Changes in / [6bd4235:c7634fd] in sasview


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Files:
7 added
1 deleted
24 edited

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  • build_tools/requirements.txt

    r36ca21e rc16172d  
    33pylint 
    44unittest-xml-reporting==1.10.0 
    5 pyparsing==1.5.5 
     5pyparsing>=2.0 
    66html5lib==0.95 
    77reportlab==2.5 

  • docs/sphinx-docs/source/user/marketplace.rst

    r59dfb53 r1eb86a5  
    66plug-in fitting models for *SasView* for all to use. 
    77 
    8 .. note:: These plug-in models require SasView version 4.0 or later. 
     8.. note::  
     9    These plug-in models require SasView version 4.0 or later. However,  
     10    not *all* models may work with *every* version of SasView because  
     11    of changes to our API. 
    912 
    1013Contributed models should be written in Python (only version 2.7.x is 
    … …  
    1215combination of Python and C. You only need to upload the .py/.c source 
    1316code files to the Marketplace! 
     17 
     18Please put a comment in your code to indicate which version of SasView you  
     19wrote the model for. 
    1420 
    1521For guidance on how to write a plugin model see :ref:`Writing_a_Plugin` . It 

  • setup.py

    r1a3602d rc16172d  
    402402 
    403403required = [ 
    404     'bumps>=0.7.5.9', 'periodictable>=1.5.0', 'pyparsing<2.0.0', 
     404    'bumps>=0.7.5.9', 'periodictable>=1.5.0', 'pyparsing>=2.0.0', 
    405405 
    406406    # 'lxml>=2.2.2', 

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

    ra58b5a0 r4a8d55c  
    3131FIELDS_2D = ('data', 'qx_data', 'qy_data', 'q_data', 'err_data', 
    3232                 'dqx_data', 'dqy_data', 'mask') 
    33  
     33DEPRECATION_MESSAGE = ("\rThe extension of this file suggests the data set migh" 
     34                       "t not be fully reduced. Support for the reader associat" 
     35                       "ed with this file type has been removed. An attempt to " 
     36                       "load the file was made, but, should it be successful, " 
     37                       "SasView cannot guarantee the accuracy of the data.") 
    3438 
    3539class FileReader(object): 
    … …  
    4044    # List of allowed extensions 
    4145    ext = ['.txt'] 
     46    # Deprecated extensions 
     47    deprecated_extensions = ['.asc', '.nxs'] 
    4248    # Bypass extension check and try to load anyway 
    4349    allow_all = False 
    … …  
    8793                    if not self.f_open.closed: 
    8894                        self.f_open.close() 
     95                    if any(filepath.lower().endswith(ext) for ext in 
     96                           self.deprecated_extensions): 
     97                        self.handle_error_message(DEPRECATION_MESSAGE) 
    8998                    if len(self.output) > 0: 
    9099                        # Sort the data that's been loaded 
    … …  
    146155        else: 
    147156            logger.warning(msg) 
     157            raise NoKnownLoaderException(msg) 
    148158 
    149159    def send_to_output(self): 

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

    rdc8d1c2 r4a8d55c  
    9090            ascii_loader = ascii_reader.Reader() 
    9191            return ascii_loader.read(path) 
     92        except NoKnownLoaderException: 
     93            pass  # Try the Cansas XML reader 
    9294        except DefaultReaderException: 
    9395            pass  # Loader specific error to try the cansas XML reader 
    … …  
    100102            cansas_loader = cansas_reader.Reader() 
    101103            return cansas_loader.read(path) 
     104        except NoKnownLoaderException: 
     105            pass  # Try the NXcanSAS reader 
    102106        except DefaultReaderException: 
    103107            pass  # Loader specific error to try the NXcanSAS reader 

  • src/sas/sascalc/fit/pagestate.py

    r574adc7 r3b070a0  
    646646                    name = value.split(':', 1)[1].strip() 
    647647                    file_value = "File name:" + name 
     648                    #Truncating string so print doesn't complain of being outside margins 
     649                    if sys.platform != "win32": 
     650                        MAX_STRING_LENGHT = 50 
     651                        if len(file_value) > MAX_STRING_LENGHT: 
     652                            file_value = "File name:.."+file_value[-MAX_STRING_LENGHT+10:] 
    648653                    file_name = CENTRE % file_value 
    649654                    if len(title) == 0: 
    … …  
    721726        html_str, text_str, title = self._get_report_string() 
    722727        # Allow 2 figures to append 
    723         image_links = [FEET_2%fig for fig in fig_urls] 
    724  
     728        #Constraining image width for OSX and linux, so print doesn't complain of being outside margins 
     729        if sys.platform == "win32": 
     730            image_links = [FEET_2%fig for fig in fig_urls] 
     731        else: 
     732            image_links = [FEET_2_unix%fig for fig in fig_urls] 
    725733        # final report html strings 
    726734        report_str = html_str + ELINE.join(image_links) 
    727  
     735        report_str += FEET_3 
    728736        return report_str, text_str 
    729737 
    … …  
    13681376""" 
    13691377FEET_2 = \ 
    1370 """<img src="%s" ></img> 
     1378"""<img src="%s"></img> 
     1379""" 
     1380FEET_2_unix = \ 
     1381"""<img src="%s" width="540"></img> 
    13711382""" 
    13721383FEET_3 = \ 

  • src/sas/sasgui/guiframe/local_perspectives/data_loader/data_loader.py

    r20fa5fe r2924532  
    185185            try: 
    186186                message = "Loading {}...\n".format(p_file) 
    187                 self.load_update(output=output, message=message, info="info") 
     187                self.load_update(message=message, info="info") 
    188188                temp = self.loader.load(p_file, format) 
    189189                if not isinstance(temp, list): 
    … …  
    201201                        else: 
    202202                            file_errors[basename] = [error_message] 
    203                         self.load_update(output=output, 
    204                             message=error_message, info="warning") 
    205  
    206                 self.load_update(output=output, 
    207                 message="Loaded {}\n".format(p_file), 
    208                 info="info") 
     203 
     204                self.load_update(message="Loaded {}\n".format(p_file), 
     205                                 info="info") 
    209206 
    210207            except NoKnownLoaderException as e: 
    211208                exception_occurred = True 
    212                 logger.error(e.message) 
    213  
    214209                error_message = "Loading data failed!\n" + e.message 
    215                 self.load_update(output=None, message=e.message, info="warning") 
     210                self.load_complete(output=None, 
     211                                   message=error_message, 
     212                                   info="warning") 
    216213 
    217214            except Exception as e: 
    218215                exception_occurred = True 
    219                 logger.error(e.message) 
    220  
    221216                file_err = "The Data file you selected could not be " 
    222217                file_err += "loaded.\nMake sure the content of your file" 
    … …  
    225220                file_err += " following:\n" 
    226221                file_err += e.message 
    227                 file_errors[basename] = [file_err] 
     222                self.load_complete(output=None, 
     223                                   message=file_err, 
     224                                   info="error") 
    228225 
    229226        if len(file_errors) > 0: 
    230227            error_message = "" 
    231228            for filename, error_array in file_errors.iteritems(): 
    232                 error_message += "The following errors occured whilst " 
     229                error_message += "The following issues were found whilst " 
    233230                error_message += "loading {}:\n".format(filename) 
    234231                for message in error_array: 
    235232                    error_message += message + "\n" 
    236                 error_message += "\n" 
    237             if not exception_occurred: # Some data loaded but with errors 
    238                 self.load_update(output=output, message=error_message, info="error") 
    239  
    240         if not exception_occurred: # Everything loaded as expected 
     233                error_message = error_message[:-1] 
     234            self.load_complete(output=output, 
     235                               message=error_message, 
     236                               info="error") 
     237 
     238        elif not exception_occurred: # Everything loaded as expected 
    241239            self.load_complete(output=output, message="Loading data complete!", 
    242240                               info="info") 
    … …  
    244242            self.load_complete(output=None, message=error_message, info="error") 
    245243 
    246  
    247     def load_update(self, output=None, message="", info="warning"): 
     244    def load_update(self, message="", info="warning"): 
    248245        """ 
    249246        print update on the status bar 
    250247        """ 
    251248        if message != "": 
    252             wx.PostEvent(self.parent, StatusEvent(status=message, info=info, 
     249            wx.PostEvent(self.parent, StatusEvent(status=message, 
     250                                                  info=info, 
    253251                                                  type="progress")) 
    254252 
    … …  
    257255         post message to status bar and return list of data 
    258256        """ 
    259         wx.PostEvent(self.parent, StatusEvent(status=message, info=info, 
     257        wx.PostEvent(self.parent, StatusEvent(status=message, 
     258                                              info=info, 
    260259                                              type="stop")) 
    261260        if output is not None: 

  • src/sas/sasgui/guiframe/media/data_formats_help.rst

    r959eb01 r1eb86a5  
    2828 
    2929*  .TXT 
    30 *  .ASC 
    3130*  .DAT 
    3231*  .XML (in canSAS format v1.0 and 1.1) 
     32*  .H5  (as NeXus NXcanSAS only) 
     33*  .NXS (as NeXus NXcanSAS only) 
     34 
     35.. note:: 
     36    From SasView version 4.2 onwards files written in the NIST .ASC format are no longer read. This is because that  
     37    format normally represents *raw* and not reduced data. 
    3338 
    3439If using CSV output from, for example, a spreadsheet, ensure that it is not using commas as delimiters for thousands. 
    … …  
    4045 
    4146For a description of the ISIS 1D format see: 
    42 http://www.isis.stfc.ac.uk/instruments/loq/software/colette-ascii-file-format-descriptions9808.pdf 
     47https://www.isis.stfc.ac.uk/Pages/colette-ascii-file-format-descriptions.pdf 
    4348 
    4449For a description of the NXcanSAS format see: 
    … …  
    5863-------------- 
    5964 
    60 SasView will read ASCII ('text') files in the NIST 2D format (with the extensions .ASC or .DAT) or files in the NeXus NXcanSAS (HDF5) format (with the extension .H5). File extensions are not case-sensitive. Both of these formats are written by the `Mantid Framework <http://www.mantidproject.org/>`_. 
     65SasView will read ASCII ('text') files in the NIST 2D format (with the extension .DAT) or files in the NeXus NXcanSAS (HDF5) format (with the extension .H5 or .NXS). File extensions are not case-sensitive. Both of these formats are written by the `Mantid Framework <http://www.mantidproject.org/>`_. 
    6166 
    6267Most of the header lines in the NIST 2D format can actually be removed except the last line, and only the first three columns (*Qx, Qy,* and *I(Qx,Qy)*) are actually required. 
     68 
     69.. note:: 
     70    From SasView version 4.2 onwards files written in the NIST .ASC format are no longer read. This is because that  
     71    format normally represents *raw* and not reduced data. 
     72 
     73.. note:: 
     74    SasView does not read the standard NeXus format, only the NXcanSAS subset.  
    6375 
    6476The SasView :ref:`File_Converter_Tool` available in SasView 4.1 onwards can be used to convert data sets in the 2D BSL/OTOKO format into the NeXus NXcanSAS (HDF5) format. 

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

    r69a6897 r91552b5  
    2727class BaseReportDialog(wx.Dialog): 
    2828 
    29     def __init__(self, report_list, *args, **kwds): 
     29    def __init__(self, report_list, imgRAM, fig_urls, *args, **kwds): 
    3030        """ 
    3131        Initialization. The parameters added to Dialog are: 
    … …  
    3737        kwds["image"] = 'Dynamic Image' 
    3838 
     39        #MemoryFSHandle for storing images 
     40        self.imgRAM = imgRAM 
     41        #Images location in urls 
     42        self.fig_urls = fig_urls 
    3943        # title 
    4044        self.SetTitle("Report") 
    … …  
    7579        hbox.Add(button_print) 
    7680 
    77         button_save = wx.Button(self, wx.NewId(), "Save") 
    78         button_save.SetToolTipString("Save this report.") 
    79         button_save.Bind(wx.EVT_BUTTON, self.onSave, id=button_save.GetId()) 
    80         hbox.Add(button_save) 
     81        if sys.platform != "darwin": 
     82            button_save = wx.Button(self, wx.NewId(), "Save") 
     83            button_save.SetToolTipString("Save this report.") 
     84            button_save.Bind(wx.EVT_BUTTON, self.onSave, id=button_save.GetId()) 
     85            hbox.Add(button_save) 
    8186 
    8287        # panel for report page 
    … …  
    111116        printh.PrintText(self.report_html) 
    112117 
     118 
    113119    def OnClose(self, event=None): 
    114120        """ 
    … …  
    116122        : event: Close button event 
    117123        """ 
     124        for fig in self.fig_urls: 
     125            self.imgRAM.RemoveFile(fig) 
     126 
    118127        self.Close() 
    119128 

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

    r235f514 r61bfd36  
    8686                ("Generic Scattering Calculator", 
    8787                        gensas_help, self.on_gen_model), 
     88                ("Orientation Viewer", "Show 3-D view of oriented shape", self.on_show_orientation), 
    8889                ("Python Shell/Editor", pyconsole_help, self.on_python_console), 
    8990                ("Image Viewer", imageviewer_help, self.on_image_viewer), ] 
    … …  
    190191            self.gen_frame.Show(False) 
    191192        self.gen_frame.Show(True) 
     193 
     194    def on_show_orientation(self, event): 
     195        """ 
     196        Make sasmodels orientation & jitter viewer available 
     197        """ 
     198        from sasmodels.jitter import run 
     199        run() 
    192200 
    193201    def on_image_viewer(self, event): 

  • src/sas/sasgui/perspectives/calculator/media/resolution_calculator_help.rst

    r5ed76f8 r3bd58f0  
    2929   careful to note that distances are specified in cm! 
    3030 
    31 4) Enter values for the source wavelength(s), $\lambda$, and its spread (= $\text{FWHM}/\lambda$). 
     314) Enter values for the source wavelength(s), $\lambda$, and its spread (= $\mathrm{FWHM}/\lambda$). 
    3232 
    3333   For monochromatic sources, the inputs are just one value. For TOF sources, 
    … …  
    5858   region near the beam block/stop 
    5959 
    60    [i.e., $Q < (2 \pi \cdot \text{beam block diameter}) / (\text{sample-to-detector distance} \cdot \lambda_\text{min})$] 
     60   [i.e., $Q < (2 \pi \cdot w) / (d_s \cdot \lambda_\mathrm{min})$, where $w$ is the beam block diameter, $d_s$ is the sample-to-detector distance, and $\lambda_\mathrm{min}$ is the minimum wavelength.] 
    6161 
    6262   the variance is slightly under estimated. 

  • src/sas/sasgui/perspectives/calculator/media/sas_calculator_help.rst

    r1b67f3e r55abe4f  
    8888 
    8989Now let us assume that the angles of the $\vec Q$ vector and the spin-axis ($x'$) 
    90 to the $x$-axis are $\phi$ and $\theta_\text{up}$ respectively (see above). Then, 
     90to the $x$-axis are $\phi$ and $\theta_\mathrm{up}$ respectively (see above). Then, 
    9191depending upon the polarization (spin) state of neutrons, the scattering 
    9292length densities, including the nuclear scattering length density ($\beta_N$) 
    … …  
    107107.. math:: 
    108108 
    109     M_{\perp x'} &= M_{0q_x}\cos\theta_\text{up} + M_{0q_y}\sin\theta_\text{up} \\ 
    110     M_{\perp y'} &= M_{0q_y}\cos\theta_\text{up} - M_{0q_x}\sin\theta_\text{up} \\ 
     109    M_{\perp x'} &= M_{0q_x}\cos\theta_\mathrm{up} + M_{0q_y}\sin\theta_\mathrm{up} \\ 
     110    M_{\perp y'} &= M_{0q_y}\cos\theta_\mathrm{up} - M_{0q_x}\sin\theta_\mathrm{up} \\ 
    111111    M_{\perp z'} &= M_{0z} \\ 
    112112    M_{0q_x} &= (M_{0x}\cos\phi - M_{0y}\sin\phi)\cos\phi \\ 

  • src/sas/sasgui/perspectives/calculator/model_editor.py

    r2469df7 rd247504b  
    391391        self._msg_box.SetLabel(msg) 
    392392        self._msg_box.SetForegroundColour(color) 
     393        self._set_model_list() 
    393394        if self.parent.parent is not None: 
    394395            from sas.sasgui.guiframe.events import StatusEvent 
    … …  
    432433        if len(main_list) > 1: 
    433434            main_list.sort() 
     435        self.model1.Clear() 
     436        self.model2.Clear() 
    434437        for idx in range(len(main_list)): 
    435438            self.model1.Append(str(main_list[idx]), idx) 
    … …  
    660663        Do the layout for parameter related widgets 
    661664        """ 
    662         param_txt = wx.StaticText(self, -1, 'Fit Parameters NOT requiring' + \ 
    663                                   ' polydispersity (if any): ') 
    664  
    665         param_tip = "#Set the parameters NOT requiring polydispersity " + \ 
    666         "and their initial values.\n" 
     665        param_txt = wx.StaticText(self, -1, 'Fit Parameters: ') 
     666 
     667        param_tip = "#Set the parameters and their initial values.\n" 
    667668        param_tip += "#Example:\n" 
    668669        param_tip += "A = 1\nB = 1" 
    … …  
    678679                                  (self.param_tcl, 1, wx.EXPAND | wx.ALL, 10)]) 
    679680 
    680         # Parameters with polydispersity 
    681         pd_param_txt = wx.StaticText(self, -1, 'Fit Parameters requiring ' + \ 
    682                                      'polydispersity (if any): ') 
    683  
    684         pd_param_tip = "#Set the parameters requiring polydispersity and " + \ 
    685         "their initial values.\n" 
    686         pd_param_tip += "#Example:\n" 
    687         pd_param_tip += "C = 2\nD = 2" 
    688         newid = wx.NewId() 
    689         self.pd_param_tcl = EditWindow(self, newid, wx.DefaultPosition, 
    690                                     wx.DefaultSize, 
    691                                     wx.CLIP_CHILDREN | wx.SUNKEN_BORDER) 
    692         self.pd_param_tcl.setDisplayLineNumbers(True) 
    693         self.pd_param_tcl.SetToolTipString(pd_param_tip) 
    694  
    695         self.param_sizer.AddMany([(pd_param_txt, 0, wx.LEFT, 10), 
    696                                   (self.pd_param_tcl, 1, wx.EXPAND | wx.ALL, 10)]) 
    697681 
    698682    def _layout_function(self): 
    … …  
    896880            description = self.desc_tcl.GetValue() 
    897881            param_str = self.param_tcl.GetText() 
    898             pd_param_str = self.pd_param_tcl.GetText() 
    899882            func_str = self.function_tcl.GetText() 
    900883            # No input for the model function 
    … …  
    902885                if func_str.count('return') > 0: 
    903886                    self.write_file(self.fname, name, description, param_str, 
    904                                     pd_param_str, func_str) 
     887                                    func_str) 
    905888                    try: 
    906889                        result, msg = check_model(self.fname), None 
    … …  
    942925        self.warning = msg 
    943926 
    944     def write_file(self, fname, name, desc_str, param_str, pd_param_str, func_str): 
     927    def write_file(self, fname, name, desc_str, param_str, func_str): 
    945928        """ 
    946929        Write content in file 
    … …  
    949932        :param desc_str: content of the description strings 
    950933        :param param_str: content of params; Strings 
    951         :param pd_param_str: content of params requiring polydispersity; Strings 
    952934        :param func_str: content of func; Strings 
    953935        """ 
    … …  
    963945        # Write out parameters 
    964946        param_names = []    # to store parameter names 
    965         pd_params = [] 
    966947        out_f.write('parameters = [ \n') 
    967948        out_f.write('#   ["name", "units", default, [lower, upper], "type", "description"],\n') 
    … …  
    970951            out_f.write("    ['%s', '', %s, [-inf, inf], '', '%s'],\n" 
    971952                        % (pname, pvalue, desc)) 
    972         for pname, pvalue, desc in self.get_param_helper(pd_param_str): 
    973             param_names.append(pname) 
    974             pd_params.append(pname) 
    975             out_f.write("    ['%s', '', %s, [-inf, inf], 'volume', '%s'],\n" 
    976                         % (pname, pvalue, desc)) 
    977953        out_f.write('    ]\n') 
    978954 
    979955        # Write out function definition 
     956        out_f.write('\n') 
    980957        out_f.write('def Iq(%s):\n' % ', '.join(['x'] + param_names)) 
    981958        out_f.write('    """Absolute scattering"""\n') 
    … …  
    987964            out_f.write('    import numpy as np') 
    988965        for func_line in func_str.split('\n'): 
    989             out_f.write('%s%s\n' % (spaces4, func_line)) 
     966            out_f.write('%s%s\n' % ('    ', func_line)) 
    990967        out_f.write('## uncomment the following if Iq works for vector x\n') 
    991968        out_f.write('#Iq.vectorized = True\n') 
    992  
    993         # If polydisperse, create place holders for form_volume, ER and VR 
    994         if pd_params: 
    995             out_f.write('\n') 
    996             out_f.write(CUSTOM_TEMPLATE_PD % {'args': ', '.join(pd_params)}) 
    997969 
    998970        # Create place holder for Iqxy 
    … …  
    11251097description = """%(description)s""" 
    11261098 
    1127 ''' 
    1128  
    1129 CUSTOM_TEMPLATE_PD = '''\ 
    1130 def form_volume(%(args)s): 
    1131     """ 
    1132     Volume of the particles used to compute absolute scattering intensity 
    1133     and to weight polydisperse parameter contributions. 
    1134     """ 
    1135     return 0.0 
    1136  
    1137 def ER(%(args)s): 
    1138     """ 
    1139     Effective radius of particles to be used when computing structure factors. 
    1140  
    1141     Input parameters are vectors ranging over the mesh of polydispersity values. 
    1142     """ 
    1143     return 0.0 
    1144  
    1145 def VR(%(args)s): 
    1146     """ 
    1147     Volume ratio of particles to be used when computing structure factors. 
    1148  
    1149     Input parameters are vectors ranging over the mesh of polydispersity values. 
    1150     """ 
    1151     return 1.0 
    11521099''' 
    11531100 

  • src/sas/sasgui/perspectives/calculator/resolution_calculator_panel.py

    r7432acb r1cf490b6  
    1818matplotlib.use('WXAgg') 
    1919from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas 
    20 from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar 
     20from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg as Toolbar 
    2121from matplotlib.backend_bases import FigureManagerBase 
    2222# Wx-Pylab magic for displaying plots within an application's window. 

  • src/sas/sasgui/perspectives/corfunc/media/corfunc_help.rst

    rad476d1 r501712f  
    188188*   Average Hard Block Thickness :math:`= L_c` 
    189189*   Average Core Thickness :math:`= D_0` 
    190 *   Average Interface Thickness :math:`\text{} = D_{tr}` 
    191 *   Polydispersity :math:`= \Gamma_{\text{min}}/\Gamma_{\text{max}}` 
     190*   Average Interface Thickness :math:`= D_{tr}` 
     191*   Polydispersity :math:`= \Gamma_{\mathrm{min}}/\Gamma_{\mathrm{max}}` 
    192192*   Local Crystallinity :math:`= L_c/L_p` 
    193193 
    … …  
    203203*   Bound Fraction :math:`= <p>` 
    204204*   Second Moment :math:`= \sigma` 
    205 *   Maximum Extent :math:`= \delta_{\text{h}}` 
     205*   Maximum Extent :math:`= \delta_{\mathrm{h}}` 
    206206*   Adsorbed Amount :math:`= \Gamma` 
    207207 

  • src/sas/sasgui/perspectives/file_converter/media/file_converter_help.rst

    r59decb81 rfafb396  
    1919    or with a comma or semi-colon delimiter 
    2020*   2D `ISIS ASCII formatted 
    21     <http://www.isis.stfc.ac.uk/instruments/loq/software/ 
    22     colette-ascii-file-format-descriptions9808.pdf>`_ data 
     21    <https://www.isis.stfc.ac.uk/Pages/colette-ascii-file-format-descriptions.pdf>`_ data 
    2322*   `1D BSL/OTOKO format 
    2423    <http://www.diamond.ac.uk/Beamlines/Soft-Condensed-Matter/small-angle/ 

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

    r58a8f76 rc192960  
    641641        # get the strings for report 
    642642        report_str, text_str = self.state.report(fig_urls=refs) 
    643  
    644643        # Show the dialog 
    645644        report_list = [report_str, text_str, images] 
    646         dialog = ReportDialog(report_list, None, wx.ID_ANY, "") 
     645        dialog = ReportDialog(report_list, imgRAM, refs, None, wx.ID_ANY, "") 
    647646        dialog.Show() 
    648647 
    … …  
    677676            refs.append('memory:' + name) 
    678677            imgRAM.AddFile(name, canvas.bitmap, wx.BITMAP_TYPE_PNG) 
    679  
    680678            # append figs 
    681679            images.append(fig) 
    … …  
    13671365            except Exception: 
    13681366                logger.error(traceback.format_exc()) 
    1369             selection = self._find_polyfunc_selection(disp_model) 
     1367            index, selection = self._find_polyfunc_selection(disp_model) 
    13701368            for list in self.fittable_param: 
    13711369                if list[1] == key and list[7] is not None: 
    1372                     list[7].SetSelection(selection) 
     1370                    list[7].SetSelection(index) 
    13731371                    # For the array disp_model, set the values and weights 
    1374                     if selection == 1: 
     1372                    if selection == 'array': 
    13751373                        disp_model.set_weights(self.values[key], 
    13761374                                               self.weights[key]) 
    … …  
    13851383                            logger.error(traceback.format_exc()) 
    13861384            # For array, disable all fixed params 
    1387             if selection == 1: 
     1385            if selection == 'array': 
    13881386                for item in self.fixed_param: 
    13891387                    if item[1].split(".")[0] == key.split(".")[0]: 
    … …  
    14721470            # we need to check here ourselves. 
    14731471            if not is_modified: 
    1474                 is_modified = (self._check_value_enter(self.fittable_param) 
    1475                                or self._check_value_enter(self.fixed_param) 
    1476                                or self._check_value_enter(self.parameters)) 
     1472                is_modified = self._check_value_enter(self.fittable_param) 
     1473                is_modified = self._check_value_enter( 
     1474                    self.fixed_param) or is_modified 
     1475                is_modified = self._check_value_enter( 
     1476                    self.parameters) or is_modified 
    14771477 
    14781478            # Here we should check whether the boundaries have been modified. 
    … …  
    15361536                        data=[self.data]) 
    15371537            # Check the values 
    1538             is_modified = (self._check_value_enter(self.fittable_param) 
    1539                            or self._check_value_enter(self.fixed_param) 
    1540                            or self._check_value_enter(self.parameters)) 
     1538            is_modified = self._check_value_enter(self.fittable_param) 
     1539            is_modified = self._check_value_enter(self.fixed_param) or is_modified 
     1540            is_modified = self._check_value_enter(self.parameters) or is_modified 
    15411541 
    15421542            # If qmin and qmax have been modified, update qmin and qmax and 
    … …  
    23242324 
    23252325            # Update value in model if it has changed 
    2326             if value != self.model.getParam(name): 
     2326            if (value != self.model.getParam(name) or 
     2327                    (np.isnan(value) and np.isnan(self.model.getParam(name)))): 
    23272328                self.model.setParam(name, value) 
    23282329                is_modified = True 
    … …  
    26682669    def _find_polyfunc_selection(self, disp_func=None): 
    26692670        """ 
    2670         FInd Comboox selection from disp_func 
     2671        Find Combobox selection from disp_func 
    26712672 
    26722673        :param disp_function: dispersion distr. function 
    … …  
    26752676        if disp_func is not None: 
    26762677            try: 
    2677                 return POLYDISPERSITY_MODELS.values().index(disp_func.__class__) 
     2678                return (list(POLYDISPERSITY_MODELS).index(disp_func.type), 
     2679                       disp_func.type) 
    26782680            except ValueError: 
    26792681                pass  # Fall through to default class 
    2680         return POLYDISPERSITY_MODELS.keys().index('gaussian') 
     2682        return (list(POLYDISPERSITY_MODELS).index('gaussian'), 'gaussian') 
    26812683 
    26822684    def on_reset_clicked(self, event): 

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

    rbfeb823 ra7c6f38  
    365365        # StaticText for chi2, N(for fitting), Npts + Log/linear spacing 
    366366        self.tcChi = BGTextCtrl(self, wx.ID_ANY, "-", size=(75, 20), style=0) 
    367         self.tcChi.SetToolTipString("Chi2/Npts(Fit)") 
     367        self.tcChi.SetToolTipString("Chi2/DOF (DOF=Npts-Npar fitted)") 
    368368        self.Npts_fit = BGTextCtrl(self, wx.ID_ANY, "-", size=(75, 20), style=0) 
    369369        self.Npts_fit.SetToolTipString( 
    … …  
    391391        self.points_sizer.Add(self.pointsbox) 
    392392 
    393         box_description_1 = wx.StaticText(self, wx.ID_ANY, '   Chi2/Npts') 
     393        box_description_1 = wx.StaticText(self, wx.ID_ANY, 'Reduced Chi2') 
    394394        box_description_2 = wx.StaticText(self, wx.ID_ANY, 'Npts(Fit)') 
    395395 

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

    r5005ae0 r8b89396  
    180180*checked*\ . 
    181181 
    182 Also note that the 'Fit Parameters' have been split into two sections: those 
    183 which can be polydisperse (shape and orientation parameters) and those which are 
    184 not (eg, scattering length densities). 
    185  
    186182A model file generated by this option can be viewed and further modified using 
    187183the :ref:`Advanced_Plugin_Editor` . 
    188184 
    189 **SasView version 4.2** made it possible to specify whether a plugin created with 
    190 the *New Plugin Model* dialog is actually a form factor P(Q) or a structure factor 
    191 S(Q). To do this, simply add one or other of the following lines under the *import* 
    192 statements. 
     185Note that the New Plugin Model Feature currently does not allow for parameters 
     186to be polydisperse.  However they can be edited in the Advanced Editor. 
     187 
     188 
     189**SasView version 4.2** made it possible to specify whether a plugin created 
     190with the *New Plugin Model* dialog is actually a form factor P(Q) or a structure 
     191factor S(Q). To do this, simply add one or other of the following lines under 
     192the *import* statements. 
    193193 
    194194For a form factor:: 
    … …  
    200200     structure_factor = True 
    201201 
    202 If the plugin is a structure factor it is *also* necessary to add two variables to 
    203 the parameter list:: 
     202If the plugin is a structure factor it is *also* necessary to add two variables 
     203to the parameter list:: 
    204204 
    205205     parameters = [ 
    … …  
    426426See :ref:`Assessing_Fit_Quality`. 
    427427 
    428 The objective of model-fitting is to find a *physically-plausible* model, and set 
    429 of model parameters, that generate a theory that reproduces the experimental data 
    430 and gives residual values as close to zero as possible. 
     428The objective of model-fitting is to find a *physically-plausible* model, and 
     429set of model parameters, that generate a theory that reproduces the experimental 
     430data and minimizes the values of the residuals. 
    431431 
    432432Change the default values of the model parameters by hand until the theory line 
    433 starts to represent the experimental data. Then uncheck the tick boxes alongside 
    434 all parameters *except* the 'background' and the 'scale'. Click the *Fit* button. 
    435 SasView will optimise the values of the 'background' and 'scale' and also display 
    436 the corresponding uncertainties on the optimised values. 
    437  
    438 *NB: If no uncertainty is shown it generally means that the model is not very* 
    439 *dependent on the corresponding parameter (or that one or more parameters are* 
    440 *'correlated').* 
    441  
    442 In the bottom left corner of the *Fit Page* is a box displaying the normalised value 
    443 of the statistical $\chi^2$ parameter returned by the optimiser. 
     433starts to represent the experimental data. Then check the tick boxes alongside 
     434the 'background' and 'scale' parameters. Click the *Fit* button. SasView 
     435will optimise the values of the 'background' and 'scale' and also display the 
     436corresponding uncertainties on the optimised values. 
     437 
     438.. note:: 
     439   If the uncertainty on a fitted parameter is unrealistically large, or if it 
     440   displays as NaN, the model is most likely a poor representation of the data, 
     441   the parameter in question is highly correlated with one or more of the other 
     442   fitted parameters, or the model is relatively insensitive to the value of 
     443   that particular parameter. 
     444 
     445In the bottom left corner of the *Fit Page* is a box displaying a normalised 
     446value of the statistical $\chi^2$ parameter (the reduced $\chi^2$, 
     447See :ref:`Assessing_Fit_Quality`) returned by the optimiser. 
    444448 
    445449Now check the box for another model parameter and click *Fit* again. Repeat this 
    446 process until most or all parameters are checked and have been optimised. As the 
    447 fit of the theory to the experimental data improves the value of 'chi2/Npts' will 
    448 decrease. A good model fit should easily produce values of 'chi2/Npts' that are 
    449 close to one, and certainly <100. See :ref:`Assessing_Fit_Quality`. 
     450process until all relevant parameters are checked and have been optimised. As 
     451the fit of the theory to the experimental data improves, the value of 'Reduced 
     452Chi2' will decrease. A good model fit should produce values of Reduced Chi2 
     453close to one, and certainly << 100. See :ref:`Assessing_Fit_Quality`. 
    450454 
    451455SasView has a number of different optimisers (see the section :ref:`Fitting_Options`). 
    … …  
    462466*the Data Explorer is checked (see the section* :ref:`Loading_data` *).* 
    463467 
    464 This mode is an extension of the :ref:`Single_Fit_Mode` that fits two or more data 
    465 sets *to the same model* simultaneously. If necessary it is possible to constrain 
    466 fit parameters between data sets (eg, to fix a background level, or radius, etc). 
     468This mode is an extension of the :ref:`Single_Fit_Mode` that allows for some 
     469relatively extensive constraints between fitted parameters in a single *FitPage* 
     470or between several *FitPage*'s (eg, to constrain all fitted parameters to be the 
     471same in a contrast series of *FitPages* except for the solvent sld parameter, 
     472constrain the length to be twice that of the radius in a single *FitPage*, 
     473fix the radius of the sphere in one *FitPage* to be the same as the radius of 
     474the cylinder in a second *FitPage*, etc). 
    467475 
    468476If the data to be fit are in multiple files, load each file, then select each file 
    … …  
    501509next to *Add Constraint?* in the *Fit Constraints* box. 
    502510 
     511To constrain all identically named parameters to fit *simultaneously* to the 
     512same value across all the *Fitpages* use the *Easy Setup* drop-down buttons in 
     513the *Const & Simul Fit* page. 
     514 
    503515*NB: You can only constrain parameters that are set to refine.* 
     516 
     517Constraints will generally be of the form 
     518 
     519  Mi Parameter1 = Mj.Parameter1 
     520 
     521however the text box after the '=' sign can be used to adjust this 
     522relationship; for example 
     523 
     524  Mi Parameter1 = scalar \* Mj.Parameter1 
     525 
     526A 'free-form' constraint box is also provided. 
     527 
     528Many constraints can be entered for a single fit. 
    504529 
    505530When ready, click the *Fit* button on the *Const & Simul Fit* page, NOT the *Fit* 
    506531button on the individual *FitPage*'s. 
    507532 
    508 Simultaneous Fits without Constraints 
    509 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    510  
    511533The results of the model-fitting will be returned to each of the individual 
    512534*FitPage*'s. 
    513535 
    514 Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To 
    515 see the chi2/Npts value for a specific *FitPage*, click the *Compute* button at the 
    516 bottom of that *FitPage* to recalculate. Also see :ref:`Assessing_Fit_Quality`. 
    517  
    518 Simultaneous Fits with Constraints 
    519 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    520  
    521 Use the *Easy Setup* drop-down buttons in the *Const & Simul Fit* page to set 
    522 up constraints between *FitPage*'s. 
    523  
    524 Constraints will generally be of the form 
    525  
    526   Mi Parameter1 = Mj.Parameter1 
    527  
    528 however the text box after the '=' sign can be used to adjust this 
    529 relationship; for example 
    530  
    531   Mi Parameter1 = scalar \* Mj.Parameter1 
    532  
    533 A 'free-form' constraint box is also provided. 
    534  
    535 Many constraints can be entered for a single fit. 
    536  
    537 The results of the model-fitting will be returned to each of the individual 
    538 *FitPage*'s. 
    539  
    540 Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To 
    541 see the chi2/Npts value for a specific *FitPage*, click the *Compute* button at the 
    542 bottom of that *FitPage* to recalculate. Also see :ref:`Assessing_Fit_Quality`. 
     536Note that the Reduced Chi2 value returned is the SUM of the Reduced Chi2 of 
     537each fit. To see the Reduced Chi2 value for a specific *FitPage*, click the  
     538*Compute* button at the bottom of that *FitPage* to recalculate. Note that in 
     539doing so the degrees of freedom will be set to Npts. 
     540See :ref:`Assessing_Fit_Quality`.  Moreover in the case of constraints the 
     541degrees of freedom are less than one might think due to those constraints. 
    543542 
    544543.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    766765.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    767766 
    768 .. note::  This help document was last changed by Paul Butler, 10 September 
    769    2017 
     767.*Document History* 
     768 
     769| 2017-09-10 Paul Butler 
     770| 2017-09-15 Steve King 
     771| 2018-03-05 Paul Butler 

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

    r99ded31 r84ac3f1  
    2727 
    2828$\chi^2$ is a statistical parameter that quantifies the differences between 
    29 an observed data set and an expected dataset (or 'theory'). 
    30  
    31 When showing the a model with the data, *SasView* displays this parameter 
    32 normalized to the number of data points, $N_\mathrm{pts}$ such that 
     29an observed data set and an expected dataset (or 'theory') calculated as 
    3330 
    3431.. math:: 
    3532 
    36   \chi^2_N 
    37   =  \sum[(Y_i - \mathrm{theory}_i)^2 / \mathrm{error}_i^2] / N_\mathrm{pts} 
     33  \chi^2 
     34  =  \sum[(Y_i - \mathrm{theory}_i)^2 / \mathrm{error}_i^2] 
    3835 
    39 When performing a fit, *SasView* instead displays the reduced $\chi^2_R$, 
    40 which takes into account the number of fitting parameters $N_\mathrm{par}$ 
    41 (to calculate the number of 'degrees of freedom'). This is computed as 
     36Fitting typically minimizes the value of $\chi^2$.  For assessing the quality of 
     37the model and its "fit" however, *SasView* displays the traditional reduced 
     38$\chi^2_R$ which normalizes this parameter by dividing it by the number of 
     39degrees of freedom (or DOF). The DOF is the number of data points being 
     40considered, $N_\mathrm{pts}$, reduced by the number of free (i.e. fitted) 
     41parameters, $N_\mathrm{par}$. Note that model parameters that are kept fixed do 
     42*not* contribute to the DOF (they are not "free"). This reduced value is then 
     43given as 
    4244 
    4345.. math:: 
    … …  
    4749  / [N_\mathrm{pts} - N_\mathrm{par}] 
    4850 
    49 The normalized $\chi^2_N$ and the reduced $\chi^2_R$ are very close to each 
    50 other when $N_\mathrm{pts} \gg N_\mathrm{par}$. 
     51Note that this means the displayed value will vary depending on the number of 
     52parameters used in the fit. In particular, when doing a calculation without a 
     53fit (e.g. manually changing a parameter) the DOF will now equal $N_\mathrm{pts}$ 
     54and the $\chi^2_R$ will be the smallest possible for that combination of model, 
     55data set, and set of parameter values. 
     56 
     57When $N_\mathrm{pts} \gg N_\mathrm{par}$ as it should for proper fitting, the 
     58value of the reduced $\chi^2_R$ will not change very much. 
    5159 
    5260For a good fit, $\chi^2_R$ tends to 1. 
    … …  
    9098| 2015-06-08 Steve King 
    9199| 2017-09-28 Paul Kienzle 
     100| 2018-03-04 Paul Butler 

  • src/sas/sasview/sasview.py

    r20fa5fe r1270e3c  
    4343        from sas.sasgui.guiframe.gui_manager import SasViewApp 
    4444        self.gui = SasViewApp(0) 
     45        if sys.platform == "darwin": 
     46            self.check_sasmodels_compiler() 
    4547        # Set the application manager for the GUI 
    4648        self.gui.set_manager(self) 
    … …  
    130132        self.gui.MainLoop() 
    131133 
     134    def check_sasmodels_compiler(self): 
     135        """ 
     136        Checking c compiler for sasmodels and raises xcode command line 
     137        tools for installation 
     138        """ 
     139        #wx should be importable at this stage 
     140        import wx 
     141        import subprocess 
     142        #Generic message box created becuase standard MessageBox is not moveable 
     143        class GenericMessageBox(wx.Dialog): 
     144            def __init__(self, parent, text, title = ''): 
     145 
     146                wx.Dialog.__init__(self, parent, -1, title = title, 
     147                               size = (360,200), pos=(20,60), 
     148                               style = wx.STAY_ON_TOP | wx.DEFAULT_DIALOG_STYLE) 
     149                panel = wx.Panel(self, -1) 
     150                top_row_sizer = wx.BoxSizer(wx.HORIZONTAL) 
     151 
     152                error_bitmap = wx.ArtProvider.GetBitmap( 
     153                    wx.ART_ERROR, wx.ART_MESSAGE_BOX 
     154                ) 
     155                error_bitmap_ctrl = wx.StaticBitmap(panel, -1) 
     156                error_bitmap_ctrl.SetBitmap(error_bitmap) 
     157                label = wx.StaticText(panel, -1, text) 
     158                top_row_sizer.Add(error_bitmap_ctrl, flag=wx.ALL, border=10) 
     159                top_row_sizer.Add(label, flag=wx.ALIGN_CENTER_VERTICAL) 
     160 
     161                #Create the OK button in the bottom row. 
     162                ok_button = wx.Button(panel, wx.ID_OK ) 
     163                self.Bind(wx.EVT_BUTTON, self.on_ok, source=ok_button) 
     164                ok_button.SetFocus() 
     165                ok_button.SetDefault() 
     166 
     167                sizer = wx.BoxSizer(wx.VERTICAL) 
     168                sizer.Add(top_row_sizer) 
     169                sizer.Add(ok_button, flag=wx.ALIGN_CENTER | wx.ALL, border=5) 
     170                panel.SetSizer(sizer) 
     171 
     172            def on_ok(self, event): 
     173                self.Destroy() 
     174 
     175        logger = logging.getLogger(__name__) 
     176        try: 
     177            subprocess.check_output(["cc","--version"], stderr=subprocess.STDOUT) 
     178        except subprocess.CalledProcessError as exc: 
     179            dlg = GenericMessageBox(parent=None, 
     180            text='No compiler installed. Please install command line\n' 
     181                'developers tools by clicking \"Install\" in another winodw\n\n' 
     182                'Alternatively click \"Not Now\" and use OpenCL\n' 
     183                 'compiler, which can be set up from menu Fitting->OpenCL Options\n\n', 
     184            title = 'Compiler Info') 
     185            dlg.Show() 
     186            logger.error("No compiler installed. %s\n"%(exc)) 
     187            logger.error(traceback.format_exc()) 
    132188 
    133189def setup_logging(): 

  • test/corfunc/test/utest_corfunc.py

    rf53d684 r6ef75fa6  
    7474        while True: 
    7575            time.sleep(0.001) 
    76             if not self.calculator.transform_isrunning(): 
     76            if (not self.calculator.transform_isrunning() and 
     77                self.transformation is not None): 
    7778                break 
    7879 
    79     def transform_callback(self, transforms): 
    80         transform1, transform3, idf = transforms 
     80        transform1, transform3, idf = self.transformation 
    8181        self.assertIsNotNone(transform1) 
    8282        self.assertAlmostEqual(transform1.y[0], 1) 
    8383        self.assertAlmostEqual(transform1.y[-1], 0, 5) 
     84 
     85    def transform_callback(self, transforms): 
    8486        self.transformation = transforms 
    8587 

  • test/sascalculator/test/utest_sas_gen.py

    rf53d684 r39a018b  
    6060        Test that the calculator calculates. 
    6161        """ 
    62         f = self.omfloader.read("A_Raw_Example-1.omf") 
     62        f = self.omfloader.read(find("A_Raw_Example-1.omf")) 
    6363        omf2sld = sas_gen.OMF2SLD() 
    6464        omf2sld.set_data(f) 

  • test/sasdataloader/test/utest_generic_file_reader_class.py

    rf53d684 r4a8d55c  
    88import numpy as np 
    99 
    10 from sas.sascalc.dataloader.data_info import DataInfo, plottable_1D 
     10from sas.sascalc.dataloader.data_info import DataInfo, plottable_1D, Data1D 
     11from sas.sascalc.dataloader.loader import Loader 
     12from sas.sascalc.dataloader.loader_exceptions import NoKnownLoaderException 
    1113from sas.sascalc.dataloader.file_reader_base_class import FileReader 
    1214 
    … …  
    2426        self.bad_file = find("ACB123.txt") 
    2527        self.good_file = find("123ABC.txt") 
     28        self.generic_reader = Loader() 
     29        self.deprecated_file_type = find("FEB18012.ASC") 
    2630 
    2731    def test_bad_file_path(self): 
    28         output = self.reader.read(self.bad_file) 
    29         self.assertEqual(output, []) 
     32        self.assertRaises(NoKnownLoaderException, self.reader.read, 
     33                          self.bad_file) 
    3034 
    3135    def test_good_file_path(self): 
    … …  
    3640        self.assertEqual(len(output), 1) 
    3741        self.assertEqual(output[0].meta_data["blah"], '123ABC exists!') 
     42 
     43    def test_old_file_types(self): 
     44        f = self.generic_reader.load(self.deprecated_file_type) 
     45        last_f = f[0] 
     46        if hasattr(last_f, "errors"): 
     47            self.assertEquals(len(last_f.errors), 1) 
     48        else: 
     49            self.fail("Errors did not propogate to the file properly.") 
     50 
     51    def test_same_file_unknown_extensions(self): 
     52        # Five files, all with the same content, but different file extensions 
     53        no_ext = find("test_data//TestExtensions") 
     54        not_xml = find("test_data//TestExtensions.notxml") 
     55        # Deprecated extensions 
     56        asc_dep = find("test_data//TestExtensions.asc") 
     57        nxs_dep = find("test_data//TestExtensions.nxs") 
     58        # Native extension as a baseline 
     59        xml_native = find("test_data//TestExtensions.xml") 
     60        # Load the files and check contents 
     61        no_ext_load = self.generic_reader.load(no_ext) 
     62        asc_load = self.generic_reader.load(asc_dep) 
     63        nxs_load = self.generic_reader.load(nxs_dep) 
     64        not_xml_load = self.generic_reader.load(not_xml) 
     65        xml_load = self.generic_reader.load(xml_native) 
     66        self.check_unknown_extension(no_ext_load[0]) 
     67        self.check_unknown_extension(asc_load[0]) 
     68        self.check_unknown_extension(nxs_load[0]) 
     69        self.check_unknown_extension(not_xml_load[0]) 
     70        self.check_unknown_extension(xml_load[0]) 
     71        # Be sure the deprecation warning is passed with the file 
     72        self.assertEquals(len(asc_load[0].errors), 1) 
     73        self.assertEquals(len(nxs_load[0].errors), 1) 
     74 
     75    def check_unknown_extension(self, data): 
     76        self.assertTrue(isinstance(data, Data1D)) 
     77        self.assertEquals(len(data.x), 138) 
     78        self.assertEquals(data.sample.ID, "TK49 c10_SANS") 
     79        self.assertEquals(data.meta_data["loader"], "CanSAS XML 1D") 
    3880 
    3981    def tearDown(self): 
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