Changeset ade01a0 in sasmodels for README.rst
- Timestamp:
- Feb 24, 2019 7:11:27 PM (6 years ago)
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- master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
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- c03e0cc
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- cd28947
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README.rst
re30d645 rade01a0 10 10 is available. 11 11 12 Example 12 Install 13 13 ------- 14 15 The easiest way to use sasmodels is from `SasView <http://www.sasview.org/>`. 16 17 You can also install sasmodels as a standalone package in python. Using 18 `miniconda <https://docs.conda.io/en/latest/miniconda.html>` 19 (or `anaconda <https://www.anaconda.com/>`), 20 create a python environment with the sasmodels dependencies:: 21 22 $ conda create -n sasmodels -c conda-forge numpy scipy matplotlib pyopencl 23 24 The option `-n sasmodels` names the environment sasmodels, and the option 25 `-c conda-forge` selects the conda-forge package channel because pyopencl 26 is not part of the base anaconda distribution. 27 28 Activate the environment and install sasmodels:: 29 30 $ conda activate sasmodels 31 (sasmodels) $ pip install sasmodels 32 33 Install `bumps <https://github.com/bumps/bumps>` if you want to use it to fit 34 your data:: 35 36 (sasmodels) $ pip install bumps 37 38 Usage 39 ----- 40 41 Check that the works:: 42 43 (sasmodels) $ python -m sasmodels.compare cylinder 44 45 To show the orientation explorer:: 46 47 (sasmodels) $ python -m sasmodels.jitter 48 49 Documentation is available online as part of the SasView 50 `fitting perspective <http://www.sasview.org/docs/index.html>`_ 51 as well as separate pages for 52 `individual models <http://www.sasview.org/docs/user/sasgui/perspectives/fitting/models/index.html>`_. 53 Programming details for sasmodels are available in the 54 `developer documentation <http://www.sasview.org/docs/dev/dev.html>`_. 55 56 57 Fitting Example 58 --------------- 14 59 15 60 The example directory contains a radial+tangential data set for an oriented 16 61 rod-like shape. 17 62 18 The data is loaded by sas.dataloader from the sasview package, so sasview 19 is needed to run the example. 63 To load the example data, you will need the SAS data loader from the sasview 64 package. This is not yet available on PyPI, so you will need a copy of the 65 SasView source code to run it. Create a directory somewhere to hold the 66 sasview and sasmodels source code, which we will refer to as $SOURCE. 20 67 21 To run the example, you need sasview, sasmodels and bumps. Assuming these 22 repositories are installed side by side, change to the sasmodels/example 23 directory and enter:: 68 Use the following to install sasview, and the sasmodels examples:: 24 69 25 PYTHONPATH=..:../../sasview/src ../../bumps/run.py fit.py \ 26 cylinder --preview 70 (sasmodels) $ cd $SOURCE 71 (sasmodels) $ conda install git 72 (sasmodels) $ git clone https://github.com/sasview/sasview.git 73 (sasmodels) $ git clone https://github.com/sasview/sasmodels.git 27 74 28 See bumps documentation for instructions on running the fit. With the 29 python packages installed, e.g., into a virtual environment, then the 30 python path need not be set, and the command would be:: 75 Set the path to the sasview source on your python path within the sasmodels 76 environment. On Windows, this will be:: 31 77 32 bumps fit.py cylinder --preview 78 (sasmodels)> set PYTHONPATH="$SOURCE\sasview\src" 79 (sasmodels)> cd $SOURCE/sasmodels/example 80 (sasmodels)> python -m bumps.cli fit.py cylinder --preview 81 82 On Mac/Linux with the standard shell this will be:: 83 84 (sasmodels) $ export PYTHONPATH="$SOURCE/sasview/src" 85 (sasmodels) $ cd $SOURCE/sasmodels/example 86 (sasmodels) $ bumps fit.py cylinder --preview 33 87 34 88 The fit.py model accepts up to two arguments. The first argument is the … … 38 92 both radial and tangential simultaneously, use the word "both". 39 93 40 Notes 41 ----- 42 43 cylinder.c + cylinder.py is the cylinder model with renamed variables and 44 sld scaled by 1e6 so the numbers are nicer. The model name is "cylinder" 45 46 lamellar.py is an example of a single file model with embedded C code. 94 See `bumps documentation <https://bumps.readthedocs.io/>` for detailed 95 instructions on running the fit. 47 96 48 97 |TravisStatus|_
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