def __init__(self, element_subshell, GOS=None):
# Declare the parameters
Component.__init__(self, ["intensity", "fine_structure_coeff", "effective_angle", "onset_energy"])
self.name = element_subshell
self.element, self.subshell = element_subshell.split("_")
self.energy_scale = None
self.effective_angle.free = False
self.fine_structure_active = preferences.EELS.fine_structure_active
self.fine_structure_width = preferences.EELS.fine_structure_width
self.fine_structure_coeff.ext_force_positive = False
self.GOS = None
# Set initial actions
if GOS is None:
try:
self.GOS = HartreeSlaterGOS(element_subshell)
GOS = "Hartree-Slater"
except IOError:
GOS = "hydrogenic"
messages.information("Hartree-Slater GOS not available" "Using hydrogenic GOS")
if self.GOS is None:
if GOS == "Hartree-Slater":
self.GOS = HartreeSlaterGOS(element_subshell)
elif GOS == "hydrogenic":
self.GOS = HydrogenicGOS(element_subshell)
else:
raise ValueError("gos must be one of: None, 'hydrogenic'" " or 'Hartree-Slater'")
self.onset_energy.value = self.GOS.onset_energy
self.onset_energy.free = False
self._position = self.onset_energy
self.free_onset_energy = False
self.intensity.grad = self.grad_intensity
self.intensity.value = 1
self.intensity.bmin = 0.0
self.intensity.bmax = None
def __init__(self, element_subshell, GOS=None):
# Declare the parameters
Component.__init__(self,
['intensity',
'fine_structure_coeff',
'effective_angle',
'onset_energy'])
if isinstance(element_subshell, dict):
self.element = element_subshell['element']
self.subshell = element_subshell['subshell']
else:
self.element, self.subshell = element_subshell.split('_')
self.name = "_".join([self.element, self.subshell])
self.energy_scale = None
self.effective_angle.free = False
self.fine_structure_active = preferences.EELS.fine_structure_active
self.fine_structure_width = preferences.EELS.fine_structure_width
self.fine_structure_coeff.ext_force_positive = False
self.GOS = None
# Set initial actions
if GOS is None:
try:
self.GOS = HartreeSlaterGOS(element_subshell)
GOS = 'Hartree-Slater'
except IOError:
GOS = 'hydrogenic'
messages.information(
'Hartree-Slater GOS not available. '
'Using hydrogenic GOS')
if self.GOS is None:
if GOS == 'Hartree-Slater':
self.GOS = HartreeSlaterGOS(element_subshell)
elif GOS == 'hydrogenic':
self.GOS = HydrogenicGOS(element_subshell)
else:
raise ValueError(
'gos must be one of: None, \'hydrogenic\''
' or \'Hartree-Slater\'')
self.onset_energy.value = self.GOS.onset_energy
self.onset_energy.free = False
self._position = self.onset_energy
self.free_onset_energy = False
self.intensity.grad = self.grad_intensity
self.intensity.value = 1
self.intensity.bmin = 0.
self.intensity.bmax = None
self._whitelist['GOS'] = ('init', GOS)
if GOS == 'Hartree-Slater':
self._whitelist['element_subshell'] = (
'init',
self.GOS.as_dictionary(True))
elif GOS == 'hydrogenic':
self._whitelist['element_subshell'] = ('init', element_subshell)
self._whitelist['fine_structure_active'] = None
self._whitelist['fine_structure_width'] = None
self._whitelist['fine_structure_smoothing'] = None
def __init__(self, element_subshell, GOS=None):
# Declare the parameters
Component.__init__(self, ["intensity", "fine_structure_coeff", "effective_angle", "onset_energy"])
if isinstance(element_subshell, dict):
self.element = element_subshell["element"]
self.subshell = element_subshell["subshell"]
else:
self.element, self.subshell = element_subshell.split("_")
self.name = "_".join([self.element, self.subshell])
self.energy_scale = None
self.effective_angle.free = False
self.fine_structure_active = preferences.EELS.fine_structure_active
self.fine_structure_width = preferences.EELS.fine_structure_width
self.fine_structure_coeff.ext_force_positive = False
self.GOS = None
# Set initial actions
if GOS is None:
try:
self.GOS = HartreeSlaterGOS(element_subshell)
GOS = "Hartree-Slater"
except IOError:
GOS = "hydrogenic"
messages.information("Hartree-Slater GOS not available. " "Using hydrogenic GOS")
if self.GOS is None:
if GOS == "Hartree-Slater":
self.GOS = HartreeSlaterGOS(element_subshell)
elif GOS == "hydrogenic":
self.GOS = HydrogenicGOS(element_subshell)
else:
raise ValueError("gos must be one of: None, 'hydrogenic'" " or 'Hartree-Slater'")
self.onset_energy.value = self.GOS.onset_energy
self.onset_energy.free = False
self._position = self.onset_energy
self.free_onset_energy = False
self.intensity.grad = self.grad_intensity
self.intensity.value = 1
self.intensity.bmin = 0.0
self.intensity.bmax = None
self._whitelist["GOS"] = ("init", GOS)
if GOS == "Hartree-Slater":
self._whitelist["element_subshell"] = ("init", self.GOS.as_dictionary(True))
elif GOS == "hydrogenic":
self._whitelist["element_subshell"] = ("init", element_subshell)
self._whitelist["fine_structure_active"] = None
self._whitelist["fine_structure_width"] = None
self._whitelist["fine_structure_smoothing"] = None
self.effective_angle.events.value_changed.connect(self._integrate_GOS, [])
self.onset_energy.events.value_changed.connect(self._integrate_GOS, [])
self.onset_energy.events.value_changed.connect(self._calculate_knots, [])
class EELSCLEdge(Component):
"""EELS core loss ionisation edge from hydrogenic or tabulated
Hartree-Slater GOS with splines for fine structure fitting.
Hydrogenic GOS are limited to K and L shells.
Currently it only supports Peter Rez's Hartree Slater cross sections
parametrised as distributed by Gatan in their
Digital Micrograph (DM) software. If Digital Micrograph is installed
in the system HyperSpy in the standard location HyperSpy should
find the path to the HS GOS folder. Otherwise, the location of the
folder can be defined in HyperSpy preferences, which can be done through
preferences.gui() or the preferences.EELS.eels_gos_files_path variable.
Calling this class with a numpy.array
Parameters
----------
element_subshell : str
For example, 'Ti_L3' for the GOS of the titanium L3 subshell
GOS : {'hydrogenic', 'Hartree-Slater', None}
The GOS to use. If None it will use the Hartree-Slater GOS if
they are available, otherwise it will use the hydrogenic GOS.
Attributes
----------
onset_energy : Parameter
The edge onset position
intensity : Parameter
The factor by which the cross section is multiplied, what in
favourable cases is proportional to the number of atoms of
the element. It is a component.Parameter instance.
It is fixed by default.
fine_structure_coeff : Parameter
The coefficients of the spline that fits the fine structure.
Fix this parameter to fix the fine structure. It is a
component.Parameter instance.
effective_angle : Parameter
The effective collection angle. It is automatically
calculated by set_microscope_parameters. It is a
component.Parameter instance. It is fixed by default.
fine_structure_smoothing : float between 0 and 1
Controls the level of smoothing of the fine structure model.
Decreasing the value increases the level of smoothing.
fine_structure_active : bool
Activates/deactivates the fine structure feature. Its
default value can be choosen in the preferences.
"""
_fine_structure_smoothing = \
preferences.EELS.fine_structure_smoothing
def __init__(self, element_subshell, GOS=None):
# Declare the parameters
Component.__init__(self,
['intensity',
'fine_structure_coeff',
'effective_angle',
'onset_energy'])
self.name = element_subshell
self.element, self.subshell = element_subshell.split('_')
self.energy_scale = None
self.effective_angle.free = False
self.fine_structure_active = preferences.EELS.fine_structure_active
self.fine_structure_width = preferences.EELS.fine_structure_width
self.fine_structure_coeff.ext_force_positive = False
self.GOS = None
# Set initial actions
if GOS is None:
try:
self.GOS = HartreeSlaterGOS(element_subshell)
GOS = 'Hartree-Slater'
except IOError:
GOS = 'hydrogenic'
messages.information(
'Hartree-Slater GOS not available'
'Using hydrogenic GOS')
if self.GOS is None:
if GOS == 'Hartree-Slater':
self.GOS = HartreeSlaterGOS(element_subshell)
elif GOS == 'hydrogenic':
self.GOS = HydrogenicGOS(element_subshell)
else:
raise ValueError(
'gos must be one of: None, \'hydrogenic\''
' or \'Hartree-Slater\'')
self.onset_energy.value = self.GOS.onset_energy
self.onset_energy.free = False
self._position = self.onset_energy
self.free_onset_energy = False
self.intensity.grad = self.grad_intensity
self.intensity.value = 1
self.intensity.bmin = 0.
self.intensity.bmax = None
# Automatically fix the fine structure when the fine structure is
# disable.
# In this way we avoid a common source of problems when fitting
# However the fine structure must be *manually* freed when we
# reactivate the fine structure.
def _get_fine_structure_active(self):
return self.__fine_structure_active
def _set_fine_structure_active(self, arg):
if arg is False:
self.fine_structure_coeff.free = False
self.__fine_structure_active = arg
# Force replot
self.intensity.value = self.intensity.value
fine_structure_active = property(_get_fine_structure_active,
_set_fine_structure_active)
def _get_fine_structure_width(self):
return self.__fine_structure_width
def _set_fine_structure_width(self, arg):
self.__fine_structure_width = arg
self._set_fine_structure_coeff()
fine_structure_width = property(_get_fine_structure_width,
_set_fine_structure_width)
# E0
def _get_E0(self):
return self.__E0
def _set_E0(self, arg):
self.__E0 = arg
self._calculate_effective_angle()
E0 = property(_get_E0, _set_E0)
# Collection angles
def _get_collection_angle(self):
return self.__collection_angle
def _set_collection_angle(self, arg):
self.__collection_angle = arg
self._calculate_effective_angle()
collection_angle = property(_get_collection_angle,
_set_collection_angle)
# Convergence angle
def _get_convergence_angle(self):
return self.__convergence_angle
def _set_convergence_angle(self, arg):
self.__convergence_angle = arg
self._calculate_effective_angle()
convergence_angle = property(_get_convergence_angle,
_set_convergence_angle)
def _calculate_effective_angle(self):
try:
self.effective_angle.value = effective_angle(
self.E0,
self.GOS.onset_energy,
self.convergence_angle,
self.collection_angle)
except:
# All the parameters may not be defined yet...
pass
@property
def fine_structure_smoothing(self):
"""Controls the level of the smoothing of the fine structure.
It must a real number between 0 and 1. The higher close to 0
the higher the smoothing.
"""
return self._fine_structure_smoothing
@fine_structure_smoothing.setter
def fine_structure_smoothing(self, value):
if 0 <= value <= 1:
self._fine_structure_smoothing = value
self._set_fine_structure_coeff()
else:
raise ValueError(
"The value must be a number between 0 and 1")
# It is needed because the property cannot be used to sort the edges
def _onset_energy(self):
return self.onset_energy.value
def _set_fine_structure_coeff(self):
if self.energy_scale is None:
return
self.fine_structure_coeff._number_of_elements = int(
round(self.fine_structure_smoothing *
self.fine_structure_width /
self.energy_scale)) + 4
self.fine_structure_coeff.bmin = None
self.fine_structure_coeff.bmax = None
self._calculate_knots()
if self.fine_structure_coeff.map is not None:
self.fine_structure_coeff._create_array()
def set_microscope_parameters(self, E0, alpha, beta, energy_scale):
"""
Parameters
----------
E0 : float
Electron beam energy in keV.
alpha: float
Convergence angle in mrad.
beta: float
Collection angle in mrad.
energy_scale : float
The energy step in eV.
"""
# Relativistic correction factors
self.convergence_angle = alpha
self.collection_angle = beta
self.energy_scale = energy_scale
self.E0 = E0
self._integrate_GOS()
def _integrate_GOS(self):
# Integration over q using splines
angle = self.effective_angle.value * 1e-3 # in rad
self.tab_xsection = self.GOS.integrateq(
self.onset_energy.value, angle, self.E0)
# Calculate extrapolation powerlaw extrapolation parameters
E1 = self.GOS.energy_axis[-2] + self.GOS.energy_shift
E2 = self.GOS.energy_axis[-1] + self.GOS.energy_shift
y1 = self.GOS.qint[-2] # in m**2/bin */
y2 = self.GOS.qint[-1] # in m**2/bin */
self.r = math.log(y2 / y1) / math.log(E1 / E2)
self.A = y1 / E1 ** -self.r
# Connect them at this point where it is certain that all the
# parameters are well defined
self.effective_angle.connect(self._integrate_GOS)
self.onset_energy.connect(self._integrate_GOS)
self.onset_energy.connect(self._calculate_knots)
def _calculate_knots(self):
start = self.onset_energy.value
stop = start + self.fine_structure_width
self.__knots = np.r_[[start] * 4,
np.linspace(start,
stop,
self.fine_structure_coeff._number_of_elements
)[2:-2], [stop] * 4]
def function(self, E):
"""Returns the number of counts in barns
"""
Emax = self.GOS.energy_axis[-1] + self.GOS.energy_shift
cts = np.zeros((len(E)))
bsignal = (E >= self.onset_energy.value)
if self.fine_structure_active is True:
bfs = bsignal * (
E < (self.onset_energy.value + self.fine_structure_width))
cts[bfs] = splev(E[bfs],
(self.__knots, self.fine_structure_coeff.value + (0,) * 4,
3))
bsignal[bfs] = False
itab = bsignal * (E <= Emax)
cts[itab] = self.tab_xsection(E[itab])
bsignal[itab] = False
cts[bsignal] = self.A * E[bsignal] ** -self.r
return cts * self.intensity.value
def grad_intensity(self, E):
return self.function(E) / self.intensity.value
def fine_structure_coeff_to_txt(self, filename):
np.savetxt(filename + '.dat', self.fine_structure_coeff.value,
fmt="%12.6G")
def txt_to_fine_structure_coeff(self, filename):
fs = np.loadtxt(filename)
self._calculate_knots()
if len(fs) == len(self.__knots):
self.fine_structure_coeff.value = fs
else:
messages.warning_exit("The provided fine structure file "
"doesn't match the size of the current fine structure")
def get_fine_structure_as_spectrum(self):
"""Returns a spectrum containing the fine structure.
Notes
-----
The fine structure is corrected from multiple scattering if
the model was convolved with a low-loss spectrum
"""
from hyperspy._signals.eels import EELSSpectrum
channels = int(np.floor(
self.fine_structure_width / self.energy_scale))
data = np.zeros(self.fine_structure_coeff.map.shape +
(channels,))
s = EELSSpectrum(
data,
axes=self.intensity._axes_manager._get_axes_dicts())
s.get_dimensions_from_data()
s.axes_manager.signal_axes[0].offset = self.onset_energy.value
# Backup the axes_manager
original_axes_manager = self._axes_manager
self._axes_manager = s.axes_manager
for spectrum in s:
self.fetch_stored_values()
spectrum.data[:] = self.function(
s.axes_manager.signal_axes[0].axis)
# Restore the axes_manager and the values
self._axes_manager = original_axes_manager
self.fetch_stored_values()
s.metadata.General.title = self.name.replace(
'_', ' ') + ' fine structure'
return s
class EELSCLEdge(Component):
"""EELS core loss ionisation edge from hydrogenic or tabulated
Hartree-Slater GOS with splines for fine structure fitting.
Hydrogenic GOS are limited to K and L shells.
Currently it only supports Peter Rez's Hartree Slater cross sections
parametrised as distributed by Gatan in their Digital Micrograph (DM)
software. If Digital Micrograph is installed in the system HyperSpy in the
standard location HyperSpy should find the path to the HS GOS folder.
Otherwise, the location of the folder can be defined in HyperSpy
preferences, which can be done through hs.preferences.gui() or the
hs.preferences.EELS.eels_gos_files_path variable.
Parameters
----------
element_subshell : {str, dict}
Usually a string, for example, 'Ti_L3' for the GOS of the titanium L3
subshell. If a dictionary is passed, it is assumed that Hartree Slater
GOS was exported using `GOS.as_dictionary`, and will be reconstructed.
GOS : {'hydrogenic', 'Hartree-Slater', None}
The GOS to use. If None it will use the Hartree-Slater GOS if
they are available, otherwise it will use the hydrogenic GOS.
Attributes
----------
onset_energy : Parameter
The edge onset position
intensity : Parameter
The factor by which the cross section is multiplied, what in
favourable cases is proportional to the number of atoms of
the element. It is a component.Parameter instance.
It is fixed by default.
fine_structure_coeff : Parameter
The coefficients of the spline that fits the fine structure.
Fix this parameter to fix the fine structure. It is a
component.Parameter instance.
effective_angle : Parameter
The effective collection semi-angle. It is automatically
calculated by set_microscope_parameters. It is a
component.Parameter instance. It is fixed by default.
fine_structure_smoothing : float between 0 and 1
Controls the level of smoothing of the fine structure model.
Decreasing the value increases the level of smoothing.
fine_structure_active : bool
Activates/deactivates the fine structure feature. Its
default value can be choosen in the preferences.
"""
_fine_structure_smoothing = \
preferences.EELS.fine_structure_smoothing
def __init__(self, element_subshell, GOS=None):
# Declare the parameters
Component.__init__(self,
['intensity',
'fine_structure_coeff',
'effective_angle',
'onset_energy'])
if isinstance(element_subshell, dict):
self.element = element_subshell['element']
self.subshell = element_subshell['subshell']
else:
self.element, self.subshell = element_subshell.split('_')
self.name = "_".join([self.element, self.subshell])
self.energy_scale = None
self.effective_angle.free = False
self.fine_structure_active = preferences.EELS.fine_structure_active
self.fine_structure_width = preferences.EELS.fine_structure_width
self.fine_structure_coeff.ext_force_positive = False
self.GOS = None
# Set initial actions
if GOS is None:
try:
self.GOS = HartreeSlaterGOS(element_subshell)
GOS = 'Hartree-Slater'
except IOError:
GOS = 'hydrogenic'
_logger.info(
'Hartree-Slater GOS not available. '
'Using hydrogenic GOS')
if self.GOS is None:
if GOS == 'Hartree-Slater':
self.GOS = HartreeSlaterGOS(element_subshell)
elif GOS == 'hydrogenic':
self.GOS = HydrogenicGOS(element_subshell)
else:
raise ValueError(
'gos must be one of: None, \'hydrogenic\''
' or \'Hartree-Slater\'')
self.onset_energy.value = self.GOS.onset_energy
self.onset_energy.free = False
self._position = self.onset_energy
self.free_onset_energy = False
self.intensity.grad = self.grad_intensity
self.intensity.value = 1
self.intensity.bmin = 0.
self.intensity.bmax = None
self._whitelist['GOS'] = ('init', GOS)
if GOS == 'Hartree-Slater':
self._whitelist['element_subshell'] = (
'init',
self.GOS.as_dictionary(True))
elif GOS == 'hydrogenic':
self._whitelist['element_subshell'] = ('init', element_subshell)
self._whitelist['fine_structure_active'] = None
self._whitelist['fine_structure_width'] = None
self._whitelist['fine_structure_smoothing'] = None
self.effective_angle.events.value_changed.connect(
self._integrate_GOS, [])
self.onset_energy.events.value_changed.connect(self._integrate_GOS, [])
self.onset_energy.events.value_changed.connect(
self._calculate_knots, [])
# Automatically fix the fine structure when the fine structure is
# disable.
# In this way we avoid a common source of problems when fitting
# However the fine structure must be *manually* freed when we
# reactivate the fine structure.
def _get_fine_structure_active(self):
return self.__fine_structure_active
def _set_fine_structure_active(self, arg):
if arg is False:
self.fine_structure_coeff.free = False
self.__fine_structure_active = arg
# Force replot
self.intensity.value = self.intensity.value
fine_structure_active = property(_get_fine_structure_active,
_set_fine_structure_active)
def _get_fine_structure_width(self):
return self.__fine_structure_width
def _set_fine_structure_width(self, arg):
self.__fine_structure_width = arg
self._set_fine_structure_coeff()
fine_structure_width = property(_get_fine_structure_width,
_set_fine_structure_width)
# E0
def _get_E0(self):
return self.__E0
def _set_E0(self, arg):
self.__E0 = arg
self._calculate_effective_angle()
E0 = property(_get_E0, _set_E0)
# Collection semi-angle
def _get_collection_angle(self):
return self.__collection_angle
def _set_collection_angle(self, arg):
self.__collection_angle = arg
self._calculate_effective_angle()
collection_angle = property(_get_collection_angle,
_set_collection_angle)
# Convergence semi-angle
def _get_convergence_angle(self):
return self.__convergence_angle
def _set_convergence_angle(self, arg):
self.__convergence_angle = arg
self._calculate_effective_angle()
convergence_angle = property(_get_convergence_angle,
_set_convergence_angle)
def _calculate_effective_angle(self):
try:
self.effective_angle.value = effective_angle(
self.E0,
self.GOS.onset_energy,
self.convergence_angle,
self.collection_angle)
except:
# All the parameters may not be defined yet...
pass
@property
def fine_structure_smoothing(self):
"""Controls the level of the smoothing of the fine structure.
It must a real number between 0 and 1. The higher close to 0
the higher the smoothing.
"""
return self._fine_structure_smoothing
@fine_structure_smoothing.setter
def fine_structure_smoothing(self, value):
if 0 <= value <= 1:
self._fine_structure_smoothing = value
self._set_fine_structure_coeff()
else:
raise ValueError(
"The value must be a number between 0 and 1")
# It is needed because the property cannot be used to sort the edges
def _onset_energy(self):
return self.onset_energy.value
def _set_fine_structure_coeff(self):
if self.energy_scale is None:
return
self.fine_structure_coeff._number_of_elements = int(
round(self.fine_structure_smoothing *
self.fine_structure_width /
self.energy_scale)) + 4
self.fine_structure_coeff.bmin = None
self.fine_structure_coeff.bmax = None
self._calculate_knots()
if self.fine_structure_coeff.map is not None:
self.fine_structure_coeff._create_array()
def set_microscope_parameters(self, E0, alpha, beta, energy_scale):
"""
Parameters
----------
E0 : float
Electron beam energy in keV.
alpha: float
Convergence semi-angle in mrad.
beta: float
Collection semi-angle in mrad.
energy_scale : float
The energy step in eV.
"""
# Relativistic correction factors
old = self.effective_angle.value
with self.effective_angle.events.value_changed.suppress_callback(
self._integrate_GOS):
self.convergence_angle = alpha
self.collection_angle = beta
self.energy_scale = energy_scale
self.E0 = E0
if self.effective_angle.value != old:
self._integrate_GOS()
def _integrate_GOS(self):
# Integration over q using splines
angle = self.effective_angle.value * 1e-3 # in rad
self.tab_xsection = self.GOS.integrateq(
self.onset_energy.value, angle, self.E0)
# Calculate extrapolation powerlaw extrapolation parameters
E1 = self.GOS.energy_axis[-2] + self.GOS.energy_shift
E2 = self.GOS.energy_axis[-1] + self.GOS.energy_shift
y1 = self.GOS.qint[-2] # in m**2/bin */
y2 = self.GOS.qint[-1] # in m**2/bin */
self.r = math.log(y2 / y1) / math.log(E1 / E2)
self.A = y1 / E1 ** -self.r
def _calculate_knots(self):
start = self.onset_energy.value
stop = start + self.fine_structure_width
self.__knots = np.r_[
[start] * 4,
np.linspace(
start,
stop,
self.fine_structure_coeff._number_of_elements)[
2:-2],
[stop] * 4]
def function(self, E):
"""Returns the number of counts in barns
"""
shift = self.onset_energy.value - self.GOS.onset_energy
if shift != self.GOS.energy_shift:
# Because hspy Events are not executed in any given order,
# an external function could be in the same event execution list
# as _integrate_GOS and be executed first. That can potentially
# cause an error that enforcing _integrate_GOS here prevents. Note
# that this is suboptimal because _integrate_GOS is computed twice
# unnecessarily.
self._integrate_GOS()
Emax = self.GOS.energy_axis[-1] + self.GOS.energy_shift
cts = np.zeros((len(E)))
bsignal = (E >= self.onset_energy.value)
if self.fine_structure_active is True:
bfs = bsignal * (
E < (self.onset_energy.value + self.fine_structure_width))
cts[bfs] = splev(
E[bfs], (
self.__knots,
self.fine_structure_coeff.value + (0,) * 4,
3))
bsignal[bfs] = False
itab = bsignal * (E <= Emax)
cts[itab] = self.tab_xsection(E[itab])
bsignal[itab] = False
cts[bsignal] = self.A * E[bsignal] ** -self.r
return cts * self.intensity.value
def grad_intensity(self, E):
return self.function(E) / self.intensity.value
def fine_structure_coeff_to_txt(self, filename):
np.savetxt(filename + '.dat', self.fine_structure_coeff.value,
fmt="%12.6G")
def txt_to_fine_structure_coeff(self, filename):
fs = np.loadtxt(filename)
self._calculate_knots()
if len(fs) == len(self.__knots):
self.fine_structure_coeff.value = fs
else:
raise ValueError(
"The provided fine structure file "
"doesn't match the size of the current fine structure")
def get_fine_structure_as_signal1D(self):
"""Returns a spectrum containing the fine structure.
Notes
-----
The fine structure is corrected from multiple scattering if
the model was convolved with a low-loss spectrum
"""
from hyperspy._signals.eels import EELSSpectrum
channels = int(np.floor(
self.fine_structure_width / self.energy_scale))
data = np.zeros(self.fine_structure_coeff.map.shape +
(channels,))
s = EELSSpectrum(
data,
axes=self.intensity._axes_manager._get_axes_dicts())
s.get_dimensions_from_data()
s.axes_manager.signal_axes[0].offset = self.onset_energy.value
# Backup the axes_manager
original_axes_manager = self._axes_manager
self._axes_manager = s.axes_manager
for spectrum in s:
self.fetch_stored_values()
spectrum.data[:] = self.function(
s.axes_manager.signal_axes[0].axis)
# Restore the axes_manager and the values
self._axes_manager = original_axes_manager
self.fetch_stored_values()
s.metadata.General.title = self.name.replace(
'_', ' ') + ' fine structure'
return s
def notebook_interaction(self, display=True):
from ipywidgets import (Checkbox, FloatSlider, VBox)
from traitlets import TraitError as TraitletError
from IPython.display import display as ip_display
try:
active = Checkbox(description='active', value=self.active)
def on_active_change(change):
self.active = change['new']
active.observe(on_active_change, names='value')
fine_structure = Checkbox(description='Fine structure',
value=self.fine_structure_active)
def on_fine_structure_active_change(change):
self.fine_structure_active = change['new']
fine_structure.observe(on_fine_structure_active_change,
names='value')
fs_smoothing = FloatSlider(description='Fine structure smoothing',
min=0, max=1, step=0.001,
value=self.fine_structure_smoothing)
def on_fs_smoothing_change(change):
self.fine_structure_smoothing = change['new']
fs_smoothing.observe(on_fs_smoothing_change, names='value')
container = VBox([active, fine_structure, fs_smoothing])
for parameter in [self.intensity, self.effective_angle,
self.onset_energy]:
container.children += parameter.notebook_interaction(False),
if not display:
return container
ip_display(container)
except TraitletError:
if display:
print('This function is only avialable when running in a'
' notebook')
else:
raise
notebook_interaction.__doc__ = Component.notebook_interaction.__doc__
class EELSCLEdge(Component):
"""EELS core loss ionisation edge from hydrogenic or tabulated
Hartree-Slater GOS with splines for fine structure fitting.
Hydrogenic GOS are limited to K and L shells.
Currently it only supports Peter Rez's Hartree Slater cross sections
parametrised as distributed by Gatan in their Digital Micrograph (DM)
software. If Digital Micrograph is installed in the system HyperSpy in the
standard location HyperSpy should find the path to the HS GOS folder.
Otherwise, the location of the folder can be defined in HyperSpy
preferences, which can be done through hs.preferences.gui() or the
hs.preferences.EELS.eels_gos_files_path variable.
Parameters
----------
element_subshell : {str, dict}
Usually a string, for example, 'Ti_L3' for the GOS of the titanium L3
subshell. If a dictionary is passed, it is assumed that Hartree Slater
GOS was exported using `GOS.as_dictionary`, and will be reconstructed.
GOS : {'hydrogenic', 'Hartree-Slater', None}
The GOS to use. If None it will use the Hartree-Slater GOS if
they are available, otherwise it will use the hydrogenic GOS.
Attributes
----------
onset_energy : Parameter
The edge onset position
intensity : Parameter
The factor by which the cross section is multiplied, what in
favourable cases is proportional to the number of atoms of
the element. It is a component.Parameter instance.
It is fixed by default.
fine_structure_coeff : Parameter
The coefficients of the spline that fits the fine structure.
Fix this parameter to fix the fine structure. It is a
component.Parameter instance.
effective_angle : Parameter
The effective collection semi-angle. It is automatically
calculated by set_microscope_parameters. It is a
component.Parameter instance. It is fixed by default.
fine_structure_smoothing : float between 0 and 1
Controls the level of smoothing of the fine structure model.
Decreasing the value increases the level of smoothing.
fine_structure_active : bool
Activates/deactivates the fine structure feature.
"""
_fine_structure_smoothing = 0.3
def __init__(self, element_subshell, GOS=None):
# Declare the parameters
Component.__init__(self,
['intensity',
'fine_structure_coeff',
'effective_angle',
'onset_energy'])
if isinstance(element_subshell, dict):
self.element = element_subshell['element']
self.subshell = element_subshell['subshell']
else:
self.element, self.subshell = element_subshell.split('_')
self.name = "_".join([self.element, self.subshell])
self.energy_scale = None
self.effective_angle.free = False
self.fine_structure_active = False
self.fine_structure_width = 30.
self.fine_structure_coeff.ext_force_positive = False
self.GOS = None
# Set initial actions
if GOS is None:
try:
self.GOS = HartreeSlaterGOS(element_subshell)
GOS = 'Hartree-Slater'
except IOError:
GOS = 'hydrogenic'
_logger.info(
'Hartree-Slater GOS not available. '
'Using hydrogenic GOS')
if self.GOS is None:
if GOS == 'Hartree-Slater':
self.GOS = HartreeSlaterGOS(element_subshell)
elif GOS == 'hydrogenic':
self.GOS = HydrogenicGOS(element_subshell)
else:
raise ValueError(
'gos must be one of: None, \'hydrogenic\''
' or \'Hartree-Slater\'')
self.onset_energy.value = self.GOS.onset_energy
self.onset_energy.free = False
self._position = self.onset_energy
self.free_onset_energy = False
self.intensity.grad = self.grad_intensity
self.intensity.value = 1
self.intensity.bmin = 0.
self.intensity.bmax = None
self._whitelist['GOS'] = ('init', GOS)
if GOS == 'Hartree-Slater':
self._whitelist['element_subshell'] = (
'init',
self.GOS.as_dictionary(True))
elif GOS == 'hydrogenic':
self._whitelist['element_subshell'] = ('init', element_subshell)
self._whitelist['fine_structure_active'] = None
self._whitelist['fine_structure_width'] = None
self._whitelist['fine_structure_smoothing'] = None
self.effective_angle.events.value_changed.connect(
self._integrate_GOS, [])
self.onset_energy.events.value_changed.connect(self._integrate_GOS, [])
self.onset_energy.events.value_changed.connect(
self._calculate_knots, [])
# Automatically fix the fine structure when the fine structure is
# disable.
# In this way we avoid a common source of problems when fitting
# However the fine structure must be *manually* freed when we
# reactivate the fine structure.
def _get_fine_structure_active(self):
return self.__fine_structure_active
def _set_fine_structure_active(self, arg):
if arg is False:
self.fine_structure_coeff.free = False
self.__fine_structure_active = arg
# Force replot
self.intensity.value = self.intensity.value
fine_structure_active = property(_get_fine_structure_active,
_set_fine_structure_active)
def _get_fine_structure_width(self):
return self.__fine_structure_width
def _set_fine_structure_width(self, arg):
self.__fine_structure_width = arg
self._set_fine_structure_coeff()
fine_structure_width = property(_get_fine_structure_width,
_set_fine_structure_width)
# E0
def _get_E0(self):
return self.__E0
def _set_E0(self, arg):
self.__E0 = arg
self._calculate_effective_angle()
E0 = property(_get_E0, _set_E0)
# Collection semi-angle
def _get_collection_angle(self):
return self.__collection_angle
def _set_collection_angle(self, arg):
self.__collection_angle = arg
self._calculate_effective_angle()
collection_angle = property(_get_collection_angle,
_set_collection_angle)
# Convergence semi-angle
def _get_convergence_angle(self):
return self.__convergence_angle
def _set_convergence_angle(self, arg):
self.__convergence_angle = arg
self._calculate_effective_angle()
convergence_angle = property(_get_convergence_angle,
_set_convergence_angle)
def _calculate_effective_angle(self):
try:
self.effective_angle.value = effective_angle(
self.E0,
self.GOS.onset_energy,
self.convergence_angle,
self.collection_angle)
except:
# All the parameters may not be defined yet...
pass
@property
def fine_structure_smoothing(self):
"""Controls the level of the smoothing of the fine structure.
It must a real number between 0 and 1. The higher close to 0
the higher the smoothing.
"""
return self._fine_structure_smoothing
@fine_structure_smoothing.setter
def fine_structure_smoothing(self, value):
if 0 <= value <= 1:
self._fine_structure_smoothing = value
self._set_fine_structure_coeff()
else:
raise ValueError(
"The value must be a number between 0 and 1")
# It is needed because the property cannot be used to sort the edges
def _onset_energy(self):
return self.onset_energy.value
def _set_fine_structure_coeff(self):
if self.energy_scale is None:
return
self.fine_structure_coeff._number_of_elements = int(
round(self.fine_structure_smoothing *
self.fine_structure_width /
self.energy_scale)) + 4
self.fine_structure_coeff.bmin = None
self.fine_structure_coeff.bmax = None
self._calculate_knots()
if self.fine_structure_coeff.map is not None:
self.fine_structure_coeff._create_array()
def set_microscope_parameters(self, E0, alpha, beta, energy_scale):
"""
Parameters
----------
E0 : float
Electron beam energy in keV.
alpha: float
Convergence semi-angle in mrad.
beta: float
Collection semi-angle in mrad.
energy_scale : float
The energy step in eV.
"""
# Relativistic correction factors
old = self.effective_angle.value
with self.effective_angle.events.value_changed.suppress_callback(
self._integrate_GOS):
self.convergence_angle = alpha
self.collection_angle = beta
self.energy_scale = energy_scale
self.E0 = E0
if self.effective_angle.value != old:
self._integrate_GOS()
def _integrate_GOS(self):
# Integration over q using splines
angle = self.effective_angle.value * 1e-3 # in rad
self.tab_xsection = self.GOS.integrateq(
self.onset_energy.value, angle, self.E0)
# Calculate extrapolation powerlaw extrapolation parameters
E1 = self.GOS.energy_axis[-2] + self.GOS.energy_shift
E2 = self.GOS.energy_axis[-1] + self.GOS.energy_shift
y1 = self.GOS.qint[-2] # in m**2/bin */
y2 = self.GOS.qint[-1] # in m**2/bin */
self.r = math.log(y2 / y1) / math.log(E1 / E2)
self.A = y1 / E1 ** -self.r
def _calculate_knots(self):
start = self.onset_energy.value
stop = start + self.fine_structure_width
self.__knots = np.r_[
[start] * 4,
np.linspace(
start,
stop,
self.fine_structure_coeff._number_of_elements)[
2:-2],
[stop] * 4]
def function(self, E):
"""Returns the number of counts in barns
"""
shift = self.onset_energy.value - self.GOS.onset_energy
if shift != self.GOS.energy_shift:
# Because hspy Events are not executed in any given order,
# an external function could be in the same event execution list
# as _integrate_GOS and be executed first. That can potentially
# cause an error that enforcing _integrate_GOS here prevents. Note
# that this is suboptimal because _integrate_GOS is computed twice
# unnecessarily.
self._integrate_GOS()
Emax = self.GOS.energy_axis[-1] + self.GOS.energy_shift
cts = np.zeros((len(E)))
bsignal = (E >= self.onset_energy.value)
if self.fine_structure_active is True:
bfs = bsignal * (
E < (self.onset_energy.value + self.fine_structure_width))
cts[bfs] = splev(
E[bfs], (
self.__knots,
self.fine_structure_coeff.value + (0,) * 4,
3))
bsignal[bfs] = False
itab = bsignal * (E <= Emax)
cts[itab] = self.tab_xsection(E[itab])
bsignal[itab] = False
cts[bsignal] = self.A * E[bsignal] ** -self.r
return cts * self.intensity.value
def grad_intensity(self, E):
return self.function(E) / self.intensity.value
def fine_structure_coeff_to_txt(self, filename):
np.savetxt(filename + '.dat', self.fine_structure_coeff.value,
fmt="%12.6G")
def txt_to_fine_structure_coeff(self, filename):
fs = np.loadtxt(filename)
self._calculate_knots()
if len(fs) == len(self.__knots):
self.fine_structure_coeff.value = fs
else:
raise ValueError(
"The provided fine structure file "
"doesn't match the size of the current fine structure")
def get_fine_structure_as_signal1D(self):
"""Returns a spectrum containing the fine structure.
Notes
-----
The fine structure is corrected from multiple scattering if
the model was convolved with a low-loss spectrum
"""
from hyperspy._signals.eels import EELSSpectrum
channels = int(np.floor(
self.fine_structure_width / self.energy_scale))
data = np.zeros(self.fine_structure_coeff.map.shape +
(channels,))
s = EELSSpectrum(
data,
axes=self.intensity._axes_manager._get_axes_dicts())
s.get_dimensions_from_data()
s.axes_manager.signal_axes[0].offset = self.onset_energy.value
# Backup the axes_manager
original_axes_manager = self._axes_manager
self._axes_manager = s.axes_manager
for spectrum in s:
self.fetch_stored_values()
spectrum.data[:] = self.function(
s.axes_manager.signal_axes[0].axis)
# Restore the axes_manager and the values
self._axes_manager = original_axes_manager
self.fetch_stored_values()
s.metadata.General.title = self.name.replace(
'_', ' ') + ' fine structure'
return s