def test_peak_statistics_with_derivatives(RE):
"""peak statistics calculation on simple gaussian function with derivatives
"""
x = "motor"
y = "det"
num_points = 100
ps = PeakStats(x, y, calc_derivative_and_stats=True)
RE.subscribe(ps)
RE(scan([det], motor, -5, 5, num_points))
assert hasattr(ps, "derivative_stats")
der_fields = [
"x", "y", "min", "max", "com", "cen", "crossings", "fwhm", "lin_bkg"
]
for field in der_fields:
assert hasattr(ps.derivative_stats,
field), f"{field} is not an attribute of ps.der"
assert type(ps.derivative_stats.x) is np.ndarray
assert type(ps.derivative_stats.y) is np.ndarray
assert type(ps.derivative_stats.min) is tuple
assert type(ps.derivative_stats.max) is tuple
assert type(ps.derivative_stats.com) is np.float64
assert type(ps.derivative_stats.cen) is np.float64
assert type(ps.derivative_stats.crossings) is np.ndarray
if len(ps.derivative_stats.crossings) >= 2:
assert type(ps.derivative_stats.fwhm) is float
else:
assert ps.derivative_stats.fwhm is None
assert len(ps.derivative_stats.x) == num_points - 1
assert len(ps.derivative_stats.y) == num_points - 1
assert np.allclose(np.diff(ps.y_data), ps.derivative_stats.y, atol=1e-10)
def tune(signal, motor, width=None, num=None, peak_choice=None, md=None):
"""tune an axis, single pass. Scans axis centered at current position
from ``-width/2`` to ``width/2`` with ``num`` observations
"""
# set up parameters for tune
name = motor.name
try: # if both exist, take provided parameter
# if argument defined, short circuting ignores KeyError
width = width or tune_params[name]['width']
num = num or tune_params[name]['num']
peak_choice = peak_choice or tune_params[name]['peak_choice']
except KeyError as ke:
msg = f'Tuning parameters not defined for provided motor: {name}'
raise KeyError(msg)
initial_position = motor.position
# TO-DO Check to make sure params are in dictionary, abort if not
# gather metadata
_md = {'plan_name': motor.name + '.tune',
'motors': motor.name,
'detectors': signal.name,
'hints': dict(
dimensions = [ ([motor.name], 'primary')]
)
}
_md.update(md or {})
peak_stats = PeakStats(x=motor.name, y=signal.name)
# start plans
@subs_decorator(peak_stats)
@inject_md_decorator(_md)
def _scan(md=None):
yield from bp.rel_scan([signal], motor, -width/2, width/2, num)
# Grab final position from subscribed peak_stats
valid_peak = peak_stats.max[-1] >= (4 * peak_stats.min[-1])
if peak_stats.max is None:
valid_peak = False
final_position = initial_position
if valid_peak: # Condition for finding a peak
if peak_choice == 'cen':
final_position = peak_stats.cen
elif peak_choice == 'com':
final_position = peak_stats.com
yield from bps.mv(motor, final_position)
return (yield from _scan())
def test_peak_statistics(RE):
"""peak statistics calculation on simple gaussian function
"""
x = 'motor'
y = 'det'
ps = PeakStats(x, y)
RE.subscribe(ps)
RE(scan([det], motor, -5, 5, 100))
np.allclose(ps.cen, 0, atol=1e-6)
np.allclose(ps.com, 0, atol=1e-6)
fwhm_gauss = 2 * np.sqrt(2 * np.log(2)) # theoretical value with std=1
np.allclose(ps.fwhm, fwhm_gauss, atol=1e-2)
def inner():
y_signal = peaky.calculated_value
x_signal = mot
ps = PeakStats(x_signal.name, y_signal.name)
RE.subscribe(ps) # collects data during scan # FIXME: trouble here
yield from bp.scan([y_signal, calc.calculated_value],
x_signal,
-2,
0,
41,
md=md)
tbl = pyRestTable.Table()
tbl.labels = "PeakStats value".split()
tbl.rows = [[k, ps.__getattribute__(k)]
for k in sorted("min max cen com fwhm".split())]
h = db[-1]
logger.info(f"scan_id={RE.md['scan_id']}")
logger.info(f"uid={h.start['uid']}")
logger.info(tbl)
calc.reset()
def check_tth():
'''Align the spectrometer rotation angle'''
yield from bps.mv(geo.det_mode, 1)
yield from bps.mv(abs2, 6)
yield from mabt(0, 0, 0)
tmp1 = geo.tth.position
print('resetting tth')
yield from bps.mv(sh, -1)
yield from bps.mv(shutter, 1) # open shutter
local_peaks = PeakStats(tth.user_readback.name,
quadem.current3.mean_value.name)
#yield from bp.rel_scan([quadem],tth,-0.1,0.1,21)
yield from bpp.subs_wrapper(bp.rel_scan([quadem], tth, -0.1, 0.1, 21),
local_peaks)
tmp2 = local_peaks.cen #get the height for roi2 of quadem with a max intens
yield from bps.mv(tth, tmp2)
yield from set_tth(tmp1)
yield from bps.mv(shutter, 0) # close shutter
def check_astth(detector=lambda_det):
'''Align the detector arm rotation angle'''
yield from bps.mv(geo.det_mode, 1)
yield from bps.mv(abs2, 6)
yield from mabt(0.0, 0.0, 0)
tmp1 = geo.astth.position
yield from bps.mvr(sh, -1)
print('setting astth')
yield from bps.mv(shutter, 1) # open shutter
# yield from bp.rel_scan([detector],astth,-0.1,0.1,21)
# tmp2=peaks.cen['%s_stats2_total'%detector.name]
local_peaks = PeakStats(astth.user_readback.name,
'%s_stats2_total' % detector.name)
yield from bpp.subs_wrapper(bp.rel_scan([detector], astth, -0.1, 0.1, 21),
local_peaks)
tmp2 = local_peaks.cen #get the height for roi2 of detector.name with max intens
yield from bps.mv(astth, tmp2)
yield from bps.mv(shutter, 0) # close shutter
yield from set_astth(tmp1)
def check_ih():
'''Align the Align the spectrometer stage height
'''
yield from bps.mv(geo.det_mode, 1) #move lamda detector in ?
yield from bps.mv(abs2, 6) #move the second absorber in
yield from mabt(0, 0, 0) # don't understand???,
yield from bps.mv(sh, -1) # move the Sample vertical translation to -1
yield from bps.mv(shutter, 1) # open shutter
print('resetting ih')
#yield from bp.rel_scan([quadem],ih,-0.15,0.15,16) #scan the quadem detector against XtalDfl-height
#tmp=peaks.cen['quadem_current3_mean_value'] #get the height for roi2 of quadem with a max intensity
local_peaks = PeakStats(ih.user_readback.name,
quadem.current3.mean_value.name)
yield from bpp.subs_wrapper(bp.rel_scan([quadem], ih, -0.15, 0.15, 16),
local_peaks)
tmp = local_peaks.cen #get the height for roi2 of quadem with a max intens
yield from bps.mv(ih, tmp) #move the XtalDfl to this height
yield from set_ih(0) #set this height as 0
yield from bps.mv(shutter, 0) # close shutter
def test_peak_statistics(RE):
"""peak statistics calculation on simple gaussian function
"""
x = 'motor'
y = 'det'
ps = PeakStats(x, y)
RE.subscribe(ps)
RE(scan([det], motor, -5, 5, 100))
fields = [
"x", "y", "min", "max", "com", "cen", "crossings", "fwhm", "lin_bkg"
]
for field in fields:
assert hasattr(ps, field), f"{field} is not an attribute of ps"
np.allclose(ps.cen, 0, atol=1e-6)
np.allclose(ps.com, 0, atol=1e-6)
fwhm_gauss = 2 * np.sqrt(2 * np.log(2)) # theoretical value with std=1
assert np.allclose(ps.fwhm, fwhm_gauss, atol=1e-2)
def check_sh_coarse(value=0, detector=lambda_det):
'''
Aligh the sample height
'''
yield from bps.mv(geo.det_mode, 1)
yield from bps.mv(abs2, 6)
yield from mabt(value, value, 0)
tmp1 = geo.sh.position
#Msg('reset_settle_time', sh.settle_time, 2)
print('Start the height scan before GID')
# yield from bp.rel_scan([detector],sh,-1,1,21,per_step=shutter_flash_scan)
# tmp2=peaks.cen['%s_stats2_total'%detector.name]
local_peaks = PeakStats(sh.user_readback.name,
'%s_stats2_total' % detector.name)
yield from bpp.subs_wrapper(
bp.rel_scan([detector], sh, -1, 1, 21, per_step=shutter_flash_scan),
local_peaks)
tmp2 = local_peaks.cen #get the height for roi2 of detector.name with max intens )
yield from bps.mv(sh, tmp2)
yield from set_sh(tmp1)
Msg('reset_settle_time', sh.settle_time, 0)
def test_peak_statistics_compare_chx(RE):
"""This test focuses on gaussian function with noise.
"""
s = np.random.RandomState(1)
noisy_det_fix = SynGauss('noisy_det_fix',
motor,
'motor',
center=0,
Imax=1,
noise='uniform',
sigma=1,
noise_multiplier=0.1,
random_state=s)
x = 'motor'
y = 'noisy_det_fix'
ps = PeakStats(x, y)
RE.subscribe(ps)
RE(scan([noisy_det_fix], motor, -5, 5, 100))
ps_chx = get_ps(ps.x_data, ps.y_data)
assert np.allclose(ps.cen, ps_chx['cen'], atol=1e-6)
assert np.allclose(ps.com, ps_chx['com'], atol=1e-6)
assert np.allclose(ps.fwhm, ps_chx['fwhm'], atol=1e-6)
def check_sh_fine(value=0.05, detector=lambda_det):
yield from bps.mv(geo.det_mode, 1)
yield from bps.mv(abs2, 5)
yield from mabt(value, value, 0)
tmp1 = geo.sh.position
print('Start the height scan before GID')
# Msg('reset_settle_time', sh.settle_time, value)
# yield from bp.rel_scan([detector],sh,-0.1,0.1,21,per_step=shutter_flash_scan)
# tmp2=peaks.cen['%s_stats2_total'%detector.name]
local_peaks = PeakStats(sh.user_readback.name,
'%s_stats2_total' % detector.name)
yield from bpp.subs_wrapper(
bp.rel_scan([detector],
sh,
-0.15,
0.15,
16,
per_step=shutter_flash_scan), local_peaks)
print("at #1")
tmp2 = local_peaks.cen #get the height for roi2 of detector.name with max intens
print("at #2")
yield from bps.mv(sh, tmp2)
yield from set_sh(tmp1)
Msg('reset_settle_time', sh.settle_time, 0)
if not SimAlign:
motor2.move(det4offset+10.0)
motor.move(alignRange[0])
if plotter is None:
figTh, thAx = plt.subplots()
else:
thAx = plotter
cur_color = fit_colors[iteration % len(fit_colors)]
coarsePlot = LivePlot(detector_name,x=motor_name, linestyle = 'none',
marker = '^', markerfacecolor = 'none',
markeredgecolor = cur_color, ax = thAx,
label = '{} - coarse'.format(iteration))
coarsePeak = PeakStats(motor_name,detector_name)
lt = LiveTable([detector, motor])
if verbose:
coarse_cbs = [coarsePlot,coarsePeak, lt]
else:
coarse_cbs = [coarsePlot,coarsePeak]
@subs_decorator(coarse_cbs)
def coarseScan(detector, motor, cRange, pts = 10):
#Coarse scan to find region of peak
yield from scan([detector], motor, cRange[0], cRange[1], num = pts)
yield from coarseScan(detector, motor, alignRange, pts = coarsePTS)
def tune(self, width=None, num=None, md=None):
"""
BlueSky plan to execute one pass through the current scan range
Scan self.axis centered about current position from
``-width/2`` to ``+width/2`` with ``num`` observations.
If a peak was detected (default check is that max >= 4*min),
then set ``self.tune_ok = True``.
PARAMETERS
width : float
width of the tuning scan in the units of ``self.axis``
Default value in ``self.width`` (initially 1)
num : int
number of steps
Default value in ``self.num`` (initially 10)
md : dict, optional
metadata
"""
width = width or self.width
num = num or self.num
if self.peak_choice not in self._peak_choices_:
msg = "peak_choice must be one of {}, geave {}"
msg = msg.format(self._peak_choices_, self.peak_choice)
raise ValueError(msg)
initial_position = self.axis.position
final_position = initial_position # unless tuned
start = initial_position - width/2
finish = initial_position + width/2
self.tune_ok = False
tune_md = dict(
width = width,
initial_position = self.axis.position,
time_iso8601 = str(datetime.datetime.now()),
)
_md = {'tune_md': tune_md,
'plan_name': self.__class__.__name__ + '.tune',
'tune_parameters': dict(
num = num,
width = width,
initial_position = self.axis.position,
peak_choice = self.peak_choice,
x_axis = self.axis.name,
y_axis = self.signal_name,
),
'hints': dict(
dimensions = [
(
[self.axis.name],
'primary')]
)
}
_md.update(md or {})
if "pass_max" not in _md:
self.stats = []
self.peaks = PeakStats(x=self.axis.name, y=self.signal_name)
class Results(Device):
"""because bps.read() needs a Device or a Signal)"""
tune_ok = Component(Signal)
initial_position = Component(Signal)
final_position = Component(Signal)
center = Component(Signal)
# - - - - -
x = Component(Signal)
y = Component(Signal)
cen = Component(Signal)
com = Component(Signal)
fwhm = Component(Signal)
min = Component(Signal)
max = Component(Signal)
crossings = Component(Signal)
peakstats_attrs = "x y cen com fwhm min max crossings".split()
def report(self):
keys = self.peakstats_attrs + "tune_ok center initial_position final_position".split()
for key in keys:
print("{} : {}".format(key, getattr(self, key).value))
@bpp.subs_decorator(self.peaks)
def _scan(md=None):
yield from bps.open_run(md)
position_list = np.linspace(start, finish, num)
signal_list = list(self.signals)
signal_list += [self.axis,]
for pos in position_list:
yield from bps.mv(self.axis, pos)
yield from bps.trigger_and_read(signal_list)
final_position = initial_position
if self.peak_detected():
self.tune_ok = True
if self.peak_choice == "cen":
final_position = self.peaks.cen
elif self.peak_choice == "com":
final_position = self.peaks.com
else:
final_position = None
self.center = final_position
# add stream with results
# yield from add_results_stream()
stream_name = "PeakStats"
results = Results(name=stream_name)
for key in "tune_ok center".split():
getattr(results, key).put(getattr(self, key))
results.final_position.put(final_position)
results.initial_position.put(initial_position)
for key in results.peakstats_attrs:
v = getattr(self.peaks, key)
if key in ("crossings", "min", "max"):
v = np.array(v)
getattr(results, key).put(v)
if results.tune_ok.value:
yield from bps.create(name=stream_name)
yield from bps.read(results)
yield from bps.save()
yield from bps.mv(self.axis, final_position)
self.stats.append(self.peaks)
yield from bps.close_run()
results.report()
return (yield from _scan(md=_md))
class TuneAxis(object):
"""
tune an axis with a signal
This class provides a tuning object so that a Device or other entity
may gain its own tuning process, keeping track of the particulars
needed to tune this device again. For example, one could add
a tuner to a motor stage::
motor = EpicsMotor("xxx:motor", "motor")
motor.tuner = TuneAxis([det], motor)
Then the ``motor`` could be tuned individually::
RE(motor.tuner.tune(md={"activity": "tuning"}))
or the :meth:`tune()` could be part of a plan with other steps.
Example::
tuner = TuneAxis([det], axis)
live_table = LiveTable(["axis", "det"])
RE(tuner.multi_pass_tune(width=2, num=9), live_table)
RE(tuner.tune(width=0.05, num=9), live_table)
Also see the jupyter notebook referenced here:
:ref:`example_tuneaxis`.
.. autosummary::
~tune
~multi_pass_tune
~peak_detected
"""
_peak_choices_ = "cen com".split()
def __init__(self, signals, axis, signal_name=None):
self.signals = signals
self.signal_name = signal_name or signals[0].name
self.axis = axis
self.stats = {}
self.tune_ok = False
self.peaks = None
self.peak_choice = self._peak_choices_[0]
self.center = None
self.stats = []
# defaults
self.width = 1
self.num = 10
self.step_factor = 4
self.pass_max = 6
self.snake = True
def tune(self, width=None, num=None, md=None):
"""
BlueSky plan to execute one pass through the current scan range
Scan self.axis centered about current position from
``-width/2`` to ``+width/2`` with ``num`` observations.
If a peak was detected (default check is that max >= 4*min),
then set ``self.tune_ok = True``.
PARAMETERS
width : float
width of the tuning scan in the units of ``self.axis``
Default value in ``self.width`` (initially 1)
num : int
number of steps
Default value in ``self.num`` (initially 10)
md : dict, optional
metadata
"""
width = width or self.width
num = num or self.num
if self.peak_choice not in self._peak_choices_:
msg = "peak_choice must be one of {}, geave {}"
msg = msg.format(self._peak_choices_, self.peak_choice)
raise ValueError(msg)
initial_position = self.axis.position
final_position = initial_position # unless tuned
start = initial_position - width/2
finish = initial_position + width/2
self.tune_ok = False
tune_md = dict(
width = width,
initial_position = self.axis.position,
time_iso8601 = str(datetime.datetime.now()),
)
_md = {'tune_md': tune_md,
'plan_name': self.__class__.__name__ + '.tune',
'tune_parameters': dict(
num = num,
width = width,
initial_position = self.axis.position,
peak_choice = self.peak_choice,
x_axis = self.axis.name,
y_axis = self.signal_name,
),
'hints': dict(
dimensions = [
(
[self.axis.name],
'primary')]
)
}
_md.update(md or {})
if "pass_max" not in _md:
self.stats = []
self.peaks = PeakStats(x=self.axis.name, y=self.signal_name)
class Results(Device):
"""because bps.read() needs a Device or a Signal)"""
tune_ok = Component(Signal)
initial_position = Component(Signal)
final_position = Component(Signal)
center = Component(Signal)
# - - - - -
x = Component(Signal)
y = Component(Signal)
cen = Component(Signal)
com = Component(Signal)
fwhm = Component(Signal)
min = Component(Signal)
max = Component(Signal)
crossings = Component(Signal)
peakstats_attrs = "x y cen com fwhm min max crossings".split()
def report(self):
keys = self.peakstats_attrs + "tune_ok center initial_position final_position".split()
for key in keys:
print("{} : {}".format(key, getattr(self, key).value))
@bpp.subs_decorator(self.peaks)
def _scan(md=None):
yield from bps.open_run(md)
position_list = np.linspace(start, finish, num)
signal_list = list(self.signals)
signal_list += [self.axis,]
for pos in position_list:
yield from bps.mv(self.axis, pos)
yield from bps.trigger_and_read(signal_list)
final_position = initial_position
if self.peak_detected():
self.tune_ok = True
if self.peak_choice == "cen":
final_position = self.peaks.cen
elif self.peak_choice == "com":
final_position = self.peaks.com
else:
final_position = None
self.center = final_position
# add stream with results
# yield from add_results_stream()
stream_name = "PeakStats"
results = Results(name=stream_name)
for key in "tune_ok center".split():
getattr(results, key).put(getattr(self, key))
results.final_position.put(final_position)
results.initial_position.put(initial_position)
for key in results.peakstats_attrs:
v = getattr(self.peaks, key)
if key in ("crossings", "min", "max"):
v = np.array(v)
getattr(results, key).put(v)
if results.tune_ok.value:
yield from bps.create(name=stream_name)
yield from bps.read(results)
yield from bps.save()
yield from bps.mv(self.axis, final_position)
self.stats.append(self.peaks)
yield from bps.close_run()
results.report()
return (yield from _scan(md=_md))
def multi_pass_tune(self, width=None, step_factor=None,
num=None, pass_max=None, snake=None, md=None):
"""
BlueSky plan for tuning this axis with this signal
Execute multiple passes to refine the centroid determination.
Each subsequent pass will reduce the width of scan by ``step_factor``.
If ``snake=True`` then the scan direction will reverse with
each subsequent pass.
PARAMETERS
width : float
width of the tuning scan in the units of ``self.axis``
Default value in ``self.width`` (initially 1)
num : int
number of steps
Default value in ``self.num`` (initially 10)
step_factor : float
This reduces the width of the next tuning scan by the given factor.
Default value in ``self.step_factor`` (initially 4)
pass_max : int
Maximum number of passes to be executed (avoids runaway
scans when a centroid is not found).
Default value in ``self.pass_max`` (initially 10)
snake : bool
If ``True``, reverse scan direction on next pass.
Default value in ``self.snake`` (initially True)
md : dict, optional
metadata
"""
width = width or self.width
num = num or self.num
step_factor = step_factor or self.step_factor
snake = snake or self.snake
pass_max = pass_max or self.pass_max
self.stats = []
def _scan(width=1, step_factor=10, num=10, snake=True):
for _pass_number in range(pass_max):
_md = {'pass': _pass_number+1,
'pass_max': pass_max,
'plan_name': self.__class__.__name__ + '.multi_pass_tune',
}
_md.update(md or {})
yield from self.tune(width=width, num=num, md=_md)
if not self.tune_ok:
return
width /= step_factor
if snake:
width *= -1
return (
yield from _scan(
width=width, step_factor=step_factor, num=num, snake=snake))
def peak_detected(self):
"""
returns True if a peak was detected, otherwise False
The default algorithm identifies a peak when the maximum
value is four times the minimum value. Change this routine
by subclassing :class:`TuneAxis` and override :meth:`peak_detected`.
"""
if self.peaks is None:
return False
self.peaks.compute()
if self.peaks.max is None:
return False
ymax = self.peaks.max[-1]
ymin = self.peaks.min[-1]
return ymax > 4*ymin # this works for USAXS@APS
from bluesky import RunEngine
from bluesky.callbacks.fitting import PeakStats
from bluesky.callbacks.mpl_plotting import plot_peak_stats
from ophyd.sim import motor, det
from bluesky.plans import scan
RE = RunEngine({})
ps = PeakStats('motor', 'det')
RE(scan([det], motor, -5, 5, 10), ps)
plot_peak_stats(ps)
class TuneAxis(object):
"""
tune an axis with a signal
This class provides a tuning object so that a Device or other entity
may gain its own tuning process, keeping track of the particulars
needed to tune this device again. For example, one could add
a tuner to a motor stage::
motor = EpicsMotor("xxx:motor", "motor")
motor.tuner = TuneAxis([det], motor)
Then the ``motor`` could be tuned individually::
RE(motor.tuner.tune(md={"activity": "tuning"}))
or the :meth:`tune()` could be part of a plan with other steps.
Example::
tuner = TuneAxis([det], axis)
live_table = LiveTable(["axis", "det"])
RE(tuner.multi_pass_tune(width=2, num=9), live_table)
RE(tuner.tune(width=0.05, num=9), live_table)
Also see the jupyter notebook referenced here:
:ref:`example_tuneaxis`.
.. autosummary::
~tune
~multi_pass_tune
~peak_detected
SEE ALSO
.. autosummary::
~tune_axes
"""
_peak_choices_ = "cen com".split()
def __init__(self, signals, axis, signal_name=None):
self.signals = signals
self.signal_name = signal_name or signals[0].name
self.axis = axis
self.tune_ok = False
self.peaks = None
self.peak_choice = self._peak_choices_[0]
self.center = None
self.stats = []
# defaults
self.width = 1
self.num = 10
self.step_factor = 4
self.peak_factor = 4
self.pass_max = 4
self.snake = True
def tune(self, width=None, num=None, peak_factor=None, md=None):
"""
Bluesky plan to execute one pass through the current scan range
Scan self.axis centered about current position from
``-width/2`` to ``+width/2`` with ``num`` observations.
If a peak was detected (default check is that max >= 4*min),
then set ``self.tune_ok = True``.
PARAMETERS
width : float
width of the tuning scan in the units of ``self.axis``
Default value in ``self.width`` (initially 1)
num : int
number of steps
Default value in ``self.num`` (initially 10)
md : dict, optional
metadata
"""
width = width or self.width
num = num or self.num
peak_factor = peak_factor or self.peak_factor
if self.peak_choice not in self._peak_choices_:
msg = "peak_choice must be one of {}, geave {}"
msg = msg.format(self._peak_choices_, self.peak_choice)
raise ValueError(msg)
initial_position = self.axis.position
# final_position = initial_position # unless tuned
start = initial_position - width/2
finish = initial_position + width/2
self.tune_ok = False
tune_md = dict(
width = width,
initial_position = self.axis.position,
time_iso8601 = str(datetime.datetime.now()),
)
_md = {'tune_md': tune_md,
'plan_name': self.__class__.__name__ + '.tune',
'tune_parameters': dict(
num = num,
width = width,
initial_position = self.axis.position,
peak_choice = self.peak_choice,
x_axis = self.axis.name,
y_axis = self.signal_name,
),
'motors': (self.axis.name,),
'detectors': (self.signal_name,),
'hints': dict(
dimensions = [
(
[self.axis.name],
'primary')]
)
}
_md.update(md or {})
if "pass_max" not in _md:
self.stats = []
self.peaks = PeakStats(x=self.axis.name, y=self.signal_name)
@bpp.subs_decorator(self.peaks)
def _scan(md=None):
yield from bps.open_run(md)
position_list = np.linspace(start, finish, num)
signal_list = list(self.signals)
signal_list += [self.axis,]
for pos in position_list:
yield from bps.mv(self.axis, pos)
yield from bps.trigger_and_read(signal_list)
final_position = initial_position
if self.peak_detected(peak_factor=peak_factor):
self.tune_ok = True
if self.peak_choice == "cen":
final_position = self.peaks.cen
elif self.peak_choice == "com":
final_position = self.peaks.com
else:
final_position = None
self.center = final_position
# add stream with results
# yield from add_results_stream()
stream_name = "PeakStats"
results = TuneResults(name=stream_name)
results.tune_ok.put(self.tune_ok)
results.center.put(self.center)
results.final_position.put(final_position)
results.initial_position.put(initial_position)
results.set_stats(self.peaks)
self.stats.append(results)
if results.tune_ok.get():
yield from bps.create(name=stream_name)
try:
yield from bps.read(results)
except ValueError as ex:
separator = " "*8 + "-"*12
print(separator)
print(f"Error saving stream {stream_name}:\n{ex}")
print(separator)
yield from bps.save()
yield from bps.mv(self.axis, final_position)
yield from bps.close_run()
results.report(stream_name)
return (yield from _scan(md=_md))
def multi_pass_tune(self, width=None, step_factor=None,
num=None, pass_max=None,
peak_factor=None,
snake=None, md=None):
"""
Bluesky plan for tuning this axis with this signal
Execute multiple passes to refine the centroid determination.
Each subsequent pass will reduce the width of scan by ``step_factor``.
If ``snake=True`` then the scan direction will reverse with
each subsequent pass.
PARAMETERS
width : float
width of the tuning scan in the units of ``self.axis``
Default value in ``self.width`` (initially 1)
num : int
number of steps
Default value in ``self.num`` (initially 10)
step_factor : float
This reduces the width of the next tuning scan by the given factor.
Default value in ``self.step_factor`` (initially 4)
pass_max : int
Maximum number of passes to be executed (avoids runaway
scans when a centroid is not found).
Default value in ``self.pass_max`` (initially 4)
peak_factor : float (default: 4)
peak maximum must be greater than ``peak_factor*minimum``
snake : bool
If ``True``, reverse scan direction on next pass.
Default value in ``self.snake`` (initially True)
md : dict, optional
metadata
"""
width = width or self.width
num = num or self.num
step_factor = step_factor or self.step_factor
snake = snake or self.snake
pass_max = pass_max or self.pass_max
peak_factor = peak_factor or self.peak_factor
self.stats = []
def _scan(width=1, step_factor=10, num=10, snake=True):
for _pass_number in range(pass_max):
logger.info("Multipass tune %d of %d", _pass_number+1, pass_max)
_md = {'pass': _pass_number+1,
'pass_max': pass_max,
'plan_name': self.__class__.__name__ + '.multi_pass_tune',
}
_md.update(md or {})
yield from self.tune(width=width, num=num, peak_factor=peak_factor, md=_md)
if not self.tune_ok:
return
if width > 0:
sign = 1
else:
sign = -1
width = sign * 2 * self.stats[-1].fwhm.get()
if snake:
width *= -1
return (
yield from _scan(
width=width, step_factor=step_factor, num=num, snake=snake))
def multi_pass_tune_summary(self):
t = pyRestTable.Table()
t.labels = "pass Ok? center width max.X max.Y".split()
for i, stat in enumerate(self.stats):
row = [i+1,]
row.append(stat.tune_ok.get())
row.append(stat.cen.get())
row.append(stat.fwhm.get())
x, y = stat.max.get()
row += [x, y]
t.addRow(row)
return t
def peak_detected(self, peak_factor=None):
"""
returns True if a peak was detected, otherwise False
The default algorithm identifies a peak when the maximum
value is four times the minimum value. Change this routine
by subclassing :class:`TuneAxis` and override :meth:`peak_detected`.
"""
peak_factor = peak_factor or self.peak_factor
if self.peaks is None:
return False
self.peaks.compute()
if self.peaks.max is None:
return False
ymax = self.peaks.max[-1]
ymin = self.peaks.min[-1]
ok = ymax >= peak_factor*ymin # this works for USAXS@APS
if not ok:
logger.info("ymax < ymin * %f: is it a peak?", peak_factor)
return ok
def peakup_dcm(correct_roll=True, plot=False, shutter=True, use_calib=False):
"""
Scan the HDCM fine pitch and, optionally, roll against the ion chamber in the D Hutch
correct_roll <Bool> If True, align the beam in the vertical (roll)
plot <Bool> If True, plot the intensity as a function of pitch/roll
shutter <Bool> If True, the shutter will be automatically opened/closed
use_calib <Bool> If True, use a previous calibration as an initial guess
"""
e_value = energy.energy.get()[1]
pitch_old = dcm.c2_pitch.position
roll_old = dcm.c1_roll.position
det = [sclr1]
ps = PeakStats(dcm.c2_pitch.name, im.name)
ps1 = PeakStats(dcm.c1_roll.name, im.name)
if (shutter == True):
RE(mv(shut_b, 'Open'))
c2pitch_kill = EpicsSignal("XF:05IDA-OP:1{Mono:HDCM-Ax:P2}Cmd:Kill-Cmd")
# Turn off the ePID loop for the pitch motor
# 'XF:05IDD-CT{FbPid:02}PID:on'
c2_pid = EpicsSignal("XF:05IDD-CT{FbPid:02}PID:on")
c2_pid.put(0) # Turn off the ePID loop
c2_V = EpicsSignal("XF:05ID-BI{EM:BPM1}DAC1")
c2_V.put(3.0) # Reset the piezo voltage to 3 V
# pitch_lim = (-19.320, -19.370)
# pitch_num = 51
# roll_lim = (-4.9, -5.14)
# roll_num = 45
# pitch_lim = (-19.375, -19.425)
# pitch_num = 51
# roll_lim = (-4.9, -5.6)
# roll_num = 51
pitch_lim = (pitch_old - 0.025, pitch_old + 0.025)
roll_lim = (roll_old - 0.2, roll_old + 0.2)
pitch_num = 51
roll_num = 51
if (use_calib):
# Factor to convert eV to keV
K = 1
if (e_value > 1000):
K = 1 / 1000
# Pitch calibration
pitch_guess = -0.00055357 * K * e_value - 19.39382381
dcm.c2_pitch.move(pitch_guess, wait=True)
# Roll calibration
roll_guess = -0.01124286 * K * e_value - 4.93568571
dcm.c1_roll.move(roll_guess, wait=True)
# Output guess
print('\nMoving to guess:')
print('\tC2 Pitch: %f' % (pitch_guess))
print('\tC1 Roll: %f\n' % (roll_guess))
#if e_value < 10.:
# sclr1.preset_time.put(0.1)
# RE(scan([sclr1], dcm.c2_pitch, -19.335, -19.305, 31), [ps])
#else:
# sclr1.preset_time.put(1.)
# RE(scan([sclr1], dcm.c2_pitch, -19.355, -19.310, 46), [ps])
if e_value < 14.:
# sclr1.preset_time.put(0.1)
sclr1.preset_time.put(1.0)
else:
sclr1.preset_time.put(1.0)
if (plot == True):
sclr1.preset_time.put(
1.0) # Let's collect a longer scan since we're plotting it
RE(scan(det, dcm.c2_pitch, pitch_lim[0], pitch_lim[1], pitch_num),
[ps])
print('Pitch: Centroid at %f\n\n' % (ps.cen))
plt.figure()
plt.plot(ps.x_data, ps.y_data, label='Data')
plt.plot((ps.cen, ps.cen), (np.amin(ps.y_data), np.amax(ps.y_data)),
'--k',
label='Centroid')
plt.xlabel('HDCM C2 PITCH')
plt.ylabel('Counts')
plt.legend()
else:
RE(scan(det, dcm.c2_pitch, pitch_lim[0], pitch_lim[1], pitch_num),
[ps])
time.sleep(0.5)
dcm.c2_pitch.move(ps.cen, wait=True)
time.sleep(0.5)
if (np.abs(dcm.c2_pitch.position - ps.cen) > 0.001):
print('The pitch motor did not move on the first try. Trying again...',
end='')
dcm.c2_pitch.move(ps.cen, wait=True)
if (np.abs(dcm.c2_pitch.position - ps.cen) > 0.001):
print('FAIL! Check motor location.\n')
else:
print('OK\n')
logscan('peakup_pitch')
c2pitch_kill.put(1)
if correct_roll == True:
if (plot == True):
sclr1.preset_time.put(
1.0) # If we are debugging, let's collect a longer scan
RE(scan(det, dcm.c1_roll, roll_lim[0], roll_lim[1], roll_num),
[ps1])
# print('Roll: Maximum flux at %f' % (ps1.max[0]))
print('Roll: Centroid at %f\n\n' % (ps1.cen))
plt.figure()
plt.plot(ps1.x_data, ps1.y_data, label='Data')
plt.plot((ps1.cen, ps1.cen),
(np.amin(ps1.y_data), np.amax(ps1.y_data)),
'--k',
label='Centroid')
plt.xlabel('HDCM ROLL')
plt.ylabel('Counts')
plt.legend()
else:
RE(scan(det, dcm.c1_roll, roll_lim[0], roll_lim[1], roll_num),
[ps1])
time.sleep(0.5)
dcm.c1_roll.move(ps1.cen, wait=True)
time.sleep(0.5)
if (np.abs(dcm.c1_roll.position - ps1.cen) > 0.001):
print(
'The roll motor did not move on the first try. Trying again...',
end='')
dcm.c1_roll.move(ps1.cen, wait=True)
if (np.abs(dcm.c1_roll.position - ps1.cen) > 0.001):
print('FAIL! Check motor location.\n')
else:
print('OK\n')
logscan('peakup_roll')
# Output old/new values
print('Old pitch value:\t%f' % pitch_old)
print('New pitch value:\t%f' % ps.cen)
print('Current pitch value:\t%f' % dcm.c2_pitch.position)
print('Old roll value: \t%f' % roll_old)
print('New roll value: \t%f' % ps1.cen)
print('Current roll value: \t%f\n' % dcm.c1_roll.position)
if (shutter == True):
RE(mv(shut_b, 'Close'))
#for some reason we now need to kill the pitch motion to keep it from overheating. 6/8/17
#this need has disappeared mysteriously after the shutdown - gjw 2018/01/19
# This has now reappeared - amk 2018/06/06
time.sleep(1)
c2pitch_kill.put(1)
c2_pid.put(1) # Turn on the ePID loop
def tune(self, width=None, num=None, md=None):
"""
Bluesky plan to execute one pass through the current scan range
Scan self.axis centered about current position from
``-width/2`` to ``+width/2`` with ``num`` observations.
If a peak was detected (default check is that max >= 4*min),
then set ``self.tune_ok = True``.
PARAMETERS
width : float
width of the tuning scan in the units of ``self.axis``
Default value in ``self.width`` (initially 1)
num : int
number of steps
Default value in ``self.num`` (initially 10)
md : dict, optional
metadata
"""
width = width or self.width
num = num or self.num
if self.peak_choice not in self._peak_choices_:
raise ValueError(
f"peak_choice must be one of {self._peak_choices_},"
f" gave {self.peak_choice}")
initial_position = self.axis.position
start = initial_position - width / 2
finish = initial_position + width / 2
self.tune_ok = False
signal_list = list(self.signals)
signal_list += [
self.axis,
]
tune_md = dict(
width=width,
initial_position=self.axis.position,
time_iso8601=str(datetime.datetime.now()),
)
_md = {
'tune_md':
tune_md,
'plan_name':
self.__class__.__name__ + '.tune',
'tune_parameters':
dict(
num=num,
width=width,
initial_position=self.axis.position,
peak_choice=self.peak_choice,
x_axis=self.axis.name,
y_axis=self.signal_name,
),
'motors': (self.axis.name, ),
'detectors': (self.signal_name, ),
'hints':
dict(dimensions=[([self.axis.name], 'primary')])
}
_md.update(md or {})
if "pass_max" not in _md:
self.stats = []
self.peaks = PeakStats(x=self.axis.name, y=self.signal_name)
@bpp.subs_decorator(self.peaks)
def _scan(md=None):
yield from bp.scan(signal_list,
self.axis,
start,
finish,
num,
md=_md)
yield from self.peak_analysis(initial_position)
yield from _scan()
class UsaxsTuneAxis(TuneAxis):
"""use bp.rel_scan() for the tune()"""
width_signal = None
_width_default = 1 # fallback default when width_signal is None
def __init__(self, signals, axis, signal_name=None, width_signal=None):
"""
Adds to the ``apstools.devices.TuneAxis()`` signature
signal_width (obj):
Instance of `ophyd.EpicsSignal` connected to PV
with default tune width for this axis.
If undefined (set to ``None``), then a private attribute
(``_width_default``) will be used for the value.
"""
super().__init__(signals, axis, signal_name=signal_name)
self.width_signal = width_signal
@property
def width(self):
"""Get default tune width for this axis."""
if self.width_signal is None:
return self._width_default
else:
return self.width_signal.get()
@width.setter
def width(self, value):
"""
Set the width PV value - blocking call, not a plan.
To set the width PV in a plan, use ``yield from bps.mv(self.width_signal, value)``.
CAUTION: Do NOT call this setter from a bluesky plan!
"""
if self.width_signal is None:
self._width_default = value
else:
self.width_signal.put(value)
def peak_analysis(self, initial_position):
if self.peak_detected():
self.tune_ok = True
if self.peak_choice == "cen":
final_position = self.peaks.cen
elif self.peak_choice == "com":
final_position = self.peaks.com
else:
final_position = None
self.center = final_position
else:
self.tune_ok = False
final_position = initial_position
yield from bps.mv(self.axis, final_position)
stream_name = "PeakStats"
results = TuningResults(name=stream_name)
results.tune_ok.put(self.tune_ok)
results.center.put(self.center)
results.final_position.put(final_position)
results.initial_position.put(initial_position)
if self.peaks is None:
logger.info("PeakStats object is None.")
results.put_results({})
else:
results.put_results(self.peaks)
self.stats.append(results)
t = results.report(print_enable=False)
logger.info("%s\n%s", stream_name, str(t))
def tune(self, width=None, num=None, md=None):
"""
Bluesky plan to execute one pass through the current scan range
Scan self.axis centered about current position from
``-width/2`` to ``+width/2`` with ``num`` observations.
If a peak was detected (default check is that max >= 4*min),
then set ``self.tune_ok = True``.
PARAMETERS
width : float
width of the tuning scan in the units of ``self.axis``
Default value in ``self.width`` (initially 1)
num : int
number of steps
Default value in ``self.num`` (initially 10)
md : dict, optional
metadata
"""
width = width or self.width
num = num or self.num
if self.peak_choice not in self._peak_choices_:
raise ValueError(
f"peak_choice must be one of {self._peak_choices_},"
f" gave {self.peak_choice}")
initial_position = self.axis.position
start = initial_position - width / 2
finish = initial_position + width / 2
self.tune_ok = False
signal_list = list(self.signals)
signal_list += [
self.axis,
]
tune_md = dict(
width=width,
initial_position=self.axis.position,
time_iso8601=str(datetime.datetime.now()),
)
_md = {
'tune_md':
tune_md,
'plan_name':
self.__class__.__name__ + '.tune',
'tune_parameters':
dict(
num=num,
width=width,
initial_position=self.axis.position,
peak_choice=self.peak_choice,
x_axis=self.axis.name,
y_axis=self.signal_name,
),
'motors': (self.axis.name, ),
'detectors': (self.signal_name, ),
'hints':
dict(dimensions=[([self.axis.name], 'primary')])
}
_md.update(md or {})
if "pass_max" not in _md:
self.stats = []
self.peaks = PeakStats(x=self.axis.name, y=self.signal_name)
@bpp.subs_decorator(self.peaks)
def _scan(md=None):
yield from bp.scan(signal_list,
self.axis,
start,
finish,
num,
md=_md)
yield from self.peak_analysis(initial_position)
yield from _scan()
def multi_pass_tune(self,
width=None,
step_factor=None,
num=None,
pass_max=None,
snake=None,
md=None):
"""
BlueSky plan for tuning this axis with this signal
Execute multiple passes to refine the centroid determination.
Each subsequent pass will reduce the width of scan by ``step_factor``.
If ``snake=True`` then the scan direction will reverse with
each subsequent pass.
PARAMETERS
width : float
width of the tuning scan in the units of ``self.axis``
Default value in ``self.width`` (initially 1)
num : int
number of steps
Default value in ``self.num`` (initially 10)
step_factor : float
This reduces the width of the next tuning scan by the given factor.
Default value in ``self.step_factor`` (initially 4)
pass_max : int
Maximum number of passes to be executed (avoids runaway
scans when a centroid is not found).
Default value in ``self.pass_max`` (initially 10)
snake : bool
If ``True``, reverse scan direction on next pass.
Default value in ``self.snake`` (initially True)
md : dict, optional
metadata
"""
width = width or self.width
num = num or self.num
step_factor = step_factor or self.step_factor
snake = snake or self.snake
pass_max = pass_max or self.pass_max
self.stats = []
def _scan(width=1, step_factor=10, num=10, snake=True):
for _pass_number in range(pass_max):
_md = {
'pass': _pass_number + 1,
'pass_max': pass_max,
'plan_name': self.__class__.__name__ + '.multi_pass_tune',
}
_md.update(md or {})
yield from self.tune(width=width, num=num, md=_md)
if not self.tune_ok:
break
width /= step_factor
if snake:
width *= -1
t = pyRestTable.Table()
t.labels = "pass Ok? center width max.X max.Y".split()
for i, stat in enumerate(self.stats):
row = [
i + 1,
]
row.append(stat.tune_ok.get())
row.append(stat.cen.get())
row.append(stat.fwhm.get())
x, y = stat.max.get()
row += [x, y]
t.addRow(row)
logger.info("Results\n%s", str(t))
logger.info("Final tune position: %s = %f", self.axis.name,
self.axis.position)
return (yield from _scan(width=width,
step_factor=step_factor,
num=num,
snake=snake))
def peak_detected(self):
"""
returns True if a peak was detected, otherwise False
The default algorithm identifies a peak when the maximum
value is four times the minimum value. Change this routine
by subclassing :class:`TuneAxis` and override :meth:`peak_detected`.
"""
if self.peaks is None:
logger.info("PeakStats = None")
return False
self.peaks.compute()
if self.peaks.max is None:
logger.info("PeakStats : no max reported")
return False
ymax = self.peaks.max[-1]
ymin = self.peaks.min[-1]
ok = ymax > 4 * ymin # this works for USAXS@APS
if not ok:
logger.info("ymax/yman not big enough: is it a peak?")
return ok
def undulator_calibration(outfile=None,
UCalibDir='/home/xf05id1/current_user_data/',
u_gap_start=6500,
u_gap_end=12000,
u_gap_step=500):
'''
outfile string filename for a txt file for the lookup table
desirable to name it with the date of the calibration
e.g. SRXUgapCalibration20161225.txt
undulator gap set point range are defined in:
u_gap_start float
u_gap_end float
u_gap_step float
'''
# Format a default filename
if (outfile is None):
outfile = f"{datetime.datetime.now().strftime('%Y%m%d')}_SRXUgapCalibration.txt"
# Check if the file exists
if (not os.path.exists(UCalibDir + outfile)):
with open(UCalibDir + outfile, 'w') as f:
f.write('Undulator_gap\tFundemental_energy\n')
# Bragg scan setup default
energy_res = 0.002 # keV
bragg_scanwidth = 0.2 # keV +/- this value
bragg_scanpoint = (np.floor(
(2 * bragg_scanwidth) / (energy_res)) + 1).astype('int')
harmonic = 3
energy.harmonic.put(harmonic)
# Generate lookup table by scanning Bragg at each undulator gap set point
for u_gap_setpoint in np.arange(u_gap_start, u_gap_end + u_gap_step,
u_gap_step):
# Look up the energy from the previous lookup table
# Right now, the lookup table is in mm, not um!
# A new lookup table should be created with the correct units
energy_setpoint = (float(energy.utoelookup(u_gap_setpoint / 1000)) *
harmonic)
print('Move u_gap to:\t', u_gap_setpoint)
print('Move Bragg energy to:\t', energy_setpoint)
# energy.move_c2_x.put(False)
energy.move_u_gap.put(True)
yield from mv(energy, energy_setpoint)
energy.move_u_gap.put(False)
# Setup LiveCallbacks
# liveplotfig1 = plt.figure()
liveplotx = energy.energy.name
liveploty = xbpm1.sumT.name
livetableitem = [
energy.energy.name, ring_current.name, xbpm1.sumT.name
]
ps = PeakStats(energy.energy.name, xbpm1.sumT.name)
livecallbacks = [
LiveTable(livetableitem),
LivePlot(liveploty, x=liveplotx), ps
]
# Setup the scan
@subs_decorator(livecallbacks)
def braggscan():
yield from scan([xbpm1, ring_current], energy,
energy_setpoint - bragg_scanwidth,
energy_setpoint + bragg_scanwidth, bragg_scanpoint)
# Run the scan
yield from braggscan()
# Find the maximum and output result to file
maxenergy = ps.max[0]
maxintensity = ps.max[1]
fwhm = ps.fwhm
print('Max energy is:\t', maxenergy)
print('Fundemental energy:\t', maxenergy / harmonic)
with open(UCalibDir + outfile, 'a') as f:
f.write(
f"{energy.u_gap.position:.3f}\t{(maxenergy / harmonic):.8f}\n")
# Return moving u_gap
energy.move_u_gap.put(True)
def undulator_calibration(
outfile=None,
UCalibDir='/nsls2/xf05id1/shared/config/undulator_calibration/',
u_gap_start=6500,
u_gap_end=12000,
u_gap_step=500):
'''
outfile string filename for a txt file for the lookup table
desirable to name it with the date of the calibration
e.g. SRXUgapCalibration20161225.txt
undulator gap set point range are defined in:
u_gap_start float
u_gap_end float
u_gap_step float
'''
bpmAD.cam.read_attrs = ['acquire_time']
bpmAD.configuration_attrs = ['cam']
# Format a default filename
if (outfile is None):
outfile = '%s_SRXUgapCalibration.txt' % (
datetime.datetime.now().strftime('%Y%m%d'))
# Check if the file exists
if (not os.path.exists(UCalibDir + outfile)):
f = open(UCalibDir + outfile, 'w')
f.write('Undulator_gap\tFundemental_energy\n')
f.close()
# Bragg scan setup default
energy_res = 0.002 # keV
bragg_scanwidth = 0.1 # keV
bragg_scanpoint = int(bragg_scanwidth * 2 / energy_res + 1)
harmonic = 3
energy.harmonic.put(harmonic)
# Generate lookup table by scanning Bragg at each undulator gap set point
for u_gap_setpoint in np.arange(u_gap_start, u_gap_end + u_gap_step,
u_gap_step):
# Look up the energy from the previous lookup table
# Right now, the lookup table is in mm, not um!
# A new lookup table should be created with the correct units
energy_setpoint = (float(energy.utoelookup(u_gap_setpoint / 1000)) *
harmonic)
print('Move u_gap to:\t', u_gap_setpoint)
print('Move Bragg energy to:\t', energy_setpoint)
energy.move_c2_x.put(False)
energy.move_u_gap.put(True)
yield from bps.sleep(0.2)
yield from mv(energy, energy_setpoint)
yield from bpmAD_exposuretime_adjust()
energy.move_u_gap.put(False)
# Setup LiveCallbacks
liveplotfig1 = plt.figure()
liveploty = bpmAD.stats1.total.name
livetableitem = [energy.energy, bpmAD.stats1.total, ring_current]
liveplotx = energy.energy.name
ps = PeakStats(energy.energy.name, bpmAD.stats1.total.name)
livecallbacks = [
LiveTable(livetableitem),
LivePlot(liveploty, x=liveplotx, fig=liveplotfig1), ps
]
# Setup the scan
@subs_decorator(livecallbacks)
def braggscan():
yield from scan([bpmAD, pu, ring_current], energy,
energy_setpoint - bragg_scanwidth,
energy_setpoint + bragg_scanwidth, bragg_scanpoint)
# Run the scan
yield from braggscan()
# Find the maximum and output result to file
maxenergy = ps.max[0]
maxintensity = ps.max[1]
fwhm = ps.fwhm
print('Max energy is:\t', maxenergy)
print('Fundemental energy:\t', maxenergy / harmonic)
f = open(UCalibDir + outfile, 'a')
f.write(f"{str(energy.u_gap.position)}\t{str(maxenergy / harmonic)}\n")
f.close()
def tune(self, width=None, num=None, peak_factor=None, md=None):
"""
Bluesky plan to execute one pass through the current scan range
Scan self.axis centered about current position from
``-width/2`` to ``+width/2`` with ``num`` observations.
If a peak was detected (default check is that max >= 4*min),
then set ``self.tune_ok = True``.
PARAMETERS
width : float
width of the tuning scan in the units of ``self.axis``
Default value in ``self.width`` (initially 1)
num : int
number of steps
Default value in ``self.num`` (initially 10)
md : dict, optional
metadata
"""
width = width or self.width
num = num or self.num
peak_factor = peak_factor or self.peak_factor
if self.peak_choice not in self._peak_choices_:
msg = "peak_choice must be one of {}, geave {}"
msg = msg.format(self._peak_choices_, self.peak_choice)
raise ValueError(msg)
initial_position = self.axis.position
# final_position = initial_position # unless tuned
start = initial_position - width/2
finish = initial_position + width/2
self.tune_ok = False
tune_md = dict(
width = width,
initial_position = self.axis.position,
time_iso8601 = str(datetime.datetime.now()),
)
_md = {'tune_md': tune_md,
'plan_name': self.__class__.__name__ + '.tune',
'tune_parameters': dict(
num = num,
width = width,
initial_position = self.axis.position,
peak_choice = self.peak_choice,
x_axis = self.axis.name,
y_axis = self.signal_name,
),
'motors': (self.axis.name,),
'detectors': (self.signal_name,),
'hints': dict(
dimensions = [
(
[self.axis.name],
'primary')]
)
}
_md.update(md or {})
if "pass_max" not in _md:
self.stats = []
self.peaks = PeakStats(x=self.axis.name, y=self.signal_name)
@bpp.subs_decorator(self.peaks)
def _scan(md=None):
yield from bps.open_run(md)
position_list = np.linspace(start, finish, num)
signal_list = list(self.signals)
signal_list += [self.axis,]
for pos in position_list:
yield from bps.mv(self.axis, pos)
yield from bps.trigger_and_read(signal_list)
final_position = initial_position
if self.peak_detected(peak_factor=peak_factor):
self.tune_ok = True
if self.peak_choice == "cen":
final_position = self.peaks.cen
elif self.peak_choice == "com":
final_position = self.peaks.com
else:
final_position = None
self.center = final_position
# add stream with results
# yield from add_results_stream()
stream_name = "PeakStats"
results = TuneResults(name=stream_name)
results.tune_ok.put(self.tune_ok)
results.center.put(self.center)
results.final_position.put(final_position)
results.initial_position.put(initial_position)
results.set_stats(self.peaks)
self.stats.append(results)
if results.tune_ok.get():
yield from bps.create(name=stream_name)
try:
yield from bps.read(results)
except ValueError as ex:
separator = " "*8 + "-"*12
print(separator)
print(f"Error saving stream {stream_name}:\n{ex}")
print(separator)
yield from bps.save()
yield from bps.mv(self.axis, final_position)
yield from bps.close_run()
results.report(stream_name)
return (yield from _scan(md=_md))
def undulator_calibration(outfile='SRXUgapCalibration.txt',
u_gap_start=9.53,
u_gap_end=18.03,
u_gap_step=0.5):
'''
outfile (string) is a .txt file for the lookup table, desirable to name it with the date of the calibration, e.g. SRXUgapCalibration20161225.txt
undulator gap set point range are defined in:
u_gap_start (float)
u_gap_end (float)
u_gap_step (float)
'''
bpmAD.cam.read_attrs = ['acquire_time']
bpmAD.configuration_attrs = ['cam']
#default output directory for the lookup table
UCalibDir = '/nfs/xf05id1/UndulatorCalibration/'
newfile = False
if newfile is True:
f = open(UCalibDir + outfile, 'w')
f.write('undulator_gap fundemental_energy\n')
f.close()
#bragg scan setup default
energy_res = 0.002 #keV
bragg_scanwidth = 0.1 #keV
bragg_scanpoint = int(bragg_scanwidth * 2 / energy_res + 1)
harmonic = 3
energy.harmonic.set(harmonic)
#generate lookup table by scanning Bragg at each undulator gap set point
for u_gap_setpoint in numpy.arange(u_gap_start, u_gap_end + u_gap_step,
u_gap_step):
energy_setpoint = float(
energy.u_gap.utoelookup(u_gap_setpoint)) * harmonic
print('move u_gap to:', u_gap_setpoint)
print('move bragg energy to:', energy_setpoint)
energy.move_c2_x.put(False)
energy.move_u_gap.set(True)
time.sleep(0.2)
energy.move(energy_setpoint)
ps = PeakStats(energy.energy.name, bpmAD.stats1.total.name)
bpmAD_exposuretime_adjust()
energy.move_u_gap.set(False)
braggscan = bp.scan([bpmAD, pu, ring_current], energy,
energy_setpoint - bragg_scanwidth,
energy_setpoint + bragg_scanwidth, bragg_scanpoint)
liveploty = bpmAD.stats1.total.name
livetableitem = [energy.energy, bpmAD.stats1.total, ring_current]
liveplotx = energy.energy.name
liveplotfig1 = plt.figure()
plt.show()
RE(braggscan, [
LiveTable(livetableitem),
LivePlot(liveploty, x=liveplotx, fig=liveplotfig1), ps
])
maxenergy = ps.max[0]
maxintensity = ps.max[1]
fwhm = ps.fwhm
print('max energy is:', maxenergy)
print('fundemental energy:', maxenergy / harmonic)
f = open(UCalibDir + outfile, 'a')
f.write(
str(energy.u_gap.position) + ' ' + str(maxenergy / harmonic) +
'\n')
f.close()