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, click the Show 2D button on the Fit Page. To return to 1D fitting model, click the same button (which will now say Show 1D).

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.

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 Selected button. Then click Done.

Showing/hiding models

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

NB: It may be necessary to change to a different category and then back again before any changes take effect.

New Plugin Model

Relatively straightforward models can be programmed directly from the SasView GUI using the New Plugin Model Function.

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:`Advanced_Plugin_Editor` .

SasView version 4.2 made 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).

Sum|Multi(p1,p2)

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 Sum/Multi Editor give the new model a function name and brief description (to appear under the Details button on the FitPage). Then select two existing models, as p1 and 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. If the model is not listed you can force a recompilation of the plugins by selecting Fitting > Plugin Model Operations > Load Plugin Models.

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.

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

To create a P(Q)*S(Q) model use the @ symbol instead of * like this:

sphere@hardsphere

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.

Advanced Plugin Editor

Selecting this option shows all the plugin models in the plugin model folder, on Windows this is

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

You can edit, modify, and save the Python code in any of these models using the Advanced Plugin Model Editor. Note that this is actually the same tool as the :ref:`Python_shell` .

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

When editing is complete, select Run > Check Model from the Advanced Plugin Model Editor menu bar. An Info box will appear with the results of the compilation and model unit tests. The model will only be usable if the tests 'pass'.

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.

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

Delete Plugin Models

Simply highlight the plugin model to be removed. The operation is final!!!

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

Load Plugin Models

This option loads (or re-loads) all models present in the ~\.sasview\plugin_models folder.

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.

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!).

To tie parameters between the data sets with constraints, check the 'yes' radio button next to Add Constraint? in the Fit Constraints box.

NB: You can only constrain parameters that are set to refine.

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.

Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To see the chi2/Npts value for a specific FitPage, click the Compute button at the bottom of that FitPage to recalculate. Also see :ref:`Assessing_Fit_Quality`.

Simultaneous Fits with Constraints

Use the Easy Setup drop-down buttons in the Const & Simul Fit page to set up constraints between FitPage's.

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.

Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To see the chi2/Npts value for a specific FitPage, click the Compute button at the bottom of that FitPage to recalculate. Also see :ref:`Assessing_Fit_Quality`.

Method

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

NB: The Batch Page can also be created by checking the Batch Mode radio 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 View Fits button. The data and the model fit will be displayed. If you select mutliple data sets they will all appear on one graph.

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.

If you select a 'Chi2' value and click the View Fits button a graph of the residuals for that data set is displayed. Again, if you select multiple 'Chi2' values then all the residuals data will appear on one graph. Also see :ref:`Assessing_Fit_Quality`.

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.

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.

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.

NB: 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.

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.

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]

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. At this point the Combine Batch Fit menu item under the Fitting menu should be active (if there is one or no BatchPage the menu item will be greyed out and inactive). Clicking on Combine Batch Fit will bring up a new panel, similar to the Const & Simult Fit panel. In this case there will be a checkbox for each BatchPage instead of each FitPage that should be included in the fit. Once all are selected, click the Fit button on the BatchPage 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:

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.

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.