_name, moves, check_distance=True):
"""
move (in absolute) the axis of the given component to the specified position
comp_name (str): name of the component
check_distance (bool): if the axis is in meters, check that the move is not
too big.
moves (dict str -> str): axis -> position (as text)
"""
component = get_component(comp_name)
act_mv = {} # axis -> value
for axis_name, str_position in moves.items():
try:
if axis_name not in component.axes:
raise ValueError("Actuator %s has no axis '%s'" % (comp_name, axis_name))
ad = component.axes[axis_name]
except (TypeError, AttributeError):
raise ValueError("Component %s is not an actuator" % comp_name)
# Allow the user to indicate the position via the user-friendly choice entry
position = None
if (hasattr(ad, "choices") and isinstance(ad.choices, dict)):
for key, value in ad.choices.items():
if value == str_position:
logging.info("Converting '%s' into %s", str_position, key)
position = key
# Even if it's a big distance, we don't complain as it's likely
# that all choices are safe
break
if position is None:
if ad.unit == "m":
try:
position = float(str_position)
except ValueError:
raise ValueError("Position '%s' cannot be converted to a number" % str_position)
# compare to the current position, to see if the new position sounds reasonable
cur_pos = component.position.value[axis_name]
if check_distance and abs(cur_pos - position) > MAX_DISTANCE:
raise IOError("Distance of %f m is too big (> %f m), use '--big-distance' to allow the move." %
(abs(cur_pos - position), MAX_DISTANCE))
else:
position = convert_to_object(str_position)
# If only a couple of positions are possible, and asking for a float,
# avoid the rounding error by looking for the closest possible
if (isinstance(position, numbers.Real) and
hasattr(ad, "choices") and
isinstance(ad.choices, collections.Iterable) and
position not in ad.choices):
closest = util.find_closest(position, ad.choices)
if util.almost_equal(closest, position, rtol=1e-3):
logging.debug("Adjusting value %.15g to %.15g", position, closest)
position = closest
act_mv[axis_name] = position
logging.info(u"Will move %s.%s to %s", comp_name, axis_name,
units.readable_str(position, ad.unit, sig=3))
try:
m = component.moveAbs(act_mv)
try:
m.result(120)
except KeyboardInterrupt:
logging.warning("Cancelling absolute move of component %s", comp_name)
m.cancel()
raise
except Exception as exc:
raise IOError("Failed to move component %s to %s: %s" %
(comp_name, act_mv, exc))
def move_abs(comp_name, moves, check_distance=True):
"""
move (in absolute) the axis of the given component to the specified position
comp_name (str): name of the component
check_distance (bool): if the axis is in meters, check that the move is not
too big.
moves (dict str -> str): axis -> position (as text)
"""
component = get_component(comp_name)
act_mv = {} # axis -> value
for axis_name, str_position in moves.items():
try:
if axis_name not in component.axes:
raise ValueError("Actuator %s has no axis '%s'" % (comp_name, axis_name))
ad = component.axes[axis_name]
except (TypeError, AttributeError):
raise ValueError("Component %s is not an actuator" % comp_name)
# Allow the user to indicate the position via the user-friendly choice entry
position = None
if hasattr(ad, "choices") and isinstance(ad.choices, dict):
for key, value in ad.choices.items():
if value == str_position:
logging.info("Converting '%s' into %s", str_position, key)
position = key
# Even if it's a big distance, we don't complain as it's likely
# that all choices are safe
break
if position is None:
if ad.unit == "m":
try:
position = float(convert_to_object(str_position))
except ValueError:
raise ValueError("Position '%s' cannot be converted to a number" % str_position)
# compare to the current position, to see if the new position sounds reasonable
cur_pos = component.position.value[axis_name]
if check_distance and abs(cur_pos - position) > MAX_DISTANCE:
raise IOError("Distance of %f m is too big (> %f m), use '--big-distance' to allow the move." %
(abs(cur_pos - position), MAX_DISTANCE))
else:
position = convert_to_object(str_position)
# If only a couple of positions are possible, and asking for a float,
# avoid the rounding error by looking for the closest possible
if (isinstance(position, numbers.Real) and
hasattr(ad, "choices") and
isinstance(ad.choices, collections.Iterable) and
position not in ad.choices):
closest = util.find_closest(position, ad.choices)
if util.almost_equal(closest, position, rtol=1e-3):
logging.debug("Adjusting value %.15g to %.15g", position, closest)
position = closest
act_mv[axis_name] = position
if isinstance(position, numbers.Real):
pos_pretty = units.readable_str(position, ad.unit, sig=3)
else:
pos_pretty = "%s" % (position,)
logging.info(u"Will move %s.%s to %s", comp_name, axis_name, pos_pretty)
try:
m = component.moveAbs(act_mv)
try:
m.result(120)
except KeyboardInterrupt:
logging.warning("Cancelling absolute move of component %s", comp_name)
m.cancel()
raise
except Exception as exc:
raise IOError("Failed to move component %s to %s: %s" %
(comp_name, act_mv, exc))
