Changeset f845454 in sasview for src/sas


Ignore:
Timestamp:
Dec 19, 2016 1:52:12 PM (8 years ago)
Author:
GitHub <noreply@…>
Branches:
master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.1.1, release-4.1.2, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
Children:
b61bd57
Parents:
99f3e053 (diff), 50f1477 (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:
Jeff Krzywon <krzywon@…> (12/19/16 13:52:12)
git-committer:
GitHub <noreply@…> (12/19/16 13:52:12)
Message:

Merge branch 'master' into ticket-753

Location:
src/sas
Files:
11 edited

Legend:

Unmodified
Added
Removed

  • src/sas/sascalc/dataloader/manipulations.py

    rb699768 rb2b36932  
    143143        :return: Data1D object 
    144144        """ 
    145         if len(data2D.detector) != 1: 
     145        if len(data2D.detector) > 1: 
    146146            msg = "_Slab._avg: invalid number of " 
    147147            msg += " detectors: %g" % len(data2D.detector) 
    … …  
    299299            error on number of counts, number of entries summed 
    300300        """ 
    301         if len(data2D.detector) != 1: 
     301        if len(data2D.detector) > 1: 
    302302            msg = "Circular averaging: invalid number " 
    303303            msg += "of detectors: %g" % len(data2D.detector) 

  • src/sas/sascalc/dataloader/readers/ascii_reader.py

    r7d94915 rd2471870  
    172172                input_f.close() 
    173173                if not is_data: 
    174                     return None 
     174                    msg = "ascii_reader: x has no data" 
     175                    raise RuntimeError, msg 
    175176                # Sanity check 
    176177                if has_error_dy == True and not len(ty) == len(tdy): 

  • src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py

    r5e906207 rbbd0f37  
    162162                    else: 
    163163                        self.current_dataset.x = data_set.flatten() 
     164                    continue 
     165                elif key == u'Qdev': 
     166                    self.current_dataset.dx = data_set.flatten() 
    164167                    continue 
    165168                elif key == u'Qy': 

  • src/sas/sascalc/fit/BumpsFitting.py

    rb699768 r345e7e4  
    44import os 
    55from datetime import timedelta, datetime 
     6import traceback 
    67 
    78import numpy 
    … …  
    293294            R.success = result['success'] 
    294295            if R.success: 
    295                 R.stderr = numpy.hstack((result['stderr'][fitted_index], 
    296                                          numpy.NaN*numpy.ones(len(fitness.computed_pars)))) 
     296                if result['stderr'] is None: 
     297                    R.stderr = numpy.NaN*numpy.ones(len(param_list)) 
     298                else: 
     299                    R.stderr = numpy.hstack((result['stderr'][fitted_index], 
     300                                             numpy.NaN*numpy.ones(len(fitness.computed_pars)))) 
    297301                R.pvec = numpy.hstack((result['value'][fitted_index], 
    298302                                      [p.value for p in fitness.computed_pars])) 
    … …  
    306310                R.uncertainty_state = result['uncertainty'] 
    307311            all_results.append(R) 
     312        all_results[0].mesg = result['errors'] 
    308313 
    309314        if q is not None: 
    … …  
    344349    try: 
    345350        best, fbest = fitdriver.fit() 
    346     except: 
    347         import traceback; traceback.print_exc() 
    348         raise 
     351        errors = [] 
     352    except Exception as exc: 
     353        best, fbest = None, numpy.NaN 
     354        errors = [str(exc), traceback.traceback.format_exc()] 
    349355    finally: 
    350356        mapper.stop_mapper(fitdriver.mapper) 
    … …  
    356362 
    357363    success = best is not None 
     364    try: 
     365        stderr = fitdriver.stderr() if success else None 
     366    except Exception as exc: 
     367        errors.append(str(exc)) 
     368        errors.append(traceback.format_exc()) 
     369        stderr = None 
    358370    return { 
    359371        'value': best if success else None, 
    360         'stderr': fitdriver.stderr() if success else None, 
     372        'stderr': stderr, 
    361373        'success': success, 
    362374        'convergence': convergence, 
    363375        'uncertainty': getattr(fitdriver.fitter, 'state', None), 
     376        'errors': '\n'.join(errors), 
    364377        } 
    365378 

  • src/sas/sasgui/guiframe/gui_manager.py

    rc8e1996 r67b0a99  
    19501950                    item, _, _ = value 
    19511951                    item.Check(True) 
    1952             self._data_panel.on_remove(None, False) 
    19531952 
    19541953            wx.PostEvent(self, StatusEvent(status="Loading Project file...")) 
    … …  
    19631962                # Reset to a base state 
    19641963                self._on_reset_state() 
     1964                self._data_panel.on_remove(None, False) 
    19651965                # Load the project file 
    19661966                self.load_state(path=path, is_project=True) 
    … …  
    24562456                                                group_id=group_id, 
    24572457                                                action='remove')) 
    2458                 # remove res plot: Todo: improve 
    24592458                wx.CallAfter(self._remove_res_plot, new_plot.id) 
    24602459        self._data_manager.delete_data(data_id=data_id, 

  • src/sas/sasgui/guiframe/local_perspectives/plotting/Plotter2D.py

    r1a696bf rb2b36932  
    316316 
    317317        slicerpop.AppendSeparator() 
    318         if len(self.data2D.detector) == 1: 
     318        if len(self.data2D.detector) <= 1: 
    319319            item_list = self.parent.get_current_context_menu(self) 
    320320            if (not item_list == None) and (not len(item_list) == 0) and\ 

  • src/sas/sasgui/perspectives/fitting/basepage.py

    r99f3e053 rf845454  
    15321532                        val = len(val) if isinstance(val, list) else 1 
    15331533                        self.Npts_fit.SetValue(str(val)) 
     1534 
    15341535                    else: 
    15351536                        # No data in the panel 

  • src/sas/sasgui/perspectives/fitting/fitpanel.py

    rc8e1996 r67b0a99  
    189189        # use while-loop, for-loop will not do the job well. 
    190190        while (self.GetPageCount() > 0): 
    191             # delete the first page until no page exists 
    192             page = self.GetPage(0) 
     191            page = self.GetPage(self.GetPageCount() - 1) 
    193192            if self._manager.parent.panel_on_focus == page: 
    194193                self._manager.parent.panel_on_focus = None 
    195194            self._close_helper(selected_page=page) 
    196             self.DeletePage(0) 
     195            self.DeletePage(self.GetPageCount() - 1) 
    197196        # Clear list of names 
    198197        self.fit_page_name = {} 
    … …  
    400399                    temp = self.GetSelection() 
    401400                    self.DeletePage(temp) 
     401            if self.sim_page is not None: 
     402                if len(self.sim_page.model_list) == 0: 
     403                    pos = self.GetPageIndex(self.sim_page) 
     404                    self.SetSelection(pos) 
     405                    self.on_close_page(event=None) 
     406                    temp = self.GetSelection() 
     407                    self.DeletePage(temp) 
     408                    self.sim_page = None 
     409                    self.batch_on = False 
    402410            if self.GetPageCount() == 0: 
    403411                self._manager.on_add_new_page(event=None) 

  • src/sas/sasgui/perspectives/fitting/fitting.py

    rec72ceb r1a5d5f2  
    15211521            for uid in page_id: 
    15221522                res = result[index] 
     1523                fit_msg = res.mesg 
    15231524                if res.fitness is None or \ 
    15241525                    not numpy.isfinite(res.fitness) or \ 
    15251526                    numpy.any(res.pvec == None) or \ 
    15261527                    not numpy.all(numpy.isfinite(res.pvec)): 
    1527                     msg = "Fitting did not converge!!!" 
    1528                     evt = StatusEvent(status=msg, info="warning", type="stop") 
    1529                     wx.PostEvent(self.parent, evt) 
     1528                    fit_msg += "\nFitting did not converge!!!" 
    15301529                    wx.CallAfter(self._update_fit_button, page_id) 
    15311530                else: 
    … …  
    15501549                        wx.CallAfter(cpage._on_fit_complete) 
    15511550                    except KeyboardInterrupt: 
    1552                         msg = "Singular point: Fitting Stoped." 
    1553                         evt = StatusEvent(status=msg, info="info", type="stop") 
    1554                         wx.PostEvent(self.parent, evt) 
     1551                        fit_msg += "\nSingular point: Fitting stopped." 
    15551552                    except: 
    1556                         msg = "Singular point: Fitting Error occurred." 
    1557                         evt = StatusEvent(status=msg, info="error", type="stop") 
    1558                         wx.PostEvent(self.parent, evt) 
     1553                        fit_msg += "\nSingular point: Fitting error occurred." 
     1554                if fit_msg: 
     1555                   evt = StatusEvent(status=fit_msg, info="warning", type="stop") 
     1556                   wx.PostEvent(self.parent, evt) 
    15591557 
    15601558        except: 

  • src/sas/sasgui/perspectives/fitting/media/plugin.rst

    r20cfa23 rca1eaeb  
    560560 
    561561    M_PI_180, M_4PI_3: 
    562         $\pi/{180}$, $\tfrac{4}{3}\pi$ 
     562        $\frac{\pi}{180}$, $\frac{4\pi}{3}$ 
    563563    SINCOS(x, s, c): 
    564564        Macro which sets s=sin(x) and c=cos(x). The variables *c* and *s* 
    … …  
    596596These functions have been tuned to be fast and numerically stable down 
    597597to $q=0$ even in single precision.  In some cases they work around bugs 
    598 which appear on some platforms but not others. So use them where needed!!! 
     598which appear on some platforms but not others, so use them where needed. 
     599Add the files listed in :code:`source = ["lib/file.c", ...]` to your *model.py* 
     600file in the order given, otherwise these functions will not be available. 
    599601 
    600602    polevl(x, c, n): 
    601         Polynomial evaluation $p(x) = \sum_{i=0}^n c_i x^{n-i}$ using Horner's 
     603        Polynomial evaluation $p(x) = \sum_{i=0}^n c_i x^i$ using Horner's 
    602604        method so it is faster and more accurate. 
    603605 
     606        $c = \{c_n, c_{n-1}, \ldots, c_0 \}$ is the table of coefficients, 
     607        sorted from highest to lowest. 
     608 
     609        :code:`source = ["lib/polevl.c", ...]` (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/polevl.c>`_) 
     610 
     611    p1evl(x, c, n): 
     612        Evaluation of normalized polynomial $p(x) = x^n + \sum_{i=0}^{n-1} c_i x^i$ 
     613        using Horner's method so it is faster and more accurate. 
     614 
     615        $c = \{c_{n-1}, c_{n-2} \ldots, c_0 \}$ is the table of coefficients, 
     616        sorted from highest to lowest. 
     617 
    604618        :code:`source = ["lib/polevl.c", ...]` 
    605  
    606     sas_gamma: 
    607         Gamma function $\text{sas_gamma}(x) = \Gamma(x)$.  The standard math 
    608         library gamma function, tgamma(x) is unstable below 1 on some platforms. 
     619        (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/polevl.c>`_) 
     620 
     621    sas_gamma(x): 
     622        Gamma function $\text{sas_gamma}(x) = \Gamma(x)$. 
     623 
     624        The standard math function, tgamma(x) is unstable for $x < 1$ 
     625        on some platforms. 
    609626 
    610627        :code:`source = ["lib/sasgamma.c", ...]` 
    611  
    612     erf, erfc: 
     628        (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gamma.c>`_) 
     629 
     630    sas_erf(x), sas_erfc(x): 
    613631        Error function 
    614         $\text{erf}(x) = \frac{1}{\sqrt\pi}\int_0^x e^{-t^2}\,dt$ 
     632        $\text{sas_erf}(x) = \frac{2}{\sqrt\pi}\int_0^x e^{-t^2}\,dt$ 
    615633        and complementary error function 
    616         $\text{erfc}(x) = \frac{1}{\sqrt\pi}\int_x^\inf e^{-t^2}\,dt$. 
    617         The standard math library erf and erfc are slower and broken 
     634        $\text{sas_erfc}(x) = \frac{2}{\sqrt\pi}\int_x^{\infty} e^{-t^2}\,dt$. 
     635 
     636        The standard math functions erf(x) and erfc(x) are slower and broken 
    618637        on some platforms. 
    619638 
    620639        :code:`source = ["lib/polevl.c", "lib/sas_erf.c", ...]` 
    621  
    622     sas_J0: 
    623         Bessel function of the first kind where 
     640        (`link to error functions' code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_erf.c>`_) 
     641 
     642    sas_J0(x): 
     643        Bessel function of the first kind $\text{sas_J0}(x)=J_0(x)$ where 
    624644        $J_0(x) = \frac{1}{\pi}\int_0^\pi \cos(x\sin(\tau))\,d\tau$. 
    625645 
     646        The standard math function j0(x) is not available on all platforms. 
     647 
    626648        :code:`source = ["lib/polevl.c", "lib/sas_J0.c", ...]` 
    627  
    628     sas_J1: 
    629         Bessel function of the first kind where 
     649        (`link to Bessel function's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J0.c>`_) 
     650 
     651    sas_J1(x): 
     652        Bessel function of the first kind  $\text{sas_J1}(x)=J_1(x)$ where 
    630653        $J_1(x) = \frac{1}{\pi}\int_0^\pi \cos(\tau - x\sin(\tau))\,d\tau$. 
    631654 
     655        The standard math function j1(x) is not available on all platforms. 
     656 
    632657        :code:`source = ["lib/polevl.c", "lib/sas_J1.c", ...]` 
    633  
    634     sas_JN: 
    635         Bessel function of the first kind where 
     658        (`link to Bessel function's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_) 
     659 
     660    sas_JN(n, x): 
     661        Bessel function of the first kind and integer order $n$: 
     662        $\text{sas_JN}(n, x)=J_n(x)$ where 
    636663        $J_n(x) = \frac{1}{\pi}\int_0^\pi \cos(n\tau - x\sin(\tau))\,d\tau$. 
     664        If $n$ = 0 or 1, it uses sas_J0(x) or sas_J1(x), respectively. 
     665 
     666        The standard math function jn(n, x) is not available on all platforms. 
    637667 
    638668        :code:`source = ["lib/polevl.c", "lib/sas_J0.c", "lib/sas_J1.c", "lib/sas_JN.c", ...]` 
    639  
    640     Si: 
     669        (`link to Bessel function's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_JN.c>`_) 
     670 
     671    Si(x): 
    641672        Sine integral $\text{Si}(x) = \int_0^x \tfrac{\sin t}{t}\,dt$. 
    642673 
    643         :code:`soure = ["lib/Si.c", ...]` 
    644  
    645     sph_j1c(qr): 
     674        This function uses Taylor series for small and large arguments: 
     675 
     676        For large arguments, 
     677 
     678        .. math:: 
     679 
     680             \text{Si}(x) \sim \frac{\pi}{2} 
     681             - \frac{\cos(x)}{x}\left(1 - \frac{2!}{x^2} + \frac{4!}{x^4} - \frac{6!}{x^6} \right) 
     682             - \frac{\sin(x)}{x}\left(\frac{1}{x} - \frac{3!}{x^3} + \frac{5!}{x^5} - \frac{7!}{x^7}\right) 
     683 
     684        For small arguments, 
     685 
     686        .. math:: 
     687 
     688           \text{Si}(x) \sim x 
     689           - \frac{x^3}{3\times 3!} + \frac{x^5}{5 \times 5!} - \frac{x^7}{7 \times 7!} 
     690           + \frac{x^9}{9\times 9!} - \frac{x^{11}}{11\times 11!} 
     691 
     692        :code:`source = ["lib/Si.c", ...]` 
     693        (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/Si.c>`_) 
     694 
     695    sph_j1c(x): 
    646696        Spherical Bessel form 
    647         $F(qr) = 3 j_1(qr)/(qr) = 3 (\sin(qr) - qr \cos(qr))/{(qr)^3}$, 
    648         with a limiting value of 1 at $qr=0$.  This function uses a Taylor 
    649         series for small $qr$ for numerical accuracy. 
     697        $\text{sph_j1c}(x) = 3 j_1(x)/x = 3 (\sin(x) - x \cos(x))/x^3$, 
     698        with a limiting value of 1 at $x=0$, where $j_1(x)$ is the spherical 
     699        Bessel function of the first kind and first order. 
     700 
     701        This function uses a Taylor series for small $x$ for numerical accuracy. 
    650702 
    651703        :code:`source = ["lib/sph_j1c.c", ...]` 
    652  
    653     sas_J1c(qr): 
    654         Bessel form $F(qr) = 2 J_1(qr)/{(qr)}$, with a limiting value of 1 at $qr=0$. 
     704        (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sph_j1c.c>`_) 
     705 
     706 
     707    sas_J1c(x): 
     708        Bessel form $\text{sas_J1c}(x) = 2 J_1(x)/x$, with a limiting value 
     709        of 1 at $x=0$, where $J_1(x)$ is the Bessel function of first kind 
     710        and first order. 
    655711 
    656712        :code:`source = ["lib/polevl.c", "lib/sas_J1.c", ...]` 
    657  
    658     Gauss76z[i], Gauss76Wt[i]: 
    659         Points $z_i$ and weights $w_i$ for 76-point Gaussian quadrature, 
    660         computing $\int_{-1}^1 f(z)\,dz \approx \sum_{i=1}^{76} w_i f(z_i)$. 
    661         Similar arrays are available in :code:`gauss20.c` for 20 point 
    662         quadrature and in :code:`gauss150.c` for 150 point quadrature. 
    663  
    664         :code:`source = ["gauss76.c", ...]` 
     713        (`link to Bessel form's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_) 
     714 
     715 
     716    Gauss76Z[i], Gauss76Wt[i]: 
     717        Points $z_i$ and weights $w_i$ for 76-point Gaussian quadrature, respectively, 
     718        computing $\int_{-1}^1 f(z)\,dz \approx \sum_{i=1}^{76} w_i\,f(z_i)$. 
     719 
     720        Similar arrays are available in :code:`gauss20.c` for 20-point 
     721        quadrature and in :code:`gauss150.c` for 150-point quadrature. 
     722 
     723        :code:`source = ["lib/gauss76.c", ...]` 
     724        (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/gauss76.c>`_) 
     725 
     726 
    665727 
    666728Problems with C models 

  • src/sas/sasgui/perspectives/invariant/media/invariant_help.rst

    rb64b87c r484141c  
    116116Academic Press, New York, 1982 
    117117 
    118 http://physchem.kfunigraz.ac.at/sm/ 
     118http://web.archive.org/web/20110824105537/http://physchem.kfunigraz.ac.at/sm/Service/Glatter_Kratky_SAXS_1982.zip 
    119119 
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