-                      ra0637de
+                      ra6f3613
 ===================
+Preparing_to_fit_data_
+Single_Fit_
+Simultaneous_Fitting_
+Batch_Fitting_
+Model_Selection_
+Model_Category_Manager_
+Model_Functions_
+Custom_Model_Editor_
+Key_Combinations_
+Status_Bar_Help_
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+.. _Preparing_to_fit_data:
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
 Preparing to fit data
 …
 To fit some data you must first load some data, activate one or more data sets,
+then send those data sets to the fitting perspective.
+Instructions on how to do this are in the User Documentation section *Loading*
+*Data*.
+send those data sets to the fitting perspective, and select a model to fit to
+each data set.
+Instructions on how to load and activate data are in the User Documentation
+section :ref:`Loading_data`.
 SasView can fit data in one of three ways:
+*  in *Single* fit mode
+*  in *Simultaneous* fit mode
+*  in *Batch* fit mode
+These modes of operation are described below.
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+.. _Single_Fit:
+Single Fit
+----------
+*  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!)
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+Selecting a model
+-----------------
+By default, the models in SasView are grouped into five categories
+*  *Shapes* - models describing 'objects' (spheres, cylinders, 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)
+*  *Structure Factor* - S(Q) models
+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`.
+Once you have selected a model you can read its help documentation by clicking
+on the *Description* button to the right.
+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*).
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+Model Functions
+---------------
+For a complete list of all the 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
+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.
+.. image:: edit_model_menu.bmp
+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
+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
+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.
+Delete
+^^^^^^
+The menu option is to delete the custom models. Just select the file name to
+delete.
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+Key Combinations
+----------------
+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
+bottom of the SasView window.
+Bookmark
+^^^^^^^^
+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.
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+Single Fit Mode
+---------------
 One of two fit-engines can be chosen from the Fitting menu bar. The Simple Fit-
 …
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+..  _Simultaneous_Fitting:
+Simultaneous Fitting
+--------------------
+Simultaneous Fit Mode
+---------------------
 This fitting option enables to set a number of the constraints between the
 …
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+..  _Batch_Fitting:
+Batch Fitting
+-------------
+Batch_Fit_
+Batch_Window_
+Edit_Grid_
+Save_Grid_
+Open_Batch_Results_
+Plot_
+View_Column_Cell_
+.. _Batch_Fit:
+Batch Fit Mode
+--------------
 Batch Fit
+---------
+^^^^^^^^^
 Create a *Batch Page* by selecting the *Batch* radio button on the DataExplorer
 …
 lots of, and similar, data sets.
-.. _Batch_Window:
 Batch Window
+------------
+^^^^^^^^^^^^
 Batch Window provides an easy way to view the fit results, i.e., plot data,
 fits, and residuals. Batch window will be automatically shown after a batch
 …
 Figure 2: Edit Menu:
-.. _Edit_Grid:
 Edit Grid
+---------
+^^^^^^^^^
 Once a batch fit is completed, all fitted and fixed model parameters are
 …
 Figure 3: Edit Menu:
-.. _Save_Grid:
 Save Grid
+---------
+^^^^^^^^^
 To save the current page on the batch window, select the *'File'*  menubar
 item(see Figure 4), then choose the *'Save as'*  menu item to save it as a
 …
 the current grid before modifying it .
+.. _Open_Batch_Results:
+Open Batch Results
+------------------
+Open Batch Results
+^^^^^^^^^^^^^^^^^^
 Any *csv*  file can be opened in the grid by selecting the *'Open'*  under
 …
 Figure 4: MenuBar:
-.. _Plot:
 Plot
+----
+^^^^
 To *plot*  a column versus another, select one column at the time, click the
 …
 Figure 5: Plotting
-.. _View_Column_Cell:
 View Column/Cell(s)
+-------------------
+^^^^^^^^^^^^^^^^^^^
 Select 1 or more cells from the same column, click the 'View Fits' button to
 …
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-..  _Model_Selection:
-Model_Type_
-Change_Model_Parameters_
-Write_your_Own_Model_
-.. _Model_Type:
-Model Type
-----------
-Models are grouped into three classes
-*  *Shapes*
-*  *Shape-Independent*
-*  *Uncategorised*
-*  *Customized Models*
-*  *Structure Factor*
-.. _Change_Model_Parameters:
-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:
-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
-..  _Model_Category_Manager:
-Model Category Manager
-----------------------
-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
-..  _Model_Functions:
-Model Functions
----------------
-See *Model Documentation*.
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-..  _Custom_Model_Editor:
-Custom Model Editor
--------------------
-Description_
-New_
-Sum_Multi_p1_p2_
-Advanced_
-Delete_
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-.. _Description:
-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.
-.. image:: edit_model_menu.bmp
-.. _New:
-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
-.. _Sum_Multi_p1_p2:
-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
-.. _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.
-.. _Delete:
-Delete
-------
-The menu option is to delete the custom models. Just select the file name to
-delete.
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-.. _Key_Combinations:
-Key Combinations
-----------------
-Copy_Paste_
-Bookmark_
-Graph_Context_Menu_
-FTolerance_
-.. _Copy_Paste:
-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
-bottom of the SasView window.
-.. _Bookmark:
-Bookmark
---------
-Bookmark of a fit-panel or model-panel status:
-*(Mouse)Right-Click*  and select the bookmark in the popup list.
-.. _Graph_Context_Menu:
-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:
-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.
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-.. _Status_Bar_Help:
 Status Bar Help
+---------------
+Message_Warning_Hint_
+Console_
+.. _Message_Warning_Hint:
+^^^^^^^^^^^^^^^
 Message/Warning/Hint
+--------------------
+^^^^^^^^^^^^^^^^^^^^
 The status bar located at the bottom of the application frame, displays
 messages, hints, warnings and errors.
-.. _Console:
 Console
+-------
+^^^^^^^
 Select *light bulb/info icon*  button in the status bar at the bottom of the

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Changeset a6f3613 in sasview for src/sas/perspectives/fitting

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

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