.. fitting_help.rst

.. This is a port of the original SasView html help file to ReSTructured text
.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.

Fitting
=======

.. note:: If some code blocks are not readable, expand the documentation window

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Preparing to fit data
---------------------

To fit some data you must first load some data, activate one or more data sets,
send those data sets to fitting, and select a model to fit to each data set.

Instructions on how to load and activate data are in the section :ref:`Loading_data`.

SasView can fit data in one of three ways:

*  in *Single* fit mode - individual data sets are fitted independently one-by-one

*  in *Simultaneous* fit mode - multiple data sets are fitted simultaneously to
   the *same* model with/without constrained parameters (this might be useful,
   for example, if you have measured the same sample at different contrasts)

*  in *Batch* fit mode - multiple data sets are fitted sequentially to the
   *same* model (this might be useful, for example, if you have performed
   a kinetic or time-resolved experiment and have *lots* of data sets!)

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Selecting a model
-----------------

The models in SasView are grouped into categories. By default these consist of:

*  *Cylinder* - cylindrical shapes (disc, right cylinder, cylinder with end-caps
   etc)
*  *Ellipsoid* - ellipsoidal shapes (oblate, prolate, core shell, etc)
*  *Parallelepiped* - as the name implies
*  *Sphere* - spheroidal shapes (sphere, core multishell, vesicle, etc)
*  *Lamellae* - lamellar shapes (lamellar, core shell lamellar, stacked
   lamellar, etc)
*  *Shape-Independent* - models describing structure in terms of density
   correlation functions, fractals, peaks, power laws, etc
*  *Paracrystal* - semi ordered structures (bcc, fcc, etc)
*  *Structure Factor* - S(Q) models
*  *Plugin Models* - User-created (custom/non-library) Python models

Use the *Category* drop-down menu to chose a category of model, then select
a model from the drop-down menu to the right. The "Show Plot" button on the
bottom of the dialog will become active. If you click on it, 
a graph of the chosen model, calculated using default parameter values, will appear.
The graph will update dynamically as the parameter values are changed.

You can decide your own model categorizations using the :ref:`Category_Manager`.

Once you have selected a model you can read its help documentation by clicking
on the *Help* button. Additionally, right clicking on the empty space in the
parameter table will display a short description of the model.

.. image:: descr_fig.png


.. _Interaction_and_Mixture_Models:

Interaction Models
^^^^^^^^^^^^^^^^^^

Structure factor S(Q) models can be combined with many form factor P(Q) models
in the other categories to generate what SasView calls "interaction models"
(previously "product models"). The combination can be done by one of two
methods, but how they behave is slightly different.

The first, most straightforward, method is simply to use the S(Q) drop-down in
the FitPage:

.. figure:: p_and_s_buttons.png

This example would then generate an interaction model with the following
parameters:

.. figure:: p_and_s_buttons_parameters.png

The other method is to use the :ref:`Add/Multiply_Models` tool under Fitting menu:

.. figure:: p_and_s_sum_model.png

This creates an interaction model with the following parameters:

.. figure:: p_and_s_sum_model_parameters.png

As can be seen, the second method has produced an interaction model with an
extra parameter: *radius_effective*. This is the radial distance determining the
range of the $S(Q)$ interaction and may, or may not, be the same as the
*radius*, in this example, depending on the concentration of the system. In
other systems, *radius_effective* may depend on the particle form (shape).
SasView offers the flexibility to automatically constrain (tie) some of these
parameters together so that, for example, *radius_effective* = *radius*. See
:ref:`Add/Multiply_Models`.

Also see :ref:`Interaction_and_Mixture_Models` for further information.

Mixture Models
^^^^^^^^^^^^^^

SasView "mixture models" (previously called "sum models") are summations of
form factor models, or even of form factor models and an "interaction model"
(see above), and are used to describe mixed-phase systems where the scattering
is proportional to the volume fraction of each contributing phase.

Show 1D/2D
^^^^^^^^^^

Models are normally fitted to 1D (ie, I(Q) vs Q) data sets, but some models in
SasView can also be fitted to 2D (ie, I(Qx,Qy) vs Qx vs Qy) data sets.

*NB: Magnetic scattering can only be fitted in SasView in 2D.*

To activate 2D fitting mode, select the *2D view* checkbox on the *Fit Page*. To
return to 1D fitting model, de-select the same checkbox.

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.. _Category_Manager:

Category Manager
----------------

To change the model categorizations, either choose *Category Manager* from the
*View* option on the menu bar, or click on the *Modify* button on the *Fit Page*.

.. image:: cat_fig0.png

The categorization of all models except the user supplied Plugin Models can be
reassigned, added to, and removed using *Category Manager*. Models can also be
hidden from view in the drop-down menus.

.. image:: cat_fig1.png

Changing category
^^^^^^^^^^^^^^^^^

To change category, highlight a model in the list by left-clicking on its entry
and then click the *Modify* button. Use the *Change Category* panel that appears
to make the required changes.

.. image:: cat_fig2.png

To create a category for the selected model, click the *Add* button. In order
to delete a category, select the category name and click the *Remove*
button. Then click *OK*.

Showing/hiding models
^^^^^^^^^^^^^^^^^^^^^

Use the *Enable / Disable All* buttons and the check boxes beside each model
to select the models to show/hide. To apply the selection, click *OK*.

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Model Functions
---------------

For a complete list of all the library models available in SasView, see
the `Model Documentation <models/index.html>`_ .

It is also possible to add your own models.

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.. _Adding_your_own_models:

Adding your own Models
----------------------

There are essentially four ways to generate new fitting models for SasView:

*  Using the SasView :ref:`Add/Multiply_Models` dialog to sum/multiply
   together *two existing models* in the model library (best for
   beginners - provided the required models are in the model library!)
*  Using the SasView :ref:`New_Plugin_Model` helper dialog (aimed at those with
   little programming experience but works best for relatively simple models)
*  By copying/editing an existing model (this can include models generated by
   the *New Plugin Model* dialog) in the :ref:`Python_shell` or
   :ref:`Model_Editor` (suitable for all use cases)
*  By writing a model from scratch outside of SasView (only recommended for 
   experienced Python users)

In the last two cases, please read the guidance on :ref:`Writing_a_Plugin`
before proceeding.

**For your model to be found by SasView it must reside in the *~\\.sasview\\plugin_models* folder.**

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.. _Plugin_Model_Operations:

Plugin Model Operations
-----------------------

From the *Fitting* option in the menu bar, select one of the options:

.. image:: edit_model_menu.png

*  *Add Custom Model* - to create a plugin model template with a helper dialog
*  *Edit Custom Model* - to edit a plugin model in an editor window
*  *Manage Custom Models* - to list available plugin models, add one you have
   written, duplicate a model, edit a model, or delete a model
*  *Add/Multiply Models* - to create a plugin model by summing/multiplying *two
   existing models* in the model library

.. _New_Plugin_Model:

Add Custom Model
^^^^^^^^^^^^^^^^

Relatively straightforward models can be programmed directly from the SasView
GUI using the *Plugin Definition* Function.

.. image:: new_model.png

When using this feature, be aware that even if your code has errors, including
syntax errors, a model file is still generated. When you then correct the errors
and click 'Apply' again to re-compile you will get an error informing you that
the model already exists if the 'Overwrite' box is not checked. In this case you
will need to supply a new model function name. By default the 'Overwrite' box is
*checked*\ .

Also note that the 'Fit Parameters' have been split into two sections: those
which can be polydisperse (shape and orientation parameters) and those which are
not (eg, scattering length densities).

A model file generated by this option can be viewed and further modified using
the :ref:`Model_Editor`.

It possible to specify whether a plugin created with the *New Plugin Model*
dialog is actually a form factor P(Q) or a structure factor S(Q). To do this,
simply add one or other of the following lines under the *import* statements.

For a form factor::

     form_factor = True

or for a structure factor::

     structure_factor = True

If the plugin is a structure factor it is *also* necessary to add two variables
to the parameter list::

     parameters = [
                     ['radius_effective', '', 1, [0.0, numpy.inf], 'volume', ''],
                     ['volfraction', '', 1, [0.0, 1.0], '', ''],
                     [...],

and to the declarations of the functions Iq and Iqxy:::

     def Iq(x , radius_effective, volfraction, ...):

     def Iqxy(x, y, radius_effective, volfraction, ...):

Such a plugin should then be available in the S(Q) drop-down box on a FitPage
(once a P(Q) model has been selected).


.. _Add/Multiply_Models:

Add / Multiply Models
^^^^^^^^^^^^^^^^^^^^^

Choosing the *Add/Multiply models* item from the *Fitting* menu

.. image:: sum_multi_menu.png

displays the *Easy Add/Multiply Editor* dialog.

.. image:: sum_model.png

This option creates a custom Plugin Model of the form::

     Plugin Model = scale_factor * {(scale_1 * model_1) +/- (scale_2 * model_2)} + background

or::

     Plugin Model = scale_factor * (model1 * model2) + background

In the *Easy Add/Multiply Editor* give the new model a name (which will appear
in the list of plugin models on the *FitPage*) and brief description (to appear
under the *Details* button on the *FitPage*). The model name must not contain
spaces (use underscores to separate words if necessary) and if it is longer
than ~25 characters the name will not display in full in the list of models.
Now select two built-in models, as model_1 (or p1) and model_2 (or p2), and the
required operator, '+' or '*' between them. Finally, click the *Apply* button
to generate and test the model, and then click *Close*.

Any changes to a plugin model generated in this way only become effective
*after* it is re-selected from the plugin models drop-down menu on the FitPage.

**In SasView 4.x**, if the model is not listed you can try and force a
recompilation of the plugins by selecting *Fitting* > *Plugin Model Operations*
> *Load Plugin Models*. **In SasView 5.x**, you may need to restart the
program.

.. warning::

   **SasView versions 4.2.x, 5.0.0 and 5.0.1**
   The *Easy Add/Multiply Editor* dialog should *not* be used to combine a
   plugin model with a built-in model, or to combine two plugin models. The
   operation will appear to work in 4.2.x but may generate a faulty plugin
   model. In 5.0.0 the operation will fail (generating an error message in the
   Log Explorer). Whilst in 5.0.1 the operation has been blocked.
   
   If you need to generate a plugin model from more than two built-in models,
   please read the sub-sections :ref:`Model_Structure` and :ref:`Combining_multiple_models`
   below.

.. _Model_Structure:

Model Structure
^^^^^^^^^^^^^^^

**SasView version 4.2** introduced a much simplified and more extensible
structure for plugin models generated through the Easy Sum/Multi Editor. For
example, the code for a combination of a sphere model with a power law model
now looks like this::

     from sasmodels.core import load_model_info
     from sasmodels.sasview_model import make_model_from_info

     model_info = load_model_info('sphere+power_law')
     model_info.name = 'MyPluginModel'
     model_info.description = 'sphere + power_law'
     Model = make_model_from_info(model_info)

To change the models or operators contributing to this plugin it is only
necessary to edit the string in the brackets after *load_model_info*, though it
would also be a good idea to update the model name and description too!!!

The model specification string can handle multiple models and combinations of
operators ('+' or '*') which are processed according to normal conventions. Thus
'model1+model2*\model3' would be valid and would multiply model2 by model3
before adding model1. In this example, parameters in the *FitPage* would be
prefixed A (for model2), B (for model3) and C (for model1). Whilst this might
appear a little confusing, unless you were creating a plugin model from
multiple instances of the same model the parameter assignments ought to be
obvious when you load the plugin.

.. SMK 05/02/2020
.. I've commented out the lines below for now because it is not clear from
.. using SasView that it is still (ever was!) a requirement for including
.. plugin models in the new model structure.

.. If you need to include another plugin model in the model specification string,
.. just prefix the name of that model with *custom*. For instance::

..     sphere+custom.MyPluginModel

This streamlined approach to building complex plugin models from existing 
library models, or models available on the *Model Marketplace*, also permits
the creation of P(Q)*\S(Q) plugin models, something that was not possible in
earlier versions of SasView. Also see :ref:`Interaction_and_Mixture_Models`
above.

.. note::

   **Interaction Models**
   
   When the *Easy Sum/Multi Editor* creates a P(Q)*\S(Q) model it will use
   the * symbol like this::

     sphere*hardsphere

   However, it is probably advisable to edit the model file and use the @
   symbol instead, for example::

     sphere@hardsphere

   This is because * and @ confer different behavior on the model

   *  *with @* - the radius and volume fraction in the S(Q) model are
      constrained to have the *same* values as the radius and volume fraction
      in the P(Q) model.
   *  *with ** - the radii and volume fractions in the P(Q) and S(Q) models are
      unconstrained. 

.. warning::

   If combining P(Q) models with S(Q) models, *particularly if combining
   multiple instances of such models* (eg, $(P(Q)_1$ * $S(Q)_1$) + $(P(Q)_2$ * $S(Q)_2)$
   or similar), pay careful attention to the behaviour of the scale and volume
   fraction parameters and test your model thoroughly, preferably on
   well-characterised data.

.. _Combining_multiple_models:

Combining more than two models
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

If you need generate a plugin model from more than two other models, it is
tempting to think that the way to do so is simply to use the
*Easy Add/Multiply Editor* dialog to combine the first two models into a
plugin, then generate a new plugin using that first plugin as one of the
selected models, combine it with the third model, and repeat as required.

This does not currently work properly (although it *may appear to* in SasView
4.2.x).

Instead, use the *Easy Add/Multiply Editor* dialog to combine the first two
models, then navigate to the plugin folder (~\\.sasview\\plugin_models on 
Windows) and open the plugin Python file (eg, MyPluginModel.py) in a text
editor.

Now edit the Python to specify all the models to contribute to the expanded
plugin (the text string in the brackets after *load_model_info*). Make sure you
specify the model names correctly, including any capitalisation (if in doubt
use the model name dropdown on a *FitPage*)! Finally, update the model name and
description, and save the file.

So, as an example, one could take the MyPluginModel example in the preceding
section, change it to::

     from sasmodels.core import load_model_info
     from sasmodels.sasview_model import make_model_from_info

     model_info = load_model_info('power_law + fractal + gaussian_peak + gaussian_peak')
     model_info.name = 'MyBigPluginModel'
     model_info.description = 'For fitting pores in crystalline framework'
     Model = make_model_from_info(model_info)

and re-save it as MyBigPluginModel.py. When loaded into a *FitPage*, the 
parameters for the four models in the *load_model_info* string are then all
present and prefixed by A\_, B\_, C\_, and D\_, respectively.

.. _Model_Editor:

Model Editor
^^^^^^^^^^^^

Selecting "Edit Custom Model" option opens the editor window.

.. image :: model_editor_empty.png

Initially, the editor is empty. A custom model can be loaded by clicking on the *Load plugin...* button and choosing one of the existing custom plugins.

Once the model is loaded, it can be edited and saved with *Save* button.
Saving the model will perform the validation and only when the model is correct it will be saved to a file.
Successful model check is indicated by a SasView status bar message.

When *Cancel* is clicked, any changes to the model are discarded and the window is closed.


For details of the SasView plugin model format see :ref:`Writing_a_Plugin` .

To use the model, go to the relevant *Fit Page*, select the *Plugin Models*
category and then select the model from the drop-down menu.


.. Plugin_Manager:

Plugin Manager
^^^^^^^^^^^^^^

Selecting the *Manage Custom Models* option shows a list of all the plugin models in the plugin model folder, on Windows this is

  *C:\\Users\\{username}\\.sasview\\plugin_models*

You can add, edit, duplicate and delete these models using buttons on the right side of the list.

.. image:: plugin_manager.png


Add a model
^^^^^^^^^^^

Clicking the "Add" button opens the Model Editor window, allowing you to create a new plugin as described above.

Duplicate a model
^^^^^^^^^^^^^^^^^

Clicking the "Duplicate" button will create a copy of the selected model(s). Naming of the duplicate follows the standard, with added * (n)* to the plugin model name, with *n* being the first unused yet integer.

Edit a model
^^^^^^^^^^^^

When a single model is selected, clicking this button will open the Advanced *Model Editor* allowing you to edit the
Python code of the model.
If no models or multiple models are selected, the *Edit* button is disabled.

Delete Plugin Models
^^^^^^^^^^^^^^^^^^^^

Simply highlight the plugin model(s) to be removed and click on the "Delete" button. The operation is final.

*NB: Models shipped with SasView cannot be removed in this way.*

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.. _Fitting_Options:

Fit Algorithms
---------------

It is possible to specify which optimiser SasView should use to fit the data, and
to modify some of the configurational parameters for each optimiser.

From *Fitting* in the menu bar select *Fit Algorithms*, then select one of the following
optimisers:

*  DREAM
*  Levenberg-Marquardt
*  Quasi-Newton BFGS
*  Differential Evolution
*  Nelder-Mead Simplex

.. image:: fit_algorithms.png

The DREAM optimiser is the most sophisticated, but may not necessarily be the best
option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser
initially.

These optimisers form the *Bumps* package written by P Kienzle. For more information
on each optimiser, see the :ref:`Fitting_Documentation`.

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Fitting Limits
--------------

By default, *SasView* will attempt to model fit the full range of the data; ie,
across all *Q* values. If necessary, however, it is possible to specify only a
sub-region of the data for fitting.

In a *FitPage* or *BatchPage* change the tab to *Fit Options* and then change 
the *Q* values in the *Min* and/or *Max*
text boxes. 

..
  Vertical coloured bars will appear on the graph with the data and
  'theory' indicating the current *Q* limits (red = *Qmin*, purple = *Qmax*).

To return to including all data in the fit, click the *Reset* button.

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Shortcuts
---------

Copy/Paste Parameters
^^^^^^^^^^^^^^^^^^^^^

It is possible to copy the parameters from one *Fit Page* and to paste them into
another *Fit Page* using the same model.

To *copy* parameters, either:

*  Select *Edit -> Copy Params* from the menu bar, or
*  Use Ctrl(Cmd on Mac) + Left Mouse Click on the *Fit Page*.

To *paste* parameters, either:

*  Select *Edit -> Paste Params* from the menu bar, or
*  Use Ctrl(Cmd on Mac) + Shift + Left-click on the *Fit Page*.

If either operation is successful a message will appear in the info line at the
bottom of the SasView window.

Bookmark
^^^^^^^^

To *Bookmark* a *Fit Page* either:

*  Select a *Fit Page* and then click on *Bookmark* in the tool bar, or
*  Right-click and select the *Bookmark* in the popup menu.

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.. _Status_bar:

Status Bar & Log Explorer
-------------------------

The status bar is located at the bottom of the SasView window and displays
messages, warnings and errors.

.. image:: log_explorer.png

The bottom part of the SasView application window contains the *Log Explorer*.
The *Log Explorer* displays available message history and run-time traceback information.

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.. _Single_Fit_Mode:

Single Fit Mode
---------------

*NB: Before proceeding, ensure that the Batch mode checkbox at the bottom of*
*the Data Explorer is unchecked (see the section* :ref:`Loading_data` *).*

This mode fits one data set.

.. When data is sent to the fitting it is plotted in a graph window as markers.

When data is sent to the fitting, the Fit Page will show the dataset name.

.. image:: dataset_name.png

Clicking on the *Show Plot* will cause the data can be plotted in a graph window as markers.

If a graph does not appear, or a graph window appears but is empty, then the data
has not loaded correctly. Check to see if there is a message in the :ref:`Status_Bar`
or in the *Console* window.

Assuming the data has loaded correctly, when a model is selected a blue model
calculation (or what SasView calls a 'Theory') line will appear in the earlier graph
window, and a second graph window will appear displaying the residuals (the
difference between the experimental data and the theory) at the same X-data values.
See :ref:`Assessing_Fit_Quality`.

The objective of model-fitting is to find a *physically-plausible* model, and set
of model parameters, that generate a theory that reproduces the experimental data
and gives residual values as close to zero as possible.

Change the default values of the model parameters by hand until the theory line
starts to represent the experimental data. Then uncheck the tick boxes alongside
all parameters *except* the 'background' and the 'scale'. Click the *Fit* button.
SasView will optimise the values of the 'background' and 'scale' and also display
the corresponding uncertainties on the optimised values.

*NB: If no uncertainty is shown it generally means that the model is not very*
*dependent on the corresponding parameter (or that one or more parameters are*
*'correlated').*

In the bottom right corner of the *Fit Page* is a box displaying the normalised value
of the statistical $\chi^2$ parameter returned by the optimiser.

Now check the box for another model parameter and click *Fit* again. Repeat this
process until most or all parameters are checked and have been optimised. As the
fit of the theory to the experimental data improves the value of 'chi2/Npts' will
decrease. A good model fit should easily produce values of 'chi2/Npts' that are
close to one, and certainly <100. See :ref:`Assessing_Fit_Quality`.

SasView has a number of different optimisers (see the section :ref:`Fitting_Options`).
The DREAM optimiser is the most sophisticated, but may not necessarily be the best
option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser
initially.

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Simultaneous Fit Mode
---------------------

*NB: Before proceeding, ensure that the Batch Mode check button at the bottom of*
*the Data Explorer is unchecked (see the section* :ref:`Loading_data` *).*

This mode is an extension of the :ref:`Single_Fit_Mode` that fits two or more data
sets *to the same model* simultaneously. If necessary it is possible to constrain
fit parameters between data sets (eg, to fix a background level, or radius, etc).

If the data to be fit are in multiple files, load each file, then select each file
in the *Data Explorer*, and *Send To Fitting*. If multiple data sets are in one file,
load that file, *Unselect All Data*, select just those data sets to be fitted, and
*Send To Fitting*. Either way, the result should be that for *n* data sets you have
2\ *n* graphs (*n* of the data and model fit, and *n* of the resulting residuals). But
it may be helpful to minimise the residuals plots for clarity. Also see
:ref:`Assessing_Fit_Quality`.

*NB: If you need to use a custom Plugin Model, you must ensure that model is
available first (see* :ref:`Adding_your_own_models` *).*

Method
^^^^^^

Now go to each *FitPage* in turn and:

*  Select the required category and model;
*  Unselect all the model parameters;
*  Enter some starting guesses for the parameters;
*  Enter any parameter limits (recommended);
*  Select which parameters will refine (selecting all is generally a bad idea...);

When done, select *Constrained or Simultaneous Fit* under *Fitting* in the menu bar.

In the *Const & Simul Fit* page that appears, select which data sets are to be
simultaneously fitted (this will probably be all of them or you would not have loaded
them in the first place!).

.. image:: constraint_1.png

To tie parameters between the data sets with constraints, select the data sets and right click.
From the menu choose *Mutual constraint of parameters in selected models*

.. image:: constraint_menu.png

When ready, click the *Fit* button on the *Const & Simul Fit* page, NOT the *Fit*
button on the individual *FitPage*'s.

Simultaneous Fits without Constraints
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The results of the model-fitting will be returned to each of the individual
*FitPage*'s. Also see :ref:`Assessing_Fit_Quality`.

Simultaneous Fits with Constraints
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

In the *Const. & Simul. Fit* page make sure that at least two fitpages are present.
Then, click the *Add constraints* button

.. image:: add_constraint.png

Alternatively, right clicking on two selected fitpages in the
*Source choice for simultaneous fitting* area will bring up the context menu:

.. image:: constraint_menu.png

Here you can choose datasets for fitting and define constraints between parameters in
both datasets.

Clicking the *Add constraints* button or choosing the *Mutual constraint of parameters
in selected models...* option will bring up the *Complex Constraint* dialog.

.. image:: complex_constraint.png

Constraints will generally be of the form

  Mi:Parameter1 = Mj.Parameter1

however the text box after the '=' sign can be used to adjust this
relationship; for example

  Mi:Parameter1 = scalar \* Mj.Parameter1

A 'free-form' constraint box is also provided.

Many constraints can be entered for a single fit.

The results of the model-fitting will be returned to each of the individual
*FitPage*'s. Also see :ref:`Assessing_Fit_Quality`.

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.. _Batch_Fit_Mode:

Batch Fit Mode
--------------

*NB: Before proceeding, ensure that the Batch Mode check button at the bottom of*
*the Data Explorer is unchecked (see the section* :ref:`Loading_data` *). The Batch*
*Mode button will be used later on!*

This mode *sequentially* fits two or more data sets *to the same model*. Unlike in
simultaneous fitting, in batch fitting it is not possible to constrain fit parameters
between data sets.

If the data to be fit are in multiple files, load each file in the *Data Explorer*.
If multiple data sets are in one file, load just that file. *Unselect All Data*, then
select a single initial data set to be fitted. Fit that selected data set as described
above under :ref:`Single_Fit_Mode`.

*NB: If you need to use a custom Plugin Model, you must ensure that model is
available first (see* :ref:`Adding_your_own_models` *).*

Method
^^^^^^

Now *Select All Data* in the *Data Explorer*, check the *Batch Mode* check button
at the bottom of that panel and *Send To Fitting*. A *BatchPage* will be created.

.. image:: batch_button_area.png

*NB: The Batch Page can also be created by checking the Batch Mode check button*
*and selecting New Fit Page under Fitting in the menu bar.*

Using the drop-down menus in the *BatchPage*, now set up the *same* data set
with the *same* model that you just fitted in single fit mode. A quick way to
set the model parameter values is to just copy them from the earlier Single
Fit. To do this, go back to the Single Fit *FitPage*, select *Copy Params*
under *Edit* in the menu bar, then go back to the *BatchPage* and *Paste Params*.

When ready, use the *Fit* button on the *BatchPage* to perform the fitting, NOT
the *Fit* button on the individual *FitPage*'s.

Unlike in single fit mode, the results of batch fits are not returned to
the *BatchPage*. Instead, a spreadsheet-like :ref:`Grid_Window` will appear.

If you want to visually check a graph of a particular fit, click on the name of
a *Data set* in the *Grid Window* and then click the *Plot* button. The
data and the model fit will be displayed.

.. image:: view_button.png

*NB: In theory, returning to the BatchPage and changing the name of the I(Q)*
*data source should also work, but at the moment whilst this does change the*
*data set displayed it always superimposes the 'theory' corresponding to the*
*starting parameters.*

Chain Fitting
^^^^^^^^^^^^^

By default, the *same* parameter values copied from the initial single fit into
the *BatchPage* will be used as the starting parameters for all batch fits. It
is, however, possible to get *SasView* to use the results of a fit to a preceding
data set as the starting parameters for the next fit in the sequence. This
variation of batch fitting is called *Chain Fitting*, and will considerably speed
up model-fitting if you have lots of very similar data sets where a few parameters
are gradually changing. Do not use chain fitting on disparate data sets.

To use chain fitting, select *Chain Fitting* under *Fitting* in the menu bar. It
toggles on/off, so selecting it again will switch back to normal batch fitting.

To choose the order of the fitpages in the fitting process, drag and drop rows in the
*Source choice for simultaneous fitting* table. The order of the table determines
the order of the chain fitting performed.

.. _Grid_Window:

Grid Window
^^^^^^^^^^^

The *Grid Window* provides an easy way to view the results from batch fitting.
It will be displayed automatically when a batch fit completes, but may be
opened at any time by selecting *Show Grid Window* under *View* in the menu
bar.

.. image:: restore_batch_window.png

..
  Once a batch fit is completed, all model parameters are displayed but *not*
  their uncertainties. To view the uncertainties, click on a given column then
  go to *Edit* in the menu bar, select *Insert Column Before* and choose the
  required data from the list. An empty column can be inserted in the same way.


  To remove a column from the grid, click on the column header and choose
  *Remove Column* under *Edit* in the menu bar. The same functionality also
  allows you to re-order columns.

  *NB: You cannot insert/remove/re-order the rows in the Grid Window.*

  All of the above functions are also available by right-clicking on a column
  label.

  .. image:: edit_menu.png
..

If there is an existing Grid Window and another batch fit is performed,*
*an additional 'Table' tab will be added to the Grid Window.*

The parameter values in the *currently selected* table of the *Grid Window*
can be output to a CSV file by choosing *Save As* under *File* in the (*Grid*
*Window*) menu bar. The default filename includes the date and time that the
batch fit was performed.

Saved CSV files can be reloaded by choosing *Open* under *File* in the *Grid*
*Window* menu bar. The loaded parameters will appear in a new table tab.

.. image:: file_menu.png

*NB: Saving the Grid Window does not save any experimental data, residuals*
*or actual model fits. Consequently if you reload a saved CSV file the*
*ability to View Fits will be lost.*

Parameter Plots
^^^^^^^^^^^^^^^

..
  Any column of *numeric* parameter values can be plotted against another using
  the *Grid Window*. Simply select one column at the time and click the *Add*
  button next to the required *X/Y-axis Selection Range* text box. When both
  the X and Y axis boxes have been completed, click the *Plot* button.

  When the *Add* button is clicked, *SasView* also automatically completes the
  *X/Y-axis Label* text box with the heading from Row 1 of the selected table,
  but different labels and units can be entered manually.

  .. image:: plot_button.png

  The *X/Y-axis Selection Range* can be edited manually. The text control box
  recognises the operators +, -, \*, /, or 'pow', and allows the following
  types of expression :

    1) if an axis label range is a function of 1 or more *columns*, write
      this type of expression

      constant1 * column_name1 [minimum row index :  maximum  row index]
      operator constant2 * column_name2 [minimum row index :  maximum  row index]

      Example: radius [2 : 5] -3 * scale [2 : 5]

    2) if only some *values* of a given column are needed but the range between
      the first row and the last row used is not continuous, write this type of
      expression

      column_name1 [minimum row index1 :  maximum  row index1] , column_name1
      [minimum row index2 :  maximum  row index2]

      Example: radius [2 : 5] , radius [10 : 25]
..

Any row (dataset) can be plotted by selecting it and either right-clicking and choosing
*Plot selected fits* menu item or by clicking on the *Plot* button.

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Combined Batch Fit Mode
-----------------------

The purpose of the Combined Batch Fit is to allow running two or more batch
fits in sequence without overwriting the output table of results.  This may be
of interest for example if one is fitting a series of data sets where there is
a shape change occurring in the series that requires changing the model part
way through the series; for example a sphere to rod transition.  Indeed the
regular batch mode does not allow for multiple models and requires all the
files in the series to be fit with single model and set of parameters.  While
it is of course possible to just run part of the series as a batch fit using
model one followed by running another batch fit on the rest of the series with
model two (and/or model three etc), doing so will overwrite the table of
outputs from the previous batch fit(s).  This may not be desirable if one is
interested in comparing the parameters: for example the sphere radius of set
one and the cylinder radius of set two.

Method
^^^^^^

In order to use the *Combined Batch Fit*, first load all the data needed as
described in :ref:`Loading_data`. Next start up two or more *BatchPage* fits
following the instructions in :ref:`Batch_Fit_Mode` but **DO NOT PRESS FIT**.

When done, select *Constrained or Simultaneous Fit* under *Fitting* in the menu bar.

In the *Const & Simul Fit* page that appears, choose *Batch fits* radio button and
select which data sets are to be  fitted.

.. image:: simult_batch.png

Once all are selected, click the Fit button on
the *Const. Simult. Fitting* to run each batch fit in *sequence*


The batch table will then pop up at the end as for the case of the simple Batch
Fitting with the following caveats:

.. note::
   The order matters.  The parameters in the table will be taken from the model
   used in the first *BatchPage* of the list.  Any parameters from the
   second and later *BatchPage* s that have the same name as a parameter in the
   first will show up allowing for plotting of that parameter across the
   models. The other parameters will not be available in the grid.
   To choose the order of the fitpages in the fitting process, drag and drop rows in the
   *Source choice for simultaneous fitting* table.

.. note::
   a corollary of the above is that currently models created as a sum|multiply
   model will not work as desired because the generated model parameters have a
   p#_ appended to the beginning and thus radius and p1_radius will not be
   recognized as the same parameter.

.. image:: combine_batch_grid.png

In the example shown above the data is a time series with a shifting peak.
The first part of the series was fitted using the *broad_peak* model, while
the rest of the data were fit using the *gaussian_peak* model. Unfortunately the
time is not listed in the file but the file name contains the information. As
described in :ref:`Grid_Window`, a column can be added manually, in this case
called time, and the peak position plotted against time.

.. image:: combine_batch_plot.png

Note the discontinuity in the peak position.  This reflects the fact that the
Gaussian fit is a rather poor model for the data and is not actually
finding the peak.

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.. note::  This help document was last changed by Steve King, 05 Feb 2020
