def _collect_img(exposure,
dark_sub_bool,
sample_md,
tag,
RE_instance,
*,
calibrant=None,
detector=None):
"""helper function to collect image and return it"""
# grab beamtime object linked to run_engine
bto = RE_instance.beamtime
plan = ScanPlan(bto, ct, exposure).factory()
sample_md.update(bto)
if tag == "calib":
# instantiate Calibrant class
calibrant_obj = Calibration(calibrant=calibrant).calibrant
if calibrant_obj is None:
raise xpdAcqException("Invalid calibrant")
dSpacing = calibrant_obj.dSpacing
if not dSpacing:
raise xpdAcqException("empty dSpacing from calibrant")
sample_md.update({"dSpacing": dSpacing, "detector": detector})
plan = bpp.msg_mutator(plan, _inject_calibration_tag)
# collect image
uid = RE_instance(sample_md, plan)
"""
def inject_metadata(plan: typing.Generator,
metadata: dict) -> typing.Generator:
"""Inject the metadata into a plan."""
def _inject_metadata(msg: Msg):
"""Inject metadata in the start of the run."""
if msg.command == "open_run":
msg.kwargs.update(**metadata)
return msg
plan1 = bpp.msg_mutator(plan, _inject_metadata)
return plan1
def test_simple_replace():
new_cmd = 'replaced'
def change_command(msg):
return msg._replace(command=new_cmd)
num = 10
msgs = EchoRE(msg_mutator(echo_plan(num=num), change_command))
_verify_msg_seq(msgs,
m_len=num,
cmd_sq=[new_cmd] * num,
args_sq=[()] * num,
kwargs_sq=[{}] * num)
def test_simple_replace():
new_cmd = 'replaced'
def change_command(msg):
return msg._replace(command=new_cmd)
num = 10
msgs = EchoRE(msg_mutator(echo_plan(num=num),
change_command))
_verify_msg_seq(msgs, m_len=num,
cmd_sq=[new_cmd]*num,
args_sq=[()]*num,
kwargs_sq=[{}]*num)
def inner():
# Run plan (stripping open/close run messages)
yield from msg_mutator(plan, block_run_control)
# Yield result of Lorentz model
logger.debug(model.result.fit_report())
max_position = model.result.values['center']
# Check that the estimated position is reasonable
if not bounds[0] < max_position < bounds[1]:
raise ValueError("Predicted maximum position of {} is outside the "
"bounds {}".format(max_position, bounds))
# Order move to maximum position
logger.debug("Travelling to maximum of Lorentz at %s", max_position)
yield from abs_set(motor, model.result.values['center'], wait=True)
def test_msg_mutator_skip():
def skipper(msg):
if msg.command == 'SKIP':
return None
return msg
def skip_plan():
for c in 'abcd':
yield Msg(c, None)
yield Msg('SKIP', None)
pln = msg_mutator(skip_plan(), skipper)
msgs = EchoRE(pln)
_verify_msg_seq(msgs, m_len=4,
cmd_sq='abcd',
args_sq=[()]*4,
kwargs_sq=[{}]*4)
def test_msg_mutator_skip():
def skipper(msg):
if msg.command == 'SKIP':
return None
return msg
def skip_plan():
for c in 'abcd':
yield Msg(c, None)
yield Msg('SKIP', None)
pln = msg_mutator(skip_plan(), skipper)
msgs = EchoRE(pln)
_verify_msg_seq(msgs,
m_len=4,
cmd_sq='abcd',
args_sq=[()] * 4,
kwargs_sq=[{}] * 4)
def _collect_img(exposure,
dark_sub_bool,
sample_md,
RE_instance,
*,
calibrant=None,
detector=None):
"""helper function to collect image and return it"""
# grab beamtime object linked to run_engine
bto = RE_instance.beamtime
plan = ScanPlan(bto, ct, exposure).factory()
sample_md.update(bto)
dSpacing = find_dspacing(calibrant)
sample_md.update({"dSpacing": dSpacing, "detector": detector})
plan = bpp.msg_mutator(plan, _inject_calibration_tag)
# collect image
RE_instance(sample_md, plan)
def _collect_img(exposure,
dark_sub_bool,
sample_md,
tag,
RE_instance,
*,
calibrant=None,
detector=None):
"""helper function to collect image and return it"""
# grab beamtime object linked to run_engine
bto = RE_instance.beamtime
plan = ScanPlan(bto, ct, exposure).factory()
sample_md.update(bto)
if tag == "calib":
# instantiate Calibrant class
calibrant_obj = Calibration(calibrant=calibrant).calibrant
if calibrant_obj is None:
raise xpdAcqException("Invalid calibrant")
dSpacing = calibrant_obj.dSpacing
if not dSpacing:
raise xpdAcqException("empty dSpacing from calibrant")
sample_md.update({"dSpacing": dSpacing, "detector": detector})
plan = bpp.msg_mutator(plan, _inject_calibration_tag)
# collect image
uid = RE_instance(sample_md, plan)
# last one must be light
db = xpd_configuration["db"]
light_header = db[uid[-1]]
dark_uid = light_header["start"].get("sc_dk_field_uid")
dark_header = db[dark_uid]
dark_img = dark_header.data(glbl["image_field"])
dark_img = np.asarray(next(dark_img)).squeeze()
img = light_header.data(glbl["image_field"])
img = np.asarray(next(img)).squeeze()
if dark_sub_bool:
img -= dark_img
# FIXME: filename template from xpdAn
fn_template = "from_calib_func_{}.poni".format(_timestampstr(time.time()))
return img, fn_template
def translate_to_plan(self, plan, sample):
"""Translate a plan input into a generator
Parameters
----------
sample : list of int or dict-like
Sample metadata. If a beamtime object is linked,
an integer will be interpreted as the index appears in the
``bt.list()`` method, corresponding metadata will be passed.
A customized dict can also be passed as the sample
metadata.
plan : list of int or generator
Scan plan. If a beamtime object is linked, an integer
will be interpreted as the index appears in the
``bt.list()`` method, corresponding scan plan will be
A generator or that yields ``Msg`` objects (or an iterable
that returns such a generator) can also be passed.
Returns
-------
plan : generator
The generator of messages for the plan
"""
if isinstance(plan, list):
plan = [self.translate_to_plan(p, s) for p, s in zip(plan, sample)]
# If a plan is given as a int, look in up in the global registry.
else:
if isinstance(plan, int):
try:
plan = list(self.beamtime.scanplans.values())[plan]
except IndexError:
print("WARNING: hmm, there is no scanplan with index `{}`"
", please do `bt.list()` to check if it exists yet".
format(plan))
return
# If the plan is an xpdAcq 'ScanPlan', make the actual plan.
if isinstance(plan, ScanPlan):
plan = plan.factory()
mm = _sample_injector_factory(sample)
plan = bpp.msg_mutator(plan, mm)
return plan
def __call__(self,
sample,
plan,
subs=None,
*,
verify_write=False,
dark_strategy=periodic_dark,
robot=False,
**metadata_kw):
"""
Execute a plan
Any keyword arguments other than those listed below will
be interpreted as metadata and recorded with the run.
Parameters
----------
sample : int or dict-like or list of int or dict-like
Sample metadata. If a beamtime object is linked,
an integer will be interpreted as the index appears in the
``bt.list()`` method, corresponding metadata will be passed.
A customized dict can also be passed as the sample
metadata.
plan : int or generator or list of int or generator
Scan plan. If a beamtime object is linked, an integer
will be interpreted as the index appears in the
``bt.list()`` method, corresponding scan plan will be
A generator or that yields ``Msg`` objects (or an iterable
that returns such a generator) can also be passed.
subs: callable, list, or dict, optional
Temporary subscriptions (a.k.a. callbacks) to be used on
this run. Default to None. For convenience, any of the
following are accepted:
* a callable, which will be subscribed to 'all'
* a list of callables, which again will be subscribed to 'all'
* a dictionary, mapping specific subscriptions to callables or
lists of callables; valid keys are {'all', 'start', 'stop',
'event', 'descriptor'}
verify_write: bool, optional
Double check if the data have been written into database.
In general data is written in a lossless fashion at the
NSLS-II. Therefore, False by default.
dark_strategy: callable, optional.
Protocol of taking dark frame during experiment. Default
to the logic of matching dark frame and light frame with
the sample exposure time and frame rate. Details can be
found at ``http://xpdacq.github.io/xpdAcq/usb_Running.html#automated-dark-collection``
robot: bool, optional
If true run the scan as a robot scan, defaults to False
metadata_kw:
Extra keyword arguments for specifying metadata in the
run time. If the extra metdata has the same key as the
``sample``, ``ValueError`` will be raised.
Returns
-------
uids : list
list of uids (i.e. RunStart Document uids) of run(s)
"""
if self.md.get("robot", None) is not None:
raise RuntimeError("Robot must be specified at call time, not in"
"global metadata")
if robot:
metadata_kw.update(robot=True)
# The CustomizedRunEngine knows about a Beamtime object, and it
# interprets integers for 'sample' as indexes into the Beamtime's
# lists of Samples from all its Experiments.
# Turn everything into lists
sample, plan = self._normalize_sample_plan(sample, plan)
# Turn ints into actual samples
sample = self.translate_to_sample(sample)
if robot:
print("This is the current experimental plan:")
print("Sample Name: Sample Position")
for s, p in [
(k, [o[1] for o in v])
for k, v in groupby(zip(sample, plan), key=lambda x: x[0])
]:
print(
s["sample_name"],
":",
self._beamtime.robot_info[s["sa_uid"]],
)
for pp in p:
# Check if this is a registered scanplan
if isinstance(pp, int):
print(
indent(
"{}".format(
list(
self.beamtime.scanplans.values())[pp]),
"\t",
))
else:
print("This scan is not a registered scanplan so no "
"summary")
ip = input("Is this ok? [y]/n")
if ip.lower() == "n":
return
# Turn ints into generators
plan = self.translate_to_plan(plan, sample)
# Collect the plans by contiguous samples and chain them
sample, plan = zip(
*[(k, pchain(*[o[1] for o in v]))
for k, v in groupby(zip(sample, plan), key=lambda x: x[0])])
# Make the complete plan by chaining the chained plans
total_plan = []
for s, p in zip(sample, plan):
if robot:
# If robot scan inject the needed md into the sample
s.update(self._beamtime.robot_info[s["sa_uid"]])
total_plan.append(robot_wrapper(p, s))
else:
total_plan.append(p)
plan = pchain(*total_plan)
_subs = normalize_subs_input(subs)
if verify_write:
_subs.update({"stop": verify_files_saved})
if self._beamtime and self._beamtime.get("bt_wavelength") is None:
print("WARNING: there is no wavelength information in current"
"beamtime object, scan will keep going....")
if glbl["shutter_control"]:
# Alter the plan to incorporate dark frames.
# only works if user allows shutter control
if glbl["auto_dark"]:
plan = dark_strategy(plan)
plan = bpp.msg_mutator(plan, _inject_qualified_dark_frame_uid)
# force to close shutter after scan
plan = bpp.finalize_wrapper(
plan,
bps.abs_set(
xpd_configuration["shutter"],
XPD_SHUTTER_CONF["close"],
wait=True,
),
)
# Load calibration file
if glbl["auto_load_calib"]:
plan = bpp.msg_mutator(plan, _inject_calibration_md)
# Insert xpdacq md version
plan = bpp.msg_mutator(plan, _inject_xpdacq_md_version)
# Insert analysis stage tag
plan = bpp.msg_mutator(plan, _inject_analysis_stage)
# Insert filter metadata
plan = bpp.msg_mutator(plan, _inject_filter_positions)
# Execute
return super().__call__(plan, subs, **metadata_kw)
def xpdacq_composer(beamtime: Beamtime,
sample: typing.Union[int, dict, typing.List[int]],
plan: typing.Union[int, Generator, typing.List[int],
typing.Generator],
*,
robot: bool = False,
shutter_control: typing.Tuple[Device, typing.Any] = None,
dark_strategy: typing.Callable = None,
auto_load_calib: bool = False) -> typing.Generator:
"""Create a list of plans for an xpd experiment. Used in `~xpdacq.xpdacq.CumstomeizedRunEngine.__call__`.
Parameters
----------
beamtime :
The beamtime object.
sample :
If a beamtime object is linked, an integer will be interpreted as the index appears in the ``bt.list()``
method, corresponding metadata will be passed. A customized dict can also be passed as the sample
metadata.
plan :
Scan plan. If a beamtime object is linked, an integer will be interpreted as the index appears in the
``bt.list()`` method, corresponding scan plan will be A generator or that yields ``Msg`` objects (or an
iterable that returns such a generator) can also be passed.
robot :
If True, the plan is meant to be using robot.
shutter_control :
A tuple of the shutter device and its close state. The shutter will be closed after the whole scan.
If None, shutter won't be controlled and no dark will be taken.
dark_strategy :
The strategy how to take the dark frame.
auto_load_calib :
If True, the calibration meta-data will be injected into the run. Else, do nothing.
Returns
-------
grand_plan :
The grand plan to be run by the RunEngine.
"""
# check wavelength
warn_wavelength(beamtime)
# noramlize the sample and plan to two lists with the same length
lst_sample, lst_plan = _normalize_sample_plan(sample, plan)
# Turn ints into actual sample dictionary
lst_metadata = [translate_to_sample(beamtime, s) for s in lst_sample]
# Turn ints into bluesky generators
lst_bp_plan = [translate_to_plan(beamtime, p) for p in lst_plan]
# Make the complete plan by chaining the chained plans
if robot:
lst_bp_plan = gen_robot_plans(beamtime, lst_metadata, lst_bp_plan)
# shutter control and dark
if shutter_control:
shutter, close_state = shutter_control
# Alter the plan to incorporate dark frames.
if dark_strategy:
lst_bp_plan = [dark_strategy(p) for p in lst_bp_plan]
lst_bp_plan = [
bpp.msg_mutator(p, _inject_qualified_dark_frame_uid)
for p in lst_bp_plan
]
# force to close shutter after scan
lst_bp_plan = [
close_shutter_at_last(p, shutter, close_state) for p in lst_bp_plan
]
# Load calibration file
if auto_load_calib:
lst_bp_plan = [
bpp.msg_mutator(p, _inject_calibration_md) for p in lst_bp_plan
]
# Insert xpdacq md version
lst_bp_plan = [
bpp.msg_mutator(p, _inject_xpdacq_md_version) for p in lst_bp_plan
]
# Insert analysis stage tag
lst_bp_plan = [
bpp.msg_mutator(p, _inject_analysis_stage) for p in lst_bp_plan
]
# Insert filter metadata
lst_bp_plan = [
bpp.msg_mutator(p, _inject_filter_positions) for p in lst_bp_plan
]
# Inject the sample metadata
lst_bp_plan = [
inject_metadata(p, s) for p, s in zip(lst_bp_plan, lst_metadata)
]
return pchain(*lst_bp_plan)