[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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[b64b87c] | 6 | Fitting |
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| 7 | ======= |
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[ec392464] | 8 | |
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[3e1c9e5] | 9 | .. note:: If some code blocks are not readable, expand the documentation window |
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| 10 | |
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[a6f3613] | 11 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 12 | |
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| 13 | Preparing to fit data |
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| 14 | --------------------- |
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| 15 | |
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| 16 | To fit some data you must first load some data, activate one or more data sets, |
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[b64b87c] | 17 | send those data sets to fitting, and select a model to fit to each data set. |
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[a6f3613] | 18 | |
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[f3377b8] | 19 | Instructions on how to load and activate data are in the section :ref:`Loading_data`. |
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[ec392464] | 20 | |
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[a6f3613] | 21 | SasView can fit data in one of three ways: |
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[ec392464] | 22 | |
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[a6f3613] | 23 | * in *Single* fit mode - individual data sets are fitted independently one-by-one |
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[ec392464] | 24 | |
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[5295cf5] | 25 | * in *Simultaneous* fit mode - multiple data sets are fitted simultaneously to |
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| 26 | the *same* model with/without constrained parameters (this might be useful, |
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| 27 | for example, if you have measured the same sample at different contrasts) |
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[ec392464] | 28 | |
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[5005ae0] | 29 | * in *Batch* fit mode - multiple data sets are fitted sequentially to the |
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| 30 | *same* model (this might be useful, for example, if you have performed |
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| 31 | a kinetic or time-resolved experiment and have *lots* of data sets!) |
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[a6f3613] | 32 | |
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| 33 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[ec392464] | 34 | |
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[a6f3613] | 35 | Selecting a model |
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| 36 | ----------------- |
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[ec392464] | 37 | |
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[5295cf5] | 38 | The models in SasView are grouped into categories. By default these consist of: |
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[ec392464] | 39 | |
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[5295cf5] | 40 | * *Cylinder* - cylindrical shapes (disc, right cylinder, cylinder with endcaps |
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| 41 | etc) |
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| 42 | * *Ellipsoid* - ellipsoidal shapes (oblate,prolate, core shell, etc) |
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| 43 | * *Parellelepiped* - as the name implies |
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[dbc1f73] | 44 | * *Sphere* - spheroidal shapes (sphere, core multishell, vesicle, etc) |
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[5295cf5] | 45 | * *Lamellae* - lamellar shapes (lamellar, core shell lamellar, stacked |
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| 46 | lamellar, etc) |
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[5005ae0] | 47 | * *Shape-Independent* - models describing structure in terms of density |
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| 48 | correlation functions, fractals, peaks, power laws, etc |
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[5295cf5] | 49 | * *Paracrystal* - semi ordered structures (bcc, fcc, etc) |
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[a6f3613] | 50 | * *Structure Factor* - S(Q) models |
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[5295cf5] | 51 | * *Plugin Models* - User-created (custom/non-library) Python models |
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[ec392464] | 52 | |
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[a6f3613] | 53 | Use the *Category* drop-down menu to chose a category of model, then select |
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[f3377b8] | 54 | a model from the drop-down menu beneath. A graph of the chosen model, calculated |
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| 55 | using default parameter values, will appear. The graph will update dynamically |
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| 56 | as the parameter values are changed. |
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| 57 | |
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| 58 | You can decide your own model categorizations using the :ref:`Category_Manager`. |
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[ce62e75] | 59 | |
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[a6f3613] | 60 | Once you have selected a model you can read its help documentation by clicking |
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| 61 | on the *Description* button to the right. |
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| 62 | |
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[dbc1f73] | 63 | S(Q) models can be combined with models in the other categories to generate |
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[3ec78a1] | 64 | what SasView calls "product models". See :ref:`Product_Models` for more |
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| 65 | information. |
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[dbc1f73] | 66 | |
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[a6f3613] | 67 | Show 1D/2D |
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| 68 | ^^^^^^^^^^ |
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| 69 | |
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| 70 | Models are normally fitted to 1D (ie, I(Q) vs Q) data sets, but some models in |
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| 71 | SasView can also be fitted to 2D (ie, I(Qx,Qy) vs Qx vs Qy) data sets. |
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| 72 | |
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| 73 | *NB: Magnetic scattering can only be fitted in SasView in 2D.* |
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| 74 | |
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| 75 | To activate 2D fitting mode, click the *Show 2D* button on the *Fit Page*. To |
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| 76 | return to 1D fitting model, click the same button (which will now say *Show 1D*). |
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[ce62e75] | 77 | |
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[ec392464] | 78 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 79 | |
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[a6f3613] | 80 | .. _Category_Manager: |
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[a0637de] | 81 | |
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[a6f3613] | 82 | Category Manager |
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| 83 | ---------------- |
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| 84 | |
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[f3377b8] | 85 | To change the model categorizations, either choose *Category Manager* from the |
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| 86 | *View* option on the menubar, or click on the *Modify* button on the *Fit Page*. |
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[a6f3613] | 87 | |
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[6aad2e8] | 88 | .. image:: cat_fig0.png |
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[a6f3613] | 89 | |
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[5295cf5] | 90 | The categorization of all models except the user supplied Plugin Models can be |
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| 91 | reassigned, added to, and removed using *Category Manager*. Models can also be |
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| 92 | hidden from view in the drop-down menus. |
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[a6f3613] | 93 | |
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[6aad2e8] | 94 | .. image:: cat_fig1.png |
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[a6f3613] | 95 | |
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[f3377b8] | 96 | Changing category |
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| 97 | ^^^^^^^^^^^^^^^^^ |
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[a6f3613] | 98 | |
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[5295cf5] | 99 | To change category, highlight a model in the list by left-clicking on its entry |
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| 100 | and then click the *Modify* button. Use the *Change Category* panel that appears |
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| 101 | to make the required changes. |
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[a6f3613] | 102 | |
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[6aad2e8] | 103 | .. image:: cat_fig2.png |
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[a6f3613] | 104 | |
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[f3377b8] | 105 | To create a category for the selected model, click the *Add* button. In order |
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| 106 | to delete a category, select the category name and click the *Remove Selected* |
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| 107 | button. Then click *Done*. |
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[a6f3613] | 108 | |
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[f3377b8] | 109 | Showing/hiding models |
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| 110 | ^^^^^^^^^^^^^^^^^^^^^ |
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[a6f3613] | 111 | |
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[5295cf5] | 112 | Use the *Enable All / Disable All* buttons and the check boxes beside each model |
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| 113 | to select the models to show/hide. To apply the selection, click *Ok*. Otherwise |
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| 114 | click *Cancel*. |
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[a6f3613] | 115 | |
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[8570246] | 116 | *NB: It may be necessary to change to a different category and then back again* |
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[f3377b8] | 117 | *before any changes take effect.* |
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[a6f3613] | 118 | |
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| 119 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 120 | |
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[f3377b8] | 121 | Model Functions |
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| 122 | --------------- |
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[a6f3613] | 123 | |
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[5295cf5] | 124 | For a complete list of all the library models available in SasView, see |
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[dbc1f73] | 125 | the `Model Documentation <../../../sasgui/perspectives/fitting/models/index.html>`_ . |
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[a6f3613] | 126 | |
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[f3377b8] | 127 | It is also possible to add your own models. |
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[a6f3613] | 128 | |
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[f3377b8] | 129 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[a6f3613] | 130 | |
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[b5846a10] | 131 | .. _Adding_your_own_models: |
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| 132 | |
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[3e1c9e5] | 133 | Adding your own Models |
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[f3377b8] | 134 | ---------------------- |
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[a6f3613] | 135 | |
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[3e1c9e5] | 136 | There are essentially three ways to generate new fitting models for SasView: |
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| 137 | |
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[5295cf5] | 138 | * Using the SasView :ref:`New_Plugin_Model` helper dialog (best for beginners |
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| 139 | and/or relatively simple models) |
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| 140 | * By copying/editing an existing model (this can include models generated by |
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[5005ae0] | 141 | the New Plugin Model* dialog) in the :ref:`Python_shell` or |
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[5295cf5] | 142 | :ref:`Advanced_Plugin_Editor` (suitable for all use cases) |
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| 143 | * By writing a model from scratch outside of SasView (only recommended for code |
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| 144 | monkeys!) |
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[3e1c9e5] | 145 | |
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| 146 | Please read the guidance on :ref:`Writing_a_Plugin` before proceeding. |
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[f3377b8] | 147 | |
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[3e1c9e5] | 148 | **To be found by SasView your model must reside in the *~\\.sasview\\plugin_models* folder.** |
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[f3377b8] | 149 | |
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[a6f3613] | 150 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 151 | |
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[3e1c9e5] | 152 | .. _Plugin_Model_Operations: |
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[f3377b8] | 153 | |
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[3e1c9e5] | 154 | Plugin Model Operations |
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| 155 | ----------------------- |
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[a6f3613] | 156 | |
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[3e1c9e5] | 157 | From the *Fitting* option in the menu bar, select *Plugin Model Operations* |
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[a6f3613] | 158 | |
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[82b0b05e] | 159 | .. image:: edit_model_menu.png |
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[a6f3613] | 160 | |
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[3e1c9e5] | 161 | and then one of the sub-options |
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[f3377b8] | 162 | |
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[3e1c9e5] | 163 | * *New Plugin Model* - to create a plugin model template with a helper dialog |
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| 164 | * *Sum|Multi(p1,p2)* - to create a plugin model by summing/multiplying *existing models* in the model library |
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| 165 | * *Advanced Plugin Editor* - to create/edit a plugin model in a Python shell |
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| 166 | * *Delete Plugin Models* - to delete a plugin model |
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| 167 | * *Load Plugin Models* - to (re-)load plugin models |
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[a6f3613] | 168 | |
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[3e1c9e5] | 169 | .. _New_Plugin_Model: |
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| 170 | |
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| 171 | New Plugin Model |
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| 172 | ^^^^^^^^^^^^^^^^ |
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[a6f3613] | 173 | |
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[5295cf5] | 174 | Relatively straightforward models can be programmed directly from the SasView |
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| 175 | GUI using the *New Plugin Model Function*. |
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[26c8be3] | 176 | |
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[6aad2e8] | 177 | .. image:: new_model.png |
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[a6f3613] | 178 | |
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[5005ae0] | 179 | When using this feature, be aware that even if your code has errors, including |
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| 180 | syntax errors, a model file is still generated. When you then correct the errors |
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| 181 | and click 'Apply' again to re-compile you will get an error informing you that |
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| 182 | the model already exists if the 'Overwrite' box is not checked. In this case you |
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| 183 | will need to supply a new model function name. By default the 'Overwrite' box is |
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[26c8be3] | 184 | *checked*\ . |
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[f3377b8] | 185 | |
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[26c8be3] | 186 | A model file generated by this option can be viewed and further modified using |
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| 187 | the :ref:`Advanced_Plugin_Editor` . |
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[05829fb] | 188 | |
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[8b89396] | 189 | Note that the New Plugin Model Feature currently does not allow for parameters |
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| 190 | to be polydisperse. However they can be edited in the Advanced Editor. |
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| 191 | |
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| 192 | |
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| 193 | **SasView version 4.2** made it possible to specify whether a plugin created |
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| 194 | with the *New Plugin Model* dialog is actually a form factor P(Q) or a structure |
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| 195 | factor S(Q). To do this, simply add one or other of the following lines under |
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| 196 | the *import* statements. |
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[f485ba0] | 197 | |
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| 198 | For a form factor:: |
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| 199 | |
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| 200 | form_factor = True |
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[5005ae0] | 201 | |
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[f485ba0] | 202 | or for a structure factor:: |
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| 203 | |
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| 204 | structure_factor = True |
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[5005ae0] | 205 | |
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[8b89396] | 206 | If the plugin is a structure factor it is *also* necessary to add two variables |
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| 207 | to the parameter list:: |
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[f485ba0] | 208 | |
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[5005ae0] | 209 | parameters = [ |
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[ca383a0] | 210 | ['radius_effective', '', 1, [0.0, numpy.inf], 'volume', ''], |
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| 211 | ['volfraction', '', 1, [0.0, 1.0], '', ''], |
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[e081946] | 212 | [...], |
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[f485ba0] | 213 | |
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| 214 | and to the declarations of the functions Iq and Iqxy::: |
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| 215 | |
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| 216 | def Iq(x , radius_effective, volfraction, ...): |
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| 217 | |
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| 218 | def Iqxy(x, y, radius_effective, volfraction, ...): |
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| 219 | |
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[5005ae0] | 220 | Such a plugin should then be available in the S(Q) drop-down box on a FitPage (once |
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[f485ba0] | 221 | a P(Q) model has been selected). |
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| 222 | |
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[a6f3613] | 223 | Sum|Multi(p1,p2) |
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| 224 | ^^^^^^^^^^^^^^^^ |
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| 225 | |
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[6aad2e8] | 226 | .. image:: sum_model.png |
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[a0637de] | 227 | |
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[5295cf5] | 228 | This option creates a custom Plugin Model of the form:: |
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[f3377b8] | 229 | |
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[5295cf5] | 230 | Plugin Model = scale_factor * {(scale_1 * model_1) +/- (scale_2 * model_2)} + background |
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[f3377b8] | 231 | |
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[3e1c9e5] | 232 | or:: |
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| 233 | |
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[f485ba0] | 234 | Plugin Model = scale_factor * (model1 * model2) + background |
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[3e1c9e5] | 235 | |
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| 236 | In the *Easy Sum/Multi Editor* give the new model a function name and brief |
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| 237 | description (to appear under the *Details* button on the *FitPage*). Then select |
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[f3377b8] | 238 | two existing models, as p1 and p2, and the required operator, '+' or '*' between |
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[f485ba0] | 239 | them. Finally, click the *Apply* button to generate and test the model and then click *Close*. |
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[f3377b8] | 240 | |
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[5005ae0] | 241 | Any changes to a plugin model generated in this way only become effective *after* it is re-selected |
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| 242 | from the plugin models drop-down menu on the FitPage. If the model is not listed you can force a |
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[f485ba0] | 243 | recompilation of the plugins by selecting *Fitting* > *Plugin Model Operations* > *Load Plugin Models*. |
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| 244 | |
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[5005ae0] | 245 | **SasView version 4.2** introduced a much simplified and more extensible structure for plugin models |
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| 246 | generated through the Easy Sum/Multi Editor. For example, the code for a combination of a sphere model |
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[f485ba0] | 247 | with a power law model now looks like this:: |
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| 248 | |
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| 249 | from sasmodels.core import load_model_info |
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| 250 | from sasmodels.sasview_model import make_model_from_info |
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[5005ae0] | 251 | |
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[f485ba0] | 252 | model_info = load_model_info('sphere+power_law') |
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[e081946] | 253 | model_info.name = 'MyPluginModel' |
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[f485ba0] | 254 | model_info.description = 'sphere + power_law' |
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| 255 | Model = make_model_from_info(model_info) |
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| 256 | |
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[5005ae0] | 257 | To change the models or operators contributing to this plugin it is only necessary to edit the string |
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| 258 | in the brackets after *load_model_info*, though it would also be a good idea to update the model name |
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[f485ba0] | 259 | and description too!!! |
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| 260 | |
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[5005ae0] | 261 | The model specification string can handle multiple models and combinations of operators (+ or *) which |
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| 262 | are processed according to normal conventions. Thus 'model1+model2*model3' would be valid and would |
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| 263 | multiply model2 by model3 before adding model1. In this example, parameters in the *FitPage* would be |
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| 264 | prefixed A (for model2), B (for model3) and C (for model1). Whilst this might appear a little |
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| 265 | confusing, unless you were creating a plugin model from multiple instances of the same model the parameter |
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[e081946] | 266 | assignments ought to be obvious when you load the plugin. |
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[f485ba0] | 267 | |
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[5005ae0] | 268 | If you need to include another plugin model in the model specification string, just prefix the name of |
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[e081946] | 269 | that model with *custom*. For instance:: |
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| 270 | |
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| 271 | sphere+custom.MyPluginModel |
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| 272 | |
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| 273 | To create a P(Q)*\S(Q) model use the @ symbol instead of * like this:: |
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| 274 | |
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| 275 | sphere@hardsphere |
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[5005ae0] | 276 | |
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| 277 | This streamlined approach to building complex plugin models from existing library models, or models |
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| 278 | available on the *Model Marketplace*, also permits the creation of P(Q)*\S(Q) plugin models, something |
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| 279 | that was not possible in earlier versions of SasView. |
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[f3377b8] | 280 | |
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[3e1c9e5] | 281 | .. _Advanced_Plugin_Editor: |
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[f3377b8] | 282 | |
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[3e1c9e5] | 283 | Advanced Plugin Editor |
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| 284 | ^^^^^^^^^^^^^^^^^^^^^^ |
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[ec392464] | 285 | |
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[3e1c9e5] | 286 | Selecting this option shows all the plugin models in the plugin model folder, on Windows this is |
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[f3377b8] | 287 | |
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[afb93df] | 288 | *C:\\Users\\{username}\\.sasview\\plugin_models* |
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[f3377b8] | 289 | |
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| 290 | You can edit, modify, and save the Python code in any of these models using the |
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[3e1c9e5] | 291 | *Advanced Plugin Model Editor*. Note that this is actually the same tool as the :ref:`Python_shell` . |
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[f3377b8] | 292 | |
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[afb93df] | 293 | For details of the SasView plugin model format see :ref:`Writing_a_Plugin` . |
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[05829fb] | 294 | |
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[afb93df] | 295 | .. note:: Model files generated with the Sum/Multi option are still using the SasView 3.x model format. Unless you are confident about what you are doing, it is recommended that you only modify lines denoted with the ## <----- comments! |
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[f3377b8] | 296 | |
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[3e1c9e5] | 297 | When editing is complete, select *Run* > *Check Model* from the *Advanced Plugin Model Editor* menu bar. An *Info* box will appear with the results of the compilation and model unit tests. The model will only be usable if the tests 'pass'. |
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[f3377b8] | 298 | |
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[3e1c9e5] | 299 | .. image:: ../calculator/new_pycrust_example_2.png |
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| 300 | |
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| 301 | To use the model, go to the relevant *Fit Page*, select the *Plugin Models* |
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[f3377b8] | 302 | category and then select the model from the drop-down menu. |
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| 303 | |
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[3e1c9e5] | 304 | Any changes to a plugin model generated in this way only become effective *after* it is re-selected from the model drop-down menu on the FitPage. |
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[a6f3613] | 305 | |
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[3e1c9e5] | 306 | Delete Plugin Models |
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| 307 | ^^^^^^^^^^^^^^^^^^^^ |
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[a6f3613] | 308 | |
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[3e1c9e5] | 309 | Simply highlight the plugin model to be removed. The operation is final!!! |
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[f3377b8] | 310 | |
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[5295cf5] | 311 | *NB: Models shipped with SasView cannot be removed in this way.* |
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[ec392464] | 312 | |
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[3e1c9e5] | 313 | Load Plugin Models |
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| 314 | ^^^^^^^^^^^^^^^^^^ |
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[afb93df] | 315 | |
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[5295cf5] | 316 | This option loads (or re-loads) all models present in the |
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| 317 | *~\\.sasview\\plugin_models* folder. |
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[afb93df] | 318 | |
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[ec392464] | 319 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 320 | |
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[4666660] | 321 | .. _Fitting_Options: |
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| 322 | |
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[f3377b8] | 323 | Fitting Options |
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| 324 | --------------- |
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[a6f3613] | 325 | |
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[f3377b8] | 326 | It is possible to specify which optimiser SasView should use to fit the data, and |
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| 327 | to modify some of the configurational parameters for each optimiser. |
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| 328 | |
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| 329 | From *Fitting* in the menu bar select *Fit Options*, then select one of the following |
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| 330 | optimisers: |
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[a6f3613] | 331 | |
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[f3377b8] | 332 | * DREAM |
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| 333 | * Levenberg-Marquardt |
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| 334 | * Quasi-Newton BFGS |
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| 335 | * Differential Evolution |
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| 336 | * Nelder-Mead Simplex |
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[a6f3613] | 337 | |
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[6af2785] | 338 | The DREAM optimiser is the most sophisticated, but may not necessarily be the best |
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| 339 | option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser |
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| 340 | initially. |
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| 341 | |
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[f3377b8] | 342 | These optimisers form the *Bumps* package written by P Kienzle. For more information |
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[4666660] | 343 | on each optimiser, see the :ref:`Fitting_Documentation`. |
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[a6f3613] | 344 | |
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[f3377b8] | 345 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[a6f3613] | 346 | |
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[b7ce5ad] | 347 | Fitting Integer Parameters |
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| 348 | -------------------------- |
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| 349 | |
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| 350 | Most of the parameters in SasView models will naturally take floating point (decimal) |
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| 351 | values, but there are some parameters which can only have integer values. Examples |
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| 352 | include, but are not limited to, the number of shells in a multilayer vesicle, the |
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| 353 | number of beads in a pearl necklace, the number of arms of a star polymer, and so on. |
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| 354 | Wherever possible/recognised, the integer nature of a parameter is specified in the |
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| 355 | respective model documentation and/or parameter table, so read the documentation |
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| 356 | carefully! |
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| 357 | |
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| 358 | Integer parameters must be fitted with care. |
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| 359 | |
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| 360 | Start with your best possible guess for the value of the parameter. And using |
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| 361 | *a priori* knowledge, fix as many of the other parameters as possible. |
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| 362 | |
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| 363 | The SasView optimizers treat integer parameters internally as floating point |
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| 364 | numbers, but the values presented to the user are truncated or rounded, as |
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| 365 | appropriate. |
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| 366 | |
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| 367 | In most instances integer parameters will probably be greater than zero. A good |
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| 368 | policy in such cases is to use a constraint to enforce this. |
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| 369 | |
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| 370 | Because an integer parameter should, by definition, only move in integer steps, |
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| 371 | problems may be encountered if the optimizer step size is too small. Similarly, |
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| 372 | be **very careful** about applying polydispersity to integer parameters. |
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| 373 | |
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| 374 | The Levenberg-Marquardt and Quasi-Newton BFGS (and other derivative-based) |
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| 375 | optimizers are probably best avoided for fitting models with integer parameters. |
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| 376 | |
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| 377 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 378 | |
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[5ac0a7a] | 379 | Fitting Limits |
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| 380 | -------------- |
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| 381 | |
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| 382 | By default, *SasView* will attempt to model fit the full range of the data; ie, |
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| 383 | across all *Q* values. If necessary, however, it is possible to specify only a |
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| 384 | sub-region of the data for fitting. |
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| 385 | |
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| 386 | In a *FitPage* or *BatchPage* change the *Q* values in the *Min* and/or *Max* |
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| 387 | text boxes. Vertical coloured bars will appear on the graph with the data and |
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| 388 | 'theory' indicating the current *Q* limits (red = *Qmin*, purple = *Qmax*). |
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| 389 | |
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| 390 | To return to including all data in the fit, click the *Reset* button. |
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| 391 | |
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| 392 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 393 | |
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| 394 | |
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[f3377b8] | 395 | Shortcuts |
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| 396 | --------- |
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[a6f3613] | 397 | |
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[f3377b8] | 398 | Copy/Paste Parameters |
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| 399 | ^^^^^^^^^^^^^^^^^^^^^ |
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[a6f3613] | 400 | |
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[f3377b8] | 401 | It is possible to copy the parameters from one *Fit Page* and to paste them into |
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| 402 | another *Fit Page* using the same model. |
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[a6f3613] | 403 | |
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[f3377b8] | 404 | To *copy* parameters, either: |
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[a6f3613] | 405 | |
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[f3377b8] | 406 | * Select *Edit -> Copy Params* from the menu bar, or |
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| 407 | * Use Ctrl(Cmd on Mac) + Left Mouse Click on the *Fit Page*. |
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[a6f3613] | 408 | |
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[f3377b8] | 409 | To *paste* parameters, either: |
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| 410 | |
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| 411 | * Select *Edit -> Paste Params* from the menu bar, or |
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| 412 | * Use Ctrl(Cmd on Mac) + Shift + Left-click on the *Fit Page*. |
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| 413 | |
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| 414 | If either operation is successful a message will appear in the info line at the |
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| 415 | bottom of the SasView window. |
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| 416 | |
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| 417 | Bookmark |
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| 418 | ^^^^^^^^ |
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[a6f3613] | 419 | |
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[1fda506] | 420 | To *Bookmark* a *Fit Page* either: |
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[a6f3613] | 421 | |
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[f3377b8] | 422 | * Select a *Fit Page* and then click on *Bookmark* in the tool bar, or |
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| 423 | * Right-click and select the *Bookmark* in the popup menu. |
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[a6f3613] | 424 | |
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| 425 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 426 | |
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[4666660] | 427 | .. _Status_bar: |
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| 428 | |
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[1fda506] | 429 | Status Bar & Console |
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| 430 | -------------------- |
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| 431 | |
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| 432 | The status bar is located at the bottom of the SasView window and displays |
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| 433 | messages, hints, warnings and errors. |
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| 434 | |
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| 435 | At the right-hand side of the status bar is a button marked *Console*. The *Console* |
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| 436 | displays available message history and some run-time traceback information. |
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| 437 | |
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| 438 | During a long task the *Console* can also be used to monitor the progress. |
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| 439 | |
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| 440 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 441 | |
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[6af2785] | 442 | .. _Single_Fit_Mode: |
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| 443 | |
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[a6f3613] | 444 | Single Fit Mode |
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| 445 | --------------- |
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[ec392464] | 446 | |
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[4666660] | 447 | *NB: Before proceeding, ensure that the Single Mode radio button at the bottom of* |
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| 448 | *the Data Explorer is checked (see the section* :ref:`Loading_data` *).* |
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| 449 | |
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[63d314b] | 450 | This mode fits one data set. |
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| 451 | |
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[b64b87c] | 452 | When data is sent to the fitting it is plotted in a graph window as markers. |
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[4666660] | 453 | |
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| 454 | If a graph does not appear, or a graph window appears but is empty, then the data |
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| 455 | has not loaded correctly. Check to see if there is a message in the :ref:`Status_Bar` |
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| 456 | or in the *Console* window. |
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| 457 | |
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| 458 | Assuming the data has loaded correctly, when a model is selected a green model |
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| 459 | calculation (or what SasView calls a 'Theory') line will appear in the earlier graph |
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| 460 | window, and a second graph window will appear displaying the residuals (the |
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| 461 | difference between the experimental data and the theory) at the same X-data values. |
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[f9250dc] | 462 | See :ref:`Assessing_Fit_Quality`. |
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[4666660] | 463 | |
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[a7c6f38] | 464 | The objective of model-fitting is to find a *physically-plausible* model, and |
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| 465 | set of model parameters, that generate a theory that reproduces the experimental |
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| 466 | data and minimizes the values of the residuals. |
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[4666660] | 467 | |
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| 468 | Change the default values of the model parameters by hand until the theory line |
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[a7c6f38] | 469 | starts to represent the experimental data. Then check the tick boxes alongside |
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[84ac3f1] | 470 | the 'background' and 'scale' parameters. Click the *Fit* button. SasView |
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[a7c6f38] | 471 | will optimise the values of the 'background' and 'scale' and also display the |
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| 472 | corresponding uncertainties on the optimised values. |
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[4666660] | 473 | |
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[a7c6f38] | 474 | .. note:: |
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[84ac3f1] | 475 | If the uncertainty on a fitted parameter is unrealistically large, or if it |
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| 476 | displays as NaN, the model is most likely a poor representation of the data, |
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| 477 | the parameter in question is highly correlated with one or more of the other |
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| 478 | fitted parameters, or the model is relatively insensitive to the value of |
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| 479 | that particular parameter. |
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[4666660] | 480 | |
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[47ace50] | 481 | In the bottom left corner of the *Fit Page* is a box displaying a normalised |
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| 482 | value of the statistical $\chi^2$ parameter (the reduced $\chi^2$, |
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| 483 | See :ref:`Assessing_Fit_Quality`) returned by the optimiser. |
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[4666660] | 484 | |
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| 485 | Now check the box for another model parameter and click *Fit* again. Repeat this |
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[84ac3f1] | 486 | process until all relevant parameters are checked and have been optimised. As |
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| 487 | the fit of the theory to the experimental data improves, the value of 'Reduced |
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| 488 | Chi2' will decrease. A good model fit should produce values of Reduced Chi2 |
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| 489 | close to one, and certainly << 100. See :ref:`Assessing_Fit_Quality`. |
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[4666660] | 490 | |
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| 491 | SasView has a number of different optimisers (see the section :ref:`Fitting_Options`). |
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| 492 | The DREAM optimiser is the most sophisticated, but may not necessarily be the best |
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| 493 | option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser |
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| 494 | initially. |
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[ec392464] | 495 | |
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| 496 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 497 | |
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[a6f3613] | 498 | Simultaneous Fit Mode |
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| 499 | --------------------- |
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[ec392464] | 500 | |
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[63d314b] | 501 | *NB: Before proceeding, ensure that the Single Mode radio button at the bottom of* |
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| 502 | *the Data Explorer is checked (see the section* :ref:`Loading_data` *).* |
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[ec392464] | 503 | |
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[84ac3f1] | 504 | This mode is an extension of the :ref:`Single_Fit_Mode` that allows for some |
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| 505 | relatively extensive constraints between fitted parameters in a single *FitPage* |
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| 506 | or between several *FitPage*'s (eg, to constrain all fitted parameters to be the |
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| 507 | same in a contrast series of *FitPages* except for the solvent sld parameter, |
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[47ace50] | 508 | constrain the length to be twice that of the radius in a single *FitPage*, |
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[84ac3f1] | 509 | fix the radius of the sphere in one *FitPage* to be the same as the radius of |
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| 510 | the cylinder in a second *FitPage*, etc). |
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[63d314b] | 511 | |
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[b5846a10] | 512 | If the data to be fit are in multiple files, load each file, then select each file |
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| 513 | in the *Data Explorer*, and *Send To Fitting*. If multiple data sets are in one file, |
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| 514 | load that file, *Unselect All Data*, select just those data sets to be fitted, and |
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| 515 | *Send To Fitting*. Either way, the result should be that for *n* data sets you have |
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[6af2785] | 516 | 2\ *n* graphs (*n* of the data and model fit, and *n* of the resulting residuals). But |
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[f9250dc] | 517 | it may be helpful to minimise the residuals plots for clarity. Also see |
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| 518 | :ref:`Assessing_Fit_Quality`. |
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[b5846a10] | 519 | |
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[5295cf5] | 520 | *NB: If you need to use a custom Plugin Model, you must ensure that model is |
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| 521 | available first (see* :ref:`Adding_your_own_models` *).* |
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[b5846a10] | 522 | |
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[6af2785] | 523 | Method |
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| 524 | ^^^^^^ |
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| 525 | |
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[b5846a10] | 526 | Now go to each *FitPage* in turn and: |
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| 527 | |
---|
| 528 | Select the required category and model; |
---|
| 529 | |
---|
| 530 | Unselect all the model parameters; |
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| 531 | |
---|
| 532 | Enter some starting guesses for the parameters; |
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| 533 | |
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| 534 | Enter any parameter limits (recommended); |
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[63d314b] | 535 | |
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[b5846a10] | 536 | Select which parameters will refine (selecting all is generally a bad idea...); |
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[63d314b] | 537 | |
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[b5846a10] | 538 | When done, select *Constrained or Simultaneous Fit* under *Fitting* in the menu bar. |
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| 539 | |
---|
| 540 | In the *Const & Simul Fit* page that appears, select which data sets are to be |
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| 541 | simultaneously fitted (this will probably be all of them or you would not have loaded |
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| 542 | them in the first place!). |
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| 543 | |
---|
| 544 | To tie parameters between the data sets with constraints, check the 'yes' radio button |
---|
| 545 | next to *Add Constraint?* in the *Fit Constraints* box. |
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| 546 | |
---|
[84ac3f1] | 547 | To constrain all identically named parameters to fit *simultaneously* to the |
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| 548 | same value across all the *Fitpages* use the *Easy Setup* drop-down buttons in |
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| 549 | the *Const & Simul Fit* page. |
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[ec392464] | 550 | |
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[84ac3f1] | 551 | *NB: You can only constrain parameters that are set to refine.* |
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[b5846a10] | 552 | |
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[6af2785] | 553 | Constraints will generally be of the form |
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| 554 | |
---|
| 555 | Mi Parameter1 = Mj.Parameter1 |
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| 556 | |
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| 557 | however the text box after the '=' sign can be used to adjust this |
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| 558 | relationship; for example |
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| 559 | |
---|
| 560 | Mi Parameter1 = scalar \* Mj.Parameter1 |
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| 561 | |
---|
| 562 | A 'free-form' constraint box is also provided. |
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[b5846a10] | 563 | |
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| 564 | Many constraints can be entered for a single fit. |
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| 565 | |
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[84ac3f1] | 566 | When ready, click the *Fit* button on the *Const & Simul Fit* page, NOT the *Fit* |
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| 567 | button on the individual *FitPage*'s. |
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| 568 | |
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[b5846a10] | 569 | The results of the model-fitting will be returned to each of the individual |
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| 570 | *FitPage*'s. |
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[ec392464] | 571 | |
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[a7c6f38] | 572 | Note that the Reduced Chi2 value returned is the SUM of the Reduced Chi2 of |
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| 573 | each fit. To see the Reduced Chi2 value for a specific *FitPage*, click the |
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| 574 | *Compute* button at the bottom of that *FitPage* to recalculate. Note that in |
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[84ac3f1] | 575 | doing so the degrees of freedom will be set to Npts. |
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[a7c6f38] | 576 | See :ref:`Assessing_Fit_Quality`. Moreover in the case of constraints the |
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[84ac3f1] | 577 | degrees of freedom are less than one might think due to those constraints. |
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| 578 | |
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[ec392464] | 579 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 580 | |
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[e6c74e8] | 581 | .. _Batch_Fit_Mode: |
---|
| 582 | |
---|
[a6f3613] | 583 | Batch Fit Mode |
---|
| 584 | -------------- |
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[ec392464] | 585 | |
---|
[6af2785] | 586 | *NB: Before proceeding, ensure that the Single Mode radio button at the bottom of* |
---|
| 587 | *the Data Explorer is checked (see the section* :ref:`Loading_data` *). The Batch* |
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| 588 | *Mode button will be used later on!* |
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[63d314b] | 589 | |
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[6af2785] | 590 | This mode *sequentially* fits two or more data sets *to the same model*. Unlike in |
---|
| 591 | simultaneous fitting, in batch fitting it is not possible to constrain fit parameters |
---|
| 592 | between data sets. |
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[ec392464] | 593 | |
---|
[6af2785] | 594 | If the data to be fit are in multiple files, load each file in the *Data Explorer*. |
---|
| 595 | If multiple data sets are in one file, load just that file. *Unselect All Data*, then |
---|
| 596 | select a single initial data set to be fitted. Fit that selected data set as described |
---|
[5295cf5] | 597 | above under :ref:`Single_Fit_Mode`. |
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[ec392464] | 598 | |
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[5295cf5] | 599 | *NB: If you need to use a custom Plugin Model, you must ensure that model is |
---|
| 600 | available first (see* :ref:`Adding_your_own_models` *).* |
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[ec392464] | 601 | |
---|
[6af2785] | 602 | Method |
---|
| 603 | ^^^^^^ |
---|
[ec392464] | 604 | |
---|
[6af2785] | 605 | Now *Select All Data* in the *Data Explorer*, check the *Batch Mode* radio button |
---|
| 606 | at the bottom of that panel and *Send To Fitting*. A *BatchPage* will be created. |
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[ec392464] | 607 | |
---|
[6aad2e8] | 608 | .. image:: batch_button_area.png |
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[ec392464] | 609 | |
---|
[6af2785] | 610 | *NB: The Batch Page can also be created by checking the Batch Mode radio button* |
---|
| 611 | *and selecting New Fit Page under Fitting in the menu bar.* |
---|
[ec392464] | 612 | |
---|
[6af2785] | 613 | Using the drop-down menus in the *BatchPage*, now set up the *same* data set |
---|
| 614 | with the *same* model that you just fitted in single fit mode. A quick way to |
---|
| 615 | set the model parameter values is to just copy them from the earlier Single |
---|
| 616 | Fit. To do this, go back to the Single Fit *FitPage*, select *Copy Params* |
---|
| 617 | under *Edit* in the menu bar, then go back to the *BatchPage* and *Paste Params*. |
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[ec392464] | 618 | |
---|
[6af2785] | 619 | When ready, use the *Fit* button on the *BatchPage* to perform the fitting, NOT |
---|
| 620 | the *Fit* button on the individual *FitPage*'s. |
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[ec392464] | 621 | |
---|
[6af2785] | 622 | Unlike in single fit mode, the results of batch fits are not returned to |
---|
| 623 | the *BatchPage*. Instead, a spreadsheet-like :ref:`Grid_Window` will appear. |
---|
[ec392464] | 624 | |
---|
[6af2785] | 625 | If you want to visually check a graph of a particular fit, click on the name of |
---|
| 626 | a *Data set* in the *Grid Window* and then click the *View Fits* button. The |
---|
| 627 | data and the model fit will be displayed. If you select mutliple data sets they |
---|
| 628 | will all appear on one graph. |
---|
[ec392464] | 629 | |
---|
[6aad2e8] | 630 | .. image:: view_button.png |
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[ec392464] | 631 | |
---|
[6af2785] | 632 | *NB: In theory, returning to the BatchPage and changing the name of the I(Q)* |
---|
| 633 | *data source should also work, but at the moment whilst this does change the* |
---|
| 634 | *data set displayed it always superimposes the 'theory' corresponding to the* |
---|
| 635 | *starting parameters.* |
---|
[ec392464] | 636 | |
---|
[6af2785] | 637 | If you select a 'Chi2' value and click the *View Fits* button a graph of the |
---|
| 638 | residuals for that data set is displayed. Again, if you select multiple 'Chi2' |
---|
[f9250dc] | 639 | values then all the residuals data will appear on one graph. Also see |
---|
| 640 | :ref:`Assessing_Fit_Quality`. |
---|
[ec392464] | 641 | |
---|
[6af2785] | 642 | Chain Fitting |
---|
| 643 | ^^^^^^^^^^^^^ |
---|
[ec392464] | 644 | |
---|
[6af2785] | 645 | By default, the *same* parameter values copied from the initial single fit into |
---|
| 646 | the *BatchPage* will be used as the starting parameters for all batch fits. It |
---|
| 647 | is, however, possible to get *SasView* to use the results of a fit to a preceding |
---|
| 648 | data set as the starting parameters for the next fit in the sequence. This |
---|
| 649 | variation of batch fitting is called *Chain Fitting*, and will considerably speed |
---|
| 650 | up model-fitting if you have lots of very similar data sets where a few parameters |
---|
| 651 | are gradually changing. Do not use chain fitting on disparate data sets. |
---|
[ec392464] | 652 | |
---|
[6af2785] | 653 | To use chain fitting, select *Chain Fitting* under *Fitting* in the menu bar. It |
---|
| 654 | toggles on/off, so selecting it again will switch back to normal batch fitting. |
---|
[ec392464] | 655 | |
---|
[6af2785] | 656 | .. _Grid_Window: |
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[ec392464] | 657 | |
---|
[6af2785] | 658 | Grid Window |
---|
| 659 | ^^^^^^^^^^^ |
---|
[ec392464] | 660 | |
---|
[6af2785] | 661 | The *Grid Window* provides an easy way to view the results from batch fitting. |
---|
| 662 | It will be displayed automatically when a batch fit completes, but may be |
---|
| 663 | opened at any time by selecting *Show Grid Window* under *View* in the menu |
---|
| 664 | bar. |
---|
[ec392464] | 665 | |
---|
[6aad2e8] | 666 | .. image:: restore_batch_window.png |
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[ec392464] | 667 | |
---|
[6af2785] | 668 | Once a batch fit is completed, all model parameters are displayed but *not* |
---|
| 669 | their uncertainties. To view the uncertainties, click on a given column then |
---|
| 670 | go to *Edit* in the menu bar, select *Insert Column Before* and choose the |
---|
| 671 | required data from the list. An empty column can be inserted in the same way. |
---|
[ec392464] | 672 | |
---|
[6af2785] | 673 | To remove a column from the grid, click on the column header and choose |
---|
| 674 | *Remove Column* under *Edit* in the menu bar. The same functionality also |
---|
| 675 | allows you to re-order columns. |
---|
[ec392464] | 676 | |
---|
[6af2785] | 677 | *NB: You cannot insert/remove/re-order the rows in the Grid Window.* |
---|
[ec392464] | 678 | |
---|
[6af2785] | 679 | All of the above functions are also available by right-clicking on a column |
---|
| 680 | label. |
---|
[ec392464] | 681 | |
---|
[6aad2e8] | 682 | .. image:: edit_menu.png |
---|
[ec392464] | 683 | |
---|
[6af2785] | 684 | *NB: If there is an existing Grid Window and another batch fit is performed,* |
---|
| 685 | *an additional 'Table' tab will be added to the Grid Window.* |
---|
[ec392464] | 686 | |
---|
[6af2785] | 687 | The parameter values in the *currently selected* table of the *Grid Window* |
---|
| 688 | can be output to a CSV file by choosing *Save As* under *File* in the (*Grid* |
---|
| 689 | *Window*) menu bar. The default filename includes the date and time that the |
---|
| 690 | batch fit was performed. |
---|
[ec392464] | 691 | |
---|
[6af2785] | 692 | Saved CSV files can be reloaded by choosing *Open* under *File* in the *Grid* |
---|
| 693 | *Window* menu bar. The loaded parameters will appear in a new table tab. |
---|
[ec392464] | 694 | |
---|
[6aad2e8] | 695 | .. image:: file_menu.png |
---|
[ec392464] | 696 | |
---|
[6af2785] | 697 | *NB: Saving the Grid Window does not save any experimental data, residuals* |
---|
| 698 | *or actual model fits. Consequently if you reload a saved CSV file the* |
---|
| 699 | *ability to View Fits will be lost.* |
---|
[ec392464] | 700 | |
---|
[6af2785] | 701 | Parameter Plots |
---|
| 702 | ^^^^^^^^^^^^^^^ |
---|
[ec392464] | 703 | |
---|
[6af2785] | 704 | Any column of *numeric* parameter values can be plotted against another using |
---|
| 705 | the *Grid Window*. Simply select one column at the time and click the *Add* |
---|
| 706 | button next to the required *X/Y-axis Selection Range* text box. When both |
---|
| 707 | the X and Y axis boxes have been completed, click the *Plot* button. |
---|
[ec392464] | 708 | |
---|
[6af2785] | 709 | When the *Add* button is clicked, *SasView* also automatically completes the |
---|
| 710 | *X/Y-axis Label* text box with the heading from Row 1 of the selected table, |
---|
| 711 | but different labels and units can be entered manually. |
---|
[ec392464] | 712 | |
---|
[6aad2e8] | 713 | .. image:: plot_button.png |
---|
[ec392464] | 714 | |
---|
[6af2785] | 715 | The *X/Y-axis Selection Range* can be edited manually. The text control box |
---|
| 716 | recognises the operators +, -, \*, /, or 'pow', and allows the following |
---|
| 717 | types of expression : |
---|
[5005ae0] | 718 | |
---|
[6af2785] | 719 | 1) if an axis label range is a function of 1 or more *columns*, write |
---|
| 720 | this type of expression |
---|
[ec392464] | 721 | |
---|
[6af2785] | 722 | constant1 * column_name1 [minimum row index : maximum row index] |
---|
| 723 | operator constant2 * column_name2 [minimum row index : maximum row index] |
---|
[ec392464] | 724 | |
---|
[6af2785] | 725 | Example: radius [2 : 5] -3 * scale [2 : 5] |
---|
[ec392464] | 726 | |
---|
[6af2785] | 727 | 2) if only some *values* of a given column are needed but the range between |
---|
| 728 | the first row and the last row used is not continuous, write this type of |
---|
| 729 | expression |
---|
[ec392464] | 730 | |
---|
[6af2785] | 731 | column_name1 [minimum row index1 : maximum row index1] , column_name1 |
---|
| 732 | [minimum row index2 : maximum row index2] |
---|
[ec392464] | 733 | |
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[6af2785] | 734 | Example: radius [2 : 5] , radius [10 : 25] |
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[5005ae0] | 735 | |
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[9d93c37] | 736 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 737 | |
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| 738 | Combined Batch Fit Mode |
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| 739 | ----------------------- |
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| 740 | |
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[e6c74e8] | 741 | The purpose of the Combined Batch Fit is to allow running two or more batch |
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| 742 | fits in sequence without overwriting the output table of results. This may be |
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| 743 | of interest for example if one is fitting a series of data sets where there is |
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| 744 | a shape change occurring in the series that requires changing the model part |
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| 745 | way through the series; for example a sphere to rod transition. Indeed the |
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| 746 | regular batch mode does not allow for multiple models and requires all the |
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| 747 | files in the series to be fit with single model and set of parameters. While |
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| 748 | it is of course possible to just run part of the series as a batch fit using |
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| 749 | model one followed by running another batch fit on the rest of the series with |
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| 750 | model two (and/or model three etc), doing so will overwrite the table of |
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| 751 | outputs from the previous batch fit(s). This may not be desirable if one is |
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| 752 | interested in comparing the parameters: for example the sphere radius of set |
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[05b0bf6] | 753 | one and the cylinder radius of set two. |
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[e6c74e8] | 754 | |
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| 755 | Method |
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| 756 | ^^^^^^ |
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[9d93c37] | 757 | |
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[e6c74e8] | 758 | In order to use the *Combined Batch Fit*, first load all the data needed as |
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| 759 | described in :ref:`Loading_data`. Next start up two or more *BatchPage* fits |
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| 760 | following the instructions in :ref:`Batch_Fit_Mode` but **DO NOT PRESS FIT**. |
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| 761 | At this point the *Combine Batch Fit* menu item under the *Fitting menu* should |
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| 762 | be active (if there is one or no *BatchPage* the menu item will be greyed out |
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| 763 | and inactive). Clicking on *Combine Batch Fit* will bring up a new panel, |
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| 764 | similar to the *Const & Simult Fit* panel. In this case there will be a |
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| 765 | checkbox for each *BatchPage* instead of each *FitPage* that should be included |
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| 766 | in the fit. Once all are selected, click the Fit button on |
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| 767 | the *BatchPage* to run each batch fit in *sequence* |
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[9d93c37] | 768 | |
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| 769 | .. image:: combine_batch_page.png |
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| 770 | |
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[e6c74e8] | 771 | The batch table will then pop up at the end as for the case of the simple Batch |
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| 772 | Fitting with the following caveats: |
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[9d93c37] | 773 | |
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| 774 | .. note:: |
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| 775 | The order matters. The parameters in the table will be taken from the model |
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[e6c74e8] | 776 | used in the first *BatchPage* of the list. Any parameters from the |
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| 777 | second and later *BatchPage* s that have the same name as a parameter in the |
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| 778 | first will show up allowing for plotting of that parameter across the |
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| 779 | models. The other parameters will not be available in the grid. |
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[9d93c37] | 780 | .. note:: |
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| 781 | a corralary of the above is that currently models created as a sum|multiply |
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| 782 | model will not work as desired because the generated model parameters have a |
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| 783 | p#_ appended to the beginning and thus radius and p1_radius will not be |
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| 784 | recognized as the same parameter. |
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[5005ae0] | 785 | |
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[9d93c37] | 786 | .. image:: combine_batch_grid.png |
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| 787 | |
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[e6c74e8] | 788 | In the example shown above the data is a time series with a shifting peak. |
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| 789 | The first part of the series was fitted using the *broad_peak* model, while |
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| 790 | the rest of the data were fit using the *gaussian_peak* model. Unfortunately the |
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| 791 | time is not listed in the file but the file name contains the information. As |
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| 792 | described in :ref:`Grid_Window`, a column can be added manually, in this case |
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[5005ae0] | 793 | called time, and the peak position plotted against time. |
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[9d93c37] | 794 | |
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| 795 | .. image:: combine_batch_plot.png |
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| 796 | |
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[05b0bf6] | 797 | Note the discontinuity in the peak position. This reflects the fact that the |
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| 798 | Gaussian fit is a rather poor model for the data and is not actually |
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[e6c74e8] | 799 | finding the peak. |
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[ec392464] | 800 | |
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| 801 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[6af2785] | 802 | |
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[84ac3f1] | 803 | .*Document History* |
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| 804 | |
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| 805 | | 2017-09-10 Paul Butler |
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| 806 | | 2017-09-15 Steve King |
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| 807 | | 2018-03-05 Paul Butler |
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