source: sasview/src/sas/sasgui/perspectives/fitting/media/fitting_help.rst @ 5005ae0

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalcmagnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload
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[ec392464]1.. fitting_help.rst
2
3.. This is a port of the original SasView html help file to ReSTructured text
4.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
5
[b64b87c]6Fitting
7=======
[ec392464]8
[3e1c9e5]9.. note:: If some code blocks are not readable, expand the documentation window
10
[a6f3613]11.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
12
13Preparing to fit data
14---------------------
15
16To fit some data you must first load some data, activate one or more data sets,
[b64b87c]17send those data sets to fitting, and select a model to fit to each data set.
[a6f3613]18
[f3377b8]19Instructions on how to load and activate data are in the section :ref:`Loading_data`.
[ec392464]20
[a6f3613]21SasView can fit data in one of three ways:
[ec392464]22
[a6f3613]23*  in *Single* fit mode - individual data sets are fitted independently one-by-one
[ec392464]24
[5295cf5]25*  in *Simultaneous* fit mode - multiple data sets are fitted simultaneously to
26   the *same* model with/without constrained parameters (this might be useful,
27   for example, if you have measured the same sample at different contrasts)
[ec392464]28
[5005ae0]29*  in *Batch* fit mode - multiple data sets are fitted sequentially to the
30   *same* model (this might be useful, for example, if you have performed
31   a kinetic or time-resolved experiment and have *lots* of data sets!)
[a6f3613]32
33.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
[ec392464]34
[a6f3613]35Selecting a model
36-----------------
[ec392464]37
[5295cf5]38The models in SasView are grouped into categories. By default these consist of:
[ec392464]39
[5295cf5]40*  *Cylinder* - cylindrical shapes (disc, right cylinder, cylinder with endcaps
41   etc)
42*  *Ellipsoid* - ellipsoidal shapes (oblate,prolate, core shell, etc)
43*  *Parellelepiped* - as the name implies
44*  *Sphere* - sheroidal shapes (sphere, core multishell, vesicle, etc)
45*  *Lamellae* - lamellar shapes (lamellar, core shell lamellar, stacked
46   lamellar, etc)
[5005ae0]47*  *Shape-Independent* - models describing structure in terms of density
48   correlation functions, fractals, peaks, power laws, etc
[5295cf5]49*  *Paracrystal* - semi ordered structures (bcc, fcc, etc)
[a6f3613]50*  *Structure Factor* - S(Q) models
[5295cf5]51*  *Plugin Models* - User-created (custom/non-library) Python models
[ec392464]52
[a6f3613]53Use the *Category* drop-down menu to chose a category of model, then select
[f3377b8]54a model from the drop-down menu beneath. A graph of the chosen model, calculated
55using default parameter values, will appear. The graph will update dynamically
56as the parameter values are changed.
57
58You can decide your own model categorizations using the :ref:`Category_Manager`.
[ce62e75]59
[a6f3613]60Once you have selected a model you can read its help documentation by clicking
61on the *Description* button to the right.
62
63Show 1D/2D
64^^^^^^^^^^
65
66Models are normally fitted to 1D (ie, I(Q) vs Q) data sets, but some models in
67SasView can also be fitted to 2D (ie, I(Qx,Qy) vs Qx vs Qy) data sets.
68
69*NB: Magnetic scattering can only be fitted in SasView in 2D.*
70
71To activate 2D fitting mode, click the *Show 2D* button on the *Fit Page*. To
72return to 1D fitting model, click the same button (which will now say *Show 1D*).
[ce62e75]73
[ec392464]74.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
75
[a6f3613]76.. _Category_Manager:
[a0637de]77
[a6f3613]78Category Manager
79----------------
80
[f3377b8]81To change the model categorizations, either choose *Category Manager* from the
82*View* option on the menubar, or click on the *Modify* button on the *Fit Page*.
[a6f3613]83
[6aad2e8]84.. image:: cat_fig0.png
[a6f3613]85
[5295cf5]86The categorization of all models except the user supplied Plugin Models can be
87reassigned, added to, and removed using *Category Manager*. Models can also be
88hidden from view in the drop-down menus.
[a6f3613]89
[6aad2e8]90.. image:: cat_fig1.png
[a6f3613]91
[f3377b8]92Changing category
93^^^^^^^^^^^^^^^^^
[a6f3613]94
[5295cf5]95To change category, highlight a model in the list by left-clicking on its entry
96and then click the *Modify* button. Use the *Change Category* panel that appears
97to make the required changes.
[a6f3613]98
[6aad2e8]99.. image:: cat_fig2.png
[a6f3613]100
[f3377b8]101To create a category for the selected model, click the *Add* button. In order
102to delete a category, select the category name and click the *Remove Selected*
103button. Then click *Done*.
[a6f3613]104
[f3377b8]105Showing/hiding models
106^^^^^^^^^^^^^^^^^^^^^
[a6f3613]107
[5295cf5]108Use the *Enable All / Disable All* buttons and the check boxes beside each model
109to select the models to show/hide. To apply the selection, click *Ok*. Otherwise
110click *Cancel*.
[a6f3613]111
[8570246]112*NB: It may be necessary to change to a different category and then back again*
[f3377b8]113*before any changes take effect.*
[a6f3613]114
115.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
116
[f3377b8]117Model Functions
118---------------
[a6f3613]119
[5295cf5]120For a complete list of all the library models available in SasView, see
121the `Model Documentation <../../../index.html>`_ .
[a6f3613]122
[f3377b8]123It is also possible to add your own models.
[a6f3613]124
[f3377b8]125.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
[a6f3613]126
[b5846a10]127.. _Adding_your_own_models:
128
[3e1c9e5]129Adding your own Models
[f3377b8]130----------------------
[a6f3613]131
[3e1c9e5]132There are essentially three ways to generate new fitting models for SasView:
133
[5295cf5]134*  Using the SasView :ref:`New_Plugin_Model` helper dialog (best for beginners
135   and/or relatively simple models)
136*  By copying/editing an existing model (this can include models generated by
[5005ae0]137   the New Plugin Model* dialog) in the :ref:`Python_shell` or
[5295cf5]138   :ref:`Advanced_Plugin_Editor` (suitable for all use cases)
139*  By writing a model from scratch outside of SasView (only recommended for code
140   monkeys!)
[3e1c9e5]141
142Please read the guidance on :ref:`Writing_a_Plugin` before proceeding.
[f3377b8]143
[3e1c9e5]144**To be found by SasView your model must reside in the *~\\.sasview\\plugin_models* folder.**
[f3377b8]145
[a6f3613]146.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
147
[3e1c9e5]148.. _Plugin_Model_Operations:
[f3377b8]149
[3e1c9e5]150Plugin Model Operations
151-----------------------
[a6f3613]152
[3e1c9e5]153From the *Fitting* option in the menu bar, select *Plugin Model Operations*
[a6f3613]154
[82b0b05e]155.. image:: edit_model_menu.png
[a6f3613]156
[3e1c9e5]157and then one of the sub-options
[f3377b8]158
[3e1c9e5]159*  *New Plugin Model* - to create a plugin model template with a helper dialog
160*  *Sum|Multi(p1,p2)* - to create a plugin model by summing/multiplying *existing models* in the model library
161*  *Advanced Plugin Editor* - to create/edit a plugin model in a Python shell
162*  *Delete Plugin Models* - to delete a plugin model
163*  *Load Plugin Models* - to (re-)load plugin models
[a6f3613]164
[3e1c9e5]165.. _New_Plugin_Model:
166
167New Plugin Model
168^^^^^^^^^^^^^^^^
[a6f3613]169
[5295cf5]170Relatively straightforward models can be programmed directly from the SasView
171GUI using the *New Plugin Model Function*.
[26c8be3]172
[6aad2e8]173.. image:: new_model.png
[a6f3613]174
[5005ae0]175When using this feature, be aware that even if your code has errors, including
176syntax errors, a model file is still generated. When you then correct the errors
177and click 'Apply' again to re-compile you will get an error informing you that
178the model already exists if the 'Overwrite' box is not checked. In this case you
179will need to supply a new model function name. By default the 'Overwrite' box is
[26c8be3]180*checked*\ .
[f3377b8]181
[5295cf5]182Also note that the 'Fit Parameters' have been split into two sections: those
183which can be polydisperse (shape and orientation parameters) and those which are
184not (eg, scattering length densities).
[26c8be3]185
186A model file generated by this option can be viewed and further modified using
187the :ref:`Advanced_Plugin_Editor` .
[05829fb]188
[5005ae0]189**SasView version 4.2** made it possible to specify whether a plugin created with
190the *New Plugin Model* dialog is actually a form factor P(Q) or a structure factor
191S(Q). To do this, simply add one or other of the following lines under the *import*
[f485ba0]192statements.
193
194For a form factor::
195
196     form_factor = True
[5005ae0]197
[f485ba0]198or for a structure factor::
199
200     structure_factor = True
[5005ae0]201
202If the plugin is a structure factor it is *also* necessary to add two variables to
[f485ba0]203the parameter list::
204
[5005ae0]205     parameters = [
[ca383a0]206                     ['radius_effective', '', 1, [0.0, numpy.inf], 'volume', ''],
207                     ['volfraction', '', 1, [0.0, 1.0], '', ''],
[e081946]208                     [...],
[f485ba0]209
210and to the declarations of the functions Iq and Iqxy:::
211
212     def Iq(x , radius_effective, volfraction, ...):
213
214     def Iqxy(x, y, radius_effective, volfraction, ...):
215
[5005ae0]216Such a plugin should then be available in the S(Q) drop-down box on a FitPage (once
[f485ba0]217a P(Q) model has been selected).
218
[a6f3613]219Sum|Multi(p1,p2)
220^^^^^^^^^^^^^^^^
221
[6aad2e8]222.. image:: sum_model.png
[a0637de]223
[5295cf5]224This option creates a custom Plugin Model of the form::
[f3377b8]225
[5295cf5]226     Plugin Model = scale_factor * {(scale_1 * model_1) +/- (scale_2 * model_2)} + background
[f3377b8]227
[3e1c9e5]228or::
229
[f485ba0]230     Plugin Model = scale_factor * (model1 * model2) + background
[3e1c9e5]231
232In the *Easy Sum/Multi Editor* give the new model a function name and brief
233description (to appear under the *Details* button on the *FitPage*). Then select
[f3377b8]234two existing models, as p1 and p2, and the required operator, '+' or '*' between
[f485ba0]235them. Finally, click the *Apply* button to generate and test the model and then click *Close*.
[f3377b8]236
[5005ae0]237Any changes to a plugin model generated in this way only become effective *after* it is re-selected
238from the plugin models drop-down menu on the FitPage. If the model is not listed you can force a
[f485ba0]239recompilation of the plugins by selecting *Fitting* > *Plugin Model Operations* > *Load Plugin Models*.
240
[5005ae0]241**SasView version 4.2** introduced a much simplified and more extensible structure for plugin models
242generated through the Easy Sum/Multi Editor. For example, the code for a combination of a sphere model
[f485ba0]243with a power law model now looks like this::
244
245     from sasmodels.core import load_model_info
246     from sasmodels.sasview_model import make_model_from_info
[5005ae0]247
[f485ba0]248     model_info = load_model_info('sphere+power_law')
[e081946]249     model_info.name = 'MyPluginModel'
[f485ba0]250     model_info.description = 'sphere + power_law'
251     Model = make_model_from_info(model_info)
252
[5005ae0]253To change the models or operators contributing to this plugin it is only necessary to edit the string
254in the brackets after *load_model_info*, though it would also be a good idea to update the model name
[f485ba0]255and description too!!!
256
[5005ae0]257The model specification string can handle multiple models and combinations of operators (+ or *) which
258are processed according to normal conventions. Thus 'model1+model2*model3' would be valid and would
259multiply model2 by model3 before adding model1. In this example, parameters in the *FitPage* would be
260prefixed A (for model2), B (for model3) and C (for model1). Whilst this might appear a little
261confusing, unless you were creating a plugin model from multiple instances of the same model the parameter
[e081946]262assignments ought to be obvious when you load the plugin.
[f485ba0]263
[5005ae0]264If you need to include another plugin model in the model specification string, just prefix the name of
[e081946]265that model with *custom*. For instance::
266
267     sphere+custom.MyPluginModel
268
269To create a P(Q)*\S(Q) model use the @ symbol instead of * like this::
270
271     sphere@hardsphere
[5005ae0]272
273This streamlined approach to building complex plugin models from existing library models, or models
274available on the *Model Marketplace*, also permits the creation of P(Q)*\S(Q) plugin models, something
275that was not possible in earlier versions of SasView.
[f3377b8]276
[3e1c9e5]277.. _Advanced_Plugin_Editor:
[f3377b8]278
[3e1c9e5]279Advanced Plugin Editor
280^^^^^^^^^^^^^^^^^^^^^^
[ec392464]281
[3e1c9e5]282Selecting this option shows all the plugin models in the plugin model folder, on Windows this is
[f3377b8]283
[afb93df]284  *C:\\Users\\{username}\\.sasview\\plugin_models*
[f3377b8]285
286You can edit, modify, and save the Python code in any of these models using the
[3e1c9e5]287*Advanced Plugin Model Editor*. Note that this is actually the same tool as the :ref:`Python_shell` .
[f3377b8]288
[afb93df]289For details of the SasView plugin model format see :ref:`Writing_a_Plugin` .
[05829fb]290
[afb93df]291.. note:: Model files generated with the Sum/Multi option are still using the SasView 3.x model format. Unless you are confident about what you are doing, it is recommended that you only modify lines denoted with the ## <----- comments!
[f3377b8]292
[3e1c9e5]293When 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'.
[f3377b8]294
[3e1c9e5]295.. image:: ../calculator/new_pycrust_example_2.png
296
297To use the model, go to the relevant *Fit Page*, select the *Plugin Models*
[f3377b8]298category and then select the model from the drop-down menu.
299
[3e1c9e5]300Any 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.
[a6f3613]301
[3e1c9e5]302Delete Plugin Models
303^^^^^^^^^^^^^^^^^^^^
[a6f3613]304
[3e1c9e5]305Simply highlight the plugin model to be removed. The operation is final!!!
[f3377b8]306
[5295cf5]307*NB: Models shipped with SasView cannot be removed in this way.*
[ec392464]308
[3e1c9e5]309Load Plugin Models
310^^^^^^^^^^^^^^^^^^
[afb93df]311
[5295cf5]312This option loads (or re-loads) all models present in the
313*~\\.sasview\\plugin_models* folder.
[afb93df]314
[ec392464]315.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
316
[4666660]317.. _Fitting_Options:
318
[f3377b8]319Fitting Options
320---------------
[a6f3613]321
[f3377b8]322It is possible to specify which optimiser SasView should use to fit the data, and
323to modify some of the configurational parameters for each optimiser.
324
325From *Fitting* in the menu bar select *Fit Options*, then select one of the following
326optimisers:
[a6f3613]327
[f3377b8]328*  DREAM
329*  Levenberg-Marquardt
330*  Quasi-Newton BFGS
331*  Differential Evolution
332*  Nelder-Mead Simplex
[a6f3613]333
[6af2785]334The DREAM optimiser is the most sophisticated, but may not necessarily be the best
335option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser
336initially.
337
[f3377b8]338These optimisers form the *Bumps* package written by P Kienzle. For more information
[4666660]339on each optimiser, see the :ref:`Fitting_Documentation`.
[a6f3613]340
[f3377b8]341.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
[a6f3613]342
[5ac0a7a]343Fitting Limits
344--------------
345
346By default, *SasView* will attempt to model fit the full range of the data; ie,
347across all *Q* values. If necessary, however, it is possible to specify only a
348sub-region of the data for fitting.
349
350In a *FitPage* or *BatchPage* change the *Q* values in the *Min* and/or *Max*
351text boxes. Vertical coloured bars will appear on the graph with the data and
352'theory' indicating the current *Q* limits (red = *Qmin*, purple = *Qmax*).
353
354To return to including all data in the fit, click the *Reset* button.
355
356.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
357
358
[f3377b8]359Shortcuts
360---------
[a6f3613]361
[f3377b8]362Copy/Paste Parameters
363^^^^^^^^^^^^^^^^^^^^^
[a6f3613]364
[f3377b8]365It is possible to copy the parameters from one *Fit Page* and to paste them into
366another *Fit Page* using the same model.
[a6f3613]367
[f3377b8]368To *copy* parameters, either:
[a6f3613]369
[f3377b8]370*  Select *Edit -> Copy Params* from the menu bar, or
371*  Use Ctrl(Cmd on Mac) + Left Mouse Click on the *Fit Page*.
[a6f3613]372
[f3377b8]373To *paste* parameters, either:
374
375*  Select *Edit -> Paste Params* from the menu bar, or
376*  Use Ctrl(Cmd on Mac) + Shift + Left-click on the *Fit Page*.
377
378If either operation is successful a message will appear in the info line at the
379bottom of the SasView window.
380
381Bookmark
382^^^^^^^^
[a6f3613]383
[1fda506]384To *Bookmark* a *Fit Page* either:
[a6f3613]385
[f3377b8]386*  Select a *Fit Page* and then click on *Bookmark* in the tool bar, or
387*  Right-click and select the *Bookmark* in the popup menu.
[a6f3613]388
389.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
390
[4666660]391.. _Status_bar:
392
[1fda506]393Status Bar & Console
394--------------------
395
396The status bar is located at the bottom of the SasView window and displays
397messages, hints, warnings and errors.
398
399At the right-hand side of the status bar is a button marked *Console*. The *Console*
400displays available message history and some run-time traceback information.
401
402During a long task the *Console* can also be used to monitor the progress.
403
404.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
405
[6af2785]406.. _Single_Fit_Mode:
407
[a6f3613]408Single Fit Mode
409---------------
[ec392464]410
[4666660]411*NB: Before proceeding, ensure that the Single Mode radio button at the bottom of*
412*the Data Explorer is checked (see the section* :ref:`Loading_data` *).*
413
[63d314b]414This mode fits one data set.
415
[b64b87c]416When data is sent to the fitting it is plotted in a graph window as markers.
[4666660]417
418If a graph does not appear, or a graph window appears but is empty, then the data
419has not loaded correctly. Check to see if there is a message in the :ref:`Status_Bar`
420or in the *Console* window.
421
422Assuming the data has loaded correctly, when a model is selected a green model
423calculation (or what SasView calls a 'Theory') line will appear in the earlier graph
424window, and a second graph window will appear displaying the residuals (the
425difference between the experimental data and the theory) at the same X-data values.
[f9250dc]426See :ref:`Assessing_Fit_Quality`.
[4666660]427
428The objective of model-fitting is to find a *physically-plausible* model, and set
429of model parameters, that generate a theory that reproduces the experimental data
430and gives residual values as close to zero as possible.
431
432Change the default values of the model parameters by hand until the theory line
433starts to represent the experimental data. Then uncheck the tick boxes alongside
434all parameters *except* the 'background' and the 'scale'. Click the *Fit* button.
435SasView will optimise the values of the 'background' and 'scale' and also display
436the corresponding uncertainties on the optimised values.
437
438*NB: If no uncertainty is shown it generally means that the model is not very*
439*dependent on the corresponding parameter (or that one or more parameters are*
440*'correlated').*
441
442In the bottom left corner of the *Fit Page* is a box displaying the normalised value
[5ed76f8]443of the statistical $\chi^2$ parameter returned by the optimiser.
[4666660]444
445Now check the box for another model parameter and click *Fit* again. Repeat this
446process until most or all parameters are checked and have been optimised. As the
447fit of the theory to the experimental data improves the value of 'chi2/Npts' will
448decrease. A good model fit should easily produce values of 'chi2/Npts' that are
[5ed76f8]449close to one, and certainly <100. See :ref:`Assessing_Fit_Quality`.
[4666660]450
451SasView has a number of different optimisers (see the section :ref:`Fitting_Options`).
452The DREAM optimiser is the most sophisticated, but may not necessarily be the best
453option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser
454initially.
[ec392464]455
456.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
457
[a6f3613]458Simultaneous Fit Mode
459---------------------
[ec392464]460
[63d314b]461*NB: Before proceeding, ensure that the Single Mode radio button at the bottom of*
462*the Data Explorer is checked (see the section* :ref:`Loading_data` *).*
[ec392464]463
[6af2785]464This mode is an extension of the :ref:`Single_Fit_Mode` that fits two or more data
[5005ae0]465sets *to the same model* simultaneously. If necessary it is possible to constrain
[63d314b]466fit parameters between data sets (eg, to fix a background level, or radius, etc).
467
[b5846a10]468If the data to be fit are in multiple files, load each file, then select each file
469in the *Data Explorer*, and *Send To Fitting*. If multiple data sets are in one file,
470load that file, *Unselect All Data*, select just those data sets to be fitted, and
471*Send To Fitting*. Either way, the result should be that for *n* data sets you have
[6af2785]4722\ *n* graphs (*n* of the data and model fit, and *n* of the resulting residuals). But
[f9250dc]473it may be helpful to minimise the residuals plots for clarity. Also see
474:ref:`Assessing_Fit_Quality`.
[b5846a10]475
[5295cf5]476*NB: If you need to use a custom Plugin Model, you must ensure that model is
477available first (see* :ref:`Adding_your_own_models` *).*
[b5846a10]478
[6af2785]479Method
480^^^^^^
481
[b5846a10]482Now go to each *FitPage* in turn and:
483
484  Select the required category and model;
485
486  Unselect all the model parameters;
487
488  Enter some starting guesses for the parameters;
489
490  Enter any parameter limits (recommended);
[63d314b]491
[b5846a10]492  Select which parameters will refine (selecting all is generally a bad idea...);
[63d314b]493
[b5846a10]494When done, select *Constrained or Simultaneous Fit* under *Fitting* in the menu bar.
495
496In the *Const & Simul Fit* page that appears, select which data sets are to be
497simultaneously fitted (this will probably be all of them or you would not have loaded
498them in the first place!).
499
500To tie parameters between the data sets with constraints, check the 'yes' radio button
501next to *Add Constraint?* in the *Fit Constraints* box.
502
503*NB: You can only constrain parameters that are set to refine.*
504
505When ready, click the *Fit* button on the *Const & Simul Fit* page, NOT the *Fit*
506button on the individual *FitPage*'s.
[63d314b]507
508Simultaneous Fits without Constraints
509^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[ec392464]510
[b5846a10]511The results of the model-fitting will be returned to each of the individual
512*FitPage*'s.
[ec392464]513
[b5846a10]514Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To
[6af2785]515see the chi2/Npts value for a specific *FitPage*, click the *Compute* button at the
[f9250dc]516bottom of that *FitPage* to recalculate. Also see :ref:`Assessing_Fit_Quality`.
[ec392464]517
[63d314b]518Simultaneous Fits with Constraints
519^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[ec392464]520
[b5846a10]521Use the *Easy Setup* drop-down buttons in the *Const & Simul Fit* page to set
522up constraints between *FitPage*'s.
523
[6af2785]524Constraints will generally be of the form
525
526  Mi Parameter1 = Mj.Parameter1
527
528however the text box after the '=' sign can be used to adjust this
529relationship; for example
530
531  Mi Parameter1 = scalar \* Mj.Parameter1
532
533A 'free-form' constraint box is also provided.
[b5846a10]534
535Many constraints can be entered for a single fit.
536
537The results of the model-fitting will be returned to each of the individual
538*FitPage*'s.
[ec392464]539
[b5846a10]540Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To
[6af2785]541see the chi2/Npts value for a specific *FitPage*, click the *Compute* button at the
[f9250dc]542bottom of that *FitPage* to recalculate. Also see :ref:`Assessing_Fit_Quality`.
[ec392464]543
544.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
545
[e6c74e8]546.. _Batch_Fit_Mode:
547
[a6f3613]548Batch Fit Mode
549--------------
[ec392464]550
[6af2785]551*NB: Before proceeding, ensure that the Single Mode radio button at the bottom of*
552*the Data Explorer is checked (see the section* :ref:`Loading_data` *). The Batch*
553*Mode button will be used later on!*
[63d314b]554
[6af2785]555This mode *sequentially* fits two or more data sets *to the same model*. Unlike in
556simultaneous fitting, in batch fitting it is not possible to constrain fit parameters
557between data sets.
[ec392464]558
[6af2785]559If the data to be fit are in multiple files, load each file in the *Data Explorer*.
560If multiple data sets are in one file, load just that file. *Unselect All Data*, then
561select a single initial data set to be fitted. Fit that selected data set as described
[5295cf5]562above under :ref:`Single_Fit_Mode`.
[ec392464]563
[5295cf5]564*NB: If you need to use a custom Plugin Model, you must ensure that model is
565available first (see* :ref:`Adding_your_own_models` *).*
[ec392464]566
[6af2785]567Method
568^^^^^^
[ec392464]569
[6af2785]570Now *Select All Data* in the *Data Explorer*, check the *Batch Mode* radio button
571at the bottom of that panel and *Send To Fitting*. A *BatchPage* will be created.
[ec392464]572
[6aad2e8]573.. image:: batch_button_area.png
[ec392464]574
[6af2785]575*NB: The Batch Page can also be created by checking the Batch Mode radio button*
576*and selecting New Fit Page under Fitting in the menu bar.*
[ec392464]577
[6af2785]578Using the drop-down menus in the *BatchPage*, now set up the *same* data set
579with the *same* model that you just fitted in single fit mode. A quick way to
580set the model parameter values is to just copy them from the earlier Single
581Fit. To do this, go back to the Single Fit *FitPage*, select *Copy Params*
582under *Edit* in the menu bar, then go back to the *BatchPage* and *Paste Params*.
[ec392464]583
[6af2785]584When ready, use the *Fit* button on the *BatchPage* to perform the fitting, NOT
585the *Fit* button on the individual *FitPage*'s.
[ec392464]586
[6af2785]587Unlike in single fit mode, the results of batch fits are not returned to
588the *BatchPage*. Instead, a spreadsheet-like :ref:`Grid_Window` will appear.
[ec392464]589
[6af2785]590If you want to visually check a graph of a particular fit, click on the name of
591a *Data set* in the *Grid Window* and then click the *View Fits* button. The
592data and the model fit will be displayed. If you select mutliple data sets they
593will all appear on one graph.
[ec392464]594
[6aad2e8]595.. image:: view_button.png
[ec392464]596
[6af2785]597*NB: In theory, returning to the BatchPage and changing the name of the I(Q)*
598*data source should also work, but at the moment whilst this does change the*
599*data set displayed it always superimposes the 'theory' corresponding to the*
600*starting parameters.*
[ec392464]601
[6af2785]602If you select a 'Chi2' value and click the *View Fits* button a graph of the
603residuals for that data set is displayed. Again, if you select multiple 'Chi2'
[f9250dc]604values then all the residuals data will appear on one graph. Also see
605:ref:`Assessing_Fit_Quality`.
[ec392464]606
[6af2785]607Chain Fitting
608^^^^^^^^^^^^^
[ec392464]609
[6af2785]610By default, the *same* parameter values copied from the initial single fit into
611the *BatchPage* will be used as the starting parameters for all batch fits. It
612is, however, possible to get *SasView* to use the results of a fit to a preceding
613data set as the starting parameters for the next fit in the sequence. This
614variation of batch fitting is called *Chain Fitting*, and will considerably speed
615up model-fitting if you have lots of very similar data sets where a few parameters
616are gradually changing. Do not use chain fitting on disparate data sets.
[ec392464]617
[6af2785]618To use chain fitting, select *Chain Fitting* under *Fitting* in the menu bar. It
619toggles on/off, so selecting it again will switch back to normal batch fitting.
[ec392464]620
[6af2785]621.. _Grid_Window:
[ec392464]622
[6af2785]623Grid Window
624^^^^^^^^^^^
[ec392464]625
[6af2785]626The *Grid Window* provides an easy way to view the results from batch fitting.
627It will be displayed automatically when a batch fit completes, but may be
628opened at any time by selecting *Show Grid Window* under *View* in the menu
629bar.
[ec392464]630
[6aad2e8]631.. image:: restore_batch_window.png
[ec392464]632
[6af2785]633Once a batch fit is completed, all model parameters are displayed but *not*
634their uncertainties. To view the uncertainties, click on a given column then
635go to *Edit* in the menu bar, select *Insert Column Before* and choose the
636required data from the list. An empty column can be inserted in the same way.
[ec392464]637
[6af2785]638To remove a column from the grid, click on the column header and choose
639*Remove Column* under *Edit* in the menu bar. The same functionality also
640allows you to re-order columns.
[ec392464]641
[6af2785]642*NB: You cannot insert/remove/re-order the rows in the Grid Window.*
[ec392464]643
[6af2785]644All of the above functions are also available by right-clicking on a column
645label.
[ec392464]646
[6aad2e8]647.. image:: edit_menu.png
[ec392464]648
[6af2785]649*NB: If there is an existing Grid Window and another batch fit is performed,*
650*an additional 'Table' tab will be added to the Grid Window.*
[ec392464]651
[6af2785]652The parameter values in the *currently selected* table of the *Grid Window*
653can be output to a CSV file by choosing *Save As* under *File* in the (*Grid*
654*Window*) menu bar. The default filename includes the date and time that the
655batch fit was performed.
[ec392464]656
[6af2785]657Saved CSV files can be reloaded by choosing *Open* under *File* in the *Grid*
658*Window* menu bar. The loaded parameters will appear in a new table tab.
[ec392464]659
[6aad2e8]660.. image:: file_menu.png
[ec392464]661
[6af2785]662*NB: Saving the Grid Window does not save any experimental data, residuals*
663*or actual model fits. Consequently if you reload a saved CSV file the*
664*ability to View Fits will be lost.*
[ec392464]665
[6af2785]666Parameter Plots
667^^^^^^^^^^^^^^^
[ec392464]668
[6af2785]669Any column of *numeric* parameter values can be plotted against another using
670the *Grid Window*. Simply select one column at the time and click the *Add*
671button next to the required *X/Y-axis Selection Range* text box. When both
672the X and Y axis boxes have been completed, click the *Plot* button.
[ec392464]673
[6af2785]674When the *Add* button is clicked, *SasView* also automatically completes the
675*X/Y-axis Label* text box with the heading from Row 1 of the selected table,
676but different labels and units can be entered manually.
[ec392464]677
[6aad2e8]678.. image:: plot_button.png
[ec392464]679
[6af2785]680The *X/Y-axis Selection Range* can be edited manually. The text control box
681recognises the operators +, -, \*, /, or 'pow', and allows the following
682types of expression :
[5005ae0]683
[6af2785]684  1) if an axis label range is a function of 1 or more *columns*, write
685     this type of expression
[ec392464]686
[6af2785]687     constant1 * column_name1 [minimum row index :  maximum  row index]
688     operator constant2 * column_name2 [minimum row index :  maximum  row index]
[ec392464]689
[6af2785]690     Example: radius [2 : 5] -3 * scale [2 : 5]
[ec392464]691
[6af2785]692  2) if only some *values* of a given column are needed but the range between
693     the first row and the last row used is not continuous, write this type of
694     expression
[ec392464]695
[6af2785]696     column_name1 [minimum row index1 :  maximum  row index1] , column_name1
697     [minimum row index2 :  maximum  row index2]
[ec392464]698
[6af2785]699     Example: radius [2 : 5] , radius [10 : 25]
[5005ae0]700
[9d93c37]701.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
702
703Combined Batch Fit Mode
704-----------------------
705
[e6c74e8]706The purpose of the Combined Batch Fit is to allow running two or more batch
707fits in sequence without overwriting the output table of results.  This may be
708of interest for example if one is fitting a series of data sets where there is
709a shape change occurring in the series that requires changing the model part
710way through the series; for example a sphere to rod transition.  Indeed the
711regular batch mode does not allow for multiple models and requires all the
712files in the series to be fit with single model and set of parameters.  While
713it is of course possible to just run part of the series as a batch fit using
714model one followed by running another batch fit on the rest of the series with
715model two (and/or model three etc), doing so will overwrite the table of
716outputs from the previous batch fit(s).  This may not be desirable if one is
717interested in comparing the parameters: for example the sphere radius of set
[05b0bf6]718one and the cylinder radius of set two.
[e6c74e8]719
720Method
721^^^^^^
[9d93c37]722
[e6c74e8]723In order to use the *Combined Batch Fit*, first load all the data needed as
724described in :ref:`Loading_data`. Next start up two or more *BatchPage* fits
725following the instructions in :ref:`Batch_Fit_Mode` but **DO NOT PRESS FIT**.
726At this point the *Combine Batch Fit* menu item under the *Fitting menu* should
727be active (if there is one or no *BatchPage* the menu item will be greyed out
728and inactive).  Clicking on *Combine Batch Fit* will bring up a new panel,
729similar to the *Const & Simult Fit* panel. In this case there will be a
730checkbox for each *BatchPage* instead of each *FitPage* that should be included
731in the fit.  Once all are selected, click the Fit button on
732the *BatchPage* to run each batch fit in *sequence*
[9d93c37]733
734.. image:: combine_batch_page.png
735
[e6c74e8]736The batch table will then pop up at the end as for the case of the simple Batch
737Fitting with the following caveats:
[9d93c37]738
739.. note::
740   The order matters.  The parameters in the table will be taken from the model
[e6c74e8]741   used in the first *BatchPage* of the list.  Any parameters from the
742   second and later *BatchPage* s that have the same name as a parameter in the
743   first will show up allowing for plotting of that parameter across the
744   models. The other parameters will not be available in the grid.
[9d93c37]745.. note::
746   a corralary of the above is that currently models created as a sum|multiply
747   model will not work as desired because the generated model parameters have a
748   p#_ appended to the beginning and thus radius and p1_radius will not be
749   recognized as the same parameter.
[5005ae0]750
[9d93c37]751.. image:: combine_batch_grid.png
752
[e6c74e8]753In the example shown above the data is a time series with a shifting peak.
754The first part of the series was fitted using the *broad_peak* model, while
755the rest of the data were fit using the *gaussian_peak* model. Unfortunately the
756time is not listed in the file but the file name contains the information. As
757described in :ref:`Grid_Window`, a column can be added manually, in this case
[5005ae0]758called time, and the peak position plotted against time.
[9d93c37]759
760.. image:: combine_batch_plot.png
761
[05b0bf6]762Note the discontinuity in the peak position.  This reflects the fact that the
763Gaussian fit is a rather poor model for the data and is not actually
[e6c74e8]764finding the peak.
[ec392464]765
766.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
[6af2785]767
[e6c74e8]768.. note::  This help document was last changed by Paul Butler, 10 September
769   2017
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