-                      ra6f3613
+                      rf3377b8
 each data set.
+Instructions on how to load and activate data are in the User Documentation
+section :ref:`Loading_data`.
+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!)
+*  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!)
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
 …
 *  *Shapes* - models describing 'objects' (spheres, cylinders, etc)
+*  *Shape-Independent* - models describing structure in terms of density
+correlation functions, fractals, peaks, power laws, etc
+*  *Shape-Independent* - models describing structure in terms of density correlation functions, fractals, peaks, power laws, etc
 *  *Customized Models* - SasView-created (non-library) Python models
 *  *Uncategorised* - other models (for reflectivity, etc)
 …
 Use the *Category* drop-down menu to chose a category of model, then select
+a model from the drop-down menu beneath. You can decide your own model
+categorizations using the :ref:`Category_Manager`.
+a model from the drop-down menu beneath. 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
 …
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+.. _Category_Manager:
+Category Manager
+----------------
+To change the model categorizations, either choose *Category Manager* from the
+*View* option on the menubar, or click on the *Modify* button on the *Fit Page*.
+.. image:: cat_fig0.bmp
+The categorization of all models except the customized 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.bmp
+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.bmp
+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.*
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
 Model Functions
 ---------------
 For a complete list of all the models available in SasView, see the section
+For a complete list of all the library models available in SasView, see the section
 :ref:`SasView_model_functions`.
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+.. _Category_Manager:
+Category Manager
+----------------
+To change the model categorizations, click on the *Modify* button on the *Fit Page*.
+Our SAS models are, by default, classified into 5 categories; shapes,
+shape-independent, structure factor, and customized models, where these
+categories (except the customized models) can be reassigned, added, and
+removed using 'Category Manager'. Each models can also be enabled(shown)/
+disabled(hidden) from the category that they belong. The Category Manager
+panel is accessible from the model category 'Modify' button in the fitting
+panel or the 'View/Category Manager' menu in the menu bar (Fig. 1).
+) Enable/Disable models: Check/uncheck the check boxes to enable/disable the
+models (Fig. 2).
+) Change category: Highlight a model in the list by left-clicking and click
+the 'Modify' button. In the 'Change Category' panel, one can create/use a
+category for the model, then click the 'Add' button. In order to delete a
+category, select a category name and click the 'Remove Selected' button
+(Fig. 3).
+) To apply the changes made, hit the OK button. Otherwise, click the 'Cancel'
+button (Fig. 2).
+.. image:: cat_fig0.bmp
+Fig.1
+.. image:: cat_fig1.bmp
+Fig.2
+.. image:: cat_fig2.bmp
+Fig.3
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+Change Model Parameters
+^^^^^^^^^^^^^^^^^^^^^^^
+To visualize model in a different window, from menu click on *Model*. Select
+a type of model and then the name of your model.A new window will appear with
+the plot of your model with default values. Change model's parameters on
+*model view*  tab and view the plotted model with its new parameters.
+Write your Own Model
+^^^^^^^^^^^^^^^^^^^^
+The custom model editors are provided from 'Fitting' menu in the menu bar.
+See 'Custom model editor' in the side menu on left. Advanced users can write
+your own model and save it (in .py format) into *plugin_models*  directory in
+.sasview of your home directory (eg., username\.sasview>\plugin_models). Your
+plugin model will be added into "<>Customized Models" on the next model
+selection.
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+It is also possible to add your own models.
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+Adding your own models
+----------------------
+There are currently two ways to add your own models to SasView:
+* using the :ref:`Custom_Model_Editor`
+* by :ref:`Writing_a_Plugin`
+*NB: Because of the way these options are implemented, it is not possible for them*
+*to use the polydispersity algorithms in SasView. Only models in the model library*
+*can do this. At the time of writing (Release 3.1.0) work is in hand to make it*
+*easier to add new models to the model library.*
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+.. _Custom_Model_Editor:
 Custom Model Editor
 -------------------
+Description
+^^^^^^^^^^^
+This menu (Fitting/Edit Custom Model in the menu bar) interface is to provide
+you an easy way to write your own custom models. The changes in a model
+function are effective after it is re-selected from the combo-box menu.
+From the *Fitting* option in the menu bar, select *Edit Custom Model*.
 .. image:: edit_model_menu.bmp
+and then one of the options
+*  *New* - to create a new custom model template
+*  *Sum|Multi(p1,p2)* - to create a new model by summing/multiplying existing models in the model library
+*  *Advanced* - to edit a new custom model
+*  *Delete* - to delete a custom model
 New
+---
+This option is used to make a new model. A model code generated by this option
+can be viewed and further modified by the 'Advanced' option below.
+^^^^
 .. image:: new_model.bmp
+A model template generated by this option can be viewed and further modified using
+the :ref:`Advanced` option.
 Sum|Multi(p1,p2)
 ^^^^^^^^^^^^^^^^
-This option create a new sum (or multiplication) model. Fill up the (sum
-model function) name and the description. The description will show up on
-details button in the application. Then select the p1 or p2 model for the
-sum/multi model, select an operator as necessary and click the Apply button
-for activation. Hit the 'Close' button when it's done.
 .. image:: sum_model.bmp
+This option creates a custom model of the form
+Custom Model = scale_factor * (model1 +/* model2)
+In the *Easy Sum/Multi Editor* give the new custom model a function name and brief
+description (to appear under the *Details* button on the *Fit Page*). Then select
+two existing models, as p1 and p2, and the required operator, '+' or '*' between
+them. Finally, click the *Apply* button to generate the model and then click *Close*.
+*NB: Any changes to a custom model generated in this way only become effective after*
+*it is re-selected from the model drop-down menu on the Fit Page.*
+.. _Advanced:
 Advanced
 ^^^^^^^^
+The menu option shows all the files in the plugin_models folder. You can edit,
+modify, and save it. It is recommended to modify only the lines with arrow
+(-------). In the end of edit, 'Compile' and 'Run' from the menu bar to
+activate or to see the model working properly.
+Selecting this option shows all the custom models in the plugin model folder
+C:\Users\[username]\.sasview\plugin_models - (on Windows)
+You can edit, modify, and save the Python code in any of these models using the
+*Advanced Custom Model Editor*.
+*NB: Unless you are confident about what you are doing, it is recommended that you*
+*only modify lines denoted with the ## <----- comments!*
+When editing is complete, select *Run -> Compile* from the *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 *Customized Models*
+category and then select the model from the drop-down menu.
+*NB: Any changes to a custom model generated in this way only become effective after*
+*it is re-selected from the model drop-down menu on the Fit Page.*
 Delete
 ^^^^^^
+The menu option is to delete the custom models. Just select the file name to
+delete.
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+Key Combinations
+Simply highlight the custom model to be removed. This operation is final!
+*NB: Custom models shipped with SasView cannot be removed in this way.*
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+.. _Writing_a_Plugin:
+Writing a Plugin
 ----------------
+Copy & Paste
+^^^^^^^^^^^^
+To copy the parameter values in a Fit(Model) panel to the clipboard:
+*Ctrl(Cmd on MAC) + Left(Mouse)Click*  on the panel.
+To paste the parameter values to a Fit(Model)panel from the clipboard:
+*Ctrl(Cmd on MAC) + Shift + Left(Mouse)Click*  on the panel.
+If this operation is successful, it will say so in the info line at the
+Advanced users can write their own model in Python and save it to the the SasView
+*plugin_models* folder
+C:\Users\[username]\.sasview\plugin_models - (on Windows)
+in .py format. The next time SasView is started it will compile the plugin and add
+it to the list of *Customized Models*.
+It is recommended that existing plugin models be used as templates.
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+Fitting Options
+---------------
+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 Options*, then select one of the following
+optimisers:
+*  DREAM
+*  Levenberg-Marquardt
+*  Quasi-Newton BFGS
+*  Differential Evolution
+*  Nelder-Mead Simplex
+These optimisers form the *Bumps* package written by P Kienzle. For more information
+on each optimiser, see *Information on the SasView Optimisers* in the documentation
+for the :ref:`Fitting Perspective`.
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+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 of a fit-panel or model-panel status:
+*(Mouse)Right-Click*  and select the bookmark in the popup list.
+Graph Context Menu
+^^^^^^^^^^^^^^^^^^
+To get the graph context menu to print, copy, save data, (2D)average, etc.:
+*Locate the mouse point on the plot to highlight and *(Mouse) Right Click*
+to bring up the full menu.
+FTolerance (SciPy)
+^^^^^^^^^^^^^^^^^^
+To change the ftol value of the Scipy FitEngine (leastsq):
+First, make sure that the Fit panel has data and a model selected.
+*Ctrl(Cmd on MAC) + Shift + Alt + Right(Mouse)Click*  on the panel.
+Then, set up the value in the dialog panel.
+If this operation is successful, the new ftol value will be displayed in the
+info line at the bottom of the SV window.Note that increasing the ftol value
+may cause for the fitting to terminate with higher |chi| sq.
+To *Bookmark* a *Fit Page* or model-panel status, 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.
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
 …
 an empty batch page exists, it will be set there. Otherwise it will create a
 new Batch Page. Set up the model and the parameter values as same as a single
 fitting (see Single Fit help) <Single_Fit_>. Then use 'Fit' button to
+fitting (see Single Fit help). Then use 'Fit' button to
 perform the fitting.

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SasView

Changeset f3377b8 in sasview for src/sas/perspectives

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src/sas/perspectives/fitting/media/fitting_help.rst

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