def test_acq_getScalingTable(self):
"""Get the scaling table (correction for mapping vertical px with timestamps)
for the streak Time Range chosen for one sweep."""
# test a first value
self.streakunit.timeRange.value = util.find_closest(
0.000000002, self.streakunit.timeRange.choices) # 2ns
self.streakunit.streakMode.value = True
# Note: RemoteEx automatically stops and restarts "Live" acq when changing settings
img = self.readoutcam.data.get()
self.assertIn(model.MD_TIME_LIST, img.metadata)
self.assertIsNotNone(img.metadata[model.MD_TIME_LIST])
# check first value in table is the same order as the conversion factor
# the quotient should be greater than zero
firstCorrectedValue = img.metadata[model.MD_TIME_LIST][0]
conversionFactor = self.streakunit.timeRangeFactor
self.assertGreater(firstCorrectedValue / conversionFactor, 0)
# test a second value
# test a second value)
self.streakunit.timeRange.value = util.find_closest(
0.001, self.streakunit.timeRange.choices) # 1ms
img = self.readoutcam.data.get()
self.assertIn(model.MD_TIME_LIST, img.metadata)
self.assertIsNotNone(img.metadata[model.MD_TIME_LIST])
# check first value in table is the same order as the conversion factor
# the quotient should be greater than zero
firstCorrectedValue = img.metadata[model.MD_TIME_LIST][0]
conversionFactor = self.streakunit.timeRangeFactor
self.assertGreater(firstCorrectedValue / conversionFactor, 0)
# check that scaling correction is not included when image is acquired in Focus mode
# Note: In case we only acquire images in operate mode, we can skip that test.
self.streakunit.streakMode.value = False
img = self.readoutcam.data.get()
self.assertNotIn(model.MD_TIME_LIST, img.metadata)
self.assertFalse(img.metadata[model.MD_STREAK_MODE])
# change again to operate mode
self.streakunit.streakMode.value = True
img = self.readoutcam.data.get()
self.assertIn(model.MD_TIME_LIST, img.metadata)
self.assertIsNotNone(img.metadata[model.MD_TIME_LIST])
# check first value in table is the same order as the conversion factor
# the quotient should be greater than zero
firstCorrectedValue = img.metadata[model.MD_TIME_LIST][0]
conversionFactor = self.streakunit.timeRangeFactor
self.assertGreater(firstCorrectedValue / conversionFactor, 0)
def test_acq_getScalingTable(self):
"""Get the scaling table (correction for mapping vertical px with timestamps)
for the streak Time Range chosen for one sweep."""
# test a first value
self.streakunit.timeRange.value = util.find_closest(0.000000002, self.streakunit.timeRange.choices) # 2ns
self.streakunit.streakMode.value = True
# Note: RemoteEx automatically stops and restarts "Live" acq when changing settings
img = self.readoutcam.data.get()
self.assertIn(model.MD_TIME_LIST, img.metadata)
self.assertIsNotNone(img.metadata[model.MD_TIME_LIST])
# check first value in table is the same order as the conversion factor
# the quotient should be greater than zero
firstCorrectedValue = img.metadata[model.MD_TIME_LIST][0]
conversionFactor = self.streakunit.timeRangeFactor
self.assertGreater(firstCorrectedValue/conversionFactor, 0)
# test a second value
# test a second value)
self.streakunit.timeRange.value = util.find_closest(0.001, self.streakunit.timeRange.choices) # 1ms
img = self.readoutcam.data.get()
self.assertIn(model.MD_TIME_LIST, img.metadata)
self.assertIsNotNone(img.metadata[model.MD_TIME_LIST])
# check first value in table is the same order as the conversion factor
# the quotient should be greater than zero
firstCorrectedValue = img.metadata[model.MD_TIME_LIST][0]
conversionFactor = self.streakunit.timeRangeFactor
self.assertGreater(firstCorrectedValue/conversionFactor, 0)
# check that scaling correction is not included when image is acquired in Focus mode
# Note: In case we only acquire images in operate mode, we can skip that test.
self.streakunit.streakMode.value = False
img = self.readoutcam.data.get()
self.assertNotIn(model.MD_TIME_LIST, img.metadata)
self.assertFalse(img.metadata[model.MD_STREAK_MODE])
# change again to operate mode
self.streakunit.streakMode.value = True
img = self.readoutcam.data.get()
self.assertIn(model.MD_TIME_LIST, img.metadata)
self.assertIsNotNone(img.metadata[model.MD_TIME_LIST])
# check first value in table is the same order as the conversion factor
# the quotient should be greater than zero
firstCorrectedValue = img.metadata[model.MD_TIME_LIST][0]
conversionFactor = self.streakunit.timeRangeFactor
self.assertGreater(firstCorrectedValue/conversionFactor, 0)
def test_acq_Live_RingBuffer_subscribe(self):
"""Acquire single image and receive it via the dataport."""
# Note: AcqStop can be called multiple times even if the acq is already stopped without causing an error
# However, AcqStart can be only called once and raises an error if called while an acq is running.
# AcqStop is not an asynchronous command. But it takes time until the status of the async command
# "AcqStart" is properly finished.
# Changing settings is not async. RemoteEx blocks as long as the settings are changed.
# RemoteEx also stops the "Live" mode if a settings change is requested but does not restarts the "Live" mode.
self.streakunit.streakMode.value = True
self.streakunit.timeRange.value = util.find_closest(0.000000002, self.streakunit.timeRange.choices)
self.streakunit.MCPGain.value = 2
self.readoutcam.exposureTime.value = 0.1 # 100ms
time.sleep(1)
# start Live mode
# and subscribe to dataflow afterwards in order to request one image while acq in Live mode is already running
# The acq should be automatically stopped and restarted, otherwise a RemoteEx error will be received.
# error returned: ['7', 'AcqStart', 'async command pending', 'HAcq_mLive']
self.streakcam.StartAcquisition(self.readoutcam.acqMode) # acquire images
def callback(dataflow, image):
# self.streakcam.AcqAcqMonitor("Off") # TODO?
self.readoutcam.data.unsubscribe(callback)
# Note: MCPGain set to 0 is handled by stream not by driver except when changing from
# "Operate" mode to "Focus" mode
size = self.readoutcam.resolution.value
self.assertEqual(image.shape, size[::-1]) # invert size
self.assertIn(model.MD_EXP_TIME, image.metadata)
logging.debug("Got image.")
self.readoutcam.data.subscribe(callback)
time.sleep(5)
def test_acq_wavelengthTable(self):
"""Get the scaling table (correction for mapping vertical px with timestamps)
for the streak Time Range chosen for one sweep."""
# test a first value
self.readoutcam.binning.value = (1, 1)
self.streakunit.timeRange.value = util.find_closest(0.000000002, self.streakunit.timeRange.choices) # 2ns
self.streakunit.streakMode.value = True
# Note: RemoteEx automatically stops and restarts "Live" acq when changing settings
img = self.readoutcam.data.get()
wl_list_bin1 = img.metadata[model.MD_WL_LIST]
self.assertIn(model.MD_TIME_LIST, img.metadata)
self.assertIn(model.MD_WL_LIST, img.metadata)
# check wavelength list changes when changing binning
self.readoutcam.binning.value = (2, 2)
img = self.readoutcam.data.get()
wl_list_bin2 = img.metadata[model.MD_WL_LIST]
self.assertEqual(len(wl_list_bin1)/2, len(wl_list_bin2))
with self.assertRaises(AssertionError):
self.assertListEqual(wl_list_bin1, wl_list_bin2) # there is not assertListNotEqual...
def _on_em_view_mpp_change(self, mpp):
""" Set the microscope's hfw when the MicroscopeView's mpp value changes
The canvas calculates the new hfw value.
"""
# Only change the fov of the hardware if:
# * this Viewport was *not* responsible for setting the mpp
# (by calling `self.set_horizontal_field_width`)
# * _and_ if it's displayed on screen (so we don't interfere with
# viewports in other tabs that are not currently displayed)
# This way, we prevent mpp/fov setting loops.
if not self.self_set_mpp and self.IsShownOnScreen():
logging.debug("View mpp changed to %s on %s", mpp, self)
hfw = self.get_fov_from_mpp()
if hfw is None:
return
fov_va = self.microscope_view.fov_va
try:
# TODO: Test with a simulated SEM that has HFW choices
choices = fov_va.choices
# Get the choice that matches hfw most closely
hfw = util.find_closest(hfw, choices)
except NotApplicableError:
hfw = fov_va.clip(hfw)
# Indicate that this object was responsible for updating the hardware's HFW, so it won't
# get updated again in `_on_hw_fov_change`
self.self_set_fov = True
logging.debug("Setting hardware FoV to %s", hfw)
fov_va.value = hfw
else:
self.self_set_mpp = False
def test_acq_wavelengthTable(self):
"""Get the scaling table (correction for mapping vertical px with timestamps)
for the streak Time Range chosen for one sweep."""
# test a first value
self.readoutcam.binning.value = (1, 1)
self.streakunit.timeRange.value = util.find_closest(
0.000000002, self.streakunit.timeRange.choices) # 2ns
self.streakunit.streakMode.value = True
# Note: RemoteEx automatically stops and restarts "Live" acq when changing settings
img1 = self.readoutcam.data.get()
wl_list_bin1 = img1.metadata[model.MD_WL_LIST]
self.assertIn(model.MD_TIME_LIST, img1.metadata)
self.assertIn(model.MD_WL_LIST, img1.metadata)
# check wavelength list changes when changing binning
self.readoutcam.binning.value = (2, 2)
img2 = self.readoutcam.data.get()
wl_list_bin2 = img2.metadata[model.MD_WL_LIST]
self.assertEqual(len(wl_list_bin1) / 2, len(wl_list_bin2))
with self.assertRaises(AssertionError):
self.assertListEqual(
wl_list_bin1,
wl_list_bin2) # there is not assertListNotEqual...
def set_attr(comp_name, attr_val_str):
"""
set the value of vigilant attribute of the given component.
attr_val_str (dict str->str): attribute name -> value as a string
"""
component = get_component(comp_name)
for attr_name, str_val in attr_val_str.items():
try:
attr = getattr(component, attr_name)
except Exception:
raise ValueError("Failed to find attribute '%s' on component '%s'" % (attr_name, comp_name))
if not isinstance(attr, model.VigilantAttributeBase):
raise ValueError("'%s' is not a vigilant attribute of component %s" % (attr_name, comp_name))
new_val = convert_to_object(str_val)
# Special case for floats, due to rounding error, it's very hard to put the
# exact value if it's an enumerated VA. So just pick the closest one in this
# case.
if isinstance(new_val, float) and (
hasattr(attr, "choices") and isinstance(attr.choices, collections.Iterable)):
orig_val = new_val
new_val = util.find_closest(new_val, attr.choices)
if new_val != orig_val:
logging.debug("Adjusting value to %s", new_val)
try:
attr.value = new_val
except Exception as exc:
raise IOError("Failed to set %s.%s = '%s': %s" % (comp_name, attr_name, str_val, exc))
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 test_TimeRange(self):
"""Test time range VA for sweeping of streak unit."""
for timeRange in self.streakunit.timeRange.choices:
# change timeRange VA to value in range
self.streakunit.timeRange.value = util.find_closest(timeRange, self.streakunit.timeRange.choices)
self.assertAlmostEqual(self.streakunit.timeRange.value, timeRange)
tr2d = self.delaybox._metadata.get(model.MD_TIME_RANGE_TO_DELAY)
if tr2d:
key = util.find_closest(timeRange, tr2d.keys())
# check that the corresponding trigger delay is set when changing the .timeRange VA
md_triggerDelay = tr2d[key]
self.assertAlmostEqual(self.delaybox.triggerDelay.value, md_triggerDelay)
# request value, which is not in choices of VA
with self.assertRaises(IndexError):
self.streakunit.timeRange.value = 0.000004 # 4us
def test_TimeRange(self):
"""Test time range VA for sweeping of streak unit."""
for timeRange in self.streakunit.timeRange.choices:
# change timeRange VA to value in range
self.streakunit.timeRange.value = util.find_closest(timeRange, self.streakunit.timeRange.choices)
self.assertAlmostEqual(self.streakunit.timeRange.value, timeRange)
tr2d = self.delaybox._metadata.get(model.MD_TIME_RANGE_TO_DELAY)
if tr2d:
key = util.find_closest(timeRange, tr2d.keys())
# check that the corresponding trigger delay is set when changing the .timeRange VA
md_triggerDelay = tr2d[key]
self.assertAlmostEqual(self.delaybox.triggerDelay.value, md_triggerDelay)
# request value, which is not in choices of VA
with self.assertRaises(IndexError):
self.streakunit.timeRange.value = 0.000004 # 4us
def _setCCDFan(self, enable):
"""
Turn on/off the fan of the CCD
enable (boolean): True to turn on/restore the fan, and False to turn if off
"""
if not self._has_fan_speed:
return
if self._fan_enabled == enable:
return
self._fan_enabled = enable
comp = self._getComponent("ccd")
if enable:
if self._enabled_fan_speed is not None:
logging.debug("Turning fan on of %s", comp.name)
comp.fanSpeed.value = max(comp.fanSpeed.value,
self._enabled_fan_speed)
else:
if comp.fanSpeed.value == 0:
# Already off => don't touch it
self._enabled_fan_speed = None
self._enabled_fan_temp = None
else:
logging.debug("Turning fan off of %s", comp.name)
self._enabled_fan_speed = comp.fanSpeed.value
comp.fanSpeed.value = 0
# Raise targetTemperature to max/ambient to avoid the fan from
# automatically starting again. (Some hardware have this built-in when
# the current temperature is too high compared to the target)
if self._has_fan_temp:
temp = comp.targetTemperature
if enable:
if self._enabled_fan_temp is not None:
temp.value = min(comp.targetTemperature.value,
self._enabled_fan_temp)
try:
self._waitTemperatureReached(comp, timeout=60)
except Exception as ex:
logging.warning(
"Failed to reach target temperature of CCD: %s",
ex)
else:
# Set ~25°C == ambient temperature
self._enabled_fan_temp = temp.value
try:
try:
temp.value = min(comp.targetTemperature.range[1], 25)
except AttributeError:
temp.value = util.find_closest(
25, comp.targetTemperature.choices)
except Exception:
logging.warning(
"Failed to change targetTemperature when disabling fan",
exc_info=True)
def _setPower(self, value):
powers = self.power.choices
self._power = util.find_closest(value, powers)
if self._power == 0:
self.parent._device.HVBeamOff()
else:
self.parent._device.HVBeamOn()
return self._power
def _setPower(self, value):
powers = self.power.choices
self._power = util.find_closest(value, powers)
if self._power == 0:
self.parent._device.HVBeamOff()
else:
self.parent._device.HVBeamOn()
return self._power
def _doReference(self, axes):
logging.debug("Referencing axis %s (-> %s)", self._axis, self._caxis)
f = self._child.reference({self._caxis})
f.result()
# If we just did homing and ended up to an unsupported position, move to
# the nearest supported position
cp = self._child.position.value[self._caxis]
if (cp not in self._positions):
nearest = util.find_closest(cp, self._positions.keys())
self._doMoveAbs({self._axis: nearest})
def _doReference(self, axes):
logging.debug("Referencing axis %s (-> %s)", self._axis, self._caxis)
f = self._child.reference({self._caxis})
f.result()
# If we just did homing and ended up to an unsupported position, move to
# the nearest supported position
cp = self._child.position.value[self._caxis]
if (cp not in self._positions):
nearest = util.find_closest(cp, self._positions.keys())
self._doMoveAbs({self._axis: nearest})
def _setCCDFan(self, enable):
"""
Turn on/off the fan of the CCD
enable (boolean): True to turn on/restore the fan, and False to turn if off
"""
if not self._has_fan_speed:
return
if self._fan_enabled == enable:
return
self._fan_enabled = enable
comp = self._getComponent("ccd")
if enable:
if self._enabled_fan_speed is not None:
logging.debug("Turning fan on of %s", comp.name)
comp.fanSpeed.value = max(comp.fanSpeed.value, self._enabled_fan_speed)
else:
if comp.fanSpeed.value == 0:
# Already off => don't touch it
self._enabled_fan_speed = None
self._enabled_fan_temp = None
else:
logging.debug("Turning fan off of %s", comp.name)
self._enabled_fan_speed = comp.fanSpeed.value
comp.fanSpeed.value = 0
# Raise targetTemperature to max/ambient to avoid the fan from
# automatically starting again. (Some hardware have this built-in when
# the current temperature is too high compared to the target)
if self._has_fan_temp:
temp = comp.targetTemperature
if enable:
if self._enabled_fan_temp is not None:
temp.value = min(comp.targetTemperature.value, self._enabled_fan_temp)
try:
self._waitTemperatureReached(comp, timeout=60)
except Exception as ex:
logging.warning("Failed to reach target temperature of CCD: %s",
ex)
else:
# Set ~25°C == ambient temperature
self._enabled_fan_temp = temp.value
try:
try:
temp.value = min(comp.targetTemperature.range[1], 25)
except (AttributeError, NotApplicableError):
temp.value = util.find_closest(25, comp.targetTemperature.choices)
except Exception:
logging.warning("Failed to change targetTemperature when disabling fan",
exc_info=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 _setPC(self, value):
currents = self.probeCurrent.choices
self._probeCurrent = util.find_closest(value, currents)
self._indexCurrent = util.index_closest(value, self._list_currents)
# Set the corresponding current index to Tescan SEM
self.parent._device.SetPCIndex(self._indexCurrent + 1)
# Adjust brightness and contrast
with self.parent._acquisition_init_lock:
self.parent._device.DtAutoSignal(self.parent._detector._channel)
return self._probeCurrent
def _setPC(self, value):
currents = self.probeCurrent.choices
self._probeCurrent = util.find_closest(value, currents)
self._indexCurrent = util.index_closest(value, self._list_currents)
# Set the corresponding current index to Tescan SEM
self.parent._device.SetPCIndex(self._indexCurrent + 1)
# Adjust brightness and contrast
with self.parent._acquisition_init_lock:
self.parent._device.DtAutoSignal(self.parent._detector._channel)
return self._probeCurrent
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 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 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 set_attr(comp_name, attr_name, str_val):
"""
set the value of vigilant attribute of the given component using the type
of the current value of the attribute.
"""
try:
component = get_component(comp_name)
except LookupError:
logging.error("Failed to find component '%s'", comp_name)
return 127
except:
logging.error("Failed to contact the back-end")
return 127
try:
attr = getattr(component, attr_name)
except:
logging.error("Failed to find attribute '%s' on component '%s'",
attr_name, comp_name)
return 129
if not isinstance(attr, model.VigilantAttributeBase):
logging.error("'%s' is not a vigilant attribute of component '%s'",
attr_name, comp_name)
return 129
try:
new_val = convertToObject(str_val)
except Exception:
return 127
# Special case for floats, due to rounding error, it's very hard to put the
# exact value if it's an enumerated VA. So just pick the closest one in this
# case.
if isinstance(new_val, float) and (hasattr(attr, "choices") and isinstance(
attr.choices, collections.Iterable)):
orig_val = new_val
new_val = util.find_closest(new_val, attr.choices)
if new_val != orig_val:
logging.debug("Adjusting value to %s", new_val)
try:
attr.value = new_val
except:
logging.exception("Failed to set %s.%s = '%s'", comp_name, attr_name,
str_val)
return 127
return 0
def set_attr(comp_name, attr_val_str):
"""
set the value of vigilant attribute of the given component.
attr_val_str (dict str->str): attribute name -> value as a string
"""
component = get_component(comp_name)
for attr_name, str_val in attr_val_str.items():
try:
attr = getattr(component, attr_name)
except Exception:
raise ValueError(
"Failed to find attribute '%s' on component '%s'" %
(attr_name, comp_name))
if not isinstance(attr, model.VigilantAttributeBase):
raise ValueError(
"'%s' is not a vigilant attribute of component %s" %
(attr_name, comp_name))
new_val = convert_to_object(str_val)
# Special case for floats, due to rounding error, it's very hard to put the
# exact value if it's an enumerated VA. So just pick the closest one in this
# case.
if (isinstance(new_val, float) and hasattr(attr, "choices")
and isinstance(attr.choices, collections.Iterable)):
orig_val = new_val
choices = [
v for v in attr.choices if isinstance(v, numbers.Number)
]
new_val = util.find_closest(new_val, choices)
if new_val != orig_val:
logging.debug("Adjusting value to %s", new_val)
# Special case for None being referred to as "null" in YAML, but we should
# also accept "None"
elif new_val == "None" and not isinstance(attr.value, basestring):
new_val = None
logging.debug("Adjusting value to %s (null)", new_val)
try:
attr.value = new_val
except Exception as exc:
raise IOError("Failed to set %s.%s = '%s': %s" %
(comp_name, attr_name, str_val, exc))
def _onOpenCalibFile(self, event):
"""
Loads a calibration file (*csv) containing the time range and the corresponding trigger delay
for streak camera calibration.
"""
logging.debug(
"Open trigger delay calibration file for temporal acquisition.")
dialog = wx.FileDialog(self.panel,
message="Choose a calibration file to load",
defaultDir=self._calib_path,
defaultFile="",
style=wx.FD_OPEN,
wildcard="csv files (*.csv)|*.csv")
# Show the dialog and check whether is was accepted or cancelled
if dialog.ShowModal() != wx.ID_OK:
return
# get selected path + filename and update default directory
self._calib_path = dialog.GetDirectory()
path = dialog.GetPath()
filename = dialog.GetFilename()
# read file
try:
tr2d = calibration.read_trigger_delay_csv(
path, self.streak_unit.timeRange.choices,
self.streak_delay.triggerDelay.range)
except ValueError as error:
self._onUpdateTriggerDelayGUI("Error while loading file!",
odemis.gui.FG_COLOUR_HIGHLIGHT)
logging.error("Failed loading %s: %s", filename, error)
return
# update the MD: overwrite the complete dict
self.streak_delay.updateMetadata({model.MD_TIME_RANGE_TO_DELAY: tr2d})
# update triggerDelay shown in GUI
cur_timeRange = self.streak_unit.timeRange.value
# find the corresponding trigger delay
key = util.find_closest(cur_timeRange, tr2d.keys())
# Note: no need to check almost_equal again as we do that already when loading the file
self.streak_delay.triggerDelay.value = tr2d[key] # set the new value
self._onUpdateTriggerDelayGUI(filename) # update txt displayed in GUI
def set_attr(comp_name, attr_name, str_val):
"""
set the value of vigilant attribute of the given component using the type
of the current value of the attribute.
"""
try:
component = get_component(comp_name)
except LookupError:
logging.error("Failed to find component '%s'", comp_name)
return 127
except:
logging.error("Failed to contact the back-end")
return 127
try:
attr = getattr(component, attr_name)
except:
logging.error("Failed to find attribute '%s' on component '%s'", attr_name, comp_name)
return 129
if not isinstance(attr, model.VigilantAttributeBase):
logging.error("'%s' is not a vigilant attribute of component '%s'", attr_name, comp_name)
return 129
try:
new_val = convertToObject(str_val)
except Exception:
return 127
# Special case for floats, due to rounding error, it's very hard to put the
# exact value if it's an enumerated VA. So just pick the closest one in this
# case.
if isinstance(new_val, float) and (
hasattr(attr, "choices") and isinstance(attr.choices, collections.Iterable)):
orig_val = new_val
new_val = util.find_closest(new_val, attr.choices)
if new_val != orig_val:
logging.debug("Adjusting value to %s", new_val)
try:
attr.value = new_val
except:
logging.exception("Failed to set %s.%s = '%s'", comp_name, attr_name, str_val)
return 127
return 0
def test_acqSync_EarlyEvents(self):
"""Test early events triggered in synchronous acquisition mode."""
# AsyncCommandStatus() returns: pending, preparing, active
# AsyncCommandPreparing = True # action has not yet been started
# AsyncCommandActive = True # action has been started
# AsyncCommandPending = False # action has been ended, if True: action still going on
# Note: async commands are: AcqStart, SeqStart, SeqSave, SeqLoad
# choose very small exposure time to trigger for asynchronous commands are handled correctly
self.readoutcam.exposureTime.value = 0.00001 # 10us
self.streakunit.timeRange.value = util.find_closest(
0.000001, self.streakunit.timeRange.choices)
size = self.readoutcam.resolution.value
self.readoutcam.data.synchronizedOn(self.readoutcam.softwareTrigger)
num_images = 5
self.camera_left = num_images
def receive_image(dataflow, image):
"""Callback for readout camera"""
self.assertEqual(image.shape, size[::-1]) # invert size
self.assertIn(model.MD_EXP_TIME, image.metadata)
self.camera_left -= 1
logging.debug("Got image.")
if self.camera_left <= 0:
dataflow.unsubscribe(receive_image)
self.readoutcam.data.subscribe(receive_image)
# Wait for the image
for i in range(num_images):
# call notify quickly to trigger an early event
self.readoutcam.softwareTrigger.notify()
if i == num_images - 1:
time.sleep(0.01)
# if trigger event was fast enough we should get more than one acq waiting in queue
self.assertGreater(len(self.readoutcam.queue_events), 1)
time.sleep(num_images * 0.2 *
2) # wait some time for acquisition to finish
self.assertEqual(len(self.readoutcam.queue_events), 0)
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 _on_em_view_mpp_change(self, mpp):
"""
Set the microscope's hfw when the MicroscopeView's mpp value changes
(or the viewport size changes)
The canvas calculates the new hfw value.
"""
fov = self.get_fov_from_mpp()
self.microscope_view.fov.value = fov
self.microscope_view.fov_buffer.value = self.get_buffer_fov_from_mpp()
# Only change the FoV of the hardware if:
# * this Viewport was *not* responsible for setting the mpp
# (by calling `self.set_mpp_from_fov`)
# * _and_ if it's displayed on screen (so we don't interfere with
# viewports in other tabs that are not currently displayed)
# This way, we prevent mpp/fov setting loops.
if not self.self_set_mpp and self.IsShownOnScreen():
logging.debug("View mpp changed to %s on %s", mpp, self)
if fov is None:
return
fov_va = self.microscope_view.fov_hw.horizontalFoV
shape = self.microscope_view.fov_hw.shape
# Compute the hfov, so that the whole HW FoV just fully fit
hfov = min(fov[0], fov[1] * shape[0] / shape[1])
try:
# TODO: Test with a simulated SEM that has HFW choices
choices = fov_va.choices
# Get the choice that matches hfw most closely
hfov = util.find_closest(hfov, choices)
except NotApplicableError:
hfov = fov_va.clip(hfov)
# Indicate that this object was responsible for updating the hardware's HFW, so it won't
# get updated again in `_on_hw_fov_change`
self.self_set_fov = True
logging.debug("Setting hardware FoV to %s", hfov)
fov_va.value = hfov
else:
self.self_set_mpp = False
def test_acqSync_EarlyEvents(self):
"""Test early events triggered in synchronous acquisition mode."""
# AsyncCommandStatus() returns: pending, preparing, active
# AsyncCommandPreparing = True # action has not yet been started
# AsyncCommandActive = True # action has been started
# AsyncCommandPending = False # action has been ended, if True: action still going on
# Note: async commands are: AcqStart, SeqStart, SeqSave, SeqLoad
# choose very small exposure time to trigger for asynchronous commands are handled correctly
self.readoutcam.exposureTime.value = 0.00001 # 10us
self.streakunit.timeRange.value = util.find_closest(0.000001, self.streakunit.timeRange.choices)
size = self.readoutcam.resolution.value
self.readoutcam.data.synchronizedOn(self.readoutcam.softwareTrigger)
num_images = 5
self.camera_left = num_images
def receive_image(dataflow, image):
"""Callback for readout camera"""
self.assertEqual(image.shape, size[::-1]) # invert size
self.assertIn(model.MD_EXP_TIME, image.metadata)
self.camera_left -= 1
logging.debug("Got image.")
if self.camera_left <= 0:
dataflow.unsubscribe(receive_image)
self.readoutcam.data.subscribe(receive_image)
# Wait for the image
for i in range(num_images):
# call notify quickly to trigger an early event
self.readoutcam.softwareTrigger.notify()
if i == num_images - 1:
time.sleep(0.01)
# if trigger event was fast enough we should get more than one acq waiting in queue
self.assertGreater(len(self.readoutcam.queue_events), 1)
time.sleep(num_images * 0.2 * 2) # wait some time for acquisition to finish
self.assertEqual(len(self.readoutcam.queue_events), 0)
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 set_attr(comp_name, attr_val_str):
"""
set the value of vigilant attribute of the given component.
attr_val_str (dict str->str): attribute name -> value as a string
"""
component = get_component(comp_name)
for attr_name, str_val in attr_val_str.items():
try:
attr = getattr(component, attr_name)
except Exception:
raise ValueError(
"Failed to find attribute '%s' on component '%s'" %
(attr_name, comp_name))
if not isinstance(attr, model.VigilantAttributeBase):
raise ValueError(
"'%s' is not a vigilant attribute of component %s" %
(attr_name, comp_name))
new_val = convertToObject(str_val)
# Special case for floats, due to rounding error, it's very hard to put the
# exact value if it's an enumerated VA. So just pick the closest one in this
# case.
if isinstance(new_val,
float) and (hasattr(attr, "choices") and isinstance(
attr.choices, collections.Iterable)):
orig_val = new_val
new_val = util.find_closest(new_val, attr.choices)
if new_val != orig_val:
logging.debug("Adjusting value to %s", new_val)
try:
attr.value = new_val
except Exception as exc:
raise IOError("Failed to set %s.%s = '%s': %s" %
(comp_name, attr_name, str_val, exc))
def test_acq_Live_RingBuffer_subscribe(self):
"""Acquire single image and receive it via the dataport."""
# Note: AcqStop can be called multiple times even if the acq is already stopped without causing an error
# However, AcqStart can be only called once and raises an error if called while an acq is running.
# AcqStop is not an asynchronous command. But it takes time until the status of the async command
# "AcqStart" is properly finished.
# Changing settings is not async. RemoteEx blocks as long as the settings are changed.
# RemoteEx also stops the "Live" mode if a settings change is requested but does not restarts the "Live" mode.
self.streakunit.streakMode.value = True
self.streakunit.timeRange.value = util.find_closest(
0.000000002, self.streakunit.timeRange.choices)
self.streakunit.MCPGain.value = 2
self.readoutcam.exposureTime.value = 0.1 # 100ms
time.sleep(1)
# start Live mode
# and subscribe to dataflow afterwards in order to request one image while acq in Live mode is already running
# The acq should be automatically stopped and restarted, otherwise a RemoteEx error will be received.
# error returned: ['7', 'AcqStart', 'async command pending', 'HAcq_mLive']
self.streakcam.StartAcquisition(
self.readoutcam.acqMode) # acquire images
def callback(dataflow, image):
# self.streakcam.AcqAcqMonitor("Off") # TODO?
self.readoutcam.data.unsubscribe(callback)
# Note: MCPGain set to 0 is handled by stream not by driver except when changing from
# "Operate" mode to "Focus" mode
size = self.readoutcam.resolution.value
self.assertEqual(image.shape, size[::-1]) # invert size
self.assertIn(model.MD_EXP_TIME, image.metadata)
logging.debug("Got image.")
self.readoutcam.data.subscribe(callback)
time.sleep(5)
def _setWavelength(self, value):
return find_closest(value, self._wl_px_values)
def test_acqSync_SingleLive_RingBuffer_subscribe(self):
"""Test to acquire synchronized images by subscribing."""
# test sync acq in focus mode
self.streakunit.streakMode.value = False
size = self.readoutcam.resolution.value
# Note: When using self.acqMode = "SingleLive" parameters regarding the readout camera
# need to be changed via location = "Live"! For now hardcoded in driver...
self.readoutcam.exposureTime.value = 2 # s
exp_time = self.readoutcam.exposureTime.value
num_images = 5
self.images_left = num_images # unsubscribe after receiving number of images
self.readoutcam.data.synchronizedOn(self.readoutcam.softwareTrigger)
def receive_image(dataflow, image):
"""Callback for readout camera"""
self.assertEqual(image.shape, size[::-1]) # invert size
self.assertIn(model.MD_EXP_TIME, image.metadata)
self.assertNotIn(model.MD_TIME_LIST, image.metadata)
self.assertFalse(image.metadata[model.MD_STREAK_MODE])
self.images_left -= 1
logging.debug("Got image.")
if self.images_left == 0:
dataflow.unsubscribe(receive_image)
self.assertEqual(self.streakunit.MCPGain.value, 0) # MCPGain should be zero when acq finished
self.end_time = time.time()
self.readoutcam.data.subscribe(receive_image)
# Wait for the image
for i in range(num_images):
self.readoutcam.softwareTrigger.notify()
time.sleep(i * 0.1) # wait a bit to simulate some processing
# Waiting long enough
time.sleep(num_images * exp_time + 2)
self.assertEqual(self.images_left, 0)
self.readoutcam.data.synchronizedOn(None)
# check we can still get data normally
img = self.readoutcam.data.get()
# test sync acq in operate mode
self.streakunit.streakMode.value = True
self.streakunit.timeRange.value = util.find_closest(0.001, self.streakunit.timeRange.choices)
num_images = 5
self.images_left = num_images # unsubscribe after receiving number of images
self.readoutcam.data.synchronizedOn(self.readoutcam.softwareTrigger)
def receive_image(dataflow, image):
"""Callback for readout camera"""
self.assertEqual(image.shape, size[::-1]) # invert size
self.assertIn(model.MD_EXP_TIME, image.metadata)
self.assertIn(model.MD_TIME_LIST, image.metadata)
self.assertTrue(image.metadata[model.MD_STREAK_MODE])
self.images_left -= 1
logging.debug("Got image.")
if self.images_left == 0:
dataflow.unsubscribe(receive_image)
self.end_time = time.time()
self.readoutcam.data.subscribe(receive_image)
# Wait for the image
for i in range(num_images):
self.readoutcam.softwareTrigger.notify()
time.sleep(i * 0.1) # wait a bit to simulate some processing
# Waiting long enough
time.sleep(num_images * exp_time + 2)
self.assertEqual(self.images_left, 0)
self.readoutcam.data.synchronizedOn(None)
# check we can still get data normally
img = self.readoutcam.data.get()
def _setWavelength(self, value):
return find_closest(value, self._wl_px_values)
def _setTime(self, value):
return find_closest(value, self._tl_px_values)
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 _setTime(self, value):
return find_closest(value, self._tl_px_values)
def __init__(self, name, role, children, axis_name, positions, cycle=None, **kwargs):
"""
name (string)
role (string)
children (dict str -> actuator): axis name (in this actuator) -> actuator to be used for this axis
axis_name (str): axis name in the child actuator
positions (set or dict value -> str): positions where the actuator is allowed to move
cycle (float): if not None, it means the actuator does a cyclic move and this value represents a full cycle
"""
# TODO: forbid inverted
if len(children) != 1:
raise ValueError("FixedPositionsActuator needs precisely one child")
self._cycle = cycle
self._move_sum = 0
self._position = {}
self._referenced = {}
axis, child = children.items()[0]
self._axis = axis
self._child = child
self._caxis = axis_name
self._positions = positions
# Executor used to reference and move to nearest position
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
if not isinstance(child, model.ComponentBase):
raise ValueError("Child %s is not a component." % (child,))
if not hasattr(child, "axes") or not isinstance(child.axes, dict):
raise ValueError("Child %s is not an actuator." % child.name)
if cycle is not None:
# just an offset to reference switch position
self._offset = self._cycle / len(self._positions)
if not all(0 <= p < cycle for p in positions.keys()):
raise ValueError("Positions must be between 0 and %s (non inclusive)" % (cycle,))
ac = child.axes[axis_name]
axes = {axis: model.Axis(choices=positions, unit=ac.unit)} # TODO: allow the user to override the unit?
model.Actuator.__init__(self, name, role, axes=axes, children=children, **kwargs)
self._position = {}
self.position = model.VigilantAttribute({}, readonly=True)
logging.debug("Subscribing to position of child %s", child.name)
child.position.subscribe(self._update_child_position, init=True)
if model.hasVA(child, "referenced") and axis_name in child.referenced.value:
self._referenced[axis] = child.referenced.value[axis_name]
self.referenced = model.VigilantAttribute(self._referenced.copy(), readonly=True)
child.referenced.subscribe(self._update_child_ref)
# If the axis can be referenced => do it now (and move to a known position)
# In case of cyclic move always reference
if not self._referenced.get(axis, True) or (self._cycle and axis in self._referenced):
# The initialisation will not fail if the referencing fails
f = self.reference({axis})
f.add_done_callback(self._on_referenced)
else:
# If not at a known position => move to the closest known position
nearest = util.find_closest(self._child.position.value[self._caxis], self._positions.keys())
self.moveAbs({self._axis: nearest}).result()
def __init__(self, name, role, children, axis_name, positions, cycle=None, **kwargs):
"""
name (string)
role (string)
children (dict str -> actuator): axis name (in this actuator) -> actuator to be used for this axis
axis_name (str): axis name in the child actuator
positions (set or dict value -> str): positions where the actuator is allowed to move
cycle (float): if not None, it means the actuator does a cyclic move and this value represents a full cycle
"""
# TODO: forbid inverted
if len(children) != 1:
raise ValueError("FixedPositionsActuator needs precisely one child")
self._cycle = cycle
self._move_sum = 0
self._position = {}
self._referenced = {}
axis, child = children.items()[0]
self._axis = axis
self._child = child
self._caxis = axis_name
self._positions = positions
# Executor used to reference and move to nearest position
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
if not isinstance(child, model.ComponentBase):
raise ValueError("Child %s is not a component." % (child,))
if not hasattr(child, "axes") or not isinstance(child.axes, dict):
raise ValueError("Child %s is not an actuator." % child.name)
if cycle is not None:
# just an offset to reference switch position
self._offset = self._cycle / len(self._positions)
if not all(0 <= p < cycle for p in positions.keys()):
raise ValueError("Positions must be between 0 and %s (non inclusive)" % (cycle,))
ac = child.axes[axis_name]
axes = {axis: model.Axis(choices=positions, unit=ac.unit)} # TODO: allow the user to override the unit?
model.Actuator.__init__(self, name, role, axes=axes, children=children, **kwargs)
self._position = {}
self.position = model.VigilantAttribute({}, readonly=True)
logging.debug("Subscribing to position of child %s", child.name)
child.position.subscribe(self._update_child_position, init=True)
if model.hasVA(child, "referenced") and axis_name in child.referenced.value:
self._referenced[axis] = child.referenced.value[axis_name]
self.referenced = model.VigilantAttribute(self._referenced.copy(), readonly=True)
child.referenced.subscribe(self._update_child_ref)
# If the axis can be referenced => do it now (and move to a known position)
# In case of cyclic move always reference
if not self._referenced.get(axis, True) or (self._cycle and axis in self._referenced):
# The initialisation will not fail if the referencing fails
f = self.reference({axis})
f.add_done_callback(self._on_referenced)
else:
# If not at a known position => move to the closest known position
nearest = util.find_closest(self._child.position.value[self._caxis], self._positions.keys())
self.moveAbs({self._axis: nearest}).result()
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))
def test_acqSync_SingleLive_RingBuffer_subscribe(self):
"""Test to acquire synchronized images by subscribing."""
# test sync acq in focus mode
self.streakunit.streakMode.value = False
size = self.readoutcam.resolution.value
# Note: When using self.acqMode = "SingleLive" parameters regarding the readout camera
# need to be changed via location = "Live"! For now hardcoded in driver...
self.readoutcam.exposureTime.value = 2 # s
exp_time = self.readoutcam.exposureTime.value
num_images = 5
self.images_left = num_images # unsubscribe after receiving number of images
self.readoutcam.data.synchronizedOn(self.readoutcam.softwareTrigger)
def receive_image(dataflow, image):
"""Callback for readout camera"""
self.assertEqual(image.shape, size[::-1]) # invert size
self.assertIn(model.MD_EXP_TIME, image.metadata)
self.assertNotIn(model.MD_TIME_LIST, image.metadata)
self.assertFalse(image.metadata[model.MD_STREAK_MODE])
self.images_left -= 1
logging.debug("Got image.")
if self.images_left == 0:
dataflow.unsubscribe(receive_image)
self.assertEqual(self.streakunit.MCPGain.value,
0) # MCPGain should be zero when acq finished
self.end_time = time.time()
self.readoutcam.data.subscribe(receive_image)
# Wait for the image
for i in range(num_images):
self.readoutcam.softwareTrigger.notify()
time.sleep(i * 0.1) # wait a bit to simulate some processing
# Waiting long enough
time.sleep(num_images * exp_time + 2)
self.assertEqual(self.images_left, 0)
self.readoutcam.data.synchronizedOn(None)
# check we can still get data normally
img = self.readoutcam.data.get()
# test sync acq in operate mode
self.streakunit.streakMode.value = True
self.streakunit.timeRange.value = util.find_closest(
0.001, self.streakunit.timeRange.choices)
num_images = 5
self.images_left = num_images # unsubscribe after receiving number of images
self.readoutcam.data.synchronizedOn(self.readoutcam.softwareTrigger)
def receive_image(dataflow, image):
"""Callback for readout camera"""
self.assertEqual(image.shape, size[::-1]) # invert size
self.assertIn(model.MD_EXP_TIME, image.metadata)
self.assertIn(model.MD_TIME_LIST, image.metadata)
self.assertTrue(image.metadata[model.MD_STREAK_MODE])
self.images_left -= 1
logging.debug("Got image.")
if self.images_left == 0:
dataflow.unsubscribe(receive_image)
self.end_time = time.time()
self.readoutcam.data.subscribe(receive_image)
# Wait for the image
for i in range(num_images):
self.readoutcam.softwareTrigger.notify()
time.sleep(i * 0.1) # wait a bit to simulate some processing
# Waiting long enough
time.sleep(num_images * exp_time + 2)
self.assertEqual(self.images_left, 0)
self.readoutcam.data.synchronizedOn(None)
# check we can still get data normally
img = self.readoutcam.data.get()
