def test_rank_models():
RE = RunEngine()
# Create accurate fit
motor = SynAxis(name='motor')
det = SynSignal(name='centroid',
func=lambda: 5 * motor.read()['motor']['value'] + 2)
fit1 = LinearFit('centroid', 'motor', update_every=None, name='Accurate')
RE(scan([det], motor, -1, 1, 50), fit1)
# Create inaccurate fit
det2 = SynSignal(name='centroid',
func=lambda: 25 * motor.read()['motor']['value'] + 2)
fit2 = LinearFit('centroid', 'motor', update_every=None, name='Inaccurate')
RE(scan([det2], motor, -1, 1, 50), fit2)
# Create inaccurate fit
det3 = SynSignal(name='centroid',
func=lambda: 12 * motor.read()['motor']['value'] + 2)
fit3 = LinearFit('centroid',
'motor',
update_every=None,
name='Midly Inaccurate')
RE(scan([det3], motor, -1, 1, 50), fit3)
# Rank models
ranking = rank_models([fit2, fit1, fit3], target=22, x=4)
assert ranking[0] == fit1
assert ranking[1] == fit3
assert ranking[2] == fit2
def describe_plans(self):
from bluesky import RunEngine
import bluesky.plans as bp
from bluesky.callbacks.fitting import PeakStats
start, end = 10, 13
min_step = 0.01
max_step = 0.15
min_change = 1
steps = 10
dets = [ self.DEVICES['inj_kicker'].current, self.DEVICES['inj_kicker'].offset ]
indep = self.DEVICES['inj_kicker'].offset
plan = bp.scan(dets, indep, start, end, steps)
self.PLANS.append(plan)
start, end = 11, 12
steps = 30
plan2 = bp.scan(dets, indep, start, end, steps)
self.PLANS.append(plan2)
def test_rank_models():
RE = RunEngine()
#Create accurate fit
motor = Mover('motor', {'motor': lambda x: x}, {'x': 0})
det = Reader('det',
{'centroid': lambda: 5 * motor.read()['motor']['value'] + 2})
fit1 = LinearFit('centroid', 'motor', update_every=None, name='Accurate')
RE(scan([det], motor, -1, 1, 50), fit1)
#Create inaccurate fit
det2 = Reader(
'det', {'centroid': lambda: 25 * motor.read()['motor']['value'] + 2})
fit2 = LinearFit('centroid', 'motor', update_every=None, name='Inaccurate')
RE(scan([det2], motor, -1, 1, 50), fit2)
#Create inaccurate fit
det3 = Reader(
'det', {'centroid': lambda: 12 * motor.read()['motor']['value'] + 2})
fit3 = LinearFit('centroid',
'motor',
update_every=None,
name='Midly Inaccurate')
RE(scan([det3], motor, -1, 1, 50), fit3)
#Rank models
ranking = rank_models([fit2, fit1, fit3], target=22, x=4)
assert ranking[0] == fit1
assert ranking[1] == fit3
assert ranking[2] == fit2
def test_to_event_model_new_api_e_stop(RE, hw):
source = Stream()
t = FromEventStream("event", ("data", "motor"), source, principle=True)
assert t.principle
n = simple_to_event_stream_new_api(
{t: {"data_keys": {"ct": {"units": "arb", "precision": 2}}}}
)
tt = t.sink_to_list()
p = n.pluck(0).sink_to_list()
d = n.pluck(1).sink_to_list()
def f(*x):
if x[0] == "stop":
return
source.emit(x)
RE.subscribe(f)
RE(scan([hw.motor], hw.motor, 0, 9, 10))
rs = d[0]["uid"]
assert tt
assert set(p) == {"start", "event", "descriptor"}
assert d[1]["hints"] == {"analyzer": {"fields": ["ct"]}}
assert d[1]["data_keys"]["ct"]["units"] == "arb"
ll = len(d)
RE(scan([hw.motor], hw.motor, 0, 9, 10))
assert d[ll]["run_start"] == rs
assert set(p) == {"start", "stop", "event", "descriptor"}
def test_dbfriendly(RE, hw):
source = Stream()
t = FromEventStream("event", ("data", "motor"), source, principle=True)
z = t.map(op.add, 1)
n = ToEventStream(z, "out").DBFriendly()
d = n.pluck(1).sink_to_list()
RE.subscribe(unstar(source.emit))
RE(scan([hw.motor], hw.motor, 0, 9, 10))
assert isinstance(d[0]["graph"], dict)
h1 = d[0].get("graph_hash")
assert h1
d.clear()
RE(scan([hw.motor], hw.motor, 0, 9, 10))
h2 = d[0].get("graph_hash")
assert h1 == h2
assert len(d) == 10 + 3
d.clear()
z.args = (2, )
RE(scan([hw.motor], hw.motor, 0, 9, 10))
h2 = d[0].get("graph_hash")
assert h1 != h2
assert len(d) == 10 + 3
def test_disable(RE, hw):
det, motor = hw.ab_det, hw.motor
bec = BestEffortCallback()
RE.subscribe(bec)
bec.disable_table()
RE(scan([det], motor, 1, 5, 5))
assert bec._table is None
bec.enable_table()
RE(scan([det], motor, 1, 5, 5))
assert bec._table is not None
bec.peaks.com
bec.peaks['com']
assert ast.literal_eval(repr(bec.peaks)) == vars(bec.peaks)
bec.clear()
assert bec._table is None
# smoke test
bec.disable_plots()
bec.enable_plots()
bec.disable_baseline()
bec.enable_baseline()
bec.disable_heading()
bec.enable_heading()
def test_check_limits(hw):
det = hw.det
motor = hw.motor
# The motor object does not currently implement limits.
# Use an assert to help us out if this changes in the future.
assert not hasattr(motor, 'limits')
# # check_limits should warn if it can't find check_value
# TODO: Is there _any_ object to test?
# with pytest.warns(UserWarning):
# check_limits(scan([det], motor, -1, 1, 3))
# monkey-patch some limits
motor.limits = (-2, 2)
# check_limits should do nothing here
check_limits(scan([det], motor, -1, 1, 3))
# check_limits should error if limits are exceeded only if object raises
# this object does not raise
check_limits(scan([det], motor, -3, 3, 3))
# check_limits should raise if limits are equal only if object raises
# this object does not raise
motor.limits = (2, 2)
check_limits(scan([det], motor, -1, 1, 3))
def test_disable(RE, hw):
det, motor = hw.ab_det, hw.motor
bec = BestEffortCallback()
RE.subscribe(bec)
bec.disable_table()
RE(scan([det], motor, 1, 5, 5))
assert bec._table is None
bec.enable_table()
RE(scan([det], motor, 1, 5, 5))
assert bec._table is not None
bec.peaks.com
bec.peaks['com']
assert ast.literal_eval(repr(bec.peaks)) == vars(bec.peaks)
bec.clear()
assert bec._table is None
# smoke test
bec.disable_plots()
bec.enable_plots()
bec.disable_baseline()
bec.enable_baseline()
bec.disable_heading()
bec.enable_heading()
def generate_example_catalog(data_path):
data_path = Path(data_path)
def factory(name, doc):
serializer = Serializer(data_path / 'abc')
serializer('start', doc)
return [serializer], []
RE = RunEngine()
sd = SupplementalData()
RE.preprocessors.append(sd)
sd.baseline.extend([motor1, motor2])
rr = RunRouter([factory])
RE.subscribe(rr)
RE(count([det]))
RE(count([noisy_det], 5))
RE(scan([det], motor, -1, 1, 7))
RE(grid_scan([det4], motor1, -1, 1, 4, motor2, -1, 1, 7, False))
RE(scan([det], motor, -1, 1, motor2, -1, 1, 5))
RE(count([noisy_det, det], 5))
RE(count([random_img], 5))
RE(count([img], 5))
def factory(name, doc):
serializer = Serializer(data_path / 'xyz')
serializer('start', doc)
return [serializer], []
RE = RunEngine()
rr = RunRouter([factory])
RE.subscribe(rr)
RE(count([det], 3))
catalog_filepath = data_path / 'catalog.yml'
with open(catalog_filepath, 'w') as file:
file.write(f'''
sources:
abc:
description: Some imaginary beamline
driver: bluesky-jsonl-catalog
container: catalog
args:
paths: {Path(data_path) / 'abc' / '*.jsonl'}
handler_registry:
NPY_SEQ: ophyd.sim.NumpySeqHandler
metadata:
beamline: "00-ID"
xyz:
description: Some imaginary beamline
driver: bluesky-jsonl-catalog
container: catalog
args:
paths: {Path(data_path) / 'xyz' / '*.jsonl'}
handler_registry:
NPY_SEQ: ophyd.sim.NumpySeqHandler
metadata:
beamline: "99-ID"
''')
return str(catalog_filepath)
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_per_step(RE, hw):
# Check default behavior, using one motor and then two.
RE(scan([hw.det], hw.motor, -1, 1, 3, per_step=one_nd_step))
RE(
scan([hw.det],
hw.motor,
-1,
1,
hw.motor2,
-1,
1,
3,
per_step=one_nd_step))
RE(inner_product_scan([hw.det], 3, hw.motor, -1, 1, per_step=one_nd_step))
RE(
inner_product_scan([hw.det],
3,
hw.motor,
-1,
1,
hw.motor2,
-1,
1,
per_step=one_nd_step))
# Check that scan still accepts old one_1d_step signature:
RE(scan([hw.det], hw.motor, -1, 1, 3, per_step=one_1d_step))
RE(rel_scan([hw.det], hw.motor, -1, 1, 3, per_step=one_1d_step))
# Test that various error paths include a useful error message identifying
# that the problem is with 'per_step':
# You can't usage one_1d_step signature with more than one motor.
with pytest.raises(TypeError) as excinfo:
RE(
scan([hw.det],
hw.motor,
-1,
1,
hw.motor2,
-1,
1,
3,
per_step=one_1d_step))
assert excinfo.match("Signature of per_step assumes 1D trajectory")
# The signature must be either like one_1d_step or one_nd_step:
def bad_sig(detectors, mtr, step):
...
with pytest.raises(TypeError) as excinfo:
RE(scan([hw.det], hw.motor, -1, 1, 3, per_step=bad_sig))
assert excinfo.match("per_step must be a callable with the signature")
def test_scan_num(RE, hw):
RE(bp.scan([hw.det], hw.motor1, -1, 1, num=1))
RE(bp.scan([hw.det], hw.motor1, -1, 1, num=1.0))
with pytest.raises(ValueError):
RE(bp.scan([hw.det], hw.motor1, -1, 1, num=0))
with pytest.raises(ValueError):
RE(bp.scan([hw.det], hw.motor1, -1, 1, num=0.5))
with pytest.raises(ValueError):
RE(bp.scan([hw.det], hw.motor1, -1, 1, num=float('nan')))
def test_daq_step_scan_args(hw, daq, daq_step_scan):
"""
Basic args and message inspection tests.
Can I decorate a scan?
Can I call a decorated scan at all?
Does a decorated scan produce the messages I expect?
"""
logger.debug('test_daq_step_scan_args')
def assert_daq_messages(msg_list):
"""
Make sure the msg_list is properly mutated.
Checks for a daq configure message with controls arg
Checks for a daq trigger/read in every bundle
"""
found_configure = False
found_trigger = False
found_read = False
for msg in msg_list:
if msg.command == 'configure' and msg.obj is daq:
found_configure = True
assert msg.kwargs['controls'] == [hw.motor]
elif msg.command == 'trigger' and msg.obj is daq:
found_trigger = True
elif msg.command == 'read' and msg.obj is daq:
found_read = True
assert found_configure, 'Did not find daq configure in msg list.'
assert found_trigger, 'Did not find daq trigger in msg list.'
assert found_read, 'Did not find daq read in msg list.'
daq_with_det = list(daq_step_scan([hw.det], hw.motor, 0, 10, 11, events=10,
record=False, use_l3t=True))
assert_daq_messages(daq_with_det)
daq_none_det = list(daq_step_scan([], hw.motor, 0, 10, 11, events=10,
record=False, use_l3t=True))
assert_daq_messages(daq_none_det)
def assert_no_lost_msg(daq_msg_list, nodaq_msg_list):
"""
Make sure no message from the original plan is lost.
"""
daq_without_daq = [msg for msg in daq_msg_list if msg.obj is not daq]
assert daq_without_daq == nodaq_msg_list
nodaq_with_det = list(bp.scan([hw.det], hw.motor, 0, 10, 11))
assert_no_lost_msg(nodaq_with_det, nodaq_with_det)
nodaq_none_det = list(bp.scan([], hw.motor, 0, 10, 11))
assert_no_lost_msg(nodaq_none_det, nodaq_none_det)
def test_old_module_name(hw):
det = hw.det
motor = hw.motor
motor1 = hw.motor1
motor2 = hw.motor2
from bluesky.plan_tools import (print_summary, print_summary_wrapper,
plot_raster_path)
with pytest.warns(UserWarning):
print_summary(scan([det], motor, -1, 1, 10))
with pytest.warns(UserWarning):
list(print_summary_wrapper(scan([det], motor, -1, 1, 10)))
with pytest.warns(UserWarning):
plan = grid_scan([det], motor1, -5, 5, 10, motor2, -7, 7, 15, True)
plot_raster_path(plan, 'motor1', 'motor2', probe_size=.3)
def _generate_simulation_data():
""" priviate function to insert data to exp_db
"""
if os.environ['XPDAN_SETUP'] != str(2):
raise RuntimeError("ONLY insert data if you are running"
"simulation")
# simulated det
pe1c = SimulatedPE1C('pe1c',
{'pe1_image': lambda: np.random.randn(25, 25)})
# TODO : add md schema later
RE = RunEngine({})
RE.subscribe(an_glbl['exp_db'].db.insert, 'all', )
RE(count([pe1c]))
RE(scan([pe1c], motor, 1, 5, 5))
RE(scan([pe1c], motor, 1, 10, 10))
def test_SaveTiff(RE, hw, tmpdir):
sbc = SaveTiff(
handler_reg={"NPY_SEQ": NumpySeqHandler},
template="{base_folder}/{folder_prefix}/{start[hello]}{"
"__independent_vars__}{ext}",
base_folders=tmpdir.strpath,
)
L = []
RE.subscribe(lambda *x: L.append(x))
RE(
bp.scan(
[hw.img],
hw.motor,
0,
10,
1,
md={
"hello": "world",
"folder_tag_list": ["a", "b", "c"],
"a": "a",
"b": "b",
"c": "c",
},
)
)
for n, d in L:
sbc(n, d)
if n == "event":
assert os.path.exists(
tmpdir.strpath + "/a/b/c//world_motor_0,000_arb_img.tiff"
)
def test_SaveTiff(RE, hw, tmpdir):
sbc = SaveTiff(
handler_reg={"NPY_SEQ": NumpySeqHandler},
template="{base_folder}/{folder_prefix}/{start[hello]}{"
"__independent_vars__}{ext}",
base_folders=tmpdir.strpath,
)
L = []
RE.subscribe(lambda *x: L.append(x))
RE(
bp.scan(
[hw.img],
hw.motor,
0,
10,
1,
md={
"hello": "world",
"folder_tag_list": ["a", "b", "c"],
"a": "a",
"b": "b",
"c": "c",
},
))
for n, d in L:
sbc(n, d)
if n == "event":
assert os.path.exists(tmpdir.strpath +
"/a/b/c//world_motor_0,000_arb_img.tiff")
def _gen(self):
return scan(self.detectors,
self.motor,
self.start,
self.stop,
self.num,
md=self.md)
def scan_gui_plan():
yield from scan(self.dets,
self.motor,
self.start.value(),
self.stop.value(),
self.steps.value(),
md={'created_by': 'GUI'})
def scan_bpm(bpm_num, bpm_motor, start, end, step):
detector_name = 'bpm' + str(bpm_num)
device_name = 'mbpm' + str(bpm_num)
motor_name = '_'.join((device_name, bpm_motor))
detector = globals()[detector_name]
device = globals()[device_name]
motor = getattr(device, bpm_motor)
egu = motor.motor_egu.get()
plan = bp.scan([detector], motor, start, end, step)
result_uid = RE(plan)
table = db[result_uid].table()
channels = ['A', 'B', 'C', 'D']
ydata = [table['_'.join((detector_name, ch.lower()))] for ch in channels]
xdata = table[motor_name]
plt.xlabel('Motor position ({})'.format(egu))
plt.ylabel('Currents')
plt.title('BPM {} Currents vs Motor Position'.format(bpm_num))
plots = [
plt.plot(xdata, ydata[i], label=ch) for i, ch in enumerate(channels)
]
plt.legend(channels)
return result_uid
def test_live_fit_plot(fresh_RE):
RE = fresh_RE
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([det], 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 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 test_scan_vars(RE, daq):
logger.debug('test_scan_vars')
daq.configure(events=120)
scan_vars = ScanVars('TST', name='tst', RE=RE)
scan_vars.enable()
check = CheckVals(scan_vars)
RE.subscribe(check)
check.plan = 'scan'
RE(
scan([det1, det2], motor1, 0, 10, motor2, 20, 0, motor3, 0, 1, motor,
0, 1, 11))
check.plan = 'count'
RE(count([det1, det2], 11))
def custom(detector):
for i in range(3):
yield from create()
yield from read(detector)
yield from save()
check.plan = 'custom'
daq.configure(duration=4)
RE(stage_wrapper(run_wrapper(custom(det1)), [det1]))
scan_vars.disable()
# Last, let's force an otherwise uncaught error to cover the catch-all
# try-except block to make sure the log message doesn't error
scan_vars.start({'motors': 4})
def energy_scan(start, stop, num, flyers=None, name='', **metadata):
"""
Example
-------
>>> RE(energy_scan(11350, 11450, 2))
"""
if flyers is None:
flyers = [pb9.enc1, pba2.adc6, pba1.adc7]
def inner():
md = {'plan_args': {}, 'plan_name': 'step scan', 'name': name}
md.update(**metadata)
yield from bps.open_run(md=md)
# Start with a step scan.
plan = bp.scan([hhm_en.energy], hhm_en.energy, start, stop, num, md={'name': name})
# Wrap it in a fly scan with the Pizza Box.
plan = bpp.fly_during_wrapper(plan, flyers)
# Working around a bug in fly_during_wrapper, stage and unstage the pizza box manually.
for flyer in flyers:
yield from bps.stage(flyer)
yield from bps.stage(hhm)
plan = bpp.pchain(plan)
yield from plan
def test_to_event_model_new_api_multi(RE, hw):
source = Stream()
stop = FromEventStream("stop", (), source)
t = FromEventStream(
"event", ("data", "motor"), source, principle=True, stream_name="hi"
)
assert t.principle
tt = t.zip(stop)
n = simple_to_event_stream_new_api(
{
t: {"data_keys": {"ct": {"units": "arb", "precision": 2}}},
tt: {
"name": "final",
"data_keys": {"ct": {"units": "arb", "precision": 2}},
},
},
hello="world",
)
tt = t.sink_to_list()
p = n.pluck(0).sink_to_list()
d = n.pluck(1).sink_to_list()
RE.subscribe(unstar(source.emit))
RE.subscribe(print)
RE(scan([hw.motor], hw.motor, 0, 9, 10))
assert tt
assert set(p) == {"start", "stop", "event", "descriptor"}
assert d[0]["hello"] == "world"
assert d[1]["hints"] == {"analyzer": {"fields": ["ct"]}}
assert d[1]["data_keys"]["ct"]["units"] == "arb"
assert d[-3]["name"] == "final"
assert d[-1]["run_start"]
def test_to_event_model_new_api_multi_parent(RE, hw):
source = Stream()
t = FromEventStream("event", ("data", "motor"), source, principle=True)
t2 = FromEventStream("event", ("data", "motor"), source, principle=True)
assert t.principle
n = simple_to_event_stream_new_api(
{
t.zip(t2).pluck(0): {
"data_keys": {"ct": {"units": "arb", "precision": 2}}
}
}
)
tt = t.sink_to_list()
p = n.pluck(0).sink_to_list()
d = n.pluck(1).sink_to_list()
RE.subscribe(unstar(source.emit))
RE.subscribe(print)
RE(scan([hw.motor], hw.motor, 0, 9, 10))
assert tt
assert set(p) == {"start", "stop", "event", "descriptor"}
assert d[1]["hints"] == {"analyzer": {"fields": ["ct"]}}
assert d[1]["data_keys"]["ct"]["units"] == "arb"
assert d[-1]["run_start"]
def cam_scan(detectors, camera, motor, start, stop, num, md=None, idle_time=1):
def per_step(dets, motor, step):
yield from one_1d_step(dets, motor, step)
yield from bp.abs_set(camera, 1, wait=True)
yield from bp.abs_set(camera, 0, wait=True)
yield from bp.sleep(idle_time)
if md is None:
md = {}
md = ChainMap(
md,
{'plan_args': {'detectors': list(map(repr, detectors)), 'num': num,
'motor': repr(motor),
'start': start, 'stop': stop,
'per_step': repr(per_step),
'idle_time': float(idle_time)},
'plan_name': 'cam_scan',
})
return (yield from bp.subs_wrapper(
bp.scan(detectors, motor, start, stop, num, per_step=per_step, md=md),
LiveTable(detectors + [motor]))
)
def basic_scan():
print('start basic scan')
basic_scan_plan = scan([], tomo_stage.finex_top, 0, 10, 5)
basic_scan_gen = yield from basic_scan_plan
print('done with basic scan')
return basic_scan_gen
def test_last_cache(RE, hw):
source = Stream()
t = FromEventStream("event", ("data", "motor"), source, principle=True)
assert t.principle
n = ToEventStream(
t, ("ct",), data_key_md={"ct": {"units": "arb"}}
).LastCache()
tt = t.sink_to_list()
names = n.pluck(0).sink_to_list()
docs = n.pluck(1).sink_to_list()
RE.subscribe(unstar(source.emit))
RE.subscribe(print)
RE(scan([hw.motor], hw.motor, 0, 9, 10))
assert len(docs) == 10 + 3 + 2
assert names[-3] == "descriptor"
assert names[-2] == "event"
assert tt
assert set(names) == {"start", "stop", "event", "descriptor"}
assert docs[1]["hints"] == {"analyzer": {"fields": ["ct"]}}
assert docs[1]["data_keys"]["ct"]["units"] == "arb"
assert docs[-1]["run_start"]
def test_full_field_tomo_pipeline(RE, hw, db):
L = []
rr = RunRouter(
[lambda x: tomo_callback_factory(x,
publisher=lambda *x: L.append(x),
handler_reg=db.reg.handler_reg)]
)
RE.subscribe(rr)
direct_img = SynSignal(
func=lambda: np.array(np.random.random((10, 10))),
name="img",
labels={"detectors"},
)
RE(
bp.scan(
[direct_img],
hw.motor1,
0,
180,
30,
md={
"tomo": {
"type": "full_field",
"rotation": "motor1",
"center": 0.0,
}
},
)
)
# det1
# sinogram and recon
# 30 events + start, stop, descriptor
assert len(L) == (30 + 2 + 1 + 2) * 2
assert len(L[7][1]["data"]["img_tomo"].shape) == 3
assert len(L[6][1]["data"]["img_sinogram"].shape) == 3
def test_linear_fit():
#Create RunEngine
RE = RunEngine()
#Excepted values of fit
expected = {'slope': 5, 'intercept': 2}
#Create simulated devices
motor = Mover('motor', {'motor': lambda x: x}, {'x': 0})
det = Reader('det',
{'centroid': lambda: 5 * motor.read()['motor']['value'] + 2})
#Assemble fitting callback
cb = LinearFit('centroid', 'motor', update_every=None)
#Scan through variables
RE(scan([det], motor, -1, 1, 50), cb)
#Check accuracy of fit
for k, v in expected.items():
assert np.allclose(cb.result.values[k], v, atol=1e-6)
#Check we create an accurate estimate
assert np.allclose(cb.eval(x=10), 52, atol=1e-5)
assert np.allclose(cb.eval(motor=10), 52, atol=1e-5)
assert np.allclose(cb.backsolve(52)['x'], 10, atol=1e-5)
def newport_dscan(self, motor, start, end, nsteps, nEvents, record=None, use_l3t=False, post=False):
self.cleanup_RE()
daq.configure(nEvents, record=record, controls=[motor], use_l3t=use_l3t)
currPos = motor.wm()
# remove backlash for small scans
motor.mvr(-.1, wait=True)
try:
RE(scan([daq], motor, currPos+start, currPos+end, nsteps))
except Exception:
logger.debug('RE Exit', exc_info=True)
finally:
self.cleanup_RE()
# move back to starting point and remove backlash
motor.mv(currPos, wait=True)
motor.mvr(-0.1, wait=True)
motor.mv(currPos)
if post:
run = get_run()
message = 'scan {name} from {min1:.3f} to {max1:.3f} in {num1} steps'.format(name=motor.name,
min1=start+currPos,max1=end+currPos,
num1=nsteps)
self.elog.post(message,run=int(run))
def MED(init_gas, other_gas, minT, maxT, num_steps, num_steady, num_trans, num_loops=2):
"""
1. Start flowing the initial gas.
2. Scan the temperature from minT to maxT in `num_steps` evenly-spaced steps.
3. Hold temperature at maxT and take `num_steady` images.
4. Repeat (2) and (3) `num_loops` times.
5. Switch the gas to `other_gas` and take `num_trans` acquisitions.
6. Switch it back and take another `num_trans` acquisitions.
Example
-------
Set the gasses. They can be in any other, nothing to do with
the order they are used in the plan.
>>> gas.gas_list = ['O2', 'CO2']
Optionally, preview the plan.
>>> print_summary(MED('O2', 'C02', 200, 300, 21, 20, 60))
Execute it.
>>> RE(MED('O2', 'C02', 200, 300, 21, 20, 60))
"""
# Step 1
yield from abs_set(gas, init_gas)
# Steps 2 and 3 in a loop.
for _ in range(num_loops):
yield from subs_wrapper(scan([pe1, gas.current_gas], eurotherm, minT, maxT, num_steps),
LiveTable([eurotherm, gas.current_gas]))
yield from subs_wrapper(count([pe1], num_steady), LiveTable([]))
# Step 4
yield from abs_set(gas, other_gas)
yield from subs_wrapper(count([pe1], num_steady), LiveTable([]))
# Step 6
yield from abs_set(gas, init_gas)
yield from subs_wrapper(count([pe1], num_steady), LiveTable([]))
def stepping_ct(dets, exposure, motor, start, stop, *, md=None, num=3):
"""Take data at several points along the y-direction"""
_md = md or {}
sp_md = yield from _xpd_pre_plan(dets, exposure)
_md.update(sp_md)
return (yield from bp.scan(dets, motor, start, stop, num, md=_md))
def ascan_wimagerh5_slow(self,
imagerh5,
motor,
start,
end,
nsteps,
nEvents,
record=True):
plan_duration = (nsteps * nEvents / 120. + 0.3 * (nsteps - 1) + 4) * 10
try:
imagerh5.prepare(nSec=plan_duration)
except:
print('imager preparation failed')
return
daq.configure(nEvents, record=record, controls=[motor])
this_plan = scan([daq], motor, start, end, nsteps)
#we assume DAQ runs at 120Hz (event code 40 or 140)
# a DAQ transition time of 0.3 seconds
# a DAQ start time of about 1 sec
# two extra seconds.
# one extra second to wait for hdf5 file to start being written
imagerh5.write()
time.sleep(1)
RE(this_plan)
imagerh5.write_stop()
def cam_scan(detectors, camera, motor, start, stop, num, md=None, idle_time=1):
def per_step(dets, motor, step):
yield from one_1d_step(dets, motor, step)
yield from bp.abs_set(camera, 1, wait=True)
yield from bp.abs_set(camera, 0, wait=True)
yield from bp.sleep(idle_time)
if md is None:
md = {}
md = ChainMap(
md,
{'plan_args': {'detectors': list(map(repr, detectors)), 'num': num,
'motor': repr(motor),
'start': start, 'stop': stop,
'per_step': repr(per_step),
'idle_time': float(idle_time)},
'plan_name': 'cam_scan',
})
return (yield from bp.subs_wrapper(
bp.scan(detectors, motor, start, stop, num, per_step=per_step, md=md),
LiveTable(detectors + [motor]))
)
def Tramp(dets, exposure, Tstart, Tstop, Tstep, *, md=None):
"""
Scan over temeprature controller in steps.
temeprature steps are defined by starting point,
stoping point and step size
Parameters
----------
detectors : list
list of 'readable' objects
exposure : float
exposure time at each temeprature step in seconds
Tstart : float
starting point of temperature sequence
Tstop : float
stoping point of temperature sequence
Tstep : float
step size between Tstart and Tstop of this sequence
md : dict, optional
extra metadata
Note
----
temperature controller that is driven will always be the one configured in
global state. Please refer to http://xpdacq.github.io for more information
"""
pe1c, = dets
if md is None:
md = {}
# setting up area_detector
(num_frame, acq_time, computed_exposure) = _configure_pe1c(exposure)
# compute Nsteps
(Nsteps, computed_step_size) = _nstep(Tstart, Tstop, Tstep)
# update md
_md = ChainMap(md, {'sp_time_per_frame': acq_time,
'sp_num_frames': num_frame,
'sp_requested_exposure': exposure,
'sp_computed_exposure': computed_exposure,
'sp_type': 'Tramp',
'sp_startingT': Tstart,
'sp_endingT': Tstop,
'sp_requested_Tstep': Tstep,
'sp_computed_Tstep': computed_step_size,
'sp_Nsteps': Nsteps,
# need a name that shows all parameters values
# 'sp_name': 'Tramp_<exposure_time>',
'sp_uid': str(uuid.uuid4()),
'sp_plan_name': 'Tramp'})
plan = bp.scan([glbl.area_det], glbl.temp_controller, Tstart, Tstop,
Nsteps, md=_md)
plan = bp.subs_wrapper(plan,
LiveTable([glbl.area_det, glbl.temp_controller]))
yield from plan
def test_hints(RE, hw):
motor = hw.motor
expected_hint = {'fields': [motor.name]}
assert motor.hints == expected_hint
collector = []
def collect(*args):
collector.append(args)
RE(scan([], motor, 1, 2, 2), {'descriptor': collect})
name, doc = collector.pop()
assert doc['hints'][motor.name] == expected_hint
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 test_per_step(RE, hw):
# Check default behavior, using one motor and then two.
RE(scan([hw.det], hw.motor, -1, 1, 3, per_step=one_nd_step))
RE(scan([hw.det],
hw.motor, -1, 1,
hw.motor2, -1, 1,
3,
per_step=one_nd_step))
RE(inner_product_scan([hw.det], 3, hw.motor, -1, 1, per_step=one_nd_step))
RE(inner_product_scan([hw.det],
3,
hw.motor, -1, 1,
hw.motor2, -1, 1,
per_step=one_nd_step))
# Check that scan still accepts old one_1d_step signature:
RE(scan([hw.det], hw.motor, -1, 1, 3, per_step=one_1d_step))
RE(rel_scan([hw.det], hw.motor, -1, 1, 3, per_step=one_1d_step))
# Test that various error paths include a useful error message identifying
# that the problem is with 'per_step':
# You can't usage one_1d_step signature with more than one motor.
with pytest.raises(TypeError) as exc:
RE(scan([hw.det],
hw.motor, -1, 1,
hw.motor2, -1, 1,
3,
per_step=one_1d_step))
assert "Signature of per_step assumes 1D trajectory" in str(exc)
# The signature must be either like one_1d_step or one_nd_step:
def bad_sig(detectors, mtr, step):
...
with pytest.raises(TypeError) as exc:
RE(scan([hw.det], hw.motor, -1, 1, 3, per_step=bad_sig))
assert "per_step must be a callable with the signature" in str(exc)
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 test_SaveBaseClass(RE, hw, tmpdir):
sbc = SaveBaseClass(
"{base_folder}/{folder_prefix}/{start[hello]}{"
"__independent_vars__}",
handler_reg={},
base_folders=tmpdir.strpath,
)
L = []
RE.subscribe(lambda *x: L.append(x))
RE(
bp.scan(
[hw.direct_img],
hw.motor,
0,
10,
1,
md={
"hello": "world",
"folder_tag_list": ["a", "b", "c"],
"a": "a",
"b": "b",
"c": "c",
},
)
)
name_param = {
"start": (
"start_template",
"{base_folder}/a/b/c//world{__independent_vars__}",
),
"event": (
"filenames",
[f"{tmpdir.strpath}/a/b/c//world_motor_0,000_arb_"],
),
}
for n, d in L:
sbc(n, d)
key = name_param.get(n, "")
if key:
assert getattr(sbc, key[0], "") == name_param[n][1]
def test_live_fit():
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}
cb = LiveFit(model, 'det', {'x': 'motor'}, init_guess)
RE(scan([det], motor, -1, 1, 100), cb)
# results are in cb.result.values
expected = {'A': 1, 'sigma': 1, 'x0': 0}
for k, v in expected.items():
assert np.allclose(cb.result.values[k], v, atol=1e-6)
def test_plan_md(RE, hw):
mutable = []
md = {'color': 'red'}
def collector(name, doc):
mutable.append(doc)
# test genereator
mutable.clear()
RE(count([hw.det], md=md), collector)
assert 'color' in mutable[0]
# test Plan with explicit __init__
mutable.clear()
RE(bp.count([hw.det], md=md), collector)
assert 'color' in mutable[0]
# test Plan with implicit __init__ (created via metaclasss)
mutable.clear()
RE(bp.scan([hw.det], hw.motor, 1, 2, 2, md=md), collector)
assert 'color' in mutable[0]
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 test_save_server(RE, hw, tmpdir):
L = []
RE.subscribe(lambda *x: L.append(x))
RE.subscribe(
RunRouter(
[setup_saver],
base_folders=tmpdir.strpath,
template="{base_folder}/{folder_prefix}/"
"{start[analysis_stage]}/"
"{start[sample_name]}_"
"{human_timestamp}_"
"{__independent_vars__}"
"{start[uid]:.6}_"
"{event[seq_num]:04d}{ext}",
handler_reg={"NPY_SEQ": NumpySeqHandler},
)
)
RE(
bp.scan(
[hw.img],
hw.motor,
0,
10,
1,
md={
"sample_name": "world",
"folder_tag_list": ["a", "b", "c"],
"a": "a",
"b": "b",
"c": "c",
"analysis_stage": "dark_sub",
},
)
)
for n, d in L:
if n == "event":
start = L[0][1]
s = f"/a/b/c//{start['analysis_stage']}/world_{_timestampstr(start['time'])}_motor_0,000_arb_{start['uid']:.6}_{d['seq_num']:04d}_img.tiff"
assert os.path.exists(tmpdir.strpath + s)
def test_live_fit(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,
}
cb = LiveFit(model, "det", {"x": "motor"}, init_guess, update_every=50)
RE(scan([hw.det], hw.motor, -1, 1, 50), cb)
# results are in cb.result.values
expected = {"A": 1, "sigma": 1, "x0": 0}
for k, v in expected.items():
assert np.allclose(cb.result.values[k], v, atol=1e-6)
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 test_strip_dep_var(RE, hw):
L = []
LL = []
RE.subscribe(lambda *x: L.append(x))
sdv = StripDepVar()
RE.subscribe(lambda *x: LL.append(sdv(*x)))
RE(scan([hw.ab_det], hw.motor1, 0, 10, 10))
for (n1, d1), (n2, d2) in zip(L, LL):
assert n1 == n2
if n1 == "descriptor":
assert d1 != d2
for k in ["data_keys", "hints", "configuration", "object_keys"]:
for kk in ["det"]:
assert kk not in d2[k]
elif n1 == "event":
assert d1 != d2
for k in ["data", "timestamps"]:
for kk in ["det_a", "det_b"]:
assert kk not in d2[k]
else:
assert d1 == d2
def run_exp(delay): # pragma: no cover
time.sleep(delay)
print("running exp")
p = Publisher(proxy[0], prefix=b"an")
RE.subscribe(p)
det = SynSignal(func=lambda: np.ones((10, 10)), name="gr")
RE(
bp.scan(
[det],
hw.motor1,
0,
2,
2,
md={
"tomo": {
"type": "full_field",
"rotation": "motor1",
"center": 1,
}
},
)
)
def generate_data(RE):
# This adds {'proposal_id': 1} to all future runs, unless overridden.
RE.md['proposal_id'] = 1
RE(count([det]))
RE(scan([det], motor, 1, 5, 5))
RE(scan([det], motor, 1, 10, 10))
RE.md['proposal_id'] = 2
RE(count([det]))
RE(scan([det], motor, -1, 1, 5))
RE(relative_scan([det], motor, 1, 10, 10))
RE(scan([det], motor, -1, 1, 1000))
RE.md['proposal_id'] = 3
# This adds {'operator': 'Ken'} to all future runs, unless overridden.
RE.md['operator'] = 'Ken'
RE(count([det]), purpose='calibration', sample='A')
RE(scan([det], motor, 1, 10, 10), operator='Dan') # temporarily overrides Ken
RE(count([det]), sample='A') # (now back to Ken)
RE(count([det]), sample='B')
RE.md['operator'] = 'Dan'
RE(count([det]), purpose='calibration')
RE(scan([det], motor, 1, 10, 10))
del RE.md['operator'] # clean up by un-setting operator
def test_with_baseline(RE, hw):
bec = BestEffortCallback()
RE.subscribe(bec)
sd = SupplementalData(baseline=[hw.det])
RE.preprocessors.append(sd)
RE(scan([hw.ab_det], hw.motor, 1, 5, 5))
def escan(*args, **kwargs):
return (yield from bp.scan(*args, per_step=one_1d_step_pseudo_shutter, **kwargs))
def test_simple(RE, hw):
bec = BestEffortCallback()
RE.subscribe(bec)
RE(scan([hw.ab_det], hw.motor, 1, 5, 5))
def generate_example_catalog(data_path):
data_path = Path(data_path)
def factory(name, doc):
serializer = Serializer(data_path / 'abc')
serializer('start', doc)
return [serializer], []
RE = RunEngine()
sd = SupplementalData()
RE.preprocessors.append(sd)
sd.baseline.extend([motor1, motor2])
rr = RunRouter([factory])
RE.subscribe(rr)
RE(count([det]))
RE(count([noisy_det], 5))
RE(scan([det], motor, -1, 1, 7))
RE(grid_scan([det4], motor1, -1, 1, 4, motor2, -1, 1, 7, False))
RE(scan([det], motor, -1, 1, motor2, -1, 1, 5))
RE(count([noisy_det, det], 5))
# RE(count([img], 5))
def factory(name, doc):
serializer = Serializer(data_path / 'xyz')
serializer('start', doc)
return [serializer], []
RE = RunEngine()
rr = RunRouter([factory])
RE.subscribe(rr)
RE(count([det], 3))
catalog_filepath = data_path / 'catalog.yml'
with open(catalog_filepath, 'w') as file:
file.write(f'''
plugins:
source:
- module: intake_bluesky
sources:
abc:
description: Some imaginary beamline
driver: intake_bluesky.jsonl.BlueskyJSONLCatalog
container: catalog
args:
paths: {Path(data_path) / 'abc' / '*.jsonl'}
handler_registry:
NPY_SEQ: ophyd.sim.NumpySeqHandler
metadata:
beamline: "00-ID"
xyz:
description: Some imaginary beamline
driver: intake_bluesky.jsonl.BlueskyJSONLCatalog
container: catalog
args:
paths: {Path(data_path) / 'xyz' / '*.jsonl'}
handler_registry:
NPY_SEQ: ophyd.sim.NumpySeqHandler
metadata:
beamline: "99-ID"
''')
return str(catalog_filepath)
def absolute_scan(dets, motor, start, finish, intervals, time=None, *,
md=None):
yield from _pre_scan(dets, total_points=intervals + 1, count_time=time)
return (yield from plans.scan(dets, motor, start, finish, intervals, md=md))
def cscan(*args, **kwargs):
return (yield from bp.scan(*args, per_step=one_1d_step_check_beam, **kwargs))
res = SimpleToEventStream(pipeline, ("result",))
merge = AlignEventStreams(raw_source.starmap(StripDepVar()), res)
merge.sink(pprint)
# send to viz server
merge.starsink(p)
RE.subscribe(lambda *x: raw_source.emit(x))
RE.subscribe(lambda *x: p(*x))
RE.subscribe(lambda *x: time.sleep(.1))
RE.subscribe(lambda *x: time.sleep(1), "stop")
RE(
pchain(
bp.scan([hw.noisy_det], hw.motor, 0, 10, 10),
bp.grid_scan(
[hw.ab_det],
hw.motor,
0,
5,
5,
hw.motor2,
0,
5,
5,
True,
per_step=one_nd_step,
),
bp.grid_scan(
[hw.ab_det],
def inner():
yield from bp.scan([camera], motor, start, end, steps)
def test_blank_hints(RE, hw):
bec = BestEffortCallback()
RE.subscribe(bec)
RE(scan([hw.ab_det], hw.motor, 1, 5, 5, md={'hints': {}}))
