[ec392464] | 1 | .. fitting_help.rst |
---|
| 2 | |
---|
| 3 | .. This is a port of the original SasView html help file to ReSTructured text |
---|
| 4 | .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. |
---|
| 5 | |
---|
[b64b87c] | 6 | Fitting |
---|
| 7 | ======= |
---|
[ec392464] | 8 | |
---|
[3e1c9e5] | 9 | .. note:: If some code blocks are not readable, expand the documentation window |
---|
| 10 | |
---|
[a6f3613] | 11 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 12 | |
---|
| 13 | Preparing to fit data |
---|
| 14 | --------------------- |
---|
| 15 | |
---|
| 16 | To fit some data you must first load some data, activate one or more data sets, |
---|
[b64b87c] | 17 | send those data sets to fitting, and select a model to fit to each data set. |
---|
[a6f3613] | 18 | |
---|
[f3377b8] | 19 | Instructions on how to load and activate data are in the section :ref:`Loading_data`. |
---|
[ec392464] | 20 | |
---|
[a6f3613] | 21 | SasView can fit data in one of three ways: |
---|
[ec392464] | 22 | |
---|
[a6f3613] | 23 | * in *Single* fit mode - individual data sets are fitted independently one-by-one |
---|
[ec392464] | 24 | |
---|
[5295cf5] | 25 | * in *Simultaneous* fit mode - multiple data sets are fitted simultaneously to |
---|
| 26 | the *same* model with/without constrained parameters (this might be useful, |
---|
| 27 | for example, if you have measured the same sample at different contrasts) |
---|
[ec392464] | 28 | |
---|
[5005ae0] | 29 | * in *Batch* fit mode - multiple data sets are fitted sequentially to the |
---|
| 30 | *same* model (this might be useful, for example, if you have performed |
---|
| 31 | a kinetic or time-resolved experiment and have *lots* of data sets!) |
---|
[a6f3613] | 32 | |
---|
| 33 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
[ec392464] | 34 | |
---|
[a6f3613] | 35 | Selecting a model |
---|
| 36 | ----------------- |
---|
[ec392464] | 37 | |
---|
[5295cf5] | 38 | The models in SasView are grouped into categories. By default these consist of: |
---|
[ec392464] | 39 | |
---|
[5295cf5] | 40 | * *Cylinder* - cylindrical shapes (disc, right cylinder, cylinder with endcaps |
---|
| 41 | etc) |
---|
| 42 | * *Ellipsoid* - ellipsoidal shapes (oblate,prolate, core shell, etc) |
---|
| 43 | * *Parellelepiped* - as the name implies |
---|
[dbc1f73] | 44 | * *Sphere* - spheroidal shapes (sphere, core multishell, vesicle, etc) |
---|
[5295cf5] | 45 | * *Lamellae* - lamellar shapes (lamellar, core shell lamellar, stacked |
---|
| 46 | lamellar, etc) |
---|
[5005ae0] | 47 | * *Shape-Independent* - models describing structure in terms of density |
---|
| 48 | correlation functions, fractals, peaks, power laws, etc |
---|
[5295cf5] | 49 | * *Paracrystal* - semi ordered structures (bcc, fcc, etc) |
---|
[a6f3613] | 50 | * *Structure Factor* - S(Q) models |
---|
[5295cf5] | 51 | * *Plugin Models* - User-created (custom/non-library) Python models |
---|
[ec392464] | 52 | |
---|
[a6f3613] | 53 | Use the *Category* drop-down menu to chose a category of model, then select |
---|
[f3377b8] | 54 | a model from the drop-down menu beneath. A graph of the chosen model, calculated |
---|
| 55 | using default parameter values, will appear. The graph will update dynamically |
---|
| 56 | as the parameter values are changed. |
---|
| 57 | |
---|
| 58 | You can decide your own model categorizations using the :ref:`Category_Manager`. |
---|
[ce62e75] | 59 | |
---|
[a6f3613] | 60 | Once you have selected a model you can read its help documentation by clicking |
---|
| 61 | on the *Description* button to the right. |
---|
| 62 | |
---|
[dbc1f73] | 63 | S(Q) models can be combined with models in the other categories to generate |
---|
| 64 | what SasView calls :ref:`Product_Models`. |
---|
| 65 | |
---|
[a6f3613] | 66 | Show 1D/2D |
---|
| 67 | ^^^^^^^^^^ |
---|
| 68 | |
---|
| 69 | Models are normally fitted to 1D (ie, I(Q) vs Q) data sets, but some models in |
---|
| 70 | SasView can also be fitted to 2D (ie, I(Qx,Qy) vs Qx vs Qy) data sets. |
---|
| 71 | |
---|
| 72 | *NB: Magnetic scattering can only be fitted in SasView in 2D.* |
---|
| 73 | |
---|
| 74 | To activate 2D fitting mode, click the *Show 2D* button on the *Fit Page*. To |
---|
| 75 | return to 1D fitting model, click the same button (which will now say *Show 1D*). |
---|
[ce62e75] | 76 | |
---|
[ec392464] | 77 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 78 | |
---|
[a6f3613] | 79 | .. _Category_Manager: |
---|
[a0637de] | 80 | |
---|
[a6f3613] | 81 | Category Manager |
---|
| 82 | ---------------- |
---|
| 83 | |
---|
[f3377b8] | 84 | To change the model categorizations, either choose *Category Manager* from the |
---|
| 85 | *View* option on the menubar, or click on the *Modify* button on the *Fit Page*. |
---|
[a6f3613] | 86 | |
---|
[6aad2e8] | 87 | .. image:: cat_fig0.png |
---|
[a6f3613] | 88 | |
---|
[5295cf5] | 89 | The categorization of all models except the user supplied Plugin Models can be |
---|
| 90 | reassigned, added to, and removed using *Category Manager*. Models can also be |
---|
| 91 | hidden from view in the drop-down menus. |
---|
[a6f3613] | 92 | |
---|
[6aad2e8] | 93 | .. image:: cat_fig1.png |
---|
[a6f3613] | 94 | |
---|
[f3377b8] | 95 | Changing category |
---|
| 96 | ^^^^^^^^^^^^^^^^^ |
---|
[a6f3613] | 97 | |
---|
[5295cf5] | 98 | To change category, highlight a model in the list by left-clicking on its entry |
---|
| 99 | and then click the *Modify* button. Use the *Change Category* panel that appears |
---|
| 100 | to make the required changes. |
---|
[a6f3613] | 101 | |
---|
[6aad2e8] | 102 | .. image:: cat_fig2.png |
---|
[a6f3613] | 103 | |
---|
[f3377b8] | 104 | To create a category for the selected model, click the *Add* button. In order |
---|
| 105 | to delete a category, select the category name and click the *Remove Selected* |
---|
| 106 | button. Then click *Done*. |
---|
[a6f3613] | 107 | |
---|
[f3377b8] | 108 | Showing/hiding models |
---|
| 109 | ^^^^^^^^^^^^^^^^^^^^^ |
---|
[a6f3613] | 110 | |
---|
[5295cf5] | 111 | Use the *Enable All / Disable All* buttons and the check boxes beside each model |
---|
| 112 | to select the models to show/hide. To apply the selection, click *Ok*. Otherwise |
---|
| 113 | click *Cancel*. |
---|
[a6f3613] | 114 | |
---|
[8570246] | 115 | *NB: It may be necessary to change to a different category and then back again* |
---|
[f3377b8] | 116 | *before any changes take effect.* |
---|
[a6f3613] | 117 | |
---|
| 118 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 119 | |
---|
[f3377b8] | 120 | Model Functions |
---|
| 121 | --------------- |
---|
[a6f3613] | 122 | |
---|
[5295cf5] | 123 | For a complete list of all the library models available in SasView, see |
---|
[dbc1f73] | 124 | the `Model Documentation <../../../sasgui/perspectives/fitting/models/index.html>`_ . |
---|
[a6f3613] | 125 | |
---|
[f3377b8] | 126 | It is also possible to add your own models. |
---|
[a6f3613] | 127 | |
---|
[f3377b8] | 128 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
[a6f3613] | 129 | |
---|
[b5846a10] | 130 | .. _Adding_your_own_models: |
---|
| 131 | |
---|
[3e1c9e5] | 132 | Adding your own Models |
---|
[f3377b8] | 133 | ---------------------- |
---|
[a6f3613] | 134 | |
---|
[3e1c9e5] | 135 | There are essentially three ways to generate new fitting models for SasView: |
---|
| 136 | |
---|
[5295cf5] | 137 | * Using the SasView :ref:`New_Plugin_Model` helper dialog (best for beginners |
---|
| 138 | and/or relatively simple models) |
---|
| 139 | * By copying/editing an existing model (this can include models generated by |
---|
[5005ae0] | 140 | the New Plugin Model* dialog) in the :ref:`Python_shell` or |
---|
[5295cf5] | 141 | :ref:`Advanced_Plugin_Editor` (suitable for all use cases) |
---|
| 142 | * By writing a model from scratch outside of SasView (only recommended for code |
---|
| 143 | monkeys!) |
---|
[3e1c9e5] | 144 | |
---|
| 145 | Please read the guidance on :ref:`Writing_a_Plugin` before proceeding. |
---|
[f3377b8] | 146 | |
---|
[3e1c9e5] | 147 | **To be found by SasView your model must reside in the *~\\.sasview\\plugin_models* folder.** |
---|
[f3377b8] | 148 | |
---|
[a6f3613] | 149 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 150 | |
---|
[3e1c9e5] | 151 | .. _Plugin_Model_Operations: |
---|
[f3377b8] | 152 | |
---|
[3e1c9e5] | 153 | Plugin Model Operations |
---|
| 154 | ----------------------- |
---|
[a6f3613] | 155 | |
---|
[3e1c9e5] | 156 | From the *Fitting* option in the menu bar, select *Plugin Model Operations* |
---|
[a6f3613] | 157 | |
---|
[82b0b05e] | 158 | .. image:: edit_model_menu.png |
---|
[a6f3613] | 159 | |
---|
[3e1c9e5] | 160 | and then one of the sub-options |
---|
[f3377b8] | 161 | |
---|
[3e1c9e5] | 162 | * *New Plugin Model* - to create a plugin model template with a helper dialog |
---|
| 163 | * *Sum|Multi(p1,p2)* - to create a plugin model by summing/multiplying *existing models* in the model library |
---|
| 164 | * *Advanced Plugin Editor* - to create/edit a plugin model in a Python shell |
---|
| 165 | * *Delete Plugin Models* - to delete a plugin model |
---|
| 166 | * *Load Plugin Models* - to (re-)load plugin models |
---|
[a6f3613] | 167 | |
---|
[3e1c9e5] | 168 | .. _New_Plugin_Model: |
---|
| 169 | |
---|
| 170 | New Plugin Model |
---|
| 171 | ^^^^^^^^^^^^^^^^ |
---|
[a6f3613] | 172 | |
---|
[5295cf5] | 173 | Relatively straightforward models can be programmed directly from the SasView |
---|
| 174 | GUI using the *New Plugin Model Function*. |
---|
[26c8be3] | 175 | |
---|
[6aad2e8] | 176 | .. image:: new_model.png |
---|
[a6f3613] | 177 | |
---|
[5005ae0] | 178 | When using this feature, be aware that even if your code has errors, including |
---|
| 179 | syntax errors, a model file is still generated. When you then correct the errors |
---|
| 180 | and click 'Apply' again to re-compile you will get an error informing you that |
---|
| 181 | the model already exists if the 'Overwrite' box is not checked. In this case you |
---|
| 182 | will need to supply a new model function name. By default the 'Overwrite' box is |
---|
[26c8be3] | 183 | *checked*\ . |
---|
[f3377b8] | 184 | |
---|
[26c8be3] | 185 | A model file generated by this option can be viewed and further modified using |
---|
| 186 | the :ref:`Advanced_Plugin_Editor` . |
---|
[05829fb] | 187 | |
---|
[8b89396] | 188 | Note that the New Plugin Model Feature currently does not allow for parameters |
---|
| 189 | to be polydisperse. However they can be edited in the Advanced Editor. |
---|
| 190 | |
---|
| 191 | |
---|
| 192 | **SasView version 4.2** made it possible to specify whether a plugin created |
---|
| 193 | with the *New Plugin Model* dialog is actually a form factor P(Q) or a structure |
---|
| 194 | factor S(Q). To do this, simply add one or other of the following lines under |
---|
| 195 | the *import* statements. |
---|
[f485ba0] | 196 | |
---|
| 197 | For a form factor:: |
---|
| 198 | |
---|
| 199 | form_factor = True |
---|
[5005ae0] | 200 | |
---|
[f485ba0] | 201 | or for a structure factor:: |
---|
| 202 | |
---|
| 203 | structure_factor = True |
---|
[5005ae0] | 204 | |
---|
[8b89396] | 205 | If the plugin is a structure factor it is *also* necessary to add two variables |
---|
| 206 | to the parameter list:: |
---|
[f485ba0] | 207 | |
---|
[5005ae0] | 208 | parameters = [ |
---|
[ca383a0] | 209 | ['radius_effective', '', 1, [0.0, numpy.inf], 'volume', ''], |
---|
| 210 | ['volfraction', '', 1, [0.0, 1.0], '', ''], |
---|
[e081946] | 211 | [...], |
---|
[f485ba0] | 212 | |
---|
| 213 | and to the declarations of the functions Iq and Iqxy::: |
---|
| 214 | |
---|
| 215 | def Iq(x , radius_effective, volfraction, ...): |
---|
| 216 | |
---|
| 217 | def Iqxy(x, y, radius_effective, volfraction, ...): |
---|
| 218 | |
---|
[5005ae0] | 219 | Such a plugin should then be available in the S(Q) drop-down box on a FitPage (once |
---|
[f485ba0] | 220 | a P(Q) model has been selected). |
---|
| 221 | |
---|
[a6f3613] | 222 | Sum|Multi(p1,p2) |
---|
| 223 | ^^^^^^^^^^^^^^^^ |
---|
| 224 | |
---|
[6aad2e8] | 225 | .. image:: sum_model.png |
---|
[a0637de] | 226 | |
---|
[5295cf5] | 227 | This option creates a custom Plugin Model of the form:: |
---|
[f3377b8] | 228 | |
---|
[5295cf5] | 229 | Plugin Model = scale_factor * {(scale_1 * model_1) +/- (scale_2 * model_2)} + background |
---|
[f3377b8] | 230 | |
---|
[3e1c9e5] | 231 | or:: |
---|
| 232 | |
---|
[f485ba0] | 233 | Plugin Model = scale_factor * (model1 * model2) + background |
---|
[3e1c9e5] | 234 | |
---|
| 235 | In the *Easy Sum/Multi Editor* give the new model a function name and brief |
---|
| 236 | description (to appear under the *Details* button on the *FitPage*). Then select |
---|
[f3377b8] | 237 | two existing models, as p1 and p2, and the required operator, '+' or '*' between |
---|
[f485ba0] | 238 | them. Finally, click the *Apply* button to generate and test the model and then click *Close*. |
---|
[f3377b8] | 239 | |
---|
[5005ae0] | 240 | Any changes to a plugin model generated in this way only become effective *after* it is re-selected |
---|
| 241 | from the plugin models drop-down menu on the FitPage. If the model is not listed you can force a |
---|
[f485ba0] | 242 | recompilation of the plugins by selecting *Fitting* > *Plugin Model Operations* > *Load Plugin Models*. |
---|
| 243 | |
---|
[5005ae0] | 244 | **SasView version 4.2** introduced a much simplified and more extensible structure for plugin models |
---|
| 245 | generated through the Easy Sum/Multi Editor. For example, the code for a combination of a sphere model |
---|
[f485ba0] | 246 | with a power law model now looks like this:: |
---|
| 247 | |
---|
| 248 | from sasmodels.core import load_model_info |
---|
| 249 | from sasmodels.sasview_model import make_model_from_info |
---|
[5005ae0] | 250 | |
---|
[f485ba0] | 251 | model_info = load_model_info('sphere+power_law') |
---|
[e081946] | 252 | model_info.name = 'MyPluginModel' |
---|
[f485ba0] | 253 | model_info.description = 'sphere + power_law' |
---|
| 254 | Model = make_model_from_info(model_info) |
---|
| 255 | |
---|
[5005ae0] | 256 | To change the models or operators contributing to this plugin it is only necessary to edit the string |
---|
| 257 | in the brackets after *load_model_info*, though it would also be a good idea to update the model name |
---|
[f485ba0] | 258 | and description too!!! |
---|
| 259 | |
---|
[5005ae0] | 260 | The model specification string can handle multiple models and combinations of operators (+ or *) which |
---|
| 261 | are processed according to normal conventions. Thus 'model1+model2*model3' would be valid and would |
---|
| 262 | multiply model2 by model3 before adding model1. In this example, parameters in the *FitPage* would be |
---|
| 263 | prefixed A (for model2), B (for model3) and C (for model1). Whilst this might appear a little |
---|
| 264 | confusing, unless you were creating a plugin model from multiple instances of the same model the parameter |
---|
[e081946] | 265 | assignments ought to be obvious when you load the plugin. |
---|
[f485ba0] | 266 | |
---|
[5005ae0] | 267 | If you need to include another plugin model in the model specification string, just prefix the name of |
---|
[e081946] | 268 | that model with *custom*. For instance:: |
---|
| 269 | |
---|
| 270 | sphere+custom.MyPluginModel |
---|
| 271 | |
---|
| 272 | To create a P(Q)*\S(Q) model use the @ symbol instead of * like this:: |
---|
| 273 | |
---|
| 274 | sphere@hardsphere |
---|
[5005ae0] | 275 | |
---|
| 276 | This streamlined approach to building complex plugin models from existing library models, or models |
---|
| 277 | available on the *Model Marketplace*, also permits the creation of P(Q)*\S(Q) plugin models, something |
---|
| 278 | that was not possible in earlier versions of SasView. |
---|
[f3377b8] | 279 | |
---|
[3e1c9e5] | 280 | .. _Advanced_Plugin_Editor: |
---|
[f3377b8] | 281 | |
---|
[3e1c9e5] | 282 | Advanced Plugin Editor |
---|
| 283 | ^^^^^^^^^^^^^^^^^^^^^^ |
---|
[ec392464] | 284 | |
---|
[3e1c9e5] | 285 | Selecting this option shows all the plugin models in the plugin model folder, on Windows this is |
---|
[f3377b8] | 286 | |
---|
[afb93df] | 287 | *C:\\Users\\{username}\\.sasview\\plugin_models* |
---|
[f3377b8] | 288 | |
---|
| 289 | You can edit, modify, and save the Python code in any of these models using the |
---|
[3e1c9e5] | 290 | *Advanced Plugin Model Editor*. Note that this is actually the same tool as the :ref:`Python_shell` . |
---|
[f3377b8] | 291 | |
---|
[afb93df] | 292 | For details of the SasView plugin model format see :ref:`Writing_a_Plugin` . |
---|
[05829fb] | 293 | |
---|
[afb93df] | 294 | .. note:: Model files generated with the Sum/Multi option are still using the SasView 3.x model format. Unless you are confident about what you are doing, it is recommended that you only modify lines denoted with the ## <----- comments! |
---|
[f3377b8] | 295 | |
---|
[3e1c9e5] | 296 | 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'. |
---|
[f3377b8] | 297 | |
---|
[3e1c9e5] | 298 | .. image:: ../calculator/new_pycrust_example_2.png |
---|
| 299 | |
---|
| 300 | To use the model, go to the relevant *Fit Page*, select the *Plugin Models* |
---|
[f3377b8] | 301 | category and then select the model from the drop-down menu. |
---|
| 302 | |
---|
[3e1c9e5] | 303 | 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. |
---|
[a6f3613] | 304 | |
---|
[3e1c9e5] | 305 | Delete Plugin Models |
---|
| 306 | ^^^^^^^^^^^^^^^^^^^^ |
---|
[a6f3613] | 307 | |
---|
[3e1c9e5] | 308 | Simply highlight the plugin model to be removed. The operation is final!!! |
---|
[f3377b8] | 309 | |
---|
[5295cf5] | 310 | *NB: Models shipped with SasView cannot be removed in this way.* |
---|
[ec392464] | 311 | |
---|
[3e1c9e5] | 312 | Load Plugin Models |
---|
| 313 | ^^^^^^^^^^^^^^^^^^ |
---|
[afb93df] | 314 | |
---|
[5295cf5] | 315 | This option loads (or re-loads) all models present in the |
---|
| 316 | *~\\.sasview\\plugin_models* folder. |
---|
[afb93df] | 317 | |
---|
[ec392464] | 318 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 319 | |
---|
[4666660] | 320 | .. _Fitting_Options: |
---|
| 321 | |
---|
[f3377b8] | 322 | Fitting Options |
---|
| 323 | --------------- |
---|
[a6f3613] | 324 | |
---|
[f3377b8] | 325 | It is possible to specify which optimiser SasView should use to fit the data, and |
---|
| 326 | to modify some of the configurational parameters for each optimiser. |
---|
| 327 | |
---|
| 328 | From *Fitting* in the menu bar select *Fit Options*, then select one of the following |
---|
| 329 | optimisers: |
---|
[a6f3613] | 330 | |
---|
[f3377b8] | 331 | * DREAM |
---|
| 332 | * Levenberg-Marquardt |
---|
| 333 | * Quasi-Newton BFGS |
---|
| 334 | * Differential Evolution |
---|
| 335 | * Nelder-Mead Simplex |
---|
[a6f3613] | 336 | |
---|
[6af2785] | 337 | The DREAM optimiser is the most sophisticated, but may not necessarily be the best |
---|
| 338 | option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser |
---|
| 339 | initially. |
---|
| 340 | |
---|
[f3377b8] | 341 | These optimisers form the *Bumps* package written by P Kienzle. For more information |
---|
[4666660] | 342 | on each optimiser, see the :ref:`Fitting_Documentation`. |
---|
[a6f3613] | 343 | |
---|
[f3377b8] | 344 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
[a6f3613] | 345 | |
---|
[b7ce5ad] | 346 | Fitting Integer Parameters |
---|
| 347 | -------------------------- |
---|
| 348 | |
---|
| 349 | Most of the parameters in SasView models will naturally take floating point (decimal) |
---|
| 350 | values, but there are some parameters which can only have integer values. Examples |
---|
| 351 | include, but are not limited to, the number of shells in a multilayer vesicle, the |
---|
| 352 | number of beads in a pearl necklace, the number of arms of a star polymer, and so on. |
---|
| 353 | Wherever possible/recognised, the integer nature of a parameter is specified in the |
---|
| 354 | respective model documentation and/or parameter table, so read the documentation |
---|
| 355 | carefully! |
---|
| 356 | |
---|
| 357 | Integer parameters must be fitted with care. |
---|
| 358 | |
---|
| 359 | Start with your best possible guess for the value of the parameter. And using |
---|
| 360 | *a priori* knowledge, fix as many of the other parameters as possible. |
---|
| 361 | |
---|
| 362 | The SasView optimizers treat integer parameters internally as floating point |
---|
| 363 | numbers, but the values presented to the user are truncated or rounded, as |
---|
| 364 | appropriate. |
---|
| 365 | |
---|
| 366 | In most instances integer parameters will probably be greater than zero. A good |
---|
| 367 | policy in such cases is to use a constraint to enforce this. |
---|
| 368 | |
---|
| 369 | Because an integer parameter should, by definition, only move in integer steps, |
---|
| 370 | problems may be encountered if the optimizer step size is too small. Similarly, |
---|
| 371 | be **very careful** about applying polydispersity to integer parameters. |
---|
| 372 | |
---|
| 373 | The Levenberg-Marquardt and Quasi-Newton BFGS (and other derivative-based) |
---|
| 374 | optimizers are probably best avoided for fitting models with integer parameters. |
---|
| 375 | |
---|
| 376 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 377 | |
---|
[5ac0a7a] | 378 | Fitting Limits |
---|
| 379 | -------------- |
---|
| 380 | |
---|
| 381 | By default, *SasView* will attempt to model fit the full range of the data; ie, |
---|
| 382 | across all *Q* values. If necessary, however, it is possible to specify only a |
---|
| 383 | sub-region of the data for fitting. |
---|
| 384 | |
---|
| 385 | In a *FitPage* or *BatchPage* change the *Q* values in the *Min* and/or *Max* |
---|
| 386 | text boxes. Vertical coloured bars will appear on the graph with the data and |
---|
| 387 | 'theory' indicating the current *Q* limits (red = *Qmin*, purple = *Qmax*). |
---|
| 388 | |
---|
| 389 | To return to including all data in the fit, click the *Reset* button. |
---|
| 390 | |
---|
| 391 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 392 | |
---|
| 393 | |
---|
[f3377b8] | 394 | Shortcuts |
---|
| 395 | --------- |
---|
[a6f3613] | 396 | |
---|
[f3377b8] | 397 | Copy/Paste Parameters |
---|
| 398 | ^^^^^^^^^^^^^^^^^^^^^ |
---|
[a6f3613] | 399 | |
---|
[f3377b8] | 400 | It is possible to copy the parameters from one *Fit Page* and to paste them into |
---|
| 401 | another *Fit Page* using the same model. |
---|
[a6f3613] | 402 | |
---|
[f3377b8] | 403 | To *copy* parameters, either: |
---|
[a6f3613] | 404 | |
---|
[f3377b8] | 405 | * Select *Edit -> Copy Params* from the menu bar, or |
---|
| 406 | * Use Ctrl(Cmd on Mac) + Left Mouse Click on the *Fit Page*. |
---|
[a6f3613] | 407 | |
---|
[f3377b8] | 408 | To *paste* parameters, either: |
---|
| 409 | |
---|
| 410 | * Select *Edit -> Paste Params* from the menu bar, or |
---|
| 411 | * Use Ctrl(Cmd on Mac) + Shift + Left-click on the *Fit Page*. |
---|
| 412 | |
---|
| 413 | If either operation is successful a message will appear in the info line at the |
---|
| 414 | bottom of the SasView window. |
---|
| 415 | |
---|
| 416 | Bookmark |
---|
| 417 | ^^^^^^^^ |
---|
[a6f3613] | 418 | |
---|
[1fda506] | 419 | To *Bookmark* a *Fit Page* either: |
---|
[a6f3613] | 420 | |
---|
[f3377b8] | 421 | * Select a *Fit Page* and then click on *Bookmark* in the tool bar, or |
---|
| 422 | * Right-click and select the *Bookmark* in the popup menu. |
---|
[a6f3613] | 423 | |
---|
| 424 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 425 | |
---|
[4666660] | 426 | .. _Status_bar: |
---|
| 427 | |
---|
[1fda506] | 428 | Status Bar & Console |
---|
| 429 | -------------------- |
---|
| 430 | |
---|
| 431 | The status bar is located at the bottom of the SasView window and displays |
---|
| 432 | messages, hints, warnings and errors. |
---|
| 433 | |
---|
| 434 | At the right-hand side of the status bar is a button marked *Console*. The *Console* |
---|
| 435 | displays available message history and some run-time traceback information. |
---|
| 436 | |
---|
| 437 | During a long task the *Console* can also be used to monitor the progress. |
---|
| 438 | |
---|
| 439 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 440 | |
---|
[6af2785] | 441 | .. _Single_Fit_Mode: |
---|
| 442 | |
---|
[a6f3613] | 443 | Single Fit Mode |
---|
| 444 | --------------- |
---|
[ec392464] | 445 | |
---|
[4666660] | 446 | *NB: Before proceeding, ensure that the Single Mode radio button at the bottom of* |
---|
| 447 | *the Data Explorer is checked (see the section* :ref:`Loading_data` *).* |
---|
| 448 | |
---|
[63d314b] | 449 | This mode fits one data set. |
---|
| 450 | |
---|
[b64b87c] | 451 | When data is sent to the fitting it is plotted in a graph window as markers. |
---|
[4666660] | 452 | |
---|
| 453 | If a graph does not appear, or a graph window appears but is empty, then the data |
---|
| 454 | has not loaded correctly. Check to see if there is a message in the :ref:`Status_Bar` |
---|
| 455 | or in the *Console* window. |
---|
| 456 | |
---|
| 457 | Assuming the data has loaded correctly, when a model is selected a green model |
---|
| 458 | calculation (or what SasView calls a 'Theory') line will appear in the earlier graph |
---|
| 459 | window, and a second graph window will appear displaying the residuals (the |
---|
| 460 | difference between the experimental data and the theory) at the same X-data values. |
---|
[f9250dc] | 461 | See :ref:`Assessing_Fit_Quality`. |
---|
[4666660] | 462 | |
---|
[a7c6f38] | 463 | The objective of model-fitting is to find a *physically-plausible* model, and |
---|
| 464 | set of model parameters, that generate a theory that reproduces the experimental |
---|
| 465 | data and minimizes the values of the residuals. |
---|
[4666660] | 466 | |
---|
| 467 | Change the default values of the model parameters by hand until the theory line |
---|
[a7c6f38] | 468 | starts to represent the experimental data. Then check the tick boxes alongside |
---|
[84ac3f1] | 469 | the 'background' and 'scale' parameters. Click the *Fit* button. SasView |
---|
[a7c6f38] | 470 | will optimise the values of the 'background' and 'scale' and also display the |
---|
| 471 | corresponding uncertainties on the optimised values. |
---|
[4666660] | 472 | |
---|
[a7c6f38] | 473 | .. note:: |
---|
[84ac3f1] | 474 | If the uncertainty on a fitted parameter is unrealistically large, or if it |
---|
| 475 | displays as NaN, the model is most likely a poor representation of the data, |
---|
| 476 | the parameter in question is highly correlated with one or more of the other |
---|
| 477 | fitted parameters, or the model is relatively insensitive to the value of |
---|
| 478 | that particular parameter. |
---|
[4666660] | 479 | |
---|
[47ace50] | 480 | In the bottom left corner of the *Fit Page* is a box displaying a normalised |
---|
| 481 | value of the statistical $\chi^2$ parameter (the reduced $\chi^2$, |
---|
| 482 | See :ref:`Assessing_Fit_Quality`) returned by the optimiser. |
---|
[4666660] | 483 | |
---|
| 484 | Now check the box for another model parameter and click *Fit* again. Repeat this |
---|
[84ac3f1] | 485 | process until all relevant parameters are checked and have been optimised. As |
---|
| 486 | the fit of the theory to the experimental data improves, the value of 'Reduced |
---|
| 487 | Chi2' will decrease. A good model fit should produce values of Reduced Chi2 |
---|
| 488 | close to one, and certainly << 100. See :ref:`Assessing_Fit_Quality`. |
---|
[4666660] | 489 | |
---|
| 490 | SasView has a number of different optimisers (see the section :ref:`Fitting_Options`). |
---|
| 491 | The DREAM optimiser is the most sophisticated, but may not necessarily be the best |
---|
| 492 | option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser |
---|
| 493 | initially. |
---|
[ec392464] | 494 | |
---|
| 495 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 496 | |
---|
[a6f3613] | 497 | Simultaneous Fit Mode |
---|
| 498 | --------------------- |
---|
[ec392464] | 499 | |
---|
[63d314b] | 500 | *NB: Before proceeding, ensure that the Single Mode radio button at the bottom of* |
---|
| 501 | *the Data Explorer is checked (see the section* :ref:`Loading_data` *).* |
---|
[ec392464] | 502 | |
---|
[84ac3f1] | 503 | This mode is an extension of the :ref:`Single_Fit_Mode` that allows for some |
---|
| 504 | relatively extensive constraints between fitted parameters in a single *FitPage* |
---|
| 505 | or between several *FitPage*'s (eg, to constrain all fitted parameters to be the |
---|
| 506 | same in a contrast series of *FitPages* except for the solvent sld parameter, |
---|
[47ace50] | 507 | constrain the length to be twice that of the radius in a single *FitPage*, |
---|
[84ac3f1] | 508 | fix the radius of the sphere in one *FitPage* to be the same as the radius of |
---|
| 509 | the cylinder in a second *FitPage*, etc). |
---|
[63d314b] | 510 | |
---|
[b5846a10] | 511 | If the data to be fit are in multiple files, load each file, then select each file |
---|
| 512 | in the *Data Explorer*, and *Send To Fitting*. If multiple data sets are in one file, |
---|
| 513 | load that file, *Unselect All Data*, select just those data sets to be fitted, and |
---|
| 514 | *Send To Fitting*. Either way, the result should be that for *n* data sets you have |
---|
[6af2785] | 515 | 2\ *n* graphs (*n* of the data and model fit, and *n* of the resulting residuals). But |
---|
[f9250dc] | 516 | it may be helpful to minimise the residuals plots for clarity. Also see |
---|
| 517 | :ref:`Assessing_Fit_Quality`. |
---|
[b5846a10] | 518 | |
---|
[5295cf5] | 519 | *NB: If you need to use a custom Plugin Model, you must ensure that model is |
---|
| 520 | available first (see* :ref:`Adding_your_own_models` *).* |
---|
[b5846a10] | 521 | |
---|
[6af2785] | 522 | Method |
---|
| 523 | ^^^^^^ |
---|
| 524 | |
---|
[b5846a10] | 525 | Now go to each *FitPage* in turn and: |
---|
| 526 | |
---|
| 527 | Select the required category and model; |
---|
| 528 | |
---|
| 529 | Unselect all the model parameters; |
---|
| 530 | |
---|
| 531 | Enter some starting guesses for the parameters; |
---|
| 532 | |
---|
| 533 | Enter any parameter limits (recommended); |
---|
[63d314b] | 534 | |
---|
[b5846a10] | 535 | Select which parameters will refine (selecting all is generally a bad idea...); |
---|
[63d314b] | 536 | |
---|
[b5846a10] | 537 | When done, select *Constrained or Simultaneous Fit* under *Fitting* in the menu bar. |
---|
| 538 | |
---|
| 539 | In the *Const & Simul Fit* page that appears, select which data sets are to be |
---|
| 540 | simultaneously fitted (this will probably be all of them or you would not have loaded |
---|
| 541 | them in the first place!). |
---|
| 542 | |
---|
| 543 | To tie parameters between the data sets with constraints, check the 'yes' radio button |
---|
| 544 | next to *Add Constraint?* in the *Fit Constraints* box. |
---|
| 545 | |
---|
[84ac3f1] | 546 | To constrain all identically named parameters to fit *simultaneously* to the |
---|
| 547 | same value across all the *Fitpages* use the *Easy Setup* drop-down buttons in |
---|
| 548 | the *Const & Simul Fit* page. |
---|
[ec392464] | 549 | |
---|
[84ac3f1] | 550 | *NB: You can only constrain parameters that are set to refine.* |
---|
[b5846a10] | 551 | |
---|
[6af2785] | 552 | Constraints will generally be of the form |
---|
| 553 | |
---|
| 554 | Mi Parameter1 = Mj.Parameter1 |
---|
| 555 | |
---|
| 556 | however the text box after the '=' sign can be used to adjust this |
---|
| 557 | relationship; for example |
---|
| 558 | |
---|
| 559 | Mi Parameter1 = scalar \* Mj.Parameter1 |
---|
| 560 | |
---|
| 561 | A 'free-form' constraint box is also provided. |
---|
[b5846a10] | 562 | |
---|
| 563 | Many constraints can be entered for a single fit. |
---|
| 564 | |
---|
[84ac3f1] | 565 | When ready, click the *Fit* button on the *Const & Simul Fit* page, NOT the *Fit* |
---|
| 566 | button on the individual *FitPage*'s. |
---|
| 567 | |
---|
[b5846a10] | 568 | The results of the model-fitting will be returned to each of the individual |
---|
| 569 | *FitPage*'s. |
---|
[ec392464] | 570 | |
---|
[a7c6f38] | 571 | Note that the Reduced Chi2 value returned is the SUM of the Reduced Chi2 of |
---|
| 572 | each fit. To see the Reduced Chi2 value for a specific *FitPage*, click the |
---|
| 573 | *Compute* button at the bottom of that *FitPage* to recalculate. Note that in |
---|
[84ac3f1] | 574 | doing so the degrees of freedom will be set to Npts. |
---|
[a7c6f38] | 575 | See :ref:`Assessing_Fit_Quality`. Moreover in the case of constraints the |
---|
[84ac3f1] | 576 | degrees of freedom are less than one might think due to those constraints. |
---|
| 577 | |
---|
[ec392464] | 578 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 579 | |
---|
[e6c74e8] | 580 | .. _Batch_Fit_Mode: |
---|
| 581 | |
---|
[a6f3613] | 582 | Batch Fit Mode |
---|
| 583 | -------------- |
---|
[ec392464] | 584 | |
---|
[6af2785] | 585 | *NB: Before proceeding, ensure that the Single Mode radio button at the bottom of* |
---|
| 586 | *the Data Explorer is checked (see the section* :ref:`Loading_data` *). The Batch* |
---|
| 587 | *Mode button will be used later on!* |
---|
[63d314b] | 588 | |
---|
[6af2785] | 589 | This mode *sequentially* fits two or more data sets *to the same model*. Unlike in |
---|
| 590 | simultaneous fitting, in batch fitting it is not possible to constrain fit parameters |
---|
| 591 | between data sets. |
---|
[ec392464] | 592 | |
---|
[6af2785] | 593 | If the data to be fit are in multiple files, load each file in the *Data Explorer*. |
---|
| 594 | If multiple data sets are in one file, load just that file. *Unselect All Data*, then |
---|
| 595 | select a single initial data set to be fitted. Fit that selected data set as described |
---|
[5295cf5] | 596 | above under :ref:`Single_Fit_Mode`. |
---|
[ec392464] | 597 | |
---|
[5295cf5] | 598 | *NB: If you need to use a custom Plugin Model, you must ensure that model is |
---|
| 599 | available first (see* :ref:`Adding_your_own_models` *).* |
---|
[ec392464] | 600 | |
---|
[6af2785] | 601 | Method |
---|
| 602 | ^^^^^^ |
---|
[ec392464] | 603 | |
---|
[6af2785] | 604 | Now *Select All Data* in the *Data Explorer*, check the *Batch Mode* radio button |
---|
| 605 | at the bottom of that panel and *Send To Fitting*. A *BatchPage* will be created. |
---|
[ec392464] | 606 | |
---|
[6aad2e8] | 607 | .. image:: batch_button_area.png |
---|
[ec392464] | 608 | |
---|
[6af2785] | 609 | *NB: The Batch Page can also be created by checking the Batch Mode radio button* |
---|
| 610 | *and selecting New Fit Page under Fitting in the menu bar.* |
---|
[ec392464] | 611 | |
---|
[6af2785] | 612 | Using the drop-down menus in the *BatchPage*, now set up the *same* data set |
---|
| 613 | with the *same* model that you just fitted in single fit mode. A quick way to |
---|
| 614 | set the model parameter values is to just copy them from the earlier Single |
---|
| 615 | Fit. To do this, go back to the Single Fit *FitPage*, select *Copy Params* |
---|
| 616 | under *Edit* in the menu bar, then go back to the *BatchPage* and *Paste Params*. |
---|
[ec392464] | 617 | |
---|
[6af2785] | 618 | When ready, use the *Fit* button on the *BatchPage* to perform the fitting, NOT |
---|
| 619 | the *Fit* button on the individual *FitPage*'s. |
---|
[ec392464] | 620 | |
---|
[6af2785] | 621 | Unlike in single fit mode, the results of batch fits are not returned to |
---|
| 622 | the *BatchPage*. Instead, a spreadsheet-like :ref:`Grid_Window` will appear. |
---|
[ec392464] | 623 | |
---|
[6af2785] | 624 | If you want to visually check a graph of a particular fit, click on the name of |
---|
| 625 | a *Data set* in the *Grid Window* and then click the *View Fits* button. The |
---|
| 626 | data and the model fit will be displayed. If you select mutliple data sets they |
---|
| 627 | will all appear on one graph. |
---|
[ec392464] | 628 | |
---|
[6aad2e8] | 629 | .. image:: view_button.png |
---|
[ec392464] | 630 | |
---|
[6af2785] | 631 | *NB: In theory, returning to the BatchPage and changing the name of the I(Q)* |
---|
| 632 | *data source should also work, but at the moment whilst this does change the* |
---|
| 633 | *data set displayed it always superimposes the 'theory' corresponding to the* |
---|
| 634 | *starting parameters.* |
---|
[ec392464] | 635 | |
---|
[6af2785] | 636 | If you select a 'Chi2' value and click the *View Fits* button a graph of the |
---|
| 637 | residuals for that data set is displayed. Again, if you select multiple 'Chi2' |
---|
[f9250dc] | 638 | values then all the residuals data will appear on one graph. Also see |
---|
| 639 | :ref:`Assessing_Fit_Quality`. |
---|
[ec392464] | 640 | |
---|
[6af2785] | 641 | Chain Fitting |
---|
| 642 | ^^^^^^^^^^^^^ |
---|
[ec392464] | 643 | |
---|
[6af2785] | 644 | By default, the *same* parameter values copied from the initial single fit into |
---|
| 645 | the *BatchPage* will be used as the starting parameters for all batch fits. It |
---|
| 646 | is, however, possible to get *SasView* to use the results of a fit to a preceding |
---|
| 647 | data set as the starting parameters for the next fit in the sequence. This |
---|
| 648 | variation of batch fitting is called *Chain Fitting*, and will considerably speed |
---|
| 649 | up model-fitting if you have lots of very similar data sets where a few parameters |
---|
| 650 | are gradually changing. Do not use chain fitting on disparate data sets. |
---|
[ec392464] | 651 | |
---|
[6af2785] | 652 | To use chain fitting, select *Chain Fitting* under *Fitting* in the menu bar. It |
---|
| 653 | toggles on/off, so selecting it again will switch back to normal batch fitting. |
---|
[ec392464] | 654 | |
---|
[6af2785] | 655 | .. _Grid_Window: |
---|
[ec392464] | 656 | |
---|
[6af2785] | 657 | Grid Window |
---|
| 658 | ^^^^^^^^^^^ |
---|
[ec392464] | 659 | |
---|
[6af2785] | 660 | The *Grid Window* provides an easy way to view the results from batch fitting. |
---|
| 661 | It will be displayed automatically when a batch fit completes, but may be |
---|
| 662 | opened at any time by selecting *Show Grid Window* under *View* in the menu |
---|
| 663 | bar. |
---|
[ec392464] | 664 | |
---|
[6aad2e8] | 665 | .. image:: restore_batch_window.png |
---|
[ec392464] | 666 | |
---|
[6af2785] | 667 | Once a batch fit is completed, all model parameters are displayed but *not* |
---|
| 668 | their uncertainties. To view the uncertainties, click on a given column then |
---|
| 669 | go to *Edit* in the menu bar, select *Insert Column Before* and choose the |
---|
| 670 | required data from the list. An empty column can be inserted in the same way. |
---|
[ec392464] | 671 | |
---|
[6af2785] | 672 | To remove a column from the grid, click on the column header and choose |
---|
| 673 | *Remove Column* under *Edit* in the menu bar. The same functionality also |
---|
| 674 | allows you to re-order columns. |
---|
[ec392464] | 675 | |
---|
[6af2785] | 676 | *NB: You cannot insert/remove/re-order the rows in the Grid Window.* |
---|
[ec392464] | 677 | |
---|
[6af2785] | 678 | All of the above functions are also available by right-clicking on a column |
---|
| 679 | label. |
---|
[ec392464] | 680 | |
---|
[6aad2e8] | 681 | .. image:: edit_menu.png |
---|
[ec392464] | 682 | |
---|
[6af2785] | 683 | *NB: If there is an existing Grid Window and another batch fit is performed,* |
---|
| 684 | *an additional 'Table' tab will be added to the Grid Window.* |
---|
[ec392464] | 685 | |
---|
[6af2785] | 686 | The parameter values in the *currently selected* table of the *Grid Window* |
---|
| 687 | can be output to a CSV file by choosing *Save As* under *File* in the (*Grid* |
---|
| 688 | *Window*) menu bar. The default filename includes the date and time that the |
---|
| 689 | batch fit was performed. |
---|
[ec392464] | 690 | |
---|
[6af2785] | 691 | Saved CSV files can be reloaded by choosing *Open* under *File* in the *Grid* |
---|
| 692 | *Window* menu bar. The loaded parameters will appear in a new table tab. |
---|
[ec392464] | 693 | |
---|
[6aad2e8] | 694 | .. image:: file_menu.png |
---|
[ec392464] | 695 | |
---|
[6af2785] | 696 | *NB: Saving the Grid Window does not save any experimental data, residuals* |
---|
| 697 | *or actual model fits. Consequently if you reload a saved CSV file the* |
---|
| 698 | *ability to View Fits will be lost.* |
---|
[ec392464] | 699 | |
---|
[6af2785] | 700 | Parameter Plots |
---|
| 701 | ^^^^^^^^^^^^^^^ |
---|
[ec392464] | 702 | |
---|
[6af2785] | 703 | Any column of *numeric* parameter values can be plotted against another using |
---|
| 704 | the *Grid Window*. Simply select one column at the time and click the *Add* |
---|
| 705 | button next to the required *X/Y-axis Selection Range* text box. When both |
---|
| 706 | the X and Y axis boxes have been completed, click the *Plot* button. |
---|
[ec392464] | 707 | |
---|
[6af2785] | 708 | When the *Add* button is clicked, *SasView* also automatically completes the |
---|
| 709 | *X/Y-axis Label* text box with the heading from Row 1 of the selected table, |
---|
| 710 | but different labels and units can be entered manually. |
---|
[ec392464] | 711 | |
---|
[6aad2e8] | 712 | .. image:: plot_button.png |
---|
[ec392464] | 713 | |
---|
[6af2785] | 714 | The *X/Y-axis Selection Range* can be edited manually. The text control box |
---|
| 715 | recognises the operators +, -, \*, /, or 'pow', and allows the following |
---|
| 716 | types of expression : |
---|
[5005ae0] | 717 | |
---|
[6af2785] | 718 | 1) if an axis label range is a function of 1 or more *columns*, write |
---|
| 719 | this type of expression |
---|
[ec392464] | 720 | |
---|
[6af2785] | 721 | constant1 * column_name1 [minimum row index : maximum row index] |
---|
| 722 | operator constant2 * column_name2 [minimum row index : maximum row index] |
---|
[ec392464] | 723 | |
---|
[6af2785] | 724 | Example: radius [2 : 5] -3 * scale [2 : 5] |
---|
[ec392464] | 725 | |
---|
[6af2785] | 726 | 2) if only some *values* of a given column are needed but the range between |
---|
| 727 | the first row and the last row used is not continuous, write this type of |
---|
| 728 | expression |
---|
[ec392464] | 729 | |
---|
[6af2785] | 730 | column_name1 [minimum row index1 : maximum row index1] , column_name1 |
---|
| 731 | [minimum row index2 : maximum row index2] |
---|
[ec392464] | 732 | |
---|
[6af2785] | 733 | Example: radius [2 : 5] , radius [10 : 25] |
---|
[5005ae0] | 734 | |
---|
[9d93c37] | 735 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
| 736 | |
---|
| 737 | Combined Batch Fit Mode |
---|
| 738 | ----------------------- |
---|
| 739 | |
---|
[e6c74e8] | 740 | The purpose of the Combined Batch Fit is to allow running two or more batch |
---|
| 741 | fits in sequence without overwriting the output table of results. This may be |
---|
| 742 | of interest for example if one is fitting a series of data sets where there is |
---|
| 743 | a shape change occurring in the series that requires changing the model part |
---|
| 744 | way through the series; for example a sphere to rod transition. Indeed the |
---|
| 745 | regular batch mode does not allow for multiple models and requires all the |
---|
| 746 | files in the series to be fit with single model and set of parameters. While |
---|
| 747 | it is of course possible to just run part of the series as a batch fit using |
---|
| 748 | model one followed by running another batch fit on the rest of the series with |
---|
| 749 | model two (and/or model three etc), doing so will overwrite the table of |
---|
| 750 | outputs from the previous batch fit(s). This may not be desirable if one is |
---|
| 751 | interested in comparing the parameters: for example the sphere radius of set |
---|
[05b0bf6] | 752 | one and the cylinder radius of set two. |
---|
[e6c74e8] | 753 | |
---|
| 754 | Method |
---|
| 755 | ^^^^^^ |
---|
[9d93c37] | 756 | |
---|
[e6c74e8] | 757 | In order to use the *Combined Batch Fit*, first load all the data needed as |
---|
| 758 | described in :ref:`Loading_data`. Next start up two or more *BatchPage* fits |
---|
| 759 | following the instructions in :ref:`Batch_Fit_Mode` but **DO NOT PRESS FIT**. |
---|
| 760 | At this point the *Combine Batch Fit* menu item under the *Fitting menu* should |
---|
| 761 | be active (if there is one or no *BatchPage* the menu item will be greyed out |
---|
| 762 | and inactive). Clicking on *Combine Batch Fit* will bring up a new panel, |
---|
| 763 | similar to the *Const & Simult Fit* panel. In this case there will be a |
---|
| 764 | checkbox for each *BatchPage* instead of each *FitPage* that should be included |
---|
| 765 | in the fit. Once all are selected, click the Fit button on |
---|
| 766 | the *BatchPage* to run each batch fit in *sequence* |
---|
[9d93c37] | 767 | |
---|
| 768 | .. image:: combine_batch_page.png |
---|
| 769 | |
---|
[e6c74e8] | 770 | The batch table will then pop up at the end as for the case of the simple Batch |
---|
| 771 | Fitting with the following caveats: |
---|
[9d93c37] | 772 | |
---|
| 773 | .. note:: |
---|
| 774 | The order matters. The parameters in the table will be taken from the model |
---|
[e6c74e8] | 775 | used in the first *BatchPage* of the list. Any parameters from the |
---|
| 776 | second and later *BatchPage* s that have the same name as a parameter in the |
---|
| 777 | first will show up allowing for plotting of that parameter across the |
---|
| 778 | models. The other parameters will not be available in the grid. |
---|
[9d93c37] | 779 | .. note:: |
---|
| 780 | a corralary of the above is that currently models created as a sum|multiply |
---|
| 781 | model will not work as desired because the generated model parameters have a |
---|
| 782 | p#_ appended to the beginning and thus radius and p1_radius will not be |
---|
| 783 | recognized as the same parameter. |
---|
[5005ae0] | 784 | |
---|
[9d93c37] | 785 | .. image:: combine_batch_grid.png |
---|
| 786 | |
---|
[e6c74e8] | 787 | In the example shown above the data is a time series with a shifting peak. |
---|
| 788 | The first part of the series was fitted using the *broad_peak* model, while |
---|
| 789 | the rest of the data were fit using the *gaussian_peak* model. Unfortunately the |
---|
| 790 | time is not listed in the file but the file name contains the information. As |
---|
| 791 | described in :ref:`Grid_Window`, a column can be added manually, in this case |
---|
[5005ae0] | 792 | called time, and the peak position plotted against time. |
---|
[9d93c37] | 793 | |
---|
| 794 | .. image:: combine_batch_plot.png |
---|
| 795 | |
---|
[05b0bf6] | 796 | Note the discontinuity in the peak position. This reflects the fact that the |
---|
| 797 | Gaussian fit is a rather poor model for the data and is not actually |
---|
[e6c74e8] | 798 | finding the peak. |
---|
[ec392464] | 799 | |
---|
| 800 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
---|
[6af2785] | 801 | |
---|
[84ac3f1] | 802 | .*Document History* |
---|
| 803 | |
---|
| 804 | | 2017-09-10 Paul Butler |
---|
| 805 | | 2017-09-15 Steve King |
---|
| 806 | | 2018-03-05 Paul Butler |
---|