source: sasview/src/sas/sasgui/perspectives/fitting/media/plugin.rst @ b2a3814

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Writing a Plugin Model

Note

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Overview

You can write your own model and save it to the the SasView plugin_models folder

C:\Users\[username]\.sasview\plugin_models (on Windows)

The next time SasView is started it will compile the plugin and add it to the list of Customized Models in a FitPage. It is recommended that an existing model be used as a template.

SasView has three ways of writing models:

The built-in modules are available in the sasmodels-data\models subdirectory of your SasView installation folder. On Windows, this will be something like C:\Program Files (x86)\SasView\sasmodels-data\models. On Mac OSX, these will be within the application bundle as /Applications/SasView 4.0.app/Contents/Resources/sasmodels-data/models.

Other models are available for download from our Model Marketplace. You can contribute your own models to the Marketplace aswell.

Create New Model Files

In the ~\.sasview\plugin_models directory, copy the appropriate files (using the examples above as templates) to mymodel.py (and mymodel.c, etc) as required, where "mymodel" is the name for the model you are creating.

Please follow these naming rules:

  • No capitalization and thus no CamelCase
  • If necessary use underscore to separate words (i.e. barbell not BarBell or broad_peak not BroadPeak)
  • Do not include “modelâ€ᅵ in the name (i.e. barbell not BarBellModel)

Edit New Model Files

Model Contents

The model interface definition is in the .py file. This file contains:

  • a model name:
    • this is the name string in the .py file
    • titles should be:
    • all in lower case
    • without spaces (use underscores to separate words instead)
    • without any capitalization or CamelCase
    • without incorporating the word "model"
    • examples: barbell not BarBell; broad_peak not BroadPeak; barbell not BarBellModel
  • a model title:
    • this is the title string in the .py file
    • this is a one or two line description of the model, which will appear at the start of the model documentation and as a tooltip in the SasView GUI
  • a short discription:
    • this is the description string in the .py file
    • this is a medium length description which appears when you click Description on the model FitPage
  • a parameter table:
    • this will be auto-generated from the parameters in the .py file
  • a long description:
    • this is ReStructuredText enclosed between the r""" and """ delimiters at the top of the .py file
    • what you write here is abstracted into the SasView help documentation
    • this is what other users will refer to when they want to know what your model does; so please be helpful!
  • a definition of the model:
    • as part of the long description
  • a formula defining the function the model calculates:
    • as part of the long description
  • an explanation of the parameters:
    • as part of the long description
    • explaining how the symbols in the formula map to the model parameters
  • a plot of the function, with a figure caption:
    • this is automatically generated from your default parameters
  • at least one reference:
    • as part of the long description
    • specifying where the reader can obtain more information about the model
  • the name of the author
    • as part of the long description
    • the .py file should also contain a comment identifying who converted/created the model file

Models that do not conform to these requirements will never be incorporated into the built-in library.

More complete documentation for the sasmodels package can be found at http://www.sasview.org/sasmodels. In particular, http://www.sasview.org/sasmodels/api/generate.html#module-sasmodels.generate describes the structure of a model.

Model Documentation

The .py file starts with an r (for raw) and three sets of quotes to start the doc string and ends with a second set of three quotes. For example:

r"""
Definition
----------
The 1D scattering intensity of the sphere is calculated in the following
way (Guinier, 1955)
.. math::
    I(q) = \frac{\text{scale}}{V} \cdot \left[
        3V(\Delta\rho) \cdot \frac{\sin(qr) - qr\cos(qr))}{(qr)^3}
        \right]^2 + \text{background}
where *scale* is a volume fraction, $V$ is the volume of the scatterer,
$r$ is the radius of the sphere and *background* is the background level.
*sld* and *sld_solvent* are the scattering length densities (SLDs) of the
scatterer and the solvent respectively, whose difference is $\Delta\rho$.
You can included figures in your documentation, as in the following
figure for the cylinder model.
.. figure:: img/cylinder_angle_definition.jpg
    Definition of the angles for oriented cylinders.
References
----------
A Guinier, G Fournet, *Small-Angle Scattering of X-Rays*,
John Wiley and Sons, New York, (1955)
"""

This is where the FULL documentation for the model goes (to be picked up by the automatic documentation system). Although it feels odd, you should start the documentation immediately with the definition---the model name, a brief description and the parameter table are automatically inserted above the definition, and the a plot of the model is automatically inserted before the reference.

Figures can be included using the figure command, with the name of the .png file containing the figure and a caption to appear below the figure. Figure numbers will be added automatically.

See this Sphinx cheat sheet for a quick guide to the documentation layout commands, or the Sphinx Documentation for complete details.

The model should include a formula written using LaTeX markup. The example above uses the math command to make a displayed equation. You can also use $formula$ for an inline formula. This is handy for defining the relationship between the model parameters and formula variables, such as the phrase "$r$ is the radius" used above. The live demo MathJax page http://www.mathjax.org/ is handy for checking that the equations will look like you intend.

Math layout uses the amsmath package for aligning equations (see amsldoc.pdf on that page for complete documentation). You will automatically be in an aligned environment, with blank lines separating the lines of the equation. Place an ampersand before the operator on which to align. For example:

.. math::
  x + y &= 1 \\
  y &= x - 1

produces

x + y  = 1 y  = x − 1

If you need more control, use:

.. math::
    :nowrap:

Model Definition

Following the documentation string, there are a series of definitions:

name = "sphere"  # optional: defaults to the filename without .py
title = "Spheres with uniform scattering length density"
description = """\
P(q)=(scale/V)*[3V(sld-sld_solvent)*(sin(qr)-qr cos(qr))
                /(qr)^3]^2 + background
    r: radius of sphere
    V: The volume of the scatter
    sld: the SLD of the sphere
    sld_solvent: the SLD of the solvent
"""
category = "shape:sphere"
single = True   # optional: defaults to True
opencl = False  # optional: defaults to False
structure_factor = False  # optional: defaults to False

name = "mymodel" defines the name of the model that is shown to the user. If it is not provided, it will use the name of the model file, with '_' replaced by spaces and the parts capitalized. So adsorbed_layer.py will become Adsorbed Layer. The predefined models all use the name of the model file as the name of the model, so the default may be changed.

title = "short description" is short description of the model which is included after the model name in the automatically generated documentation. The title can also be used for a tooltip.

description = """doc string""" is a longer description of the model. It shows up when you press the "Description" button of the SasView FitPage. It should give a brief description of the equation and the parameters without the need to read the entire model documentation. The triple quotes allow you to write the description over multiple lines. Keep the lines short since the GUI will wrap each one separately if they are too long. Make sure the parameter names in the description match the model definition!

category = "shape:sphere" defines where the model will appear in the model documentation. In this example, the model will appear alphabetically in the list of spheroid models in the Shape category.

single = True indicates that the model can be run using single precision floating point values. Set it to False if the numerical calculation for the model is unstable, which is the case for about 20 of the built in models. It is worthwhile modifying the calculation to support single precision, allowing models to run up to 10 times faster. The section Test_Your_New_Model describes how to compare model values for single vs. double precision so you can decide if you need to set single to False.

opencl = False indicates that the model should not be run using OpenCL. This may be because the model definition includes code that cannot be compiled for the GPU (for example, goto statements). It can also be used for large models which can't run on most GPUs. This flag has not been used on any of the built in models; models which were failing were streamlined so this flag was not necessary.

structure_factor = True indicates that the model can be used as a structure factor to account for interactions between particles. See Form_Factors for more details.

Model Parameters

Next comes the parameter table. For example:

# pylint: disable=bad-whitespace, line-too-long
#   ["name",        "units", default, [min, max], "type",    "description"],
parameters = [
    ["sld",         "1e-6/Ang^2",  1, [-inf, inf], "sld",    "Layer scattering length density"],
    ["sld_solvent", "1e-6/Ang^2",  6, [-inf, inf], "sld",    "Solvent scattering length density"],
    ["radius",      "Ang",        50, [0, inf],    "volume", "Sphere radius"],
]
# pylint: enable=bad-whitespace, line-too-long

parameters = [["name", "units", default, [min,max], "type", "tooltip"],...] defines the parameters that form the model.

Note: The order of the parameters in the definition will be the order of the parameters in the user interface and the order of the parameters in Iq(), Iqxy() and form_volume(). And scale and background parameters are implicit to all models, so they do not need to be included in the parameter table.

  • "name" is the name of the parameter shown on the FitPage.

    • parameter names should follow the mathematical convention; e.g., radius_core not core_radius, or sld_solvent not solvent_sld.

    • model parameter names should be consistent between different models, so sld_solvent, for example, should have exactly the same name in every model.

    • to see all the parameter names currently in use, type the following in the python shell/editor under the Tools menu:

      import sasmodels.list_pars
      sasmodels.list_pars.list_pars()
      

      re-use as many as possible!!!

    • use "name[n]" for multiplicity parameters, where n is the name of the parameter defining the number of shells/layers/segments, etc.

  • "units" are displayed along with the parameter name

    • every parameter should have units; use "None" if there are no units.

    • sld's should be given in units of 1e-6/Ang^2, and not simply 1/Ang^2 to be consistent with the builtin models. Adjust your formulas appropriately.

    • fancy units markup is available for some units, including:

      Ang, 1/Ang, 1/Ang^2, 1e-6/Ang^2, degrees, 1/cm, Ang/cm, g/cm^3, mg/m^2
      
    • the list of units is defined in the variable RST_UNITS within sasmodels/generate.py

      • new units can be added using the macros defined in doc/rst_prolog in the sasmodels source.
      • units should be properly formatted using sub-/super-scripts and using negative exponents instead of the / operator, though the unit name should use the / operator for consistency.
      • please post a message to the SasView developers mailing list with your changes.
  • default is the initial value for the parameter.

    • the parameter default values are used to auto-generate a plot of the model function in the documentation.
  • [min, max] are the lower and upper limits on the parameter.

    • lower and upper limits can be any number, or -inf or inf.
    • the limits will show up as the default limits for the fit making it easy, for example, to force the radius to always be greater than zero.
  • "type" can be one of: "", "sld", "volume", or "orientation".

    • "sld" parameters can have magnetic moments when fitting magnetic models; depending on the spin polarization of the beam and the $q$ value being examined, the effective sld for that material will be used to compute the scattered intensity.
    • "volume" parameters are passed to Iq(), Iqxy(), and form_volume(), and have polydispersity loops generated automatically.
    • "orientation" parameters are only passed to Iqxy(), and have angular dispersion.

Model Computation

Models can be defined as pure python models, or they can be a mixture of python and C models. C models are run on the GPU if it is available, otherwise they are compiled and run on the CPU.

Models are defined by the scattering kernel, which takes a set of parameter values defining the shape, orientation and material, and returns the expected scattering. Polydispersity and angular dispersion are defined by the computational infrastructure. Any parameters defined as "volume" parameters are polydisperse, with polydispersity defined in proportion to their value. "orientation" parameters use angular dispersion defined in degrees, and are not relative to the current angle.

Based on a weighting function $G(x)$ and a number of points $n$, the computed value is

(q) = (G(x)I(q, x) dx)/(G(x)V(x) dx) ≈ (ni = 1G(xi)I(q, xi))/(ni = 1G(xi)V(xi))

That is, the indivdual models do not need to include polydispersity calculations, but instead rely on numerical integration to compute the appropriately smeared pattern. Angular dispersion values over polar angle $theta$ requires an additional $cos theta$ weighting due to decreased arc length for the equatorial angle $phi$ with increasing latitude.

Python Models

For pure python models, define the Iq function:

import numpy as np
from numpy import cos, sin, ...
def Iq(q, par1, par2, ...):
    return I(q, par1, par2, ...)
Iq.vectorized = True

The parameters par1, par2, ... are the list of non-orientation parameters to the model in the order that they appear in the parameter table. Note that the autogenerated model file uses x rather than q.

The .py file should import trigonometric and exponential functions from numpy rather than from math. This lets us evaluate the model for the whole range of $q$ values at once rather than looping over each $q$ separately in python. With $q$ as a vector, you cannot use if statements, but must instead do tricks like

a = x*q*(q>0) + y*q*(q<=0)

or

a = np.empty_like(q)
index = q>0
a[index] = x*q[index]
a[~index] = y*q[~index]

which sets $a$ to $q cdot x$ if $q$ is positive or $q cdot y$ if $q$ is zero or negative. If you have not converted your function to use $q$ vectors, you can set the following and it will only receive one $q$ value at a time:

Iq.vectorized = False

Return np.NaN if the parameters are not valid (e.g., cap_radius < radius in barbell). If I(q; pars) is NaN for any $q$, then those parameters will be ignored, and not included in the calculation of the weighted polydispersity.

Similar to Iq, you can define Iqxy(qx, qy, par1, par2, ...) where the parameter list includes any orientation parameters. If Iqxy is not defined, then it will default to Iqxy = Iq(sqrt(qx**2+qy**2), par1, par2, ...).

Models should define form_volume(par1, par2, ...) where the parameter list includes the volume parameters in order. This is used for a weighted volume normalization so that scattering is on an absolute scale. If form_volume is not defined, then the default form_volume = 1.0 will be used.

Embedded C Models

Like pure python models, inline C models need to define an Iq function:

Iq = """
    return I(q, par1, par2, ...);
"""

This expands into the equivalent C code:

#include <math.h>
double Iq(double q, double par1, double par2, ...);
double Iq(double q, double par1, double par2, ...)
{
    return I(q, par1, par2, ...);
}

The C model operates on a single $q$ value at a time. The code will be run in parallel across different $q$ values, either on the graphics card or the processor.

Rather than returning NAN from Iq, you must define the INVALID(v). The v parameter lets you access all the parameters in the model using v.par1, v.par2, etc. For example:

#define INVALID(v) (v.bell_radius < v.radius)

Iqxy is similar to Iq, except it uses parameters qx, qy instead of q, and it includes orientation parameters. As in python models, form_volume includes only the volume parameters. Iqxy will default to Iq(sqrt(qx**2 + qy**2), par1, ...) and form_volume will default to 1.0.

The C code follows the C99 standard, including the usual math functions, as defined in OpenCL.

The standard constants and functions include the following:

M_PI = pi
M_PI_2 = pi/2
M_PI_4 = pi/4
M_E = e
M_SQRT1_2 = 1/sqrt(2)
NAN = NaN
INFINITY = 1/0
erf(x) = error function
erfc(x) = 1-erf(x)
expm1(x) = exp(x) - 1
tgamma(x) = gamma function

Some non-standard constants and functions are also provided:

M_PI_180 = pi/180
M_4PI_3 = 4pi/3
square(x) = x*x
cube(x) = x*x*x
sinc(x) = sin(x)/x, with sin(0)/0 -> 1
SINCOS(x, s, c) sets s=sin(angle) and c=cos(angle)
powr(x, y) = x^y for x >= 0
pown(x, n) = x^n for n integer

source=['lib/fn.c', ...] includes the listed C source files in the program before Iq and Iqxy are defined. This allows you to extend the library of available C functions. Additional special functions and scattering calculations are defined in sasmodels/models/lib, including:

sph_j1c(x) = 3 j1(x)/x = 3 (sin(x) - x cos(x))/x^3  [spherical bessel function]
sas_J1c(x) = 2 J1(x)/x  [bessel function of the first kind]
sas_gamma(x) = gamma function  [tgamma is unstable below 1]
sas_erf(x) = error function [erf is broken on some Intel OpenCL drivers]
sas_erfc(x) = 1-erf(x)
sas_J0(x) = J0(x)
sas_J1(x) = J1(x)
sas_JN(x) = JN(x)
Si(x) = integral sin(z)/z from 0 to x
Gauss76Wt = gaussian quadrature weights for 76 point integral
Gauss76Z = gaussian quadrature values for 76 point integral

These functions have been tuned to be fast and numerically stable down to $q=0$ even in single precision. In some cases they work around bugs which appear on some platforms but not others. So use them where needed!!!

Models are defined using double precision declarations for the parameters and return values. Declarations and constants will be converted to float or long double depending on the precision requested.

Floating point constants must include the decimal point. This allows us to convert values such as 1.0 (double precision) to 1.0f (single precision) so that expressions that use these values are not promoted to double precision expressions. Some graphics card drivers are confused when functions that expect floating point values are passed integers, such as 4*atan(1); it is safest to not use integers in floating point expressions. Even better, use the builtin constant M_PI rather than 4*atan(1); it is faster and smaller!

FLOAT_SIZE is the number of bytes in the converted variables. If your algorithm depends on precision (which is not uncommon for numerical algorithms), use the following:

#if FLOAT_SIZE>4
... code for double precision ...
#else
... code for single precision ...
#endif

A value defined as SAS_DOUBLE will stay double precision; this should not be used since some graphics cards do not support double precision.

External C Models

External C models are very much like embedded C models, except that Iq, Iqxy and form_volume are defined in an external source file loaded using the source=[...] method. You need to supply the function declarations for each of these that you need instead of building them automatically from the parameter table.

Form Factors

Away from the dilute limit you can estimate scattering including particle-particle interactions using $I(q) = P(q)*S(q)$ where $P(q)$ is the form factor and $S(q)$ is the structure factor. The simplest structure factor is the hardsphere interaction, which uses the effective radius of the form factor as an input to the structure factor model. The effective radius is the average radius of the form averaged over all the polydispersity values.

def ER(radius, thickness):
    """Effective radius of a core-shell sphere."""
    return radius + thickness

Now consider the core_shell_sphere, which has a simple effective radius equal to the radius of the core plus the thickness of the shell, as shown above. Given polydispersity over (r1, r2, ..., rm) in radius and (t1, t2, ..., tn) in thickness, ER is called with a mesh grid covering all possible combinations of radius and thickness. That is, radius is (r1, r2, ..., rm, r1, r2, ..., rm, ...) and thickness is (t1, t1, ... t1, t2, t2, ..., t2, ...). The ER function returns one effective radius for each combination. The effective radius calculator weights each of these according to the polydispersity distributions and calls the structure factor with the average ER.

def VR(radius, thickness):
    """Sphere and shell volumes for a core-shell sphere."""
    whole = 4.0/3.0 * pi * (radius + thickness)**3
    core = 4.0/3.0 * pi * radius**3
    return whole, whole - core

Core-shell type models have an additional volume ratio which scales the structure factor. The VR function returns the volume of the whole sphere and the volume of the shell. Like ER, there is one return value for each point in the mesh grid.

NOTE: we may be removing or modifying this feature soon. As of the time of writing, core-shell sphere returns (1., 1.) for VR, giving a volume ratio of 1.0.

Unit Tests

THESE ARE VERY IMPORTANT. Include at least one test for each model and PLEASE make sure that the answer value is correct (i.e. not a random number).

tests = [
    [{}, 0.2, 0.726362],
    [{"scale": 1., "background": 0., "sld": 6., "sld_solvent": 1.,
      "radius": 120., "radius_pd": 0.2, "radius_pd_n":45},
     0.2, 0.228843],
    [{"radius": 120., "radius_pd": 0.2, "radius_pd_n":45}, "ER", 120.],
    [{"radius": 120., "radius_pd": 0.2, "radius_pd_n":45}, "VR", 1.],
]

tests=[[{parameters}, q, result], ...] is a list of lists. Each list is one test and contains, in order:

  • a dictionary of parameter values. This can be {} using the default parameters, or filled with some parameters that will be different from the default, such as {‘radius’:10.0, ‘sld’:4}. Unlisted parameters will be given the default values.
  • the input $q$ value or tuple of $(q_x, q_y)$ values.
  • the output $I(q)$ or $I(q_x,q_y)$ expected of the model for the parameters and input value given.
  • input and output values can themselves be lists if you have several $q$ values to test for the same model parameters.
  • for testing ER and VR, give the inputs as "ER" and "VR" respectively; the output for VR should be the sphere/shell ratio, not the individual sphere and shell values.

Test Your New Model

Installed SasView

If you are editing your model from the SasView GUI, you can test it by selecting Run > Check Model from the Model Editor menu bar. An Info box will appear with the results of the compilation and a check that the model runs.

Built SasView

If the model compiles and runs, you can next run the unit tests that you have added using the test = values. Switch to the Shell tab and type the following:

from sasmodels.model_test import run_one
run_one("~/.sasview/plugin_models/model.py")

This should print:

test_model_python (sasmodels.model_test.ModelTestCase) ... ok

To check whether single precision is good enough, type the following:

from sasmodels.compare import main
main("~/.sasview/plugin_models/model.py")

This will pop up a plot showing the difference between single precision and double precision on a range of $q$ values.

demo = dict(scale=1, background=0,
            sld=6, sld_solvent=1,
            radius=120,
            radius_pd=.2, radius_pd_n=45)

demo={'par': value, ...} in the model file sets the default values for the comparison. You can include polydispersity parameters such as radius_pd=0.2, radius_pd_n=45 which would otherwise be zero.

The options to compare are quite extensive; type the following for help:

main()

Options will need to be passed as separate strings. For example to run your model with a random set of parameters:

main("-random", "-pars", "~/.sasview/plugin_models/model.py")

For the random models,

  • sld will be in the range (-0.5,10.5),
  • angles (theta, phi, psi) will be in the range (-180,180),
  • angular dispersion will be in the range (0,45),
  • polydispersity will be in the range (0,1)
  • other values will be in the range (0, 2v), where v is the value of the parameter in demo.

Dispersion parameters n, sigma and type will be unchanged from demo so that run times are predictable.

If your model has 2D orientational calculation, then you should also test with:

main("-2d", "~/.sasview/plugin_models/model.py")

Clean Lint - (Developer Version Only)

NB: For now we are not providing pylint with the installer version of SasView; so unless you have a SasView build environment available, you can ignore this section!

Run the lint check with:

python -m pylint --rcfile=extra/pylint.rc ~/.sasview/plugin_models/model.py

We are not aiming for zero lint just yet, only keeping it to a minimum. For now, don't worry too much about invalid-name. If you really want a variable name Rg for example because $R_g$ is the right name for the model parameter then ignore the lint errors. Also, ignore missing-docstring for standard model functions Iq, Iqxy, etc.

We will have delinting sessions at the SasView Code Camps, where we can decide on standards for model files, parameter names, etc.

For now, you can tell pylint to ignore things. For example, to align your parameters in blocks:

# pylint: disable=bad-whitespace,line-too-long
#   ["name",                  "units", default, [lower, upper], "type", "description"],
parameters = [
    ["contrast_factor",       "barns",    10.0,  [-inf, inf], "", "Contrast factor of the polymer"],
    ["bjerrum_length",        "Ang",       7.1,  [0, inf],    "", "Bjerrum length"],
    ["virial_param",          "1/Ang^2",  12.0,  [-inf, inf], "", "Virial parameter"],
    ["monomer_length",        "Ang",      10.0,  [0, inf],    "", "Monomer length"],
    ["salt_concentration",    "mol/L",     0.0,  [-inf, inf], "", "Concentration of monovalent salt"],
    ["ionization_degree",     "",          0.05, [0, inf],    "", "Degree of ionization"],
    ["polymer_concentration", "mol/L",     0.7,  [0, inf],    "", "Polymer molar concentration"],
    ]
# pylint: enable=bad-whitespace,line-too-long

Don't put in too many pylint statements, though, since they make the code ugly.

Check The Docs - (Developer Version Only)

You can get a rough idea of how the documentation will look using the following:

from sasmodels.generate import view_html
view_html('~/.sasview/plugin_models/model.py')

This does not use the same styling as the SasView docs, but it will allow you to check that your ReStructuredText and LaTeX formatting. Here are some tools to help with the inevitable syntax errors:

There is also a neat online WYSIWYG ReStructuredText editor at http://rst.ninjs.org.

Share Your Model!

Once compare and the unit test(s) pass properly and everything is done, consider adding your model to the Model Marketplace so that others may use it!

Note: See TracBrowser for help on using the repository browser.