Changeset b6e0636 in sasmodels for sasmodels


Ignore:
Timestamp:
Apr 5, 2017 9:36:59 AM (7 years ago)
Author:
richardh
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
0b56f38, 4aaf89a
Parents:
4b0a294 (diff), 6e5c0b7 (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.
Message:

Merge branch 'ticket-890' of ​https://github.com/sasview/sasmodels into ticket-890

Location:
sasmodels
Files:
7 edited

Legend:

Unmodified
Added
Removed

  • sasmodels/compare.py

    r01ea374 r6e5c0b7  
    3030 
    3131import sys 
     32import os 
    3233import math 
    3334import datetime 
    … …  
    4041from . import kerneldll 
    4142from . import exception 
    42 from .data import plot_theory, empty_data1D, empty_data2D 
     43from .data import plot_theory, empty_data1D, empty_data2D, load_data 
    4344from .direct_model import DirectModel 
    4445from .convert import revert_name, revert_pars, constrain_new_to_old 
    … …  
    8586    -help/-html shows the model docs instead of running the model 
    8687    -title="note" adds note to the plot title, after the model name 
     88    -data="path" uses q, dq from the data file 
    8789 
    8890Any two calculation engines can be selected for comparison: 
    … …  
    747749    comp = opts['engines'][1] if have_comp else None 
    748750    data = opts['data'] 
     751    use_data = have_base ^ have_comp 
    749752 
    750753    # Plot if requested 
    … …  
    763766    if have_base: 
    764767        if have_comp: plt.subplot(131) 
    765         plot_theory(data, base_value, view=view, use_data=False, limits=limits) 
     768        plot_theory(data, base_value, view=view, use_data=use_data, limits=limits) 
    766769        plt.title("%s t=%.2f ms"%(base.engine, base_time)) 
    767770        #cbar_title = "log I" 
    … …  
    769772        if have_base: plt.subplot(132) 
    770773        if not opts['is2d'] and have_base: 
    771             plot_theory(data, base_value, view=view, use_data=False, limits=limits) 
    772         plot_theory(data, comp_value, view=view, use_data=False, limits=limits) 
     774            plot_theory(data, base_value, view=view, use_data=use_data, limits=limits) 
     775        plot_theory(data, comp_value, view=view, use_data=use_data, limits=limits) 
    773776        plt.title("%s t=%.2f ms"%(comp.engine, comp_time)) 
    774777        #cbar_title = "log I" 
    … …  
    784787            err[err>cutoff] = cutoff 
    785788        #err,errstr = base/comp,"ratio" 
    786         plot_theory(data, None, resid=err, view=errview, use_data=False) 
     789        plot_theory(data, None, resid=err, view=errview, use_data=use_data) 
    787790        if view == 'linear': 
    788791            plt.xscale('linear') 
    … …  
    834837VALUE_OPTIONS = [ 
    835838    # Note: random is both a name option and a value option 
    836     'cutoff', 'random', 'nq', 'res', 'accuracy', 'title', 
     839    'cutoff', 'random', 'nq', 'res', 'accuracy', 'title', 'data', 
    837840    ] 
    838841 
    … …  
    951954        'html'      : False, 
    952955        'title'     : None, 
     956        'data'      : None, 
    953957    } 
    954958    engines = [] 
    … …  
    971975        elif arg.startswith('-cutoff='):   opts['cutoff'] = float(arg[8:]) 
    972976        elif arg.startswith('-random='):   opts['seed'] = int(arg[8:]) 
    973         elif arg.startswith('-title'):     opts['title'] = arg[7:] 
     977        elif arg.startswith('-title='):    opts['title'] = arg[7:] 
     978        elif arg.startswith('-data='):     opts['data'] = arg[6:] 
    974979        elif arg == '-random':  opts['seed'] = np.random.randint(1000000) 
    975980        elif arg == '-preset':  opts['seed'] = -1 
    … …  
    11131118 
    11141119    # Create the computational engines 
    1115     data, _ = make_data(opts) 
     1120    if opts['data'] is not None: 
     1121        data = load_data(os.path.expanduser(opts['data'])) 
     1122    else: 
     1123        data, _ = make_data(opts) 
    11161124    if n1: 
    11171125        base = make_engine(model_info, data, engines[0], opts['cutoff']) 
    … …  
    11431151    show html docs for the model 
    11441152    """ 
    1145     import wx  # type: ignore 
    1146     from .generate import view_html_from_info 
    1147     app = wx.App() if wx.GetApp() is None else None 
    1148     view_html_from_info(opts['def'][0]) 
    1149     if app: app.MainLoop() 
    1150  
     1153    import os 
     1154    from .generate import make_html 
     1155    from . import rst2html 
     1156 
     1157    info = opts['def'][0] 
     1158    html = make_html(info) 
     1159    path = os.path.dirname(info.filename) 
     1160    url = "file://"+path.replace("\\","/")[2:]+"/" 
     1161    rst2html.view_html_qtapp(html, url) 
    11511162 
    11521163def explore(opts): 

  • sasmodels/data.py

    r40a87fa ra769b54  
    5454    if data is None: 
    5555        raise IOError("Data %r could not be loaded" % filename) 
     56    if hasattr(data, 'x'): 
     57        data.qmin, data.qmax = data.x.min(), data.x.max() 
     58        data.mask = (np.isnan(data.y) if data.y is not None 
     59                     else np.zeros_like(data.x, dtype='bool')) 
    5660    return data 
    5761 
    … …  
    348352    # data, but they already handle the masking and graph markup already, so 
    349353    # do not repeat. 
    350     if hasattr(data, 'lam'): 
     354    if hasattr(data, 'isSesans') and data.isSesans: 
    351355        _plot_result_sesans(data, None, None, use_data=True, limits=limits) 
    352356    elif hasattr(data, 'qx_data'): 
    … …  
    376380    *Iq_calc* is the raw theory values without resolution smearing 
    377381    """ 
    378     if hasattr(data, 'lam'): 
     382    if hasattr(data, 'isSesans') and data.isSesans: 
    379383        _plot_result_sesans(data, theory, resid, use_data=True, limits=limits) 
    380384    elif hasattr(data, 'qx_data'): 

  • sasmodels/direct_model.py

    rb397165 ra769b54  
    192192 
    193193        # interpret data 
    194         if hasattr(data, 'lam'): 
     194        if hasattr(data, 'isSesans') and data.isSesans: 
    195195            self.data_type = 'sesans' 
    196196        elif hasattr(data, 'qx_data'): 

  • sasmodels/generate.py

    r1e7b0db0 rc4e3215  
    928928    from . import rst2html 
    929929    url = "file://"+dirname(info.filename)+"/" 
    930     rst2html.wxview(make_html(info), url=url) 
     930    rst2html.view_html(make_html(info), url=url) 
    931931 
    932932def demo_time(): 

  • sasmodels/rst2html.py

    r0890871 rc4e3215  
    2929from docutils.writers.html4css1 import HTMLTranslator 
    3030from docutils.nodes import SkipNode 
    31  
    32 def wxview(html, url="", size=(850, 540)): 
    33     import wx 
    34     from wx.html2 import WebView 
    35     frame = wx.Frame(None, -1, size=size) 
    36     view = WebView.New(frame) 
    37     view.SetPage(html, url) 
    38     frame.Show() 
    39     return frame 
    40  
    41 def view_rst(filename): 
    42     from os.path import expanduser 
    43     with open(expanduser(filename)) as fid: 
    44         rst = fid.read() 
    45     html = rst2html(rst) 
    46     wxview(html) 
    4731 
    4832def rst2html(rst, part="whole", math_output="mathjax"): 
    … …  
    155139    assert replace_dollar(u"a (again $in parens$) a") == u"a (again :math:`in parens`) a" 
    156140 
    157 def view_rst_app(filename): 
     141def load_rst_as_html(filename): 
     142    from os.path import expanduser 
     143    with open(expanduser(filename)) as fid: 
     144        rst = fid.read() 
     145    html = rst2html(rst) 
     146    return html 
     147 
     148def wxview(html, url="", size=(850, 540)): 
     149    import wx 
     150    from wx.html2 import WebView 
     151    frame = wx.Frame(None, -1, size=size) 
     152    view = WebView.New(frame) 
     153    view.SetPage(html, url) 
     154    frame.Show() 
     155    return frame 
     156 
     157def qtview(html, url=""): 
     158    try: 
     159        from PyQt5.QtWebKitWidgets import QWebView 
     160        from PyQt5.QtCore import QUrl 
     161    except ImportError: 
     162        from PyQt4.QtWebkit import QWebView 
     163        from PyQt4.QtCore import QUrl 
     164    helpView = QWebView() 
     165    helpView.setHtml(html, QUrl(url)) 
     166    helpView.show() 
     167    return helpView 
     168 
     169def view_html_wxapp(html, url=""): 
    158170    import wx  # type: ignore 
    159171    app = wx.App() 
    160     view_rst(filename) 
     172    frame = wxview(html, url) 
    161173    app.MainLoop() 
    162174 
     175def view_html_qtapp(html, url=""): 
     176    import sys 
     177    try: 
     178        from PyQt5.QtWidgets import QApplication 
     179    except ImportError: 
     180        from PyQt4.QtGui import QApplication 
     181    app = QApplication([]) 
     182    frame = qtview(html, url) 
     183    sys.exit(app.exec_()) 
     184 
     185def view_rst_app(filename, qt=False): 
     186    import os 
     187    html = load_rst_as_html(filename) 
     188    url="file://"+os.path.abspath(filename)+"/" 
     189    if qt: 
     190        view_html_qtapp(html, url) 
     191    else: 
     192        view_html_wxapp(html, url) 
    163193 
    164194if __name__ == "__main__": 
    165195    import sys 
    166     view_rst_app(sys.argv[1]) 
     196    view_rst_app(sys.argv[1], qt=True) 
    167197 

  • sasmodels/models/ellipsoid.py

    r3b571ae r4b0a294  
    161161def ER(radius_polar, radius_equatorial): 
    162162    import numpy as np 
    163  
     163# see equation (26) in A.Isihara, J.Chem.Phys. 18(1950)1446-1449 
    164164    ee = np.empty_like(radius_polar) 
    165165    idx = radius_polar > radius_equatorial 

  • sasmodels/models/triaxial_ellipsoid.py

    r28d3067 r4b0a294  
    1616    \frac{X^2}{R_a^2} + \frac{Y^2}{R_b^2} + \frac{Z^2}{R_c^2} = 1 
    1717 
    18 the scattering is defined by the average over all orientations $\Omega$, 
     18the scattering for randomly oriented particles is defined by the average over all orientations $\Omega$ of: 
    1919 
    2020.. math:: 
    2121 
    22     P(q) = \text{scale}\frac{V}{4 \pi}\int_\Omega \Phi^2(qr) d\Omega + \text{background} 
     22    P(q) = \text{scale}(\Delta\rho)^2\frac{V}{4 \pi}\int_\Omega \Phi^2(qr) d\Omega + \text{background} 
    2323 
    2424where 
    … …  
    7979The radius-of-gyration for this system is  $R_g^2 = (R_a R_b R_c)^2/5$. 
    8080 
    81 The contrast is defined as SLD(ellipsoid) - SLD(solvent).  In the 
     81The contrast $\Delta\rho$ is defined as SLD(ellipsoid) - SLD(solvent).  In the 
    8282parameters, $R_a$ is the minor equatorial radius, $R_b$ is the major 
    8383equatorial radius, and $R_c$ is the polar radius of the ellipsoid. 
    … …  
    102102*Light scattering by ellipsoidal particles in solution*, 
    103103J. Phys. D: Appl. Phys. 4, 72-77. doi:10.1088/0022-3727/4/1/310 
     104 
     105Authorship and Verification 
     106---------------------------- 
     107 
     108* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     109* **Last Modified by:** Paul Kienzle (improved calculation) **Date:** April 4, 2017 
     110* **Last Reviewed by:** Paul Kienzle &Richard Heenan **Date:**  April 4, 2017 
    104111 
    105112""" 
    … …  
    144151    import numpy as np 
    145152    from .ellipsoid import ER as ellipsoid_ER 
     153     # now that radii can be in any size order, radii need sorting a,b,c where a~b and c is either much smaller or much larger 
     154     # also need some unit tests! 
     155     
    146156    return ellipsoid_ER(radius_polar, np.sqrt(radius_equat_minor * radius_equat_major)) 
    147157 
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