Changes in / [997c9ca:793d802] in sasmodels


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22 added
13 deleted
14 edited

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  • .gitignore

    r8a5f021 r8a5f021  
    1111/doc/api/ 
    1212/doc/model/ 
    13 /doc/ref/models 
     13/doc/guide/models 
    1414.mplconfig 
    1515/pylint_violations.txt 

  • doc/conf.py

    r40a87fa r8ae8532  
    4242             ] 
    4343 
     44# Redirect mathjax to a different CDN 
     45mathjax_path = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-MML-AM_CHTML" 
     46 
    4447# Add any paths that contain templates here, relative to this directory. 
    4548templates_path = ['_templates'] 

  • doc/developer/calculator.rst

    re822c97 r870a2f4  
    11.. currentmodule:: sasmodels 
     2 
     3.. _Calculator_Interface: 
    24 
    35Calculator Interface 
    … …  
    79model calculator which implements the polydispersity and magnetic SLD 
    810calculations.  There are three separate implementations of this layer, 
    9 *kernelcl.py* for OpenCL, which operates on a single Q value at a time, 
    10 *kerneldll.c* for the DLL, which loops over a vector of Q values, and 
    11 *kernelpy.py* for python models which operates on vector Q values. 
     11:mod:`kernelcl` for OpenCL, which operates on a single Q value at a time, 
     12:mod:`kerneldll` for the DLL, which loops over a vector of Q values, and 
     13:mod:`kernelpy` for python models which operates on vector Q values. 
    1214 
    1315Each implementation provides three different calls *Iq*, *Iqxy* and *Imagnetic* 

  • doc/developer/index.rst

    rb85be2d r2e66ef5  
    77   :maxdepth: 4 
    88 
     9   overview.rst 
    910   calculator.rst 

  • doc/genapi.py

    ra5b8477 r2e66ef5  
    22import os.path 
    33 
    4 MODULE_TEMPLATE=""".. Autogenerated by genmods.py 
     4MODULE_TEMPLATE = """.. Autogenerated by genmods.py 
    55 
    66****************************************************************************** 
    … …  
    1919""" 
    2020 
    21 INDEX_TEMPLATE=""".. Autogenerated by genmods.py 
     21INDEX_TEMPLATE = """.. Autogenerated by genmods.py 
    2222 
    2323.. _api-index: 
    … …  
    4646        os.makedirs(dir) 
    4747 
    48     for module,name in modules: 
    49         with open(os.path.join(dir,module+'.rst'), 'w') as f: 
     48    for module, name in modules: 
     49        with open(os.path.join(dir, module+'.rst'), 'w') as f: 
    5050            f.write(MODULE_TEMPLATE%locals()) 
    5151 
    52     rsts = "\n   ".join(module+'.rst' for module,name in modules) 
    53     with open(os.path.join(dir,'index.rst'),'w') as f: 
     52    rsts = "\n   ".join(module+'.rst' for module, name in modules) 
     53    with open(os.path.join(dir, 'index.rst'), 'w') as f: 
    5454        f.write(INDEX_TEMPLATE%locals()) 
    5555 
    5656 
    57 modules=[ 
    58     #('__init__', 'Top level namespace'), 
     57modules = [ 
     58    ('__init__', 'Sasmodels package'), 
    5959    #('alignment', 'GPU data alignment [unused]'), 
    6060    ('bumps_model', 'Bumps interface'), 
     61    ('compare_many', 'Batch compare models on different compute engines'), 
    6162    ('compare', 'Compare models on different compute engines'), 
    6263    ('convert', 'Sasview to sasmodel converter'), 
    … …  
    6667    ('direct_model', 'Simple interface'), 
    6768    ('exception', 'Annotate exceptions'), 
    68     #('frozendict', 'Freeze a dictionary to make it immutable'), 
    6969    ('generate', 'Model parser'), 
    7070    ('kernel', 'Evaluator type definitions'), 
    … …  
    7979    ('resolution', '1-D resolution functions'), 
    8080    ('resolution2d', '2-D resolution functions'), 
     81    ('rst2html', 'Convert doc strings the web pages'), 
    8182    ('sasview_model', 'Sasview interface'), 
    8283    ('sesans', 'SESANS calculation routines'), 
    83     #('transition', 'Model stepper for automatic model selection'), 
    8484    ('weights', 'Distribution functions'), 
    8585] 
    86 package='sasmodels' 
    87 package_name='Reference' 
     86package = 'sasmodels' 
     87package_name = 'Reference' 
    8888genfiles(package, package_name, modules) 

  • doc/gentoc.py

    r40a87fa r990d8df  
    1616    from sasmodels.modelinfo import ModelInfo 
    1717 
    18 TEMPLATE="""\ 
     18TEMPLATE = """\ 
    1919.. 
    2020    Generated from doc/gentoc.py -- DO NOT EDIT -- 
    … …  
    3030""" 
    3131 
    32 MODEL_TOC_PATH = "ref/models" 
     32MODEL_TOC_PATH = "guide/models" 
    3333 
    3434def _make_category(category_name, label, title, parent=None): 
    … …  
    6565        # assume model is in sasmodels/models/name.py, and ignore the full path 
    6666        model_name = basename(item)[:-3] 
    67         if model_name.startswith('_'): continue 
     67        if model_name.startswith('_'): 
     68            continue 
    6869        model_info = load_model_info(model_name) 
    6970        if model_info.category is None: 
    7071            print("Missing category for", item, file=sys.stderr) 
    7172        else: 
    72             category.setdefault(model_info.category,[]).append(model_name) 
     73            category.setdefault(model_info.category, []).append(model_name) 
    7374 
    7475    # Check category names 
    75     for k,v in category.items(): 
     76    for k, v in category.items(): 
    7677        if len(v) == 1: 
    77             print("Category %s contains only %s"%(k,v[0]), file=sys.stderr) 
     78            print("Category %s contains only %s"%(k, v[0]), file=sys.stderr) 
    7879 
    7980    # Generate category files for the table of contents. 
    … …  
    8687    # alphabetical order before them. 
    8788 
    88     if not exists(MODEL_TOC_PATH): mkdir(MODEL_TOC_PATH) 
     89    if not exists(MODEL_TOC_PATH): 
     90        mkdir(MODEL_TOC_PATH) 
    8991    model_toc = _make_category( 
    90         'index',  'Models', 'Model Functions') 
     92        'index', 'Models', 'Model Functions') 
    9193    #shape_toc = _make_category( 
    9294    #    'shape',  'Shapes', 'Shape Functions', model_toc) 
    9395    free_toc = _make_category( 
    94         'shape-independent',  'Shape-independent', 
     96        'shape-independent', 'Shape-independent', 
    9597        'Shape-Independent Functions') 
    9698    struct_toc = _make_category( 
    97         'structure-factor',  'Structure-factor', 'Structure Factors') 
    98     custom_toc = _make_category( 
    99         'custom-models', 'Custom-models', 'Custom Models') 
     99        'structure-factor', 'Structure-factor', 'Structure Factors') 
     100    #custom_toc = _make_category( 
     101    #    'custom-models', 'Custom-models', 'Custom Models') 
    100102 
    101103    # remember to top level categories 
    … …  
    105107        'shape-independent':free_toc, 
    106108        'structure-factor': struct_toc, 
    107         'custom': custom_toc, 
     109        #'custom': custom_toc, 
    108110        } 
    109111 
    110112    # Process the model lists 
    111     for k,v in sorted(category.items()): 
     113    for k, v in sorted(category.items()): 
    112114        if ':' in k: 
    113             cat,subcat = k.split(':') 
     115            cat, subcat = k.split(':') 
    114116            _maybe_make_category(cat, v, cat_files, model_toc) 
    115117            cat_file = cat_files[cat] 
    116             label = "-".join((cat,subcat)) 
     118            label = "-".join((cat, subcat)) 
    117119            filename = label 
    118             title = subcat.capitalize()+" Functions" 
     120            title = subcat.capitalize() + " Functions" 
    119121            sub_toc = _make_category(filename, label, title, cat_file) 
    120122            for model in sorted(v): 
    … …  
    130132    _add_subcategory('shape-independent', model_toc) 
    131133    _add_subcategory('structure-factor', model_toc) 
    132     _add_subcategory('custom-models', model_toc) 
     134    #_add_subcategory('custom-models', model_toc) 
    133135 
    134136    # Close the top-level category files 
    135137    #model_toc.close() 
    136     for f in cat_files.values(): f.close() 
     138    for f in cat_files.values(): 
     139        f.close() 
    137140 
    138141 

  • doc/guide/index.rst

    rbb6f0f3 r2e66ef5  
    1 ********** 
    2 SAS Models 
    3 ********** 
     1**************** 
     2SAS Models Guide 
     3**************** 
    44 
    5 Small angle X-ray and Neutron (SAXS and SANS) scattering examines the 
    6 scattering patterns produced by a beam travelling through the sample 
    7 and scattering at low angles.  The scattering is computed as a function 
    8 of $q_x$ and $q_y$, which for a given beam wavelength corresponds to 
    9 particular scattering angles. Each pixel on the detector corresponds to 
    10 a different scattering angle. If the sample is unoriented, the scattering 
    11 pattern will appear as rings on the detector.  In this case, a circular 
    12 average can be taken with 1-dimension data at $q = \surd (q_x^2 + q_y^2)$ 
    13 compared to the orientationally averaged SAS scattering pattern. 
     5.. toctree:: 
     6   :numbered: 4 
     7   :maxdepth: 4 
    148 
    15 Models have certain features in common. 
    16  
    17 Every model has a *scale* and a *background*. 
    18  
    19 Talk about orientation, with diagrams for orientation so that we don't need 
    20 a link on every model page? 
    21  
    22 .. _orientation: 
    23  
    24 .. figure: img/orientation1.jpg 
    25  
    26     Orientation in 3D 
    27  
    28 .. figure: img/orientation2.jpg 
    29  
    30     Orientation cross sections 
    31  
    32 Talk about polydispersity. 
    33  
    34 Talk about magnetism, converting the magnetism help file to inline text here, 
    35 with links so that models can point back to it. 
    36  
    37 Need to talk about structure factors even though we don't have any 
    38 implemented yet. 
     9   intro.rst 
     10   install.rst 
     11   pd/polydispersity.rst 
     12   resolution.rst 
     13   magnetism/magnetism.rst 
     14   sesans/sans_to_sesans.rst 
     15   sesans/sesans_fitting.rst 
     16   plugin.rst 
     17   scripting.rst 
     18   refs.rst 

  • doc/index.rst

    r5e1d6b0 r8ae8532  
    1 Introduction 
    2 ============ 
     1sasmodels 
     2========= 
     3Small angle X-ray and Neutron scattering (SAXS and SANS) examines the 
     4scattering patterns produced by a beam travelling through the sample 
     5and scattering at low angles.  The scattering is computed as a function 
     6of reciprocal space $q$, which arises from a combination of beam wavelength 
     7and scattering angles. Each pixel on the detector corresponds to 
     8a different scattering angle, and has a distinct $q_x$ and $q_y$. If the 
     9sample is unoriented, the scattering pattern will appear as rings on the 
     10detector.  In this case, a circular average can be taken with 1-dimension 
     11data at $q = \surd (q_x^2 + q_y^2)$ compared to the orientationally 
     12averaged SAS scattering pattern. 
     13 
    314The sasmodels package provides theory functions for small angle scattering 
    4 calculations. 
     15calculations for different shapes, including the effects of resolution, 
     16polydispersity and orientational dispersion. 
    517 
    618.. htmlonly:: 
    … …  
    1527 
    1628   guide/index.rst 
     29   guide/models/index.rst 
    1730   developer/index.rst 
    18    ref/index.rst 
    19    ref/models/index.rst 
    2031   api/index.rst 
    2132 
    … …  
    2839.. htmlonly:: 
    2940  * :ref:`search` 
    30  
    31  
    32  
    33  
    34    
    35  

  • example/model.py

    r1182da5 r2e66ef5  
    1717model = Model(kernel, 
    1818    scale=0.08, 
    19     r_polar=15, r_equatorial=800, 
     19    radius_polar=15, radius_equatorial=800, 
    2020    sld=.291, sld_solvent=7.105, 
    2121    background=0, 
    2222    theta=90, phi=0, 
    2323    theta_pd=15, theta_pd_n=40, theta_pd_nsigma=3, 
    24     r_polar_pd=0.222296, r_polar_pd_n=1, r_polar_pd_nsigma=0, 
    25     r_equatorial_pd=.000128, r_equatorial_pd_n=1, r_equatorial_pd_nsigma=0, 
     24    radius_polar_pd=0.222296, radius_polar_pd_n=1, radius_polar_pd_nsigma=0, 
     25    radius_equatorial_pd=.000128, radius_equatorial_pd_n=1, radius_equatorial_pd_nsigma=0, 
    2626    phi_pd=0, phi_pd_n=20, phi_pd_nsigma=3, 
    2727    ) 
    2828 
    2929# SET THE FITTING PARAMETERS 
    30 model.r_polar.range(15, 1000) 
    31 model.r_equatorial.range(15, 1000) 
     30model.radius_polar.range(15, 1000) 
     31model.radius_equatorial.range(15, 1000) 
    3232model.theta_pd.range(0, 360) 
    3333model.background.range(0,1000) 

  • sasmodels/alignment.py

    r7ae2b7f r870a2f4  
    4242    view[:] = x 
    4343    return view 
    44  

  • sasmodels/core.py

    r650c6d2 r2e66ef5  
    117117    Load model info and build model. 
    118118 
    119     *model_name* is the name of the model as used by :func:`load_model_info`. 
    120     Additional keyword arguments are passed directly to :func:`build_model`. 
     119    *model_name* is the name of the model, or perhaps a model expression 
     120    such as sphere*hardsphere or sphere+cylinder. 
     121 
     122    *dtype* and *platform* are given by :func:`build_model`. 
    121123    """ 
    122124    return build_model(load_model_info(model_name), 
    … …  
    128130    """ 
    129131    Load a model definition given the model name. 
     132 
     133    *model_name* is the name of the model, or perhaps a model expression 
     134    such as sphere*hardsphere or sphere+cylinder. 
    130135 
    131136    This returns a handle to the module defining the model.  This can be 
    … …  
    227232 
    228233    Possible types include 'half', 'single', 'double' and 'quad'.  If the 
    229     type is 'fast', then this is equivalent to dtype 'single' with the 
    230     fast flag set to True. 
     234    type is 'fast', then this is equivalent to dtype 'single' but using 
     235    fast native functions rather than those with the precision level guaranteed 
     236    by the OpenCL standard. 
     237 
     238    Platform preference can be specfied ("ocl" vs "dll"), with the default 
     239    being OpenCL if it is availabe.  If the dtype name ends with '!' then 
     240    platform is forced to be DLL rather than OpenCL. 
     241 
     242    This routine ignores the preferences within the model definition.  This 
     243    is by design.  It allows us to test models in single precision even when 
     244    we have flagged them as requiring double precision so we can easily check 
     245    the performance on different platforms without having to change the model 
     246    definition. 
    231247    """ 
    232248    # Assign default platform, overriding ocl with dll if OpenCL is unavailable 

  • 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/resolution.py

    rb32caab r990d8df  
    437437    .. math:: 
    438438 
    439          \log \Delta q = (\log q_n - log q_1) / (n - 1) 
     439         \log \Delta q = (\log q_n - \log q_1) / (n - 1) 
    440440 
    441441    From this we can compute the number of steps required to extend $q$ 
    … …  
    451451 
    452452         n_\text{extend} = (n-1) (\log q_\text{max} - \log q_n) 
    453             / (\log q_n - log q_1) 
     453            / (\log q_n - \log q_1) 
    454454    """ 
    455455    q = np.sort(q) 
    … …  
    459459        log_delta_q = log(10.) / points_per_decade 
    460460    if q_min < q[0]: 
    461         if q_min < 0: q_min = q[0]*MINIMUM_ABSOLUTE_Q 
     461        if q_min < 0: 
     462            q_min = q[0]*MINIMUM_ABSOLUTE_Q 
    462463        n_low = log_delta_q * (log(q[0])-log(q_min)) 
    463464        q_low = np.logspace(log10(q_min), log10(q[0]), np.ceil(n_low)+1)[:-1] 

  • sasmodels/rst2html.py

    rf2f5413 r870a2f4  
    3838    - mathml 
    3939    - mathjax 
    40     See `http://docutils.sourceforge.net/docs/user/config.html#math-output`_ 
     40    See `<http://docutils.sourceforge.net/docs/user/config.html#math-output>`_ 
    4141    for details. 
    4242 
    … …  
    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() 
    … …  
    211211    sys.exit(app.exec_()) 
    212212 
     213def can_use_qt(): 
     214    """ 
     215    Return True if QWebView exists. 
     216 
     217    Checks first in PyQt5 then in PyQt4 
     218    """ 
     219    try: 
     220        from PyQt5.QtWebKitWidgets import QWebView 
     221        return True 
     222    except ImportError: 
     223        try: 
     224            from PyQt4.QtWebKit import QWebView 
     225            return True 
     226        except ImportError: 
     227            return False 
     228 
    213229def view_help(filename, qt=False): 
    214230    import os 
    215     url="file:///"+os.path.abspath(filename).replace("\\","/") 
     231 
     232    if qt: 
     233        qt = can_use_qt() 
     234 
     235    url = "file:///"+os.path.abspath(filename).replace("\\", "/") 
    216236    if filename.endswith('.rst'): 
    217237        html = load_rst_as_html(filename) 
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