1 | Sasmodels |
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2 | ========= |
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3 | |
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4 | Theory models for small angle scattering. |
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5 | |
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6 | The models provided are usable directly in the bumps fitting package and |
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7 | in the sasview analysis package. If OpenCL is available, the models will |
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8 | run much faster. If not, then precompiled versions will be included with |
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9 | the distributed package. New models can be added if OpenCL or a C compiler |
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10 | is available. |
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11 | |
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12 | Install |
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13 | ------- |
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14 | |
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15 | The easiest way to use sasmodels is from `SasView <http://www.sasview.org/>`_. |
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16 | |
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17 | You can also install sasmodels as a standalone package in python. Using |
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18 | `miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ |
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19 | (or `anaconda <https://www.anaconda.com/>`_), |
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20 | create a python environment with the sasmodels dependencies:: |
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21 | |
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22 | $ conda create -n sasmodels -c conda-forge numpy scipy matplotlib pyopencl |
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23 | |
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24 | The option `-n sasmodels` names the environment sasmodels, and the option |
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25 | `-c conda-forge` selects the conda-forge package channel because pyopencl |
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26 | is not part of the base anaconda distribution. |
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27 | |
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28 | Activate the environment and install sasmodels:: |
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29 | |
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30 | $ conda activate sasmodels |
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31 | (sasmodels) $ pip install sasmodels |
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32 | |
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33 | Install `bumps <https://github.com/bumps/bumps>`_ if you want to use it to fit |
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34 | your data:: |
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35 | |
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36 | (sasmodels) $ pip install bumps |
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37 | |
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38 | Usage |
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39 | ----- |
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40 | |
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41 | Check that the works:: |
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42 | |
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43 | (sasmodels) $ python -m sasmodels.compare cylinder |
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44 | |
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45 | To show the orientation explorer:: |
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46 | |
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47 | (sasmodels) $ python -m sasmodels.jitter |
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48 | |
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49 | Documentation is available online as part of the SasView |
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50 | `fitting perspective <http://www.sasview.org/docs/index.html>`_ |
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51 | as well as separate pages for |
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52 | `individual models <http://www.sasview.org/docs/user/sasgui/perspectives/fitting/models/index.html>`_. |
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53 | Programming details for sasmodels are available in the |
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54 | `developer documentation <http://www.sasview.org/docs/dev/dev.html>`_. |
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55 | |
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56 | |
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57 | Fitting Example |
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58 | --------------- |
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59 | |
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60 | The example directory contains a radial+tangential data set for an oriented |
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61 | rod-like shape. |
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62 | |
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63 | To load the example data, you will need the SAS data loader from the sasview |
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64 | package. This is not yet available on PyPI, so you will need a copy of the |
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65 | SasView source code to run it. Create a directory somewhere to hold the |
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66 | sasview and sasmodels source code, which we will refer to as $SOURCE. |
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67 | |
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68 | Use the following to install sasview, and the sasmodels examples:: |
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69 | |
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70 | (sasmodels) $ cd $SOURCE |
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71 | (sasmodels) $ conda install git |
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72 | (sasmodels) $ git clone https://github.com/sasview/sasview.git |
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73 | (sasmodels) $ git clone https://github.com/sasview/sasmodels.git |
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74 | |
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75 | Set the path to the sasview source on your python path within the sasmodels |
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76 | environment. On Windows, this will be:: |
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77 | |
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78 | (sasmodels)> set PYTHONPATH="$SOURCE\sasview\src" |
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79 | (sasmodels)> cd $SOURCE/sasmodels/example |
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80 | (sasmodels)> python -m bumps.cli fit.py cylinder --preview |
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81 | |
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82 | On Mac/Linux with the standard shell this will be:: |
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83 | |
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84 | (sasmodels) $ export PYTHONPATH="$SOURCE/sasview/src" |
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85 | (sasmodels) $ cd $SOURCE/sasmodels/example |
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86 | (sasmodels) $ bumps fit.py cylinder --preview |
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87 | |
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88 | The fit.py model accepts up to two arguments. The first argument is the |
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89 | model type, which has been defined for cylinder, capped_cylinder, |
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90 | core_shell_cylinder, ellipsoid, triaxial_ellipsoid and lamellar. The |
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91 | second argument is view, which can be radial or tangential. To fit |
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92 | both radial and tangential simultaneously, use the word "both". |
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93 | |
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94 | See `bumps documentation <https://bumps.readthedocs.io/>`_ for detailed |
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95 | instructions on running the fit. |
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96 | |
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97 | |TravisStatus|_ |
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98 | |
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99 | .. |TravisStatus| image:: https://travis-ci.org/SasView/sasmodels.svg?branch=master |
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100 | .. _TravisStatus: https://travis-ci.org/SasView/sasmodels |
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