def get_data(self):
prefix = self.get_prefix()
if prefix:
self.import_file = prefix
else:
self.import_file = self.get_directory()
filenames = self.get_files()
v0 = self.read_image(filenames[0])
x = NXfield(range(v0.shape[1]), dtype=np.uint16, name='x')
y = NXfield(range(v0.shape[0]), dtype=np.uint16, name='y')
z = NXfield(range(1,len(filenames)+1), dtype=np.uint16, name='z')
v = NXfield(shape=(len(filenames),v0.shape[0],v0.shape[1]),
dtype=v0.dtype, name='v')
v[0] = v0
if v._memfile:
chunk_size = v._memfile['data'].chunks[0]
else:
chunk_size = v.shape[0]/10
self.progress_bar.setVisible(True)
self.progress_bar.setRange(0, len(filenames))
for i in range(0, len(filenames)):
try:
files = []
for j in range(i,i+chunk_size):
files.append(filenames[j])
self.progress_bar.setValue(j)
self.update_progress()
v[i:i+chunk_size,:,:] = self.read_images(files)
except IndexError as error:
pass
global maximum
v.maximum = maximum
return NXentry(NXdata(v,(z,y,x)))
def write_sample_counts(self, total, rate):
self._entry.sample.total_counts = NXfield(int(total),
dtype='int32',
units=string_attr('counts'))
self._entry.sample.total_count_rate = NXfield(float(rate),
dtype='float32',
units=string_attr('1/s'))
def get_model(self, f=None):
self.read_parameters()
fit = Fit(self.data, self.functions)
if self.plot_checkbox.isChecked():
x = fit.x
else:
x = np.linspace(float(self.plot_minbox.text()),
float(self.plot_maxbox.text()), 1001)
return NXdata(NXfield(fit.get_model(x, f), name='model'),
NXfield(x, name=fit.data.nxaxes[0].nxname),
title='Fit Results')
def write_chopper_vacuum(self, vac0, vac1, vac2, vac3):
if vac0 is not None:
self._entry.instrument.chopper_vac0 = NXfield(
float(vac0), dtype='float32', units=string_attr('mbar'))
if vac1 is not None:
self._entry.instrument.chopper_vac1 = NXfield(
float(vac1), dtype='float32', units=string_attr('mbar'))
if vac2 is not None:
self._entry.instrument.chopper_vac2 = NXfield(
float(vac2), dtype='float32', units=string_attr('mbar'))
if vac3 is not None:
self._entry.instrument.chopper_vac3 = NXfield(
float(vac3), dtype='float32', units=string_attr('mbar'))
def write_sample_temperature(self, average, std, minimum, maximum):
val, unit = average.split()
self._entry.sample.temperature = NXfield(float(val),
dtype='float32',
units=string_attr(unit))
val, unit = std.split()
self._entry.sample.standard_deviation_of_temperature = NXfield(
float(val), dtype='float32', units=string_attr(unit))
val, unit = minimum.split()
self._entry.sample.minimum_temperature = NXfield(
float(val), dtype='float32', units=string_attr(unit))
val, unit = maximum.split()
self._entry.sample.maximum_temperature = NXfield(
float(val), dtype='float32', units=string_attr(unit))
def get_data(self):
self.import_file = self.get_filename()
if not self.import_file:
raise NeXusError("No file specified")
try:
import tifffile as TIFF
except ImportError:
raise NeXusError("Please install the 'tifffile' module")
im = TIFF.imread(self.import_file)
z = NXfield(im, name='z')
y = NXfield(np.arange(z.shape[0], dtype=float), name='y')
x = NXfield(np.arange(z.shape[1], dtype=float), name='x')
return NXentry(NXdata(z, (y, x)))
def convert_QE(entry, dQ, dE):
"""Convert S(phi,eps) to S(Q,eps)"""
az = entry.data.azimuthal.nxdata[:]
pol = entry.data.polar.nxdata[:]
pol, en = centers(entry.data.nxsignal, entry.data.nxaxes)
data = entry.data.data.nxdata[:]
errors = entry.data.errors.nxdata[:]
Ei = entry.instrument.monochromator.incident_energy.nxdata
Q = np.zeros((len(pol), len(en)))
E = np.zeros((len(pol), len(en)))
for i in range(0, len(pol)):
for j in range(0, len(en)):
Q[i][j] = np.sqrt((2*Ei - en[j] - 2*np.sqrt(Ei*(Ei-en[j]))
* np.cos(pol[i]*np.pi/180.0))/2.0721)
E[i][j] = en[j]
s = Q.shape
Qin = Q.reshape(s[0]*s[1])
Ein = E.reshape(s[0]*s[1])
datain = data.reshape(s[0]*s[1])
errorsin = errors.reshape(s[0]*s[1])
qmin = Q.min()
qmax = Q.max()
emin = E.min()
emax = E.max()
NQ = int((qmax-qmin)/dQ) + 1
NE = int((emax-emin)/dE) + 1
Qb = np.linspace(qmin, qmax, NQ)
Eb = np.linspace(emin, emax, NE)
# histogram and normalize
norm, nbin = np.histogramdd((Ein, Qin), bins=(Eb, Qb))
hist, hbin = np.histogramdd((Ein, Qin), bins=(Eb, Qb), weights=datain)
histe, hbin = np.histogramdd(
(Ein, Qin),
bins=(Eb, Qb),
weights=errorsin * errorsin)
histe = histe**0.5
Ib = NXfield(hist/norm, name='S(Q,E)')
err = histe/norm
Qb = NXfield(Qb[:-1]+dQ/2., name='Q')
Eb = NXfield(Eb[:-1]+dE/2., name='E')
return NXdata(Ib, (Eb, Qb), errors=NXfield(err))
def write_sample_pressure(self, average, std, minimum=None, maximum=None):
val, unit = average.split()
self._entry.sample.pressure = NXfield(float(val),
dtype='float32',
units=string_attr(unit))
val, unit = std.split()
self._entry.sample.standard_deviation_of_pressure = NXfield(
float(val), dtype='float32', units=string_attr(unit))
if minimum:
val, unit = minimum.split()
self._entry.sample.minimum_pressure = NXfield(
float(val), dtype='float32', units=string_attr(unit))
if maximum:
val, unit = maximum.split()
self._entry.sample.maximum_pressure = NXfield(
float(val), dtype='float32', units=string_attr(unit))
def write_monitor_data(self, value):
self._entry.monitor.data = NXfield(
value,
signal=1,
dtype='int64',
# axis=string_attr('channel_number'),
units=string_attr('counts'))
def save(self, x=None):
"""Save the fit results in a NXprocess group.
Parameters
----------
x : ndarray, optional
x-values at which to calculate the model. Defaults to `self.x`
Returns
-------
group : NXprocess
NXprocess group that contains the data, models and parameters.
"""
group = NXprocess(program='lmfit', version=__version__)
group['data'] = self.data
for f in self.functions:
group[f.name] = NXdata(NXfield(self.get_model(x, f), name='model'),
NXfield(x, name=self.data.nxaxes[0].nxname),
title='Fit Results')
parameters = NXparameters()
for p in f.parameters:
parameters[p.name] = NXfield(p.value,
error=p.stderr,
initial_value=p.init_value,
min=str(p.min),
max=str(p.max))
group[f.name]['parameters'] = parameters
group['title'] = 'Fit Results'
group['fit'] = NXdata(NXfield(self.get_model(x), name='model'),
NXfield(x, name=self.data.nxaxes[0].nxname),
title='Fit Results')
if self.result is not None:
fit = NXparameters()
fit.nfev = self.result.nfev
fit.chisq = self.result.chisqr
fit.redchi = self.result.redchi
fit.message = self.result.message
group['statistics'] = fit
group.note = NXnote(
self.fit.result.message, f'Chi^2 = {self.fit.result.chisqr}\n'
f'Reduced Chi^2 = {self.fit.result.redchi}\n'
f'No. of Function Evaluations = {self.fit.result.nfev}\n'
f'No. of Variables = {self.fit.result.nvarys}\n'
f'No. of Data Points = {self.fit.result.ndata}\n'
f'No. of Degrees of Freedom = {self.fit.result.nfree}\n'
f'{self.fit.fit_report()}')
return group
def get_data(self):
group = NXgroup(name=self.groupbox.text())
group.nxclass = self.groupcombo.selected
for i, col in enumerate(
[c for c in self.data if self.data[c]['signal'] != 'exclude']):
name = self.data[col]['name']
group[name] = NXfield(self.data[col]['data'],
dtype=self.data[col]['dtype'])
if self.header and name != self.headers[i]:
group[name].long_name = self.headers[i]
if isinstance(group, NXdata):
if self.data[col]['signal'] == 'signal':
group.nxsignal = group[name]
elif self.data[col]['signal'] == 'axis':
group.nxaxes = [group[name]]
elif self.data[col]['signal'] == 'signal':
group.nxerrors = group[name]
return NXentry(group)
def setup_instrument(self):
default = self.settings['nxrefine']
entry = self.configuration_file['entry']
entry['instrument/detector/distance'] = NXfield(default['distance'],
dtype=float)
entry['instrument/detector/distance'].attrs['units'] = 'mm'
self.instrument = GridParameters()
self.instrument.add('distance', entry['instrument/detector/distance'],
'Detector Distance (mm)')
detector_list = sorted(
list(set([detector().name
for detector in ALL_DETECTORS.values()])))
self.instrument.add('detector', detector_list, 'Detector')
self.instrument['detector'].value = 'Pilatus CdTe 2M'
self.instrument.add('positions', [0, 1, 2, 3, 4, 5, 6, 7, 8],
'Number of Detector Positions',
slot=self.set_entries)
self.instrument['positions'].value = '0'
def save_fit(self):
"""Saves fit results to an NXentry"""
self.read_parameters()
group = NXprocess()
group['data'] = self.data
for f in self.functions:
group[f.name] = self.get_model(f)
parameters = NXparameters()
for p in f.parameters:
parameters[p.name] = NXfield(p.value,
error=p.stderr,
initial_value=p.init_value,
min=str(p.min),
max=str(p.max))
group[f.name].insert(parameters)
if self.fit is not None:
group['program'] = 'lmfit'
group['version'] = lmfit.__version__
group['title'] = 'Fit Results'
group['fit'] = self.get_model()
fit = NXparameters()
fit.nfev = self.fit.result.nfev
fit.ier = self.fit.result.ier
fit.chisq = self.fit.result.chisqr
fit.redchi = self.fit.result.redchi
fit.message = self.fit.result.message
fit.lmdif_message = self.fit.result.lmdif_message
group['statistics'] = fit
group.note = NXnote(
self.fit.result.message,
('%s\n' % self.fit.result.lmdif_message +
'scipy.optimize.leastsq error value = %s\n' %
self.fit.result.ier +
'Chi^2 = %s\n' % self.fit.result.chisqr +
'Reduced Chi^2 = %s\n' % self.fit.result.redchi +
'No. of Function Evaluations = %s\n' % self.fit.result.nfev +
'No. of Variables = %s\n' % self.fit.result.nvarys +
'No. of Data Points = %s\n' % self.fit.result.ndata +
'No. of Degrees of Freedom = %s\n' % self.fit.result.nfree +
'%s' % self.fit.fit_report()))
else:
group['title'] = 'Fit Model'
group['model'] = self.get_model()
if 'w0' not in self.tree:
self.tree['w0'] = nxload(self.mainwindow.scratch_file, 'rw')
ind = []
for key in self.tree['w0']:
try:
if key.startswith('f'):
ind.append(int(key[1:]))
except ValueError:
pass
if not ind:
ind = [0]
name = 'f' + str(sorted(ind)[-1] + 1)
self.tree['w0'][name] = group
def setup_scan(self):
default = self.settings['nxrefine']
entry = self.configuration_file['entry']
entry['instrument/goniometer/chi'] = (NXfield(default['chi'],
dtype=float))
entry['instrument/goniometer/chi'].attrs['units'] = 'degree'
entry['instrument/goniometer/phi'] = (NXfield(default['phi'],
dtype=float))
entry['instrument/goniometer/phi'].attrs['step'] = (NXfield(
default['phi_step'], dtype=float))
entry['instrument/goniometer/phi'].attrs['end'] = (NXfield(
default['phi_end'], dtype=float))
entry['instrument/goniometer/phi'].attrs['units'] = 'degree'
entry['instrument/detector/frame_time'] = (NXfield(
1 / float(default['frame_rate']), dtype=float))
self.scan = GridParameters()
self.scan.add('chi', default['chi'], 'Chi (deg)')
self.scan.add('phi_start', default['phi'], 'Phi Start (deg)')
self.scan.add('phi_end', default['phi_end'], 'Phi End (deg)')
self.scan.add('phi_step', default['phi_step'], 'Phi Step (deg)')
self.scan.add('frame_rate', default['frame_rate'], 'Frame Rate (Hz)')
def rebin2D(self, spw, phi, psi, omega, dphi, dpsi):
rot = np.linspace(np.round(phi.min() - 0.5 * dphi, 2),
np.round(phi.max() + 0.5 * dphi, 2),
np.round(phi.ptp() / dphi)).astype(np.float32)
tilt = np.linspace(np.round(psi.min() - 0.5 * dpsi, 2),
np.round(psi.max() + 0.5 * dpsi, 2),
np.round(psi.ptp() / dpsi)).astype(np.float32)
en = 0.5*(omega[1:]+omega[:-1])
data = NXfield(name='data', dtype='float32', shape=[
rot.size-1, tilt.size-1, omega.size-1])
rotation_angle = NXfield(rot, name='rotation_angle', units='degree')
tilt_angle = NXfield(tilt, name='tilt_angle', units='degree')
energy_transfer = NXfield(omega, name='energy_transfer', units='meV')
pixels = np.array(zip(np.repeat(phi, en.size), np.repeat(
psi, en.size), np.tile(en, phi.size)))
hist, edges = np.histogramdd(
pixels, [rot, tilt, omega],
weights=spw.reshape(spw.size))
return NXdata(
NXfield(hist, name='intensity'),
(rotation_angle, tilt_angle, energy_transfer))
def get_data(self):
prefix = self.get_prefix()
if prefix:
self.import_file = prefix
else:
self.import_file = self.get_directory()
filenames = self.get_files()
v0 = self.read_image(filenames[0])
x = NXfield(range(v0.shape[1]), dtype=np.uint16, name='x')
y = NXfield(range(v0.shape[0]), dtype=np.uint16, name='y')
z = NXfield(range(1, len(filenames) + 1), dtype=np.uint16, name='z')
v = NXfield(shape=(len(filenames), v0.shape[0], v0.shape[1]),
dtype=v0.dtype,
name='v')
v[0] = v0
if v._memfile:
chunk_size = v._memfile['data'].chunks[0]
else:
chunk_size = v.shape[0] / 10
self.progress_bar.setVisible(True)
self.progress_bar.setRange(0, len(filenames))
for i in range(0, len(filenames)):
try:
files = []
for j in range(i, i + chunk_size):
files.append(filenames[j])
self.progress_bar.setValue(j)
self.update_progress()
v[i:i + chunk_size, :, :] = self.read_images(files)
except IndexError as error:
pass
global maximum
v.maximum = maximum
return NXentry(NXdata(v, (z, y, x)))
def write_data(self, block, channels):
try:
self._entry.data.makelink(
self._entry.instrument.detector.polar_angle)
except NeXusError:
pass
nDet = len(self.eleTotal)
data = []
for i in range(nDet):
data += block[self.eleTotal[i] - 1].tolist()
data = np.array(data, dtype='int32').reshape(nDet, 1, int(channels))
self._entry.data.data = NXfield(
data,
signal=1,
dtype='int32',
# compression='lzf',
axes=string_attr('2theta:channel_number'),
units=string_attr('counts'))
channel_number = np.arange(int(channels), dtype='float32')
self._entry.data.channel_number = NXfield(channel_number)
def write_times(self, stime, etime, duration=None):
fmtin = '%d.%m.%YT%H:%M:%S'
fmtout = '%Y-%m-%dT%H:%M:%S%z'
tzinfo = pytz.timezone('Europe/Berlin')
t0 = datetime.strptime(stime, fmtin).replace(tzinfo=tzinfo)
t1 = datetime.strptime(etime, fmtin).replace(tzinfo=tzinfo)
if duration is None:
duration = (t1 - t0).total_seconds()
assert (duration >= 0)
self._entry.start_time = string_(t0.strftime(fmtout))
self._entry.end_time = string_(t1.strftime(fmtout))
self._entry.duration = NXfield(int(duration),
dtype='int32',
units=string_attr('s'))
def plot_cake(self):
if 'Cake Plot' in plotviews:
plotview = plotviews['Cake Plot']
else:
plotview = NXPlotView('Cake Plot')
if not self.is_calibrated:
raise NeXusError('No refinement performed')
res = self.cake_geometry.integrate2d(self.counts,
1024, 1024,
method='csr',
unit='2th_deg',
correctSolidAngle=True)
self.cake_data = NXdata(res[0],
(NXfield(res[2], name='azimumthal_angle'),
NXfield(res[1], name='polar_angle')))
self.cake_data['title'] = 'Cake Plot'
plotview.plot(self.cake_data, log=True)
wavelength = self.parameters['wavelength'].value
polar_angles = [2 * np.degrees(np.arcsin(wavelength/(2*d)))
for d in self.calibrant.dSpacing]
plotview.vlines([polar_angle for polar_angle in polar_angles
if polar_angle < plotview.xaxis.max],
linestyle=':', color='r')
def get_data(self):
prefix = self.get_prefix()
if prefix:
self.import_file = prefix
else:
self.import_file = self.get_directory()
filenames = self.get_files()
try:
import fabio
except ImportError:
raise NeXusError("Please install the 'fabio' module")
im = self.read_image(filenames[0])
v0 = im.data
x = NXfield(range(v0.shape[1]), dtype=np.uint16, name='x')
y = NXfield(range(v0.shape[0]), dtype=np.uint16, name='y')
z = NXfield(range(1, len(filenames)+1), dtype=np.uint16, name='z')
v = NXfield(shape=(len(filenames), v0.shape[0], v0.shape[1]),
dtype=v0.dtype, name='v')
v[0] = v0
if v._memfile:
chunk_size = v._memfile['data'].chunks[0]
else:
chunk_size = v.shape[0]/10
self.progress_bar.setVisible(True)
self.progress_bar.setRange(0, len(filenames))
for i in range(0, len(filenames), chunk_size):
try:
files = []
for j in range(i, i+chunk_size):
files.append(filenames[j])
self.progress_bar.setValue(j)
self.update_progress()
v[i:i+chunk_size, :, :] = self.read_images(files)
except IndexError as error:
pass
global maximum
v.maximum = maximum
if im.getclassname() == 'CbfImage':
note = NXnote(type='text/plain', file_name=self.import_file)
note.data = im.header.pop('_array_data.header_contents', '')
note.description = im.header.pop(
'_array_data.header_convention', '')
else:
note = None
header = NXcollection()
for key, value in im.header.items():
header[key] = value
if note:
return NXentry(
NXdata(
v, (z, y, x),
CBF_header=note, header=header))
else:
return NXentry(NXdata(v, (z, y, x), header=header))
def NXchi(self, T=None):
"""Returns the susceptibility as a NeXus NXentry"""
from nexusformat.nexus import NXfield, NXentry, NXdata
ChiC_zz, ChiC_xx, ChiV_zz, ChiV_xx = self.chi(T)
entry = NXentry()
entry.title = self.title
temperature = NXfield(T, name="temperature")
temperature.units = "K"
chi = NXfield(ChiC_zz + ChiV_zz + 2 * (ChiC_xx + ChiV_xx), name="chi")
entry.chi = NXdata(chi, temperature)
entry.chi.title = "Susceptibility of %s" % self.title
entry.invchi = NXdata(1 / chi, temperature)
entry.invchi.title = "Inverse Susceptibility of %s" % self.title
entry.chiz = NXdata(ChiC_zz + ChiV_zz, temperature)
entry.chiz.title = "Susceptibility of %s (z-axis)" % self.title
entry.chix = NXdata(ChiC_xx + ChiV_xx, temperature)
entry.chix.title = "Susceptibility of %s (x-axis)" % self.title
return entry
def get_nxspe(self):
spe_file = nxload(self.import_file)
entry = NXentry()
entry.title = self.get_title()
Ei = self.get_energy()
if Ei and Ei > 0.0:
entry.instrument = NXinstrument()
entry.instrument.monochromator = NXmonochromator(
NXfield(Ei, name="incident_energy", units="meV"))
entry.data = spe_file.NXentry[0].data
entry.data.nxsignal = entry.data.data
if 'energy' in entry.data.entries:
entry.data.energy.rename('energy_transfer')
entry.data.nxaxes = [entry.data.polar, entry.data.energy_transfer]
if 'error' in entry.data.entries:
entry.data.error.rename('errors')
return entry
def save_fit(self):
"""Saves fit results to an NXentry"""
self.read_parameters()
entry = NXentry()
entry['data'] = self.data
for f in self.functions:
entry[f.name] = self.get_model(f)
parameters = NXparameters()
for p in f.parameters:
parameters[p.name] = NXfield(p.value,
error=p.stderr,
initial_value=p.init_value,
min=str(p.min),
max=str(p.max))
entry[f.name].insert(parameters)
if self.fit is not None:
entry['title'] = 'Fit Results'
entry['fit'] = self.get_model()
fit = NXparameters()
fit.nfev = self.fit.result.nfev
fit.ier = self.fit.result.ier
fit.chisq = self.fit.result.chisqr
fit.redchi = self.fit.result.redchi
fit.message = self.fit.result.message
fit.lmdif_message = self.fit.result.lmdif_message
entry['statistics'] = fit
else:
entry['title'] = 'Fit Model'
entry['model'] = self.get_model()
if 'w0' not in self.tree.keys():
self.tree.add(NXroot(name='w0'))
ind = []
for key in self.tree['w0'].keys():
try:
if key.startswith('f'):
ind.append(int(key[1:]))
except ValueError:
pass
if not ind:
ind = [0]
name = 'f' + str(sorted(ind)[-1] + 1)
self.tree['w0'][name] = entry
def plot_peaks(self, x, y):
try:
polar_angles, azimuthal_angles = self.refine.calculate_angles(x, y)
if polar_angles[0] > polar_angles[-1]:
polar_angles = polar_angles[::-1]
azimuthal_angles = azimuthal_angles[::-1]
azimuthal_field = NXfield(azimuthal_angles, name='azimuthal_angle')
azimuthal_field.long_name = 'Azimuthal Angle'
polar_field = NXfield(polar_angles, name='polar_angle')
polar_field.long_name = 'Polar Angle'
plotview = get_plotview()
plotview.plot(
NXdata(azimuthal_field, polar_field, title='Peak Angles'))
except NeXusError as error:
report_error("Plotting Lattice", error)
def plot_peaks(self):
try:
x, y = (self.refine.xp[self.refine.idx],
self.refine.yp[self.refine.idx])
polar_angles, azimuthal_angles = self.refine.calculate_angles(x, y)
if polar_angles[0] > polar_angles[-1]:
polar_angles = polar_angles[::-1]
azimuthal_angles = azimuthal_angles[::-1]
azimuthal_field = NXfield(azimuthal_angles, name='azimuthal_angle')
azimuthal_field.long_name = 'Azimuthal Angle'
polar_field = NXfield(polar_angles, name='polar_angle')
polar_field.long_name = 'Polar Angle'
plotview = get_plotview()
plotview.plot(NXdata(azimuthal_field,
polar_field,
title=f'{self.refine.name} Peak Angles'),
xmax=self.get_polar_max())
except NeXusError as error:
report_error('Plotting Lattice', error)
def setup_configuration(self):
default = self.settings['nxrefine']
entry = self.configuration_file['entry']
entry['instrument/monochromator/wavelength'] = NXfield(
default['wavelength'], dtype=np.float32)
entry['instrument/monochromator/wavelength'].attrs['units'] = (
'Angstroms')
entry['instrument/monochromator/energy'] = NXfield(12.398419739640717 /
0.5,
dtype=np.float32)
entry['instrument/monochromator/energy'].attrs['units'] = 'keV'
entry['instrument/goniometer'] = NXgoniometer()
entry['instrument/detector'] = NXdetector()
self.configuration = GridParameters()
self.configuration.add('configuration', 'configuration',
'Configuration Filename')
self.configuration.add('wavelength',
entry['instrument/monochromator/wavelength'],
'Wavelength (Å)')
def setup_analysis(self):
default = self.settings['nxreduce']
entry = self.configuration_file['entry']
entry['nxreduce/threshold'] = NXfield(default['threshold'],
dtype=float)
entry['nxreduce/monitor'] = NXfield(default['monitor'])
entry['nxreduce/norm'] = NXfield(default['norm'], dtype=float)
entry['nxreduce/first_frame'] = NXfield(default['first'], dtype=int)
entry['nxreduce/last_frame'] = NXfield(default['last'], dtype=int)
entry['nxreduce/radius'] = NXfield(default['radius'], dtype=float)
self.analysis = GridParameters()
self.analysis.add('threshold', entry['nxreduce/threshold'],
'Peak Threshold')
self.analysis.add('first', entry['nxreduce/first_frame'],
'First Frame')
self.analysis.add('last', entry['nxreduce/last_frame'], 'Last Frame')
self.analysis.add('monitor', ['monitor1', 'monitor2'],
'Normalization Monitor')
self.analysis['monitor'].value = default['monitor']
self.analysis.add('norm', entry['nxreduce/norm'],
'Normalization Value')
self.analysis.add('radius', entry['nxreduce/radius'],
'Punch Radius (Å)')
def string_(value):
if not value:
value = ' '
f = NXfield(value, dtype='|S%d' % (len(value) + 1))
return f
def convert_QE(self):
"""Convert S(phi,eps) to S(Q,eps)"""
self.read_parameters()
Ei = self.Ei
dQ = self.dQ
dE = self.dE
signal = self.entry['data'].nxsignal
pol = centers(self.entry['data/polar_angle'], signal.shape[0])
tof = centers(self.entry['data/time_of_flight'], signal.shape[1])
en = self.convert_tof(tof)
idx_max = min(np.where(np.abs(en - 0.75 * Ei) < 0.1)[0])
en = en[:idx_max]
data = signal.nxdata[:, :idx_max]
if self.entry['data'].nxerrors:
errors = self.entry['data'].nxerrors.nxdata[:]
Q = np.zeros((len(pol), len(en)))
E = np.zeros((len(pol), len(en)))
for i in range(0, len(pol)):
p = pol[i]
Q[i, :] = np.array(
np.sqrt(
(2 * Ei - en -
2 * np.sqrt(Ei * (Ei - en)) * np.cos(p * np.pi / 180.0)) /
2.0721))
E[i, :] = np.array(en)
s = Q.shape
Qin = Q.reshape(s[0] * s[1])
Ein = E.reshape(s[0] * s[1])
datain = data.reshape(s[0] * s[1])
if self.entry['data'].nxerrors:
errorsin = errors.reshape(s[0] * s[1])
qmin = Q.min()
qmax = Q.max()
emin = E.min()
emax = E.max()
NQ = int((qmax - qmin) / dQ) + 1
NE = int((emax - emin) / dE) + 1
Qb = np.linspace(qmin, qmax, NQ)
Eb = np.linspace(emin, emax, NE)
# histogram and normalize
norm, nbin = np.histogramdd((Ein, Qin), bins=(Eb, Qb))
hist, hbin = np.histogramdd((Ein, Qin), bins=(Eb, Qb), weights=datain)
if self.entry['data'].nxerrors:
histe, hbin = np.histogramdd((Ein, Qin),
bins=(Eb, Qb),
weights=errorsin * errorsin)
histe = histe**0.5
err = histe / norm
Ib = NXfield(hist / norm, name='S(Q,E)')
Qb = NXfield(Qb[:-1] + dQ / 2., name='Q')
Eb = NXfield(Eb[:-1] + dE / 2., name='E')
result = NXdata(Ib, (Eb, Qb))
if self.entry.data.nxerrors:
result.errors = NXfield(err)
return result
def get_spe(self, phxfile=None):
entry = NXentry()
phi, omega, spw, errors = readspe(self.get_filename())
if phxfile:
theta, phi, dtheta, dpsi = readphx(phxfile)
phip, psi = angles(theta, phi)
instrument = NXinstrument(NXdetector())
instrument.detector.polar_angle = NXfield(theta, units="degrees")
Ei = self.get_energy()
if Ei and Ei > 0.0:
instrument.monochromator = NXmonochromator(
NXfield(Ei, name="incident_energy", units="meV"))
if phi.ptp() > 1.0: # i.e., the azimuthal angle is specified
instrument.detector.azimuthal_angle = NXfield(
phi, units="degrees")
instrument.detector.rotation_angle = NXfield(
phip, units="degrees")
instrument.detector.tilt_angle = NXfield(psi, units="degrees")
data = NXdata(
NXfield(
spw, name="intensity",
long_name="Neutron Intensity"),
(
NXfield(
np.arange(1, len(theta) + 1),
name="spectrum_index",
long_name="Spectrum Index"),
NXfield(
omega, name="energy_transfer", units="meV",
long_name="Energy Transfer")),
errors=NXfield(
np.sqrt(errors),
name="errors", long_name="Errors"))
if np.median(dtheta) > 0.0 and np.median(dpsi) > 0.0:
data2D = rebin2D(
spw, phip, psi, omega, np.median(dtheta),
np.median(dpsi))
return NXentry(instrument, data, data2D=data2D)
else:
return NXentry(instrument, data)
else:
phi = np.zeros(theta.size+1)
phi[:-1] = theta - 0.5*dtheta
phi[-1] = theta[-1] + 0.5*dtheta[-1]
data = NXdata(
NXfield(
spw, name="intensity",
long_name="Neutron Intensity"),
(
NXfield(
phi, name="polar_angle",
long_name="Polar Angle", units="degrees"),
NXfield(
omega, name="energy_transfer", units="meV",
long_name="Energy Transfer")),
errors=NXfield(
np.sqrt(errors),
name="errors", long_name="Errors"))
return NXentry(instrument, data)
else:
Ei = self.get_energy()
if Ei and Ei > 0.0:
entry = NXentry(
NXinstrument(
NXmonochromator(
NXfield(
Ei, name="incident_energy",
units="meV"))))
else:
entry = NXentry()
if phi.ptp() > 1.0:
entry.data = NXdata(
NXfield(spw, name="intensity",
long_name="Neutron Intensity"),
(NXfield(phi, name="polar_angle", units="degrees",
long_name="Polar Angle"),
NXfield(omega, name="energy_transfer", units="meV",
long_name="Energy Transfer")),
errors=NXfield(np.sqrt(errors), name="errors",
long_name="Errors"))
else:
entry.data = NXdata(
NXfield(spw, name="intensity",
long_name="Neutron Intensity"),
(NXfield(np.arange(1, len(phi)+1), name="spectrum_index",
long_name="Spectrum Index"),
NXfield(omega, name="energy_transfer", units="meV",
long_name="Energy Transfer")),
errors=NXfield(np.sqrt(errors), name="errors",
long_name="Errors"))
return entry
def write_wavelength(self, value):
val, unit = value.split()
self._entry.wavelength = NXfield(float(val),
dtype='float32',
units=string_attr(unit))
def plot(self, data_group, fmt, xmin, xmax, ymin, ymax, zmin, zmax,
**opts):
"""
Plot the data entry.
Raises NeXusError if the data cannot be plotted.
"""
try:
import matplotlib.pyplot as plt
except ImportError:
raise NeXusError(
"Default plotting package (matplotlib) not available.")
over = opts.pop("over", False)
image = opts.pop("image", False)
log = opts.pop("log", False)
logx = opts.pop("logx", False)
logy = opts.pop("logy", False)
if fmt == '':
fmt = 'o'
if over:
plt.autoscale(enable=False)
else:
plt.autoscale(enable=True)
plt.clf()
signal = data_group.nxsignal
errors = data_group.nxerrors
title = data_group.nxtitle
# Provide a new view of the data if there is a dimension of length 1
data, axes = (signal.nxdata.reshape(data_group.plot_shape),
data_group.plot_axes)
#One-dimensional Plot
if len(data.shape) == 1:
if hasattr(signal, 'units'):
if not errors and signal.units == 'counts':
errors = NXfield(np.sqrt(data))
if errors:
ebars = errors.nxdata
plt.errorbar(centers(axes[0], data.shape[0]),
data,
ebars,
fmt=fmt,
**opts)
else:
plt.plot(centers(axes[0], data.shape[0]), data, fmt, **opts)
if not over:
ax = plt.gca()
xlo, xhi = ax.set_xlim(auto=True)
ylo, yhi = ax.set_ylim(auto=True)
if xmin: xlo = xmin
if xmax: xhi = xmax
ax.set_xlim(xlo, xhi)
if ymin: ylo = ymin
if ymax: yhi = ymax
ax.set_ylim(ylo, yhi)
if logx: ax.set_xscale('symlog')
if log or logy: ax.set_yscale('symlog')
plt.xlabel(label(axes[0]))
plt.ylabel(label(signal))
plt.title(title)
#Two dimensional plot
else:
from matplotlib.image import NonUniformImage
from matplotlib.colors import LogNorm, Normalize
if len(data.shape) > 2:
slab = []
if image:
for _dim in data.shape[:-3]:
slab.append(0)
slab.extend([slice(None), slice(None), slice(None)])
else:
for _dim in data.shape[:-2]:
slab.append(0)
slab.extend([slice(None), slice(None)])
data = data[slab]
if 0 in slab:
print "Warning: Only the top 2D slice of the data is plotted"
if image:
x = boundaries(axes[-2], data.shape[-2])
y = boundaries(axes[-3], data.shape[-3])
xlabel, ylabel = label(axes[-2]), label(axes[-3])
else:
x = boundaries(axes[-1], data.shape[-1])
y = boundaries(axes[-2], data.shape[-2])
xlabel, ylabel = label(axes[-1]), label(axes[-2])
if not zmin:
zmin = np.nanmin(data[data > -np.inf])
if not zmax:
zmax = np.nanmax(data[data < np.inf])
if not image:
if log:
zmin = max(zmin, 0.01)
zmax = max(zmax, 0.01)
opts["norm"] = LogNorm(zmin, zmax)
else:
opts["norm"] = Normalize(zmin, zmax)
ax = plt.gca()
if image:
im = ax.imshow(data, **opts)
ax.set_aspect('equal')
else:
im = ax.pcolormesh(x, y, data, **opts)
im.get_cmap().set_bad('k', 1.0)
ax.set_xlim(x[0], x[-1])
ax.set_ylim(y[0], y[-1])
ax.set_aspect('auto')
if not image:
plt.colorbar(im)
if 'origin' in opts and opts['origin'] == 'lower':
image = False
if xmin:
ax.set_xlim(left=xmin)
if xmax:
ax.set_xlim(right=xmax)
if ymin:
if image:
ax.set_ylim(top=ymin)
else:
ax.set_ylim(bottom=ymin)
if ymax:
if image:
ax.set_ylim(bottom=ymax)
else:
ax.set_ylim(top=ymax)
plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title)
plt.gcf().canvas.draw_idle()
plt.ion()
plt.show()