Changeset b6e0636 in sasmodels


Ignore:
Timestamp:
Apr 5, 2017 9:36:59 AM (8 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

Files:
8 edited

Legend:

Unmodified
Added
Removed

  • LICENSE.txt

    rc8de1bd rf68e2a5  
    1 This program is in the public domain. 
     1Copyright (c) 2009-2017, SasView Developers 
     2All rights reserved. 
    23 
    3 Individual files may be copyright different authors, with licences that 
    4 allow modification and redistribution in source or binary form with or 
    5 without modification, and a disclaimer of warranty. 
     4Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 
     5 
     61. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 
     7 
     82. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 
     9 
     103. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 
     11 
     12THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 

  • 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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