# Model fitting¶

HyperSpy can perform curve fitting of one-dimensional signals (spectra) and two-dimensional signals (images) in n-dimensional data sets. Models can be created as a linear combination of predefined components and multiple optimisation algorithms can be used to fit the model to experimental data. Bounds and weights are supported. The syntax for creating both kinds of model is essentially the same as in this documentation any method referred to in the :py:class`~.model.BaseModel` class is available for both kinds.

New in version 1.0: 2D models. Note that this first implementation lacks many of the features of 1D models e.g. plotting. Those will be added in future releases.

Models can be created and and fit to experimental data in both one and two
dimensions i.e. spectra and images respectively. Most of the syntax is
identical in either case. A one-dimensional model is created when a model
is created for a `Signal1D`

whereas a two-
dimensional model is created for a `_signals.signal2D.Signal2D`

.
At present plotting and gradient fitting methods tools for are not yet
provided for the `Model2D`

class.

New in version 0.7: Binned/unbinned signals

Before creating a model verify that the `Signal.binned`

metadata
attribute of the signal is set to the correct value because the resulting
model depends on this parameter. See Binned and unbinned signals for more details.

## Creating a model¶

A `Model1D`

can be created for data in the
`Signal1D`

class using the
`create_model()`

method:

```
>>> s = hs.signals.Signal1D('SomeDataHere') # or load the data from a file
>>> m = s.create_model() # Creates the 1D-Model and asign it to the variable m
```

Similarly A `Model2D`

can be created for data in the
`Signal2D`

class using the
`create_model()`

method:

```
>>> im = hs.signals.Signal2D('SomeDataHere') # Load the data from a file
>>> mod = im.create_model() # Create the 2D-Model and asign it to the variable mod
```

The syntax for creating both one-dimensional and two-dimensional models is thus identical for the user in practice. When a model is created you may be prompted to provide important information not already included in the datafile, e.g.if s is EELS data, you may be asked for the accelerating voltage, convergence and collection semi-angles etc.

## Adding components to the model¶

Changed in version 1.0: hyperspy.api.model.components renamed to hyperspy.api.model.components1D

New in version 1.0: hyperspy.api.model.components2D.

In HyperSpy a model consists of a linear combination of components
and various components are available in one (`components1d`

)and
two-dimensions (`components2d`

) to construct a
model.

The following components are currently available for one-dimensional models:

`EELSCLEdge`

`VolumePlasmonDrude`

`PowerLaw`

`Offset`

`Exponential`

`ScalableFixedPattern`

`Gaussian`

`GaussianHF`

`Lorentzian`

`Voigt`

`Polynomial`

`Logistic`

`Bleasdale`

`Erf`

`SEE`

`Arctan`

`HeavisideStep`

New in version 1.0: The following components are currently available for two-dimensional models:

However, this doesn’t mean that you have to limit yourself to this meagre list of functions. A new function can easily be written or a custom function may be specified as below.

### Specifying custom components¶

New in version 0.8.1: `Expression`

component

The easiest way to turn a mathematical expression into a component is using the
`Expression`

component. For example, the
following is all you need to create a`Gaussian` component with more sensible
parameters for spectroscopy than the one that ships with HyperSpy:

```
>>> g = hs.model.components1D.Expression(
... expression="height * exp(-(x - x0) ** 2 * 4 * log(2)/ fwhm ** 2)",
... name="Gaussian",
... position="x0",
... height=1,
... fwhm=1,
... centre=0,
... module="numpy")
```

`Expression`

uses Sympy internally to turn the string into
a funtion. By default it “translates” the expression using
numpy, but often it is possible to boost performance by using
numexpr instead.

`Expression`

is only useful for analytical
functions. If you know how to write the function with Python, turning it into
a component is very easy modifying the following template:

```
from hyperspy.component import Component
class My_Component(Component):
"""
"""
def __init__(self, parameter_1=1, parameter_2=2):
# Define the parameters
Component.__init__(self, ('parameter_1', 'parameter_2'))
# Optionally we can set the initial values
self.parameter_1.value = parameter_1
self.parameter_1.value = parameter_1
# The units (optional)
self.parameter_1.units = 'Tesla'
self.parameter_2.units = 'Kociak'
# Once defined we can give default values to the attribute is we want
# For example we fix the attribure_1 (optional)
self.parameter_1.attribute_1.free = False
# And we set the boundaries (optional)
self.parameter_1.bmin = 0.
self.parameter_1.bmax = None
# Optionally, to boost the optimization speed we can define also define
# the gradients of the function we the syntax:
# self.parameter.grad = function
self.parameter_1.grad = self.grad_parameter_1
self.parameter_2.grad = self.grad_parameter_2
# Define the function as a function of the already defined parameters, x
# being the independent variable value
def function(self, x):
p1 = self.parameter_1.value
p2 = self.parameter_2.value
return p1 + x * p2
# Optionally define the gradients of each parameter
def grad_parameter_1(self, x):
"""
Returns d(function)/d(parameter_1)
"""
return 0
def grad_parameter_2(self, x):
"""
Returns d(function)/d(parameter_2)
"""
return x
```

If you need help with the task please submit your question to the users mailing list.

Changed in version 0.8.1: printing current model components

To print the current components in a model use `components`

of the
variable. A table with component number, attribute name, component name and
component type will be printed:

```
>>> m
<Model, title: my signal title>
>>> m.components # an empty model
# | Attribute Name | Component Name | Component Type
---- | ------------------------- | ------------------------- | -------------------------
```

In fact, components may be created automatically in some cases. For example, if
the Signal1D is recognised as EELS data, a power-law background component will
automatically be placed in the model. To add a component first we have to create
an instance of the component. Once the instance has been created we can add the
component to the model using the `append()`

method, e.g. for a type of
data that can be modelled using gaussians we might proceed as follows:

```
>>> gaussian = hs.model.components1D.Gaussian() # Create a Gaussian function component
>>> m.append(gaussian) # Add it to the model
>>> m.components # Print the model components
# | Attribute Name | Component Name | Component Type
---- | ------------------------- | ------------------------- | -------------------------
0 | Gaussian | Gaussian | Gaussian
>>> gaussian2 = hs.components.Gaussian() # Create another gaussian components
>>> gaussian3 = hs.components.Gaussian() # Create a third gaussian components
```

We could use the append method two times to add the two gaussians, but when adding multiple components it is handier to use the extend method that enables adding a list of components at once.

```
>>> m.extend((gaussian2, gaussian3)) # note the double brackets!
>>> m.components
# | Attribute Name | Component Name | Component Type
---- | ------------------------- | ------------------------- | -------------------------
0 | Gaussian | Gaussian | Gaussian
1 | Gaussian_0 | Gaussian_0 | Gaussian
2 | Gaussian_1 | Gaussian_1 | Gaussian
```

We can customise the name of the components.

```
>>> gaussian.name = 'Carbon'
>>> gaussian2.name = 'Long Hydrogen name'
>>> gaussian3.name = 'Nitrogen'
>>> m.components
# | Attribute Name | Component Name | Component Type
---- | ------------------------- | ------------------------- | -------------------------
0 | Carbon | Carbon | Gaussian
1 | Long_Hydrogen_name | Long Hydrogen name | Gaussian
2 | Nitrogen | Nitrogen | Gaussian
```

Two components cannot have the same name.

```
>>> gaussian2.name = 'Carbon'
Traceback (most recent call last):
File "<ipython-input-5-2b5669fae54a>", line 1, in <module>
g2.name = "Carbon"
File "/home/fjd29/Python/hyperspy/hyperspy/component.py", line 466, in name
"the name " + str(value))
ValueError: Another component already has the name Carbon
```

It is possible to access the components in the model by their name or by the index in the model.

```
>>> m
# | Attribute Name | Component Name | Component Type
---- | ------------------------- | ------------------------- | -------------------------
0 | Carbon | Carbon | Gaussian
1 | Long_Hydrogen_name | Long Hydrogen name | Gaussian
2 | Nitrogen | Nitrogen | Gaussian
>>> m[0]
<Carbon (Gaussian component)>
>>> m["Long Hydrogen name"]
<Long Hydrogen name (Gaussian component)>
```

New in version 0.8.1: `components`

attribute

In addition, the components can be accessed in the
`components`

Model attribute. This is specially
useful when working in interactive data analysis with IPython because it
enables tab completion.

```
>>> m
# | Attribute Name | Component Name | Component Type
---- | ------------------------- | ------------------------- | -------------------------
0 | Carbon | Carbon | Gaussian
1 | Long_Hydrogen_name | Long Hydrogen name | Gaussian
2 | Nitrogen | Nitrogen | Gaussian
>>> m.components.Long_Hydrogen_name
<Long Hydrogen name (Gaussian component)>
```

It is possible to “switch off” a component by setting its
`active`

to False. When a components is
switched off, to all effects it is as if it was not part of the model. To
switch it on simply set the `active`

attribute
back to True.

New in version 0.7.1: `active_is_multidimensional`

In multidimensional signals it is possible to store the value of the
`active`

attribute at each navigation index.
To enable this feature for a given component set the
`active_is_multidimensional`

attribute to
True.

```
>>> s = hs.signals.Signal1D(np.arange(100).reshape(10,10))
>>> m = s.create_model()
>>> g1 = hs.model.components1D.Gaussian()
>>> g2 = hs.model.components1D.Gaussian()
>>> m.extend([g1,g2])
>>> g1.active_is_multidimensional = True
>>> g1._active_array
array([ True, True, True, True, True, True, True, True, True, True], dtype=bool)
>>> g2._active_array is None
True
>>> m.set_component_active_value(False)
>>> g1._active_array
array([False, False, False, False, False, False, False, False, False, False], dtype=bool)
>>> m.set_component_active_value(True, only_current=True)
>>> g1._active_array
array([ True, False, False, False, False, False, False, False, False, False], dtype=bool)
>>> g1.active_is_multidimensional = False
>>> g1._active_array is None
True
```

## Indexing model¶

New in version 1.0: model indexing

Often it is useful to consider only part of the model - for example at
a particular location (i.e. a slice in the navigation space) or energy range
(i.e. a slice in the signal space). This can be done using exactly the same
syntax that we use for signal indexing (Indexing).
`red_chisq`

and `dof`

are automatically
recomputed for the resulting slices.

```
>>> s = hs.signals.Signal1D(np.arange(100).reshape(10,10))
>>> m = s.create_model()
>>> m.append(hs.model.components1D.Gaussian())
>>> # select first three navigation pixels and last five signal channels
>>> m1 = m.inav[:3].isig[-5:]
>>> m1.signal1D
<Signal1D, title: , dimensions: (3|5)>
```

## Getting and setting parameter values and attributes¶

`print_current_values()`

prints the value of the
parameters of the components in the current coordinates.

`parameters`

contains a list of the parameters
of a component and `free_parameters`

lists only
the free parameters.

The value of a particular parameter can be accessed in the
`value`

.

If a model contains several components with the same parameters, it is possible
to change them all by using `set_parameters_value()`

.
Example:

```
>>> s = hs.signals.Signal1D(np.arange(100).reshape(10,10))
>>> m = s.create_model()
>>> g1 = hs.model.components1D.Gaussian()
>>> g2 = hs.model.components1D.Gaussian()
>>> m.extend([g1,g2])
>>> m.set_parameters_value('A', 20)
>>> g1.A.map['values']
array([ 20., 20., 20., 20., 20., 20., 20., 20., 20., 20.])
>>> g2.A.map['values']
array([ 20., 20., 20., 20., 20., 20., 20., 20., 20., 20.])
>>> m.set_parameters_value('A', 40, only_current=True)
>>> g1.A.map['values']
array([ 40., 20., 20., 20., 20., 20., 20., 20., 20., 20.])
>>> m.set_parameters_value('A',30, component_list=[g2])
>>> g2.A.map['values']
array([ 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.])
>>> g1.A.map['values']
array([ 40., 20., 20., 20., 20., 20., 20., 20., 20., 20.])
```

To set the the free state of a parameter change the
`free`

attribute. To change the free state of
all parameters in a component to True use
`set_parameters_free()`

, and
`set_parameters_not_free()`

for setting them to
False. Specific parameter-names can also be specified by using
parameter_name_list, shown in the example:

```
>>> g = hs.model.components1D.Gaussian()
>>> g.free_parameters
set([<Parameter A of Gaussian component>,
<Parameter sigma of Gaussian component>,
<Parameter centre of Gaussian component>])
>>> g.set_parameters_not_free()
set([])
>>> g.set_parameters_free(parameter_name_list=['A','centre'])
set([<Parameter A of Gaussian component>,
<Parameter centre of Gaussian component>])
```

Similar functions exist for `BaseModel`

:
`set_parameters_free()`

and
`set_parameters_not_free()`

. Which sets the
`free`

states for the parameters in components
in a model. Specific components and parameter-names can also be specified. For
example:

```
>>> g1 = hs.model.components1D.Gaussian()
>>> g2 = hs.model.components1D.Gaussian()
>>> m.extend([g1,g2])
>>> m.set_parameters_not_free()
>>> g1.free_parameters
set([])
>>> g2.free_parameters
set([])
>>> m.set_parameters_free(parameter_name_list=['A'])
>>> g1.free_parameters
set([<Parameter A of Gaussian component>])
>>> g2.free_parameters
set([<Parameter A of Gaussian component>])
>>> m.set_parameters_free([g1], parameter_name_list=['sigma'])
>>> g1.free_parameters
set([<Parameter A of Gaussian component>,
<Parameter sigma of Gaussian component>])
>>> g2.free_parameters
set([<Parameter A of Gaussian component>])
```

The value of a parameter can be coupled to the value of another by setting the
`twin`

attribute.

For example:

```
>>> gaussian.parameters # Print the parameters of the gaussian components
(A, sigma, centre)
>>> gaussian.centre.free = False # Fix the centre
>>> gaussian.free_parameters # Print the free parameters
set([A, sigma])
>>> m.print_current_values() # Print the current value of all the free parameters
Components Parameter Value
Normalized Gaussian
A 1.000000
sigma 1.000000
Normalized Gaussian
centre 0.000000
A 1.000000
sigma 1.000000
Normalized Gaussian
A 1.000000
sigma 1.000000
centre 0.000000
>>> gaussian2.A.twin = gaussian3.A # Couple the A parameter of gaussian2 to the A parameter of gaussian 3
>>> gaussian2.A.value = 10 # Set the gaussian2 centre value to 10
>>> m.print_current_values()
Components Parameter Value
Carbon
sigma 1.000000
A 1.000000
centre 0.000000
Hydrogen
sigma 1.000000
A 10.000000
centre 10.000000
Nitrogen
sigma 1.000000
A 10.000000
centre 0.000000
>>> gaussian3.A.value = 5 # Set the gaussian1 centre value to 5
>>> m.print_current_values()
Components Parameter Value
Carbon
sigma 1.000000
A 1.000000
centre 0.000000
Hydrogen
sigma 1.000000
A 5.000000
centre 10.000000
Nitrogen
sigma 1.000000
A 5.000000
centre 0.000000
```

By default the coupling function is the identity function. However it is
possible to set a different coupling function by setting the
`twin_function`

and
`twin_inverse_function`

attributes. For
example:

```
>>> gaussian2.A.twin_function = lambda x: x**2
>>> gaussian2.A.twin_inverse_function = lambda x: np.sqrt(np.abs(x))
>>> gaussian2.A.value = 4
>>> m.print_current_values()
Components Parameter Value
Carbon
sigma 1.000000
A 1.000000
centre 0.000000
Hydrogen
sigma 1.000000
A 4.000000
centre 10.000000
Nitrogen
sigma 1.000000
A 2.000000
centre 0.000000
```

```
>>> gaussian3.A.value = 4
>>> m.print_current_values()
Components Parameter Value
Carbon
sigma 1.000000
A 1.000000
centre 0.000000
Hydrogen
sigma 1.000000
A 16.000000
centre 10.000000
Nitrogen
sigma 1.000000
A 4.000000
centre 0.000000
```

## Fitting the model to the data¶

To fit the model to the data at the current coordinates (e.g. to fit one
spectrum at a particular point in a spectrum-image) use
`fit()`

.

The following table summarizes the features of the currently available optimizers. For more information on the local and global optimization algorithms, see the Scipy documentation.

New in version 1.1: Global optimizer Differential Evolution added.

Changed in version 1.1: leastsq supports bound constraints. fmin_XXX methods changed to the scipy.optimze.minimize() notation.

Optimizer | Bounds | Error estimation | Method | Type |
---|---|---|---|---|

“leastsq” | Yes | Yes | ‘ls’ | local |

“mpfit” | Yes | Yes | ‘ls’ | local |

“odr” | No | Yes | ‘ls’ | local |

“Nelder-Mead” | No | No | ‘ls’, ‘ml’ | local |

“Powell” | No | No | ‘ls’, ‘ml’ | local |

“CG” | No | No | ‘ls’, ‘ml’ | local |

“BFGS” | No | No | ‘ls’, ‘ml’ | local |

“Newton-CG” | No | No | ‘ls’, ‘ml’ | local |

“L-BFGS-B” | Yes | No | ‘ls’, ‘ml’ | local |

“TNC” | Yes | No | ‘ls’, ‘ml’ | local |

“Differential Evolution” | Yes | No | ‘ls’, ‘ml’ | global |

The following example shows how to perfom least squares with error estimation.

First we create data consisting of a line line `y = a*x + b`

with `a = 1`

and `b = 100`

and we add white noise to it:

```
>>> s = hs.signals.SpectrumSimulation(
... np.arange(100, 300))
>>> s.add_gaussian_noise(std=100)
```

To fit it we create a model consisting of a
`Polynomial`

component of order 1 and fit it
to the data.

```
>>> m = s.create_model()
>>> line = hs.model.components1D.Polynomial(order=1)
>>> m.append(line)
>>> m.fit()
```

On fitting completion, the optimized value of the parameters and their estimated standard deviation are stored in the following line attributes:

```
>>> line.coefficients.value
(0.99246156488437653, 103.67507406125888)
>>> line.coefficients.std
(0.11771053738516088, 13.541061301257537)
```

When the noise is heterocedastic, only if the
`metadata.Signal.Noise_properties.variance`

attribute of the
`Signal1D`

instance is defined can the errors be
estimated accurately. If the variance is not defined, the standard deviation of
the parameters are still computed and stored in the
`std`

attribute by setting variance equal 1.
However, the value won’t be correct unless an accurate value of the variance is
defined in `metadata.Signal.Noise_properties.variance`

. See
Setting the noise properties for more information.

In the following example, we add poissonian noise to the data instead of gaussian noise and proceed to fit as in the previous example.

```
>>> s = hs.signals.SpectrumSimulation(
... np.arange(300))
>>> s.add_poissonian_noise()
>>> m = s.create_model()
>>> line = hs.model.components1D.Polynomial(order=1)
>>> m.append(line)
>>> m.fit()
>>> line.coefficients.value
(1.0052331707848698, -1.0723588390873573)
>>> line.coefficients.std
(0.0081710549764721901, 1.4117294994070277)
```

Because the noise is heterocedastic, the least squares optimizer estimation is biased. A more accurate result can be obtained by using weighted least squares instead that, although still biased for poissonian noise, is a good approximation in most cases.

```
>>> s.estimate_poissonian_noise_variance(expected_value=hs.signals.Signal1D(np.arange(300)))
>>> m.fit()
>>> line.coefficients.value
(1.0004224896604759, -0.46982916592391377)
>>> line.coefficients.std
(0.0055752036447948173, 0.46950832982673557)
```

We can use Poisson maximum likelihood estimation instead, which is an unbiased estimator for poissonian noise. To do so, we use a general optimizer called “Nelder-Mead”.

```
>>> m.fit(fitter="Nelder-Mead", method="ml")
>>> line.coefficients.value
(1.0030718094185611, -0.63590210946134107)
```

Problems of ill-conditioning and divergence can be ameliorated by using bounded
optimization. Currently, only the “mpfit” optimizer supports bounds. In the
following example a gaussian histogram is fitted using a
`Gaussian`

component using mpfit and bounds on
the `centre`

parameter.

```
>>> s = hs.signals.BaseSignal(np.random.normal(loc=10, scale=0.01,
size=1e5)).get_histogram()
>>> s.metadata.Signal.binned = True
>>> m = s.create_model()
>>> g1 = hs.model.components1D.Gaussian()
>>> m.append(g1)
>>> g1.centre.value = 7
>>> g1.centre.bmin = 7
>>> g1.centre.bmax = 14
>>> g1.centre.bounded = True
>>> m.fit(fitter="mpfit", bounded=True)
>>> m.print_current_values()
Components Parameter Value
Gaussian
sigma 0.00996345
A 99918.7
centre 9.99976
```

New in version 0.7: chi-squared and reduced chi-squared

The chi-squared, reduced chi-squared and the degrees of freedom are
computed automatically when fitting. They are stored as signals, in the
`chisq`

, `red_chisq`

and
`dof`

attributes of the model respectively. Note that,
unless `metadata.Signal.Noise_properties.variance`

contains an accurate
estimation of the variance of the data, the chi-squared and reduced
chi-squared cannot be computed correctly. This is also true for
homocedastic noise.

### Visualizing the model¶

To visualise the result use the `plot()`

method:

```
>>> m.plot() # Visualise the results
```

New in version 0.7.

By default only the full model line is displayed in the plot. In addition, it
is possible to display the individual components by calling
`enable_plot_components()`

or directly using
`plot()`

:

```
>>> m.plot(plot_components=True) # Visualise the results
```

To disable this feature call `disable_plot_components()`

.

New in version 0.7.1: `suspend_update()`

and `resume_update()`

By default the model plot is automatically updated when any parameter value
changes. It is possible to suspend this feature with
`suspend_update()`

. To resume it use
`resume_update()`

.

### Setting the initial parameters¶

Non-linear regression often requires setting sensible starting parameters. This can be done by plotting the model and adjusting the parameters by hand.

New in version 0.7: In addition, it is possible to fit a given component independently using
the `fit_component()`

method.

New in version 0.8.5: `notebook_interaction()`

,

If running in a Jupyter Notebook, interactive widgets can be used to
conveniently adjust the parameter values by running
`notebook_interaction()`

for `Model`

,
`Component`

and
`Parameter`

.

Warning

`notebook_interaction()`

functions require
`ipywidgets`

, which is an optional dependency of HyperSpy.

New in version 0.6: `enable_adjust_position()`

and
`disable_adjust_position()`

Also, `enable_adjust_position()`

provides an interactive
way of setting the position of the components with a well define position.
`disable_adjust_position()`

disables the tool.

### Exclude data from the fitting process¶

The following `BaseModel`

methods can be used to exclude
undesired spectral channels from the fitting process:

`set_signal_range()`

`remove_signal_range()`

`reset_signal_range()`

### Fitting multidimensional datasets¶

To fit the model to all the elements of a multidimensional datataset use
`multifit()`

, e.g.:

```
>>> m.multifit() # warning: this can be a lengthy process on large datasets
```

`multifit()`

fits the model at the first position,
store the result of the fit internally and move to the next position until
reaching the end of the dataset.

Sometimes one may like to store and fetch the value of the parameters at a
given position manually. This is possible using
`store_current_values()`

and
`fetch_stored_values()`

.

## Storing models¶

New in version 1.0: `ModelManager`

Multiple models can be stored in the same signal. In particular, when
`store()`

is called, a full “frozen” copy of the model is stored
in `models`

. The stored models can be recreated at any time
by calling `restore()`

with the stored model name as an
argument. To remove a model from storage, simply call
`remove()`

The stored models can be either given a name, or assigned one automatically. The automatic naming follows alphabetical scheme, with the sequence being (a, b, ..., z, aa, ab, ..., az, ba, ...).

Note

If you want to slice a model, you have to perform the operation on the model itself, not its stored version

Warning

Modifying a signal in-place (e.g. `map()`

,
`crop()`

, `align1D()`

,
`align2D()`

and similar) will invalidate all stored models.
This is done intentionally.

Current stored models can be listed by calling `models`

:

```
>>> m = s.create_model()
>>> m.append(hs.model.components1D.Lorentzian())
>>> m.store('myname')
>>> s.models
└── myname
├── components
│ └── Lorentzian
├── date = 2015-09-07 12:01:50
└── dimensions = (|100)
>>> m.append(hs.model.components1D.Exponential())
>>> m.store() # assign model name automatically
>>> s.models
├── a
│ ├── components
│ │ ├── Exponential
│ │ └── Lorentzian
│ ├── date = 2015-09-07 12:01:57
│ └── dimensions = (|100)
└── myname
├── components
│ └── Lorentzian
├── date = 2015-09-07 12:01:50
└── dimensions = (|100)
>>> m1 = s.models.restore('myname')
>>> m1.components
# | Attribute Name | Component Name | Component Type
---- | ------------------------- | ------------------------- | -------------------------
0 | Lorentzian | Lorentzian | Lorentzian
```

### Saving and loading the result of the fit¶

New in version 1.0.

To save a model, a convenience function `save()`

is provided,
which stores the current model into its signal and saves the signal. As
described in storing_models, more than just one model can be saved with
one signal.

```
>>> m = s.create_model()
>>> # analysis and fitting goes here
>>> m.save('my_filename', 'model_name')
>>> l = hs.load('my_filename.hdf5')
>>> m = l.models.restore('model_name') # or l.models.model_name.restore()
```

For older versions of HyperSpy (before 0.9), the instructions were as follows:

Note that this method is known to be brittle i.e. there is no guarantee that a version of HyperSpy different from the one used to save the model will be able to load it successfully. Also, it is advisable not to use this method in combination with functions that alter the value of the parameters interactively (e.g. enable_adjust_position) as the modifications made by this functions are normally not stored in the IPython notebook or Python script.

To save a model:

- Save the parameter arrays to a file using
`save_parameters2file()`

.- Save all the commands that used to create the model to a file. This can be done in the form of an IPython notebook or a Python script.
- (Optional) Comment out or delete the fitting commangs (e.g. multifit).
To recreate the model:

- Execute the IPython notebook or Python script.
- Use
`load_parameters_from_file()`

to load back the parameter values and arrays.

## Batch setting of parameter attributes¶

New in version 0.6.

The following methods can be used to ease the task of setting some important parameter attributes:

## Smart Adaptive Multi-dimensional Fitting (SAMFire)¶

New in version 1.0: SAMFire

SAMFire (Smart Adaptive Multi-dimensional Fitting) is an algorithm created to reduce the starting value (or local / false minima) problem, which often arises when fitting multi-dimensional datasets.

The algorithm will be described in full when accompanying paper is published, but we are making the implementation available now.

### The idea¶

The main idea of SAMFire is to change two things compared to the traditional way of fitting datasets with many dimensions in the navigation space:

- Pick a more sensible pixel fitting order.
- Calculate the pixel starting parameters from already fitted parts of the dataset.

Both of these aspects are linked one to another and are represented by two different strategy families that SAMFfire uses while operating.

### Strategies¶

During operation SAMFire uses a list of strategies to determine how to select the next pixel and estimate its starting parameters. Only one strategy is used at a time. Next strategy is chosen when no new pixels are can be fitted with the current strategy. Once either the strategy list is exhausted or the full dataset fitted, the algorithm terminates.

There are two families of strategies. In each family there may be many strategies, using different statistical or significance measures.

As a rule of thumb, the first strategy in the list should always be from the local family, followed by a strategy from the global family.

### Local strategy family¶

These strategies assume that locally neighbouring pixels are similar. As a result, the pixel fitting order seems to follow data-suggested order, and the starting values are computed from the surrounding already fitted pixels.

More information about the exact procedure will be available once the accompanying paper is published.

### Global strategy family¶

Global strategies assume that the navigation coordinates of each pixel bear no relation to it’s signal (i.e. the location of pixels is meaningless). As a result, the pixels are selected at random to ensure uniform sampling of the navigation space.

A number of candidate starting values are computed form global statistical measures. These values are all attempted in order until a satisfactory result is found (not necessarily testing all available starting guesses). As a result, on average each pixel requires significantly more computations when compared to a local strategy.

More information about the exact procedure will be available once the accompanying paper is published.

### Seed points¶

Due to the strategies using already fitted pixels to estimate the starting values, at least one pixel has to be fitted beforehand by the user.

The seed pixel(s) should be selected to require the most complex model present in the dataset, however in-built goodness of fit checks ensure that only sufficiently well fitted values are allowed to propagate.

If the dataset consists of regions (in the navigation space) of highly dissimilar pixels, often called “domain structures”, at least one seed pixel should be given for each unique region.

If the starting pixels were not optimal, only part of the dataset will be fitted. In such cases it is best to allow the algorithm terminate, then provide new (better) seed pixels by hand, and restart SAMFire. It will use the new seed together with the already computed parts of the data.

### Usage¶

After creating a model and fitting suitable seed pixels, to fit the rest of the multi-dimensional dataset using SAMFire we must craete a SAMFire instance as follows:

```
>>> samf = m.create_samfire(workers=None, ipyparallel=False)
```

By default SAMFire will look for an ipyparallel cluster for the
workers for around 30 seconds. If none is available, it will use
multiprocessing instead. However, if you are not planning to use ipyparallel,
it’s recommended specify it explicitly via the `ipyparallel=False`

argument,
to use the fall-back option of multiprocessing.

By default a new SAMFire object already has two (and currently only) strategies added to its strategist list:

```
>>> samf.strategies
A | # | Strategy
-- | ---- | -------------------------
x | 0 | Reduced chi squared strategy
| 1 | Histogram global strategy
```

The currently active strategy is marked by an ‘x’ in the first column.

If a new datapoint (i.e. pixel) is added manually, the “database” of the
currently active strategy has to be refreshed using the
`refresh_database()`

call.

The current strategy “database” can be plotted using the
`plot()`

method.

Whilst SAMFire is running, each pixel is checked by a `goodness_test`

,
which is by default `red_chisq_test`

, checking the
reduced chi-squared to be in the bounds of [0, 2].

This tolerance can (and most likely should!) be changed appropriately for the data as follows:

```
>>> samf.metadata.goodness_test.tolerance = 0.3 # use a sensible value
```

The SAMFire managed multi-dimensional fit can be started using the
`start()`

method. All keyword arguments are passed to
the underlying (i.e. usual) `fit()`

call:

```
>>> samf.start(fitter='mpfit', bounded=True)
```