def test_live_fit_plot(RE, hw):
try:
import lmfit
except ImportError:
raise pytest.skip('requires lmfit')
def gaussian(x, A, sigma, x0):
return A * np.exp(-(x - x0)**2 / (2 * sigma**2))
model = lmfit.Model(gaussian)
init_guess = {
'A': 2,
'sigma': lmfit.Parameter('sigma', 3, min=0),
'x0': -0.2
}
livefit = LiveFit(model,
'det', {'x': 'motor'},
init_guess,
update_every=50)
lfplot = LiveFitPlot(livefit, color='r')
lplot = LivePlot('det', 'motor', ax=plt.gca(), marker='o', ls='none')
RE(scan([hw.det], hw.motor, -1, 1, 50), [lplot, lfplot])
expected = {'A': 1, 'sigma': 1, 'x0': 0}
for k, v in expected.items():
assert np.allclose(livefit.result.values[k], v, atol=1e-6)
def my_plan():
motor = hw.motor
det = hw.det
motor.delay = 1
plan = bp.scan([det], motor, -5, 5, 25)
plan = subs_wrapper(bp.scan([det], motor, -5, 5, 25),
LivePlot(det.name, motor.name))
return (yield from plan)
def test_live_plotter(RE, hw):
RE.ignore_callback_exceptions = False
try:
import matplotlib.pyplot as plt
del plt
except ImportError as ie:
pytest.skip("Skipping live plot test because matplotlib is not installed."
"Error was: {}".format(ie))
my_plotter = LivePlot('det', 'motor')
assert RE.state == 'idle'
RE(stepscan(hw.det, hw.motor), {'all': my_plotter})
assert RE.state == 'idle'
xlen = len(my_plotter.x_data)
assert xlen > 0
ylen = len(my_plotter.y_data)
assert xlen == ylen
RE.ignore_callback_exceptions = True
import numpy as np
import lmfit
from bluesky.plans import scan
from ophyd.sim import motor, noisy_det
from bluesky.callbacks import LiveFit
from bluesky.callbacks.mpl_plotting import LivePlot, LiveFitPlot
from bluesky import RunEngine
RE = RunEngine({})
def gaussian(x, A, sigma, x0):
return A * np.exp(-(x - x0)**2 / (2 * sigma**2))
model = lmfit.Model(gaussian)
init_guess = {'A': 2, 'sigma': lmfit.Parameter('sigma', 3, min=0), 'x0': -0.2}
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
lf = LiveFit(model, 'noisy_det', {'x': 'motor'}, init_guess)
lfp = LiveFitPlot(lf, ax=ax, color='r')
lp = LivePlot('noisy_det', 'motor', ax=ax, marker='o', linestyle='none')
RE(scan([noisy_det], motor, -1, 1, 50), [lfp, lp])
plt.draw()
from bluesky import RunEngine
from bluesky.plans import scan
from ophyd.sim import det, motor
from bluesky.callbacks.mpl_plotting import LivePlot
RE = RunEngine({})
RE(scan([det], motor, -5, 5, 30),
LivePlot('det', 'motor', marker='x', markersize=10, color='red'))
from bluesky import RunEngine
from bluesky.plans import scan
from ophyd.sim import det, motor
from bluesky.callbacks.mpl_plotting import LivePlot
RE = RunEngine({})
RE(scan([det], motor, -5, 5, 30), LivePlot('det', 'motor'))
def rocking_curve(start=-0.10, stop=0.10, nsteps=101, choice="peak"):
"""Perform a relative scan of the DCM 2nd crystal pitch around the current
position to find the peak of the crystal rocking curve. Begin by opening
the hutch slits to 3 mm. At the end, move to the position of maximum
intensity on I0, then return to the hutch slits to their original height.
Input:
start: (float) starting position relative to current [-0.1]
end: (float) ending position relative to current [0.1]
nsteps: (int) number of steps [101]
choice: (string) 'peak', fit' or 'com' (center of mass) ['peak']
If choice is fit, the fit is performed using the
SkewedGaussianModel from lmfit, which works pretty well for this
measurement at BMM. The line shape is a bit skewed due to the
convolution with the slightly misaligned entrance slits.
"""
# Cache the data here as it is collected so we can examine it here and use
# it to make decisions.
src = SingleRunCache()
@subs_decorator(LivePlot("I0", pitch.name, ax=plt.gca()))
@subs_decorator(src.callback)
def scan_dcm_pitch():
line1 = "%s, %s, %.3f, %.3f, %d -- starting at %.3f\n" % (
pitch.name,
"I0",
start,
stop,
nsteps,
pitch.readback.get(),
)
uid = yield from rel_scan([I0], pitch, start, stop, nsteps)
# The data that we just acquired has been cached in memory by src.
# Access it as a pandas DataFrame so that we can conveniently do some
# math on it.
run = src.retrieve()
t = run.primary.read().to_dataframe()
if choice.lower() == "com":
signal = numpy.array(t["I0"])
position = com(signal)
top = t['pitch'].iloc[position]
elif choice.lower() == "fit":
signal = numpy.array(t["I0"])
pitch_ = numpy.array(t["pitch"])
mod = SkewedGaussianModel()
pars = mod.guess(signal, x=pitch_)
out = mod.fit(signal, pars, x=pitch_)
print(out.fit_report(min_correl=0))
out.plot()
top = out.params["center"].value
else:
signal = t['I0']
position = peak(signal)
top = t[pitch.name][position]
print(
"rocking curve scan: %s\tuid = %s, scan_id = %d"
% (line1, uid, run.metadata["start"]["scan_id"])
)
print(f"Found and moved to peak at {top:.3} via method {choice}")
yield from mv(pitch, top)
yield from scan_dcm_pitch()