def beginScan(self):
# since for every scan interval the underlying motor will be driven
# to the starting point as described in `moveDevices` instead of the
# originating motor it is necessary to replace the motor with the
# underlying one in the dataset. Otherwise datasets will contain
# ``None`` values because ``resdict`` in `PointDataset._reslist` will
# contain just values for the underlying motor although values for
# the originating/microstepping motor are requested.
copydevices = list(self._devices)
self._devices = underlying_motor(self._devices)
Scan.beginScan(self)
self._devices = copydevices
def __init__(self,
devices,
startpositions,
endpositions,
speed=None,
firstmoves=None,
multistep=None,
detlist=None,
envlist=None,
scaninfo=None,
subscan=False):
self._speed = speed if speed is not None else devices[0].speed
preset = {'live': True}
Scan.__init__(self, devices, startpositions, endpositions, firstmoves,
multistep, detlist, envlist, preset, scaninfo, subscan)
def cscan(dev, *args, **kwargs):
"""Scan around a center.
This command is a specialisation of the `scan()` command to scan around a
center a number of points left from the center and the same number right
from the center with a certain step size.
The command takes as parameters the center, a step size, and number of
points on each side of the center:
>>> cscan(dev, 0, 1, 5) # scans around 0 from -5 to 5 in steps of 1.
The total number of points is (2 * numperside) + 1. The above commands
counts at -5, -4, ..., 5.
The equivalent `scan()` command would be:
>>> scan(dev, -5, 1, 11)
The device can also be a list of devices that should be moved for each
step. In this case, the center and step width also have to be lists:
>>> cscan([dev1, dev2], [0, 0], [0.5, 1], 3)
Resulting positions:
==== ==== ====
Step dev1 dev2
==== ==== ====
1 -1.5 -3.0
2 -1.0 -2.0
3 -0.5 -1.0
4 0.0 0.0
5 0.5 1.0
6 1.0 2.0
7 1.5 3.0
==== ==== ====
"""
def mkpos(centers, steps, numperside):
return [[
center + (i - numperside) * step
for (center, step) in zip(centers, steps)
] for i in range(2 * numperside + 1)]
scanstr = _infostr('cscan', (dev, ) + args, kwargs)
devs, values, restargs = _fixType(dev, args, mkpos)
subscan = kwargs.pop(SUBSCAN, False)
preset, scaninfo, detlist, envlist, move, multistep = \
_handleScanArgs(restargs, kwargs, scanstr)
Scan(devs,
values,
None,
move,
multistep,
detlist,
envlist,
preset,
scaninfo,
subscan=subscan).run()
def preparePoint(self, num, xvalues):
if num > 0: # skip starting point, because of range scan (0..1, ...)
Scan.preparePoint(self, num, xvalues)
# Open Shutters before movement of scan devices (e.g. motor).
# Just for RScan because movement and counting should be done
# simultaneous.
where = []
for det in self._detlist:
if isinstance(det, BiodiffDetector):
det.prepare()
if det.ctrl_gammashutter:
where.append((det._attached_gammashutter, OPEN))
if det.ctrl_photoshutter:
where.append((det._attached_photoshutter, OPEN))
if where:
where = list(zip(*where))
self.moveDevices(where[0], where[1])
def doStart(self):
positions = [[p] for p in self.positions]
dataset = Scan([self._adevs['scandev']], positions, positions,
detlist=[self._adevs['detector']], preset=self._preset,
subscan=True).run()
# process the values...
yvalues = [subset.detvaluelist[0] for subset in dataset.subsets]
self._last = [sum(yvalues) / float(len(yvalues)), dataset.filenames[0]]
def doStart(self):
positions = [[p] for p in self.positions]
self.readresult = self._processDataset(
Scan([self._attached_scandev],
positions,
None,
detlist=[self._attached_detector],
preset=self._preset,
subscan=True).run())
def __init__(self,
positions,
firstmoves=None,
multistep=None,
detlist=None,
envlist=None,
preset=None,
scaninfo=None,
subscan=False):
inst = session.instrument
if not isinstance(inst, SXTalBase):
raise NicosError('cannot do a Q scan, your instrument device '
'is not a sxtal device')
Scan.__init__(self, [inst], positions, [], firstmoves, multistep,
detlist, envlist, preset, scaninfo, subscan)
self._envlist[0:0] = [
inst._attached_gamma, inst._attached_omega, inst._attached_nu
]
if inst in self._envlist:
self._envlist.remove(inst)
def sscan(dev, *args, **kwargs):
"""Scan over device(s) and count detector(s).
The general syntax is either to give start, step and end:
>>> sscan(dev, 0, 1, 10) # scans from 0 to 10 in steps of 1.
or a list of positions to scan:
>>> sscan(dev, [0, 1, 2, 3, 7, 8, 9, 10]) # scans at the given positions.
For floating point arguments, the length of the result is
``int(round((end - start) / step + 1)``. Because of floating point
overflow, this rule may result in the last element being greater than
``end``, e.g.
>>> sscan(dev, 30, .1, 30.19) # scans from 30 to 30.2 in steps of 0.1.
"""
def mkpos(starts, steps, ends):
def mk(starts, steps, numpoints):
return [[start + i * step for (start, step) in zip(starts, steps)]
for i in range(numpoints)]
# use round to handle floating point overflows
numpoints = [
int(round((end - start) / step + 1))
for (start, step, end) in zip(starts, steps, ends)
]
if all(n == numpoints[0] for n in numpoints):
if numpoints[0] > 0:
if numpoints[0] > 1:
return mk(starts, steps, numpoints[0])
else:
raise UsageError("invalid number of points. At least two "
"points are necessary to define a range "
"scan. Please check parameters.")
else:
raise UsageError("negative number of points. Please check "
"parameters. Maybe step parameter has wrong"
"sign.")
else:
raise UsageError("all entries must generate the same number of "
"points")
scanstr = _infostr("sscan", (dev, ) + args, kwargs)
devs, values, restargs = _fixType(dev, args, mkpos)
preset, scaninfo, detlist, envlist, move, multistep = \
_handleScanArgs(restargs, kwargs, scanstr)
Scan(devs, values, None, move, multistep, detlist, envlist, preset,
scaninfo).run()
def amplscan(dev1, start1, step1, numpoints1, dev2, start2, step2, numpoints2,
t):
scandet = session.getDevice('scandet')
scandet.scandev = str(dev2)
scandet.positions = [start2 + i * step2 for i in range(numpoints2)]
dev1pos = [[start1 + i * step1] for i in range(numpoints1)]
ds = Scan([session.getDevice(dev1)],
dev1pos,
None,
detlist=[scandet],
preset={
't': t
}).run()
fit(CosineFit, 'A', dataset=ds)
def gridscan(dev, *args, **kwargs):
"""Scans over a grid of device positions and count detector(s).
The orthogonal grid will spanned by the positions of each device.
>>> gridscan([dev1, dev2], [-1, -2], [1, 1], [3, 5])
which generates a measurement over a grid with positions:
==== ==== ====
Step dev1 dev2
==== ==== ====
1 -1.0 -2.0
2 0.0 -2.0
3 1.0 -2.0
4 -1.0 -1.0
5 0.0 -1.0
6 1.0 -1.0
7 -1.0 0.0
8 0.0 0.0
9 1.0 0.0
10 -1.0 1.0
11 0.0 1.0
12 1.0 1.0
13 -1.0 2.0
14 0.0 2.0
15 1.0 2.0
==== ==== ====
"""
def mkpos(starts, steps, numpoints):
if isinstance(numpoints, (list, tuple)):
if len(starts) != len(numpoints):
raise UsageError('start, steps, and numpoint arguments must '
'have the same length')
scanvals = [[
start + j * step for j in range(numpoint)
] for start, step, numpoint in zip(starts, steps, numpoints)]
values = meshgrid(*scanvals)
for i, grid in enumerate(values):
values[i] = list(grid.reshape(grid.size))
return [tuple(v[i] for v in values) for i in range(len(values[0]))]
raise UsageError('numpoints must be a list')
scanstr = _infostr('gridscan', (dev, ) + args, kwargs)
devs, values, restargs = _fixType(dev, args, mkpos)
preset, scaninfo, detlist, envlist, move, multistep = \
_handleScanArgs(restargs, kwargs, scanstr)
Scan(devs, values, None, move, multistep, detlist, envlist, preset,
scaninfo).run()
def handleError(self, what, err):
# consider all movement errors fatal
if what in ('move', 'wait'):
session.log.warning(
'Positioning problem, stopping all moving '
'motors and detectors',
exc=1)
try:
for dev in self._devices:
if isinstance(dev, NicosMotor):
dev.stop()
for det in self._detlist:
det.stop()
finally:
raise # pylint: disable=misplaced-bare-raise
return Scan.handleError(self, what, err)
def moveDevices(self, devices, positions, wait=True):
if wait:
# stop running microstep sequence if wait is true because
# in the following code the attached motor will be used which will
# interference with the microstepping device.
# (If there is a running sequence the microstepping device will be
# busy but the attached motor is just busy when it gets a move
# command from the sequence)
# A general stop for microstepping motors avoids this interference.
for dev in devices:
if isinstance(dev, MicrostepMotor):
dev.stop()
waitForCompletion(dev, ignore_errors=True)
# movement and counting separate
# do not use software based micro stepping
devices = underlying_motor(devices)
return Scan.moveDevices(self, devices, positions, wait)
def doStart(self):
positions = [[p] for p in self.positions]
ds = Scan([session.getDevice(self.scandev)],
positions,
None,
detlist=[self._attached_detector],
preset=self._preset,
subscan=True).run()
xs, ys, dys, _, ds = _getData()
fit = self.fitcls()
res = fit.run(xs, ys, dys)
if res._failed:
self.log.warning('Fit failed: %s.' % res._message)
self.readresult = [0] * (self._nparams * 2)
else:
session.notifyFitCurve(ds, fit.fit_title, res.curve_x, res.curve_y)
readres = []
for par, err in zip(res._pars[1], res._pars[2]):
readres.append(par)
readres.append(err)
self.readresult = readres
def preparePoint(self, num, xvalues):
if num > 1 and self._nsettings > 1 and (num -
1) % self._nsettings == 0:
for sink in self._sinks:
sink.addBreak(self.dataset)
Scan.preparePoint(self, num, xvalues)
def finishPoint(self):
self._data.finishPoint()
Scan.finishPoint(self)
def endScan(self):
device = self._devices[0]
device.speed = self._original_speed
device.accel = self._original_accel
device.decel = self._original_decel
Scan.endScan(self)
def scan(dev, *args, **kwargs):
"""Scan over device(s) and count detector(s).
A scan is used to collect data during the experiment depending on the
position of one or more devices:
- Move the devices to a new position, called a **point**, and wait until
all devices have reached their position.
- Start the detectors and wait until the requested time and/or monitor
counts, called a **preset**, are reached.
The output is a sequence of detector data corresponding to the device
positions.
The command has two basic modes:
- Equidistant steps between the points
A start value, the step size, and the number of points are given to the
command:
>>> scan(dev, 0, 1, 11) # counts at positions from 0 to 10 in steps of 1
For scans *around* a center, use the `cscan()` command.
- A user defined list of points
Here, the command expects a list of points:
>>> scan(dev, [0, 1, 2, 3, 7, 8, 9]) # counts at the given positions
Instead of one device, the command also handles a list of devices that
should be moved for each step. In this case, the start and step width
also have to be lists:
>>> scan([dev1, dev2], [0, 0], [0.5, 1], 4)
The list of points will be:
==== ==== ====
Step dev1 dev2
==== ==== ====
1 0.0 0.0
2 0.5 1.0
3 1.0 2.0
4 1.5 3.0
==== ==== ====
This also works for the second operation mode:
>>> scan([dev1, dev2], [[0, 1, 2, 3], [0, 1, 5, 7]])
with positions:
==== ==== ====
Step dev1 dev2
==== ==== ====
1 0.0 0.0
2 1.0 1.0
3 2.0 5.0
4 3.0 7.0
==== ==== ====
"""
def mkpos(starts, steps, numpoints):
return [[start + i * step for (start, step) in zip(starts, steps)]
for i in range(numpoints)]
scanstr = _infostr('scan', (dev, ) + args, kwargs)
devs, values, restargs = _fixType(dev, args, mkpos)
preset, scaninfo, detlist, envlist, move, multistep = \
_handleScanArgs(restargs, kwargs, scanstr)
Scan(devs, values, None, move, multistep, detlist, envlist, preset,
scaninfo).run()
def beginScan(self):
if self._notherdevs == 0:
self.dataset.xindex = 1 # plot against tau
Scan.beginScan(self)
def appendscan(numpoints=5, stepsize=None):
"""Go on *numpoints* steps from the end of the last scan.
*numpoints* can also be negative to prepend scan points.
Examples:
>>> appendscan(5) # append 5 more points to last scan
>>> appendscan(-5) # append 5 more points to beginning of last scan
If *stepsize* is given, the step size of the last scan will be overridden.
Example:
>>> scan(x, 10, 0.1, 10) # original scan
>>> appendscan(10, 0.5) # continue the scan, but with other step size
If the previous scan wasn't a scan with fixed step size and *stepsize* is
not given, the new step size will be calculated as the averaged step size
from the previous scan:
>>> scan(x, [0, 0.1, 0.2, 0.5, 1])
>>> appendscan(5)
moves x to the following positions:
==== ====
Step x
==== ====
1/5 1.25
2/5 1.50
3/5 1.75
4/5 2.00
5/5 2.25
==== ====
The scan data will be plotted into the same live plot, if possible, but
will be saved into a separate data file.
Scans with multiple devices are supported:
>>> scan([x, y], [0, 1], [0.1, 0.2], 10)
>>> appendscan(3, [0.05, 0.1]) # append 5 points with new stepsizes
If the original scan was made over multiple devices, the *stepsize* must
be a list with the same number of elements.
"""
if numpoints == 0:
raise UsageError('number of points must be either positive or '
'negative')
direction = numpoints / abs(numpoints)
dslist = session.experiment.data.getLastScans()
if not dslist:
raise NicosError('no last scan saved')
contuids = []
# Find the last scan that wasn't an appendscan.
i = len(dslist) - 1
while i >= 0:
contuids.append(dslist[i].uid)
if not dslist[i].continuation:
break
i -= 1
# If the last scan was an appendscan in the same direction, append to it,
# else append to the original scan. This DWUMs for
# scan(...)
# appendscan(5)
# appendscan(2)
# appendscan(-3)
if dslist[-1].cont_direction == direction:
scan = dslist[-1]
# to continue an appendscan in the negative direction, which has
# the points reversed, we need to reverse the direction again
if scan.cont_direction == -1:
numpoints = -numpoints
else:
scan = dslist[i]
n_devs = len(scan.devices)
n_steps = len(scan.subsets)
if n_steps < 2:
raise NicosError('cannot append to scan with no positions')
if stepsize is not None:
if isinstance(stepsize, number_types):
stepsize = [stepsize]
if n_devs != len(stepsize):
raise NicosError('the stepsize must have %d elements' % n_devs)
else:
stepsize = [None] * n_devs
# create the new list of positions
positions = [[None] * n_devs for _ in range(abs(numpoints))]
# for each device involved in the scan
for i in range(n_devs):
# determine step size by first and last position
pos1 = scan.startpositions[0][i]
pos2 = scan.startpositions[n_steps - 1][i]
if isinstance(pos1, (tuple, ndarray)):
stepsizes = tuple(
(b - a) / (n_steps - 1) for (a, b) in zip(pos1, pos2))
if numpoints > 0:
for j in range(1, numpoints + 1):
positions[j - 1][i] = tuple(
b + j * s for (b, s) in zip(pos2, stepsizes))
else:
for j in range(1, -numpoints + 1):
positions[j - 1][i] = tuple(
a - j * s for (a, s) in zip(pos1, stepsizes))
elif isinstance(pos1, number_types):
if stepsize[i] is None:
stepsize[i] = (pos2 - pos1) / (n_steps - 1)
if numpoints > 0:
startpos = pos2 + stepsize[i]
else:
stepsize[i] = -stepsize[i]
startpos = pos1 + stepsize[i]
for j in range(abs(numpoints)):
positions[j][i] = startpos + j * stepsize[i]
else:
# we can't produce new values for this device
raise NicosError('cannot append to this scan; some devices '
'have nonnumeric values')
numpoints = abs(numpoints)
s = Scan(scan.devices, positions, [], None, None, scan.detectors,
scan.environment, scan.preset,
'%d more steps of last scan' % numpoints)
s._xindex = scan.xindex
s._continuation = contuids
s._cont_direction = direction
# envlist must be reset since Scan.__init__ messes with the ordering
s._envlist[:] = scan.environment
s.run()