[ec392464] | 1 | .. fitting_help.rst |
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| 2 | |
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| 3 | .. This is a port of the original SasView html help file to ReSTructured text |
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| 4 | .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. |
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| 5 | |
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[98b30b4] | 6 | .. |inlineimage004| image:: sm_image004.gif |
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| 7 | .. |inlineimage005| image:: sm_image005.gif |
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| 8 | .. |inlineimage008| image:: sm_image008.gif |
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| 9 | .. |inlineimage009| image:: sm_image009.gif |
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| 10 | .. |inlineimage010| image:: sm_image010.gif |
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| 11 | .. |inlineimage011| image:: sm_image011.gif |
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| 12 | .. |inlineimage012| image:: sm_image012.gif |
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| 13 | .. |inlineimage018| image:: sm_image018.gif |
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| 14 | .. |inlineimage019| image:: sm_image019.gif |
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| 15 | |
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[ec392464] | 16 | |
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[1f1e4f0] | 17 | Fitting |
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| 18 | ======= |
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[ec392464] | 19 | |
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[a6f3613] | 20 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 21 | |
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| 22 | Preparing to fit data |
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| 23 | --------------------- |
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| 24 | |
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| 25 | To fit some data you must first load some data, activate one or more data sets, |
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[1f1e4f0] | 26 | send those data sets to fitting, and select a model to fit to each data set. |
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[a6f3613] | 27 | |
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[f3377b8] | 28 | Instructions on how to load and activate data are in the section :ref:`Loading_data`. |
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[ec392464] | 29 | |
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[a6f3613] | 30 | SasView can fit data in one of three ways: |
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[ec392464] | 31 | |
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[a6f3613] | 32 | * in *Single* fit mode - individual data sets are fitted independently one-by-one |
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[ec392464] | 33 | |
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[f3377b8] | 34 | * 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) |
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[ec392464] | 35 | |
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[f3377b8] | 36 | * 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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[a6f3613] | 37 | |
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| 38 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[ec392464] | 39 | |
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[a6f3613] | 40 | Selecting a model |
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| 41 | ----------------- |
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[ec392464] | 42 | |
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[a6f3613] | 43 | By default, the models in SasView are grouped into five categories |
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[ec392464] | 44 | |
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[a6f3613] | 45 | * *Shapes* - models describing 'objects' (spheres, cylinders, etc) |
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[f3377b8] | 46 | * *Shape-Independent* - models describing structure in terms of density correlation functions, fractals, peaks, power laws, etc |
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[8570246] | 47 | * *Customized Models* - SasView- or User-created (non-library) Python models |
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[a6f3613] | 48 | * *Uncategorised* - other models (for reflectivity, etc) |
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| 49 | * *Structure Factor* - S(Q) models |
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[ec392464] | 50 | |
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[a6f3613] | 51 | Use the *Category* drop-down menu to chose a category of model, then select |
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[f3377b8] | 52 | a model from the drop-down menu beneath. A graph of the chosen model, calculated |
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| 53 | using default parameter values, will appear. The graph will update dynamically |
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| 54 | as the parameter values are changed. |
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| 55 | |
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| 56 | You can decide your own model categorizations using the :ref:`Category_Manager`. |
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[ce62e75] | 57 | |
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[a6f3613] | 58 | Once you have selected a model you can read its help documentation by clicking |
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| 59 | on the *Description* button to the right. |
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| 60 | |
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| 61 | Show 1D/2D |
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| 62 | ^^^^^^^^^^ |
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| 63 | |
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| 64 | Models are normally fitted to 1D (ie, I(Q) vs Q) data sets, but some models in |
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| 65 | SasView can also be fitted to 2D (ie, I(Qx,Qy) vs Qx vs Qy) data sets. |
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| 66 | |
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| 67 | *NB: Magnetic scattering can only be fitted in SasView in 2D.* |
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| 68 | |
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| 69 | To activate 2D fitting mode, click the *Show 2D* button on the *Fit Page*. To |
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| 70 | return to 1D fitting model, click the same button (which will now say *Show 1D*). |
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[ce62e75] | 71 | |
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[ec392464] | 72 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 73 | |
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[a6f3613] | 74 | .. _Category_Manager: |
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[a0637de] | 75 | |
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[a6f3613] | 76 | Category Manager |
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| 77 | ---------------- |
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| 78 | |
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[f3377b8] | 79 | To change the model categorizations, either choose *Category Manager* from the |
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| 80 | *View* option on the menubar, or click on the *Modify* button on the *Fit Page*. |
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[a6f3613] | 81 | |
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[f3377b8] | 82 | .. image:: cat_fig0.bmp |
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[a6f3613] | 83 | |
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[f3377b8] | 84 | The categorization of all models except the customized models can be reassigned, |
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| 85 | added to, and removed using *Category Manager*. Models can also be hidden from view |
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| 86 | in the drop-down menus. |
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[a6f3613] | 87 | |
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[f3377b8] | 88 | .. image:: cat_fig1.bmp |
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[a6f3613] | 89 | |
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[f3377b8] | 90 | Changing category |
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| 91 | ^^^^^^^^^^^^^^^^^ |
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[a6f3613] | 92 | |
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[f3377b8] | 93 | To change category, highlight a model in the list by left-clicking on its entry and |
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| 94 | then click the *Modify* button. Use the *Change Category* panel that appears to make |
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| 95 | the required changes. |
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[a6f3613] | 96 | |
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[f3377b8] | 97 | .. image:: cat_fig2.bmp |
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[a6f3613] | 98 | |
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[f3377b8] | 99 | To create a category for the selected model, click the *Add* button. In order |
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| 100 | to delete a category, select the category name and click the *Remove Selected* |
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| 101 | button. Then click *Done*. |
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[a6f3613] | 102 | |
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[f3377b8] | 103 | Showing/hiding models |
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| 104 | ^^^^^^^^^^^^^^^^^^^^^ |
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[a6f3613] | 105 | |
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[8570246] | 106 | Use the *Enable All / Disable All* buttons and the check boxes beside each model to |
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[f3377b8] | 107 | select the models to show/hide. To apply the selection, click *Ok*. Otherwise click |
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| 108 | *Cancel*. |
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[a6f3613] | 109 | |
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[8570246] | 110 | *NB: It may be necessary to change to a different category and then back again* |
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[f3377b8] | 111 | *before any changes take effect.* |
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[a6f3613] | 112 | |
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| 113 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 114 | |
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[f3377b8] | 115 | Model Functions |
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| 116 | --------------- |
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[a6f3613] | 117 | |
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[20846be] | 118 | For a complete list of all the library models available in SasView, see the Model Documentation. |
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[a6f3613] | 119 | |
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[f3377b8] | 120 | It is also possible to add your own models. |
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[a6f3613] | 121 | |
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[f3377b8] | 122 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[a6f3613] | 123 | |
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[b5846a10] | 124 | .. _Adding_your_own_models: |
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| 125 | |
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[f3377b8] | 126 | Adding your own models |
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| 127 | ---------------------- |
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[a6f3613] | 128 | |
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[f3377b8] | 129 | There are currently two ways to add your own models to SasView: |
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| 130 | |
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[8570246] | 131 | * Using the :ref:`Custom_Model_Editor` |
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| 132 | * By :ref:`Writing_a_Plugin` |
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[f3377b8] | 133 | |
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| 134 | *NB: Because of the way these options are implemented, it is not possible for them* |
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| 135 | *to use the polydispersity algorithms in SasView. Only models in the model library* |
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| 136 | *can do this. At the time of writing (Release 3.1.0) work is in hand to make it* |
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| 137 | *easier to add new models to the model library.* |
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[a6f3613] | 138 | |
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| 139 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 140 | |
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[f3377b8] | 141 | .. _Custom_Model_Editor: |
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| 142 | |
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[a6f3613] | 143 | Custom Model Editor |
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| 144 | ------------------- |
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| 145 | |
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[f3377b8] | 146 | From the *Fitting* option in the menu bar, select *Edit Custom Model*. |
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[a6f3613] | 147 | |
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| 148 | .. image:: edit_model_menu.bmp |
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| 149 | |
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[f3377b8] | 150 | and then one of the options |
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| 151 | |
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| 152 | * *New* - to create a new custom model template |
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| 153 | * *Sum|Multi(p1,p2)* - to create a new model by summing/multiplying existing models in the model library |
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| 154 | * *Advanced* - to edit a new custom model |
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| 155 | * *Delete* - to delete a custom model |
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[a6f3613] | 156 | |
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[f3377b8] | 157 | New |
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| 158 | ^^^^ |
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[a6f3613] | 159 | |
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| 160 | .. image:: new_model.bmp |
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| 161 | |
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[f3377b8] | 162 | A model template generated by this option can be viewed and further modified using |
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| 163 | the :ref:`Advanced` option. |
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| 164 | |
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[a6f3613] | 165 | Sum|Multi(p1,p2) |
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| 166 | ^^^^^^^^^^^^^^^^ |
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| 167 | |
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| 168 | .. image:: sum_model.bmp |
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[a0637de] | 169 | |
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[f3377b8] | 170 | This option creates a custom model of the form |
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| 171 | |
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[8570246] | 172 | Custom Model = scale_factor \* (model1 +/\* model2) |
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[f3377b8] | 173 | |
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| 174 | In the *Easy Sum/Multi Editor* give the new custom model a function name and brief |
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| 175 | description (to appear under the *Details* button on the *Fit Page*). Then select |
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| 176 | two existing models, as p1 and p2, and the required operator, '+' or '*' between |
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| 177 | them. Finally, click the *Apply* button to generate the model and then click *Close*. |
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| 178 | |
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| 179 | *NB: Any changes to a custom model generated in this way only become effective after* |
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| 180 | *it is re-selected from the model drop-down menu on the Fit Page.* |
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| 181 | |
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| 182 | .. _Advanced: |
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| 183 | |
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[a6f3613] | 184 | Advanced |
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| 185 | ^^^^^^^^ |
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[ec392464] | 186 | |
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[f3377b8] | 187 | Selecting this option shows all the custom models in the plugin model folder |
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| 188 | |
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[8570246] | 189 | *C:\\Users\\[username]\\.sasview\\plugin_models* - (on Windows) |
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[f3377b8] | 190 | |
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| 191 | You can edit, modify, and save the Python code in any of these models using the |
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| 192 | *Advanced Custom Model Editor*. |
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| 193 | |
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| 194 | *NB: Unless you are confident about what you are doing, it is recommended that you* |
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| 195 | *only modify lines denoted with the ## <----- comments!* |
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| 196 | |
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| 197 | When editing is complete, select *Run -> Compile* from the *Model Editor* menu bar. An |
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| 198 | *Info* box will appear with the results of the compilation and model unit tests. The |
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| 199 | model will only be usable if the tests 'pass'. |
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| 200 | |
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| 201 | To use the model, go to the relevant *Fit Page*, select the *Customized Models* |
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| 202 | category and then select the model from the drop-down menu. |
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| 203 | |
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| 204 | *NB: Any changes to a custom model generated in this way only become effective after* |
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| 205 | *it is re-selected from the model drop-down menu on the Fit Page.* |
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[a6f3613] | 206 | |
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| 207 | Delete |
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| 208 | ^^^^^^ |
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| 209 | |
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[f3377b8] | 210 | Simply highlight the custom model to be removed. This operation is final! |
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| 211 | |
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| 212 | *NB: Custom models shipped with SasView cannot be removed in this way.* |
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[ec392464] | 213 | |
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| 214 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 215 | |
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[f3377b8] | 216 | .. _Writing_a_Plugin: |
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| 217 | |
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| 218 | Writing a Plugin |
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[a6f3613] | 219 | ---------------- |
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| 220 | |
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[f3377b8] | 221 | Advanced users can write their own model in Python and save it to the the SasView |
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| 222 | *plugin_models* folder |
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[a6f3613] | 223 | |
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[8570246] | 224 | *C:\\Users\\[username]\\.sasview\\plugin_models* - (on Windows) |
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[a6f3613] | 225 | |
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[f3377b8] | 226 | in .py format. The next time SasView is started it will compile the plugin and add |
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| 227 | it to the list of *Customized Models*. |
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[a6f3613] | 228 | |
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[f3377b8] | 229 | It is recommended that existing plugin models be used as templates. |
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[a6f3613] | 230 | |
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[f3377b8] | 231 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[ec392464] | 232 | |
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[4666660] | 233 | .. _Fitting_Options: |
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| 234 | |
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[f3377b8] | 235 | Fitting Options |
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| 236 | --------------- |
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[a6f3613] | 237 | |
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[f3377b8] | 238 | It is possible to specify which optimiser SasView should use to fit the data, and |
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| 239 | to modify some of the configurational parameters for each optimiser. |
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| 240 | |
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| 241 | From *Fitting* in the menu bar select *Fit Options*, then select one of the following |
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| 242 | optimisers: |
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[a6f3613] | 243 | |
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[f3377b8] | 244 | * DREAM |
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| 245 | * Levenberg-Marquardt |
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| 246 | * Quasi-Newton BFGS |
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| 247 | * Differential Evolution |
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| 248 | * Nelder-Mead Simplex |
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[a6f3613] | 249 | |
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[6af2785] | 250 | The DREAM optimiser is the most sophisticated, but may not necessarily be the best |
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| 251 | option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser |
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| 252 | initially. |
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| 253 | |
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[f3377b8] | 254 | These optimisers form the *Bumps* package written by P Kienzle. For more information |
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[4666660] | 255 | on each optimiser, see the :ref:`Fitting_Documentation`. |
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[a6f3613] | 256 | |
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[f3377b8] | 257 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[a6f3613] | 258 | |
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[5ac0a7a] | 259 | Fitting Limits |
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| 260 | -------------- |
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| 261 | |
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| 262 | By default, *SasView* will attempt to model fit the full range of the data; ie, |
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| 263 | across all *Q* values. If necessary, however, it is possible to specify only a |
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| 264 | sub-region of the data for fitting. |
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| 265 | |
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| 266 | In a *FitPage* or *BatchPage* change the *Q* values in the *Min* and/or *Max* |
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| 267 | text boxes. Vertical coloured bars will appear on the graph with the data and |
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| 268 | 'theory' indicating the current *Q* limits (red = *Qmin*, purple = *Qmax*). |
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| 269 | |
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| 270 | To return to including all data in the fit, click the *Reset* button. |
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| 271 | |
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| 272 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 273 | |
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| 274 | |
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[f3377b8] | 275 | Shortcuts |
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| 276 | --------- |
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[a6f3613] | 277 | |
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[f3377b8] | 278 | Copy/Paste Parameters |
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| 279 | ^^^^^^^^^^^^^^^^^^^^^ |
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[a6f3613] | 280 | |
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[f3377b8] | 281 | It is possible to copy the parameters from one *Fit Page* and to paste them into |
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| 282 | another *Fit Page* using the same model. |
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[a6f3613] | 283 | |
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[f3377b8] | 284 | To *copy* parameters, either: |
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[a6f3613] | 285 | |
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[f3377b8] | 286 | * Select *Edit -> Copy Params* from the menu bar, or |
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| 287 | * Use Ctrl(Cmd on Mac) + Left Mouse Click on the *Fit Page*. |
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[a6f3613] | 288 | |
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[f3377b8] | 289 | To *paste* parameters, either: |
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| 290 | |
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| 291 | * Select *Edit -> Paste Params* from the menu bar, or |
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| 292 | * Use Ctrl(Cmd on Mac) + Shift + Left-click on the *Fit Page*. |
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| 293 | |
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| 294 | If either operation is successful a message will appear in the info line at the |
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| 295 | bottom of the SasView window. |
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| 296 | |
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| 297 | Bookmark |
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| 298 | ^^^^^^^^ |
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[a6f3613] | 299 | |
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[1fda506] | 300 | To *Bookmark* a *Fit Page* either: |
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[a6f3613] | 301 | |
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[f3377b8] | 302 | * Select a *Fit Page* and then click on *Bookmark* in the tool bar, or |
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| 303 | * Right-click and select the *Bookmark* in the popup menu. |
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[a6f3613] | 304 | |
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| 305 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 306 | |
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[4666660] | 307 | .. _Status_bar: |
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| 308 | |
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[1fda506] | 309 | Status Bar & Console |
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| 310 | -------------------- |
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| 311 | |
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| 312 | The status bar is located at the bottom of the SasView window and displays |
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| 313 | messages, hints, warnings and errors. |
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| 314 | |
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| 315 | At the right-hand side of the status bar is a button marked *Console*. The *Console* |
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| 316 | displays available message history and some run-time traceback information. |
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| 317 | |
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| 318 | During a long task the *Console* can also be used to monitor the progress. |
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| 319 | |
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| 320 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 321 | |
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[6af2785] | 322 | .. _Single_Fit_Mode: |
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| 323 | |
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[a6f3613] | 324 | Single Fit Mode |
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| 325 | --------------- |
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[ec392464] | 326 | |
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[4666660] | 327 | *NB: Before proceeding, ensure that the Single Mode radio button at the bottom of* |
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| 328 | *the Data Explorer is checked (see the section* :ref:`Loading_data` *).* |
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| 329 | |
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[63d314b] | 330 | This mode fits one data set. |
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| 331 | |
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[1f1e4f0] | 332 | When data is sent to the fitting it is plotted in a graph window as markers. |
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[4666660] | 333 | |
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| 334 | If a graph does not appear, or a graph window appears but is empty, then the data |
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| 335 | has not loaded correctly. Check to see if there is a message in the :ref:`Status_Bar` |
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| 336 | or in the *Console* window. |
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| 337 | |
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| 338 | Assuming the data has loaded correctly, when a model is selected a green model |
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| 339 | calculation (or what SasView calls a 'Theory') line will appear in the earlier graph |
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| 340 | window, and a second graph window will appear displaying the residuals (the |
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| 341 | difference between the experimental data and the theory) at the same X-data values. |
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[f9250dc] | 342 | See :ref:`Assessing_Fit_Quality`. |
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[4666660] | 343 | |
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| 344 | The objective of model-fitting is to find a *physically-plausible* model, and set |
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| 345 | of model parameters, that generate a theory that reproduces the experimental data |
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| 346 | and gives residual values as close to zero as possible. |
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| 347 | |
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| 348 | Change the default values of the model parameters by hand until the theory line |
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| 349 | starts to represent the experimental data. Then uncheck the tick boxes alongside |
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| 350 | all parameters *except* the 'background' and the 'scale'. Click the *Fit* button. |
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| 351 | SasView will optimise the values of the 'background' and 'scale' and also display |
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| 352 | the corresponding uncertainties on the optimised values. |
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| 353 | |
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| 354 | *NB: If no uncertainty is shown it generally means that the model is not very* |
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| 355 | *dependent on the corresponding parameter (or that one or more parameters are* |
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| 356 | *'correlated').* |
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| 357 | |
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| 358 | In the bottom left corner of the *Fit Page* is a box displaying the normalised value |
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| 359 | of the statistical |chi|\ :sup:`2` parameter returned by the optimiser. |
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| 360 | |
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| 361 | Now check the box for another model parameter and click *Fit* again. Repeat this |
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| 362 | process until most or all parameters are checked and have been optimised. As the |
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| 363 | fit of the theory to the experimental data improves the value of 'chi2/Npts' will |
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| 364 | decrease. A good model fit should easily produce values of 'chi2/Npts' that are |
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[ff42a26] | 365 | close to zero, and certainly <100. See :ref:`Assessing_Fit_Quality`. |
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[4666660] | 366 | |
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| 367 | SasView has a number of different optimisers (see the section :ref:`Fitting_Options`). |
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| 368 | The DREAM optimiser is the most sophisticated, but may not necessarily be the best |
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| 369 | option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser |
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| 370 | initially. |
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[ec392464] | 371 | |
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| 372 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 373 | |
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[a6f3613] | 374 | Simultaneous Fit Mode |
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| 375 | --------------------- |
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[ec392464] | 376 | |
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[63d314b] | 377 | *NB: Before proceeding, ensure that the Single Mode radio button at the bottom of* |
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| 378 | *the Data Explorer is checked (see the section* :ref:`Loading_data` *).* |
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[ec392464] | 379 | |
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[6af2785] | 380 | This mode is an extension of the :ref:`Single_Fit_Mode` that fits two or more data |
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[63d314b] | 381 | sets *to the same model* simultaneously. If necessary it is possible to constrain |
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| 382 | fit parameters between data sets (eg, to fix a background level, or radius, etc). |
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| 383 | |
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[b5846a10] | 384 | If the data to be fit are in multiple files, load each file, then select each file |
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| 385 | in the *Data Explorer*, and *Send To Fitting*. If multiple data sets are in one file, |
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| 386 | load that file, *Unselect All Data*, select just those data sets to be fitted, and |
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| 387 | *Send To Fitting*. Either way, the result should be that for *n* data sets you have |
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[6af2785] | 388 | 2\ *n* graphs (*n* of the data and model fit, and *n* of the resulting residuals). But |
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[f9250dc] | 389 | it may be helpful to minimise the residuals plots for clarity. Also see |
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| 390 | :ref:`Assessing_Fit_Quality`. |
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[b5846a10] | 391 | |
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| 392 | *NB: If you need to use a customized model, you must ensure that model is available* |
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| 393 | *first (see* :ref:`Adding_your_own_models` *).* |
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| 394 | |
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[6af2785] | 395 | Method |
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| 396 | ^^^^^^ |
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| 397 | |
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[b5846a10] | 398 | Now go to each *FitPage* in turn and: |
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| 399 | |
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| 400 | Select the required category and model; |
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| 401 | |
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| 402 | Unselect all the model parameters; |
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| 403 | |
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| 404 | Enter some starting guesses for the parameters; |
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| 405 | |
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| 406 | Enter any parameter limits (recommended); |
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[63d314b] | 407 | |
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[b5846a10] | 408 | Select which parameters will refine (selecting all is generally a bad idea...); |
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[63d314b] | 409 | |
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[b5846a10] | 410 | When done, select *Constrained or Simultaneous Fit* under *Fitting* in the menu bar. |
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| 411 | |
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| 412 | In the *Const & Simul Fit* page that appears, select which data sets are to be |
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| 413 | simultaneously fitted (this will probably be all of them or you would not have loaded |
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| 414 | them in the first place!). |
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| 415 | |
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| 416 | To tie parameters between the data sets with constraints, check the 'yes' radio button |
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| 417 | next to *Add Constraint?* in the *Fit Constraints* box. |
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| 418 | |
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| 419 | *NB: You can only constrain parameters that are set to refine.* |
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| 420 | |
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| 421 | When ready, click the *Fit* button on the *Const & Simul Fit* page, NOT the *Fit* |
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| 422 | button on the individual *FitPage*'s. |
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[63d314b] | 423 | |
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| 424 | Simultaneous Fits without Constraints |
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| 425 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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[ec392464] | 426 | |
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[b5846a10] | 427 | The results of the model-fitting will be returned to each of the individual |
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| 428 | *FitPage*'s. |
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[ec392464] | 429 | |
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[b5846a10] | 430 | Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To |
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[6af2785] | 431 | see the chi2/Npts value for a specific *FitPage*, click the *Compute* button at the |
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[f9250dc] | 432 | bottom of that *FitPage* to recalculate. Also see :ref:`Assessing_Fit_Quality`. |
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[ec392464] | 433 | |
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[63d314b] | 434 | Simultaneous Fits with Constraints |
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| 435 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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[ec392464] | 436 | |
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[b5846a10] | 437 | Use the *Easy Setup* drop-down buttons in the *Const & Simul Fit* page to set |
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| 438 | up constraints between *FitPage*'s. |
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| 439 | |
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[6af2785] | 440 | Constraints will generally be of the form |
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| 441 | |
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| 442 | Mi Parameter1 = Mj.Parameter1 |
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| 443 | |
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| 444 | however the text box after the '=' sign can be used to adjust this |
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| 445 | relationship; for example |
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| 446 | |
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| 447 | Mi Parameter1 = scalar \* Mj.Parameter1 |
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| 448 | |
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| 449 | A 'free-form' constraint box is also provided. |
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[b5846a10] | 450 | |
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| 451 | Many constraints can be entered for a single fit. |
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| 452 | |
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| 453 | The results of the model-fitting will be returned to each of the individual |
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| 454 | *FitPage*'s. |
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[ec392464] | 455 | |
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[b5846a10] | 456 | Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To |
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[6af2785] | 457 | see the chi2/Npts value for a specific *FitPage*, click the *Compute* button at the |
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[f9250dc] | 458 | bottom of that *FitPage* to recalculate. Also see :ref:`Assessing_Fit_Quality`. |
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[ec392464] | 459 | |
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| 460 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 461 | |
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[a6f3613] | 462 | Batch Fit Mode |
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| 463 | -------------- |
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[ec392464] | 464 | |
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[6af2785] | 465 | *NB: Before proceeding, ensure that the Single Mode radio button at the bottom of* |
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| 466 | *the Data Explorer is checked (see the section* :ref:`Loading_data` *). The Batch* |
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| 467 | *Mode button will be used later on!* |
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[63d314b] | 468 | |
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[6af2785] | 469 | This mode *sequentially* fits two or more data sets *to the same model*. Unlike in |
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| 470 | simultaneous fitting, in batch fitting it is not possible to constrain fit parameters |
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| 471 | between data sets. |
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[ec392464] | 472 | |
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[6af2785] | 473 | If the data to be fit are in multiple files, load each file in the *Data Explorer*. |
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| 474 | If multiple data sets are in one file, load just that file. *Unselect All Data*, then |
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| 475 | select a single initial data set to be fitted. Fit that selected data set as described |
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| 476 | above under :ref:`Single_Fit_Mode` . |
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[ec392464] | 477 | |
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[6af2785] | 478 | *NB: If you need to use a customized model, you must ensure that model is available* |
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| 479 | *first (see* :ref:`Adding_your_own_models` *).* |
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[ec392464] | 480 | |
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[6af2785] | 481 | Method |
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| 482 | ^^^^^^ |
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[ec392464] | 483 | |
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[6af2785] | 484 | Now *Select All Data* in the *Data Explorer*, check the *Batch Mode* radio button |
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| 485 | at the bottom of that panel and *Send To Fitting*. A *BatchPage* will be created. |
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[ec392464] | 486 | |
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[6af2785] | 487 | .. image:: batch_button_area.bmp |
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[ec392464] | 488 | |
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[6af2785] | 489 | *NB: The Batch Page can also be created by checking the Batch Mode radio button* |
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| 490 | *and selecting New Fit Page under Fitting in the menu bar.* |
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[ec392464] | 491 | |
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[6af2785] | 492 | Using the drop-down menus in the *BatchPage*, now set up the *same* data set |
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| 493 | with the *same* model that you just fitted in single fit mode. A quick way to |
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| 494 | set the model parameter values is to just copy them from the earlier Single |
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| 495 | Fit. To do this, go back to the Single Fit *FitPage*, select *Copy Params* |
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| 496 | under *Edit* in the menu bar, then go back to the *BatchPage* and *Paste Params*. |
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[ec392464] | 497 | |
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[6af2785] | 498 | When ready, use the *Fit* button on the *BatchPage* to perform the fitting, NOT |
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| 499 | the *Fit* button on the individual *FitPage*'s. |
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[ec392464] | 500 | |
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[6af2785] | 501 | Unlike in single fit mode, the results of batch fits are not returned to |
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| 502 | the *BatchPage*. Instead, a spreadsheet-like :ref:`Grid_Window` will appear. |
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[ec392464] | 503 | |
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[6af2785] | 504 | If you want to visually check a graph of a particular fit, click on the name of |
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| 505 | a *Data set* in the *Grid Window* and then click the *View Fits* button. The |
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| 506 | data and the model fit will be displayed. If you select mutliple data sets they |
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| 507 | will all appear on one graph. |
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[ec392464] | 508 | |
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[6af2785] | 509 | .. image:: view_button.bmp |
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[ec392464] | 510 | |
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[6af2785] | 511 | *NB: In theory, returning to the BatchPage and changing the name of the I(Q)* |
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| 512 | *data source should also work, but at the moment whilst this does change the* |
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| 513 | *data set displayed it always superimposes the 'theory' corresponding to the* |
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| 514 | *starting parameters.* |
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[ec392464] | 515 | |
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[6af2785] | 516 | If you select a 'Chi2' value and click the *View Fits* button a graph of the |
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| 517 | residuals for that data set is displayed. Again, if you select multiple 'Chi2' |
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[f9250dc] | 518 | values then all the residuals data will appear on one graph. Also see |
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| 519 | :ref:`Assessing_Fit_Quality`. |
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[ec392464] | 520 | |
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[6af2785] | 521 | Chain Fitting |
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| 522 | ^^^^^^^^^^^^^ |
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[ec392464] | 523 | |
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[6af2785] | 524 | By default, the *same* parameter values copied from the initial single fit into |
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| 525 | the *BatchPage* will be used as the starting parameters for all batch fits. It |
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| 526 | is, however, possible to get *SasView* to use the results of a fit to a preceding |
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| 527 | data set as the starting parameters for the next fit in the sequence. This |
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| 528 | variation of batch fitting is called *Chain Fitting*, and will considerably speed |
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| 529 | up model-fitting if you have lots of very similar data sets where a few parameters |
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| 530 | are gradually changing. Do not use chain fitting on disparate data sets. |
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[ec392464] | 531 | |
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[6af2785] | 532 | To use chain fitting, select *Chain Fitting* under *Fitting* in the menu bar. It |
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| 533 | toggles on/off, so selecting it again will switch back to normal batch fitting. |
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[ec392464] | 534 | |
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[6af2785] | 535 | .. _Grid_Window: |
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[ec392464] | 536 | |
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[6af2785] | 537 | Grid Window |
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| 538 | ^^^^^^^^^^^ |
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[ec392464] | 539 | |
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[6af2785] | 540 | The *Grid Window* provides an easy way to view the results from batch fitting. |
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| 541 | It will be displayed automatically when a batch fit completes, but may be |
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| 542 | opened at any time by selecting *Show Grid Window* under *View* in the menu |
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| 543 | bar. |
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[ec392464] | 544 | |
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[6af2785] | 545 | .. image:: restore_batch_window.bmp |
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[ec392464] | 546 | |
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[6af2785] | 547 | Once a batch fit is completed, all model parameters are displayed but *not* |
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| 548 | their uncertainties. To view the uncertainties, click on a given column then |
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| 549 | go to *Edit* in the menu bar, select *Insert Column Before* and choose the |
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| 550 | required data from the list. An empty column can be inserted in the same way. |
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[ec392464] | 551 | |
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[6af2785] | 552 | To remove a column from the grid, click on the column header and choose |
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| 553 | *Remove Column* under *Edit* in the menu bar. The same functionality also |
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| 554 | allows you to re-order columns. |
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[ec392464] | 555 | |
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[6af2785] | 556 | *NB: You cannot insert/remove/re-order the rows in the Grid Window.* |
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[ec392464] | 557 | |
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[6af2785] | 558 | All of the above functions are also available by right-clicking on a column |
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| 559 | label. |
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[ec392464] | 560 | |
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[6af2785] | 561 | .. image:: edit_menu.bmp |
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[ec392464] | 562 | |
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[6af2785] | 563 | *NB: If there is an existing Grid Window and another batch fit is performed,* |
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| 564 | *an additional 'Table' tab will be added to the Grid Window.* |
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[ec392464] | 565 | |
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[6af2785] | 566 | The parameter values in the *currently selected* table of the *Grid Window* |
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| 567 | can be output to a CSV file by choosing *Save As* under *File* in the (*Grid* |
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| 568 | *Window*) menu bar. The default filename includes the date and time that the |
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| 569 | batch fit was performed. |
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[ec392464] | 570 | |
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[6af2785] | 571 | Saved CSV files can be reloaded by choosing *Open* under *File* in the *Grid* |
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| 572 | *Window* menu bar. The loaded parameters will appear in a new table tab. |
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[ec392464] | 573 | |
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[6af2785] | 574 | .. image:: file_menu.bmp |
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[ec392464] | 575 | |
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[6af2785] | 576 | *NB: Saving the Grid Window does not save any experimental data, residuals* |
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| 577 | *or actual model fits. Consequently if you reload a saved CSV file the* |
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| 578 | *ability to View Fits will be lost.* |
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[ec392464] | 579 | |
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[6af2785] | 580 | Parameter Plots |
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| 581 | ^^^^^^^^^^^^^^^ |
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[ec392464] | 582 | |
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[6af2785] | 583 | Any column of *numeric* parameter values can be plotted against another using |
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| 584 | the *Grid Window*. Simply select one column at the time and click the *Add* |
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| 585 | button next to the required *X/Y-axis Selection Range* text box. When both |
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| 586 | the X and Y axis boxes have been completed, click the *Plot* button. |
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[ec392464] | 587 | |
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[6af2785] | 588 | When the *Add* button is clicked, *SasView* also automatically completes the |
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| 589 | *X/Y-axis Label* text box with the heading from Row 1 of the selected table, |
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| 590 | but different labels and units can be entered manually. |
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[ec392464] | 591 | |
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| 592 | .. image:: plot_button.bmp |
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| 593 | |
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[6af2785] | 594 | The *X/Y-axis Selection Range* can be edited manually. The text control box |
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| 595 | recognises the operators +, -, \*, /, or 'pow', and allows the following |
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| 596 | types of expression : |
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| 597 | |
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| 598 | 1) if an axis label range is a function of 1 or more *columns*, write |
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| 599 | this type of expression |
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[ec392464] | 600 | |
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[6af2785] | 601 | constant1 * column_name1 [minimum row index : maximum row index] |
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| 602 | operator constant2 * column_name2 [minimum row index : maximum row index] |
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[ec392464] | 603 | |
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[6af2785] | 604 | Example: radius [2 : 5] -3 * scale [2 : 5] |
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[ec392464] | 605 | |
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[6af2785] | 606 | 2) if only some *values* of a given column are needed but the range between |
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| 607 | the first row and the last row used is not continuous, write this type of |
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| 608 | expression |
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[ec392464] | 609 | |
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[6af2785] | 610 | column_name1 [minimum row index1 : maximum row index1] , column_name1 |
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| 611 | [minimum row index2 : maximum row index2] |
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[ec392464] | 612 | |
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[6af2785] | 613 | Example: radius [2 : 5] , radius [10 : 25] |
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[ec392464] | 614 | |
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| 615 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[6af2785] | 616 | |
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| 617 | .. note:: This help document was last changed by Steve King, 04Jun2015 |
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