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fixes #320
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@prjemian
prjemian committed Jun 1, 2020
1 parent 9a5c053 commit 0f22934
Showing 1 changed file with 85 additions and 51 deletions.
136 changes: 85 additions & 51 deletions apstools/plans.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,8 @@
from . import utils as APS_utils


logger = logging.getLogger(__name__).addHandler(logging.NullHandler())
logger = logging.getLogger(__name__)
logger.info(__file__)


class CommandFileReadError(IOError): ...
Expand Down Expand Up @@ -229,7 +230,7 @@ def lineup(
count time per step (if counter is ScalerChannel object)
peak_factor : float (default: 4)
maximum must be greater than ``peak_factor*minimum``
peak maximum must be greater than ``peak_factor*minimum``
width_factor : float (default: 0.8)
fwhm must be less than ``width_factor*plot_range``
Expand Down Expand Up @@ -874,6 +875,43 @@ def phase_cb(value, timestamp, **kwargs):
return sscan_status


class TuneResults(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, title=None):
keys = self.peakstats_attrs + "tune_ok center initial_position final_position".split()
t = pyRestTable.Table()
t.addLabel("key")
t.addLabel("result")
for key in keys:
v = getattr(self, key).get()
t.addRow((key, str(v)))
if title is not None:
print(title)
print(t)

def set_stats(self, peaks):
for key in self.peakstats_attrs:
v = getattr(peaks, key)
if key in ("crossings", "min", "max"):
v = np.array(v)
getattr(self, key).put(v)


class TuneAxis(object):
"""
tune an axis with a signal
Expand Down Expand Up @@ -922,7 +960,6 @@ 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]
Expand All @@ -933,12 +970,13 @@ def __init__(self, signals, axis, signal_name=None):
self.width = 1
self.num = 10
self.step_factor = 4
self.pass_max = 6
self.peak_factor = 4
self.pass_max = 4
self.snake = True

def tune(self, width=None, num=None, md=None):
def tune(self, width=None, num=None, peak_factor=None, md=None):
"""
BlueSky plan to execute one pass through the current scan range
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.
Expand All @@ -958,6 +996,7 @@ def tune(self, width=None, num=None, md=None):
"""
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 {}"
Expand Down Expand Up @@ -999,35 +1038,6 @@ def tune(self, width=None, num=None, md=None):
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, title=None):
keys = self.peakstats_attrs + "tune_ok center initial_position final_position".split()
t = pyRestTable.Table()
t.addLabel("key")
t.addLabel("result")
for key in keys:
v = getattr(self, key).get()
t.addRow((key, str(v)))
if title is not None:
print(title)
print(t)

@bpp.subs_decorator(self.peaks)
def _scan(md=None):
yield from bps.open_run(md)
Expand All @@ -1040,7 +1050,7 @@ def _scan(md=None):
yield from bps.trigger_and_read(signal_list)

final_position = initial_position
if self.peak_detected():
if self.peak_detected(peak_factor=peak_factor):
self.tune_ok = True
if self.peak_choice == "cen":
final_position = self.peaks.cen
Expand All @@ -1053,17 +1063,14 @@ def _scan(md=None):
# add stream with results
# yield from add_results_stream()
stream_name = "PeakStats"
results = Results(name=stream_name)
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)
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)
results.set_stats(self.peaks)
self.stats.append(results)

if results.tune_ok.get():
yield from bps.create(name=stream_name)
Expand All @@ -1077,7 +1084,6 @@ def _scan(md=None):
yield from bps.save()

yield from bps.mv(self.axis, final_position)
self.stats.append(self.peaks)
yield from bps.close_run()

results.report(stream_name)
Expand All @@ -1086,7 +1092,9 @@ def _scan(md=None):


def multi_pass_tune(self, width=None, step_factor=None,
num=None, pass_max=None, snake=None, md=None):
num=None, pass_max=None,
peak_factor=None,
snake=None, md=None):
"""
BlueSky plan for tuning this axis with this signal
Expand All @@ -1109,7 +1117,9 @@ def multi_pass_tune(self, width=None, step_factor=None,
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)
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)
Expand All @@ -1121,37 +1131,58 @@ def multi_pass_tune(self, width=None, step_factor=None,
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, md=_md)
yield from self.tune(width=width, num=num, peak_factor=peak_factor, md=_md)

if not self.tune_ok:
return
width /= step_factor
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 peak_detected(self):

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()
Expand All @@ -1160,7 +1191,10 @@ def peak_detected(self):

ymax = self.peaks.max[-1]
ymin = self.peaks.min[-1]
return ymax > 4*ymin # this works for USAXS@APS
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 tune_axes(axes):
Expand Down

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