def sigmoid(*columns):
"""Fit a Sigmoid through the data of the last scan.
The return value is a pair of tuples::
((a, b, x0, c), (d_a, d_b, d_x0, d_c))
where the elemets of the second tuple the estimated standard errors of the
fit parameters. The fit parameters are:
* a - amplitude of the Sigmoid
* b - steepness of the curve
* x0 - center
* c - background
if the fit failed, the result is ``(None, None)``.
Example::
cscan(...)
values, stderr = sigmoid('h', 'adet')
"""
xs, ys, dys, _, ds = _getData(columns)
fit = SigmoidFit()
res = fit.run(xs, ys, dys)
if res._failed:
return None, None
session.notifyFitCurve(ds, 'sigmoid', res.curve_x, res.curve_y)
descrs = ['amplitude', 'steepness', 'center', 'background']
vals = []
for par, err, descr in zip(res._pars[1], res._pars[2], descrs):
vals.append((descr, '%.4f' % par, '%.4f' % err))
printTable(('parameter', 'value', 'error'), vals, session.log.info)
return CommandLineFitResult((tuple(res._pars[1]), tuple(res._pars[2])))
def ListSetups(listall=False):
"""Print a list of setups.
Example:
>>> ListSetups()
To list also low-level and simulation setups:
>>> ListSetups(True)
see also: `NewSetup`, `AddSetup`, `RemoveSetup`
"""
session.log.info('Available setups:')
items = []
for name, info in iteritems(session.getSetupInfo()):
if info is None:
items.append((name, '', '<could not be read, check syntax>', ''))
continue
if info['group'] in ('special', 'configdata'):
continue
if info['group'] == 'lowlevel' and not listall:
continue
items.append((name, name in session.loaded_setups and 'yes' or '',
info['description'],
', '.join(sorted(info['devices']))))
items.sort()
printTable(('name', 'loaded', 'description', 'devices'), items, session.log.info)
def _logvalues(self, values, isheader=False):
if isheader:
values = ['{0: <13}'.format(val) for val in values]
printTable(values, [], self.log.info)
else:
values = ['{0: >13}'.format(val) for val in values]
printTable([], [values], self.log.info)
def info(*devlist):
"""Print general information of the given device or all devices.
Information is the device value, status and any other parameters that are
marked as "interesting" by giving them a category.
Examples:
>>> info() # show all information
>>> info(Sample) # show information relevant to the Sample object
"""
if not devlist:
devlist = [
dev for dev in itervalues(session.devices) if not dev.lowlevel
]
bycategory = {}
for dev in devlist:
for key, _value, strvalue, unit, category in dev.info():
bycategory.setdefault(category, []).append(
(str(dev), key + ':', strvalue + ' ' + unit))
for catname, catinfo in INFO_CATEGORIES:
if catname not in bycategory:
continue
session.log.info(catinfo)
session.log.info('=' * len(catinfo))
printTable(None,
sorted(bycategory[catname]),
session.log.info,
minlen=8)
session.log.info()
def ListMethods(dev):
"""List user-callable methods for the device.
Example:
>>> ListMethods(phi)
"""
dev = session.getDevice(dev, Device)
items = []
listed = builtins.set()
def _list(cls):
if cls in listed:
return
listed.add(cls)
for name, (args, doc, mcls, is_user) in sorted(iteritems(cls.methods)):
if cls is mcls and is_user:
items.append((dev.name + '.' + name + args, cls.__name__, doc))
for base in cls.__bases__:
if issubclass(base, (Device, DeviceMixinBase)):
_list(base)
_list(dev.__class__)
dev.log.info('Device methods:')
printTable(('method', 'from class', 'description'), items,
session.log.info)
def __call__(self, components=None):
# Print the distances of specified components from
# Laser, Sample and Chopper
if not components:
components = self._components()
sample = getattr(self, 'sample', None)
chopper = getattr(self, 'chopper', None)
table = []
self.log.info('Horizontal distances of components:')
for component in components:
distance = getattr(self, component, None)
row = [component]
if isinstance(distance, number_types):
if isinstance(sample, number_types):
row.append(str(sample - distance))
else:
row.append('-')
if isinstance(chopper, number_types):
row.append(str(chopper - distance))
else:
row.append('-')
table.append(row)
printTable(['Component', 'From SAMPLE', 'From CHOPPER'],
table,
self.log.info,
rjust=True)
def ListCommands():
"""List all available commands.
Example:
>>> ListCommands()
"""
session.log.info('Available commands:')
items = []
for name, obj in session.getExportedObjects():
if getattr(obj, 'is_usercommand', False):
real_func = getattr(obj, 'real_func', obj)
if getattr(real_func, 'is_hidden', False):
continue
if real_func.__name__ != name:
# it's an alias, don't show it again
continue
if hasattr(real_func, 'help_arglist'):
argspec = '(%s)' % real_func.help_arglist
else:
argspec = formatArgs(real_func)
docstring = real_func.__doc__ or ' '
signature = real_func.__name__ + argspec
if len(signature) > 50:
signature = signature[:47] + '...'
if not real_func.__name__.startswith('_'):
items.append((signature, docstring.splitlines()[0]))
items.sort()
printTable(('name', 'description'), items, session.log.info)
def listtunings(self):
"""List all existing tuning tables."""
data = []
for name, table in self.tunetables.items():
data.append((name,
', '.join(setting['_name_'] for setting in table)))
self.log.info('all tuning tables:')
printTable(('name', 'settings'), data, session.log.info)
def show(self):
"""
Shows the list of stored positions
"""
session.log.info('Stored positions on %s\n', self.name)
items = []
for key, val in self.positions.items():
items.append((key, str(val)))
printTable(('Name', 'Device positions'), items, session.log.info)
def ListDatasinks():
"""List the standard data sinks."""
if session.datasinks:
session.log.info('Currently used data sinks are:')
items = [(ds.name, ', '.join(ds.settypes), ', '.join(ds.detectors))
for ds in session.datasinks]
printTable(('name', 'used for', 'active for detectors'), items,
session.log.info)
else:
session.log.info('At the moment no data sinks are set.')
def ListFitters():
"""Print a table with all known fitters.
These fitters are usable for `center()`, `checkoffset()` and related
commands.
"""
items = []
for k, v in FitterRegistry.fitters.items():
items.append((k, 'yes' if v.center_index is not None else 'no'))
items.sort()
printTable(('name', 'can center'), items, session.log.info)
def TacoRes(dev):
"""List all resources for the given TACO device."""
cl = _client(dev)
items = []
for res, info in sorted(cl.deviceQueryResourceInfo().items()):
try:
rv = cl.deviceQueryResource(res)
except Exception:
rv = '<n/a>'
items.append((res, info['info'], rv))
session.log.info('TACO resources for %s:', cl.deviceName())
printTable(('name', 'info', 'value'), items, session.log.info)
def showModules(self):
"""show modules of the connected SECoP server
and intended devices names using the given prefix
"""
prefix = self._get_prefix()
if prefix is None:
self.log.error('secnode is not connected')
return
items = [(prefix + m, m, mod_desc.get('properties', {}).get('description', '').split('\n')[0])
for m, mod_desc in self._secnode.modules.items()]
printTable(['foreseen device name', 'SECoP module', 'description'], items, self.log.info)
def ListDevices():
"""List all currently created devices.
Example:
>>> ListDevices()
"""
session.log.info('All created devices:')
items = []
for devname in sorted(session.explicit_devices, key=lambda d: d.lower()):
dev = session.devices[devname]
items.append((dev.name, dev.__class__.__name__, dev.description))
printTable(('name', 'type', 'description'), items, session.log.info)
def history(dev, key='value', fromtime=None, totime=None):
"""Print history of a device parameter.
The optional argument *key* selects a parameter of the device. "value" is
the main value, and "status" is the device status.
*fromtime* and *totime* are eithernumbers giving **hours** in the past, or
otherwise strings with a time specification (see below). The default is to
list history of the last hour for "value" and "status", or from the last
day for other parameters. For example:
>>> history(mth) # show value of mth in the last hour
>>> history(mth, 48) # show value of mth in the last two days
>>> history(mtt, 'offset') # show offset of mth in the last day
Examples for time specification:
>>> history(mth, '1 day') # allowed: d/day/days
>>> history(mth, 'offset', '1 week') # allowed: w/week/weeks
>>> history(mth, 'speed', '30 minutes') # allowed: m/min/minutes
>>> history(mth, 'speed', '2012-05-04 14:00') # from that date/time on
>>> history(mth, 'speed', '14:00', '17:00') # between 14h and 17h today
>>> history(mth, 'speed', '2012-05-04', '2012-05-08') # between two days
"""
# support calling history(dev, -3600)
if isinstance(key, string_types):
try:
key = parseDateString(key)
except ValueError:
pass
if isinstance(key, number_types):
totime = fromtime
fromtime = key
key = 'value'
if key not in ('value', 'status') and fromtime is None:
fromtime = -24
# Device.history() accepts number of hours only when negative (anything
# > 10000 is taken to be a Unix timestamp)
if isinstance(fromtime, number_types) and 0 < fromtime < 10000:
fromtime = -fromtime
if isinstance(totime, number_types) and 0 < totime < 10000:
totime = -totime
# history() already accepts strings as fromtime and totime arguments
hist = session.getDevice(dev, Device).history(key, fromtime, totime)
entries = []
ltime = time.localtime
ftime = time.strftime
for t, v in hist:
entries.append((ftime('%Y-%m-%d %H:%M:%S', ltime(t)), repr(v)))
printTable(('timestamp', 'value'), entries, session.log.info)
def version(*devlist):
"""List version info of the device(s).
If no device is given, the version of nicos-core is printed.
"""
if devlist:
for dev in devlist:
dev = session.getDevice(dev, Device)
versions = dev.version()
dev.log.info('relevant versions for this device:')
printTable(('module/component', 'version'), versions,
session.log.info)
else:
session.log.info('NICOS version: %s (rev %s)', nicos_version,
nicos_revision)
def fit(fitclass, *columns, **kwargs):
xs, ys, dys, _, ds = _getData(columns, dataset=kwargs.pop('dataset', None))
fit = fitclass(**kwargs)
res = fit.run(xs, ys, dys)
if res._failed:
session.log.info('Fit failed.')
return CommandLineFitResult((None, None))
session.notifyFitCurve(ds, fit.fit_title, res.curve_x, res.curve_y)
descrs = fit.fit_p_descr
vals = []
for par, err, descr in zip(res._pars[1], res._pars[2], descrs):
vals.append((descr, '%.5g' % par, '+/- %.5g' % err,
'+/- {:.1%}'.format(err / par) if par else '-'))
printTable(('parameter', 'value', 'error', 'rel. error'), vals,
session.log.info)
return CommandLineFitResult((tuple(res._pars[1]), tuple(res._pars[2])))
def ListMailReceivers():
"""List all mail addresses for notifications.
Example:
>>> ListMailReceivers()
see also: `SetMailReceivers`
"""
session.log.info('Email addresses for notifications:')
items = []
for notifier, recipients in iteritems(_listReceivers(Mailer)):
for rec in recipients:
items.append((notifier,) + rec)
printTable(('mailer', 'email address', 'info'), sorted(items),
session.log.info)
def _generate_protocol(self, first=None, last=None, with_ts=False):
data = []
senv = set()
for fname in os.listdir(self.datapath):
if not fname.endswith(self.DATA_SUFFIX):
continue
parts = fname.split('_')
if not (len(parts) > 1 and parts[self.RUNNO_INDEX].isdigit()):
continue
runno = int(parts[self.RUNNO_INDEX])
if first is not None and runno < first:
continue
if last is not None and runno > last:
continue
try:
data.append(
self._read_data_file(runno, senv,
path.join(self.datapath, fname)))
except Exception as err:
self.log.warning('could not read %s: %s', fname, err)
continue
data.sort(key=lambda x: x['#'])
headers = self.PROTO_HEADERS[:]
if with_ts:
headers.insert(1, 'Started')
for sename in sorted(senv):
if sename not in self.IGNORE_SENV:
headers.append(sename)
items = []
day = ''
for info in data:
if 'Sample' not in info:
continue
if with_ts and info['Day'] != day:
day = info['Day']
items.append([''] * len(headers))
items.append(['', day] + [''] * (len(headers) - 2))
items.append([info.get(key, '') for key in headers])
lines = [
'Protocol for proposal %s, generated on %s' %
(self.proposal, time.strftime('%Y-%m-%d %H:%M')), ''
]
printTable(headers, items, lines.append)
return '\n'.join(lines) + '\n'
def ListDataReceivers():
"""List email addresses to which experimental data will be sent.
Data is sent once when a proposal is finished. See also
`SetDataReceivers`.
Example:
>>> ListDataReceivers()
see also: `SetDataReceivers`
"""
session.log.info('Email addresses the data will be sent to:')
propinfo = dict(session.experiment.propinfo)
items = set()
for addr in propinfo.get('user_email', ()):
items.add((addr,))
printTable(('email address', ), sorted(items), session.log.info)
def printtuning(self):
"""Print out the current tuning table."""
data = []
valueidx = {}
all_values = set()
for setting in self.curtable:
all_values.update(key for key in setting if not key.startswith('_'))
all_values = sorted(all_values)
valueidx = {val: idx for idx, val in enumerate(all_values)}
for idx, setting in enumerate(self.curtable):
values = ['---'] * len(all_values)
for devname, devvalue in setting.items():
if not devname.startswith('_'):
values[valueidx[devname]] = str(devvalue)[:15]
data.append((str(idx), setting['_name_'], '%.3f' %
setting['_tau_']) + tuple(values))
self.log.info('current MIEZE settings (%s):', self.tuning)
printTable(('#', 'name', 'tau (ps)') + tuple(all_values), data,
session.log.info)
def getall(*names):
"""List the given parameters for all existing devices that have them.
Example:
>>> getall('offset')
lists the offset for all devices with an "offset" parameter.
"""
items = []
for name, dev in sorted(iteritems(session.devices),
key=lambda nd: nd[0].lower()):
pvalues = []
for param in names:
if param in dev.parameters:
pvalues.append(repr(getattr(dev, param)))
else:
pvalues.append(None)
if any(v is not None for v in pvalues):
items.append([name] + list(map(str, pvalues)))
printTable(('device', ) + names, items, session.log.info)
def PosListShow(listname='default'):
"""Show the positions in the given position list.
Examples:
>>> PosListShow() # show default position list
>>> PosListShow('other') # show named position list
"""
sample = session.experiment.sample
instr = session.instrument
lists = dict(sample.poslists)
if listname not in lists:
session.log.warning('Position list %r does not exist', listname)
return
if not lists[listname]:
session.log.info('<empty>')
return
items = []
R2D = math.degrees
for i, item in enumerate(lists[listname]):
calcpos = instr._calcPos(item[1]) if item[1] is not None else None
items.append((
'%d' % (i + 1),
'%.3f' % R2D(item[0].gamma),
'%.3f' % R2D(item[0].omega),
'%.3f' % R2D(item[0].nu),
'%.1f' % item[2][0],
'%.1f' % item[2][1],
'' if item[1] is None else '%.4g' % item[1][0],
'' if item[1] is None else '%.4g' % item[1][1],
'' if item[1] is None else '%.4g' % item[1][2],
'' if calcpos is None else '%.3f' % R2D(calcpos.gamma),
'' if calcpos is None else '%.3f' % R2D(calcpos.omega),
'' if calcpos is None else '%.3f' % R2D(calcpos.nu),
))
printTable(('pos#', 'γ', 'ω', 'ν', 'I', 'σ(I)', 'h', 'k', 'l', 'γ_calc',
'ω_calc', 'ν_calc'),
items,
session.log.info,
rjust=True)
def ListParams(dev):
"""List all parameters of the device.
Example:
>>> ListParams(phi)
"""
dev = session.getDevice(dev, Device)
dev.log.info('Device parameters:')
items = []
aliasdev = getattr(dev, 'alias', None)
if aliasdev is not None:
aliasdev = session.getDevice(aliasdev, Device)
items.append(
(dev.name + '.alias', '-> ' + aliasdev.name, '', 'yes', 'string',
'Aliased device, parameters of that device follow'))
dev = aliasdev
devunit = getattr(dev, 'unit', '')
for name, info in sorted(iteritems(dev.parameters)):
if not info.userparam:
continue
try:
value = getattr(dev, name)
except Exception:
value = '<could not get value>'
unit = (info.unit or '').replace('main', devunit)
vstr = repr(value)
if len(vstr) > 40:
vstr = vstr[:37] + '...'
settable = info.settable and 'yes' or 'no'
name = dev.name + '.' + name
if isinstance(info.type, type):
ptype = info.type.__name__
else:
ptype = info.type.__doc__ or '?'
items.append((name, vstr, unit, settable, ptype, info.description))
printTable(('name', 'value', 'unit', 'r/w?', 'value type', 'description'),
items, session.log.info)
def ListSamples():
"""List all information about defined samples.
Example:
>>> ListSamples()
see also: `NewSample`, `SetSample`, `SelectSample`, `ClearSamples`
"""
rows = []
all_cols = set()
index = {}
for info in session.experiment.sample.samples.values():
all_cols.update(info)
all_cols.discard('name')
index = {key: i for (i, key) in enumerate(sorted(all_cols), start=2)}
index['name'] = 1
for number, info in session.experiment.sample.samples.items():
rows.append([str(number), info['name']] + [''] * len(all_cols))
for key in info:
rows[-1][index[key]] = str(info[key])
printTable(['number', 'sample name'] + sorted(all_cols), rows,
session.log.info)
def activation(formula=None,
instrument=None,
flux=None,
cdratio=0,
fastratio=0,
mass=None,
exposure=24,
getdata=False):
"""Calculate sample activation using the FRM II activation web services.
``formula``:
the chemical formula, see below for possible formats
The *flux* can be specified either by:
``instrument``:
the instrument name to select flux data
or:
``flux``:
The thermal flux (for cold instruments use the equivalent
thermal flux)
``cdratio``:
The ratio between full flux and flux with 1mm Cd in the beam,
0 to deactivate
``fastratio``:
Thermal/fast neutron ratio, 0 to deactivate
``mass``:
the sample mass in g
``exposure``:
exposure time in h, default 24h
``getdata``:
In addition to printing the result table,
return a dict with the full results for further
processing
**Formula input format**
Formula:
``CaCO3``
Formula with fragments:
``CaCO3+6H2O``
Formula with parentheses:
``HO ((CH2)2O)6 H``
Formula with isotope:
``CaCO[18]3+6H2O``
Counts can be integer or decimal:
``CaCO3+(3HO1.5)2``
Mass fractions use %wt, with the final portion adding to 100%:
``10%wt Fe // 15% Co // Ni``
Volume fractions use %vol, with the final portion adding to 100%:
``10%vol [email protected] // [email protected]``
For volume fractions you have to specify the density using
``@<density>``!
Mixtures can nest. The following is a 10% salt solution by weight \
mixed 20:80 by volume with D2O:
``20%vol (10%wt [email protected] // H2O@1) // D2O@1``
"""
if formula is None:
try:
# preparation for a future enhanced sample class
formula = session.experiment.sample.formula
except (ConfigurationError, AttributeError):
# ConfigurationError is raised if no experiment is in session
pass
if formula is None:
raise UsageError('Please give a formula')
if flux:
instrument = 'Manual'
if instrument is None:
try:
instrument = session.instrument.instrument or None
except ConfigurationError:
pass
if instrument is None:
raise UsageError('Please specifiy an instrument or flux')
if mass is None:
try:
formula = session.experiment.sample.mass
except (ConfigurationError, AttributeError):
pass
if mass is None:
raise UsageError('Please specify the sample mass')
qs = '?json=1&formula=%(formula)s&instrument=%(instrument)s&mass=%(mass)g' \
% locals()
if flux:
qs += '&fluence=%(flux)f&cdratio=%(cdratio)f&fastratio=%(fastratio)f' \
% locals()
qs = ACTIVATIONURL + qs
try:
response = urllib.request.urlopen(qs)
except urllib.error.HTTPError as e:
session.log.warning('Error opening: %s', qs)
session.log.warning(e)
return None
data = json.load(response)
if data['ecode'] == 'unknown instrument' and flux is None:
session.log.warning(
'Instrument %s unknown to calculator, '
'specify flux manually', instrument)
session.log.info('Known instruments')
printTable(['instrument'], [(d, ) for d in data['instruments']],
session.log.info)
if data['result']['activation']:
h = data['result']['activation']['headers']
th = [h['isotope'], h['daughter'], h['reaction'], h['Thalf_str']]
for ha in h['activities']:
th.append(ha)
rows = []
for r in data['result']['activation']['rows']:
rd = [r['isotope'], r['daughter'], r['reaction'], r['Thalf_str']]
for a in r['activities']:
rd.append('%.3g' % a if a > 1e-6 else '<1e-6')
rows.append(rd)
dr = ['', '', '', 'Dose (uSv/h)']
for d in data['result']['activation']['doses']:
dr.append('%.3g' % d)
rows.append(dr)
printTable(th, rows, session.log.info)
else:
session.log.info('No activation')
if getdata:
return data
return
def IndexPeaks(max_deviation=0.2, listname='default'):
"""Index crystal reflections using Indexus.
Uses the positions and intensities either the default position list, or the
given name.
You can also select the maximum deviation of HKL indices from integers
using the *max_deviation* parameter (default is 0.2).
After indexing is complete, the calculated HKLs and matrix are shown.
You can accept the indexing with the `AcceptIndexing()` command.
Examples:
>>> IndexPeaks() # use default position list
>>> IndexPeaks(0.1) # use different maximum deviation
>>> IndexPeaks('other') # use other position list
This command will generate input files for Indexus (indexus.txt and
angles.txt) in the experiment data directory and run Indexus. Then it will
read the output files and show the calculated matrix and positions, as well
as the gamma/nu offsets.
If you want to manually run Indexus, you can use the generated input files
as a template.
"""
if isinstance(max_deviation, str):
listname = max_deviation
max_deviation = 0.2
sample = session.experiment.sample
wavelength = session.getDevice('wavelength').read()
lists = dict(sample.poslists)
if listname not in lists:
session.log.warning('Position list %r does not exist', listname)
return
posl = lists[listname]
if len(posl) < 2:
session.log.warning(
'Cannot calculate: need at least two positions in list')
return
params = (
len(posl),
1.0,
1.0,
max_deviation,
wavelength,
sample.bravais,
sample.a,
sample.b,
sample.c,
sample.alpha,
sample.beta,
sample.gamma,
)
# write input file for Indexus
root = session.experiment.samplepath
with open(path.join(root, 'indexus.txt'), 'w', encoding='utf-8') as fp:
fp.write('''\
poli ! instrument
n ! extended output
%d ! num of spots
%f %f ! delta theta, delta angle
%f ! max deviation
%f ! wavelength
%s ! lattice type
%.4f %.4f %.4f %.3f %.3f %.3f ! lattice parameters
.0 .1 -1.0 1.0 ! offset gamma, step, low and high limits
.0 .1 -1.0 1.0 ! offset nu, step, low and high limits
''' % params)
R2D = math.degrees
with open(path.join(root, 'angles.txt'), 'w', encoding='utf-8') as fp:
fp.write(' gamma omega nu I sigI\n')
for pos, _hkl, (intensity, sigma) in posl:
fp.write('%8.3f %8.3f %8.3f %8.2f %8.2f\n' % (R2D(
pos.gamma), R2D(pos.omega), R2D(pos.nu), intensity, sigma))
session.log.info('Running Indexus...')
proc = createSubprocess(['indexus'],
cwd=root,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
output = proc.communicate()[0]
if 'unable to find solution' in output:
session.log.warning('Indexus could not find a solution.')
IndexPeaks._last_result = None
return
# read output from Indexus
p1, p2 = None, None
table = []
peaks = []
dgamma = 0.
dnu = 0.
chi2 = 0.
with open(path.join(root, 'indexus.lis'), 'r', encoding='utf-8') as fp:
lines = iter(fp)
for line in lines:
if line.startswith(' best combination:'):
parts = line.split()
p1, p2 = int(parts[2]) - 1, int(parts[4]) - 1
elif line.startswith(' offset gamma:'):
dgamma = float(line.split()[2])
elif line.startswith(' offset nu:'):
dnu = float(line.split()[2])
elif line.startswith(' chi2:'):
chi2 = float(line.split()[1])
elif line.startswith(' list:'):
session.log.info('Indexed reflections:')
for i, line in enumerate(lines):
if not line.strip(): # empty line after table
break
cols = line.strip().strip('*').split()
if cols[0] == 'H': # header
continue
peaks.append([float(ix) for ix in cols[:3]])
table.append([str(i)] + cols)
break
printTable(('pos#', 'h', 'k', 'l', 'γ', 'ω', 'ν', 'I', 'σ(I)'),
table,
session.log.info,
rjust=True)
# calculate UB matrix from "best combination" of two peaks
or_calc = orient(*sample.cell.cellparams())
pos1 = posl[p1][0]
pos2 = posl[p2][0]
hkl1 = [int(round(ix)) for ix in peaks[p1]]
hkl2 = [int(round(ix)) for ix in peaks[p2]]
new_cell = or_calc.Reorient(hkl1, pos1, hkl2, pos2)
IndexPeaks._last_result = (new_cell.rmat.T, (dgamma, dnu), listname, peaks)
session.log.info(
'Using (%.4g %.4g %.4g) and (%.4g %.4g %.4g) to calculate'
' UB matrix:', *(tuple(hkl1) + tuple(hkl2)))
for row in new_cell.rmat.T: # pylint: disable=not-an-iterable
session.log.info(' %8.4f %8.4f %8.4f', *row)
session.log.info('')
session.log.info('Fit quality χ²: %8.4f', chi2)
session.log.info('')
session.log.info('Offsets:')
session.log.info(' delta gamma = %8.4f delta nu = %8.4f', dgamma, dnu)
session.log.info('')
session.log.info('Use AcceptIndexing() to use this indexing.')