def test_appendscan(session):
m1 = session.getDevice('motor')
m2 = session.getDevice('motor2')
det = session.getDevice('det')
scan(m1, 0, 1, 3, det, t=0.)
dataman = session.experiment.data
dataset1 = dataman.getLastScans()[-1]
assert dataset1.startpositions == [[0], [1], [2]]
appendscan(3, 2)
dataset2 = dataman.getLastScans()[-1]
assert dataset2.continuation == [dataset1.uid]
assert dataset2.startpositions == [[4], [6], [8]]
appendscan(-3)
dataset3 = dataman.getLastScans()[-1]
assert dataset3.continuation == [dataset2.uid, dataset1.uid]
assert dataset3.startpositions == [[-1], [-2], [-3]]
appendscan(-3)
dataset4 = dataman.getLastScans()[-1]
assert dataset4.continuation == [dataset3.uid, dataset2.uid, dataset1.uid]
assert dataset4.startpositions == [[-4], [-5], [-6]]
scan([m2, m1], [0, 10], [1, 2], 3, det, t=0.)
appendscan(3)
dataset5 = dataman.getLastScans()[-1]
assert dataset5.startpositions == [[3, 16], [4, 18], [5, 20]]
appendscan(3, [0, 1])
dataset5 = dataman.getLastScans()[-1]
assert dataset5.startpositions == [[5, 21], [5, 22], [5, 23]]
def test_scan_invalidpreset(session, log):
m = session.getDevice('motor')
# invalid preset
session.experiment.setDetectors([session.getDevice('det')])
with log.assert_warns('these preset keys were not recognized by any of '
'the detectors: .*'):
scan(m, 0, 1, 1, preset=5, t=0.)
def test_scan2(session):
m = session.getDevice('motor')
det = session.getDevice('det')
mm = session.getDevice('manual')
mm.move(0)
session.experiment.setDetectors([session.getDevice('det')])
dataman = session.experiment.data
try:
session.experiment.setEnvironment([])
# scan with different detectors
scan(m, [0, 1], det, m=1, t=0.)
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[0.], [1.]]
# 2 points, 5 detector channels
assert len(dataset.detvaluelists) == 2
assert len(dataset.detvaluelists[0]) == 5
assert [v.name for v in dataset.detvalueinfo] == \
['timer', 'mon1', 'ctr1', 'ctr2', 'img.sum']
# scan with multistep
scan(m, [0, 1], det, manual=[3, 4], t=0.)
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[0., 3.], [0., 4.], [1., 3.],
[1., 4.]]
finally:
session.experiment.envlist = []
session.experiment.detlist = []
def prepare(session, dataroot):
"""Prepare a dataset for StressSpec"""
session.experiment.setDetectors(['adet'])
# Create devices needed in data sinks
for dev in ['xt', 'yt', 'zt', 'slits', 'slitm', 'slite', 'slitp', 'omgm']:
session.getDevice(dev)
# Adjust the monochromator to reasonable position and check it
tthm = session.getDevice('tthm')
tthm.maw(69)
transm = session.getDevice('transm')
wav = session.getDevice('wav')
assert wav.plane == '' # pylint: disable=compare-to-empty-string
transm.maw('Ge')
wav.plane = '311'
wav.maw(1.7)
# Perform different scans
phis = session.getDevice('phis')
timescan(1, t=0.05)
scan(phis, 0, 0.1, 1, t=0.05, info='phi scan on time')
scan(phis, 0, 0.1, 1, mon1=50, info='phi scan on monitor')
contscan(phis, 0, 1, 1000, 0.001)
yield
def test_simmode(session):
m = session.getDevice('motor')
det = session.getDevice('det')
scan(m, 0, 1, 5, 0., det, 'test scan')
assert m._sim_min == 0
assert m._sim_max == 4
assert m._sim_value == 4
def setup_module(session):
"""Setup dataroot and generate a dataset by scanning"""
exp = session.experiment
dataroot = path.join(config.nicos_root, 'testdata')
os.makedirs(dataroot)
counter = path.join(dataroot, exp.counterfile)
open(counter, 'w').close()
updateFileCounter(counter, 'scan', 42)
updateFileCounter(counter, 'point', 167)
exp._setROParam('dataroot', dataroot)
exp.new(1234, user='******', localcontact=exp.localcontact)
exp.sample.new({'name': 'mysample'})
assert path.abspath(exp.datapath) == \
path.abspath(path.join(config.nicos_root, 'testdata',
year, 'p1234', 'data'))
m = session.getDevice('motor2')
det = session.getDevice('det')
tdev = session.getDevice('tdev')
session.experiment.setEnvironment([])
scan(m, 0, 1, 5, det, tdev, t=0.005)
yield
def test_live_count(session):
det = session.getDevice('det')
m = session.getDevice('motor')
def _go_live(det):
live(det)
waitForState(det, BUSY)
_go_live(det)
det.stop()
waitForState(det, OK)
session._thd_acquire.join()
_go_live(det)
waitForState(det, BUSY)
count(det, t=0)
_go_live(det)
waitForState(det, BUSY)
scan(m, [0, 4, 5], 0., det)
count(t=0)
_go_live(det)
count() # t=0
count() # t=0
scan(m, [0, 4, 5], 0., det, live=1) # live will be ignored
def NutatorsZeros_In(start=45, stop=135, step=5, t=2):
adet = session.getDevice('adet')
lam = session.getDevice('wavelength')()
Cryopad = session.getDevice('Cryopad')
maw('pc2', 0, 'pc1', 180.0 / (Cryopad.coefficients[0] * lam), 'Fout',
'off')
nsteps = int((stop - start) / step)
scan(['nutator1', 'nutator2'], [start, start - 90], [step, step],
nsteps,
adet,
t=t)
fit(ZerosFit, 'Asym')
def test_scan_gen_elog(session):
m = session.getDevice('motor')
mm = session.getDevice('manual')
mm.move(0)
session.experiment.setDetectors([session.getDevice('det')])
try:
# plain scan, with some extras: infostring, firstmove
scan(m, 0, 1, 5, 0., 'test scan', manual=1)
dataset = ScanData(session.experiment.data.getLastScans()[-1])
genplot.plotDataset(dataset, path.join(runtime_root, 'testplt'), 'svg')
finally:
session.experiment.detlist = []
def PeakSearch(reflist=None, threshold=100, **preset):
sample, inst = getSampleInst()
if not hasattr(inst, 'searchpars'):
session.log.error('%s does not support peak search', inst.name)
return
rfl = sample.getRefList(reflist)
if rfl is None:
session.log.error('Reflection list %s not found', reflist)
return
mots = inst.get_motors()
dstt = session.getDevice(mots[0])
dom = session.getDevice(mots[1])
dchi = session.getDevice(mots[2])
dphi = session.getDevice(mots[3])
mots = [dstt, dom, dchi, dphi]
sttpars = inst.searchpars['stt']
chipars = inst.searchpars['chi']
phipars = inst.searchpars['phi']
nphi = (phipars[1] - phipars[0]) / phipars[2]
for stt in np.arange(sttpars[0], sttpars[1], sttpars[2]):
for chi in np.arange(chipars[0], chipars[1], chipars[2]):
dstt.start(stt)
dstt.start(stt / 2.)
dchi.start(chi)
multiWait([dstt, dom, dchi])
session.log.info('Searching at stt = %f, chi = %f', stt, chi)
scan(dphi, phipars[0], phipars[2], int(nphi), **preset)
peaks = findpeaks(mots[3].name, inst.center_counter, npoints=4)
if peaks:
session.log.info('%d candidate peaks found in phi scan',
len(peaks))
for p in peaks:
dphi.maw(p)
ang = [m.read(0) for m in mots]
r = ((0, 0, 0), tuple(ang), ())
if not test_threshold(dphi.name, inst.center_counter, p,
threshold):
session.log.info('Peak at %f below threshold %f', p,
threshold)
continue
if test_proximity(rfl, ang):
session.log.info('Peak at %f failed proximity test', p)
continue
session.log.info('Centering reflection at phi = %f', p)
ok, maxang = inner_center(r, **preset)
if ok:
rfl.append(None, tuple(maxang), None)
else:
session.log.warning('Failed centering at phi = %f', p)
def test_Scan(self, session):
template = {
'entry:NXentry': {
'time': DetectorDataset('timer', 'float32'),
'mon': DetectorDataset('mon1', 'uint32'),
'counts': ImageDataset(0, 0, signal=NXAttribute(1, 'int32')),
'sry': DeviceDataset('sry'),
},
'data:NXdata': {
'None': NXScanLink(),
}
}
setTemplate(template)
self.setScanCounter(session, 48)
session.experiment.setDetectors([
'det',
])
sry = session.getDevice('sry')
scan(sry, 0, 1, 5, t=0.001)
fin = h5py.File(
path.join(session.experiment.datapath, 'test%sn000049.hdf' % year),
'r')
ds = fin['entry/sry']
assert (len(ds) == 5)
ds = fin['entry/time']
assert (len(ds) == 5)
ds = fin['entry/mon']
assert (len(ds) == 5)
ds = fin['entry/counts']
assert (len(ds) == 5)
ds = fin['data/sry']
assert (len(ds) == 5)
assert (ds[0] == 0)
assert (ds[1] == 1)
assert (ds[2] == 2)
assert (ds[3] == 3)
assert (ds.attrs['target'] == b'/entry/sry')
fin.close()
def nGI_stepping(n_images, p=1, angle=0, *detlist, **preset):
"""Performs a nGI stepping scan of G0 over p periods in n_images-1 steps.
Calculates the stepping period from the angle of the grating lines to the
vertical axis *angle*.
Example:
>>> nGI_stepping(11,1,0,t=30) # steps G0 over one period from 0 to 1.6 mm
>>> # in 0.16 mm steps and count for 30 s
"""
import numpy as np
stepwidth = 1.6 / np.cos(angle * 2 * np.pi / 360) * p / (n_images - 1)
session.log.info('Starting nGI scan.')
scan('G0tx', 0, stepwidth, n_images, *detlist, **preset)
maw('fastshutter', 'closed')
session.log.info('fastshutter closed')
def test_scan_plotindex(session):
m = session.getDevice('motor')
m2 = session.getDevice('motor2')
mm = session.getDevice('manual')
mm.move(0)
dataman = session.experiment.data
session.experiment.setDetectors([session.getDevice('det')])
# first device is moving
scan([m, m2], [0, 0], [2, 0], 2, t=0)
assert dataman.getLastScans()[-1].xindex == 0
# second device is moving
scan([m, m2], [0, 0], [0, 2], 2, t=0)
assert dataman.getLastScans()[-1].xindex == 1
# second device is moving, with multistep (issue #4030, #4031)
scan([m, m2], [0, 0], [0, 2], 2, t=0., manual=[1, 2])
assert dataman.getLastScans()[-1].xindex == 1
# degenerate case only multistep moving, with multistep (issue #4030, #4031)
scan([m, m2], [0, 0], [0, 0], 2, t=0., manual=[1, 2])
assert dataman.getLastScans()[-1].xindex == 0
def test_scan_errorhandling(session, log):
t = session.getDevice('tdev')
m = session.getDevice('motor')
dataman = session.experiment.data
# no errors, works fine
scan(t, [0, 1, 2])
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[0], [1], [2]]
with log.allow_errors():
# limit error: skips the data points
scan(t, [-10, 0, 10, 3])
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[0], [3]]
# communication error during move: also skips the data points
t._value = 0
t._start_exception = CommunicationError()
scan(t, [0, 1, 2, 3])
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[
0
]] # tdev.move only raises when target != 0
# position error during move: ignored
t._value = 0
t._read_exception = None
t._start_exception = PositionError()
scan(t, [0, 1, 2, 3])
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[0], [None], [None], [None]]
# position error during readout: ignored
t._read_exception = PositionError()
t._start_exception = None
scan(t, [0, 1, 2, 3])
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[None], [None], [None], [None]]
# also as an environment device
scan(m, [0, 1], t)
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[0.], [1.]]
assert dataset.envvaluelists == [[None], [None]]
# other errors: reraised
t._start_exception = RuntimeError()
assert raises(RuntimeError, scan, t, [0, 1, 2, 3])
def NutatorPerpendicularity(start=45, stop=135, step=5, t=2):
adet = session.getDevice('adet')
maw('nutator2', 0, 'nutator1', start, 'Fout', 'off', 'pc1', 0, 'pc2', 0)
nsteps = int((stop - start) / step)
scan('nutator1', start, step, nsteps, adet, t=t)
fit(PerpFit, 'Asym')
def PC2Current(start=-4, stop=4, step=0.25, t=2):
adet = session.getDevice('adet')
maw('nutator2', 0, 'nutator1', 0, 'Fout', 'off', 'pc1', 0)
nsteps = int((stop - start) / step)
scan('pc2', start, step, nsteps, adet, t=t)
fit(PCurrentFit, 'Asym')
def test_scan(session, log):
m = session.getDevice('motor')
m2 = session.getDevice('motor2')
c = session.getDevice('coder')
mm = session.getDevice('manual')
mm.move(0)
# check that scans are impossible in slave mode
session.setMode(SLAVE)
assert raises(ModeError, scan, m, [0, 1, 2, 10])
session.setMode(MASTER)
session.experiment.setDetectors([session.getDevice('det')])
session.experiment.setEnvironment([avg(mm), minmax(mm)])
dataman = session.experiment.data
try:
# plain scan, with some extras: infostring, firstmove
scan(m, 0, 1, 5, 0.005, 'test scan', manual=1)
dataset = dataman.getLastScans()[-1]
assert [v.name for v in dataset.devvalueinfo] == ['motor']
assert [v.unit for v in dataset.devvalueinfo] == ['mm']
assert dataset.devvaluelists == [[float(i)] for i in range(5)]
assert [v.name for v in dataset.detvalueinfo] == \
['timer', 'mon1', 'ctr1', 'ctr2', 'img.sum']
assert [v.unit for v in dataset.detvalueinfo] == \
['s', 'cts', 'cts', 'cts', 'cts']
assert dataset.info.startswith('test scan')
assert len(dataset.detvaluelists) == 5
assert len(dataset.envvaluelists[0]) == 3
assert dataset.envvaluelists[0] == [1., 1., 1.] # avg, min, max
assert mm.read() == 1
session.experiment.setEnvironment([])
# scan with second basic syntax
scan(m, [0, 4, 5], 0.)
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[float(i)] for i in [0, 4, 5]]
# scan with multiple devices
scan([m, m2], [0, 0], [1, 2], 3, t=0.)
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[float(i), float(i * 2)]
for i in [0, 1, 2]]
# same with tuple arguments
scan((m, m2), (0, 0), (1, 2), 2, t=0.)
# scan with multiple devices and second basic syntax
scan([m, m2], [[0, 0, 1], [4, 2, 1]], t=0.)
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[0., 4.], [0., 2.], [1., 1.]]
# scan with different environment
scan(m, [0, 1], c)
dataset = dataman.getLastScans()[-1]
assert dataset.devvaluelists == [[0.], [1.]]
assert dataset.envvaluelists == [[0.], [1.]]
assert dataset.devvalueinfo[0].name == 'motor'
assert dataset.devvalueinfo[0].unit == 'mm'
assert dataset.envvalueinfo[0].name == 'coder'
assert dataset.envvalueinfo[0].unit == 'mm'
finally:
session.experiment.envlist = []
session.experiment.detlist = []
def test_experiment(session, cleanup):
exp = session.experiment
# setup test scenario
exp._setROParam('dataroot', path.join(runtime_root, 'data'))
exp.proposal = 'service'
exp._setROParam('proptype', 'service')
# if there is no exp.new, we need to adjust proposalpath ourselfs!
exp.proposalpath = exp.proposalpath_of(exp.proposal)
# create the needed script file
spath = path.join(runtime_root, 'data', year, 'service', 'scripts')
assert exp.scriptpath == spath
ensureDirectory(spath)
with open(path.join(spath, 'servicestart.py'), 'w') as fp:
fp.write('Remark("service time")\n')
# first, go in service mode
exp.servicescript = 'servicestart.py'
try:
exp.new('service', localcontact=exp.localcontact)
finally:
exp.servicescript = ''
assert exp.proposal == 'service'
assert exp.proptype == 'service'
assert exp.remark == 'service time'
assert exp.scriptpath == spath
# check correct operation of sampledir
exp.sampledir = 'sample'
assert exp.datapath == path.join(exp.dataroot, year, 'service', 'sample',
'data')
exp.sampledir = ''
# for this proposal, remove access rights after switching back
exp._setROParam('managerights', dict(disableFileMode=0, disableDirMode=0))
# then, go in proposal mode
exp.new(999, 'etitle', 'me <*****@*****.**>', 'you')
# check that all properties have been set accordingly
assert exp.proposal == 'p999'
assert exp.proptype == 'user'
assert exp.title == 'etitle'
assert exp.localcontact == 'me <*****@*****.**>'
assert exp.users == 'you'
assert exp.remark == '' #pylint: disable=compare-to-empty-string
# check that directories have been created
assert path.isdir(datapath('p999'))
assert path.isdir(datapath('p999', 'scripts'))
assert path.isdir(datapath('p999', 'data'))
# check that templating works
assert path.isfile(datapath('p999', 'scripts', 'start_p999.py'))
run('start_p999.py')
assert exp.remark == 'proposal p999 started by you; sample is unknown'
# try a small scan; check for data file written
scan(session.getDevice('axis'), 0, 1, 5, 0.01, u'Meßzeit')
assert path.isfile(datapath('..', 'counters'))
nr = readFileCounter(datapath('..', 'counters'), 'scan')
fn = datapath('p999', 'data', 'p999_%08d.dat' % nr)
assert path.isfile(fn)
with open(fn, 'rb') as fp:
assert u'Meßzeit'.encode('utf-8') in fp.read()
# now, finish the experiment
thd = exp.finish()
if thd:
thd.join()
# have the access rights been revoked?
if os.name != 'nt':
assert not os.access(datapath('p999'), os.X_OK)
# did we switch back to service proposal?
assert exp.proposal == 'service'
# switch back to proposal (should re-enable directory)
exp.new('p999', localcontact=exp.localcontact)
assert os.access(datapath('p999'), os.X_OK)
assert exp.users == '' #pylint: disable=compare-to-empty-string
# has the zip file been created?
assert path.isfile(datapath('p999', 'p999.zip'))
exp.addUser('A User')
assert exp.users == 'A User'
exp.addUser('Another User', '*****@*****.**')
assert exp.users == 'A User, Another User <*****@*****.**>'
exp.addUser('Athird User', '*****@*****.**',
'An Institute, Anywhere street, 12345 Anywhere')
assert exp.users == 'A User, Another User <*****@*****.**>, '\
'Athird User <*****@*****.**> ' \
'(An Institute, Anywhere street, 12345 Anywhere)'
exp.users = 'Jülich'
exp.users = u'Jülich'
exp.scripts = ['Test ümlauts']
exp.scripts = [u'Test ümlauts']
assert exp.scripts == ['Test ümlauts']
# and back to service
exp.new('service', localcontact=exp.localcontact)
