def grid_fly(flyer, y, ystart, ystop, ynum, x, xstart, xstop, xnum):
generator = CompoundGenerator(
generators=[
LineGenerator(y.name, "mm", ystart, ystop, ynum),
LineGenerator(x.name, "mm", xstart, xstop, xnum),
],
duration=0.1,
)
mapping.configure(dict(generator=generator))
md = dict(
hints=dict(
gridding="rectilinear",
dimensions=[([y.name], "primary"), ([x.name], "primary")],
),
shape=(ynum, xnum),
extents=([ystart, ystop], [xstart, xstop]),
)
uid = yield from bps.open_run(md)
yield from bps.kickoff(flyer, wait=True)
yield from bps.collect(flyer, stream=True)
yield from bps.checkpoint()
yield from bps.complete(flyer, group="flyer")
for _ in range(int(ynum * xnum * 0.1)):
yield from bps.sleep(1)
yield from bps.collect(flyer, stream=True)
yield from bps.checkpoint()
yield from bps.wait(group="flyer")
yield from bps.collect(flyer, stream=True)
yield from bps.close_run()
return uid
def move_and_do_one(bt: Beamtime,
sample_ind: tp.Union[int, str],
plan_ind: tp.Union[int, str, tp.Generator],
wait_time: float = 0.,
sample_x: str = "sample_x",
sample_y: str = "sample_y",
x_controller: str = "x_controller",
y_controller: str = "y_controller") -> tp.Generator:
"""Move to the sample and conduct the plan."""
sample = translate_to_sample(bt, sample_ind)
plan = translate_to_plan(bt, plan_ind, sample)
xc = xpd_configuration[x_controller]
yc = xpd_configuration[y_controller]
x = float(get_from_sample(sample, sample_x))
y = float(get_from_sample(sample, sample_y))
yield from bps.checkpoint()
print("Start moving to sample {} at ({}, {}).".format(sample_ind, x, y))
yield from bps.mv(xc, x, yc, y)
print("Finish. ")
yield from bps.checkpoint()
print("Start sleeping for {} s.".format(wait_time))
yield from bps.sleep(wait_time)
print("Wake up.")
yield from bps.checkpoint()
print("Start plan {} for sample {}".format(plan_ind, sample_ind))
yield from plan
print("Finish.")
def cryostat_plan(bt: object, temp_motor: object, temperatures: List[float], posi_motor: object,
positions: List[float],
samples: List[int], exposures: List[float], temp_to_power: dict = None):
"""
The scanplan of cryostat measurement.
Parameters
----------
bt : beamtime object
The beamtime object.
temp_motor : motor object
The controller of temperature.
temperatures : List[float]
A list of temperature setpoints.
posi_motor : motor object
The controller of positions.
positions : List[float]
A list of positions.
samples : List[int]
A list of index of samples in bt.
exposures : List[float]
A list of exposure time.
temp_to_power : dict
A mapping from temperature range to power. The range is open at left and close at right. If None,
default setting (see function 'get_heater_range') is used. Default None.
Yields
------
Message of the plan
"""
samples = translate_to_sample(bt, samples)
for temperature in temperatures:
yield from set_power(temp_motor, temperature, temp_to_power)
yield from checkpoint()
yield from mv(temp_motor, temperature)
yield from checkpoint()
if not (len(positions) == len(samples) and len(samples) == len(exposures)):
raise ValueError("Unmatched length of positions, samples and exposures: "
f"{len(positions)}, {len(samples)}, {len(exposures)}.")
for position, sample, exposure in zip(positions, samples, exposures):
yield from mv(posi_motor, position)
yield from checkpoint()
yield from config_det_and_count([temp_motor, posi_motor], sample, exposure)
yield from checkpoint()
def my_move_per_step(step: dict, pos_cache: dict):
yield from bps.checkpoint()
for motor, pos in step.items():
if pos == pos_cache[motor]:
continue
yield from bps.mv(motor, pos)
pos_cache[motor] = pos
def simple_plan():
nonlocal flag
try:
yield from checkpoint()
yield Msg('pause')
except excp:
flag = True
def inner_per_step(detectors, motor, step):
# Set a checkpoint in case the scan is interrupted
yield from checkpoint()
"""
# Notify the user where we are trying to move to
goal_sample = inner_motor.position + inner_step_size
goal_index = inner_motor.locate_1d(goal_sample)
logger.info('Inner Step: Moving {0} to {1} (sample {2})'.format(
inner_motor.name, goal_index, goal_sample))
"""
# Move the motor to the inputted step
yield from rel_set(inner_motor, inner_step_size, wait=True)
if use_sequencer:
# # Start and wait for the sequencer
logger.info('Inner Step: Starting the sequencer')
yield from abs_set(sequencer, 1, wait=True)
# Wait the specified amount of time
if wait:
logger.info(
"Inner Step: Waiting for {0} second(s)...".format(wait))
time.sleep(wait)
# Fill the dataframe
scan_positions.append((
outer_motor.position,
#inner_motor.chip,
inner_motor.position,
#*inner_motor.index,
#*inner_motor.coordinates
))
def close_shutter_stub():
"""simple function to return a generator that yields messages to
close the shutter"""
yield from bps.abs_set(
xpd_configuration["shutter"], XPD_SHUTTER_CONF["close"], wait=True
)
yield from bps.checkpoint()
def motor_dark_step(detectors, motor, step):
"""
Take darks while moving motors, wait for all to be finished before
taking light
"""
yield from bps.checkpoint()
print('l120')
# close the shutter
#yield from _close_shutter_stub() COMMENTED OUT (dark per light)
print('l123')
# move motors don't wait yet.
# Note for Soham: use `group=None` to ramp temp after dark collected
# (Broken and replaced below) yield from bps.abs_set(motor, step, group="dark_motor")
yield from bps.abs_set(motor, step, group="dark_motor")
print('l127')
# take dark (this has an internal wait on the readback)
#yield from bps.trigger_and_read(list(detectors), name="dark") COMMENTED OUT (dark per light)
print('l130')
# (Broken) now wait for the motors to be done too
yield from bps.wait(group="dark_motor")
print('l133')
# open shutter
yield from open_shutter_stub()
print('l136')
# take data
yield from bps.trigger_and_read(list(detectors) + [motor])
print('l139')
def open_shutter_stub():
"""simple function to return a generator that yields messages to
open the shutter"""
yield from bps.abs_set(
xpd_configuration["shutter"], XPD_SHUTTER_CONF["open"], wait=True
)
yield from bps.sleep(glbl["shutter_sleep"])
yield from bps.checkpoint()
def xpdacq_trigger_and_read(detectors: list,
name: str = "primary") -> typing.Generator:
"""Open shutter, wait, trigger and read detectors, close shutter."""
yield from bps.checkpoint()
yield from xb.open_shutter_stub()
yield from bps.sleep(xb.glbl["shutter_sleep"])
yield from bps.trigger_and_read(detectors, name=name)
yield from xb.close_shutter_stub()
def dull_scan(mot, count, sig=None, sleep_time=0):
if sig:
thread = threading.Thread(target=sig_sequence, args=(sig, ))
thread.start()
for i in range(count):
yield from checkpoint()
try:
yield from mv(mot, i)
except:
pass
# make every step take 1s extra
yield from sleep(sleep_time)
yield from checkpoint()
yield from create()
yield from read(mot)
yield from save()
yield from checkpoint()
def measure(detectors, motor, step):
# Perform step
logger.debug("Measuring average at step %s ...", step)
yield from checkpoint()
yield from abs_set(motor, step, wait=True)
# Measure the average
return (yield from measure_average([motor, detector],
num=average,
filters=filters))
def move():
yield from 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 from abs_set(motor, pos, group=grp)
pos_cache[motor] = pos
yield from wait(group=grp)
def move():
yield from 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 from abs_set(motor, pos, group=grp)
pos_cache[motor] = pos
yield from wait(group=grp)
def one_1d_step(detectors, motor, step):
"""
Inner loop of a 1D step scan
This is the default function for ``per_step`` param in 1D plans.
"""
yield from checkpoint()
yield from abs_set(motor, step, wait=True)
yield from trigger_and_read(list(detectors) + [motor], name="dark")
return (yield from trigger_and_read(list(detectors) + [motor]))
def plan():
while True:
for step in np.linspace(start, stop, num):
yield from bps.abs_set(motor, step, wait=True)
yield from bps.trigger_and_read(list(detectors) + [motor])
yield from bps.checkpoint()
err = errorbar(lf.result, 'sigma')
if err < err_thresh:
break
def shutter_step(detectors, motor, step):
""" customized step to ensure shutter is open before
reading at each motor point and close shutter after reading
"""
yield from bps.checkpoint()
yield from bps.abs_set(motor, step, wait=True)
yield from open_shutter_stub()
yield from bps.sleep(glbl["shutter_sleep"])
yield from bps.trigger_and_read(list(detectors) + [motor])
yield from close_shutter_stub()
def custom_step(detectors, motor, step):
"""
Inner loop of a 1D step scan
This is the default function for ``per_step`` param in 1D plans.
"""
yield from checkpoint()
print('Set attenuator to {}'.format(step))
yield from pause()
yield from abs_set(motor, step, wait=True)
return (yield from trigger_and_read(list(detectors) + [motor]))
def robot_wrapper(plan, sample):
"""Wrap a plan in load/unload messages.
Parameters
----------
plan : a bluesky plan
sample : dict
must contain 'position'; optionally also 'geometry'
Example
-------
>>> plan = count([pe1c])
>>> new_plan = robot_wrapper(plan, {'position': 1})
"""
yield from bps.checkpoint()
yield from load_sample(sample['robot_identifier'],
sample.get('robot_geometry', None))
yield from bps.checkpoint()
yield from plan
yield from bps.checkpoint()
yield from unload_sample()
yield from bps.checkpoint()
def per_step(detectors, motor, step):
# Perform step
yield from checkpoint()
logger.debug("Measuring average at step {0} ...".format(step))
yield from abs_set(motor, step, wait=True)
# Measure the average
reads = (yield from measure_average(all_devices, num=average,
filters=filters, *args, **kwargs))
# Fill the dataframe at this step with the centroid difference
for fld in all_fields:
df.loc[step, fld] = reads[fld]
def per_step(detectors, step: dict, pos_cache):
""" customized step to ensure shutter is open before
reading at each motor point and close shutter after reading
"""
yield from bps.checkpoint()
for motor, pos in step.items():
yield from bps.mv(motor, pos)
yield from bps.sleep(wait)
yield from open_shutter_stub()
yield from bps.sleep(glbl["shutter_sleep"])
yield from bps.trigger_and_read(list(detectors) + list(step.keys()))
yield from close_shutter_stub()
def move_to_start_fly():
"See http://nsls-ii.github.io/bluesky/plans.html#the-per-step-hook"
# row_str = short_uid('row')
# yield from abs_set(xmotor, row_start, group=row_str)
# yield from one_1d_step([temp_nanoKB], motor, step)
# yield from bps.wait(group=row_str)
row_str = short_uid('row')
yield from bps.checkpoint()
yield from bps.abs_set(xmotor, row_start, group=row_str)
yield from bps.abs_set(motor, step, group=row_str)
yield from bps.wait(group=row_str)
yield from bps.trigger_and_read([temp_nanoKB, motor])
def _shutter_step(detectors, motor, step):
""" customized step to ensure shutter is open before
reading at each motor point and close shutter after reading
"""
yield from bps.checkpoint()
yield from bps.abs_set(motor, step, wait=True)
yield from bps.abs_set(
xpd_configuration["shutter"], XPD_SHUTTER_CONF["open"], wait=True
)
yield from bps.sleep(glbl['shutter_sleep'])
yield from bps.trigger_and_read(list(detectors) + [motor])
yield from bps.abs_set(
xpd_configuration["shutter"], XPD_SHUTTER_CONF["close"], wait=True
)
def outer_per_step(detectors, motor, step):
# Set a checkpoint in case the scan is interrupted
yield from checkpoint()
# Move the monochrometer to the inputted energy
logger.info('Outer Step: Moving {0} to {1}'.format(
outer_motor.name, step))
yield from abs_set(outer_motor, step, wait=True)
# Define what we will do at every motor step
def inner_per_step(detectors, motor, step):
# Set a checkpoint in case the scan is interrupted
yield from checkpoint()
"""
# Notify the user where we are trying to move to
goal_sample = inner_motor.position + inner_step_size
goal_index = inner_motor.locate_1d(goal_sample)
logger.info('Inner Step: Moving {0} to {1} (sample {2})'.format(
inner_motor.name, goal_index, goal_sample))
"""
# Move the motor to the inputted step
yield from rel_set(inner_motor, inner_step_size, wait=True)
if use_sequencer:
# # Start and wait for the sequencer
logger.info('Inner Step: Starting the sequencer')
yield from abs_set(sequencer, 1, wait=True)
# Wait the specified amount of time
if wait:
logger.info(
"Inner Step: Waiting for {0} second(s)...".format(wait))
time.sleep(wait)
# Fill the dataframe
scan_positions.append((
outer_motor.position,
#inner_motor.chip,
inner_motor.position,
#*inner_motor.index,
#*inner_motor.coordinates
))
# Define the larger inner scan as a list_scan. We cannot use
# rel_list_scan because it includes the reset_positions_decorator,
# which we do not want to do
yield from stub_wrapper(
list_scan([], inner_motor, inner_steps, per_step=inner_per_step))
def move_to_start_fly():
"See http://nsls-ii.github.io/bluesky/plans.html#the-per-step-hook"
# row_str = short_uid('row')
# yield from abs_set(xmotor, row_start, group=row_str)
# yield from one_1d_step([temp_nanoKB], motor, step)
# yield from bps.wait(group=row_str)
print(f"Start moving to beginning of the row")
row_str = short_uid('row')
yield from bps.checkpoint()
yield from bps.abs_set(xmotor, row_start, group=row_str)
yield from bps.abs_set(motor, step, group=row_str)
yield from bps.wait(group=row_str)
# yield from bps.trigger_and_read([temp_nanoKB, motor]) ## Uncomment this
print(f"Finished moving to the beginning of the row")
print(f"Fast axis: {xmotor.read()} Slow axis: {motor.read()}")
def solve_stub(detectors, motor, step, log=None):
'''
This stub should be a bit more generic
'''
bk_dev = detectors[0]
yield from bps.checkpoint()
yield from bps.mv(bk_dev.status, SolverState.unknown)
def step_stub(detectors, motor, x):
yield from bps.checkpoint()
yield from bps.mv(motor, x)
all_dev = list(detectors) + [motor]
r = (yield from bps.trigger_and_read(all_dev))
return r
def cb(val):
cmd = partial(step_stub, detectors, motor, val)
r = bridge.submit(cmd)
val = r[motor.readback.name]['value']
return val - step
bridge = setup_bridge()
def run_solver():
a, b = -10, 10
r = brentq(cb, a, b)
bridge.stopDelegation()
return r
yield from bps.mv(bk_dev.status, SolverState.searching)
yield from bps.mv(bk_dev.target, step)
thread = threading.Thread(target=run_solver, name='run_solver')
thread.start()
try:
(yield from bridge_plan_stub(bridge, log=log))
except Exception:
yield from bps.mv(bk_dev.status, SolverState.failed)
else:
yield from bps.mv(bk_dev.status, SolverState.finished)
thread.join()
del thread
def setup_plan(detectors, motors, *args, log=None, **kwargs):
'''retrieve the actual status
Reads the detectors and returns the state
Args:
detectors: detectors to read from
Motors are passed for convenience for a user that intends to
implement his own plan.
'''
if log is None:
log = logger
yield from bps.checkpoint()
log.info(f'Reading detectors {detectors}')
r = (yield from bps.trigger_and_read(detectors))
log.info(f'setup returned {r}')
return r
def custom_step(detectors, motor, step):
"""
Inner loop of a 1D step scan
Modified the default function for ``per_step`` param in 1D plans.
Add a pause to adjust the attenuator
"""
yield from checkpoint()
print('Set attenuator to {}'.format(step))
# adjust DMM range
if step < 12:
yield from abs_set(dmm.volt_range_dc, 10)
elif step < 30:
yield from abs_set(dmm.volt_range_dc, 1)
elif step >= 30:
yield from abs_set(dmm.volt_range_dc, 0.1)
yield from pause()
yield from abs_set(motor, step, wait=True)
return (yield from trigger_and_read(list(detectors) + [motor]))
def fly_once(y):
# for y in range(num_scans):
# go to start of row
yield from bps.checkpoint()
yield from bps.mv(mono.linear.velocity, 1)
yield from bps.mv(mono.linear, l_start)
# set the fly speed
yield from bps.mv(mono.linear.velocity, flyspeed)
yield from bps.trigger_and_read([mono], name="row_ends")
for v in ["p1600=0", "p1600=1"]:
yield from bps.mv(dtt, v)
yield from bps.sleep(0.1)
# arm the Struck
yield from bps.trigger(sclr, group=f"fly_energy_{y}")
if xspress3 is not None:
yield from bps.trigger(xspress3, group=f"fly_energy_{y}")
# fly the motor
yield from bps.abs_set(mono.linear,
l_stop + a_l_step_size,
group=f"fly_energy_{y}")
yield from bps.wait(group=f"fly_energy_{y}")
yield from bps.trigger_and_read([mono], name="row_ends")
yield from bps.mv(mono.linear.velocity, flyspeed)
# hard coded to let the sclr count its fingers and toes
yield from bps.sleep(0.1)
# read and save the struck
yield from bps.create(name="primary")
yield from bps.read(sclr)
if xspress3 is not None:
yield from bps.read(xspress3)
yield from bps.save()
def step_scan(experiment, cfg_tomo):
"""
Collect projects with step motion
"""
# unpack devices
det = experiment.det
tomostage = experiment.tomostage
yield from bps.mv(det.hdf1.nd_array_port, 'PROC1')
yield from bps.mv(det.tiff1.nd_array_port, 'PROC1')
yield from bps.mv(det.proc1.enable, 1)
yield from bps.mv(det.proc1.reset_filter, 1)
yield from bps.mv(det.proc1.num_filter, cfg_tomo['n_frames'])
angs = np.arange(
cfg_tomo['omega_start'],
cfg_tomo['omega_end'] + cfg_tomo['omega_step'] / 2,
cfg_tomo['omega_step'],
)
for ang in angs:
yield from bps.checkpoint()
yield from bps.mv(tomostage.preci, ang)
yield from bps.trigger_and_read([det])
def scan_closure():
# -------------------
# collect white field
# -------------------
# 1-1 monitor shutter status, auto-puase scan if beam is lost
yield from bps.open_run()
yield from bps.mv(A_shutter, 'open')
yield from bps.install_suspender(suspend_A_shutter)
#1-1.5 configure output plugins edited by Jason 07/19/2019
for me in [det.tiff1, det.hdf1]:
yield from bps.mv(me.file_path, fp)
yield from bps.mv(me.file_name, fn)
yield from bps.mv(me.file_write_mode, 2)
yield from bps.mv(me.num_capture, total_images)
yield from bps.mv(
me.file_template,
".".join([r"%s%s_%06d", config['output']['type'].lower()]))
if config['output']['type'] in ['tif', 'tiff']:
yield from bps.mv(det.tiff1.enable, 1)
yield from bps.mv(det.tiff1.capture, 1)
yield from bps.mv(det.hdf1.enable, 0)
elif config['output']['type'] in ['hdf', 'hdf1', 'hdf5']:
yield from bps.mv(det.tiff1.enable, 0)
yield from bps.mv(det.hdf1.enable, 1)
yield from bps.mv(det.hdf1.capture, 1)
else:
raise ValueError(f"Unsupported output type {output_dict['type']}")
# 1-2 move sample out of the way
initial_samx = samX.position
initial_samy = samY.position
initial_preci = preci.position
dx = config['tomo']['sample_out_position']['samX']
dy = config['tomo']['sample_out_position']['samY']
r = config['tomo']['sample_out_position']['preci']
yield from bps.mv(samX, initial_samx + dx)
yield from bps.mv(samY, initial_samy + dy)
yield from bps.mv(preci, r)
# 1-2.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 0)
# 1-3 collect front white field images
yield from bps.mv(det.hdf1.nd_array_port, 'PROC1')
yield from bps.mv(det.tiff1.nd_array_port, 'PROC1')
yield from bps.mv(det.proc1.enable, 1)
yield from bps.mv(det.proc1.reset_filter, 1)
yield from bps.mv(det.proc1.num_filter, n_frames)
yield from bps.mv(det.cam.trigger_mode, "Internal")
yield from bps.mv(det.cam.image_mode, "Multiple")
yield from bps.mv(det.cam.num_images, n_frames * n_white)
yield from bps.mv(det.cam.acquire_time, acquire_time)
yield from bps.mv(det.cam.acquire_period, acquire_period)
yield from bps.trigger_and_read([det])
# 1-4 move sample back
yield from bps.mv(samX, initial_samx)
yield from bps.mv(samY, initial_samy)
#yield from bps.mv(preci, initial_preci)
# -------------------
# collect projections
# -------------------
# 1-5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 1)
# 1-6 step and fly scan are differnt
if config['tomo']['type'].lower() == 'step':
yield from bps.mv(det.proc1.reset_filter, 1)
yield from bps.mv(det.cam.num_images, n_frames)
# 1-6 collect projections
for ang in angs:
yield from bps.checkpoint()
yield from bps.mv(preci, ang)
yield from bps.trigger_and_read([det])
elif config['tomo']['type'].lower() == 'fly':
yield from bps.mv(det.proc1.num_filter, 1)
yield from bps.mv(det.hdf1.nd_array_port, 'PG1')
yield from bps.mv(det.tiff1.nd_array_port, 'PG1')
yield from bps.mv(
psofly.start,
config['tomo']['omega_start'],
psofly.end,
config['tomo']['omega_end'],
psofly.scan_delta,
abs(config['tomo']['omega_step']),
psofly.slew_speed,
slew_speed,
)
# taxi
yield from bps.mv(psofly.taxi, "Taxi")
# setup detector to overlap for fly scan
yield from bps.mv(
det.cam.num_images,
n_projections,
det.cam.trigger_mode,
"Overlapped",
)
# start the fly scan
print("before trigger")
yield from bps.trigger(det, group='trigger')
print("waiting for trigger")
# yield from bps.wait(group='trigger')
print("before plan()")
try:
yield from psofly.plan()
except NotEnoughTriggers as err:
reason = (
f"{err.expected:.0f} were expected but {err.actual:.0f} were received."
)
yield from bps.close_run('fail', reason=reason)
return # short-circuit
# fly scan finished. switch image port and trigger_mode back
yield from bps.mv(det.cam.trigger_mode, "Internal")
yield from bps.mv(det.hdf1.nd_array_port, 'PROC1')
yield from bps.mv(det.tiff1.nd_array_port, 'PROC1')
else:
raise ValueError(f"Unknown scan type: {config['tomo']['type']}")
# ------------------
# collect back white
# ------------------
# 1-7 move the sample out of the way
# NOTE:
# this will return ALL motors to starting positions, we need a
# smart way to calculate a shorter trajectory to move sample
# out of way
yield from bps.mv(preci, r)
yield from bps.mv(samX, initial_samx + dx)
yield from bps.mv(samY, initial_samy + dy)
# 1-7.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 2)
# 1-8 take the back white
yield from bps.mv(det.proc1.num_filter, n_frames)
yield from bps.mv(det.cam.num_images, n_frames * n_white)
yield from bps.trigger_and_read([det])
# 1-9 move sample back
yield from bps.mv(samX, initial_samx)
yield from bps.mv(samY, initial_samy)
# -----------------
# collect back dark
# -----------------
# 1-10 close the shutter
yield from bps.remove_suspender(suspend_A_shutter)
yield from bps.mv(A_shutter, "close")
# 1-10.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 3)
# 1-11 collect the back dark
yield from bps.mv(det.cam.num_images, n_frames * n_dark)
yield from bps.trigger_and_read([det])
yield from bps.close_run('success')