Changeset 870a2f4 in sasmodels


Ignore:
Timestamp:
Aug 8, 2017 6:18:53 PM (3 years ago)
Author:
Paul Kienzle <pkienzle@…>
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
793d802
Parents:
c26897a
Message:

fix doc builds

Files:
2 deleted
6 edited

Legend:

Unmodified
Added
Removed
  • doc/developer/calculator.rst

    r2e66ef5 r870a2f4  
    11.. currentmodule:: sasmodels 
     2 
     3.. _Calculator_Interface: 
    24 
    35Calculator Interface 
  • doc/developer/overview.rst

    r2e66ef5 r870a2f4  
    77Computational kernels 
    88--------------------- 
     9 
     10* :mod:`core` 
     11* :mod:`modelinfo` 
     12* :mod:`kernel` 
     13* :mod:`product` 
     14* :mod:`mixture` 
    915 
    1016At the heart of *sasmodels* are the individual computational kernels.  These 
     
    1218return the expected scattering for that $q$. The instructions for writing 
    1319a kernel are documented in :ref:`Writing_a_Plugin`.  The source code for 
    14 the kernels is stored in :mod:`sasmodels.models`. 
    15  
    16 The primary interface to the models is through :mod:`sasmodels.core`, which 
     20the kernels is stored in :mod:`models`. 
     21 
     22The primary interface to the models is through :mod:`core`, which 
    1723provides functions for listing available models, loading the model definition 
    18 and compiling the model.  Use :func:`sasmodels.core.load_model` to load in 
    19 a model definition and compile it. 
    20  
    21 The computational kernels are difficult to call directly, but an example 
    22 was provided in :ref:`Scripting_Interface`. 
    23  
    24 The code for loading the kernel is in 
    25 :mod:`sasmodels.generate`, but a big part of it, which is interpreting the 
    26 definition, lives in :mod:`sasmodels.modelinfo`.  This defines the properties 
    27 of the model in :class:`sasmodels.modelinfo.ModelInfo`, the available 
    28 model parameters in :class:`sasmodels.modelinfo.ParameterTable` and the 
    29 individual parameter attributes such as units and hard limits in 
    30 :class:`sasmodels.modelinfo.Parameter`. 
     24and compiling the model.  Use :func:`core.load_model` to load in 
     25a model definition and compile it.  This makes use of 
     26:func:`core.load_model_info` to load the model definition and 
     27:func:`core.build_model` to turn it into a computational kernel model 
     28:class:`kernel.KernelModel`. 
     29 
     30The :class:`modelinfo.ModelInfo` class defines the properties 
     31of the model including the available model parameters 
     32:class:`modelinfo.ParameterTable` with individual parameter attributes 
     33such as units and hard limits defined in :class:`modelinfo.Parameter`. 
     34 
     35The :class:`product.ProductModel` and :class:`mixture.MixtureModel` classes 
     36are derived models, created automatically for models with names like 
     37"hardsphere*sphere" and "cylinder+sphere". 
     38 
     39Data loaders 
     40------------ 
     41 
     42* :mod:`data` 
     43 
     44In order to test models a minimal set of data management routines is 
     45provided in :mod:`data`.  In particular, it provides mock :class:`data.Data1D` 
     46and :class:`data.Data2D` classes which mimic those classes in *SasView*. 
     47The functions :func:`data.empty_data1D` and :func:`data.empty_data2D` 
     48are handy for creating containers with a particular set of $q$, $\Delta q$ 
     49points which can later be evaluated, and :func:`data.plot_theory` to show 
     50the result.  If *SasView* is available on the path then :func:`data.load_data` 
     51can be used to load any data type defined in *SasView*.  The function 
     52:func:`data.plot_data` can plot that data alone without the theory value. 
     53 
     54Kernel execution 
     55---------------- 
     56 
     57* :mod:`resolution` 
     58* :mod:`resolution2d` 
     59* :mod:`sesans` 
     60* :mod:`weights` 
     61* :mod:`details` 
     62* :mod:`direct_model` 
     63* :mod:`bumps_model` 
     64* :mod:`sasview_model` 
     65 
     66To execute a computational kernel at a particular set of $q$ values, the 
     67use :meth:`kernel.KernelModel.make_kernel`, which returns a callable 
     68:class:`kernel.Kernel` for that $q$ vector (or a pair of $q_x$, $q_y$ 
     69for 2-D datasets). 
     70 
     71The calculated $q$ values should include the measured 
     72data points as well as additional $q$ values required to properly compute the 
     73$q$ resolution function.  The *Resolution* subclasses in :mod:`resolution` 
     74define the *q_calc* attribute for this purpose.  These are 
     75:class:`resolution.Perfect1D` for perfect resolution, 
     76:class:`resolution.Pinhole1D` for the usual SANS pinhole aperture, 
     77:class:`resolution.Slit1D` for the usual USANS slit aperture and 
     78:class:`resolution2d.Pinhole2D` for 2-D pinhole data. 
     79In addition, :class:`resolution2d.Slit2D` defines 1-D slit smeared data 
     80for oriented samples, which require calculation at particular $q_x$ and 
     81$q_y$ values instead of $|q|$ as is the case for orientationally averaged 
     82USANS.  The :class:`sesans.SesansTransform` class acts like a 1-D resolution, 
     83having a *q_calc* attribute that defines the calculated $q$ values for 
     84the SANS models that get converted to spin-echo values by the 
     85:meth:`sesnas.SesansTransform.apply` method. 
     86 
     87Polydispersity is defined by :class:`weights.Dispersion` classes, 
     88:class:`weights.RectangleDispersion`, :class:`weights.ArrayDispersion`, 
     89:class:`weights.LogNormalDispersion`, :class:`weights.GaussianDispersion`, 
     90:class:`weights.SchulzDispersion`.  The :func:`weights.get_weights` 
     91function creates a dispersion object of the class matching 
     92:attr:`weights.Dispersion.type`, and calls it with the current value 
     93of the parameter.  This returns a vector of values and weights for a 
     94weighted average polydispersity. 
     95 
     96In order to call the :class:`kernel.Kernel`, the values and weights for 
     97all parameters must be composed into a :class:`details.CallDetails` object. 
     98This is a compact vector representation of the entire polydispersity 
     99loop that can be passed easily to the kernel.  Additionally, the magnetic 
     100parameters must be converted from polar to cartesian coordinates.  This 
     101work is done by the :func:`details.make_kernel_args` function, which returns 
     102values that can be sent directly to the kernel.  It uses 
     103:func:`details.make_details` to set the details object and 
     104:func:`details.convert_magnetism` for the coordinate transform. 
     105 
     106In the end, making a simple theory function evaluation requires a lot of 
     107setup. To make calling them a little easier, the *DirectModel* and 
     108*BumpsModel* interfaces are provided.  See :ref:`Scripting_Interface` 
     109for an example. 
     110 
     111The :class:`direct_model.DirectModel` interface accepts a data object 
     112and a kernel model.  Within the class, 
     113the :meth:`direct_model.DataMixin._interpret_data` method is called to 
     114query the data and set the resolution. 
     115The :meth:`direct_model.DataMixin._calc_theory` takes a set of parameter 
     116values, builds the kernel arguments, calls the kernel, and applies the 
     117resolution function, returning the predicted value for the data $q$ values. 
     118The :class:`bumps_model.Experiment` class is like the DirectModel class, 
     119but it defines a Fitness class that can be handed directly to the 
     120bumps optimization and uncertainty analysis program. 
     121 
     122The :class:`sasview_model.SasviewModel` class defines a SasView 4.x 
     123compatible interface to the sasmodels definitions, allowing sasmodels 
     124to be used directly from SasView.  Over time the SasView shim should 
     125disappear as SasView access the :class:`modelinfo.ModelInfo` and 
     126computational kernels directly. 
     127 
     128Kernel execution 
     129---------------- 
     130 
     131* :mod:`kernelcl` 
     132* :mod:`kerneldll` 
     133* :mod:`kernelpy` 
     134* :mod:`generate` 
     135 
    31136 
    32137The kernel functions for the most part do not define polydispersity, 
    33 resolution functions or magnetism.  Instead, code for these is generated in 
    34 :mod:`sasmodels.generate` 
    35  
    36  
    37  
    38 Sasview kernels: 
    39  
    40 * :mod:` 
    41     ('kernel', 'Evaluator type definitions'), 
    42     ('kernelcl', 'OpenCL model evaluator'), 
    43     ('kerneldll', 'Ctypes model evaluator'), 
    44     ('kernelpy', 'Python model evaluator'), 
    45  
    46 Bumps fitting routines: 
    47  
    48 * :mod:`sasmodels.bumps_model` is a wrapper around 
    49     ('bumps_model', 'Bumps interface'), 
    50     ('direct_model', 'Simple interface'), 
    51  
    52  
    53 Utility functions: 
    54  
    55 * :mod:`sasmodels` provides :func:`sasmodels.__init__.data_files` for the installer. 
    56 * :mod:`sasmodels.rst2html` provides tools for converting model docs to html and viewing 
    57   the html.  When run as a main program, it can display arbitrary rst files. 
    58 * :mod:`sasmodels.exception` annotates the current exception with a context string, 
    59   such as "while opening myfile.dat" without adjusting the traceback. 
    60  
    61  
    62 And so on:: 
    63  
    64  
    65     ('compare_many', 'Batch compare models on different compute engines'), 
    66     ('compare', 'Compare models on different compute engines'), 
    67     ('convert', 'Sasview to sasmodel converter'), 
    68     ('core', 'Model access'), 
    69     ('data', 'Data layout and plotting routines'), 
    70     ('details', 'Parameter packing for kernel calls'), 
    71     ('generate', 'Model parser'), 
    72     ('list_pars', 'Identify all parameters in all models'), 
    73     ('mixture', 'Mixture model evaluator'), 
    74     ('model_test', 'Unit test support'), 
    75     ('modelinfo', 'Parameter and model definitions'), 
    76     ('product', 'Product model evaluator'), 
    77     ('resolution', '1-D resolution functions'), 
    78     ('resolution2d', '2-D resolution functions'), 
    79     ('sasview_model', 'Sasview interface'), 
    80     ('sesans', 'SESANS calculation routines'), 
    81     ('weights', 'Distribution functions'), 
     138resolution or magnetism directly.  Instead sasmodels automatically 
     139applies these, calling the computation kernel as needed. 
     140 
     141The outermost loop is the resolution calculation.  For the 1-D case 
     142this computes a single vector of $I(q)$ values and applies the convolution 
     143to the resulting set.  Since the same $I(q)$ vector is used to compute the 
     144convolution at each point, it can be precomputed before the convolution, 
     145and so the convolution is reasonably efficient.  The 2-D case is not 
     146that efficient, and instead recomputes the entire shifted/scaled set 
     147of $q_x$, $q_y$ values many times, or very many times depending on the 
     148accuracy requested. 
     149 
     150Polydispersity is handled as a mesh over the polydisperse parameters. 
     151This is the next level of the loop.  For C kernels run in a DLL or 
     152using OpenCL, the polydisperisty loop is generated separately for each 
     153model as C code.  Inside the polydispersity loop there is a loop over 
     154the magnetic cross sections for magnetic models, updating the SLD 
     155parameters with the effective magnetic SLD for that particular $q$ 
     156value. For OpenCL, each $q$ value loops over the 
     157polydispersity mesh on a separate processor. For DLL, the outer loop 
     158cycles through polydispersity, and the inner loop distributes q values 
     159amongst the processors.  Like the DLL, the Python kernel execution 
     160cycles over the polydisperse parameters and the magnetic cross sections, 
     161calling the computation kernel with a vector of $q$ values.  Assuming 
     162the kernel code accepts vectors, this can be fast enough (though it is 
     163painfully slow if not vectorized). 
     164 
     165Further details are provided in the next section, 
     166:ref:`Calculator_Interface` 
     167 
     168 
     169Testing 
     170------- 
     171 
     172* :mod:`model_test` 
     173* :mod:`compare` 
     174* :mod:`compare_many` 
     175* :mod:`rst2html` 
     176* :mod:`list_pars` 
     177 
     178Individual models should all have test values to make sure that the 
     179evaluation is correct.  This is particularly important in the context 
     180of OpenCL since sasmodels doesn't control the compiler or the hardware, 
     181and since GPUs are notorious for preferring speed over precision.  The 
     182tests can be run as a group using :mod:`model_test` as main:: 
     183 
     184    $ python -m sasmodels.model_test all 
     185 
     186Individual models can be listed instead of *all*, which is convenient when 
     187adding new models. 
     188 
     189The :mod:`compare` module, usually invoked using *./sascomp* provides a 
     190rich interface for exploring model accuracy, execution speed and parameter 
     191ranges.  It also allows different models to be compared. 
     192The :mod:`compare_many` module does batch comparisons, keeping a list of 
     193the particular random seeds which lead to large differences in output 
     194between different computing platforms. 
     195 
     196The :mod:`rst2html` module provides tools for converting model docs to 
     197html and viewing the html.  This is used by :mod:`compare` to display 
     198the model description, such as:: 
     199 
     200    $ ./sascomp -html sphere 
     201 
     202This makes debugging the latex much faster, though this may require 
     203Qt in order for mathjax to work correctly. 
     204 
     205When run as main, it can display arbitrary ReStructuredText files. E.g., 
     206 
     207:: 
     208 
     209    $ python -m sasmodels.rst2html doc/developer/overview.rst 
     210 
     211This is handy for sorting out rst and latex syntax.  With some work 
     212the results could be improved so that it recognizes sphinx roles 
     213such as *mod*, *class* and *func*, and so that it uses the style sheets 
     214from the sasmodels docs. 
     215 
     216The :mod:`list_pars` module lists all instances of parameters across 
     217all models.  This helps to make sure that similar parameters have 
     218similar names across the different models.  With the verbose flag, 
     219the particular models which use each named parameter are listed. 
     220 
     221 
     222Model conversion 
     223---------------- 
     224 
     225* :mod:`convert` 
     226* :mod:`conversion_table` 
     227 
     228Model definitions are not static.  As needs change or problems are found, 
     229models may be updated with new model names or may be reparameterized 
     230with new parameter definitions.  For example, in translating the 
     231Teubner-Strey model from SasView 3.x to sasmodels, the definition 
     232in terms of *drho*, *k*, *c1*, *c2*, *a2* and prefactor was replaced 
     233by the defintion in terms of *volfraction_a*, *xi*, *d*, *sld_a* and 
     234*sld_b*.  Within :mod:`convert`, the *_hand_convert_3_1_2_to_4_1* 
     235function must be called when loading a 3.x model definition to update it to 
     2364.1, and then the model should be further updated to 4.2, 5.0, and so on. 
     237The :func:`convert.convert_model` function does this, using the conversion 
     238table in :mod:`conversion_table` (which handled the major renaming from 
     239SasView 3.x to sasmodels), and using the internal *_hand_convert* function 
     240for the more complicated cases. 
     241 
     242Other 
     243----- 
     244 
     245* :mod:`exception` 
     246* :mod:`alignment` 
     247 
     248The :func:`exception.annotate_exception` function annotates the current 
     249exception with a context string, such as "while opening myfile.dat" without 
     250adjusting the traceback. 
     251 
     252The :mod:`alignment` module is unused. 
  • doc/guide/plugin.rst

    r990d8df r870a2f4  
    610610 
    611611        :code:`source = ["lib/polevl.c", ...]` 
    612         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/polevl.c>`_) 
     612        (`polevl.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/polevl.c>`_) 
    613613 
    614614    sas_gamma(x): 
     
    618618        on some platforms. 
    619619 
    620         :code:`source = ["lib/sasgamma.c", ...]` 
    621         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gamma.c>`_) 
     620        :code:`source = ["lib/sas_gamma.c", ...]` 
     621        (`sas_gamma.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gamma.c>`_) 
    622622 
    623623    sas_erf(x), sas_erfc(x): 
     
    631631 
    632632        :code:`source = ["lib/polevl.c", "lib/sas_erf.c", ...]` 
    633         (`link to error functions' code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_erf.c>`_) 
     633        (`sas_erf.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_erf.c>`_) 
    634634 
    635635    sas_J0(x): 
     
    640640 
    641641        :code:`source = ["lib/polevl.c", "lib/sas_J0.c", ...]` 
    642         (`link to Bessel function's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J0.c>`_) 
     642        (`sas_J0.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J0.c>`_) 
    643643 
    644644    sas_J1(x): 
     
    649649 
    650650        :code:`source = ["lib/polevl.c", "lib/sas_J1.c", ...]` 
    651         (`link to Bessel function's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_) 
     651        (`sas_J1.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_) 
    652652 
    653653    sas_JN(n, x): 
     
    660660 
    661661        :code:`source = ["lib/polevl.c", "lib/sas_J0.c", "lib/sas_J1.c", "lib/sas_JN.c", ...]` 
    662         (`link to Bessel function's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_JN.c>`_) 
     662        (`sas_JN.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_JN.c>`_) 
    663663 
    664664    sas_Si(x): 
     
    684684 
    685685        :code:`source = ["lib/Si.c", ...]` 
    686         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/Si.c>`_) 
     686        (`Si.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/Si.c>`_) 
    687687 
    688688    sas_3j1x_x(x): 
     
    695695 
    696696        :code:`source = ["lib/sas_3j1x_x.c", ...]` 
    697         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_3j1x_x.c>`_) 
     697        (`sas_3j1x_x.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_3j1x_x.c>`_) 
    698698 
    699699 
     
    704704 
    705705        :code:`source = ["lib/polevl.c", "lib/sas_J1.c", ...]` 
    706         (`link to Bessel form's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_) 
     706        (`sas_J1.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_) 
    707707 
    708708 
     
    715715 
    716716        :code:`source = ["lib/gauss76.c", ...]` 
    717         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/gauss76.c>`_) 
     717        (`gauss76.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/gauss76.c>`_) 
    718718 
    719719 
  • sasmodels/alignment.py

    r7ae2b7f r870a2f4  
    4242    view[:] = x 
    4343    return view 
    44  
  • sasmodels/models/multilayer_vesicle.py

    r5d23de2 r870a2f4  
    7171  sufficiently fine grained in certain cases. Please report any such occurences 
    7272  to the SasView team. Generally, for the best possible experience: 
    73  * Start with the best possible guess 
    74  * Using a priori knowledge, hold as many parameters fixed as possible 
    75  * if N=1, tw (water thickness) must by definition be zero. Both N and tw should 
     73 
     74 - Start with the best possible guess 
     75 - Using a priori knowledge, hold as many parameters fixed as possible 
     76 - if N=1, tw (water thickness) must by definition be zero. Both N and tw should 
    7677   be fixed during fitting. 
    77  * If N>1, use constraints to keep N > 1 
    78  * Because N only really moves in integer steps, it may get "stuck" if the 
     78 - If N>1, use constraints to keep N > 1 
     79 - Because N only really moves in integer steps, it may get "stuck" if the 
    7980   optimizer step size is too small so care should be taken 
    8081   If you experience problems with this please contact the SasView team and let 
  • sasmodels/rst2html.py

    r990d8df r870a2f4  
    176176        from PyQt5.QtCore import QUrl 
    177177    except ImportError: 
    178         from PyQt4.QtWebkit import QWebView 
     178        from PyQt4.QtWebKit import QWebView 
    179179        from PyQt4.QtCore import QUrl 
    180180    helpView = QWebView() 
     
    204204        from PyQt5.QtCore import QUrl 
    205205    except ImportError: 
    206         from PyQt4.QtWebkit import QWebView 
     206        from PyQt4.QtWebKit import QWebView 
    207207        from PyQt4.QtCore import QUrl 
    208208    frame = QWebView() 
     
    222222    except ImportError: 
    223223        try: 
    224             from PyQt4.QtWebkit import QWebView 
     224            from PyQt4.QtWebKit import QWebView 
    225225            return True 
    226226        except ImportError: 
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