def kickoff_and_collect(block=False, magic=False):
"""Make a flyer or magic_flyer object and maybe block
Returns
-------
msg1 : Msg
kickoff message for flyer or magic_flyer created in this function
msg2 : Msg
collect message for flyer or magic_flyer created in this function
"""
args = []
kwargs = {}
if magic:
flyer = get_magic_flyer()
else:
flyer = get_flyer()
args = [
random.randrange(-5, -1), # start
random.randrange(0, 5), # stop
random.randint(1, 10)
] # step
if block:
kwargs = {'group': unique_name()}
return [Msg('kickoff', flyer, *args, **kwargs), Msg('collect', flyer)]
def checkpoint_forever():
# simplest pauseable scan
yield Msg('open_run')
while True:
ttime.sleep(0.1)
yield Msg('checkpoint')
yield Msg('close_run')
def do_nothing(timeout=5):
"Generate 'checkpoint' messages until timeout."
t = ttime.time()
yield Msg('open_run')
while True:
if ttime.time() > t + timeout:
break
ttime.sleep(0.1)
yield Msg('checkpoint')
yield Msg('close_run')
def move():
yield Msg("checkpoint")
grp = _short_uid("set")
for motor, pos in step.items():
if pos == pos_cache[motor]:
# This step does not move this motor.
continue
yield Msg("set", motor, pos, group=grp)
pos_cache[motor] = pos
yield Msg("wait", None, group=grp)
def conditional_break(det, motor, threshold):
"""Set, trigger, read until the detector reads intensity < threshold"""
i = 0
yield Msg('open_run')
while True:
print("LOOP %d" % i)
yield Msg('set', motor, i)
yield Msg('trigger', det)
reading = yield Msg('read', det)
if reading[det.name]['value'] < threshold:
print('DONE')
yield Msg('close_run')
break
i += 1
def cautious_stepscan(det, motor):
yield Msg('open_run')
for i in range(-5, 5):
yield Msg('checkpoint')
yield Msg('create')
yield Msg('set', motor, i)
yield Msg('trigger', det)
ret_m = yield Msg('read', motor)
ret_d = yield Msg('read', det)
yield Msg('save')
print("Value at {m} is {d}. Pausing.".format(
m=ret_m[motor.name]['value'], d=ret_d[det.name]['value']))
yield Msg('pause', None, defer=True)
yield Msg('close_run')
def test_single_msg_to_gen():
m = Msg('set', None, 0)
m_list = [m for m in ensure_generator(m)]
assert len(m_list) == 1
assert m_list[0] == m
def simple_scan_saving(det, motor):
"Set, trigger, read"
yield Msg('open_run')
yield Msg('create')
yield Msg('set', motor, 5)
yield Msg('read', motor)
yield Msg('trigger', det)
yield Msg('read', det)
yield Msg('save')
yield Msg('close_run')
def stepscan(det, motor):
yield Msg('open_run')
for i in range(-5, 5):
yield Msg('create')
yield Msg('set', motor, i)
yield Msg('trigger', det)
yield Msg('read', motor)
yield Msg('read', det)
yield Msg('save')
yield Msg('close_run')
def stepscan(det, motor):
"""Old example scan from bluesky deprecated submodule."""
yield Msg('open_run')
for i in range(-5, 5):
yield Msg('create', name='primary')
yield Msg('set', motor, i)
yield Msg('trigger', det)
yield Msg('read', motor)
yield Msg('read', det)
yield Msg('save')
yield Msg('close_run')
def wait_complex(det, motors):
"Set motors, trigger motors, wait for all motors to move in groups."
# Same as above...
yield Msg('open_run')
for motor in motors[:-1]:
yield Msg('set', motor, 5, group='A')
# ...but put the last motor is separate group.
yield Msg('set', motors[-1], 5, group='B')
# Wait for everything in group 'A' to report done.
yield Msg('wait', None, group='A')
yield Msg('trigger', det)
yield Msg('read', det)
# Wait for everything in group 'B' to report done.
yield Msg('wait', None, group='B')
yield Msg('trigger', det)
yield Msg('read', det)
yield Msg('close_run')
def annotate(message):
"""
Plan stub to add messages to a plan inspection routine.
Parameters
----------
message: str
The message to include.
"""
return (yield Msg('annotate', message))
def restore_value(obj):
"""
Plan stub that restores a cached value using .put.
Parameters
----------
obj : OphydObject
The object we will call .put() on.
"""
return (yield Msg('restore_value', obj))
def cache_value(obj):
"""
Plan stub that caches an object's .get for later restoration.
Parameters
----------
obj : OphydObject
The object we will call .get() on.
"""
return (yield Msg('cache_value', obj))
def multi_sample_temperature_ramp(detector, sample_names, sample_positions,
scan_motor, start, stop, step,
temp_controller, tstart, tstop, tstep):
def read_and_store_temp():
yield Msg('create')
yield Msg('read', temp_controller)
yield Msg('save')
peak_centers = [-1 + 3 * n for n in range(len((sample_names)))]
detector.noise = True
for idx, temp in enumerate(np.arange(tstart, tstop, tstep)):
# todo would be cute to have the temperature reduce peak noise
yield Msg('set', temp_controller, temp)
for sample, sample_position, peak_pos in zip(sample_names,
sample_positions,
peak_centers):
yield Msg('open_run', sample_name=sample, target_temp=temp)
detector.center = peak_pos
detector.sigma = .5 + .25 * idx
detector.noise_factor = .05 + idx * 0.1
for scan_pos in np.arange(start, stop, step):
yield Msg('set', scan_motor, scan_pos)
# be super paranoid about the temperature. Grab it before and
# after each trigger!
# Capturing the temperature data before and after each
# trigger is resulting in unintended behavior. Uncomment the
# two `yield from` statements and run this example to see
# what I'm talking about.
# yield from read_and_store_temp()
yield Msg('trigger', detector)
# yield from read_and_store_temp()
yield Msg('create')
yield Msg('read', scan_motor)
yield Msg('read', detector)
yield Msg('read', temp_controller)
# yield Msg('sleep', None, .1)
yield Msg('save')
# generate the end of the run document
yield Msg('close_run')
def sleepy(det, motor):
"Set, trigger motor, sleep for a fixed time, trigger detector, read"
yield Msg('open_run')
yield Msg('set', motor, 5)
yield Msg('sleep', None, 2) # units: seconds
yield Msg('trigger', det)
yield Msg('read', det)
yield Msg('close_run')
def conditional_pause(det, motor, defer, include_checkpoint):
yield Msg('open_run')
for i in range(5):
if include_checkpoint:
yield Msg('checkpoint')
yield Msg('set', motor, i)
yield Msg('trigger', det)
reading = yield Msg('read', det)
if reading['det']['value'] < 0.2:
yield Msg('pause', defer=defer)
print("I'm not pausing yet.")
yield Msg('close_run')
def wait_one(det, motor):
"Set, trigger, read"
yield Msg('open_run')
yield Msg('set', motor, 5, group='A') # Add to group 'A'.
yield Msg('wait', None,
group='A') # Wait for everything in group 'A' to finish.
yield Msg('trigger', det)
yield Msg('read', det)
yield Msg('close_run')
def tweak_core():
nonlocal step
while True:
yield Msg('create', None, name='primary')
ret_mot = yield Msg('read', motor)
if ret_mot is None:
return
key = list(ret_mot.keys())[0]
pos = ret_mot[key]['value']
yield Msg('trigger', d, group='A')
yield Msg('wait', None, 'A')
reading = yield Msg('read', d)
val = reading[target_field]['value']
yield Msg('save')
prompt = prompt_str.format(motor.name, float(pos), float(val),
step)
# print(prompt)
# wait until user click
while obj.wait:
yield Msg('sleep', None, 0.1)
# change tweak step
new_step = obj.step
if new_step:
try:
step = float(new_step)
except ValueError:
print("step is not valid input")
break
yield Msg('set', motor, pos + step, group='A')
print('Motor moving...')
sys.stdout.flush()
yield Msg('wait', None, 'A')
clear_output(wait=True)
# stackoverflow.com/a/12586667/380231
#print('\x1b[1A\x1b[2K\x1b[1A')
obj.wait = True
def wait_multiple(det, motors):
"Set motors, trigger all motors, wait for all motors to move."
yield Msg('open_run')
for motor in motors:
yield Msg('set', motor, 5, group='A')
# Wait for everything in group 'A' to report done.
yield Msg('wait', None, group='A')
yield Msg('trigger', det)
yield Msg('read', det)
yield Msg('close_run')
def _inner_Escan_list():
yield from moveE(energy_list[0]+0.001)
for energy, factor in zip(energy_list, factor_list):
# Change counting time
for detector, original_preset in zip(detectors, dets_preset):
yield from mv(detector.preset_monitor, factor*original_preset)
# Move and scan
grp = short_uid('set')
yield Msg('checkpoint')
yield from moveE(energy, group=grp)
if dichro:
yield from dichro_steps(detectors, _positioners,
trigger_and_read)
else:
yield from trigger_and_read(list(detectors)+_positioners)
def assert_equals(obj, value, error_message='', halt=True):
"""
Plan stub that asserts an object's .get equals a particular value.
Parameters
----------
obj : OphydObject
The object we will call .get() on.
value : any
The value we will compare against.
error_message : str, optional
The error to present in the test suite if this fails.
halt : bool, optional
If True, end the test on failure. Otherwise, bundle for assertion at
the end of the test with use of this module's fixtures.
"""
return (yield Msg('assert_equals',
obj,
value,
error_message=error_message,
halt=halt))
def fitwalk(detectors, motor, models, target,
naive_step=None, average=120,
filters=None, drop_missing=True,
tolerance=10, delay=None, max_steps=10):
"""
Parameters
----------
detectors : list
List of detectors to read at each step of walk
motor : ``ophyd.Object``
Ophyd object that supports the set and wait. This should have a one to
one relationship with the independent variable in the model you plan to
optimize
models : list
List of models to evaluate during the walk
target : float
Desired end position for the walk
naive_step : bluesky.plan, optional
Plan to execute when there is not an accurate enough model available.
By default this is ``mv(0.01)``
average : int, optional
Number of readings to take and average at each event. Models are
allowed to take a subset of each reading and average, however if the
two settings will create an average over multiple steps in the walk the
:attr:`.LiveBuild.average` setting is automatically updated. For
example, if the walk is told to average over 10 events, your model can
either average over 10, 5, 2, or 1 shots.
filters : dict, optional
Key, callable pairs of event keys and single input functions that
evaluate to True or False. For more infromation see
:meth:`.apply_filters`
drop_missing : bool, optional
Choice to include events where event keys are missing
tolerance : float, optional
Maximum distance from target considered successful
delay : float, optional
Mininum time between consecutive readings
max_steps : int, optional
Maximum number of steps the scan will attempt before faulting.
There is a max of 10 by default, but you may disable this by setting
this option to None. Note that this may cause the walk to run indefinitely.
"""
#Check all models are fitting the same key
if len(set([model.y for model in models])) > 1:
raise RuntimeError("Provided models must predict "\
"the same dependent variable.")
#Prepare model callbacks
for model in models:
#Modify averaging
if average % model.average != 0:
logger.warning("Model {} was set to an incompatible averaging "
"setting, changing setting to {}".format(model.name,
average))
model.average = average
#Subscribe callbacks
yield Msg('subscribe', None, model, 'all')
#Target field
target_field = models[0].y
#Install filters
filters = filters or {}
[m.install_filters(filters) for m in models]
#Link motor to independent variables
detectors.insert(1, motor)
field_names = list(set(var for model in models
for var in model.independent_vars.values()))
motors = dict((key, motor) for key in field_names
if key in motor.read_attrs)
#Initialize variables
steps = 0
if not naive_step:
def naive_step():
return (yield from rel_set(motor, 0.01, wait=True))
#Measurement method
def model_measure():
#Take average measurement
avg = yield from measure_average(detectors,
num=average, delay=delay,
drop_missing=drop_missing,
filters=filters)
#Save current target position
last_shot = avg.pop(target_field)
logger.debug("Averaged data yielded {} is at {}"
"".format(target_field, last_shot))
#Rank models based on accuracy of fit
model_ranking = rank_models(models, last_shot, **avg)
#Determine if any models are accurate enough
if len(model_ranking):
model = model_ranking[0]
else:
model = None
return avg, last_shot, model
#Make first measurements
averaged_data, last_shot, accurate_model = yield from model_measure()
#Begin walk
while not np.isclose(last_shot, target, atol=tolerance):
#Log error
if not steps:
logger.debug("Initial error before fitwalk is {}"
"".format(int(target-last_shot)))
else:
logger.debug("fitwalk is reporting an error {} of after step #{}"\
"".format(int(target-last_shot), steps))
#Break on maximum step count
if max_steps and steps >= max_steps:
raise RuntimeError("fitwalk failed to converge after {} steps"\
"".format(steps))
#Use naive step plan if no model is accurate enough
#or we have not made a step yet
if not accurate_model or steps==0:
logger.debug("No model yielded accurate prediction, "\
"using naive plan")
yield from naive_step()
else:
logger.debug("Using model {} to determine next step."\
"".format(accurate_model.name))
#Calculate estimate of next step from accurate model
fixed_motors = dict((key, averaged_data[key])
for key in field_names
if key not in motors.keys())
#Try and step off model prediction
try:
estimates = accurate_model.backsolve(target, **fixed_motors)
#Report model faults
except Exception as e:
logger.warning("Accurate model {} was unable to backsolve "
"for target {}".format(accurate_model.name,
target))
logger.warning(e)
#Reuse naive step
logger.debug("Reusing naive step due to lack of accurate model")
yield from naive_step()
else:
#Move system to match estimate
for param, pos in estimates.items():
#Watch for NaN
if pd.isnull(pos) or np.isinf(pos):
raise RuntimeError("Invalid position return by fit")
#Attempt to move
try:
logger.debug("Adjusting motor {} to position {:.1f}"\
"".format(motor.name, pos))
yield from mv(motor, pos)
except KeyboardInterrupt as e:
logger.debug("No motor found to adjust variable {}"\
"".format(e))
#Count our steps
steps += 1
#Take a new measurement
logger.debug("Resampling after successfull move")
averaged_data, last_shot, accurate_model = yield from model_measure()
#Report a succesfull run
logger.info("Succesfully walked to value {} (target={}) after {} steps."\
"".format(int(last_shot), target, steps))
return last_shot, accurate_model
def measure(detectors, num=1, delay=None, filters=None, drop_missing=True,
max_dropped=50):
"""
Gather a fixed number of measurements from a group of detectors
Parameters
----------
detectors : list
List of detector objects to read and bundle
num : int
Number of measurements that pass filters
delay : float
Minimum time between consecutive reads of the detectors.
filters : dict, optional
Key, callable pairs of event keys and single input functions that
evaluate to True or False. For more infromation see
:meth:`.apply_filters`
drop_missing : bool, optional
Choice to include events where event keys are missing
max_dropped : int, optional
Maximum number of events to drop before raising a ValueError
Returns
-------
data : list
List of mock-event documents
"""
#Log setup
logger.debug("Running measure")
logger.debug("Arguments passed: detectors: {0}, "\
"num: {1}, delay: {2}, drop_missing: {3}"\
"".format([d.name for d in detectors],
num, delay,drop_missing))
#If scalable, repeat forever
if not isinstance(delay, Iterable):
delay = itertools.repeat(delay)
else:
#Number of supplied delays
try:
num_delays = len(delay)
#Invalid delay
except TypeError as err:
err_msg = "Supplied delay must be scalar or iterable"
logger.error(err_msg)
raise ValueError(err_msg) from err
#Handle provided iterable
else:
#Invalid number of delays for shot counts
if num -1 > num_delays:
err = "num={:} but delays only provides "\
"{:} entries".format(num, num_delays)
logger.error(err, stack_info=True)
raise ValueError(err)
#Ensure it is an iterable
delay = iter(delay)
#Gather shots
logger.debug("Gathering shots..")
shots = 0
dropped = 0
data = list()
filters = filters or dict()
#Gather fixed number of shots
while shots < num:
#Timestamp earliest possible moment
now = time.time()
#Trigger detector and wait for completion
for det in detectors:
yield Msg('trigger', det, group='B')
#Wait for completion and start bundling
yield Msg('wait', None, 'B')
yield Msg('create', None, name='primary')
#Mock-event document
det_reads = dict()
#Gather shots
for det in detectors:
cur_det = yield Msg('read', det)
det_reads.update(dict([(k,v['value'])
for k,v in cur_det.items()]))
#Emit Event doc to callbacks
yield Msg('save')
#Apply filters
unfiltered = apply_filters(det_reads, filters=filters, drop_missing=drop_missing)
#Increment shots if filters are passed
shots += int(unfiltered)
#Do not delay if we have not passed filter
if unfiltered:
#Append recent read to data list
data.append(det_reads)
#Gather next delay
try:
d = next(delay)
#Out of delays
except StopIteration:
#If our last measurement that is fine
if shots == num:
break
#Otherwise raise exception
else:
err = "num={:} but delays only provides {:} entries".format(
num, shots)
logger.error(err, stack_info=True)
raise ValueError(err)
#If we have a delay, sleep
if d is not None:
d = d - (time.time() - now)
if d > 0:
yield Msg('sleep', None, d)
#Report filtered event
else:
dropped += 1
logger.debug('Ignoring inadequate measurement, '\
'attempting to gather again...')
if dropped > max_dropped:
dropped_dict = {}
for key in filters.keys():
dropped_dict[key] = det_reads[key]
logger.debug(('Dropped too many events, raising exception. Latest '
'bad values were %s'), dropped_dict)
raise FilterCountError
#Report finished
logger.debug("Finished taking {} measurements, "\
"filters removed {} events"\
"".format(len(data), dropped))
return data
def read_and_store_temp():
yield Msg('create')
yield Msg('read', temp_controller)
yield Msg('save')
def fly_gen(flyer):
yield Msg('open_run')
yield Msg('kickoff', flyer, group='fly-kickoff')
yield Msg('wait', None, group='fly-kickoff')
yield Msg('complete', flyer, group='fly-complete')
yield Msg('wait', None, group='fly-complete')
yield Msg('collect', flyer)
yield Msg('kickoff', flyer, group='fly-kickoff2')
yield Msg('wait', None, group='fly-kickoff2')
yield Msg('complete', flyer, group='fly-complete2')
yield Msg('wait', None, group='fly-complete2')
yield Msg('collect', flyer)
yield Msg('close_run')
def unload_sample():
# TODO: I think this can be simpler.
return (yield from
single_gen(Msg("unload_sample", xpd_configuration["robot"])))
def adaptive_core():
next_pos = start
step = (stop - start) / 2
past_I = None
cur_I = target_val + 99 # start the while loop
repeat = 0
largest_out_of_bound = stop
cnt = 0
if stop >= start:
direction_sign = 1
else:
direction_sign = -1
while cur_I > target_val or (
(largest_out_of_bound - next_pos) > accuracy) or repeat < 3:
debug = False
if debug:
print(
'Current value = {}; largest_out_of_bound = {}; repeat = {}'
.format(cur_I, largest_out_of_bound, repeat))
yield Msg('checkpoint')
yield from bps.mv(motor, next_pos)
yield Msg('create', None, name='primary')
for det in detectors:
yield Msg('trigger', det, group='B')
yield Msg('wait', None, 'B')
for det in utils.separate_devices(detectors + [motor] +
[outer_motor]):
cur_det = yield Msg('read', det)
if target_field in cur_det:
cur_I = calc_function(
value=cur_det[target_field]['value'])
yield Msg('save')
# special case first first loop
if past_I is None:
past_I = cur_I
next_pos += step * direction_sign
continue
# binary search
if cur_I > past_I:
if cur_I < target_val:
direction_sign = 1
else:
direction_sign = -1
largest_out_of_bound = np.min(
[largest_out_of_bound, next_pos])
elif cur_I <= past_I:
if cur_I < target_val:
direction_sign = 1
else:
direction_sign = -1
largest_out_of_bound = np.min(
[largest_out_of_bound, next_pos])
else:
print('binary search error')
# the logic here is non-conventional:
# once the dynamic reserve is exceeded measurements jump around significantly
# so we search for the largest interfering amplitude that does NOT cause a
# deviation over 5% (target_val)
# and that is a specified voltage maximum voltage away from an interferer amplitude that did cause
# a deviation greater than the target value.
past_I = cur_I
step = np.max([step / 2, min_step])
if (cur_I < target_val) and (
abs(largest_out_of_bound - next_pos) < accuracy):
repeat += 1
next_pos = next_pos
else:
repeat = 0
next_pos += step * direction_sign
next_pos = np.clip(
next_pos, start, stop
) # by binary search this shouldn't be needed. Just in case
# handle conditions that might get stuck. Only run 30 loops,
if ((next_pos == start) or (next_pos == stop) and
(repeat == 0) and (cnt > 8)) or (cnt > 50):
break
cnt += 1
def outer_loop():
for step in outer_steps:
yield Msg('checkpoint')
yield from bps.mv(outer_motor, step)
yield from adaptive_core()
def simple_scan(motor):
yield Msg('open_run')
yield Msg('set', motor, 5)
yield Msg('read', motor)
yield Msg('close_run')
