Changeset a8a1d48 in sasmodels


Ignore:
Timestamp:
Mar 5, 2019 10:35:27 AM (6 years ago)
Author:
GitHub <noreply@…>
Branches:
master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
e589e9a
Parents:
e5bbe64 (diff), c1799d3 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
git-author:
Paul Kienzle <pkienzle@…> (03/05/19 10:35:27)
git-committer:
GitHub <noreply@…> (03/05/19 10:35:27)
Message:

Set structure factor background default to 0.0. Closes #1157.

Files:
11 edited
6 moved

Legend:

Unmodified
Added
Removed

  • sasmodels/compare.py

    r07646b6 rc1799d3  
    11521152        'rel_err'   : True, 
    11531153        'explore'   : False, 
    1154         'use_demo'  : True, 
     1154        'use_demo'  : False, 
    11551155        'zero'      : False, 
    11561156        'html'      : False, 

  • sasmodels/direct_model.py

    r5024a56 rc1799d3  
    332332 
    333333        # Need to pull background out of resolution for multiple scattering 
    334         background = pars.get('background', DEFAULT_BACKGROUND) 
     334        default_background = self._model.info.parameters.common_parameters[1].default 
     335        background = pars.get('background', default_background) 
    335336        pars = pars.copy() 
    336337        pars['background'] = 0. 

  • sasmodels/generate.py

    rcd28947 ra8a1d48  
    10061006        pars = model_info.parameters.kernel_parameters 
    10071007    else: 
    1008         pars = model_info.parameters.COMMON + model_info.parameters.kernel_parameters 
     1008        pars = (model_info.parameters.common_parameters 
     1009                + model_info.parameters.kernel_parameters) 
    10091010    partable = make_partable(pars) 
    10101011    subst = dict(id=model_info.id.replace('_', '-'), 

  • sasmodels/modelinfo.py

    r39a06c9 rc1799d3  
    404404      parameters counted as n individual parameters p1, p2, ... 
    405405 
     406    * *common_parameters* is the list of common parameters, with a unique 
     407      copy for each model so that structure factors can have a default 
     408      background of 0.0. 
     409 
    406410    * *call_parameters* is the complete list of parameters to the kernel, 
    407411      including scale and background, with vector parameters recorded as 
    … …  
    416420    parameters don't use vector notation, and instead use p1, p2, ... 
    417421    """ 
    418     # scale and background are implicit parameters 
    419     COMMON = [Parameter(*p) for p in COMMON_PARAMETERS] 
    420  
    421422    def __init__(self, parameters): 
    422423        # type: (List[Parameter]) -> None 
     424 
     425        # scale and background are implicit parameters 
     426        # Need them to be unique to each model in case they have different 
     427        # properties, such as default=0.0 for structure factor backgrounds. 
     428        self.common_parameters = [Parameter(*p) for p in COMMON_PARAMETERS] 
     429 
    423430        self.kernel_parameters = parameters 
    424431        self._set_vector_lengths() 
    … …  
    468475                         if p.polydisperse and p.type not in ('orientation', 'magnetic')) 
    469476        self.pd_2d = set(p.name for p in self.call_parameters if p.polydisperse) 
     477 
     478    def set_zero_background(self): 
     479        """ 
     480        Set the default background to zero for this model.  This is done for 
     481        structure factor models. 
     482        """ 
     483        # type: () -> None 
     484        # Make sure background is the second common parameter. 
     485        assert self.common_parameters[1].id == "background" 
     486        self.common_parameters[1].default = 0.0 
     487        self.defaults = self._get_defaults() 
    470488 
    471489    def check_angles(self): 
    … …  
    567585    def _get_call_parameters(self): 
    568586        # type: () -> List[Parameter] 
    569         full_list = self.COMMON[:] 
     587        full_list = self.common_parameters[:] 
    570588        for p in self.kernel_parameters: 
    571589            if p.length == 1: 
    … …  
    670688 
    671689        # Gather the user parameters in order 
    672         result = control + self.COMMON 
     690        result = control + self.common_parameters 
    673691        for p in self.kernel_parameters: 
    674692            if not is2d and p.type in ('orientation', 'magnetic'): 
    … …  
    770788 
    771789    info = ModelInfo() 
     790 
     791    # Build the parameter table 
    772792    #print("make parameter table", kernel_module.parameters) 
    773793    parameters = make_parameter_table(getattr(kernel_module, 'parameters', [])) 
     794 
     795    # background defaults to zero for structure factor models 
     796    structure_factor = getattr(kernel_module, 'structure_factor', False) 
     797    if structure_factor: 
     798        parameters.set_zero_background() 
     799 
     800    # TODO: remove demo parameters 
     801    # The plots in the docs are generated from the model default values. 
     802    # Sascomp set parameters from the command line, and so doesn't need 
     803    # demo values for testing. 
    774804    demo = expand_pars(parameters, getattr(kernel_module, 'demo', None)) 
     805 
    775806    filename = abspath(kernel_module.__file__).replace('.pyc', '.py') 
    776807    kernel_id = splitext(basename(filename))[0] 

  • sasmodels/models/hardsphere.py

    r304c775 rc1799d3  
    162162    return pars 
    163163 
    164 demo = dict(radius_effective=200, volfraction=0.2, 
    165             radius_effective_pd=0.1, radius_effective_pd_n=40) 
    166164# Q=0.001 is in the Taylor series, low Q part, so add Q=0.1, 
    167165# assuming double precision sasview is correct 

  • sasmodels/sasview_model.py

    r3a1afed ra8a1d48  
    382382            hidden.add('scale') 
    383383            hidden.add('background') 
    384             self._model_info.parameters.defaults['background'] = 0. 
    385384 
    386385        # Update the parameter lists to exclude any hidden parameters 
    … …  
    931930    CylinderModel().evalDistribution([0.1, 0.1]) 
    932931 
     932def test_structure_factor_background(): 
     933    # type: () -> None 
     934    """ 
     935    Check that sasview model and direct model match, with background=0. 
     936    """ 
     937    from .data import empty_data1D 
     938    from .core import load_model_info, build_model 
     939    from .direct_model import DirectModel 
     940 
     941    model_name = "hardsphere" 
     942    q = [0.0] 
     943 
     944    sasview_model = _make_standard_model(model_name)() 
     945    sasview_value = sasview_model.evalDistribution(np.array(q))[0] 
     946 
     947    data = empty_data1D(q) 
     948    model_info = load_model_info(model_name) 
     949    model = build_model(model_info) 
     950    direct_model = DirectModel(data, model) 
     951    direct_value_zero_background = direct_model(background=0.0) 
     952 
     953    assert sasview_value == direct_value_zero_background 
     954 
     955    # Additionally check that direct value background defaults to zero 
     956    direct_value_default = direct_model() 
     957    assert sasview_value == direct_value_default 
     958 
     959 
    933960def magnetic_demo(): 
    934961    Model = _make_standard_model('sphere') 
    … …  
    951978    #print("rpa:", test_rpa()) 
    952979    #test_empty_distribution() 
     980    #test_structure_factor_background() 

  • README.rst

    re30d645 r2a64722  
    1010is available. 
    1111 
    12 Example 
     12Install 
    1313------- 
     14 
     15The easiest way to use sasmodels is from `SasView <http://www.sasview.org/>`_. 
     16 
     17You can also install sasmodels as a standalone package in python. Use 
     18`miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ 
     19or `anaconda <https://www.anaconda.com/>`_ 
     20to create a python environment with the sasmodels dependencies:: 
     21 
     22    $ conda create -n sasmodels -c conda-forge numpy scipy matplotlib pyopencl 
     23 
     24The option ``-n sasmodels`` names the environment sasmodels, and the option 
     25``-c conda-forge`` selects the conda-forge package channel because pyopencl 
     26is not part of the base anaconda distribution. 
     27 
     28Activate the environment and install sasmodels:: 
     29 
     30    $ conda activate sasmodels 
     31    (sasmodels) $ pip install sasmodels 
     32 
     33Install `bumps <https://github.com/bumps/bumps>`_ if you want to use it to fit 
     34your data:: 
     35 
     36    (sasmodels) $ pip install bumps 
     37 
     38Usage 
     39----- 
     40 
     41Check that the works:: 
     42 
     43    (sasmodels) $ python -m sasmodels.compare cylinder 
     44 
     45To show the orientation explorer:: 
     46 
     47    (sasmodels) $ python -m sasmodels.jitter 
     48 
     49Documentation is available online as part of the SasView 
     50`fitting perspective <http://www.sasview.org/docs/index.html>`_ 
     51as well as separate pages for 
     52`individual models <http://www.sasview.org/docs/user/sasgui/perspectives/fitting/models/index.html>`_. 
     53Programming details for sasmodels are available in the 
     54`developer documentation <http://www.sasview.org/docs/dev/dev.html>`_. 
     55 
     56 
     57Fitting Example 
     58--------------- 
    1459 
    1560The example directory contains a radial+tangential data set for an oriented 
    1661rod-like shape. 
    1762 
    18 The data is loaded by sas.dataloader from the sasview package, so sasview 
    19 is needed to run the example. 
     63To load the example data, you will need the SAS data loader from the sasview 
     64package. This is not yet available on PyPI, so you will need a copy of the 
     65SasView source code to run it.  Create a directory somewhere to hold the 
     66sasview and sasmodels source code, which we will refer to as $SOURCE. 
    2067 
    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:: 
     68Use the following to install sasview, and the sasmodels examples:: 
    2469 
    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 
    2774 
    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:: 
     75Set the path to the sasview source on your python path within the sasmodels 
     76environment.  On Windows, this will be:: 
    3177 
    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 
     82On 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 
    3387 
    3488The fit.py model accepts up to two arguments.  The first argument is the 
    … …  
    3892both radial and tangential simultaneously, use the word "both". 
    3993 
    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. 
     94See `bumps documentation <https://bumps.readthedocs.io/>`_ for detailed 
     95instructions on running the fit. 
    4796 
    4897|TravisStatus|_ 

  • explore/beta/sasfit_compare.py

    r2a12351b r119073a  
    505505    } 
    506506 
    507     Q, IQ = load_sasfit(data_file('richard_test.txt')) 
    508     Q, IQSD = load_sasfit(data_file('richard_test2.txt')) 
    509     Q, IQBD = load_sasfit(data_file('richard_test3.txt')) 
     507    Q, IQ = load_sasfit(data_file('sasfit_sphere_schulz_IQD.txt')) 
     508    Q, IQSD = load_sasfit(data_file('sasfit_sphere_schulz_IQSD.txt')) 
     509    Q, IQBD = load_sasfit(data_file('sasfit_sphere_schulz_IQBD.txt')) 
    510510    target = Theory(Q=Q, F1=None, F2=None, P=IQ, S=None, I=IQSD, Seff=None, Ibeta=IQBD) 
    511511    actual = sphere_r(Q, norm="sasfit", **pars) 
    … …  
    526526    } 
    527527 
    528     Q, IQ = load_sasfit(data_file('richard_test4.txt')) 
    529     Q, IQSD = load_sasfit(data_file('richard_test5.txt')) 
    530     Q, IQBD = load_sasfit(data_file('richard_test6.txt')) 
     528    Q, IQ = load_sasfit(data_file('sasfit_ellipsoid_shulz_IQD.txt')) 
     529    Q, IQSD = load_sasfit(data_file('sasfit_ellipsoid_shulz_IQSD.txt')) 
     530    Q, IQBD = load_sasfit(data_file('sasfit_ellipsoid_shulz_IQBD.txt')) 
    531531    target = Theory(Q=Q, F1=None, F2=None, P=IQ, S=None, I=IQSD, Seff=None, Ibeta=IQBD) 
    532532    actual = ellipsoid_pe(Q, norm="sasfit", **pars) 

  • explore/precision.py

    raa8c6e0 rcd28947  
    207207    return model_info 
    208208 
    209 # Hack to allow second parameter A in two parameter functions 
     209# Hack to allow second parameter A in the gammainc and gammaincc functions. 
     210# Create a 2-D variant of the precision test if we need to handle other two 
     211# parameter functions. 
    210212A = 1 
    211213def parse_extra_pars(): 
     214    """ 
     215    Parse the command line looking for the second parameter "A=..." for the 
     216    gammainc/gammaincc functions. 
     217    """ 
    212218    global A 
    213219 
    … …  
    333339) 
    334340add_function( 
     341    # Note: "a" is given as A=... on the command line via parse_extra_pars 
    335342    name="gammainc(x)", 
    336343    mp_function=lambda x, a=A: mp.gammainc(a, a=0, b=x)/mp.gamma(a), 
    … …  
    339346) 
    340347add_function( 
     348    # Note: "a" is given as A=... on the command line via parse_extra_pars 
    341349    name="gammaincc(x)", 
    342350    mp_function=lambda x, a=A: mp.gammainc(a, a=x, b=mp.inf)/mp.gamma(a), 

  • sasmodels/kernel.py

    re44432d rcd28947  
    133133        nout = 2 if self.info.have_Fq and self.dim == '1d' else 1 
    134134        total_weight = self.result[nout*self.q_input.nq + 0] 
     135        # Note: total_weight = sum(weight > cutoff), with cutoff >= 0, so it 
     136        # is okay to test directly against zero.  If weight is zero then I(q), 
     137        # etc. must also be zero. 
    135138        if total_weight == 0.: 
    136139            total_weight = 1. 

  • sasmodels/models/pearl_necklace.c

    r99658f6 r9b5fd42  
    4040    const double si = sas_sinx_x(q*A_s); 
    4141    const double omsi = 1.0 - si; 
    42     const double pow_si = pow(si, num_pearls); 
     42    const double pow_si = pown(si, num_pearls); 
    4343 
    4444    // form factor for num_pearls 
    … …  
    8181radius_from_volume(double radius, double edge_sep, double thick_string, double fp_num_pearls) 
    8282{ 
    83     const int num_pearls = (int) fp_num_pearls +0.5; 
    8483    const double vol_tot = form_volume(radius, edge_sep, thick_string, fp_num_pearls); 
    8584    return cbrt(vol_tot/M_4PI_3); 
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